# 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/T0348/
# command:# Making conformation for sequence T0348 numbered 1 through 68
Created new target T0348 from T0348.a2m
# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0348/
# command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0348//projects/compbio/experiments/protein-predict/casp7/T0348/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0348//projects/compbio/experiments/protein-predict/casp7/T0348/align.constraints_v3.costfcn.gz for input
Trying /projects/compbio/experiments/protein-predict/casp7/T0348/align.constraints_v3.costfcn
# reading script from file /projects/compbio/experiments/protein-predict/casp7/T0348/align.constraints_v3.costfcn
# future Constraint commands -> align
# future HelixConstraint commands -> align
# future StrandConstraint commands -> align
# future SheetConstraint commands -> align
# future Hbond commands -> align
# future SSbond commands -> align
# Constraint # added constraint: constraint((T0348)L27.CB, (T0348)F36.CB) [> 3.0925 = 5.1542 < 6.7005] w=0.8458 to align
# Constraint # added constraint: constraint((T0348)L18.CB, (T0348)L27.CB) [> 3.1831 = 5.3052 < 6.8968] w=0.8063 to align
# Constraint # added constraint: constraint((T0348)L18.CB, (T0348)C29.CB) [> 3.1947 = 5.3245 < 6.9218] w=0.7873 to align
# Constraint # added constraint: constraint((T0348)C14.CB, (T0348)G31.CA) [> 4.0200 = 6.7001 < 8.7101] w=0.7784 to align
# Constraint # added constraint: constraint((T0348)C11.CB, (T0348)C29.CB) [> 2.6475 = 4.4125 < 5.7363] w=0.7784 to align
# Constraint # added constraint: constraint((T0348)L18.CB, (T0348)I28.CB) [> 4.0365 = 6.7275 < 8.7457] w=0.7442 to align
# Constraint # added constraint: constraint((T0348)V19.CB, (T0348)I28.CB) [> 3.4062 = 5.6771 < 7.3802] w=0.7442 to align
# Constraint # added constraint: constraint((T0348)E26.CB, (T0348)F36.CB) [> 3.9985 = 6.6641 < 8.6633] w=0.7381 to align
# Constraint # added constraint: constraint((T0348)V19.CB, (T0348)K30.CB) [> 3.7385 = 6.2309 < 8.1001] w=0.7244 to align
# Constraint # added constraint: constraint((T0348)C14.CB, (T0348)C29.CB) [> 3.9582 = 6.5970 < 8.5761] w=0.7184 to align
# Constraint # added constraint: constraint((T0348)G16.CA, (T0348)C29.CB) [> 4.1271 = 6.8785 < 8.9420] w=0.7181 to align
# Constraint # added constraint: constraint((T0348)L13.CB, (T0348)C29.CB) [> 4.1017 = 6.8362 < 8.8871] w=0.6728 to align
# Constraint # added constraint: constraint((T0348)C11.CB, (T0348)L34.CB) [> 3.7636 = 6.2727 < 8.1545] w=0.6579 to align
# Constraint # added constraint: constraint((T0348)L13.CB, (T0348)L34.CB) [> 3.1901 = 5.3168 < 6.9119] w=0.6490 to align
# Constraint # added constraint: constraint((T0348)E26.CB, (T0348)P37.CB) [> 3.5204 = 5.8674 < 7.6276] w=0.5961 to align
# Constraint # added constraint: constraint((T0348)L27.CB, (T0348)P37.CB) [> 4.4160 = 7.3600 < 9.5680] w=0.5585 to align
# Constraint # added constraint: constraint((T0348)P12.CB, (T0348)L34.CB) [> 4.0205 = 6.7009 < 8.7112] w=0.5045 to align
# Constraint # added constraint: constraint((T0348)P12.CB, (T0348)F36.CB) [> 3.8414 = 6.4022 < 8.3229] w=0.4524 to align
# Constraint # added constraint: constraint((T0348)P17.CB, (T0348)C29.CB) [> 3.7102 = 6.1837 < 8.0388] w=0.4174 to align
# Constraint # added constraint: constraint((T0348)E26.CB, (T0348)I38.CB) [> 4.2955 = 7.1591 < 9.3069] w=0.4146 to align
# Constraint # added constraint: constraint((T0348)C14.CB, (T0348)L34.CB) [> 4.2489 = 7.0815 < 9.2059] w=0.4083 to align
# Constraint # added constraint: constraint((T0348)L18.CB, (T0348)F36.CB) [> 4.1590 = 6.9316 < 9.0111] w=0.3701 to align
# Constraint # added constraint: constraint((T0348)L18.CB, (T0348)L34.CB) [> 4.3743 = 7.2905 < 9.4777] w=0.3092 to align
# Constraint # added constraint: constraint((T0348)D21.CB, (T0348)A35.CB) [> 4.3010 = 7.1684 < 9.3189] w=0.2419 to align
# Constraint # added constraint: constraint((T0348)C11.CB, (T0348)F36.CB) [> 3.4585 = 5.7642 < 7.4935] w=0.1820 to align
# Constraint # added constraint: constraint((T0348)P12.CB, (T0348)P43.CB) [> 3.5293 = 5.8821 < 7.6468] w=0.1249 to align
# Constraint # added constraint: constraint((T0348)P43.CB, (T0348)L53.CB) [> 3.3735 = 5.6226 < 7.3094] w=0.1246 to align
# Constraint # added constraint: constraint((T0348)I42.CB, (T0348)L53.CB) [> 3.1845 = 5.3075 < 6.8998] w=0.1246 to align
# Constraint # added constraint: constraint((T0348)L13.CB, (T0348)F36.CB) [> 3.2192 = 5.3654 < 6.9750] w=0.1182 to align
# Constraint # added constraint: constraint((T0348)F36.CB, (T0348)L46.CB) [> 3.6710 = 6.1183 < 7.9538] w=0.1056 to align
# Constraint # added constraint: constraint((T0348)K15.CB, (T0348)G31.CA) [> 3.5735 = 5.9559 < 7.7426] w=0.1055 to align
# Constraint # added constraint: constraint((T0348)K15.CB, (T0348)C29.CB) [> 3.9391 = 6.5652 < 8.5347] w=0.1055 to align
# Constraint # added constraint: constraint((T0348)I38.CB, (T0348)L61.CB) [> 3.4868 = 5.8113 < 7.5546] w=0.1055 to align
# Constraint # added constraint: constraint((T0348)P12.CB, (T0348)M44.CB) [> 4.1044 = 6.8406 < 8.8928] w=0.1048 to align
# Constraint # added constraint: constraint((T0348)P37.CB, (T0348)A50.CB) [> 3.6268 = 6.0447 < 7.8581] w=0.1043 to align
# Constraint # added constraint: constraint((T0348)A35.CB, (T0348)L46.CB) [> 3.2701 = 5.4502 < 7.0852] w=0.1043 to align
# Constraint # added constraint: constraint((T0348)A35.CB, (T0348)M45.CB) [> 4.4349 = 7.3916 < 9.6090] w=0.1043 to align
# Constraint # added constraint: constraint((T0348)A35.CB, (T0348)M44.CB) [> 3.1712 = 5.2853 < 6.8709] w=0.1031 to align
# Constraint # added constraint: constraint((T0348)C29.CB, (T0348)I38.CB) [> 4.2430 = 7.0717 < 9.1932] w=0.0846 to align
# Constraint # added constraint: constraint((T0348)I28.CB, (T0348)I38.CB) [> 4.0407 = 6.7344 < 8.7548] w=0.0846 to align
# Constraint # added constraint: constraint((T0348)L18.CB, (T0348)P43.CB) [> 3.4177 = 5.6961 < 7.4049] w=0.0831 to align
# Constraint # added constraint: constraint((T0348)F20.CB, (T0348)G41.CA) [> 4.0736 = 6.7893 < 8.8261] w=0.0831 to align
# Constraint # added constraint: constraint((T0348)L27.CB, (T0348)P43.CB) [> 2.8367 = 4.7278 < 6.1461] w=0.0831 to align
# Constraint # added constraint: constraint((T0348)I42.CB, (T0348)A54.CB) [> 3.6380 = 6.0634 < 7.8824] w=0.0831 to align
# Constraint # added constraint: constraint((T0348)D40.CB, (T0348)L61.CB) [> 3.3569 = 5.5948 < 7.2732] w=0.0818 to align
# Constraint # added constraint: constraint((T0348)L9.CB, (T0348)L18.CB) [> 3.8206 = 6.3677 < 8.2780] w=0.0710 to align
# Constraint # added constraint: constraint((T0348)C11.CB, (T0348)P43.CB) [> 4.6839 = 7.8064 < 10.1484] w=0.0641 to align
# Constraint # added constraint: constraint((T0348)F20.CB, (T0348)I38.CB) [> 3.8869 = 6.4781 < 8.4215] w=0.0641 to align
# Constraint # added constraint: constraint((T0348)D25.CB, (T0348)L46.CB) [> 4.3767 = 7.2944 < 9.4828] w=0.0641 to align
# Constraint # added constraint: constraint((T0348)D25.CB, (T0348)A50.CB) [> 4.2545 = 7.0908 < 9.2180] w=0.0641 to align
# Constraint # added constraint: constraint((T0348)L34.CB, (T0348)M45.CB) [> 4.2167 = 7.0279 < 9.1363] w=0.0641 to align
# Constraint # added constraint: constraint((T0348)P37.CB, (T0348)L46.CB) [> 3.2927 = 5.4879 < 7.1343] w=0.0641 to align
# Constraint # added constraint: constraint((T0348)E26.CB, (T0348)K39.CB) [> 4.0713 = 6.7854 < 8.8210] w=0.0639 to align
# Constraint # added constraint: constraint((T0348)L34.CB, (T0348)P43.CB) [> 4.6395 = 7.7325 < 10.0522] w=0.0629 to align
# Constraint # added constraint: constraint((T0348)I42.CB, (T0348)L61.CB) [> 4.1555 = 6.9258 < 9.0035] w=0.0603 to align
# Constraint # added constraint: constraint((T0348)C11.CB, (T0348)L27.CB) [> 4.7345 = 7.8908 < 10.2581] w=0.0596 to align
# Constraint # added constraint: constraint((T0348)F5.CB, (T0348)L18.CB) [> 3.9930 = 6.6550 < 8.6516] w=0.0515 to align
# Constraint # added constraint: constraint((T0348)F5.CB, (T0348)L27.CB) [> 4.3353 = 7.2255 < 9.3931] w=0.0515 to align
# Constraint # added constraint: constraint((T0348)I8.CB, (T0348)P17.CB) [> 4.2969 = 7.1615 < 9.3100] w=0.0515 to align
# Constraint # added constraint: constraint((T0348)I8.CB, (T0348)L18.CB) [> 3.0447 = 5.0744 < 6.5967] w=0.0515 to align
# Constraint # added constraint: constraint((T0348)L9.CB, (T0348)V19.CB) [> 4.6426 = 7.7377 < 10.0591] w=0.0515 to align
# Constraint # added constraint: constraint((T0348)L9.CB, (T0348)F20.CB) [> 3.8485 = 6.4142 < 8.3384] w=0.0515 to align
# Constraint # added constraint: constraint((T0348)L9.CB, (T0348)L27.CB) [> 3.6388 = 6.0647 < 7.8841] w=0.0515 to align
# Constraint # added constraint: constraint((T0348)V10.CB, (T0348)C29.CB) [> 4.6185 = 7.6976 < 10.0069] w=0.0427 to align
# Constraint # added constraint: constraint((T0348)E47.CB, (T0348)E58.CB) [> 4.1304 = 6.8840 < 8.9492] w=0.0427 to align
# Constraint # added constraint: constraint((T0348)E49.CB, (T0348)E58.CB) [> 3.8181 = 6.3635 < 8.2726] w=0.0427 to align
# Constraint # added constraint: constraint((T0348)D25.CB, (T0348)I42.CB) [> 2.5337 = 4.2228 < 5.4896] w=0.0426 to align
# Constraint # added constraint: constraint((T0348)L18.CB, (T0348)L46.CB) [> 3.4894 = 5.8157 < 7.5604] w=0.0403 to align
# Constraint # added constraint: constraint((T0348)G16.CA, (T0348)L46.CB) [> 4.2716 = 7.1193 < 9.2551] w=0.0403 to align
# Constraint # added constraint: constraint((T0348)L13.CB, (T0348)M45.CB) [> 3.0315 = 5.0526 < 6.5683] w=0.0403 to align
# Constraint # added constraint: constraint((T0348)P37.CB, (T0348)L53.CB) [> 4.2553 = 7.0922 < 9.2199] w=0.0403 to align
# Constraint # added constraint: constraint((T0348)A35.CB, (T0348)A50.CB) [> 4.5300 = 7.5499 < 9.8149] w=0.0403 to align
# Constraint # added constraint: constraint((T0348)A35.CB, (T0348)E47.CB) [> 4.1113 = 6.8521 < 8.9078] w=0.0403 to align
# Constraint # added constraint: constraint((T0348)R33.CB, (T0348)M44.CB) [> 4.2418 = 7.0697 < 9.1906] w=0.0403 to align
# Constraint # added constraint: constraint((T0348)D32.CB, (T0348)E47.CB) [> 3.8394 = 6.3991 < 8.3188] w=0.0403 to align
# Constraint # added constraint: constraint((T0348)D32.CB, (T0348)L46.CB) [> 3.3984 = 5.6640 < 7.3632] w=0.0403 to align
# Constraint # added constraint: constraint((T0348)C14.CB, (T0348)P37.CB) [> 3.4883 = 5.8139 < 7.5580] w=0.0392 to align
# Constraint # added constraint: constraint((T0348)G16.CA, (T0348)I28.CB) [> 3.4298 = 5.7164 < 7.4313] w=0.0210 to align
# Constraint # added constraint: constraint((T0348)P17.CB, (T0348)I28.CB) [> 2.5612 = 4.2687 < 5.5493] w=0.0210 to align
# Constraint # added constraint: constraint((T0348)P37.CB, (T0348)R51.CB) [> 3.9392 = 6.5654 < 8.5351] w=0.0208 to align
# Constraint # added constraint: constraint((T0348)C14.CB, (T0348)M45.CB) [> 4.7983 = 7.9972 < 10.3963] w=0.0207 to align
# Constraint # added constraint: constraint((T0348)C14.CB, (T0348)L46.CB) [> 3.4263 = 5.7105 < 7.4237] w=0.0207 to align
# Constraint # added constraint: constraint((T0348)L6.CB, (T0348)L18.CB) [> 4.3950 = 7.3249 < 9.5224] w=0.0195 to align
# Constraint # added constraint: constraint((T0348)P12.CB, (T0348)M45.CB) [> 4.7103 = 7.8505 < 10.2057] w=0.0195 to align
# Constraint # added constraint: constraint((T0348)L13.CB, (T0348)A50.CB) [> 4.7223 = 7.8705 < 10.2316] w=0.0195 to align
# Constraint # added constraint: constraint((T0348)L18.CB, (T0348)M44.CB) [> 4.6389 = 7.7316 < 10.0510] w=0.0195 to align
# Constraint # added constraint: constraint((T0348)D32.CB, (T0348)M44.CB) [> 4.6351 = 7.7252 < 10.0427] w=0.0195 to align
# Constraint # added constraint: constraint((T0348)D32.CB, (T0348)M45.CB) [> 4.7753 = 7.9588 < 10.3465] w=0.0195 to align
# SetCost created cost = 
#	( 1.0000 * align )
# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0348/
# command:# reading script from file servers-clean.under
# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0348/decoys/
# ReadConformPDB reading from PDB file chimera-M1-K60-2-8.pdb.gz looking for model 1
# choosing archetypes in rotamer library
# Found a chain break before 45
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1
# Found a chain break before 58
# 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 42
# copying to AlignedFragments data structure
# naming current conformation 3D-JIGSAW_POPULUS_TS2
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0348 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation 3D-JIGSAW_POPULUS_TS3
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS4.pdb.gz looking for model 1
# Found a chain break before 58
# 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 58
# 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 T0348 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation 3D-JIGSAW_RECOM_TS1
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0348 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# 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 T0348 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# 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 T0348 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# 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 T0348 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# 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 T0348 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation 3D-JIGSAW_TS1
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0348 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 T0348 can't currently be optimized by undertaker
# 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 T0348 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
# Found a chain break before 58
# copying to AlignedFragments data structure
# naming current conformation 3D-JIGSAW_TS5
# ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1
# naming current conformation 3Dpro_TS1
# ReadConformPDB reading from PDB file servers/3Dpro_TS2.pdb.gz looking for model 1
# naming current conformation 3Dpro_TS2
# ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1
# Found a chain break before 17
# 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 57
# 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 59
# 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 57
# 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 59
# 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 63
# 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 45
# 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 34
# 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 48
# 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
# naming current conformation Bilab-ENABLE_TS1
# ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS2.pdb.gz looking for model 1
# Found a chain break before 67
# copying to AlignedFragments data structure
# naming current conformation Bilab-ENABLE_TS2
# ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS3.pdb.gz looking for model 1
# Found a chain break before 67
# 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 67
# 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 67
# 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 64
# 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 T0348 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 54
# copying to AlignedFragments data structure
# naming current conformation CIRCLE_TS3
# ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1
# Found a chain break before 43
# copying to AlignedFragments data structure
# naming current conformation CIRCLE_TS4
# ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1
# Found a chain break before 43
# copying to AlignedFragments data structure
# naming current conformation CIRCLE_TS5
# ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0348 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
# Found a chain break before 54
# copying to AlignedFragments data structure
# naming current conformation CaspIta-FOX_TS2
# ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0348 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 T0348 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: atoms too close: (T0348)S48.C and (T0348)E49.N only 0 apart, marking (T0348)E49.N as missing
WARNING: atoms too close: (T0348)E49.N and (T0348)E49.CA only 0 apart, marking (T0348)E49.CA as missing
WARNING: atoms too close: (T0348)S48.C and (T0348)E49.CA only 0 apart, marking (T0348)E49.CA as missing
WARNING: atoms too close: (T0348)E49.CA and (T0348)E49.CB only 0 apart, marking (T0348)E49.CB as missing
WARNING: atoms too close: (T0348)E49.N and (T0348)E49.CB only 0 apart, marking (T0348)E49.CB as missing
WARNING: atoms too close: (T0348)S48.C and (T0348)E49.CB only 0 apart, marking (T0348)E49.CB as missing
WARNING: atoms too close: (T0348)E49.CB and (T0348)E49.CG only 0 apart, marking (T0348)E49.CG as missing
WARNING: atoms too close: (T0348)E49.CA and (T0348)E49.CG only 0 apart, marking (T0348)E49.CG as missing
WARNING: atoms too close: (T0348)E49.N and (T0348)E49.CG only 0 apart, marking (T0348)E49.CG as missing
WARNING: atoms too close: (T0348)S48.C and (T0348)E49.CG only 0 apart, marking (T0348)E49.CG as missing
WARNING: atoms too close: (T0348)E49.CG and (T0348)E49.CD only 0 apart, marking (T0348)E49.CD as missing
WARNING: atoms too close: (T0348)E49.CB and (T0348)E49.CD only 0 apart, marking (T0348)E49.CD as missing
WARNING: atoms too close: (T0348)E49.CA and (T0348)E49.CD only 0 apart, marking (T0348)E49.CD as missing
WARNING: atoms too close: (T0348)E49.N and (T0348)E49.CD only 0 apart, marking (T0348)E49.CD as missing
WARNING: atoms too close: (T0348)S48.C and (T0348)E49.CD only 0 apart, marking (T0348)E49.CD as missing
WARNING: atoms too close: (T0348)E49.CD and (T0348)E49.OE1 only 0 apart, marking (T0348)E49.OE1 as missing
WARNING: atoms too close: (T0348)E49.CG and (T0348)E49.OE1 only 0 apart, marking (T0348)E49.OE1 as missing
WARNING: atoms too close: (T0348)E49.CB and (T0348)E49.OE1 only 0 apart, marking (T0348)E49.OE1 as missing
WARNING: atoms too close: (T0348)E49.CA and (T0348)E49.OE1 only 0 apart, marking (T0348)E49.OE1 as missing
WARNING: atoms too close: (T0348)E49.N and (T0348)E49.OE1 only 0 apart, marking (T0348)E49.OE1 as missing
WARNING: atoms too close: (T0348)S48.C and (T0348)E49.OE1 only 0 apart, marking (T0348)E49.OE1 as missing
WARNING: atoms too close: (T0348)E49.OE1 and (T0348)E49.OE2 only 0 apart, marking (T0348)E49.OE2 as missing
WARNING: atoms too close: (T0348)E49.CD and (T0348)E49.OE2 only 0 apart, marking (T0348)E49.OE2 as missing
WARNING: atoms too close: (T0348)E49.CG and (T0348)E49.OE2 only 0 apart, marking (T0348)E49.OE2 as missing
WARNING: atoms too close: (T0348)E49.CB and (T0348)E49.OE2 only 0 apart, marking (T0348)E49.OE2 as missing
WARNING: atoms too close: (T0348)E49.CA and (T0348)E49.OE2 only 0 apart, marking (T0348)E49.OE2 as missing
WARNING: atoms too close: (T0348)E49.N and (T0348)E49.OE2 only 0 apart, marking (T0348)E49.OE2 as missing
WARNING: atoms too close: (T0348)S48.C and (T0348)E49.OE2 only 0 apart, marking (T0348)E49.OE2 as missing
WARNING: atoms too close: (T0348)E49.OE2 and (T0348)E49.O only 0 apart, marking (T0348)E49.O as missing
WARNING: atoms too close: (T0348)E49.OE1 and (T0348)E49.O only 0 apart, marking (T0348)E49.O as missing
WARNING: atoms too close: (T0348)E49.CD and (T0348)E49.O only 0 apart, marking (T0348)E49.O as missing
WARNING: atoms too close: (T0348)E49.CG and (T0348)E49.O only 0 apart, marking (T0348)E49.O as missing
WARNING: atoms too close: (T0348)E49.CB and (T0348)E49.O only 0 apart, marking (T0348)E49.O as missing
WARNING: atoms too close: (T0348)E49.CA and (T0348)E49.O only 0 apart, marking (T0348)E49.O as missing
WARNING: atoms too close: (T0348)E49.N and (T0348)E49.O only 0 apart, marking (T0348)E49.O as missing
WARNING: atoms too close: (T0348)S48.C and (T0348)E49.O only 0 apart, marking (T0348)E49.O as missing
WARNING: atoms too close: (T0348)E49.O and (T0348)E49.C only 0 apart, marking (T0348)E49.C as missing
WARNING: atoms too close: (T0348)E49.OE2 and (T0348)E49.C only 0 apart, marking (T0348)E49.C as missing
WARNING: atoms too close: (T0348)E49.OE1 and (T0348)E49.C only 0 apart, marking (T0348)E49.C as missing
WARNING: atoms too close: (T0348)E49.CD and (T0348)E49.C only 0 apart, marking (T0348)E49.C as missing
WARNING: atoms too close: (T0348)E49.CG and (T0348)E49.C only 0 apart, marking (T0348)E49.C as missing
WARNING: atoms too close: (T0348)E49.CB and (T0348)E49.C only 0 apart, marking (T0348)E49.C as missing
WARNING: atoms too close: (T0348)E49.CA and (T0348)E49.C only 0 apart, marking (T0348)E49.C as missing
WARNING: atoms too close: (T0348)E49.N and (T0348)E49.C only 0 apart, marking (T0348)E49.C as missing
WARNING: atoms too close: (T0348)S48.C and (T0348)E49.C only 0 apart, marking (T0348)E49.C as missing
# WARNING: incomplete conformation T0348 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 T0348 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 T0348 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 T0348 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 T0348 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 T0348 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 66
# copying to AlignedFragments data structure
# naming current conformation FAMSD_TS1
# ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1
# Found a chain break before 57
# copying to AlignedFragments data structure
# naming current conformation FAMSD_TS2
# ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0348 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FAMSD_TS3
# ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation FAMSD_TS4
# ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1
# Found a chain break before 46
# copying to AlignedFragments data structure
# naming current conformation FAMSD_TS5
# ReadConformPDB reading from PDB file servers/FAMS_TS1.pdb.gz looking for model 1
# Found a chain break before 65
# 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 64
# 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 T0348 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 54
# 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 T0348 can't currently be optimized by undertaker
# 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 38
# 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
# 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
# naming current conformation FOLDpro_TS5
# ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0348 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 30, because occupancy 1 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 32, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 34, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 36, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
# WARNING: incomplete conformation T0348 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 T0348 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FORTE1_AL3
# ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0348 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FORTE1_AL4
# ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0348 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FORTE1_AL5
# ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0348 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 T0348 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FORTE2_AL2
# ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1
Skipped atom 30, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz
Skipped atom 32, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz
Skipped atom 34, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz
Skipped atom 36, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz
# WARNING: incomplete conformation T0348 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 T0348 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FORTE2_AL4
# ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0348 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FORTE2_AL5
# ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS1.pdb.gz looking for model 1
# 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 23
# 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 16
# 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
# naming current conformation FPSOLVER-SERVER_TS4
# ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS5.pdb.gz looking for model 1
# 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 21
# copying to AlignedFragments data structure
# naming current conformation FUGMOD_TS1
# ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1
# naming current conformation FUGMOD_TS2
# ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1
# naming current conformation FUGMOD_TS3
# ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1
# 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
# WARNING: incomplete conformation T0348 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 T0348 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FUGUE_AL2
# ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0348 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 T0348 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 T0348 can't currently be optimized by undertaker
# naming current conformation FUGUE_AL5
# ReadConformPDB reading from PDB file servers/FUNCTION_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0348 can't currently be optimized by undertaker
# naming current conformation FUNCTION_TS1
# ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1
# Found a chain break before 67
# 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 63
# 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 55
# 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 58
# 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 5
# copying to AlignedFragments data structure
# naming current conformation Frankenstein_TS2
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0348 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
# naming current conformation GeneSilicoMetaServer_TS2
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0348 can't currently be optimized by undertaker
# naming current conformation GeneSilicoMetaServer_TS3
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0348 can't currently be optimized by undertaker
# naming current conformation GeneSilicoMetaServer_TS4
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0348 can't currently be optimized by undertaker
# naming current conformation GeneSilicoMetaServer_TS5
# ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1
# Found a chain break before 10
# 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 10
# copying to AlignedFragments data structure
# naming current conformation HHpred2_TS1
# ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1
# naming current conformation HHpred3_TS1
# ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0348 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 T0348 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 T0348 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 T0348 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 T0348 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 T0348 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 T0348 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 T0348 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 T0348 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 T0348 can't currently be optimized by undertaker
# naming current conformation LOOPP_TS5
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS1.pdb.gz looking for model 1
# naming current conformation Ma-OPUS-server2_TS1
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS2.pdb.gz looking for model 1
# 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
# naming current conformation Ma-OPUS-server2_TS4
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS5.pdb.gz looking for model 1
# naming current conformation Ma-OPUS-server2_TS5
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1
# 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 37
# 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 52
# 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
# 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 49
# 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 66
# 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 64
# 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 54
# 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 67
# 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 T0348 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
# Found a chain break before 28
# copying to AlignedFragments data structure
# naming current conformation POMYSL_TS1
# ReadConformPDB reading from PDB file servers/POMYSL_TS2.pdb.gz looking for model 1
# Found a chain break before 33
# copying to AlignedFragments data structure
# naming current conformation POMYSL_TS2
# ReadConformPDB reading from PDB file servers/POMYSL_TS3.pdb.gz looking for model 1
# Found a chain break before 67
# 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 65
# 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 39
# copying to AlignedFragments data structure
# naming current conformation POMYSL_TS5
# ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1
# naming current conformation PROTINFO-AB_TS1
# ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1
# naming current conformation PROTINFO-AB_TS2
# ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1
# naming current conformation PROTINFO-AB_TS3
# ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1
# naming current conformation PROTINFO-AB_TS4
# ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1
# naming current conformation PROTINFO-AB_TS5
# ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1
# Found a chain break before 37
# copying to AlignedFragments data structure
# naming current conformation PROTINFO_TS1
# ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0348 can't currently be optimized by undertaker
# naming current conformation PROTINFO_TS2
# ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1
# Found a chain break before 46
# 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 37
# copying to AlignedFragments data structure
# naming current conformation PROTINFO_TS4
# ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0348 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 T0348 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 T0348 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 T0348 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 T0348 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 T0348 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 T0348 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 65
# 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 65
# 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 65
# 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
# 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 20
# 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 T0348 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 T0348 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 T0348 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 T0348 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
# naming current conformation Pmodeller6_TS5
# ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1
# naming current conformation RAPTOR-ACE_TS1
# ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1
# naming current conformation RAPTOR-ACE_TS2
# ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1
# naming current conformation RAPTOR-ACE_TS3
# ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS4.pdb.gz looking for model 1
# Found a chain break before 10
# 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 17
# 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
# naming current conformation RAPTORESS_TS1
# ReadConformPDB reading from PDB file servers/RAPTORESS_TS2.pdb.gz looking for model 1
# Found a chain break before 36
# 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 36
# 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 36
# 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 42
# 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 40
# 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 21
# copying to AlignedFragments data structure
# naming current conformation RAPTOR_TS5
# ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1
# naming current conformation ROBETTA_TS1
# ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1
# naming current conformation ROBETTA_TS2
# ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1
# naming current conformation ROBETTA_TS3
# ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1
# naming current conformation ROBETTA_TS4
# ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1
# naming current conformation ROBETTA_TS5
# ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0348 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 T0348 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 T0348 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 T0348 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 T0348 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation ROKKY_TS5
# ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0348 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 T0348 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 T0348 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 T0348 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 T0348 can't currently be optimized by undertaker
# naming current conformation SAM-T02_AL5
# ReadConformPDB reading from PDB file servers/SAM-T99_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0348 can't currently be optimized by undertaker
# naming current conformation SAM-T99_AL1
# ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1
# Found a chain break before 62
# 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 T0348 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 T0348 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 T0348 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 T0348 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
# 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 8
# copying to AlignedFragments data structure
# naming current conformation SP3_TS3
# ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1
# 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
# naming current conformation SP4_TS1
# ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1
# Found a chain break before 8
# copying to AlignedFragments data structure
# 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
# naming current conformation SP4_TS4
# ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1
# naming current conformation SP4_TS5
# ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1
# Found a chain break before 26
# 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 37
# 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
# naming current conformation SPARKS2_TS4
# ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1
# Found a chain break before 43
# 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 T0348 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 T0348 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 T0348 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 T0348 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 T0348 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: incomplete conformation T0348 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 T0348 can't currently be optimized by undertaker
# naming current conformation UNI-EID_sfst_AL1
# ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0348 can't currently be optimized by undertaker
# naming current conformation UNI-EID_sfst_AL2
# ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0348 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 T0348 can't currently be optimized by undertaker
# naming current conformation UNI-EID_sfst_AL4
# ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0348 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 55
# 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 45
# 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 64
# 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 54
# 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 65
# 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 65
# 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 T0348 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 T0348 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation forecast-s_AL1
# ReadConformPDB reading from PDB file servers/forecast-s_AL2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0348 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 T0348 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation forecast-s_AL3
# ReadConformPDB reading from PDB file servers/forecast-s_AL4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0348 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 T0348 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation forecast-s_AL5
# ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1
# naming current conformation karypis.srv.2_TS1
# ReadConformPDB reading from PDB file servers/karypis.srv.2_TS2.pdb.gz looking for model 1
# Found a chain break before 11
# 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
# 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 42
# 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 49
# 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 65
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.4_TS1
# ReadConformPDB reading from PDB file servers/karypis.srv.4_TS3.pdb.gz looking for model 1
WARNING: atoms too close: (T0348)H65.O and (T0348)H66.N only 0.000 apart, marking (T0348)H66.N as missing
# WARNING: incomplete conformation T0348 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_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0348 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 T0348 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 T0348 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 T0348 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 T0348 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 T0348 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 T0348 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 T0348 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 T0348 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 T0348 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 T0348 can't currently be optimized by undertaker
# naming current conformation nFOLD_TS5
# ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0348 can't currently be optimized by undertaker
# naming current conformation shub_TS1
# command:Using radius: 8.0000
Metaserver mode
NUMB_ALIGNS: 257
model score -0.2510
model score 1.5937
model score 2.4659
model score 1.7250
model score 2.1619
model score 2.4382
model score 1.3014
model score 1.1953
model score 1.1815
model score 1.1891
model score 1.1888
model score 1.4187
model score 0.8407
model score 1.5075
model score 1.4118
model score 2.2686
model score 0.1909
model score 1.1824
model score 0.3162
model score 0.0696
model score 0.4665
model score 0.0696
model score 0.4665
model score 0.2824
model score 0.5892
model score 0.2354
model score 0.1476
model score 1.6976
model score 2.0642
model score 2.0456
model score 2.0846
model score 2.1088
model score 0.6309
model score 0.6093
model score 1.3636
model score 1.1202
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weight: 0.6860 eval: 0.7339 min: -0.2935 max: 2.6511
weight: 0.4087 eval: 1.6413 min: -0.2935 max: 2.6511
weight: 0.5486 eval: 1.1834 min: -0.2935 max: 2.6511
weight: 0.4990 eval: 1.3458 min: -0.2935 max: 2.6511
weight: 0.3576 eval: 1.8082 min: -0.2935 max: 2.6511
weight: 0.3645 eval: 1.7858 min: -0.2935 max: 2.6511
weight: 0.4391 eval: 1.5415 min: -0.2935 max: 2.6511
weight: 0.4568 eval: 1.4839 min: -0.2935 max: 2.6511
weight: 0.4965 eval: 1.3539 min: -0.2935 max: 2.6511
weight: 0.5757 eval: 1.0947 min: -0.2935 max: 2.6511
weight: 0.8810 eval: 0.0959 min: -0.2935 max: 2.6511
weight: 0.9666 eval: -0.1843 min: -0.2935 max: 2.6511
weight: 0.8295 eval: 0.2642 min: -0.2935 max: 2.6511
weight: 0.9582 eval: -0.1568 min: -0.2935 max: 2.6511
weight: 0.9004 eval: 0.0324 min: -0.2935 max: 2.6511
weight: 0.8162 eval: 0.3077 min: -0.2935 max: 2.6511
weight: 0.3183 eval: 1.9368 min: -0.2935 max: 2.6511
weight: 0.6676 eval: 0.7942 min: -0.2935 max: 2.6511
weight: 0.4463 eval: 1.5181 min: -0.2935 max: 2.6511
weight: 0.4645 eval: 1.4584 min: -0.2935 max: 2.6511
weight: 0.3485 eval: 1.8380 min: -0.2935 max: 2.6511
weight: 0.8700 eval: 0.1318 min: -0.2935 max: 2.6511
Adding 1677 constraints to all2.constraints
Done adding distance constraints
# command:Reading probabilities from probabilities.dat
Reading constraints from ConstraintSet all2.constraints
maxweight: 1.0000
Optimizing...
 Probability sum: -109.3150, CN propb: -109.3150 weights: 0.2805 constraints: 102
# command:Found ConstraintSet
# PrintContacts align.constraints_meta02
Number of constraints in align2.constraints 102
# command:Found ConstraintSet
# PrintContacts align_bonus.constraints_meta02
Number of constraints in align2.constraints.bonus 102
# command:Found ConstraintSet
# PrintContacts rejected.constraints_meta02
Number of constraints in rejected2.constraints 1575
# command:Found ConstraintSet
# PrintContacts rejected_bonus.constraints_meta02
Number of constraints in rejected2.constraints.bonus 1575
# command:Found ConstraintSet
# PrintContacts non_contacts.constraints_meta02
Number of constraints in noncontact2.constraints 0
# command:Found ConstraintSet
# PrintContacts non_contacts_bonus.constraints_meta02
Number of constraints in noncontact2.constraints.bonus 0
# command:Found ConstraintSet
# PrintContacts all.constraints_meta02
Number of constraints in all2.constraints 1677
# command: