core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: rosetta.source.release-234 r234 2019.40+release.513cc22 513cc22d17d203e95eda08f3e66a985d92be7bfe https://www.rosettacommons.org 2019-10-06T18:20:18.207239 core.init: command: /lwork01/rosetta_src_2019.40.60963_bundle/main/source/bin/remodel.default.linuxgccrelease @flags basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=1650540439 seed_offset=0 real_seed=1650540439 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1650540439 RG_type=mt19937 core.init: Resolved executable path: /lwork01/rosetta_src_2019.40.60963_bundle/main/source/bin/remodel.default.linuxgccrelease core.init: Looking for database based on location of executable: /lwork01/rosetta_src_2019.40.60963_bundle/main/database/ 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 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 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 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. core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 45 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.12 seconds. 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/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 protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: pushed PTPRB_2i5xB_UA5.pdb nstruct index 1 protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from PDB PTPRB_2i5xB_UA5.pdb core.import_pose.import_pose: File 'PTPRB_2i5xB_UA5.pdb' automatically determined to be of type PDB core.chemical.GlobalResidueTypeSet: Loading (but possibly not actually using) 'UA5' from the PDB components dictionary for residue type 'pdb_UA5' protocols.forge.remodel.RemodelMover: apply(): entered RemodelMover apply(). pose.size(): 282 protocols.forge.remodel.RemodelMover: 282 protocols.forge.remodel.RemodelMover: apply(): input PDB dssp assignment: (based on start structure) protocols.forge.remodel.RemodelMover: LLLLLEEHHHHHHHHHHHLHHHHHHHHHHHHHHLLLLLLLLLLLLLLHHHHHHLLLLLLLELLLLEEELLLLLLEEEEEEELLLLLLLLEEEELLLLLLLHHHHHHHHHHLLLLEEEELLLLEELLEELLLLLLLLLLLEEEELLEEEEEEEEEELLLEEEEEEEEELLEEEEEEEELLLLLLLLLLLHHHHHHHHHHHHHHHHHLLLLLLEEEELLLLLLHHHHHHHHHHHHHHHHHLLEELHHHHHHHHHHHELLLLLLHHHHHHHHHHHHHHHHHHHLL protocols.forge.remodel.RemodelMover: apply(): reading blueprint file protocols.forge.remodel.RemodelData: Found token 71 on blueprint line '71' protocols.forge.remodel.RemodelData: Found token N on blueprint line '71' protocols.forge.remodel.RemodelData: Found token L on blueprint line '71' protocols.forge.remodel.RemodelData: Found token PIKAA on blueprint line '71' protocols.forge.remodel.RemodelData: Found token N on blueprint line '71' protocols.forge.remodel.RemodelData: Do remodeling on chain A protocols.forge.remodel.RemodelData: design position 71 to N ASN protocols.forge.remodel.RemodelData: Found token 0 on blueprint line '72' protocols.forge.remodel.RemodelData: Found token X on blueprint line '72' protocols.forge.remodel.RemodelData: Found token L on blueprint line '72' protocols.forge.remodel.RemodelData: Found token PIKAA on blueprint line '72' protocols.forge.remodel.RemodelData: Found token V on blueprint line '72' protocols.forge.remodel.RemodelData: Do remodeling on chain A protocols.forge.remodel.RemodelData: design position 72 to V VAL protocols.forge.remodel.RemodelData: Found token 0 on blueprint line '73' protocols.forge.remodel.RemodelData: Found token X on blueprint line '73' protocols.forge.remodel.RemodelData: Found token L on blueprint line '73' protocols.forge.remodel.RemodelData: Found token PIKAA on blueprint line '73' protocols.forge.remodel.RemodelData: Found token D on blueprint line '73' protocols.forge.remodel.RemodelData: Do remodeling on chain A protocols.forge.remodel.RemodelData: design position 73 to D ASP protocols.forge.remodel.RemodelData: Found token 0 on blueprint line '74' protocols.forge.remodel.RemodelData: Found token X on blueprint line '74' protocols.forge.remodel.RemodelData: Found token L on blueprint line '74' protocols.forge.remodel.RemodelData: Found token PIKAA on blueprint line '74' protocols.forge.remodel.RemodelData: Found token D on blueprint line '74' protocols.forge.remodel.RemodelData: Do remodeling on chain A protocols.forge.remodel.RemodelData: design position 74 to D ASP protocols.forge.remodel.RemodelData: Found token 0 on blueprint line '75' protocols.forge.remodel.RemodelData: Found token X on blueprint line '75' protocols.forge.remodel.RemodelData: Found token L on blueprint line '75' protocols.forge.remodel.RemodelData: Found token PIKAA on blueprint line '75' protocols.forge.remodel.RemodelData: Found token D on blueprint line '75' protocols.forge.remodel.RemodelData: Do remodeling on chain A protocols.forge.remodel.RemodelData: design position 75 to D ASP protocols.forge.remodel.RemodelData: Found token 0 on blueprint line '76' protocols.forge.remodel.RemodelData: Found token X on blueprint line '76' protocols.forge.remodel.RemodelData: Found token L on blueprint line '76' protocols.forge.remodel.RemodelData: Found token PIKAA on blueprint line '76' protocols.forge.remodel.RemodelData: Found token P on blueprint line '76' protocols.forge.remodel.RemodelData: Do remodeling on chain A protocols.forge.remodel.RemodelData: design position 76 to P PRO protocols.forge.remodel.RemodelData: Found token 72 on blueprint line '77' protocols.forge.remodel.RemodelData: Found token C on blueprint line '77' protocols.forge.remodel.RemodelData: Found token L on blueprint line '77' protocols.forge.remodel.RemodelData: Found token PIKAA on blueprint line '77' protocols.forge.remodel.RemodelData: Found token C on blueprint line '77' protocols.forge.remodel.RemodelData: Do remodeling on chain A protocols.forge.remodel.RemodelData: design position 77 to C CYS protocols.forge.remodel.RemodelData: Found token 168 on blueprint line '173' protocols.forge.remodel.RemodelData: Found token G on blueprint line '173' protocols.forge.remodel.RemodelData: Found token L on blueprint line '173' protocols.forge.remodel.RemodelData: Found token PIKAA on blueprint line '173' protocols.forge.remodel.RemodelData: Found token G on blueprint line '173' protocols.forge.remodel.RemodelData: Do remodeling on chain A protocols.forge.remodel.RemodelData: design position 173 to G GLY protocols.forge.remodel.RemodelData: Found token 0 on blueprint line '174' protocols.forge.remodel.RemodelData: Found token X on blueprint line '174' protocols.forge.remodel.RemodelData: Found token E on blueprint line '174' protocols.forge.remodel.RemodelData: Found token PIKAA on blueprint line '174' protocols.forge.remodel.RemodelData: Found token E on blueprint line '174' protocols.forge.remodel.RemodelData: Do remodeling on chain A protocols.forge.remodel.RemodelData: design position 174 to E GLU protocols.forge.remodel.RemodelData: Found token 0 on blueprint line '175' protocols.forge.remodel.RemodelData: Found token X on blueprint line '175' protocols.forge.remodel.RemodelData: Found token E on blueprint line '175' protocols.forge.remodel.RemodelData: Found token PIKAA on blueprint line '175' protocols.forge.remodel.RemodelData: Found token E on blueprint line '175' protocols.forge.remodel.RemodelData: Do remodeling on chain A protocols.forge.remodel.RemodelData: design position 175 to E GLU protocols.forge.remodel.RemodelData: Found token 0 on blueprint line '176' protocols.forge.remodel.RemodelData: Found token X on blueprint line '176' protocols.forge.remodel.RemodelData: Found token Q on blueprint line '176' protocols.forge.remodel.RemodelData: Found token PIKAA on blueprint line '176' protocols.forge.remodel.RemodelData: Found token Q on blueprint line '176' protocols.forge.remodel.RemodelData: Do remodeling on chain A protocols.forge.remodel.RemodelData: design position 176 to Q GLN protocols.forge.remodel.RemodelData: Found token 0 on blueprint line '177' protocols.forge.remodel.RemodelData: Found token X on blueprint line '177' protocols.forge.remodel.RemodelData: Found token L on blueprint line '177' protocols.forge.remodel.RemodelData: Found token PIKAA on blueprint line '177' protocols.forge.remodel.RemodelData: Found token L on blueprint line '177' protocols.forge.remodel.RemodelData: Do remodeling on chain A protocols.forge.remodel.RemodelData: design position 177 to L LEU protocols.forge.remodel.RemodelData: Found token 0 on blueprint line '178' protocols.forge.remodel.RemodelData: Found token X on blueprint line '178' protocols.forge.remodel.RemodelData: Found token D on blueprint line '178' protocols.forge.remodel.RemodelData: Found token PIKAA on blueprint line '178' protocols.forge.remodel.RemodelData: Found token D on blueprint line '178' protocols.forge.remodel.RemodelData: Do remodeling on chain A protocols.forge.remodel.RemodelData: design position 178 to D ASP protocols.forge.remodel.RemodelData: Found token 0 on blueprint line '179' protocols.forge.remodel.RemodelData: Found token X on blueprint line '179' protocols.forge.remodel.RemodelData: Found token A on blueprint line '179' protocols.forge.remodel.RemodelData: Found token PIKAA on blueprint line '179' protocols.forge.remodel.RemodelData: Found token A on blueprint line '179' protocols.forge.remodel.RemodelData: Do remodeling on chain A protocols.forge.remodel.RemodelData: design position 179 to A ALA protocols.forge.remodel.RemodelData: Found token 169 on blueprint line '180' protocols.forge.remodel.RemodelData: Found token H on blueprint line '180' protocols.forge.remodel.RemodelData: Found token L on blueprint line '180' protocols.forge.remodel.RemodelData: Found token PIKAA on blueprint line '180' protocols.forge.remodel.RemodelData: Found token H on blueprint line '180' protocols.forge.remodel.RemodelData: Do remodeling on chain A protocols.forge.remodel.RemodelData: design position 180 to H HIS protocols.forge.remodel.RemodelData: Resfile to be used for design: NATRO start 71 A PIKAA N 72 A PIKAA V 73 A PIKAA D 74 A PIKAA D 75 A PIKAA D 76 A PIKAA P 77 A PIKAA C 173 A PIKAA G 174 A PIKAA E 175 A PIKAA E 176 A PIKAA Q 177 A PIKAA L 178 A PIKAA D 179 A PIKAA A 180 A PIKAA H protocols.forge.remodel.RemodelData: ABEGO based assignment found protocols.forge.remodel.RemodelData: sequence (based on blueprint): protocols.forge.remodel.RemodelData: KTSCPIKINQFEGHFMKLQADSNYLLSKEYEELKDVGRNQSCDIALLPENRGKNRYNNILPYDATRVKLSNXXXXXCSDYINASYIPGNNFRREYIVTQGPLPGTKDDFWKMVWEQNVHNIVMVTQCVEKGRVKCDHYWPADQDSLYYGDLILQMLSESVLPEWTIREFKICGXXXXXXHRLIRHFHYTVWPDHGVPETTQSLIQFVRTVRDYINRSPGAGPTVVHCSAGVGRTGTFIALDRILQQLDSKDSVDIYGAVHDLRLHRVHMVQTECQYVYLHQCVRDVLRARKL protocols.forge.remodel.RemodelData: ss (based on blueprint): protocols.forge.remodel.RemodelData: ......................................................................LLLLLLL...............................................................................................LDDQLDDL................................................................................................................ protocols.forge.remodel.RemodelData: ABEGOtype: protocols.forge.remodel.RemodelData: XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXLLLLLLLXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXLEEQLDALXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX protocols.forge.remodel.RemodelData: LD_types: protocols.forge.remodel.RemodelData: LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL protocols.forge.remodel.RemodelData: dssp_updated_ss: lengths = 292 protocols.forge.remodel.RemodelData: LLLLLEEHHHHHHHHHHHLHHHHHHHHHHHHHHLLLLLLLLLLLLLLHHHHHHLLLLLLLELLLLEEELLLLLLLLLLLEEEEEEELLLLLLLLEEEELLLLLLLHHHHHHHHHHLLLLEEEELLLLEELLEELLLLLLLLLLLEEEELLEEEEEEEEEELLLEEEEEEEEELDDQLDDLEEEEEEEELLLLLLLLLLLHHHHHHHHHHHHHHHHHLLLLLLEEEELLLLLLHHHHHHHHHHHHHHHHHLLEELHHHHHHHHHHHELLLLLLHHHHHHHHHHHHHHHHHHHL core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /lwork01/rosetta_src_2019.40.60963_bundle/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/lwork01/rosetta_src_2019.40.60963_bundle/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.26 seconds to load from binary protocols.forge.remodel.RemodelWorkingSet: workingSetGen(): length change found. last blueprint line index: 292, last blueprint line original_index: 281 protocols.forge.remodel.RemodelWorkingSet: Adding lines to temp_for_truncation vector. protocols.forge.remodel.RemodelWorkingSet: data.dssp_updated_ss: LLLLLEEHHHHHHHHHHHLHHHHHHHHHHHHHHLLLLLLLLLLLLLLHHHHHHLLLLLLLELLLLEEELLLLLLLLLLLEEEEEEELLLLLLLLEEEELLLLLLLHHHHHHHHHHLLLLEEEELLLLEELLEELLLLLLLLLLLEEEELLEEEEEEEEEELLLEEEEEEEEELDDQLDDLEEEEEEEELLLLLLLLLLLHHHHHHHHHHHHHHHHHLLLLLLEEEELLLLLLHHHHHHHHHHHHHHHHHLLEELHHHHHHHHHHHELLLLLLHHHHHHHHHHHHHHHHHHHL AA for build: VVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVV protocols.forge.remodel.RemodelWorkingSet: head 71:71, tail 72:77, gap: 7, dssp_updated_ss.size(): 292, insert_ss: LLLLLLL protocols.forge.remodel.RemodelWorkingSet: normal rebuild protocols.forge.remodel.RemodelWorkingSet: head 168:173, tail 169:180, gap: 8, dssp_updated_ss.size(): 292, insert_ss: LDDQLDDL protocols.forge.remodel.RemodelWorkingSet: normal rebuild core.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree. core.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 74 BB 3 protocols.forge.build.BuildManager: FOLD_TREE EDGE 1 287 1 EDGE 1 70 -1 EDGE 70 74 -1 JEDGE 70 78 2 N C END EDGE 78 286 -1 EDGE 78 75 -1 core.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree. core.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 174 BB 3 protocols.forge.build.BuildManager: FOLD_TREE EDGE 1 293 1 EDGE 1 70 -1 EDGE 70 74 -1 JEDGE 70 78 2 N C END EDGE 78 75 -1 EDGE 78 172 -1 EDGE 172 174 -1 JEDGE 172 181 3 N C END EDGE 181 292 -1 EDGE 181 175 -1 protocols.forge.remodel.RemodelDesignMover: Creating NeighborhoodByDistanceCalculator using und_pos: [ 71 72 73 74 75 76 77 173 174 175 176 177 178 179 180 ] protocols.forge.remodel.RemodelMover: protocols.forge.remodel.RemodelMover: apply(): BUILD CYCLE REMAINING 1 protocols.forge.remodel.RemodelMover: ORIGINAL TREE: FOLD_TREE EDGE 1 293 1 EDGE 1 70 -1 EDGE 70 74 -1 JEDGE 70 78 2 N C END EDGE 78 75 -1 EDGE 78 172 -1 EDGE 172 174 -1 JEDGE 172 181 3 N C END EDGE 181 292 -1 EDGE 181 175 -1 protocols.forge.remodel.RemodelMover: centroid_build(): calling VariableLengthBuild apply. protocols.forge.components.VarLengthBuild: Abego size=292 and pose size=293 core.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set. Created 62 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.03 seconds. core.chemical.residue_support: [ WARNING ] Atom type 'S' on atom 'S1' from residue type 'UA5' does not have a centroid mode equivalent: assuming CAbb. core.chemical.GlobalResidueTypeSet: Loading (but possibly not actually using) 'UA5' from the PDB components dictionary for residue type 'pdb_UA5' protocols.forge.components.VarLengthBuild: VLB count_cutpoints 1 interval.left 71 interval.right 77 protocols.forge.components.VarLengthBuild: picking 200 7-mers for position 71 protocols.forge.components.VarLengthBuild: complete_ss length: 292 complete_abego size: 293 core.fragment.picking_old.vall.vall_io: Reading Vall library from /lwork01/rosetta_src_2019.40.60963_bundle/main/database//sampling/filtered.vall.dat.2006-05-05 ... core.fragment.picking_old.vall.vall_io: 100000 core.fragment.picking_old.vall.vall_io: 200000 core.fragment.picking_old.vall.vall_io: 300000 core.fragment.picking_old.vall.vall_io: 400000 core.fragment.picking_old.vall.vall_io: 500000 core.fragment.picking_old.vall.vall_io: 600000 core.fragment.picking_old.vall.vall_io: 700000 core.fragment.picking_old.vall.vall_io: 800000 core.fragment.picking_old.vall.vall_io: 900000 core.fragment.picking_old.vall.vall_io: 1000000 core.fragment.picking_old.vall.vall_io: 1100000 core.fragment.picking_old.vall.vall_io: 1200000 core.fragment.picking_old.vall.vall_io: 1300000 core.fragment.picking_old.vall.vall_io: 1400000 core.fragment.picking_old.vall.vall_io: ... done. Read 1400124 lines. Time elapsed: 10 seconds. core.fragment.picking_old.vall.vall_io: Prior library contained 0 sections totaling 0 residues. core.fragment.picking_old.vall.vall_io: Added 62471 sections to library totaling 1400124 residues. core.fragment.picking_old.vall.eval.IdentityEval: ss = LLLLLLL | aa = ....... core.fragment.picking_old.vall.eval.ABEGOEval: abego = LLLLLLL core.sequence.ABEGOManager: [ ERROR ] Unrecognized abego index: L protocols.jd2.JobDistributor: [ ERROR ] [ERROR] Exception caught by JobDistributor for job PTPRB_2i5xB_UA5_0001 protocols.jd2.JobDistributor: [ WARNING ] PTPRB_2i5xB_UA5_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 12 seconds