# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading dunbrack-2191.atoms # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 53157 examples # computed average trans backbone unit before proline from 2010 examples # computed average cis backbone unit from 97 examples # trans (non-proline) backbone unit: # CA= -2.2087 1.0126 -0.0030 # O= -0.1499 2.2440 0.0016 # C= -0.6889 1.1368 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4581 -0.0000 0.0000 # cis backbone unit: # CA= -0.1436 2.4534 -0.0002 # O= -2.0284 0.9742 0.0015 # C= -0.8018 1.0771 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4668 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2100 1.0631 -0.0014 # O= -0.1236 2.2458 0.0075 # C= -0.6872 1.1517 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading dunbrack-2191.atoms have 2191 chains in training database # Count of chains,residues,atoms: 2191,500310,3902258 # 493341 residues have no bad marker # 3226 residues lack atoms needed to compute omega # 1453 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 4 # HAS_OXT 1167 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 3052 # HAS_UNKNOWN_ATOMS 9 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 979 # NON_PLANAR_PEPTIDE 888 # BAD_PEPTIDE 2680 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-2191.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0356/ # command:# Making conformation for sequence T0356 numbered 1 through 505 Created new target T0356 from T0356.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0356/ # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0356/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0356/decoys/ # ReadConformPDB reading from PDB file 2nd-chimera-domain-1-and-2-and-3+tag.pdb.gz looking for model 1 # choosing archetypes in rotamer library # Found a chain break before 496 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file 2nd-chimera-domain-1-and-2-and-3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # ReadConformPDB reading from PDB file 2nd-chimera-domain-1-and-2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # ReadConformPDB reading from PDB file 3rd-chimera-domain-1-and-2-and-3+tag.pdb.gz looking for model 1 # Found a chain break before 496 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file 3rd-chimera-domain-1-and-2-and-3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # ReadConformPDB reading from PDB file 3rd-chimera-domain-1-and-2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # ReadConformPDB reading from PDB file chimera-domain-1-and-2-and-3-proteinshop+tag.pdb.gz looking for model 1 # Found a chain break before 496 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file chimera-domain-1-and-2-and-3-proteinshop.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # ReadConformPDB reading from PDB file chimera-domain-1-and-2-and-3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS1.pdb.gz looking for model 1 # Found a chain break before 494 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_RECOM_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS1.pdb.gz looking for model 1 # Found a chain break before 494 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS5 # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # Found a chain break before 415 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS1 # ReadConformPDB reading from PDB file servers/3Dpro_TS2.pdb.gz looking for model 1 # Found a chain break before 471 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS2 # ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1 # Found a chain break before 457 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS3 # ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1 # Found a chain break before 468 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS4 # ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1 # Found a chain break before 380 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS5 # ReadConformPDB reading from PDB file servers/ABIpro_TS1.pdb.gz looking for model 1 # Found a chain break before 457 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS1 # ReadConformPDB reading from PDB file servers/ABIpro_TS2.pdb.gz looking for model 1 # Found a chain break before 474 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS2 # ReadConformPDB reading from PDB file servers/ABIpro_TS3.pdb.gz looking for model 1 # Found a chain break before 501 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS3 # ReadConformPDB reading from PDB file servers/ABIpro_TS4.pdb.gz looking for model 1 # Found a chain break before 490 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS4 # ReadConformPDB reading from PDB file servers/ABIpro_TS5.pdb.gz looking for model 1 # Found a chain break before 501 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS5 # ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1 # Found a chain break before 401 # copying to AlignedFragments data structure # naming current conformation BayesHH_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS1.pdb.gz looking for model 1 # Found a chain break before 504 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS2.pdb.gz looking for model 1 # Found a chain break before 468 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS2 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS3.pdb.gz looking for model 1 # Found a chain break before 468 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS3 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS4.pdb.gz looking for model 1 # Found a chain break before 504 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS4 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS5.pdb.gz looking for model 1 # naming current conformation Bilab-ENABLE_TS5 # ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1 # Found a chain break before 485 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS1 # ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS3 # ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS4 # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # Found a chain break before 477 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS5 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS2 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS3 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS4 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS5 # ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation Distill_TS1 # ReadConformPDB reading from PDB file servers/Distill_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation Distill_TS2 # ReadConformPDB reading from PDB file servers/Distill_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation Distill_TS3 # ReadConformPDB reading from PDB file servers/Distill_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation Distill_TS4 # ReadConformPDB reading from PDB file servers/Distill_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation Distill_TS5 # ReadConformPDB reading from PDB file servers/FAMSD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation FAMSD_TS1 # ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation FAMSD_TS2 # ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation FAMSD_TS3 # ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation FAMSD_TS4 # ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation FAMSD_TS5 # ReadConformPDB reading from PDB file servers/FAMS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation FAMS_TS1 # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation FAMS_TS3 # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # Found a chain break before 485 # copying to AlignedFragments data structure # naming current conformation FAMS_TS4 # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation FAMS_TS5 # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # Found a chain break before 471 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS1 # ReadConformPDB reading from PDB file servers/FOLDpro_TS2.pdb.gz looking for model 1 # Found a chain break before 376 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS2 # ReadConformPDB reading from PDB file servers/FOLDpro_TS3.pdb.gz looking for model 1 # Found a chain break before 457 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS3 # ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1 # Found a chain break before 422 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS4 # ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1 # Found a chain break before 473 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS5 # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation FORTE1_AL1 # ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation FORTE1_AL2 # ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation FORTE1_AL3 # ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation FORTE1_AL4 # ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation FORTE1_AL5 # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation FORTE2_AL1 # ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation FORTE2_AL2 # ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation FORTE2_AL3 # ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation FORTE2_AL4 # ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation FORTE2_AL5 # ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation FUGUE_AL1 # ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation FUGUE_AL2 # ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation FUGUE_AL3 # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation FUGUE_AL4 # ReadConformPDB reading from PDB file servers/FUGUE_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation FUGUE_AL5 # ReadConformPDB reading from PDB file servers/FUNCTION_TS1.pdb.gz looking for model 1 # Found a chain break before 504 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS1 # ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS2 # ReadConformPDB reading from PDB file servers/FUNCTION_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation FUNCTION_TS3 # ReadConformPDB reading from PDB file servers/FUNCTION_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation FUNCTION_TS4 # ReadConformPDB reading from PDB file servers/FUNCTION_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation FUNCTION_TS5 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS1 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # Found a chain break before 499 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS3 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1 # Found a chain break before 447 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS4 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS5 # ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation HHpred1_TS1 # ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1 WARNING: atom 1 has residue number 1 < previous residue 491 in servers/HHpred2_TS1.pdb.gz # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation HHpred2_TS1 # ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1 WARNING: atom 1 has residue number 1 < previous residue 499 in servers/HHpred3_TS1.pdb.gz # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation HHpred3_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS2 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS3 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS4 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS5 # ReadConformPDB reading from PDB file servers/LOOPP_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation LOOPP_TS1 # ReadConformPDB reading from PDB file servers/LOOPP_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation LOOPP_TS2 # ReadConformPDB reading from PDB file servers/LOOPP_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation LOOPP_TS3 # ReadConformPDB reading from PDB file servers/LOOPP_TS4.pdb.gz looking for model 1 # Found a chain break before 460 # copying to AlignedFragments data structure # naming current conformation LOOPP_TS4 # ReadConformPDB reading from PDB file servers/LOOPP_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation LOOPP_TS5 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation Ma-OPUS-server2_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation Ma-OPUS-server2_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation Ma-OPUS-server2_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation Ma-OPUS-server2_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation Ma-OPUS-server2_TS5 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation Ma-OPUS-server_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation Ma-OPUS-server_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation Ma-OPUS-server_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation Ma-OPUS-server_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation Ma-OPUS-server_TS5 # ReadConformPDB reading from PDB file servers/MetaTasser_TS1.pdb.gz looking for model 1 # Found a chain break before 504 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS1 # ReadConformPDB reading from PDB file servers/MetaTasser_TS2.pdb.gz looking for model 1 # Found a chain break before 502 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS2 # ReadConformPDB reading from PDB file servers/MetaTasser_TS3.pdb.gz looking for model 1 # Found a chain break before 504 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS3 # ReadConformPDB reading from PDB file servers/MetaTasser_TS4.pdb.gz looking for model 1 # Found a chain break before 503 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS4 # ReadConformPDB reading from PDB file servers/MetaTasser_TS5.pdb.gz looking for model 1 # Found a chain break before 502 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS5 # ReadConformPDB reading from PDB file servers/NN_PUT_lab_TS1.pdb.gz looking for model 1 # Found a chain break before 301 # copying to AlignedFragments data structure # naming current conformation NN_PUT_lab_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS1.pdb.gz looking for model 1 # Found a chain break before 469 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation POMYSL_TS2 # ReadConformPDB reading from PDB file servers/POMYSL_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation POMYSL_TS3 # ReadConformPDB reading from PDB file servers/POMYSL_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation POMYSL_TS4 # ReadConformPDB reading from PDB file servers/POMYSL_TS5.pdb.gz looking for model 1 # Found a chain break before 474 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS5 # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation Pcons6_TS1 # ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation Pcons6_TS2 # ReadConformPDB reading from PDB file servers/Pcons6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation Pcons6_TS3 # ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation Pcons6_TS4 # ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation Pcons6_TS5 # ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation Phyre-1_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation Phyre-2_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation Phyre-2_TS2 # ReadConformPDB reading from PDB file servers/Phyre-2_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation Phyre-2_TS3 # ReadConformPDB reading from PDB file servers/Phyre-2_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation Phyre-2_TS4 # ReadConformPDB reading from PDB file servers/Phyre-2_TS5.pdb.gz looking for model 1 # Found a chain break before 504 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS5 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS1 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS2 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS3 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS4 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1 # Found a chain break before 498 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1 # Found a chain break before 498 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1 # Found a chain break before 427 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS4.pdb.gz looking for model 1 # Found a chain break before 472 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1 # Found a chain break before 466 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS5 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS1.pdb.gz looking for model 1 # Found a chain break before 433 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS1 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS2.pdb.gz looking for model 1 # Found a chain break before 495 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS2 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS3.pdb.gz looking for model 1 # Found a chain break before 442 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS3 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS4.pdb.gz looking for model 1 # Found a chain break before 469 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS4 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS5.pdb.gz looking for model 1 # Found a chain break before 498 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR_TS1.pdb.gz looking for model 1 # Found a chain break before 394 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1 # Found a chain break before 488 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR_TS3.pdb.gz looking for model 1 # Found a chain break before 447 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR_TS4.pdb.gz looking for model 1 # Found a chain break before 497 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR_TS5.pdb.gz looking for model 1 # Found a chain break before 390 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS5 # ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation ROBETTA_TS1 # ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1 # Found a chain break before 323 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS2 # ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation ROBETTA_TS3 # ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1 # Found a chain break before 323 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS4 # ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation ROBETTA_TS5 # ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1 WARNING: atoms too close: (T0356)M4.CA and (T0356)M4.CB only 0 apart, marking (T0356)M4.CB as missing WARNING: atoms too close: (T0356)N7.CA and (T0356)N7.CB only 0 apart, marking (T0356)N7.CB as missing WARNING: atoms too close: (T0356)D11.CA and (T0356)D11.CB only 0 apart, marking (T0356)D11.CB as missing WARNING: atoms too close: (T0356)L13.CA and (T0356)L13.CB only 0 apart, marking (T0356)L13.CB as missing WARNING: atoms too close: (T0356)L22.CA and (T0356)L22.CB only 0 apart, marking (T0356)L22.CB as missing WARNING: atoms too close: (T0356)V29.CA and (T0356)V29.CB only 0 apart, marking (T0356)V29.CB as missing WARNING: atoms too close: (T0356)I35.CA and (T0356)I35.CB only 0 apart, marking (T0356)I35.CB as missing WARNING: atoms too close: (T0356)T36.CA and (T0356)T36.CB only 0 apart, marking (T0356)T36.CB as missing WARNING: atoms too close: (T0356)E53.CA and (T0356)E53.CB only 0 apart, marking (T0356)E53.CB as missing WARNING: atoms too close: (T0356)L63.CA and (T0356)L63.CB only 0 apart, marking (T0356)L63.CB as missing WARNING: atoms too close: (T0356)F67.CA and (T0356)F67.CB only 0 apart, marking (T0356)F67.CB as missing WARNING: atoms too close: (T0356)T69.CA and (T0356)T69.CB only 0 apart, marking (T0356)T69.CB as missing WARNING: atoms too close: (T0356)K71.CA and (T0356)K71.CB only 0 apart, marking (T0356)K71.CB as missing WARNING: atoms too close: (T0356)Q79.CA and (T0356)Q79.CB only 0 apart, marking (T0356)Q79.CB as missing WARNING: atoms too close: (T0356)E80.CA and (T0356)E80.CB only 0 apart, marking (T0356)E80.CB as missing WARNING: atoms too close: (T0356)A84.CA and (T0356)A84.CB only 0 apart, marking (T0356)A84.CB as missing WARNING: atoms too close: (T0356)K90.CA and (T0356)K90.CB only 0 apart, marking (T0356)K90.CB as missing WARNING: atoms too close: (T0356)L92.CA and (T0356)L92.CB only 0 apart, marking (T0356)L92.CB as missing WARNING: atoms too close: (T0356)E97.CA and (T0356)E97.CB only 0 apart, marking (T0356)E97.CB as missing WARNING: atoms too close: (T0356)F108.CA and (T0356)F108.CB only 0 apart, marking (T0356)F108.CB as missing WARNING: atoms too close: (T0356)Q113.CA and (T0356)Q113.CB only 0 apart, marking (T0356)Q113.CB as missing WARNING: atoms too close: (T0356)F114.CA and (T0356)F114.CB only 0 apart, marking (T0356)F114.CB as missing WARNING: atoms too close: (T0356)L125.CA and (T0356)L125.CB only 0 apart, marking (T0356)L125.CB as missing WARNING: atoms too close: (T0356)Q131.CA and (T0356)Q131.CB only 0 apart, marking (T0356)Q131.CB as missing WARNING: atoms too close: (T0356)V135.CA and (T0356)V135.CB only 0 apart, marking (T0356)V135.CB as missing WARNING: atoms too close: (T0356)D141.CA and (T0356)D141.CB only 0 apart, marking (T0356)D141.CB as missing WARNING: atoms too close: (T0356)I147.CA and (T0356)I147.CB only 0 apart, marking (T0356)I147.CB as missing WARNING: atoms too close: (T0356)W151.CA and (T0356)W151.CB only 0 apart, marking (T0356)W151.CB as missing WARNING: atoms too close: (T0356)L158.CA and (T0356)L158.CB only 0 apart, marking (T0356)L158.CB as missing WARNING: atoms too close: (T0356)T160.CA and (T0356)T160.CB only 0 apart, marking (T0356)T160.CB as missing WARNING: atoms too close: (T0356)K171.CA and (T0356)K171.CB only 0 apart, marking (T0356)K171.CB as missing WARNING: atoms too close: (T0356)L189.CA and (T0356)L189.CB only 0 apart, marking (T0356)L189.CB as missing WARNING: atoms too close: (T0356)I190.CA and (T0356)I190.CB only 0 apart, marking (T0356)I190.CB as missing WARNING: atoms too close: (T0356)W193.CA and (T0356)W193.CB only 0 apart, marking (T0356)W193.CB as missing WARNING: atoms too close: (T0356)V219.CA and (T0356)V219.CB only 0 apart, marking (T0356)V219.CB as missing WARNING: atoms too close: (T0356)L229.CA and (T0356)L229.CB only 0 apart, marking (T0356)L229.CB as missing WARNING: atoms too close: (T0356)P234.CA and (T0356)P234.CB only 0 apart, marking (T0356)P234.CB as missing WARNING: atoms too close: (T0356)L239.CA and (T0356)L239.CB only 0 apart, marking (T0356)L239.CB as missing WARNING: atoms too close: (T0356)L247.CA and (T0356)L247.CB only 0 apart, marking (T0356)L247.CB as missing WARNING: atoms too close: (T0356)R249.CA and (T0356)R249.CB only 0 apart, marking (T0356)R249.CB as missing WARNING: atoms too close: (T0356)T251.CA and (T0356)T251.CB only 0 apart, marking (T0356)T251.CB as missing WARNING: atoms too close: (T0356)K252.CA and (T0356)K252.CB only 0 apart, marking (T0356)K252.CB as missing WARNING: atoms too close: (T0356)V255.CA and (T0356)V255.CB only 0 apart, marking (T0356)V255.CB as missing WARNING: atoms too close: (T0356)K257.CA and (T0356)K257.CB only 0 apart, marking (T0356)K257.CB as missing WARNING: atoms too close: (T0356)I259.CA and (T0356)I259.CB only 0 apart, marking (T0356)I259.CB as missing WARNING: atoms too close: (T0356)L263.CA and (T0356)L263.CB only 0 apart, marking (T0356)L263.CB as missing WARNING: atoms too close: (T0356)V265.CA and (T0356)V265.CB only 0 apart, marking (T0356)V265.CB as missing WARNING: atoms too close: (T0356)P266.CA and (T0356)P266.CB only 0 apart, marking (T0356)P266.CB as missing WARNING: atoms too close: (T0356)E274.CA and (T0356)E274.CB only 0 apart, marking (T0356)E274.CB as missing WARNING: atoms too close: (T0356)E281.CA and (T0356)E281.CB only 0 apart, marking (T0356)E281.CB as missing WARNING: atoms too close: (T0356)Y295.CA and (T0356)Y295.CB only 0 apart, marking (T0356)Y295.CB as missing WARNING: atoms too close: (T0356)P302.CA and (T0356)P302.CB only 0 apart, marking (T0356)P302.CB as missing WARNING: atoms too close: (T0356)P325.CA and (T0356)P325.CB only 0 apart, marking (T0356)P325.CB as missing WARNING: atoms too close: (T0356)D327.CA and (T0356)D327.CB only 0 apart, marking (T0356)D327.CB as missing WARNING: atoms too close: (T0356)E328.CA and (T0356)E328.CB only 0 apart, marking (T0356)E328.CB as missing WARNING: atoms too close: (T0356)L336.CA and (T0356)L336.CB only 0 apart, marking (T0356)L336.CB as missing WARNING: atoms too close: (T0356)P342.CA and (T0356)P342.CB only 0 apart, marking (T0356)P342.CB as missing WARNING: atoms too close: (T0356)I343.CA and (T0356)I343.CB only 0 apart, marking (T0356)I343.CB as missing WARNING: atoms too close: (T0356)Q347.CA and (T0356)Q347.CB only 0 apart, marking (T0356)Q347.CB as missing WARNING: atoms too close: (T0356)F348.CA and (T0356)F348.CB only 0 apart, marking (T0356)F348.CB as missing WARNING: atoms too close: (T0356)I351.CA and (T0356)I351.CB only 0 apart, marking (T0356)I351.CB as missing WARNING: atoms too close: (T0356)P357.CA and (T0356)P357.CB only 0 apart, marking (T0356)P357.CB as missing WARNING: atoms too close: (T0356)R364.CA and (T0356)R364.CB only 0 apart, marking (T0356)R364.CB as missing WARNING: atoms too close: (T0356)L365.CA and (T0356)L365.CB only 0 apart, marking (T0356)L365.CB as missing WARNING: atoms too close: (T0356)K372.CA and (T0356)K372.CB only 0 apart, marking (T0356)K372.CB as missing WARNING: atoms too close: (T0356)Q373.CA and (T0356)Q373.CB only 0 apart, marking (T0356)Q373.CB as missing WARNING: atoms too close: (T0356)A375.CA and (T0356)A375.CB only 0 apart, marking (T0356)A375.CB as missing WARNING: atoms too close: (T0356)A378.CA and (T0356)A378.CB only 0 apart, marking (T0356)A378.CB as missing WARNING: atoms too close: (T0356)V381.CA and (T0356)V381.CB only 0 apart, marking (T0356)V381.CB as missing WARNING: atoms too close: (T0356)M383.CA and (T0356)M383.CB only 0 apart, marking (T0356)M383.CB as missing WARNING: atoms too close: (T0356)V400.CA and (T0356)V400.CB only 0 apart, marking (T0356)V400.CB as missing WARNING: atoms too close: (T0356)R408.CA and (T0356)R408.CB only 0 apart, marking (T0356)R408.CB as missing WARNING: atoms too close: (T0356)D409.CA and (T0356)D409.CB only 0 apart, marking (T0356)D409.CB as missing WARNING: atoms too close: (T0356)W410.CA and (T0356)W410.CB only 0 apart, marking (T0356)W410.CB as missing WARNING: atoms too close: (T0356)D426.CA and (T0356)D426.CB only 0 apart, marking (T0356)D426.CB as missing WARNING: atoms too close: (T0356)T427.CA and (T0356)T427.CB only 0 apart, marking (T0356)T427.CB as missing WARNING: atoms too close: (T0356)D436.CA and (T0356)D436.CB only 0 apart, marking (T0356)D436.CB as missing WARNING: atoms too close: (T0356)Y437.CA and (T0356)Y437.CB only 0 apart, marking (T0356)Y437.CB as missing WARNING: atoms too close: (T0356)S445.CA and (T0356)S445.CB only 0 apart, marking (T0356)S445.CB as missing WARNING: atoms too close: (T0356)K450.CA and (T0356)K450.CB only 0 apart, marking (T0356)K450.CB as missing WARNING: atoms too close: (T0356)W459.CA and (T0356)W459.CB only 0 apart, marking (T0356)W459.CB as missing WARNING: atoms too close: (T0356)E466.CA and (T0356)E466.CB only 0 apart, marking (T0356)E466.CB as missing WARNING: atoms too close: (T0356)W467.CA and (T0356)W467.CB only 0 apart, marking (T0356)W467.CB as missing WARNING: atoms too close: (T0356)P470.CA and (T0356)P470.CB only 0 apart, marking (T0356)P470.CB as missing WARNING: atoms too close: (T0356)K473.CA and (T0356)K473.CB only 0 apart, marking (T0356)K473.CB as missing WARNING: atoms too close: (T0356)D476.CA and (T0356)D476.CB only 0 apart, marking (T0356)D476.CB as missing WARNING: atoms too close: (T0356)V478.CA and (T0356)V478.CB only 0 apart, marking (T0356)V478.CB as missing WARNING: atoms too close: (T0356)A479.CA and (T0356)A479.CB only 0 apart, marking (T0356)A479.CB as missing WARNING: atoms too close: (T0356)W485.CA and (T0356)W485.CB only 0 apart, marking (T0356)W485.CB as missing WARNING: atoms too close: (T0356)A497.CA and (T0356)A497.CB only 0 apart, marking (T0356)A497.CB as missing WARNING: atoms too close: (T0356)E499.CA and (T0356)E499.CB only 0 apart, marking (T0356)E499.CB as missing WARNING: atoms too close: (T0356)H505.CA and (T0356)H505.CB only 0 apart, marking (T0356)H505.CB as missing # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS1 # ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1 WARNING: atoms too close: (T0356)D8.CA and (T0356)D8.CB only 0 apart, marking (T0356)D8.CB as missing WARNING: atoms too close: (T0356)K23.CA and (T0356)K23.CB only 0 apart, marking (T0356)K23.CB as missing WARNING: atoms too close: (T0356)R24.CA and (T0356)R24.CB only 0 apart, marking (T0356)R24.CB as missing WARNING: atoms too close: (T0356)L27.CA and (T0356)L27.CB only 0 apart, marking (T0356)L27.CB as missing WARNING: atoms too close: (T0356)V29.CA and (T0356)V29.CB only 0 apart, marking (T0356)V29.CB as missing WARNING: atoms too close: (T0356)D30.CA and (T0356)D30.CB only 0 apart, marking (T0356)D30.CB as missing WARNING: atoms too close: (T0356)L51.CA and (T0356)L51.CB only 0 apart, marking (T0356)L51.CB as missing WARNING: atoms too close: (T0356)K56.CA and (T0356)K56.CB only 0 apart, marking (T0356)K56.CB as missing WARNING: atoms too close: (T0356)K71.CA and (T0356)K71.CB only 0 apart, marking (T0356)K71.CB as missing WARNING: atoms too close: (T0356)V73.CA and (T0356)V73.CB only 0 apart, marking (T0356)V73.CB as missing WARNING: atoms too close: (T0356)M77.CA and (T0356)M77.CB only 0 apart, marking (T0356)M77.CB as missing WARNING: atoms too close: (T0356)K90.CA and (T0356)K90.CB only 0 apart, marking (T0356)K90.CB as missing WARNING: atoms too close: (T0356)A93.CA and (T0356)A93.CB only 0 apart, marking (T0356)A93.CB as missing WARNING: atoms too close: (T0356)E99.CA and (T0356)E99.CB only 0 apart, marking (T0356)E99.CB as missing WARNING: atoms too close: (T0356)Q113.CA and (T0356)Q113.CB only 0 apart, marking (T0356)Q113.CB as missing WARNING: atoms too close: (T0356)S136.CA and (T0356)S136.CB only 0 apart, marking (T0356)S136.CB as missing WARNING: atoms too close: (T0356)D139.CA and (T0356)D139.CB only 0 apart, marking (T0356)D139.CB as missing WARNING: atoms too close: (T0356)I145.CA and (T0356)I145.CB only 0 apart, marking (T0356)I145.CB as missing WARNING: atoms too close: (T0356)T149.CA and (T0356)T149.CB only 0 apart, marking (T0356)T149.CB as missing WARNING: atoms too close: (T0356)P152.CA and (T0356)P152.CB only 0 apart, marking (T0356)P152.CB as missing WARNING: atoms too close: (T0356)L158.CA and (T0356)L158.CB only 0 apart, marking (T0356)L158.CB as missing WARNING: atoms too close: (T0356)I159.CA and (T0356)I159.CB only 0 apart, marking (T0356)I159.CB as missing WARNING: atoms too close: (T0356)L163.CA and (T0356)L163.CB only 0 apart, marking (T0356)L163.CB as missing WARNING: atoms too close: (T0356)T164.CA and (T0356)T164.CB only 0 apart, marking (T0356)T164.CB as missing WARNING: atoms too close: (T0356)Q174.CA and (T0356)Q174.CB only 0 apart, marking (T0356)Q174.CB as missing WARNING: atoms too close: (T0356)Y179.CA and (T0356)Y179.CB only 0 apart, marking (T0356)Y179.CB as missing WARNING: atoms too close: (T0356)L189.CA and (T0356)L189.CB only 0 apart, marking (T0356)L189.CB as missing WARNING: atoms too close: (T0356)I190.CA and (T0356)I190.CB only 0 apart, marking (T0356)I190.CB as missing WARNING: atoms too close: (T0356)R192.CA and (T0356)R192.CB only 0 apart, marking (T0356)R192.CB as missing WARNING: atoms too close: (T0356)R197.CA and (T0356)R197.CB only 0 apart, marking (T0356)R197.CB as missing WARNING: atoms too close: (T0356)W206.CA and (T0356)W206.CB only 0 apart, marking (T0356)W206.CB as missing WARNING: atoms too close: (T0356)A209.CA and (T0356)A209.CB only 0 apart, marking (T0356)A209.CB as missing WARNING: atoms too close: (T0356)A231.CA and (T0356)A231.CB only 0 apart, marking (T0356)A231.CB as missing WARNING: atoms too close: (T0356)V235.CA and (T0356)V235.CB only 0 apart, marking (T0356)V235.CB as missing WARNING: atoms too close: (T0356)K252.CA and (T0356)K252.CB only 0 apart, marking (T0356)K252.CB as missing WARNING: atoms too close: (T0356)L263.CA and (T0356)L263.CB only 0 apart, marking (T0356)L263.CB as missing WARNING: atoms too close: (T0356)I277.CA and (T0356)I277.CB only 0 apart, marking (T0356)I277.CB as missing WARNING: atoms too close: (T0356)Q279.CA and (T0356)Q279.CB only 0 apart, marking (T0356)Q279.CB as missing WARNING: atoms too close: (T0356)T282.CA and (T0356)T282.CB only 0 apart, marking (T0356)T282.CB as missing WARNING: atoms too close: (T0356)P287.CA and (T0356)P287.CB only 0 apart, marking (T0356)P287.CB as missing WARNING: atoms too close: (T0356)D290.CA and (T0356)D290.CB only 0 apart, marking (T0356)D290.CB as missing WARNING: atoms too close: (T0356)Y295.CA and (T0356)Y295.CB only 0 apart, marking (T0356)Y295.CB as missing WARNING: atoms too close: (T0356)E297.CA and (T0356)E297.CB only 0 apart, marking (T0356)E297.CB as missing WARNING: atoms too close: (T0356)S300.CA and (T0356)S300.CB only 0 apart, marking (T0356)S300.CB as missing WARNING: atoms too close: (T0356)V303.CA and (T0356)V303.CB only 0 apart, marking (T0356)V303.CB as missing WARNING: atoms too close: (T0356)T307.CA and (T0356)T307.CB only 0 apart, marking (T0356)T307.CB as missing WARNING: atoms too close: (T0356)H308.CA and (T0356)H308.CB only 0 apart, marking (T0356)H308.CB as missing WARNING: atoms too close: (T0356)T310.CA and (T0356)T310.CB only 0 apart, marking (T0356)T310.CB as missing WARNING: atoms too close: (T0356)E313.CA and (T0356)E313.CB only 0 apart, marking (T0356)E313.CB as missing WARNING: atoms too close: (T0356)Y317.CA and (T0356)Y317.CB only 0 apart, marking (T0356)Y317.CB as missing WARNING: atoms too close: (T0356)S319.CA and (T0356)S319.CB only 0 apart, marking (T0356)S319.CB as missing WARNING: atoms too close: (T0356)P342.CA and (T0356)P342.CB only 0 apart, marking (T0356)P342.CB as missing WARNING: atoms too close: (T0356)I351.CA and (T0356)I351.CB only 0 apart, marking (T0356)I351.CB as missing WARNING: atoms too close: (T0356)P357.CA and (T0356)P357.CB only 0 apart, marking (T0356)P357.CB as missing WARNING: atoms too close: (T0356)S362.CA and (T0356)S362.CB only 0 apart, marking (T0356)S362.CB as missing WARNING: atoms too close: (T0356)R364.CA and (T0356)R364.CB only 0 apart, marking (T0356)R364.CB as missing WARNING: atoms too close: (T0356)L365.CA and (T0356)L365.CB only 0 apart, marking (T0356)L365.CB as missing WARNING: atoms too close: (T0356)A378.CA and (T0356)A378.CB only 0 apart, marking (T0356)A378.CB as missing WARNING: atoms too close: (T0356)L389.CA and (T0356)L389.CB only 0 apart, marking (T0356)L389.CB as missing WARNING: atoms too close: (T0356)Q391.CA and (T0356)Q391.CB only 0 apart, marking (T0356)Q391.CB as missing WARNING: atoms too close: (T0356)K396.CA and (T0356)K396.CB only 0 apart, marking (T0356)K396.CB as missing WARNING: atoms too close: (T0356)I399.CA and (T0356)I399.CB only 0 apart, marking (T0356)I399.CB as missing WARNING: atoms too close: (T0356)V400.CA and (T0356)V400.CB only 0 apart, marking (T0356)V400.CB as missing WARNING: atoms too close: (T0356)D402.CA and (T0356)D402.CB only 0 apart, marking (T0356)D402.CB as missing WARNING: atoms too close: (T0356)D403.CA and (T0356)D403.CB only 0 apart, marking (T0356)D403.CB as missing WARNING: atoms too close: (T0356)A407.CA and (T0356)A407.CB only 0 apart, marking (T0356)A407.CB as missing WARNING: atoms too close: (T0356)R420.CA and (T0356)R420.CB only 0 apart, marking (T0356)R420.CB as missing WARNING: atoms too close: (T0356)A424.CA and (T0356)A424.CB only 0 apart, marking (T0356)A424.CB as missing WARNING: atoms too close: (T0356)T427.CA and (T0356)T427.CB only 0 apart, marking (T0356)T427.CB as missing WARNING: atoms too close: (T0356)A441.CA and (T0356)A441.CB only 0 apart, marking (T0356)A441.CB as missing WARNING: atoms too close: (T0356)S445.CA and (T0356)S445.CB only 0 apart, marking (T0356)S445.CB as missing WARNING: atoms too close: (T0356)L447.CA and (T0356)L447.CB only 0 apart, marking (T0356)L447.CB as missing WARNING: atoms too close: (T0356)E466.CA and (T0356)E466.CB only 0 apart, marking (T0356)E466.CB as missing WARNING: atoms too close: (T0356)P470.CA and (T0356)P470.CB only 0 apart, marking (T0356)P470.CB as missing WARNING: atoms too close: (T0356)I471.CA and (T0356)I471.CB only 0 apart, marking (T0356)I471.CB as missing WARNING: atoms too close: (T0356)D476.CA and (T0356)D476.CB only 0 apart, marking (T0356)D476.CB as missing WARNING: atoms too close: (T0356)A479.CA and (T0356)A479.CB only 0 apart, marking (T0356)A479.CB as missing WARNING: atoms too close: (T0356)W485.CA and (T0356)W485.CB only 0 apart, marking (T0356)W485.CB as missing WARNING: atoms too close: (T0356)D486.CA and (T0356)D486.CB only 0 apart, marking (T0356)D486.CB as missing WARNING: atoms too close: (T0356)N492.CA and (T0356)N492.CB only 0 apart, marking (T0356)N492.CB as missing WARNING: atoms too close: (T0356)E499.CA and (T0356)E499.CB only 0 apart, marking (T0356)E499.CB as missing WARNING: atoms too close: (T0356)H501.CA and (T0356)H501.CB only 0 apart, marking (T0356)H501.CB as missing # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS2 # ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1 WARNING: atoms too close: (T0356)M1.CA and (T0356)M1.CB only 0 apart, marking (T0356)M1.CB as missing WARNING: atoms too close: (T0356)A3.CA and (T0356)A3.CB only 0 apart, marking (T0356)A3.CB as missing WARNING: atoms too close: (T0356)Y6.CA and (T0356)Y6.CB only 0 apart, marking (T0356)Y6.CB as missing WARNING: atoms too close: (T0356)D11.CA and (T0356)D11.CB only 0 apart, marking (T0356)D11.CB as missing WARNING: atoms too close: (T0356)L13.CA and (T0356)L13.CB only 0 apart, marking (T0356)L13.CB as missing WARNING: atoms too close: (T0356)T26.CA and (T0356)T26.CB only 0 apart, marking (T0356)T26.CB as missing WARNING: atoms too close: (T0356)P31.CA and (T0356)P31.CB only 0 apart, marking (T0356)P31.CB as missing WARNING: atoms too close: (T0356)I38.CA and (T0356)I38.CB only 0 apart, marking (T0356)I38.CB as missing WARNING: atoms too close: (T0356)A49.CA and (T0356)A49.CB only 0 apart, marking (T0356)A49.CB as missing WARNING: atoms too close: (T0356)L51.CA and (T0356)L51.CB only 0 apart, marking (T0356)L51.CB as missing WARNING: atoms too close: (T0356)C64.CA and (T0356)C64.CB only 0 apart, marking (T0356)C64.CB as missing WARNING: atoms too close: (T0356)K71.CA and (T0356)K71.CB only 0 apart, marking (T0356)K71.CB as missing WARNING: atoms too close: (T0356)K90.CA and (T0356)K90.CB only 0 apart, marking (T0356)K90.CB as missing WARNING: atoms too close: (T0356)K96.CA and (T0356)K96.CB only 0 apart, marking (T0356)K96.CB as missing WARNING: atoms too close: (T0356)R124.CA and (T0356)R124.CB only 0 apart, marking (T0356)R124.CB as missing WARNING: atoms too close: (T0356)C130.CA and (T0356)C130.CB only 0 apart, marking (T0356)C130.CB as missing WARNING: atoms too close: (T0356)Q131.CA and (T0356)Q131.CB only 0 apart, marking (T0356)Q131.CB as missing WARNING: atoms too close: (T0356)I147.CA and (T0356)I147.CB only 0 apart, marking (T0356)I147.CB as missing WARNING: atoms too close: (T0356)D154.CA and (T0356)D154.CB only 0 apart, marking (T0356)D154.CB as missing WARNING: atoms too close: (T0356)A155.CA and (T0356)A155.CB only 0 apart, marking (T0356)A155.CB as missing WARNING: atoms too close: (T0356)T164.CA and (T0356)T164.CB only 0 apart, marking (T0356)T164.CB as missing WARNING: atoms too close: (T0356)P169.CA and (T0356)P169.CB only 0 apart, marking (T0356)P169.CB as missing WARNING: atoms too close: (T0356)Q174.CA and (T0356)Q174.CB only 0 apart, marking (T0356)Q174.CB as missing WARNING: atoms too close: (T0356)I178.CA and (T0356)I178.CB only 0 apart, marking (T0356)I178.CB as missing WARNING: atoms too close: (T0356)Q182.CA and (T0356)Q182.CB only 0 apart, marking (T0356)Q182.CB as missing WARNING: atoms too close: (T0356)L183.CA and (T0356)L183.CB only 0 apart, marking (T0356)L183.CB as missing WARNING: atoms too close: (T0356)I184.CA and (T0356)I184.CB only 0 apart, marking (T0356)I184.CB as missing WARNING: atoms too close: (T0356)L189.CA and (T0356)L189.CB only 0 apart, marking (T0356)L189.CB as missing WARNING: atoms too close: (T0356)R192.CA and (T0356)R192.CB only 0 apart, marking (T0356)R192.CB as missing WARNING: atoms too close: (T0356)W193.CA and (T0356)W193.CB only 0 apart, marking (T0356)W193.CB as missing WARNING: atoms too close: (T0356)A200.CA and (T0356)A200.CB only 0 apart, marking (T0356)A200.CB as missing WARNING: atoms too close: (T0356)C207.CA and (T0356)C207.CB only 0 apart, marking (T0356)C207.CB as missing WARNING: atoms too close: (T0356)P234.CA and (T0356)P234.CB only 0 apart, marking (T0356)P234.CB as missing WARNING: atoms too close: (T0356)V235.CA and (T0356)V235.CB only 0 apart, marking (T0356)V235.CB as missing WARNING: atoms too close: (T0356)A245.CA and (T0356)A245.CB only 0 apart, marking (T0356)A245.CB as missing WARNING: atoms too close: (T0356)K252.CA and (T0356)K252.CB only 0 apart, marking (T0356)K252.CB as missing WARNING: atoms too close: (T0356)E254.CA and (T0356)E254.CB only 0 apart, marking (T0356)E254.CB as missing WARNING: atoms too close: (T0356)D262.CA and (T0356)D262.CB only 0 apart, marking (T0356)D262.CB as missing WARNING: atoms too close: (T0356)V265.CA and (T0356)V265.CB only 0 apart, marking (T0356)V265.CB as missing WARNING: atoms too close: (T0356)L273.CA and (T0356)L273.CB only 0 apart, marking (T0356)L273.CB as missing WARNING: atoms too close: (T0356)Y276.CA and (T0356)Y276.CB only 0 apart, marking (T0356)Y276.CB as missing WARNING: atoms too close: (T0356)E278.CA and (T0356)E278.CB only 0 apart, marking (T0356)E278.CB as missing WARNING: atoms too close: (T0356)Q279.CA and (T0356)Q279.CB only 0 apart, marking (T0356)Q279.CB as missing WARNING: atoms too close: (T0356)T282.CA and (T0356)T282.CB only 0 apart, marking (T0356)T282.CB as missing WARNING: atoms too close: (T0356)T292.CA and (T0356)T292.CB only 0 apart, marking (T0356)T292.CB as missing WARNING: atoms too close: (T0356)Y295.CA and (T0356)Y295.CB only 0 apart, marking (T0356)Y295.CB as missing WARNING: atoms too close: (T0356)D299.CA and (T0356)D299.CB only 0 apart, marking (T0356)D299.CB as missing WARNING: atoms too close: (T0356)R312.CA and (T0356)R312.CB only 0 apart, marking (T0356)R312.CB as missing WARNING: atoms too close: (T0356)I316.CA and (T0356)I316.CB only 0 apart, marking (T0356)I316.CB as missing WARNING: atoms too close: (T0356)Y317.CA and (T0356)Y317.CB only 0 apart, marking (T0356)Y317.CB as missing WARNING: atoms too close: (T0356)H318.CA and (T0356)H318.CB only 0 apart, marking (T0356)H318.CB as missing WARNING: atoms too close: (T0356)N337.CA and (T0356)N337.CB only 0 apart, marking (T0356)N337.CB as missing WARNING: atoms too close: (T0356)Q347.CA and (T0356)Q347.CB only 0 apart, marking (T0356)Q347.CB as missing WARNING: atoms too close: (T0356)P358.CA and (T0356)P358.CB only 0 apart, marking (T0356)P358.CB as missing WARNING: atoms too close: (T0356)Y363.CA and (T0356)Y363.CB only 0 apart, marking (T0356)Y363.CB as missing WARNING: atoms too close: (T0356)L365.CA and (T0356)L365.CB only 0 apart, marking (T0356)L365.CB as missing WARNING: atoms too close: (T0356)H377.CA and (T0356)H377.CB only 0 apart, marking (T0356)H377.CB as missing WARNING: atoms too close: (T0356)K396.CA and (T0356)K396.CB only 0 apart, marking (T0356)K396.CB as missing WARNING: atoms too close: (T0356)V398.CA and (T0356)V398.CB only 0 apart, marking (T0356)V398.CB as missing WARNING: atoms too close: (T0356)I399.CA and (T0356)I399.CB only 0 apart, marking (T0356)I399.CB as missing WARNING: atoms too close: (T0356)A407.CA and (T0356)A407.CB only 0 apart, marking (T0356)A407.CB as missing WARNING: atoms too close: (T0356)R408.CA and (T0356)R408.CB only 0 apart, marking (T0356)R408.CB as missing WARNING: atoms too close: (T0356)A416.CA and (T0356)A416.CB only 0 apart, marking (T0356)A416.CB as missing WARNING: atoms too close: (T0356)R425.CA and (T0356)R425.CB only 0 apart, marking (T0356)R425.CB as missing WARNING: atoms too close: (T0356)V430.CA and (T0356)V430.CB only 0 apart, marking (T0356)V430.CB as missing WARNING: atoms too close: (T0356)N457.CA and (T0356)N457.CB only 0 apart, marking (T0356)N457.CB as missing WARNING: atoms too close: (T0356)T463.CA and (T0356)T463.CB only 0 apart, marking (T0356)T463.CB as missing WARNING: atoms too close: (T0356)K472.CA and (T0356)K472.CB only 0 apart, marking (T0356)K472.CB as missing WARNING: atoms too close: (T0356)K473.CA and (T0356)K473.CB only 0 apart, marking (T0356)K473.CB as missing WARNING: atoms too close: (T0356)D476.CA and (T0356)D476.CB only 0 apart, marking (T0356)D476.CB as missing WARNING: atoms too close: (T0356)L488.CA and (T0356)L488.CB only 0 apart, marking (T0356)L488.CB as missing WARNING: atoms too close: (T0356)N493.CA and (T0356)N493.CB only 0 apart, marking (T0356)N493.CB as missing # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS3 # ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1 WARNING: atoms too close: (T0356)I25.CA and (T0356)I25.CB only 0 apart, marking (T0356)I25.CB as missing WARNING: atoms too close: (T0356)V29.CA and (T0356)V29.CB only 0 apart, marking (T0356)V29.CB as missing WARNING: atoms too close: (T0356)P31.CA and (T0356)P31.CB only 0 apart, marking (T0356)P31.CB as missing WARNING: atoms too close: (T0356)I38.CA and (T0356)I38.CB only 0 apart, marking (T0356)I38.CB as missing WARNING: atoms too close: (T0356)L51.CA and (T0356)L51.CB only 0 apart, marking (T0356)L51.CB as missing WARNING: atoms too close: (T0356)Y58.CA and (T0356)Y58.CB only 0 apart, marking (T0356)Y58.CB as missing WARNING: atoms too close: (T0356)L63.CA and (T0356)L63.CB only 0 apart, marking (T0356)L63.CB as missing WARNING: atoms too close: (T0356)C64.CA and (T0356)C64.CB only 0 apart, marking (T0356)C64.CB as missing WARNING: atoms too close: (T0356)T69.CA and (T0356)T69.CB only 0 apart, marking (T0356)T69.CB as missing WARNING: atoms too close: (T0356)M75.CA and (T0356)M75.CB only 0 apart, marking (T0356)M75.CB as missing WARNING: atoms too close: (T0356)K96.CA and (T0356)K96.CB only 0 apart, marking (T0356)K96.CB as missing WARNING: atoms too close: (T0356)D109.CA and (T0356)D109.CB only 0 apart, marking (T0356)D109.CB as missing WARNING: atoms too close: (T0356)K110.CA and (T0356)K110.CB only 0 apart, marking (T0356)K110.CB as missing WARNING: atoms too close: (T0356)P112.CA and (T0356)P112.CB only 0 apart, marking (T0356)P112.CB as missing WARNING: atoms too close: (T0356)Q113.CA and (T0356)Q113.CB only 0 apart, marking (T0356)Q113.CB as missing WARNING: atoms too close: (T0356)V117.CA and (T0356)V117.CB only 0 apart, marking (T0356)V117.CB as missing WARNING: atoms too close: (T0356)L118.CA and (T0356)L118.CB only 0 apart, marking (T0356)L118.CB as missing WARNING: atoms too close: (T0356)R124.CA and (T0356)R124.CB only 0 apart, marking (T0356)R124.CB as missing WARNING: atoms too close: (T0356)K133.CA and (T0356)K133.CB only 0 apart, marking (T0356)K133.CB as missing WARNING: atoms too close: (T0356)I147.CA and (T0356)I147.CB only 0 apart, marking (T0356)I147.CB as missing WARNING: atoms too close: (T0356)W151.CA and (T0356)W151.CB only 0 apart, marking (T0356)W151.CB as missing WARNING: atoms too close: (T0356)E153.CA and (T0356)E153.CB only 0 apart, marking (T0356)E153.CB as missing WARNING: atoms too close: (T0356)D154.CA and (T0356)D154.CB only 0 apart, marking (T0356)D154.CB as missing WARNING: atoms too close: (T0356)A156.CA and (T0356)A156.CB only 0 apart, marking (T0356)A156.CB as missing WARNING: atoms too close: (T0356)W161.CA and (T0356)W161.CB only 0 apart, marking (T0356)W161.CB as missing WARNING: atoms too close: (T0356)P169.CA and (T0356)P169.CB only 0 apart, marking (T0356)P169.CB as missing WARNING: atoms too close: (T0356)K171.CA and (T0356)K171.CB only 0 apart, marking (T0356)K171.CB as missing WARNING: atoms too close: (T0356)Q174.CA and (T0356)Q174.CB only 0 apart, marking (T0356)Q174.CB as missing WARNING: atoms too close: (T0356)I184.CA and (T0356)I184.CB only 0 apart, marking (T0356)I184.CB as missing WARNING: atoms too close: (T0356)N187.CA and (T0356)N187.CB only 0 apart, marking (T0356)N187.CB as missing WARNING: atoms too close: (T0356)R192.CA and (T0356)R192.CB only 0 apart, marking (T0356)R192.CB as missing WARNING: atoms too close: (T0356)L194.CA and (T0356)L194.CB only 0 apart, marking (T0356)L194.CB as missing WARNING: atoms too close: (T0356)H196.CA and (T0356)H196.CB only 0 apart, marking (T0356)H196.CB as missing WARNING: atoms too close: (T0356)R197.CA and (T0356)R197.CB only 0 apart, marking (T0356)R197.CB as missing WARNING: atoms too close: (T0356)E205.CA and (T0356)E205.CB only 0 apart, marking (T0356)E205.CB as missing WARNING: atoms too close: (T0356)C207.CA and (T0356)C207.CB only 0 apart, marking (T0356)C207.CB as missing WARNING: atoms too close: (T0356)H210.CA and (T0356)H210.CB only 0 apart, marking (T0356)H210.CB as missing WARNING: atoms too close: (T0356)S218.CA and (T0356)S218.CB only 0 apart, marking (T0356)S218.CB as missing WARNING: atoms too close: (T0356)V219.CA and (T0356)V219.CB only 0 apart, marking (T0356)V219.CB as missing WARNING: atoms too close: (T0356)A220.CA and (T0356)A220.CB only 0 apart, marking (T0356)A220.CB as missing WARNING: atoms too close: (T0356)K252.CA and (T0356)K252.CB only 0 apart, marking (T0356)K252.CB as missing WARNING: atoms too close: (T0356)D262.CA and (T0356)D262.CB only 0 apart, marking (T0356)D262.CB as missing WARNING: atoms too close: (T0356)L263.CA and (T0356)L263.CB only 0 apart, marking (T0356)L263.CB as missing WARNING: atoms too close: (T0356)V265.CA and (T0356)V265.CB only 0 apart, marking (T0356)V265.CB as missing WARNING: atoms too close: (T0356)P266.CA and (T0356)P266.CB only 0 apart, marking (T0356)P266.CB as missing WARNING: atoms too close: (T0356)L273.CA and (T0356)L273.CB only 0 apart, marking (T0356)L273.CB as missing WARNING: atoms too close: (T0356)E274.CA and (T0356)E274.CB only 0 apart, marking (T0356)E274.CB as missing WARNING: atoms too close: (T0356)Q279.CA and (T0356)Q279.CB only 0 apart, marking (T0356)Q279.CB as missing WARNING: atoms too close: (T0356)P287.CA and (T0356)P287.CB only 0 apart, marking (T0356)P287.CB as missing WARNING: atoms too close: (T0356)Y295.CA and (T0356)Y295.CB only 0 apart, marking (T0356)Y295.CB as missing WARNING: atoms too close: (T0356)D299.CA and (T0356)D299.CB only 0 apart, marking (T0356)D299.CB as missing WARNING: atoms too close: (T0356)D314.CA and (T0356)D314.CB only 0 apart, marking (T0356)D314.CB as missing WARNING: atoms too close: (T0356)I316.CA and (T0356)I316.CB only 0 apart, marking (T0356)I316.CB as missing WARNING: atoms too close: (T0356)R324.CA and (T0356)R324.CB only 0 apart, marking (T0356)R324.CB as missing WARNING: atoms too close: (T0356)P342.CA and (T0356)P342.CB only 0 apart, marking (T0356)P342.CB as missing WARNING: atoms too close: (T0356)Q345.CA and (T0356)Q345.CB only 0 apart, marking (T0356)Q345.CB as missing WARNING: atoms too close: (T0356)C361.CA and (T0356)C361.CB only 0 apart, marking (T0356)C361.CB as missing WARNING: atoms too close: (T0356)A366.CA and (T0356)A366.CB only 0 apart, marking (T0356)A366.CB as missing WARNING: atoms too close: (T0356)T369.CA and (T0356)T369.CB only 0 apart, marking (T0356)T369.CB as missing WARNING: atoms too close: (T0356)H377.CA and (T0356)H377.CB only 0 apart, marking (T0356)H377.CB as missing WARNING: atoms too close: (T0356)V385.CA and (T0356)V385.CB only 0 apart, marking (T0356)V385.CB as missing WARNING: atoms too close: (T0356)L389.CA and (T0356)L389.CB only 0 apart, marking (T0356)L389.CB as missing WARNING: atoms too close: (T0356)F397.CA and (T0356)F397.CB only 0 apart, marking (T0356)F397.CB as missing WARNING: atoms too close: (T0356)V400.CA and (T0356)V400.CB only 0 apart, marking (T0356)V400.CB as missing WARNING: atoms too close: (T0356)R408.CA and (T0356)R408.CB only 0 apart, marking (T0356)R408.CB as missing WARNING: atoms too close: (T0356)W410.CA and (T0356)W410.CB only 0 apart, marking (T0356)W410.CB as missing WARNING: atoms too close: (T0356)A416.CA and (T0356)A416.CB only 0 apart, marking (T0356)A416.CB as missing WARNING: atoms too close: (T0356)R425.CA and (T0356)R425.CB only 0 apart, marking (T0356)R425.CB as missing WARNING: atoms too close: (T0356)E431.CA and (T0356)E431.CB only 0 apart, marking (T0356)E431.CB as missing WARNING: atoms too close: (T0356)N432.CA and (T0356)N432.CB only 0 apart, marking (T0356)N432.CB as missing WARNING: atoms too close: (T0356)I435.CA and (T0356)I435.CB only 0 apart, marking (T0356)I435.CB as missing WARNING: atoms too close: (T0356)T456.CA and (T0356)T456.CB only 0 apart, marking (T0356)T456.CB as missing WARNING: atoms too close: (T0356)W467.CA and (T0356)W467.CB only 0 apart, marking (T0356)W467.CB as missing WARNING: atoms too close: (T0356)K473.CA and (T0356)K473.CB only 0 apart, marking (T0356)K473.CB as missing WARNING: atoms too close: (T0356)D474.CA and (T0356)D474.CB only 0 apart, marking (T0356)D474.CB as missing WARNING: atoms too close: (T0356)V478.CA and (T0356)V478.CB only 0 apart, marking (T0356)V478.CB as missing WARNING: atoms too close: (T0356)A479.CA and (T0356)A479.CB only 0 apart, marking (T0356)A479.CB as missing WARNING: atoms too close: (T0356)I481.CA and (T0356)I481.CB only 0 apart, marking (T0356)I481.CB as missing WARNING: atoms too close: (T0356)N493.CA and (T0356)N493.CB only 0 apart, marking (T0356)N493.CB as missing # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS4 # ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1 WARNING: atoms too close: (T0356)D11.CA and (T0356)D11.CB only 0 apart, marking (T0356)D11.CB as missing WARNING: atoms too close: (T0356)F12.CA and (T0356)F12.CB only 0 apart, marking (T0356)F12.CB as missing WARNING: atoms too close: (T0356)E17.CA and (T0356)E17.CB only 0 apart, marking (T0356)E17.CB as missing WARNING: atoms too close: (T0356)L51.CA and (T0356)L51.CB only 0 apart, marking (T0356)L51.CB as missing WARNING: atoms too close: (T0356)N54.CA and (T0356)N54.CB only 0 apart, marking (T0356)N54.CB as missing WARNING: atoms too close: (T0356)P70.CA and (T0356)P70.CB only 0 apart, marking (T0356)P70.CB as missing WARNING: atoms too close: (T0356)K96.CA and (T0356)K96.CB only 0 apart, marking (T0356)K96.CB as missing WARNING: atoms too close: (T0356)E99.CA and (T0356)E99.CB only 0 apart, marking (T0356)E99.CB as missing WARNING: atoms too close: (T0356)D109.CA and (T0356)D109.CB only 0 apart, marking (T0356)D109.CB as missing WARNING: atoms too close: (T0356)K110.CA and (T0356)K110.CB only 0 apart, marking (T0356)K110.CB as missing WARNING: atoms too close: (T0356)L111.CA and (T0356)L111.CB only 0 apart, marking (T0356)L111.CB as missing WARNING: atoms too close: (T0356)Q113.CA and (T0356)Q113.CB only 0 apart, marking (T0356)Q113.CB as missing WARNING: atoms too close: (T0356)F114.CA and (T0356)F114.CB only 0 apart, marking (T0356)F114.CB as missing WARNING: atoms too close: (T0356)R126.CA and (T0356)R126.CB only 0 apart, marking (T0356)R126.CB as missing WARNING: atoms too close: (T0356)A128.CA and (T0356)A128.CB only 0 apart, marking (T0356)A128.CB as missing WARNING: atoms too close: (T0356)P146.CA and (T0356)P146.CB only 0 apart, marking (T0356)P146.CB as missing WARNING: atoms too close: (T0356)T149.CA and (T0356)T149.CB only 0 apart, marking (T0356)T149.CB as missing WARNING: atoms too close: (T0356)L158.CA and (T0356)L158.CB only 0 apart, marking (T0356)L158.CB as missing WARNING: atoms too close: (T0356)T166.CA and (T0356)T166.CB only 0 apart, marking (T0356)T166.CB as missing WARNING: atoms too close: (T0356)P169.CA and (T0356)P169.CB only 0 apart, marking (T0356)P169.CB as missing WARNING: atoms too close: (T0356)H170.CA and (T0356)H170.CB only 0 apart, marking (T0356)H170.CB as missing WARNING: atoms too close: (T0356)Q174.CA and (T0356)Q174.CB only 0 apart, marking (T0356)Q174.CB as missing WARNING: atoms too close: (T0356)Q182.CA and (T0356)Q182.CB only 0 apart, marking (T0356)Q182.CB as missing WARNING: atoms too close: (T0356)I184.CA and (T0356)I184.CB only 0 apart, marking (T0356)I184.CB as missing WARNING: atoms too close: (T0356)K188.CA and (T0356)K188.CB only 0 apart, marking (T0356)K188.CB as missing WARNING: atoms too close: (T0356)L201.CA and (T0356)L201.CB only 0 apart, marking (T0356)L201.CB as missing WARNING: atoms too close: (T0356)Y203.CA and (T0356)Y203.CB only 0 apart, marking (T0356)Y203.CB as missing WARNING: atoms too close: (T0356)Q204.CA and (T0356)Q204.CB only 0 apart, marking (T0356)Q204.CB as missing WARNING: atoms too close: (T0356)C207.CA and (T0356)C207.CB only 0 apart, marking (T0356)C207.CB as missing WARNING: atoms too close: (T0356)P216.CA and (T0356)P216.CB only 0 apart, marking (T0356)P216.CB as missing WARNING: atoms too close: (T0356)S218.CA and (T0356)S218.CB only 0 apart, marking (T0356)S218.CB as missing WARNING: atoms too close: (T0356)V219.CA and (T0356)V219.CB only 0 apart, marking (T0356)V219.CB as missing WARNING: atoms too close: (T0356)L221.CA and (T0356)L221.CB only 0 apart, marking (T0356)L221.CB as missing WARNING: atoms too close: (T0356)A223.CA and (T0356)A223.CB only 0 apart, marking (T0356)A223.CB as missing WARNING: atoms too close: (T0356)I228.CA and (T0356)I228.CB only 0 apart, marking (T0356)I228.CB as missing WARNING: atoms too close: (T0356)A231.CA and (T0356)A231.CB only 0 apart, marking (T0356)A231.CB as missing WARNING: atoms too close: (T0356)V235.CA and (T0356)V235.CB only 0 apart, marking (T0356)V235.CB as missing WARNING: atoms too close: (T0356)F244.CA and (T0356)F244.CB only 0 apart, marking (T0356)F244.CB as missing WARNING: atoms too close: (T0356)A245.CA and (T0356)A245.CB only 0 apart, marking (T0356)A245.CB as missing WARNING: atoms too close: (T0356)R249.CA and (T0356)R249.CB only 0 apart, marking (T0356)R249.CB as missing WARNING: atoms too close: (T0356)E254.CA and (T0356)E254.CB only 0 apart, marking (T0356)E254.CB as missing WARNING: atoms too close: (T0356)V255.CA and (T0356)V255.CB only 0 apart, marking (T0356)V255.CB as missing WARNING: atoms too close: (T0356)I259.CA and (T0356)I259.CB only 0 apart, marking (T0356)I259.CB as missing WARNING: atoms too close: (T0356)D262.CA and (T0356)D262.CB only 0 apart, marking (T0356)D262.CB as missing WARNING: atoms too close: (T0356)V265.CA and (T0356)V265.CB only 0 apart, marking (T0356)V265.CB as missing WARNING: atoms too close: (T0356)I271.CA and (T0356)I271.CB only 0 apart, marking (T0356)I271.CB as missing WARNING: atoms too close: (T0356)E274.CA and (T0356)E274.CB only 0 apart, marking (T0356)E274.CB as missing WARNING: atoms too close: (T0356)T282.CA and (T0356)T282.CB only 0 apart, marking (T0356)T282.CB as missing WARNING: atoms too close: (T0356)T292.CA and (T0356)T292.CB only 0 apart, marking (T0356)T292.CB as missing WARNING: atoms too close: (T0356)Y295.CA and (T0356)Y295.CB only 0 apart, marking (T0356)Y295.CB as missing WARNING: atoms too close: (T0356)F304.CA and (T0356)F304.CB only 0 apart, marking (T0356)F304.CB as missing WARNING: atoms too close: (T0356)Q311.CA and (T0356)Q311.CB only 0 apart, marking (T0356)Q311.CB as missing WARNING: atoms too close: (T0356)R312.CA and (T0356)R312.CB only 0 apart, marking (T0356)R312.CB as missing WARNING: atoms too close: (T0356)Y317.CA and (T0356)Y317.CB only 0 apart, marking (T0356)Y317.CB as missing WARNING: atoms too close: (T0356)S319.CA and (T0356)S319.CB only 0 apart, marking (T0356)S319.CB as missing WARNING: atoms too close: (T0356)R324.CA and (T0356)R324.CB only 0 apart, marking (T0356)R324.CB as missing WARNING: atoms too close: (T0356)N337.CA and (T0356)N337.CB only 0 apart, marking (T0356)N337.CB as missing WARNING: atoms too close: (T0356)F340.CA and (T0356)F340.CB only 0 apart, marking (T0356)F340.CB as missing WARNING: atoms too close: (T0356)F348.CA and (T0356)F348.CB only 0 apart, marking (T0356)F348.CB as missing WARNING: atoms too close: (T0356)P358.CA and (T0356)P358.CB only 0 apart, marking (T0356)P358.CB as missing WARNING: atoms too close: (T0356)Y363.CA and (T0356)Y363.CB only 0 apart, marking (T0356)Y363.CB as missing WARNING: atoms too close: (T0356)H377.CA and (T0356)H377.CB only 0 apart, marking (T0356)H377.CB as missing WARNING: atoms too close: (T0356)R390.CA and (T0356)R390.CB only 0 apart, marking (T0356)R390.CB as missing WARNING: atoms too close: (T0356)R408.CA and (T0356)R408.CB only 0 apart, marking (T0356)R408.CB as missing WARNING: atoms too close: (T0356)D409.CA and (T0356)D409.CB only 0 apart, marking (T0356)D409.CB as missing WARNING: atoms too close: (T0356)V413.CA and (T0356)V413.CB only 0 apart, marking (T0356)V413.CB as missing WARNING: atoms too close: (T0356)D422.CA and (T0356)D422.CB only 0 apart, marking (T0356)D422.CB as missing WARNING: atoms too close: (T0356)T433.CA and (T0356)T433.CB only 0 apart, marking (T0356)T433.CB as missing WARNING: atoms too close: (T0356)P434.CA and (T0356)P434.CB only 0 apart, marking (T0356)P434.CB as missing WARNING: atoms too close: (T0356)I435.CA and (T0356)I435.CB only 0 apart, marking (T0356)I435.CB as missing WARNING: atoms too close: (T0356)T463.CA and (T0356)T463.CB only 0 apart, marking (T0356)T463.CB as missing WARNING: atoms too close: (T0356)W467.CA and (T0356)W467.CB only 0 apart, marking (T0356)W467.CB as missing WARNING: atoms too close: (T0356)P470.CA and (T0356)P470.CB only 0 apart, marking (T0356)P470.CB as missing WARNING: atoms too close: (T0356)P475.CA and (T0356)P475.CB only 0 apart, marking (T0356)P475.CB as missing WARNING: atoms too close: (T0356)W485.CA and (T0356)W485.CB only 0 apart, marking (T0356)W485.CB as missing WARNING: atoms too close: (T0356)N493.CA and (T0356)N493.CB only 0 apart, marking (T0356)N493.CB as missing WARNING: atoms too close: (T0356)S496.CA and (T0356)S496.CB only 0 apart, marking (T0356)S496.CB as missing # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS5 # ReadConformPDB reading from PDB file servers/SAM-T02_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL3 # ReadConformPDB reading from PDB file servers/SAM-T02_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL4 # ReadConformPDB reading from PDB file servers/SAM-T02_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL5 # ReadConformPDB reading from PDB file servers/SAM-T99_AL1.pdb.gz looking for model 1 Skipped atom 186, because occupancy 1 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 188, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 190, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 192, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL1 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1 # Found a chain break before 491 # copying to AlignedFragments data structure # naming current conformation SAM_T06_server_TS1 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS2 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS3 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS4 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS5 # ReadConformPDB reading from PDB file servers/SP3_TS1.pdb.gz looking for model 1 # Found a chain break before 418 # copying to AlignedFragments data structure # naming current conformation SP3_TS1 # ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1 # Found a chain break before 319 # copying to AlignedFragments data structure # naming current conformation SP3_TS2 # ReadConformPDB reading from PDB file servers/SP3_TS3.pdb.gz looking for model 1 # Found a chain break before 470 # copying to AlignedFragments data structure # naming current conformation SP3_TS3 # ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1 # Found a chain break before 427 # copying to AlignedFragments data structure # naming current conformation SP3_TS4 # ReadConformPDB reading from PDB file servers/SP3_TS5.pdb.gz looking for model 1 # Found a chain break before 466 # copying to AlignedFragments data structure # naming current conformation SP3_TS5 # ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1 # Found a chain break before 488 # copying to AlignedFragments data structure # naming current conformation SP4_TS1 # ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1 # Found a chain break before 420 # copying to AlignedFragments data structure # naming current conformation SP4_TS2 # ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1 # Found a chain break before 487 # copying to AlignedFragments data structure # naming current conformation SP4_TS3 # ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1 # Found a chain break before 471 # copying to AlignedFragments data structure # naming current conformation SP4_TS4 # ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1 # Found a chain break before 489 # copying to AlignedFragments data structure # naming current conformation SP4_TS5 # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # Found a chain break before 301 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS1 # ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1 # Found a chain break before 326 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS2 # ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1 # Found a chain break before 478 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS3 # ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1 # Found a chain break before 473 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS4 # ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1 # Found a chain break before 434 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS2 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS3 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS4 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_expm_TS1.pdb.gz looking for model 1 WARNING: atoms too close: (T0356)D314.CA and (T0356)V352.CA only 0.000 apart, marking (T0356)V352.CA as missing WARNING: atoms too close: (T0356)A315.CA and (T0356)D353.CA only 0.000 apart, marking (T0356)D353.CA as missing WARNING: atoms too close: (T0356)I316.CA and (T0356)F354.CA only 0.000 apart, marking (T0356)F354.CA as missing # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation UNI-EID_expm_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL2 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL3 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL4 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL5 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1 # Found a chain break before 475 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS1 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS2.pdb.gz looking for model 1 # Found a chain break before 496 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS2 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS3.pdb.gz looking for model 1 # Found a chain break before 493 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS3 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS4.pdb.gz looking for model 1 # Found a chain break before 490 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS4 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS5.pdb.gz looking for model 1 # Found a chain break before 469 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS5 # ReadConformPDB reading from PDB file servers/beautshot_TS1.pdb.gz looking for model 1 # Found a chain break before 504 # copying to AlignedFragments data structure # naming current conformation beautshot_TS1 # ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1 # Found a chain break before 503 # copying to AlignedFragments data structure # naming current conformation beautshotbase_TS1 # ReadConformPDB reading from PDB file servers/forecast-s_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation forecast-s_AL1 # ReadConformPDB reading from PDB file servers/forecast-s_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation forecast-s_AL2 # ReadConformPDB reading from PDB file servers/forecast-s_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation forecast-s_AL3 # ReadConformPDB reading from PDB file servers/forecast-s_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation forecast-s_AL4 # ReadConformPDB reading from PDB file servers/forecast-s_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation forecast-s_AL5 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # Found a chain break before 500 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS2.pdb.gz looking for model 1 # Found a chain break before 453 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS3.pdb.gz looking for model 1 # Found a chain break before 457 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS4.pdb.gz looking for model 1 # Found a chain break before 420 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS5.pdb.gz looking for model 1 # Found a chain break before 420 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS1.pdb.gz looking for model 1 WARNING: atoms too close: (T0356)E297.O and (T0356)V298.N only 0.000 apart, marking (T0356)V298.N as missing WARNING: atoms too close: (T0356)I435.O and (T0356)D436.N only 0.000 apart, marking (T0356)D436.N as missing # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS2.pdb.gz looking for model 1 # Found a chain break before 502 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS3.pdb.gz looking for model 1 # Found a chain break before 502 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS4.pdb.gz looking for model 1 WARNING: atoms too close: (T0356)K56.O and (T0356)G57.N only 0.000 apart, marking (T0356)G57.N as missing WARNING: atoms too close: (T0356)E487.O and (T0356)L488.N only 0.000 apart, marking (T0356)L488.N as missing # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS5.pdb.gz looking for model 1 # Found a chain break before 502 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS5 # ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation keasar-server_TS1 # ReadConformPDB reading from PDB file servers/keasar-server_TS2.pdb.gz looking for model 1 # naming current conformation keasar-server_TS2 # ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation keasar-server_TS3 # ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation keasar-server_TS5 # ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation mGen-3D_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation nFOLD_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation nFOLD_TS2 # ReadConformPDB reading from PDB file servers/nFOLD_TS3.pdb.gz looking for model 1 WARNING: atom 1 has residue number 1 < previous residue 470 in servers/nFOLD_TS3.pdb.gz # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation nFOLD_TS3 # ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation nFOLD_TS4 # ReadConformPDB reading from PDB file servers/nFOLD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation nFOLD_TS5 # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0356 can't currently be optimized by undertaker # naming current conformation shub_TS1 # command:Using radius: 8.0000 Metaserver mode NUMB_ALIGNS: 248 Adding 60827 constraints to all.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all.constraints maxweight: 48.0000 Optimizing... Probability sum: -921.7694, CN propb: -921.7694 weights: 0.2148 constraints: 3448 # command:Found ConstraintSet # PrintContacts align.constraints_meta01 Number of constraints in align.constraints 3448 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta01 Number of constraints in align.constraints.bonus 3448 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta01 Number of constraints in rejected.constraints 57379 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta01 Number of constraints in rejected.constraints.bonus 57379 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_meta01 Number of constraints in noncontact.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_meta01 Number of constraints in noncontact.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_meta01 Number of constraints in all.constraints 60827 # command: