# 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/T0369/
# command:# Making conformation for sequence T0369 numbered 1 through 148
Created new target T0369 from T0369.a2m
# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0369/
# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0369/
# command:# reading script from file servers-clean.under
# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0369/decoys/
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1
# choosing archetypes in rotamer library
# Found a chain break before 144
# copying to AlignedFragments data structure
# naming current conformation 3D-JIGSAW_POPULUS_TS1
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS2.pdb.gz looking for model 1
# Found a chain break before 146
# copying to AlignedFragments data structure
# naming current conformation 3D-JIGSAW_POPULUS_TS2
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS3.pdb.gz looking for model 1
# Found a chain break before 139
# copying to AlignedFragments data structure
# naming current conformation 3D-JIGSAW_POPULUS_TS3
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS4.pdb.gz looking for model 1
# Found a chain break before 144
# copying to AlignedFragments data structure
# naming current conformation 3D-JIGSAW_POPULUS_TS4
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS5.pdb.gz looking for model 1
# Found a chain break before 144
# copying to AlignedFragments data structure
# naming current conformation 3D-JIGSAW_POPULUS_TS5
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0369 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 T0369 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 T0369 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 T0369 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 T0369 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 T0369 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 T0369 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
# Found a chain break before 143
# copying to AlignedFragments data structure
# naming current conformation 3D-JIGSAW_TS3
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0369 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_TS4
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0369 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_TS5
# ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1
# Found a chain break before 146
# 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 66
# 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 103
# 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 134
# 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 140
# 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 103
# 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 146
# 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 104
# 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 142
# 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 141
# 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 144
# 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 67
# copying to AlignedFragments data structure
# naming current conformation Bilab-ENABLE_TS1
# ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1
# Found a chain break before 71
# 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 144
# 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 T0369 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 T0369 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 T0369 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 T0369 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 T0369 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 T0369 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 T0369 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 T0369 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 T0369 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 T0369 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 T0369 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 T0369 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 T0369 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 132
# 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 T0369 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
# Found a chain break before 140
# copying to AlignedFragments data structure
# naming current conformation FAMSD_TS3
# ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0369 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FAMSD_TS4
# ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0369 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 115
# 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 T0369 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 T0369 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 T0369 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FAMS_TS4
# ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0369 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 95
# 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 145
# copying to AlignedFragments data structure
# naming current conformation FOLDpro_TS3
# ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1
# naming current conformation FOLDpro_TS4
# ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1
# Found a chain break before 76
# 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 T0369 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
Skipped atom 2, because occupancy 1 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 4, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 6, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 8, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 11, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 52, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 57, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 58, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 87, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 92, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 109, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 234, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 307, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 415, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 417, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 419, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 421, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 424, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 525, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 534, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 559, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 564, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
# WARNING: incomplete conformation T0369 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 T0369 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
Skipped atom 98, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz
Skipped atom 100, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz
Skipped atom 102, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz
Skipped atom 104, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz
Skipped atom 146, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz
Skipped atom 148, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz
Skipped atom 150, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz
Skipped atom 152, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz
Skipped atom 178, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz
Skipped atom 180, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz
Skipped atom 182, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz
Skipped atom 184, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz
Skipped atom 262, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz
Skipped atom 264, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz
Skipped atom 266, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz
Skipped atom 268, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz
Skipped atom 362, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz
Skipped atom 364, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz
Skipped atom 366, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz
Skipped atom 368, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz
Skipped atom 522, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz
Skipped atom 524, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz
Skipped atom 526, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz
Skipped atom 528, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz
# WARNING: incomplete conformation T0369 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 T0369 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 T0369 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
Skipped atom 2, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz
Skipped atom 4, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz
Skipped atom 6, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz
Skipped atom 8, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz
Skipped atom 11, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz
Skipped atom 52, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz
Skipped atom 57, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz
Skipped atom 58, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz
Skipped atom 87, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz
Skipped atom 92, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz
Skipped atom 109, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz
Skipped atom 234, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz
Skipped atom 307, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz
Skipped atom 415, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz
Skipped atom 417, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz
Skipped atom 419, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz
Skipped atom 421, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz
Skipped atom 424, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz
Skipped atom 525, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz
Skipped atom 534, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz
Skipped atom 559, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz
Skipped atom 564, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz
# WARNING: incomplete conformation T0369 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 T0369 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
Skipped atom 98, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 100, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 102, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 104, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 146, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 148, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 150, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 152, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 178, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 180, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 182, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 184, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 262, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 264, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 266, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 268, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 362, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 364, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 366, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 368, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 522, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 524, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 526, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 528, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
# WARNING: incomplete conformation T0369 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 T0369 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 103
# 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 133
# 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
# 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 147
# 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 61
# 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 T0369 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FUGMOD_TS1
# ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1
# Found a chain break before 97
# 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 65
# 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 73
# copying to AlignedFragments data structure
# naming current conformation FUGMOD_TS4
# ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1
# naming current conformation FUGMOD_TS5
# ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1
Skipped atom 2, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz
Skipped atom 4, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz
Skipped atom 6, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz
Skipped atom 8, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz
Skipped atom 47, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz
Skipped atom 76, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz
Skipped atom 81, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz
Skipped atom 98, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz
Skipped atom 223, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz
Skipped atom 300, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz
Skipped atom 400, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz
Skipped atom 402, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz
Skipped atom 404, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz
Skipped atom 406, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz
Skipped atom 409, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz
Skipped atom 506, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz
Skipped atom 515, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz
Skipped atom 540, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz
Skipped atom 545, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz
# WARNING: incomplete conformation T0369 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 T0369 can't currently be optimized by undertaker
# naming current conformation FUGUE_AL2
# ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0369 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 T0369 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 T0369 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FUGUE_AL5
# ReadConformPDB reading from PDB file servers/FUNCTION_TS1.pdb.gz looking for model 1
# Found a chain break before 142
# 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 116
# 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 139
# copying to AlignedFragments data structure
# naming current conformation FUNCTION_TS3
# ReadConformPDB reading from PDB file servers/FUNCTION_TS4.pdb.gz looking for model 1
# Found a chain break before 147
# copying to AlignedFragments data structure
# naming current conformation FUNCTION_TS4
# ReadConformPDB reading from PDB file servers/FUNCTION_TS5.pdb.gz looking for model 1
# Found a chain break before 144
# copying to AlignedFragments data structure
# naming current conformation FUNCTION_TS5
# ReadConformPDB reading from PDB file servers/Frankenstein_TS1.pdb.gz looking for model 1
# naming current conformation Frankenstein_TS1
# ReadConformPDB reading from PDB file servers/Frankenstein_TS2.pdb.gz looking for model 1
# Found a chain break before 76
# copying to AlignedFragments data structure
# naming current conformation Frankenstein_TS2
# ReadConformPDB reading from PDB file servers/Frankenstein_TS3.pdb.gz looking for model 1
# naming current conformation Frankenstein_TS3
# ReadConformPDB reading from PDB file servers/Frankenstein_TS4.pdb.gz looking for model 1
# Found a chain break before 72
# copying to AlignedFragments data structure
# naming current conformation Frankenstein_TS4
# ReadConformPDB reading from PDB file servers/Frankenstein_TS5.pdb.gz looking for model 1
# naming current conformation Frankenstein_TS5
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0369 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 T0369 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 T0369 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
# Found a chain break before 73
# 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 T0369 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
# naming current conformation HHpred1_TS1
# ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1
# Found a chain break before 25
# 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 87
# 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 T0369 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 T0369 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 T0369 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 T0369 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 T0369 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 T0369 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
# Found a chain break before 111
# copying to AlignedFragments data structure
# naming current conformation LOOPP_TS2
# ReadConformPDB reading from PDB file servers/LOOPP_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0369 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 T0369 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 T0369 can't currently be optimized by undertaker
# naming current conformation LOOPP_TS5
# ReadConformPDB reading from PDB file servers/MIG_FROST_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0369 can't currently be optimized by undertaker
# naming current conformation MIG_FROST_AL1
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS1.pdb.gz looking for model 1
# Found a chain break before 131
# 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 136
# 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
# 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 74
# 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 133
# 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 131
# 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
# 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 14
# 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
# 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 145
# 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 139
# 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 112
# 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 139
# 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 140
# 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 112
# 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 T0369 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: atom 1 has residue number 27  < previous residue 148  in servers/POMYSL_TS1.pdb.gz
# WARNING: incomplete conformation T0369 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: atom 1 has residue number 27  < previous residue 148  in servers/POMYSL_TS2.pdb.gz
# WARNING: incomplete conformation T0369 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
# Found a chain break before 134
# 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 142
# 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 129
# 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
# Found a chain break before 88
# 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 92
# 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 96
# 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 88
# 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
# naming current conformation PROTINFO-AB_TS5
# ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1
# naming current conformation PROTINFO_TS1
# ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1
# naming current conformation PROTINFO_TS2
# ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1
# Found a chain break before 146
# 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 119
# 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 88
# 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 T0369 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 T0369 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 T0369 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 T0369 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 T0369 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 T0369 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 80
# 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 145
# 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 146
# 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 143
# 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 T0369 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
# WARNING: incomplete conformation T0369 can't currently be optimized by undertaker
# 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 97
# 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 108
# 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 T0369 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
# Found a chain break before 106
# copying to AlignedFragments data structure
# naming current conformation Pmodeller6_TS5
# ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0369 can't currently be optimized by undertaker
# 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 67
# 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 T0369 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
# Found a chain break before 114
# 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 77
# 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 74
# 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 143
# 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 146
# 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 147
# 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 116
# 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
# naming current conformation RAPTOR_TS2
# ReadConformPDB reading from PDB file servers/RAPTOR_TS3.pdb.gz looking for model 1
# Found a chain break before 134
# copying to AlignedFragments data structure
# naming current conformation RAPTOR_TS3
# ReadConformPDB reading from PDB file servers/RAPTOR_TS4.pdb.gz looking for model 1
# naming current conformation RAPTOR_TS4
# ReadConformPDB reading from PDB file servers/RAPTOR_TS5.pdb.gz looking for model 1
# Found a chain break before 90
# 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 108
# 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 97
# 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 68
# 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 65
# 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 110
# 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: incomplete conformation T0369 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: incomplete conformation T0369 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: incomplete conformation T0369 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: incomplete conformation T0369 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: incomplete conformation T0369 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 27, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz
Skipped atom 32, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz
Skipped atom 33, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz
Skipped atom 62, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz
Skipped atom 67, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz
Skipped atom 84, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz
Skipped atom 209, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz
Skipped atom 282, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz
Skipped atom 390, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz
Skipped atom 392, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz
Skipped atom 394, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz
Skipped atom 396, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz
Skipped atom 399, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz
Skipped atom 500, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz
Skipped atom 509, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz
# WARNING: incomplete conformation T0369 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 T0369 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 T0369 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 T0369 can't currently be optimized by undertaker
# naming current conformation SAM-T02_AL4
# ReadConformPDB reading from PDB file servers/SAM-T99_AL1.pdb.gz looking for model 1
Skipped atom 31, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz
Skipped atom 36, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz
Skipped atom 37, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz
Skipped atom 66, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz
Skipped atom 71, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz
Skipped atom 88, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz
Skipped atom 213, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz
Skipped atom 290, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz
Skipped atom 398, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz
Skipped atom 400, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz
Skipped atom 402, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz
Skipped atom 404, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz
Skipped atom 407, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz
Skipped atom 508, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz
Skipped atom 517, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz
# WARNING: incomplete conformation T0369 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
Skipped atom 31, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL2.pdb.gz
Skipped atom 84, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL2.pdb.gz
Skipped atom 97, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL2.pdb.gz
Skipped atom 142, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL2.pdb.gz
Skipped atom 171, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL2.pdb.gz
Skipped atom 348, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL2.pdb.gz
Skipped atom 369, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL2.pdb.gz
Skipped atom 402, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL2.pdb.gz
Skipped atom 503, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL2.pdb.gz
# WARNING: incomplete conformation T0369 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
# WARNING: incomplete conformation T0369 can't currently be optimized by undertaker
# naming current conformation SAM-T99_AL3
# ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1
# Found a chain break before 145
# 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 T0369 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 T0369 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 T0369 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 T0369 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 114
# 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 73
# 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 69
# 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 97
# copying to AlignedFragments data structure
# naming current conformation SP3_TS4
# ReadConformPDB reading from PDB file servers/SP3_TS5.pdb.gz looking for model 1
# naming current conformation SP3_TS5
# ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1
# Found a chain break before 107
# copying to AlignedFragments data structure
# naming current conformation SP4_TS1
# ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1
# naming current conformation SP4_TS2
# ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1
# naming current conformation SP4_TS3
# ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1
# Found a chain break before 73
# 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 97
# 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 107
# 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 70
# copying to AlignedFragments data structure
# naming current conformation SPARKS2_TS2
# ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1
# naming current conformation SPARKS2_TS3
# ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1
# Found a chain break before 143
# 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 72
# 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 T0369 can't currently be optimized by undertaker
# naming current conformation UNI-EID_bnmx_TS1
# ReadConformPDB reading from PDB file servers/UNI-EID_expm_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0369 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 T0369 can't currently be optimized by undertaker
# naming current conformation UNI-EID_sfst_AL1
# ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1
# Found a chain break before 108
# 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 133
# 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 108
# 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 142
# 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 102
# 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 147
# 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 T0369 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 T0369 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 T0369 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 T0369 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 T0369 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 T0369 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 118
# 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 90
# 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 71
# 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 119
# 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
# naming current conformation karypis.srv.2_TS5
# ReadConformPDB reading from PDB file servers/karypis.srv.4_TS1.pdb.gz looking for model 1
WARNING: atoms too close: (T0369)G139.O and (T0369)Y140.N only 0.000 apart, marking (T0369)Y140.N as missing
# WARNING: incomplete conformation T0369 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.4_TS1
# ReadConformPDB reading from PDB file servers/karypis.srv.4_TS2.pdb.gz looking for model 1
WARNING: atoms too close: (T0369)Q90.O and (T0369)Y91.N only 0.000 apart, marking (T0369)Y91.N as missing
# WARNING: incomplete conformation T0369 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 145
# 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 143
# 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 145
# 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 T0369 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 T0369 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 T0369 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 T0369 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 T0369 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
# 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: incomplete conformation T0369 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 T0369 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 T0369 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 T0369 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation nFOLD_TS3
# ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0369 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 T0369 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: atoms too close: (T0369)A63.N and (T0369)T64.N only 0.000 apart, marking (T0369)T64.N as missing
WARNING: atoms too close: (T0369)A63.CA and (T0369)T64.CA only 0.000 apart, marking (T0369)T64.CA as missing
WARNING: atoms too close: (T0369)A63.CB and (T0369)T64.CB only 0.000 apart, marking (T0369)T64.CB as missing
WARNING: atoms too close: (T0369)A63.O and (T0369)T64.O only 0.000 apart, marking (T0369)T64.O as missing
WARNING: atoms too close: (T0369)A63.C and (T0369)T64.C only 0.000 apart, marking (T0369)T64.C as missing
WARNING: atoms too close: (T0369)T64.N and (T0369)A65.N only 0.000 apart, marking (T0369)T64.N as missing
WARNING: atoms too close: (T0369)A63.N and (T0369)A65.N only 0.000 apart, marking (T0369)A65.N as missing
WARNING: atoms too close: (T0369)T64.CA and (T0369)A65.CA only 0.000 apart, marking (T0369)A65.CA as missing
WARNING: atoms too close: (T0369)A63.CA and (T0369)A65.CA only 0.000 apart, marking (T0369)A65.CA as missing
WARNING: atoms too close: (T0369)T64.CB and (T0369)A65.CB only 0.000 apart, marking (T0369)A65.CB as missing
WARNING: atoms too close: (T0369)A63.CB and (T0369)A65.CB only 0.000 apart, marking (T0369)A65.CB as missing
WARNING: atoms too close: (T0369)T64.O and (T0369)A65.O only 0.000 apart, marking (T0369)A65.O as missing
WARNING: atoms too close: (T0369)A63.O and (T0369)A65.O only 0.000 apart, marking (T0369)A65.O as missing
WARNING: atoms too close: (T0369)T64.C and (T0369)A65.C only 0.000 apart, marking (T0369)A65.C as missing
WARNING: atoms too close: (T0369)A63.C and (T0369)A65.C only 0.000 apart, marking (T0369)A65.C as missing
WARNING: atoms too close: (T0369)A65.N and (T0369)D66.N only 0.000 apart, marking (T0369)A65.N as missing
WARNING: atoms too close: (T0369)T64.N and (T0369)D66.N only 0.000 apart, marking (T0369)T64.N as missing
WARNING: atoms too close: (T0369)A63.N and (T0369)D66.N only 0.000 apart, marking (T0369)D66.N as missing
WARNING: atoms too close: (T0369)A65.CA and (T0369)D66.CA only 0.000 apart, marking (T0369)D66.CA as missing
WARNING: atoms too close: (T0369)T64.CA and (T0369)D66.CA only 0.000 apart, marking (T0369)D66.CA as missing
WARNING: atoms too close: (T0369)A63.CA and (T0369)D66.CA only 0.000 apart, marking (T0369)D66.CA as missing
WARNING: atoms too close: (T0369)A65.CB and (T0369)D66.CB only 0.000 apart, marking (T0369)D66.CB as missing
WARNING: atoms too close: (T0369)T64.CB and (T0369)D66.CB only 0.000 apart, marking (T0369)D66.CB as missing
WARNING: atoms too close: (T0369)A63.CB and (T0369)D66.CB only 0.000 apart, marking (T0369)D66.CB as missing
WARNING: atoms too close: (T0369)T64.CG2 and (T0369)D66.CG only 0.000 apart, marking (T0369)D66.CG as missing
WARNING: atoms too close: (T0369)A65.O and (T0369)D66.O only 0.000 apart, marking (T0369)D66.O as missing
WARNING: atoms too close: (T0369)T64.O and (T0369)D66.O only 0.000 apart, marking (T0369)D66.O as missing
WARNING: atoms too close: (T0369)A63.O and (T0369)D66.O only 0.000 apart, marking (T0369)D66.O as missing
WARNING: atoms too close: (T0369)A65.C and (T0369)D66.C only 0.000 apart, marking (T0369)D66.C as missing
WARNING: atoms too close: (T0369)T64.C and (T0369)D66.C only 0.000 apart, marking (T0369)D66.C as missing
WARNING: atoms too close: (T0369)A63.C and (T0369)D66.C only 0.000 apart, marking (T0369)D66.C as missing
WARNING: atoms too close: (T0369)D66.N and (T0369)E67.N only 0.000 apart, marking (T0369)D66.N as missing
WARNING: atoms too close: (T0369)A65.N and (T0369)E67.N only 0.000 apart, marking (T0369)A65.N as missing
WARNING: atoms too close: (T0369)T64.N and (T0369)E67.N only 0.000 apart, marking (T0369)T64.N as missing
WARNING: atoms too close: (T0369)A63.N and (T0369)E67.N only 0.000 apart, marking (T0369)E67.N as missing
WARNING: atoms too close: (T0369)D66.CA and (T0369)E67.CA only 0.000 apart, marking (T0369)E67.CA as missing
WARNING: atoms too close: (T0369)A65.CA and (T0369)E67.CA only 0.000 apart, marking (T0369)E67.CA as missing
WARNING: atoms too close: (T0369)T64.CA and (T0369)E67.CA only 0.000 apart, marking (T0369)E67.CA as missing
WARNING: atoms too close: (T0369)A63.CA and (T0369)E67.CA only 0.000 apart, marking (T0369)E67.CA as missing
WARNING: atoms too close: (T0369)D66.CB and (T0369)E67.CB only 0.000 apart, marking (T0369)E67.CB as missing
WARNING: atoms too close: (T0369)A65.CB and (T0369)E67.CB only 0.000 apart, marking (T0369)E67.CB as missing
WARNING: atoms too close: (T0369)T64.CB and (T0369)E67.CB only 0.000 apart, marking (T0369)E67.CB as missing
WARNING: atoms too close: (T0369)A63.CB and (T0369)E67.CB only 0.000 apart, marking (T0369)E67.CB as missing
WARNING: atoms too close: (T0369)D66.CG and (T0369)E67.CG only 0.000 apart, marking (T0369)E67.CG as missing
WARNING: atoms too close: (T0369)T64.CG2 and (T0369)E67.CG only 0.000 apart, marking (T0369)E67.CG as missing
WARNING: atoms too close: (T0369)D66.O and (T0369)E67.O only 0.000 apart, marking (T0369)E67.O as missing
WARNING: atoms too close: (T0369)A65.O and (T0369)E67.O only 0.000 apart, marking (T0369)E67.O as missing
WARNING: atoms too close: (T0369)T64.O and (T0369)E67.O only 0.000 apart, marking (T0369)E67.O as missing
WARNING: atoms too close: (T0369)A63.O and (T0369)E67.O only 0.000 apart, marking (T0369)E67.O as missing
WARNING: atoms too close: (T0369)D66.C and (T0369)E67.C only 0.000 apart, marking (T0369)E67.C as missing
WARNING: atoms too close: (T0369)A65.C and (T0369)E67.C only 0.000 apart, marking (T0369)E67.C as missing
WARNING: atoms too close: (T0369)T64.C and (T0369)E67.C only 0.000 apart, marking (T0369)E67.C as missing
WARNING: atoms too close: (T0369)A63.C and (T0369)E67.C only 0.000 apart, marking (T0369)E67.C as missing
WARNING: atoms too close: (T0369)E67.N and (T0369)M68.N only 0.000 apart, marking (T0369)E67.N as missing
WARNING: atoms too close: (T0369)D66.N and (T0369)M68.N only 0.000 apart, marking (T0369)D66.N as missing
WARNING: atoms too close: (T0369)A65.N and (T0369)M68.N only 0.000 apart, marking (T0369)A65.N as missing
WARNING: atoms too close: (T0369)T64.N and (T0369)M68.N only 0.000 apart, marking (T0369)T64.N as missing
WARNING: atoms too close: (T0369)A63.N and (T0369)M68.N only 0.000 apart, marking (T0369)M68.N as missing
WARNING: atoms too close: (T0369)E67.CA and (T0369)M68.CA only 0.000 apart, marking (T0369)M68.CA as missing
WARNING: atoms too close: (T0369)D66.CA and (T0369)M68.CA only 0.000 apart, marking (T0369)M68.CA as missing
WARNING: atoms too close: (T0369)A65.CA and (T0369)M68.CA only 0.000 apart, marking (T0369)M68.CA as missing
WARNING: atoms too close: (T0369)T64.CA and (T0369)M68.CA only 0.000 apart, marking (T0369)M68.CA as missing
WARNING: atoms too close: (T0369)A63.CA and (T0369)M68.CA only 0.000 apart, marking (T0369)M68.CA as missing
WARNING: atoms too close: (T0369)E67.CB and (T0369)M68.CB only 0.000 apart, marking (T0369)M68.CB as missing
WARNING: atoms too close: (T0369)D66.CB and (T0369)M68.CB only 0.000 apart, marking (T0369)M68.CB as missing
WARNING: atoms too close: (T0369)A65.CB and (T0369)M68.CB only 0.000 apart, marking (T0369)M68.CB as missing
WARNING: atoms too close: (T0369)T64.CB and (T0369)M68.CB only 0.000 apart, marking (T0369)M68.CB as missing
WARNING: atoms too close: (T0369)A63.CB and (T0369)M68.CB only 0.000 apart, marking (T0369)M68.CB as missing
WARNING: atoms too close: (T0369)E67.CG and (T0369)M68.CG only 0.000 apart, marking (T0369)M68.CG as missing
WARNING: atoms too close: (T0369)D66.CG and (T0369)M68.CG only 0.000 apart, marking (T0369)M68.CG as missing
WARNING: atoms too close: (T0369)T64.CG2 and (T0369)M68.CG only 0.000 apart, marking (T0369)M68.CG as missing
WARNING: atoms too close: (T0369)E67.O and (T0369)M68.O only 0.000 apart, marking (T0369)M68.O as missing
WARNING: atoms too close: (T0369)D66.O and (T0369)M68.O only 0.000 apart, marking (T0369)M68.O as missing
WARNING: atoms too close: (T0369)A65.O and (T0369)M68.O only 0.000 apart, marking (T0369)M68.O as missing
WARNING: atoms too close: (T0369)T64.O and (T0369)M68.O only 0.000 apart, marking (T0369)M68.O as missing
WARNING: atoms too close: (T0369)A63.O and (T0369)M68.O only 0.000 apart, marking (T0369)M68.O as missing
WARNING: atoms too close: (T0369)E67.C and (T0369)M68.C only 0.000 apart, marking (T0369)M68.C as missing
WARNING: atoms too close: (T0369)D66.C and (T0369)M68.C only 0.000 apart, marking (T0369)M68.C as missing
WARNING: atoms too close: (T0369)A65.C and (T0369)M68.C only 0.000 apart, marking (T0369)M68.C as missing
WARNING: atoms too close: (T0369)T64.C and (T0369)M68.C only 0.000 apart, marking (T0369)M68.C as missing
WARNING: atoms too close: (T0369)A63.C and (T0369)M68.C only 0.000 apart, marking (T0369)M68.C as missing
WARNING: atoms too close: (T0369)M68.N and (T0369)A69.N only 0.000 apart, marking (T0369)M68.N as missing
WARNING: atoms too close: (T0369)E67.N and (T0369)A69.N only 0.000 apart, marking (T0369)E67.N as missing
WARNING: atoms too close: (T0369)D66.N and (T0369)A69.N only 0.000 apart, marking (T0369)D66.N as missing
WARNING: atoms too close: (T0369)A65.N and (T0369)A69.N only 0.000 apart, marking (T0369)A65.N as missing
WARNING: atoms too close: (T0369)T64.N and (T0369)A69.N only 0.000 apart, marking (T0369)T64.N as missing
WARNING: atoms too close: (T0369)A63.N and (T0369)A69.N only 0.000 apart, marking (T0369)A69.N as missing
WARNING: atoms too close: (T0369)M68.CA and (T0369)A69.CA only 0.000 apart, marking (T0369)A69.CA as missing
WARNING: atoms too close: (T0369)E67.CA and (T0369)A69.CA only 0.000 apart, marking (T0369)A69.CA as missing
WARNING: atoms too close: (T0369)D66.CA and (T0369)A69.CA only 0.000 apart, marking (T0369)A69.CA as missing
WARNING: atoms too close: (T0369)A65.CA and (T0369)A69.CA only 0.000 apart, marking (T0369)A69.CA as missing
WARNING: atoms too close: (T0369)T64.CA and (T0369)A69.CA only 0.000 apart, marking (T0369)A69.CA as missing
WARNING: atoms too close: (T0369)A63.CA and (T0369)A69.CA only 0.000 apart, marking (T0369)A69.CA as missing
WARNING: atoms too close: (T0369)M68.CB and (T0369)A69.CB only 0.000 apart, marking (T0369)A69.CB as missing
WARNING: atoms too close: (T0369)E67.CB and (T0369)A69.CB only 0.000 apart, marking (T0369)A69.CB as missing
WARNING: atoms too close: (T0369)D66.CB and (T0369)A69.CB only 0.000 apart, marking (T0369)A69.CB as missing
WARNING: atoms too close: (T0369)A65.CB and (T0369)A69.CB only 0.000 apart, marking (T0369)A69.CB as missing
WARNING: atoms too close: (T0369)T64.CB and (T0369)A69.CB only 0.000 apart, marking (T0369)A69.CB as missing
WARNING: atoms too close: (T0369)A63.CB and (T0369)A69.CB only 0.000 apart, marking (T0369)A69.CB as missing
WARNING: atoms too close: (T0369)M68.O and (T0369)A69.O only 0.000 apart, marking (T0369)A69.O as missing
WARNING: atoms too close: (T0369)E67.O and (T0369)A69.O only 0.000 apart, marking (T0369)A69.O as missing
WARNING: atoms too close: (T0369)D66.O and (T0369)A69.O only 0.000 apart, marking (T0369)A69.O as missing
WARNING: atoms too close: (T0369)A65.O and (T0369)A69.O only 0.000 apart, marking (T0369)A69.O as missing
WARNING: atoms too close: (T0369)T64.O and (T0369)A69.O only 0.000 apart, marking (T0369)A69.O as missing
WARNING: atoms too close: (T0369)A63.O and (T0369)A69.O only 0.000 apart, marking (T0369)A69.O as missing
WARNING: atoms too close: (T0369)M68.C and (T0369)A69.C only 0.000 apart, marking (T0369)A69.C as missing
WARNING: atoms too close: (T0369)E67.C and (T0369)A69.C only 0.000 apart, marking (T0369)A69.C as missing
WARNING: atoms too close: (T0369)D66.C and (T0369)A69.C only 0.000 apart, marking (T0369)A69.C as missing
WARNING: atoms too close: (T0369)A65.C and (T0369)A69.C only 0.000 apart, marking (T0369)A69.C as missing
WARNING: atoms too close: (T0369)T64.C and (T0369)A69.C only 0.000 apart, marking (T0369)A69.C as missing
WARNING: atoms too close: (T0369)A63.C and (T0369)A69.C only 0.000 apart, marking (T0369)A69.C as missing
WARNING: atoms too close: (T0369)A69.N and (T0369)Q70.N only 0.000 apart, marking (T0369)A69.N as missing
WARNING: atoms too close: (T0369)M68.N and (T0369)Q70.N only 0.000 apart, marking (T0369)M68.N as missing
WARNING: atoms too close: (T0369)E67.N and (T0369)Q70.N only 0.000 apart, marking (T0369)E67.N as missing
WARNING: atoms too close: (T0369)D66.N and (T0369)Q70.N only 0.000 apart, marking (T0369)D66.N as missing
WARNING: atoms too close: (T0369)A65.N and (T0369)Q70.N only 0.000 apart, marking (T0369)A65.N as missing
WARNING: atoms too close: (T0369)T64.N and (T0369)Q70.N only 0.000 apart, marking (T0369)T64.N as missing
WARNING: atoms too close: (T0369)A63.N and (T0369)Q70.N only 0.000 apart, marking (T0369)Q70.N as missing
WARNING: atoms too close: (T0369)A69.CA and (T0369)Q70.CA only 0.000 apart, marking (T0369)Q70.CA as missing
WARNING: atoms too close: (T0369)M68.CA and (T0369)Q70.CA only 0.000 apart, marking (T0369)Q70.CA as missing
WARNING: atoms too close: (T0369)E67.CA and (T0369)Q70.CA only 0.000 apart, marking (T0369)Q70.CA as missing
WARNING: atoms too close: (T0369)D66.CA and (T0369)Q70.CA only 0.000 apart, marking (T0369)Q70.CA as missing
WARNING: atoms too close: (T0369)A65.CA and (T0369)Q70.CA only 0.000 apart, marking (T0369)Q70.CA as missing
WARNING: atoms too close: (T0369)T64.CA and (T0369)Q70.CA only 0.000 apart, marking (T0369)Q70.CA as missing
WARNING: atoms too close: (T0369)A63.CA and (T0369)Q70.CA only 0.000 apart, marking (T0369)Q70.CA as missing
WARNING: atoms too close: (T0369)A69.CB and (T0369)Q70.CB only 0.000 apart, marking (T0369)Q70.CB as missing
WARNING: atoms too close: (T0369)M68.CB and (T0369)Q70.CB only 0.000 apart, marking (T0369)Q70.CB as missing
WARNING: atoms too close: (T0369)E67.CB and (T0369)Q70.CB only 0.000 apart, marking (T0369)Q70.CB as missing
WARNING: atoms too close: (T0369)D66.CB and (T0369)Q70.CB only 0.000 apart, marking (T0369)Q70.CB as missing
WARNING: atoms too close: (T0369)A65.CB and (T0369)Q70.CB only 0.000 apart, marking (T0369)Q70.CB as missing
WARNING: atoms too close: (T0369)T64.CB and (T0369)Q70.CB only 0.000 apart, marking (T0369)Q70.CB as missing
WARNING: atoms too close: (T0369)A63.CB and (T0369)Q70.CB only 0.000 apart, marking (T0369)Q70.CB as missing
WARNING: atoms too close: (T0369)M68.CG and (T0369)Q70.CG only 0.000 apart, marking (T0369)Q70.CG as missing
WARNING: atoms too close: (T0369)E67.CG and (T0369)Q70.CG only 0.000 apart, marking (T0369)Q70.CG as missing
WARNING: atoms too close: (T0369)D66.CG and (T0369)Q70.CG only 0.000 apart, marking (T0369)Q70.CG as missing
WARNING: atoms too close: (T0369)T64.CG2 and (T0369)Q70.CG only 0.000 apart, marking (T0369)Q70.CG as missing
WARNING: atoms too close: (T0369)E67.CD and (T0369)Q70.CD only 0.000 apart, marking (T0369)Q70.CD as missing
WARNING: atoms too close: (T0369)A69.O and (T0369)Q70.O only 0.000 apart, marking (T0369)Q70.O as missing
WARNING: atoms too close: (T0369)M68.O and (T0369)Q70.O only 0.000 apart, marking (T0369)Q70.O as missing
WARNING: atoms too close: (T0369)E67.O and (T0369)Q70.O only 0.000 apart, marking (T0369)Q70.O as missing
WARNING: atoms too close: (T0369)D66.O and (T0369)Q70.O only 0.000 apart, marking (T0369)Q70.O as missing
WARNING: atoms too close: (T0369)A65.O and (T0369)Q70.O only 0.000 apart, marking (T0369)Q70.O as missing
WARNING: atoms too close: (T0369)T64.O and (T0369)Q70.O only 0.000 apart, marking (T0369)Q70.O as missing
WARNING: atoms too close: (T0369)A63.O and (T0369)Q70.O only 0.000 apart, marking (T0369)Q70.O as missing
WARNING: atoms too close: (T0369)A69.C and (T0369)Q70.C only 0.000 apart, marking (T0369)Q70.C as missing
WARNING: atoms too close: (T0369)M68.C and (T0369)Q70.C only 0.000 apart, marking (T0369)Q70.C as missing
WARNING: atoms too close: (T0369)E67.C and (T0369)Q70.C only 0.000 apart, marking (T0369)Q70.C as missing
WARNING: atoms too close: (T0369)D66.C and (T0369)Q70.C only 0.000 apart, marking (T0369)Q70.C as missing
WARNING: atoms too close: (T0369)A65.C and (T0369)Q70.C only 0.000 apart, marking (T0369)Q70.C as missing
WARNING: atoms too close: (T0369)T64.C and (T0369)Q70.C only 0.000 apart, marking (T0369)Q70.C as missing
WARNING: atoms too close: (T0369)A63.C and (T0369)Q70.C only 0.000 apart, marking (T0369)Q70.C as missing
WARNING: atoms too close: (T0369)Q70.N and (T0369)F71.N only 0.000 apart, marking (T0369)Q70.N as missing
WARNING: atoms too close: (T0369)A69.N and (T0369)F71.N only 0.000 apart, marking (T0369)A69.N as missing
WARNING: atoms too close: (T0369)M68.N and (T0369)F71.N only 0.000 apart, marking (T0369)M68.N as missing
WARNING: atoms too close: (T0369)E67.N and (T0369)F71.N only 0.000 apart, marking (T0369)E67.N as missing
WARNING: atoms too close: (T0369)D66.N and (T0369)F71.N only 0.000 apart, marking (T0369)D66.N as missing
WARNING: atoms too close: (T0369)A65.N and (T0369)F71.N only 0.000 apart, marking (T0369)A65.N as missing
WARNING: atoms too close: (T0369)T64.N and (T0369)F71.N only 0.000 apart, marking (T0369)T64.N as missing
WARNING: atoms too close: (T0369)A63.N and (T0369)F71.N only 0.000 apart, marking (T0369)F71.N as missing
WARNING: atoms too close: (T0369)Q70.CA and (T0369)F71.CA only 0.000 apart, marking (T0369)F71.CA as missing
WARNING: atoms too close: (T0369)A69.CA and (T0369)F71.CA only 0.000 apart, marking (T0369)F71.CA as missing
WARNING: atoms too close: (T0369)M68.CA and (T0369)F71.CA only 0.000 apart, marking (T0369)F71.CA as missing
WARNING: atoms too close: (T0369)E67.CA and (T0369)F71.CA only 0.000 apart, marking (T0369)F71.CA as missing
WARNING: atoms too close: (T0369)D66.CA and (T0369)F71.CA only 0.000 apart, marking (T0369)F71.CA as missing
WARNING: atoms too close: (T0369)A65.CA and (T0369)F71.CA only 0.000 apart, marking (T0369)F71.CA as missing
WARNING: atoms too close: (T0369)T64.CA and (T0369)F71.CA only 0.000 apart, marking (T0369)F71.CA as missing
WARNING: atoms too close: (T0369)A63.CA and (T0369)F71.CA only 0.000 apart, marking (T0369)F71.CA as missing
WARNING: atoms too close: (T0369)Q70.CB and (T0369)F71.CB only 0.000 apart, marking (T0369)F71.CB as missing
WARNING: atoms too close: (T0369)A69.CB and (T0369)F71.CB only 0.000 apart, marking (T0369)F71.CB as missing
WARNING: atoms too close: (T0369)M68.CB and (T0369)F71.CB only 0.000 apart, marking (T0369)F71.CB as missing
WARNING: atoms too close: (T0369)E67.CB and (T0369)F71.CB only 0.000 apart, marking (T0369)F71.CB as missing
WARNING: atoms too close: (T0369)D66.CB and (T0369)F71.CB only 0.000 apart, marking (T0369)F71.CB as missing
WARNING: atoms too close: (T0369)A65.CB and (T0369)F71.CB only 0.000 apart, marking (T0369)F71.CB as missing
WARNING: atoms too close: (T0369)T64.CB and (T0369)F71.CB only 0.000 apart, marking (T0369)F71.CB as missing
WARNING: atoms too close: (T0369)A63.CB and (T0369)F71.CB only 0.000 apart, marking (T0369)F71.CB as missing
WARNING: atoms too close: (T0369)Q70.CG and (T0369)F71.CG only 0.000 apart, marking (T0369)F71.CG as missing
WARNING: atoms too close: (T0369)M68.CG and (T0369)F71.CG only 0.000 apart, marking (T0369)F71.CG as missing
WARNING: atoms too close: (T0369)E67.CG and (T0369)F71.CG only 0.000 apart, marking (T0369)F71.CG as missing
WARNING: atoms too close: (T0369)D66.CG and (T0369)F71.CG only 0.000 apart, marking (T0369)F71.CG as missing
WARNING: atoms too close: (T0369)T64.CG2 and (T0369)F71.CG only 0.000 apart, marking (T0369)F71.CG as missing
WARNING: atoms too close: (T0369)Q70.O and (T0369)F71.O only 0.000 apart, marking (T0369)F71.O as missing
WARNING: atoms too close: (T0369)A69.O and (T0369)F71.O only 0.000 apart, marking (T0369)F71.O as missing
WARNING: atoms too close: (T0369)M68.O and (T0369)F71.O only 0.000 apart, marking (T0369)F71.O as missing
WARNING: atoms too close: (T0369)E67.O and (T0369)F71.O only 0.000 apart, marking (T0369)F71.O as missing
WARNING: atoms too close: (T0369)D66.O and (T0369)F71.O only 0.000 apart, marking (T0369)F71.O as missing
WARNING: atoms too close: (T0369)A65.O and (T0369)F71.O only 0.000 apart, marking (T0369)F71.O as missing
WARNING: atoms too close: (T0369)T64.O and (T0369)F71.O only 0.000 apart, marking (T0369)F71.O as missing
WARNING: atoms too close: (T0369)A63.O and (T0369)F71.O only 0.000 apart, marking (T0369)F71.O as missing
WARNING: atoms too close: (T0369)Q70.C and (T0369)F71.C only 0.000 apart, marking (T0369)F71.C as missing
WARNING: atoms too close: (T0369)A69.C and (T0369)F71.C only 0.000 apart, marking (T0369)F71.C as missing
WARNING: atoms too close: (T0369)M68.C and (T0369)F71.C only 0.000 apart, marking (T0369)F71.C as missing
WARNING: atoms too close: (T0369)E67.C and (T0369)F71.C only 0.000 apart, marking (T0369)F71.C as missing
WARNING: atoms too close: (T0369)D66.C and (T0369)F71.C only 0.000 apart, marking (T0369)F71.C as missing
WARNING: atoms too close: (T0369)A65.C and (T0369)F71.C only 0.000 apart, marking (T0369)F71.C as missing
WARNING: atoms too close: (T0369)T64.C and (T0369)F71.C only 0.000 apart, marking (T0369)F71.C as missing
WARNING: atoms too close: (T0369)A63.C and (T0369)F71.C only 0.000 apart, marking (T0369)F71.C as missing
# WARNING: incomplete conformation T0369 can't currently be optimized by undertaker
# naming current conformation panther2_TS1
# ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0369 can't currently be optimized by undertaker
# naming current conformation shub_TS1
# command:Using radius: 8.0000
Metaserver mode
NUMB_ALIGNS: 253
Adding 7268 constraints to all.constraints
Done adding distance constraints
# command:Reading probabilities from probabilities.dat
Reading constraints from ConstraintSet all.constraints
maxweight: 118.0000
Optimizing...
 Probability sum: -247.7024, CN propb: -247.7024 weights: 0.3490 constraints: 224
# command:Found ConstraintSet
# PrintContacts align.constraints_meta01
Number of constraints in align.constraints 224
# command:Found ConstraintSet
# PrintContacts align_bonus.constraints_meta01
Number of constraints in align.constraints.bonus 224
# command:Found ConstraintSet
# PrintContacts rejected.constraints_meta01
Number of constraints in rejected.constraints 7044
# command:Found ConstraintSet
# PrintContacts rejected_bonus.constraints_meta01
Number of constraints in rejected.constraints.bonus 7044
# 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 7268
# command: