Bug reports for Ralph 5.30 and 5.31 and 5.32

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

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Leffe

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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

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Profile anders n

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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

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Leffe

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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

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Chu
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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

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MatrixCrawler

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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))
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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

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ID: 2407 · Report as offensive    Reply Quote
Lee Carre

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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
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ID: 2408 · Report as offensive    Reply Quote
Chu
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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]

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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

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



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