Running ProFit... Running antibody_graft 0 cd "grafting/details" && "/mnt/share/stagePitie/rosetta_2014.35.57232_bundle/main/source/bin/antibody_graft.linuxgccrelease" -database /mnt/share/stagePitie/rosetta_2014.35.57232_bundle/main/database -overwrite -s FR.pdb -antibody::h3_no_stem_graft -scorefile score-graft.sf -check_cdr_chainbreaks false core.init: Rosetta version exported from http://www.rosettacommons.org core.init: command: /mnt/share/stagePitie/rosetta_2014.35.57232_bundle/main/source/bin/antibody_graft.linuxgccrelease -database /mnt/share/stagePitie/rosetta_2014.35.57232_bundle/main/database -overwrite -s FR.pdb -antibody::h3_no_stem_graft -scorefile score-graft.sf -check_cdr_chainbreaks false core.init: 'RNG device' seed mode, using '/dev/urandom', seed=1123348245 seed_offset=0 real_seed=1123348245 core.init.random: RandomGenerator:init: Normal mode, seed=1123348245 RG_type=mt19937 protocols.antibody.GraftCDRLoopsProtocol: Setting default settings protocols.antibody.GraftCDRLoopsProtocol: Reading Options 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/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/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.antibody: //////////////////////////////////////////////////////////////////////////////// protocols.antibody: /// Rosetta 3 Antibody Modeler /// protocols.antibody: /// CDR Assembling /// protocols.antibody: /// /// protocols.antibody: /// Graft_l1: 1 protocols.antibody: /// Graft_l2: 1 protocols.antibody: /// Graft_l3: 1 protocols.antibody: /// Graft_h1: 1 protocols.antibody: /// Graft_h2: 1 protocols.antibody: /// Graft_h3: 1 protocols.antibody: /// camelid: 0 protocols.antibody: //////////////////////////////////////////////////////////////////////////////// protocols.antibody: protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: pushed FR.pdb nstruct index 1 protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from PDB FR.pdb core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 737 residue types core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue GLU:NtermProteinFull 1 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU:NtermProteinFull 1 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU:NtermProteinFull 1 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU:NtermProteinFull 1 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU:NtermProteinFull 1 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue ASN 2 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASN 2 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASN 2 core.conformation.Conformation: [ WARNING ] missing heavyatom: ND2 on residue ASN 2 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue LEU 4 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LEU 4 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue LEU 4 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue LEU 4 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue ARG 24 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 24 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 24 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 24 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 24 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 24 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 24 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue VAL 29 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG1 on residue VAL 29 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG2 on residue VAL 29 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue SER 31 core.conformation.Conformation: [ WARNING ] missing heavyatom: OG on residue SER 31 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue SER 32 core.conformation.Conformation: [ WARNING ] missing heavyatom: OG on residue SER 32 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue LEU 34 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LEU 34 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue LEU 34 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue LEU 34 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue HIS 35 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue HIS 35 core.conformation.Conformation: [ WARNING ] missing heavyatom: ND1 on residue HIS 35 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue HIS 35 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE1 on residue HIS 35 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue HIS 35 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue HIS 35 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue SER 41 core.conformation.Conformation: [ WARNING ] missing heavyatom: OG on residue SER 41 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue ALA 43 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue LEU 47 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LEU 47 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue LEU 47 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue LEU 47 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue SER 51 core.conformation.Conformation: [ WARNING ] missing heavyatom: OG on residue SER 51 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue ASN 54 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASN 54 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASN 54 core.conformation.Conformation: [ WARNING ] missing heavyatom: ND2 on residue ASN 54 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue VAL 79 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG1 on residue VAL 79 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG2 on residue VAL 79 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue GLN 90 core.conformation.Conformation: [ WARNING ] missing heavyatom: CGTraceback (most recent call last): File "/mnt/share/stagePitie/rosetta_2014.35.57232_bundle/tools/antibody/antibody.py", line 1374, in on residue GLN 90 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN 90 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN 90 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN 90 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue TYR 92 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue TYR 92 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue TYR 92 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue TYR 92 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE1 on residue TYR 92 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE2 on residue TYR 92 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue TYR 92 core.conformation.Conformation: [ WARNING ] missing heavyatom: OH on residue TYR 92 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue PRO 96 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue PRO 96 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue PRO 96 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue TYR 97 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue TYR 97 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue TYR 97 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue TYR 97 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE1 on residue TYR 97 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE2 on residue TYR 97 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue TYR 97 core.conformation.Conformation: [ WARNING ] missing heavyatom: OH on residue TYR 97 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ALA:CtermProteinFull 110 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue ALA:CtermProteinFull 110 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue ALA:NtermProteinFull 111 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue VAL 112 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG1 on residue VAL 112 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG2 on residue VAL 112 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue GLU 115 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 115 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 115 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 115 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 115 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue THR 140 core.conformation.Conformation: [ WARNING ] missing heavyatom: OG1 on residue THR 140 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG2 on residue THR 140 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue ILE 161 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG1 on residue ILE 161 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG2 on residue ILE 161 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue ILE 161 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue TYR 164 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue TYR 164 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue TYR 164 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue TYR 164 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE1 on residue TYR 164 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE2 on residue TYR 164 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue TYR 164 core.conformation.Conformation: [ WARNING ] missing heavyatom: OH on residue TYR 164 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue PRO 168 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue PRO 168 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue PRO 168 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue ALA 171 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue ASP 172 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 172 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 172 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 172 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue ASP 173 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 173 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 173 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 173 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue LYS 175 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 175 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 175 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 175 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 175 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue GLU 176 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 176 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 176 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 176 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 176 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue ALA 186 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue ALA 188 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue TYR 210 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue TYR 210 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue TYR 210 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue TYR 210 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE1 on residue TYR 210 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE2 on residue TYR 210 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue TYR 210 core.conformation.Conformation: [ WARNING ] missing heavyatom: OH on residue TYR 210 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue TYR 211 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue TYR 211 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue TYR 211 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue TYR 211 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE1 on residue TYR 211 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE2 on residue TYR 211 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue TYR 211 core.conformation.Conformation: [ WARNING ] missing heavyatom: OH on residue TYR 211 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue SER 213 core.conformation.Conformation: [ WARNING ] missing heavyatom: OG on residue SER 213 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue THR 214 core.conformation.Conformation: [ WARNING ] missing heavyatom: OG1 on residue THR 214 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG2 on residue THR 214 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue TYR 215 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue TYR 215 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue TYR 215 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue TYR 215 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE1 on residue TYR 215 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE2 on residue TYR 215 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue TYR 215 core.conformation.Conformation: [ WARNING ] missing heavyatom: OH on residue TYR 215 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue PRO 216 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue PRO 216 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue PRO 216 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue TYR 217 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue TYR 217 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue TYR 217 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue TYR 217 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE1 on residue TYR 217 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE2 on residue TYR 217 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue TYR 217 core.conformation.Conformation: [ WARNING ] missing heavyatom: OH on residue TYR 217 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue TYR 218 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue TYR 218 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue TYR 218 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue TYR 218 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE1 on residue TYR 218 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE2 on residue TYR 218 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue TYR 218 core.conformation.Conformation: [ WARNING ] missing heavyatom: OH on residue TYR 218 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue ALA 219 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue MET 220 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue MET 220 core.conformation.Conformation: [ WARNING ] missing heavyatom: SD on residue MET 220 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue MET 220 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue SER:CtermProteinFull 232 core.conformation.Conformation: Found disulfide between residues 23 89 core.conformation.Conformation: current variant for 23 CYS core.conformation.Conformation: current variant for 89 CYS core.conformation.Conformation: current variant for 23 CYD core.conformation.Conformation: current variant for 89 CYD core.conformation.Conformation: Found disulfide between residues 132 206 core.conformation.Conformation: current variant for 132 CYS core.conformation.Conformation: current variant for 206 CYS core.conformation.Conformation: current variant for 132 CYD core.conformation.Conformation: current variant for 206 CYD core.pack.task: Packer task: initialize from command line() core.pack.pack_missing_sidechains: packing residue number 1 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 2 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 4 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 24 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 29 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 31 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 32 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 34 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 35 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 41 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 43 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 47 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 51 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 54 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 79 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 90 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 92 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 96 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 97 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 110 because of missing atom number 6 atom name CB core.pack.pack_missing_sidechains: packing residue number 111 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 112 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 115 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 140 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 161 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 164 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 168 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 171 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 172 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 173 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 175 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 176 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 186 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 188 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 210 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 211 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 213 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 214 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 215 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 216 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 217 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 218 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 219 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 220 because of missing atom number 5 atom name CB core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2013 core.pack.dunbrack: Dunbrack 2010 library took 0.043569 seconds to load from binary core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 521 rotamers at 44 positions. core.pack.pack_rotamers: IG: 78240 bytes protocols.antibody.GraftCDRLoopsProtocol: in the apply function protocols.antibody.GraftCDRLoopsProtocol: AAAAAAAA cst_weight: 0 protocols.antibody.GraftCDRLoopsProtocol: Danger Will Robinson! Native is an impostor! protocols.antibody.GraftCDRLoopsProtocol: 'native_pose' is just a copy of the 'input_pose' protocols.antibody.GraftCDRLoopsProtocol: since you didn't sepcifiy the native pdb name basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: ARDYYGSTYPYYAMDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Clusters core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue ARG 5 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 5 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 5 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 5 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 5 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 5 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 5 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue GLN:CtermProteinFull 20 core.pack.task: Packer task: initialize from command line() core.pack.pack_missing_sidechains: packing residue number 5 because of missing atom number 5 atom name CB core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2013 core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 25 rotamers at 1 positions. core.pack.pack_rotamers: IG: 888 bytes core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue TRP 2 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue TRP 2 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue TRP 2 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue TRP 2 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE1 on residue TRP 2 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE2 on residue TRP 2 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE3 on residue TRP 2 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ2 on residue TRP 2 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ3 on residue TRP 2 core.conformation.Conformation: [ WARNING ] missing heavyatom: CH2 on residue TRP 2 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue TRP 2 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE3 on residue TRP 2 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ3 on residue TRP 2 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue TRP 2 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE3 on residue TRP 2 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue TRP 2 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ALA:CtermProteinFull 15 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue ALA:CtermProteinFull 15 core.pack.task: Packer task: initialize from command line() core.pack.pack_missing_sidechains: packing residue number 2 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 15 because of missing atom number 6 atom name CB core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2013 core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 6 rotamers at 2 positions. core.pack.pack_rotamers: IG: 1120 bytes core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue TYR 7 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue TYR 7 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue TYR 7 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue TYR 7 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE1 on residue TYR 7 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE2 on residue TYR 7 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue TYR 7 core.conformation.Conformation: [ WARNING ] missing heavyatom: OH on residue TYR 7 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue TYR 10 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue TYR 10 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue TYR 10 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue TYR 10 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE1 on residue TYR 10 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE2 on residue TYR 10 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue TYR 10 core.conformation.Conformation: [ WARNING ] missing heavyatom: OH on residue TYR 10 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue TYR 12 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue TYR 12 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue TYR 12 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue TYR 12 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE1 on residue TYR 12 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE2 on residue TYR 12 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue TYR 12 core.conformation.Conformation: [ WARNING ] missing heavyatom: OH on residue TYR 12 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue GLY:CtermProteinFull 17 core.pack.task: Packer task: initialize from command line() core.pack.pack_missing_sidechains: packing residue number 7 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 10 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 12 because of missing atom number 5 atom name CB core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2013 core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 11 rotamers at 3 positions. core.pack.pack_rotamers: IG: 2728 bytes core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue LYS 17 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 17 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 17 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 17 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 17 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue GLN:CtermProteinFull 18 core.pack.task: Packer task: initialize from command line() core.pack.pack_missing_sidechains: packing residue number 17 because of missing atom number 5 atom name CB core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2013 core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 23 rotamers at 1 positions. core.pack.pack_rotamers: IG: 880 bytes core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue GLU 21 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 21 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 21 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 21 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 21 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue PHE:CtermProteinFull 25 core.pack.task: Packer task: initialize from command line() core.pack.pack_missing_sidechains: packing residue number 21 because of missing atom number 5 atom name CB core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2013 core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 1 rotamers at 1 positions. core.pack.pack_rotamers: IG: 792 bytes core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue PHE:NtermProteinFull 1 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue PHE:NtermProteinFull 1 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue PHE:NtermProteinFull 1 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue PHE:NtermProteinFull 1 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE1 on residue PHE:NtermProteinFull 1 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE2 on residue PHE:NtermProteinFull 1 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue PHE:NtermProteinFull 1 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue PHE:NtermProteinFull 1 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE2 on residue PHE:NtermProteinFull 1 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue PHE:NtermProteinFull 1 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue ALA 3 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue ASP 5 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 5 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 5 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 5 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue TYR 6 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue TYR 6 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue TYR 6 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue TYR 6 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE1 on residue TYR 6 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE2 on residue TYR 6 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue TYR 6 core.conformation.Conformation: [ WARNING ] missing heavyatom: OH on residue TYR 6 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue SER 9 core.conformation.Conformation: [ WARNING ] missing heavyatom: OG on residue SER 9 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue THR 10 core.conformation.Conformation: [ WARNING ] missing heavyatom: OG1 on residue THR 10 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG2 on residue THR 10 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue TYR 11 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue TYR 11 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue TYR 11 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue TYR 11 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE1 on residue TYR 11 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE2 on residue TYR 11 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue TYR 11 core.conformation.Conformation: [ WARNING ] missing heavyatom: OH on residue TYR 11 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue PRO 12 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue PRO 12 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue PRO 12 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue GLY:CtermProteinFull 22 core.pack.task: Packer task: initialize from command line() core.pack.pack_missing_sidechains: packing residue number 1 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 3 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 5 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 6 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 9 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 10 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 11 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 12 because of missing atom number 5 atom name CB core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2013 core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 57 rotamers at 8 positions. core.pack.pack_rotamers: IG: 10184 bytes protocols.antibody.GraftCDRLoopsProtocol: Checking AntibodyInfo object: protocols.antibody.GraftCDRLoopsProtocol: //////////////////////////////////////////////////////////////////////////////// protocols.antibody.GraftCDRLoopsProtocol: /// Rosetta Antibody Info /// protocols.antibody.GraftCDRLoopsProtocol: /// /// protocols.antibody.GraftCDRLoopsProtocol: /// Antibody Type: Regular Antibody protocols.antibody.GraftCDRLoopsProtocol: /// Predict H3 Cterminus Base: KINKED protocols.antibody.GraftCDRLoopsProtocol: /// protocols.antibody.GraftCDRLoopsProtocol: /// H1 info: protocols.antibody.GraftCDRLoopsProtocol: /// length: 10 protocols.antibody.GraftCDRLoopsProtocol: /// sequence: GYTFTNYGMN protocols.antibody.GraftCDRLoopsProtocol: /// north_cluster: H1-13-1 protocols.antibody.GraftCDRLoopsProtocol: /// loop_info: LOOP start: 136 stop: 145 cut: 141 size: 10 skip rate: 0 extended?: False protocols.antibody.GraftCDRLoopsProtocol: protocols.antibody.GraftCDRLoopsProtocol: /// H2 info: protocols.antibody.GraftCDRLoopsProtocol: /// length: 17 protocols.antibody.GraftCDRLoopsProtocol: /// sequence: WINTYTGEPTYADDFKE protocols.antibody.GraftCDRLoopsProtocol: /// north_cluster: H2-10-1 protocols.antibody.GraftCDRLoopsProtocol: /// loop_info: LOOP start: 160 stop: 176 cut: 168 size: 17 skip rate: 0 extended?: False protocols.antibody.GraftCDRLoopsProtocol: protocols.antibody.GraftCDRLoopsProtocol: /// H3 info: protocols.antibody.GraftCDRLoopsProtocol: /// length: 14 protocols.antibody.GraftCDRLoopsProtocol: /// sequence: DYYGSTYPYYAMDY protocols.antibody.GraftCDRLoopsProtocol: /// north_cluster: NA protocols.antibody.GraftCDRLoopsProtocol: /// loop_info: LOOP start: 209 stop: 222 cut: 210 size: 14 skip rate: 0 extended?: False protocols.antibody.GraftCDRLoopsProtocol: protocols.antibody.GraftCDRLoopsProtocol: /// L1 info: protocols.antibody.GraftCDRLoopsProtocol: /// length: 12 protocols.antibody.GraftCDRLoopsProtocol: /// sequence: RASSSVSSSYLH protocols.antibody.GraftCDRLoopsProtocol: /// north_cluster: NA protocols.antibody.GraftCDRLoopsProtocol: /// loop_info: LOOP start: 24 stop: 35 cut: 30 size: 12 skip rate: 0 extended?: False protocols.antibody.GraftCDRLoopsProtocol: protocols.antibody.GraftCDRLoopsProtocol: /// L2 info: protocols.antibody.GraftCDRLoopsProtocol: /// length: 7 protocols.antibody.GraftCDRLoopsProtocol: /// sequence: STSNLAS protocols.antibody.GraftCDRLoopsProtocol: /// north_cluster: L2-8-2 protocols.antibody.GraftCDRLoopsProtocol: /// loop_info: LOOP start: 51 stop: 57 cut: 54 size: 7 skip rate: 0 extended?: False protocols.antibody.GraftCDRLoopsProtocol: protocols.antibody.GraftCDRLoopsProtocol: /// L3 info: protocols.antibody.GraftCDRLoopsProtocol: /// length: 9 protocols.antibody.GraftCDRLoopsProtocol: /// sequence: QQYSGYPYT protocols.antibody.GraftCDRLoopsProtocol: /// north_cluster: NA protocols.antibody.GraftCDRLoopsProtocol: /// loop_info: LOOP start: 90 stop: 98 cut: 94 size: 9 skip rate: 0 extended?: False protocols.antibody.GraftCDRLoopsProtocol: protocols.antibody.GraftCDRLoopsProtocol: //////////////////////////////////////////////////////////////////////////////// protocols.antibody.GraftCDRLoopsProtocol: protocols.antibody.GraftCDRLoopsProtocol: protocols.antibody.GraftCDRLoopsProtocol: Checking Ab_TemplateInfo object: protocols.antibody.GraftCDRLoopsProtocol: //////////////////////////////////////////////////////////////////////////////// protocols.antibody.GraftCDRLoopsProtocol: /// Rosetta Antibody Template Info /// protocols.antibody.GraftCDRLoopsProtocol: /// /// protocols.antibody.GraftCDRLoopsProtocol: /// L1 template: protocols.antibody.GraftCDRLoopsProtocol: /// template_name: protocols.antibody.GraftCDRLoopsProtocol: ///PDB file name: ./L1.pdb protocols.antibody.GraftCDRLoopsProtocol: Total residues:20 protocols.antibody.GraftCDRLoopsProtocol: Sequence: TMTCRASSSVSSSYLHWYQQ protocols.antibody.GraftCDRLoopsProtocol: Fold tree: protocols.antibody.GraftCDRLoopsProtocol: FOLD_TREE EDGE 1 20 -1 protocols.antibody.GraftCDRLoopsProtocol: protocols.antibody.GraftCDRLoopsProtocol: /// L2 template: protocols.antibody.GraftCDRLoopsProtocol: /// template_name: protocols.antibody.GraftCDRLoopsProtocol: ///PDB file name: ./L2.pdb protocols.antibody.GraftCDRLoopsProtocol: Total residues:15 protocols.antibody.GraftCDRLoopsProtocol: Sequence: LWIYSTSNLASGVPA protocols.antibody.GraftCDRLoopsProtocol: Fold tree: protocols.antibody.GraftCDRLoopsProtocol: FOLD_TREE EDGE 1 15 -1 protocols.antibody.GraftCDRLoopsProtocol: protocols.antibody.GraftCDRLoopsProtocol: /// L3 template: protocols.antibody.GraftCDRLoopsProtocol: /// template_name: protocols.antibody.GraftCDRLoopsProtocol: ///PDB file name: ./L3.pdb protocols.antibody.GraftCDRLoopsProtocol: Total residues:17 protocols.antibody.GraftCDRLoopsProtocol: Sequence: TYYCQQYSGYPYTFGGG protocols.antibody.GraftCDRLoopsProtocol: Fold tree: protocols.antibody.GraftCDRLoopsProtocol: FOLD_TREE EDGE 1 17 -1 protocols.antibody.GraftCDRLoopsProtocol: protocols.antibody.GraftCDRLoopsProtocol: /// H1 template: protocols.antibody.GraftCDRLoopsProtocol: /// template_name: protocols.antibody.GraftCDRLoopsProtocol: ///PDB file name: ./H1.pdb protocols.antibody.GraftCDRLoopsProtocol: Total residues:18 protocols.antibody.GraftCDRLoopsProtocol: Sequence: CKASGYTFTNYGMNWVKQ protocols.antibody.GraftCDRLoopsProtocol: Fold tree: protocols.antibody.GraftCDRLoopsProtocol: FOLD_TREE EDGE 1 18 -1 protocols.antibody.GraftCDRLoopsProtocol: protocols.antibody.GraftCDRLoopsProtocol: /// H2 template: protocols.antibody.GraftCDRLoopsProtocol: /// template_name: protocols.antibody.GraftCDRLoopsProtocol: ///PDB file name: ./H2.pdb protocols.antibody.GraftCDRLoopsProtocol: Total residues:25 protocols.antibody.GraftCDRLoopsProtocol: Sequence: KWMGWINTYTGEPTYADDFKERFAF protocols.antibody.GraftCDRLoopsProtocol: Fold tree: protocols.antibody.GraftCDRLoopsProtocol: FOLD_TREE EDGE 1 25 -1 protocols.antibody.GraftCDRLoopsProtocol: protocols.antibody.GraftCDRLoopsProtocol: /// H3 template: protocols.antibody.GraftCDRLoopsProtocol: /// template_name: protocols.antibody.GraftCDRLoopsProtocol: ///PDB file name: ./H3.pdb protocols.antibody.GraftCDRLoopsProtocol: Total residues:22 protocols.antibody.GraftCDRLoopsProtocol: Sequence: FCARDYYGSTYPYYAMDYWGQG protocols.antibody.GraftCDRLoopsProtocol: Fold tree: protocols.antibody.GraftCDRLoopsProtocol: FOLD_TREE EDGE 1 22 -1 protocols.antibody.GraftCDRLoopsProtocol: protocols.antibody.GraftCDRLoopsProtocol: //////////////////////////////////////////////////////////////////////////////// protocols.antibody.GraftCDRLoopsProtocol: protocols.antibody.GraftCDRLoopsProtocol: protocols.antibody.GraftCDRLoopsProtocol: Creating movers for H1 protocols.antibody.GraftCDRLoopsProtocol: start (chothia): 136 protocols.antibody.GraftCDRLoopsProtocol: stop (chothia): 145 protocols.antibody.GraftCDRLoopsProtocol: Creating movers for H2 protocols.antibody.GraftCDRLoopsProtocol: start (chothia): 160 protocols.antibody.GraftCDRLoopsProtocol: stop (chothia): 176 protocols.antibody.GraftCDRLoopsProtocol: Creating movers for H3 protocols.antibody.GraftCDRLoopsProtocol: start (chothia): 209 protocols.antibody.GraftCDRLoopsProtocol: stop (chothia): 222 protocols.antibody.GraftCDRLoopsProtocol: Creating movers for L1 protocols.antibody.GraftCDRLoopsProtocol: start (chothia): 24 protocols.antibody.GraftCDRLoopsProtocol: stop (chothia): 35 protocols.antibody.GraftCDRLoopsProtocol: Creating movers for L2 protocols.antibody.GraftCDRLoopsProtocol: start (chothia): 51 protocols.antibody.GraftCDRLoopsProtocol: stop (chothia): 57 protocols.antibody.GraftCDRLoopsProtocol: Creating movers for L3 protocols.antibody.GraftCDRLoopsProtocol: start (chothia): 90 protocols.antibody.GraftCDRLoopsProtocol: stop (chothia): 98 core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2013 protocols.antibody.GraftOneCDRLoop: Start to Graft CDRs H1 ............ protocols.antibody.GraftOneCDRLoop: flank_size: 4 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue GLN:CtermProteinFull 18 protocols.antibody.GraftOneCDRLoop: template_pose: protocols.antibody.GraftOneCDRLoop: PDB file name: ./H1.pdb protocols.antibody.GraftOneCDRLoop: Total residues:18 protocols.antibody.GraftOneCDRLoop: Sequence: CKASGYTFTNYGMNWVKQ protocols.antibody.GraftOneCDRLoop: Fold tree: protocols.antibody.GraftOneCDRLoop: FOLD_TREE EDGE 1 18 -1 protocols.antibody.GraftOneCDRLoop: protocols.antibody.GraftOneCDRLoop: Start to Graft CDRs H2 ............ protocols.antibody.GraftOneCDRLoop: flank_size: 4 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue PHE:CtermProteinFull 25 protocols.antibody.GraftOneCDRLoop: template_pose: protocols.antibody.GraftOneCDRLoop: PDB file name: ./H2.pdb protocols.antibody.GraftOneCDRLoop: Total residues:25 protocols.antibody.GraftOneCDRLoop: Sequence: KWMGWINTYTGEPTYADDFKERFAF protocols.antibody.GraftOneCDRLoop: Fold tree: protocols.antibody.GraftOneCDRLoop: FOLD_TREE EDGE 1 25 -1 protocols.antibody.GraftOneCDRLoop: protocols.antibody.GraftOneCDRLoop: Start to Graft CDRs H3 ............ protocols.antibody.GraftOneCDRLoop: flank_size: 4 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue GLY:CtermProteinFull 22 protocols.antibody.GraftOneCDRLoop: template_pose: protocols.antibody.GraftOneCDRLoop: PDB file name: ./H3.pdb protocols.antibody.GraftOneCDRLoop: Total residues:22 protocols.antibody.GraftOneCDRLoop: Sequence: FCARDYYGSTYPYYAMDYWGQG protocols.antibody.GraftOneCDRLoop: Fold tree: protocols.antibody.GraftOneCDRLoop: FOLD_TREE EDGE 1 22 -1 protocols.antibody.GraftOneCDRLoop: protocols.antibody.GraftOneCDRLoop: Start to Graft CDRs L1 ............ protocols.antibody.GraftOneCDRLoop: flank_size: 4 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue GLN:CtermProteinFull 20 protocols.antibody.GraftOneCDRLoop: template_pose: protocols.antibody.GraftOneCDRLoop: PDB file name: ./L1.pdb protocols.antibody.GraftOneCDRLoop: Total residues:20 protocols.antibody.GraftOneCDRLoop: Sequence: TMTCRASSSVSSSYLHWYQQ protocols.antibody.GraftOneCDRLoop: Fold tree: protocols.antibody.GraftOneCDRLoop: FOLD_TREE EDGE 1 20 -1 protocols.antibody.GraftOneCDRLoop: protocols.antibody.GraftOneCDRLoop: Start to Graft CDRs L2 ............ protocols.antibody.GraftOneCDRLoop: flank_size: 4 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ALA:CtermProteinFull 15 protocols.antibody.GraftOneCDRLoop: template_pose: protocols.antibody.GraftOneCDRLoop: PDB file name: ./L2.pdb protocols.antibody.GraftOneCDRLoop: Total residues:15 protocols.antibody.GraftOneCDRLoop: Sequence: LWIYSTSNLASGVPA protocols.antibody.GraftOneCDRLoop: Fold tree: protocols.antibody.GraftOneCDRLoop: FOLD_TREE EDGE 1 15 -1 protocols.antibody.GraftOneCDRLoop: protocols.antibody.GraftOneCDRLoop: Start to Graft CDRs L3 ............ protocols.antibody.GraftOneCDRLoop: flank_size: 4 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue GLY:CtermProteinFull 17 protocols.antibody.GraftOneCDRLoop: template_pose: protocols.antibody.GraftOneCDRLoop: PDB file name: ./L3.pdb protocols.antibody.GraftOneCDRLoop: Total residues:17 protocols.antibody.GraftOneCDRLoop: Sequence: TYYCQQYSGYPYTFGGG protocols.antibody.GraftOneCDRLoop: Fold tree: protocols.antibody.GraftOneCDRLoop: FOLD_TREE EDGE 1 17 -1 protocols.antibody.GraftOneCDRLoop: protocols.antibody.CDRsMinPackMin: FOLD_TREE EDGE 1 23 -1 EDGE 23 30 -1 EDGE 23 36 1 EDGE 36 31 -1 EDGE 36 50 -1 EDGE 50 54 -1 EDGE 50 58 2 EDGE 58 55 -1 EDGE 58 89 -1 EDGE 89 94 -1 EDGE 89 99 3 EDGE 99 95 -1 EDGE 99 135 -1 EDGE 135 141 -1 EDGE 135 146 4 EDGE 146 142 -1 EDGE 146 159 -1 EDGE 159 168 -1 EDGE 159 177 5 EDGE 177 169 -1 EDGE 177 208 -1 EDGE 208 210 -1 EDGE 208 223 6 EDGE 223 211 -1 EDGE 223 232 -1 protocols.antibody.CDRsMinPackMin: protocols.loops.loops_main: Added cutpoint variant to residue 30 protocols.loops.loops_main: Added cutpoint variant to residue 31 protocols.loops.loops_main: Added cutpoint variant to residue 54 protocols.loops.loops_main: Added cutpoint variant to residue 55 protocols.loops.loops_main: Added cutpoint variant to residue 94 protocols.loops.loops_main: Added cutpoint variant to residue 95 protocols.loops.loops_main: Added cutpoint variant to residue 141 protocols.loops.loops_main: Added cutpoint variant to residue 142 protocols.loops.loops_main: Added cutpoint variant to residue 168 protocols.loops.loops_main: Added cutpoint variant to residue 169 protocols.loops.loops_main: Added cutpoint variant to residue 210 protocols.loops.loops_main: Added cutpoint variant to residue 211 core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 3706 rotamers at 228 positions. core.pack.pack_rotamers: IG: 3036420 bytes protocols.antibody.GraftedStemOptimizer: Optimizing the stem of the Grafted CDR H1 ............ protocols.antibody.GraftedStemOptimizer: Setting Up the Optimizer Mover ..... core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2013 protocols.antibody.GraftedStemOptimizer: Finished Setting Up the Optimizer Mover!! basic.io.database: Database file opened: scoring/score_functions/disulfides/fa_SS_distance_score protocols.antibody.GraftedStemOptimizer: Score Before Stem Idealization: -140.243 protocols.loops.loops_main: Added cutpoint variant to residue 133 protocols.loops.loops_main: Added cutpoint variant to residue 134 protocols.loops.loops_main: Added cutpoint variant to residue 147 protocols.loops.loops_main: Added cutpoint variant to residue 148 protocols.antibody.GraftedStemOptimizer: Score After Idealization, but Before Stem Optimization: -142.992 protocols.loops.loop_closure.ccd.CCDLoopClosureMover: Closing loop 132 139 protocols.loops.loop_closure.ccd.RamaCheck: Initializing starting_rama_scores with current conformation. protocols.jd2.JobDistributor: [ERROR] Exception caught by JobDistributor for job FR_0001CCDLoopClosureMover::get_anchors( core::conformation::Residue const & residue ): Residue is not a cutpoint variant! You must add cutpoint variants before applying this Mover. protocols.jd2.JobDistributor: protocols.jd2.JobDistributor: FR_0001 reported that its input was bad and will not retry protocols.jd2.FileSystemJobDistributor: job failed, reporting bad input; other jobs of same input will be canceled: FR_0001 protocols.jd2.JobDistributor: no more batches to process... protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 2 seconds