# 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/T0366/
# command:# Making conformation for sequence T0366 numbered 1 through 106
Created new target T0366 from T0366.a2m
# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0366/
# command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0366//projects/compbio/experiments/protein-predict/casp7/T0366/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0366//projects/compbio/experiments/protein-predict/casp7/T0366/align.constraints_v3.costfcn.gz for input
Trying /projects/compbio/experiments/protein-predict/casp7/T0366/align.constraints_v3.costfcn
# reading script from file /projects/compbio/experiments/protein-predict/casp7/T0366/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((T0366)V65.CB, (T0366)V96.CB) [> 3.4422 = 5.7370 < 7.4581] w=1.0000 to align
# Constraint # added constraint: constraint((T0366)M46.CB, (T0366)V60.CB) [> 3.8664 = 6.4440 < 8.3771] w=1.0000 to align
# Constraint # added constraint: constraint((T0366)I43.CB, (T0366)I64.CB) [> 4.0472 = 6.7453 < 8.7690] w=1.0000 to align
# Constraint # added constraint: constraint((T0366)I43.CB, (T0366)D62.CB) [> 2.8532 = 4.7553 < 6.1819] w=1.0000 to align
# Constraint # added constraint: constraint((T0366)I43.CB, (T0366)G61.CA) [> 3.2854 = 5.4757 < 7.1184] w=1.0000 to align
# Constraint # added constraint: constraint((T0366)I43.CB, (T0366)V60.CB) [> 3.5483 = 5.9139 < 7.6880] w=1.0000 to align
# Constraint # added constraint: constraint((T0366)F42.CB, (T0366)G61.CA) [> 3.1235 = 5.2058 < 6.7675] w=1.0000 to align
# Constraint # added constraint: constraint((T0366)R63.CB, (T0366)V96.CB) [> 2.8516 = 4.7527 < 6.1785] w=0.9904 to align
# Constraint # added constraint: constraint((T0366)C68.CB, (T0366)I91.CB) [> 3.5563 = 5.9272 < 7.7054] w=0.9904 to align
# Constraint # added constraint: constraint((T0366)C68.CB, (T0366)E92.CB) [> 3.2639 = 5.4398 < 7.0718] w=0.9904 to align
# Constraint # added constraint: constraint((T0366)M46.CB, (T0366)L58.CB) [> 3.5459 = 5.9099 < 7.6828] w=0.9714 to align
# Constraint # added constraint: constraint((T0366)I43.CB, (T0366)L58.CB) [> 3.6100 = 6.0166 < 7.8216] w=0.9714 to align
# Constraint # added constraint: constraint((T0366)V65.CB, (T0366)V95.CB) [> 3.9793 = 6.6322 < 8.6219] w=0.9713 to align
# Constraint # added constraint: constraint((T0366)I64.CB, (T0366)V95.CB) [> 3.4944 = 5.8240 < 7.5712] w=0.9713 to align
# Constraint # added constraint: constraint((T0366)F42.CB, (T0366)R63.CB) [> 3.2024 = 5.3373 < 6.9385] w=0.9713 to align
# Constraint # added constraint: constraint((T0366)A44.CB, (T0366)V60.CB) [> 3.9987 = 6.6645 < 8.6638] w=0.9713 to align
# Constraint # added constraint: constraint((T0366)M45.CB, (T0366)V60.CB) [> 3.8954 = 6.4924 < 8.4401] w=0.9713 to align
# Constraint # added constraint: constraint((T0366)I43.CB, (T0366)R59.CB) [> 4.1684 = 6.9474 < 9.0316] w=0.9684 to align
# Constraint # added constraint: constraint((T0366)R63.CB, (T0366)V95.CB) [> 3.8363 = 6.3938 < 8.3120] w=0.9617 to align
# Constraint # added constraint: constraint((T0366)I67.CB, (T0366)I91.CB) [> 3.5938 = 5.9897 < 7.7866] w=0.9617 to align
# Constraint # added constraint: constraint((T0366)G25.CA, (T0366)M46.CB) [> 3.9249 = 6.5414 < 8.5038] w=0.9564 to align
# Constraint # added constraint: constraint((T0366)G25.CA, (T0366)H47.CB) [> 2.4566 = 4.0943 < 5.3225] w=0.9564 to align
# Constraint # added constraint: constraint((T0366)I26.CB, (T0366)I43.CB) [> 3.2216 = 5.3694 < 6.9802] w=0.9564 to align
# Constraint # added constraint: constraint((T0366)I26.CB, (T0366)M46.CB) [> 3.1060 = 5.1767 < 6.7297] w=0.9564 to align
# Constraint # added constraint: constraint((T0366)I26.CB, (T0366)H47.CB) [> 4.0485 = 6.7475 < 8.7718] w=0.9564 to align
# Constraint # added constraint: constraint((T0366)S27.CB, (T0366)I43.CB) [> 4.2578 = 7.0964 < 9.2253] w=0.9564 to align
# Constraint # added constraint: constraint((T0366)S27.CB, (T0366)A44.CB) [> 2.8511 = 4.7518 < 6.1774] w=0.9564 to align
# Constraint # added constraint: constraint((T0366)S27.CB, (T0366)M45.CB) [> 2.6069 = 4.3449 < 5.6483] w=0.9564 to align
# Constraint # added constraint: constraint((T0366)I28.CB, (T0366)F42.CB) [> 4.0001 = 6.6668 < 8.6668] w=0.9564 to align
# Constraint # added constraint: constraint((T0366)I28.CB, (T0366)I43.CB) [> 3.6469 = 6.0782 < 7.9017] w=0.9564 to align
# Constraint # added constraint: constraint((T0366)I28.CB, (T0366)A44.CB) [> 3.7977 = 6.3296 < 8.2285] w=0.9564 to align
# Constraint # added constraint: constraint((T0366)I28.CB, (T0366)I64.CB) [> 4.1365 = 6.8941 < 8.9623] w=0.9564 to align
# Constraint # added constraint: constraint((T0366)A29.CB, (T0366)F42.CB) [> 3.3199 = 5.5332 < 7.1931] w=0.9564 to align
# Constraint # added constraint: constraint((T0366)A29.CB, (T0366)A44.CB) [> 2.7013 = 4.5021 < 5.8527] w=0.9564 to align
# Constraint # added constraint: constraint((T0366)F42.CB, (T0366)D62.CB) [> 4.0717 = 6.7862 < 8.8221] w=0.9497 to align
# Constraint # added constraint: constraint((T0366)F42.CB, (T0366)I64.CB) [> 4.3234 = 7.2056 < 9.3673] w=0.9470 to align
# Constraint # added constraint: constraint((T0366)T70.CB, (T0366)L83.CB) [> 3.6198 = 6.0330 < 7.8428] w=0.9427 to align
# Constraint # added constraint: constraint((T0366)D62.CB, (T0366)V95.CB) [> 2.5854 = 4.3091 < 5.6018] w=0.9426 to align
# Constraint # added constraint: constraint((T0366)I67.CB, (T0366)L83.CB) [> 3.4477 = 5.7461 < 7.4700] w=0.9426 to align
# Constraint # added constraint: constraint((T0366)I41.CB, (T0366)T72.CB) [> 3.2535 = 5.4225 < 7.0493] w=0.9426 to align
# Constraint # added constraint: constraint((T0366)I41.CB, (T0366)I64.CB) [> 2.9027 = 4.8378 < 6.2892] w=0.9426 to align
# Constraint # added constraint: constraint((T0366)I67.CB, (T0366)M93.CB) [> 3.0937 = 5.1561 < 6.7030] w=0.9426 to align
# Constraint # added constraint: constraint((T0366)L24.CB, (T0366)V51.CB) [> 3.2908 = 5.4847 < 7.1301] w=0.9351 to align
# Constraint # added constraint: constraint((T0366)L24.CB, (T0366)A52.CB) [> 3.3374 = 5.5623 < 7.2309] w=0.9349 to align
# Constraint # added constraint: constraint((T0366)I64.CB, (T0366)M93.CB) [> 3.5422 = 5.9036 < 7.6747] w=0.9330 to align
# Constraint # added constraint: constraint((T0366)T66.CB, (T0366)M93.CB) [> 4.1737 = 6.9562 < 9.0431] w=0.9330 to align
# Constraint # added constraint: constraint((T0366)I67.CB, (T0366)E92.CB) [> 3.9965 = 6.6609 < 8.6591] w=0.9330 to align
# Constraint # added constraint: constraint((T0366)I26.CB, (T0366)L58.CB) [> 3.7777 = 6.2962 < 8.1851] w=0.9279 to align
# Constraint # added constraint: constraint((T0366)G25.CA, (T0366)G50.CA) [> 3.0521 = 5.0868 < 6.6129] w=0.9279 to align
# Constraint # added constraint: constraint((T0366)I26.CB, (T0366)A52.CB) [> 2.7053 = 4.5088 < 5.8615] w=0.9277 to align
# Constraint # added constraint: constraint((T0366)G25.CA, (T0366)A52.CB) [> 2.8606 = 4.7676 < 6.1979] w=0.9277 to align
# Constraint # added constraint: constraint((T0366)I26.CB, (T0366)M45.CB) [> 3.9893 = 6.6488 < 8.6434] w=0.9277 to align
# Constraint # added constraint: constraint((T0366)I67.CB, (T0366)L84.CB) [> 3.8911 = 6.4851 < 8.4306] w=0.9140 to align
# Constraint # added constraint: constraint((T0366)D62.CB, (T0366)A97.CB) [> 3.4215 = 5.7026 < 7.4134] w=0.9140 to align
# Constraint # added constraint: constraint((T0366)T66.CB, (T0366)Q94.CB) [> 2.4052 = 4.0086 < 5.2112] w=0.9139 to align
# Constraint # added constraint: constraint((T0366)I41.CB, (T0366)R63.CB) [> 4.0885 = 6.8142 < 8.8584] w=0.9139 to align
# Constraint # added constraint: constraint((T0366)I41.CB, (T0366)A80.CB) [> 3.0167 = 5.0278 < 6.5361] w=0.9139 to align
# Constraint # added constraint: constraint((T0366)A44.CB, (T0366)G61.CA) [> 4.3816 = 7.3027 < 9.4935] w=0.9139 to align
# Constraint # added constraint: constraint((T0366)G30.CA, (T0366)H77.CB) [> 3.2974 = 5.4957 < 7.1444] w=0.9087 to align
# Constraint # added constraint: constraint((T0366)G30.CA, (T0366)F42.CB) [> 3.6874 = 6.1458 < 7.9895] w=0.9087 to align
# Constraint # added constraint: constraint((T0366)V65.CB, (T0366)Q94.CB) [> 2.8287 = 4.7146 < 6.1289] w=0.9043 to align
# Constraint # added constraint: constraint((T0366)G25.CA, (T0366)V51.CB) [> 3.4986 = 5.8310 < 7.5804] w=0.8992 to align
# Constraint # added constraint: constraint((T0366)A29.CB, (T0366)I41.CB) [> 4.4217 = 7.3695 < 9.5803] w=0.8990 to align
# Constraint # added constraint: constraint((T0366)I28.CB, (T0366)I41.CB) [> 3.1655 = 5.2759 < 6.8586] w=0.8990 to align
# Constraint # added constraint: constraint((T0366)I64.CB, (T0366)A80.CB) [> 4.1527 = 6.9212 < 8.9976] w=0.8852 to align
# Constraint # added constraint: constraint((T0366)I64.CB, (T0366)Q94.CB) [> 4.3989 = 7.3315 < 9.5310] w=0.8852 to align
# Constraint # added constraint: constraint((T0366)M46.CB, (T0366)R59.CB) [> 4.1137 = 6.8562 < 8.9131] w=0.8852 to align
# Constraint # added constraint: constraint((T0366)I41.CB, (T0366)H77.CB) [> 3.9974 = 6.6623 < 8.6610] w=0.8833 to align
# Constraint # added constraint: constraint((T0366)L24.CB, (T0366)I91.CB) [> 3.8268 = 6.3781 < 8.2915] w=0.8800 to align
# Constraint # added constraint: constraint((T0366)G69.CA, (T0366)E92.CB) [> 4.2090 = 7.0150 < 9.1195] w=0.8758 to align
# Constraint # added constraint: constraint((T0366)I28.CB, (T0366)A80.CB) [> 3.6975 = 6.1624 < 8.0112] w=0.8703 to align
# Constraint # added constraint: constraint((T0366)C68.CB, (T0366)A87.CB) [> 3.4470 = 5.7450 < 7.4684] w=0.8609 to align
# Constraint # added constraint: constraint((T0366)G30.CA, (T0366)I41.CB) [> 3.3408 = 5.5679 < 7.2383] w=0.8514 to align
# Constraint # added constraint: constraint((T0366)L24.CB, (T0366)L84.CB) [> 3.9772 = 6.6286 < 8.6172] w=0.8488 to align
# Constraint # added constraint: constraint((T0366)M16.CB, (T0366)I91.CB) [> 3.1371 = 5.2285 < 6.7970] w=0.8418 to align
# Constraint # added constraint: constraint((T0366)V14.CB, (T0366)E92.CB) [> 4.2632 = 7.1053 < 9.2369] w=0.8322 to align
# Constraint # added constraint: constraint((T0366)I67.CB, (T0366)A87.CB) [> 4.1132 = 6.8553 < 8.9119] w=0.8322 to align
# Constraint # added constraint: constraint((T0366)I28.CB, (T0366)V81.CB) [> 4.1244 = 6.8740 < 8.9361] w=0.8321 to align
# Constraint # added constraint: constraint((T0366)I67.CB, (T0366)Q94.CB) [> 4.3766 = 7.2943 < 9.4826] w=0.8278 to align
# Constraint # added constraint: constraint((T0366)I43.CB, (T0366)R63.CB) [> 4.6430 = 7.7384 < 10.0599] w=0.8278 to align
# Constraint # added constraint: constraint((T0366)K17.CB, (T0366)S90.CB) [> 3.4025 = 5.6709 < 7.3721] w=0.8227 to align
# Constraint # added constraint: constraint((T0366)I28.CB, (T0366)H77.CB) [> 4.0521 = 6.7535 < 8.7796] w=0.8130 to align
# Constraint # added constraint: constraint((T0366)M16.CB, (T0366)S90.CB) [> 4.1263 = 6.8771 < 8.9403] w=0.8035 to align
# Constraint # added constraint: constraint((T0366)G30.CA, (T0366)P40.CB) [> 4.0032 = 6.6721 < 8.6737] w=0.8035 to align
# Constraint # added constraint: constraint((T0366)V14.CB, (T0366)V95.CB) [> 3.8122 = 6.3536 < 8.2597] w=0.7940 to align
# Constraint # added constraint: constraint((T0366)R12.CB, (T0366)V95.CB) [> 3.4351 = 5.7252 < 7.4427] w=0.7844 to align
# Constraint # added constraint: constraint((T0366)V14.CB, (T0366)M93.CB) [> 3.1524 = 5.2540 < 6.8302] w=0.7844 to align
# Constraint # added constraint: constraint((T0366)M16.CB, (T0366)M93.CB) [> 4.0868 = 6.8113 < 8.8547] w=0.7844 to align
# Constraint # added constraint: constraint((T0366)A29.CB, (T0366)H77.CB) [> 4.2889 = 7.1482 < 9.2926] w=0.7843 to align
# Constraint # added constraint: constraint((T0366)G25.CA, (T0366)A53.CB) [> 4.2513 = 7.0856 < 9.2113] w=0.7843 to align
# Constraint # added constraint: constraint((T0366)L11.CB, (T0366)V96.CB) [> 3.3573 = 5.5954 < 7.2741] w=0.7748 to align
# Constraint # added constraint: constraint((T0366)K18.CB, (T0366)V51.CB) [> 3.6158 = 6.0263 < 7.8342] w=0.7748 to align
# Constraint # added constraint: constraint((T0366)K18.CB, (T0366)G89.CA) [> 3.1680 = 5.2801 < 6.8641] w=0.7748 to align
# Constraint # added constraint: constraint((T0366)I43.CB, (T0366)V95.CB) [> 4.4851 = 7.4752 < 9.7177] w=0.7747 to align
# Constraint # added constraint: constraint((T0366)P40.CB, (T0366)R63.CB) [> 3.0007 = 5.0012 < 6.5015] w=0.7704 to align
# Constraint # added constraint: constraint((T0366)T13.CB, (T0366)Q94.CB) [> 3.3938 = 5.6564 < 7.3533] w=0.7653 to align
# Constraint # added constraint: constraint((T0366)M16.CB, (T0366)E92.CB) [> 4.3326 = 7.2209 < 9.3872] w=0.7653 to align
# Constraint # added constraint: constraint((T0366)R12.CB, (T0366)Q94.CB) [> 4.2751 = 7.1252 < 9.2627] w=0.7366 to align
# Constraint # added constraint: constraint((T0366)K18.CB, (T0366)I91.CB) [> 3.9704 = 6.6172 < 8.6024] w=0.7366 to align
# Constraint # added constraint: constraint((T0366)M16.CB, (T0366)A52.CB) [> 3.7683 = 6.2805 < 8.1646] w=0.7270 to align
# Constraint # added constraint: constraint((T0366)M16.CB, (T0366)V51.CB) [> 3.0837 = 5.1396 < 6.6814] w=0.7270 to align
# Constraint # added constraint: constraint((T0366)V14.CB, (T0366)L58.CB) [> 3.6904 = 6.1507 < 7.9959] w=0.7270 to align
# Constraint # added constraint: constraint((T0366)E15.CB, (T0366)I91.CB) [> 4.3295 = 7.2159 < 9.3807] w=0.7174 to align
# Constraint # added constraint: constraint((T0366)C68.CB, (T0366)L83.CB) [> 4.0837 = 6.8062 < 8.8480] w=0.7174 to align
# Constraint # added constraint: constraint((T0366)T66.CB, (T0366)E92.CB) [> 4.6424 = 7.7373 < 10.0585] w=0.7106 to align
# Constraint # added constraint: constraint((T0366)G31.CA, (T0366)I41.CB) [> 3.7722 = 6.2870 < 8.1731] w=0.7079 to align
# Constraint # added constraint: constraint((T0366)G31.CA, (T0366)P40.CB) [> 3.8635 = 6.4392 < 8.3709] w=0.7079 to align
# Constraint # added constraint: constraint((T0366)S23.CB, (T0366)V51.CB) [> 4.3590 = 7.2651 < 9.4446] w=0.6983 to align
# Constraint # added constraint: constraint((T0366)T13.CB, (T0366)E92.CB) [> 3.8543 = 6.4239 < 8.3510] w=0.6983 to align
# Constraint # added constraint: constraint((T0366)I28.CB, (T0366)L84.CB) [> 4.4545 = 7.4241 < 9.6513] w=0.6887 to align
# Constraint # added constraint: constraint((T0366)E15.CB, (T0366)S90.CB) [> 3.6558 = 6.0931 < 7.9210] w=0.6887 to align
# Constraint # added constraint: constraint((T0366)T72.CB, (T0366)L83.CB) [> 4.0704 = 6.7840 < 8.8192] w=0.6843 to align
# Constraint # added constraint: constraint((T0366)G31.CA, (T0366)H77.CB) [> 3.1583 = 5.2639 < 6.8431] w=0.6792 to align
# Constraint # added constraint: constraint((T0366)E15.CB, (T0366)M93.CB) [> 4.2734 = 7.1223 < 9.2590] w=0.6792 to align
# Constraint # added constraint: constraint((T0366)T13.CB, (T0366)M93.CB) [> 4.3124 = 7.1873 < 9.3435] w=0.6696 to align
# Constraint # added constraint: constraint((T0366)L11.CB, (T0366)V95.CB) [> 4.2296 = 7.0493 < 9.1641] w=0.6600 to align
# Constraint # added constraint: constraint((T0366)L11.CB, (T0366)V65.CB) [> 4.1601 = 6.9335 < 9.0135] w=0.6505 to align
# Constraint # added constraint: constraint((T0366)K17.CB, (T0366)G89.CA) [> 3.6955 = 6.1592 < 8.0070] w=0.6505 to align
# Constraint # added constraint: constraint((T0366)K18.CB, (T0366)S90.CB) [> 4.1618 = 6.9363 < 9.0172] w=0.6409 to align
# Constraint # added constraint: constraint((T0366)K17.CB, (T0366)I91.CB) [> 4.2277 = 7.0462 < 9.1601] w=0.6122 to align
# Constraint # added constraint: constraint((T0366)G69.CA, (T0366)Q94.CB) [> 4.3643 = 7.2738 < 9.4560] w=0.6079 to align
# Constraint # added constraint: constraint((T0366)G19.CA, (T0366)V51.CB) [> 3.5582 = 5.9304 < 7.7095] w=0.6026 to align
# Constraint # added constraint: constraint((T0366)S27.CB, (T0366)M46.CB) [> 4.6155 = 7.6925 < 10.0003] w=0.5907 to align
# Constraint # added constraint: constraint((T0366)V14.CB, (T0366)T55.CB) [> 3.4120 = 5.6867 < 7.3927] w=0.5835 to align
# Constraint # added constraint: constraint((T0366)R12.CB, (T0366)V96.CB) [> 4.1935 = 6.9892 < 9.0859] w=0.5739 to align
# Constraint # added constraint: constraint((T0366)I67.CB, (T0366)A80.CB) [> 4.1745 = 6.9575 < 9.0447] w=0.5695 to align
# Constraint # added constraint: constraint((T0366)V14.CB, (T0366)Q94.CB) [> 4.2798 = 7.1329 < 9.2728] w=0.5644 to align
# Constraint # added constraint: constraint((T0366)S23.CB, (T0366)H47.CB) [> 4.4343 = 7.3904 < 9.6076] w=0.5644 to align
# Constraint # added constraint: constraint((T0366)G30.CA, (T0366)V39.CB) [> 3.5975 = 5.9958 < 7.7946] w=0.5548 to align
# Constraint # added constraint: constraint((T0366)T13.CB, (T0366)V95.CB) [> 4.3213 = 7.2021 < 9.3628] w=0.5548 to align
# Constraint # added constraint: constraint((T0366)R12.CB, (T0366)A97.CB) [> 3.9167 = 6.5278 < 8.4861] w=0.5548 to align
# Constraint # added constraint: constraint((T0366)L24.CB, (T0366)G50.CA) [> 4.5147 = 7.5245 < 9.7818] w=0.5261 to align
# Constraint # added constraint: constraint((T0366)I26.CB, (T0366)A44.CB) [> 4.6104 = 7.6840 < 9.9892] w=0.4974 to align
# Constraint # added constraint: constraint((T0366)G31.CA, (T0366)T76.CB) [> 3.4759 = 5.7932 < 7.5311] w=0.4879 to align
# Constraint # added constraint: constraint((T0366)V14.CB, (T0366)K57.CB) [> 2.9730 = 4.9550 < 6.4415] w=0.4879 to align
# Constraint # added constraint: constraint((T0366)G10.CA, (T0366)A97.CB) [> 3.4440 = 5.7399 < 7.4619] w=0.4879 to align
# Constraint # added constraint: constraint((T0366)E15.CB, (T0366)T55.CB) [> 4.0093 = 6.6821 < 8.6868] w=0.4879 to align
# Constraint # added constraint: constraint((T0366)G31.CA, (T0366)A80.CB) [> 3.9880 = 6.6467 < 8.6407] w=0.4496 to align
# Constraint # added constraint: constraint((T0366)P40.CB, (T0366)T72.CB) [> 4.1387 = 6.8979 < 8.9672] w=0.4261 to align
# Constraint # added constraint: constraint((T0366)D22.CB, (T0366)V51.CB) [> 3.9655 = 6.6091 < 8.5919] w=0.4018 to align
# Constraint # added constraint: constraint((T0366)M16.CB, (T0366)L58.CB) [> 4.4856 = 7.4759 < 9.7187] w=0.4018 to align
# Constraint # added constraint: constraint((T0366)P40.CB, (T0366)I64.CB) [> 4.1956 = 6.9927 < 9.0905] w=0.3974 to align
# Constraint # added constraint: constraint((T0366)C68.CB, (T0366)M93.CB) [> 4.4432 = 7.4053 < 9.6268] w=0.3946 to align
# Constraint # added constraint: constraint((T0366)V32.CB, (T0366)H77.CB) [> 4.0420 = 6.7367 < 8.7578] w=0.3922 to align
# Constraint # added constraint: constraint((T0366)L11.CB, (T0366)A97.CB) [> 4.2641 = 7.1069 < 9.2389] w=0.3922 to align
# Constraint # added constraint: constraint((T0366)M9.CB, (T0366)A97.CB) [> 3.6382 = 6.0637 < 7.8828] w=0.3826 to align
# Constraint # added constraint: constraint((T0366)S27.CB, (T0366)H47.CB) [> 4.4285 = 7.3808 < 9.5950] w=0.3801 to align
# Constraint # added constraint: constraint((T0366)A29.CB, (T0366)I43.CB) [> 4.5852 = 7.6419 < 9.9345] w=0.3157 to align
# Constraint # added constraint: constraint((T0366)P40.CB, (T0366)V65.CB) [> 4.1308 = 6.8847 < 8.9502] w=0.3113 to align
# Constraint # added constraint: constraint((T0366)R12.CB, (T0366)K57.CB) [> 4.1083 = 6.8472 < 8.9014] w=0.3061 to align
# Constraint # added constraint: constraint((T0366)G30.CA, (T0366)A80.CB) [> 4.6215 = 7.7024 < 10.0132] w=0.3061 to align
# Constraint # added constraint: constraint((T0366)G31.CA, (T0366)F42.CB) [> 3.3106 = 5.5176 < 7.1729] w=0.3061 to align
# Constraint # added constraint: constraint((T0366)C68.CB, (T0366)S88.CB) [> 4.3509 = 7.2515 < 9.4269] w=0.2870 to align
# Constraint # added constraint: constraint((T0366)G33.CA, (T0366)H77.CB) [> 4.2754 = 7.1257 < 9.2634] w=0.2487 to align
# Constraint # added constraint: constraint((T0366)I64.CB, (T0366)L84.CB) [> 4.6750 = 7.7916 < 10.1291] w=0.2296 to align
# Constraint # added constraint: constraint((T0366)D38.CB, (T0366)E73.CB) [> 4.2245 = 7.0409 < 9.1532] w=0.2296 to align
# Constraint # added constraint: constraint((T0366)P20.CB, (T0366)G89.CA) [> 3.9628 = 6.6047 < 8.5861] w=0.2296 to align
# Constraint # added constraint: constraint((T0366)V14.CB, (T0366)A52.CB) [> 4.5827 = 7.6378 < 9.9291] w=0.2200 to align
# Constraint # added constraint: constraint((T0366)L24.CB, (T0366)A87.CB) [> 4.5528 = 7.5879 < 9.8643] w=0.2009 to align
# Constraint # added constraint: constraint((T0366)M16.CB, (T0366)K57.CB) [> 3.7538 = 6.2564 < 8.1333] w=0.1913 to align
# Constraint # added constraint: constraint((T0366)G19.CA, (T0366)S90.CB) [> 4.1695 = 6.9492 < 9.0340] w=0.1913 to align
# Constraint # added constraint: constraint((T0366)R12.CB, (T0366)D62.CB) [> 4.6037 = 7.6728 < 9.9746] w=0.1913 to align
# Constraint # added constraint: constraint((T0366)M16.CB, (T0366)G25.CA) [> 4.6122 = 7.6870 < 9.9931] w=0.1913 to align
# Constraint # added constraint: constraint((T0366)M9.CB, (T0366)G99.CA) [> 4.1789 = 6.9648 < 9.0542] w=0.1817 to align
# Constraint # added constraint: constraint((T0366)E15.CB, (T0366)K57.CB) [> 3.6002 = 6.0003 < 7.8004] w=0.1722 to align
# Constraint # added constraint: constraint((T0366)S8.CB, (T0366)A97.CB) [> 3.9239 = 6.5398 < 8.5017] w=0.1722 to align
# Constraint # added constraint: constraint((T0366)T21.CB, (T0366)G89.CA) [> 4.0935 = 6.8224 < 8.8692] w=0.1722 to align
# Constraint # added constraint: constraint((T0366)C68.CB, (T0366)L84.CB) [> 3.9851 = 6.6418 < 8.6344] w=0.1722 to align
# Constraint # added constraint: constraint((T0366)P40.CB, (T0366)M75.CB) [> 4.1586 = 6.9310 < 9.0103] w=0.1722 to align
# Constraint # added constraint: constraint((T0366)V65.CB, (T0366)M93.CB) [> 4.7283 = 7.8804 < 10.2445] w=0.1650 to align
# Constraint # added constraint: constraint((T0366)I41.CB, (T0366)V65.CB) [> 4.3642 = 7.2736 < 9.4557] w=0.1464 to align
# Constraint # added constraint: constraint((T0366)T13.CB, (T0366)T66.CB) [> 4.5833 = 7.6388 < 9.9305] w=0.1435 to align
# Constraint # added constraint: constraint((T0366)E15.CB, (T0366)V95.CB) [> 3.9297 = 6.5495 < 8.5143] w=0.1435 to align
# Constraint # added constraint: constraint((T0366)S23.CB, (T0366)K85.CB) [> 4.1235 = 6.8725 < 8.9342] w=0.1435 to align
# Constraint # added constraint: constraint((T0366)V39.CB, (T0366)T72.CB) [> 4.0709 = 6.7849 < 8.8203] w=0.1435 to align
# Constraint # added constraint: constraint((T0366)P40.CB, (T0366)V96.CB) [> 4.4896 = 7.4826 < 9.7274] w=0.1391 to align
# Constraint # added constraint: constraint((T0366)M16.CB, (T0366)I26.CB) [> 4.4733 = 7.4556 < 9.6922] w=0.1339 to align
# Constraint # added constraint: constraint((T0366)K17.CB, (T0366)Q54.CB) [> 4.5766 = 7.6277 < 9.9160] w=0.1244 to align
# Constraint # added constraint: constraint((T0366)A29.CB, (T0366)V39.CB) [> 4.5790 = 7.6317 < 9.9212] w=0.1148 to align
# Constraint # added constraint: constraint((T0366)G37.CA, (T0366)T76.CB) [> 4.0945 = 6.8242 < 8.8714] w=0.1148 to align
# Constraint # added constraint: constraint((T0366)F42.CB, (T0366)G98.CA) [> 4.5504 = 7.5839 < 9.8591] w=0.1148 to align
# Constraint # added constraint: constraint((T0366)G30.CA, (T0366)A44.CB) [> 4.7274 = 7.8790 < 10.2427] w=0.1148 to align
# Constraint # added constraint: constraint((T0366)G31.CA, (T0366)R63.CB) [> 4.0158 = 6.6929 < 8.7008] w=0.1148 to align
# Constraint # added constraint: constraint((T0366)T13.CB, (T0366)V96.CB) [> 4.2115 = 7.0191 < 9.1248] w=0.1148 to align
# Constraint # added constraint: constraint((T0366)V39.CB, (T0366)R63.CB) [> 3.1193 = 5.1989 < 6.7586] w=0.1148 to align
# Constraint # added constraint: constraint((T0366)G25.CA, (T0366)M45.CB) [> 4.7064 = 7.8440 < 10.1972] w=0.1148 to align
# Constraint # added constraint: constraint((T0366)I41.CB, (T0366)V81.CB) [> 4.4082 = 7.3470 < 9.5510] w=0.1147 to align
# Constraint # added constraint: constraint((T0366)I41.CB, (T0366)Q79.CB) [> 4.3560 = 7.2600 < 9.4379] w=0.1104 to align
# Constraint # added constraint: constraint((T0366)R12.CB, (T0366)V65.CB) [> 3.9341 = 6.5568 < 8.5239] w=0.1052 to align
# Constraint # added constraint: constraint((T0366)T13.CB, (T0366)A97.CB) [> 4.2192 = 7.0321 < 9.1417] w=0.1052 to align
# Constraint # added constraint: constraint((T0366)E15.CB, (T0366)Q94.CB) [> 4.2689 = 7.1148 < 9.2492] w=0.1052 to align
# Constraint # added constraint: constraint((T0366)R12.CB, (T0366)R59.CB) [> 4.5299 = 7.5498 < 9.8147] w=0.1052 to align
# Constraint # added constraint: constraint((T0366)S34.CB, (T0366)H77.CB) [> 3.1091 = 5.1819 < 6.7365] w=0.0957 to align
# Constraint # added constraint: constraint((T0366)V39.CB, (T0366)H77.CB) [> 4.2378 = 7.0630 < 9.1819] w=0.0861 to align
# Constraint # added constraint: constraint((T0366)L24.CB, (T0366)L58.CB) [> 4.7511 = 7.9185 < 10.2940] w=0.0861 to align
# Constraint # added constraint: constraint((T0366)V39.CB, (T0366)I64.CB) [> 3.8764 = 6.4607 < 8.3989] w=0.0861 to align
# Constraint # added constraint: constraint((T0366)I26.CB, (T0366)I64.CB) [> 4.6436 = 7.7393 < 10.0611] w=0.0861 to align
# Constraint # added constraint: constraint((T0366)G25.CA, (T0366)T49.CB) [> 4.1056 = 6.8426 < 8.8954] w=0.0861 to align
# Constraint # added constraint: constraint((T0366)I26.CB, (T0366)L84.CB) [> 4.2800 = 7.1333 < 9.2733] w=0.0861 to align
# Constraint # added constraint: constraint((T0366)P40.CB, (T0366)A80.CB) [> 3.3182 = 5.5303 < 7.1894] w=0.0860 to align
# Constraint # added constraint: constraint((T0366)P40.CB, (T0366)H77.CB) [> 3.2652 = 5.4419 < 7.0745] w=0.0860 to align
# Constraint # added constraint: constraint((T0366)L11.CB, (T0366)G98.CA) [> 3.4288 = 5.7146 < 7.4290] w=0.0765 to align
# Constraint # added constraint: constraint((T0366)R63.CB, (T0366)V101.CB) [> 4.0117 = 6.6862 < 8.6920] w=0.0670 to align
# Constraint # added constraint: constraint((T0366)V32.CB, (T0366)T78.CB) [> 3.8641 = 6.4402 < 8.3723] w=0.0574 to align
# Constraint # added constraint: constraint((T0366)A29.CB, (T0366)M45.CB) [> 4.5827 = 7.6378 < 9.9291] w=0.0574 to align
# Constraint # added constraint: constraint((T0366)V14.CB, (T0366)D62.CB) [> 4.5234 = 7.5390 < 9.8007] w=0.0574 to align
# Constraint # added constraint: constraint((T0366)V14.CB, (T0366)I91.CB) [> 4.7338 = 7.8897 < 10.2566] w=0.0574 to align
# Constraint # added constraint: constraint((T0366)G69.CA, (T0366)M93.CB) [> 4.5219 = 7.5364 < 9.7973] w=0.0574 to align
# Constraint # added constraint: constraint((T0366)S27.CB, (T0366)V60.CB) [> 4.2982 = 7.1637 < 9.3128] w=0.0574 to align
# Constraint # added constraint: constraint((T0366)L24.CB, (T0366)H47.CB) [> 4.6749 = 7.7914 < 10.1289] w=0.0574 to align
# Constraint # added constraint: constraint((T0366)I28.CB, (T0366)I67.CB) [> 4.7666 = 7.9443 < 10.3275] w=0.0574 to align
# Constraint # added constraint: constraint((T0366)I28.CB, (T0366)T72.CB) [> 3.9837 = 6.6396 < 8.6314] w=0.0574 to align
# Constraint # added constraint: constraint((T0366)T70.CB, (T0366)A80.CB) [> 2.9156 = 4.8593 < 6.3171] w=0.0574 to align
# Constraint # added constraint: constraint((T0366)S71.CB, (T0366)A80.CB) [> 4.6479 = 7.7464 < 10.0703] w=0.0574 to align
# Constraint # added constraint: constraint((T0366)I26.CB, (T0366)V51.CB) [> 4.5163 = 7.5271 < 9.7852] w=0.0574 to align
# Constraint # added constraint: constraint((T0366)S27.CB, (T0366)V81.CB) [> 4.0298 = 6.7164 < 8.7313] w=0.0574 to align
# Constraint # added constraint: constraint((T0366)F42.CB, (T0366)H77.CB) [> 4.3274 = 7.2123 < 9.3760] w=0.0511 to align
# Constraint # added constraint: constraint((T0366)T13.CB, (T0366)D62.CB) [> 4.6393 = 7.7322 < 10.0518] w=0.0383 to align
# Constraint # added constraint: constraint((T0366)V14.CB, (T0366)T66.CB) [> 4.7474 = 7.9122 < 10.2859] w=0.0383 to align
# Constraint # added constraint: constraint((T0366)G30.CA, (T0366)E73.CB) [> 4.4694 = 7.4489 < 9.6836] w=0.0383 to align
# Constraint # added constraint: constraint((T0366)L24.CB, (T0366)A80.CB) [> 4.5880 = 7.6467 < 9.9408] w=0.0357 to align
# Constraint # added constraint: constraint((T0366)P35.CB, (T0366)H77.CB) [> 4.5556 = 7.5927 < 9.8705] w=0.0287 to align
# Constraint # added constraint: constraint((T0366)T13.CB, (T0366)V65.CB) [> 4.5076 = 7.5127 < 9.7665] w=0.0287 to align
# Constraint # added constraint: constraint((T0366)S8.CB, (T0366)D100.CB) [> 4.5121 = 7.5201 < 9.7761] w=0.0287 to align
# Constraint # added constraint: constraint((T0366)L11.CB, (T0366)T66.CB) [> 4.1562 = 6.9271 < 9.0052] w=0.0287 to align
# Constraint # added constraint: constraint((T0366)V32.CB, (T0366)F42.CB) [> 4.4781 = 7.4634 < 9.7024] w=0.0287 to align
# Constraint # added constraint: constraint((T0366)E15.CB, (T0366)Q54.CB) [> 4.6537 = 7.7561 < 10.0829] w=0.0287 to align
# Constraint # added constraint: constraint((T0366)G69.CA, (T0366)I91.CB) [> 4.3116 = 7.1859 < 9.3417] w=0.0287 to align
# Constraint # added constraint: constraint((T0366)T70.CB, (T0366)V81.CB) [> 4.5367 = 7.5611 < 9.8294] w=0.0287 to align
# Constraint # added constraint: constraint((T0366)V14.CB, (T0366)A97.CB) [> 3.4841 = 5.8069 < 7.5490] w=0.0287 to align
# Constraint # added constraint: constraint((T0366)S23.CB, (T0366)P48.CB) [> 3.3988 = 5.6646 < 7.3640] w=0.0287 to align
# Constraint # added constraint: constraint((T0366)L24.CB, (T0366)I67.CB) [> 4.5676 = 7.6126 < 9.8964] w=0.0287 to align
# Constraint # added constraint: constraint((T0366)G25.CA, (T0366)P48.CB) [> 2.4418 = 4.0697 < 5.2906] w=0.0287 to align
# Constraint # added constraint: constraint((T0366)G30.CA, (T0366)T72.CB) [> 3.6341 = 6.0568 < 7.8738] w=0.0287 to align
# Constraint # added constraint: constraint((T0366)T66.CB, (T0366)V96.CB) [> 3.7612 = 6.2686 < 8.1492] w=0.0287 to align
# Constraint # added constraint: constraint((T0366)G30.CA, (T0366)M75.CB) [> 4.1352 = 6.8920 < 8.9596] w=0.0287 to align
# Constraint # added constraint: constraint((T0366)A29.CB, (T0366)A80.CB) [> 4.6582 = 7.7637 < 10.0928] w=0.0287 to align
# Constraint # added constraint: constraint((T0366)T66.CB, (T0366)V101.CB) [> 4.4040 = 7.3401 < 9.5421] w=0.0235 to align
# Constraint # added constraint: constraint((T0366)V32.CB, (T0366)A80.CB) [> 4.1280 = 6.8801 < 8.9441] w=0.0191 to align
# Constraint # added constraint: constraint((T0366)G33.CA, (T0366)A44.CB) [> 4.6252 = 7.7087 < 10.0214] w=0.0191 to align
# Constraint # added constraint: constraint((T0366)R12.CB, (T0366)M93.CB) [> 4.7051 = 7.8418 < 10.1944] w=0.0191 to align
# Constraint # added constraint: constraint((T0366)M9.CB, (T0366)G61.CA) [> 4.7957 = 7.9928 < 10.3906] w=0.0191 to align
# Constraint # added constraint: constraint((T0366)T66.CB, (T0366)V95.CB) [> 3.6683 = 6.1138 < 7.9480] w=0.0124 to align
# Constraint # added constraint: constraint((T0366)G25.CA, (T0366)T55.CB) [> 4.7910 = 7.9850 < 10.3805] w=0.0096 to align
# Constraint # added constraint: constraint((T0366)E15.CB, (T0366)T66.CB) [> 4.3720 = 7.2867 < 9.4726] w=0.0096 to align
# Constraint # added constraint: constraint((T0366)L36.CB, (T0366)A80.CB) [> 4.0259 = 6.7099 < 8.7229] w=0.0096 to align
# Constraint # added constraint: constraint((T0366)L36.CB, (T0366)H77.CB) [> 4.2067 = 7.0112 < 9.1145] w=0.0096 to align
# Constraint # added constraint: constraint((T0366)V65.CB, (T0366)A97.CB) [> 4.0203 = 6.7006 < 8.7107] w=0.0096 to align
# Constraint # added constraint: constraint((T0366)S34.CB, (T0366)V65.CB) [> 4.1976 = 6.9960 < 9.0947] w=0.0096 to align
# Constraint # added constraint: constraint((T0366)S27.CB, (T0366)G50.CA) [> 2.3813 = 3.9688 < 5.1595] w=0.0072 to align
# Constraint # added constraint: constraint((T0366)S27.CB, (T0366)A52.CB) [> 2.6350 = 4.3916 < 5.7091] w=0.0072 to align
# Constraint # added constraint: constraint((T0366)M46.CB, (T0366)D62.CB) [> 4.6962 = 7.8271 < 10.1752] w=0.0029 to align
# Constraint # added constraint: constraint((T0366)F42.CB, (T0366)M75.CB) [> 3.8088 = 6.3480 < 8.2524] w=0.0019 to align
# SetCost created cost = 
#	( 1.0000 * align )
# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0366/
# command:# reading script from file servers-clean.under
# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0366/decoys/
# ReadConformPDB reading from PDB file tr366.gromacs0.pdb.gz looking for model 1
# choosing archetypes in rotamer library
# Found a chain break before 99
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file tr366.gromacs0.repack-nonPC.pdb.gz looking for model 1
# Found a chain break before 99
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file tr366.pdb.gz looking for model 1
# Found a chain break before 99
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file tr366.repack-nonPC.pdb.gz looking for model 1
# Found a chain break before 99
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file ../dimer/decoys/dimer-tr366-1g9oA.pdb.gz looking for chain 'A' model 1
# Found a chain break before 99
# copying to AlignedFragments data structure
# naming current conformation dimer//dimer-tr366-1g9oA
# ReadConformPDB reading from PDB file ../dimer/decoys/dimer-tr366-1tp5A.pdb.gz looking for chain 'A' model 1
# Found a chain break before 99
# copying to AlignedFragments data structure
# naming current conformation dimer//dimer-tr366-1tp5A
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0366 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 T0366 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 T0366 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 T0366 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 T0366 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 T0366 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 T0366 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 T0366 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 T0366 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 T0366 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 T0366 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 T0366 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 T0366 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 T0366 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 T0366 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_TS5
# ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1
# Found a chain break before 71
# 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 71
# copying to AlignedFragments data structure
# naming current conformation 3Dpro_TS2
# ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1
# naming current conformation 3Dpro_TS3
# ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1
# Found a chain break before 71
# 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 71
# 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 104
# 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 79
# 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 100
# 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 94
# 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 93
# copying to AlignedFragments data structure
# naming current conformation ABIpro_TS5
# ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1
# 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
# 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 20
# 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 93
# 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 38
# 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 101
# copying to AlignedFragments data structure
# naming current conformation CIRCLE_TS1
# ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1
# Found a chain break before 98
# copying to AlignedFragments data structure
# naming current conformation CIRCLE_TS2
# ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1
# Found a chain break before 89
# 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 T0366 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
# Found a chain break before 99
# 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 T0366 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 T0366 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 T0366 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 T0366 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 T0366 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation CaspIta-FOX_TS4
# ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0366 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 T0366 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 T0366 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 T0366 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 T0366 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 T0366 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 98
# 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 T0366 can't currently be optimized by undertaker
# naming current conformation FAMSD_TS2
# ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0366 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
# WARNING: incomplete conformation T0366 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FAMSD_TS4
# ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0366 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 98
# 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 98
# copying to AlignedFragments data structure
# naming current conformation FAMS_TS2
# ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1
# Found a chain break before 96
# copying to AlignedFragments data structure
# naming current conformation FAMS_TS3
# ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1
# Found a chain break before 89
# 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 102
# 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 71
# 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 33
# 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 71
# copying to AlignedFragments data structure
# naming current conformation FOLDpro_TS3
# ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1
# naming current conformation FOLDpro_TS4
# ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1
# Found a chain break before 71
# 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 T0366 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FORTE1_AL1
# ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0366 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FORTE1_AL2
# ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0366 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 T0366 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 T0366 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 T0366 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FORTE2_AL1
# ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0366 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
# WARNING: incomplete conformation T0366 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FORTE2_AL3
# ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0366 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 T0366 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
# Found a chain break before 62
# 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 79
# 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 81
# 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
# Found a chain break before 33
# copying to AlignedFragments data structure
# naming current conformation FPSOLVER-SERVER_TS5
# ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0366 can't currently be optimized by undertaker
# naming current conformation FUGMOD_TS1
# ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1
# naming current conformation FUGMOD_TS2
# ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0366 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
# naming current conformation FUGMOD_TS4
# ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0366 can't currently be optimized by undertaker
# naming current conformation FUGMOD_TS5
# ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0366 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 T0366 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
Skipped atom 211, because occupancy 1 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz
# WARNING: incomplete conformation T0366 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 T0366 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 T0366 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 102
# 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 98
# 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 105
# 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 105
# 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 96
# 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
# naming current conformation Frankenstein_TS2
# ReadConformPDB reading from PDB file servers/Frankenstein_TS3.pdb.gz looking for model 1
# Found a chain break before 12
# copying to AlignedFragments data structure
# naming current conformation Frankenstein_TS3
# ReadConformPDB reading from PDB file servers/Frankenstein_TS4.pdb.gz looking for model 1
# Found a chain break before 71
# copying to AlignedFragments data structure
# naming current conformation Frankenstein_TS4
# ReadConformPDB reading from PDB file servers/Frankenstein_TS5.pdb.gz looking for model 1
# Found a chain break before 59
# copying to AlignedFragments data structure
# naming current conformation Frankenstein_TS5
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0366 can't currently be optimized by undertaker
# naming current conformation GeneSilicoMetaServer_TS1
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0366 can't currently be optimized by undertaker
# naming current conformation GeneSilicoMetaServer_TS2
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0366 can't currently be optimized by undertaker
# naming current conformation GeneSilicoMetaServer_TS3
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1
# Found a chain break before 59
# copying to AlignedFragments data structure
# naming current conformation GeneSilicoMetaServer_TS4
# ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1
# Found a chain break before 72
# 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 72
# 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 72
# 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 T0366 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 T0366 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# 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 T0366 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 T0366 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 T0366 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 T0366 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 T0366 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 T0366 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 T0366 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 T0366 can't currently be optimized by undertaker
# naming current conformation LOOPP_TS5
# ReadConformPDB reading from PDB file servers/MIG_FROST_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0366 can't currently be optimized by undertaker
# naming current conformation MIG_FROST_AL1
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS1.pdb.gz looking for model 1
# Found a chain break before 9
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server2_TS1
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS2.pdb.gz looking for model 1
# Found a chain break before 39
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server2_TS2
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS3.pdb.gz looking for model 1
# naming current conformation Ma-OPUS-server2_TS3
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS4.pdb.gz looking for model 1
# Found a chain break before 101
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server2_TS4
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS5.pdb.gz looking for model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server2_TS5
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1
# Found a chain break before 9
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server_TS1
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS2.pdb.gz looking for model 1
# naming current conformation Ma-OPUS-server_TS2
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS3.pdb.gz looking for model 1
# 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 39
# 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 56
# 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 105
# 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 105
# 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 105
# 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 102
# 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 105
# 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 T0366 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# 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 39
# copying to AlignedFragments data structure
# naming current conformation PROTINFO_TS1
# ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1
# naming current conformation PROTINFO_TS2
# ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1
# naming current conformation PROTINFO_TS3
# ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1
# naming current conformation PROTINFO_TS4
# ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1
# Found a chain break before 39
# copying to AlignedFragments data structure
# naming current conformation PROTINFO_TS5
# ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0366 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 T0366 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 T0366 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 T0366 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation Pcons6_TS4
# ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0366 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 T0366 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
# WARNING: incomplete conformation T0366 can't currently be optimized by undertaker
# 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
# WARNING: incomplete conformation T0366 can't currently be optimized by undertaker
# 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
# WARNING: incomplete conformation T0366 can't currently be optimized by undertaker
# 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
# WARNING: incomplete conformation T0366 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation Phyre-2_TS4
# ReadConformPDB reading from PDB file servers/Phyre-2_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0366 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation Phyre-2_TS5
# ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1
# Found a chain break before 22
# copying to AlignedFragments data structure
# naming current conformation Pmodeller6_TS1
# ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0366 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
# naming current conformation Pmodeller6_TS3
# ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0366 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 T0366 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 71
# 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
# 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 71
# 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
# naming current conformation RAPTOR-ACE_TS4
# ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1
# 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 103
# 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 103
# 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 103
# 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 34
# 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 34
# 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
# naming current conformation RAPTOR_TS3
# ReadConformPDB reading from PDB file servers/RAPTOR_TS4.pdb.gz looking for model 1
# Found a chain break before 89
# 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 89
# 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
# Found a chain break before 22
# 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 100
# copying to AlignedFragments data structure
# 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
# naming current conformation ROKKY_TS1
# ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1
# Found a chain break before 71
# 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 67
# 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 72
# 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 33
# 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 T0366 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 T0366 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 T0366 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 15, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 292, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 304, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 306, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 308, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 310, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 312, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 314, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 316, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 318, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 320, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 322, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 324, 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
# WARNING: incomplete conformation T0366 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 T0366 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 31, 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
# WARNING: incomplete conformation T0366 can't currently be optimized by undertaker
# naming current conformation SAM-T99_AL1
# ReadConformPDB reading from PDB file servers/SAM-T99_AL2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0366 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 T0366 can't currently be optimized by undertaker
# naming current conformation SAM-T99_AL3
# ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1
# Found a chain break before 103
# 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 T0366 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 T0366 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 T0366 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 T0366 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 56
# copying to AlignedFragments data structure
# naming current conformation SP3_TS2
# ReadConformPDB reading from PDB file servers/SP3_TS3.pdb.gz looking for model 1
# 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
# Found a chain break before 61
# 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 56
# copying to AlignedFragments data structure
# naming current conformation SP4_TS1
# ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1
# naming current conformation SP4_TS2
# ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1
# naming current conformation SP4_TS3
# ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1
# 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 100
# 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 56
# 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 71
# copying to AlignedFragments data structure
# 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 90
# 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 T0366 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 T0366 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 T0366 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# 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 T0366 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 T0366 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 T0366 can't currently be optimized by undertaker
# naming current conformation UNI-EID_expm_TS1
# ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL1.pdb.gz looking for model 1
Skipped atom 11, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz
Skipped atom 364, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz
# WARNING: incomplete conformation T0366 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 T0366 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 T0366 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 T0366 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 T0366 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 99
# 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 99
# 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 99
# 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 99
# 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
# 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 105
# 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 T0366 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 T0366 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 T0366 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation forecast-s_AL2
# ReadConformPDB reading from PDB file servers/forecast-s_AL3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0366 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 T0366 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 T0366 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
# Found a chain break before 23
# 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
# 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 55
# 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 39
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.2_TS5
# ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0366 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 T0366 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 T0366 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 T0366 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 T0366 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation karypis.srv_TS5
# ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1
# Found a chain break before 93
# 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 96
# 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
# 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 T0366 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 T0366 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation nFOLD_TS1
# ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0366 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation nFOLD_TS2
# ReadConformPDB reading from PDB file servers/nFOLD_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0366 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 T0366 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 T0366 can't currently be optimized by undertaker
# naming current conformation nFOLD_TS5
# ReadConformPDB reading from PDB file servers/panther2_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0366 can't currently be optimized by undertaker
# naming current conformation panther2_TS1
# ReadConformPDB reading from PDB file servers/panther3_TS1.pdb.gz looking for model 1
WARNING: atoms too close: (T0366)M9.N and (T0366)P20.N only 0.000 apart, marking (T0366)P20.N as missing
WARNING: atoms too close: (T0366)M9.CA and (T0366)P20.CA only 0.000 apart, marking (T0366)P20.CA as missing
WARNING: atoms too close: (T0366)M9.CB and (T0366)P20.CB only 0.000 apart, marking (T0366)P20.CB as missing
WARNING: atoms too close: (T0366)M9.O and (T0366)P20.O only 0.000 apart, marking (T0366)P20.O as missing
WARNING: atoms too close: (T0366)M9.C and (T0366)P20.C only 0.000 apart, marking (T0366)P20.C as missing
# WARNING: incomplete conformation T0366 can't currently be optimized by undertaker
# naming current conformation panther3_TS1
# ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0366 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation shub_TS1
# command:Using radius: 8.0000
Metaserver mode
NUMB_ALIGNS: 263
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weight: 0.9681 eval: -0.6457 min: -0.7549 max: 2.3217
weight: 0.9416 eval: -0.5554 min: -0.7549 max: 2.3217
weight: 0.9866 eval: -0.7093 min: -0.7549 max: 2.3217
weight: 0.9563 eval: -0.6056 min: -0.7549 max: 2.3217
weight: 0.9445 eval: -0.5653 min: -0.7549 max: 2.3217
weight: 0.9561 eval: -0.6047 min: -0.7549 max: 2.3217
weight: 0.8609 eval: -0.2795 min: -0.7549 max: 2.3217
weight: 0.4097 eval: 1.2631 min: -0.7549 max: 2.3217
weight: 0.4101 eval: 1.2615 min: -0.7549 max: 2.3217
weight: 0.4097 eval: 1.2630 min: -0.7549 max: 2.3217
weight: 0.4101 eval: 1.2616 min: -0.7549 max: 2.3217
weight: 0.4099 eval: 1.2624 min: -0.7549 max: 2.3217
weight: 0.9853 eval: -0.7048 min: -0.7549 max: 2.3217
weight: 0.4097 eval: 1.2631 min: -0.7549 max: 2.3217
weight: 0.4101 eval: 1.2615 min: -0.7549 max: 2.3217
weight: 0.4097 eval: 1.2630 min: -0.7549 max: 2.3217
weight: 0.4101 eval: 1.2616 min: -0.7549 max: 2.3217
weight: 0.4099 eval: 1.2624 min: -0.7549 max: 2.3217
weight: 0.9858 eval: -0.7062 min: -0.7549 max: 2.3217
weight: 0.9817 eval: -0.6922 min: -0.7549 max: 2.3217
weight: 0.9935 eval: -0.7327 min: -0.7549 max: 2.3217
weight: 0.9837 eval: -0.6991 min: -0.7549 max: 2.3217
weight: 0.9682 eval: -0.6461 min: -0.7549 max: 2.3217
weight: 0.9777 eval: -0.6788 min: -0.7549 max: 2.3217
weight: 0.9755 eval: -0.6711 min: -0.7549 max: 2.3217
weight: 0.4098 eval: 1.2625 min: -0.7549 max: 2.3217
weight: 0.4092 eval: 1.2647 min: -0.7549 max: 2.3217
weight: 0.4080 eval: 1.2688 min: -0.7549 max: 2.3217
weight: 0.4080 eval: 1.2687 min: -0.7549 max: 2.3217
weight: 0.4103 eval: 1.2611 min: -0.7549 max: 2.3217
weight: 0.8373 eval: -0.1989 min: -0.7549 max: 2.3217
weight: 0.9582 eval: -0.6121 min: -0.7549 max: 2.3217
weight: 0.9454 eval: -0.5684 min: -0.7549 max: 2.3217
weight: 0.9264 eval: -0.5034 min: -0.7549 max: 2.3217
weight: 0.9172 eval: -0.4717 min: -0.7549 max: 2.3217
weight: 0.8370 eval: -0.1979 min: -0.7549 max: 2.3217
weight: 0.9221 eval: -0.4887 min: -0.7549 max: 2.3217
weight: 0.9680 eval: -0.6454 min: -0.7549 max: 2.3217
weight: 0.9037 eval: -0.4259 min: -0.7549 max: 2.3217
weight: 0.9372 eval: -0.5402 min: -0.7549 max: 2.3217
weight: 0.9769 eval: -0.6759 min: -0.7549 max: 2.3217
weight: 0.9788 eval: -0.6826 min: -0.7549 max: 2.3217
weight: 0.9325 eval: -0.5243 min: -0.7549 max: 2.3217
weight: 0.9417 eval: -0.5556 min: -0.7549 max: 2.3217
weight: 0.9417 eval: -0.5556 min: -0.7549 max: 2.3217
weight: 0.9476 eval: -0.5757 min: -0.7549 max: 2.3217
weight: 0.9433 eval: -0.5610 min: -0.7549 max: 2.3217
weight: 0.9454 eval: -0.5682 min: -0.7549 max: 2.3217
weight: 0.7476 eval: 0.1080 min: -0.7549 max: 2.3217
weight: 0.9235 eval: -0.4933 min: -0.7549 max: 2.3217
weight: 0.9638 eval: -0.6311 min: -0.7549 max: 2.3217
weight: 0.9104 eval: -0.4487 min: -0.7549 max: 2.3217
weight: 0.9485 eval: -0.5789 min: -0.7549 max: 2.3217
weight: 0.9720 eval: -0.6593 min: -0.7549 max: 2.3217
Adding 2148 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: -188.3774, CN propb: -188.3774 weights: 0.4900 constraints: 277
# command:Found ConstraintSet
# PrintContacts align.constraints_meta02
Number of constraints in align2.constraints 277
# command:Found ConstraintSet
# PrintContacts align_bonus.constraints_meta02
Number of constraints in align2.constraints.bonus 277
# command:Found ConstraintSet
# PrintContacts rejected.constraints_meta02
Number of constraints in rejected2.constraints 1871
# command:Found ConstraintSet
# PrintContacts rejected_bonus.constraints_meta02
Number of constraints in rejected2.constraints.bonus 1871
# 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 2148
# command: