core.init: Rosetta version exported from http://www.rosettacommons.org core.init: command: /home/dancebean/Cheng/rosetta_2014.30.57114_bundle/main/source/bin/remodel.linuxgccrelease -database /home/dancebean/Cheng/rosetta_2014.30.57114_bundle/main/database -s /mnt/hgfs/Cheng/remodel/4KMT_HC_native_442residue_FullAtom_looped.pdb -remodel:blueprint /mnt/hgfs/Cheng/remodel/blueprint.4KMT_223_228.domaininsertion -remodel:quick_and_dirty -run:chain H -remodel:num_trajectory 3 -overwrite core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-1133840701 seed_offset=0 real_seed=-1133840701 core.init.random: RandomGenerator:init: Normal mode, seed=-1133840701 RG_type=mt19937 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 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 protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: pushed /mnt/hgfs/Cheng/remodel/4KMT_HC_native_442residue_FullAtom_looped.pdb nstruct index 1 protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from PDB /mnt/hgfs/Cheng/remodel/4KMT_HC_native_442residue_FullAtom_looped.pdb core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 737 residue types core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue CYS:CtermProteinFull 222 core.conformation.Conformation: Found disulfide between residues 22 96 core.conformation.Conformation: current variant for 22 CYS core.conformation.Conformation: current variant for 96 CYS core.conformation.Conformation: current variant for 22 CYD core.conformation.Conformation: current variant for 96 CYD core.conformation.Conformation: Found disulfide between residues 146 202 core.conformation.Conformation: current variant for 146 CYS core.conformation.Conformation: current variant for 202 CYS core.conformation.Conformation: current variant for 146 CYD core.conformation.Conformation: current variant for 202 CYD core.pack.task: Packer task: initialize from command line() protocols.forge.remodel.RemodelMover: apply(): entered RemodelMover apply(). pose.total_residue(): 222 protocols.forge.remodel.RemodelMover: 222 protocols.forge.remodel.RemodelMover: apply(): input PDB dssp assignment: (based on start structure) protocols.forge.remodel.RemodelMover: LLEEEELLLEEELLLLLEEEEEEEELLLHHHLEEEEEEELLLLLLEEEEEEELLLLEEEELLLLELLEEEEEEHHHLEEEEEELLLLHHHLEEEEEEEEELLLLEEEEELLLEEEEELLLLLELLEEEEELLLLLLLLLLEEEEEEEEEEEELLLLEEEEHHHLELLLEEELLLEELLLLLEEEEEEEEEEHHHLLLLLLEEEEEELLLLEEEEEELLLLLL protocols.forge.remodel.RemodelMover: apply(): reading blueprint file protocols.forge.remodel.RemodelData: Found token 217 on blueprint line '1' protocols.forge.remodel.RemodelData: Found token V on blueprint line '1' protocols.forge.remodel.RemodelData: Found token L on blueprint line '1' protocols.forge.remodel.RemodelData: Found token PIKAA on blueprint line '1' protocols.forge.remodel.RemodelData: Found token V on blueprint line '1' protocols.forge.remodel.RemodelData: design position 1 to V VAL protocols.forge.remodel.RemodelData: Found token 218 on blueprint line '2' protocols.forge.remodel.RemodelData: Found token E on blueprint line '2' protocols.forge.remodel.RemodelData: Found token L on blueprint line '2' protocols.forge.remodel.RemodelData: Found token PIKAA on blueprint line '2' protocols.forge.remodel.RemodelData: Found token E on blueprint line '2' protocols.forge.remodel.RemodelData: design position 2 to E GLU protocols.forge.remodel.RemodelData: Found token 219 on blueprint line '3' protocols.forge.remodel.RemodelData: Found token P on blueprint line '3' protocols.forge.remodel.RemodelData: Found token L on blueprint line '3' protocols.forge.remodel.RemodelData: Found token PIKAA on blueprint line '3' protocols.forge.remodel.RemodelData: Found token P on blueprint line '3' protocols.forge.remodel.RemodelData: design position 3 to P PRO protocols.forge.remodel.RemodelData: Found token 220 on blueprint line '4' protocols.forge.remodel.RemodelData: Found token K on blueprint line '4' protocols.forge.remodel.RemodelData: Found token L on blueprint line '4' protocols.forge.remodel.RemodelData: Found token PIKAA on blueprint line '4' protocols.forge.remodel.RemodelData: Found token K on blueprint line '4' protocols.forge.remodel.RemodelData: design position 4 to K LYS protocols.forge.remodel.RemodelData: Found token 221 on blueprint line '5' protocols.forge.remodel.RemodelData: Found token S on blueprint line '5' protocols.forge.remodel.RemodelData: Found token L on blueprint line '5' protocols.forge.remodel.RemodelData: Found token PIKAA on blueprint line '5' protocols.forge.remodel.RemodelData: Found token S on blueprint line '5' protocols.forge.remodel.RemodelData: design position 5 to S SER protocols.forge.remodel.RemodelData: Found token 222 on blueprint line '6' protocols.forge.remodel.RemodelData: Found token C on blueprint line '6' protocols.forge.remodel.RemodelData: Found token L on blueprint line '6' protocols.forge.remodel.RemodelData: Found token PIKAA on blueprint line '6' protocols.forge.remodel.RemodelData: Found token C on blueprint line '6' protocols.forge.remodel.RemodelData: design position 6 to C CYS protocols.forge.remodel.RemodelData: Found token 0 on blueprint line '7' protocols.forge.remodel.RemodelData: Found token x on blueprint line '7' protocols.forge.remodel.RemodelData: Found token L on blueprint line '7' protocols.forge.remodel.RemodelData: Found token PIKAA on blueprint line '7' protocols.forge.remodel.RemodelData: Found token H on blueprint line '7' protocols.forge.remodel.RemodelData: design position 7 to H HIS protocols.forge.remodel.RemodelData: Found token 0 on blueprint line '8' protocols.forge.remodel.RemodelData: Found token x on blueprint line '8' protocols.forge.remodel.RemodelData: Found token L on blueprint line '8' protocols.forge.remodel.RemodelData: Found token PIKAA on blueprint line '8' protocols.forge.remodel.RemodelData: Found token H on blueprint line '8' protocols.forge.remodel.RemodelData: design position 8 to H HIS protocols.forge.remodel.RemodelData: Found token 0 on blueprint line '9' protocols.forge.remodel.RemodelData: Found token x on blueprint line '9' protocols.forge.remodel.RemodelData: Found token L on blueprint line '9' protocols.forge.remodel.RemodelData: Found token PIKAA on blueprint line '9' protocols.forge.remodel.RemodelData: Found token H on blueprint line '9' protocols.forge.remodel.RemodelData: design position 9 to H HIS protocols.forge.remodel.RemodelData: Found token 0 on blueprint line '10' protocols.forge.remodel.RemodelData: Found token x on blueprint line '10' protocols.forge.remodel.RemodelData: Found token L on blueprint line '10' protocols.forge.remodel.RemodelData: Found token PIKAA on blueprint line '10' protocols.forge.remodel.RemodelData: Found token H on blueprint line '10' protocols.forge.remodel.RemodelData: design position 10 to H HIS protocols.forge.remodel.RemodelData: Found token 0 on blueprint line '11' protocols.forge.remodel.RemodelData: Found token x on blueprint line '11' protocols.forge.remodel.RemodelData: Found token L on blueprint line '11' protocols.forge.remodel.RemodelData: Found token PIKAA on blueprint line '11' protocols.forge.remodel.RemodelData: Found token H on blueprint line '11' protocols.forge.remodel.RemodelData: design position 11 to H HIS protocols.forge.remodel.RemodelData: Found token 0 on blueprint line '12' protocols.forge.remodel.RemodelData: Found token x on blueprint line '12' protocols.forge.remodel.RemodelData: Found token L on blueprint line '12' protocols.forge.remodel.RemodelData: Found token PIKAA on blueprint line '12' protocols.forge.remodel.RemodelData: Found token H on blueprint line '12' protocols.forge.remodel.RemodelData: design position 12 to H HIS protocols.forge.remodel.RemodelData: Resfile to be used for design: NATRO start 1 H PIKAA V 2 H PIKAA E 3 H PIKAA P 4 H PIKAA K 5 H PIKAA S 6 H PIKAA C 7 H PIKAA H 8 H PIKAA H 9 H PIKAA H 10 H PIKAA H 11 H PIKAA H 12 H PIKAA H protocols.forge.remodel.RemodelData: SS based assignment found protocols.forge.remodel.RemodelData: sequence (based on blueprint): protocols.forge.remodel.RemodelData: VEPKSCxxxxxx protocols.forge.remodel.RemodelData: ss (based on blueprint): protocols.forge.remodel.RemodelData: LLLLLLLLLLLL protocols.forge.remodel.RemodelData: ABEGOtype: protocols.forge.remodel.RemodelData: protocols.forge.remodel.RemodelData: dssp_updated_ss: lengths = 12 protocols.forge.remodel.RemodelData: LLLLLLLLLLLL core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2013 core.pack.dunbrack: Dunbrack 2010 library took 0.377684 seconds to load from binary protocols.forge.remodel.RemodelWorkingSet: workingSetGen(): C-terminal is extended protocols.forge.remodel.RemodelWorkingSet: workingSetGen(): length change found. last blueprint line index: 12, last blueprint line original_index: 0 protocols.forge.remodel.RemodelWorkingSet: Adding lines to temp_for_truncation vector. protocols.forge.remodel.RemodelWorkingSet: temp_for_truncation.size():6 protocols.forge.remodel.RemodelWorkingSet: Setting up translate_index. protocols.forge.remodel.RemodelWorkingSet: temp_for_copy (lines_residues_to_remodel): [ ] protocols.forge.remodel.RemodelWorkingSet: segmentStorageVector: [ segment 0: [ 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, ], ] protocols.forge.remodel.RemodelWorkingSet: data.dssp_updated_ss: LLLLLLLLLLLL AA for build: VVVVVVVVVVVV protocols.forge.remodel.RemodelWorkingSet: head 217:1, tail 0:12, gap: 12, dssp_updated_ss.size(): 12, insert_ss: LLLLLLLLLLLL protocols.forge.remodel.RemodelWorkingSet: C-terminal extension found protocols.forge.build.BuildManager: FOLD_TREE EDGE 1 228 -1 protocols.forge.build.BuildManager: protocols.forge.remodel.RemodelDesignMover: Creating NeighborhoodByDistanceCalculator using und_pos: [ 217 218 219 220 221 222 223 224 225 226 227 228 ] protocols.forge.remodel.RemodelMover: protocols.forge.remodel.RemodelMover: apply(): BUILD CYCLE REMAINING 3 protocols.forge.remodel.RemodelMover: ORIGINAL TREE: FOLD_TREE EDGE 1 228 -1 protocols.forge.remodel.RemodelMover: protocols.forge.remodel.RemodelMover: centroid_build(): calling VariableLengthBuild apply. core.chemical.ResidueTypeSet: Finished initializing centroid residue type set. Created 1010 residue types protocols.forge.components.VarLengthBuild: VLB count_cutpoints 0 interval.left 217 interval.right 228 protocols.forge.components.VarLengthBuild: picking 200 12-mers for position 217 Got some signal... It is:6 Process was aborted!