core.init: Rosetta version: rosetta.binary.mac.release-164 r164 2017.52+release.7984dbe 7984dbe8f2d8944cc7af321c625dd9f256ab1598 https://www.rosettacommons.org 2017-12-30T21:34:42.824086 core.init: command: remodel.static.macosclangrelease -s 1pgaA_0001.pdb -blueprint template.blueprint -jd2:no_output -num_trajectory 1 -save_top 1 -out:prefix long_loop -remodel:quick_and_dirty core.init: 'RNG device' seed mode, using '/dev/urandom', seed=360500043 seed_offset=0 real_seed=360500043 core.init.random: RandomGenerator:init: Normal mode, seed=360500043 RG_type=mt19937 core.init: Resolved executable path: /Users/zhouti8/software/rosetta/rosetta_bin_mac_2017.52.59948_bundle/main/source/bin/remodel.static.macosclangrelease core.init: Looking for database based on location of executable: /Users/zhouti8/software/rosetta/rosetta_bin_mac_2017.52.59948_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 587 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.768329 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 1pgaA_0001.pdb nstruct index 1 protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from PDB 1pgaA_0001.pdb core.import_pose.import_pose: File '1pgaA_0001.pdb' automatically determined to be of type PDB protocols.forge.remodel.RemodelMover: apply(): entered RemodelMover apply(). pose.size(): 56 protocols.forge.remodel.RemodelMover: 56 protocols.forge.remodel.RemodelMover: apply(): input PDB dssp assignment: (based on start structure) protocols.forge.remodel.RemodelMover: LEEEEEEELLLLEEEEEEELLLHHHHHHHHHHHHHHLLLLLEEEEELLLLEEEEEL protocols.forge.remodel.RemodelMover: apply(): reading blueprint file protocols.forge.remodel.RemodelData: SS based assignment found protocols.forge.remodel.RemodelData: sequence (based on blueprint): protocols.forge.remodel.RemodelData: MTYKLILNGKTLKGETTTEAxxxxDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTE protocols.forge.remodel.RemodelData: ss (based on blueprint): protocols.forge.remodel.RemodelData: ...................LLLLLL.................................. protocols.forge.remodel.RemodelData: ABEGOtype: protocols.forge.remodel.RemodelData: protocols.forge.remodel.RemodelData: LD_types: protocols.forge.remodel.RemodelData: LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL protocols.forge.remodel.RemodelData: dssp_updated_ss: lengths = 59 protocols.forge.remodel.RemodelData: LEEEEEEELLLLEEEEEEELLLLLLHHHHHHHHHHHHHHLLLLLEEEEELLLLEEEEEL 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: /Users/zhouti8/software/rosetta/rosetta_bin_mac_2017.52.59948_bundle/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Users/zhouti8/software/rosetta/rosetta_bin_mac_2017.52.59948_bundle/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.509149 seconds to load from binary protocols.forge.remodel.RemodelWorkingSet: workingSetGen(): length change found. last blueprint line index: 59, last blueprint line original_index: 56 protocols.forge.remodel.RemodelWorkingSet: Adding lines to temp_for_truncation vector. protocols.forge.remodel.RemodelWorkingSet: data.dssp_updated_ss: LEEEEEEELLLLEEEEEEELLLLLLHHHHHHHHHHHHHHLLLLLEEEEELLLLEEEEEL AA for build: VVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVV protocols.forge.remodel.RemodelWorkingSet: head 20:20, tail 22:25, gap: 6, dssp_updated_ss.size(): 59, insert_ss: LLLLLL protocols.forge.remodel.RemodelWorkingSet: normal rebuild core.kinematics.AtomTree: [ ERROR ] No proper DoF can be found for these four atoms: 23-2, 23-3, 24-1, 24-2! 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 23 BB 3 protocols.forge.build.BuildManager: FOLD_TREE EDGE 1 19 -1 EDGE 19 23 -1 JEDGE 19 26 1 N C END EDGE 26 59 -1 EDGE 26 24 -1 protocols.forge.remodel.RemodelDesignMover: Creating NeighborhoodByDistanceCalculator using und_pos: [ 20 21 22 23 24 25 ] protocols.forge.remodel.RemodelMover: protocols.forge.remodel.RemodelMover: apply(): BUILD CYCLE REMAINING 1 protocols.forge.remodel.RemodelMover: ORIGINAL TREE: FOLD_TREE EDGE 1 19 -1 EDGE 19 23 -1 JEDGE 19 26 1 N C END EDGE 26 59 -1 EDGE 26 24 -1 protocols.forge.remodel.RemodelMover: centroid_build(): calling VariableLengthBuild apply. core.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set. Created 62 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.02778 seconds. protocols.forge.components.VarLengthBuild: VLB count_cutpoints 1 interval.left 20 interval.right 25 protocols.forge.components.VarLengthBuild: picking 200 6-mers for position 20 protocols.forge.components.VarLengthBuild: complete_ss length: 59 complete_abego size: 0 core.fragment.picking_old.vall.vall_io: Reading Vall library from /Users/zhouti8/software/rosetta/rosetta_bin_mac_2017.52.59948_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: 8 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 = LLLLLL | aa = ...... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 1.26971e-08 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 1.82339e-06 protocols.forge.components.VarLengthBuild: picking 200 6-mers for position 21 protocols.forge.components.VarLengthBuild: complete_ss length: 59 complete_abego size: 0 core.fragment.picking_old.vall.eval.IdentityEval: ss = LLLLLH | aa = ...... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 3.56231e-08 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 1.36216e-05 protocols.forge.components.VarLengthBuild: picking 200 6-mers for position 22 protocols.forge.components.VarLengthBuild: complete_ss length: 59 complete_abego size: 0 core.fragment.picking_old.vall.eval.IdentityEval: ss = LLLLHH | aa = ...... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 7.61212e-09 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 9.70028e-06 protocols.forge.components.VarLengthBuild: picking 200 6-mers for position 23 protocols.forge.components.VarLengthBuild: complete_ss length: 59 complete_abego size: 0 core.fragment.picking_old.vall.eval.IdentityEval: ss = LLLHHH | aa = ...... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 1.7871e-08 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 6.76719e-06 protocols.forge.components.VarLengthBuild: picking 200 6-mers for position 24 protocols.forge.components.VarLengthBuild: complete_ss length: 59 complete_abego size: 0 core.fragment.picking_old.vall.eval.IdentityEval: ss = LLHHHH | aa = ...... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 6.08278e-10 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 6.66587e-06 protocols.forge.components.VarLengthBuild: picking 200 6-mers for position 25 protocols.forge.components.VarLengthBuild: complete_ss length: 59 complete_abego size: 0 core.fragment.picking_old.vall.eval.IdentityEval: ss = LHHHHH | aa = ...... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 2.70271e-08 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 5.35174e-06 protocols.forge.components.VarLengthBuild: picking 200 9-mers for position 20 protocols.forge.components.VarLengthBuild: complete_ss length: 59 complete_abego size: 0 core.fragment.picking_old.vall.eval.IdentityEval: ss = LLLLLLHHH | aa = ......... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 1.24019e-07 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 1.51854e-05 protocols.forge.components.VarLengthBuild: picking 200 9-mers for position 21 protocols.forge.components.VarLengthBuild: complete_ss length: 59 complete_abego size: 0 core.fragment.picking_old.vall.eval.IdentityEval: ss = LLLLLHHHH | aa = ......... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 6.52926e-09 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 1.48368e-05 protocols.forge.components.VarLengthBuild: picking 200 9-mers for position 22 protocols.forge.components.VarLengthBuild: complete_ss length: 59 complete_abego size: 0 core.fragment.picking_old.vall.eval.IdentityEval: ss = LLLLHHHHH | aa = ......... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 3.05961e-07 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 1.35228e-05 protocols.forge.components.VarLengthBuild: picking 200 9-mers for position 23 protocols.forge.components.VarLengthBuild: complete_ss length: 59 complete_abego size: 0 core.fragment.picking_old.vall.eval.IdentityEval: ss = LLLHHHHHH | aa = ......... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 3.59211e-09 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 1.06578e-05 protocols.forge.components.VarLengthBuild: picking 200 9-mers for position 24 protocols.forge.components.VarLengthBuild: complete_ss length: 59 complete_abego size: 0 core.fragment.picking_old.vall.eval.IdentityEval: ss = LLHHHHHHH | aa = ......... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 7.52864e-08 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 8.01325e-06 protocols.forge.components.VarLengthBuild: picking 200 9-mers for position 25 protocols.forge.components.VarLengthBuild: complete_ss length: 59 complete_abego size: 0 core.fragment.picking_old.vall.eval.IdentityEval: ss = LHHHHHHHH | aa = ......... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 1.53363e-08 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 7.24645e-06 protocols.forge.components.VarLengthBuild: picking 200 3-mers for position 20 protocols.forge.components.VarLengthBuild: complete_ss length: 59 complete_abego size: 0 core.fragment.picking_old.vall.eval.IdentityEval: ss = LLL | aa = ... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 6.07559e-09 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 6.55764e-07 protocols.forge.components.VarLengthBuild: picking 200 3-mers for position 21 protocols.forge.components.VarLengthBuild: complete_ss length: 59 complete_abego size: 0 core.fragment.picking_old.vall.eval.IdentityEval: ss = LLL | aa = ... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 9.07792e-09 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 7.51474e-07 protocols.forge.components.VarLengthBuild: picking 200 3-mers for position 22 protocols.forge.components.VarLengthBuild: complete_ss length: 59 complete_abego size: 0 core.fragment.picking_old.vall.eval.IdentityEval: ss = LLL | aa = ... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 3.3879e-11 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 5.85186e-07 protocols.forge.components.VarLengthBuild: picking 200 3-mers for position 23 protocols.forge.components.VarLengthBuild: complete_ss length: 59 complete_abego size: 0 core.fragment.picking_old.vall.eval.IdentityEval: ss = LLL | aa = ... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 3.40013e-10 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 7.49342e-07 protocols.forge.components.VarLengthBuild: picking 200 3-mers for position 24 protocols.forge.components.VarLengthBuild: complete_ss length: 59 complete_abego size: 0 core.fragment.picking_old.vall.eval.IdentityEval: ss = LLH | aa = ... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 1.35755e-08 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 4.93631e-06 protocols.forge.components.VarLengthBuild: picking 200 3-mers for position 25 protocols.forge.components.VarLengthBuild: complete_ss length: 59 complete_abego size: 0 core.fragment.picking_old.vall.eval.IdentityEval: ss = LHH | aa = ... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 3.30581e-08 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 4.18757e-06 protocols.forge.components.VarLengthBuild: total full-mer fragments: 1200 protocols.forge.components.VarLengthBuild: total 9-mer fragments: 1200 protocols.forge.components.VarLengthBuild: total 3-mer fragments: 1200 protocols.forge.components.VarLengthBuild: total 1-mer fragments: 1200 protocols.forge.remodel.RemodelMover: ** randomize_stage core.kinematics.AtomTree: [ ERROR ] No proper DoF can be found for these four atoms: 23-1, 23-2, 23-3, 24-1! 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 23 BB 2 core.kinematics.AtomTree: [ ERROR ] No proper DoF can be found for these four atoms: 23-2, 23-3, 24-1, 24-2! 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 23 BB 3 core.kinematics.AtomTree: [ ERROR ] No proper DoF can be found for these four atoms: 23-3, 24-1, 24-2, 24-3! 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 24 BB 1 core.kinematics.AtomTree: [ ERROR ] No proper DoF can be found for these four atoms: 23-3, 24-1, 24-2, 24-3! 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 24 BB 1 core.kinematics.AtomTree: [ ERROR ] No proper DoF can be found for these four atoms: 23-1, 23-2, 23-3, 24-1! 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 23 BB 2 core.kinematics.AtomTree: [ ERROR ] No proper DoF can be found for these four atoms: 23-2, 23-3, 24-1, 24-2! 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 23 BB 3 core.kinematics.AtomTree: [ ERROR ] No proper DoF can be found for these four atoms: 23-3, 24-1, 24-2, 24-3! 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 24 BB 1 core.kinematics.AtomTree: [ ERROR ] No proper DoF can be found for these four atoms: 23-1, 23-2, 23-3, 24-1! 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 23 BB 2 core.kinematics.AtomTree: [ ERROR ] No proper DoF can be found for these four atoms: 23-2, 23-3, 24-1, 24-2! 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 23 BB 3 core.kinematics.AtomTree: [ ERROR ] No proper DoF can be found for these four atoms: 23-3, 24-1, 24-2, 24-3! 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 24 BB 1 core.kinematics.AtomTree: [ ERROR ] No proper DoF can be found for these four atoms: 23-1, 23-2, 23-3, 24-1! 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 23 BB 2 core.kinematics.AtomTree: [ ERROR ] No proper DoF can be found for these four atoms: 23-2, 23-3, 24-1, 24-2! 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 23 BB 3 core.kinematics.AtomTree: [ ERROR ] No proper DoF can be found for these four atoms: 23-3, 24-1, 24-2, 24-3! 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 24 BB 1 core.kinematics.AtomTree: [ ERROR ] No proper DoF can be found for these four atoms: 23-3, 24-1, 24-2, 24-3! 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 24 BB 1 core.kinematics.AtomTree: [ ERROR ] No proper DoF can be found for these four atoms: 23-3, 24-1, 24-2, 24-3! 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 24 BB 1 core.kinematics.AtomTree: [ ERROR ] No proper DoF can be found for these four atoms: 23-1, 23-2, 23-3, 24-1! 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 23 BB 2 core.kinematics.AtomTree: [ ERROR ] No proper DoF can be found for these four atoms: 23-2, 23-3, 24-1, 24-2! 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 23 BB 3 core.kinematics.AtomTree: [ ERROR ] No proper DoF can be found for these four atoms: 23-3, 24-1, 24-2, 24-3! 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 24 BB 1 core.kinematics.AtomTree: [ ERROR ] No proper DoF can be found for these four atoms: 23-1, 23-2, 23-3, 24-1! 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 23 BB 2 core.kinematics.AtomTree: [ ERROR ] No proper DoF can be found for these four atoms: 23-2, 23-3, 24-1, 24-2! 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 23 BB 3 core.kinematics.AtomTree: [ ERROR ] No proper DoF can be found for these four atoms: 23-3, 24-1, 24-2, 24-3! 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 24 BB 1 core.kinematics.AtomTree: [ ERROR ] No proper DoF can be found for these four atoms: 23-1, 23-2, 23-3, 24-1! 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 23 BB 2 core.kinematics.AtomTree: [ ERROR ] No proper DoF can be found for these four atoms: 23-2, 23-3, 24-1, 24-2! 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 23 BB 3 core.kinematics.AtomTree: [ ERROR ] No proper DoF can be found for these four atoms: 23-1, 23-2, 23-3, 24-1! 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 23 BB 2 core.kinematics.AtomTree: [ ERROR ] No proper DoF can be found for these four atoms: 23-2, 23-3, 24-1, 24-2! 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 23 BB 3 core.kinematics.AtomTree: [ ERROR ] No proper DoF can be found for these four atoms: 23-3, 24-1, 24-2, 24-3! 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 24 BB 1 core.kinematics.AtomTree: [ ERROR ] No proper DoF can be found for these four atoms: 23-3, 24-1, 24-2, 24-3! 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 24 BB 1 core.kinematics.AtomTree: [ ERROR ] No proper DoF can be found for these four atoms: 23-3, 24-1, 24-2, 24-3! 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 24 BB 1 core.kinematics.AtomTree: [ ERROR ] No proper DoF can be found for these four atoms: 23-1, 23-2, 23-3, 24-1! 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 23 BB 2 core.kinematics.AtomTree: [ ERROR ] No proper DoF can be found for these four atoms: 23-2, 23-3, 24-1, 24-2! 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 23 BB 3 core.kinematics.AtomTree: [ ERROR ] No proper DoF can be found for these four atoms: 23-3, 24-1, 24-2, 24-3! 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 24 BB 1 core.kinematics.AtomTree: [ ERROR ] No proper DoF can be found for these four atoms: 23-3, 24-1, 24-2, 24-3! 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 24 BB 1 protocols.forge.remodel.RemodelMover: start stop cut cbreak protocols.forge.remodel.RemodelMover: 20 25 23 9.27756 protocols.forge.remodel.RemodelMover: * closure_attempt 1 protocols.forge.remodel.RemodelMover: ** simultaneous_stage protocols.forge.remodel.RemodelMover: n_loops = 1 protocols.loops.loops_main: Added cutpoint variant to residue 23 protocols.loops.loops_main: Added cutpoint variant to residue 24 protocols.forge.remodel.RemodelMover: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ vdw 1.000 0.000 0.000 hbond_sr_bb 1.000 -15.424 -15.424 hbond_lr_bb 1.000 -22.378 -22.378 rama 0.100 -22.521 -2.252 omega 1.000 3.519 3.519 rg 1.000 11.453 11.453 linear_chainbreak 0.556 3.740 2.078 --------------------------------------------------- Total weighted score: -23.005 protocols.forge.remodel.RemodelMover: protocols.moves.MonteCarlo: MC: 2 -15.6399 -23.005 -15.6399 -23.005 0 0 0 rejected protocols.moves.TrialCounter: ccd_move trials= 15 NO ACCEPTS. protocols.moves.TrialCounter: simul_frag trials= 420; accepts= 0.3381; energy_drop/trial= -0.31415 protocols.forge.remodel.RemodelMover: start stop cut cbreak protocols.forge.remodel.RemodelMover: 20 25 23 3.74033 protocols.forge.remodel.RemodelMover: ** independent_stage protocols.forge.remodel.RemodelMover: n_loops = 1 protocols.loops.loops_main: Added cutpoint variant to residue 23 protocols.loops.loops_main: Added cutpoint variant to residue 24 protocols.forge.remodel.RemodelMover: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ vdw 1.000 0.607 0.607 hbond_sr_bb 1.000 -15.511 -15.511 hbond_lr_bb 1.000 -22.378 -22.378 rama 0.100 -16.741 -1.674 omega 1.000 2.518 2.518 rg 1.000 11.319 11.319 linear_chainbreak 2.778 2.217 6.160 --------------------------------------------------- Total weighted score: -18.960 protocols.forge.remodel.RemodelMover: protocols.moves.MonteCarlo: MC: 2 -16.8963 -18.9601 -16.8963 -18.9601 0 0 0 accepted thermally protocols.moves.TrialCounter: ccd_move trials= 189; accepts= 0.1217; energy_drop/trial= -0.03653 protocols.moves.TrialCounter: frag trials= 1164; accepts= 0.1031; energy_drop/trial= 0.00404 protocols.forge.remodel.RemodelMover: start stop cut cbreak protocols.forge.remodel.RemodelMover: 20 25 23 2.22065 protocols.forge.remodel.RemodelMover: ** boost_closure_stage protocols.forge.remodel.RemodelMover: at least one loop is beyond tolerance protocols.forge.remodel.RemodelMover: * 0 / 1 closed / attempts protocols.forge.components.VarLengthBuild: centroid_build: loop: 20-25, final chainbreak = 2.21748, max_linear_chainbreak_: 0.07 protocols.forge.components.VarLengthBuild: centroid_build: final chainbreak at 23 = 2.21748 max tolerance 0.07 protocols.forge.remodel.RemodelMover: centroid_build(): variable length build failed. resetting pose to archived pose. protocols.forge.remodel.RemodelMover: centroid_build(): centroid_build unable to close loop. retrying. protocols.forge.remodel.RemodelMover: apply(): number of attempts at loop closure made: 1 protocols.forge.remodel.RemodelMover: clustered poses count: 0 protocols.forge.remodel.RemodelMover: Remodel poses remaining from original run: 0 protocols.jd2.JobDistributor: long_loop1pgaA_0001_0001 reported success in 20 seconds protocols.jd2.JobDistributor: no more batches to process... protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 20 seconds protocols.jd2.JobDistributor: [ WARNING ] The following options have been set, but have not yet been used: -remodel:quick_and_dirty -remodel:save_top 1