core.init: Rosetta version exported from http://www.rosettacommons.org core.init: command: /share/src/rosetta/clang-1.1.3/rosetta_2014.22.56873_bundle/main/rosetta_source/bin/mr_protocols.default.linuxgccrelease @rebuild.flags core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-104234080 seed_offset=0 real_seed=-104234080 core.init.random: RandomGenerator:init: Normal mode, seed=-104234080 RG_type=mt19937 rosetta_MR: The flag -MR::mode is no longer used. Ignoring. 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 basic.io.database: Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.HS.resmooth basic.io.database: Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.SS.resmooth basic.io.database: Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/rama/Rama_smooth_dyn.dat_ss_6.4 basic.io.database: Database file opened: scoring/score_functions/centroid_smooth/cen_smooth_params.txt core.scoring.CartesianBondedEnergy: Initializing IdealParametersDatabase with default Ks=300 , 80 , 20 , 10 , 40 basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-lengths.txt core.scoring.CartesianBondedEnergy: Read 770 bb-independent lengths. basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-angles.txt core.scoring.CartesianBondedEnergy: Read 1464 bb-independent angles. basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-torsions.txt core.scoring.CartesianBondedEnergy: Read 2110 bb-independent torsions. core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2013 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/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_pp core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 722 residue types core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ASP:CtermProteinFull 7 core.pack.task: Packer task: initialize from command line() protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... core.scoring.electron_density.ElectronDensity: Loading Density Map core.scoring.electron_density.ElectronDensity: Loading density map/home/smas036/phenix_test/test_fixed_model/WORK_2/AutoBuild_run_1_/overall_best_denmod_map_coeffs_nf.map core.scoring.electron_density.ElectronDensity: Setting resolution to 3A core.scoring.electron_density.ElectronDensity: atom mask to 3.2A core.scoring.electron_density.ElectronDensity: CA mask to 6A core.scoring.electron_density.ElectronDensity: Read density map'/home/smas036/phenix_test/test_fixed_model/WORK_2/AutoBuild_run_1_/overall_best_denmod_map_coeffs_nf.map' core.scoring.electron_density.ElectronDensity: extent: 40 x 48 x 40 core.scoring.electron_density.ElectronDensity: origin: 1 x 1 x 1 core.scoring.electron_density.ElectronDensity: altorigin: 0 x 0 x 0 core.scoring.electron_density.ElectronDensity: grid: 40 x 48 x 40 core.scoring.electron_density.ElectronDensity: celldim: 30 x 35 x 30 core.scoring.electron_density.ElectronDensity: cellangles: 90 x 100 x 90 core.scoring.electron_density.ElectronDensity: Symmetry records found: core.scoring.electron_density.ElectronDensity: X, Y, Z core.scoring.electron_density.ElectronDensity: -X, Y+1/2, -Z core.scoring.electron_density.ElectronDensity: voxel vol.: 0.403925 core.scoring.electron_density.ElectronDensity: Resizing 40x48x40 to 20x24x20 core.scoring.electron_density.ElectronDensity: new extent: 20 x 24 x 20 core.scoring.electron_density.ElectronDensity: new origin: 0.5 x 0.5 x 0.5 core.scoring.electron_density.ElectronDensity: new grid: 20 x 24 x 20 core.scoring.electron_density.ElectronDensity: new VV: 3.2314 core.scoring.electron_density.ElectronDensity: Minimum resolution = 3 core.scoring.electron_density.ElectronDensity: Minimum B factor = 36 core.scoring.electron_density.ElectronDensity: Effective resolution = 3 core.scoring.electron_density.ElectronDensity: Effective B factor = 36 core.scoring.electron_density.ElectronDensity: Override ATOM_MASK (was 3.2, now 4.05142) core.scoring.electron_density.ElectronDensity: Override CA_MASK (was 6, now 9.72342) core.io.fragments: reading fragments from file: /share/apps/phenix/phenix-1.9-1692/phenix/phenix/rosetta/dummy_fragments_file_9.gz ... core.io.fragments: rosetta++ fileformat detected! Calling legacy reader... core.fragments.ConstantLengthFragSet: finished reading top 90 9mer fragments from file /share/apps/phenix/phenix-1.9-1692/phenix/phenix/rosetta/dummy_fragments_file_9.gz core.io.fragments: reading fragments from file: /share/apps/phenix/phenix-1.9-1692/phenix/phenix/rosetta/dummy_fragments_file_3.gz ... core.io.fragments: rosetta++ fileformat detected! Calling legacy reader... core.fragments.ConstantLengthFragSet: finished reading top 75 3mer fragments from file /share/apps/phenix/phenix-1.9-1692/phenix/phenix/rosetta/dummy_fragments_file_3.gz protocols.comparative_modeling.util: No unaligned residues, no loops found. core.chemical.ResidueTypeSet: Finished initializing centroid residue type set. Created 1010 residue types basic.io.database: Database file opened: scoring/score_functions/hbonds/score12_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/score12_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/score12_params/HBEval.csv core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2013 protocols.hybridization.HybridizeProtocol: FRAGMENTS small max length: 3 protocols.hybridization.HybridizeProtocol: FRAGMENTS big max length: 9 protocols.hybridization.HybridizeProtocol: Using initial template: 1 default protocols.hybridization.HybridizeProtocol: Found 1 domains for template default protocols.hybridization.HybridizeProtocol: domain 1: LOOP begin end cut skip_rate extended protocols.hybridization.HybridizeProtocol: LOOP 1 7 0 0 0 protocols.hybridization.HybridizeProtocol: protocols.hybridization.HybridizeProtocol: Final decision: 1 domains protocols.hybridization.HybridizeProtocol: domain 1: LOOP begin end cut skip_rate extended protocols.hybridization.HybridizeProtocol: LOOP 1 7 0 0 0 protocols.hybridization.HybridizeProtocol: core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2013 core.fragment: compute strand/loop fractions for 7 residues... protocols.hybridization.FoldTreeHybridize: Secondary structure from fragments: LLLLLLLL protocols.hybridization.FoldTreeHybridize: Chunks used for foldtree setup: protocols.hybridization.FoldTreeHybridize: LOOP begin end cut skip_rate extended protocols.hybridization.FoldTreeHybridize: LOOP 1 7 0 0 0 protocols.hybridization.FoldTreeHybridize: protocols.hybridization.HybridizeFoldtreeDynamic: Identified template core chunk with index: 1 protocols.hybridization.HybridizeFoldtreeDynamic: LOOP 1 7 0 0 0 core.pose.util: addVirtualResAsRoot() called but pose is already rooted on a VRT residue ... continuing. protocols.loops.loops_main: Residue 7 is not compatible with cutpoints; variant type not changed. protocols.loops.loops_main: Residue 8 is not compatible with cutpoints; variant type not changed. protocols.hybridization.FoldTreeHybridize: FOLD_TREE EDGE 8 3 1 EDGE 3 1 -1 EDGE 3 7 -1 protocols.hybridization.FoldTreeHybridize: protocols.hybridization.FoldTreeHybridize: auto_frag_insertion_weight for 1mer fragments: 0.00000 0 protocols.hybridization.FoldTreeHybridize: auto_frag_insertion_weight for small fragments: 0.00000 0 protocols.hybridization.FoldTreeHybridize: auto_frag_insertion_weight for big fragments: 0.00000 0 protocols.hybridization.FoldTreeHybridize: auto_frag_insertion_weight for template chunks: 1.00000 1 protocols.hybridization.FoldTreeHybridize: =================================================================== Stage 2 Folding with score1 for 2000 core.scoring.electron_density.ElectronDensity: Setting [kmin_,kmax_] to [-0.00256679,1.09662] core.scoring.electron_density.ElectronDensity: Bin 1: B(C/N/O/S)=16.4641 / 15.664 / 16.2854 / 24.2963 sum=(0,0) protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -16.9701 -16.9701 protocols.moves.TrialCounter: ChunkTrialMover trials= 2000; accepts= 1.0000; energy_drop/trial= 0.00000 protocols.hybridization.FoldTreeHybridize: =================================================================== Stage 3 Folding with score2 and score5 for 2000 protocols.hybridization.FoldTreeHybridize: Stage 3 select score2... protocols.hybridization.FoldTreeHybridize: Stage 3 loop iteration 1 protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -15.9099 -15.9099 protocols.moves.TrialCounter: ChunkTrialMover trials= 2000; accepts= 1.0000; energy_drop/trial= 0.00000 protocols.hybridization.FoldTreeHybridize: Stage 3 select score5... protocols.hybridization.FoldTreeHybridize: Stage 3 loop iteration 2 protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -15.9099 -15.9099 protocols.moves.TrialCounter: ChunkTrialMover trials= 2000; accepts= 1.0000; energy_drop/trial= 0.00000 protocols.hybridization.FoldTreeHybridize: Stage 3 select score2... protocols.hybridization.FoldTreeHybridize: Stage 3 loop iteration 3 protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -15.9099 -15.9099 protocols.moves.TrialCounter: ChunkTrialMover trials= 2000; accepts= 1.0000; energy_drop/trial= 0.00000 protocols.hybridization.FoldTreeHybridize: Stage 3 select score5... protocols.hybridization.FoldTreeHybridize: Stage 3 loop iteration 4 protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -15.9099 -15.9099 protocols.moves.TrialCounter: ChunkTrialMover trials= 2000; accepts= 1.0000; energy_drop/trial= 0.00000 protocols.hybridization.FoldTreeHybridize: Stage 3 select score2... protocols.hybridization.FoldTreeHybridize: Stage 3 loop iteration 5 protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -15.9099 -15.9099 protocols.moves.TrialCounter: ChunkTrialMover trials= 2000; accepts= 1.0000; energy_drop/trial= 0.00000 protocols.hybridization.FoldTreeHybridize: Stage 3 select score5... protocols.hybridization.FoldTreeHybridize: Stage 3 loop iteration 6 protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -15.9099 -15.9099 protocols.moves.TrialCounter: ChunkTrialMover trials= 2000; accepts= 1.0000; energy_drop/trial= 0.00000 protocols.hybridization.FoldTreeHybridize: Stage 3 select score2... protocols.hybridization.FoldTreeHybridize: Stage 3 loop iteration 7 protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -15.9099 -15.9099 protocols.moves.TrialCounter: ChunkTrialMover trials= 2000; accepts= 1.0000; energy_drop/trial= 0.00000 protocols.hybridization.FoldTreeHybridize: Stage 3 select score2... protocols.hybridization.FoldTreeHybridize: Stage 3 loop iteration 8 protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -15.9099 -15.9099 protocols.moves.TrialCounter: ChunkTrialMover trials= 2000; accepts= 1.0000; energy_drop/trial= 0.00000 protocols.hybridization.FoldTreeHybridize: Stage 3 select score2... protocols.hybridization.FoldTreeHybridize: Stage 3 loop iteration 9 protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -15.9099 -15.9099 protocols.moves.TrialCounter: ChunkTrialMover trials= 2000; accepts= 1.0000; energy_drop/trial= 0.00000 protocols.hybridization.FoldTreeHybridize: Stage 3 select score2... protocols.hybridization.FoldTreeHybridize: Stage 3 loop iteration 10 protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -15.9099 -15.9099 protocols.moves.TrialCounter: ChunkTrialMover trials= 2000; accepts= 1.0000; energy_drop/trial= 0.00000 protocols.hybridization.FoldTreeHybridize: =================================================================== Stage 4 Folding with score3 for 400 protocols.hybridization.FoldTreeHybridize: Stage 4 loop iteration 1: small fragments trials protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 10.5963 10.5963 protocols.moves.TrialCounter: ChunkTrialMover trials= 400; accepts= 1.0000; energy_drop/trial= 0.00000 protocols.hybridization.FoldTreeHybridize: Stage 4 loop iteration 2: small fragments smooth trials protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 10.5963 10.5963 protocols.moves.TrialCounter: ChunkTrialMover trials= 400; accepts= 1.0000; energy_drop/trial= 0.00000 protocols.hybridization.FoldTreeHybridize: Stage 4 loop iteration 3: small fragments smooth trials protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 10.5963 10.5963 protocols.moves.TrialCounter: ChunkTrialMover trials= 400; accepts= 1.0000; energy_drop/trial= 0.00000 core.util.switchresiduetypeset: core::util::switch_to_residue_type_set: residue 1 already in centroid residue_type_set core.util.switchresiduetypeset: core::util::switch_to_residue_type_set: residue 2 already in centroid residue_type_set core.util.switchresiduetypeset: core::util::switch_to_residue_type_set: residue 3 already in centroid residue_type_set core.util.switchresiduetypeset: core::util::switch_to_residue_type_set: residue 4 already in centroid residue_type_set core.util.switchresiduetypeset: core::util::switch_to_residue_type_set: residue 5 already in centroid residue_type_set core.util.switchresiduetypeset: core::util::switch_to_residue_type_set: residue 6 already in centroid residue_type_set core.util.switchresiduetypeset: core::util::switch_to_residue_type_set: residue 7 already in centroid residue_type_set core.util.switchresiduetypeset: core::util::switch_to_residue_type_set: residue 8 already in centroid residue_type_set protocols.hybridization.CartesianHybridize: RUNNING FOR 4 MACROCYCLES protocols.hybridization.CartesianHybridize: CYCLE 1 protocols.hybridization.CartesianHybridize: setting bonded weight = 0 protocols.hybridization.CartesianHybridize: setting bonded angle weight = 0 protocols.hybridization.CartesianHybridize: setting bonded length weight = 0 protocols.hybridization.CartesianHybridize: setting bonded torsion weight = 0 protocols.hybridization.CartesianHybridize: setting cst weight = 0 protocols.hybridization.CartesianHybridize: setting vdw weight = 0.1 ERROR: conformation.size() >= seqpos ERROR:: Exit from: src/core/conformation/util.cc line: 308 protocols.jd2.JobDistributor: [ERROR] Exception caught by JobDistributor for job S_COORD_0001 [ERROR] EXCN_utility_exit has been thrown from: src/core/conformation/util.cc line: 308 ERROR: conformation.size() >= seqpos protocols.jd2.JobDistributor: S_COORD_0001 reported failure and will NOT retry protocols.jd2.JobDistributor: no more batches to process... protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 5 seconds