Posts by Saenger

1) Message boards : RALPH@home bug list : MiniRosetta Beta 3.26 (Message 5520)
Posted 9 Apr 2012 by Profile Saenger
Post:
18,800 seconds for 1.95 credits, that's incredible:
2646029 	21363 	5 Apr 2012 23:19:34 UTC 	9 Apr 2012 21:11:20 UTC 	Over 	Success 	Done 	18,800.09 	187.68 	1.95


Any idea what went so terribly wrong?
http://ralph.bakerlab.org/result.php?resultid=2646029
2) Message boards : RALPH@home bug list : Minirosetta Beta 3.06 (Message 5277)
Posted 4 May 2011 by Profile Saenger
Post:
Woke up this morning to an idling computer, while it pretended to run 3 RALPH on parallel.
I suspended RALPH for 15 seconds, CPU-usage resumed.
I reactivated RALPH, the WUs started again one after the other.
One was reset in CPU-time from 8h to 0, the second one from 8:30 to 2:20, the last one is still at 4:40,.
The CPU-usage is all right again, let's see what will wait for me once I return from work ;)

Here's a picture from my system monitor:
3) Message boards : Number crunching : minirosetta v2.03 (Message 5027)
Posted 5 Jan 2010 by Profile Saenger
Post:
I had some of that kind as well in former batches, they will probably stop before they reach 100% at +/- 6h.
4) Message boards : RALPH@home bug list : minirosetta 2.03 (Message 5026)
Posted 5 Jan 2010 by Profile Saenger
Post:
I got a bunch of errors, but more valids 'til now.

Typical error:
stderr out	

<core_client_version>6.10.17</core_client_version>
<![CDATA[
<message>
process exited with code 1 (0x1, -255)
</message>
<stderr_txt>
[2010- 1- 5  2:32: 2:] :: BOINC:: Initializing ... ok.
[2010- 1- 5  2:32: 2:] :: BOINC :: boinc_init()
BOINC:: Setting up shared resources ... ok.
BOINC:: Setting up semaphores ... ok.
BOINC:: Updating status ... ok.
BOINC:: Registering timer callback... ok.
BOINC:: Worker initialized successfully. 
Registering options.. 
Registered extra options.
Initializing broker options ...
Registered extra options.
Initializing core...
Initializing options.... ok 
Options::initialize()
Options::adding_options()
Options::initialize() Check specs.
Options::initialize()  End reached
Loaded options.... ok 
Processed options.... ok 
Initializing random generators... ok 
Initialization complete. 
Setting WU description ...
Unpacking zip data: ../../projects/ralph.bakerlab.org/minirosetta_database_rev34260.zip
Unpacking WU data ...
Unpacking data: ../../projects/ralph.bakerlab.org/job_boinc_t373__loopbuild_threading_tex.boinc.zip
Setting database description ...
Setting up checkpointing ...
Setting up graphics native ...

ERROR: Cannot open PDB file "native.pdb"
ERROR:: Exit from: src/core/io/pdb/pose_io.cc line: 170
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

</stderr_txt>
]]>
5) Message boards : RALPH@home bug list : minirosetta 2.01/2.02 (Message 5014)
Posted 12 Dec 2009 by Profile Saenger
Post:
As reported by svincent and Evan, all completed results have been purged.
This is not much help to you or us as we can't see the ones that fail and therefore are unable to tell you about it.

Indeed, a Beta project that purges it's WU asap is doing something decidedly wrong. It may be OK for production level, but in beta you have to be able to have a look at your results some time afterwards, and with such an irregular sending projects that "some time" should be in the order of weeks, as was before.

Please adjust the file deleter and the db_purge accordingly, like it was before the last batch.
6) Message boards : RALPH@home bug list : minirosetta 1.80 (Message 4851)
Posted 24 Jun 2009 by Profile Saenger
Post:
Most ran fine, but the last one errored out with this stderr:


<core_client_version>6.4.5</core_client_version>
<![CDATA[
<message>
process exited with code 1 (0x1, -255)
</message>
<stderr_txt>
[2009- 6-24 12:37: 2:] :: BOINC:: Initializing ... ok.
[2009- 6-24 12:37: 2:] :: BOINC :: boinc_init()
BOINC:: Setting up shared resources ... ok.
BOINC:: Setting up semaphores ... ok.
BOINC:: Updating status ... ok.
BOINC:: Registering timer callback... ok.
BOINC:: Worker initialized successfully.
Registering options..
Registered extra options.
Initializing broker options ...
Registered extra options.
Initializing core...
Initializing options.... ok
Options::initialize()
Options::adding_options()
Options::initialize() Check specs.
Options::initialize() End reached
Loaded options.... ok
Processed options.... ok
Initializing random generators... ok
Initialization complete.
Setting WU description ...
Unpacking zip data: ../../projects/ralph.bakerlab.org/minirosetta_database_rev30680.zip
Unpacking WU data ...
Unpacking data: ../../projects/ralph.bakerlab.org/real_core_1.5_low200_beta_low200.broker_corebuild.t303_.olange.boinc_files.zip
Setting database description ...
Setting up checkpointing ...
Setting up graphics native ...
BOINC:: Worker startup.
Starting watchdog...
Watchdog active.

ERROR: choice != 0
ERROR:: Exit from: src/protocols/jd2/ShuffleJobDistributor.cc line: 83
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

</stderr_txt>
]]>


This are the messages for the errored WU:
Mi 24 Jun 2009 12:36:21 CEST|ralph@home|Sending scheduler request: To fetch work. Requesting 4004 seconds of work, reporting 0 completed tasks
Mi 24 Jun 2009 12:36:27 CEST|ralph@home|Scheduler request completed: got 1 new tasks
Mi 24 Jun 2009 12:36:29 CEST|ralph@home|Started download of real_core_1.5_low200_beta_low200.broker_corebuild.t303_.olange.flags.boinc
Mi 24 Jun 2009 12:36:29 CEST|ralph@home|Started download of real_core_1.5_low200_beta_low200.broker_corebuild.t303_.olange.boinc_files.zip
Mi 24 Jun 2009 12:36:30 CEST|ralph@home|Finished download of real_core_1.5_low200_beta_low200.broker_corebuild.t303_.olange.flags.boinc
Mi 24 Jun 2009 12:37:00 CEST|ralph@home|Finished download of real_core_1.5_low200_beta_low200.broker_corebuild.t303_.olange.boinc_files.zip
Mi 24 Jun 2009 12:37:01 CEST|ralph@home|Starting real_core_1.5_low200_beta_low200_hb_t303__IGNORE_THE_REST_10771_1_1
Mi 24 Jun 2009 12:37:01 CEST|ralph@home|Starting task real_core_1.5_low200_beta_low200_hb_t303__IGNORE_THE_REST_10771_1_1 using minirosetta version 180
Mi 24 Jun 2009 12:37:16 CEST|ralph@home|Computation for task real_core_1.5_low200_beta_low200_hb_t303__IGNORE_THE_REST_10771_1_1 finished
Mi 24 Jun 2009 12:37:16 CEST|ralph@home|Output file real_core_1.5_low200_beta_low200_hb_t303__IGNORE_THE_REST_10771_1_1_0 for task real_core_1.5_low200_beta_low200_hb_t303__IGNORE_THE_REST_10771_1_1 absent
Mi 24 Jun 2009 12:40:32 CEST|ralph@home|Sending scheduler request: To fetch work. Requesting 4004 seconds of work, reporting 1 completed tasks
Mi 24 Jun 2009 12:40:37 CEST|ralph@home|Scheduler request completed: got 0 new tasks


My computer ist this.
(ubuntu64 on C2Q)
7) Message boards : RALPH@home bug list : minirosetta 1.13 bug thread (Message 3925)
Posted 18 Apr 2008 by Profile Saenger
Post:
Juhuu!
My first minirosetta without error just arrived on your servers. As you can see here most other ones have errored out.
I hope I will get soon some more than my 2 tasks per day, the limit that the older minis have put my puter to ;)
8) Message boards : RALPH@home bug list : Bug Reports for Rosetta Mini Versions 1.+ (Message 3853)
Posted 8 Apr 2008 by Profile Saenger
Post:
My first result for quite some time produced this error as well on my ubuntu 7.10_64 Computer running BOINC 5.10.45 on a C2D E6750@3,2GHz



stderr out	

<core_client_version>5.10.45</core_client_version>
<![CDATA[
<message>
process exited with code 1 (0x1, -255)
</message>
<stderr_txt>
  End-of-central-directory signature not found.  Either this file is not
  a zipfile, or it constitutes one disk of a multi-part archive.  In the
  latter case the central directory and zipfile comment will be found on
  the last disk(s) of this archive.
unzip:  cannot find zipfile directory in one of minirosetta_database_rev20940.zip or
        minirosetta_database_rev20940.zip.zip, and cannot find minirosetta_database_rev20940.zip.ZIP, period.

ERROR: Unable to open file: minirosetta_database/chemical/residue_type_sets/fa_standard/residue_types.txt

ERROR:: Exit from: src/core/chemical/ResidueTypeSet.cc line: 85
called boinc_finish

</stderr_txt>
]]>



Edith says:
I just looked in the projects directory and found the missing .zip, inly a second .ZIP was missing ;). In the described thread in there was the residue_types.txt, but if the stupid minirosetta looks for a double-zipped file, it can't find any of course.
Opening the .zip was no problem
9) Message boards : RALPH@home bug list : Bug Report for Ralph 5.41 (Message 2581)
Posted 5 Dec 2006 by Profile Saenger
Post:
Here's my last result:
stderr out

<core_client_version>5.4.9</core_client_version>
<stderr_txt>
Graphics are disabled due to configuration...
# random seed: 2844030
# cpu_run_time_pref: 14400
Graphics are disabled due to configuration...
# cpu_run_time_pref: 14400
No heartbeat from core client for 31 sec - exiting
Graphics are disabled due to configuration...
# cpu_run_time_pref: 14400
======================================================
DONE :: 1 starting structures built 34 (nstruct) times
This process generated 34 decoys from 34 attempts
0 starting pdbs were skipped
======================================================


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

</stderr_txt>
<message>
<file_xfer_error>
<file_name>t103_test_LARS_constraints_6_IGNORE_THE_RESTS_00001_0000492_0.pdb_1528_16_1_0</file_name>
<error_code>-161</error_code>
</file_xfer_error>

</message>

Validate state Invalid
Claimed credit 20.4061201355507
Granted credit 0
application version 5.41


The WU has been crunched by another guy/gal with an error as well.
10) Message boards : RALPH@home bug list : Bug reports for Ralph 5.37 through 5.40 (Message 2499)
Posted 7 Nov 2006 by Profile Saenger
Post:
I've got one as well:
BOINC messages:
Die 07 Nov 2006 21:25:01 CET|ralph@home|Resuming task fibril_abeta40_test1_1463_19_2 using rosetta_beta version 538
Die 07 Nov 2006 23:14:51 CET|ralph@home|Computation for task fibril_abeta40_test1_1463_19_2 finished
Die 07 Nov 2006 23:14:52 CET|ralph@home|Unrecoverable error for result fibril_abeta40_test1_1463_19_2 (<file_xfer_error> <file_name>fibril_abeta40_test1_1463_19_2_0</file_name> <error_code>-161</error_code></file_xfer_error>)
Die 07 Nov 2006 23:14:52 CET|ralph@home|Deferring scheduler requests for 1 minutes and 0 seconds


From the stderr.txt:
</stderr_txt>
<message>
<file_xfer_error>
<file_name>fibril_abeta40_test1_1463_19_2_0</file_name>
<error_code>-161</error_code>
</file_xfer_error>

</message>


As you can see, all other Wus failed as well.
11) Message boards : RALPH@home bug list : Bug reports for Ralph 5.30 and 5.31 and 5.32 (Message 2412)
Posted 17 Oct 2006 by Profile Saenger
Post:
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.
12) Message boards : RALPH@home bug list : Bug reports for Ralph 5.30 and 5.31 and 5.32 (Message 2407)
Posted 13 Oct 2006 by Profile Saenger
Post:
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]






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