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

LogFile log Basic usage: /home/benchmark/rosetta/source/bin/rna_denovo.default.linuxgccaddsan -fasta <fasta file with sequence> [ -native <native pdb file> ] Type -help for full slate of options. ******** (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/rna_denovo.default.linuxgccaddsan -in:path:database_cache_dir /home/benchmark/rosetta/.database-binaries/ubuntugccaddsan @flags -database /home/benchmark/rosetta/database -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 The use of -superimpose_over_all is deprecated. The behavior in question now defaults to TRUE and is turned off by providing a particular residue that is part of an anchoring input domain as -alignment_anchor_res. core.import_pose.import_pose: File 'srp_domainIV_fixed_START1_native_1lnt_RNA.pdb' automatically determined to be of type PDB from contents. protocols.rna.denovo.movers.RNA_DeNovoProtocolMover: Sequence: gucaggucgaagcagc protocols.rna.denovo.movers.RNA_DeNovoProtocolMover: Secstruct: ................ protocols.rna.denovo.movers.RNA_DeNovoProtocolMover: Secstruct [general]: (((((((()))))))) core.import_pose.import_pose: File 'bps_rebuild_srp_domainIV_native_1lnt_RNA.pdb' automatically determined to be of type PDB from contents. core.import_pose.import_pose: File 'bps_rebuild_srp_domainIV_native_1lnt_RNA.pdb' automatically determined to be of type PDB from contents. protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: pushed srp_domainIV_fixed_START1_native_1lnt_RNA.pdb nstruct index 1 core.import_pose.import_pose: File 'bps_rebuild_srp_domainIV_native_1lnt_RNA.pdb' automatically determined to be of type PDB from contents. protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... basic.io.database: Database file opened: scoring/rna/rna_atom_vdw.txt basic.io.database: Database file opened: scoring/rna/rnp_atom_vdw_min_distances_reformat_MIN.txt core.scoring.ScoringManager: Reading in: /home/benchmark/rosetta/database/scoring/rna/rna_base_pair_xy.dat core.scoring.rna.RNA_LowResolutionPotential: Reading basepair x - y potential file: scoring/rna/rna_base_pair_xy.dat core.scoring.rna.RNA_LowResolutionPotential: Finished reading basepair x - y potential file: scoring/rna/rna_base_pair_xy.dat core.scoring.rna.RNA_LowResolutionPotential: Reading non - base - base x - y potential file: scoring/rna/rna_base_backbone_xy.dat core.scoring.rna.RNA_LowResolutionPotential: Reading RNA backbone backbone potential file: scoring/rna/rna_backbone_backbone.dat core.scoring.ScoreFunctionFactory: SCOREFUNCTION: rna/denovo/rna_hires.wts 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/carbon_hbond/ch_o_bond_potential.dat protocols.rna.denovo.setup.RNA_DeNovoPoseInitializer: Setting desired secondary structure to: XXXXXXXXXXXXXXXX core.import_pose.import_pose: File 'srp_domainIV_fixed_START1_native_1lnt_RNA.pdb' automatically determined to be of type PDB from contents. core.io.silent.SilentFileData: Reading all structures from /home/benchmark/rosetta/database/sampling/rna/base_pair_steps/general/standard/ca_ca.out.gz core.io.silent.SilentFileData: Finished reading 19 structures from /home/benchmark/rosetta/database/sampling/rna/base_pair_steps/general/standard/ca_ca.out.gz core.io.silent.SilentFileData: Reading all structures from /home/benchmark/rosetta/database/sampling/rna/base_pair_steps/general/standard/ag_gc.out.gz core.io.silent.SilentFileData: Finished reading 4 structures from /home/benchmark/rosetta/database/sampling/rna/base_pair_steps/general/standard/ag_gc.out.gz core.io.silent.SilentFileData: Reading all structures from /home/benchmark/rosetta/database/sampling/rna/base_pair_steps/general/standard/gg_ag.out.gz core.io.silent.SilentFileData: Finished reading 6 structures from /home/benchmark/rosetta/database/sampling/rna/base_pair_steps/general/standard/gg_ag.out.gz protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Reading in vall_torsions file: /home/benchmark/rosetta/database/sampling/rna/RICHARDSON_RNA09.torsions protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Lines read from vall_torsions file: 24459 protocols.rna.denovo.RNA_FragmentMonteCarlo: Using user-defined 500 cycles in de novo modeling. protocols.rna.denovo.libraries.RNA_JumpLibrary: Reading RNA jump library: /home/benchmark/rosetta/database/sampling/rna/1jj2_RNA_jump_library.dat protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 48 cycles. protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence a and sec. struct X ... found 5709 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence c and sec. struct X ... found 6239 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence g and sec. struct X ... found 7881 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence u and sec. struct X ... found 4630 potential fragments protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence guc and sec. struct XXX ... found 383 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence ggu and sec. struct XXX ... found 604 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence gca and sec. struct XXX ... found 392 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence uca and sec. struct XXX ... found 242 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence agc and sec. struct XXX ... found 523 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence agg and sec. struct XXX ... found 587 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence cag and sec. struct XXX ... found 414 potential fragments protocols.rna.denovo.RNA_FragmentMonteCarlo: In loop modeling mode, since there is a single user-inputted pose protocols.rna.denovo.RNA_FragmentMonteCarlo: 10.7318 is all atom rmsd. protocols.moves.TrialCounter: chunk trials= 30; accepts= 0.4000; energy_drop/trial= -4.26989 protocols.moves.TrialCounter: frag 3 trials= 14; accepts= 0.8571; energy_drop/trial= 0.12848 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence aag and sec. struct XXX ... found 560 potential fragments protocols.rna.denovo.RNA_FragmentMonteCarlo: In loop modeling mode, since there is a single user-inputted pose protocols.rna.denovo.RNA_FragmentMonteCarlo: 13.2902 is all atom rmsd. protocols.moves.TrialCounter: chunk trials= 33; accepts= 0.0909; energy_drop/trial= -1.27174 protocols.moves.TrialCounter: frag 3 trials= 10; accepts= 0.5000; energy_drop/trial= -0.28040 core.scoring.rna.RNA_LowResolutionPotential: Reading basepair x - y potential file: scoring/rna/rna_base_pair_xy.dat core.scoring.rna.RNA_LowResolutionPotential: Finished reading basepair x - y potential file: scoring/rna/rna_base_pair_xy.dat core.scoring.rna.RNA_LowResolutionPotential: Reading non - base - base x - y potential file: scoring/rna/rna_base_backbone_xy.dat core.scoring.rna.RNA_LowResolutionPotential: Reading RNA backbone backbone potential file: scoring/rna/rna_backbone_backbone.dat protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: In loop modeling mode, since there is a single user-inputted pose protocols.rna.denovo.RNA_FragmentMonteCarlo: 12.9891 is all atom rmsd. protocols.moves.TrialCounter: chunk trials= 40; accepts= 0.1500; energy_drop/trial= -0.38542 protocols.moves.TrialCounter: frag 3 trials= 7; accepts= 0.8571; energy_drop/trial= -0.51324 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence gc and sec. struct XX ... found 1956 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence ca and sec. struct XX ... found 1250 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence uc and sec. struct XX ... found 1147 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence ag and sec. struct XX ... found 1819 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence ga and sec. struct XX ... found 1820 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence gu and sec. struct XX ... found 1551 potential fragments protocols.rna.denovo.RNA_FragmentMonteCarlo: In loop modeling mode, since there is a single user-inputted pose protocols.rna.denovo.RNA_FragmentMonteCarlo: 11.4658 is all atom rmsd. protocols.moves.TrialCounter: chunk trials= 36; accepts= 0.1389; energy_drop/trial= -0.74457 protocols.moves.TrialCounter: frag 2 trials= 11; accepts= 0.1818; energy_drop/trial= -1.26313 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence aa and sec. struct XX ... found 1674 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence gg and sec. struct XX ... found 2553 potential fragments protocols.rna.denovo.RNA_FragmentMonteCarlo: In loop modeling mode, since there is a single user-inputted pose protocols.rna.denovo.RNA_FragmentMonteCarlo: 11.8097 is all atom rmsd. protocols.moves.TrialCounter: chunk trials= 29; accepts= 0.1034; energy_drop/trial= -0.08678 protocols.moves.TrialCounter: frag 2 trials= 17; accepts= 0.3529; energy_drop/trial= -0.41665 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 0 protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 2 out of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 48 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3 protocols.rna.denovo.RNA_FragmentMonteCarlo: In loop modeling mode, since there is a single user-inputted pose protocols.rna.denovo.RNA_FragmentMonteCarlo: 12.9635 is all atom rmsd. protocols.moves.TrialCounter: chunk trials= 30; accepts= 0.3667; energy_drop/trial= -11.27983 protocols.moves.TrialCounter: frag 3 trials= 14; accepts= 0.7143; energy_drop/trial= -2.70402 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence gaa and sec. struct XXX ... found 603 potential fragments protocols.rna.denovo.RNA_FragmentMonteCarlo: In loop modeling mode, since there is a single user-inputted pose protocols.rna.denovo.RNA_FragmentMonteCarlo: 2.47928 is all atom rmsd. protocols.moves.TrialCounter: chunk trials= 32; accepts= 0.1875; energy_drop/trial= -0.65066 protocols.moves.TrialCounter: frag 3 trials= 11; accepts= 0.8182; energy_drop/trial= -4.18326 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: In loop modeling mode, since there is a single user-inputted pose protocols.rna.denovo.RNA_FragmentMonteCarlo: 2.36239 is all atom rmsd. protocols.moves.TrialCounter: chunk trials= 33; accepts= 0.1818; energy_drop/trial= -0.30521 protocols.moves.TrialCounter: frag 3 trials= 10; accepts= 0.3000; energy_drop/trial= -0.02684 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.rna.denovo.RNA_FragmentMonteCarlo: In loop modeling mode, since there is a single user-inputted pose protocols.rna.denovo.RNA_FragmentMonteCarlo: 1.4285 is all atom rmsd. protocols.moves.TrialCounter: chunk trials= 30; accepts= 0.1000; energy_drop/trial= 0.05681 protocols.moves.TrialCounter: frag 2 trials= 14; accepts= 0.5000; energy_drop/trial= -0.05727 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: In loop modeling mode, since there is a single user-inputted pose protocols.rna.denovo.RNA_FragmentMonteCarlo: 2.3998 is all atom rmsd. protocols.moves.TrialCounter: chunk trials= 38; accepts= 0.3421; energy_drop/trial= 0.03928 protocols.moves.TrialCounter: frag 2 trials= 6 NO ACCEPTS. protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: In loop modeling mode, since there is a single user-inputted pose protocols.rna.denovo.RNA_FragmentMonteCarlo: 2.42727 is all atom rmsd. protocols.moves.TrialCounter: chunk trials= 31; accepts= 0.1935; energy_drop/trial= 0.03779 protocols.moves.TrialCounter: frag 2 trials= 13; accepts= 0.5385; energy_drop/trial= 0.29718 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: In loop modeling mode, since there is a single user-inputted pose protocols.rna.denovo.RNA_FragmentMonteCarlo: 2.36239 is all atom rmsd. protocols.moves.TrialCounter: chunk trials= 34; accepts= 0.2353; energy_drop/trial= 0.00000 protocols.moves.TrialCounter: frag 1 trials= 10; accepts= 0.1000; energy_drop/trial= -0.05188 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: In loop modeling mode, since there is a single user-inputted pose protocols.rna.denovo.RNA_FragmentMonteCarlo: 2.36059 is all atom rmsd. protocols.moves.TrialCounter: chunk trials= 28; accepts= 0.0714; energy_drop/trial= 0.00003 protocols.moves.TrialCounter: frag 1 trials= 12; accepts= 0.3333; energy_drop/trial= 0.00740 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: In loop modeling mode, since there is a single user-inputted pose protocols.rna.denovo.RNA_FragmentMonteCarlo: 2.3597 is all atom rmsd. protocols.moves.TrialCounter: chunk trials= 41; accepts= 0.1220; energy_drop/trial= -0.00002 protocols.moves.TrialCounter: frag 1 trials= 5; accepts= 0.8000; energy_drop/trial= 0.43598 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: In loop modeling mode, since there is a single user-inputted pose protocols.rna.denovo.RNA_FragmentMonteCarlo: 2.31794 is all atom rmsd. protocols.moves.TrialCounter: chunk trials= 30; accepts= 0.1667; energy_drop/trial= -0.64028 protocols.moves.TrialCounter: frag 1 trials= 14; accepts= 0.4286; energy_drop/trial= 0.21509 protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -90.6908 to automatically determined cutoff: -90.6908 based on 0.2 quantile from 1 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ rna_data_backbone 1.000 0.000 0.000 rna_vdw 1.000 5.050 5.050 rna_base_backbone 1.000 -2.479 -2.479 rna_backbone_backbone 1.000 0.000 0.000 rna_repulsive 1.000 1.177 1.177 rna_base_pair 1.000 -51.051 -51.051 rna_base_axis 0.200 -30.830 -6.166 rna_base_stagger 1.000 -21.458 -21.458 rna_base_stack 1.000 -15.605 -15.605 rna_base_stack_axis 0.200 -106.737 -21.347 rna_rg 1.000 8.354 8.354 atom_pair_constraint 1.000 0.000 0.000 base_pair_constraint 1.000 0.000 0.000 linear_chainbreak 5.000 2.567 12.835 --------------------------------------------------- Total weighted score: -90.691 protocols.rna.denovo.RNA_FragmentMonteCarlo: protocols.rna.denovo.RNA_FragmentMonteCarlo: In loop modeling mode, since there is a single user-inputted pose protocols.rna.denovo.RNA_FragmentMonteCarlo: In loop modeling mode, since there is a single user-inputted pose protocols.rna.denovo.RNA_FragmentMonteCarlo: In loop modeling mode, since there is a single user-inputted pose protocols.rna.denovo.movers.RNA_DeNovoProtocolMover: All atom rmsd: 2.39392 for this model. 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/