# 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/T0305/
# command:# Making conformation for sequence T0305 numbered 1 through 297
Created new target T0305 from T0305.a2m
# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0305/
# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0305/
# command:# reading script from file servers-clean.under
# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0305/decoys/
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0305 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 T0305 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 T0305 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 T0305 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 T0305 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 T0305 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 T0305 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 T0305 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 T0305 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 T0305 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 T0305 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 T0305 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 T0305 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 T0305 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 T0305 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
# choosing archetypes in rotamer library
# Found a chain break before 234
# 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 286
# 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 290
# 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 290
# 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 246
# 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 292
# 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 279
# 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 292
# 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 266
# 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 269
# 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 188
# 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 40
# 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
# 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 275
# copying to AlignedFragments data structure
# naming current conformation Bilab-ENABLE_TS3
# ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS4.pdb.gz looking for model 1
# Found a chain break before 209
# copying to AlignedFragments data structure
# naming current conformation Bilab-ENABLE_TS4
# ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS5.pdb.gz looking for model 1
# Found a chain break before 222
# copying to AlignedFragments data structure
# naming current conformation Bilab-ENABLE_TS5
# ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1
# Found a chain break before 284
# copying to AlignedFragments data structure
# naming current conformation CIRCLE_TS1
# ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0305 can't currently be optimized by undertaker
# naming current conformation CIRCLE_TS2
# ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1
# Found a chain break before 294
# copying to AlignedFragments data structure
# naming current conformation CIRCLE_TS3
# ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0305 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 T0305 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation CIRCLE_TS5
# ReadConformPDB reading from PDB file servers/CPHmodels_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0305 can't currently be optimized by undertaker
# naming current conformation CPHmodels_TS1
# ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0305 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 T0305 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 T0305 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 T0305 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 T0305 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 T0305 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 T0305 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 T0305 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 T0305 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 T0305 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 275
# 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 T0305 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 283
# 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 T0305 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 T0305 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 275
# copying to AlignedFragments data structure
# naming current conformation FAMS_TS1
# ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1
# Found a chain break before 295
# copying to AlignedFragments data structure
# naming current conformation FAMS_TS2
# ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0305 can't currently be optimized by undertaker
# naming current conformation FAMS_TS3
# ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1
# Found a chain break before 290
# copying to AlignedFragments data structure
# naming current conformation FAMS_TS4
# ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1
# Found a chain break before 294
# copying to AlignedFragments data structure
# naming current conformation FAMS_TS5
# ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1
# Found a chain break before 234
# copying to AlignedFragments data structure
# naming current conformation FOLDpro_TS1
# ReadConformPDB reading from PDB file servers/FOLDpro_TS2.pdb.gz looking for model 1
# Found a chain break before 276
# copying to AlignedFragments data structure
# naming current conformation FOLDpro_TS2
# ReadConformPDB reading from PDB file servers/FOLDpro_TS3.pdb.gz looking for model 1
# Found a chain break before 244
# 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 256
# 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 255
# 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 T0305 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 T0305 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
Skipped atom 26, because occupancy 1 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 28, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 30, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 32, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 210, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 212, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 214, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 216, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 262, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 264, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 266, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 268, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 270, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 272, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 274, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 276, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 278, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 280, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 282, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 284, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 286, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 288, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 290, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 292, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 386, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 388, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 390, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 392, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 462, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 464, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 466, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 468, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 518, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 520, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 522, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 524, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 526, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 528, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 530, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 532, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 666, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 668, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 670, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 672, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 678, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 680, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 682, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 684, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 754, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 756, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 758, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 760, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 762, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 764, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 766, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 768, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 770, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 772, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 774, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 776, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 778, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 780, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 782, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 784, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 786, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 788, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 790, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 792, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 794, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 796, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 798, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 800, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 802, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 804, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 806, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 808, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 810, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 812, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 814, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 816, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 818, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 820, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 822, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 824, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 826, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 828, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 830, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 832, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 834, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 836, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 838, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 840, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 842, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 844, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 846, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 848, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 854, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 856, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 858, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 860, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 954, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 956, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 958, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 960, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 978, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 980, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 982, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 984, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 1002, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 1004, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 1006, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 1008, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 1074, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 1076, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 1078, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 1080, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 1106, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 1107, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 1109, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 1110, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 1112, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 1113, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 1115, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 1116, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
# WARNING: incomplete conformation T0305 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 T0305 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 T0305 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 T0305 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 T0305 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 T0305 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 T0305 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 T0305 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 280
# 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 289
# 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 260
# 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 228
# 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 296
# 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
# Found a chain break before 173
# 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 224
# copying to AlignedFragments data structure
# naming current conformation FUGMOD_TS2
# ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0305 can't currently be optimized by undertaker
# naming current conformation FUGMOD_TS3
# ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0305 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FUGMOD_TS4
# ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1
# Found a chain break before 248
# copying to AlignedFragments data structure
# naming current conformation FUGMOD_TS5
# ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0305 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 T0305 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 T0305 can't currently be optimized by undertaker
# naming current conformation FUGUE_AL3
# ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0305 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 T0305 can't currently be optimized by undertaker
# naming current conformation FUGUE_AL5
# ReadConformPDB reading from PDB file servers/FUNCTION_TS1.pdb.gz looking for model 1
# Found a chain break before 286
# 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 295
# 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 275
# 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 292
# 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 290
# copying to AlignedFragments data structure
# naming current conformation FUNCTION_TS5
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1
# Found a chain break before 124
# 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 124
# copying to AlignedFragments data structure
# naming current conformation GeneSilicoMetaServer_TS2
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1
# Found a chain break before 124
# copying to AlignedFragments data structure
# naming current conformation GeneSilicoMetaServer_TS3
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0305 can't currently be optimized by undertaker
# naming current conformation GeneSilicoMetaServer_TS4
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1
# Found a chain break before 124
# copying to AlignedFragments data structure
# naming current conformation GeneSilicoMetaServer_TS5
# ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1
# Found a chain break before 144
# copying to AlignedFragments data structure
# naming current conformation HHpred1_TS1
# ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1
# Found a chain break before 34
# 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 33
# 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 T0305 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 T0305 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 T0305 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 T0305 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 T0305 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 T0305 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 T0305 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 T0305 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 T0305 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 T0305 can't currently be optimized by undertaker
# naming current conformation LOOPP_TS5
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1
# Found a chain break before 124
# 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 40
# 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 124
# 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 199
# 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 162
# 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 296
# 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 290
# 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 284
# 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 239
# 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 278
# 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 T0305 can't currently be optimized by undertaker
# naming current conformation NN_PUT_lab_TS1
# 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 185
# 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 278
# copying to AlignedFragments data structure
# naming current conformation PROTINFO_TS2
# ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1
# naming current conformation PROTINFO_TS3
# ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0305 can't currently be optimized by undertaker
# naming current conformation PROTINFO_TS4
# ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0305 can't currently be optimized by undertaker
# naming current conformation PROTINFO_TS5
# ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0305 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 T0305 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 T0305 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 T0305 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 T0305 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 T0305 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 175
# 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 171
# 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 171
# 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 171
# copying to AlignedFragments data structure
# naming current conformation Phyre-2_TS4
# ReadConformPDB reading from PDB file servers/Phyre-2_TS5.pdb.gz looking for model 1
# Found a chain break before 175
# 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 T0305 can't currently be optimized by undertaker
# naming current conformation Pmodeller6_TS1
# ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0305 can't currently be optimized by undertaker
# naming current conformation Pmodeller6_TS2
# ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0305 can't currently be optimized by undertaker
# naming current conformation Pmodeller6_TS3
# ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0305 can't currently be optimized by undertaker
# naming current conformation Pmodeller6_TS4
# ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0305 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 124
# 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 40
# copying to AlignedFragments data structure
# naming current conformation RAPTOR-ACE_TS2
# ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1
# Found a chain break before 275
# 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 234
# 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 124
# 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 183
# 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 271
# 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 261
# 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 277
# copying to AlignedFragments data structure
# naming current conformation RAPTORESS_TS5
# ReadConformPDB reading from PDB file servers/RAPTOR_TS1.pdb.gz looking for model 1
# Found a chain break before 40
# copying to AlignedFragments data structure
# naming current conformation RAPTOR_TS1
# ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1
# Found a chain break before 124
# 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 191
# 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 174
# 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 174
# 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 225
# 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 225
# 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 225
# 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 225
# 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 225
# copying to AlignedFragments data structure
# naming current conformation ROBETTA_TS5
# ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1
# Found a chain break before 234
# copying to AlignedFragments data structure
# naming current conformation ROKKY_TS1
# ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1
# Found a chain break before 185
# copying to AlignedFragments data structure
# naming current conformation ROKKY_TS2
# ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1
# Found a chain break before 124
# copying to AlignedFragments data structure
# naming current conformation ROKKY_TS3
# ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1
# Found a chain break before 275
# copying to AlignedFragments data structure
# naming current conformation ROKKY_TS4
# ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1
# Found a chain break before 277
# 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 T0305 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 T0305 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 T0305 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
Skipped atom 26, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 28, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 30, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 32, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 162, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 164, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 166, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 168, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 326, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 328, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 330, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 332, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 622, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 624, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 626, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 628, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 830, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 832, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 834, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 836, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 914, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 916, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 918, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 920, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
# WARNING: incomplete conformation T0305 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 T0305 can't currently be optimized by undertaker
# naming current conformation SAM-T02_AL5
# ReadConformPDB reading from PDB file servers/SAM-T99_AL1.pdb.gz looking for model 1
Skipped atom 38, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz
Skipped atom 40, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz
Skipped atom 42, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz
Skipped atom 44, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz
Skipped atom 174, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz
Skipped atom 176, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz
Skipped atom 178, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz
Skipped atom 180, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz
Skipped atom 338, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz
Skipped atom 340, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz
Skipped atom 342, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz
Skipped atom 344, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz
Skipped atom 634, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz
Skipped atom 636, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz
Skipped atom 638, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz
Skipped atom 640, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz
Skipped atom 842, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz
Skipped atom 844, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz
Skipped atom 846, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz
Skipped atom 848, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz
Skipped atom 926, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz
Skipped atom 928, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz
Skipped atom 930, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz
Skipped atom 932, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz
# WARNING: incomplete conformation T0305 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 585, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL2.pdb.gz
Skipped atom 770, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL2.pdb.gz
# WARNING: incomplete conformation T0305 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 T0305 can't currently be optimized by undertaker
# naming current conformation SAM-T99_AL3
# ReadConformPDB reading from PDB file servers/SAM-T99_AL4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0305 can't currently be optimized by undertaker
# naming current conformation SAM-T99_AL4
# ReadConformPDB reading from PDB file servers/SAM-T99_AL5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0305 can't currently be optimized by undertaker
# naming current conformation SAM-T99_AL5
# ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1
# Found a chain break before 279
# 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 T0305 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 T0305 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 T0305 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 T0305 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 258
# 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 41
# 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 124
# 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 184
# 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 283
# copying to AlignedFragments data structure
# naming current conformation SP3_TS5
# ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1
# Found a chain break before 258
# copying to AlignedFragments data structure
# naming current conformation SP4_TS1
# ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1
# Found a chain break before 124
# 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 92
# 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 184
# 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 278
# 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 258
# 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 227
# 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 92
# 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 124
# 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 40
# 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 T0305 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 T0305 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 T0305 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 T0305 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 T0305 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: (T0305)T174.CA and (T0305)K185.CA only 0.000 apart, marking (T0305)K185.CA as missing
# WARNING: incomplete conformation T0305 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 T0305 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
Skipped atom 131, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz
Skipped atom 792, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz
Skipped atom 1049, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz
# WARNING: incomplete conformation T0305 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 987, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz
# WARNING: incomplete conformation T0305 can't currently be optimized by undertaker
# naming current conformation UNI-EID_sfst_AL3
# ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0305 can't currently be optimized by undertaker
# naming current conformation UNI-EID_sfst_AL4
# ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL5.pdb.gz looking for model 1
Skipped atom 585, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz
Skipped atom 770, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz
# WARNING: incomplete conformation T0305 can't currently be optimized by undertaker
# naming current conformation UNI-EID_sfst_AL5
# ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1
# Found a chain break before 239
# 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 279
# 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 279
# 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 74
# 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 279
# 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 278
# copying to AlignedFragments data structure
# naming current conformation beautshot_TS1
# ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1
# Found a chain break before 278
# copying to AlignedFragments data structure
# naming current conformation beautshotbase_TS1
# ReadConformPDB reading from PDB file servers/forecast-s_AL1.pdb.gz looking for model 1
Skipped atom 18, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 20, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 22, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 24, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 202, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 204, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 206, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 208, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 254, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 256, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 258, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 260, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 262, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 264, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 266, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 268, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 270, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 272, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 274, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 276, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 278, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 280, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 282, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 284, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 378, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 380, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 382, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 384, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 454, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 456, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 458, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 460, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 510, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 512, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 514, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 516, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 518, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 520, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 522, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 524, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 658, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 660, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 662, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 664, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 670, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 672, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 674, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 676, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 746, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 748, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 750, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 752, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 754, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 756, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 758, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 760, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 762, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 764, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 766, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 768, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 770, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 772, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 774, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 776, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 778, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 780, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 782, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 784, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 786, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 788, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 790, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 792, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 794, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 796, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 798, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 800, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 802, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 804, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 806, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 808, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 810, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 812, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 814, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 816, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 818, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 820, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 822, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 824, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 826, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 828, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 830, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 832, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 834, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 836, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 838, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 840, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 846, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 848, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 850, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 852, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 946, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 948, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 950, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 952, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 970, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 972, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 974, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 976, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 994, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 996, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 998, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 1000, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 1066, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 1068, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 1070, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 1072, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 1098, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 1099, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 1101, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 1102, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 1104, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 1105, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 1107, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 1108, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
# WARNING: incomplete conformation T0305 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 T0305 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 T0305 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 T0305 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 T0305 can't currently be optimized by undertaker
# naming current conformation forecast-s_AL5
# ReadConformPDB reading from PDB file servers/gtg_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0305 can't currently be optimized by undertaker
# naming current conformation gtg_AL1
# ReadConformPDB reading from PDB file servers/gtg_AL2.pdb.gz looking for model 1
Skipped atom 622, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz
Skipped atom 624, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz
Skipped atom 626, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz
Skipped atom 628, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz
# WARNING: incomplete conformation T0305 can't currently be optimized by undertaker
# naming current conformation gtg_AL2
# ReadConformPDB reading from PDB file servers/gtg_AL3.pdb.gz looking for model 1
Skipped atom 585, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL3.pdb.gz
Skipped atom 770, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL3.pdb.gz
# WARNING: incomplete conformation T0305 can't currently be optimized by undertaker
# naming current conformation gtg_AL3
# ReadConformPDB reading from PDB file servers/gtg_AL4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0305 can't currently be optimized by undertaker
# naming current conformation gtg_AL4
# ReadConformPDB reading from PDB file servers/gtg_AL5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0305 can't currently be optimized by undertaker
# naming current conformation gtg_AL5
# ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1
# Found a chain break before 275
# 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 174
# 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 40
# 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 209
# 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 147
# 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 294
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.4_TS1
# ReadConformPDB reading from PDB file servers/karypis.srv.4_TS2.pdb.gz looking for model 1
# Found a chain break before 294
# 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
WARNING: atoms too close: (T0305)S157.O and (T0305)T158.N only 0.000 apart, marking (T0305)T158.N as missing
# WARNING: incomplete conformation T0305 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.4_TS3
# ReadConformPDB reading from PDB file servers/karypis.srv.4_TS4.pdb.gz looking for model 1
WARNING: atoms too close: (T0305)V129.O and (T0305)E130.N only 0.000 apart, marking (T0305)E130.N as missing
# WARNING: incomplete conformation T0305 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.4_TS4
# ReadConformPDB reading from PDB file servers/karypis.srv.4_TS5.pdb.gz looking for model 1
WARNING: atoms too close: (T0305)Q3.O and (T0305)S4.N only 0.000 apart, marking (T0305)S4.N as missing
WARNING: atoms too close: (T0305)L68.O and (T0305)R69.N only 0.000 apart, marking (T0305)R69.N as missing
# WARNING: incomplete conformation T0305 can't currently be optimized by undertaker
# 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 T0305 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 T0305 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 T0305 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 T0305 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 T0305 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
# Found a chain break before 233
# copying to AlignedFragments data structure
# naming current conformation keasar-server_TS1
# ReadConformPDB reading from PDB file servers/keasar-server_TS2.pdb.gz looking for model 1
# Found a chain break before 233
# copying to AlignedFragments data structure
# naming current conformation keasar-server_TS2
# ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1
# Found a chain break before 274
# copying to AlignedFragments data structure
# naming current conformation keasar-server_TS3
# ReadConformPDB reading from PDB file servers/keasar-server_TS4.pdb.gz looking for model 1
# Found a chain break before 235
# copying to AlignedFragments data structure
# naming current conformation keasar-server_TS4
# ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1
# Found a chain break before 233
# copying to AlignedFragments data structure
# naming current conformation keasar-server_TS5
# ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0305 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 T0305 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 T0305 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 T0305 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 T0305 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 T0305 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
# Found a chain break before 278
# copying to AlignedFragments data structure
# naming current conformation shub_TS1
# command:Using radius: 8.0000
Metaserver mode
NUMB_ALIGNS: 257
Adding 11856 constraints to all.constraints
Done adding distance constraints
# command:Reading probabilities from probabilities.dat
Reading constraints from ConstraintSet all.constraints
maxweight: 229.0000
Optimizing...
 Probability sum: -513.3979, CN propb: -513.3979 weights: 0.3963 constraints: 877
# command:Found ConstraintSet
# PrintContacts align.constraints_meta01
Number of constraints in align.constraints 877
# command:Found ConstraintSet
# PrintContacts align_bonus.constraints_meta01
Number of constraints in align.constraints.bonus 877
# command:Found ConstraintSet
# PrintContacts rejected.constraints_meta01
Number of constraints in rejected.constraints 10979
# command:Found ConstraintSet
# PrintContacts rejected_bonus.constraints_meta01
Number of constraints in rejected.constraints.bonus 10979
# 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 11856
# command: