RALPH@home

Bug reports for Ralph 5.30 and 5.31 and 5.32

  UW Seal
 
[ Home ] [ Join ] [ About ] [ Participants ] [ Community ] [ Statistics ]
  [ login/out ]


Advanced search

Message boards : RALPH@home bug list : Bug reports for Ralph 5.30 and 5.31 and 5.32

AuthorMessage
Rhiju
Forum moderator
Project developer
Project scientist

Joined: Feb 14 06
Posts: 161
ID: 4
Credit: 3,725
RAC: 0
Message 2351 - Posted 8 Oct 2006 5:43:07 UTC

    Thanks for your help in our updates over the last week!
    This one may be our last, or our second-to-last one, before update Rosetta@home. We\'re testing a new strategy for folding that will allow rosetta to handle non-linear protein topologies with all the atoms present. We already have a version of this protocol (\"jumping\") in earlier versions, but it couldn\'t handle all the sidechain atoms.
    ____________

    Norman_RKN

    Joined: Mar 26 06
    Posts: 5
    ID: 1187
    Credit: 4,877
    RAC: 0
    Message 2352 - Posted 8 Oct 2006 7:11:05 UTC - in response to Message 2351.

      Last modified: 8 Oct 2006 7:05:18 UTC

      Unzul�ssige Funktion. (0x1) - exit code 1 (0x1)
      </message>
      <stderr_txt>
      # cpu_run_time_pref: 3600
      # random seed: 2897923
      ERROR:: Exit at: .\\chuck.cc line:1028

      </stderr_txt>

      08.10.2006 08:54:59|ralph@home|Unrecoverable error for result JUMPTEST_POSERELAX_1tul__1336_10_0 (Unzulässige Funktion. (0x1) - exit code 1 (0x1))


      ------------------

      08.10.2006 09:16:03|ralph@home|Unrecoverable error for result JUMPTEST_POSERELAX_1tul__1336_19_0 (Unzulässige Funktion. (0x1) - exit code 1 (0x1))

      <core_client_version>5.5.0</core_client_version>
      <message>
      Unzul�ssige Funktion. (0x1) - exit code 1 (0x1)
      </message>
      <stderr_txt>
      # random seed: 2897914
      # cpu_run_time_pref: 3600
      ERROR:: Exit at: .\\chuck.cc line:1028

      </stderr_txt>




      285228

      285274

      ____________

      SafeAggie

      Joined: Oct 5 06
      Posts: 6
      ID: 1943
      Credit: 4,207
      RAC: 0
      Message 2354 - Posted 8 Oct 2006 13:48:23 UTC

        Unrecoverable error for result IDL_RLX_NT_t305_CASP7_hom001_1_1335_6_0 (<file_xfer_error> <file_name>IDL_RLX_NT_t305_CASP7_hom001_1_1335_6_0_0</file_name> <error_code>-161</error_code></file_xfer_error>)

        resultid=284811

        Profile paul and kirsty yates
        Avatar

        Joined: Feb 16 06
        Posts: 11
        ID: 310
        Credit: 949
        RAC: 0
        Message 2355 - Posted 8 Oct 2006 18:11:23 UTC

          Last modified: 8 Oct 2006 17:57:44 UTC

          just got another error on this one
          08/10/2006 14:35:41|ralph@home|Unrecoverable error for result IDL_RLX_NT_t304_CASP7_hom001_1_1332_7_1 (<file_xfer_error>

          <file_name>IDL_RLX_NT_t304_CASP7_hom001_1_1332_7_1_0</file_name> <error_code>-161</error_code></file_xfer_error>)

          <core_client_version>5.4.11</core_client_version>
          <stderr_txt>
          ERROR:: Unable to determine sequence length from pdb file
          ======================================================
          DONE :: 1 starting structures built 5 (nstruct) times
          This process generated 0 decoys from 0 attempts
          1 starting pdbs were skipped
          ======================================================


          BOINC :: Watchdog shutting down...
          BOINC :: BOINC support services shutting down...

          </stderr_txt>
          <message>
          <file_xfer_error>
          <file_name>IDL_RLX_NT_t296_CASP7_hom001_1_1332_7_2_0</file_name>
          <error_code>-161</error_code>
          </file_xfer_error>

          </message>


          ____________

          Profile William Senn
          Avatar

          Joined: Feb 16 06
          Posts: 4
          ID: 183
          Credit: 30,895
          RAC: 0
          Message 2357 - Posted 8 Oct 2006 19:05:10 UTC

            Hi,

            Reporting an error as can be seen in result 285411:

            resultid=285411

            Hope it helps you...

            Cheers,

            William Senn...


            ____________

            Pieface

            Joined: Feb 16 06
            Posts: 64
            ID: 234
            Credit: 203,513
            RAC: 0
            Message 2358 - Posted 8 Oct 2006 19:14:55 UTC

              I\'m also getting a couple of errors on the jumptest units:

              resid 285431
              and
              resid 285518

              error info was:

              Incorrect function. (0x1) - exit code 1 (0x1)
              </message>
              <stderr_txt>
              # random seed: 2897927
              ERROR:: Exit at: .\\chuck.cc line:1028

              Rhiju
              Forum moderator
              Project developer
              Project scientist

              Joined: Feb 14 06
              Posts: 161
              ID: 4
              Credit: 3,725
              RAC: 0
              Message 2360 - Posted 8 Oct 2006 21:03:52 UTC - in response to Message 2358.

                Thanks to everyone for posting! I\'m working on the fix. Hopefully it will go into an update later today, but that might get delayed. Several of our computers are down today because of an air conditioning problem.

                I\'m also getting a couple of errors on the jumptest units:

                resid 285431
                and
                resid 285518

                error info was:

                Incorrect function. (0x1) - exit code 1 (0x1)
                </message>
                <stderr_txt>
                # random seed: 2897927
                ERROR:: Exit at: .\\chuck.cc line:1028



                ____________

                Profile paul and kirsty yates
                Avatar

                Joined: Feb 16 06
                Posts: 11
                ID: 310
                Credit: 949
                RAC: 0
                Message 2361 - Posted 8 Oct 2006 22:09:50 UTC

                  just had another 2
                  this one
                  and this one

                  all mine are 161 errors
                  ____________

                  Mike Gelvin
                  Avatar

                  Joined: Feb 17 06
                  Posts: 50
                  ID: 468
                  Credit: 55,397
                  RAC: 0
                  Message 2362 - Posted 9 Oct 2006 1:02:10 UTC

                    A -161 error
                    http://ralph.bakerlab.org/workunit.php?wuid=248602

                    ____________

                    SafeAggie

                    Joined: Oct 5 06
                    Posts: 6
                    ID: 1943
                    Credit: 4,207
                    RAC: 0
                    Message 2363 - Posted 9 Oct 2006 3:15:37 UTC

                      Unrecoverable error for result IDL_RLX_NT_t326_CASP7_hom001_1_1335_6_0 (Incorrect function. (0x1) - exit code 1 (0x1))

                      resultid=284828

                      Rhiju
                      Forum moderator
                      Project developer
                      Project scientist

                      Joined: Feb 14 06
                      Posts: 161
                      ID: 4
                      Credit: 3,725
                      RAC: 0
                      Message 2364 - Posted 9 Oct 2006 6:35:27 UTC - in response to Message 2351.

                        Ralph 5.31 should fix some of the issues that you reported. The other issues were apparently not due to the new application but due to a bad workunit, and is getting fixed.

                        Thanks for your help in our updates over the last week!
                        This one may be our last, or our second-to-last one, before update Rosetta@home. We\'re testing a new strategy for folding that will allow rosetta to handle non-linear protein topologies with all the atoms present. We already have a version of this protocol (\"jumping\") in earlier versions, but it couldn\'t handle all the sidechain atoms.


                        ____________

                        SafeAggie

                        Joined: Oct 5 06
                        Posts: 6
                        ID: 1943
                        Credit: 4,207
                        RAC: 0
                        Message 2365 - Posted 9 Oct 2006 12:02:34 UTC

                          Unrecoverable error for result IDL_RLX_NT_t339_CASP7_hom001_1_1335_6_0 (One or more arguments are invalid (0x80000003) - exit code -2147483645 (0x80000003))

                          resultid=284837

                          Tobie

                          Joined: Oct 4 06
                          Posts: 3
                          ID: 1934
                          Credit: 582
                          RAC: 0
                          Message 2366 - Posted 9 Oct 2006 14:02:49 UTC

                            09/10/06 14:34:39 PM|ralph@home|Starting task IDL_RLX_NT_t345_CASP7_hom001_1_1332_10_2 using rosetta_beta version 531
                            09/10/06 14:35:16 PM||Rescheduling CPU: application exited
                            09/10/06 14:35:16 PM|ralph@home|Computation for task IDL_RLX_NT_t345_CASP7_hom001_1_1332_10_2 finished
                            09/10/06 14:35:16 PM|ralph@home|Starting task IDL_RLX_NT_t350_CASP7_hom001_1_1332_10_2 using rosetta_beta version 531
                            09/10/06 14:35:18 PM|ralph@home|Unrecoverable error for result IDL_RLX_NT_t345_CASP7_hom001_1_1332_10_2 (<file_xfer_error> <file_name>IDL_RLX_NT_t345_CASP7_hom001_1_1332_10_2_0</file_name> <error_code>-161</error_code></file_xfer_error>)
                            09/10/06 14:35:18 PM|ralph@home|Deferring scheduler requests for 1 minutes and 0 seconds
                            09/10/06 14:35:48 PM||Rescheduling CPU: application exited
                            09/10/06 14:35:48 PM|ralph@home|Computation for task IDL_RLX_NT_t350_CASP7_hom001_1_1332_10_2 finished
                            09/10/06 14:35:49 PM|ralph@home|Unrecoverable error for result IDL_RLX_NT_t350_CASP7_hom001_1_1332_10_2 (<file_xfer_error> <file_name>IDL_RLX_NT_t350_CASP7_hom001_1_1332_10_2_0</file_name> <error_code>-161</error_code></file_xfer_error>)
                            09/10/06 14:35:49 PM|ralph@home|Deferring scheduler requests for 1 minutes and 0 seconds

                            Profile [B^S] thierry@home
                            Avatar

                            Joined: Feb 15 06
                            Posts: 20
                            ID: 12
                            Credit: 17,624
                            RAC: 0
                            Message 2369 - Posted 9 Oct 2006 20:41:11 UTC

                              Last modified: 9 Oct 2006 20:26:52 UTC

                              I have a WU: JUMPTEST_POSERELAX_VARY_BOND_ANGLES_1tul__1336_32_0 (5.31)

                              stuck at 1% - Model 1 - Step 360000 for 20 minutes. Then starts working.




                              Profile [B^S] thierry@home
                              Avatar

                              Joined: Feb 15 06
                              Posts: 20
                              ID: 12
                              Credit: 17,624
                              RAC: 0
                              Message 2370 - Posted 9 Oct 2006 21:12:16 UTC - in response to Message 2369.

                                I have a WU: JUMPTEST_POSERELAX_VARY_BOND_ANGLES_1tul__1336_32_0 (5.31)

                                stuck at 1% - Model 1 - Step 360000 for 20 minutes. Then starts working.



                                After 45 minutes: step 360131 but still at 1%. Don\'t know if it\'s normal or not.

                                Brian B

                                Joined: Feb 17 06
                                Posts: 9
                                ID: 362
                                Credit: 2,632
                                RAC: 0
                                Message 2371 - Posted 10 Oct 2006 1:14:32 UTC

                                  This wu/result failed with these messages:

                                  10/09/2006 09:03:07 PM|ralph@home|Starting result IDL_RLX_NT_t376_CASP7_hom001_1_1332_1_2 using rosetta_beta version 530
                                  10/09/2006 09:03:33 PM|ralph@home|Sending scheduler request to http://ralph.bakerlab.org/ralph_cgi/cgi
                                  10/09/2006 09:03:33 PM|ralph@home|Reason: To fetch work
                                  10/09/2006 09:03:33 PM|ralph@home|Requesting 8640 seconds of new work
                                  10/09/2006 09:03:38 PM|ralph@home|Scheduler request to http://ralph.bakerlab.org/ralph_cgi/cgi succeeded
                                  10/09/2006 09:03:40 PM|ralph@home|Started download of rosetta_beta_5.31_windows_intelx86.exe
                                  10/09/2006 09:03:40 PM|ralph@home|Started download of 1BRC.pdb
                                  10/09/2006 09:03:43 PM||request_reschedule_cpus: process exited
                                  10/09/2006 09:03:43 PM|ralph@home|Computation for result IDL_RLX_NT_t376_CASP7_hom001_1_1332_1_2 finished
                                  10/09/2006 09:03:44 PM|ralph@home|Unrecoverable error for result IDL_RLX_NT_t376_CASP7_hom001_1_1332_1_2 (<file_xfer_error> <file_name>IDL_RLX_NT_t376_CASP7_hom001_1_1332_1_2_0</file_name> <error_code>-161</error_code> <error_message></error_message></file_xfer_error>)

                                  This was on 5.30 though...

                                  Good luck
                                  ____________

                                  rbpeake

                                  Joined: Feb 16 06
                                  Posts: 19
                                  ID: 218
                                  Credit: 3,370
                                  RAC: 0
                                  Message 2372 - Posted 10 Oct 2006 2:29:06 UTC

                                    Result ID 286395
                                    Name DOC_1WEJ_u_pert_mcm_bbmin_1338_8_0
                                    Workunit 252472
                                    Created 9 Oct 2006 22:58:45 UTC
                                    Sent 9 Oct 2006 23:06:02 UTC
                                    Received 10 Oct 2006 2:07:08 UTC
                                    Server state Over
                                    Outcome Validate error
                                    Client state Done
                                    Exit status 0 (0x0)
                                    Computer ID 2078
                                    Report deadline 13 Oct 2006 23:06:02 UTC
                                    CPU time 5628.653606
                                    stderr out

                                    <core_client_version>5.6.5</core_client_version>
                                    <![CDATA[
                                    <stderr_txt>
                                    # random seed: 2896945
                                    # cpu_run_time_pref: 7200
                                    WARNING! error deleting file .\\aa1WEJ.out
                                    WARNING! error deleting file .\\aa1WEJ.out.bonds
                                    WARNING! error deleting file .\\aa1WEJ.out.rot_templates
                                    ======================================================
                                    DONE :: 1 starting structures built 3 (nstruct) times
                                    This process generated 3 decoys from 4 attempts
                                    0 starting pdbs were skipped
                                    ======================================================


                                    BOINC :: Watchdog shutting down...
                                    BOINC :: BOINC support services shutting down...

                                    </stderr_txt>
                                    ]]>

                                    Validate state Invalid
                                    Claimed credit 9.54912155099347
                                    Granted credit 0
                                    application version 5.31
                                    ____________

                                    Profile Conan
                                    Avatar

                                    Joined: Feb 16 06
                                    Posts: 344
                                    ID: 145
                                    Credit: 1,309,534
                                    RAC: 0
                                    Message 2373 - Posted 10 Oct 2006 3:43:04 UTC

                                      >>> Getting a few errors:-
                                      http://ralph.bakerlab.org/workunit.php?wuid=252767
                                      http://ralph.bakerlab.org/workunit.php?wuid=252768

                                      Windows machine, getting error message
                                      \"Incorrect function. (0x1)-exit code 1 (0x1)
                                      ERROR:: Exit at: dock_structure.cc line:431\"

                                      Also error on Linux machine:-
                                      http://ralph.bakerlab.org/workunit.php?wuid=252033

                                      \"process exited with code 1 (0x1)
                                      ERROR:: Exit at: dock_structure.cc line:431\"


                                      Note:-- Thanks Chu for responding to my troubles with 5.28, hopefully I will have no more trouble like that, although I now have my 4800+ AMD machine duplicated across Ralph, Rosetta and Einstein projects, I will have to live with it.

                                      ____________

                                      Chu
                                      Forum moderator
                                      Project developer
                                      Project scientist

                                      Joined: Sep 26 06
                                      Posts: 61
                                      ID: 1900
                                      Credit: 12,545
                                      RAC: 0
                                      Message 2374 - Posted 10 Oct 2006 5:25:14 UTC - in response to Message 2373.

                                        We have noticed this kind of errors under 5.31 and just updated the app to 5.32. Hopefully it will be fixed.

                                        >>> Getting a few errors:-
                                        http://ralph.bakerlab.org/workunit.php?wuid=252767
                                        http://ralph.bakerlab.org/workunit.php?wuid=252768

                                        Windows machine, getting error message
                                        \"Incorrect function. (0x1)-exit code 1 (0x1)
                                        ERROR:: Exit at: dock_structure.cc line:431\"

                                        Also error on Linux machine:-
                                        http://ralph.bakerlab.org/workunit.php?wuid=252033

                                        \"process exited with code 1 (0x1)
                                        ERROR:: Exit at: dock_structure.cc line:431\"


                                        Note:-- Thanks Chu for responding to my troubles with 5.28, hopefully I will have no more trouble like that, although I now have my 4800+ AMD machine duplicated across Ralph, Rosetta and Einstein projects, I will have to live with it.

                                        Profile Conan
                                        Avatar

                                        Joined: Feb 16 06
                                        Posts: 344
                                        ID: 145
                                        Credit: 1,309,534
                                        RAC: 0
                                        Message 2375 - Posted 10 Oct 2006 12:04:58 UTC

                                          > On my Windows machine, I am still having screensaver lockups. It has carried over from 5.28. The screensaver will be processing and showing data fine but after a long time on (probably greater than 1 hour?) when I move the mouse nothing happens and the screensaver is doing nothing either. Task manager shows the programme is still working fine but not the screensaver. I tried stopping BoincManager.exe and boinc.exe but this did nothing, I can still get the start menu up but unable to get rid of screensaver background. I was about to reboot when I thought to double click on the screensaver and my computer was returned to me.
                                          Has anyone else had this happen?
                                          Not a problem on Linux machines as they don\'t have the screensaver function. Can it be turned of in Windows?
                                          ____________

                                          Profile feet1st

                                          Joined: Mar 7 06
                                          Posts: 312
                                          ID: 1028
                                          Credit: 110,522
                                          RAC: 0
                                          Message 2377 - Posted 10 Oct 2006 16:42:42 UTC

                                            V5.31 docking. The graphic doesn\'t react properly to mouse control when not fully maximized. If I attempt to rotate the Low Energy image, the Native image does the rotating...if any reaction at all. Although I was able to right click and enlarge the low energy image. I could not enlarge the Native structure.

                                            Is there any details on what to expect of a docking WU?? i.e. long running models, and low numbers of steps?
                                            ____________

                                            Profile paul and kirsty yates
                                            Avatar

                                            Joined: Feb 16 06
                                            Posts: 11
                                            ID: 310
                                            Credit: 949
                                            RAC: 0
                                            Message 2378 - Posted 10 Oct 2006 16:47:50 UTC

                                              not an error as the w/u finished ok but did get this
                                              stderr out <core_client_version>5.4.11</core_client_version>
                                              <stderr_txt>
                                              # random seed: 2896098
                                              # cpu_run_time_pref: 3600
                                              WARNING! error deleting file .\\aa1IGC.out
                                              WARNING! error deleting file .\\aa1IGC.out.bonds
                                              WARNING! error deleting file .\\aa1IGC.out.rot_templates
                                              ======================================================
                                              DONE :: 1 starting structures built 1 (nstruct) times
                                              This process generated 1 decoys from 1 attempts
                                              0 starting pdbs were skipped
                                              ======================================================


                                              ____________

                                              rbpeake

                                              Joined: Feb 16 06
                                              Posts: 19
                                              ID: 218
                                              Credit: 3,370
                                              RAC: 0
                                              Message 2379 - Posted 10 Oct 2006 19:41:53 UTC - in response to Message 2378.

                                                not an error as the w/u finished ok but did get this
                                                stderr out <core_client_version>5.4.11</core_client_version>
                                                <stderr_txt>
                                                # random seed: 2896098
                                                # cpu_run_time_pref: 3600
                                                WARNING! error deleting file .\\aa1IGC.out
                                                WARNING! error deleting file .\\aa1IGC.out.bonds
                                                WARNING! error deleting file .\\aa1IGC.out.rot_templates
                                                ======================================================
                                                DONE :: 1 starting structures built 1 (nstruct) times
                                                This process generated 1 decoys from 1 attempts
                                                0 starting pdbs were skipped
                                                ======================================================



                                                I had the same issue.

                                                Result ID 288375
                                                Name DOC_4HTC_u_pert_mcm_bbmin_1340_20_0
                                                Workunit 254288
                                                Created 10 Oct 2006 11:51:18 UTC
                                                Sent 10 Oct 2006 12:13:39 UTC
                                                Received 10 Oct 2006 16:10:29 UTC
                                                Server state Over
                                                Outcome Success
                                                Client state Done
                                                Exit status 0 (0x0)
                                                Computer ID 250
                                                Report deadline 14 Oct 2006 12:13:39 UTC
                                                CPU time 13897.25
                                                stderr out

                                                <core_client_version>5.6.5</core_client_version>
                                                <![CDATA[
                                                <stderr_txt>
                                                # random seed: 2895533
                                                # cpu_run_time_pref: 14400
                                                WARNING! error deleting file .\\aa4HTC.out
                                                WARNING! error deleting file .\\aa4HTC.out.bonds
                                                WARNING! error deleting file .\\aa4HTC.out.rot_templates
                                                ======================================================
                                                DONE :: 1 starting structures built 23 (nstruct) times
                                                This process generated 23 decoys from 23 attempts
                                                0 starting pdbs were skipped
                                                ======================================================


                                                BOINC :: Watchdog shutting down...
                                                BOINC :: BOINC support services shutting down...

                                                </stderr_txt>
                                                ]]>

                                                Validate state Valid
                                                Claimed credit 47.6463856052397
                                                Granted credit 50.3978804981935
                                                application version 5.32
                                                ____________

                                                Chu
                                                Forum moderator
                                                Project developer
                                                Project scientist

                                                Joined: Sep 26 06
                                                Posts: 61
                                                ID: 1900
                                                Credit: 12,545
                                                RAC: 0
                                                Message 2380 - Posted 10 Oct 2006 21:25:47 UTC - in response to Message 2377.

                                                  Hi, this is a known issue, not just for V5.31. it might be due to the sensitivity of the mouse control setup in the graphics and will be fixed in the futural release.

                                                  To answer the second question, for docking WUs, there will be two proteins drawn. One in blue and the other in red. The calculation is, given the structures of two proteins, to search the optimal relatvie orientation between these two \"objects\" which gives the best anergy according to Rosetta scoring function. The docking protocol mainly comprises two parts. The first step is with low-resolution (only backbone is shown in the graphic) and is meant to find quickly a roughly fit shape complementarity between the two proteins. In the second step, the two proteins are represented by full atoms and the search space is mainly confined locally aiming at refining detailed protein-protein interactions across the interface. This step is relatively time-consuming and a lot of computation is used for optimizing sidechain interactions. Appearing on the graphics, the proteins sometimes do not move at all and that is because we currently have a hard time showing every step of sidechain movement ( we tried that in 5.28, but it resulted in a lot of errors probably due to some graphic issue) But generally users should be able to see in the fullatom docking stage that sidechains wiggle and the relative orientation of the two proteins changes from time to time in a small scale. Compared to ab initio and relax WUs, there are less steps and the run time is about on the same scale. And currently some dianostics on the screen saver such as score and rmsd do not always update timely due to some limitations in Rosetta code and since rmsd is calculated differently in docking, the value might be too large to be shown in the plot area. I will try to put more information explaing scientific aspect of docking soon.

                                                  Thanks for everybody\'s help here.

                                                  V5.31 docking. The graphic doesn\'t react properly to mouse control when not fully maximized. If I attempt to rotate the Low Energy image, the Native image does the rotating...if any reaction at all. Although I was able to right click and enlarge the low energy image. I could not enlarge the Native structure.

                                                  Is there any details on what to expect of a docking WU?? i.e. long running models, and low numbers of steps?

                                                  Chu
                                                  Forum moderator
                                                  Project developer
                                                  Project scientist

                                                  Joined: Sep 26 06
                                                  Posts: 61
                                                  ID: 1900
                                                  Credit: 12,545
                                                  RAC: 0
                                                  Message 2381 - Posted 10 Oct 2006 21:28:51 UTC - in response to Message 2379.

                                                    Your runs are ok, and we have known for a while on Windows platform those output files are gzipped but the original files can not be deleted right away. They will evnentually be after the WU is finished.

                                                    not an error as the w/u finished ok but did get this
                                                    stderr out <core_client_version>5.4.11</core_client_version>
                                                    <stderr_txt>
                                                    # random seed: 2896098
                                                    # cpu_run_time_pref: 3600
                                                    WARNING! error deleting file .\\aa1IGC.out
                                                    WARNING! error deleting file .\\aa1IGC.out.bonds
                                                    WARNING! error deleting file .\\aa1IGC.out.rot_templates
                                                    ======================================================
                                                    DONE :: 1 starting structures built 1 (nstruct) times
                                                    This process generated 1 decoys from 1 attempts
                                                    0 starting pdbs were skipped
                                                    ======================================================



                                                    I had the same issue.

                                                    Result ID 288375
                                                    Name DOC_4HTC_u_pert_mcm_bbmin_1340_20_0
                                                    Workunit 254288
                                                    Created 10 Oct 2006 11:51:18 UTC
                                                    Sent 10 Oct 2006 12:13:39 UTC
                                                    Received 10 Oct 2006 16:10:29 UTC
                                                    Server state Over
                                                    Outcome Success
                                                    Client state Done
                                                    Exit status 0 (0x0)
                                                    Computer ID 250
                                                    Report deadline 14 Oct 2006 12:13:39 UTC
                                                    CPU time 13897.25
                                                    stderr out

                                                    <core_client_version>5.6.5</core_client_version>
                                                    [CDATA[
                                                    <stderr_txt>
                                                    # random seed: 2895533
                                                    # cpu_run_time_pref: 14400
                                                    WARNING! error deleting file .\\aa4HTC.out
                                                    WARNING! error deleting file .\\aa4HTC.out.bonds
                                                    WARNING! error deleting file .\\aa4HTC.out.rot_templates
                                                    ======================================================
                                                    DONE :: 1 starting structures built 23 (nstruct) times
                                                    This process generated 23 decoys from 23 attempts
                                                    0 starting pdbs were skipped
                                                    ======================================================


                                                    BOINC :: Watchdog shutting down...
                                                    BOINC :: BOINC support services shutting down...

                                                    </stderr_txt>
                                                    ]]

                                                    Validate state Valid
                                                    Claimed credit 47.6463856052397
                                                    Granted credit 50.3978804981935
                                                    application version 5.32

                                                    Profile Astro

                                                    Joined: Feb 16 06
                                                    Posts: 141
                                                    ID: 48
                                                    Credit: 32,977
                                                    RAC: 0
                                                    Message 2382 - Posted 10 Oct 2006 21:49:08 UTC - in response to Message 2375.

                                                      Last modified: 10 Oct 2006 21:36:44 UTC

                                                      > On my Windows machine, I am still having screensaver lockups. It has carried over from 5.28. The screensaver will be processing and showing data fine but after a long time on (probably greater than 1 hour?) when I move the mouse nothing happens and the screensaver is doing nothing either. Task manager shows the programme is still working fine but not the screensaver. I tried stopping BoincManager.exe and boinc.exe but this did nothing, I can still get the start menu up but unable to get rid of screensaver background. I was about to reboot when I thought to double click on the screensaver and my computer was returned to me.
                                                      Has anyone else had this happen?
                                                      Not a problem on Linux machines as they don\'t have the screensaver function. Can it be turned of in Windows?

                                                      Yes, I have. On my laptop(never on a desktop). I\'ve seen it predominately with Rosetta dating back to 5.22, but have seen it twice with Setibeta or seti. The screensaver will lock itself on top and will not go away. By clicking on places I can hear that it\'s actually still interfacing with the IE browser window below and it makes noise. Example, the browser window beneath the screensaver had a box game that if you shot a duck you\'d win some fantastic prize. I could hear the gun shots from my clicking the mouse over where that area used to be. Rebooting has been my only option. Not even ctrl/alt/del works. Rom Walton has recieved my message about this many times. It only happens once every week or so, so it\'s hard to track. If you turn screensaver OFF it doesn\'t happen.

                                                      tony

                                                      Profile paul and kirsty yates
                                                      Avatar

                                                      Joined: Feb 16 06
                                                      Posts: 11
                                                      ID: 310
                                                      Credit: 949
                                                      RAC: 0
                                                      Message 2383 - Posted 10 Oct 2006 22:31:23 UTC

                                                        thanks for the reply chu

                                                        thought i should say something in case it was an unknown prob
                                                        ____________

                                                        Profile Astro

                                                        Joined: Feb 16 06
                                                        Posts: 141
                                                        ID: 48
                                                        Credit: 32,977
                                                        RAC: 0
                                                        Message 2384 - Posted 10 Oct 2006 22:34:38 UTC - in response to Message 2383.

                                                          thanks for the reply chu

                                                          thought i should say something in case it was an unknown prob

                                                          indeed. Perhaps if more report it, it\'ll become a priority??? LOL

                                                          Profile Astro

                                                          Joined: Feb 16 06
                                                          Posts: 141
                                                          ID: 48
                                                          Credit: 32,977
                                                          RAC: 0
                                                          Message 2385 - Posted 10 Oct 2006 22:37:32 UTC

                                                            To me it seems like it doesn\'t happen when the screensaver turns on, but more \"maybe\" when my power options turns OFF the monitor. Like I said, It doesn\'t happen often enough for me to even be sure of any efforts to fix it.

                                                            Conrad Poohs
                                                            Avatar

                                                            Joined: Aug 29 06
                                                            Posts: 9
                                                            ID: 1758
                                                            Credit: 1,955
                                                            RAC: 0
                                                            Message 2386 - Posted 11 Oct 2006 5:24:38 UTC

                                                              I got two WUs which started while Monitor was switched off. One had an error regarding screensaver, it then stopped processing but did not exit (though it said it did) until end of time slot, it then fell over:-

                                                              2006-10-11 02:03:43 [ralph@home] rosetta_beta not responding to screensaver, exiting

                                                              2006-10-11 05:47:10 [ralph@home] Unrecoverable error for result IDL_RLX_NT_t364_CASP7_hom001_1_1342_3_0 ( - exit code -1 (0xffffffff))

                                                              The second WU ran alongside and seems fine so far, having completed one two hour time slot, another 3.5 hours to run, fingers crossed.
                                                              ____________

                                                              Profile Krzychu P.

                                                              Joined: Feb 16 06
                                                              Posts: 19
                                                              ID: 114
                                                              Credit: 10,236
                                                              RAC: 0
                                                              Message 2387 - Posted 11 Oct 2006 7:30:14 UTC

                                                                Today I get:

                                                                2006-10-11 08:05:30|ralph@home|Unrecoverable error for result 1t4o_1_CASPR_1_1t4o_1_xxidid_model_50_core_0001IGNORE_THE_REST_idl_1344_3_0 (Niepoprawna funkcja. (0x1) - exit code 1 (0x1))

                                                                Niepoprawna funkcja. (0x1) - exit code 1 (0x1)
                                                                </message>
                                                                <stderr_txt>
                                                                # random seed: 2894240
                                                                ABORT: bad to aa_rotno_to_packedrotno
                                                                aa,rot1/2/3/4: ARG 15 3 2 2 0
                                                                chi no 4 nchi 4 aav 1 is_chi_proton_rotamer(aa,aav,i) 0
                                                                ERROR:: Exit at: .\\rotamer_functions.cc line:1458

                                                                And

                                                                2006-10-11 09:23:23|ralph@home|Unrecoverable error for result 1hz6A_BOINC_NATIVEJUMPS_CLOSE_CHAINBREAKS_VARY_BOND_ANGLES_SAVE_ALL_OUT__1343_28_0 (Niepoprawna funkcja. (0x1) - exit code 1 (0x1))

                                                                Niepoprawna funkcja. (0x1) - exit code 1 (0x1)
                                                                </message>
                                                                <stderr_txt>
                                                                # random seed: 2894605
                                                                sin_cos_range ERROR: -1.#IND000 is outside of [-1,+1] range
                                                                sin_cos_range ERROR: -1.#IND000 is outside of [-1,+1] range
                                                                sin_cos_range ERROR: -1.#IND000 is outside of [-1,+1] range
                                                                sin_cos_range ERROR: -1.#IND000 is outside of [-1,+1] range
                                                                ABORT: bad to aa_rotno_to_packedrotno
                                                                aa,rot1/2/3/4: GLU 4 2 0 1 0
                                                                chi no 2 nchi 3 aav 1 is_chi_proton_rotamer(aa,aav,i) 0
                                                                ERROR:: Exit at: .\\rotamer_functions.cc line:1458

                                                                One WU went good.

                                                                ____________

                                                                SafeAggie

                                                                Joined: Oct 5 06
                                                                Posts: 6
                                                                ID: 1943
                                                                Credit: 4,207
                                                                RAC: 0
                                                                Message 2388 - Posted 11 Oct 2006 11:39:50 UTC

                                                                  Unrecoverable error for result IDL_RLX_NT_t326_CASP7_hom001_1_1342_3_0 (Incorrect function. (0x1) - exit code 1 (0x1))

                                                                  resultid=288651

                                                                  Profile Krzychu P.

                                                                  Joined: Feb 16 06
                                                                  Posts: 19
                                                                  ID: 114
                                                                  Credit: 10,236
                                                                  RAC: 0
                                                                  Message 2389 - Posted 11 Oct 2006 12:01:34 UTC

                                                                    Last modified: 11 Oct 2006 12:08:36 UTC

                                                                    and next one:

                                                                    2006-10-11 14:02:26|ralph@home|Unrecoverable error for result DOC_2VIR_u_pert_mcm_bbmin_1340_17_2 (Niepoprawna funkcja. (0x1) - exit code 1 (0x1))

                                                                    Niepoprawna funkcja. (0x1) - exit code 1 (0x1)
                                                                    </message>
                                                                    <stderr_txt>
                                                                    # random seed: 2895576
                                                                    sin_cos_range ERROR: -1.#IND000 is outside of [-1,+1] range
                                                                    sin_cos_range ERROR: -1.#IND000 is outside of [-1,+1] range
                                                                    ABORT: bad to aa_rotno_to_packedrotno
                                                                    aa,rot1/2/3/4: LYS 9 3 0 2 0
                                                                    chi no 2 nchi 4 aav 1 is_chi_proton_rotamer(aa,aav,i) 0
                                                                    ERROR:: Exit at: .\\rotamer_functions.cc line:1458


                                                                    2006-10-11 14:19:44|ralph@home|Unrecoverable error for result IDL_RLX_NT_t291_CASP7_hom001_1_1342_4_1 (Niepoprawna funkcja. (0x1) - exit code 1 (0x1))

                                                                    Niepoprawna funkcja. (0x1) - exit code 1 (0x1)
                                                                    </message>
                                                                    <stderr_txt>
                                                                    # random seed: 2895459
                                                                    # cpu_run_time_pref: 3600
                                                                    ABORT: bad to aa_rotno_to_packedrotno
                                                                    aa,rot1/2/3/4: ARG 15 3 2 1 0
                                                                    chi no 4 nchi 4 aav 1 is_chi_proton_rotamer(aa,aav,i) 0
                                                                    ERROR:: Exit at: .\\rotamer_functions.cc line:1458


                                                                    2006-10-11 14:29:43|ralph@home|Unrecoverable error for result 5croA_BOINC_ABRELAX_SAVE_ALL_OUT_truess__1334_17_1 (Niepoprawna funkcja. (0x1) - exit code 1 (0x1))

                                                                    Niepoprawna funkcja. (0x1) - exit code 1 (0x1)
                                                                    </message>
                                                                    <stderr_txt>
                                                                    # random seed: 2898706
                                                                    ABORT: bad to aa_rotno_to_packedrotno
                                                                    aa,rot1/2/3/4: LYS 9 3 2 0 0
                                                                    chi no 3 nchi 4 aav 1 is_chi_proton_rotamer(aa,aav,i) 0
                                                                    ERROR:: Exit at: .\\rotamer_functions.cc line:1458
                                                                    ____________

                                                                    Profile anders n

                                                                    Joined: Feb 16 06
                                                                    Posts: 166
                                                                    ID: 91
                                                                    Credit: 131,419
                                                                    RAC: 0
                                                                    Message 2390 - Posted 11 Oct 2006 16:15:44 UTC

                                                                      What does this text mean?

                                                                      2006-10-11 09:26:56|ralph@home|Started upload of file DOC_2VIR_u_pert_mcm_bbmin_1340_5_0_0
                                                                      2006-10-11 09:26:56|ralph@home|Started upload of file DOC_2VIR_u_pert_mcm_bbmin_1340_5_0_1
                                                                      2006-10-11 09:26:59||Curl error: a libcurl function was given a bad argument
                                                                      2006-10-11 09:26:59||Curl error: a libcurl function was given a bad argument
                                                                      2006-10-11 09:27:06|ralph@home|Finished upload of file DOC_2VIR_u_pert_mcm_bbmin_1340_5_0_1


                                                                      Anders n

                                                                      ____________

                                                                      Chu
                                                                      Forum moderator
                                                                      Project developer
                                                                      Project scientist

                                                                      Joined: Sep 26 06
                                                                      Posts: 61
                                                                      ID: 1900
                                                                      Credit: 12,545
                                                                      RAC: 0
                                                                      Message 2391 - Posted 11 Oct 2006 16:36:02 UTC - in response to Message 2389.

                                                                        Hi, it looks like that you may have a corrupted rosetta_database which could be caused by various reasons...

                                                                        and next one:

                                                                        2006-10-11 14:02:26|ralph@home|Unrecoverable error for result DOC_2VIR_u_pert_mcm_bbmin_1340_17_2 (Niepoprawna funkcja. (0x1) - exit code 1 (0x1))

                                                                        Niepoprawna funkcja. (0x1) - exit code 1 (0x1)
                                                                        </message>
                                                                        <stderr_txt>
                                                                        # random seed: 2895576
                                                                        sin_cos_range ERROR: -1.#IND000 is outside of [-1,+1] range
                                                                        sin_cos_range ERROR: -1.#IND000 is outside of [-1,+1] range
                                                                        ABORT: bad to aa_rotno_to_packedrotno
                                                                        aa,rot1/2/3/4: LYS 9 3 0 2 0
                                                                        chi no 2 nchi 4 aav 1 is_chi_proton_rotamer(aa,aav,i) 0
                                                                        ERROR:: Exit at: .\\rotamer_functions.cc line:1458


                                                                        2006-10-11 14:19:44|ralph@home|Unrecoverable error for result IDL_RLX_NT_t291_CASP7_hom001_1_1342_4_1 (Niepoprawna funkcja. (0x1) - exit code 1 (0x1))

                                                                        Niepoprawna funkcja. (0x1) - exit code 1 (0x1)
                                                                        </message>
                                                                        <stderr_txt>
                                                                        # random seed: 2895459
                                                                        # cpu_run_time_pref: 3600
                                                                        ABORT: bad to aa_rotno_to_packedrotno
                                                                        aa,rot1/2/3/4: ARG 15 3 2 1 0
                                                                        chi no 4 nchi 4 aav 1 is_chi_proton_rotamer(aa,aav,i) 0
                                                                        ERROR:: Exit at: .\\rotamer_functions.cc line:1458


                                                                        2006-10-11 14:29:43|ralph@home|Unrecoverable error for result 5croA_BOINC_ABRELAX_SAVE_ALL_OUT_truess__1334_17_1 (Niepoprawna funkcja. (0x1) - exit code 1 (0x1))

                                                                        Niepoprawna funkcja. (0x1) - exit code 1 (0x1)
                                                                        </message>
                                                                        <stderr_txt>
                                                                        # random seed: 2898706
                                                                        ABORT: bad to aa_rotno_to_packedrotno
                                                                        aa,rot1/2/3/4: LYS 9 3 2 0 0
                                                                        chi no 3 nchi 4 aav 1 is_chi_proton_rotamer(aa,aav,i) 0
                                                                        ERROR:: Exit at: .\\rotamer_functions.cc line:1458

                                                                        Pieface

                                                                        Joined: Feb 16 06
                                                                        Posts: 64
                                                                        ID: 234
                                                                        Credit: 203,513
                                                                        RAC: 0
                                                                        Message 2392 - Posted 11 Oct 2006 19:47:50 UTC

                                                                          I just finished what may be a \'problem\' unit:
                                                                          wuid 252995
                                                                          someone else did it in 5.31 and mine ran 5.32, but we both got \'validate\' errors.

                                                                          Leffe

                                                                          Joined: Feb 19 06
                                                                          Posts: 10
                                                                          ID: 596
                                                                          Credit: 3,683
                                                                          RAC: 0
                                                                          Message 2393 - Posted 12 Oct 2006 2:54:43 UTC

                                                                            there was another error in visual basic (or C++ don\'t remember for sure) \"pure virtual call\"

                                                                            11/10/2006 20:53:30|SETI@home|Deferring task 21au02ab.16275.8016.234634.3.146_2
                                                                            11/10/2006 20:53:31|ralph@home|Resuming task IDL_RLX_NT_t288_CASP7_hom001_1_1342_5_0 using rosetta_beta version 532
                                                                            11/10/2006 20:53:32||Using earliest-deadline-first scheduling because computer is overcommitted.
                                                                            11/10/2006 20:53:32||Suspending work fetch because computer is overcommitted.
                                                                            12/10/2006 05:49:40|ralph@home|Unrecoverable error for result IDL_RLX_NT_t288_CASP7_hom001_1_1342_5_0 (The system cannot find the path specified. (0x3) - exit code 3 (0x3))
                                                                            12/10/2006 05:49:40|ralph@home|Deferring scheduler requests for 1 minutes and 0 seconds

                                                                            ____________

                                                                            Profile Astro

                                                                            Joined: Feb 16 06
                                                                            Posts: 141
                                                                            ID: 48
                                                                            Credit: 32,977
                                                                            RAC: 0
                                                                            Message 2394 - Posted 12 Oct 2006 2:59:09 UTC - in response to Message 2390.

                                                                              What does this text mean?

                                                                              2006-10-11 09:26:56|ralph@home|Started upload of file DOC_2VIR_u_pert_mcm_bbmin_1340_5_0_0
                                                                              2006-10-11 09:26:56|ralph@home|Started upload of file DOC_2VIR_u_pert_mcm_bbmin_1340_5_0_1
                                                                              2006-10-11 09:26:59||Curl error: a libcurl function was given a bad argument
                                                                              2006-10-11 09:26:59||Curl error: a libcurl function was given a bad argument
                                                                              2006-10-11 09:27:06|ralph@home|Finished upload of file DOC_2VIR_u_pert_mcm_bbmin_1340_5_0_1


                                                                              Anders n

                                                                              If you\'re using 5.6.5 then Rom has submitted a fix for this to show up in the next version.

                                                                              tony

                                                                              Chu
                                                                              Forum moderator
                                                                              Project developer
                                                                              Project scientist

                                                                              Joined: Sep 26 06
                                                                              Posts: 61
                                                                              ID: 1900
                                                                              Credit: 12,545
                                                                              RAC: 0
                                                                              Message 2395 - Posted 12 Oct 2006 3:32:15 UTC

                                                                                We have seen errors (stop in options.cc ) for jobs batch 1349 and will fix that soon. Sorry about this.

                                                                                Profile KSMarksPsych
                                                                                Avatar

                                                                                Joined: Feb 16 06
                                                                                Posts: 40
                                                                                ID: 72
                                                                                Credit: 8,226
                                                                                RAC: 0
                                                                                Message 2396 - Posted 12 Oct 2006 3:34:10 UTC

                                                                                  This one and this one died before they even got started.

                                                                                  The error is

                                                                                  <core_client_version>5.4.11</core_client_version>
                                                                                  <message>
                                                                                  Incorrect function. (0x1) - exit code 1 (0x1)
                                                                                  </message>
                                                                                  <stderr_txt>
                                                                                  ERROR:: Exit at: .\\options.cc line:453

                                                                                  </stderr_txt>

                                                                                  Leffe

                                                                                  Joined: Feb 19 06
                                                                                  Posts: 10
                                                                                  ID: 596
                                                                                  Credit: 3,683
                                                                                  RAC: 0
                                                                                  Message 2400 - Posted 12 Oct 2006 17:23:46 UTC


                                                                                    this was a screensaver lockup had to open task manager twice before i could abort the screensaver

                                                                                    12/10/2006 18:53:14||Rescheduling CPU: application exited
                                                                                    12/10/2006 18:53:14|ralph@home|Computation for task IDL_RLX_NT_t290_CASP7_hom001_1_1342_5_0 finished
                                                                                    12/10/2006 18:53:14|ralph@home|Starting task IDL_RLX_NT_t291_CASP7_hom001_1_1342_5_0 using rosetta_beta version 532
                                                                                    12/10/2006 18:53:16|ralph@home|Started upload of file IDL_RLX_NT_t290_CASP7_hom001_1_1342_5_0_0
                                                                                    12/10/2006 18:53:22|ralph@home|Finished upload of file IDL_RLX_NT_t290_CASP7_hom001_1_1342_5_0_0
                                                                                    12/10/2006 18:53:22|ralph@home|Throughput 6582 bytes/sec
                                                                                    12/10/2006 19:48:47|ralph@home|Unrecoverable error for result IDL_RLX_NT_t291_CASP7_hom001_1_1342_5_0 ( - exit code 1073807364 (0x40010004))
                                                                                    12/10/2006 19:48:47|ralph@home|Deferring scheduler requests for 1 minutes and 0 seconds
                                                                                    12/10/2006 19:48:47||Rescheduling CPU: application exited

                                                                                    ____________

                                                                                    Profile anders n

                                                                                    Joined: Feb 16 06
                                                                                    Posts: 166
                                                                                    ID: 91
                                                                                    Credit: 131,419
                                                                                    RAC: 0
                                                                                    Message 2401 - Posted 12 Oct 2006 17:38:14 UTC - in response to Message 2394.

                                                                                      What does this text mean?

                                                                                      2006-10-11 09:26:56|ralph@home|Started upload of file DOC_2VIR_u_pert_mcm_bbmin_1340_5_0_0
                                                                                      2006-10-11 09:26:56|ralph@home|Started upload of file DOC_2VIR_u_pert_mcm_bbmin_1340_5_0_1
                                                                                      2006-10-11 09:26:59||Curl error: a libcurl function was given a bad argument
                                                                                      2006-10-11 09:26:59||Curl error: a libcurl function was given a bad argument
                                                                                      2006-10-11 09:27:06|ralph@home|Finished upload of file DOC_2VIR_u_pert_mcm_bbmin_1340_5_0_1


                                                                                      Anders n

                                                                                      If you\'re using 5.6.5 then Rom has submitted a fix for this to show up in the next version.

                                                                                      tony



                                                                                      Thanks

                                                                                      Anders n

                                                                                      ____________

                                                                                      Leffe

                                                                                      Joined: Feb 19 06
                                                                                      Posts: 10
                                                                                      ID: 596
                                                                                      Credit: 3,683
                                                                                      RAC: 0
                                                                                      Message 2402 - Posted 13 Oct 2006 2:06:20 UTC

                                                                                        this was a new one...

                                                                                        13/10/2006 01:07:22|ralph@home|Computation for task IDL_RLX_NT_t293_CASP7_hom001_1_1342_5_0 finished
                                                                                        13/10/2006 01:07:22|ralph@home|Starting task IDL_RLX_NT_t294_CASP7_hom001_1_1342_5_0 using rosetta_beta version 532
                                                                                        13/10/2006 01:07:24|ralph@home|Started upload of file IDL_RLX_NT_t293_CASP7_hom001_1_1342_5_0_0
                                                                                        13/10/2006 01:07:29|ralph@home|Finished upload of file IDL_RLX_NT_t293_CASP7_hom001_1_1342_5_0_0
                                                                                        13/10/2006 01:07:29|ralph@home|Throughput 12437 bytes/sec
                                                                                        13/10/2006 03:37:37|ralph@home|Unrecoverable error for result IDL_RLX_NT_t294_CASP7_hom001_1_1342_5_0 (One or more arguments are invalid (0x80000003) - exit code -2147483645 (0x80000003))
                                                                                        13/10/2006 03:37:37|ralph@home|Deferring scheduler requests for 1 minutes and 0 seconds
                                                                                        13/10/2006 03:37:37||Rescheduling CPU: application exited
                                                                                        13/10/2006 03:37:37|ralph@home|Computation for task IDL_RLX_NT_t294_CASP7_hom001_1_1342_5_0 finished

                                                                                        ____________

                                                                                        Chu
                                                                                        Forum moderator
                                                                                        Project developer
                                                                                        Project scientist

                                                                                        Joined: Sep 26 06
                                                                                        Posts: 61
                                                                                        ID: 1900
                                                                                        Credit: 12,545
                                                                                        RAC: 0
                                                                                        Message 2403 - Posted 13 Oct 2006 4:25:23 UTC - in response to Message 2402.

                                                                                          It looks that the run was stuck and the score was not changed for a long time. So it was forced to stop ... Why that happened will be investigated. Thanks for the report.

                                                                                          this was a new one...

                                                                                          13/10/2006 01:07:22|ralph@home|Computation for task IDL_RLX_NT_t293_CASP7_hom001_1_1342_5_0 finished
                                                                                          13/10/2006 01:07:22|ralph@home|Starting task IDL_RLX_NT_t294_CASP7_hom001_1_1342_5_0 using rosetta_beta version 532
                                                                                          13/10/2006 01:07:24|ralph@home|Started upload of file IDL_RLX_NT_t293_CASP7_hom001_1_1342_5_0_0
                                                                                          13/10/2006 01:07:29|ralph@home|Finished upload of file IDL_RLX_NT_t293_CASP7_hom001_1_1342_5_0_0
                                                                                          13/10/2006 01:07:29|ralph@home|Throughput 12437 bytes/sec
                                                                                          13/10/2006 03:37:37|ralph@home|Unrecoverable error for result IDL_RLX_NT_t294_CASP7_hom001_1_1342_5_0 (One or more arguments are invalid (0x80000003) - exit code -2147483645 (0x80000003))
                                                                                          13/10/2006 03:37:37|ralph@home|Deferring scheduler requests for 1 minutes and 0 seconds
                                                                                          13/10/2006 03:37:37||Rescheduling CPU: application exited
                                                                                          13/10/2006 03:37:37|ralph@home|Computation for task IDL_RLX_NT_t294_CASP7_hom001_1_1342_5_0 finished

                                                                                          MatrixCrawler

                                                                                          Joined: Oct 8 06
                                                                                          Posts: 1
                                                                                          ID: 1980
                                                                                          Credit: 709
                                                                                          RAC: 0
                                                                                          Message 2405 - Posted 13 Oct 2006 11:39:17 UTC

                                                                                            13.10.2006 13:13:41|ralph@home|Unrecoverable error for result DOC_2KAI_bound_perturb_benchmark_1349_2_2 (Unzulässige Funktion. (0x1) - exit code 1 (0x1))
                                                                                            13.10.2006 13:13:44|ralph@home|Unrecoverable error for result DOC_2PCC_bound_perturb_benchmark_1349_2_2 (Unzulässige Funktion. (0x1) - exit code 1 (0x1))
                                                                                            13.10.2006 13:13:47|ralph@home|Unrecoverable error for result DOC_2PTC_bound_perturb_benchmark_1349_2_2 (Unzulässige Funktion. (0x1) - exit code 1 (0x1))
                                                                                            13.10.2006 13:13:51|ralph@home|Unrecoverable error for result DOC_2SIC_bound_perturb_benchmark_1349_2_2 (Unzulässige Funktion. (0x1) - exit code 1 (0x1))

                                                                                            Profile Saenger
                                                                                            Avatar

                                                                                            Joined: Feb 28 06
                                                                                            Posts: 12
                                                                                            ID: 861
                                                                                            Credit: 44,776
                                                                                            RAC: 6
                                                                                            Message 2407 - Posted 13 Oct 2006 16:54:06 UTC

                                                                                              My Ralph just stopped the progress @1.002%. CPU-time went up, but nothing else seems to happen.
                                                                                              I\'ve suspended the WU for now, should I abort it or do anything else?

                                                                                              This is the stderr.txt:

                                                                                              Graphics are disabled due to configuration...
                                                                                              # random seed: 2898263
                                                                                              # cpu_run_time_pref: 14400
                                                                                              Graphics are disabled due to configuration...
                                                                                              # cpu_run_time_pref: 14400

                                                                                              And this is the stdout.txt:
                                                                                              [REAL OPT]Default value for [-cpu_frac] 10
                                                                                              [REAL OPT]Default value for [-frame_rate] 10
                                                                                              [INT OPT]New value for [-cpu_run_time] 3600
                                                                                              command executed: rosetta_beta_5.32_i686-pc-linux-gnu aa t339 _ -relax -looprlx -nstruct 5 -farlx -ex1 -ex2 -loop_model -termini -short_range_hb_weight 0.50 -long_range_hb_weight 1.0 -farlx_cycle_ratio 1.0 -idl_no_chain_break -vary_omega -output_silent_gz -output_chi_silent -protein_name_prefix idlrlx_hom001_ -frags_name_prefix idlrlx_boinc_hom001_ -s T0339_t339_1_2.pdb -paths paths_200_idlrlx.txt -do_farlx_checkpointing -checkpointing_interval 10 -cpu_run_time 3600 -watchdog -constant_seed -jran 2898263
                                                                                              [STR OPT]New value for [-paths] paths_200_idlrlx.txt.
                                                                                              [INT OPT]Default value for [-seed_offset] 0
                                                                                              [T/F OPT]Default FALSE value for [-version]
                                                                                              [T/F OPT]Default FALSE value for [-score]
                                                                                              [T/F OPT]Default FALSE value for [-abinitio]
                                                                                              [T/F OPT]Default FALSE value for [-refine]
                                                                                              [T/F OPT]Default FALSE value for [-assemble]
                                                                                              [T/F OPT]Default FALSE value for [-idealize]
                                                                                              [T/F OPT]New TRUE value for [-relax]
                                                                                              [T/F OPT]Default FALSE value for [-sim_aneal]
                                                                                              [T/F OPT]Default FALSE value for [-cenrlx]
                                                                                              [T/F OPT]New TRUE value for [-farlx]
                                                                                              [T/F OPT]Default FALSE value for [-record_irms_before_relax]
                                                                                              [T/F OPT]Default FALSE value for [-force_expand]
                                                                                              [T/F OPT]New TRUE value for [-looprlx]
                                                                                              [T/F OPT]Default FALSE value for [-pose_relax]
                                                                                              [T/F OPT]Default FALSE value for [-minimize]
                                                                                              [T/F OPT]Default FALSE value for [-loop_farlx_only]
                                                                                              Rosetta mode: relax
                                                                                              [T/F OPT]Default FALSE value for [-chain]
                                                                                              [T/F OPT]Default FALSE value for [-protein]
                                                                                              [T/F OPT]Default FALSE value for [-series]
                                                                                              series_code = aa :: protein_name is t339:: chain_id is _.
                                                                                              [INT OPT]New value for [-nstruct] 5
                                                                                              [T/F OPT]Default FALSE value for [-read_all_chains]
                                                                                              [T/F OPT]Default FALSE value for [-preserve_header]
                                                                                              [T/F OPT]Default FALSE value for [-use_pdb_numbering]
                                                                                              [T/F OPT]Default FALSE value for [-flip_symmetric_sidechains]
                                                                                              [T/F OPT]Default FALSE value for [-fa_input]
                                                                                              [T/F OPT]Default FALSE value for [-overwrite]
                                                                                              [T/F OPT]Default FALSE value for [-output_pdb_gz]
                                                                                              [T/F OPT]New TRUE value for [-output_silent_gz]
                                                                                              [T/F OPT]Default FALSE value for [-output_scorefile_gz]
                                                                                              [T/F OPT]Default FALSE value for [-sasapack_bvalues]
                                                                                              [T/F OPT]Default FALSE value for [-cenlist_values]
                                                                                              [T/F OPT]New TRUE value for [-termini]
                                                                                              [T/F OPT]Default FALSE value for [-use_trie]
                                                                                              [T/F OPT]Default FALSE value for [-no_trie]
                                                                                              [T/F OPT]Default FALSE value for [-use_conformer]
                                                                                              [T/F OPT]Default FALSE value for [-use_bbind_conformer]
                                                                                              [T/F OPT]Default FALSE value for [-trials_trie]
                                                                                              [T/F OPT]Default FALSE value for [-no_trials_trie]
                                                                                              [T/F OPT]Default FALSE value for [-output_interaction_graph_memory_usage]
                                                                                              [T/F OPT]Default FALSE value for [-read_interaction_graph]
                                                                                              [T/F OPT]Default FALSE value for [-write_interaction_graph]
                                                                                              [STR OPT]Default value for [-ig_file] .
                                                                                              [T/F OPT]Default FALSE value for [-use_sasa_pack_score]
                                                                                              [T/F OPT]Default FALSE value for [-output_dot_kinemage]
                                                                                              [T/F OPT]Default FALSE value for [-pack_low_temp_annealing]
                                                                                              [T/F OPT]Default FALSE value for [-no_his_his_pairE]
                                                                                              [T/F OPT]Default FALSE value for [-silent_input]
                                                                                              [T/F OPT]Default FALSE value for [-timer]
                                                                                              [T/F OPT]Default FALSE value for [-count_attempts]
                                                                                              [T/F OPT]Default FALSE value for [-status]
                                                                                              [T/F OPT]Default FALSE value for [-ise_movie]
                                                                                              [T/F OPT]Default FALSE value for [-output_all]
                                                                                              [T/F OPT]New TRUE value for [-output_chi_silent]
                                                                                              [T/F OPT]Default FALSE value for [-accept_all]
                                                                                              [T/F OPT]Default FALSE value for [-skip_missing_residues]
                                                                                              [STR OPT]Default value for [-cst] cst.
                                                                                              [STR OPT]Default value for [-dpl] dpl.
                                                                                              [STR OPT]Default value for [-resfile] none.
                                                                                              [STR OPT]Default value for [-equiv_resfile] none.
                                                                                              [T/F OPT]Default FALSE value for [-auto_resfile]
                                                                                              [T/F OPT]Default FALSE value for [-chain_inc]
                                                                                              WARNING::refold_input T, allow_missing T
                                                                                              setting refold_input F
                                                                                              [T/F OPT]Default FALSE value for [-full_filename]
                                                                                              [T/F OPT]Default FALSE value for [-map_sequence]
                                                                                              [INT OPT]Default value for [-max_frags] 200
                                                                                              [T/F OPT]Default FALSE value for [-output_centroids]
                                                                                              [STR OPT]New value for [-protein_name_prefix] idlrlx_hom001_.
                                                                                              [STR OPT]New value for [-frags_name_prefix] idlrlx_boinc_hom001_.
                                                                                              [T/F OPT]Default FALSE value for [-protein_name_prefix_homolog]
                                                                                              [REAL OPT]Default value for [-vdw_reweight] 1
                                                                                              [REAL OPT]Default value for [-env_reweight] 1
                                                                                              [REAL OPT]Default value for [-pair_reweight] 1
                                                                                              [REAL OPT]Default value for [-cb_reweight] 1
                                                                                              [REAL OPT]Default value for [-sheet_reweight] 1
                                                                                              [REAL OPT]Default value for [-ss_reweight] 1
                                                                                              [REAL OPT]Default value for [-hs_reweight] 1
                                                                                              [REAL OPT]Default value for [-rsigma_reweight] 1
                                                                                              [REAL OPT]Default value for [-rg_reweight] 1
                                                                                              [REAL OPT]Default value for [-pc_reweight] 1
                                                                                              [REAL OPT]Default value for [-fa_atr_reweight] 1
                                                                                              [REAL OPT]Default value for [-fa_rep_reweight] 1
                                                                                              [REAL OPT]Default value for [-fa_dun_reweight ] 1
                                                                                              [REAL OPT]Default value for [-fa_pair_reweight] 1
                                                                                              [REAL OPT]Default value for [-fa_plane_reweight] 1
                                                                                              [REAL OPT]Default value for [-fa_solv_reweight] 1
                                                                                              [REAL OPT]Default value for [-fa_ref_reweight ] 1
                                                                                              [REAL OPT]Default value for [-fa_pH_reweight] 1
                                                                                              [REAL OPT]Default value for [-fa_h2o_reweight] 1
                                                                                              [REAL OPT]Default value for [-fa_prob1b_reweight] 1
                                                                                              [REAL OPT]Default value for [-fa_gb_elec_reweigh] 1
                                                                                              [REAL OPT]Default value for [-hb_srbb_reweight] 1
                                                                                              [REAL OPT]Default value for [-hb_lrbb_reweight] 1
                                                                                              [REAL OPT]Default value for [-hb_sc_reweight] 1
                                                                                              [REAL OPT]Default value for [-chainbreak_reweight] 1
                                                                                              [T/F OPT]Default FALSE value for [-find_disulf]
                                                                                              [T/F OPT]Default FALSE value for [-fix_disulf]
                                                                                              [T/F OPT]Default FALSE value for [-enable_ligand_aa]
                                                                                              [T/F OPT]Default FALSE value for [-phospho_ser]
                                                                                              [T/F OPT]Default FALSE value for [-surface]
                                                                                              [T/F OPT]Default FALSE value for [-loops]
                                                                                              [T/F OPT]Default FALSE value for [-taboo]
                                                                                              [T/F OPT]New TRUE value for [-vary_omega]
                                                                                              [T/F OPT]Default FALSE value for [-geometric_sol]
                                                                                              [T/F OPT]Default FALSE value for [-multi_chain]
                                                                                              [T/F OPT]New TRUE value for [-ex1]
                                                                                              [T/F OPT]New TRUE value for [-ex2]
                                                                                              [T/F OPT]Default FALSE value for [-ex3]
                                                                                              [T/F OPT]Default FALSE value for [-ex4]
                                                                                              [T/F OPT]Default FALSE value for [-ex1aro]
                                                                                              [T/F OPT]Default FALSE value for [-ex1aro_half]
                                                                                              [T/F OPT]Default FALSE value for [-ex2aro_only]
                                                                                              [INT OPT]Default value for [-extrachi_cutoff] 18
                                                                                              [T/F OPT]Default FALSE value for [-rot_pert]
                                                                                              [T/F OPT]Default FALSE value for [-rot_pert_input]
                                                                                              [T/F OPT]Default FALSE value for [-exdb]
                                                                                              [T/F OPT]Default FALSE value for [-use_electrostatic_repulsion]
                                                                                              [T/F OPT]Default FALSE value for [-explicit_h2o]
                                                                                              [T/F OPT]Default FALSE value for [-solvate]
                                                                                              [T/F OPT]Default FALSE value for [-pH]
                                                                                              [T/F OPT]Default FALSE value for [-try_both_his_tautomers]
                                                                                              [T/F OPT]Default FALSE value for [-hydrate_dna]
                                                                                              [T/F OPT]Default FALSE value for [-ex_dna_waters]
                                                                                              [T/F OPT]Default FALSE value for [-minimize_rot]
                                                                                              [T/F OPT]Default FALSE value for [-read_hetero_h2o]
                                                                                              [T/F OPT]Default FALSE value for [-Wint_score_only]
                                                                                              [T/F OPT]Default FALSE value for [-Wint_repack_only]
                                                                                              [T/F OPT]Default FALSE value for [-ligand]
                                                                                              [T/F OPT]Default FALSE value for [-enzyme_design]
                                                                                              [T/F OPT]Default FALSE value for [-score_contact_flag]
                                                                                              [T/F OPT]Default FALSE value for [-score_contact_weight]
                                                                                              [T/F OPT]Default FALSE value for [-score_contact_threshold]
                                                                                              [T/F OPT]Default FALSE value for [-scorefxn]
                                                                                              default centroid scorefxn: 6
                                                                                              default fullatom scorefxn: 12
                                                                                              [INT OPT]Default value for [-run_level] 0
                                                                                              [T/F OPT]Default FALSE value for [-silent]
                                                                                              [T/F OPT]New TRUE value for [-output_silent_gz]
                                                                                              run level: -4
                                                                                              [T/F OPT]Default FALSE value for [-benchmark]
                                                                                              [T/F OPT]Default FALSE value for [-debug]
                                                                                              [INT OPT]Default value for [-sym_des_units] 1
                                                                                              [T/F OPT]Default FALSE value for [-mj_min]
                                                                                              [REAL OPT]Default value for [-mod_hhrep_height] 1
                                                                                              [REAL OPT]Default value for [-mod_hhrep_width] 1
                                                                                              [REAL OPT]Default value for [-mod_hhrep_center] 2.79999995
                                                                                              [REAL OPT]Default value for [-mod_hhrep_exponent] 4
                                                                                              [REAL OPT]Default value for [-smooth_etable_ljweight] 1.15999997
                                                                                              [REAL OPT]Default value for [-smooth_etable_solvweight] 1.5
                                                                                              [STR OPT]New value for [-s] T0339_t339_1_2.pdb.
                                                                                              Starting structure: T0339_t339_1_2
                                                                                              Reading ./Rama_smooth_dyn.dat_ss_6.4.gz
                                                                                              Reading ./phi.theta.36.HS.resmooth.gz
                                                                                              Reading ./phi.theta.36.SS.resmooth.gz
                                                                                              [STR OPT]Default value for [-atom_vdw_set] hybrid.
                                                                                              [T/F OPT]Default FALSE value for [-IUPAC]
                                                                                              Atom_mode set to all
                                                                                              Reading ./paircutoffs.gz
                                                                                              [T/F OPT]Default FALSE value for [-decoystats]
                                                                                              set_decoystats_flag: from,to F F
                                                                                              [T/F OPT]Default FALSE value for [-decoyfeatures]
                                                                                              [T/F OPT]Default FALSE value for [-evolution]
                                                                                              [T/F OPT]Default FALSE value for [-evol_recomb]
                                                                                              [T/F OPT]Default FALSE value for [-profile]
                                                                                              BOINC :: [2006-10-12 12:51:59] :: mode: relax :: nstartnum: 1 :: number_of_output: 5 :: num_decoys: 0 :: pct_complete: 0.01
                                                                                              [T/F OPT]New TRUE value for [-watchdog]
                                                                                              [INT OPT]Default value for [-watchdog_time] 3600
                                                                                              [REAL OPT]Default value for [-cpu_run_timeout_factor] 4
                                                                                              [T/F OPT]Default FALSE value for [-dummy_model]
                                                                                              Searching for dat file: ./idlrlx_hom001_t339.dat
                                                                                              Searching for dat file: ./idlrlx_hom001_t339.dat
                                                                                              WARNING!! .dat file not found!
                                                                                              Looking for fasta file: ./idlrlx_hom001_t339_.fasta
                                                                                              Looking for psipred file: ./idlrlx_hom001_t339_.psipred_ss2
                                                                                              Looking for psipred file: ./idlrlx_hom001_t339_.psipred_ss2
                                                                                              Looking for psipred file: ./idlrlx_hom001_t339_.jones
                                                                                              Looking for psipred file: ./idlrlx_hom001_t339_.psipred
                                                                                              Looking for psipred file: ./idlrlx_hom001_t339_.jones
                                                                                              Looking for psipred file: ./idlrlx_hom001_t339_.psipred
                                                                                              WARNING :: Unable to find psipred file!
                                                                                              [T/F OPT]Default FALSE value for [-tight_hb]
                                                                                              File: ./idlrlx_hom001_t339_.cst not found
                                                                                              Running without distance constraints
                                                                                              File: ./idlrlx_hom001_t339_.dpl not found
                                                                                              Dipolar constraints will not be used
                                                                                              fragment file: ./idlrlx_boinc_hom001_aat339_03_05.200_v1_3.gz
                                                                                              Total Residue 416
                                                                                              frag size: 3 frags/residue: 200
                                                                                              fragment file: ./idlrlx_boinc_hom001_aat339_09_05.200_v1_3.gz
                                                                                              Total Residue 416
                                                                                              frag size: 9 frags/residue: 25
                                                                                              generating 1mer library from 3mer library
                                                                                              [T/F OPT]Default FALSE value for [-ssblocks]
                                                                                              [T/F OPT]Default FALSE value for [-check_homs]
                                                                                              calculating fragment_diversity...
                                                                                              dihedral_bin: unusual angle
                                                                                              dihedral_bin: unusual angle
                                                                                              dihedral_bin: unusual angle
                                                                                              dihedral_bin: unusual angle
                                                                                              dihedral_bin: unusual angle
                                                                                              dihedral_bin: unusual angle
                                                                                              dihedral_bin: unusual angle
                                                                                              dihedral_bin: unusual angle
                                                                                              dihedral_bin: unusual angle
                                                                                              dihedral_bin: unusual angle
                                                                                              dihedral_bin: unusual angle
                                                                                              dihedral_bin: unusual angle
                                                                                              dihedral_bin: unusual angle
                                                                                              [T/F OPT]Default FALSE value for [-barcode_mode]
                                                                                              disabling all filters
                                                                                              [REAL OPT]Default value for [-co] -1
                                                                                              [REAL OPT]Default value for [-rms] -1
                                                                                              Searching for pdb...: ./idlrlx_hom001_t339.pdb
                                                                                              Searching for pdb...: ./idlrlx_hom001_t339.pdb
                                                                                              no pdb file for idlrlx_hom001_t339
                                                                                              [T/F OPT]Default FALSE value for [-repeatin]
                                                                                              [T/F OPT]Default FALSE value for [-repeatout]
                                                                                              [T/F OPT]Default FALSE value for [-clnt]
                                                                                              reading starting structure: ./T0339_t339_1_2.pdb.gz
                                                                                              [T/F OPT]Default FALSE value for [-use_native_centroid]
                                                                                              [T/F OPT]New TRUE value for [-constant_seed]
                                                                                              [INT OPT]New value for [-jran] 2898263
                                                                                              # =====================================
                                                                                              # random seed: 2898263
                                                                                              # =====================================
                                                                                              WARNING: 52 missing backbone atoms at 13 residues in pdb file
                                                                                              allow_missing= 1
                                                                                              skip_missing= 0
                                                                                              WARNING: 13 centroids were placed at 0,0,0
                                                                                              WARNING:: end of pdb file reached: angle, secstruct, & res info not found
                                                                                              Looking for dssp file: ./T0339_t339_1_2.dssp
                                                                                              dssp file not found
                                                                                              Looking for secondary structure assignment file: ./T0339_t339_1_2.ssa
                                                                                              ssa file not found
                                                                                              calculating secondary structure from torsion angles
                                                                                              [T/F OPT]Default FALSE value for [-use_input_bond]
                                                                                              [T/F OPT]Default FALSE value for [-regions]
                                                                                              [T/F OPT]Default FALSE value for [-apply_filters]
                                                                                              [T/F OPT]Default FALSE value for [-knot_filter]
                                                                                              [T/F OPT]Default FALSE value for [-poke_filter]
                                                                                              [T/F OPT]Default FALSE value for [-score_contact_fullatom]
                                                                                              [T/F OPT]New TRUE value for [-long_range_hb_weight]
                                                                                              [T/F OPT]New TRUE value for [-long_range_hb_weight]
                                                                                              [REAL OPT]New value for [-long_range_hb_weight] 1
                                                                                              [T/F OPT]New TRUE value for [-short_range_hb_weight]
                                                                                              [T/F OPT]New TRUE value for [-short_range_hb_weight]
                                                                                              [REAL OPT]New value for [-short_range_hb_weight] 0.5
                                                                                              [REAL OPT]Default value for [-fa_plane_weight] 0
                                                                                              [REAL OPT]Default value for [-omega_weight] 0.5
                                                                                              [T/F OPT]Default FALSE value for [-rand_envpair_res_wt]
                                                                                              [REAL OPT]Default value for [-parallel_weight] 1
                                                                                              [REAL OPT]Default value for [-antiparallel_weight] 1
                                                                                              [T/F OPT]Default FALSE value for [-rand_SS_wt]
                                                                                              [T/F OPT]Default FALSE value for [-random_parallel_antiparallel]
                                                                                              [T/F OPT]Default FALSE value for [-rand_cst_res_wt]
                                                                                              [T/F OPT]Default FALSE value for [-use_barcode_to_score]
                                                                                              initializing full atom functions
                                                                                              [T/F OPT]Default FALSE value for [-soft_rep]
                                                                                              [T/F OPT]Default FALSE value for [-soft_rep_design]
                                                                                              [T/F OPT]Default FALSE value for [-smooth_etable]
                                                                                              [T/F OPT]Default FALSE value for [-reduce_templates]
                                                                                              [T/F OPT]Default FALSE value for [-gen_born]
                                                                                              [T/F OPT]Default FALSE value for [-small_radii]
                                                                                              [T/F OPT]Default FALSE value for [-use_bw]
                                                                                              [T/F OPT]Default FALSE value for [-use_aw]
                                                                                              [T/F OPT]Default FALSE value for [-dna_weights]
                                                                                              [STR OPT]Default value for [-fa_lj_rep_slope] highres.
                                                                                              Reading ./bbdep02.May.sortlib.gz
                                                                                              Reading ./plane_data_table_1015.dat.gz
                                                                                              Reading ./pdbpairstats_fine.gz
                                                                                              Reading ./Paa.gz
                                                                                              Reading ./Paa_n.gz
                                                                                              Reading ./Paa_pp.gz
                                                                                              generating Etable...
                                                                                              Starting energy table calculation
                                                                                              Energy table parameter set: polh_aroh Revision: 10024 Date: 2006-08-28 13:54:52 -0700 (Mon, 28 Aug 2006)
                                                                                              [T/F OPT]Default FALSE value for [-mod_hhrep]
                                                                                              [T/F OPT]Default FALSE value for [-output_etables]
                                                                                              [T/F OPT]Default FALSE value for [-mod_etable]
                                                                                              Finished calculating energy tables.
                                                                                              Reading ./avgE_from_pdb.gz
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 92
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 93
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 94
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 95
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 96
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 97
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 98
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 99
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 100
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 101
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 102
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 103
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 104
                                                                                              [REAL OPT]Default value for [-rsd_wt_helix] 1
                                                                                              [REAL OPT]Default value for [-rsd_wt_strand] 1
                                                                                              [REAL OPT]Default value for [-rsd_wt_loop] 1
                                                                                              [T/F OPT]Default FALSE value for [-burial_code]
                                                                                              [T/F OPT]Default FALSE value for [-new_centroid_packing]
                                                                                              [REAL OPT]Default value for [-cb_weight] 1
                                                                                              [REAL OPT]Default value for [-strand_dist_cutoff] 6.5
                                                                                              [T/F OPT]Default FALSE value for [-stretch_strand_dist_cutoff]
                                                                                              [REAL OPT]Default value for [-localstrandpair_penalty] 0
                                                                                              [T/F OPT]Default FALSE value for [-handedness_score]
                                                                                              [T/F OPT]Default FALSE value for [-separate_centroid_pack_score]
                                                                                              Reading ./SASA-masks.dat.gz
                                                                                              Reading ./SASA-angles.dat.gz
                                                                                              ========================================
                                                                                              Reading ./sasa_offsets.txt.gz
                                                                                              Reading ./sasa_prob_cdf.txt.gz
                                                                                              NEXT STRUCTURE: ./aaT0339_t339_1_2_0001.pdb
                                                                                              [T/F OPT]Default FALSE value for [-fullatom_loop]
                                                                                              setting pose_flag from: 0 to: 1
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 92
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 93
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 94
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 95
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 96
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 97
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 98
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 99
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 100
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 101
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 102
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 103
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 104
                                                                                              setting pose_flag from: 1 to: 0
                                                                                              [T/F OPT]Default FALSE value for [-obligate_loops]
                                                                                              [INT OPT]New value for [-checkpointing_interval] 10
                                                                                              [T/F OPT]Default FALSE value for [-loop_farlx_only]
                                                                                              [T/F OPT]New TRUE value for [-loop_model]
                                                                                              [STR OPT]Default value for [-loop_file] .
                                                                                              No loop_file specified! Try to find loopfile in start_path!
                                                                                              loop: 91 105
                                                                                              [T/F OPT]Default FALSE value for [-coordcst]
                                                                                              [REAL OPT]Default value for [-score_filter_cutoff] 1
                                                                                              setting pose_flag from: 0 to: 1
                                                                                              [T/F OPT]Default FALSE value for [-ccd_closure]
                                                                                              [T/F OPT]Default FALSE value for [-random_frag]
                                                                                              [T/F OPT]Default FALSE value for [-loops_subset]
                                                                                              [REAL OPT]Default value for [-loop_combine_rate] 0
                                                                                              [T/F OPT]Default FALSE value for [-random_loop]
                                                                                              loop_begin: 91 loop_end: 105 loop_sequence: TSKGHTGGHHSPVKG
                                                                                              [T/F OPT]Default FALSE value for [-alter_seqs]
                                                                                              cutpoint: 93
                                                                                              [REAL OPT]Default value for [-looprlx_cycle_ratio] 1
                                                                                              starting loop pose
                                                                                              pre-computing chuck/gunn move set for frag length 3
                                                                                              pre-computing chuck/gunn move set for frag length 1
                                                                                              accepts: frag,ccd 1 300 1 39.6667 0
                                                                                              accepts: frag,ccd 2 300 1 18.3333 0
                                                                                              accepts: frag,ccd 3 300 1 13.6667 0
                                                                                              accepts: frag,ccd 4 300 1 9 0
                                                                                              accepts: frag,ccd 5 300 1 11.3333 0
                                                                                              accepts: frag,ccd 6 114 93 11.4035 68.8172
                                                                                              accepts: frag,ccd 7 96 102 7.29167 93.1373
                                                                                              accepts: frag,ccd 8 54 123 5.55556 100
                                                                                              accepts: frag,ccd 9 36 132 13.8889 100
                                                                                              accepts: frag,ccd 10 1 150 0 100
                                                                                              [REAL OPT]Default value for [-chain_break_tol] 0.200000003
                                                                                              folded loops: 0
                                                                                              setting pose_flag from: 1 to: 0
                                                                                              score_filter: tag= looprlx score= -29.9825 rank= 1 max_rank= 1 nscores= 1 filter_score= -29.9825
                                                                                              [T/F OPT]Default FALSE value for [-output_loops_built]
                                                                                              [T/F OPT]New TRUE value for [-do_farlx_checkpointing]
                                                                                              BOINC :: [2006-10-12 12:54:48] :: checkpoint_decoys() :: saved decoy info :: attempted_decoys: 0 :: num_decoys: 0 :: farlx_stage: 2
                                                                                              setting pose_flag from: 0 to: 1
                                                                                              Pose::dump_pdb: farlxcheck
                                                                                              setting pose_flag from: 1 to: 0
                                                                                              [T/F OPT]Default FALSE value for [-loop_farlx]
                                                                                              setting pose_flag from: 0 to: 1
                                                                                              setting pose_flag from: 1 to: 0
                                                                                              [T/F OPT]Default FALSE value for [-pose_idlz]
                                                                                              setting pose_flag from: 0 to: 1
                                                                                              setting pose_flag from: 1 to: 0
                                                                                              [T/F OPT]Default FALSE value for [-local]
                                                                                              [T/F OPT]New TRUE value for [-idl_no_chain_break]
                                                                                              idealizing residues 1 to 416
                                                                                              minimization
                                                                                              window weight vomega iter fret rms rama bump tether omega phipsi
                                                                                              ------ ------ ------ ---- --------- -------- -------- -------- -------- -------- --------
                                                                                              416 1.000 T 0 55202.14 11.096 -23.078 4884.500 49098.828 0.000 0.000
                                                                                              166 0.100 F 8 3034.97 7.120 -22.254 1763.530 2816.730 0.000 0.135
                                                                                              416 0.001 T 93 4.10 0.232 -98.510 7.183 8.220 4.300 7.103
                                                                                              416 1.000 T 23 9.43 0.268 -98.736 2.432 10.462 4.373 7.135
                                                                                              rms to starting angles 2.4926393
                                                                                              root mean dme to starting coordinates 0.166341007
                                                                                              global ca_rms to starting coordinates 0.268366277
                                                                                              [T/F OPT]Default FALSE value for [-looprlx_idealization]
                                                                                              BOINC :: [2006-10-12 12:59:22] :: checkpoint_decoys() :: saved decoy info :: attempted_decoys: 0 :: num_decoys: 0 :: farlx_stage: 9
                                                                                              dump_pdb: farlxcheck
                                                                                              [INT OPT]Default value for [-lj_ramp_cycles] 8
                                                                                              [REAL OPT]Default value for [-stage2_lj_rep_weight] 1
                                                                                              [T/F OPT]Default FALSE value for [-minimize_exclude_helix]
                                                                                              [T/F OPT]Default FALSE value for [-minimize_exclude_strand]
                                                                                              [INT OPT]Default value for [-local_min_window] 5
                                                                                              [T/F OPT]Default FALSE value for [-no_minimize_set_local_min]
                                                                                              [T/F OPT]Default FALSE value for [-no_farlx_rot_trials]
                                                                                              [T/F OPT]Default FALSE value for [-stringent_relax]
                                                                                              [REAL OPT]New value for [-farlx_cycle_ratio] 1
                                                                                              CYCLES::number is 1 x total_residue: 416
                                                                                              [T/F OPT]Default FALSE value for [-more_relax_cycles]
                                                                                              initializing full atom coordinates
                                                                                              BOINC :: [2006-10-12 13:00:51] :: checkpoint_decoys() :: saved decoy info :: attempted_decoys: 0 :: num_decoys: 0 :: farlx_stage: 10
                                                                                              dump_fullatom_pdb: farlxcheck
                                                                                              [T/F OPT]Default FALSE value for [-vary_chi_before_stage1]
                                                                                              starting score -367.7052 rms 0
                                                                                              starting full atom minimization
                                                                                              [REAL OPT]Default value for [-ediff_cutoff] 15
                                                                                              BOINC :: [2006-10-12 13:20:45] :: checkpoint_decoys() :: saved decoy info :: attempted_decoys: 0 :: num_decoys: 0 :: farlx_stage: 11
                                                                                              dump_fullatom_pdb: farlxcheck
                                                                                              ---------------------------------------------------
                                                                                              repack trials: 11 accepts: 4 %: 36.36 e/trial: -1.36356
                                                                                              smallmin trials: 90 accepts: 0 %: 0.00 e/trial: 0.00000
                                                                                              stage1 score: -777.302795
                                                                                              ---------------------------------------------------
                                                                                              [T/F OPT]Default FALSE value for [-relax_score_filter]
                                                                                              [T/F OPT]Default FALSE value for [-stringentrelax_before_stage2]
                                                                                              [T/F OPT]Default FALSE value for [-vary_chi_before_stage2]
                                                                                              [INT OPT]Default value for [-stage2_cycles] 416
                                                                                              [INT OPT]Default value for [-nwobble1_crank] 3
                                                                                              [INT OPT]Default value for [-nwobble2_crank] 2
                                                                                              [INT OPT]Default value for [-nwobble_wobble] 1
                                                                                              [INT OPT]Default value for [-crank_size] 3
                                                                                              [INT OPT]Default value for [-wobble_size] 3
                                                                                              [INT OPT]Default value for [-stage2_repack_period] 25
                                                                                              [T/F OPT]Default FALSE value for [-wobble_CCD]
                                                                                              [T/F OPT]Default FALSE value for [-skip_fragment_moves]
                                                                                              [T/F OPT]Default FALSE value for [-no_minimize_exclude_frag_in_crank]
                                                                                              [T/F OPT]Default FALSE value for [-no_minimize_exclude_frag_in_wobble]
                                                                                              [REAL OPT]Default value for [-cpu_frac] 10
                                                                                              [REAL OPT]Default value for [-frame_rate] 10
                                                                                              [INT OPT]New value for [-cpu_run_time] 3600
                                                                                              command executed: rosetta_beta_5.32_i686-pc-linux-gnu aa t339 _ -relax -looprlx -nstruct 5 -farlx -ex1 -ex2 -loop_model -termini -short_range_hb_weight 0.50 -long_range_hb_weight 1.0 -farlx_cycle_ratio 1.0 -idl_no_chain_break -vary_omega -output_silent_gz -output_chi_silent -protein_name_prefix idlrlx_hom001_ -frags_name_prefix idlrlx_boinc_hom001_ -s T0339_t339_1_2.pdb -paths paths_200_idlrlx.txt -do_farlx_checkpointing -checkpointing_interval 10 -cpu_run_time 3600 -watchdog -constant_seed -jran 2898263
                                                                                              [STR OPT]New value for [-paths] paths_200_idlrlx.txt.
                                                                                              [INT OPT]Default value for [-seed_offset] 0
                                                                                              [T/F OPT]Default FALSE value for [-version]
                                                                                              [T/F OPT]Default FALSE value for [-score]
                                                                                              [T/F OPT]Default FALSE value for [-abinitio]
                                                                                              [T/F OPT]Default FALSE value for [-refine]
                                                                                              [T/F OPT]Default FALSE value for [-assemble]
                                                                                              [T/F OPT]Default FALSE value for [-idealize]
                                                                                              [T/F OPT]New TRUE value for [-relax]
                                                                                              [T/F OPT]Default FALSE value for [-sim_aneal]
                                                                                              [T/F OPT]Default FALSE value for [-cenrlx]
                                                                                              [T/F OPT]New TRUE value for [-farlx]
                                                                                              [T/F OPT]Default FALSE value for [-record_irms_before_relax]
                                                                                              [T/F OPT]Default FALSE value for [-force_expand]
                                                                                              [T/F OPT]New TRUE value for [-looprlx]
                                                                                              [T/F OPT]Default FALSE value for [-pose_relax]
                                                                                              [T/F OPT]Default FALSE value for [-minimize]
                                                                                              [T/F OPT]Default FALSE value for [-loop_farlx_only]
                                                                                              Rosetta mode: relax
                                                                                              [T/F OPT]Default FALSE value for [-chain]
                                                                                              [T/F OPT]Default FALSE value for [-protein]
                                                                                              [T/F OPT]Default FALSE value for [-series]
                                                                                              series_code = aa :: protein_name is t339:: chain_id is _.
                                                                                              [INT OPT]New value for [-nstruct] 5
                                                                                              [T/F OPT]Default FALSE value for [-read_all_chains]
                                                                                              [T/F OPT]Default FALSE value for [-preserve_header]
                                                                                              [T/F OPT]Default FALSE value for [-use_pdb_numbering]
                                                                                              [T/F OPT]Default FALSE value for [-flip_symmetric_sidechains]
                                                                                              [T/F OPT]Default FALSE value for [-fa_input]
                                                                                              [T/F OPT]Default FALSE value for [-overwrite]
                                                                                              [T/F OPT]Default FALSE value for [-output_pdb_gz]
                                                                                              [T/F OPT]New TRUE value for [-output_silent_gz]
                                                                                              [T/F OPT]Default FALSE value for [-output_scorefile_gz]
                                                                                              [T/F OPT]Default FALSE value for [-sasapack_bvalues]
                                                                                              [T/F OPT]Default FALSE value for [-cenlist_values]
                                                                                              [T/F OPT]New TRUE value for [-termini]
                                                                                              [T/F OPT]Default FALSE value for [-use_trie]
                                                                                              [T/F OPT]Default FALSE value for [-no_trie]
                                                                                              [T/F OPT]Default FALSE value for [-use_conformer]
                                                                                              [T/F OPT]Default FALSE value for [-use_bbind_conformer]
                                                                                              [T/F OPT]Default FALSE value for [-trials_trie]
                                                                                              [T/F OPT]Default FALSE value for [-no_trials_trie]
                                                                                              [T/F OPT]Default FALSE value for [-output_interaction_graph_memory_usage]
                                                                                              [T/F OPT]Default FALSE value for [-read_interaction_graph]
                                                                                              [T/F OPT]Default FALSE value for [-write_interaction_graph]
                                                                                              [STR OPT]Default value for [-ig_file] .
                                                                                              [T/F OPT]Default FALSE value for [-use_sasa_pack_score]
                                                                                              [T/F OPT]Default FALSE value for [-output_dot_kinemage]
                                                                                              [T/F OPT]Default FALSE value for [-pack_low_temp_annealing]
                                                                                              [T/F OPT]Default FALSE value for [-no_his_his_pairE]
                                                                                              [T/F OPT]Default FALSE value for [-silent_input]
                                                                                              [T/F OPT]Default FALSE value for [-timer]
                                                                                              [T/F OPT]Default FALSE value for [-count_attempts]
                                                                                              [T/F OPT]Default FALSE value for [-status]
                                                                                              [T/F OPT]Default FALSE value for [-ise_movie]
                                                                                              [T/F OPT]Default FALSE value for [-output_all]
                                                                                              [T/F OPT]New TRUE value for [-output_chi_silent]
                                                                                              [T/F OPT]Default FALSE value for [-accept_all]
                                                                                              [T/F OPT]Default FALSE value for [-skip_missing_residues]
                                                                                              [STR OPT]Default value for [-cst] cst.
                                                                                              [STR OPT]Default value for [-dpl] dpl.
                                                                                              [STR OPT]Default value for [-resfile] none.
                                                                                              [STR OPT]Default value for [-equiv_resfile] none.
                                                                                              [T/F OPT]Default FALSE value for [-auto_resfile]
                                                                                              [T/F OPT]Default FALSE value for [-chain_inc]
                                                                                              WARNING::refold_input T, allow_missing T
                                                                                              setting refold_input F
                                                                                              [T/F OPT]Default FALSE value for [-full_filename]
                                                                                              [T/F OPT]Default FALSE value for [-map_sequence]
                                                                                              [INT OPT]Default value for [-max_frags] 200
                                                                                              [T/F OPT]Default FALSE value for [-output_centroids]
                                                                                              [STR OPT]New value for [-protein_name_prefix] idlrlx_hom001_.
                                                                                              [STR OPT]New value for [-frags_name_prefix] idlrlx_boinc_hom001_.
                                                                                              [T/F OPT]Default FALSE value for [-protein_name_prefix_homolog]
                                                                                              [REAL OPT]Default value for [-vdw_reweight] 1
                                                                                              [REAL OPT]Default value for [-env_reweight] 1
                                                                                              [REAL OPT]Default value for [-pair_reweight] 1
                                                                                              [REAL OPT]Default value for [-cb_reweight] 1
                                                                                              [REAL OPT]Default value for [-sheet_reweight] 1
                                                                                              [REAL OPT]Default value for [-ss_reweight] 1
                                                                                              [REAL OPT]Default value for [-hs_reweight] 1
                                                                                              [REAL OPT]Default value for [-rsigma_reweight] 1
                                                                                              [REAL OPT]Default value for [-rg_reweight] 1
                                                                                              [REAL OPT]Default value for [-pc_reweight] 1
                                                                                              [REAL OPT]Default value for [-fa_atr_reweight] 1
                                                                                              [REAL OPT]Default value for [-fa_rep_reweight] 1
                                                                                              [REAL OPT]Default value for [-fa_dun_reweight ] 1
                                                                                              [REAL OPT]Default value for [-fa_pair_reweight] 1
                                                                                              [REAL OPT]Default value for [-fa_plane_reweight] 1
                                                                                              [REAL OPT]Default value for [-fa_solv_reweight] 1
                                                                                              [REAL OPT]Default value for [-fa_ref_reweight ] 1
                                                                                              [REAL OPT]Default value for [-fa_pH_reweight] 1
                                                                                              [REAL OPT]Default value for [-fa_h2o_reweight] 1
                                                                                              [REAL OPT]Default value for [-fa_prob1b_reweight] 1
                                                                                              [REAL OPT]Default value for [-fa_gb_elec_reweigh] 1
                                                                                              [REAL OPT]Default value for [-hb_srbb_reweight] 1
                                                                                              [REAL OPT]Default value for [-hb_lrbb_reweight] 1
                                                                                              [REAL OPT]Default value for [-hb_sc_reweight] 1
                                                                                              [REAL OPT]Default value for [-chainbreak_reweight] 1
                                                                                              [T/F OPT]Default FALSE value for [-find_disulf]
                                                                                              [T/F OPT]Default FALSE value for [-fix_disulf]
                                                                                              [T/F OPT]Default FALSE value for [-enable_ligand_aa]
                                                                                              [T/F OPT]Default FALSE value for [-phospho_ser]
                                                                                              [T/F OPT]Default FALSE value for [-surface]
                                                                                              [T/F OPT]Default FALSE value for [-loops]
                                                                                              [T/F OPT]Default FALSE value for [-taboo]
                                                                                              [T/F OPT]New TRUE value for [-vary_omega]
                                                                                              [T/F OPT]Default FALSE value for [-geometric_sol]
                                                                                              [T/F OPT]Default FALSE value for [-multi_chain]
                                                                                              [T/F OPT]New TRUE value for [-ex1]
                                                                                              [T/F OPT]New TRUE value for [-ex2]
                                                                                              [T/F OPT]Default FALSE value for [-ex3]
                                                                                              [T/F OPT]Default FALSE value for [-ex4]
                                                                                              [T/F OPT]Default FALSE value for [-ex1aro]
                                                                                              [T/F OPT]Default FALSE value for [-ex1aro_half]
                                                                                              [T/F OPT]Default FALSE value for [-ex2aro_only]
                                                                                              [INT OPT]Default value for [-extrachi_cutoff] 18
                                                                                              [T/F OPT]Default FALSE value for [-rot_pert]
                                                                                              [T/F OPT]Default FALSE value for [-rot_pert_input]
                                                                                              [T/F OPT]Default FALSE value for [-exdb]
                                                                                              [T/F OPT]Default FALSE value for [-use_electrostatic_repulsion]
                                                                                              [T/F OPT]Default FALSE value for [-explicit_h2o]
                                                                                              [T/F OPT]Default FALSE value for [-solvate]
                                                                                              [T/F OPT]Default FALSE value for [-pH]
                                                                                              [T/F OPT]Default FALSE value for [-try_both_his_tautomers]
                                                                                              [T/F OPT]Default FALSE value for [-hydrate_dna]
                                                                                              [T/F OPT]Default FALSE value for [-ex_dna_waters]
                                                                                              [T/F OPT]Default FALSE value for [-minimize_rot]
                                                                                              [T/F OPT]Default FALSE value for [-read_hetero_h2o]
                                                                                              [T/F OPT]Default FALSE value for [-Wint_score_only]
                                                                                              [T/F OPT]Default FALSE value for [-Wint_repack_only]
                                                                                              [T/F OPT]Default FALSE value for [-ligand]
                                                                                              [T/F OPT]Default FALSE value for [-enzyme_design]
                                                                                              [T/F OPT]Default FALSE value for [-score_contact_flag]
                                                                                              [T/F OPT]Default FALSE value for [-score_contact_weight]
                                                                                              [T/F OPT]Default FALSE value for [-score_contact_threshold]
                                                                                              [T/F OPT]Default FALSE value for [-scorefxn]
                                                                                              default centroid scorefxn: 6
                                                                                              default fullatom scorefxn: 12
                                                                                              [INT OPT]Default value for [-run_level] 0
                                                                                              [T/F OPT]Default FALSE value for [-silent]
                                                                                              [T/F OPT]New TRUE value for [-output_silent_gz]
                                                                                              run level: -4
                                                                                              [T/F OPT]Default FALSE value for [-benchmark]
                                                                                              [T/F OPT]Default FALSE value for [-debug]
                                                                                              [INT OPT]Default value for [-sym_des_units] 1
                                                                                              [T/F OPT]Default FALSE value for [-mj_min]
                                                                                              [REAL OPT]Default value for [-mod_hhrep_height] 1
                                                                                              [REAL OPT]Default value for [-mod_hhrep_width] 1
                                                                                              [REAL OPT]Default value for [-mod_hhrep_center] 2.79999995
                                                                                              [REAL OPT]Default value for [-mod_hhrep_exponent] 4
                                                                                              [REAL OPT]Default value for [-smooth_etable_ljweight] 1.15999997
                                                                                              [REAL OPT]Default value for [-smooth_etable_solvweight] 1.5
                                                                                              [STR OPT]New value for [-s] T0339_t339_1_2.pdb.
                                                                                              Starting structure: T0339_t339_1_2
                                                                                              Reading ./Rama_smooth_dyn.dat_ss_6.4.gz
                                                                                              Reading ./phi.theta.36.HS.resmooth.gz
                                                                                              Reading ./phi.theta.36.SS.resmooth.gz
                                                                                              [STR OPT]Default value for [-atom_vdw_set] hybrid.
                                                                                              [T/F OPT]Default FALSE value for [-IUPAC]
                                                                                              Atom_mode set to all
                                                                                              Reading ./paircutoffs.gz
                                                                                              [T/F OPT]Default FALSE value for [-decoystats]
                                                                                              set_decoystats_flag: from,to F F
                                                                                              [T/F OPT]Default FALSE value for [-decoyfeatures]
                                                                                              [T/F OPT]Default FALSE value for [-evolution]
                                                                                              [T/F OPT]Default FALSE value for [-evol_recomb]
                                                                                              [T/F OPT]Default FALSE value for [-profile]
                                                                                              BOINC :: [2006-10-12 19:33:06] :: mode: relax :: nstartnum: 1 :: number_of_output: 5 :: num_decoys: 0 :: pct_complete: 0.01
                                                                                              [T/F OPT]New TRUE value for [-watchdog]
                                                                                              [INT OPT]Default value for [-watchdog_time] 3600
                                                                                              [REAL OPT]Default value for [-cpu_run_timeout_factor] 4
                                                                                              [T/F OPT]Default FALSE value for [-dummy_model]
                                                                                              Searching for dat file: ./idlrlx_hom001_t339.dat
                                                                                              Searching for dat file: ./idlrlx_hom001_t339.dat
                                                                                              WARNING!! .dat file not found!
                                                                                              Looking for fasta file: ./idlrlx_hom001_t339_.fasta
                                                                                              Looking for psipred file: ./idlrlx_hom001_t339_.psipred_ss2
                                                                                              Looking for psipred file: ./idlrlx_hom001_t339_.psipred_ss2
                                                                                              Looking for psipred file: ./idlrlx_hom001_t339_.jones
                                                                                              Looking for psipred file: ./idlrlx_hom001_t339_.psipred
                                                                                              Looking for psipred file: ./idlrlx_hom001_t339_.jones
                                                                                              Looking for psipred file: ./idlrlx_hom001_t339_.psipred
                                                                                              WARNING :: Unable to find psipred file!
                                                                                              [T/F OPT]Default FALSE value for [-tight_hb]
                                                                                              File: ./idlrlx_hom001_t339_.cst not found
                                                                                              Running without distance constraints
                                                                                              File: ./idlrlx_hom001_t339_.dpl not found
                                                                                              Dipolar constraints will not be used
                                                                                              fragment file: ./idlrlx_boinc_hom001_aat339_03_05.200_v1_3.gz
                                                                                              Total Residue 416
                                                                                              frag size: 3 frags/residue: 200
                                                                                              fragment file: ./idlrlx_boinc_hom001_aat339_09_05.200_v1_3.gz
                                                                                              Total Residue 416
                                                                                              frag size: 9 frags/residue: 25
                                                                                              generating 1mer library from 3mer library
                                                                                              [T/F OPT]Default FALSE value for [-ssblocks]
                                                                                              [T/F OPT]Default FALSE value for [-check_homs]
                                                                                              calculating fragment_diversity...
                                                                                              dihedral_bin: unusual angle
                                                                                              dihedral_bin: unusual angle
                                                                                              dihedral_bin: unusual angle
                                                                                              dihedral_bin: unusual angle
                                                                                              dihedral_bin: unusual angle
                                                                                              dihedral_bin: unusual angle
                                                                                              dihedral_bin: unusual angle
                                                                                              dihedral_bin: unusual angle
                                                                                              dihedral_bin: unusual angle
                                                                                              dihedral_bin: unusual angle
                                                                                              dihedral_bin: unusual angle
                                                                                              dihedral_bin: unusual angle
                                                                                              dihedral_bin: unusual angle
                                                                                              [T/F OPT]Default FALSE value for [-barcode_mode]
                                                                                              disabling all filters
                                                                                              [REAL OPT]Default value for [-co] -1
                                                                                              [REAL OPT]Default value for [-rms] -1
                                                                                              Searching for pdb...: ./idlrlx_hom001_t339.pdb
                                                                                              Searching for pdb...: ./idlrlx_hom001_t339.pdb
                                                                                              no pdb file for idlrlx_hom001_t339
                                                                                              [T/F OPT]Default FALSE value for [-repeatin]
                                                                                              [T/F OPT]Default FALSE value for [-repeatout]
                                                                                              [T/F OPT]Default FALSE value for [-clnt]
                                                                                              WARNING: check_decoy_exists: unexpected decoy number: start#,decoy#,lastdecoy# 1 1 5 0
                                                                                              reading starting structure: ./T0339_t339_1_2.pdb.gz
                                                                                              [T/F OPT]Default FALSE value for [-use_native_centroid]
                                                                                              [T/F OPT]New TRUE value for [-constant_seed]
                                                                                              WARNING: 52 missing backbone atoms at 13 residues in pdb file
                                                                                              allow_missing= 1
                                                                                              skip_missing= 0
                                                                                              WARNING: 13 centroids were placed at 0,0,0
                                                                                              WARNING:: end of pdb file reached: angle, secstruct, & res info not found
                                                                                              Looking for dssp file: ./T0339_t339_1_2.dssp
                                                                                              dssp file not found
                                                                                              Looking for secondary structure assignment file: ./T0339_t339_1_2.ssa
                                                                                              ssa file not found
                                                                                              calculating secondary structure from torsion angles
                                                                                              [T/F OPT]Default FALSE value for [-use_input_bond]
                                                                                              [T/F OPT]Default FALSE value for [-regions]
                                                                                              [T/F OPT]Default FALSE value for [-apply_filters]
                                                                                              [T/F OPT]Default FALSE value for [-knot_filter]
                                                                                              [T/F OPT]Default FALSE value for [-poke_filter]
                                                                                              [T/F OPT]Default FALSE value for [-score_contact_fullatom]
                                                                                              [T/F OPT]New TRUE value for [-long_range_hb_weight]
                                                                                              [T/F OPT]New TRUE value for [-long_range_hb_weight]
                                                                                              [REAL OPT]New value for [-long_range_hb_weight] 1
                                                                                              [T/F OPT]New TRUE value for [-short_range_hb_weight]
                                                                                              [T/F OPT]New TRUE value for [-short_range_hb_weight]
                                                                                              [REAL OPT]New value for [-short_range_hb_weight] 0.5
                                                                                              [REAL OPT]Default value for [-fa_plane_weight] 0
                                                                                              [REAL OPT]Default value for [-omega_weight] 0.5
                                                                                              [T/F OPT]Default FALSE value for [-rand_envpair_res_wt]
                                                                                              [REAL OPT]Default value for [-parallel_weight] 1
                                                                                              [REAL OPT]Default value for [-antiparallel_weight] 1
                                                                                              [T/F OPT]Default FALSE value for [-rand_SS_wt]
                                                                                              [T/F OPT]Default FALSE value for [-random_parallel_antiparallel]
                                                                                              [T/F OPT]Default FALSE value for [-rand_cst_res_wt]
                                                                                              [T/F OPT]Default FALSE value for [-use_barcode_to_score]
                                                                                              initializing full atom functions
                                                                                              [T/F OPT]Default FALSE value for [-soft_rep]
                                                                                              [T/F OPT]Default FALSE value for [-soft_rep_design]
                                                                                              [T/F OPT]Default FALSE value for [-smooth_etable]
                                                                                              [T/F OPT]Default FALSE value for [-reduce_templates]
                                                                                              [T/F OPT]Default FALSE value for [-gen_born]
                                                                                              [T/F OPT]Default FALSE value for [-small_radii]
                                                                                              [T/F OPT]Default FALSE value for [-use_bw]
                                                                                              [T/F OPT]Default FALSE value for [-use_aw]
                                                                                              [T/F OPT]Default FALSE value for [-dna_weights]
                                                                                              [STR OPT]Default value for [-fa_lj_rep_slope] highres.
                                                                                              Reading ./bbdep02.May.sortlib.gz
                                                                                              Reading ./plane_data_table_1015.dat.gz
                                                                                              Reading ./pdbpairstats_fine.gz
                                                                                              Reading ./Paa.gz
                                                                                              Reading ./Paa_n.gz
                                                                                              Reading ./Paa_pp.gz
                                                                                              generating Etable...
                                                                                              Starting energy table calculation
                                                                                              Energy table parameter set: polh_aroh Revision: 10024 Date: 2006-08-28 13:54:52 -0700 (Mon, 28 Aug 2006)
                                                                                              [T/F OPT]Default FALSE value for [-mod_hhrep]
                                                                                              [T/F OPT]Default FALSE value for [-output_etables]
                                                                                              [T/F OPT]Default FALSE value for [-mod_etable]
                                                                                              Finished calculating energy tables.
                                                                                              Reading ./avgE_from_pdb.gz
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 92
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 93
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 94
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 95
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 96
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 97
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 98
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 99
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 100
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 101
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 102
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 103
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 104
                                                                                              [REAL OPT]Default value for [-rsd_wt_helix] 1
                                                                                              [REAL OPT]Default value for [-rsd_wt_strand] 1
                                                                                              [REAL OPT]Default value for [-rsd_wt_loop] 1
                                                                                              [T/F OPT]Default FALSE value for [-burial_code]
                                                                                              [T/F OPT]Default FALSE value for [-new_centroid_packing]
                                                                                              [REAL OPT]Default value for [-cb_weight] 1
                                                                                              [REAL OPT]Default value for [-strand_dist_cutoff] 6.5
                                                                                              [T/F OPT]Default FALSE value for [-stretch_strand_dist_cutoff]
                                                                                              [REAL OPT]Default value for [-localstrandpair_penalty] 0
                                                                                              [T/F OPT]Default FALSE value for [-handedness_score]
                                                                                              [T/F OPT]Default FALSE value for [-separate_centroid_pack_score]
                                                                                              Reading ./SASA-masks.dat.gz
                                                                                              Reading ./SASA-angles.dat.gz
                                                                                              ========================================
                                                                                              Reading ./sasa_offsets.txt.gz
                                                                                              Reading ./sasa_prob_cdf.txt.gz
                                                                                              NEXT STRUCTURE: ./aaT0339_t339_1_2_0001.pdb
                                                                                              [T/F OPT]Default FALSE value for [-fullatom_loop]
                                                                                              [INT OPT]Default value for [-lj_ramp_cycles] 8
                                                                                              [REAL OPT]Default value for [-stage2_lj_rep_weight] 1
                                                                                              [T/F OPT]Default FALSE value for [-minimize_exclude_helix]
                                                                                              [T/F OPT]Default FALSE value for [-minimize_exclude_strand]
                                                                                              [INT OPT]Default value for [-local_min_window] 5
                                                                                              [T/F OPT]Default FALSE value for [-no_minimize_set_local_min]
                                                                                              [T/F OPT]Default FALSE value for [-no_farlx_rot_trials]
                                                                                              [T/F OPT]Default FALSE value for [-stringent_relax]
                                                                                              [REAL OPT]New value for [-farlx_cycle_ratio] 1
                                                                                              CYCLES::number is 1 x total_residue: 416
                                                                                              [T/F OPT]Default FALSE value for [-more_relax_cycles]
                                                                                              initializing full atom coordinates
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 92
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 93
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 94
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 95
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 96
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 97
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 98
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 99
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 100
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 101
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 102
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 103
                                                                                              WARNING: Pose::set_coords: backbone missing for residue 104
                                                                                              [T/F OPT]New TRUE value for [-do_farlx_checkpointing]
                                                                                              reading starting structure: farlxcheck
                                                                                              Filling missing atoms
                                                                                              optimizing missing atoms
                                                                                              optimizing hydrogen positions
                                                                                              [T/F OPT]New TRUE value for [-constant_seed]
                                                                                              ---------------------------------------------------
                                                                                              repack trials: 1 accepts: 1 %: 100.00 e/trial: -1.15601
                                                                                              stage1 score: -779.712646
                                                                                              ---------------------------------------------------
                                                                                              [T/F OPT]Default FALSE value for [-relax_score_filter]
                                                                                              [T/F OPT]Default FALSE value for [-stringentrelax_before_stage2]
                                                                                              [T/F OPT]Default FALSE value for [-vary_chi_before_stage2]
                                                                                              [INT OPT]Default value for [-stage2_cycles] 416
                                                                                              [INT OPT]Default value for [-nwobble1_crank] 3
                                                                                              [INT OPT]Default value for [-nwobble2_crank] 2
                                                                                              [INT OPT]Default value for [-nwobble_wobble] 1
                                                                                              [INT OPT]Default value for [-crank_size] 3
                                                                                              [INT OPT]Default value for [-wobble_size] 3
                                                                                              [INT OPT]Default value for [-stage2_repack_period] 25
                                                                                              [T/F OPT]Default FALSE value for [-wobble_CCD]
                                                                                              [REAL OPT]Default value for [-ediff_cutoff] 15
                                                                                              [T/F OPT]Default FALSE value for [-skip_fragment_moves]
                                                                                              pre-computing chuck/gunn move set for frag length 3
                                                                                              [T/F OPT]Default FALSE value for [-no_minimize_exclude_frag_in_crank]
                                                                                              [T/F OPT]Default FALSE value for [-no_minimize_exclude_frag_in_wobble]

                                                                                              ____________
                                                                                              Gruesse vom Saenger

                                                                                              For questions about Boinc look in the BOINC-Wiki

                                                                                              Lee Carre

                                                                                              Joined: Feb 16 06
                                                                                              Posts: 21
                                                                                              ID: 219
                                                                                              Credit: 2,102
                                                                                              RAC: 0
                                                                                              Message 2408 - Posted 14 Oct 2006 17:28:10 UTC

                                                                                                Last modified: 14 Oct 2006 18:18:55 UTC

                                                                                                while crunching the result named FRA_2rio_CASP7_hom001_1_2rio_1_1a06__IGNORE_THE_REST_232_1281_3_0, when i showed the graphics, the rosetta application stopped responding
                                                                                                the version was 5.32 on a windows system

                                                                                                each thread (science and graphics) each took up all the cycles on 2 of my CPUs (i have a multiCPU machine)

                                                                                                stopping/exiting boinc closed the app without a problem, and it was working again when boinc was restarted

                                                                                                it was working fine before i viewed the graphics too, no problems at all since 5.32 was released
                                                                                                ____________
                                                                                                Want to search the BOINC Wiki, BOINCstats, or various BOINC forums from within firefox? Try the BOINC related Firefox Search Plugins

                                                                                                Chu
                                                                                                Forum moderator
                                                                                                Project developer
                                                                                                Project scientist

                                                                                                Joined: Sep 26 06
                                                                                                Posts: 61
                                                                                                ID: 1900
                                                                                                Credit: 12,545
                                                                                                RAC: 0
                                                                                                Message 2410 - Posted 17 Oct 2006 3:48:53 UTC - in response to Message 2407.

                                                                                                  Sometimes the protein being simulated blows up and then the run is stuck. Not sure that is responsible for your error, but that should be stopped by the watchdog after a while if you do not abort it.

                                                                                                  My Ralph just stopped the progress @1.002%. CPU-time went up, but nothing else seems to happen.
                                                                                                  I\'ve suspended the WU for now, should I abort it or do anything else?

                                                                                                  This is the stderr.txt:
                                                                                                  Graphics are disabled due to configuration...
                                                                                                  # random seed: 2898263
                                                                                                  # cpu_run_time_pref: 14400
                                                                                                  Graphics are disabled due to configuration...
                                                                                                  # cpu_run_time_pref: 14400

                                                                                                  And this is the stdout.txt:
                                                                                                  [REAL OPT]Default value for [-cpu_frac] 10
                                                                                                  [REAL OPT]Default value for [-frame_rate] 10
                                                                                                  [INT OPT]New value for [-cpu_run_time] 3600
                                                                                                  command executed: rosetta_beta_5.32_i686-pc-linux-gnu aa t339 _ -relax -looprlx -nstruct 5 -farlx -ex1 -ex2 -loop_model -termini -short_range_hb_weight 0.50 -long_range_hb_weight 1.0 -farlx_cycle_ratio 1.0 -idl_no_chain_break -vary_omega -output_silent_gz -output_chi_silent -protein_name_prefix idlrlx_hom001_ -frags_name_prefix idlrlx_boinc_hom001_ -s T0339_t339_1_2.pdb -paths paths_200_idlrlx.txt -do_farlx_checkpointing -checkpointing_interval 10 -cpu_run_time 3600 -watchdog -constant_seed -jran 2898263
                                                                                                  [STR OPT]New value for [-paths] paths_200_idlrlx.txt.
                                                                                                  [INT OPT]Default value for [-seed_offset] 0
                                                                                                  [T/F OPT]Default FALSE value for [-version]
                                                                                                  [T/F OPT]Default FALSE value for [-score]
                                                                                                  [T/F OPT]Default FALSE value for [-abinitio]
                                                                                                  [T/F OPT]Default FALSE value for [-refine]
                                                                                                  [T/F OPT]Default FALSE value for [-assemble]
                                                                                                  [T/F OPT]Default FALSE value for [-idealize]
                                                                                                  [T/F OPT]New TRUE value for [-relax]
                                                                                                  [T/F OPT]Default FALSE value for [-sim_aneal]
                                                                                                  [T/F OPT]Default FALSE value for [-cenrlx]
                                                                                                  [T/F OPT]New TRUE value for [-farlx]
                                                                                                  [T/F OPT]Default FALSE value for [-record_irms_before_relax]
                                                                                                  [T/F OPT]Default FALSE value for [-force_expand]
                                                                                                  [T/F OPT]New TRUE value for [-looprlx]
                                                                                                  [T/F OPT]Default FALSE value for [-pose_relax]
                                                                                                  [T/F OPT]Default FALSE value for [-minimize]
                                                                                                  [T/F OPT]Default FALSE value for [-loop_farlx_only]
                                                                                                  Rosetta mode: relax
                                                                                                  [T/F OPT]Default FALSE value for [-chain]
                                                                                                  [T/F OPT]Default FALSE value for [-protein]
                                                                                                  [T/F OPT]Default FALSE value for [-series]
                                                                                                  series_code = aa :: protein_name is t339:: chain_id is _.
                                                                                                  [INT OPT]New value for [-nstruct] 5
                                                                                                  [T/F OPT]Default FALSE value for [-read_all_chains]
                                                                                                  [T/F OPT]Default FALSE value for [-preserve_header]
                                                                                                  [T/F OPT]Default FALSE value for [-use_pdb_numbering]
                                                                                                  [T/F OPT]Default FALSE value for [-flip_symmetric_sidechains]
                                                                                                  [T/F OPT]Default FALSE value for [-fa_input]
                                                                                                  [T/F OPT]Default FALSE value for [-overwrite]
                                                                                                  [T/F OPT]Default FALSE value for [-output_pdb_gz]
                                                                                                  [T/F OPT]New TRUE value for [-output_silent_gz]
                                                                                                  [T/F OPT]Default FALSE value for [-output_scorefile_gz]
                                                                                                  [T/F OPT]Default FALSE value for [-sasapack_bvalues]
                                                                                                  [T/F OPT]Default FALSE value for [-cenlist_values]
                                                                                                  [T/F OPT]New TRUE value for [-termini]
                                                                                                  [T/F OPT]Default FALSE value for [-use_trie]
                                                                                                  [T/F OPT]Default FALSE value for [-no_trie]
                                                                                                  [T/F OPT]Default FALSE value for [-use_conformer]
                                                                                                  [T/F OPT]Default FALSE value for [-use_bbind_conformer]
                                                                                                  [T/F OPT]Default FALSE value for [-trials_trie]
                                                                                                  [T/F OPT]Default FALSE value for [-no_trials_trie]
                                                                                                  [T/F OPT]Default FALSE value for [-output_interaction_graph_memory_usage]
                                                                                                  [T/F OPT]Default FALSE value for [-read_interaction_graph]
                                                                                                  [T/F OPT]Default FALSE value for [-write_interaction_graph]
                                                                                                  [STR OPT]Default value for [-ig_file] .
                                                                                                  [T/F OPT]Default FALSE value for [-use_sasa_pack_score]
                                                                                                  [T/F OPT]Default FALSE value for [-output_dot_kinemage]
                                                                                                  [T/F OPT]Default FALSE value for [-pack_low_temp_annealing]
                                                                                                  [T/F OPT]Default FALSE value for [-no_his_his_pairE]
                                                                                                  [T/F OPT]Default FALSE value for [-silent_input]
                                                                                                  [T/F OPT]Default FALSE value for [-timer]
                                                                                                  [T/F OPT]Default FALSE value for [-count_attempts]
                                                                                                  [T/F OPT]Default FALSE value for [-status]
                                                                                                  [T/F OPT]Default FALSE value for [-ise_movie]
                                                                                                  [T/F OPT]Default FALSE value for [-output_all]
                                                                                                  [T/F OPT]New TRUE value for [-output_chi_silent]
                                                                                                  [T/F OPT]Default FALSE value for [-accept_all]
                                                                                                  [T/F OPT]Default FALSE value for [-skip_missing_residues]
                                                                                                  [STR OPT]Default value for [-cst] cst.
                                                                                                  [STR OPT]Default value for [-dpl] dpl.
                                                                                                  [STR OPT]Default value for [-resfile] none.
                                                                                                  [STR OPT]Default value for [-equiv_resfile] none.
                                                                                                  [T/F OPT]Default FALSE value for [-auto_resfile]
                                                                                                  [T/F OPT]Default FALSE value for [-chain_inc]
                                                                                                  WARNING::refold_input T, allow_missing T
                                                                                                  setting refold_input F
                                                                                                  [T/F OPT]Default FALSE value for [-full_filename]
                                                                                                  [T/F OPT]Default FALSE value for [-map_sequence]
                                                                                                  [INT OPT]Default value for [-max_frags] 200
                                                                                                  [T/F OPT]Default FALSE value for [-output_centroids]
                                                                                                  [STR OPT]New value for [-protein_name_prefix] idlrlx_hom001_.
                                                                                                  [STR OPT]New value for [-frags_name_prefix] idlrlx_boinc_hom001_.
                                                                                                  [T/F OPT]Default FALSE value for [-protein_name_prefix_homolog]
                                                                                                  [REAL OPT]Default value for [-vdw_reweight] 1
                                                                                                  [REAL OPT]Default value for [-env_reweight] 1
                                                                                                  [REAL OPT]Default value for [-pair_reweight] 1
                                                                                                  [REAL OPT]Default value for [-cb_reweight] 1
                                                                                                  [REAL OPT]Default value for [-sheet_reweight] 1
                                                                                                  [REAL OPT]Default value for [-ss_reweight] 1
                                                                                                  [REAL OPT]Default value for [-hs_reweight] 1
                                                                                                  [REAL OPT]Default value for [-rsigma_reweight] 1
                                                                                                  [REAL OPT]Default value for [-rg_reweight] 1
                                                                                                  [REAL OPT]Default value for [-pc_reweight] 1
                                                                                                  [REAL OPT]Default value for [-fa_atr_reweight] 1
                                                                                                  [REAL OPT]Default value for [-fa_rep_reweight] 1
                                                                                                  [REAL OPT]Default value for [-fa_dun_reweight ] 1
                                                                                                  [REAL OPT]Default value for [-fa_pair_reweight] 1
                                                                                                  [REAL OPT]Default value for [-fa_plane_reweight] 1
                                                                                                  [REAL OPT]Default value for [-fa_solv_reweight] 1
                                                                                                  [REAL OPT]Default value for [-fa_ref_reweight ] 1
                                                                                                  [REAL OPT]Default value for [-fa_pH_reweight] 1
                                                                                                  [REAL OPT]Default value for [-fa_h2o_reweight] 1
                                                                                                  [REAL OPT]Default value for [-fa_prob1b_reweight] 1
                                                                                                  [REAL OPT]Default value for [-fa_gb_elec_reweigh] 1
                                                                                                  [REAL OPT]Default value for [-hb_srbb_reweight] 1
                                                                                                  [REAL OPT]Default value for [-hb_lrbb_reweight] 1
                                                                                                  [REAL OPT]Default value for [-hb_sc_reweight] 1
                                                                                                  [REAL OPT]Default value for [-chainbreak_reweight] 1
                                                                                                  [T/F OPT]Default FALSE value for [-find_disulf]
                                                                                                  [T/F OPT]Default FALSE value for [-fix_disulf]
                                                                                                  [T/F OPT]Default FALSE value for [-enable_ligand_aa]
                                                                                                  [T/F OPT]Default FALSE value for [-phospho_ser]
                                                                                                  [T/F OPT]Default FALSE value for [-surface]
                                                                                                  [T/F OPT]Default FALSE value for [-loops]
                                                                                                  [T/F OPT]Default FALSE value for [-taboo]
                                                                                                  [T/F OPT]New TRUE value for [-vary_omega]
                                                                                                  [T/F OPT]Default FALSE value for [-geometric_sol]
                                                                                                  [T/F OPT]Default FALSE value for [-multi_chain]
                                                                                                  [T/F OPT]New TRUE value for [-ex1]
                                                                                                  [T/F OPT]New TRUE value for [-ex2]
                                                                                                  [T/F OPT]Default FALSE value for [-ex3]
                                                                                                  [T/F OPT]Default FALSE value for [-ex4]
                                                                                                  [T/F OPT]Default FALSE value for [-ex1aro]
                                                                                                  [T/F OPT]Default FALSE value for [-ex1aro_half]
                                                                                                  [T/F OPT]Default FALSE value for [-ex2aro_only]
                                                                                                  [INT OPT]Default value for [-extrachi_cutoff] 18
                                                                                                  [T/F OPT]Default FALSE value for [-rot_pert]
                                                                                                  [T/F OPT]Default FALSE value for [-rot_pert_input]
                                                                                                  [T/F OPT]Default FALSE value for [-exdb]
                                                                                                  [T/F OPT]Default FALSE value for [-use_electrostatic_repulsion]
                                                                                                  [T/F OPT]Default FALSE value for [-explicit_h2o]
                                                                                                  [T/F OPT]Default FALSE value for [-solvate]
                                                                                                  [T/F OPT]Default FALSE value for [-pH]
                                                                                                  [T/F OPT]Default FALSE value for [-try_both_his_tautomers]
                                                                                                  [T/F OPT]Default FALSE value for [-hydrate_dna]
                                                                                                  [T/F OPT]Default FALSE value for [-ex_dna_waters]
                                                                                                  [T/F OPT]Default FALSE value for [-minimize_rot]
                                                                                                  [T/F OPT]Default FALSE value for [-read_hetero_h2o]
                                                                                                  [T/F OPT]Default FALSE value for [-Wint_score_only]
                                                                                                  [T/F OPT]Default FALSE value for [-Wint_repack_only]
                                                                                                  [T/F OPT]Default FALSE value for [-ligand]
                                                                                                  [T/F OPT]Default FALSE value for [-enzyme_design]
                                                                                                  [T/F OPT]Default FALSE value for [-score_contact_flag]
                                                                                                  [T/F OPT]Default FALSE value for [-score_contact_weight]
                                                                                                  [T/F OPT]Default FALSE value for [-score_contact_threshold]
                                                                                                  [T/F OPT]Default FALSE value for [-scorefxn]
                                                                                                  default centroid scorefxn: 6
                                                                                                  default fullatom scorefxn: 12
                                                                                                  [INT OPT]Default value for [-run_level] 0
                                                                                                  [T/F OPT]Default FALSE value for [-silent]
                                                                                                  [T/F OPT]New TRUE value for [-output_silent_gz]
                                                                                                  run level: -4
                                                                                                  [T/F OPT]Default FALSE value for [-benchmark]
                                                                                                  [T/F OPT]Default FALSE value for [-debug]
                                                                                                  [INT OPT]Default value for [-sym_des_units] 1
                                                                                                  [T/F OPT]Default FALSE value for [-mj_min]
                                                                                                  [REAL OPT]Default value for [-mod_hhrep_height] 1
                                                                                                  [REAL OPT]Default value for [-mod_hhrep_width] 1
                                                                                                  [REAL OPT]Default value for [-mod_hhrep_center] 2.79999995
                                                                                                  [REAL OPT]Default value for [-mod_hhrep_exponent] 4
                                                                                                  [REAL OPT]Default value for [-smooth_etable_ljweight] 1.15999997
                                                                                                  [REAL OPT]Default value for [-smooth_etable_solvweight] 1.5
                                                                                                  [STR OPT]New value for [-s] T0339_t339_1_2.pdb.
                                                                                                  Starting structure: T0339_t339_1_2
                                                                                                  Reading ./Rama_smooth_dyn.dat_ss_6.4.gz
                                                                                                  Reading ./phi.theta.36.HS.resmooth.gz
                                                                                                  Reading ./phi.theta.36.SS.resmooth.gz
                                                                                                  [STR OPT]Default value for [-atom_vdw_set] hybrid.
                                                                                                  [T/F OPT]Default FALSE value for [-IUPAC]
                                                                                                  Atom_mode set to all
                                                                                                  Reading ./paircutoffs.gz
                                                                                                  [T/F OPT]Default FALSE value for [-decoystats]
                                                                                                  set_decoystats_flag: from,to F F
                                                                                                  [T/F OPT]Default FALSE value for [-decoyfeatures]
                                                                                                  [T/F OPT]Default FALSE value for [-evolution]
                                                                                                  [T/F OPT]Default FALSE value for [-evol_recomb]
                                                                                                  [T/F OPT]Default FALSE value for [-profile]
                                                                                                  BOINC :: [2006-10-12 12:51:59] :: mode: relax :: nstartnum: 1 :: number_of_output: 5 :: num_decoys: 0 :: pct_complete: 0.01
                                                                                                  [T/F OPT]New TRUE value for [-watchdog]
                                                                                                  [INT OPT]Default value for [-watchdog_time] 3600
                                                                                                  [REAL OPT]Default value for [-cpu_run_timeout_factor] 4
                                                                                                  [T/F OPT]Default FALSE value for [-dummy_model]
                                                                                                  Searching for dat file: ./idlrlx_hom001_t339.dat
                                                                                                  Searching for dat file: ./idlrlx_hom001_t339.dat
                                                                                                  WARNING!! .dat file not found!
                                                                                                  Looking for fasta file: ./idlrlx_hom001_t339_.fasta
                                                                                                  Looking for psipred file: ./idlrlx_hom001_t339_.psipred_ss2
                                                                                                  Looking for psipred file: ./idlrlx_hom001_t339_.psipred_ss2
                                                                                                  Looking for psipred file: ./idlrlx_hom001_t339_.jones
                                                                                                  Looking for psipred file: ./idlrlx_hom001_t339_.psipred
                                                                                                  Looking for psipred file: ./idlrlx_hom001_t339_.jones
                                                                                                  Looking for psipred file: ./idlrlx_hom001_t339_.psipred
                                                                                                  WARNING :: Unable to find psipred file!
                                                                                                  [T/F OPT]Default FALSE value for [-tight_hb]
                                                                                                  File: ./idlrlx_hom001_t339_.cst not found
                                                                                                  Running without distance constraints
                                                                                                  File: ./idlrlx_hom001_t339_.dpl not found
                                                                                                  Dipolar constraints will not be used
                                                                                                  fragment file: ./idlrlx_boinc_hom001_aat339_03_05.200_v1_3.gz
                                                                                                  Total Residue 416
                                                                                                  frag size: 3 frags/residue: 200
                                                                                                  fragment file: ./idlrlx_boinc_hom001_aat339_09_05.200_v1_3.gz
                                                                                                  Total Residue 416
                                                                                                  frag size: 9 frags/residue: 25
                                                                                                  generating 1mer library from 3mer library
                                                                                                  [T/F OPT]Default FALSE value for [-ssblocks]
                                                                                                  [T/F OPT]Default FALSE value for [-check_homs]
                                                                                                  calculating fragment_diversity...
                                                                                                  dihedral_bin: unusual angle
                                                                                                  dihedral_bin: unusual angle
                                                                                                  dihedral_bin: unusual angle
                                                                                                  dihedral_bin: unusual angle
                                                                                                  dihedral_bin: unusual angle
                                                                                                  dihedral_bin: unusual angle
                                                                                                  dihedral_bin: unusual angle
                                                                                                  dihedral_bin: unusual angle
                                                                                                  dihedral_bin: unusual angle
                                                                                                  dihedral_bin: unusual angle
                                                                                                  dihedral_bin: unusual angle
                                                                                                  dihedral_bin: unusual angle
                                                                                                  dihedral_bin: unusual angle
                                                                                                  [T/F OPT]Default FALSE value for [-barcode_mode]
                                                                                                  disabling all filters
                                                                                                  [REAL OPT]Default value for [-co] -1
                                                                                                  [REAL OPT]Default value for [-rms] -1
                                                                                                  Searching for pdb...: ./idlrlx_hom001_t339.pdb
                                                                                                  Searching for pdb...: ./idlrlx_hom001_t339.pdb
                                                                                                  no pdb file for idlrlx_hom001_t339
                                                                                                  [T/F OPT]Default FALSE value for [-repeatin]
                                                                                                  [T/F OPT]Default FALSE value for [-repeatout]
                                                                                                  [T/F OPT]Default FALSE value for [-clnt]
                                                                                                  reading starting structure: ./T0339_t339_1_2.pdb.gz
                                                                                                  [T/F OPT]Default FALSE value for [-use_native_centroid]
                                                                                                  [T/F OPT]New TRUE value for [-constant_seed]
                                                                                                  [INT OPT]New value for [-jran] 2898263
                                                                                                  # =====================================
                                                                                                  # random seed: 2898263
                                                                                                  # =====================================
                                                                                                  WARNING: 52 missing backbone atoms at 13 residues in pdb file
                                                                                                  allow_missing= 1
                                                                                                  skip_missing= 0
                                                                                                  WARNING: 13 centroids were placed at 0,0,0
                                                                                                  WARNING:: end of pdb file reached: angle, secstruct, & res info not found
                                                                                                  Looking for dssp file: ./T0339_t339_1_2.dssp
                                                                                                  dssp file not found
                                                                                                  Looking for secondary structure assignment file: ./T0339_t339_1_2.ssa
                                                                                                  ssa file not found
                                                                                                  calculating secondary structure from torsion angles
                                                                                                  [T/F OPT]Default FALSE value for [-use_input_bond]
                                                                                                  [T/F OPT]Default FALSE value for [-regions]
                                                                                                  [T/F OPT]Default FALSE value for [-apply_filters]
                                                                                                  [T/F OPT]Default FALSE value for [-knot_filter]
                                                                                                  [T/F OPT]Default FALSE value for [-poke_filter]
                                                                                                  [T/F OPT]Default FALSE value for [-score_contact_fullatom]
                                                                                                  [T/F OPT]New TRUE value for [-long_range_hb_weight]
                                                                                                  [T/F OPT]New TRUE value for [-long_range_hb_weight]
                                                                                                  [REAL OPT]New value for [-long_range_hb_weight] 1
                                                                                                  [T/F OPT]New TRUE value for [-short_range_hb_weight]
                                                                                                  [T/F OPT]New TRUE value for [-short_range_hb_weight]
                                                                                                  [REAL OPT]New value for [-short_range_hb_weight] 0.5
                                                                                                  [REAL OPT]Default value for [-fa_plane_weight] 0
                                                                                                  [REAL OPT]Default value for [-omega_weight] 0.5
                                                                                                  [T/F OPT]Default FALSE value for [-rand_envpair_res_wt]
                                                                                                  [REAL OPT]Default value for [-parallel_weight] 1
                                                                                                  [REAL OPT]Default value for [-antiparallel_weight] 1
                                                                                                  [T/F OPT]Default FALSE value for [-rand_SS_wt]
                                                                                                  [T/F OPT]Default FALSE value for [-random_parallel_antiparallel]
                                                                                                  [T/F OPT]Default FALSE value for [-rand_cst_res_wt]
                                                                                                  [T/F OPT]Default FALSE value for [-use_barcode_to_score]
                                                                                                  initializing full atom functions
                                                                                                  [T/F OPT]Default FALSE value for [-soft_rep]
                                                                                                  [T/F OPT]Default FALSE value for [-soft_rep_design]
                                                                                                  [T/F OPT]Default FALSE value for [-smooth_etable]
                                                                                                  [T/F OPT]Default FALSE value for [-reduce_templates]
                                                                                                  [T/F OPT]Default FALSE value for [-gen_born]
                                                                                                  [T/F OPT]Default FALSE value for [-small_radii]
                                                                                                  [T/F OPT]Default FALSE value for [-use_bw]
                                                                                                  [T/F OPT]Default FALSE value for [-use_aw]
                                                                                                  [T/F OPT]Default FALSE value for [-dna_weights]
                                                                                                  [STR OPT]Default value for [-fa_lj_rep_slope] highres.
                                                                                                  Reading ./bbdep02.May.sortlib.gz
                                                                                                  Reading ./plane_data_table_1015.dat.gz
                                                                                                  Reading ./pdbpairstats_fine.gz
                                                                                                  Reading ./Paa.gz
                                                                                                  Reading ./Paa_n.gz
                                                                                                  Reading ./Paa_pp.gz
                                                                                                  generating Etable...
                                                                                                  Starting energy table calculation
                                                                                                  Energy table parameter set: polh_aroh Revision: 10024 Date: 2006-08-28 13:54:52 -0700 (Mon, 28 Aug 2006)
                                                                                                  [T/F OPT]Default FALSE value for [-mod_hhrep]
                                                                                                  [T/F OPT]Default FALSE value for [-output_etables]
                                                                                                  [T/F OPT]Default FALSE value for [-mod_etable]
                                                                                                  Finished calculating energy tables.
                                                                                                  Reading ./avgE_from_pdb.gz
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 92
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 93
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 94
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 95
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 96
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 97
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 98
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 99
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 100
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 101
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 102
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 103
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 104
                                                                                                  [REAL OPT]Default value for [-rsd_wt_helix] 1
                                                                                                  [REAL OPT]Default value for [-rsd_wt_strand] 1
                                                                                                  [REAL OPT]Default value for [-rsd_wt_loop] 1
                                                                                                  [T/F OPT]Default FALSE value for [-burial_code]
                                                                                                  [T/F OPT]Default FALSE value for [-new_centroid_packing]
                                                                                                  [REAL OPT]Default value for [-cb_weight] 1
                                                                                                  [REAL OPT]Default value for [-strand_dist_cutoff] 6.5
                                                                                                  [T/F OPT]Default FALSE value for [-stretch_strand_dist_cutoff]
                                                                                                  [REAL OPT]Default value for [-localstrandpair_penalty] 0
                                                                                                  [T/F OPT]Default FALSE value for [-handedness_score]
                                                                                                  [T/F OPT]Default FALSE value for [-separate_centroid_pack_score]
                                                                                                  Reading ./SASA-masks.dat.gz
                                                                                                  Reading ./SASA-angles.dat.gz
                                                                                                  ========================================
                                                                                                  Reading ./sasa_offsets.txt.gz
                                                                                                  Reading ./sasa_prob_cdf.txt.gz
                                                                                                  NEXT STRUCTURE: ./aaT0339_t339_1_2_0001.pdb
                                                                                                  [T/F OPT]Default FALSE value for [-fullatom_loop]
                                                                                                  setting pose_flag from: 0 to: 1
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 92
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 93
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 94
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 95
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 96
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 97
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 98
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 99
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 100
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 101
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 102
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 103
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 104
                                                                                                  setting pose_flag from: 1 to: 0
                                                                                                  [T/F OPT]Default FALSE value for [-obligate_loops]
                                                                                                  [INT OPT]New value for [-checkpointing_interval] 10
                                                                                                  [T/F OPT]Default FALSE value for [-loop_farlx_only]
                                                                                                  [T/F OPT]New TRUE value for [-loop_model]
                                                                                                  [STR OPT]Default value for [-loop_file] .
                                                                                                  No loop_file specified! Try to find loopfile in start_path!
                                                                                                  loop: 91 105
                                                                                                  [T/F OPT]Default FALSE value for [-coordcst]
                                                                                                  [REAL OPT]Default value for [-score_filter_cutoff] 1
                                                                                                  setting pose_flag from: 0 to: 1
                                                                                                  [T/F OPT]Default FALSE value for [-ccd_closure]
                                                                                                  [T/F OPT]Default FALSE value for [-random_frag]
                                                                                                  [T/F OPT]Default FALSE value for [-loops_subset]
                                                                                                  [REAL OPT]Default value for [-loop_combine_rate] 0
                                                                                                  [T/F OPT]Default FALSE value for [-random_loop]
                                                                                                  loop_begin: 91 loop_end: 105 loop_sequence: TSKGHTGGHHSPVKG
                                                                                                  [T/F OPT]Default FALSE value for [-alter_seqs]
                                                                                                  cutpoint: 93
                                                                                                  [REAL OPT]Default value for [-looprlx_cycle_ratio] 1
                                                                                                  starting loop pose
                                                                                                  pre-computing chuck/gunn move set for frag length 3
                                                                                                  pre-computing chuck/gunn move set for frag length 1
                                                                                                  accepts: frag,ccd 1 300 1 39.6667 0
                                                                                                  accepts: frag,ccd 2 300 1 18.3333 0
                                                                                                  accepts: frag,ccd 3 300 1 13.6667 0
                                                                                                  accepts: frag,ccd 4 300 1 9 0
                                                                                                  accepts: frag,ccd 5 300 1 11.3333 0
                                                                                                  accepts: frag,ccd 6 114 93 11.4035 68.8172
                                                                                                  accepts: frag,ccd 7 96 102 7.29167 93.1373
                                                                                                  accepts: frag,ccd 8 54 123 5.55556 100
                                                                                                  accepts: frag,ccd 9 36 132 13.8889 100
                                                                                                  accepts: frag,ccd 10 1 150 0 100
                                                                                                  [REAL OPT]Default value for [-chain_break_tol] 0.200000003
                                                                                                  folded loops: 0
                                                                                                  setting pose_flag from: 1 to: 0
                                                                                                  score_filter: tag= looprlx score= -29.9825 rank= 1 max_rank= 1 nscores= 1 filter_score= -29.9825
                                                                                                  [T/F OPT]Default FALSE value for [-output_loops_built]
                                                                                                  [T/F OPT]New TRUE value for [-do_farlx_checkpointing]
                                                                                                  BOINC :: [2006-10-12 12:54:48] :: checkpoint_decoys() :: saved decoy info :: attempted_decoys: 0 :: num_decoys: 0 :: farlx_stage: 2
                                                                                                  setting pose_flag from: 0 to: 1
                                                                                                  Pose::dump_pdb: farlxcheck
                                                                                                  setting pose_flag from: 1 to: 0
                                                                                                  [T/F OPT]Default FALSE value for [-loop_farlx]
                                                                                                  setting pose_flag from: 0 to: 1
                                                                                                  setting pose_flag from: 1 to: 0
                                                                                                  [T/F OPT]Default FALSE value for [-pose_idlz]
                                                                                                  setting pose_flag from: 0 to: 1
                                                                                                  setting pose_flag from: 1 to: 0
                                                                                                  [T/F OPT]Default FALSE value for [-local]
                                                                                                  [T/F OPT]New TRUE value for [-idl_no_chain_break]
                                                                                                  idealizing residues 1 to 416
                                                                                                  minimization
                                                                                                  window weight vomega iter fret rms rama bump tether omega phipsi
                                                                                                  ------ ------ ------ ---- --------- -------- -------- -------- -------- -------- --------
                                                                                                  416 1.000 T 0 55202.14 11.096 -23.078 4884.500 49098.828 0.000 0.000
                                                                                                  166 0.100 F 8 3034.97 7.120 -22.254 1763.530 2816.730 0.000 0.135
                                                                                                  416 0.001 T 93 4.10 0.232 -98.510 7.183 8.220 4.300 7.103
                                                                                                  416 1.000 T 23 9.43 0.268 -98.736 2.432 10.462 4.373 7.135
                                                                                                  rms to starting angles 2.4926393
                                                                                                  root mean dme to starting coordinates 0.166341007
                                                                                                  global ca_rms to starting coordinates 0.268366277
                                                                                                  [T/F OPT]Default FALSE value for [-looprlx_idealization]
                                                                                                  BOINC :: [2006-10-12 12:59:22] :: checkpoint_decoys() :: saved decoy info :: attempted_decoys: 0 :: num_decoys: 0 :: farlx_stage: 9
                                                                                                  dump_pdb: farlxcheck
                                                                                                  [INT OPT]Default value for [-lj_ramp_cycles] 8
                                                                                                  [REAL OPT]Default value for [-stage2_lj_rep_weight] 1
                                                                                                  [T/F OPT]Default FALSE value for [-minimize_exclude_helix]
                                                                                                  [T/F OPT]Default FALSE value for [-minimize_exclude_strand]
                                                                                                  [INT OPT]Default value for [-local_min_window] 5
                                                                                                  [T/F OPT]Default FALSE value for [-no_minimize_set_local_min]
                                                                                                  [T/F OPT]Default FALSE value for [-no_farlx_rot_trials]
                                                                                                  [T/F OPT]Default FALSE value for [-stringent_relax]
                                                                                                  [REAL OPT]New value for [-farlx_cycle_ratio] 1
                                                                                                  CYCLES::number is 1 x total_residue: 416
                                                                                                  [T/F OPT]Default FALSE value for [-more_relax_cycles]
                                                                                                  initializing full atom coordinates
                                                                                                  BOINC :: [2006-10-12 13:00:51] :: checkpoint_decoys() :: saved decoy info :: attempted_decoys: 0 :: num_decoys: 0 :: farlx_stage: 10
                                                                                                  dump_fullatom_pdb: farlxcheck
                                                                                                  [T/F OPT]Default FALSE value for [-vary_chi_before_stage1]
                                                                                                  starting score -367.7052 rms 0
                                                                                                  starting full atom minimization
                                                                                                  [REAL OPT]Default value for [-ediff_cutoff] 15
                                                                                                  BOINC :: [2006-10-12 13:20:45] :: checkpoint_decoys() :: saved decoy info :: attempted_decoys: 0 :: num_decoys: 0 :: farlx_stage: 11
                                                                                                  dump_fullatom_pdb: farlxcheck
                                                                                                  ---------------------------------------------------
                                                                                                  repack trials: 11 accepts: 4 %: 36.36 e/trial: -1.36356
                                                                                                  smallmin trials: 90 accepts: 0 %: 0.00 e/trial: 0.00000
                                                                                                  stage1 score: -777.302795
                                                                                                  ---------------------------------------------------
                                                                                                  [T/F OPT]Default FALSE value for [-relax_score_filter]
                                                                                                  [T/F OPT]Default FALSE value for [-stringentrelax_before_stage2]
                                                                                                  [T/F OPT]Default FALSE value for [-vary_chi_before_stage2]
                                                                                                  [INT OPT]Default value for [-stage2_cycles] 416
                                                                                                  [INT OPT]Default value for [-nwobble1_crank] 3
                                                                                                  [INT OPT]Default value for [-nwobble2_crank] 2
                                                                                                  [INT OPT]Default value for [-nwobble_wobble] 1
                                                                                                  [INT OPT]Default value for [-crank_size] 3
                                                                                                  [INT OPT]Default value for [-wobble_size] 3
                                                                                                  [INT OPT]Default value for [-stage2_repack_period] 25
                                                                                                  [T/F OPT]Default FALSE value for [-wobble_CCD]
                                                                                                  [T/F OPT]Default FALSE value for [-skip_fragment_moves]
                                                                                                  [T/F OPT]Default FALSE value for [-no_minimize_exclude_frag_in_crank]
                                                                                                  [T/F OPT]Default FALSE value for [-no_minimize_exclude_frag_in_wobble]
                                                                                                  [REAL OPT]Default value for [-cpu_frac] 10
                                                                                                  [REAL OPT]Default value for [-frame_rate] 10
                                                                                                  [INT OPT]New value for [-cpu_run_time] 3600
                                                                                                  command executed: rosetta_beta_5.32_i686-pc-linux-gnu aa t339 _ -relax -looprlx -nstruct 5 -farlx -ex1 -ex2 -loop_model -termini -short_range_hb_weight 0.50 -long_range_hb_weight 1.0 -farlx_cycle_ratio 1.0 -idl_no_chain_break -vary_omega -output_silent_gz -output_chi_silent -protein_name_prefix idlrlx_hom001_ -frags_name_prefix idlrlx_boinc_hom001_ -s T0339_t339_1_2.pdb -paths paths_200_idlrlx.txt -do_farlx_checkpointing -checkpointing_interval 10 -cpu_run_time 3600 -watchdog -constant_seed -jran 2898263
                                                                                                  [STR OPT]New value for [-paths] paths_200_idlrlx.txt.
                                                                                                  [INT OPT]Default value for [-seed_offset] 0
                                                                                                  [T/F OPT]Default FALSE value for [-version]
                                                                                                  [T/F OPT]Default FALSE value for [-score]
                                                                                                  [T/F OPT]Default FALSE value for [-abinitio]
                                                                                                  [T/F OPT]Default FALSE value for [-refine]
                                                                                                  [T/F OPT]Default FALSE value for [-assemble]
                                                                                                  [T/F OPT]Default FALSE value for [-idealize]
                                                                                                  [T/F OPT]New TRUE value for [-relax]
                                                                                                  [T/F OPT]Default FALSE value for [-sim_aneal]
                                                                                                  [T/F OPT]Default FALSE value for [-cenrlx]
                                                                                                  [T/F OPT]New TRUE value for [-farlx]
                                                                                                  [T/F OPT]Default FALSE value for [-record_irms_before_relax]
                                                                                                  [T/F OPT]Default FALSE value for [-force_expand]
                                                                                                  [T/F OPT]New TRUE value for [-looprlx]
                                                                                                  [T/F OPT]Default FALSE value for [-pose_relax]
                                                                                                  [T/F OPT]Default FALSE value for [-minimize]
                                                                                                  [T/F OPT]Default FALSE value for [-loop_farlx_only]
                                                                                                  Rosetta mode: relax
                                                                                                  [T/F OPT]Default FALSE value for [-chain]
                                                                                                  [T/F OPT]Default FALSE value for [-protein]
                                                                                                  [T/F OPT]Default FALSE value for [-series]
                                                                                                  series_code = aa :: protein_name is t339:: chain_id is _.
                                                                                                  [INT OPT]New value for [-nstruct] 5
                                                                                                  [T/F OPT]Default FALSE value for [-read_all_chains]
                                                                                                  [T/F OPT]Default FALSE value for [-preserve_header]
                                                                                                  [T/F OPT]Default FALSE value for [-use_pdb_numbering]
                                                                                                  [T/F OPT]Default FALSE value for [-flip_symmetric_sidechains]
                                                                                                  [T/F OPT]Default FALSE value for [-fa_input]
                                                                                                  [T/F OPT]Default FALSE value for [-overwrite]
                                                                                                  [T/F OPT]Default FALSE value for [-output_pdb_gz]
                                                                                                  [T/F OPT]New TRUE value for [-output_silent_gz]
                                                                                                  [T/F OPT]Default FALSE value for [-output_scorefile_gz]
                                                                                                  [T/F OPT]Default FALSE value for [-sasapack_bvalues]
                                                                                                  [T/F OPT]Default FALSE value for [-cenlist_values]
                                                                                                  [T/F OPT]New TRUE value for [-termini]
                                                                                                  [T/F OPT]Default FALSE value for [-use_trie]
                                                                                                  [T/F OPT]Default FALSE value for [-no_trie]
                                                                                                  [T/F OPT]Default FALSE value for [-use_conformer]
                                                                                                  [T/F OPT]Default FALSE value for [-use_bbind_conformer]
                                                                                                  [T/F OPT]Default FALSE value for [-trials_trie]
                                                                                                  [T/F OPT]Default FALSE value for [-no_trials_trie]
                                                                                                  [T/F OPT]Default FALSE value for [-output_interaction_graph_memory_usage]
                                                                                                  [T/F OPT]Default FALSE value for [-read_interaction_graph]
                                                                                                  [T/F OPT]Default FALSE value for [-write_interaction_graph]
                                                                                                  [STR OPT]Default value for [-ig_file] .
                                                                                                  [T/F OPT]Default FALSE value for [-use_sasa_pack_score]
                                                                                                  [T/F OPT]Default FALSE value for [-output_dot_kinemage]
                                                                                                  [T/F OPT]Default FALSE value for [-pack_low_temp_annealing]
                                                                                                  [T/F OPT]Default FALSE value for [-no_his_his_pairE]
                                                                                                  [T/F OPT]Default FALSE value for [-silent_input]
                                                                                                  [T/F OPT]Default FALSE value for [-timer]
                                                                                                  [T/F OPT]Default FALSE value for [-count_attempts]
                                                                                                  [T/F OPT]Default FALSE value for [-status]
                                                                                                  [T/F OPT]Default FALSE value for [-ise_movie]
                                                                                                  [T/F OPT]Default FALSE value for [-output_all]
                                                                                                  [T/F OPT]New TRUE value for [-output_chi_silent]
                                                                                                  [T/F OPT]Default FALSE value for [-accept_all]
                                                                                                  [T/F OPT]Default FALSE value for [-skip_missing_residues]
                                                                                                  [STR OPT]Default value for [-cst] cst.
                                                                                                  [STR OPT]Default value for [-dpl] dpl.
                                                                                                  [STR OPT]Default value for [-resfile] none.
                                                                                                  [STR OPT]Default value for [-equiv_resfile] none.
                                                                                                  [T/F OPT]Default FALSE value for [-auto_resfile]
                                                                                                  [T/F OPT]Default FALSE value for [-chain_inc]
                                                                                                  WARNING::refold_input T, allow_missing T
                                                                                                  setting refold_input F
                                                                                                  [T/F OPT]Default FALSE value for [-full_filename]
                                                                                                  [T/F OPT]Default FALSE value for [-map_sequence]
                                                                                                  [INT OPT]Default value for [-max_frags] 200
                                                                                                  [T/F OPT]Default FALSE value for [-output_centroids]
                                                                                                  [STR OPT]New value for [-protein_name_prefix] idlrlx_hom001_.
                                                                                                  [STR OPT]New value for [-frags_name_prefix] idlrlx_boinc_hom001_.
                                                                                                  [T/F OPT]Default FALSE value for [-protein_name_prefix_homolog]
                                                                                                  [REAL OPT]Default value for [-vdw_reweight] 1
                                                                                                  [REAL OPT]Default value for [-env_reweight] 1
                                                                                                  [REAL OPT]Default value for [-pair_reweight] 1
                                                                                                  [REAL OPT]Default value for [-cb_reweight] 1
                                                                                                  [REAL OPT]Default value for [-sheet_reweight] 1
                                                                                                  [REAL OPT]Default value for [-ss_reweight] 1
                                                                                                  [REAL OPT]Default value for [-hs_reweight] 1
                                                                                                  [REAL OPT]Default value for [-rsigma_reweight] 1
                                                                                                  [REAL OPT]Default value for [-rg_reweight] 1
                                                                                                  [REAL OPT]Default value for [-pc_reweight] 1
                                                                                                  [REAL OPT]Default value for [-fa_atr_reweight] 1
                                                                                                  [REAL OPT]Default value for [-fa_rep_reweight] 1
                                                                                                  [REAL OPT]Default value for [-fa_dun_reweight ] 1
                                                                                                  [REAL OPT]Default value for [-fa_pair_reweight] 1
                                                                                                  [REAL OPT]Default value for [-fa_plane_reweight] 1
                                                                                                  [REAL OPT]Default value for [-fa_solv_reweight] 1
                                                                                                  [REAL OPT]Default value for [-fa_ref_reweight ] 1
                                                                                                  [REAL OPT]Default value for [-fa_pH_reweight] 1
                                                                                                  [REAL OPT]Default value for [-fa_h2o_reweight] 1
                                                                                                  [REAL OPT]Default value for [-fa_prob1b_reweight] 1
                                                                                                  [REAL OPT]Default value for [-fa_gb_elec_reweigh] 1
                                                                                                  [REAL OPT]Default value for [-hb_srbb_reweight] 1
                                                                                                  [REAL OPT]Default value for [-hb_lrbb_reweight] 1
                                                                                                  [REAL OPT]Default value for [-hb_sc_reweight] 1
                                                                                                  [REAL OPT]Default value for [-chainbreak_reweight] 1
                                                                                                  [T/F OPT]Default FALSE value for [-find_disulf]
                                                                                                  [T/F OPT]Default FALSE value for [-fix_disulf]
                                                                                                  [T/F OPT]Default FALSE value for [-enable_ligand_aa]
                                                                                                  [T/F OPT]Default FALSE value for [-phospho_ser]
                                                                                                  [T/F OPT]Default FALSE value for [-surface]
                                                                                                  [T/F OPT]Default FALSE value for [-loops]
                                                                                                  [T/F OPT]Default FALSE value for [-taboo]
                                                                                                  [T/F OPT]New TRUE value for [-vary_omega]
                                                                                                  [T/F OPT]Default FALSE value for [-geometric_sol]
                                                                                                  [T/F OPT]Default FALSE value for [-multi_chain]
                                                                                                  [T/F OPT]New TRUE value for [-ex1]
                                                                                                  [T/F OPT]New TRUE value for [-ex2]
                                                                                                  [T/F OPT]Default FALSE value for [-ex3]
                                                                                                  [T/F OPT]Default FALSE value for [-ex4]
                                                                                                  [T/F OPT]Default FALSE value for [-ex1aro]
                                                                                                  [T/F OPT]Default FALSE value for [-ex1aro_half]
                                                                                                  [T/F OPT]Default FALSE value for [-ex2aro_only]
                                                                                                  [INT OPT]Default value for [-extrachi_cutoff] 18
                                                                                                  [T/F OPT]Default FALSE value for [-rot_pert]
                                                                                                  [T/F OPT]Default FALSE value for [-rot_pert_input]
                                                                                                  [T/F OPT]Default FALSE value for [-exdb]
                                                                                                  [T/F OPT]Default FALSE value for [-use_electrostatic_repulsion]
                                                                                                  [T/F OPT]Default FALSE value for [-explicit_h2o]
                                                                                                  [T/F OPT]Default FALSE value for [-solvate]
                                                                                                  [T/F OPT]Default FALSE value for [-pH]
                                                                                                  [T/F OPT]Default FALSE value for [-try_both_his_tautomers]
                                                                                                  [T/F OPT]Default FALSE value for [-hydrate_dna]
                                                                                                  [T/F OPT]Default FALSE value for [-ex_dna_waters]
                                                                                                  [T/F OPT]Default FALSE value for [-minimize_rot]
                                                                                                  [T/F OPT]Default FALSE value for [-read_hetero_h2o]
                                                                                                  [T/F OPT]Default FALSE value for [-Wint_score_only]
                                                                                                  [T/F OPT]Default FALSE value for [-Wint_repack_only]
                                                                                                  [T/F OPT]Default FALSE value for [-ligand]
                                                                                                  [T/F OPT]Default FALSE value for [-enzyme_design]
                                                                                                  [T/F OPT]Default FALSE value for [-score_contact_flag]
                                                                                                  [T/F OPT]Default FALSE value for [-score_contact_weight]
                                                                                                  [T/F OPT]Default FALSE value for [-score_contact_threshold]
                                                                                                  [T/F OPT]Default FALSE value for [-scorefxn]
                                                                                                  default centroid scorefxn: 6
                                                                                                  default fullatom scorefxn: 12
                                                                                                  [INT OPT]Default value for [-run_level] 0
                                                                                                  [T/F OPT]Default FALSE value for [-silent]
                                                                                                  [T/F OPT]New TRUE value for [-output_silent_gz]
                                                                                                  run level: -4
                                                                                                  [T/F OPT]Default FALSE value for [-benchmark]
                                                                                                  [T/F OPT]Default FALSE value for [-debug]
                                                                                                  [INT OPT]Default value for [-sym_des_units] 1
                                                                                                  [T/F OPT]Default FALSE value for [-mj_min]
                                                                                                  [REAL OPT]Default value for [-mod_hhrep_height] 1
                                                                                                  [REAL OPT]Default value for [-mod_hhrep_width] 1
                                                                                                  [REAL OPT]Default value for [-mod_hhrep_center] 2.79999995
                                                                                                  [REAL OPT]Default value for [-mod_hhrep_exponent] 4
                                                                                                  [REAL OPT]Default value for [-smooth_etable_ljweight] 1.15999997
                                                                                                  [REAL OPT]Default value for [-smooth_etable_solvweight] 1.5
                                                                                                  [STR OPT]New value for [-s] T0339_t339_1_2.pdb.
                                                                                                  Starting structure: T0339_t339_1_2
                                                                                                  Reading ./Rama_smooth_dyn.dat_ss_6.4.gz
                                                                                                  Reading ./phi.theta.36.HS.resmooth.gz
                                                                                                  Reading ./phi.theta.36.SS.resmooth.gz
                                                                                                  [STR OPT]Default value for [-atom_vdw_set] hybrid.
                                                                                                  [T/F OPT]Default FALSE value for [-IUPAC]
                                                                                                  Atom_mode set to all
                                                                                                  Reading ./paircutoffs.gz
                                                                                                  [T/F OPT]Default FALSE value for [-decoystats]
                                                                                                  set_decoystats_flag: from,to F F
                                                                                                  [T/F OPT]Default FALSE value for [-decoyfeatures]
                                                                                                  [T/F OPT]Default FALSE value for [-evolution]
                                                                                                  [T/F OPT]Default FALSE value for [-evol_recomb]
                                                                                                  [T/F OPT]Default FALSE value for [-profile]
                                                                                                  BOINC :: [2006-10-12 19:33:06] :: mode: relax :: nstartnum: 1 :: number_of_output: 5 :: num_decoys: 0 :: pct_complete: 0.01
                                                                                                  [T/F OPT]New TRUE value for [-watchdog]
                                                                                                  [INT OPT]Default value for [-watchdog_time] 3600
                                                                                                  [REAL OPT]Default value for [-cpu_run_timeout_factor] 4
                                                                                                  [T/F OPT]Default FALSE value for [-dummy_model]
                                                                                                  Searching for dat file: ./idlrlx_hom001_t339.dat
                                                                                                  Searching for dat file: ./idlrlx_hom001_t339.dat
                                                                                                  WARNING!! .dat file not found!
                                                                                                  Looking for fasta file: ./idlrlx_hom001_t339_.fasta
                                                                                                  Looking for psipred file: ./idlrlx_hom001_t339_.psipred_ss2
                                                                                                  Looking for psipred file: ./idlrlx_hom001_t339_.psipred_ss2
                                                                                                  Looking for psipred file: ./idlrlx_hom001_t339_.jones
                                                                                                  Looking for psipred file: ./idlrlx_hom001_t339_.psipred
                                                                                                  Looking for psipred file: ./idlrlx_hom001_t339_.jones
                                                                                                  Looking for psipred file: ./idlrlx_hom001_t339_.psipred
                                                                                                  WARNING :: Unable to find psipred file!
                                                                                                  [T/F OPT]Default FALSE value for [-tight_hb]
                                                                                                  File: ./idlrlx_hom001_t339_.cst not found
                                                                                                  Running without distance constraints
                                                                                                  File: ./idlrlx_hom001_t339_.dpl not found
                                                                                                  Dipolar constraints will not be used
                                                                                                  fragment file: ./idlrlx_boinc_hom001_aat339_03_05.200_v1_3.gz
                                                                                                  Total Residue 416
                                                                                                  frag size: 3 frags/residue: 200
                                                                                                  fragment file: ./idlrlx_boinc_hom001_aat339_09_05.200_v1_3.gz
                                                                                                  Total Residue 416
                                                                                                  frag size: 9 frags/residue: 25
                                                                                                  generating 1mer library from 3mer library
                                                                                                  [T/F OPT]Default FALSE value for [-ssblocks]
                                                                                                  [T/F OPT]Default FALSE value for [-check_homs]
                                                                                                  calculating fragment_diversity...
                                                                                                  dihedral_bin: unusual angle
                                                                                                  dihedral_bin: unusual angle
                                                                                                  dihedral_bin: unusual angle
                                                                                                  dihedral_bin: unusual angle
                                                                                                  dihedral_bin: unusual angle
                                                                                                  dihedral_bin: unusual angle
                                                                                                  dihedral_bin: unusual angle
                                                                                                  dihedral_bin: unusual angle
                                                                                                  dihedral_bin: unusual angle
                                                                                                  dihedral_bin: unusual angle
                                                                                                  dihedral_bin: unusual angle
                                                                                                  dihedral_bin: unusual angle
                                                                                                  dihedral_bin: unusual angle
                                                                                                  [T/F OPT]Default FALSE value for [-barcode_mode]
                                                                                                  disabling all filters
                                                                                                  [REAL OPT]Default value for [-co] -1
                                                                                                  [REAL OPT]Default value for [-rms] -1
                                                                                                  Searching for pdb...: ./idlrlx_hom001_t339.pdb
                                                                                                  Searching for pdb...: ./idlrlx_hom001_t339.pdb
                                                                                                  no pdb file for idlrlx_hom001_t339
                                                                                                  [T/F OPT]Default FALSE value for [-repeatin]
                                                                                                  [T/F OPT]Default FALSE value for [-repeatout]
                                                                                                  [T/F OPT]Default FALSE value for [-clnt]
                                                                                                  WARNING: check_decoy_exists: unexpected decoy number: start#,decoy#,lastdecoy# 1 1 5 0
                                                                                                  reading starting structure: ./T0339_t339_1_2.pdb.gz
                                                                                                  [T/F OPT]Default FALSE value for [-use_native_centroid]
                                                                                                  [T/F OPT]New TRUE value for [-constant_seed]
                                                                                                  WARNING: 52 missing backbone atoms at 13 residues in pdb file
                                                                                                  allow_missing= 1
                                                                                                  skip_missing= 0
                                                                                                  WARNING: 13 centroids were placed at 0,0,0
                                                                                                  WARNING:: end of pdb file reached: angle, secstruct, & res info not found
                                                                                                  Looking for dssp file: ./T0339_t339_1_2.dssp
                                                                                                  dssp file not found
                                                                                                  Looking for secondary structure assignment file: ./T0339_t339_1_2.ssa
                                                                                                  ssa file not found
                                                                                                  calculating secondary structure from torsion angles
                                                                                                  [T/F OPT]Default FALSE value for [-use_input_bond]
                                                                                                  [T/F OPT]Default FALSE value for [-regions]
                                                                                                  [T/F OPT]Default FALSE value for [-apply_filters]
                                                                                                  [T/F OPT]Default FALSE value for [-knot_filter]
                                                                                                  [T/F OPT]Default FALSE value for [-poke_filter]
                                                                                                  [T/F OPT]Default FALSE value for [-score_contact_fullatom]
                                                                                                  [T/F OPT]New TRUE value for [-long_range_hb_weight]
                                                                                                  [T/F OPT]New TRUE value for [-long_range_hb_weight]
                                                                                                  [REAL OPT]New value for [-long_range_hb_weight] 1
                                                                                                  [T/F OPT]New TRUE value for [-short_range_hb_weight]
                                                                                                  [T/F OPT]New TRUE value for [-short_range_hb_weight]
                                                                                                  [REAL OPT]New value for [-short_range_hb_weight] 0.5
                                                                                                  [REAL OPT]Default value for [-fa_plane_weight] 0
                                                                                                  [REAL OPT]Default value for [-omega_weight] 0.5
                                                                                                  [T/F OPT]Default FALSE value for [-rand_envpair_res_wt]
                                                                                                  [REAL OPT]Default value for [-parallel_weight] 1
                                                                                                  [REAL OPT]Default value for [-antiparallel_weight] 1
                                                                                                  [T/F OPT]Default FALSE value for [-rand_SS_wt]
                                                                                                  [T/F OPT]Default FALSE value for [-random_parallel_antiparallel]
                                                                                                  [T/F OPT]Default FALSE value for [-rand_cst_res_wt]
                                                                                                  [T/F OPT]Default FALSE value for [-use_barcode_to_score]
                                                                                                  initializing full atom functions
                                                                                                  [T/F OPT]Default FALSE value for [-soft_rep]
                                                                                                  [T/F OPT]Default FALSE value for [-soft_rep_design]
                                                                                                  [T/F OPT]Default FALSE value for [-smooth_etable]
                                                                                                  [T/F OPT]Default FALSE value for [-reduce_templates]
                                                                                                  [T/F OPT]Default FALSE value for [-gen_born]
                                                                                                  [T/F OPT]Default FALSE value for [-small_radii]
                                                                                                  [T/F OPT]Default FALSE value for [-use_bw]
                                                                                                  [T/F OPT]Default FALSE value for [-use_aw]
                                                                                                  [T/F OPT]Default FALSE value for [-dna_weights]
                                                                                                  [STR OPT]Default value for [-fa_lj_rep_slope] highres.
                                                                                                  Reading ./bbdep02.May.sortlib.gz
                                                                                                  Reading ./plane_data_table_1015.dat.gz
                                                                                                  Reading ./pdbpairstats_fine.gz
                                                                                                  Reading ./Paa.gz
                                                                                                  Reading ./Paa_n.gz
                                                                                                  Reading ./Paa_pp.gz
                                                                                                  generating Etable...
                                                                                                  Starting energy table calculation
                                                                                                  Energy table parameter set: polh_aroh Revision: 10024 Date: 2006-08-28 13:54:52 -0700 (Mon, 28 Aug 2006)
                                                                                                  [T/F OPT]Default FALSE value for [-mod_hhrep]
                                                                                                  [T/F OPT]Default FALSE value for [-output_etables]
                                                                                                  [T/F OPT]Default FALSE value for [-mod_etable]
                                                                                                  Finished calculating energy tables.
                                                                                                  Reading ./avgE_from_pdb.gz
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 92
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 93
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 94
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 95
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 96
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 97
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 98
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 99
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 100
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 101
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 102
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 103
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 104
                                                                                                  [REAL OPT]Default value for [-rsd_wt_helix] 1
                                                                                                  [REAL OPT]Default value for [-rsd_wt_strand] 1
                                                                                                  [REAL OPT]Default value for [-rsd_wt_loop] 1
                                                                                                  [T/F OPT]Default FALSE value for [-burial_code]
                                                                                                  [T/F OPT]Default FALSE value for [-new_centroid_packing]
                                                                                                  [REAL OPT]Default value for [-cb_weight] 1
                                                                                                  [REAL OPT]Default value for [-strand_dist_cutoff] 6.5
                                                                                                  [T/F OPT]Default FALSE value for [-stretch_strand_dist_cutoff]
                                                                                                  [REAL OPT]Default value for [-localstrandpair_penalty] 0
                                                                                                  [T/F OPT]Default FALSE value for [-handedness_score]
                                                                                                  [T/F OPT]Default FALSE value for [-separate_centroid_pack_score]
                                                                                                  Reading ./SASA-masks.dat.gz
                                                                                                  Reading ./SASA-angles.dat.gz
                                                                                                  ========================================
                                                                                                  Reading ./sasa_offsets.txt.gz
                                                                                                  Reading ./sasa_prob_cdf.txt.gz
                                                                                                  NEXT STRUCTURE: ./aaT0339_t339_1_2_0001.pdb
                                                                                                  [T/F OPT]Default FALSE value for [-fullatom_loop]
                                                                                                  [INT OPT]Default value for [-lj_ramp_cycles] 8
                                                                                                  [REAL OPT]Default value for [-stage2_lj_rep_weight] 1
                                                                                                  [T/F OPT]Default FALSE value for [-minimize_exclude_helix]
                                                                                                  [T/F OPT]Default FALSE value for [-minimize_exclude_strand]
                                                                                                  [INT OPT]Default value for [-local_min_window] 5
                                                                                                  [T/F OPT]Default FALSE value for [-no_minimize_set_local_min]
                                                                                                  [T/F OPT]Default FALSE value for [-no_farlx_rot_trials]
                                                                                                  [T/F OPT]Default FALSE value for [-stringent_relax]
                                                                                                  [REAL OPT]New value for [-farlx_cycle_ratio] 1
                                                                                                  CYCLES::number is 1 x total_residue: 416
                                                                                                  [T/F OPT]Default FALSE value for [-more_relax_cycles]
                                                                                                  initializing full atom coordinates
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 92
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 93
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 94
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 95
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 96
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 97
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 98
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 99
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 100
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 101
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 102
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 103
                                                                                                  WARNING: Pose::set_coords: backbone missing for residue 104
                                                                                                  [T/F OPT]New TRUE value for [-do_farlx_checkpointing]
                                                                                                  reading starting structure: farlxcheck
                                                                                                  Filling missing atoms
                                                                                                  optimizing missing atoms
                                                                                                  optimizing hydrogen positions
                                                                                                  [T/F OPT]New TRUE value for [-constant_seed]
                                                                                                  ---------------------------------------------------
                                                                                                  repack trials: 1 accepts: 1 %: 100.00 e/trial: -1.15601
                                                                                                  stage1 score: -779.712646
                                                                                                  ---------------------------------------------------
                                                                                                  [T/F OPT]Default FALSE value for [-relax_score_filter]
                                                                                                  [T/F OPT]Default FALSE value for [-stringentrelax_before_stage2]
                                                                                                  [T/F OPT]Default FALSE value for [-vary_chi_before_stage2]
                                                                                                  [INT OPT]Default value for [-stage2_cycles] 416
                                                                                                  [INT OPT]Default value for [-nwobble1_crank] 3
                                                                                                  [INT OPT]Default value for [-nwobble2_crank] 2
                                                                                                  [INT OPT]Default value for [-nwobble_wobble] 1
                                                                                                  [INT OPT]Default value for [-crank_size] 3
                                                                                                  [INT OPT]Default value for [-wobble_size] 3
                                                                                                  [INT OPT]Default value for [-stage2_repack_period] 25
                                                                                                  [T/F OPT]Default FALSE value for [-wobble_CCD]
                                                                                                  [REAL OPT]Default value for [-ediff_cutoff] 15
                                                                                                  [T/F OPT]Default FALSE value for [-skip_fragment_moves]
                                                                                                  pre-computing chuck/gunn move set for frag length 3
                                                                                                  [T/F OPT]Default FALSE value for [-no_minimize_exclude_frag_in_crank]
                                                                                                  [T/F OPT]Default FALSE value for [-no_minimize_exclude_frag_in_wobble]

                                                                                                  Chu
                                                                                                  Forum moderator
                                                                                                  Project developer
                                                                                                  Project scientist

                                                                                                  Joined: Sep 26 06
                                                                                                  Posts: 61
                                                                                                  ID: 1900
                                                                                                  Credit: 12,545
                                                                                                  RAC: 0
                                                                                                  Message 2411 - Posted 17 Oct 2006 3:53:10 UTC - in response to Message 2408.

                                                                                                    Last modified: 17 Oct 2006 4:42:11 UTC

                                                                                                    I was gonna mention 2rio is a very large protein and uses a lot of meory, but that is clearly not a problem for your computer:-) Some users have reported similiar problem before, and we hope we can reproduce it reliably on our local computers in order to debug.

                                                                                                    while crunching the result named FRA_2rio_CASP7_hom001_1_2rio_1_1a06__IGNORE_THE_REST_232_1281_3_0, when i showed the graphics, the rosetta application stopped responding
                                                                                                    the version was 5.32 on a windows system

                                                                                                    each thread (science and graphics) each took up all the cycles on 2 of my CPUs (i have a multiCPU machine)

                                                                                                    stopping/exiting boinc closed the app without a problem, and it was working again when boinc was restarted

                                                                                                    it was working fine before i viewed the graphics too, no problems at all since 5.32 was released

                                                                                                    Profile Saenger
                                                                                                    Avatar

                                                                                                    Joined: Feb 28 06
                                                                                                    Posts: 12
                                                                                                    ID: 861
                                                                                                    Credit: 44,776
                                                                                                    RAC: 6
                                                                                                    Message 2412 - Posted 17 Oct 2006 13:49:41 UTC - in response to Message 2410.

                                                                                                      Sometimes the protein being simulated blows up and then the run is stuck. Not sure that is responsible for your error, but that should be stopped by the watchdog after a while if you do not abort it.

                                                                                                      I didn\'t work, I\'ve aborted this WU since. The reported time in it is some 12sec, while my boinc said something about 01:50h or such. So this watchdog didn\'t do it\'s work.
                                                                                                      I\'ve put Ralph on \"no new work\" for now, as I\'m going on a round trip through germany next wek, and don\'t want any such behaviour on my then unattended puter, I\'ll stick to steady projects for this time.

                                                                                                      But I\'ll be back in November and will look whether it happens again and will report if so.

                                                                                                      Profile Krzychu P.

                                                                                                      Joined: Feb 16 06
                                                                                                      Posts: 19
                                                                                                      ID: 114
                                                                                                      Credit: 10,236
                                                                                                      RAC: 0
                                                                                                      Message 2413 - Posted 19 Oct 2006 5:24:53 UTC

                                                                                                        After few minutes this one:
                                                                                                        2006-10-19 07:57:40|ralph@home|Unrecoverable error for result 1dcj__BOINC_NEWRELAXFLAGS_DOUBLEFARLXCYCLES_ABRELAX_SAVE_ALL_OUT__1361_15_0 (Niepoprawna funkcja. (0x1) - exit code 1 (0x1))

                                                                                                        Niepoprawna funkcja. (0x1) - exit code 1 (0x1)
                                                                                                        </message>
                                                                                                        <stderr_txt>
                                                                                                        # random seed: 2889463
                                                                                                        ABORT: bad to aa_rotno_to_packedrotno
                                                                                                        aa,rot1/2/3/4: CYS 2 0 0 0 0
                                                                                                        chi no 1 nchi 1 aav 1 is_chi_proton_rotamer(aa,aav,i) 0
                                                                                                        ERROR:: Exit at: .\\rotamer_functions.cc line:1458

                                                                                                        *and this one:
                                                                                                        2006-10-19 08:07:27|ralph@home|Unrecoverable error for result 1di2__BOINC_NEWRELAXFLAGS_DOUBLEFARLXCYCLES_ABRELAX_SAVE_ALL_OUT__1361_15_0 (Niepoprawna funkcja. (0x1) - exit code 1 (0x1))

                                                                                                        Niepoprawna funkcja. (0x1) - exit code 1 (0x1)
                                                                                                        </message>
                                                                                                        <stderr_txt>
                                                                                                        # random seed: 2889363
                                                                                                        ABORT: bad to aa_rotno_to_packedrotno
                                                                                                        aa,rot1/2/3/4: MET 11 2 0 0 0
                                                                                                        chi no 2 nchi 3 aav 2 is_chi_proton_rotamer(aa,aav,i) 0
                                                                                                        ERROR:: Exit at: .\\rotamer_functions.cc line:1458

                                                                                                        *and this one:
                                                                                                        2006-10-19 08:16:08|ralph@home|Unrecoverable error for result 1dtj__BOINC_NEWRELAXFLAGS_DOUBLEFARLXCYCLES_ABRELAX_SAVE_ALL_OUT__1361_15_0 (Niepoprawna funkcja. (0x1) - exit code 1 (0x1))

                                                                                                        <message>
                                                                                                        Niepoprawna funkcja. (0x1) - exit code 1 (0x1)
                                                                                                        </message>
                                                                                                        <stderr_txt>
                                                                                                        # random seed: 2889263
                                                                                                        ABORT: bad to aa_rotno_to_packedrotno
                                                                                                        aa,rot1/2/3/4: ARG 15 2 2 0 2
                                                                                                        chi no 3 nchi 4 aav 1 is_chi_proton_rotamer(aa,aav,i) 0
                                                                                                        ERROR:: Exit at: .\\rotamer_functions.cc line:1458

                                                                                                        *and this one too:
                                                                                                        2006-10-19 08:22:47|ralph@home|Unrecoverable error for result 1mkyA_BOINC_NEWRELAXFLAGS_DOUBLEFARLXCYCLES_ABRELAX_SAVE_ALL_OUT__1361_15_0 (Niepoprawna funkcja. (0x1) - exit code 1 (0x1))

                                                                                                        Niepoprawna funkcja. (0x1) - exit code 1 (0x1)
                                                                                                        </message>
                                                                                                        <stderr_txt>
                                                                                                        # random seed: 2889063
                                                                                                        ABORT: bad to aa_rotno_to_packedrotno
                                                                                                        aa,rot1/2/3/4: LYS 9 3 2 3 0
                                                                                                        chi no 4 nchi 4 aav 1 is_chi_proton_rotamer(aa,aav,i) 0
                                                                                                        ERROR:: Exit at: .\\rotamer_functions.cc line:1458
                                                                                                        ____________

                                                                                                        Profile Krzychu P.

                                                                                                        Joined: Feb 16 06
                                                                                                        Posts: 19
                                                                                                        ID: 114
                                                                                                        Credit: 10,236
                                                                                                        RAC: 0
                                                                                                        Message 2414 - Posted 19 Oct 2006 5:52:44 UTC

                                                                                                          Last modified: 19 Oct 2006 6:50:40 UTC

                                                                                                          and this one too:
                                                                                                          2006-10-19 08:36:44|ralph@home|Unrecoverable error for result 1n0u__BOINC_NEWRELAXFLAGS_DOUBLEFARLXCYCLES_ABRELAX_SAVE_ALL_OUT__1361_15_0 (Niepoprawna funkcja. (0x1) - exit code 1 (0x1))

                                                                                                          Niepoprawna funkcja. (0x1) - exit code 1 (0x1)
                                                                                                          </message>
                                                                                                          <stderr_txt>
                                                                                                          # random seed: 2888963
                                                                                                          sin_cos_range ERROR: -1.#IND000 is outside of [-1,+1] range
                                                                                                          ABORT: bad to aa_rotno_to_packedrotno
                                                                                                          aa,rot1/2/3/4: LEU 10 0 0 0 0
                                                                                                          chi no 1 nchi 2 aav 1 is_chi_proton_rotamer(aa,aav,i) 0
                                                                                                          ERROR:: Exit at: .\\rotamer_functions.cc line:1458

                                                                                                          *and this one too:
                                                                                                          2006-10-19 08:43:05|ralph@home|Unrecoverable error for result 1b72__BOINC_NEWRELAXFLAGS_DOUBLEFARLXCYCLES_ABRELAX_SAVE_ALL_OUT__1361_61_0 (Niepoprawna funkcja. (0x1) - exit code 1 (0x1))

                                                                                                          Niepoprawna funkcja. (0x1) - exit code 1 (0x1)
                                                                                                          </message>
                                                                                                          <stderr_txt>
                                                                                                          # random seed: 2889517
                                                                                                          sin_cos_range ERROR: -1.#IND000 is outside of [-1,+1] range
                                                                                                          sin_cos_range ERROR: -1.#IND000 is outside of [-1,+1] range
                                                                                                          sin_cos_range ERROR: -1.#IND000 is outside of [-1,+1] range
                                                                                                          sin_cos_range ERROR: -1.#IND000 is outside of [-1,+1] range
                                                                                                          ABORT: bad to aa_rotno_to_packedrotno
                                                                                                          aa,rot1/2/3/4: ASN 12 2 0 0 0
                                                                                                          chi no 2 nchi 2 aav 1 is_chi_proton_rotamer(aa,aav,i) 0
                                                                                                          ERROR:: Exit at: .\\rotamer_functions.cc line:1458

                                                                                                          *and next one :(
                                                                                                          2006-10-19 08:55:58|ralph@home|Unrecoverable error for result 1ogw__BOINC_NEWRELAXFLAGS_DOUBLEFARLXCYCLES_ABRELAX_SAVE_ALL_OUT__1361_15_0 (Niepoprawna funkcja. (0x1) - exit code 1 (0x1))

                                                                                                          Niepoprawna funkcja. (0x1) - exit code 1 (0x1)
                                                                                                          </message>
                                                                                                          <stderr_txt>
                                                                                                          # random seed: 2888863
                                                                                                          ABORT: bad to aa_rotno_to_packedrotno
                                                                                                          aa,rot1/2/3/4: GLU 4 3 2 0 0
                                                                                                          chi no 3 nchi 3 aav 1 is_chi_proton_rotamer(aa,aav,i) 0
                                                                                                          ERROR:: Exit at: .\\rotamer_functions.cc line:1458

                                                                                                          and this one:
                                                                                                          2006-10-19 09:07:07|ralph@home|Unrecoverable error for result 1r69__BOINC_NEWRELAXFLAGS_DOUBLEFARLXCYCLES_ABRELAX_SAVE_ALL_OUT__1361_15_0 (Niepoprawna funkcja. (0x1) - exit code 1 (0x1))

                                                                                                          Niepoprawna funkcja. (0x1) - exit code 1 (0x1)
                                                                                                          </message>
                                                                                                          <stderr_txt>
                                                                                                          # random seed: 2888763
                                                                                                          # cpu_run_time_pref: 3600
                                                                                                          sin_cos_range ERROR: -1.#IND000 is outside of [-1,+1] range
                                                                                                          ABORT: bad to aa_rotno_to_packedrotno
                                                                                                          aa,rot1/2/3/4: LYS 9 2 2 0 0
                                                                                                          chi no 3 nchi 4 aav 1 is_chi_proton_rotamer(aa,aav,i) 0
                                                                                                          ERROR:: Exit at: .\\rotamer_functions.cc line:1458
                                                                                                          ____________

                                                                                                          Profile Krzychu P.

                                                                                                          Joined: Feb 16 06
                                                                                                          Posts: 19
                                                                                                          ID: 114
                                                                                                          Credit: 10,236
                                                                                                          RAC: 0
                                                                                                          Message 2415 - Posted 19 Oct 2006 6:54:00 UTC

                                                                                                            and next one:
                                                                                                            2006-10-19 09:20:08|ralph@home|Unrecoverable error for result 1dcj__BOINC_NEWRELAXFLAGS_DOUBLEFARLXCYCLES_ABRELAX_SAVE_ALL_OUT__1361_16_0 (Niepoprawna funkcja. (0x1) - exit code 1 (0x1))

                                                                                                            Niepoprawna funkcja. (0x1) - exit code 1 (0x1)
                                                                                                            </message>
                                                                                                            <stderr_txt>
                                                                                                            # random seed: 2889462
                                                                                                            ABORT: bad to aa_rotno_to_packedrotno
                                                                                                            aa,rot1/2/3/4: HIS 7 2 0 0 0
                                                                                                            chi no 2 nchi 2 aav 1 is_chi_proton_rotamer(aa,aav,i) 0
                                                                                                            ERROR:: Exit at: .\\rotamer_functions.cc line:1458



                                                                                                            2006-10-19 09:29:50|ralph@home|Unrecoverable error for result 2tif__BOINC_NEWRELAXFLAGS_DOUBLEFARLXCYCLES_ABRELAX_SAVE_ALL_OUT__1361_15_0 (Niepoprawna funkcja. (0x1) - exit code 1 (0x1))

                                                                                                            Niepoprawna funkcja. (0x1) - exit code 1 (0x1)
                                                                                                            </message>
                                                                                                            <stderr_txt>
                                                                                                            # random seed: 2888563
                                                                                                            ABORT: bad to aa_rotno_to_packedrotno
                                                                                                            aa,rot1/2/3/4: GLU 4 0 0 3 0
                                                                                                            chi no 1 nchi 3 aav 1 is_chi_proton_rotamer(aa,aav,i) 0
                                                                                                            ERROR:: Exit at: .\\rotamer_functions.cc line:1458



                                                                                                            2006-10-19 09:37:40|ralph@home|Unrecoverable error for result 1di2__BOINC_NEWRELAXFLAGS_DOUBLEFARLXCYCLES_ABRELAX_SAVE_ALL_OUT__1361_16_0 (Niepoprawna funkcja. (0x1) - exit code 1 (0x1))

                                                                                                            Niepoprawna funkcja. (0x1) - exit code 1 (0x1)
                                                                                                            </message>
                                                                                                            <stderr_txt>
                                                                                                            # random seed: 2889362
                                                                                                            ABORT: bad to aa_rotno_to_packedrotno
                                                                                                            aa,rot1/2/3/4: GLU 4 0 0 1 0
                                                                                                            chi no 1 nchi 3 aav 1 is_chi_proton_rotamer(aa,aav,i) 0
                                                                                                            ERROR:: Exit at: .\\rotamer_functions.cc line:1458



                                                                                                            2006-10-19 09:52:42|ralph@home|Unrecoverable error for result 1dtj__BOINC_NEWRELAXFLAGS_DOUBLEFARLXCYCLES_ABRELAX_SAVE_ALL_OUT__1361_16_0 (Niepoprawna funkcja. (0x1) - exit code 1 (0x1))

                                                                                                            Niepoprawna funkcja. (0x1) - exit code 1 (0x1)
                                                                                                            </message>
                                                                                                            <stderr_txt>
                                                                                                            # random seed: 2889262
                                                                                                            ABORT: bad to aa_rotno_to_packedrotno
                                                                                                            aa,rot1/2/3/4: ILE 8 2 0 0 0
                                                                                                            chi no 2 nchi 2 aav 1 is_chi_proton_rotamer(aa,aav,i) 0
                                                                                                            ERROR:: Exit at: .\\rotamer_functions.cc line:1458
                                                                                                            ____________

                                                                                                            Lee Carre

                                                                                                            Joined: Feb 16 06
                                                                                                            Posts: 21
                                                                                                            ID: 219
                                                                                                            Credit: 2,102
                                                                                                            RAC: 0
                                                                                                            Message 2426 - Posted 24 Oct 2006 15:36:30 UTC - in response to Message 2411.

                                                                                                              while crunching the result named FRA_2rio_CASP7_hom001_1_2rio_1_1a06__IGNORE_THE_REST_232_1281_3_0, when i showed the graphics, the rosetta application stopped responding
                                                                                                              the version was 5.32 on a windows system

                                                                                                              each thread (science and graphics) each took up all the cycles on 2 of my CPUs (i have a multiCPU machine)

                                                                                                              stopping/exiting boinc closed the app without a problem, and it was working again when boinc was restarted

                                                                                                              it was working fine before i viewed the graphics too, no problems at all since 5.32 was released
                                                                                                              I was gonna mention 2rio is a very large protein and uses a lot of meory, but that is clearly not a problem for your computer:-) Some users have reported similiar problem before, and we hope we can reproduce it reliably on our local computers in order to debug.
                                                                                                              ah, if it\'s memory related that might be why, i have lots of memory because i use quite a few memory intensive apps, and sometimes use all of it :p

                                                                                                              so it might have been my fault, but at least the unit didn\'t fail, it continued after i restarted boinc :)
                                                                                                              ____________
                                                                                                              Want to search the BOINC Wiki, BOINCstats, or various BOINC forums from within firefox? Try the BOINC related Firefox Search Plugins

                                                                                                              Message boards : RALPH@home bug list : Bug reports for Ralph 5.30 and 5.31 and 5.32


                                                                                                              Home | Join | About | Participants | Community | Statistics

                                                                                                              Copyright © 2017 University of Washington

                                                                                                              Last Modified: 20 Nov 2008 19:41:56 UTC
                                                                                                              Back to top ^