# 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/T0327/
# command:# Making conformation for sequence T0327 numbered 1 through 102
Created new target T0327 from T0327.a2m
# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0327/
# command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0327//projects/compbio/experiments/protein-predict/casp7/T0327/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0327//projects/compbio/experiments/protein-predict/casp7/T0327/align.constraints_v3.costfcn.gz for input
Trying /projects/compbio/experiments/protein-predict/casp7/T0327/align.constraints_v3.costfcn
# reading script from file /projects/compbio/experiments/protein-predict/casp7/T0327/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((T0327)V37.CB, (T0327)I46.CB) [> 3.8872 = 6.4786 < 8.4222] w=1.0000 to align
# Constraint # added constraint: constraint((T0327)G48.CA, (T0327)Y59.CB) [> 3.5982 = 5.9969 < 7.7960] w=0.8145 to align
# Constraint # added constraint: constraint((T0327)Y45.CB, (T0327)L65.CB) [> 3.9784 = 6.6307 < 8.6199] w=0.7396 to align
# Constraint # added constraint: constraint((T0327)Y45.CB, (T0327)T66.CB) [> 3.4226 = 5.7043 < 7.4156] w=0.7206 to align
# Constraint # added constraint: constraint((T0327)G44.CA, (T0327)T66.CB) [> 3.4424 = 5.7373 < 7.4585] w=0.7206 to align
# Constraint # added constraint: constraint((T0327)G48.CA, (T0327)L58.CB) [> 3.6531 = 6.0884 < 7.9150] w=0.7150 to align
# Constraint # added constraint: constraint((T0327)Y45.CB, (T0327)G69.CA) [> 2.5601 = 4.2668 < 5.5468] w=0.7018 to align
# Constraint # added constraint: constraint((T0327)L6.CB, (T0327)A36.CB) [> 3.4400 = 5.7334 < 7.4534] w=0.6974 to align
# Constraint # added constraint: constraint((T0327)L11.CB, (T0327)L40.CB) [> 4.2632 = 7.1053 < 9.2368] w=0.6868 to align
# Constraint # added constraint: constraint((T0327)I10.CB, (T0327)L40.CB) [> 4.0639 = 6.7732 < 8.8051] w=0.6862 to align
# Constraint # added constraint: constraint((T0327)I10.CB, (T0327)A36.CB) [> 3.4983 = 5.8305 < 7.5797] w=0.6681 to align
# Constraint # added constraint: constraint((T0327)L11.CB, (T0327)Y45.CB) [> 3.9489 = 6.5815 < 8.5560] w=0.6491 to align
# Constraint # added constraint: constraint((T0327)I10.CB, (T0327)V37.CB) [> 4.2253 = 7.0422 < 9.1548] w=0.6491 to align
# Constraint # added constraint: constraint((T0327)I46.CB, (T0327)T66.CB) [> 3.8748 = 6.4579 < 8.3953] w=0.6468 to align
# Constraint # added constraint: constraint((T0327)Y45.CB, (T0327)K68.CB) [> 3.5817 = 5.9695 < 7.7603] w=0.6450 to align
# Constraint # added constraint: constraint((T0327)I47.CB, (T0327)T66.CB) [> 3.4537 = 5.7561 < 7.4830] w=0.6277 to align
# Constraint # added constraint: constraint((T0327)A9.CB, (T0327)I26.CB) [> 3.5770 = 5.9616 < 7.7502] w=0.6110 to align
# Constraint # added constraint: constraint((T0327)Y45.CB, (T0327)Y72.CB) [> 3.6592 = 6.0987 < 7.9283] w=0.6070 to align
# Constraint # added constraint: constraint((T0327)L6.CB, (T0327)V28.CB) [> 3.7689 = 6.2815 < 8.1660] w=0.5921 to align
# Constraint # added constraint: constraint((T0327)I46.CB, (T0327)L65.CB) [> 3.7231 = 6.2052 < 8.0668] w=0.5879 to align
# Constraint # added constraint: constraint((T0327)I10.CB, (T0327)F33.CB) [> 4.2740 = 7.1233 < 9.2603] w=0.5872 to align
# Constraint # added constraint: constraint((T0327)V49.CB, (T0327)Y59.CB) [> 3.3641 = 5.6069 < 7.2889] w=0.5819 to align
# Constraint # added constraint: constraint((T0327)R7.CB, (T0327)A36.CB) [> 3.3425 = 5.5708 < 7.2421] w=0.5734 to align
# Constraint # added constraint: constraint((T0327)V49.CB, (T0327)L58.CB) [> 4.0462 = 6.7437 < 8.7668] w=0.5629 to align
# Constraint # added constraint: constraint((T0327)I46.CB, (T0327)G69.CA) [> 4.2771 = 7.1285 < 9.2671] w=0.5502 to align
# Constraint # added constraint: constraint((T0327)R7.CB, (T0327)F39.CB) [> 4.1803 = 6.9672 < 9.0573] w=0.5354 to align
# Constraint # added constraint: constraint((T0327)I10.CB, (T0327)I26.CB) [> 3.8582 = 6.4303 < 8.3594] w=0.5161 to align
# Constraint # added constraint: constraint((T0327)I14.CB, (T0327)I46.CB) [> 4.0780 = 6.7966 < 8.8356] w=0.5116 to align
# Constraint # added constraint: constraint((T0327)L6.CB, (T0327)F33.CB) [> 4.0638 = 6.7730 < 8.8049] w=0.4584 to align
# Constraint # added constraint: constraint((T0327)G48.CA, (T0327)E64.CB) [> 3.8730 = 6.4550 < 8.3915] w=0.4362 to align
# Constraint # added constraint: constraint((T0327)F15.CB, (T0327)L65.CB) [> 3.8191 = 6.3652 < 8.2747] w=0.4362 to align
# Constraint # added constraint: constraint((T0327)G48.CA, (T0327)K60.CB) [> 4.0418 = 6.7363 < 8.7571] w=0.4215 to align
# Constraint # added constraint: constraint((T0327)L6.CB, (T0327)Q32.CB) [> 3.9348 = 6.5579 < 8.5253] w=0.4207 to align
# Constraint # added constraint: constraint((T0327)I46.CB, (T0327)E64.CB) [> 4.0008 = 6.6680 < 8.6684] w=0.4192 to align
# Constraint # added constraint: constraint((T0327)I47.CB, (T0327)E64.CB) [> 3.0732 = 5.1220 < 6.6586] w=0.4173 to align
# Constraint # added constraint: constraint((T0327)V37.CB, (T0327)G48.CA) [> 4.4075 = 7.3458 < 9.5496] w=0.4121 to align
# Constraint # added constraint: constraint((T0327)H50.CB, (T0327)Y59.CB) [> 4.2613 = 7.1022 < 9.2329] w=0.3992 to align
# Constraint # added constraint: constraint((T0327)I47.CB, (T0327)L65.CB) [> 4.3936 = 7.3226 < 9.5194] w=0.3983 to align
# Constraint # added constraint: constraint((T0327)L6.CB, (T0327)I26.CB) [> 3.7564 = 6.2606 < 8.1388] w=0.3957 to align
# Constraint # added constraint: constraint((T0327)F15.CB, (T0327)L73.CB) [> 3.2169 = 5.3615 < 6.9699] w=0.3794 to align
# Constraint # added constraint: constraint((T0327)I14.CB, (T0327)L65.CB) [> 2.9604 = 4.9340 < 6.4142] w=0.3794 to align
# Constraint # added constraint: constraint((T0327)L11.CB, (T0327)L73.CB) [> 3.0195 = 5.0326 < 6.5423] w=0.3794 to align
# Constraint # added constraint: constraint((T0327)E13.CB, (T0327)I26.CB) [> 4.0565 = 6.7609 < 8.7891] w=0.3789 to align
# Constraint # added constraint: constraint((T0327)I47.CB, (T0327)Y59.CB) [> 3.9767 = 6.6279 < 8.6162] w=0.3767 to align
# Constraint # added constraint: constraint((T0327)V49.CB, (T0327)E64.CB) [> 4.0732 = 6.7887 < 8.8253] w=0.3605 to align
# Constraint # added constraint: constraint((T0327)Y8.CB, (T0327)N76.CB) [> 3.9233 = 6.5388 < 8.5004] w=0.3604 to align
# Constraint # added constraint: constraint((T0327)I46.CB, (T0327)K60.CB) [> 4.0562 = 6.7604 < 8.7885] w=0.3578 to align
# Constraint # added constraint: constraint((T0327)K12.CB, (T0327)L73.CB) [> 4.0309 = 6.7181 < 8.7336] w=0.3414 to align
# Constraint # added constraint: constraint((T0327)I10.CB, (T0327)I46.CB) [> 4.5237 = 7.5396 < 9.8014] w=0.3406 to align
# Constraint # added constraint: constraint((T0327)G48.CA, (T0327)H57.CB) [> 3.6551 = 6.0918 < 7.9193] w=0.3219 to align
# Constraint # added constraint: constraint((T0327)Y45.CB, (T0327)L61.CB) [> 4.2079 = 7.0132 < 9.1172] w=0.3195 to align
# Constraint # added constraint: constraint((T0327)I46.CB, (T0327)Y59.CB) [> 3.6059 = 6.0098 < 7.8127] w=0.3009 to align
# Constraint # added constraint: constraint((T0327)Y45.CB, (T0327)L73.CB) [> 4.5197 = 7.5328 < 9.7927] w=0.2846 to align
# Constraint # added constraint: constraint((T0327)L11.CB, (T0327)N76.CB) [> 4.0917 = 6.8196 < 8.8654] w=0.2655 to align
# Constraint # added constraint: constraint((T0327)A9.CB, (T0327)V28.CB) [> 4.4409 = 7.4015 < 9.6220] w=0.2652 to align
# Constraint # added constraint: constraint((T0327)E13.CB, (T0327)D25.CB) [> 3.8469 = 6.4115 < 8.3350] w=0.2650 to align
# Constraint # added constraint: constraint((T0327)Y45.CB, (T0327)G62.CA) [> 3.8920 = 6.4867 < 8.4328] w=0.2628 to align
# Constraint # added constraint: constraint((T0327)I10.CB, (T0327)V28.CB) [> 3.6957 = 6.1595 < 8.0074] w=0.2462 to align
# Constraint # added constraint: constraint((T0327)I47.CB, (T0327)G62.CA) [> 3.5793 = 5.9655 < 7.7551] w=0.2151 to align
# Constraint # added constraint: constraint((T0327)V37.CB, (T0327)Y59.CB) [> 3.8275 = 6.3791 < 8.2928] w=0.2132 to align
# Constraint # added constraint: constraint((T0327)I14.CB, (T0327)L61.CB) [> 3.5082 = 5.8470 < 7.6010] w=0.2131 to align
# Constraint # added constraint: constraint((T0327)G48.CA, (T0327)P63.CB) [> 3.3202 = 5.5336 < 7.1937] w=0.2104 to align
# Constraint # added constraint: constraint((T0327)I14.CB, (T0327)E64.CB) [> 4.0215 = 6.7025 < 8.7133] w=0.2087 to align
# Constraint # added constraint: constraint((T0327)D4.CB, (T0327)A36.CB) [> 4.3307 = 7.2179 < 9.3832] w=0.2084 to align
# Constraint # added constraint: constraint((T0327)I46.CB, (T0327)L58.CB) [> 3.6285 = 6.0475 < 7.8618] w=0.2014 to align
# Constraint # added constraint: constraint((T0327)I47.CB, (T0327)L61.CB) [> 4.1236 = 6.8726 < 8.9344] w=0.2013 to align
# Constraint # added constraint: constraint((T0327)N18.CB, (T0327)E64.CB) [> 3.3413 = 5.5688 < 7.2394] w=0.1898 to align
# Constraint # added constraint: constraint((T0327)Y8.CB, (T0327)L73.CB) [> 3.9756 = 6.6259 < 8.6137] w=0.1897 to align
# Constraint # added constraint: constraint((T0327)I14.CB, (T0327)Y59.CB) [> 3.9631 = 6.6052 < 8.5868] w=0.1893 to align
# Constraint # added constraint: constraint((T0327)I47.CB, (T0327)L58.CB) [> 4.4225 = 7.3708 < 9.5821] w=0.1825 to align
# Constraint # added constraint: constraint((T0327)Y8.CB, (T0327)S80.CB) [> 4.2370 = 7.0616 < 9.1801] w=0.1707 to align
# Constraint # added constraint: constraint((T0327)I14.CB, (T0327)L58.CB) [> 3.7420 = 6.2366 < 8.1076] w=0.1704 to align
# Constraint # added constraint: constraint((T0327)F15.CB, (T0327)L61.CB) [> 3.7852 = 6.3086 < 8.2011] w=0.1703 to align
# Constraint # added constraint: constraint((T0327)G17.CA, (T0327)E64.CB) [> 4.1665 = 6.9442 < 9.0274] w=0.1518 to align
# Constraint # added constraint: constraint((T0327)E43.CB, (T0327)G69.CA) [> 4.7341 = 7.8901 < 10.2572] w=0.1494 to align
# Constraint # added constraint: constraint((T0327)L21.CB, (T0327)P56.CB) [> 4.1034 = 6.8390 < 8.8907] w=0.1374 to align
# Constraint # added constraint: constraint((T0327)R7.CB, (T0327)V28.CB) [> 3.6926 = 6.1544 < 8.0007] w=0.1328 to align
# Constraint # added constraint: constraint((T0327)L6.CB, (T0327)V37.CB) [> 4.3915 = 7.3192 < 9.5150] w=0.1257 to align
# Constraint # added constraint: constraint((T0327)L21.CB, (T0327)H57.CB) [> 3.2942 = 5.4903 < 7.1374] w=0.1255 to align
# Constraint # added constraint: constraint((T0327)V37.CB, (T0327)I47.CB) [> 3.9926 = 6.6543 < 8.6506] w=0.1187 to align
# Constraint # added constraint: constraint((T0327)L40.CB, (T0327)G69.CA) [> 4.6539 = 7.7565 < 10.0834] w=0.1158 to align
# Constraint # added constraint: constraint((T0327)I14.CB, (T0327)L73.CB) [> 4.0573 = 6.7622 < 8.7909] w=0.1137 to align
# Constraint # added constraint: constraint((T0327)Y45.CB, (T0327)E64.CB) [> 3.1115 = 5.1858 < 6.7415] w=0.1137 to align
# Constraint # added constraint: constraint((T0327)G44.CA, (T0327)E64.CB) [> 2.8163 = 4.6939 < 6.1021] w=0.1137 to align
# Constraint # added constraint: constraint((T0327)K5.CB, (T0327)I26.CB) [> 3.9036 = 6.5060 < 8.4578] w=0.1113 to align
# Constraint # added constraint: constraint((T0327)K41.CB, (T0327)Y59.CB) [> 4.6355 = 7.7258 < 10.0436] w=0.0996 to align
# Constraint # added constraint: constraint((T0327)L6.CB, (T0327)L40.CB) [> 3.8646 = 6.4411 < 8.3734] w=0.0876 to align
# Constraint # added constraint: constraint((T0327)L73.CB, (T0327)T85.CB) [> 4.3315 = 7.2191 < 9.3848] w=0.0803 to align
# Constraint # added constraint: constraint((T0327)F15.CB, (T0327)K74.CB) [> 4.1585 = 6.9309 < 9.0102] w=0.0759 to align
# Constraint # added constraint: constraint((T0327)Y8.CB, (T0327)Y83.CB) [> 4.1152 = 6.8586 < 8.9162] w=0.0759 to align
# Constraint # added constraint: constraint((T0327)G48.CA, (T0327)L61.CB) [> 3.6432 = 6.0721 < 7.8937] w=0.0757 to align
# Constraint # added constraint: constraint((T0327)R7.CB, (T0327)Q32.CB) [> 3.9313 = 6.5521 < 8.5178] w=0.0756 to align
# Constraint # added constraint: constraint((T0327)F15.CB, (T0327)I86.CB) [> 3.7935 = 6.3225 < 8.2193] w=0.0754 to align
# Constraint # added constraint: constraint((T0327)K41.CB, (T0327)W79.CB) [> 3.4420 = 5.7367 < 7.4577] w=0.0753 to align
# Constraint # added constraint: constraint((T0327)N38.CB, (T0327)W79.CB) [> 2.9360 = 4.8934 < 6.3614] w=0.0753 to align
# Constraint # added constraint: constraint((T0327)D34.CB, (T0327)Y83.CB) [> 3.8516 = 6.4194 < 8.3452] w=0.0753 to align
# Constraint # added constraint: constraint((T0327)F33.CB, (T0327)Y83.CB) [> 4.1879 = 6.9798 < 9.0737] w=0.0753 to align
# Constraint # added constraint: constraint((T0327)I47.CB, (T0327)N76.CB) [> 3.5997 = 5.9995 < 7.7994] w=0.0753 to align
# Constraint # added constraint: constraint((T0327)I47.CB, (T0327)A82.CB) [> 2.8876 = 4.8126 < 6.2564] w=0.0753 to align
# Constraint # added constraint: constraint((T0327)G48.CA, (T0327)A82.CB) [> 4.5496 = 7.5826 < 9.8574] w=0.0753 to align
# Constraint # added constraint: constraint((T0327)G48.CA, (T0327)T85.CB) [> 4.7749 = 7.9581 < 10.3456] w=0.0753 to align
# Constraint # added constraint: constraint((T0327)V49.CB, (T0327)T85.CB) [> 3.3639 = 5.6065 < 7.2884] w=0.0753 to align
# Constraint # added constraint: constraint((T0327)V49.CB, (T0327)I86.CB) [> 3.9456 = 6.5761 < 8.5489] w=0.0753 to align
# Constraint # added constraint: constraint((T0327)V49.CB, (T0327)I89.CB) [> 3.3654 = 5.6090 < 7.2918] w=0.0753 to align
# Constraint # added constraint: constraint((T0327)Y51.CB, (T0327)I89.CB) [> 3.5026 = 5.8377 < 7.5890] w=0.0753 to align
# Constraint # added constraint: constraint((T0327)A9.CB, (T0327)A36.CB) [> 4.2423 = 7.0704 < 9.1916] w=0.0750 to align
# Constraint # added constraint: constraint((T0327)D25.CB, (T0327)K84.CB) [> 4.5117 = 7.5194 < 9.7753] w=0.0570 to align
# Constraint # added constraint: constraint((T0327)T19.CB, (T0327)E64.CB) [> 4.1795 = 6.9659 < 9.0556] w=0.0569 to align
# Constraint # added constraint: constraint((T0327)D4.CB, (T0327)F39.CB) [> 4.0865 = 6.8108 < 8.8541] w=0.0569 to align
# Constraint # added constraint: constraint((T0327)H50.CB, (T0327)G62.CA) [> 3.2985 = 5.4976 < 7.1469] w=0.0568 to align
# Constraint # added constraint: constraint((T0327)V49.CB, (T0327)L61.CB) [> 3.7579 = 6.2632 < 8.1422] w=0.0568 to align
# Constraint # added constraint: constraint((T0327)Y45.CB, (T0327)A82.CB) [> 3.9166 = 6.5277 < 8.4860] w=0.0566 to align
# Constraint # added constraint: constraint((T0327)Y45.CB, (T0327)K81.CB) [> 4.4023 = 7.3371 < 9.5383] w=0.0566 to align
# Constraint # added constraint: constraint((T0327)Y45.CB, (T0327)T85.CB) [> 3.1576 = 5.2626 < 6.8414] w=0.0565 to align
# Constraint # added constraint: constraint((T0327)N18.CB, (T0327)H57.CB) [> 3.0773 = 5.1289 < 6.6676] w=0.0562 to align
# Constraint # added constraint: constraint((T0327)T29.CB, (T0327)Y51.CB) [> 3.8889 = 6.4815 < 8.4260] w=0.0546 to align
# Constraint # added constraint: constraint((T0327)T29.CB, (T0327)H57.CB) [> 2.6235 = 4.3726 < 5.6843] w=0.0546 to align
# Constraint # added constraint: constraint((T0327)D34.CB, (T0327)V49.CB) [> 4.3083 = 7.1805 < 9.3347] w=0.0546 to align
# Constraint # added constraint: constraint((T0327)L21.CB, (T0327)L58.CB) [> 3.0302 = 5.0504 < 6.5655] w=0.0497 to align
# Constraint # added constraint: constraint((T0327)G48.CA, (T0327)Y72.CB) [> 4.6521 = 7.7535 < 10.0796] w=0.0396 to align
# Constraint # added constraint: constraint((T0327)K12.CB, (T0327)K81.CB) [> 4.7553 = 7.9255 < 10.3032] w=0.0380 to align
# Constraint # added constraint: constraint((T0327)L40.CB, (T0327)Y59.CB) [> 4.7957 = 7.9927 < 10.3906] w=0.0380 to align
# Constraint # added constraint: constraint((T0327)L21.CB, (T0327)F33.CB) [> 4.3785 = 7.2975 < 9.4868] w=0.0380 to align
# Constraint # added constraint: constraint((T0327)F15.CB, (T0327)F33.CB) [> 4.4530 = 7.4217 < 9.6482] w=0.0379 to align
# Constraint # added constraint: constraint((T0327)E16.CB, (T0327)V28.CB) [> 4.4473 = 7.4121 < 9.6358] w=0.0379 to align
# Constraint # added constraint: constraint((T0327)E13.CB, (T0327)L58.CB) [> 4.6018 = 7.6697 < 9.9706] w=0.0379 to align
# Constraint # added constraint: constraint((T0327)S52.CB, (T0327)E64.CB) [> 3.2245 = 5.3741 < 6.9864] w=0.0379 to align
# Constraint # added constraint: constraint((T0327)Y51.CB, (T0327)E64.CB) [> 4.3824 = 7.3039 < 9.4951] w=0.0379 to align
# Constraint # added constraint: constraint((T0327)H50.CB, (T0327)L61.CB) [> 4.0050 = 6.6750 < 8.6775] w=0.0378 to align
# Constraint # added constraint: constraint((T0327)Y8.CB, (T0327)I89.CB) [> 4.5925 = 7.6542 < 9.9504] w=0.0378 to align
# Constraint # added constraint: constraint((T0327)L11.CB, (T0327)A82.CB) [> 3.5828 = 5.9714 < 7.7628] w=0.0378 to align
# Constraint # added constraint: constraint((T0327)L11.CB, (T0327)I86.CB) [> 4.7522 = 7.9203 < 10.2964] w=0.0378 to align
# Constraint # added constraint: constraint((T0327)F33.CB, (T0327)I86.CB) [> 4.5855 = 7.6425 < 9.9353] w=0.0377 to align
# Constraint # added constraint: constraint((T0327)E30.CB, (T0327)Y83.CB) [> 4.2667 = 7.1112 < 9.2446] w=0.0377 to align
# Constraint # added constraint: constraint((T0327)V49.CB, (T0327)Y72.CB) [> 4.0922 = 6.8203 < 8.8664] w=0.0377 to align
# Constraint # added constraint: constraint((T0327)L40.CB, (T0327)A82.CB) [> 4.7908 = 7.9847 < 10.3801] w=0.0377 to align
# Constraint # added constraint: constraint((T0327)L61.CB, (T0327)T85.CB) [> 3.7026 = 6.1710 < 8.0223] w=0.0377 to align
# Constraint # added constraint: constraint((T0327)K12.CB, (T0327)I89.CB) [> 3.8503 = 6.4172 < 8.3423] w=0.0377 to align
# Constraint # added constraint: constraint((T0327)L11.CB, (T0327)I89.CB) [> 4.0439 = 6.7398 < 8.7618] w=0.0377 to align
# Constraint # added constraint: constraint((T0327)I47.CB, (T0327)Y72.CB) [> 2.8945 = 4.8242 < 6.2715] w=0.0207 to align
# Constraint # added constraint: constraint((T0327)Y51.CB, (T0327)W79.CB) [> 3.4451 = 5.7419 < 7.4644] w=0.0207 to align
# Constraint # added constraint: constraint((T0327)R55.CB, (T0327)E64.CB) [> 3.8315 = 6.3858 < 8.3016] w=0.0190 to align
# Constraint # added constraint: constraint((T0327)E70.CB, (T0327)A82.CB) [> 3.4822 = 5.8037 < 7.5448] w=0.0189 to align
# Constraint # added constraint: constraint((T0327)E70.CB, (T0327)Y83.CB) [> 3.6903 = 6.1505 < 7.9956] w=0.0189 to align
# Constraint # added constraint: constraint((T0327)L61.CB, (T0327)I89.CB) [> 3.2324 = 5.3873 < 7.0034] w=0.0188 to align
# Constraint # added constraint: constraint((T0327)Y51.CB, (T0327)I93.CB) [> 3.3778 = 5.6297 < 7.3186] w=0.0188 to align
# Constraint # added constraint: constraint((T0327)D53.CB, (T0327)I93.CB) [> 3.8463 = 6.4105 < 8.3336] w=0.0188 to align
# Constraint # added constraint: constraint((T0327)T29.CB, (T0327)L58.CB) [> 2.6487 = 4.4144 < 5.7388] w=0.0182 to align
# SetCost created cost = 
#	( 1.0000 * align )
# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0327/
# command:# reading script from file servers-clean.under
# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0327/decoys/
# ReadConformPDB reading from PDB file ../dimer/decoys/dimer-1ub9A-dimer11.pdb.gz looking for chain 'A' model 1
# choosing archetypes in rotamer library
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//dimer-1ub9A-dimer11
# ReadConformPDB reading from PDB file ../dimer/decoys/dimer1-1tbxA-dimer6.pdb.gz looking for chain 'A' model 1
# Found a chain break before 79
# copying to AlignedFragments data structure
# naming current conformation dimer//dimer1-1tbxA-dimer6
# ReadConformPDB reading from PDB file ../dimer/decoys/dimer2-1tbxA-dimer6.pdb.gz looking for chain 'A' model 1
# Found a chain break before 79
# copying to AlignedFragments data structure
# naming current conformation dimer//dimer2-1tbxA-dimer6
# ReadConformPDB reading from PDB file ../dimer/decoys/dimer3-1tbxA-dimer6.pdb.gz looking for chain 'A' model 1
# Found a chain break before 79
# copying to AlignedFragments data structure
# naming current conformation dimer//dimer3-1tbxA-dimer6
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_POPULUS_TS1
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_POPULUS_TS2
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 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 T0327 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 T0327 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 T0327 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 T0327 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 T0327 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 T0327 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 T0327 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 T0327 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 T0327 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_TS2
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS3.pdb.gz looking for model 1
# Found a chain break before 100
# copying to AlignedFragments data structure
# naming current conformation 3D-JIGSAW_TS3
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_TS4
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_TS5
# ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1
# naming current conformation 3Dpro_TS1
# ReadConformPDB reading from PDB file servers/3Dpro_TS2.pdb.gz looking for model 1
# Found a chain break before 34
# copying to AlignedFragments data structure
# naming current conformation 3Dpro_TS2
# ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1
# naming current conformation 3Dpro_TS3
# ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1
# naming current conformation 3Dpro_TS4
# ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1
# Found a chain break before 97
# 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 97
# 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 78
# 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 52
# 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 97
# 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 73
# copying to AlignedFragments data structure
# naming current conformation ABIpro_TS5
# ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1
# naming current conformation BayesHH_TS1
# ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS1.pdb.gz looking for model 1
# Found a chain break before 69
# copying to AlignedFragments data structure
# naming current conformation Bilab-ENABLE_TS1
# ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS2.pdb.gz looking for model 1
# naming current conformation Bilab-ENABLE_TS2
# ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS3.pdb.gz looking for model 1
# naming current conformation Bilab-ENABLE_TS3
# ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS4.pdb.gz looking for model 1
# naming current conformation Bilab-ENABLE_TS4
# ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS5.pdb.gz looking for model 1
# 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 79
# 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 90
# copying to AlignedFragments data structure
# naming current conformation CIRCLE_TS2
# ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation CIRCLE_TS3
# ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation CIRCLE_TS4
# ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation CIRCLE_TS5
# ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 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 T0327 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 T0327 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 T0327 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 T0327 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation CaspIta-FOX_TS5
# ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 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 T0327 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 T0327 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 T0327 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 T0327 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 100
# copying to AlignedFragments data structure
# naming current conformation FAMSD_TS1
# ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation FAMSD_TS2
# ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation FAMSD_TS3
# ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation FAMSD_TS4
# ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 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 96
# 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 79
# 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 90
# copying to AlignedFragments data structure
# naming current conformation FAMS_TS3
# ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation FAMS_TS4
# ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation FAMS_TS5
# ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1
# Found a chain break before 58
# 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 61
# 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 34
# 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 62
# copying to AlignedFragments data structure
# naming current conformation FOLDpro_TS4
# ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1
# Found a chain break before 54
# copying to AlignedFragments data structure
# naming current conformation FOLDpro_TS5
# ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 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 T0327 can't currently be optimized by undertaker
# naming current conformation FORTE1_AL2
# ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1
Skipped atom 265, because occupancy 1 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
# WARNING: incomplete conformation T0327 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 T0327 can't currently be optimized by undertaker
# naming current conformation FORTE1_AL4
# ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FORTE1_AL5
# ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation FORTE2_AL1
# ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1
Skipped atom 265, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz
# WARNING: incomplete conformation T0327 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 T0327 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 T0327 can't currently be optimized by undertaker
# naming current conformation FORTE2_AL4
# ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FORTE2_AL5
# ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS1.pdb.gz looking for model 1
# Found a chain break before 98
# 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 86
# 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 101
# copying to AlignedFragments data structure
# naming current conformation FPSOLVER-SERVER_TS3
# ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS4.pdb.gz looking for model 1
# naming current conformation FPSOLVER-SERVER_TS4
# ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS5.pdb.gz looking for model 1
# Found a chain break before 48
# 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
# naming current conformation FUGMOD_TS1
# ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1
# naming current conformation FUGMOD_TS2
# ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation FUGMOD_TS3
# ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1
# Found a chain break before 27
# copying to AlignedFragments data structure
# naming current conformation FUGMOD_TS4
# ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1
# Found a chain break before 69
# copying to AlignedFragments data structure
# naming current conformation FUGMOD_TS5
# ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation FUGUE_AL1
# ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FUGUE_AL2
# ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation FUGUE_AL3
# ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 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
Skipped atom 323, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL5.pdb.gz
Skipped atom 325, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL5.pdb.gz
Skipped atom 327, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL5.pdb.gz
Skipped atom 329, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL5.pdb.gz
Skipped atom 331, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL5.pdb.gz
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FUGUE_AL5
# ReadConformPDB reading from PDB file servers/FUNCTION_TS1.pdb.gz looking for model 1
# Found a chain break before 98
# copying to AlignedFragments data structure
# naming current conformation FUNCTION_TS1
# ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1
# Found a chain break before 98
# copying to AlignedFragments data structure
# naming current conformation FUNCTION_TS2
# ReadConformPDB reading from PDB file servers/FUNCTION_TS3.pdb.gz looking for model 1
# Found a chain break before 97
# copying to AlignedFragments data structure
# naming current conformation FUNCTION_TS3
# ReadConformPDB reading from PDB file servers/FUNCTION_TS4.pdb.gz looking for model 1
# Found a chain break before 81
# 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 98
# copying to AlignedFragments data structure
# naming current conformation FUNCTION_TS5
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1
# naming current conformation GeneSilicoMetaServer_TS1
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1
# Found a chain break before 54
# copying to AlignedFragments data structure
# naming current conformation GeneSilicoMetaServer_TS2
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation GeneSilicoMetaServer_TS3
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1
# Found a chain break before 46
# copying to AlignedFragments data structure
# naming current conformation GeneSilicoMetaServer_TS4
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1
# naming current conformation GeneSilicoMetaServer_TS5
# ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1
# Found a chain break before 47
# copying to AlignedFragments data structure
# naming current conformation HHpred1_TS1
# ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1
# naming current conformation HHpred2_TS1
# ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1
# naming current conformation HHpred3_TS1
# ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 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 T0327 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 T0327 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 T0327 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 T0327 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 T0327 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 T0327 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 T0327 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 T0327 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 T0327 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
# naming current conformation Ma-OPUS-server2_TS1
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS2.pdb.gz looking for model 1
# Found a chain break before 63
# 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
# Found a chain break before 51
# 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
# 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 10
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server2_TS5
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1
# Found a chain break before 62
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server_TS1
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS2.pdb.gz looking for model 1
# Found a chain break before 24
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server_TS2
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS3.pdb.gz looking for model 1
# Found a chain break before 51
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server_TS3
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS4.pdb.gz looking for model 1
# Found a chain break before 48
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server_TS4
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS5.pdb.gz looking for model 1
# Found a chain break before 10
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server_TS5
# ReadConformPDB reading from PDB file servers/MetaTasser_TS1.pdb.gz looking for model 1
# Found a chain break before 97
# 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 99
# 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 100
# 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 97
# 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 98
# 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
# 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 70
# 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 98
# 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 90
# 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 70
# 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 100
# copying to AlignedFragments data structure
# naming current conformation POMYSL_TS5
# ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1
# naming current conformation PROTINFO-AB_TS1
# ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1
# naming current conformation PROTINFO-AB_TS2
# ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1
# naming current conformation PROTINFO-AB_TS3
# ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1
# naming current conformation PROTINFO-AB_TS4
# ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1
# naming current conformation PROTINFO-AB_TS5
# ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1
# Found a chain break before 65
# copying to AlignedFragments data structure
# naming current conformation PROTINFO_TS1
# ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1
# Found a chain break before 65
# copying to AlignedFragments data structure
# naming current conformation PROTINFO_TS2
# ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1
# Found a chain break before 65
# copying to AlignedFragments data structure
# naming current conformation PROTINFO_TS3
# ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1
# Found a chain break before 64
# copying to AlignedFragments data structure
# naming current conformation PROTINFO_TS4
# ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1
# Found a chain break before 77
# copying to AlignedFragments data structure
# naming current conformation PROTINFO_TS5
# ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation Pcons6_TS1
# ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation Pcons6_TS2
# ReadConformPDB reading from PDB file servers/Pcons6_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation Pcons6_TS3
# ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 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 T0327 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 T0327 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 T0327 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation Phyre-2_TS1
# ReadConformPDB reading from PDB file servers/Phyre-2_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation Phyre-2_TS2
# ReadConformPDB reading from PDB file servers/Phyre-2_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 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 T0327 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation Phyre-2_TS4
# ReadConformPDB reading from PDB file servers/Phyre-2_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation Phyre-2_TS5
# ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation Pmodeller6_TS1
# ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1
# Found a chain break before 77
# 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 59
# 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 T0327 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 51
# 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 79
# copying to AlignedFragments data structure
# naming current conformation RAPTOR-ACE_TS1
# ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1
# naming current conformation RAPTOR-ACE_TS2
# ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1
# naming current conformation RAPTOR-ACE_TS3
# ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS4.pdb.gz looking for model 1
# naming current conformation RAPTOR-ACE_TS4
# ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1
# Found a chain break before 65
# copying to AlignedFragments data structure
# naming current conformation RAPTOR-ACE_TS5
# ReadConformPDB reading from PDB file servers/RAPTORESS_TS1.pdb.gz looking for model 1
# Found a chain break before 99
# copying to AlignedFragments data structure
# naming current conformation RAPTORESS_TS1
# ReadConformPDB reading from PDB file servers/RAPTORESS_TS2.pdb.gz looking for model 1
# Found a chain break before 62
# copying to AlignedFragments data structure
# naming current conformation RAPTORESS_TS2
# ReadConformPDB reading from PDB file servers/RAPTORESS_TS3.pdb.gz looking for model 1
# Found a chain break before 19
# 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 101
# 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 101
# 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
# Found a chain break before 82
# copying to AlignedFragments data structure
# 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 63
# 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 59
# copying to AlignedFragments data structure
# naming current conformation ROBETTA_TS1
# ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1
# Found a chain break before 59
# copying to AlignedFragments data structure
# naming current conformation ROBETTA_TS2
# ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1
# Found a chain break before 75
# copying to AlignedFragments data structure
# naming current conformation ROBETTA_TS3
# ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1
# Found a chain break before 51
# copying to AlignedFragments data structure
# naming current conformation ROBETTA_TS4
# ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1
# Found a chain break before 77
# 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 T0327 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 T0327 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 T0327 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 T0327 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 T0327 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation ROKKY_TS5
# ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 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 T0327 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
Skipped atom 118, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz
Skipped atom 120, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz
Skipped atom 122, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz
Skipped atom 124, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz
Skipped atom 198, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz
Skipped atom 200, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz
Skipped atom 202, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz
Skipped atom 204, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz
# WARNING: incomplete conformation T0327 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 T0327 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 T0327 can't currently be optimized by undertaker
# naming current conformation SAM-T02_AL5
# ReadConformPDB reading from PDB file servers/SAM-T99_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation SAM-T99_AL1
# ReadConformPDB reading from PDB file servers/SAM-T99_AL2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation SAM-T99_AL2
# ReadConformPDB reading from PDB file servers/SAM-T99_AL3.pdb.gz looking for model 1
Skipped atom 50, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
Skipped atom 52, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
Skipped atom 54, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
Skipped atom 56, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
Skipped atom 70, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
Skipped atom 72, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
Skipped atom 74, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
Skipped atom 76, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
Skipped atom 202, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
Skipped atom 204, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
Skipped atom 206, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
Skipped atom 208, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
Skipped atom 234, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
Skipped atom 236, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
Skipped atom 238, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
Skipped atom 240, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation SAM-T99_AL3
# ReadConformPDB reading from PDB file servers/SAM-T99_AL4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation SAM-T99_AL4
# ReadConformPDB reading from PDB file servers/SAM-T99_AL5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation SAM-T99_AL5
# ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1
# Found a chain break before 100
# 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 T0327 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 T0327 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 T0327 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 T0327 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 59
# 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 75
# 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 28
# 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 79
# 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 58
# copying to AlignedFragments data structure
# naming current conformation SP4_TS1
# ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1
# naming current conformation SP4_TS2
# ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1
# Found a chain break before 29
# copying to AlignedFragments data structure
# naming current conformation SP4_TS3
# ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1
# naming current conformation SP4_TS4
# ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1
# naming current conformation SP4_TS5
# ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1
# naming current conformation SPARKS2_TS1
# ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1
# Found a chain break before 21
# copying to AlignedFragments data structure
# naming current conformation SPARKS2_TS2
# ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1
# Found a chain break before 77
# copying to AlignedFragments data structure
# naming current conformation SPARKS2_TS3
# ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1
# Found a chain break before 65
# copying to AlignedFragments data structure
# naming current conformation SPARKS2_TS4
# ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1
# Found a chain break before 29
# 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 T0327 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 T0327 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 T0327 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 T0327 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 T0327 can't currently be optimized by undertaker
# naming current conformation UNI-EID_bnmx_TS5
# ReadConformPDB reading from PDB file servers/UNI-EID_expm_TS1.pdb.gz looking for model 1
WARNING: atoms too close: (T0327)N76.CA and (T0327)K87.CA only 0.000 apart, marking (T0327)K87.CA as missing
WARNING: atoms too close: (T0327)G77.CA and (T0327)E88.CA only 0.000 apart, marking (T0327)E88.CA as missing
# WARNING: incomplete conformation T0327 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 T0327 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 T0327 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 T0327 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
Skipped atom 58, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz
Skipped atom 60, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz
Skipped atom 62, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz
Skipped atom 64, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz
Skipped atom 170, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz
Skipped atom 172, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz
Skipped atom 174, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz
Skipped atom 176, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz
Skipped atom 222, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz
Skipped atom 224, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz
Skipped atom 226, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz
Skipped atom 228, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz
# WARNING: incomplete conformation T0327 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 T0327 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 72
# 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 64
# 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 79
# 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 73
# 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 64
# copying to AlignedFragments data structure
# naming current conformation Zhang-Server_TS5
# ReadConformPDB reading from PDB file servers/beautshot_TS1.pdb.gz looking for model 1
# Found a chain break before 101
# copying to AlignedFragments data structure
# naming current conformation beautshot_TS1
# ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 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 T0327 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 T0327 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 T0327 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 T0327 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation forecast-s_AL4
# ReadConformPDB reading from PDB file servers/forecast-s_AL5.pdb.gz looking for model 1
Skipped atom 138, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL5.pdb.gz
Skipped atom 140, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL5.pdb.gz
Skipped atom 142, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL5.pdb.gz
Skipped atom 144, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL5.pdb.gz
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation forecast-s_AL5
# ReadConformPDB reading from PDB file servers/gtg_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation gtg_AL1
# ReadConformPDB reading from PDB file servers/gtg_AL2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation gtg_AL2
# ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1
# naming current conformation karypis.srv.2_TS1
# ReadConformPDB reading from PDB file servers/karypis.srv.2_TS2.pdb.gz looking for model 1
# Found a chain break before 73
# 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 63
# 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 5
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.2_TS4
# ReadConformPDB reading from PDB file servers/karypis.srv.2_TS5.pdb.gz looking for model 1
# naming current conformation karypis.srv.2_TS5
# ReadConformPDB reading from PDB file servers/karypis.srv.4_TS1.pdb.gz looking for model 1
# Found a chain break before 93
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.4_TS1
# ReadConformPDB reading from PDB file servers/karypis.srv.4_TS2.pdb.gz looking for model 1
# Found a chain break before 99
# 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 99
# 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 99
# 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 99
# 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 T0327 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 T0327 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 T0327 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation karypis.srv_TS3
# ReadConformPDB reading from PDB file servers/karypis.srv_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 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 T0327 can't currently be optimized by undertaker
# naming current conformation karypis.srv_TS5
# ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1
# Found a chain break before 84
# copying to AlignedFragments data structure
# naming current conformation keasar-server_TS1
# ReadConformPDB reading from PDB file servers/keasar-server_TS2.pdb.gz looking for model 1
# Found a chain break before 86
# copying to AlignedFragments data structure
# naming current conformation keasar-server_TS2
# ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1
# Found a chain break before 73
# copying to AlignedFragments data structure
# naming current conformation keasar-server_TS3
# ReadConformPDB reading from PDB file servers/keasar-server_TS4.pdb.gz looking for model 1
# naming current conformation keasar-server_TS4
# ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1
# Found a chain break before 19
# copying to AlignedFragments data structure
# naming current conformation keasar-server_TS5
# ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 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 T0327 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 T0327 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 T0327 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 T0327 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 T0327 can't currently be optimized by undertaker
# naming current conformation nFOLD_TS5
# ReadConformPDB reading from PDB file servers/panther2_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation panther2_TS1
# ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation shub_TS1
# command:Using radius: 8.0000
Metaserver mode
NUMB_ALIGNS: 268
model score 0.2177
model score 0.2250
model score 0.2250
model score 0.2250
model score 0.0070
model score 0.2365
model score 0.1308
model score 0.1032
model score 1.1716
model score 0.2480
model score -0.0401
model score -0.0010
model score 0.2739
model score 0.0088
model score 1.2009
model score 1.0168
model score 0.6183
model score 1.8545
model score 0.2660
model score -0.0149
model score 1.2093
model score 0.9078
model score 1.5949
model score 0.8878
model score 0.8878
model score 0.7710
model score 0.5165
model score 0.9189
model score 0.5985
model score -0.0351
model score 1.6746
model score 1.4623
model score -0.0126
model score -0.0117
model score -0.0117
model score -0.1155
model score -0.0946
model score -0.2592
model score -0.0654
model score 0.1986
model score -0.0545
model score -0.1209
model score 0.1986
model score -0.0293
model score 1.5758
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 0.0101
model score 0.1986
model score -0.1458
model score 0.0203
model score -0.0761
model score -0.0683
model score -0.1155
model score -0.0946
model score -0.2592
model score -0.1458
model score -0.0717
model score -0.2529
model score 1.2152
model score 2.0199
model score -0.0527
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 2.0091
model score 2.0925
model score 2.0313
model score 2.0649
model score 1.7033
model score 2.3320
model score 1.7267
model score 0.1129
model score 1.9217
model score 1.6760
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score -0.1260
model score 0.7195
model score -0.0656
model score 0.0311
model score 0.1265
model score 0.0696
model score 0.0074
model score -0.1736
model score 1.3273
model score 0.1335
model score -0.0432
model score -0.0351
model score -0.0351
model score 0.0553
model score 0.7707
model score 1.2084
model score 0.9861
model score 1.0440
model score -0.0708
model score 0.0984
model score -0.0233
model score 1.7313
model score 2.4199
model score -0.0184
model score -0.0754
model score 2.0109
model score 1.5176
model score 2.2464
model score 0.0066
model score 0.2795
model score 2.0109
model score 1.5014
model score 2.2464
model score -0.0896
model score 0.0469
model score -0.0398
model score -0.0361
model score -0.0505
model score -0.1140
model score 1.4268
model score 0.4898
model score 1.1104
model score 0.8184
model score 1.2637
model score -0.1086
model score -0.1348
model score -0.1306
model score -0.1199
model score -0.1495
model score -0.0550
model score -0.1247
model score -0.1330
model score -0.0792
model score -0.0914
model score 0.0154
model score -0.2712
model score -0.0242
model score 1.3422
model score -0.0432
model score 0.9310
model score 0.0409
model score 0.1285
model score 0.0529
model score 0.0409
model score 0.1682
model score -0.1850
model score -0.0700
model score 0.0161
model score -0.2289
model score 0.0803
model score -0.1659
model score 0.0283
model score -0.1140
model score -0.1401
model score -0.1766
model score -0.0915
model score 0.0576
model score 0.2884
model score -0.0248
model score -0.0012
model score -0.1356
model score 0.0448
model score 0.2646
model score -0.1559
model score -0.0352
model score 0.0161
model score 0.1988
model score 0.1151
model score 0.0803
model score -0.0700
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 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 0.7311
model score 0.5050
model score 0.7318
model score -0.2324
model score 0.8198
model score -0.1140
model score 0.3338
model score -0.0475
model score 0.2002
model score -0.1659
model score 0.0454
model score 0.0028
model score 0.0461
model score 1.5412
model score 1.7425
model score -0.1140
model score 0.0136
model score -0.0054
model score 0.3076
model score 1.9754
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 0.5047
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score -0.1034
model score -0.2473
model score -0.0685
model score -0.0047
model score -0.2256
model score -0.0977
model score -0.1944
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 -0.0066
model score -0.1659
model score 0.0961
model score 0.0336
model score 0.1539
model score 1.9117
model score 1.8922
model score 2.1149
model score 2.0236
model score 1.7840
model score -0.0025
model score -0.2344
model score 0.3843
model score 0.2915
model score 0.2116
model score -0.1832
model score -0.0848
model score -0.0370
model score 0.0165
model score 0.0223
model score 0.3466
model score 0.2766
model score 0.0111
model score 0.0102
model score -0.2317
model score 0.5369
model score 1.9117
model score -0.1351
weight: 0.8365 eval: 0.2177 min: -0.2712 max: 2.4199
weight: 0.8341 eval: 0.2250 min: -0.2712 max: 2.4199
weight: 0.8340 eval: 0.2250 min: -0.2712 max: 2.4199
weight: 0.8340 eval: 0.2250 min: -0.2712 max: 2.4199
weight: 0.9070 eval: 0.0070 min: -0.2712 max: 2.4199
weight: 0.8302 eval: 0.2365 min: -0.2712 max: 2.4199
weight: 0.8656 eval: 0.1308 min: -0.2712 max: 2.4199
weight: 0.8748 eval: 0.1032 min: -0.2712 max: 2.4199
weight: 0.5175 eval: 1.1716 min: -0.2712 max: 2.4199
weight: 0.8264 eval: 0.2480 min: -0.2712 max: 2.4199
weight: 0.9227 eval: -0.0401 min: -0.2712 max: 2.4199
weight: 0.9096 eval: -0.0010 min: -0.2712 max: 2.4199
weight: 0.8177 eval: 0.2739 min: -0.2712 max: 2.4199
weight: 0.9064 eval: 0.0088 min: -0.2712 max: 2.4199
weight: 0.5077 eval: 1.2009 min: -0.2712 max: 2.4199
weight: 0.5692 eval: 1.0168 min: -0.2712 max: 2.4199
weight: 0.7025 eval: 0.6183 min: -0.2712 max: 2.4199
weight: 0.2891 eval: 1.8545 min: -0.2712 max: 2.4199
weight: 0.8203 eval: 0.2660 min: -0.2712 max: 2.4199
weight: 0.9143 eval: -0.0149 min: -0.2712 max: 2.4199
weight: 0.5049 eval: 1.2093 min: -0.2712 max: 2.4199
weight: 0.6057 eval: 0.9078 min: -0.2712 max: 2.4199
weight: 0.3759 eval: 1.5949 min: -0.2712 max: 2.4199
weight: 0.6124 eval: 0.8878 min: -0.2712 max: 2.4199
weight: 0.6124 eval: 0.8878 min: -0.2712 max: 2.4199
weight: 0.6514 eval: 0.7710 min: -0.2712 max: 2.4199
weight: 0.7366 eval: 0.5165 min: -0.2712 max: 2.4199
weight: 0.6020 eval: 0.9189 min: -0.2712 max: 2.4199
weight: 0.7091 eval: 0.5985 min: -0.2712 max: 2.4199
weight: 0.9210 eval: -0.0351 min: -0.2712 max: 2.4199
weight: 0.3492 eval: 1.6746 min: -0.2712 max: 2.4199
weight: 0.4203 eval: 1.4623 min: -0.2712 max: 2.4199
weight: 0.9135 eval: -0.0126 min: -0.2712 max: 2.4199
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weight: 0.9132 eval: -0.0117 min: -0.2712 max: 2.4199
weight: 0.9479 eval: -0.1155 min: -0.2712 max: 2.4199
weight: 0.9409 eval: -0.0946 min: -0.2712 max: 2.4199
weight: 0.9960 eval: -0.2592 min: -0.2712 max: 2.4199
weight: 0.9312 eval: -0.0654 min: -0.2712 max: 2.4199
weight: 0.8429 eval: 0.1986 min: -0.2712 max: 2.4199
weight: 0.9275 eval: -0.0545 min: -0.2712 max: 2.4199
weight: 0.9497 eval: -0.1209 min: -0.2712 max: 2.4199
weight: 0.8429 eval: 0.1986 min: -0.2712 max: 2.4199
weight: 0.9191 eval: -0.0293 min: -0.2712 max: 2.4199
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weight: 0.4822 eval: 1.2771 min: -0.2712 max: 2.4199
weight: 0.4822 eval: 1.2771 min: -0.2712 max: 2.4199
weight: 0.4822 eval: 1.2771 min: -0.2712 max: 2.4199
weight: 0.4822 eval: 1.2771 min: -0.2712 max: 2.4199
weight: 0.9059 eval: 0.0101 min: -0.2712 max: 2.4199
weight: 0.8429 eval: 0.1986 min: -0.2712 max: 2.4199
weight: 0.9581 eval: -0.1458 min: -0.2712 max: 2.4199
weight: 0.9025 eval: 0.0203 min: -0.2712 max: 2.4199
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weight: 0.9479 eval: -0.1155 min: -0.2712 max: 2.4199
weight: 0.9409 eval: -0.0946 min: -0.2712 max: 2.4199
weight: 0.9960 eval: -0.2592 min: -0.2712 max: 2.4199
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weight: 0.4822 eval: 1.2771 min: -0.2712 max: 2.4199
weight: 0.4822 eval: 1.2771 min: -0.2712 max: 2.4199
weight: 0.4822 eval: 1.2771 min: -0.2712 max: 2.4199
weight: 0.4822 eval: 1.2771 min: -0.2712 max: 2.4199
weight: 0.4822 eval: 1.2771 min: -0.2712 max: 2.4199
weight: 0.4822 eval: 1.2771 min: -0.2712 max: 2.4199
weight: 0.4822 eval: 1.2771 min: -0.2712 max: 2.4199
weight: 0.4822 eval: 1.2771 min: -0.2712 max: 2.4199
weight: 0.4822 eval: 1.2771 min: -0.2712 max: 2.4199
weight: 0.4822 eval: 1.2771 min: -0.2712 max: 2.4199
weight: 0.2374 eval: 2.0091 min: -0.2712 max: 2.4199
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Adding 2858 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: -176.7872, CN propb: -176.7872 weights: 0.3029 constraints: 173
# command:Found ConstraintSet
# PrintContacts align.constraints_meta02
Number of constraints in align2.constraints 173
# command:Found ConstraintSet
# PrintContacts align_bonus.constraints_meta02
Number of constraints in align2.constraints.bonus 173
# command:Found ConstraintSet
# PrintContacts rejected.constraints_meta02
Number of constraints in rejected2.constraints 2685
# command:Found ConstraintSet
# PrintContacts rejected_bonus.constraints_meta02
Number of constraints in rejected2.constraints.bonus 2685
# 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 2858
# command: