# 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/T0351/
# command:# Making conformation for sequence T0351 numbered 1 through 117
Created new target T0351 from T0351.a2m
# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0351/
# command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0351//projects/compbio/experiments/protein-predict/casp7/T0351/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0351//projects/compbio/experiments/protein-predict/casp7/T0351/align.constraints_v3.costfcn.gz for input
Trying /projects/compbio/experiments/protein-predict/casp7/T0351/align.constraints_v3.costfcn
# reading script from file /projects/compbio/experiments/protein-predict/casp7/T0351/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((T0351)L53.CB, (T0351)Q64.CB) [> 3.9899 = 6.6499 < 8.6448] w=0.9817 to align
# Constraint # added constraint: constraint((T0351)W50.CB, (T0351)Y59.CB) [> 4.1343 = 6.8905 < 8.9577] w=0.9065 to align
# Constraint # added constraint: constraint((T0351)W50.CB, (T0351)E60.CB) [> 4.2584 = 7.0974 < 9.2266] w=0.8374 to align
# Constraint # added constraint: constraint((T0351)L22.CB, (T0351)I31.CB) [> 2.7557 = 4.5928 < 5.9706] w=0.8063 to align
# Constraint # added constraint: constraint((T0351)W50.CB, (T0351)L82.CB) [> 4.0691 = 6.7818 < 8.8163] w=0.6686 to align
# Constraint # added constraint: constraint((T0351)E21.CB, (T0351)Y30.CB) [> 4.0437 = 6.7395 < 8.7613] w=0.6469 to align
# Constraint # added constraint: constraint((T0351)L85.CB, (T0351)I96.CB) [> 3.5974 = 5.9957 < 7.7944] w=0.5108 to align
# Constraint # added constraint: constraint((T0351)L22.CB, (T0351)E32.CB) [> 3.3465 = 5.5776 < 7.2508] w=0.5023 to align
# Constraint # added constraint: constraint((T0351)V65.CB, (T0351)L82.CB) [> 3.3007 = 5.5012 < 7.1516] w=0.4746 to align
# Constraint # added constraint: constraint((T0351)E52.CB, (T0351)L67.CB) [> 4.3973 = 7.3288 < 9.5275] w=0.4730 to align
# Constraint # added constraint: constraint((T0351)E21.CB, (T0351)I31.CB) [> 4.7109 = 7.8515 < 10.2070] w=0.4448 to align
# Constraint # added constraint: constraint((T0351)V65.CB, (T0351)R79.CB) [> 3.7465 = 6.2442 < 8.1175] w=0.4210 to align
# Constraint # added constraint: constraint((T0351)S16.CB, (T0351)W50.CB) [> 4.3781 = 7.2968 < 9.4859] w=0.4187 to align
# Constraint # added constraint: constraint((T0351)R17.CB, (T0351)Q43.CB) [> 2.4714 = 4.1189 < 5.3546] w=0.4187 to align
# Constraint # added constraint: constraint((T0351)R17.CB, (T0351)L46.CB) [> 2.9504 = 4.9173 < 6.3925] w=0.4187 to align
# Constraint # added constraint: constraint((T0351)R17.CB, (T0351)E47.CB) [> 2.6284 = 4.3807 < 5.6950] w=0.4187 to align
# Constraint # added constraint: constraint((T0351)R17.CB, (T0351)W50.CB) [> 3.6629 = 6.1049 < 7.9364] w=0.4187 to align
# Constraint # added constraint: constraint((T0351)K18.CB, (T0351)Q43.CB) [> 3.6799 = 6.1332 < 7.9731] w=0.4187 to align
# Constraint # added constraint: constraint((T0351)F20.CB, (T0351)L46.CB) [> 3.1498 = 5.2497 < 6.8246] w=0.4187 to align
# Constraint # added constraint: constraint((T0351)L22.CB, (T0351)E45.CB) [> 4.6254 = 7.7090 < 10.0216] w=0.4187 to align
# Constraint # added constraint: constraint((T0351)L22.CB, (T0351)L46.CB) [> 3.5075 = 5.8458 < 7.5995] w=0.4187 to align
# Constraint # added constraint: constraint((T0351)L22.CB, (T0351)W49.CB) [> 4.5613 = 7.6022 < 9.8828] w=0.4187 to align
# Constraint # added constraint: constraint((T0351)W50.CB, (T0351)L68.CB) [> 3.7220 = 6.2034 < 8.0644] w=0.4120 to align
# Constraint # added constraint: constraint((T0351)L22.CB, (T0351)W34.CB) [> 3.8559 = 6.4265 < 8.3545] w=0.4091 to align
# Constraint # added constraint: constraint((T0351)L46.CB, (T0351)L85.CB) [> 3.5993 = 5.9989 < 7.7986] w=0.3980 to align
# Constraint # added constraint: constraint((T0351)L46.CB, (T0351)L82.CB) [> 4.2767 = 7.1279 < 9.2662] w=0.3904 to align
# Constraint # added constraint: constraint((T0351)D19.CB, (T0351)K33.CB) [> 3.6380 = 6.0633 < 7.8822] w=0.3678 to align
# Constraint # added constraint: constraint((T0351)F20.CB, (T0351)W50.CB) [> 4.2699 = 7.1165 < 9.2515] w=0.3532 to align
# Constraint # added constraint: constraint((T0351)E21.CB, (T0351)K33.CB) [> 3.3795 = 5.6324 < 7.3222] w=0.3429 to align
# Constraint # added constraint: constraint((T0351)F20.CB, (T0351)N35.CB) [> 4.5056 = 7.5093 < 9.7621] w=0.3429 to align
# Constraint # added constraint: constraint((T0351)D19.CB, (T0351)L36.CB) [> 3.7784 = 6.2974 < 8.1866] w=0.3429 to align
# Constraint # added constraint: constraint((T0351)Q54.CB, (T0351)V65.CB) [> 3.0549 = 5.0915 < 6.6189] w=0.3427 to align
# Constraint # added constraint: constraint((T0351)L72.CB, (T0351)I96.CB) [> 3.9211 = 6.5352 < 8.4957] w=0.3327 to align
# Constraint # added constraint: constraint((T0351)L67.CB, (T0351)A78.CB) [> 4.1103 = 6.8505 < 8.9057] w=0.3307 to align
# Constraint # added constraint: constraint((T0351)L3.CB, (T0351)V65.CB) [> 3.2922 = 5.4871 < 7.1332] w=0.3123 to align
# Constraint # added constraint: constraint((T0351)I7.CB, (T0351)K18.CB) [> 4.4951 = 7.4918 < 9.7394] w=0.3123 to align
# Constraint # added constraint: constraint((T0351)K18.CB, (T0351)W50.CB) [> 4.5602 = 7.6003 < 9.8804] w=0.3123 to align
# Constraint # added constraint: constraint((T0351)K18.CB, (T0351)E60.CB) [> 3.7160 = 6.1933 < 8.0513] w=0.3123 to align
# Constraint # added constraint: constraint((T0351)D19.CB, (T0351)E60.CB) [> 3.3839 = 5.6398 < 7.3317] w=0.3123 to align
# Constraint # added constraint: constraint((T0351)F20.CB, (T0351)I31.CB) [> 3.6332 = 6.0553 < 7.8719] w=0.3073 to align
# Constraint # added constraint: constraint((T0351)I7.CB, (T0351)L22.CB) [> 4.5554 = 7.5924 < 9.8701] w=0.3065 to align
# Constraint # added constraint: constraint((T0351)I7.CB, (T0351)F20.CB) [> 4.0353 = 6.7255 < 8.7431] w=0.3065 to align
# Constraint # added constraint: constraint((T0351)L68.CB, (T0351)A78.CB) [> 3.1867 = 5.3112 < 6.9046] w=0.2842 to align
# Constraint # added constraint: constraint((T0351)W34.CB, (T0351)L46.CB) [> 4.3043 = 7.1739 < 9.3260] w=0.2837 to align
# Constraint # added constraint: constraint((T0351)A6.CB, (T0351)L22.CB) [> 4.5732 = 7.6220 < 9.9086] w=0.2791 to align
# Constraint # added constraint: constraint((T0351)I7.CB, (T0351)W49.CB) [> 3.6487 = 6.0812 < 7.9055] w=0.2791 to align
# Constraint # added constraint: constraint((T0351)I7.CB, (T0351)W50.CB) [> 4.2342 = 7.0569 < 9.1740] w=0.2791 to align
# Constraint # added constraint: constraint((T0351)I7.CB, (T0351)L53.CB) [> 3.6251 = 6.0419 < 7.8545] w=0.2791 to align
# Constraint # added constraint: constraint((T0351)M8.CB, (T0351)L53.CB) [> 3.3829 = 5.6382 < 7.3296] w=0.2791 to align
# Constraint # added constraint: constraint((T0351)Y30.CB, (T0351)T42.CB) [> 4.5161 = 7.5269 < 9.7850] w=0.2791 to align
# Constraint # added constraint: constraint((T0351)I31.CB, (T0351)T42.CB) [> 3.3468 = 5.5780 < 7.2514] w=0.2791 to align
# Constraint # added constraint: constraint((T0351)Q54.CB, (T0351)L93.CB) [> 4.5898 = 7.6497 < 9.9446] w=0.2787 to align
# Constraint # added constraint: constraint((T0351)P39.CB, (T0351)W49.CB) [> 3.2999 = 5.4999 < 7.1499] w=0.2773 to align
# Constraint # added constraint: constraint((T0351)L82.CB, (T0351)L93.CB) [> 4.0968 = 6.8280 < 8.8764] w=0.2767 to align
# Constraint # added constraint: constraint((T0351)V65.CB, (T0351)L93.CB) [> 4.0852 = 6.8087 < 8.8513] w=0.2724 to align
# Constraint # added constraint: constraint((T0351)L68.CB, (T0351)I96.CB) [> 2.9371 = 4.8951 < 6.3637] w=0.2706 to align
# Constraint # added constraint: constraint((T0351)V65.CB, (T0351)I96.CB) [> 3.8473 = 6.4122 < 8.3359] w=0.2706 to align
# Constraint # added constraint: constraint((T0351)P62.CB, (T0351)A78.CB) [> 3.9158 = 6.5264 < 8.4843] w=0.2681 to align
# Constraint # added constraint: constraint((T0351)Y30.CB, (T0351)Q64.CB) [> 4.1246 = 6.8743 < 8.9366] w=0.2621 to align
# Constraint # added constraint: constraint((T0351)Y30.CB, (T0351)E60.CB) [> 3.5723 = 5.9538 < 7.7400] w=0.2621 to align
# Constraint # added constraint: constraint((T0351)S29.CB, (T0351)E60.CB) [> 2.2849 = 3.8081 < 4.9505] w=0.2621 to align
# Constraint # added constraint: constraint((T0351)L85.CB, (T0351)S99.CB) [> 3.1891 = 5.3151 < 6.9097] w=0.2561 to align
# Constraint # added constraint: constraint((T0351)S94.CB, (T0351)G105.CA) [> 3.9761 = 6.6268 < 8.6149] w=0.2561 to align
# Constraint # added constraint: constraint((T0351)S94.CB, (T0351)Y107.CB) [> 4.2383 = 7.0638 < 9.1830] w=0.2561 to align
# Constraint # added constraint: constraint((T0351)S94.CB, (T0351)L110.CB) [> 2.7996 = 4.6661 < 6.0659] w=0.2561 to align
# Constraint # added constraint: constraint((T0351)K97.CB, (T0351)Y107.CB) [> 3.4925 = 5.8209 < 7.5672] w=0.2561 to align
# Constraint # added constraint: constraint((T0351)D19.CB, (T0351)W50.CB) [> 4.6870 = 7.8117 < 10.1553] w=0.2487 to align
# Constraint # added constraint: constraint((T0351)W49.CB, (T0351)L68.CB) [> 3.9499 = 6.5832 < 8.5582] w=0.2271 to align
# Constraint # added constraint: constraint((T0351)Y59.CB, (T0351)L68.CB) [> 3.3226 = 5.5376 < 7.1989] w=0.2127 to align
# Constraint # added constraint: constraint((T0351)Y4.CB, (T0351)L53.CB) [> 3.6369 = 6.0615 < 7.8800] w=0.2103 to align
# Constraint # added constraint: constraint((T0351)V65.CB, (T0351)N86.CB) [> 2.7036 = 4.5060 < 5.8578] w=0.2095 to align
# Constraint # added constraint: constraint((T0351)Q64.CB, (T0351)N86.CB) [> 4.5149 = 7.5249 < 9.7823] w=0.2095 to align
# Constraint # added constraint: constraint((T0351)L40.CB, (T0351)W49.CB) [> 4.4468 = 7.4113 < 9.6348] w=0.2075 to align
# Constraint # added constraint: constraint((T0351)Y59.CB, (T0351)K97.CB) [> 4.5672 = 7.6120 < 9.8956] w=0.2061 to align
# Constraint # added constraint: constraint((T0351)E60.CB, (T0351)I96.CB) [> 4.3179 = 7.1964 < 9.3554] w=0.2061 to align
# Constraint # added constraint: constraint((T0351)E60.CB, (T0351)K97.CB) [> 2.8606 = 4.7676 < 6.1979] w=0.2061 to align
# Constraint # added constraint: constraint((T0351)E60.CB, (T0351)L100.CB) [> 2.0512 = 3.4187 < 4.4443] w=0.2061 to align
# Constraint # added constraint: constraint((T0351)E60.CB, (T0351)L101.CB) [> 3.0512 = 5.0853 < 6.6109] w=0.2061 to align
# Constraint # added constraint: constraint((T0351)E60.CB, (T0351)K104.CB) [> 4.1019 = 6.8366 < 8.8875] w=0.2061 to align
# Constraint # added constraint: constraint((T0351)P61.CB, (T0351)L101.CB) [> 4.5115 = 7.5192 < 9.7750] w=0.2061 to align
# Constraint # added constraint: constraint((T0351)P62.CB, (T0351)L101.CB) [> 3.7421 = 6.2368 < 8.1079] w=0.2061 to align
# Constraint # added constraint: constraint((T0351)P62.CB, (T0351)K104.CB) [> 3.2216 = 5.3693 < 6.9801] w=0.2061 to align
# Constraint # added constraint: constraint((T0351)Q64.CB, (T0351)L93.CB) [> 3.9625 = 6.6042 < 8.5854] w=0.2061 to align
# Constraint # added constraint: constraint((T0351)L68.CB, (T0351)K97.CB) [> 3.5495 = 5.9159 < 7.6906] w=0.2061 to align
# Constraint # added constraint: constraint((T0351)N56.CB, (T0351)V65.CB) [> 4.5338 = 7.5564 < 9.8233] w=0.2042 to align
# Constraint # added constraint: constraint((T0351)L72.CB, (T0351)L100.CB) [> 2.5479 = 4.2464 < 5.5204] w=0.2038 to align
# Constraint # added constraint: constraint((T0351)A14.CB, (T0351)A38.CB) [> 3.9513 = 6.5855 < 8.5612] w=0.2020 to align
# Constraint # added constraint: constraint((T0351)K18.CB, (T0351)L36.CB) [> 3.0202 = 5.0337 < 6.5438] w=0.2020 to align
# Constraint # added constraint: constraint((T0351)D19.CB, (T0351)W34.CB) [> 4.0089 = 6.6815 < 8.6859] w=0.2020 to align
# Constraint # added constraint: constraint((T0351)F20.CB, (T0351)W34.CB) [> 3.6776 = 6.1293 < 7.9681] w=0.2020 to align
# Constraint # added constraint: constraint((T0351)E21.CB, (T0351)E32.CB) [> 4.4816 = 7.4694 < 9.7102] w=0.2020 to align
# Constraint # added constraint: constraint((T0351)P41.CB, (T0351)W50.CB) [> 4.5402 = 7.5670 < 9.8372] w=0.1958 to align
# Constraint # added constraint: constraint((T0351)T42.CB, (T0351)Q81.CB) [> 4.6759 = 7.7931 < 10.1311] w=0.1958 to align
# Constraint # added constraint: constraint((T0351)G28.CA, (T0351)P61.CB) [> 3.9738 = 6.6230 < 8.6099] w=0.1940 to align
# Constraint # added constraint: constraint((T0351)L98.CB, (T0351)L110.CB) [> 4.3629 = 7.2715 < 9.4529] w=0.1924 to align
# Constraint # added constraint: constraint((T0351)L3.CB, (T0351)Q64.CB) [> 4.3500 = 7.2500 < 9.4250] w=0.1864 to align
# Constraint # added constraint: constraint((T0351)L3.CB, (T0351)L68.CB) [> 3.2200 = 5.3667 < 6.9767] w=0.1864 to align
# Constraint # added constraint: constraint((T0351)A6.CB, (T0351)Q64.CB) [> 4.6696 = 7.7827 < 10.1175] w=0.1864 to align
# Constraint # added constraint: constraint((T0351)A6.CB, (T0351)L68.CB) [> 4.0830 = 6.8050 < 8.8466] w=0.1864 to align
# Constraint # added constraint: constraint((T0351)I7.CB, (T0351)V65.CB) [> 4.6431 = 7.7385 < 10.0601] w=0.1864 to align
# Constraint # added constraint: constraint((T0351)K10.CB, (T0351)Q64.CB) [> 4.6507 = 7.7512 < 10.0765] w=0.1864 to align
# Constraint # added constraint: constraint((T0351)K18.CB, (T0351)Q64.CB) [> 4.1821 = 6.9701 < 9.0611] w=0.1864 to align
# Constraint # added constraint: constraint((T0351)D19.CB, (T0351)E32.CB) [> 3.3628 = 5.6048 < 7.2862] w=0.1657 to align
# Constraint # added constraint: constraint((T0351)D19.CB, (T0351)I31.CB) [> 4.1265 = 6.8775 < 8.9407] w=0.1657 to align
# Constraint # added constraint: constraint((T0351)W34.CB, (T0351)W50.CB) [> 4.7720 = 7.9534 < 10.3394] w=0.1594 to align
# Constraint # added constraint: constraint((T0351)W50.CB, (T0351)L67.CB) [> 3.7876 = 6.3127 < 8.2064] w=0.1594 to align
# Constraint # added constraint: constraint((T0351)A14.CB, (T0351)I31.CB) [> 4.2477 = 7.0795 < 9.2034] w=0.1449 to align
# Constraint # added constraint: constraint((T0351)L40.CB, (T0351)E60.CB) [> 4.6918 = 7.8197 < 10.1656] w=0.1449 to align
# Constraint # added constraint: constraint((T0351)L46.CB, (T0351)L68.CB) [> 4.2298 = 7.0497 < 9.1646] w=0.1449 to align
# Constraint # added constraint: constraint((T0351)E21.CB, (T0351)N35.CB) [> 2.7376 = 4.5627 < 5.9315] w=0.1409 to align
# Constraint # added constraint: constraint((T0351)E21.CB, (T0351)W34.CB) [> 4.5884 = 7.6474 < 9.9416] w=0.1409 to align
# Constraint # added constraint: constraint((T0351)W34.CB, (T0351)Q81.CB) [> 3.7182 = 6.1970 < 8.0561] w=0.1409 to align
# Constraint # added constraint: constraint((T0351)L3.CB, (T0351)V15.CB) [> 4.4966 = 7.4944 < 9.7427] w=0.1396 to align
# Constraint # added constraint: constraint((T0351)Y4.CB, (T0351)N13.CB) [> 3.7341 = 6.2235 < 8.0905] w=0.1396 to align
# Constraint # added constraint: constraint((T0351)Y4.CB, (T0351)A14.CB) [> 3.7970 = 6.3283 < 8.2268] w=0.1396 to align
# Constraint # added constraint: constraint((T0351)Y4.CB, (T0351)V15.CB) [> 3.8353 = 6.3922 < 8.3098] w=0.1396 to align
# Constraint # added constraint: constraint((T0351)E21.CB, (T0351)A38.CB) [> 4.3974 = 7.3290 < 9.5277] w=0.1396 to align
# Constraint # added constraint: constraint((T0351)L22.CB, (T0351)P41.CB) [> 2.4953 = 4.1589 < 5.4065] w=0.1396 to align
# Constraint # added constraint: constraint((T0351)R23.CB, (T0351)L36.CB) [> 3.9885 = 6.6475 < 8.6417] w=0.1396 to align
# Constraint # added constraint: constraint((T0351)R23.CB, (T0351)A38.CB) [> 3.1622 = 5.2704 < 6.8515] w=0.1396 to align
# Constraint # added constraint: constraint((T0351)R23.CB, (T0351)P41.CB) [> 4.4397 = 7.3996 < 9.6194] w=0.1396 to align
# Constraint # added constraint: constraint((T0351)E60.CB, (T0351)S99.CB) [> 4.7003 = 7.8338 < 10.1840] w=0.1394 to align
# Constraint # added constraint: constraint((T0351)V65.CB, (T0351)E92.CB) [> 4.3464 = 7.2440 < 9.4172] w=0.1394 to align
# Constraint # added constraint: constraint((T0351)L72.CB, (T0351)L98.CB) [> 4.5756 = 7.6261 < 9.9139] w=0.1394 to align
# Constraint # added constraint: constraint((T0351)L72.CB, (T0351)L101.CB) [> 2.8665 = 4.7775 < 6.2107] w=0.1394 to align
# Constraint # added constraint: constraint((T0351)S73.CB, (T0351)L101.CB) [> 4.6760 = 7.7933 < 10.1313] w=0.1394 to align
# Constraint # added constraint: constraint((T0351)L68.CB, (T0351)L100.CB) [> 4.6065 = 7.6775 < 9.9808] w=0.1331 to align
# Constraint # added constraint: constraint((T0351)L68.CB, (T0351)L77.CB) [> 4.3658 = 7.2763 < 9.4592] w=0.1326 to align
# Constraint # added constraint: constraint((T0351)Y9.CB, (T0351)A78.CB) [> 4.4881 = 7.4802 < 9.7242] w=0.1325 to align
# Constraint # added constraint: constraint((T0351)M8.CB, (T0351)A78.CB) [> 3.3656 = 5.6093 < 7.2921] w=0.1325 to align
# Constraint # added constraint: constraint((T0351)M8.CB, (T0351)L77.CB) [> 4.3022 = 7.1703 < 9.3214] w=0.1325 to align
# Constraint # added constraint: constraint((T0351)W50.CB, (T0351)L100.CB) [> 3.5728 = 5.9546 < 7.7410] w=0.1305 to align
# Constraint # added constraint: constraint((T0351)L89.CB, (T0351)S99.CB) [> 2.8663 = 4.7771 < 6.2102] w=0.1305 to align
# Constraint # added constraint: constraint((T0351)L46.CB, (T0351)L98.CB) [> 3.8801 = 6.4668 < 8.4069] w=0.1289 to align
# Constraint # added constraint: constraint((T0351)A6.CB, (T0351)V65.CB) [> 4.4284 = 7.3807 < 9.5949] w=0.1259 to align
# Constraint # added constraint: constraint((T0351)L3.CB, (T0351)A69.CB) [> 4.4784 = 7.4641 < 9.7033] w=0.1242 to align
# Constraint # added constraint: constraint((T0351)S16.CB, (T0351)L82.CB) [> 4.7631 = 7.9385 < 10.3200] w=0.0966 to align
# Constraint # added constraint: constraint((T0351)V15.CB, (T0351)N24.CB) [> 2.8303 = 4.7171 < 6.1322] w=0.0966 to align
# Constraint # added constraint: constraint((T0351)A14.CB, (T0351)Y30.CB) [> 4.7458 = 7.9097 < 10.2826] w=0.0966 to align
# Constraint # added constraint: constraint((T0351)E60.CB, (T0351)L98.CB) [> 4.5330 = 7.5551 < 9.8216] w=0.0731 to align
# Constraint # added constraint: constraint((T0351)N24.CB, (T0351)L89.CB) [> 4.1341 = 6.8902 < 8.9572] w=0.0704 to align
# Constraint # added constraint: constraint((T0351)F20.CB, (T0351)Q81.CB) [> 4.2933 = 7.1555 < 9.3022] w=0.0704 to align
# Constraint # added constraint: constraint((T0351)Y9.CB, (T0351)L89.CB) [> 4.4881 = 7.4802 < 9.7242] w=0.0663 to align
# Constraint # added constraint: constraint((T0351)Y9.CB, (T0351)E75.CB) [> 4.4898 = 7.4830 < 9.7278] w=0.0663 to align
# Constraint # added constraint: constraint((T0351)P39.CB, (T0351)L103.CB) [> 4.6453 = 7.7422 < 10.0648] w=0.0653 to align
# Constraint # added constraint: constraint((T0351)A69.CB, (T0351)L103.CB) [> 3.5051 = 5.8418 < 7.5943] w=0.0644 to align
# Constraint # added constraint: constraint((T0351)L68.CB, (T0351)L103.CB) [> 2.5626 = 4.2710 < 5.5523] w=0.0644 to align
# Constraint # added constraint: constraint((T0351)L68.CB, (T0351)S102.CB) [> 3.0935 = 5.1558 < 6.7026] w=0.0644 to align
# Constraint # added constraint: constraint((T0351)V65.CB, (T0351)S102.CB) [> 4.1250 = 6.8750 < 8.9375] w=0.0644 to align
# Constraint # added constraint: constraint((T0351)W50.CB, (T0351)L98.CB) [> 3.4265 = 5.7108 < 7.4240] w=0.0644 to align
# Constraint # added constraint: constraint((T0351)L72.CB, (T0351)L103.CB) [> 3.5386 = 5.8977 < 7.6670] w=0.0644 to align
# Constraint # added constraint: constraint((T0351)W50.CB, (T0351)Q64.CB) [> 4.6756 = 7.7926 < 10.1304] w=0.0628 to align
# Constraint # added constraint: constraint((T0351)D25.CB, (T0351)P39.CB) [> 2.9212 = 4.8687 < 6.3293] w=0.0623 to align
# Constraint # added constraint: constraint((T0351)Y11.CB, (T0351)I31.CB) [> 2.6997 = 4.4995 < 5.8493] w=0.0274 to align
# Constraint # added constraint: constraint((T0351)Y11.CB, (T0351)F20.CB) [> 3.5329 = 5.8882 < 7.6547] w=0.0274 to align
# Constraint # added constraint: constraint((T0351)K10.CB, (T0351)F20.CB) [> 4.6245 = 7.7076 < 10.0199] w=0.0274 to align
# Constraint # added constraint: constraint((T0351)L3.CB, (T0351)N24.CB) [> 4.6184 = 7.6974 < 10.0066] w=0.0274 to align
# Constraint # added constraint: constraint((T0351)Q64.CB, (T0351)Y107.CB) [> 3.2021 = 5.3369 < 6.9379] w=0.0137 to align
# Constraint # added constraint: constraint((T0351)Q64.CB, (T0351)D106.CB) [> 4.6306 = 7.7176 < 10.0329] w=0.0137 to align
# Constraint # added constraint: constraint((T0351)Q64.CB, (T0351)L103.CB) [> 3.1786 = 5.2976 < 6.8868] w=0.0137 to align
# Constraint # added constraint: constraint((T0351)Q64.CB, (T0351)L98.CB) [> 3.8265 = 6.3775 < 8.2907] w=0.0137 to align
# Constraint # added constraint: constraint((T0351)V65.CB, (T0351)L98.CB) [> 3.6992 = 6.1653 < 8.0149] w=0.0137 to align
# Constraint # added constraint: constraint((T0351)P39.CB, (T0351)L110.CB) [> 4.3678 = 7.2796 < 9.4635] w=0.0073 to align
# SetCost created cost = 
#	( 1.0000 * align )
# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0351/
# command:# reading script from file servers-clean.under
# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0351/decoys/
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 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
# choosing archetypes in rotamer library
# Found a chain break before 81
# copying to AlignedFragments data structure
# naming current conformation 3D-JIGSAW_POPULUS_TS2
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 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 T0351 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 T0351 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 T0351 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 T0351 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 T0351 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 T0351 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 T0351 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 T0351 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 T0351 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 T0351 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 T0351 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_TS4
# ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1
# Found a chain break before 54
# 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 19
# copying to AlignedFragments data structure
# naming current conformation 3Dpro_TS2
# ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1
# Found a chain break before 37
# copying to AlignedFragments data structure
# naming current conformation 3Dpro_TS3
# ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1
# naming current conformation 3Dpro_TS4
# ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1
# Found a chain break before 94
# 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 54
# 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 97
# 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 100
# 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 116
# copying to AlignedFragments data structure
# naming current conformation ABIpro_TS5
# ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1
# Found a chain break before 74
# copying to AlignedFragments data structure
# naming current conformation BayesHH_TS1
# ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS1.pdb.gz looking for model 1
# Found a chain break before 116
# copying to AlignedFragments data structure
# naming current conformation Bilab-ENABLE_TS1
# ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS2.pdb.gz looking for model 1
# Found a chain break before 80
# copying to AlignedFragments data structure
# naming current conformation Bilab-ENABLE_TS2
# ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS3.pdb.gz looking for model 1
# Found a chain break before 116
# 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 116
# 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 116
# 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 113
# 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 108
# 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 104
# copying to AlignedFragments data structure
# naming current conformation CIRCLE_TS3
# ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1
# Found a chain break before 107
# copying to AlignedFragments data structure
# naming current conformation CIRCLE_TS4
# ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1
# Found a chain break before 74
# copying to AlignedFragments data structure
# naming current conformation CIRCLE_TS5
# ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 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 T0351 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 T0351 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 T0351 can't currently be optimized by undertaker
# naming current conformation CaspIta-FOX_TS4
# ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 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 T0351 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 T0351 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 T0351 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 T0351 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 T0351 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 108
# copying to AlignedFragments data structure
# naming current conformation FAMSD_TS1
# ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1
# Found a chain break before 104
# copying to AlignedFragments data structure
# naming current conformation FAMSD_TS2
# ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1
# Found a chain break before 110
# 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 T0351 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 T0351 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 109
# 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 116
# 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 106
# 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 110
# 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 107
# 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 59
# 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 69
# 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 73
# copying to AlignedFragments data structure
# naming current conformation FOLDpro_TS3
# ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1
# Found a chain break before 73
# copying to AlignedFragments data structure
# naming current conformation FOLDpro_TS4
# ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1
# naming current conformation FOLDpro_TS5
# ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# naming current conformation FORTE1_AL1
# ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# naming current conformation FORTE1_AL2
# ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# naming current conformation FORTE1_AL3
# ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 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
Skipped atom 226, because occupancy 1 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz
Skipped atom 228, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz
Skipped atom 230, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz
Skipped atom 232, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# naming current conformation FORTE1_AL5
# ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# naming current conformation FORTE2_AL1
# ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# naming current conformation FORTE2_AL2
# ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# naming current conformation FORTE2_AL3
# ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 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
Skipped atom 226, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz
Skipped atom 228, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz
Skipped atom 230, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz
Skipped atom 232, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# naming current conformation FORTE2_AL5
# ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS1.pdb.gz looking for model 1
# Found a chain break before 46
# 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 77
# 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 116
# copying to AlignedFragments data structure
# naming current conformation FPSOLVER-SERVER_TS3
# ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS4.pdb.gz looking for model 1
# Found a chain break before 104
# copying to AlignedFragments data structure
# naming current conformation FPSOLVER-SERVER_TS4
# ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS5.pdb.gz looking for model 1
# Found a chain break before 114
# copying to AlignedFragments data structure
# naming current conformation FPSOLVER-SERVER_TS5
# ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1
# Found a chain break before 33
# copying to AlignedFragments data structure
# naming current conformation FUGMOD_TS1
# ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# naming current conformation FUGMOD_TS2
# ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1
# Found a chain break before 84
# copying to AlignedFragments data structure
# naming current conformation FUGMOD_TS3
# ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# naming current conformation FUGMOD_TS4
# ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 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 T0351 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FUGUE_AL1
# ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# naming current conformation FUGUE_AL2
# ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FUGUE_AL3
# ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# naming current conformation FUGUE_AL4
# ReadConformPDB reading from PDB file servers/FUGUE_AL5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# naming current conformation FUGUE_AL5
# ReadConformPDB reading from PDB file servers/FUNCTION_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# naming current conformation FUNCTION_TS1
# ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1
# Found a chain break before 113
# 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 111
# copying to AlignedFragments data structure
# naming current conformation FUNCTION_TS3
# ReadConformPDB reading from PDB file servers/FUNCTION_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# 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 109
# copying to AlignedFragments data structure
# naming current conformation FUNCTION_TS5
# ReadConformPDB reading from PDB file servers/Frankenstein_TS1.pdb.gz looking for model 1
# Found a chain break before 77
# copying to AlignedFragments data structure
# naming current conformation Frankenstein_TS1
# ReadConformPDB reading from PDB file servers/Frankenstein_TS2.pdb.gz looking for model 1
# Found a chain break before 51
# copying to AlignedFragments data structure
# naming current conformation Frankenstein_TS2
# ReadConformPDB reading from PDB file servers/Frankenstein_TS3.pdb.gz looking for model 1
# naming current conformation Frankenstein_TS3
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 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 T0351 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 T0351 can't currently be optimized by undertaker
# naming current conformation GeneSilicoMetaServer_TS3
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# naming current conformation GeneSilicoMetaServer_TS4
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# naming current conformation GeneSilicoMetaServer_TS5
# ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1
# naming current conformation HHpred1_TS1
# ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1
# Found a chain break before 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 60
# 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 T0351 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 T0351 can't currently be optimized by undertaker
# naming current conformation Huber-Torda-Server_TS2
# ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 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 T0351 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 T0351 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 T0351 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 T0351 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 T0351 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 T0351 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 T0351 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
Error: Reading chain '' from PDB file servers/MIG_FROST_AL1.pdb.gz failed---no such chain.
# naming current conformation MIG_FROST_AL1
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# 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
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# 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
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server2_TS3
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# 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 55
# 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
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# 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
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server_TS2
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server_TS3
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server_TS4
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS5.pdb.gz looking for model 1
# naming current conformation Ma-OPUS-server_TS5
# ReadConformPDB reading from PDB file servers/MetaTasser_TS1.pdb.gz looking for model 1
# Found a chain break before 111
# 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 115
# 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 98
# 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 103
# 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 108
# 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 T0351 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/POMYSL_TS1.pdb.gz looking for model 1
# Found a chain break before 44
# copying to AlignedFragments data structure
# naming current conformation POMYSL_TS1
# ReadConformPDB reading from PDB file servers/POMYSL_TS2.pdb.gz looking for model 1
# Found a chain break before 92
# copying to AlignedFragments data structure
# naming current conformation POMYSL_TS2
# ReadConformPDB reading from PDB file servers/POMYSL_TS3.pdb.gz looking for model 1
# Found a chain break before 76
# copying to AlignedFragments data structure
# naming current conformation POMYSL_TS3
# ReadConformPDB reading from PDB file servers/POMYSL_TS4.pdb.gz looking for model 1
# Found a chain break before 48
# copying to AlignedFragments data structure
# naming current conformation POMYSL_TS4
# ReadConformPDB reading from PDB file servers/POMYSL_TS5.pdb.gz looking for model 1
# Found a chain break before 34
# copying to AlignedFragments data structure
# naming current conformation POMYSL_TS5
# ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1
# naming current conformation PROTINFO-AB_TS1
# ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1
# Found a chain break before 19
# copying to AlignedFragments data structure
# naming current conformation PROTINFO-AB_TS2
# ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1
# naming current conformation PROTINFO-AB_TS3
# ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1
# Found a chain break before 113
# copying to AlignedFragments data structure
# naming current conformation PROTINFO-AB_TS4
# ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1
# Found a chain break before 113
# copying to AlignedFragments data structure
# naming current conformation PROTINFO-AB_TS5
# ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# naming current conformation PROTINFO_TS1
# ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# naming current conformation PROTINFO_TS2
# ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# naming current conformation PROTINFO_TS3
# ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# naming current conformation PROTINFO_TS4
# ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1
# naming current conformation PROTINFO_TS5
# ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1
# Found a chain break before 34
# copying to AlignedFragments data structure
# naming current conformation Pcons6_TS1
# ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 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
# Found a chain break before 37
# copying to AlignedFragments data structure
# naming current conformation Pcons6_TS3
# ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# naming current conformation Pcons6_TS4
# ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 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 T0351 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 T0351 can't currently be optimized by undertaker
# naming current conformation Phyre-2_TS1
# ReadConformPDB reading from PDB file servers/Phyre-2_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# naming current conformation Phyre-2_TS2
# ReadConformPDB reading from PDB file servers/Phyre-2_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# naming current conformation Phyre-2_TS3
# ReadConformPDB reading from PDB file servers/Phyre-2_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# naming current conformation Phyre-2_TS4
# ReadConformPDB reading from PDB file servers/Phyre-2_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# 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 35
# copying to AlignedFragments data structure
# naming current conformation Pmodeller6_TS1
# ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1
# Found a chain break before 24
# copying to AlignedFragments data structure
# naming current conformation Pmodeller6_TS2
# ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1
# Found a chain break before 34
# copying to AlignedFragments data structure
# naming current conformation Pmodeller6_TS3
# ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# naming current conformation Pmodeller6_TS4
# ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1
# Found a chain break before 29
# copying to AlignedFragments data structure
# naming current conformation Pmodeller6_TS5
# ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1
# Found a chain break before 112
# copying to AlignedFragments data structure
# naming current conformation RAPTOR-ACE_TS1
# ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation RAPTOR-ACE_TS2
# ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1
# Found a chain break before 59
# copying to AlignedFragments data structure
# naming current conformation RAPTOR-ACE_TS3
# ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS4.pdb.gz looking for model 1
# Found a chain break before 60
# copying to AlignedFragments data structure
# naming current conformation RAPTOR-ACE_TS4
# ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1
# Found a chain break before 113
# copying to AlignedFragments data structure
# naming current conformation RAPTOR-ACE_TS5
# ReadConformPDB reading from PDB file servers/RAPTORESS_TS1.pdb.gz looking for model 1
# naming current conformation RAPTORESS_TS1
# ReadConformPDB reading from PDB file servers/RAPTORESS_TS2.pdb.gz looking for model 1
# naming current conformation RAPTORESS_TS2
# ReadConformPDB reading from PDB file servers/RAPTORESS_TS3.pdb.gz looking for model 1
# Found a chain break before 57
# 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 115
# 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 115
# 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 56
# copying to AlignedFragments data structure
# naming current conformation RAPTOR_TS4
# ReadConformPDB reading from PDB file servers/RAPTOR_TS5.pdb.gz looking for model 1
# naming current conformation RAPTOR_TS5
# ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1
# Found a chain break before 24
# copying to AlignedFragments data structure
# naming current conformation ROBETTA_TS1
# ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1
# naming current conformation ROBETTA_TS2
# ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1
# Found a chain break before 37
# copying to AlignedFragments data structure
# naming current conformation ROBETTA_TS3
# ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1
# naming current conformation ROBETTA_TS4
# ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1
# Found a chain break before 29
# copying to AlignedFragments data structure
# naming current conformation ROBETTA_TS5
# ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation ROKKY_TS1
# ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation ROKKY_TS2
# ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation ROKKY_TS3
# ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation ROKKY_TS4
# ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation ROKKY_TS5
# ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1
Skipped atom 31, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz
Skipped atom 180, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz
Skipped atom 253, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz
Skipped atom 314, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz
# WARNING: incomplete conformation T0351 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 T0351 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 T0351 can't currently be optimized by undertaker
# naming current conformation SAM-T02_AL3
# ReadConformPDB reading from PDB file servers/SAM-T02_AL4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 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 T0351 can't currently be optimized by undertaker
# naming current conformation SAM-T02_AL5
# ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1
# Found a chain break before 105
# 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 T0351 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 T0351 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 T0351 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 T0351 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
# Found a chain break before 37
# copying to AlignedFragments data structure
# naming current conformation SP3_TS3
# ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1
# Found a chain break before 59
# copying to AlignedFragments data structure
# naming current conformation SP3_TS4
# ReadConformPDB reading from PDB file servers/SP3_TS5.pdb.gz looking for model 1
# Found a chain break before 41
# 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 91
# copying to AlignedFragments data structure
# naming current conformation SP4_TS1
# ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1
# Found a chain break before 25
# copying to AlignedFragments data structure
# naming current conformation SP4_TS2
# ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation SP4_TS3
# ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1
# Found a chain break before 109
# copying to AlignedFragments data structure
# 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 15
# copying to AlignedFragments data structure
# naming current conformation SPARKS2_TS1
# ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1
# naming current conformation SPARKS2_TS2
# ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1
# Found a chain break before 16
# 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 57
# 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 T0351 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 T0351 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 T0351 can't currently be optimized by undertaker
# naming current conformation UNI-EID_bnmx_TS3
# ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 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 T0351 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 T0351 can't currently be optimized by undertaker
# naming current conformation UNI-EID_expm_TS1
# ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 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 T0351 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 T0351 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 T0351 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 T0351 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 111
# 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 95
# 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 109
# 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 92
# copying to AlignedFragments data structure
# naming current conformation Zhang-Server_TS4
# ReadConformPDB reading from PDB file servers/Zhang-Server_TS5.pdb.gz looking for model 1
# Found a chain break before 114
# copying to AlignedFragments data structure
# naming current conformation Zhang-Server_TS5
# ReadConformPDB reading from PDB file servers/beautshot_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# naming current conformation beautshot_TS1
# ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 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 T0351 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 T0351 can't currently be optimized by undertaker
# naming current conformation forecast-s_AL2
# ReadConformPDB reading from PDB file servers/forecast-s_AL3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# naming current conformation forecast-s_AL3
# ReadConformPDB reading from PDB file servers/forecast-s_AL4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 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 T0351 can't currently be optimized by undertaker
# naming current conformation forecast-s_AL5
# ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1
# Found a chain break before 95
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.2_TS1
# ReadConformPDB reading from PDB file servers/karypis.srv.2_TS2.pdb.gz looking for model 1
# Found a chain break before 68
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.2_TS2
# ReadConformPDB reading from PDB file servers/karypis.srv.2_TS3.pdb.gz looking for model 1
# Found a chain break before 68
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.2_TS3
# ReadConformPDB reading from PDB file servers/karypis.srv.2_TS4.pdb.gz looking for model 1
# Found a chain break before 68
# 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 68
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.2_TS5
# ReadConformPDB reading from PDB file servers/karypis.srv.4_TS1.pdb.gz looking for model 1
WARNING: atoms too close: (T0351)A78.O and (T0351)R79.N only 0.000 apart, marking (T0351)R79.N as missing
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.4_TS1
# ReadConformPDB reading from PDB file servers/karypis.srv.4_TS2.pdb.gz looking for model 1
WARNING: atoms too close: (T0351)A108.O and (T0351)E109.N only 0.000 apart, marking (T0351)E109.N as missing
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.4_TS2
# ReadConformPDB reading from PDB file servers/karypis.srv.4_TS3.pdb.gz looking for model 1
# Found a chain break before 111
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.4_TS3
# ReadConformPDB reading from PDB file servers/karypis.srv.4_TS4.pdb.gz looking for model 1
# Found a chain break before 114
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.4_TS4
# ReadConformPDB reading from PDB file servers/karypis.srv.4_TS5.pdb.gz looking for model 1
# Found a chain break before 116
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.4_TS5
# ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 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 T0351 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 T0351 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 T0351 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 T0351 can't currently be optimized by undertaker
# naming current conformation karypis.srv_TS5
# ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# naming current conformation keasar-server_TS1
# ReadConformPDB reading from PDB file servers/keasar-server_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# naming current conformation keasar-server_TS2
# ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# naming current conformation keasar-server_TS3
# ReadConformPDB reading from PDB file servers/keasar-server_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# naming current conformation keasar-server_TS4
# ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# naming current conformation keasar-server_TS5
# ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 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 T0351 can't currently be optimized by undertaker
# naming current conformation nFOLD_TS1
# ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 can't currently be optimized by undertaker
# naming current conformation nFOLD_TS2
# ReadConformPDB reading from PDB file servers/nFOLD_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0351 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 T0351 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 T0351 can't currently be optimized by undertaker
# naming current conformation nFOLD_TS5
# ReadConformPDB reading from PDB file servers/panther2_TS1.pdb.gz looking for model 1
WARNING: atoms too close: (T0351)E45.N and (T0351)L46.N only 0.000 apart, marking (T0351)L46.N as missing
WARNING: atoms too close: (T0351)E45.CA and (T0351)L46.CA only 0.000 apart, marking (T0351)L46.CA as missing
WARNING: atoms too close: (T0351)E45.CB and (T0351)L46.CB only 0.000 apart, marking (T0351)L46.CB as missing
WARNING: atoms too close: (T0351)E45.CG and (T0351)L46.CG only 0.000 apart, marking (T0351)L46.CG as missing
WARNING: atoms too close: (T0351)E45.O and (T0351)L46.O only 0.000 apart, marking (T0351)L46.O as missing
WARNING: atoms too close: (T0351)E45.C and (T0351)L46.C only 0.000 apart, marking (T0351)L46.C as missing
WARNING: atoms too close: (T0351)L46.N and (T0351)E47.N only 0.000 apart, marking (T0351)L46.N as missing
WARNING: atoms too close: (T0351)E45.N and (T0351)E47.N only 0.000 apart, marking (T0351)E47.N as missing
WARNING: atoms too close: (T0351)L46.CA and (T0351)E47.CA only 0.000 apart, marking (T0351)E47.CA as missing
WARNING: atoms too close: (T0351)E45.CA and (T0351)E47.CA only 0.000 apart, marking (T0351)E47.CA as missing
WARNING: atoms too close: (T0351)L46.CB and (T0351)E47.CB only 0.000 apart, marking (T0351)E47.CB as missing
WARNING: atoms too close: (T0351)E45.CB and (T0351)E47.CB only 0.000 apart, marking (T0351)E47.CB as missing
WARNING: atoms too close: (T0351)L46.CG and (T0351)E47.CG only 0.000 apart, marking (T0351)E47.CG as missing
WARNING: atoms too close: (T0351)E45.CG and (T0351)E47.CG only 0.000 apart, marking (T0351)E47.CG as missing
WARNING: atoms too close: (T0351)L46.O and (T0351)E47.O only 0.000 apart, marking (T0351)E47.O as missing
WARNING: atoms too close: (T0351)E45.O and (T0351)E47.O only 0.000 apart, marking (T0351)E47.O as missing
WARNING: atoms too close: (T0351)L46.C and (T0351)E47.C only 0.000 apart, marking (T0351)E47.C as missing
WARNING: atoms too close: (T0351)E45.C and (T0351)E47.C only 0.000 apart, marking (T0351)E47.C as missing
WARNING: atoms too close: (T0351)E47.N and (T0351)T48.N only 0.000 apart, marking (T0351)E47.N as missing
WARNING: atoms too close: (T0351)L46.N and (T0351)T48.N only 0.000 apart, marking (T0351)L46.N as missing
WARNING: atoms too close: (T0351)E45.N and (T0351)T48.N only 0.000 apart, marking (T0351)T48.N as missing
WARNING: atoms too close: (T0351)E47.CA and (T0351)T48.CA only 0.000 apart, marking (T0351)T48.CA as missing
WARNING: atoms too close: (T0351)L46.CA and (T0351)T48.CA only 0.000 apart, marking (T0351)T48.CA as missing
WARNING: atoms too close: (T0351)E45.CA and (T0351)T48.CA only 0.000 apart, marking (T0351)T48.CA as missing
WARNING: atoms too close: (T0351)E47.CB and (T0351)T48.CB only 0.000 apart, marking (T0351)T48.CB as missing
WARNING: atoms too close: (T0351)L46.CB and (T0351)T48.CB only 0.000 apart, marking (T0351)T48.CB as missing
WARNING: atoms too close: (T0351)E45.CB and (T0351)T48.CB only 0.000 apart, marking (T0351)T48.CB as missing
WARNING: atoms too close: (T0351)E47.CG and (T0351)T48.CG2 only 0.000 apart, marking (T0351)T48.CG2 as missing
WARNING: atoms too close: (T0351)L46.CG and (T0351)T48.CG2 only 0.000 apart, marking (T0351)T48.CG2 as missing
WARNING: atoms too close: (T0351)E45.CG and (T0351)T48.CG2 only 0.000 apart, marking (T0351)T48.CG2 as missing
WARNING: atoms too close: (T0351)E47.O and (T0351)T48.O only 0.000 apart, marking (T0351)T48.O as missing
WARNING: atoms too close: (T0351)L46.O and (T0351)T48.O only 0.000 apart, marking (T0351)T48.O as missing
WARNING: atoms too close: (T0351)E45.O and (T0351)T48.O only 0.000 apart, marking (T0351)T48.O as missing
WARNING: atoms too close: (T0351)E47.C and (T0351)T48.C only 0.000 apart, marking (T0351)T48.C as missing
WARNING: atoms too close: (T0351)L46.C and (T0351)T48.C only 0.000 apart, marking (T0351)T48.C as missing
WARNING: atoms too close: (T0351)E45.C and (T0351)T48.C only 0.000 apart, marking (T0351)T48.C as missing
WARNING: atoms too close: (T0351)T48.N and (T0351)W49.N only 0.000 apart, marking (T0351)T48.N as missing
WARNING: atoms too close: (T0351)E47.N and (T0351)W49.N only 0.000 apart, marking (T0351)E47.N as missing
WARNING: atoms too close: (T0351)L46.N and (T0351)W49.N only 0.000 apart, marking (T0351)L46.N as missing
WARNING: atoms too close: (T0351)E45.N and (T0351)W49.N only 0.000 apart, marking (T0351)W49.N as missing
WARNING: atoms too close: (T0351)T48.CA and (T0351)W49.CA only 0.000 apart, marking (T0351)W49.CA as missing
WARNING: atoms too close: (T0351)E47.CA and (T0351)W49.CA only 0.000 apart, marking (T0351)W49.CA as missing
WARNING: atoms too close: (T0351)L46.CA and (T0351)W49.CA only 0.000 apart, marking (T0351)W49.CA as missing
WARNING: atoms too close: (T0351)E45.CA and (T0351)W49.CA only 0.000 apart, marking (T0351)W49.CA as missing
WARNING: atoms too close: (T0351)T48.CB and (T0351)W49.CB only 0.000 apart, marking (T0351)W49.CB as missing
WARNING: atoms too close: (T0351)E47.CB and (T0351)W49.CB only 0.000 apart, marking (T0351)W49.CB as missing
WARNING: atoms too close: (T0351)L46.CB and (T0351)W49.CB only 0.000 apart, marking (T0351)W49.CB as missing
WARNING: atoms too close: (T0351)E45.CB and (T0351)W49.CB only 0.000 apart, marking (T0351)W49.CB as missing
WARNING: atoms too close: (T0351)T48.CG2 and (T0351)W49.CG only 0.000 apart, marking (T0351)W49.CG as missing
WARNING: atoms too close: (T0351)E47.CG and (T0351)W49.CG only 0.000 apart, marking (T0351)W49.CG as missing
WARNING: atoms too close: (T0351)L46.CG and (T0351)W49.CG only 0.000 apart, marking (T0351)W49.CG as missing
WARNING: atoms too close: (T0351)E45.CG and (T0351)W49.CG only 0.000 apart, marking (T0351)W49.CG as missing
WARNING: atoms too close: (T0351)T48.O and (T0351)W49.O only 0.000 apart, marking (T0351)W49.O as missing
WARNING: atoms too close: (T0351)E47.O and (T0351)W49.O only 0.000 apart, marking (T0351)W49.O as missing
WARNING: atoms too close: (T0351)L46.O and (T0351)W49.O only 0.000 apart, marking (T0351)W49.O as missing
WARNING: atoms too close: (T0351)E45.O and (T0351)W49.O only 0.000 apart, marking (T0351)W49.O as missing
WARNING: atoms too close: (T0351)T48.C and (T0351)W49.C only 0.000 apart, marking (T0351)W49.C as missing
WARNING: atoms too close: (T0351)E47.C and (T0351)W49.C only 0.000 apart, marking (T0351)W49.C as missing
WARNING: atoms too close: (T0351)L46.C and (T0351)W49.C only 0.000 apart, marking (T0351)W49.C as missing
WARNING: atoms too close: (T0351)E45.C and (T0351)W49.C only 0.000 apart, marking (T0351)W49.C as missing
WARNING: atoms too close: (T0351)W49.N and (T0351)Q70.N only 0.000 apart, marking (T0351)W49.N as missing
WARNING: atoms too close: (T0351)T48.N and (T0351)Q70.N only 0.000 apart, marking (T0351)T48.N as missing
WARNING: atoms too close: (T0351)E47.N and (T0351)Q70.N only 0.000 apart, marking (T0351)E47.N as missing
WARNING: atoms too close: (T0351)L46.N and (T0351)Q70.N only 0.000 apart, marking (T0351)L46.N as missing
WARNING: atoms too close: (T0351)E45.N and (T0351)Q70.N only 0.000 apart, marking (T0351)Q70.N as missing
WARNING: atoms too close: (T0351)W49.CA and (T0351)Q70.CA only 0.000 apart, marking (T0351)Q70.CA as missing
WARNING: atoms too close: (T0351)T48.CA and (T0351)Q70.CA only 0.000 apart, marking (T0351)Q70.CA as missing
WARNING: atoms too close: (T0351)E47.CA and (T0351)Q70.CA only 0.000 apart, marking (T0351)Q70.CA as missing
WARNING: atoms too close: (T0351)L46.CA and (T0351)Q70.CA only 0.000 apart, marking (T0351)Q70.CA as missing
WARNING: atoms too close: (T0351)E45.CA and (T0351)Q70.CA only 0.000 apart, marking (T0351)Q70.CA as missing
WARNING: atoms too close: (T0351)W49.CB and (T0351)Q70.CB only 0.000 apart, marking (T0351)Q70.CB as missing
WARNING: atoms too close: (T0351)T48.CB and (T0351)Q70.CB only 0.000 apart, marking (T0351)Q70.CB as missing
WARNING: atoms too close: (T0351)E47.CB and (T0351)Q70.CB only 0.000 apart, marking (T0351)Q70.CB as missing
WARNING: atoms too close: (T0351)L46.CB and (T0351)Q70.CB only 0.000 apart, marking (T0351)Q70.CB as missing
WARNING: atoms too close: (T0351)E45.CB and (T0351)Q70.CB only 0.000 apart, marking (T0351)Q70.CB as missing
WARNING: atoms too close: (T0351)W49.CG and (T0351)Q70.CG only 0.000 apart, marking (T0351)Q70.CG as missing
WARNING: atoms too close: (T0351)T48.CG2 and (T0351)Q70.CG only 0.000 apart, marking (T0351)Q70.CG as missing
WARNING: atoms too close: (T0351)E47.CG and (T0351)Q70.CG only 0.000 apart, marking (T0351)Q70.CG as missing
WARNING: atoms too close: (T0351)L46.CG and (T0351)Q70.CG only 0.000 apart, marking (T0351)Q70.CG as missing
WARNING: atoms too close: (T0351)E45.CG and (T0351)Q70.CG only 0.000 apart, marking (T0351)Q70.CG as missing
WARNING: atoms too close: (T0351)W49.O and (T0351)Q70.O only 0.000 apart, marking (T0351)Q70.O as missing
WARNING: atoms too close: (T0351)T48.O and (T0351)Q70.O only 0.000 apart, marking (T0351)Q70.O as missing
WARNING: atoms too close: (T0351)E47.O and (T0351)Q70.O only 0.000 apart, marking (T0351)Q70.O as missing
WARNING: atoms too close: (T0351)L46.O and (T0351)Q70.O only 0.000 apart, marking (T0351)Q70.O as missing
WARNING: atoms too close: (T0351)E45.O and (T0351)Q70.O only 0.000 apart, marking (T0351)Q70.O as missing
WARNING: atoms too close: (T0351)W49.C and (T0351)Q70.C only 0.000 apart, marking (T0351)Q70.C as missing
WARNING: atoms too close: (T0351)T48.C and (T0351)Q70.C only 0.000 apart, marking (T0351)Q70.C as missing
WARNING: atoms too close: (T0351)E47.C and (T0351)Q70.C only 0.000 apart, marking (T0351)Q70.C as missing
WARNING: atoms too close: (T0351)L46.C and (T0351)Q70.C only 0.000 apart, marking (T0351)Q70.C as missing
WARNING: atoms too close: (T0351)E45.C and (T0351)Q70.C only 0.000 apart, marking (T0351)Q70.C as missing
WARNING: atoms too close: (T0351)Q70.N and (T0351)E71.N only 0.000 apart, marking (T0351)Q70.N as missing
WARNING: atoms too close: (T0351)W49.N and (T0351)E71.N only 0.000 apart, marking (T0351)W49.N as missing
WARNING: atoms too close: (T0351)T48.N and (T0351)E71.N only 0.000 apart, marking (T0351)T48.N as missing
WARNING: atoms too close: (T0351)E47.N and (T0351)E71.N only 0.000 apart, marking (T0351)E47.N as missing
WARNING: atoms too close: (T0351)L46.N and (T0351)E71.N only 0.000 apart, marking (T0351)L46.N as missing
WARNING: atoms too close: (T0351)E45.N and (T0351)E71.N only 0.000 apart, marking (T0351)E71.N as missing
WARNING: atoms too close: (T0351)Q70.CA and (T0351)E71.CA only 0.000 apart, marking (T0351)E71.CA as missing
WARNING: atoms too close: (T0351)W49.CA and (T0351)E71.CA only 0.000 apart, marking (T0351)E71.CA as missing
WARNING: atoms too close: (T0351)T48.CA and (T0351)E71.CA only 0.000 apart, marking (T0351)E71.CA as missing
WARNING: atoms too close: (T0351)E47.CA and (T0351)E71.CA only 0.000 apart, marking (T0351)E71.CA as missing
WARNING: atoms too close: (T0351)L46.CA and (T0351)E71.CA only 0.000 apart, marking (T0351)E71.CA as missing
WARNING: atoms too close: (T0351)E45.CA and (T0351)E71.CA only 0.000 apart, marking (T0351)E71.CA as missing
WARNING: atoms too close: (T0351)Q70.CB and (T0351)E71.CB only 0.000 apart, marking (T0351)E71.CB as missing
WARNING: atoms too close: (T0351)W49.CB and (T0351)E71.CB only 0.000 apart, marking (T0351)E71.CB as missing
WARNING: atoms too close: (T0351)T48.CB and (T0351)E71.CB only 0.000 apart, marking (T0351)E71.CB as missing
WARNING: atoms too close: (T0351)E47.CB and (T0351)E71.CB only 0.000 apart, marking (T0351)E71.CB as missing
WARNING: atoms too close: (T0351)L46.CB and (T0351)E71.CB only 0.000 apart, marking (T0351)E71.CB as missing
WARNING: atoms too close: (T0351)E45.CB and (T0351)E71.CB only 0.000 apart, marking (T0351)E71.CB as missing
WARNING: atoms too close: (T0351)Q70.CG and (T0351)E71.CG only 0.000 apart, marking (T0351)E71.CG as missing
WARNING: atoms too close: (T0351)W49.CG and (T0351)E71.CG only 0.000 apart, marking (T0351)E71.CG as missing
WARNING: atoms too close: (T0351)T48.CG2 and (T0351)E71.CG only 0.000 apart, marking (T0351)E71.CG as missing
WARNING: atoms too close: (T0351)E47.CG and (T0351)E71.CG only 0.000 apart, marking (T0351)E71.CG as missing
WARNING: atoms too close: (T0351)L46.CG and (T0351)E71.CG only 0.000 apart, marking (T0351)E71.CG as missing
WARNING: atoms too close: (T0351)E45.CG and (T0351)E71.CG only 0.000 apart, marking (T0351)E71.CG as missing
WARNING: atoms too close: (T0351)Q70.O and (T0351)E71.O only 0.000 apart, marking (T0351)E71.O as missing
WARNING: atoms too close: (T0351)W49.O and (T0351)E71.O only 0.000 apart, marking (T0351)E71.O as missing
WARNING: atoms too close: (T0351)T48.O and (T0351)E71.O only 0.000 apart, marking (T0351)E71.O as missing
WARNING: atoms too close: (T0351)E47.O and (T0351)E71.O only 0.000 apart, marking (T0351)E71.O as missing
WARNING: atoms too close: (T0351)L46.O and (T0351)E71.O only 0.000 apart, marking (T0351)E71.O as missing
WARNING: atoms too close: (T0351)E45.O and (T0351)E71.O only 0.000 apart, marking (T0351)E71.O as missing
WARNING: atoms too close: (T0351)Q70.C and (T0351)E71.C only 0.000 apart, marking (T0351)E71.C as missing
WARNING: atoms too close: (T0351)W49.C and (T0351)E71.C only 0.000 apart, marking (T0351)E71.C as missing
WARNING: atoms too close: (T0351)T48.C and (T0351)E71.C only 0.000 apart, marking (T0351)E71.C as missing
WARNING: atoms too close: (T0351)E47.C and (T0351)E71.C only 0.000 apart, marking (T0351)E71.C as missing
WARNING: atoms too close: (T0351)L46.C and (T0351)E71.C only 0.000 apart, marking (T0351)E71.C as missing
WARNING: atoms too close: (T0351)E45.C and (T0351)E71.C only 0.000 apart, marking (T0351)E71.C as missing
# WARNING: incomplete conformation T0351 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: incomplete conformation T0351 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 T0351 can't currently be optimized by undertaker
# naming current conformation shub_TS1
# command:Using radius: 8.0000
Metaserver mode
NUMB_ALIGNS: 260
model score 1.9872
model score 1.9057
model score 1.9779
model score 1.9605
model score 2.2689
model score 1.6855
model score 1.7177
model score 1.6201
model score 1.6912
model score 1.7727
model score 1.6523
model score 1.7759
model score 1.6388
model score 2.2110
model score 1.4954
model score 2.1317
model score 1.6070
model score 1.7301
model score 1.7508
model score 1.4954
model score 1.5105
model score 1.5355
model score 1.7258
model score 1.5520
model score 2.2288
model score 1.7718
model score 1.7599
model score 1.7718
model score 1.7729
model score 1.7726
model score 1.7685
model score 1.7922
model score 1.7649
model score 2.1147
model score 1.5858
model score 1.5858
model score 1.9349
model score 1.6482
model score 1.3772
model score 1.5329
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.7922
model score 1.7649
model score 1.4071
model score 1.4357
model score 1.6991
model score 1.6655
model score 1.7615
model score 1.8454
model score 1.9270
model score 1.9371
model score 1.9018
model score 1.7413
model score 1.6694
model score 1.7528
model score 1.6955
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 2.3236
model score 1.7953
model score 1.8775
model score 1.9227
model score 2.1276
model score 1.8342
model score 1.8513
model score 1.8271
model score 1.9307
model score 1.9067
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 2.4223
model score 1.3486
model score 2.3745
model score 1.4207
model score 1.5085
model score 1.9305
model score 1.9595
model score 2.1547
model score 1.8269
model score 1.6935
model score 1.4224
model score 1.6182
model score 1.5906
model score 2.7092
model score 2.2422
model score 2.8415
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.4874
model score 1.5645
model score 1.4390
model score 1.1005
model score 1.6322
model score 1.3258
model score 1.4536
model score 1.5502
model score 1.6569
model score 1.5647
model score 1.5502
model score 1.3258
model score 1.4536
model score 1.6569
model score 1.5399
model score 1.6511
model score 1.5858
model score 1.3745
model score 1.6721
model score 1.4543
model score 1.2771
model score 1.7304
model score 1.6228
model score 1.7815
model score 1.5686
model score 1.6832
model score 1.7967
model score 1.7934
model score 1.7962
model score 1.7958
model score 1.7958
model score 1.6537
model score 1.6381
model score 1.6279
model score 1.6554
model score 1.7967
model score 1.7170
model score 1.4037
model score 1.7115
model score 1.4921
model score 1.4844
model score 1.1947
model score 1.6728
model score 1.7564
model score 1.7076
model score 1.6011
model score 1.8145
model score 1.5502
model score 1.6484
model score 1.7170
model score 1.8489
model score 1.6645
model score 2.1008
model score 2.6133
model score 2.0907
model score 1.9380
model score 1.9082
model score 1.9004
model score 2.0057
model score 1.5467
model score 1.4835
model score 2.4229
model score 1.9004
model score 2.0057
model score 1.5104
model score 1.5149
model score 2.4336
model score 1.6484
model score 1.8404
model score 1.7115
model score 1.8644
model score 1.6645
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.8403
model score 1.5397
model score 1.3671
model score 1.1277
model score 1.3871
model score 1.8162
model score 2.6133
model score 1.4399
model score 2.0907
model score 1.5887
model score 1.7975
model score 2.0697
model score 2.6133
model score 1.5741
model score 1.6621
model score 2.1961
model score 1.9961
model score 1.7753
model score 2.0479
model score 2.2720
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.3930
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.1141
model score 1.1071
model score 1.1036
model score 1.1933
model score 1.1286
model score 1.7387
model score 1.5229
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.8728
model score 1.4854
model score 2.0182
model score 1.6696
model score 1.9084
model score 1.7647
model score 2.1181
model score 2.0551
model score 2.2193
model score 1.9521
model score 1.3488
model score 1.5135
model score 1.3628
model score 1.5256
model score 1.4177
model score 1.7378
model score 1.7776
model score 1.9560
model score 1.7617
model score 1.9186
model score 1.2984
model score 2.0031
model score 1.7849
model score 2.0477
model score 1.9782
model score 1.5651
model score 1.3981
model score 1.3000
model score 1.5860
weight: 0.5416 eval: 1.9872 min: 1.1005 max: 2.8415
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weight: 0.9087 eval: 1.2771 min: 1.1005 max: 2.8415
weight: 0.8488 eval: 1.3930 min: 1.1005 max: 2.8415
weight: 0.9087 eval: 1.2771 min: 1.1005 max: 2.8415
weight: 0.9087 eval: 1.2771 min: 1.1005 max: 2.8415
weight: 0.9087 eval: 1.2771 min: 1.1005 max: 2.8415
weight: 0.9087 eval: 1.2771 min: 1.1005 max: 2.8415
weight: 0.9087 eval: 1.2771 min: 1.1005 max: 2.8415
weight: 0.9930 eval: 1.1141 min: 1.1005 max: 2.8415
weight: 0.9966 eval: 1.1071 min: 1.1005 max: 2.8415
weight: 0.9984 eval: 1.1036 min: 1.1005 max: 2.8415
weight: 0.9520 eval: 1.1933 min: 1.1005 max: 2.8415
weight: 0.9855 eval: 1.1286 min: 1.1005 max: 2.8415
weight: 0.6701 eval: 1.7387 min: 1.1005 max: 2.8415
weight: 0.7816 eval: 1.5229 min: 1.1005 max: 2.8415
weight: 0.9087 eval: 1.2771 min: 1.1005 max: 2.8415
weight: 0.9087 eval: 1.2771 min: 1.1005 max: 2.8415
weight: 0.9087 eval: 1.2771 min: 1.1005 max: 2.8415
weight: 0.9087 eval: 1.2771 min: 1.1005 max: 2.8415
weight: 0.9087 eval: 1.2771 min: 1.1005 max: 2.8415
weight: 0.6008 eval: 1.8728 min: 1.1005 max: 2.8415
weight: 0.8010 eval: 1.4854 min: 1.1005 max: 2.8415
weight: 0.5256 eval: 2.0182 min: 1.1005 max: 2.8415
weight: 0.7058 eval: 1.6696 min: 1.1005 max: 2.8415
weight: 0.5824 eval: 1.9084 min: 1.1005 max: 2.8415
weight: 0.6567 eval: 1.7647 min: 1.1005 max: 2.8415
weight: 0.4739 eval: 2.1181 min: 1.1005 max: 2.8415
weight: 0.5065 eval: 2.0551 min: 1.1005 max: 2.8415
weight: 0.4216 eval: 2.2193 min: 1.1005 max: 2.8415
weight: 0.5598 eval: 1.9521 min: 1.1005 max: 2.8415
weight: 0.8716 eval: 1.3488 min: 1.1005 max: 2.8415
weight: 0.7865 eval: 1.5135 min: 1.1005 max: 2.8415
weight: 0.8644 eval: 1.3628 min: 1.1005 max: 2.8415
weight: 0.7802 eval: 1.5256 min: 1.1005 max: 2.8415
weight: 0.8360 eval: 1.4177 min: 1.1005 max: 2.8415
weight: 0.6706 eval: 1.7378 min: 1.1005 max: 2.8415
weight: 0.6500 eval: 1.7776 min: 1.1005 max: 2.8415
weight: 0.5577 eval: 1.9560 min: 1.1005 max: 2.8415
weight: 0.6582 eval: 1.7617 min: 1.1005 max: 2.8415
weight: 0.5771 eval: 1.9186 min: 1.1005 max: 2.8415
weight: 0.8977 eval: 1.2984 min: 1.1005 max: 2.8415
weight: 0.5334 eval: 2.0031 min: 1.1005 max: 2.8415
weight: 0.6462 eval: 1.7849 min: 1.1005 max: 2.8415
weight: 0.5103 eval: 2.0477 min: 1.1005 max: 2.8415
weight: 0.5463 eval: 1.9782 min: 1.1005 max: 2.8415
weight: 0.7598 eval: 1.5651 min: 1.1005 max: 2.8415
weight: 0.8462 eval: 1.3981 min: 1.1005 max: 2.8415
weight: 0.8968 eval: 1.3000 min: 1.1005 max: 2.8415
weight: 0.7490 eval: 1.5860 min: 1.1005 max: 2.8415
Adding 4883 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: -187.3636, CN propb: -187.3636 weights: 0.2771 constraints: 168
# command:Found ConstraintSet
# PrintContacts align.constraints_meta02
Number of constraints in align2.constraints 168
# command:Found ConstraintSet
# PrintContacts align_bonus.constraints_meta02
Number of constraints in align2.constraints.bonus 168
# command:Found ConstraintSet
# PrintContacts rejected.constraints_meta02
Number of constraints in rejected2.constraints 4715
# command:Found ConstraintSet
# PrintContacts rejected_bonus.constraints_meta02
Number of constraints in rejected2.constraints.bonus 4715
# 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 4883
# command: