# 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/T0386/ # command:# Making conformation for sequence T0386 numbered 1 through 299 Created new target T0386 from T0386.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0386/ # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0386/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0386/decoys/ # ReadConformPDB reading from PDB file T0386.chimera.pdb.gz looking for model 1 # choosing archetypes in rotamer library # Found a chain break before 293 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0386.chimera2.pdb.gz looking for model 1 # Found a chain break before 295 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0386.chimera3.pdb.gz looking for model 1 # Found a chain break before 293 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0386.chimera4.pdb.gz looking for model 1 # Found a chain break before 295 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0386.chimera5.pdb.gz looking for model 1 # Found a chain break before 296 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0386.chimera6.pdb.gz looking for model 1 # Found a chain break before 296 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0386.chimera7.pdb.gz looking for model 1 # Found a chain break before 295 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file chimera-4-1.pdb.gz looking for model 1 # Found a chain break before 295 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # 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 T0386 can't currently be optimized by undertaker # 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 T0386 can't currently be optimized by undertaker # 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 T0386 can't currently be optimized by undertaker # 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 T0386 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # 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 T0386 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 T0386 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 T0386 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 T0386 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 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 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 T0386 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS3 # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # Found a chain break before 265 # 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 255 # 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 262 # 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 253 # 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 294 # 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 289 # 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 296 # 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 294 # 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 239 # 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 273 # 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 235 # 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 263 # 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 298 # 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 288 # 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 298 # 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 # Found a chain break before 228 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS5 # ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS1 # ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 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 T0386 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 T0386 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 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS5 # ReadConformPDB reading from PDB file servers/CPHmodels_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation CPHmodels_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 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 T0386 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: atoms too close: (T0386)N235.C and (T0386)T236.N only 0 apart, marking (T0386)T236.N as missing WARNING: atoms too close: (T0386)T236.N and (T0386)T236.CA only 0 apart, marking (T0386)T236.CA as missing WARNING: atoms too close: (T0386)N235.C and (T0386)T236.CA only 0 apart, marking (T0386)T236.CA as missing WARNING: atoms too close: (T0386)T236.CA and (T0386)T236.CB only 0 apart, marking (T0386)T236.CB as missing WARNING: atoms too close: (T0386)T236.N and (T0386)T236.CB only 0 apart, marking (T0386)T236.CB as missing WARNING: atoms too close: (T0386)N235.C and (T0386)T236.CB only 0 apart, marking (T0386)T236.CB as missing WARNING: atoms too close: (T0386)T236.CB and (T0386)T236.CG2 only 0 apart, marking (T0386)T236.CG2 as missing WARNING: atoms too close: (T0386)T236.CA and (T0386)T236.CG2 only 0 apart, marking (T0386)T236.CG2 as missing WARNING: atoms too close: (T0386)T236.N and (T0386)T236.CG2 only 0 apart, marking (T0386)T236.CG2 as missing WARNING: atoms too close: (T0386)N235.C and (T0386)T236.CG2 only 0 apart, marking (T0386)T236.CG2 as missing WARNING: atoms too close: (T0386)T236.CG2 and (T0386)T236.OG1 only 0 apart, marking (T0386)T236.OG1 as missing WARNING: atoms too close: (T0386)T236.CB and (T0386)T236.OG1 only 0 apart, marking (T0386)T236.OG1 as missing WARNING: atoms too close: (T0386)T236.CA and (T0386)T236.OG1 only 0 apart, marking (T0386)T236.OG1 as missing WARNING: atoms too close: (T0386)T236.N and (T0386)T236.OG1 only 0 apart, marking (T0386)T236.OG1 as missing WARNING: atoms too close: (T0386)N235.C and (T0386)T236.OG1 only 0 apart, marking (T0386)T236.OG1 as missing WARNING: atoms too close: (T0386)T236.OG1 and (T0386)T236.O only 0 apart, marking (T0386)T236.O as missing WARNING: atoms too close: (T0386)T236.CG2 and (T0386)T236.O only 0 apart, marking (T0386)T236.O as missing WARNING: atoms too close: (T0386)T236.CB and (T0386)T236.O only 0 apart, marking (T0386)T236.O as missing WARNING: atoms too close: (T0386)T236.CA and (T0386)T236.O only 0 apart, marking (T0386)T236.O as missing WARNING: atoms too close: (T0386)T236.N and (T0386)T236.O only 0 apart, marking (T0386)T236.O as missing WARNING: atoms too close: (T0386)N235.C and (T0386)T236.O only 0 apart, marking (T0386)T236.O as missing WARNING: atoms too close: (T0386)T236.O and (T0386)T236.C only 0 apart, marking (T0386)T236.C as missing WARNING: atoms too close: (T0386)T236.OG1 and (T0386)T236.C only 0 apart, marking (T0386)T236.C as missing WARNING: atoms too close: (T0386)T236.CG2 and (T0386)T236.C only 0 apart, marking (T0386)T236.C as missing WARNING: atoms too close: (T0386)T236.CB and (T0386)T236.C only 0 apart, marking (T0386)T236.C as missing WARNING: atoms too close: (T0386)T236.CA and (T0386)T236.C only 0 apart, marking (T0386)T236.C as missing WARNING: atoms too close: (T0386)T236.N and (T0386)T236.C only 0 apart, marking (T0386)T236.C as missing WARNING: atoms too close: (T0386)N235.C and (T0386)T236.C only 0 apart, marking (T0386)T236.C as missing # WARNING: incomplete conformation T0386 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 T0386 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 T0386 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 T0386 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 T0386 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 T0386 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 T0386 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 T0386 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 # Found a chain break before 296 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS1 # ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 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 T0386 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 T0386 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 T0386 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 # Found a chain break before 291 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 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 T0386 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 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation FAMS_TS4 # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 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 265 # 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 252 # 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 294 # 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 188 # 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 112 # 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 T0386 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 T0386 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 T0386 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 T0386 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 T0386 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 T0386 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 T0386 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 T0386 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 T0386 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 T0386 can't currently be optimized by undertaker # naming current conformation FORTE2_AL5 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS1.pdb.gz looking for model 1 # Found a chain break before 269 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS1 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS2.pdb.gz looking for model 1 # Found a chain break before 283 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS2 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS3.pdb.gz looking for model 1 # Found a chain break before 274 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS3 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS4.pdb.gz looking for model 1 # Found a chain break before 224 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS4 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS5.pdb.gz looking for model 1 # Found a chain break before 248 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS5 # ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # Found a chain break before 268 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS2 # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # Found a chain break before 202 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS3 # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # Found a chain break before 291 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS4 # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS5 # ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1 Skipped atom 22, because occupancy 1 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 24, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 26, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 28, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 38, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 40, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 42, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 44, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 182, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 184, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 186, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 188, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 214, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 216, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 218, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 220, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 250, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 252, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 254, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 256, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 318, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 320, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 322, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 324, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 338, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 339, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 341, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 342, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 344, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 345, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 347, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 348, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 418, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 420, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 422, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 424, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 606, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 608, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 610, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 612, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 706, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 708, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 710, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 712, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz # WARNING: incomplete conformation T0386 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 T0386 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL2 # ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL3 # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL4 # ReadConformPDB reading from PDB file servers/FUGUE_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 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 295 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS1 # ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1 # Found a chain break before 292 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS2 # ReadConformPDB reading from PDB file servers/FUNCTION_TS3.pdb.gz looking for model 1 # Found a chain break before 291 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS3 # ReadConformPDB reading from PDB file servers/FUNCTION_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 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 # Found a chain break before 291 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # ReadConformPDB reading from PDB file servers/Frankenstein_TS1.pdb.gz looking for model 1 # Found a chain break before 239 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS1 # ReadConformPDB reading from PDB file servers/Frankenstein_TS2.pdb.gz looking for model 1 # Found a chain break before 264 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS2 # ReadConformPDB reading from PDB file servers/Frankenstein_TS3.pdb.gz looking for model 1 # Found a chain break before 236 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS3 # ReadConformPDB reading from PDB file servers/Frankenstein_TS4.pdb.gz looking for model 1 # Found a chain break before 234 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS4 # ReadConformPDB reading from PDB file servers/Frankenstein_TS5.pdb.gz looking for model 1 # Found a chain break before 292 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS5 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 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 T0386 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 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS3 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS4 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 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 # Found a chain break before 203 # copying to AlignedFragments data structure # naming current conformation HHpred1_TS1 # ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1 # Found a chain break before 236 # copying to AlignedFragments data structure # naming current conformation HHpred2_TS1 # ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1 # Found a chain break before 236 # copying to AlignedFragments data structure # naming current conformation HHpred3_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 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 T0386 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 T0386 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 T0386 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 T0386 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 T0386 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 T0386 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 T0386 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 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation LOOPP_TS4 # ReadConformPDB reading from PDB file servers/LOOPP_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 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 # Found a chain break before 274 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS2.pdb.gz looking for model 1 # Found a chain break before 297 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS3.pdb.gz looking for model 1 # Found a chain break before 212 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS4.pdb.gz looking for model 1 # Found a chain break before 138 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS5.pdb.gz looking for model 1 # Found a chain break before 249 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS5 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # Found a chain break before 285 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS2.pdb.gz looking for model 1 # Found a chain break before 297 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS3.pdb.gz looking for model 1 # Found a chain break before 172 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS4.pdb.gz looking for model 1 # Found a chain break before 160 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS5.pdb.gz looking for model 1 # Found a chain break before 273 # copying to AlignedFragments data structure # 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 298 # 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 279 # 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 298 # 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 293 # 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 297 # 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 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation NN_PUT_lab_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation POMYSL_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 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 T0386 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 T0386 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 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation POMYSL_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1 # Found a chain break before 223 # copying to AlignedFragments data structure # naming current conformation PROTINFO-AB_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1 # Found a chain break before 221 # copying to AlignedFragments data structure # naming current conformation PROTINFO-AB_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1 # Found a chain break before 223 # copying to AlignedFragments data structure # naming current conformation PROTINFO-AB_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1 # Found a chain break before 207 # copying to AlignedFragments data structure # naming current conformation PROTINFO-AB_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1 # Found a chain break before 251 # copying to AlignedFragments data structure # naming current conformation PROTINFO-AB_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 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 T0386 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 T0386 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 # Found a chain break before 221 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # Found a chain break before 226 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS5 # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 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 T0386 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 T0386 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 T0386 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 T0386 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 T0386 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 # Found a chain break before 296 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS2.pdb.gz looking for model 1 # Found a chain break before 296 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS2 # ReadConformPDB reading from PDB file servers/Phyre-2_TS3.pdb.gz looking for model 1 # Found a chain break before 296 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS3 # ReadConformPDB reading from PDB file servers/Phyre-2_TS4.pdb.gz looking for model 1 # Found a chain break before 296 # copying to AlignedFragments data structure # 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 296 # 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 # Found a chain break before 222 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS1 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # Found a chain break before 183 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS2 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # Found a chain break before 217 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS3 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 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 T0386 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 246 # 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 249 # 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 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # 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 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # 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 132 # 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 295 # 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 283 # 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 275 # 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 296 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS4 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS5.pdb.gz looking for model 1 # naming current conformation RAPTORESS_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR_TS1.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1 # Found a chain break before 218 # 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 216 # 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 216 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR_TS5.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS5 # ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1 # Found a chain break before 183 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS1 # ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1 # Found a chain break before 221 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS2 # ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1 # Found a chain break before 222 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS3 # ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1 # Found a chain break before 222 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS4 # ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1 # Found a chain break before 217 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS5 # ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1 WARNING: atoms too close: (T0386)P2.CA and (T0386)P2.CB only 0.000 apart, marking (T0386)P2.CB as missing WARNING: atoms too close: (T0386)K5.CA and (T0386)K5.CB only 0.000 apart, marking (T0386)K5.CB as missing WARNING: atoms too close: (T0386)T11.CA and (T0386)T11.CB only 0.000 apart, marking (T0386)T11.CB as missing WARNING: atoms too close: (T0386)N23.CA and (T0386)N23.CB only 0.000 apart, marking (T0386)N23.CB as missing WARNING: atoms too close: (T0386)V245.CA and (T0386)V245.CB only 0.000 apart, marking (T0386)V245.CB as missing WARNING: atoms too close: (T0386)A248.CA and (T0386)A248.CB only 0.000 apart, marking (T0386)A248.CB as missing WARNING: atoms too close: (T0386)T253.CA and (T0386)T253.CB only 0.000 apart, marking (T0386)T253.CB as missing WARNING: atoms too close: (T0386)T257.CA and (T0386)T257.CB only 0.000 apart, marking (T0386)T257.CB as missing WARNING: atoms too close: (T0386)V270.CA and (T0386)V270.CB only 0.000 apart, marking (T0386)V270.CB as missing # WARNING: incomplete conformation T0386 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: (T0386)P2.CA and (T0386)P2.CB only 0.000 apart, marking (T0386)P2.CB as missing WARNING: atoms too close: (T0386)K7.CA and (T0386)K7.CB only 0.000 apart, marking (T0386)K7.CB as missing WARNING: atoms too close: (T0386)T11.CA and (T0386)T11.CB only 0.000 apart, marking (T0386)T11.CB as missing WARNING: atoms too close: (T0386)P244.CA and (T0386)P244.CB only 0.000 apart, marking (T0386)P244.CB as missing WARNING: atoms too close: (T0386)A248.CA and (T0386)A248.CB only 0.000 apart, marking (T0386)A248.CB as missing WARNING: atoms too close: (T0386)T253.CA and (T0386)T253.CB only 0.000 apart, marking (T0386)T253.CB as missing WARNING: atoms too close: (T0386)T257.CA and (T0386)T257.CB only 0.000 apart, marking (T0386)T257.CB as missing WARNING: atoms too close: (T0386)A267.CA and (T0386)A267.CB only 0.000 apart, marking (T0386)A267.CB as missing WARNING: atoms too close: (T0386)V270.CA and (T0386)V270.CB only 0.000 apart, marking (T0386)V270.CB as missing WARNING: atoms too close: (T0386)P284.CA and (T0386)P284.CB only 0.000 apart, marking (T0386)P284.CB as missing # WARNING: incomplete conformation T0386 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: (T0386)M1.CA and (T0386)M1.CB only 0.000 apart, marking (T0386)M1.CB as missing WARNING: atoms too close: (T0386)T11.CA and (T0386)T11.CB only 0.000 apart, marking (T0386)T11.CB as missing WARNING: atoms too close: (T0386)P16.CA and (T0386)P16.CB only 0.000 apart, marking (T0386)P16.CB as missing WARNING: atoms too close: (T0386)H18.CA and (T0386)H18.CB only 0.000 apart, marking (T0386)H18.CB as missing WARNING: atoms too close: (T0386)N23.CA and (T0386)N23.CB only 0.000 apart, marking (T0386)N23.CB as missing WARNING: atoms too close: (T0386)V245.CA and (T0386)V245.CB only 0.000 apart, marking (T0386)V245.CB as missing WARNING: atoms too close: (T0386)A248.CA and (T0386)A248.CB only 0.000 apart, marking (T0386)A248.CB as missing WARNING: atoms too close: (T0386)A261.CA and (T0386)A261.CB only 0.000 apart, marking (T0386)A261.CB as missing WARNING: atoms too close: (T0386)V270.CA and (T0386)V270.CB only 0.000 apart, marking (T0386)V270.CB as missing # WARNING: incomplete conformation T0386 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: (T0386)P2.CA and (T0386)P2.CB only 0.000 apart, marking (T0386)P2.CB as missing WARNING: atoms too close: (T0386)A4.CA and (T0386)A4.CB only 0.000 apart, marking (T0386)A4.CB as missing WARNING: atoms too close: (T0386)K7.CA and (T0386)K7.CB only 0.000 apart, marking (T0386)K7.CB as missing WARNING: atoms too close: (T0386)P16.CA and (T0386)P16.CB only 0.000 apart, marking (T0386)P16.CB as missing WARNING: atoms too close: (T0386)H17.CA and (T0386)H17.CB only 0.000 apart, marking (T0386)H17.CB as missing WARNING: atoms too close: (T0386)Y19.CA and (T0386)Y19.CB only 0.000 apart, marking (T0386)Y19.CB as missing WARNING: atoms too close: (T0386)Y21.CA and (T0386)Y21.CB only 0.000 apart, marking (T0386)Y21.CB as missing WARNING: atoms too close: (T0386)T24.CA and (T0386)T24.CB only 0.000 apart, marking (T0386)T24.CB as missing WARNING: atoms too close: (T0386)N29.CA and (T0386)N29.CB only 0.000 apart, marking (T0386)N29.CB as missing WARNING: atoms too close: (T0386)T232.CA and (T0386)T232.CB only 0.000 apart, marking (T0386)T232.CB as missing WARNING: atoms too close: (T0386)P244.CA and (T0386)P244.CB only 0.000 apart, marking (T0386)P244.CB as missing WARNING: atoms too close: (T0386)T257.CA and (T0386)T257.CB only 0.000 apart, marking (T0386)T257.CB as missing WARNING: atoms too close: (T0386)T297.CA and (T0386)T297.CB only 0.000 apart, marking (T0386)T297.CB as missing # WARNING: incomplete conformation T0386 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: (T0386)K5.CA and (T0386)K5.CB only 0.000 apart, marking (T0386)K5.CB as missing WARNING: atoms too close: (T0386)K7.CA and (T0386)K7.CB only 0.000 apart, marking (T0386)K7.CB as missing WARNING: atoms too close: (T0386)P16.CA and (T0386)P16.CB only 0.000 apart, marking (T0386)P16.CB as missing WARNING: atoms too close: (T0386)V20.CA and (T0386)V20.CB only 0.000 apart, marking (T0386)V20.CB as missing WARNING: atoms too close: (T0386)Y21.CA and (T0386)Y21.CB only 0.000 apart, marking (T0386)Y21.CB as missing WARNING: atoms too close: (T0386)P22.CA and (T0386)P22.CB only 0.000 apart, marking (T0386)P22.CB as missing WARNING: atoms too close: (T0386)P244.CA and (T0386)P244.CB only 0.000 apart, marking (T0386)P244.CB as missing WARNING: atoms too close: (T0386)A248.CA and (T0386)A248.CB only 0.000 apart, marking (T0386)A248.CB as missing WARNING: atoms too close: (T0386)A261.CA and (T0386)A261.CB only 0.000 apart, marking (T0386)A261.CB as missing # WARNING: incomplete conformation T0386 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_AL1.pdb.gz looking for model 1 Skipped atom 10, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 12, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 14, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 16, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 154, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 156, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 158, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 160, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 186, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 188, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 190, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 192, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 222, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 224, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 226, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 228, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 294, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 296, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 298, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 300, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 318, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 319, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 321, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 322, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 324, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 325, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 327, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 328, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 402, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 404, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 406, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 408, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 598, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 600, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 602, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 604, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL1 # ReadConformPDB reading from PDB file servers/SAM-T02_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL2 # ReadConformPDB reading from PDB file servers/SAM-T02_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 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 T0386 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 T0386 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 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL1 # ReadConformPDB reading from PDB file servers/SAM-T99_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL2 # ReadConformPDB reading from PDB file servers/SAM-T99_AL3.pdb.gz looking for model 1 Skipped atom 138, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 140, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 142, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 144, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 170, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 172, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 174, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 176, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 206, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 208, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 210, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 212, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 278, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 280, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 282, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 284, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 302, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 303, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 305, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 306, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 308, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 309, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 311, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 312, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 386, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 388, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 390, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 392, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 578, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 580, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 582, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 584, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 678, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 680, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 682, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 684, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL3 # ReadConformPDB reading from PDB file servers/SAM-T99_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL4 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1 # Found a chain break before 295 # 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 T0386 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 T0386 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 T0386 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 T0386 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 249 # 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 219 # 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 95 # 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 291 # 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 188 # 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 183 # 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 250 # 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 282 # 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 100 # copying to AlignedFragments data structure # naming current conformation SP4_TS4 # ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1 # naming current conformation SP4_TS5 # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # Found a chain break before 197 # 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 271 # 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 257 # 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 265 # 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 275 # 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 T0386 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 T0386 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS2 # ReadConformPDB reading from PDB file servers/UNI-EID_expm_TS1.pdb.gz looking for model 1 WARNING: atoms too close: (T0386)T129.CA and (T0386)N135.CA only 0.000 apart, marking (T0386)N135.CA as missing WARNING: atoms too close: (T0386)L130.CA and (T0386)L136.CA only 0.000 apart, marking (T0386)L136.CA as missing WARNING: atoms too close: (T0386)L130.C and (T0386)L136.C only 0.000 apart, marking (T0386)L136.C as missing WARNING: atoms too close: (T0386)A131.CA and (T0386)Q137.CA only 0.000 apart, marking (T0386)Q137.CA as missing WARNING: atoms too close: (T0386)E132.CA and (T0386)E142.CA only 0.000 apart, marking (T0386)E142.CA as missing WARNING: atoms too close: (T0386)K133.CA and (T0386)E143.CA only 0.000 apart, marking (T0386)E143.CA as missing # WARNING: incomplete conformation T0386 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 Skipped atom 26, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 28, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 30, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 32, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 42, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 44, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 46, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 48, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 186, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 188, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 190, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 192, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 218, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 220, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 222, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 224, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 254, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 256, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 258, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 260, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 326, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 328, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 330, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 332, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 350, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 351, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 353, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 354, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 356, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 357, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 359, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 360, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 434, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 436, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 438, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 440, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 626, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 628, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 630, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 632, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz # WARNING: incomplete conformation T0386 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 T0386 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL2 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1 # Found a chain break before 297 # 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 292 # 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 283 # 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 281 # 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 296 # 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 298 # copying to AlignedFragments data structure # naming current conformation beautshot_TS1 # ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation beautshotbase_TS1 # ReadConformPDB reading from PDB file servers/forecast-s_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 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 T0386 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 T0386 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 T0386 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 T0386 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 177 # 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 257 # 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 211 # 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 258 # 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 177 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 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 T0386 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 T0386 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 T0386 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 T0386 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 T0386 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 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation keasar-server_TS2 # ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation keasar-server_TS3 # ReadConformPDB reading from PDB file servers/keasar-server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation keasar-server_TS4 # ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 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 T0386 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: atom 1 has residue number 1 < previous residue 252 in servers/nFOLD_TS1.pdb.gz # WARNING: incomplete conformation T0386 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 T0386 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 259 in servers/nFOLD_TS3.pdb.gz # WARNING: incomplete conformation T0386 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 T0386 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: atom 1 has residue number 1 < previous residue 252 in servers/nFOLD_TS5.pdb.gz # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation nFOLD_TS5 # ReadConformPDB reading from PDB file servers/panther2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation panther2_TS1 # ReadConformPDB reading from PDB file servers/panther3_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation panther3_TS1 # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation shub_TS1 # command:Using radius: 8.0000 Metaserver mode NUMB_ALIGNS: 263 Adding 21783 constraints to all.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all.constraints maxweight: 127.0000 Optimizing... Probability sum: -502.3602, CN propb: -502.3602 weights: 0.2550 constraints: 580 # command:Found ConstraintSet # PrintContacts align.constraints_meta01 Number of constraints in align.constraints 580 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta01 Number of constraints in align.constraints.bonus 580 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta01 Number of constraints in rejected.constraints 21203 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta01 Number of constraints in rejected.constraints.bonus 21203 # 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 21783 # command: