Branch: rosetta:main 「revision: №62162」
Test: ubuntu.gcc.integration.addsan
SubTest: AlignPDBInfoToSequences
SubTest files: 「file-system-view」
Daemon: hojo-3    
State: AlignPDBInfoToSequences

LogFile log_c1 ******** (C) Copyright Rosetta Commons Member Institutions. *************** * Use of Rosetta for commercial purposes may require purchase of a license. * ******** See LICENSE.md or email license@uw.edu for more details. ********** LogFile log_c2 ******** (C) Copyright Rosetta Commons Member Institutions. *************** * Use of Rosetta for commercial purposes may require purchase of a license. * ******** See LICENSE.md or email license@uw.edu for more details. ********** core.init: Rosetta extras: [] core.init: command: ROSETTA/source/bin/rosetta_scripts.default.linuxgccaddsan -in:path:database_cache_dir ROSETTA/.database-binaries/ubuntugccaddsan -database ROSETTA/database -s 1GL2.pdb -overwrite -parser:protocol rosetta_script2.xml -testing:INTEGRATION_TEST basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: pushed 1GL2.pdb nstruct index 1 protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from PDB 1GL2.pdb core.import_pose.import_pose: File '1GL2.pdb' automatically determined to be of type PDB from contents. core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG:NtermProteinFull 1 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG:NtermProteinFull 1 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG:NtermProteinFull 1 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG:NtermProteinFull 1 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG:NtermProteinFull 1 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG:NtermProteinFull 1 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 3 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 3 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 3 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 3 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 3 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 3 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASN 4 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASN 4 core.conformation.Conformation: [ WARNING ] missing heavyatom: ND2 on residue ASN 4 core.conformation.Conformation: [ WARNING ] missing heavyatom: O on residue VAL:CtermProteinFull 54 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue VAL:CtermProteinFull 54 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 112 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 112 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 112 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 112 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 112 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 112 core.conformation.Conformation: [ WARNING ] missing heavyatom: O on residue ALA:CtermProteinFull 114 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ALA:CtermProteinFull 114 core.conformation.Conformation: [ WARNING ] missing heavyatom: O on residue MET:CtermProteinFull 174 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue MET:CtermProteinFull 174 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP:NtermProteinFull 175 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP:NtermPr LogFile log_c3 ******** (C) Copyright Rosetta Commons Member Institutions. *************** * Use of Rosetta for commercial purposes may require purchase of a license. * ******** See LICENSE.md or email license@uw.edu for more details. ********** core.init: Rosetta extras: [] core.init: command: /home/benchmark/rosetta/source/bin/rosetta_scripts.default.linuxgccaddsan -in:path:database_cache_dir /home/benchmark/rosetta/.database-binaries/ubuntugccaddsan -database /home/benchmark/rosetta/database -s 1PEF.pdb -overwrite -out:prefix t3_ -parser:protocol rosetta_script3.xml -testing:INTEGRATION_TEST basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: pushed 1PEF.pdb nstruct index 1 protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from PDB 1PEF.pdb core.import_pose.import_pose: File '1PEF.pdb' automatically determined to be of type PDB from contents. protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=rosetta_script3.xml protocols.rosetta_scripts.RosettaScriptsParser: Validating input script... protocols.rosetta_scripts.RosettaScriptsSchemaValidator: Generating XML Schema for rosetta_scripts... protocols.rosetta_scripts.RosettaScriptsSchemaValidator: ...done protocols.rosetta_scripts.RosettaScriptsSchemaValidator: Initializing schema validator... protocols.rosetta_scripts.RosettaScriptsSchemaValidator: ...done protocols.rosetta_scripts.RosettaScriptsParser: ...done protocols.rosetta_scripts.RosettaScriptsParser: Parsed script: <ROSETTASCRIPTS> <MOVERS> <AlignPDBInfoToSequences json_fns="input3.json" mode="multiple" name="ap2s"/> </MOVERS> <PROTOCOLS> <Add mover="ap2s"/> </PROTOCOLS> </ROSETTASCRIPTS> core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt core.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "ap2s" of type AlignPDBInfoToSequences protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following settings protocols.rosetta_scripts.ParsedProtocol: Added mover "ap2s" protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from saved copy 1PEF.pdb protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER AlignPDBInfoToSequences - ap2s======================= protocols.rosetta_scripts.ParsedProtocol: setting status to success protocols.jd2.JobDistributor: no more batches to process... protocols.jd2.JobDistributor: [ WARNING ] The following options have been set, but have not yet been used: -in:path:database_cache_dir /home/benchmark/rosetta/.database-binaries/ubuntugccaddsan/ basic.citation_manager.CitationManager: The following Rosetta modules were used during this run of Rosetta, and should be cited: rosetta_scripts Application's citation(s): Fleishman SJ, Leaver-Fay A, Corn JE, Strauch E-M, Khare SD, Koga N, Ashworth J, Murphy P, Richter F, Lemmon G, Meiler J, and Baker D. (2011). RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite. PLoS ONE 6(6):e20161. doi: 10.1371/journal.pone.0020161.