# 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/T0347/
# command:# Making conformation for sequence T0347 numbered 1 through 205
Created new target T0347 from T0347.a2m
# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0347/
# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0347/
# command:# reading script from file servers-clean.under
# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0347/decoys/
# ReadConformPDB reading from PDB file T0347.chimera-renum.pdb.gz looking for model 1
# choosing archetypes in rotamer library
# Found a chain break before 200
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0347.chimera2-renum.pdb.gz looking for model 1
# Found a chain break before 200
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0347.chimera3.pdb.gz looking for model 1
WARNING: atom 1 has residue number 1  < previous residue 94  in T0347.chimera3.pdb.gz
# Found a chain break before 203
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0347.chimera3_renum.pdb.gz looking for model 1
# Found a chain break before 203
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0347.chimera4.pdb.gz looking for model 1
WARNING: atom 1 has residue number 1  < previous residue 94  in T0347.chimera4.pdb.gz
# Found a chain break before 200
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0347.chimera4_renum.pdb.gz looking for model 1
# Found a chain break before 200
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file chimera-1-2.pdb.gz looking for model 1
# Found a chain break before 203
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0347 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 T0347 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 T0347 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 T0347 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 T0347 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 T0347 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 T0347 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 T0347 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 T0347 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 T0347 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 T0347 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 T0347 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 T0347 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 T0347 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_TS4
# ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1
# Found a chain break before 166
# 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 130
# 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 189
# 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 59
# 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 199
# 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 166
# 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 189
# 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 165
# 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 178
# 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 168
# 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 193
# 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 204
# 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 204
# 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 204
# 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
# 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 190
# copying to AlignedFragments data structure
# naming current conformation CIRCLE_TS1
# ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1
# Found a chain break before 203
# copying to AlignedFragments data structure
# naming current conformation CIRCLE_TS2
# ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0347 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 T0347 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 T0347 can't currently be optimized by undertaker
# naming current conformation CIRCLE_TS5
# ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0347 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 T0347 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 T0347 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 T0347 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 T0347 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 T0347 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 T0347 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 T0347 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 T0347 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 T0347 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 T0347 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 T0347 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 T0347 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 T0347 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 T0347 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 190
# 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 T0347 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 T0347 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 T0347 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 T0347 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 181
# copying to AlignedFragments data structure
# naming current conformation FOLDpro_TS1
# ReadConformPDB reading from PDB file servers/FOLDpro_TS2.pdb.gz looking for model 1
# naming current conformation FOLDpro_TS2
# ReadConformPDB reading from PDB file servers/FOLDpro_TS3.pdb.gz looking for model 1
# Found a chain break before 142
# 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 157
# 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 134
# 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 T0347 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 T0347 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 T0347 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 T0347 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 T0347 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FORTE1_AL5
# ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0347 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 T0347 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 T0347 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 T0347 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FORTE2_AL4
# ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0347 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 204
# 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 204
# 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 204
# 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 204
# 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 156
# 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 T0347 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 157
# 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 144
# copying to AlignedFragments data structure
# naming current conformation FUGMOD_TS3
# ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0347 can't currently be optimized by undertaker
# naming current conformation FUGMOD_TS4
# ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0347 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 174, because occupancy 1 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz
Skipped atom 176, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz
Skipped atom 178, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz
Skipped atom 180, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz
Skipped atom 262, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz
Skipped atom 264, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz
Skipped atom 266, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz
Skipped atom 268, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz
Skipped atom 286, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz
Skipped atom 288, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz
Skipped atom 290, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz
Skipped atom 292, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz
# WARNING: incomplete conformation T0347 can't currently be optimized by undertaker
# naming current conformation FUGUE_AL1
# ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0347 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 T0347 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 T0347 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
# WARNING: incomplete conformation T0347 can't currently be optimized by undertaker
# naming current conformation FUNCTION_TS1
# ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0347 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 T0347 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
# Found a chain break before 202
# copying to AlignedFragments data structure
# naming current conformation FUNCTION_TS4
# ReadConformPDB reading from PDB file servers/FUNCTION_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0347 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
# Found a chain break before 50
# copying to AlignedFragments data structure
# naming current conformation GeneSilicoMetaServer_TS1
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1
# Found a chain break before 134
# copying to AlignedFragments data structure
# naming current conformation GeneSilicoMetaServer_TS2
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1
# naming current conformation GeneSilicoMetaServer_TS3
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1
# Found a chain break before 5
# 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 T0347 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 T0347 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
# Found a chain break before 175
# 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 175
# 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 T0347 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 T0347 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 T0347 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 T0347 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 T0347 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 T0347 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 T0347 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 T0347 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 T0347 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 T0347 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 135
# 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 16
# 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 147
# 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
# 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 152
# 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 135
# 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 181
# 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 65
# 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 185
# 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 169
# 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 198
# 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 202
# 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 204
# 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 198
# 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 201
# 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 135
# 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 181
# copying to AlignedFragments data structure
# naming current conformation POMYSL_TS1
# ReadConformPDB reading from PDB file servers/POMYSL_TS2.pdb.gz looking for model 1
# Found a chain break before 192
# copying to AlignedFragments data structure
# naming current conformation POMYSL_TS2
# ReadConformPDB reading from PDB file servers/POMYSL_TS3.pdb.gz looking for model 1
# Found a chain break before 170
# copying to AlignedFragments data structure
# naming current conformation POMYSL_TS3
# ReadConformPDB reading from PDB file servers/POMYSL_TS4.pdb.gz looking for model 1
# Found a chain break before 203
# copying to AlignedFragments data structure
# naming current conformation POMYSL_TS4
# ReadConformPDB reading from PDB file servers/POMYSL_TS5.pdb.gz looking for model 1
# Found a chain break before 190
# copying to AlignedFragments data structure
# naming current conformation POMYSL_TS5
# ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1
# naming current conformation PROTINFO-AB_TS1
# ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1
# naming current conformation PROTINFO-AB_TS2
# ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1
# naming current conformation PROTINFO-AB_TS3
# ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1
# naming current conformation PROTINFO-AB_TS4
# ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1
# naming current conformation PROTINFO-AB_TS5
# ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1
# Found a chain break before 82
# copying to AlignedFragments data structure
# naming current conformation PROTINFO_TS1
# ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1
# Found a chain break before 202
# copying to AlignedFragments data structure
# naming current conformation PROTINFO_TS2
# ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1
# Found a chain break before 161
# copying to AlignedFragments data structure
# naming current conformation PROTINFO_TS3
# ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1
# Found a chain break before 65
# 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 161
# 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 T0347 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation Pcons6_TS1
# ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0347 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 T0347 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 T0347 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 T0347 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 T0347 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 202
# 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 118
# 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 173
# 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 197
# 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
# WARNING: incomplete conformation T0347 can't currently be optimized by undertaker
# 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 157
# 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 177
# 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 129
# copying to AlignedFragments data structure
# naming current conformation Pmodeller6_TS3
# ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1
# Found a chain break before 153
# copying to AlignedFragments data structure
# naming current conformation Pmodeller6_TS4
# ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0347 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 134
# 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 111
# 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
# 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 173
# 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 84
# 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 134
# 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 58
# 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 154
# 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 203
# 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 202
# copying to AlignedFragments data structure
# 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 135
# 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 153
# 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 118
# 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 137
# copying to AlignedFragments data structure
# naming current conformation RAPTOR_TS5
# ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1
# Found a chain break before 177
# copying to AlignedFragments data structure
# naming current conformation ROBETTA_TS1
# ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1
# naming current conformation ROBETTA_TS2
# ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1
# Found a chain break before 177
# copying to AlignedFragments data structure
# naming current conformation ROBETTA_TS3
# ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1
# naming current conformation ROBETTA_TS4
# ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1
# Found a chain break before 153
# 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: (T0347)R8.CA and (T0347)R8.CB only 0.000 apart, marking (T0347)R8.CB as missing
WARNING: atoms too close: (T0347)A13.CA and (T0347)A13.CB only 0.000 apart, marking (T0347)A13.CB as missing
WARNING: atoms too close: (T0347)K16.CA and (T0347)K16.CB only 0.000 apart, marking (T0347)K16.CB as missing
WARNING: atoms too close: (T0347)R18.CA and (T0347)R18.CB only 0.000 apart, marking (T0347)R18.CB as missing
WARNING: atoms too close: (T0347)E28.CA and (T0347)E28.CB only 0.000 apart, marking (T0347)E28.CB as missing
WARNING: atoms too close: (T0347)E30.CA and (T0347)E30.CB only 0.000 apart, marking (T0347)E30.CB as missing
WARNING: atoms too close: (T0347)K32.CA and (T0347)K32.CB only 0.000 apart, marking (T0347)K32.CB as missing
WARNING: atoms too close: (T0347)K34.CA and (T0347)K34.CB only 0.000 apart, marking (T0347)K34.CB as missing
WARNING: atoms too close: (T0347)I52.CA and (T0347)I52.CB only 0.000 apart, marking (T0347)I52.CB as missing
WARNING: atoms too close: (T0347)V55.CA and (T0347)V55.CB only 0.000 apart, marking (T0347)V55.CB as missing
WARNING: atoms too close: (T0347)V56.CA and (T0347)V56.CB only 0.000 apart, marking (T0347)V56.CB as missing
WARNING: atoms too close: (T0347)R62.CA and (T0347)R62.CB only 0.000 apart, marking (T0347)R62.CB as missing
WARNING: atoms too close: (T0347)L73.CA and (T0347)L73.CB only 0.000 apart, marking (T0347)L73.CB as missing
WARNING: atoms too close: (T0347)V80.CA and (T0347)V80.CB only 0.000 apart, marking (T0347)V80.CB as missing
WARNING: atoms too close: (T0347)E87.CA and (T0347)E87.CB only 0.000 apart, marking (T0347)E87.CB as missing
WARNING: atoms too close: (T0347)V88.CA and (T0347)V88.CB only 0.000 apart, marking (T0347)V88.CB as missing
WARNING: atoms too close: (T0347)F99.CA and (T0347)F99.CB only 0.000 apart, marking (T0347)F99.CB as missing
WARNING: atoms too close: (T0347)V102.CA and (T0347)V102.CB only 0.000 apart, marking (T0347)V102.CB as missing
WARNING: atoms too close: (T0347)P111.CA and (T0347)P111.CB only 0.000 apart, marking (T0347)P111.CB as missing
WARNING: atoms too close: (T0347)A114.CA and (T0347)A114.CB only 0.000 apart, marking (T0347)A114.CB as missing
WARNING: atoms too close: (T0347)R118.CA and (T0347)R118.CB only 0.000 apart, marking (T0347)R118.CB as missing
WARNING: atoms too close: (T0347)I124.CA and (T0347)I124.CB only 0.000 apart, marking (T0347)I124.CB as missing
WARNING: atoms too close: (T0347)P125.CA and (T0347)P125.CB only 0.000 apart, marking (T0347)P125.CB as missing
WARNING: atoms too close: (T0347)D130.CA and (T0347)D130.CB only 0.000 apart, marking (T0347)D130.CB as missing
WARNING: atoms too close: (T0347)E132.CA and (T0347)E132.CB only 0.000 apart, marking (T0347)E132.CB as missing
WARNING: atoms too close: (T0347)D134.CA and (T0347)D134.CB only 0.000 apart, marking (T0347)D134.CB as missing
WARNING: atoms too close: (T0347)R137.CA and (T0347)R137.CB only 0.000 apart, marking (T0347)R137.CB as missing
WARNING: atoms too close: (T0347)L143.CA and (T0347)L143.CB only 0.000 apart, marking (T0347)L143.CB as missing
WARNING: atoms too close: (T0347)R144.CA and (T0347)R144.CB only 0.000 apart, marking (T0347)R144.CB as missing
WARNING: atoms too close: (T0347)A146.CA and (T0347)A146.CB only 0.000 apart, marking (T0347)A146.CB as missing
WARNING: atoms too close: (T0347)P155.CA and (T0347)P155.CB only 0.000 apart, marking (T0347)P155.CB as missing
WARNING: atoms too close: (T0347)F156.CA and (T0347)F156.CB only 0.000 apart, marking (T0347)F156.CB as missing
WARNING: atoms too close: (T0347)S157.CA and (T0347)S157.CB only 0.000 apart, marking (T0347)S157.CB as missing
WARNING: atoms too close: (T0347)D163.CA and (T0347)D163.CB only 0.000 apart, marking (T0347)D163.CB as missing
WARNING: atoms too close: (T0347)F164.CA and (T0347)F164.CB only 0.000 apart, marking (T0347)F164.CB as missing
WARNING: atoms too close: (T0347)R166.CA and (T0347)R166.CB only 0.000 apart, marking (T0347)R166.CB as missing
WARNING: atoms too close: (T0347)F178.CA and (T0347)F178.CB only 0.000 apart, marking (T0347)F178.CB as missing
WARNING: atoms too close: (T0347)R192.CA and (T0347)R192.CB only 0.000 apart, marking (T0347)R192.CB as missing
WARNING: atoms too close: (T0347)E193.CA and (T0347)E193.CB only 0.000 apart, marking (T0347)E193.CB as missing
WARNING: atoms too close: (T0347)A194.CA and (T0347)A194.CB only 0.000 apart, marking (T0347)A194.CB as missing
WARNING: atoms too close: (T0347)W200.CA and (T0347)W200.CB only 0.000 apart, marking (T0347)W200.CB as missing
# WARNING: incomplete conformation T0347 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: (T0347)E6.CA and (T0347)E6.CB only 0.000 apart, marking (T0347)E6.CB as missing
WARNING: atoms too close: (T0347)A13.CA and (T0347)A13.CB only 0.000 apart, marking (T0347)A13.CB as missing
WARNING: atoms too close: (T0347)L17.CA and (T0347)L17.CB only 0.000 apart, marking (T0347)L17.CB as missing
WARNING: atoms too close: (T0347)T20.CA and (T0347)T20.CB only 0.000 apart, marking (T0347)T20.CB as missing
WARNING: atoms too close: (T0347)E28.CA and (T0347)E28.CB only 0.000 apart, marking (T0347)E28.CB as missing
WARNING: atoms too close: (T0347)W36.CA and (T0347)W36.CB only 0.000 apart, marking (T0347)W36.CB as missing
WARNING: atoms too close: (T0347)V80.CA and (T0347)V80.CB only 0.000 apart, marking (T0347)V80.CB as missing
WARNING: atoms too close: (T0347)L84.CA and (T0347)L84.CB only 0.000 apart, marking (T0347)L84.CB as missing
WARNING: atoms too close: (T0347)E98.CA and (T0347)E98.CB only 0.000 apart, marking (T0347)E98.CB as missing
WARNING: atoms too close: (T0347)F99.CA and (T0347)F99.CB only 0.000 apart, marking (T0347)F99.CB as missing
WARNING: atoms too close: (T0347)P111.CA and (T0347)P111.CB only 0.000 apart, marking (T0347)P111.CB as missing
WARNING: atoms too close: (T0347)R119.CA and (T0347)R119.CB only 0.000 apart, marking (T0347)R119.CB as missing
WARNING: atoms too close: (T0347)P125.CA and (T0347)P125.CB only 0.000 apart, marking (T0347)P125.CB as missing
WARNING: atoms too close: (T0347)D130.CA and (T0347)D130.CB only 0.000 apart, marking (T0347)D130.CB as missing
WARNING: atoms too close: (T0347)D133.CA and (T0347)D133.CB only 0.000 apart, marking (T0347)D133.CB as missing
WARNING: atoms too close: (T0347)D134.CA and (T0347)D134.CB only 0.000 apart, marking (T0347)D134.CB as missing
WARNING: atoms too close: (T0347)R144.CA and (T0347)R144.CB only 0.000 apart, marking (T0347)R144.CB as missing
WARNING: atoms too close: (T0347)K151.CA and (T0347)K151.CB only 0.000 apart, marking (T0347)K151.CB as missing
WARNING: atoms too close: (T0347)V152.CA and (T0347)V152.CB only 0.000 apart, marking (T0347)V152.CB as missing
WARNING: atoms too close: (T0347)R166.CA and (T0347)R166.CB only 0.000 apart, marking (T0347)R166.CB as missing
WARNING: atoms too close: (T0347)D180.CA and (T0347)D180.CB only 0.000 apart, marking (T0347)D180.CB as missing
WARNING: atoms too close: (T0347)S191.CA and (T0347)S191.CB only 0.000 apart, marking (T0347)S191.CB as missing
WARNING: atoms too close: (T0347)E205.CA and (T0347)E205.CB only 0.000 apart, marking (T0347)E205.CB as missing
# WARNING: incomplete conformation T0347 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: (T0347)M1.CA and (T0347)M1.CB only 0.000 apart, marking (T0347)M1.CB as missing
WARNING: atoms too close: (T0347)P7.CA and (T0347)P7.CB only 0.000 apart, marking (T0347)P7.CB as missing
WARNING: atoms too close: (T0347)R11.CA and (T0347)R11.CB only 0.000 apart, marking (T0347)R11.CB as missing
WARNING: atoms too close: (T0347)K16.CA and (T0347)K16.CB only 0.000 apart, marking (T0347)K16.CB as missing
WARNING: atoms too close: (T0347)P19.CA and (T0347)P19.CB only 0.000 apart, marking (T0347)P19.CB as missing
WARNING: atoms too close: (T0347)R27.CA and (T0347)R27.CB only 0.000 apart, marking (T0347)R27.CB as missing
WARNING: atoms too close: (T0347)R33.CA and (T0347)R33.CB only 0.000 apart, marking (T0347)R33.CB as missing
WARNING: atoms too close: (T0347)K34.CA and (T0347)K34.CB only 0.000 apart, marking (T0347)K34.CB as missing
WARNING: atoms too close: (T0347)D45.CA and (T0347)D45.CB only 0.000 apart, marking (T0347)D45.CB as missing
WARNING: atoms too close: (T0347)D46.CA and (T0347)D46.CB only 0.000 apart, marking (T0347)D46.CB as missing
WARNING: atoms too close: (T0347)L48.CA and (T0347)L48.CB only 0.000 apart, marking (T0347)L48.CB as missing
WARNING: atoms too close: (T0347)H51.CA and (T0347)H51.CB only 0.000 apart, marking (T0347)H51.CB as missing
WARNING: atoms too close: (T0347)V55.CA and (T0347)V55.CB only 0.000 apart, marking (T0347)V55.CB as missing
WARNING: atoms too close: (T0347)P59.CA and (T0347)P59.CB only 0.000 apart, marking (T0347)P59.CB as missing
WARNING: atoms too close: (T0347)D61.CA and (T0347)D61.CB only 0.000 apart, marking (T0347)D61.CB as missing
WARNING: atoms too close: (T0347)I66.CA and (T0347)I66.CB only 0.000 apart, marking (T0347)I66.CB as missing
WARNING: atoms too close: (T0347)H70.CA and (T0347)H70.CB only 0.000 apart, marking (T0347)H70.CB as missing
WARNING: atoms too close: (T0347)L73.CA and (T0347)L73.CB only 0.000 apart, marking (T0347)L73.CB as missing
WARNING: atoms too close: (T0347)E81.CA and (T0347)E81.CB only 0.000 apart, marking (T0347)E81.CB as missing
WARNING: atoms too close: (T0347)S86.CA and (T0347)S86.CB only 0.000 apart, marking (T0347)S86.CB as missing
WARNING: atoms too close: (T0347)E87.CA and (T0347)E87.CB only 0.000 apart, marking (T0347)E87.CB as missing
WARNING: atoms too close: (T0347)L94.CA and (T0347)L94.CB only 0.000 apart, marking (T0347)L94.CB as missing
WARNING: atoms too close: (T0347)E98.CA and (T0347)E98.CB only 0.000 apart, marking (T0347)E98.CB as missing
WARNING: atoms too close: (T0347)W100.CA and (T0347)W100.CB only 0.000 apart, marking (T0347)W100.CB as missing
WARNING: atoms too close: (T0347)M103.CA and (T0347)M103.CB only 0.000 apart, marking (T0347)M103.CB as missing
WARNING: atoms too close: (T0347)D104.CA and (T0347)D104.CB only 0.000 apart, marking (T0347)D104.CB as missing
WARNING: atoms too close: (T0347)D113.CA and (T0347)D113.CB only 0.000 apart, marking (T0347)D113.CB as missing
WARNING: atoms too close: (T0347)Q115.CA and (T0347)Q115.CB only 0.000 apart, marking (T0347)Q115.CB as missing
WARNING: atoms too close: (T0347)Q120.CA and (T0347)Q120.CB only 0.000 apart, marking (T0347)Q120.CB as missing
WARNING: atoms too close: (T0347)P125.CA and (T0347)P125.CB only 0.000 apart, marking (T0347)P125.CB as missing
WARNING: atoms too close: (T0347)D130.CA and (T0347)D130.CB only 0.000 apart, marking (T0347)D130.CB as missing
WARNING: atoms too close: (T0347)L131.CA and (T0347)L131.CB only 0.000 apart, marking (T0347)L131.CB as missing
WARNING: atoms too close: (T0347)E132.CA and (T0347)E132.CB only 0.000 apart, marking (T0347)E132.CB as missing
WARNING: atoms too close: (T0347)D133.CA and (T0347)D133.CB only 0.000 apart, marking (T0347)D133.CB as missing
WARNING: atoms too close: (T0347)F136.CA and (T0347)F136.CB only 0.000 apart, marking (T0347)F136.CB as missing
WARNING: atoms too close: (T0347)R137.CA and (T0347)R137.CB only 0.000 apart, marking (T0347)R137.CB as missing
WARNING: atoms too close: (T0347)S138.CA and (T0347)S138.CB only 0.000 apart, marking (T0347)S138.CB as missing
WARNING: atoms too close: (T0347)A142.CA and (T0347)A142.CB only 0.000 apart, marking (T0347)A142.CB as missing
WARNING: atoms too close: (T0347)Y149.CA and (T0347)Y149.CB only 0.000 apart, marking (T0347)Y149.CB as missing
WARNING: atoms too close: (T0347)D163.CA and (T0347)D163.CB only 0.000 apart, marking (T0347)D163.CB as missing
WARNING: atoms too close: (T0347)D172.CA and (T0347)D172.CB only 0.000 apart, marking (T0347)D172.CB as missing
WARNING: atoms too close: (T0347)S175.CA and (T0347)S175.CB only 0.000 apart, marking (T0347)S175.CB as missing
WARNING: atoms too close: (T0347)M186.CA and (T0347)M186.CB only 0.000 apart, marking (T0347)M186.CB as missing
WARNING: atoms too close: (T0347)R192.CA and (T0347)R192.CB only 0.000 apart, marking (T0347)R192.CB as missing
WARNING: atoms too close: (T0347)E193.CA and (T0347)E193.CB only 0.000 apart, marking (T0347)E193.CB as missing
WARNING: atoms too close: (T0347)A194.CA and (T0347)A194.CB only 0.000 apart, marking (T0347)A194.CB as missing
WARNING: atoms too close: (T0347)L197.CA and (T0347)L197.CB only 0.000 apart, marking (T0347)L197.CB as missing
WARNING: atoms too close: (T0347)W200.CA and (T0347)W200.CB only 0.000 apart, marking (T0347)W200.CB as missing
# WARNING: incomplete conformation T0347 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: (T0347)T2.CA and (T0347)T2.CB only 0.000 apart, marking (T0347)T2.CB as missing
WARNING: atoms too close: (T0347)E6.CA and (T0347)E6.CB only 0.000 apart, marking (T0347)E6.CB as missing
WARNING: atoms too close: (T0347)A13.CA and (T0347)A13.CB only 0.000 apart, marking (T0347)A13.CB as missing
WARNING: atoms too close: (T0347)I14.CA and (T0347)I14.CB only 0.000 apart, marking (T0347)I14.CB as missing
WARNING: atoms too close: (T0347)K16.CA and (T0347)K16.CB only 0.000 apart, marking (T0347)K16.CB as missing
WARNING: atoms too close: (T0347)T20.CA and (T0347)T20.CB only 0.000 apart, marking (T0347)T20.CB as missing
WARNING: atoms too close: (T0347)A23.CA and (T0347)A23.CB only 0.000 apart, marking (T0347)A23.CB as missing
WARNING: atoms too close: (T0347)E28.CA and (T0347)E28.CB only 0.000 apart, marking (T0347)E28.CB as missing
WARNING: atoms too close: (T0347)H51.CA and (T0347)H51.CB only 0.000 apart, marking (T0347)H51.CB as missing
WARNING: atoms too close: (T0347)K60.CA and (T0347)K60.CB only 0.000 apart, marking (T0347)K60.CB as missing
WARNING: atoms too close: (T0347)L65.CA and (T0347)L65.CB only 0.000 apart, marking (T0347)L65.CB as missing
WARNING: atoms too close: (T0347)H68.CA and (T0347)H68.CB only 0.000 apart, marking (T0347)H68.CB as missing
WARNING: atoms too close: (T0347)L75.CA and (T0347)L75.CB only 0.000 apart, marking (T0347)L75.CB as missing
WARNING: atoms too close: (T0347)V80.CA and (T0347)V80.CB only 0.000 apart, marking (T0347)V80.CB as missing
WARNING: atoms too close: (T0347)H82.CA and (T0347)H82.CB only 0.000 apart, marking (T0347)H82.CB as missing
WARNING: atoms too close: (T0347)H93.CA and (T0347)H93.CB only 0.000 apart, marking (T0347)H93.CB as missing
WARNING: atoms too close: (T0347)L94.CA and (T0347)L94.CB only 0.000 apart, marking (T0347)L94.CB as missing
WARNING: atoms too close: (T0347)K96.CA and (T0347)K96.CB only 0.000 apart, marking (T0347)K96.CB as missing
WARNING: atoms too close: (T0347)S101.CA and (T0347)S101.CB only 0.000 apart, marking (T0347)S101.CB as missing
WARNING: atoms too close: (T0347)P111.CA and (T0347)P111.CB only 0.000 apart, marking (T0347)P111.CB as missing
WARNING: atoms too close: (T0347)A114.CA and (T0347)A114.CB only 0.000 apart, marking (T0347)A114.CB as missing
WARNING: atoms too close: (T0347)S121.CA and (T0347)S121.CB only 0.000 apart, marking (T0347)S121.CB as missing
WARNING: atoms too close: (T0347)P125.CA and (T0347)P125.CB only 0.000 apart, marking (T0347)P125.CB as missing
WARNING: atoms too close: (T0347)I128.CA and (T0347)I128.CB only 0.000 apart, marking (T0347)I128.CB as missing
WARNING: atoms too close: (T0347)E132.CA and (T0347)E132.CB only 0.000 apart, marking (T0347)E132.CB as missing
WARNING: atoms too close: (T0347)D134.CA and (T0347)D134.CB only 0.000 apart, marking (T0347)D134.CB as missing
WARNING: atoms too close: (T0347)F136.CA and (T0347)F136.CB only 0.000 apart, marking (T0347)F136.CB as missing
WARNING: atoms too close: (T0347)R137.CA and (T0347)R137.CB only 0.000 apart, marking (T0347)R137.CB as missing
WARNING: atoms too close: (T0347)L143.CA and (T0347)L143.CB only 0.000 apart, marking (T0347)L143.CB as missing
WARNING: atoms too close: (T0347)A146.CA and (T0347)A146.CB only 0.000 apart, marking (T0347)A146.CB as missing
WARNING: atoms too close: (T0347)A150.CA and (T0347)A150.CB only 0.000 apart, marking (T0347)A150.CB as missing
WARNING: atoms too close: (T0347)K151.CA and (T0347)K151.CB only 0.000 apart, marking (T0347)K151.CB as missing
WARNING: atoms too close: (T0347)P155.CA and (T0347)P155.CB only 0.000 apart, marking (T0347)P155.CB as missing
WARNING: atoms too close: (T0347)F156.CA and (T0347)F156.CB only 0.000 apart, marking (T0347)F156.CB as missing
WARNING: atoms too close: (T0347)E158.CA and (T0347)E158.CB only 0.000 apart, marking (T0347)E158.CB as missing
WARNING: atoms too close: (T0347)A162.CA and (T0347)A162.CB only 0.000 apart, marking (T0347)A162.CB as missing
WARNING: atoms too close: (T0347)R166.CA and (T0347)R166.CB only 0.000 apart, marking (T0347)R166.CB as missing
WARNING: atoms too close: (T0347)D172.CA and (T0347)D172.CB only 0.000 apart, marking (T0347)D172.CB as missing
WARNING: atoms too close: (T0347)L173.CA and (T0347)L173.CB only 0.000 apart, marking (T0347)L173.CB as missing
WARNING: atoms too close: (T0347)F178.CA and (T0347)F178.CB only 0.000 apart, marking (T0347)F178.CB as missing
WARNING: atoms too close: (T0347)D180.CA and (T0347)D180.CB only 0.000 apart, marking (T0347)D180.CB as missing
WARNING: atoms too close: (T0347)E193.CA and (T0347)E193.CB only 0.000 apart, marking (T0347)E193.CB as missing
WARNING: atoms too close: (T0347)A194.CA and (T0347)A194.CB only 0.000 apart, marking (T0347)A194.CB as missing
WARNING: atoms too close: (T0347)W200.CA and (T0347)W200.CB only 0.000 apart, marking (T0347)W200.CB as missing
WARNING: atoms too close: (T0347)E205.CA and (T0347)E205.CB only 0.000 apart, marking (T0347)E205.CB as missing
# WARNING: incomplete conformation T0347 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: (T0347)Y5.CA and (T0347)Y5.CB only 0.000 apart, marking (T0347)Y5.CB as missing
WARNING: atoms too close: (T0347)E6.CA and (T0347)E6.CB only 0.000 apart, marking (T0347)E6.CB as missing
WARNING: atoms too close: (T0347)R8.CA and (T0347)R8.CB only 0.000 apart, marking (T0347)R8.CB as missing
WARNING: atoms too close: (T0347)I12.CA and (T0347)I12.CB only 0.000 apart, marking (T0347)I12.CB as missing
WARNING: atoms too close: (T0347)I22.CA and (T0347)I22.CB only 0.000 apart, marking (T0347)I22.CB as missing
WARNING: atoms too close: (T0347)E30.CA and (T0347)E30.CB only 0.000 apart, marking (T0347)E30.CB as missing
WARNING: atoms too close: (T0347)E38.CA and (T0347)E38.CB only 0.000 apart, marking (T0347)E38.CB as missing
WARNING: atoms too close: (T0347)T39.CA and (T0347)T39.CB only 0.000 apart, marking (T0347)T39.CB as missing
WARNING: atoms too close: (T0347)R40.CA and (T0347)R40.CB only 0.000 apart, marking (T0347)R40.CB as missing
WARNING: atoms too close: (T0347)H51.CA and (T0347)H51.CB only 0.000 apart, marking (T0347)H51.CB as missing
WARNING: atoms too close: (T0347)H68.CA and (T0347)H68.CB only 0.000 apart, marking (T0347)H68.CB as missing
WARNING: atoms too close: (T0347)H70.CA and (T0347)H70.CB only 0.000 apart, marking (T0347)H70.CB as missing
WARNING: atoms too close: (T0347)L73.CA and (T0347)L73.CB only 0.000 apart, marking (T0347)L73.CB as missing
WARNING: atoms too close: (T0347)V80.CA and (T0347)V80.CB only 0.000 apart, marking (T0347)V80.CB as missing
WARNING: atoms too close: (T0347)E87.CA and (T0347)E87.CB only 0.000 apart, marking (T0347)E87.CB as missing
WARNING: atoms too close: (T0347)F91.CA and (T0347)F91.CB only 0.000 apart, marking (T0347)F91.CB as missing
WARNING: atoms too close: (T0347)K96.CA and (T0347)K96.CB only 0.000 apart, marking (T0347)K96.CB as missing
WARNING: atoms too close: (T0347)D97.CA and (T0347)D97.CB only 0.000 apart, marking (T0347)D97.CB as missing
WARNING: atoms too close: (T0347)F99.CA and (T0347)F99.CB only 0.000 apart, marking (T0347)F99.CB as missing
WARNING: atoms too close: (T0347)Q120.CA and (T0347)Q120.CB only 0.000 apart, marking (T0347)Q120.CB as missing
WARNING: atoms too close: (T0347)E132.CA and (T0347)E132.CB only 0.000 apart, marking (T0347)E132.CB as missing
WARNING: atoms too close: (T0347)D133.CA and (T0347)D133.CB only 0.000 apart, marking (T0347)D133.CB as missing
WARNING: atoms too close: (T0347)D134.CA and (T0347)D134.CB only 0.000 apart, marking (T0347)D134.CB as missing
WARNING: atoms too close: (T0347)L139.CA and (T0347)L139.CB only 0.000 apart, marking (T0347)L139.CB as missing
WARNING: atoms too close: (T0347)K151.CA and (T0347)K151.CB only 0.000 apart, marking (T0347)K151.CB as missing
WARNING: atoms too close: (T0347)V152.CA and (T0347)V152.CB only 0.000 apart, marking (T0347)V152.CB as missing
WARNING: atoms too close: (T0347)S157.CA and (T0347)S157.CB only 0.000 apart, marking (T0347)S157.CB as missing
WARNING: atoms too close: (T0347)A162.CA and (T0347)A162.CB only 0.000 apart, marking (T0347)A162.CB as missing
WARNING: atoms too close: (T0347)R166.CA and (T0347)R166.CB only 0.000 apart, marking (T0347)R166.CB as missing
WARNING: atoms too close: (T0347)R171.CA and (T0347)R171.CB only 0.000 apart, marking (T0347)R171.CB as missing
WARNING: atoms too close: (T0347)S175.CA and (T0347)S175.CB only 0.000 apart, marking (T0347)S175.CB as missing
WARNING: atoms too close: (T0347)D179.CA and (T0347)D179.CB only 0.000 apart, marking (T0347)D179.CB as missing
WARNING: atoms too close: (T0347)A194.CA and (T0347)A194.CB only 0.000 apart, marking (T0347)A194.CB as missing
WARNING: atoms too close: (T0347)W200.CA and (T0347)W200.CB only 0.000 apart, marking (T0347)W200.CB as missing
# WARNING: incomplete conformation T0347 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
# WARNING: incomplete conformation T0347 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 T0347 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 T0347 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 T0347 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 T0347 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 T0347 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 199
# 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 T0347 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 T0347 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 T0347 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 T0347 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 105
# 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 171
# 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 109
# 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 173
# 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 177
# copying to AlignedFragments data structure
# naming current conformation SP3_TS5
# ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1
# naming current conformation SP4_TS1
# ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1
# Found a chain break before 177
# 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 169
# 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 138
# 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 107
# 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 135
# 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 193
# 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 180
# 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 198
# 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 175
# 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 T0347 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 T0347 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 T0347 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 T0347 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 T0347 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: (T0347)I22.CA and (T0347)E30.CA only 0.000 apart, marking (T0347)E30.CA as missing
WARNING: atoms too close: (T0347)A23.N and (T0347)L31.N only 0.000 apart, marking (T0347)L31.N as missing
WARNING: atoms too close: (T0347)A23.CA and (T0347)L31.CA only 0.000 apart, marking (T0347)L31.CA as missing
WARNING: atoms too close: (T0347)A23.CB and (T0347)L31.CB only 0.000 apart, marking (T0347)L31.CB as missing
WARNING: atoms too close: (T0347)A23.O and (T0347)L31.O only 0.000 apart, marking (T0347)L31.O as missing
WARNING: atoms too close: (T0347)A23.C and (T0347)L31.C only 0.000 apart, marking (T0347)L31.C as missing
WARNING: atoms too close: (T0347)V24.N and (T0347)K32.N only 0.000 apart, marking (T0347)K32.N as missing
WARNING: atoms too close: (T0347)V24.CA and (T0347)K32.CA only 0.000 apart, marking (T0347)K32.CA as missing
WARNING: atoms too close: (T0347)V24.CB and (T0347)K32.CB only 0.000 apart, marking (T0347)K32.CB as missing
WARNING: atoms too close: (T0347)V24.O and (T0347)K32.O only 0.000 apart, marking (T0347)K32.O as missing
WARNING: atoms too close: (T0347)V24.C and (T0347)K32.C only 0.000 apart, marking (T0347)K32.C as missing
WARNING: atoms too close: (T0347)G25.N and (T0347)R33.N only 0.000 apart, marking (T0347)R33.N as missing
WARNING: atoms too close: (T0347)G25.CA and (T0347)R33.CA only 0.000 apart, marking (T0347)R33.CA as missing
WARNING: atoms too close: (T0347)G25.O and (T0347)R33.O only 0.000 apart, marking (T0347)R33.O as missing
WARNING: atoms too close: (T0347)G25.C and (T0347)R33.C only 0.000 apart, marking (T0347)R33.C as missing
WARNING: atoms too close: (T0347)F26.N and (T0347)K34.N only 0.000 apart, marking (T0347)K34.N as missing
WARNING: atoms too close: (T0347)F26.CA and (T0347)K34.CA only 0.000 apart, marking (T0347)K34.CA as missing
WARNING: atoms too close: (T0347)F26.CB and (T0347)K34.CB only 0.000 apart, marking (T0347)K34.CB as missing
WARNING: atoms too close: (T0347)F26.O and (T0347)K34.O only 0.000 apart, marking (T0347)K34.O as missing
WARNING: atoms too close: (T0347)F26.C and (T0347)K34.C only 0.000 apart, marking (T0347)K34.C as missing
WARNING: atoms too close: (T0347)R27.N and (T0347)E35.N only 0.000 apart, marking (T0347)E35.N as missing
WARNING: atoms too close: (T0347)R27.CA and (T0347)E35.CA only 0.000 apart, marking (T0347)E35.CA as missing
WARNING: atoms too close: (T0347)R27.CB and (T0347)E35.CB only 0.000 apart, marking (T0347)E35.CB as missing
WARNING: atoms too close: (T0347)R27.C and (T0347)E35.C only 0.000 apart, marking (T0347)E35.C as missing
WARNING: atoms too close: (T0347)E28.CA and (T0347)W36.CA only 0.000 apart, marking (T0347)W36.CA as missing
WARNING: atoms too close: (T0347)V29.CA and (T0347)R37.CA only 0.000 apart, marking (T0347)R37.CA as missing
WARNING: atoms too close: (T0347)A89.CA and (T0347)L117.CA only 0.000 apart, marking (T0347)L117.CA as missing
WARNING: atoms too close: (T0347)K90.CA and (T0347)R118.CA only 0.000 apart, marking (T0347)R118.CA as missing
WARNING: atoms too close: (T0347)V102.CA and (T0347)D130.CA only 0.000 apart, marking (T0347)D130.CA as missing
WARNING: atoms too close: (T0347)M103.N and (T0347)L131.N only 0.000 apart, marking (T0347)L131.N as missing
WARNING: atoms too close: (T0347)M103.CA and (T0347)L131.CA only 0.000 apart, marking (T0347)L131.CA as missing
WARNING: atoms too close: (T0347)M103.CB and (T0347)L131.CB only 0.000 apart, marking (T0347)L131.CB as missing
WARNING: atoms too close: (T0347)M103.O and (T0347)L131.O only 0.000 apart, marking (T0347)L131.O as missing
WARNING: atoms too close: (T0347)M103.C and (T0347)L131.C only 0.000 apart, marking (T0347)L131.C as missing
WARNING: atoms too close: (T0347)D104.N and (T0347)E132.N only 0.000 apart, marking (T0347)E132.N as missing
WARNING: atoms too close: (T0347)D104.CA and (T0347)E132.CA only 0.000 apart, marking (T0347)E132.CA as missing
WARNING: atoms too close: (T0347)D104.CB and (T0347)E132.CB only 0.000 apart, marking (T0347)E132.CB as missing
WARNING: atoms too close: (T0347)D104.C and (T0347)E132.C only 0.000 apart, marking (T0347)E132.C as missing
WARNING: atoms too close: (T0347)H105.CA and (T0347)D133.CA only 0.000 apart, marking (T0347)D133.CA as missing
WARNING: atoms too close: (T0347)R106.CA and (T0347)P135.CA only 0.000 apart, marking (T0347)P135.CA as missing
WARNING: atoms too close: (T0347)R137.CA and (T0347)F156.CA only 0.000 apart, marking (T0347)F156.CA as missing
WARNING: atoms too close: (T0347)S138.N and (T0347)S157.N only 0.000 apart, marking (T0347)S157.N as missing
WARNING: atoms too close: (T0347)S138.CA and (T0347)S157.CA only 0.000 apart, marking (T0347)S157.CA as missing
WARNING: atoms too close: (T0347)S138.CB and (T0347)S157.CB only 0.000 apart, marking (T0347)S157.CB as missing
WARNING: atoms too close: (T0347)S138.O and (T0347)S157.O only 0.000 apart, marking (T0347)S157.O as missing
WARNING: atoms too close: (T0347)S138.C and (T0347)S157.C only 0.000 apart, marking (T0347)S157.C as missing
WARNING: atoms too close: (T0347)L139.N and (T0347)E158.N only 0.000 apart, marking (T0347)E158.N as missing
WARNING: atoms too close: (T0347)L139.CA and (T0347)E158.CA only 0.000 apart, marking (T0347)E158.CA as missing
WARNING: atoms too close: (T0347)L139.CB and (T0347)E158.CB only 0.000 apart, marking (T0347)E158.CB as missing
WARNING: atoms too close: (T0347)L139.O and (T0347)E158.O only 0.000 apart, marking (T0347)E158.O as missing
WARNING: atoms too close: (T0347)L139.C and (T0347)E158.C only 0.000 apart, marking (T0347)E158.C as missing
WARNING: atoms too close: (T0347)A140.N and (T0347)F159.N only 0.000 apart, marking (T0347)F159.N as missing
WARNING: atoms too close: (T0347)A140.CA and (T0347)F159.CA only 0.000 apart, marking (T0347)F159.CA as missing
WARNING: atoms too close: (T0347)A140.CB and (T0347)F159.CB only 0.000 apart, marking (T0347)F159.CB as missing
WARNING: atoms too close: (T0347)A140.O and (T0347)F159.O only 0.000 apart, marking (T0347)F159.O as missing
WARNING: atoms too close: (T0347)A140.C and (T0347)F159.C only 0.000 apart, marking (T0347)F159.C as missing
WARNING: atoms too close: (T0347)G141.N and (T0347)G160.N only 0.000 apart, marking (T0347)G160.N as missing
WARNING: atoms too close: (T0347)G141.CA and (T0347)G160.CA only 0.000 apart, marking (T0347)G160.CA as missing
WARNING: atoms too close: (T0347)G141.O and (T0347)G160.O only 0.000 apart, marking (T0347)G160.O as missing
WARNING: atoms too close: (T0347)G141.C and (T0347)G160.C only 0.000 apart, marking (T0347)G160.C as missing
WARNING: atoms too close: (T0347)A142.N and (T0347)W161.N only 0.000 apart, marking (T0347)W161.N as missing
WARNING: atoms too close: (T0347)A142.CA and (T0347)W161.CA only 0.000 apart, marking (T0347)W161.CA as missing
WARNING: atoms too close: (T0347)A142.CB and (T0347)W161.CB only 0.000 apart, marking (T0347)W161.CB as missing
WARNING: atoms too close: (T0347)A142.O and (T0347)W161.O only 0.000 apart, marking (T0347)W161.O as missing
WARNING: atoms too close: (T0347)A142.C and (T0347)W161.C only 0.000 apart, marking (T0347)W161.C as missing
WARNING: atoms too close: (T0347)L143.N and (T0347)A162.N only 0.000 apart, marking (T0347)L143.N as missing
WARNING: atoms too close: (T0347)L143.CA and (T0347)A162.CA only 0.000 apart, marking (T0347)L143.CA as missing
WARNING: atoms too close: (T0347)L143.CB and (T0347)A162.CB only 0.000 apart, marking (T0347)L143.CB as missing
WARNING: atoms too close: (T0347)L143.C and (T0347)A162.C only 0.000 apart, marking (T0347)L143.C as missing
WARNING: atoms too close: (T0347)R144.CA and (T0347)D163.CA only 0.000 apart, marking (T0347)D163.CA as missing
WARNING: atoms too close: (T0347)M145.CA and (T0347)F164.CA only 0.000 apart, marking (T0347)F164.CA as missing
# WARNING: incomplete conformation T0347 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 T0347 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 T0347 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
Skipped atom 26, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz
Skipped atom 28, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz
Skipped atom 30, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz
Skipped atom 32, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz
# WARNING: incomplete conformation T0347 can't currently be optimized by undertaker
# naming current conformation UNI-EID_sfst_AL3
# ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1
# Found a chain break before 197
# 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 201
# 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 202
# 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 199
# 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 199
# 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 204
# 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 T0347 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
Skipped atom 163, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
# WARNING: incomplete conformation T0347 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 T0347 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 T0347 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 T0347 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 T0347 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
# naming current conformation karypis.srv.2_TS1
# ReadConformPDB reading from PDB file servers/karypis.srv.2_TS2.pdb.gz looking for model 1
# 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 43
# 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 146
# 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 138
# 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
# Found a chain break before 202
# 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
WARNING: atoms too close: (T0347)L188.O and (T0347)A189.N only 0.000 apart, marking (T0347)A189.N as missing
# WARNING: incomplete conformation T0347 can't currently be optimized by undertaker
# 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 202
# 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
# Found a chain break before 202
# 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 202
# 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 T0347 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 T0347 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 T0347 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 T0347 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 T0347 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation karypis.srv_TS5
# ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1
# 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
# naming current conformation keasar-server_TS3
# ReadConformPDB reading from PDB file servers/keasar-server_TS4.pdb.gz looking for model 1
# naming current conformation keasar-server_TS4
# ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1
# naming current conformation keasar-server_TS5
# ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1
WARNING: atom 387 has residue number 30  < previous residue 92  in servers/mGen-3D_TS1.pdb.gz
WARNING: atom 786 has residue number 23  < previous residue 205  in servers/mGen-3D_TS1.pdb.gz
# WARNING: incomplete conformation T0347 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 T0347 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 T0347 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: incomplete conformation T0347 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 T0347 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 T0347 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 T0347 can't currently be optimized by undertaker
# naming current conformation shub_TS1
# command:Using radius: 8.0000
Metaserver mode
NUMB_ALIGNS: 260
Adding 13745 constraints to all.constraints
Done adding distance constraints
# command:Reading probabilities from probabilities.dat
Reading constraints from ConstraintSet all.constraints
maxweight: 106.0000
Optimizing...
 Probability sum: -371.6927, CN propb: -371.6927 weights: 0.1882 constraints: 633
# command:Found ConstraintSet
# PrintContacts align.constraints_meta01
Number of constraints in align.constraints 633
# command:Found ConstraintSet
# PrintContacts align_bonus.constraints_meta01
Number of constraints in align.constraints.bonus 633
# command:Found ConstraintSet
# PrintContacts rejected.constraints_meta01
Number of constraints in rejected.constraints 13112
# command:Found ConstraintSet
# PrintContacts rejected_bonus.constraints_meta01
Number of constraints in rejected.constraints.bonus 13112
# 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 13745
# command: