# 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/T0314/
# command:# Making conformation for sequence T0314 numbered 1 through 106
Created new target T0314 from T0314.a2m
# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0314/
# command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0314//projects/compbio/experiments/protein-predict/casp7/T0314/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0314//projects/compbio/experiments/protein-predict/casp7/T0314/align.constraints_v3.costfcn.gz for input
Trying /projects/compbio/experiments/protein-predict/casp7/T0314/align.constraints_v3.costfcn
# reading script from file /projects/compbio/experiments/protein-predict/casp7/T0314/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((T0314)V30.CB, (T0314)M62.CB) [> 3.9388 = 6.5647 < 8.5341] w=1.0000 to align
# Constraint # added constraint: constraint((T0314)V19.CB, (T0314)L69.CB) [> 4.4205 = 7.3675 < 9.5778] w=0.7862 to align
# Constraint # added constraint: constraint((T0314)R31.CB, (T0314)I46.CB) [> 3.2098 = 5.3497 < 6.9546] w=0.7773 to align
# Constraint # added constraint: constraint((T0314)I29.CB, (T0314)I46.CB) [> 2.6683 = 4.4472 < 5.7813] w=0.7589 to align
# Constraint # added constraint: constraint((T0314)F18.CB, (T0314)R66.CB) [> 4.0105 = 6.6842 < 8.6895] w=0.7356 to align
# Constraint # added constraint: constraint((T0314)G20.CA, (T0314)V30.CB) [> 4.1590 = 6.9317 < 9.0112] w=0.6934 to align
# Constraint # added constraint: constraint((T0314)V19.CB, (T0314)R31.CB) [> 4.0023 = 6.6706 < 8.6717] w=0.6934 to align
# Constraint # added constraint: constraint((T0314)F32.CB, (T0314)L72.CB) [> 4.2461 = 7.0769 < 9.2000] w=0.6660 to align
# Constraint # added constraint: constraint((T0314)F32.CB, (T0314)L69.CB) [> 4.0616 = 6.7694 < 8.8002] w=0.6660 to align
# Constraint # added constraint: constraint((T0314)F32.CB, (T0314)Q68.CB) [> 3.1236 = 5.2060 < 6.7679] w=0.6660 to align
# Constraint # added constraint: constraint((T0314)F18.CB, (T0314)M39.CB) [> 3.3063 = 5.5104 < 7.1636] w=0.6506 to align
# Constraint # added constraint: constraint((T0314)V30.CB, (T0314)I46.CB) [> 4.3019 = 7.1698 < 9.3208] w=0.6459 to align
# Constraint # added constraint: constraint((T0314)D40.CB, (T0314)R66.CB) [> 4.1887 = 6.9812 < 9.0755] w=0.6300 to align
# Constraint # added constraint: constraint((T0314)M39.CB, (T0314)R66.CB) [> 4.5798 = 7.6331 < 9.9230] w=0.6300 to align
# Constraint # added constraint: constraint((T0314)V30.CB, (T0314)L72.CB) [> 3.1341 = 5.2235 < 6.7905] w=0.6079 to align
# Constraint # added constraint: constraint((T0314)E34.CB, (T0314)G65.CA) [> 4.3817 = 7.3028 < 9.4937] w=0.6027 to align
# Constraint # added constraint: constraint((T0314)F18.CB, (T0314)R31.CB) [> 3.5955 = 5.9925 < 7.7903] w=0.5643 to align
# Constraint # added constraint: constraint((T0314)V30.CB, (T0314)I77.CB) [> 2.9397 = 4.8994 < 6.3692] w=0.5550 to align
# Constraint # added constraint: constraint((T0314)I29.CB, (T0314)I77.CB) [> 4.0130 = 6.6883 < 8.6948] w=0.5550 to align
# Constraint # added constraint: constraint((T0314)Y28.CB, (T0314)I77.CB) [> 3.8727 = 6.4546 < 8.3909] w=0.5550 to align
# Constraint # added constraint: constraint((T0314)R27.CB, (T0314)I77.CB) [> 3.5524 = 5.9207 < 7.6969] w=0.5550 to align
# Constraint # added constraint: constraint((T0314)R27.CB, (T0314)N76.CB) [> 3.6561 = 6.0935 < 7.9216] w=0.5550 to align
# Constraint # added constraint: constraint((T0314)F21.CB, (T0314)L73.CB) [> 4.3981 = 7.3302 < 9.5293] w=0.5550 to align
# Constraint # added constraint: constraint((T0314)G20.CA, (T0314)L73.CB) [> 3.2402 = 5.4003 < 7.0204] w=0.5550 to align
# Constraint # added constraint: constraint((T0314)G20.CA, (T0314)L69.CB) [> 3.2815 = 5.4692 < 7.1099] w=0.5550 to align
# Constraint # added constraint: constraint((T0314)F18.CB, (T0314)L69.CB) [> 3.5188 = 5.8646 < 7.6240] w=0.5550 to align
# Constraint # added constraint: constraint((T0314)R31.CB, (T0314)S45.CB) [> 4.1210 = 6.8684 < 8.9289] w=0.5534 to align
# Constraint # added constraint: constraint((T0314)V19.CB, (T0314)V30.CB) [> 3.0743 = 5.1239 < 6.6611] w=0.5472 to align
# Constraint # added constraint: constraint((T0314)F37.CB, (T0314)L64.CB) [> 4.5301 = 7.5501 < 9.8152] w=0.5462 to align
# Constraint # added constraint: constraint((T0314)Y28.CB, (T0314)F52.CB) [> 3.3930 = 5.6550 < 7.3515] w=0.5343 to align
# Constraint # added constraint: constraint((T0314)V30.CB, (T0314)V89.CB) [> 3.3011 = 5.5018 < 7.1524] w=0.5294 to align
# Constraint # added constraint: constraint((T0314)F18.CB, (T0314)V30.CB) [> 3.9922 = 6.6537 < 8.6498] w=0.5273 to align
# Constraint # added constraint: constraint((T0314)V30.CB, (T0314)F52.CB) [> 3.9289 = 6.5482 < 8.5126] w=0.5265 to align
# Constraint # added constraint: constraint((T0314)G20.CA, (T0314)R31.CB) [> 3.4207 = 5.7012 < 7.4116] w=0.5239 to align
# Constraint # added constraint: constraint((T0314)Y28.CB, (T0314)L64.CB) [> 3.8123 = 6.3538 < 8.2599] w=0.5217 to align
# Constraint # added constraint: constraint((T0314)G17.CA, (T0314)Q68.CB) [> 3.3702 = 5.6170 < 7.3021] w=0.5113 to align
# Constraint # added constraint: constraint((T0314)R31.CB, (T0314)V41.CB) [> 3.7170 = 6.1951 < 8.0536] w=0.5112 to align
# Constraint # added constraint: constraint((T0314)V30.CB, (T0314)L64.CB) [> 3.8417 = 6.4029 < 8.3237] w=0.5100 to align
# Constraint # added constraint: constraint((T0314)Y28.CB, (T0314)V89.CB) [> 3.6857 = 6.1428 < 7.9857] w=0.4960 to align
# Constraint # added constraint: constraint((T0314)Y28.CB, (T0314)Y90.CB) [> 4.3411 = 7.2351 < 9.4057] w=0.4960 to align
# Constraint # added constraint: constraint((T0314)Y28.CB, (T0314)L91.CB) [> 3.7020 = 6.1699 < 8.0209] w=0.4960 to align
# Constraint # added constraint: constraint((T0314)Y28.CB, (T0314)R92.CB) [> 4.6325 = 7.7209 < 10.0371] w=0.4960 to align
# Constraint # added constraint: constraint((T0314)I29.CB, (T0314)V89.CB) [> 4.2626 = 7.1044 < 9.2357] w=0.4960 to align
# Constraint # added constraint: constraint((T0314)I29.CB, (T0314)Y90.CB) [> 2.9940 = 4.9901 < 6.4871] w=0.4960 to align
# Constraint # added constraint: constraint((T0314)I29.CB, (T0314)R92.CB) [> 3.6799 = 6.1332 < 7.9732] w=0.4960 to align
# Constraint # added constraint: constraint((T0314)V30.CB, (T0314)L88.CB) [> 4.0469 = 6.7448 < 8.7683] w=0.4960 to align
# Constraint # added constraint: constraint((T0314)V30.CB, (T0314)Y90.CB) [> 4.4356 = 7.3927 < 9.6105] w=0.4960 to align
# Constraint # added constraint: constraint((T0314)R31.CB, (T0314)L88.CB) [> 3.7612 = 6.2687 < 8.1493] w=0.4960 to align
# Constraint # added constraint: constraint((T0314)F32.CB, (T0314)L88.CB) [> 4.6287 = 7.7145 < 10.0288] w=0.4960 to align
# Constraint # added constraint: constraint((T0314)S33.CB, (T0314)E85.CB) [> 4.1878 = 6.9797 < 9.0736] w=0.4960 to align
# Constraint # added constraint: constraint((T0314)S33.CB, (T0314)P86.CB) [> 2.7621 = 4.6034 < 5.9845] w=0.4960 to align
# Constraint # added constraint: constraint((T0314)S33.CB, (T0314)L87.CB) [> 4.4750 = 7.4584 < 9.6959] w=0.4960 to align
# Constraint # added constraint: constraint((T0314)I46.CB, (T0314)Y90.CB) [> 4.5322 = 7.5536 < 9.8197] w=0.4960 to align
# Constraint # added constraint: constraint((T0314)G17.CA, (T0314)G65.CA) [> 3.9420 = 6.5700 < 8.5409] w=0.4954 to align
# Constraint # added constraint: constraint((T0314)E34.CB, (T0314)D44.CB) [> 3.1630 = 5.2717 < 6.8533] w=0.4730 to align
# Constraint # added constraint: constraint((T0314)Y28.CB, (T0314)W54.CB) [> 4.1728 = 6.9547 < 9.0412] w=0.4524 to align
# Constraint # added constraint: constraint((T0314)G20.CA, (T0314)I29.CB) [> 3.2570 = 5.4283 < 7.0568] w=0.4516 to align
# Constraint # added constraint: constraint((T0314)G26.CA, (T0314)Q94.CB) [> 3.6229 = 6.0381 < 7.8496] w=0.4352 to align
# Constraint # added constraint: constraint((T0314)D35.CB, (T0314)I46.CB) [> 3.9488 = 6.5813 < 8.5557] w=0.4337 to align
# Constraint # added constraint: constraint((T0314)F52.CB, (T0314)V89.CB) [> 3.8352 = 6.3921 < 8.3097] w=0.4332 to align
# Constraint # added constraint: constraint((T0314)R31.CB, (T0314)T47.CB) [> 4.0091 = 6.6818 < 8.6863] w=0.4319 to align
# Constraint # added constraint: constraint((T0314)A12.CB, (T0314)F21.CB) [> 4.3596 = 7.2660 < 9.4458] w=0.4295 to align
# Constraint # added constraint: constraint((T0314)F21.CB, (T0314)V30.CB) [> 3.8613 = 6.4355 < 8.3662] w=0.4232 to align
# Constraint # added constraint: constraint((T0314)F18.CB, (T0314)S36.CB) [> 4.2061 = 7.0101 < 9.1132] w=0.4224 to align
# Constraint # added constraint: constraint((T0314)S36.CB, (T0314)G65.CA) [> 3.5524 = 5.9206 < 7.6968] w=0.4177 to align
# Constraint # added constraint: constraint((T0314)I29.CB, (T0314)F52.CB) [> 4.1157 = 6.8595 < 8.9173] w=0.4172 to align
# Constraint # added constraint: constraint((T0314)R31.CB, (T0314)V53.CB) [> 3.8821 = 6.4701 < 8.4112] w=0.4071 to align
# Constraint # added constraint: constraint((T0314)R27.CB, (T0314)R92.CB) [> 3.0605 = 5.1009 < 6.6311] w=0.4061 to align
# Constraint # added constraint: constraint((T0314)R27.CB, (T0314)L91.CB) [> 4.3954 = 7.3256 < 9.5233] w=0.4061 to align
# Constraint # added constraint: constraint((T0314)T49.CB, (T0314)M62.CB) [> 3.9395 = 6.5659 < 8.5356] w=0.3989 to align
# Constraint # added constraint: constraint((T0314)D35.CB, (T0314)D44.CB) [> 3.9482 = 6.5804 < 8.5545] w=0.3989 to align
# Constraint # added constraint: constraint((T0314)S33.CB, (T0314)T47.CB) [> 2.9021 = 4.8369 < 6.2879] w=0.3956 to align
# Constraint # added constraint: constraint((T0314)S33.CB, (T0314)S45.CB) [> 3.3164 = 5.5274 < 7.1856] w=0.3956 to align
# Constraint # added constraint: constraint((T0314)A42.CB, (T0314)F52.CB) [> 3.9203 = 6.5338 < 8.4939] w=0.3818 to align
# Constraint # added constraint: constraint((T0314)L88.CB, (T0314)Q102.CB) [> 3.6419 = 6.0698 < 7.8907] w=0.3713 to align
# Constraint # added constraint: constraint((T0314)V30.CB, (T0314)W54.CB) [> 3.9196 = 6.5326 < 8.4924] w=0.3713 to align
# Constraint # added constraint: constraint((T0314)G17.CA, (T0314)M39.CB) [> 3.9976 = 6.6626 < 8.6614] w=0.3700 to align
# Constraint # added constraint: constraint((T0314)F18.CB, (T0314)G65.CA) [> 3.4470 = 5.7450 < 7.4685] w=0.3656 to align
# Constraint # added constraint: constraint((T0314)E34.CB, (T0314)E85.CB) [> 3.4592 = 5.7654 < 7.4950] w=0.3612 to align
# Constraint # added constraint: constraint((T0314)E34.CB, (T0314)G84.CA) [> 4.6326 = 7.7210 < 10.0373] w=0.3612 to align
# Constraint # added constraint: constraint((T0314)E34.CB, (T0314)I83.CB) [> 4.0297 = 6.7161 < 8.7309] w=0.3612 to align
# Constraint # added constraint: constraint((T0314)R31.CB, (T0314)L87.CB) [> 3.8498 = 6.4163 < 8.3412] w=0.3612 to align
# Constraint # added constraint: constraint((T0314)R31.CB, (T0314)A42.CB) [> 3.5170 = 5.8616 < 7.6201] w=0.3612 to align
# Constraint # added constraint: constraint((T0314)R31.CB, (T0314)D40.CB) [> 3.2750 = 5.4584 < 7.0959] w=0.3612 to align
# Constraint # added constraint: constraint((T0314)I29.CB, (T0314)L91.CB) [> 4.6467 = 7.7445 < 10.0679] w=0.3612 to align
# Constraint # added constraint: constraint((T0314)I29.CB, (T0314)A42.CB) [> 4.0964 = 6.8274 < 8.8756] w=0.3612 to align
# Constraint # added constraint: constraint((T0314)G26.CA, (T0314)R93.CB) [> 3.6330 = 6.0550 < 7.8715] w=0.3612 to align
# Constraint # added constraint: constraint((T0314)G26.CA, (T0314)L91.CB) [> 3.6305 = 6.0508 < 7.8661] w=0.3612 to align
# Constraint # added constraint: constraint((T0314)G65.CA, (T0314)I83.CB) [> 2.8575 = 4.7625 < 6.1912] w=0.3612 to align
# Constraint # added constraint: constraint((T0314)G65.CA, (T0314)N82.CB) [> 4.3675 = 7.2791 < 9.4628] w=0.3612 to align
# Constraint # added constraint: constraint((T0314)L64.CB, (T0314)I83.CB) [> 4.4346 = 7.3910 < 9.6082] w=0.3612 to align
# Constraint # added constraint: constraint((T0314)A42.CB, (T0314)Y90.CB) [> 3.7641 = 6.2734 < 8.1555] w=0.3612 to align
# Constraint # added constraint: constraint((T0314)F37.CB, (T0314)L87.CB) [> 3.3018 = 5.5030 < 7.1540] w=0.3612 to align
# Constraint # added constraint: constraint((T0314)F37.CB, (T0314)E85.CB) [> 3.7733 = 6.2888 < 8.1755] w=0.3612 to align
# Constraint # added constraint: constraint((T0314)S36.CB, (T0314)I83.CB) [> 4.7453 = 7.9088 < 10.2815] w=0.3612 to align
# Constraint # added constraint: constraint((T0314)F37.CB, (T0314)T47.CB) [> 4.1144 = 6.8573 < 8.9146] w=0.3594 to align
# Constraint # added constraint: constraint((T0314)I29.CB, (T0314)T47.CB) [> 3.8153 = 6.3588 < 8.2664] w=0.3579 to align
# Constraint # added constraint: constraint((T0314)V53.CB, (T0314)M62.CB) [> 3.0656 = 5.1093 < 6.6421] w=0.3564 to align
# Constraint # added constraint: constraint((T0314)L15.CB, (T0314)L72.CB) [> 2.3664 = 3.9440 < 5.1272] w=0.3544 to align
# Constraint # added constraint: constraint((T0314)L15.CB, (T0314)I71.CB) [> 3.9683 = 6.6137 < 8.5979] w=0.3544 to align
# Constraint # added constraint: constraint((T0314)L15.CB, (T0314)Q68.CB) [> 3.3770 = 5.6283 < 7.3169] w=0.3544 to align
# Constraint # added constraint: constraint((T0314)A12.CB, (T0314)L72.CB) [> 3.9470 = 6.5784 < 8.5519] w=0.3544 to align
# Constraint # added constraint: constraint((T0314)F32.CB, (T0314)W54.CB) [> 3.5117 = 5.8527 < 7.6086] w=0.3541 to align
# Constraint # added constraint: constraint((T0314)V19.CB, (T0314)S33.CB) [> 3.3414 = 5.5691 < 7.2398] w=0.3493 to align
# Constraint # added constraint: constraint((T0314)V19.CB, (T0314)F32.CB) [> 3.5948 = 5.9913 < 7.7887] w=0.3493 to align
# Constraint # added constraint: constraint((T0314)A14.CB, (T0314)L72.CB) [> 4.3000 = 7.1667 < 9.3168] w=0.3385 to align
# Constraint # added constraint: constraint((T0314)E34.CB, (T0314)S45.CB) [> 4.0583 = 6.7638 < 8.7929] w=0.3382 to align
# Constraint # added constraint: constraint((T0314)F32.CB, (T0314)T49.CB) [> 3.5120 = 5.8534 < 7.6094] w=0.3382 to align
# Constraint # added constraint: constraint((T0314)R31.CB, (T0314)P48.CB) [> 4.3799 = 7.2999 < 9.4899] w=0.3382 to align
# Constraint # added constraint: constraint((T0314)S5.CB, (T0314)Y28.CB) [> 4.1040 = 6.8400 < 8.8920] w=0.3223 to align
# Constraint # added constraint: constraint((T0314)V30.CB, (T0314)T49.CB) [> 4.1857 = 6.9762 < 9.0690] w=0.3204 to align
# Constraint # added constraint: constraint((T0314)I29.CB, (T0314)P48.CB) [> 3.9842 = 6.6404 < 8.6325] w=0.3204 to align
# Constraint # added constraint: constraint((T0314)L91.CB, (T0314)T100.CB) [> 3.5272 = 5.8787 < 7.6423] w=0.3184 to align
# Constraint # added constraint: constraint((T0314)Y90.CB, (T0314)A101.CB) [> 4.2060 = 7.0100 < 9.1131] w=0.3184 to align
# Constraint # added constraint: constraint((T0314)V89.CB, (T0314)Q102.CB) [> 3.8106 = 6.3510 < 8.2563] w=0.3184 to align
# Constraint # added constraint: constraint((T0314)F18.CB, (T0314)I83.CB) [> 3.8442 = 6.4070 < 8.3291] w=0.3182 to align
# Constraint # added constraint: constraint((T0314)S33.CB, (T0314)T49.CB) [> 4.3850 = 7.3083 < 9.5008] w=0.3171 to align
# Constraint # added constraint: constraint((T0314)R23.CB, (T0314)L73.CB) [> 4.0443 = 6.7406 < 8.7627] w=0.3075 to align
# Constraint # added constraint: constraint((T0314)I8.CB, (T0314)F18.CB) [> 3.8612 = 6.4354 < 8.3660] w=0.3022 to align
# Constraint # added constraint: constraint((T0314)A12.CB, (T0314)V30.CB) [> 3.8562 = 6.4270 < 8.3552] w=0.2992 to align
# Constraint # added constraint: constraint((T0314)F32.CB, (T0314)G65.CA) [> 4.0999 = 6.8332 < 8.8832] w=0.2960 to align
# Constraint # added constraint: constraint((T0314)F52.CB, (T0314)V61.CB) [> 3.9160 = 6.5267 < 8.4847] w=0.2847 to align
# Constraint # added constraint: constraint((T0314)F52.CB, (T0314)M62.CB) [> 3.7355 = 6.2258 < 8.0935] w=0.2847 to align
# Constraint # added constraint: constraint((T0314)Q70.CB, (T0314)L81.CB) [> 4.6080 = 7.6800 < 9.9840] w=0.2759 to align
# Constraint # added constraint: constraint((T0314)L15.CB, (T0314)S36.CB) [> 4.5330 = 7.5550 < 9.8215] w=0.2753 to align
# Constraint # added constraint: constraint((T0314)L15.CB, (T0314)D44.CB) [> 4.0562 = 6.7604 < 8.7885] w=0.2696 to align
# Constraint # added constraint: constraint((T0314)C9.CB, (T0314)F18.CB) [> 3.7124 = 6.1874 < 8.0436] w=0.2696 to align
# Constraint # added constraint: constraint((T0314)A14.CB, (T0314)Q75.CB) [> 4.5226 = 7.5377 < 9.7990] w=0.2642 to align
# Constraint # added constraint: constraint((T0314)G17.CA, (T0314)L72.CB) [> 4.6495 = 7.7491 < 10.0739] w=0.2642 to align
# Constraint # added constraint: constraint((T0314)F32.CB, (T0314)P48.CB) [> 3.8989 = 6.4982 < 8.4476] w=0.2642 to align
# Constraint # added constraint: constraint((T0314)E34.CB, (T0314)I46.CB) [> 4.4377 = 7.3962 < 9.6151] w=0.2642 to align
# Constraint # added constraint: constraint((T0314)E34.CB, (T0314)P48.CB) [> 3.9367 = 6.5611 < 8.5294] w=0.2642 to align
# Constraint # added constraint: constraint((T0314)S36.CB, (T0314)S45.CB) [> 3.7696 = 6.2826 < 8.1674] w=0.2642 to align
# Constraint # added constraint: constraint((T0314)A42.CB, (T0314)V53.CB) [> 3.7916 = 6.3193 < 8.2151] w=0.2610 to align
# Constraint # added constraint: constraint((T0314)V41.CB, (T0314)V53.CB) [> 4.6746 = 7.7909 < 10.1282] w=0.2610 to align
# Constraint # added constraint: constraint((T0314)P86.CB, (T0314)Q104.CB) [> 3.7396 = 6.2326 < 8.1025] w=0.2607 to align
# Constraint # added constraint: constraint((T0314)L87.CB, (T0314)Q104.CB) [> 4.5861 = 7.6435 < 9.9365] w=0.2607 to align
# Constraint # added constraint: constraint((T0314)L88.CB, (T0314)R103.CB) [> 4.3285 = 7.2141 < 9.3783] w=0.2607 to align
# Constraint # added constraint: constraint((T0314)R31.CB, (T0314)F52.CB) [> 3.7947 = 6.3245 < 8.2218] w=0.2603 to align
# Constraint # added constraint: constraint((T0314)A42.CB, (T0314)L64.CB) [> 3.6303 = 6.0505 < 7.8656] w=0.2596 to align
# Constraint # added constraint: constraint((T0314)I29.CB, (T0314)E51.CB) [> 3.5896 = 5.9827 < 7.7775] w=0.2496 to align
# Constraint # added constraint: constraint((T0314)Y28.CB, (T0314)E51.CB) [> 4.5398 = 7.5664 < 9.8363] w=0.2496 to align
# Constraint # added constraint: constraint((T0314)R27.CB, (T0314)F52.CB) [> 4.5200 = 7.5334 < 9.7934] w=0.2496 to align
# Constraint # added constraint: constraint((T0314)R27.CB, (T0314)E51.CB) [> 3.9917 = 6.6528 < 8.6487] w=0.2496 to align
# Constraint # added constraint: constraint((T0314)I29.CB, (T0314)T49.CB) [> 4.2446 = 7.0744 < 9.1967] w=0.2463 to align
# Constraint # added constraint: constraint((T0314)Y28.CB, (T0314)T49.CB) [> 2.5621 = 4.2702 < 5.5512] w=0.2463 to align
# Constraint # added constraint: constraint((T0314)Y28.CB, (T0314)P48.CB) [> 4.6611 = 7.7685 < 10.0991] w=0.2463 to align
# Constraint # added constraint: constraint((T0314)G38.CA, (T0314)T47.CB) [> 4.4060 = 7.3433 < 9.5463] w=0.2455 to align
# Constraint # added constraint: constraint((T0314)A11.CB, (T0314)D44.CB) [> 4.5042 = 7.5070 < 9.7591] w=0.2449 to align
# Constraint # added constraint: constraint((T0314)L91.CB, (T0314)A101.CB) [> 2.6648 = 4.4413 < 5.7737] w=0.2444 to align
# Constraint # added constraint: constraint((T0314)Y90.CB, (T0314)Q102.CB) [> 2.9835 = 4.9724 < 6.4642] w=0.2444 to align
# Constraint # added constraint: constraint((T0314)I8.CB, (T0314)Y28.CB) [> 4.1114 = 6.8523 < 8.9080] w=0.2418 to align
# Constraint # added constraint: constraint((T0314)I29.CB, (T0314)V61.CB) [> 3.4749 = 5.7916 < 7.5290] w=0.2399 to align
# Constraint # added constraint: constraint((T0314)V30.CB, (T0314)V61.CB) [> 4.6686 = 7.7810 < 10.1153] w=0.2399 to align
# Constraint # added constraint: constraint((T0314)Y90.CB, (T0314)I99.CB) [> 3.7471 = 6.2453 < 8.1188] w=0.2366 to align
# Constraint # added constraint: constraint((T0314)V89.CB, (T0314)A101.CB) [> 4.2283 = 7.0472 < 9.1614] w=0.2366 to align
# Constraint # added constraint: constraint((T0314)V19.CB, (T0314)S56.CB) [> 3.4195 = 5.6992 < 7.4089] w=0.2312 to align
# Constraint # added constraint: constraint((T0314)K16.CB, (T0314)V57.CB) [> 4.5486 = 7.5810 < 9.8553] w=0.2312 to align
# Constraint # added constraint: constraint((T0314)C9.CB, (T0314)V57.CB) [> 4.6785 = 7.7975 < 10.1367] w=0.2312 to align
# Constraint # added constraint: constraint((T0314)G20.CA, (T0314)W54.CB) [> 3.7513 = 6.2522 < 8.1279] w=0.2312 to align
# Constraint # added constraint: constraint((T0314)F21.CB, (T0314)F52.CB) [> 4.2418 = 7.0697 < 9.1906] w=0.2312 to align
# Constraint # added constraint: constraint((T0314)F21.CB, (T0314)V53.CB) [> 4.1215 = 6.8692 < 8.9299] w=0.2312 to align
# Constraint # added constraint: constraint((T0314)F21.CB, (T0314)W54.CB) [> 3.5244 = 5.8741 < 7.6363] w=0.2312 to align
# Constraint # added constraint: constraint((T0314)W54.CB, (T0314)L73.CB) [> 4.4348 = 7.3914 < 9.6088] w=0.2312 to align
# Constraint # added constraint: constraint((T0314)I8.CB, (T0314)G20.CA) [> 3.3247 = 5.5411 < 7.2035] w=0.2281 to align
# Constraint # added constraint: constraint((T0314)V41.CB, (T0314)F52.CB) [> 3.9826 = 6.6377 < 8.6291] w=0.2207 to align
# Constraint # added constraint: constraint((T0314)V30.CB, (T0314)S55.CB) [> 3.5485 = 5.9141 < 7.6883] w=0.2165 to align
# Constraint # added constraint: constraint((T0314)L73.CB, (T0314)L87.CB) [> 4.0639 = 6.7732 < 8.8051] w=0.2154 to align
# Constraint # added constraint: constraint((T0314)V89.CB, (T0314)R103.CB) [> 3.0555 = 5.0924 < 6.6202] w=0.2078 to align
# Constraint # added constraint: constraint((T0314)R27.CB, (T0314)V61.CB) [> 3.2514 = 5.4190 < 7.0447] w=0.2064 to align
# Constraint # added constraint: constraint((T0314)R31.CB, (T0314)D43.CB) [> 2.8292 = 4.7154 < 6.1300] w=0.2064 to align
# Constraint # added constraint: constraint((T0314)L72.CB, (T0314)I83.CB) [> 4.7113 = 7.8522 < 10.2078] w=0.2064 to align
# Constraint # added constraint: constraint((T0314)I8.CB, (T0314)V30.CB) [> 4.3621 = 7.2702 < 9.4512] w=0.2036 to align
# Constraint # added constraint: constraint((T0314)T4.CB, (T0314)N22.CB) [> 3.7006 = 6.1676 < 8.0179] w=0.2035 to align
# Constraint # added constraint: constraint((T0314)S33.CB, (T0314)A42.CB) [> 3.9846 = 6.6411 < 8.6334] w=0.2027 to align
# Constraint # added constraint: constraint((T0314)S5.CB, (T0314)F21.CB) [> 4.0726 = 6.7877 < 8.8240] w=0.1956 to align
# Constraint # added constraint: constraint((T0314)R31.CB, (T0314)S50.CB) [> 3.9680 = 6.6132 < 8.5972] w=0.1909 to align
# Constraint # added constraint: constraint((T0314)V89.CB, (T0314)T100.CB) [> 4.5285 = 7.5475 < 9.8117] w=0.1905 to align
# Constraint # added constraint: constraint((T0314)V41.CB, (T0314)E67.CB) [> 3.7091 = 6.1819 < 8.0365] w=0.1850 to align
# Constraint # added constraint: constraint((T0314)D40.CB, (T0314)G65.CA) [> 3.5257 = 5.8762 < 7.6391] w=0.1850 to align
# Constraint # added constraint: constraint((T0314)M39.CB, (T0314)G65.CA) [> 3.4529 = 5.7549 < 7.4814] w=0.1850 to align
# Constraint # added constraint: constraint((T0314)V19.CB, (T0314)N82.CB) [> 4.5686 = 7.6143 < 9.8986] w=0.1806 to align
# Constraint # added constraint: constraint((T0314)F21.CB, (T0314)L64.CB) [> 3.5310 = 5.8850 < 7.6505] w=0.1806 to align
# Constraint # added constraint: constraint((T0314)L87.CB, (T0314)L105.CB) [> 2.9338 = 4.8897 < 6.3566] w=0.1700 to align
# Constraint # added constraint: constraint((T0314)P86.CB, (T0314)L105.CB) [> 4.4893 = 7.4822 < 9.7269] w=0.1700 to align
# Constraint # added constraint: constraint((T0314)F37.CB, (T0314)I46.CB) [> 3.9490 = 6.5817 < 8.5562] w=0.1695 to align
# Constraint # added constraint: constraint((T0314)E51.CB, (T0314)G65.CA) [> 3.5357 = 5.8928 < 7.6607] w=0.1670 to align
# Constraint # added constraint: constraint((T0314)M39.CB, (T0314)V53.CB) [> 3.6510 = 6.0850 < 7.9105] w=0.1611 to align
# Constraint # added constraint: constraint((T0314)G17.CA, (T0314)D43.CB) [> 3.7652 = 6.2752 < 8.1578] w=0.1587 to align
# Constraint # added constraint: constraint((T0314)R27.CB, (T0314)T49.CB) [> 4.4513 = 7.4188 < 9.6445] w=0.1565 to align
# Constraint # added constraint: constraint((T0314)T4.CB, (T0314)V53.CB) [> 4.4552 = 7.4254 < 9.6530] w=0.1541 to align
# Constraint # added constraint: constraint((T0314)D7.CB, (T0314)G20.CA) [> 4.0874 = 6.8124 < 8.8561] w=0.1541 to align
# Constraint # added constraint: constraint((T0314)I8.CB, (T0314)S55.CB) [> 3.3487 = 5.5812 < 7.2556] w=0.1541 to align
# Constraint # added constraint: constraint((T0314)I8.CB, (T0314)V57.CB) [> 3.8240 = 6.3734 < 8.2854] w=0.1541 to align
# Constraint # added constraint: constraint((T0314)A12.CB, (T0314)Y28.CB) [> 3.6151 = 6.0253 < 7.8328] w=0.1530 to align
# Constraint # added constraint: constraint((T0314)G38.CA, (T0314)V53.CB) [> 4.0075 = 6.6791 < 8.6829] w=0.1500 to align
# Constraint # added constraint: constraint((T0314)D43.CB, (T0314)L64.CB) [> 3.5565 = 5.9276 < 7.7058] w=0.1500 to align
# Constraint # added constraint: constraint((T0314)C9.CB, (T0314)F21.CB) [> 2.8560 = 4.7599 < 6.1879] w=0.1462 to align
# Constraint # added constraint: constraint((T0314)I8.CB, (T0314)T47.CB) [> 4.5979 = 7.6632 < 9.9621] w=0.1462 to align
# Constraint # added constraint: constraint((T0314)S5.CB, (T0314)R23.CB) [> 4.5029 = 7.5049 < 9.7563] w=0.1462 to align
# Constraint # added constraint: constraint((T0314)F37.CB, (T0314)W54.CB) [> 3.8214 = 6.3689 < 8.2796] w=0.1462 to align
# Constraint # added constraint: constraint((T0314)F37.CB, (T0314)F52.CB) [> 4.5947 = 7.6579 < 9.9553] w=0.1462 to align
# Constraint # added constraint: constraint((T0314)A42.CB, (T0314)E51.CB) [> 2.8352 = 4.7254 < 6.1430] w=0.1398 to align
# Constraint # added constraint: constraint((T0314)V30.CB, (T0314)S50.CB) [> 3.3207 = 5.5345 < 7.1949] w=0.1380 to align
# Constraint # added constraint: constraint((T0314)G38.CA, (T0314)S50.CB) [> 4.5417 = 7.5696 < 9.8404] w=0.1380 to align
# Constraint # added constraint: constraint((T0314)V19.CB, (T0314)I83.CB) [> 2.6588 = 4.4313 < 5.7607] w=0.1376 to align
# Constraint # added constraint: constraint((T0314)V30.CB, (T0314)I99.CB) [> 3.9182 = 6.5303 < 8.4894] w=0.1376 to align
# Constraint # added constraint: constraint((T0314)M62.CB, (T0314)I99.CB) [> 4.0053 = 6.6755 < 8.6782] w=0.1376 to align
# Constraint # added constraint: constraint((T0314)P86.CB, (T0314)I99.CB) [> 3.2478 = 5.4130 < 7.0369] w=0.1376 to align
# Constraint # added constraint: constraint((T0314)L88.CB, (T0314)I99.CB) [> 4.4433 = 7.4055 < 9.6271] w=0.1376 to align
# Constraint # added constraint: constraint((T0314)V89.CB, (T0314)L105.CB) [> 3.9205 = 6.5342 < 8.4944] w=0.1347 to align
# Constraint # added constraint: constraint((T0314)P86.CB, (T0314)R106.CB) [> 4.0892 = 6.8153 < 8.8598] w=0.1347 to align
# Constraint # added constraint: constraint((T0314)G84.CA, (T0314)R106.CB) [> 4.1316 = 6.8861 < 8.9519] w=0.1347 to align
# Constraint # added constraint: constraint((T0314)K16.CB, (T0314)G26.CA) [> 4.6986 = 7.8311 < 10.1804] w=0.1317 to align
# Constraint # added constraint: constraint((T0314)M39.CB, (T0314)R80.CB) [> 4.2723 = 7.1205 < 9.2566] w=0.1290 to align
# Constraint # added constraint: constraint((T0314)V41.CB, (T0314)E51.CB) [> 4.0057 = 6.6762 < 8.6791] w=0.1222 to align
# Constraint # added constraint: constraint((T0314)V41.CB, (T0314)S50.CB) [> 3.4813 = 5.8021 < 7.5428] w=0.1110 to align
# Constraint # added constraint: constraint((T0314)F32.CB, (T0314)I71.CB) [> 4.5759 = 7.6266 < 9.9145] w=0.1110 to align
# Constraint # added constraint: constraint((T0314)V30.CB, (T0314)Q68.CB) [> 4.1394 = 6.8990 < 8.9687] w=0.1110 to align
# Constraint # added constraint: constraint((T0314)V30.CB, (T0314)G65.CA) [> 4.0768 = 6.7946 < 8.8330] w=0.1110 to align
# Constraint # added constraint: constraint((T0314)E51.CB, (T0314)V89.CB) [> 3.7140 = 6.1900 < 8.0471] w=0.1110 to align
# Constraint # added constraint: constraint((T0314)S33.CB, (T0314)E51.CB) [> 4.5681 = 7.6135 < 9.8975] w=0.1103 to align
# Constraint # added constraint: constraint((T0314)S33.CB, (T0314)S50.CB) [> 3.8436 = 6.4059 < 8.3277] w=0.1103 to align
# Constraint # added constraint: constraint((T0314)C9.CB, (T0314)L81.CB) [> 2.5679 = 4.2799 < 5.5639] w=0.1096 to align
# Constraint # added constraint: constraint((T0314)D13.CB, (T0314)E74.CB) [> 4.7742 = 7.9570 < 10.3441] w=0.1096 to align
# Constraint # added constraint: constraint((T0314)V41.CB, (T0314)G65.CA) [> 4.4954 = 7.4923 < 9.7400] w=0.1096 to align
# Constraint # added constraint: constraint((T0314)T4.CB, (T0314)T25.CB) [> 3.3167 = 5.5278 < 7.1861] w=0.0956 to align
# Constraint # added constraint: constraint((T0314)S5.CB, (T0314)T25.CB) [> 4.1294 = 6.8823 < 8.9470] w=0.0956 to align
# Constraint # added constraint: constraint((T0314)C9.CB, (T0314)Y28.CB) [> 4.1129 = 6.8548 < 8.9112] w=0.0956 to align
# Constraint # added constraint: constraint((T0314)M39.CB, (T0314)L69.CB) [> 3.9049 = 6.5082 < 8.4606] w=0.0750 to align
# Constraint # added constraint: constraint((T0314)A12.CB, (T0314)S33.CB) [> 3.6518 = 6.0863 < 7.9122] w=0.0740 to align
# Constraint # added constraint: constraint((T0314)F21.CB, (T0314)R93.CB) [> 4.3677 = 7.2796 < 9.4634] w=0.0740 to align
# Constraint # added constraint: constraint((T0314)Q70.CB, (T0314)L91.CB) [> 3.1460 = 5.2434 < 6.8164] w=0.0740 to align
# Constraint # added constraint: constraint((T0314)D7.CB, (T0314)D44.CB) [> 4.2118 = 7.0197 < 9.1256] w=0.0740 to align
# Constraint # added constraint: constraint((T0314)A11.CB, (T0314)S33.CB) [> 4.3172 = 7.1953 < 9.3539] w=0.0740 to align
# Constraint # added constraint: constraint((T0314)A11.CB, (T0314)V41.CB) [> 4.3545 = 7.2575 < 9.4348] w=0.0740 to align
# Constraint # added constraint: constraint((T0314)A11.CB, (T0314)D43.CB) [> 3.4990 = 5.8316 < 7.5810] w=0.0740 to align
# Constraint # added constraint: constraint((T0314)S5.CB, (T0314)I83.CB) [> 4.4222 = 7.3703 < 9.5814] w=0.0731 to align
# Constraint # added constraint: constraint((T0314)T6.CB, (T0314)L81.CB) [> 3.6394 = 6.0656 < 7.8853] w=0.0731 to align
# Constraint # added constraint: constraint((T0314)L91.CB, (T0314)R103.CB) [> 4.7941 = 7.9901 < 10.3871] w=0.0731 to align
# Constraint # added constraint: constraint((T0314)D43.CB, (T0314)L81.CB) [> 3.1507 = 5.2512 < 6.8266] w=0.0725 to align
# Constraint # added constraint: constraint((T0314)D43.CB, (T0314)R80.CB) [> 2.3516 = 3.9193 < 5.0951] w=0.0725 to align
# Constraint # added constraint: constraint((T0314)V30.CB, (T0314)V41.CB) [> 3.4762 = 5.7937 < 7.5318] w=0.0725 to align
# Constraint # added constraint: constraint((T0314)S56.CB, (T0314)L96.CB) [> 4.1143 = 6.8572 < 8.9143] w=0.0725 to align
# Constraint # added constraint: constraint((T0314)V57.CB, (T0314)L96.CB) [> 2.3653 = 3.9422 < 5.1248] w=0.0725 to align
# Constraint # added constraint: constraint((T0314)V19.CB, (T0314)A101.CB) [> 3.3165 = 5.5274 < 7.1856] w=0.0688 to align
# Constraint # added constraint: constraint((T0314)I83.CB, (T0314)A101.CB) [> 3.2039 = 5.3399 < 6.9418] w=0.0688 to align
# Constraint # added constraint: constraint((T0314)N22.CB, (T0314)D43.CB) [> 4.7739 = 7.9565 < 10.3435] w=0.0688 to align
# Constraint # added constraint: constraint((T0314)I29.CB, (T0314)D40.CB) [> 3.5601 = 5.9335 < 7.7135] w=0.0565 to align
# Constraint # added constraint: constraint((T0314)S33.CB, (T0314)G65.CA) [> 2.8280 = 4.7134 < 6.1274] w=0.0565 to align
# Constraint # added constraint: constraint((T0314)G38.CA, (T0314)R80.CB) [> 3.0911 = 5.1519 < 6.6975] w=0.0565 to align
# Constraint # added constraint: constraint((T0314)D40.CB, (T0314)R80.CB) [> 3.5310 = 5.8850 < 7.6505] w=0.0565 to align
# Constraint # added constraint: constraint((T0314)V30.CB, (T0314)L73.CB) [> 3.6649 = 6.1082 < 7.9406] w=0.0529 to align
# Constraint # added constraint: constraint((T0314)D40.CB, (T0314)T49.CB) [> 4.1574 = 6.9291 < 9.0078] w=0.0529 to align
# Constraint # added constraint: constraint((T0314)Q10.CB, (T0314)I46.CB) [> 4.7994 = 7.9990 < 10.3987] w=0.0494 to align
# Constraint # added constraint: constraint((T0314)S50.CB, (T0314)G65.CA) [> 3.9202 = 6.5337 < 8.4938] w=0.0383 to align
# Constraint # added constraint: constraint((T0314)G65.CA, (T0314)L105.CB) [> 4.0270 = 6.7117 < 8.7252] w=0.0353 to align
# Constraint # added constraint: constraint((T0314)L81.CB, (T0314)L105.CB) [> 4.1677 = 6.9461 < 9.0299] w=0.0353 to align
# Constraint # added constraint: constraint((T0314)A11.CB, (T0314)L91.CB) [> 3.9296 = 6.5494 < 8.5142] w=0.0335 to align
# Constraint # added constraint: constraint((T0314)L69.CB, (T0314)G84.CA) [> 4.1377 = 6.8962 < 8.9650] w=0.0335 to align
# Constraint # added constraint: constraint((T0314)Y28.CB, (T0314)G65.CA) [> 3.9410 = 6.5684 < 8.5389] w=0.0335 to align
# Constraint # added constraint: constraint((T0314)A11.CB, (T0314)R93.CB) [> 3.7475 = 6.2458 < 8.1195] w=0.0223 to align
# Constraint # added constraint: constraint((T0314)K24.CB, (T0314)I71.CB) [> 4.3377 = 7.2295 < 9.3984] w=0.0159 to align
# SetCost created cost = 
#	( 1.0000 * align )
# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0314/
# command:# reading script from file servers-clean.under
# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0314/decoys/
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0314 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 84
# 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 T0314 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
# Found a chain break before 91
# copying to AlignedFragments data structure
# naming current conformation 3D-JIGSAW_POPULUS_TS4
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS5.pdb.gz looking for model 1
# Found a chain break before 100
# copying to AlignedFragments data structure
# naming current conformation 3D-JIGSAW_POPULUS_TS5
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0314 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 T0314 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_RECOM_TS2
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0314 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 T0314 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 T0314 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 T0314 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 T0314 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_TS5
# ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1
# Found a chain break before 50
# 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 64
# 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 73
# copying to AlignedFragments data structure
# naming current conformation 3Dpro_TS3
# ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1
# Found a chain break before 70
# copying to AlignedFragments data structure
# naming current conformation 3Dpro_TS4
# ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1
# Found a chain break before 64
# 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 96
# 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 85
# copying to AlignedFragments data structure
# naming current conformation ABIpro_TS2
# ReadConformPDB reading from PDB file servers/ABIpro_TS3.pdb.gz looking for model 1
# naming current conformation ABIpro_TS3
# ReadConformPDB reading from PDB file servers/ABIpro_TS4.pdb.gz looking for model 1
# Found a chain break before 85
# 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 85
# 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 45
# 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 105
# 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 105
# 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 105
# 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 105
# 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 105
# 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 97
# 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 100
# 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 85
# copying to AlignedFragments data structure
# naming current conformation CIRCLE_TS3
# ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0314 can't currently be optimized by undertaker
# 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 96
# 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 T0314 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 T0314 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 T0314 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 T0314 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation CaspIta-FOX_TS4
# ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0314 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 T0314 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 T0314 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 T0314 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 T0314 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 T0314 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 95
# 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 98
# 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 96
# copying to AlignedFragments data structure
# naming current conformation FAMSD_TS3
# ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1
# Found a chain break before 93
# copying to AlignedFragments data structure
# naming current conformation FAMSD_TS4
# ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1
# Found a chain break before 97
# copying to AlignedFragments data structure
# naming current conformation FAMSD_TS5
# ReadConformPDB reading from PDB file servers/FAMS_TS1.pdb.gz looking for model 1
# Found a chain break before 101
# 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 94
# 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 97
# 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 96
# 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 98
# 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 31
# 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 53
# 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 47
# 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 101
# 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 97
# 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 T0314 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FORTE1_AL1
# ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0314 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 T0314 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FORTE1_AL3
# ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0314 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 138, because occupancy 1 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz
Skipped atom 140, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz
Skipped atom 142, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz
Skipped atom 144, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz
Skipped atom 338, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz
Skipped atom 340, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz
Skipped atom 342, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz
Skipped atom 344, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz
# WARNING: incomplete conformation T0314 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 T0314 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FORTE2_AL1
# ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0314 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 T0314 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FORTE2_AL3
# ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1
Skipped atom 138, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 140, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 142, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 144, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 338, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 340, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 342, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 344, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
# WARNING: incomplete conformation T0314 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FORTE2_AL4
# ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0314 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
# 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 105
# 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 47
# 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 90
# 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 105
# copying to AlignedFragments data structure
# naming current conformation FPSOLVER-SERVER_TS5
# ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0314 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 T0314 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 T0314 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 T0314 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FUGUE_AL4
# ReadConformPDB reading from PDB file servers/FUGUE_AL5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0314 can't currently be optimized by undertaker
# naming current conformation FUGUE_AL5
# ReadConformPDB reading from PDB file servers/FUNCTION_TS1.pdb.gz looking for model 1
# Found a chain break before 99
# copying to AlignedFragments data structure
# naming current conformation FUNCTION_TS1
# ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0314 can't currently be optimized by undertaker
# naming current conformation FUNCTION_TS2
# ReadConformPDB reading from PDB file servers/FUNCTION_TS3.pdb.gz looking for model 1
# Found a chain break before 102
# 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 94
# copying to AlignedFragments data structure
# naming current conformation FUNCTION_TS4
# ReadConformPDB reading from PDB file servers/FUNCTION_TS5.pdb.gz looking for model 1
# Found a chain break before 96
# copying to AlignedFragments data structure
# naming current conformation FUNCTION_TS5
# ReadConformPDB reading from PDB file servers/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 82
# copying to AlignedFragments data structure
# naming current conformation GeneSilicoMetaServer_TS2
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1
# naming current conformation GeneSilicoMetaServer_TS3
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1
# Found a chain break before 45
# 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 16
# 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 T0314 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 T0314 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 T0314 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# 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 T0314 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 T0314 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 T0314 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 T0314 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 T0314 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 T0314 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 T0314 can't currently be optimized by undertaker
# naming current conformation LOOPP_TS5
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1
# Found a chain break before 79
# 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 29
# 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 95
# 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
# 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 42
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server_TS5
# ReadConformPDB reading from PDB file servers/MetaTasser_TS1.pdb.gz looking for model 1
# Found a chain break before 105
# copying to AlignedFragments data structure
# naming current conformation MetaTasser_TS1
# ReadConformPDB reading from PDB file servers/MetaTasser_TS2.pdb.gz looking for model 1
# Found a chain break before 105
# copying to AlignedFragments data structure
# naming current conformation MetaTasser_TS2
# ReadConformPDB reading from PDB file servers/MetaTasser_TS3.pdb.gz looking for model 1
# Found a chain break before 105
# copying to AlignedFragments data structure
# naming current conformation MetaTasser_TS3
# ReadConformPDB reading from PDB file servers/MetaTasser_TS4.pdb.gz looking for model 1
# Found a chain break before 105
# 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 102
# 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 T0314 can't currently be optimized by undertaker
# naming current conformation NN_PUT_lab_TS1
# ReadConformPDB reading from PDB file servers/POMYSL_TS1.pdb.gz looking for model 1
WARNING: atom 1 has residue number 10  < previous residue 106  in servers/POMYSL_TS1.pdb.gz
# WARNING: incomplete conformation T0314 can't currently be optimized by undertaker
# naming current conformation POMYSL_TS1
# ReadConformPDB reading from PDB file servers/POMYSL_TS2.pdb.gz looking for model 1
WARNING: atom 1 has residue number 10  < previous residue 106  in servers/POMYSL_TS2.pdb.gz
# WARNING: incomplete conformation T0314 can't currently be optimized by undertaker
# naming current conformation POMYSL_TS2
# ReadConformPDB reading from PDB file servers/POMYSL_TS3.pdb.gz looking for model 1
# Found a chain break before 32
# 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 98
# 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 103
# 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
# Found a chain break before 100
# 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
# Found a chain break before 97
# 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 86
# 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 98
# copying to AlignedFragments data structure
# naming current conformation PROTINFO_TS3
# ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1
# naming current conformation PROTINFO_TS4
# ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1
# naming current conformation PROTINFO_TS5
# ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1
# naming current conformation Pcons6_TS1
# ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0314 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 95
# copying to AlignedFragments data structure
# naming current conformation Pcons6_TS3
# ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1
# naming current conformation Pcons6_TS4
# ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1
# Found a chain break before 97
# copying to AlignedFragments data structure
# naming current conformation Pcons6_TS5
# ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0314 can't currently be optimized by undertaker
# naming current conformation Phyre-1_TS1
# ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1
# Found a chain break before 96
# copying to AlignedFragments data structure
# naming current conformation Pmodeller6_TS1
# ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1
# naming current conformation Pmodeller6_TS2
# ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0314 can't currently be optimized by undertaker
# naming current conformation Pmodeller6_TS3
# ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0314 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 97
# 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
# naming current conformation RAPTOR-ACE_TS1
# ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1
# naming current conformation RAPTOR-ACE_TS2
# ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1
# Found a chain break before 51
# copying to AlignedFragments data structure
# naming current conformation RAPTOR-ACE_TS3
# ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS4.pdb.gz looking for model 1
# naming current conformation RAPTOR-ACE_TS4
# ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1
# Found a chain break before 82
# 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 87
# copying to AlignedFragments data structure
# naming current conformation RAPTORESS_TS1
# ReadConformPDB reading from PDB file servers/RAPTORESS_TS2.pdb.gz looking for model 1
# Found a chain break before 103
# copying to AlignedFragments data structure
# naming current conformation RAPTORESS_TS2
# ReadConformPDB reading from PDB file servers/RAPTORESS_TS3.pdb.gz looking for model 1
# Found a chain break before 83
# 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 85
# copying to AlignedFragments data structure
# naming current conformation RAPTORESS_TS4
# ReadConformPDB reading from PDB file servers/RAPTORESS_TS5.pdb.gz looking for model 1
# 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 18
# copying to AlignedFragments data structure
# naming current conformation RAPTOR_TS2
# ReadConformPDB reading from PDB file servers/RAPTOR_TS3.pdb.gz looking for model 1
# Found a chain break before 15
# copying to AlignedFragments data structure
# naming current conformation RAPTOR_TS3
# ReadConformPDB reading from PDB file servers/RAPTOR_TS4.pdb.gz looking for model 1
# Found a chain break before 78
# 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
# naming current conformation ROBETTA_TS1
# ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1
# Found a chain break before 1
# copying to AlignedFragments data structure
# naming current conformation ROBETTA_TS2
# ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1
# naming current conformation ROBETTA_TS3
# ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1
# naming current conformation ROBETTA_TS4
# ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1
# naming current conformation ROBETTA_TS5
# ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0314 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 T0314 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 T0314 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 T0314 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 T0314 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 T0314 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 T0314 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 T0314 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 T0314 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 T0314 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 96
# 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 T0314 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 T0314 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 T0314 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 T0314 can't currently be optimized by undertaker
# naming current conformation SAM_T06_server_TS5
# ReadConformPDB reading from PDB file servers/SP3_TS1.pdb.gz looking for model 1
# Found a chain break before 38
# copying to AlignedFragments data structure
# naming current conformation SP3_TS1
# ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1
# naming current conformation SP3_TS2
# ReadConformPDB reading from PDB file servers/SP3_TS3.pdb.gz looking for model 1
# naming current conformation SP3_TS3
# ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1
# Found a chain break before 58
# 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 29
# copying to AlignedFragments data structure
# naming current conformation SP3_TS5
# ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1
# naming current conformation SP4_TS1
# ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1
# naming current conformation SP4_TS2
# ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1
# naming current conformation SP4_TS3
# ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1
# naming current conformation SP4_TS4
# ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1
# Found a chain break before 32
# copying to AlignedFragments data structure
# naming current conformation SP4_TS5
# ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1
# Found a chain break before 79
# copying to AlignedFragments data structure
# naming current conformation SPARKS2_TS1
# ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1
# Found a chain break before 30
# copying to AlignedFragments data structure
# naming current conformation SPARKS2_TS2
# ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1
# naming current conformation SPARKS2_TS3
# ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1
# naming current conformation SPARKS2_TS4
# ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1
# naming current conformation SPARKS2_TS5
# ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0314 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 T0314 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 T0314 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 T0314 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 T0314 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 T0314 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 T0314 can't currently be optimized by undertaker
# naming current conformation UNI-EID_sfst_AL1
# ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL2.pdb.gz looking for model 1
Skipped atom 54, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz
Skipped atom 56, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz
Skipped atom 58, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz
Skipped atom 60, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz
Skipped atom 206, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz
Skipped atom 208, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz
Skipped atom 210, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz
Skipped atom 212, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz
# WARNING: incomplete conformation T0314 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 T0314 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 T0314 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 T0314 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 95
# 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 76
# 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 95
# 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 104
# 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 96
# 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 T0314 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 T0314 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 T0314 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 T0314 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
Skipped atom 6, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 8, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 10, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 12, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 238, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 240, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 242, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 244, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 278, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 280, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 282, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 284, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 338, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 340, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 342, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 344, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 346, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 348, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 350, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 352, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 402, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 404, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 406, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 408, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
# WARNING: incomplete conformation T0314 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 T0314 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 T0314 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 91
# 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 54
# 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 22
# 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
# 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 46
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.2_TS5
# ReadConformPDB reading from PDB file servers/karypis.srv.4_TS1.pdb.gz looking for model 1
# Found a chain break before 103
# 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: (T0314)R103.O and (T0314)Q104.N only 0.000 apart, marking (T0314)Q104.N as missing
# WARNING: incomplete conformation T0314 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 103
# 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 103
# 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 103
# 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 T0314 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation karypis.srv_TS1
# ReadConformPDB reading from PDB file servers/karypis.srv_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0314 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 T0314 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 T0314 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 T0314 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 33
# 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 61
# 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 72
# copying to AlignedFragments data structure
# naming current conformation keasar-server_TS3
# ReadConformPDB reading from PDB file servers/keasar-server_TS4.pdb.gz looking for model 1
# Found a chain break before 7
# copying to AlignedFragments data structure
# naming current conformation keasar-server_TS4
# ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1
# Found a chain break before 49
# 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 T0314 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 T0314 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation nFOLD_TS1
# ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0314 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 T0314 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation nFOLD_TS3
# ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0314 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 T0314 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 T0314 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 T0314 can't currently be optimized by undertaker
# naming current conformation shub_TS1
# command:Using radius: 8.0000
Metaserver mode
NUMB_ALIGNS: 239
model score 1.8984
model score 2.2201
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Adding 4301 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: -203.6829, CN propb: -203.6829 weights: 0.3239 constraints: 295
# command:Found ConstraintSet
# PrintContacts align.constraints_meta02
Number of constraints in align2.constraints 295
# command:Found ConstraintSet
# PrintContacts align_bonus.constraints_meta02
Number of constraints in align2.constraints.bonus 295
# command:Found ConstraintSet
# PrintContacts rejected.constraints_meta02
Number of constraints in rejected2.constraints 4006
# command:Found ConstraintSet
# PrintContacts rejected_bonus.constraints_meta02
Number of constraints in rejected2.constraints.bonus 4006
# 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 4301
# command: