# 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/T0290/
# command:# Making conformation for sequence T0290 numbered 1 through 173
Created new target T0290 from T0290.a2m
# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0290/
# command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0290//projects/compbio/experiments/protein-predict/casp7/T0290/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0290//projects/compbio/experiments/protein-predict/casp7/T0290/align.constraints_v3.costfcn.gz for input
Trying /projects/compbio/experiments/protein-predict/casp7/T0290/align.constraints_v3.costfcn
# reading script from file /projects/compbio/experiments/protein-predict/casp7/T0290/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((T0290)E21.CB, (T0290)Q137.CB) [> 3.2562 = 5.4270 < 7.0551] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)E21.CB, (T0290)I139.CB) [> 2.8661 = 4.7768 < 6.2098] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)L22.CB, (T0290)C31.CB) [> 2.5507 = 4.2512 < 5.5265] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)L22.CB, (T0290)F135.CB) [> 3.7903 = 6.3171 < 8.2123] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)L22.CB, (T0290)G136.CA) [> 3.1534 = 5.2557 < 6.8324] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)F23.CB, (T0290)F135.CB) [> 3.4589 = 5.7648 < 7.4942] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)F23.CB, (T0290)G136.CA) [> 3.0674 = 5.1123 < 6.6460] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)C27.CB, (T0290)F135.CB) [> 2.5907 = 4.3178 < 5.6132] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)T30.CB, (T0290)V133.CB) [> 3.3028 = 5.5046 < 7.1560] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)T30.CB, (T0290)F135.CB) [> 2.5255 = 4.2092 < 5.4720] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)C31.CB, (T0290)F135.CB) [> 3.2590 = 5.4317 < 7.0612] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)F34.CB, (T0290)F118.CB) [> 4.1770 = 6.9616 < 9.0501] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)L37.CB, (T0290)Y54.CB) [> 3.3148 = 5.5247 < 7.1821] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)L37.CB, (T0290)S116.CB) [> 3.4156 = 5.6927 < 7.4005] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)C38.CB, (T0290)Y54.CB) [> 3.4173 = 5.6956 < 7.4042] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)C38.CB, (T0290)C168.CB) [> 2.6698 = 4.4496 < 5.7845] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)C38.CB, (T0290)G169.CA) [> 3.0407 = 5.0678 < 6.5882] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)P14.CB, (T0290)L166.CB) [> 3.9412 = 6.5686 < 8.5392] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)A15.CB, (T0290)V144.CB) [> 3.4379 = 5.7298 < 7.4487] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)G16.CA, (T0290)V144.CB) [> 2.8944 = 4.8240 < 6.2712] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)R17.CB, (T0290)G141.CA) [> 4.0283 = 6.7138 < 8.7279] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)R17.CB, (T0290)V144.CB) [> 4.0476 = 6.7460 < 8.7698] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)V18.CB, (T0290)V138.CB) [> 3.6527 = 6.0878 < 7.9141] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)V18.CB, (T0290)S140.CB) [> 4.2217 = 7.0363 < 9.1471] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)V18.CB, (T0290)G141.CA) [> 3.0189 = 5.0316 < 6.5410] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)V18.CB, (T0290)V144.CB) [> 3.0907 = 5.1511 < 6.6965] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)V18.CB, (T0290)V145.CB) [> 3.7070 = 6.1783 < 8.0318] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)V19.CB, (T0290)V138.CB) [> 4.2846 = 7.1410 < 9.2833] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)V19.CB, (T0290)I139.CB) [> 3.0133 = 5.0222 < 6.5289] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)V19.CB, (T0290)S140.CB) [> 2.3452 = 3.9086 < 5.0812] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)V19.CB, (T0290)G141.CA) [> 3.9244 = 6.5407 < 8.5030] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)F20.CB, (T0290)G136.CA) [> 3.5451 = 5.9085 < 7.6810] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)F20.CB, (T0290)Q137.CB) [> 4.0205 = 6.7009 < 8.7111] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)F20.CB, (T0290)V138.CB) [> 3.5152 = 5.8586 < 7.6162] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)E21.CB, (T0290)G136.CA) [> 3.5101 = 5.8501 < 7.6052] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)D72.CB, (T0290)Q117.CB) [> 3.1800 = 5.3000 < 6.8900] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)F88.CB, (T0290)D112.CB) [> 4.1557 = 6.9262 < 9.0040] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)E92.CB, (T0290)V133.CB) [> 3.2343 = 5.3905 < 7.0076] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)A100.CB, (T0290)P124.CB) [> 3.0294 = 5.0491 < 6.5638] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)A101.CB, (T0290)T121.CB) [> 3.5455 = 5.9092 < 7.6819] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)L103.CB, (T0290)T121.CB) [> 2.8681 = 4.7801 < 6.2141] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)L103.CB, (T0290)V134.CB) [> 3.4660 = 5.7766 < 7.5096] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)L103.CB, (T0290)G136.CA) [> 3.9424 = 6.5706 < 8.5418] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)L103.CB, (T0290)Q137.CB) [> 3.2967 = 5.4945 < 7.1428] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)L104.CB, (T0290)F118.CB) [> 3.6917 = 6.1528 < 7.9987] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)L104.CB, (T0290)V134.CB) [> 4.2023 = 7.0038 < 9.1050] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)N114.CB, (T0290)V133.CB) [> 4.0180 = 6.6967 < 8.7057] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)T122.CB, (T0290)V145.CB) [> 3.8903 = 6.4839 < 8.4290] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)Q151.CB, (T0290)A161.CB) [> 3.4917 = 5.8194 < 7.5652] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)Y54.CB, (T0290)I165.CB) [> 3.0905 = 5.1508 < 6.6960] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)K55.CB, (T0290)I165.CB) [> 3.7827 = 6.3045 < 8.1958] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)K55.CB, (T0290)S167.CB) [> 3.4900 = 5.8166 < 7.5616] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)K55.CB, (T0290)C168.CB) [> 3.5178 = 5.8630 < 7.6219] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)S56.CB, (T0290)I165.CB) [> 4.1827 = 6.9712 < 9.0626] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)C57.CB, (T0290)G71.CA) [> 2.9988 = 4.9981 < 6.4975] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)C57.CB, (T0290)D72.CB) [> 4.0427 = 6.7378 < 8.7591] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)C57.CB, (T0290)I165.CB) [> 3.0556 = 5.0928 < 6.6206] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)D65.CB, (T0290)T122.CB) [> 3.9070 = 6.5117 < 8.4652] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)D65.CB, (T0290)K123.CB) [> 3.4403 = 5.7339 < 7.4541] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)F66.CB, (T0290)T122.CB) [> 3.8572 = 6.4288 < 8.3574] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)F66.CB, (T0290)K123.CB) [> 3.6556 = 6.0926 < 7.9204] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)G71.CA, (T0290)S116.CB) [> 3.1466 = 5.2444 < 6.8177] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)G71.CA, (T0290)Q117.CB) [> 2.9337 = 4.8895 < 6.3564] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)G71.CA, (T0290)F118.CB) [> 3.6328 = 6.0547 < 7.8712] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)D72.CB, (T0290)S116.CB) [> 4.0053 = 6.6755 < 8.6782] w=1.0000 to align
# Constraint # added constraint: constraint((T0290)H98.CB, (T0290)D129.CB) [> 3.4018 = 5.6697 < 7.3706] w=0.9986 to align
# Constraint # added constraint: constraint((T0290)D91.CB, (T0290)V133.CB) [> 3.1673 = 5.2789 < 6.8625] w=0.9971 to align
# Constraint # added constraint: constraint((T0290)H98.CB, (T0290)V134.CB) [> 3.7559 = 6.2598 < 8.1377] w=0.9971 to align
# Constraint # added constraint: constraint((T0290)F20.CB, (T0290)I139.CB) [> 3.8945 = 6.4909 < 8.4381] w=0.9957 to align
# Constraint # added constraint: constraint((T0290)L22.CB, (T0290)F34.CB) [> 3.8243 = 6.3739 < 8.2860] w=0.9957 to align
# Constraint # added constraint: constraint((T0290)L22.CB, (T0290)R35.CB) [> 3.8695 = 6.4492 < 8.3839] w=0.9957 to align
# Constraint # added constraint: constraint((T0290)C27.CB, (T0290)V134.CB) [> 4.4991 = 7.4986 < 9.7481] w=0.9957 to align
# Constraint # added constraint: constraint((T0290)F34.CB, (T0290)F135.CB) [> 3.9291 = 6.5485 < 8.5131] w=0.9957 to align
# Constraint # added constraint: constraint((T0290)C57.CB, (T0290)G70.CA) [> 3.9062 = 6.5104 < 8.4635] w=0.9957 to align
# Constraint # added constraint: constraint((T0290)H60.CB, (T0290)Q69.CB) [> 4.0220 = 6.7033 < 8.7143] w=0.9957 to align
# Constraint # added constraint: constraint((T0290)H60.CB, (T0290)G70.CA) [> 3.5158 = 5.8597 < 7.6176] w=0.9957 to align
# Constraint # added constraint: constraint((T0290)R61.CB, (T0290)G70.CA) [> 4.1500 = 6.9167 < 8.9917] w=0.9957 to align
# Constraint # added constraint: constraint((T0290)V62.CB, (T0290)I148.CB) [> 3.7961 = 6.3269 < 8.2250] w=0.9957 to align
# Constraint # added constraint: constraint((T0290)V62.CB, (T0290)E149.CB) [> 3.6938 = 6.1564 < 8.0033] w=0.9957 to align
# Constraint # added constraint: constraint((T0290)V62.CB, (T0290)Q151.CB) [> 3.7130 = 6.1883 < 8.0448] w=0.9957 to align
# Constraint # added constraint: constraint((T0290)V62.CB, (T0290)P159.CB) [> 3.2360 = 5.3934 < 7.0114] w=0.9957 to align
# Constraint # added constraint: constraint((T0290)F66.CB, (T0290)T125.CB) [> 4.1500 = 6.9167 < 8.9918] w=0.9957 to align
# Constraint # added constraint: constraint((T0290)Q69.CB, (T0290)Q117.CB) [> 3.8984 = 6.4973 < 8.4465] w=0.9957 to align
# Constraint # added constraint: constraint((T0290)Q69.CB, (T0290)F118.CB) [> 4.2978 = 7.1630 < 9.3118] w=0.9957 to align
# Constraint # added constraint: constraint((T0290)G70.CA, (T0290)Q117.CB) [> 3.4581 = 5.7635 < 7.4926] w=0.9957 to align
# Constraint # added constraint: constraint((T0290)G70.CA, (T0290)F118.CB) [> 3.7042 = 6.1737 < 8.0258] w=0.9957 to align
# Constraint # added constraint: constraint((T0290)K97.CB, (T0290)V134.CB) [> 3.8573 = 6.4288 < 8.3575] w=0.9957 to align
# Constraint # added constraint: constraint((T0290)Q151.CB, (T0290)F160.CB) [> 3.9316 = 6.5526 < 8.5184] w=0.9957 to align
# Constraint # added constraint: constraint((T0290)F102.CB, (T0290)T121.CB) [> 4.0093 = 6.6822 < 8.6869] w=0.9855 to align
# Constraint # added constraint: constraint((T0290)F102.CB, (T0290)Q137.CB) [> 3.3283 = 5.5472 < 7.2114] w=0.9855 to align
# Constraint # added constraint: constraint((T0290)F102.CB, (T0290)V138.CB) [> 2.3170 = 3.8617 < 5.0202] w=0.9855 to align
# Constraint # added constraint: constraint((T0290)K29.CB, (T0290)F89.CB) [> 3.9927 = 6.6545 < 8.6509] w=0.9855 to align
# Constraint # added constraint: constraint((T0290)L104.CB, (T0290)G136.CA) [> 2.4296 = 4.0493 < 5.2641] w=0.9566 to align
# Constraint # added constraint: constraint((T0290)A101.CB, (T0290)T122.CB) [> 3.3180 = 5.5300 < 7.1890] w=0.9566 to align
# Constraint # added constraint: constraint((T0290)M67.CB, (T0290)F119.CB) [> 2.6495 = 4.4159 < 5.7407] w=0.9565 to align
# Constraint # added constraint: constraint((T0290)M67.CB, (T0290)I120.CB) [> 3.7023 = 6.1705 < 8.0216] w=0.9565 to align
# Constraint # added constraint: constraint((T0290)M67.CB, (T0290)T121.CB) [> 3.0019 = 5.0032 < 6.5041] w=0.9565 to align
# Constraint # added constraint: constraint((T0290)M67.CB, (T0290)T122.CB) [> 3.5766 = 5.9609 < 7.7492] w=0.9565 to align
# Constraint # added constraint: constraint((T0290)V68.CB, (T0290)F119.CB) [> 3.7543 = 6.2572 < 8.1344] w=0.9565 to align
# Constraint # added constraint: constraint((T0290)V68.CB, (T0290)I120.CB) [> 3.0305 = 5.0508 < 6.5661] w=0.9565 to align
# Constraint # added constraint: constraint((T0290)V68.CB, (T0290)T122.CB) [> 4.1484 = 6.9140 < 8.9882] w=0.9565 to align
# Constraint # added constraint: constraint((T0290)V68.CB, (T0290)I148.CB) [> 3.2491 = 5.4152 < 7.0397] w=0.9565 to align
# Constraint # added constraint: constraint((T0290)I120.CB, (T0290)V138.CB) [> 3.8901 = 6.4835 < 8.4286] w=0.9565 to align
# Constraint # added constraint: constraint((T0290)I120.CB, (T0290)V145.CB) [> 3.3487 = 5.5812 < 7.2555] w=0.9565 to align
# Constraint # added constraint: constraint((T0290)C57.CB, (T0290)R164.CB) [> 4.2481 = 7.0802 < 9.2042] w=0.9565 to align
# Constraint # added constraint: constraint((T0290)I148.CB, (T0290)V163.CB) [> 3.2790 = 5.4650 < 7.1045] w=0.9565 to align
# Constraint # added constraint: constraint((T0290)F66.CB, (T0290)T121.CB) [> 4.5223 = 7.5371 < 9.7983] w=0.9565 to align
# Constraint # added constraint: constraint((T0290)F89.CB, (T0290)D112.CB) [> 4.3748 = 7.2913 < 9.4786] w=0.9565 to align
# Constraint # added constraint: constraint((T0290)S105.CB, (T0290)F118.CB) [> 3.9819 = 6.6365 < 8.6274] w=0.9565 to align
# Constraint # added constraint: constraint((T0290)S105.CB, (T0290)H132.CB) [> 2.7990 = 4.6649 < 6.0644] w=0.9565 to align
# Constraint # added constraint: constraint((T0290)S105.CB, (T0290)V133.CB) [> 3.8185 = 6.3642 < 8.2735] w=0.9565 to align
# Constraint # added constraint: constraint((T0290)S105.CB, (T0290)F135.CB) [> 4.1140 = 6.8566 < 8.9136] w=0.9565 to align
# Constraint # added constraint: constraint((T0290)M106.CB, (T0290)F118.CB) [> 3.4592 = 5.7653 < 7.4949] w=0.9565 to align
# Constraint # added constraint: constraint((T0290)M106.CB, (T0290)H132.CB) [> 3.5169 = 5.8615 < 7.6199] w=0.9565 to align
# Constraint # added constraint: constraint((T0290)A107.CB, (T0290)H132.CB) [> 4.2497 = 7.0828 < 9.2077] w=0.9565 to align
# Constraint # added constraint: constraint((T0290)A15.CB, (T0290)I148.CB) [> 3.9550 = 6.5917 < 8.5692] w=0.9565 to align
# Constraint # added constraint: constraint((T0290)A15.CB, (T0290)E147.CB) [> 3.2974 = 5.4956 < 7.1443] w=0.9565 to align
# Constraint # added constraint: constraint((T0290)V26.CB, (T0290)V96.CB) [> 3.7155 = 6.1925 < 8.0503] w=0.9565 to align
# Constraint # added constraint: constraint((T0290)N33.CB, (T0290)G115.CA) [> 4.3920 = 7.3200 < 9.5161] w=0.9565 to align
# Constraint # added constraint: constraint((T0290)Y54.CB, (T0290)G71.CA) [> 3.4901 = 5.8169 < 7.5620] w=0.9565 to align
# Constraint # added constraint: constraint((T0290)H60.CB, (T0290)D72.CB) [> 3.6442 = 6.0737 < 7.8958] w=0.9565 to align
# Constraint # added constraint: constraint((T0290)F20.CB, (T0290)L104.CB) [> 3.4119 = 5.6866 < 7.3925] w=0.9551 to align
# Constraint # added constraint: constraint((T0290)F89.CB, (T0290)N114.CB) [> 3.2275 = 5.3792 < 6.9929] w=0.9551 to align
# Constraint # added constraint: constraint((T0290)L104.CB, (T0290)V138.CB) [> 4.2070 = 7.0116 < 9.1151] w=0.9551 to align
# Constraint # added constraint: constraint((T0290)N108.CB, (T0290)H132.CB) [> 3.8860 = 6.4766 < 8.4196] w=0.9551 to align
# Constraint # added constraint: constraint((T0290)A107.CB, (T0290)Q117.CB) [> 2.4262 = 4.0437 < 5.2568] w=0.9551 to align
# Constraint # added constraint: constraint((T0290)L103.CB, (T0290)I120.CB) [> 4.2725 = 7.1208 < 9.2571] w=0.9536 to align
# Constraint # added constraint: constraint((T0290)G70.CA, (T0290)F119.CB) [> 4.1218 = 6.8697 < 8.9306] w=0.9522 to align
# Constraint # added constraint: constraint((T0290)Q69.CB, (T0290)F119.CB) [> 2.4605 = 4.1009 < 5.3312] w=0.9522 to align
# Constraint # added constraint: constraint((T0290)N33.CB, (T0290)N114.CB) [> 4.5301 = 7.5502 < 9.8153] w=0.9522 to align
# Constraint # added constraint: constraint((T0290)C27.CB, (T0290)V133.CB) [> 3.7312 = 6.2187 < 8.0843] w=0.9522 to align
# Constraint # added constraint: constraint((T0290)F102.CB, (T0290)Q142.CB) [> 3.1817 = 5.3028 < 6.8936] w=0.9406 to align
# Constraint # added constraint: constraint((T0290)A101.CB, (T0290)P124.CB) [> 4.1311 = 6.8851 < 8.9507] w=0.9406 to align
# Constraint # added constraint: constraint((T0290)A101.CB, (T0290)K123.CB) [> 3.4717 = 5.7862 < 7.5220] w=0.9406 to align
# Constraint # added constraint: constraint((T0290)L104.CB, (T0290)I120.CB) [> 3.4622 = 5.7704 < 7.5015] w=0.9406 to align
# Constraint # added constraint: constraint((T0290)A101.CB, (T0290)Q142.CB) [> 4.2876 = 7.1460 < 9.2899] w=0.9391 to align
# Constraint # added constraint: constraint((T0290)F102.CB, (T0290)I120.CB) [> 4.0575 = 6.7625 < 8.7913] w=0.9377 to align
# Constraint # added constraint: constraint((T0290)C38.CB, (T0290)E170.CB) [> 3.6471 = 6.0785 < 7.9020] w=0.9131 to align
# Constraint # added constraint: constraint((T0290)R35.CB, (T0290)E170.CB) [> 3.6040 = 6.0068 < 7.8088] w=0.9131 to align
# Constraint # added constraint: constraint((T0290)M106.CB, (T0290)V133.CB) [> 2.7998 = 4.6663 < 6.0662] w=0.9131 to align
# Constraint # added constraint: constraint((T0290)S105.CB, (T0290)V134.CB) [> 2.8492 = 4.7487 < 6.1733] w=0.9131 to align
# Constraint # added constraint: constraint((T0290)F59.CB, (T0290)P159.CB) [> 3.9543 = 6.5906 < 8.5678] w=0.9130 to align
# Constraint # added constraint: constraint((T0290)F59.CB, (T0290)I148.CB) [> 3.7774 = 6.2957 < 8.1844] w=0.9130 to align
# Constraint # added constraint: constraint((T0290)S105.CB, (T0290)F119.CB) [> 3.5817 = 5.9696 < 7.7604] w=0.9130 to align
# Constraint # added constraint: constraint((T0290)V68.CB, (T0290)V145.CB) [> 3.8021 = 6.3369 < 8.2380] w=0.9130 to align
# Constraint # added constraint: constraint((T0290)G16.CA, (T0290)G141.CA) [> 4.4457 = 7.4095 < 9.6323] w=0.9130 to align
# Constraint # added constraint: constraint((T0290)L104.CB, (T0290)F119.CB) [> 4.5457 = 7.5762 < 9.8491] w=0.9130 to align
# Constraint # added constraint: constraint((T0290)M106.CB, (T0290)Q117.CB) [> 4.2518 = 7.0863 < 9.2122] w=0.9130 to align
# Constraint # added constraint: constraint((T0290)S56.CB, (T0290)R164.CB) [> 3.9711 = 6.6185 < 8.6040] w=0.9130 to align
# Constraint # added constraint: constraint((T0290)V96.CB, (T0290)V134.CB) [> 2.2415 = 3.7358 < 4.8566] w=0.9117 to align
# Constraint # added constraint: constraint((T0290)A107.CB, (T0290)F118.CB) [> 3.5190 = 5.8650 < 7.6245] w=0.9116 to align
# Constraint # added constraint: constraint((T0290)M106.CB, (T0290)F135.CB) [> 3.9337 = 6.5561 < 8.5230] w=0.9116 to align
# Constraint # added constraint: constraint((T0290)S105.CB, (T0290)T121.CB) [> 4.1158 = 6.8597 < 8.9176] w=0.9116 to align
# Constraint # added constraint: constraint((T0290)T30.CB, (T0290)M106.CB) [> 3.7819 = 6.3031 < 8.1941] w=0.9116 to align
# Constraint # added constraint: constraint((T0290)H98.CB, (T0290)T121.CB) [> 3.4927 = 5.8212 < 7.5675] w=0.9102 to align
# Constraint # added constraint: constraint((T0290)V62.CB, (T0290)V163.CB) [> 4.3001 = 7.1669 < 9.3170] w=0.9088 to align
# Constraint # added constraint: constraint((T0290)N33.CB, (T0290)S83.CB) [> 3.1667 = 5.2777 < 6.8611] w=0.9088 to align
# Constraint # added constraint: constraint((T0290)Q69.CB, (T0290)A107.CB) [> 3.4827 = 5.8046 < 7.5460] w=0.9087 to align
# Constraint # added constraint: constraint((T0290)F59.CB, (T0290)G70.CA) [> 2.8990 = 4.8316 < 6.2811] w=0.9087 to align
# Constraint # added constraint: constraint((T0290)F59.CB, (T0290)Q69.CB) [> 3.9063 = 6.5105 < 8.4636] w=0.9087 to align
# Constraint # added constraint: constraint((T0290)L58.CB, (T0290)G70.CA) [> 4.0916 = 6.8194 < 8.8652] w=0.9087 to align
# Constraint # added constraint: constraint((T0290)R17.CB, (T0290)S140.CB) [> 4.3234 = 7.2057 < 9.3674] w=0.9087 to align
# Constraint # added constraint: constraint((T0290)C57.CB, (T0290)F73.CB) [> 2.9200 = 4.8666 < 6.3266] w=0.8942 to align
# Constraint # added constraint: constraint((T0290)T30.CB, (T0290)E92.CB) [> 2.9894 = 4.9823 < 6.4770] w=0.8826 to align
# Constraint # added constraint: constraint((T0290)C27.CB, (T0290)E92.CB) [> 2.9292 = 4.8820 < 6.3466] w=0.8826 to align
# Constraint # added constraint: constraint((T0290)M106.CB, (T0290)G115.CA) [> 4.3814 = 7.3023 < 9.4930] w=0.8811 to align
# Constraint # added constraint: constraint((T0290)D91.CB, (T0290)N108.CB) [> 4.5689 = 7.6148 < 9.8993] w=0.8797 to align
# Constraint # added constraint: constraint((T0290)K29.CB, (T0290)E92.CB) [> 3.2647 = 5.4412 < 7.0735] w=0.8797 to align
# Constraint # added constraint: constraint((T0290)N33.CB, (T0290)S116.CB) [> 4.5208 = 7.5346 < 9.7950] w=0.8697 to align
# Constraint # added constraint: constraint((T0290)F59.CB, (T0290)V68.CB) [> 3.1383 = 5.2306 < 6.7997] w=0.8696 to align
# Constraint # added constraint: constraint((T0290)L58.CB, (T0290)E162.CB) [> 3.3958 = 5.6597 < 7.3576] w=0.8696 to align
# Constraint # added constraint: constraint((T0290)L58.CB, (T0290)V163.CB) [> 3.6325 = 6.0541 < 7.8703] w=0.8696 to align
# Constraint # added constraint: constraint((T0290)L58.CB, (T0290)R164.CB) [> 3.1914 = 5.3190 < 6.9146] w=0.8696 to align
# Constraint # added constraint: constraint((T0290)F59.CB, (T0290)V163.CB) [> 2.6475 = 4.4125 < 5.7362] w=0.8696 to align
# Constraint # added constraint: constraint((T0290)L58.CB, (T0290)I165.CB) [> 4.4637 = 7.4394 < 9.6713] w=0.8696 to align
# Constraint # added constraint: constraint((T0290)F23.CB, (T0290)V96.CB) [> 3.9509 = 6.5849 < 8.5603] w=0.8682 to align
# Constraint # added constraint: constraint((T0290)A107.CB, (T0290)F119.CB) [> 3.2771 = 5.4618 < 7.1004] w=0.8681 to align
# Constraint # added constraint: constraint((T0290)S105.CB, (T0290)L128.CB) [> 4.0822 = 6.8036 < 8.8447] w=0.8681 to align
# Constraint # added constraint: constraint((T0290)N108.CB, (T0290)Q117.CB) [> 4.6241 = 7.7069 < 10.0189] w=0.8652 to align
# Constraint # added constraint: constraint((T0290)G70.CA, (T0290)A107.CB) [> 4.4972 = 7.4953 < 9.7439] w=0.8652 to align
# Constraint # added constraint: constraint((T0290)F23.CB, (T0290)Q137.CB) [> 4.6462 = 7.7437 < 10.0668] w=0.8652 to align
# Constraint # added constraint: constraint((T0290)N33.CB, (T0290)F89.CB) [> 4.1692 = 6.9486 < 9.0332] w=0.8536 to align
# Constraint # added constraint: constraint((T0290)F89.CB, (T0290)G115.CA) [> 4.0094 = 6.6824 < 8.6871] w=0.8536 to align
# Constraint # added constraint: constraint((T0290)H60.CB, (T0290)G76.CA) [> 3.2197 = 5.3661 < 6.9759] w=0.8508 to align
# Constraint # added constraint: constraint((T0290)P28.CB, (T0290)E92.CB) [> 4.5601 = 7.6002 < 9.8802] w=0.8507 to align
# Constraint # added constraint: constraint((T0290)S105.CB, (T0290)G136.CA) [> 4.6752 = 7.7920 < 10.1296] w=0.8391 to align
# Constraint # added constraint: constraint((T0290)D72.CB, (T0290)G81.CA) [> 3.2179 = 5.3632 < 6.9722] w=0.8377 to align
# Constraint # added constraint: constraint((T0290)L103.CB, (T0290)V138.CB) [> 4.6149 = 7.6915 < 9.9989] w=0.8304 to align
# Constraint # added constraint: constraint((T0290)M67.CB, (T0290)K123.CB) [> 4.5033 = 7.5054 < 9.7570] w=0.8261 to align
# Constraint # added constraint: constraint((T0290)H60.CB, (T0290)P159.CB) [> 4.4363 = 7.3938 < 9.6120] w=0.8261 to align
# Constraint # added constraint: constraint((T0290)R61.CB, (T0290)K158.CB) [> 4.1562 = 6.9270 < 9.0051] w=0.8261 to align
# Constraint # added constraint: constraint((T0290)A100.CB, (T0290)T121.CB) [> 4.0763 = 6.7938 < 8.8320] w=0.8261 to align
# Constraint # added constraint: constraint((T0290)C57.CB, (T0290)G76.CA) [> 4.2130 = 7.0216 < 9.1281] w=0.8232 to align
# Constraint # added constraint: constraint((T0290)G80.CA, (T0290)Q117.CB) [> 4.3550 = 7.2584 < 9.4359] w=0.8218 to align
# Constraint # added constraint: constraint((T0290)T39.CB, (T0290)E170.CB) [> 3.3584 = 5.5974 < 7.2766] w=0.8218 to align
# Constraint # added constraint: constraint((T0290)C31.CB, (T0290)G136.CA) [> 4.4201 = 7.3668 < 9.5769] w=0.8217 to align
# Constraint # added constraint: constraint((T0290)L37.CB, (T0290)I84.CB) [> 4.0162 = 6.6936 < 8.7017] w=0.7928 to align
# Constraint # added constraint: constraint((T0290)C36.CB, (T0290)I84.CB) [> 2.8716 = 4.7861 < 6.2219] w=0.7928 to align
# Constraint # added constraint: constraint((T0290)E32.CB, (T0290)I84.CB) [> 4.4289 = 7.3814 < 9.5959] w=0.7928 to align
# Constraint # added constraint: constraint((T0290)T39.CB, (T0290)G169.CA) [> 3.3490 = 5.5816 < 7.2561] w=0.7928 to align
# Constraint # added constraint: constraint((T0290)E92.CB, (T0290)F135.CB) [> 4.5448 = 7.5747 < 9.8471] w=0.7928 to align
# Constraint # added constraint: constraint((T0290)F23.CB, (T0290)V134.CB) [> 4.5342 = 7.5570 < 9.8242] w=0.7827 to align
# Constraint # added constraint: constraint((T0290)K55.CB, (T0290)L166.CB) [> 4.3820 = 7.3034 < 9.4944] w=0.7826 to align
# Constraint # added constraint: constraint((T0290)N108.CB, (T0290)H131.CB) [> 4.6556 = 7.7593 < 10.0871] w=0.7798 to align
# Constraint # added constraint: constraint((T0290)H60.CB, (T0290)G78.CA) [> 3.4054 = 5.6756 < 7.3783] w=0.7798 to align
# Constraint # added constraint: constraint((T0290)G81.CA, (T0290)Q117.CB) [> 3.8420 = 6.4033 < 8.3243] w=0.7638 to align
# Constraint # added constraint: constraint((T0290)R61.CB, (T0290)G78.CA) [> 4.2482 = 7.0803 < 9.2044] w=0.7638 to align
# Constraint # added constraint: constraint((T0290)N33.CB, (T0290)Y85.CB) [> 4.2423 = 7.0704 < 9.1916] w=0.7494 to align
# Constraint # added constraint: constraint((T0290)V96.CB, (T0290)F135.CB) [> 4.3158 = 7.1930 < 9.3510] w=0.7377 to align
# Constraint # added constraint: constraint((T0290)F94.CB, (T0290)G130.CA) [> 2.6104 = 4.3506 < 5.6558] w=0.7362 to align
# Constraint # added constraint: constraint((T0290)G110.CA, (T0290)H131.CB) [> 4.5310 = 7.5516 < 9.8171] w=0.7349 to align
# Constraint # added constraint: constraint((T0290)L58.CB, (T0290)P159.CB) [> 4.5547 = 7.5911 < 9.8685] w=0.7348 to align
# Constraint # added constraint: constraint((T0290)S56.CB, (T0290)L166.CB) [> 4.5066 = 7.5110 < 9.7643] w=0.7348 to align
# Constraint # added constraint: constraint((T0290)G71.CA, (T0290)G81.CA) [> 4.0279 = 6.7131 < 8.7270] w=0.7204 to align
# Constraint # added constraint: constraint((T0290)F94.CB, (T0290)V134.CB) [> 4.5769 = 7.6281 < 9.9165] w=0.7073 to align
# Constraint # added constraint: constraint((T0290)Y54.CB, (T0290)F73.CB) [> 3.7739 = 6.2898 < 8.1768] w=0.7059 to align
# Constraint # added constraint: constraint((T0290)V18.CB, (T0290)I120.CB) [> 4.5955 = 7.6591 < 9.9568] w=0.6956 to align
# Constraint # added constraint: constraint((T0290)F119.CB, (T0290)H132.CB) [> 4.7117 = 7.8529 < 10.2088] w=0.6956 to align
# Constraint # added constraint: constraint((T0290)V62.CB, (T0290)T153.CB) [> 3.1537 = 5.2562 < 6.8330] w=0.6942 to align
# Constraint # added constraint: constraint((T0290)F94.CB, (T0290)V133.CB) [> 3.9358 = 6.5597 < 8.5276] w=0.6913 to align
# Constraint # added constraint: constraint((T0290)L37.CB, (T0290)H53.CB) [> 2.8264 = 4.7107 < 6.1239] w=0.6812 to align
# Constraint # added constraint: constraint((T0290)S56.CB, (T0290)F73.CB) [> 4.3391 = 7.2318 < 9.4014] w=0.6769 to align
# Constraint # added constraint: constraint((T0290)Q69.CB, (T0290)G78.CA) [> 4.6469 = 7.7448 < 10.0682] w=0.6624 to align
# Constraint # added constraint: constraint((T0290)K29.CB, (T0290)Y85.CB) [> 4.6399 = 7.7332 < 10.0531] w=0.6624 to align
# Constraint # added constraint: constraint((T0290)R61.CB, (T0290)F119.CB) [> 4.6491 = 7.7486 < 10.0732] w=0.6521 to align
# Constraint # added constraint: constraint((T0290)L22.CB, (T0290)L104.CB) [> 4.5993 = 7.6655 < 9.9652] w=0.6507 to align
# Constraint # added constraint: constraint((T0290)F6.CB, (T0290)R17.CB) [> 4.0969 = 6.8281 < 8.8765] w=0.6479 to align
# Constraint # added constraint: constraint((T0290)F6.CB, (T0290)V18.CB) [> 2.7748 = 4.6247 < 6.0121] w=0.6479 to align
# Constraint # added constraint: constraint((T0290)F6.CB, (T0290)Y54.CB) [> 4.3356 = 7.2260 < 9.3939] w=0.6479 to align
# Constraint # added constraint: constraint((T0290)F6.CB, (T0290)I165.CB) [> 2.9711 = 4.9518 < 6.4373] w=0.6479 to align
# Constraint # added constraint: constraint((T0290)F6.CB, (T0290)C168.CB) [> 2.9831 = 4.9718 < 6.4633] w=0.6479 to align
# Constraint # added constraint: constraint((T0290)D7.CB, (T0290)G16.CA) [> 3.7574 = 6.2623 < 8.1409] w=0.6479 to align
# Constraint # added constraint: constraint((T0290)D7.CB, (T0290)R17.CB) [> 3.1479 = 5.2464 < 6.8204] w=0.6479 to align
# Constraint # added constraint: constraint((T0290)D7.CB, (T0290)I165.CB) [> 4.2463 = 7.0771 < 9.2002] w=0.6479 to align
# Constraint # added constraint: constraint((T0290)D7.CB, (T0290)L166.CB) [> 2.7946 = 4.6576 < 6.0549] w=0.6479 to align
# Constraint # added constraint: constraint((T0290)D7.CB, (T0290)S167.CB) [> 2.6248 = 4.3747 < 5.6871] w=0.6479 to align
# Constraint # added constraint: constraint((T0290)D7.CB, (T0290)C168.CB) [> 4.1135 = 6.8559 < 8.9126] w=0.6479 to align
# Constraint # added constraint: constraint((T0290)I8.CB, (T0290)R17.CB) [> 4.4310 = 7.3851 < 9.6006] w=0.6479 to align
# Constraint # added constraint: constraint((T0290)I8.CB, (T0290)V18.CB) [> 3.8287 = 6.3812 < 8.2956] w=0.6479 to align
# Constraint # added constraint: constraint((T0290)I8.CB, (T0290)V144.CB) [> 3.4139 = 5.6898 < 7.3967] w=0.6479 to align
# Constraint # added constraint: constraint((T0290)I8.CB, (T0290)I148.CB) [> 3.8728 = 6.4548 < 8.3912] w=0.6479 to align
# Constraint # added constraint: constraint((T0290)A9.CB, (T0290)L166.CB) [> 2.6018 = 4.3364 < 5.6373] w=0.6479 to align
# Constraint # added constraint: constraint((T0290)I10.CB, (T0290)E162.CB) [> 4.1302 = 6.8837 < 8.9488] w=0.6479 to align
# Constraint # added constraint: constraint((T0290)N11.CB, (T0290)A161.CB) [> 2.6905 = 4.4841 < 5.8294] w=0.6479 to align
# Constraint # added constraint: constraint((T0290)N11.CB, (T0290)E162.CB) [> 3.5560 = 5.9267 < 7.7046] w=0.6479 to align
# Constraint # added constraint: constraint((T0290)C38.CB, (T0290)H53.CB) [> 4.1435 = 6.9059 < 8.9777] w=0.6377 to align
# Constraint # added constraint: constraint((T0290)V62.CB, (T0290)K158.CB) [> 4.6085 = 7.6809 < 9.9851] w=0.6088 to align
# Constraint # added constraint: constraint((T0290)L58.CB, (T0290)D72.CB) [> 4.5995 = 7.6658 < 9.9655] w=0.6088 to align
# Constraint # added constraint: constraint((T0290)F59.CB, (T0290)I165.CB) [> 4.6564 = 7.7608 < 10.0890] w=0.6087 to align
# Constraint # added constraint: constraint((T0290)V18.CB, (T0290)Q142.CB) [> 4.6772 = 7.7953 < 10.1339] w=0.6087 to align
# Constraint # added constraint: constraint((T0290)A15.CB, (T0290)V163.CB) [> 3.9272 = 6.5454 < 8.5090] w=0.6087 to align
# Constraint # added constraint: constraint((T0290)A9.CB, (T0290)R164.CB) [> 2.9472 = 4.9121 < 6.3857] w=0.6044 to align
# Constraint # added constraint: constraint((T0290)I10.CB, (T0290)V163.CB) [> 3.0503 = 5.0839 < 6.6091] w=0.6044 to align
# Constraint # added constraint: constraint((T0290)F5.CB, (T0290)V18.CB) [> 3.9507 = 6.5845 < 8.5599] w=0.6044 to align
# Constraint # added constraint: constraint((T0290)F5.CB, (T0290)V19.CB) [> 2.8751 = 4.7919 < 6.2294] w=0.6044 to align
# Constraint # added constraint: constraint((T0290)F5.CB, (T0290)C168.CB) [> 3.7680 = 6.2800 < 8.1640] w=0.6044 to align
# Constraint # added constraint: constraint((T0290)F5.CB, (T0290)G169.CA) [> 3.4756 = 5.7927 < 7.5304] w=0.6044 to align
# Constraint # added constraint: constraint((T0290)C4.CB, (T0290)R35.CB) [> 3.5646 = 5.9409 < 7.7232] w=0.5754 to align
# Constraint # added constraint: constraint((T0290)L37.CB, (T0290)F73.CB) [> 4.6173 = 7.6955 < 10.0042] w=0.5609 to align
# Constraint # added constraint: constraint((T0290)F6.CB, (T0290)S167.CB) [> 4.6296 = 7.7159 < 10.0307] w=0.5609 to align
# Constraint # added constraint: constraint((T0290)F6.CB, (T0290)F20.CB) [> 4.6344 = 7.7241 < 10.0413] w=0.5609 to align
# Constraint # added constraint: constraint((T0290)I10.CB, (T0290)R164.CB) [> 4.4824 = 7.4707 < 9.7119] w=0.5609 to align
# Constraint # added constraint: constraint((T0290)F5.CB, (T0290)F20.CB) [> 4.4076 = 7.3460 < 9.5498] w=0.5609 to align
# Constraint # added constraint: constraint((T0290)F34.CB, (T0290)L104.CB) [> 4.5679 = 7.6131 < 9.8971] w=0.5609 to align
# Constraint # added constraint: constraint((T0290)V19.CB, (T0290)L171.CB) [> 4.1082 = 6.8469 < 8.9010] w=0.5508 to align
# Constraint # added constraint: constraint((T0290)C4.CB, (T0290)V19.CB) [> 4.2965 = 7.1608 < 9.3090] w=0.5464 to align
# Constraint # added constraint: constraint((T0290)C4.CB, (T0290)F20.CB) [> 3.2042 = 5.3404 < 6.9425] w=0.5464 to align
# Constraint # added constraint: constraint((T0290)C4.CB, (T0290)F34.CB) [> 4.2272 = 7.0453 < 9.1589] w=0.5464 to align
# Constraint # added constraint: constraint((T0290)C4.CB, (T0290)C168.CB) [> 4.0893 = 6.8154 < 8.8601] w=0.5464 to align
# Constraint # added constraint: constraint((T0290)A100.CB, (T0290)K123.CB) [> 3.7899 = 6.3166 < 8.2115] w=0.5334 to align
# Constraint # added constraint: constraint((T0290)T39.CB, (T0290)C168.CB) [> 4.5602 = 7.6002 < 9.8803] w=0.5319 to align
# Constraint # added constraint: constraint((T0290)A95.CB, (T0290)V134.CB) [> 4.6628 = 7.7713 < 10.1027] w=0.5217 to align
# Constraint # added constraint: constraint((T0290)Q69.CB, (T0290)I120.CB) [> 4.7495 = 7.9159 < 10.2906] w=0.5217 to align
# Constraint # added constraint: constraint((T0290)L104.CB, (T0290)T121.CB) [> 4.6102 = 7.6837 < 9.9888] w=0.5217 to align
# Constraint # added constraint: constraint((T0290)V63.CB, (T0290)T153.CB) [> 4.3323 = 7.2206 < 9.3867] w=0.5203 to align
# Constraint # added constraint: constraint((T0290)F59.CB, (T0290)R164.CB) [> 4.5308 = 7.5514 < 9.8167] w=0.5174 to align
# Constraint # added constraint: constraint((T0290)H53.CB, (T0290)F73.CB) [> 3.9276 = 6.5460 < 8.5098] w=0.5044 to align
# Constraint # added constraint: constraint((T0290)R3.CB, (T0290)V19.CB) [> 3.4943 = 5.8238 < 7.5709] w=0.4885 to align
# Constraint # added constraint: constraint((T0290)R3.CB, (T0290)I139.CB) [> 3.9522 = 6.5870 < 8.5631] w=0.4885 to align
# Constraint # added constraint: constraint((T0290)E21.CB, (T0290)V138.CB) [> 4.6731 = 7.7885 < 10.1251] w=0.4826 to align
# Constraint # added constraint: constraint((T0290)G71.CA, (T0290)I165.CB) [> 4.5547 = 7.5912 < 9.8686] w=0.4826 to align
# Constraint # added constraint: constraint((T0290)H60.CB, (T0290)G71.CA) [> 4.5952 = 7.6587 < 9.9563] w=0.4826 to align
# Constraint # added constraint: constraint((T0290)G71.CA, (T0290)A107.CB) [> 4.7267 = 7.8778 < 10.2412] w=0.4783 to align
# Constraint # added constraint: constraint((T0290)L103.CB, (T0290)T125.CB) [> 4.5895 = 7.6492 < 9.9440] w=0.4740 to align
# Constraint # added constraint: constraint((T0290)F102.CB, (T0290)T122.CB) [> 4.4037 = 7.3396 < 9.5414] w=0.4667 to align
# Constraint # added constraint: constraint((T0290)K42.CB, (T0290)I84.CB) [> 3.3257 = 5.5428 < 7.2056] w=0.4609 to align
# Constraint # added constraint: constraint((T0290)S105.CB, (T0290)I120.CB) [> 4.7315 = 7.8859 < 10.2516] w=0.4348 to align
# Constraint # added constraint: constraint((T0290)K64.CB, (T0290)T122.CB) [> 4.4539 = 7.4231 < 9.6500] w=0.4348 to align
# Constraint # added constraint: constraint((T0290)R61.CB, (T0290)P159.CB) [> 4.6368 = 7.7280 < 10.0464] w=0.4348 to align
# Constraint # added constraint: constraint((T0290)F5.CB, (T0290)L171.CB) [> 3.5230 = 5.8717 < 7.6332] w=0.4305 to align
# Constraint # added constraint: constraint((T0290)P2.CB, (T0290)R35.CB) [> 3.2033 = 5.3388 < 6.9404] w=0.4305 to align
# Constraint # added constraint: constraint((T0290)C4.CB, (T0290)L171.CB) [> 4.0768 = 6.7947 < 8.8331] w=0.4015 to align
# Constraint # added constraint: constraint((T0290)I10.CB, (T0290)E147.CB) [> 4.1870 = 6.9783 < 9.0718] w=0.3913 to align
# Constraint # added constraint: constraint((T0290)F59.CB, (T0290)G71.CA) [> 4.6690 = 7.7817 < 10.1162] w=0.3912 to align
# Constraint # added constraint: constraint((T0290)P2.CB, (T0290)C31.CB) [> 3.8651 = 6.4418 < 8.3744] w=0.3870 to align
# Constraint # added constraint: constraint((T0290)P2.CB, (T0290)E21.CB) [> 4.5333 = 7.5554 < 9.8221] w=0.3870 to align
# Constraint # added constraint: constraint((T0290)Q69.CB, (T0290)S157.CB) [> 4.4170 = 7.3616 < 9.5701] w=0.3870 to align
# Constraint # added constraint: constraint((T0290)V68.CB, (T0290)V163.CB) [> 4.6942 = 7.8237 < 10.1708] w=0.3869 to align
# Constraint # added constraint: constraint((T0290)D91.CB, (T0290)M106.CB) [> 4.6778 = 7.7962 < 10.1351] w=0.3768 to align
# Constraint # added constraint: constraint((T0290)A9.CB, (T0290)V19.CB) [> 4.4160 = 7.3601 < 9.5681] w=0.3521 to align
# Constraint # added constraint: constraint((T0290)A9.CB, (T0290)F20.CB) [> 2.8499 = 4.7499 < 6.1749] w=0.3521 to align
# Constraint # added constraint: constraint((T0290)A9.CB, (T0290)L22.CB) [> 3.9022 = 6.5037 < 8.4548] w=0.3521 to align
# Constraint # added constraint: constraint((T0290)A9.CB, (T0290)C168.CB) [> 3.7370 = 6.2284 < 8.0969] w=0.3521 to align
# Constraint # added constraint: constraint((T0290)I10.CB, (T0290)V19.CB) [> 3.1755 = 5.2924 < 6.8801] w=0.3521 to align
# Constraint # added constraint: constraint((T0290)N11.CB, (T0290)F20.CB) [> 4.0688 = 6.7813 < 8.8157] w=0.3521 to align
# Constraint # added constraint: constraint((T0290)N11.CB, (T0290)I165.CB) [> 3.5493 = 5.9155 < 7.6901] w=0.3521 to align
# Constraint # added constraint: constraint((T0290)N11.CB, (T0290)C168.CB) [> 3.3563 = 5.5939 < 7.2720] w=0.3521 to align
# Constraint # added constraint: constraint((T0290)N12.CB, (T0290)S167.CB) [> 2.9545 = 4.9242 < 6.4014] w=0.3521 to align
# Constraint # added constraint: constraint((T0290)Q13.CB, (T0290)V163.CB) [> 3.8471 = 6.4119 < 8.3354] w=0.3521 to align
# Constraint # added constraint: constraint((T0290)N108.CB, (T0290)V133.CB) [> 4.5492 = 7.5820 < 9.8567] w=0.3508 to align
# Constraint # added constraint: constraint((T0290)C36.CB, (T0290)H53.CB) [> 4.6792 = 7.7986 < 10.1382] w=0.3450 to align
# Constraint # added constraint: constraint((T0290)R3.CB, (T0290)L171.CB) [> 2.7284 = 4.5473 < 5.9114] w=0.3435 to align
# Constraint # added constraint: constraint((T0290)G78.CA, (T0290)A107.CB) [> 4.7232 = 7.8721 < 10.2337] w=0.3334 to align
# Constraint # added constraint: constraint((T0290)L52.CB, (T0290)F73.CB) [> 4.1354 = 6.8924 < 8.9601] w=0.3174 to align
# Constraint # added constraint: constraint((T0290)L37.CB, (T0290)L52.CB) [> 4.0477 = 6.7462 < 8.7700] w=0.3174 to align
# Constraint # added constraint: constraint((T0290)R1.CB, (T0290)E21.CB) [> 3.2922 = 5.4870 < 7.1331] w=0.3145 to align
# Constraint # added constraint: constraint((T0290)R1.CB, (T0290)D25.CB) [> 3.5496 = 5.9159 < 7.6907] w=0.3145 to align
# Constraint # added constraint: constraint((T0290)I8.CB, (T0290)V19.CB) [> 3.8753 = 6.4588 < 8.3965] w=0.3086 to align
# Constraint # added constraint: constraint((T0290)A9.CB, (T0290)E162.CB) [> 4.6255 = 7.7092 < 10.0220] w=0.3044 to align
# Constraint # added constraint: constraint((T0290)L52.CB, (T0290)E82.CB) [> 4.2532 = 7.0886 < 9.2152] w=0.3044 to align
# Constraint # added constraint: constraint((T0290)A9.CB, (T0290)F34.CB) [> 4.5337 = 7.5561 < 9.8230] w=0.3043 to align
# Constraint # added constraint: constraint((T0290)I8.CB, (T0290)L22.CB) [> 4.2414 = 7.0691 < 9.1898] w=0.2796 to align
# Constraint # added constraint: constraint((T0290)F6.CB, (T0290)L166.CB) [> 4.7523 = 7.9205 < 10.2966] w=0.2609 to align
# Constraint # added constraint: constraint((T0290)M106.CB, (T0290)V134.CB) [> 4.6320 = 7.7200 < 10.0360] w=0.2594 to align
# Constraint # added constraint: constraint((T0290)V68.CB, (T0290)K152.CB) [> 4.4955 = 7.4924 < 9.7401] w=0.2580 to align
# Constraint # added constraint: constraint((T0290)V63.CB, (T0290)K152.CB) [> 3.3264 = 5.5441 < 7.2073] w=0.2580 to align
# Constraint # added constraint: constraint((T0290)M106.CB, (T0290)F119.CB) [> 4.4929 = 7.4881 < 9.7345] w=0.2217 to align
# Constraint # added constraint: constraint((T0290)K55.CB, (T0290)F73.CB) [> 4.7829 = 7.9715 < 10.3630] w=0.2174 to align
# Constraint # added constraint: constraint((T0290)F66.CB, (T0290)E149.CB) [> 4.4391 = 7.3985 < 9.6180] w=0.2173 to align
# Constraint # added constraint: constraint((T0290)V26.CB, (T0290)E92.CB) [> 4.3808 = 7.3014 < 9.4918] w=0.2029 to align
# Constraint # added constraint: constraint((T0290)N99.CB, (T0290)T121.CB) [> 3.7482 = 6.2470 < 8.1211] w=0.1898 to align
# Constraint # added constraint: constraint((T0290)C57.CB, (T0290)S74.CB) [> 3.8566 = 6.4277 < 8.3560] w=0.1782 to align
# Constraint # added constraint: constraint((T0290)F88.CB, (T0290)R109.CB) [> 4.6294 = 7.7157 < 10.0304] w=0.1768 to align
# Constraint # added constraint: constraint((T0290)L52.CB, (T0290)S116.CB) [> 4.5651 = 7.6085 < 9.8911] w=0.1739 to align
# Constraint # added constraint: constraint((T0290)I8.CB, (T0290)F59.CB) [> 4.6858 = 7.8097 < 10.1526] w=0.1739 to align
# Constraint # added constraint: constraint((T0290)F34.CB, (T0290)G136.CA) [> 4.6919 = 7.8198 < 10.1658] w=0.1739 to align
# Constraint # added constraint: constraint((T0290)F102.CB, (T0290)I139.CB) [> 4.6582 = 7.7638 < 10.0929] w=0.1739 to align
# Constraint # added constraint: constraint((T0290)S56.CB, (T0290)S74.CB) [> 3.7390 = 6.2317 < 8.1012] w=0.1347 to align
# Constraint # added constraint: constraint((T0290)L58.CB, (T0290)E75.CB) [> 3.4275 = 5.7125 < 7.4262] w=0.1333 to align
# Constraint # added constraint: constraint((T0290)P51.CB, (T0290)F73.CB) [> 4.1293 = 6.8821 < 8.9467] w=0.1304 to align
# Constraint # added constraint: constraint((T0290)F5.CB, (T0290)S167.CB) [> 4.7364 = 7.8940 < 10.2623] w=0.1304 to align
# Constraint # added constraint: constraint((T0290)V63.CB, (T0290)T122.CB) [> 4.5647 = 7.6078 < 9.8902] w=0.1304 to align
# Constraint # added constraint: constraint((T0290)V68.CB, (T0290)T153.CB) [> 4.4407 = 7.4012 < 9.6216] w=0.1290 to align
# Constraint # added constraint: constraint((T0290)G87.CA, (T0290)T113.CB) [> 3.7553 = 6.2589 < 8.1365] w=0.1203 to align
# Constraint # added constraint: constraint((T0290)K42.CB, (T0290)C57.CB) [> 4.6344 = 7.7241 < 10.0413] w=0.1174 to align
# Constraint # added constraint: constraint((T0290)G87.CA, (T0290)N114.CB) [> 3.5358 = 5.8930 < 7.6609] w=0.1174 to align
# Constraint # added constraint: constraint((T0290)S74.CB, (T0290)S116.CB) [> 4.1782 = 6.9637 < 9.0529] w=0.1160 to align
# Constraint # added constraint: constraint((T0290)E41.CB, (T0290)S167.CB) [> 4.3627 = 7.2711 < 9.4525] w=0.1160 to align
# Constraint # added constraint: constraint((T0290)C36.CB, (T0290)S83.CB) [> 3.4667 = 5.7779 < 7.5113] w=0.1159 to align
# Constraint # added constraint: constraint((T0290)L52.CB, (T0290)S74.CB) [> 4.6371 = 7.7286 < 10.0471] w=0.1145 to align
# Constraint # added constraint: constraint((T0290)F88.CB, (T0290)N108.CB) [> 4.7188 = 7.8647 < 10.2241] w=0.1015 to align
# Constraint # added constraint: constraint((T0290)P28.CB, (T0290)D91.CB) [> 4.4935 = 7.4892 < 9.7360] w=0.1014 to align
# Constraint # added constraint: constraint((T0290)G86.CA, (T0290)S116.CB) [> 4.3909 = 7.3182 < 9.5137] w=0.0912 to align
# Constraint # added constraint: constraint((T0290)L58.CB, (T0290)F73.CB) [> 3.3181 = 5.5302 < 7.1892] w=0.0912 to align
# Constraint # added constraint: constraint((T0290)V96.CB, (T0290)S105.CB) [> 4.6962 = 7.8271 < 10.1752] w=0.0899 to align
# Constraint # added constraint: constraint((T0290)S56.CB, (T0290)E75.CB) [> 4.1974 = 6.9957 < 9.0944] w=0.0898 to align
# Constraint # added constraint: constraint((T0290)A95.CB, (T0290)V133.CB) [> 4.2193 = 7.0321 < 9.1418] w=0.0883 to align
# Constraint # added constraint: constraint((T0290)D7.CB, (T0290)V18.CB) [> 4.7605 = 7.9342 < 10.3144] w=0.0870 to align
# Constraint # added constraint: constraint((T0290)F94.CB, (T0290)H132.CB) [> 4.7796 = 7.9660 < 10.3559] w=0.0870 to align
# Constraint # added constraint: constraint((T0290)M67.CB, (T0290)S105.CB) [> 4.7865 = 7.9775 < 10.3707] w=0.0870 to align
# Constraint # added constraint: constraint((T0290)Y54.CB, (T0290)G70.CA) [> 4.6609 = 7.7682 < 10.0987] w=0.0870 to align
# Constraint # added constraint: constraint((T0290)L22.CB, (T0290)E32.CB) [> 4.7664 = 7.9439 < 10.3271] w=0.0870 to align
# Constraint # added constraint: constraint((T0290)N99.CB, (T0290)L128.CB) [> 2.5004 = 4.1674 < 5.4176] w=0.0869 to align
# Constraint # added constraint: constraint((T0290)L58.CB, (T0290)S74.CB) [> 4.1878 = 6.9796 < 9.0735] w=0.0767 to align
# Constraint # added constraint: constraint((T0290)C57.CB, (T0290)E75.CB) [> 4.3095 = 7.1825 < 9.3373] w=0.0754 to align
# Constraint # added constraint: constraint((T0290)E90.CB, (T0290)N108.CB) [> 4.4816 = 7.4693 < 9.7101] w=0.0725 to align
# Constraint # added constraint: constraint((T0290)G43.CA, (T0290)S167.CB) [> 4.3581 = 7.2635 < 9.4425] w=0.0724 to align
# Constraint # added constraint: constraint((T0290)D7.CB, (T0290)C31.CB) [> 3.6462 = 6.0771 < 7.9002] w=0.0724 to align
# Constraint # added constraint: constraint((T0290)A100.CB, (T0290)T122.CB) [> 3.7687 = 6.2812 < 8.1655] w=0.0594 to align
# Constraint # added constraint: constraint((T0290)F5.CB, (T0290)S24.CB) [> 3.3941 = 5.6569 < 7.3539] w=0.0580 to align
# Constraint # added constraint: constraint((T0290)R79.CB, (T0290)Q117.CB) [> 4.5736 = 7.6227 < 9.9095] w=0.0580 to align
# Constraint # added constraint: constraint((T0290)R61.CB, (T0290)N77.CB) [> 3.7083 = 6.1805 < 8.0347] w=0.0580 to align
# Constraint # added constraint: constraint((T0290)H53.CB, (T0290)S74.CB) [> 4.2616 = 7.1027 < 9.2335] w=0.0580 to align
# Constraint # added constraint: constraint((T0290)A101.CB, (T0290)I120.CB) [> 4.5415 = 7.5692 < 9.8399] w=0.0579 to align
# Constraint # added constraint: constraint((T0290)S93.CB, (T0290)K111.CB) [> 4.4058 = 7.3430 < 9.5459] w=0.0579 to align
# Constraint # added constraint: constraint((T0290)F20.CB, (T0290)I120.CB) [> 4.4598 = 7.4330 < 9.6630] w=0.0478 to align
# Constraint # added constraint: constraint((T0290)A107.CB, (T0290)V133.CB) [> 4.5842 = 7.6403 < 9.9324] w=0.0478 to align
# Constraint # added constraint: constraint((T0290)D7.CB, (T0290)F23.CB) [> 4.5756 = 7.6260 < 9.9139] w=0.0464 to align
# Constraint # added constraint: constraint((T0290)E21.CB, (T0290)L104.CB) [> 4.6856 = 7.8093 < 10.1521] w=0.0464 to align
# Constraint # added constraint: constraint((T0290)F23.CB, (T0290)F94.CB) [> 4.6519 = 7.7532 < 10.0792] w=0.0449 to align
# Constraint # added constraint: constraint((T0290)F20.CB, (T0290)L103.CB) [> 3.6229 = 6.0381 < 7.8495] w=0.0449 to align
# Constraint # added constraint: constraint((T0290)T30.CB, (T0290)S105.CB) [> 3.5759 = 5.9598 < 7.7477] w=0.0449 to align
# Constraint # added constraint: constraint((T0290)F102.CB, (T0290)V134.CB) [> 3.0127 = 5.0211 < 6.5274] w=0.0449 to align
# Constraint # added constraint: constraint((T0290)F102.CB, (T0290)G136.CA) [> 3.7156 = 6.1926 < 8.0504] w=0.0449 to align
# Constraint # added constraint: constraint((T0290)L103.CB, (T0290)F118.CB) [> 3.3767 = 5.6279 < 7.3163] w=0.0449 to align
# Constraint # added constraint: constraint((T0290)L103.CB, (T0290)F119.CB) [> 4.3751 = 7.2917 < 9.4793] w=0.0449 to align
# Constraint # added constraint: constraint((T0290)L103.CB, (T0290)F135.CB) [> 3.7833 = 6.3055 < 8.1971] w=0.0449 to align
# Constraint # added constraint: constraint((T0290)L104.CB, (T0290)L128.CB) [> 4.1342 = 6.8904 < 8.9575] w=0.0449 to align
# Constraint # added constraint: constraint((T0290)I8.CB, (T0290)I172.CB) [> 2.7662 = 4.6103 < 5.9934] w=0.0435 to align
# Constraint # added constraint: constraint((T0290)L103.CB, (T0290)P124.CB) [> 4.7917 = 7.9861 < 10.3820] w=0.0435 to align
# Constraint # added constraint: constraint((T0290)G43.CA, (T0290)C57.CB) [> 4.5893 = 7.6488 < 9.9434] w=0.0435 to align
# Constraint # added constraint: constraint((T0290)F6.CB, (T0290)K55.CB) [> 4.7380 = 7.8967 < 10.2657] w=0.0435 to align
# Constraint # added constraint: constraint((T0290)H60.CB, (T0290)V163.CB) [> 4.7964 = 7.9939 < 10.3921] w=0.0435 to align
# Constraint # added constraint: constraint((T0290)C38.CB, (T0290)S167.CB) [> 4.7752 = 7.9587 < 10.3463] w=0.0435 to align
# Constraint # added constraint: constraint((T0290)R61.CB, (T0290)G71.CA) [> 4.7057 = 7.8428 < 10.1957] w=0.0435 to align
# Constraint # added constraint: constraint((T0290)K64.CB, (T0290)Q151.CB) [> 4.7686 = 7.9477 < 10.3320] w=0.0435 to align
# Constraint # added constraint: constraint((T0290)I148.CB, (T0290)A161.CB) [> 4.7674 = 7.9456 < 10.3293] w=0.0435 to align
# Constraint # added constraint: constraint((T0290)F102.CB, (T0290)G141.CA) [> 4.0620 = 6.7700 < 8.8010] w=0.0435 to align
# Constraint # added constraint: constraint((T0290)D72.CB, (T0290)F118.CB) [> 4.4150 = 7.3583 < 9.5658] w=0.0435 to align
# Constraint # added constraint: constraint((T0290)Q69.CB, (T0290)M106.CB) [> 3.5001 = 5.8336 < 7.5836] w=0.0434 to align
# Constraint # added constraint: constraint((T0290)G70.CA, (T0290)M106.CB) [> 4.6105 = 7.6841 < 9.9893] w=0.0434 to align
# Constraint # added constraint: constraint((T0290)E90.CB, (T0290)A107.CB) [> 4.3253 = 7.2089 < 9.3716] w=0.0434 to align
# Constraint # added constraint: constraint((T0290)N99.CB, (T0290)H131.CB) [> 4.7260 = 7.8767 < 10.2397] w=0.0434 to align
# Constraint # added constraint: constraint((T0290)F23.CB, (T0290)A95.CB) [> 4.6630 = 7.7716 < 10.1031] w=0.0333 to align
# Constraint # added constraint: constraint((T0290)D7.CB, (T0290)L171.CB) [> 4.6882 = 7.8137 < 10.1578] w=0.0319 to align
# Constraint # added constraint: constraint((T0290)F6.CB, (T0290)C31.CB) [> 4.2112 = 7.0187 < 9.1243] w=0.0290 to align
# Constraint # added constraint: constraint((T0290)H53.CB, (T0290)I84.CB) [> 4.7593 = 7.9321 < 10.3117] w=0.0290 to align
# Constraint # added constraint: constraint((T0290)H53.CB, (T0290)D72.CB) [> 4.0955 = 6.8259 < 8.8736] w=0.0290 to align
# Constraint # added constraint: constraint((T0290)I84.CB, (T0290)S116.CB) [> 2.8004 = 4.6674 < 6.0676] w=0.0290 to align
# Constraint # added constraint: constraint((T0290)C57.CB, (T0290)E82.CB) [> 4.2777 = 7.1294 < 9.2683] w=0.0290 to align
# Constraint # added constraint: constraint((T0290)D72.CB, (T0290)M106.CB) [> 4.7706 = 7.9510 < 10.3362] w=0.0290 to align
# Constraint # added constraint: constraint((T0290)G78.CA, (T0290)R109.CB) [> 4.5234 = 7.5390 < 9.8008] w=0.0145 to align
# Constraint # added constraint: constraint((T0290)I8.CB, (T0290)Q137.CB) [> 4.4888 = 7.4813 < 9.7257] w=0.0043 to align
# Constraint # added constraint: constraint((T0290)I10.CB, (T0290)S167.CB) [> 4.6385 = 7.7308 < 10.0500] w=0.0043 to align
# Constraint # added constraint: constraint((T0290)G16.CA, (T0290)L166.CB) [> 4.5060 = 7.5100 < 9.7631] w=0.0043 to align
# Constraint # added constraint: constraint((T0290)R17.CB, (T0290)S167.CB) [> 4.6821 = 7.8036 < 10.1446] w=0.0043 to align
# Constraint # added constraint: constraint((T0290)V68.CB, (T0290)T121.CB) [> 4.7060 = 7.8433 < 10.1962] w=0.0043 to align
# Constraint # added constraint: constraint((T0290)G71.CA, (T0290)F119.CB) [> 4.6826 = 7.8043 < 10.1456] w=0.0043 to align
# Constraint # added constraint: constraint((T0290)F118.CB, (T0290)V133.CB) [> 3.9195 = 6.5325 < 8.4923] w=0.0043 to align
# Constraint # added constraint: constraint((T0290)F119.CB, (T0290)V133.CB) [> 4.7792 = 7.9653 < 10.3549] w=0.0043 to align
# Constraint # added constraint: constraint((T0290)S93.CB, (T0290)L128.CB) [> 4.2847 = 7.1411 < 9.2835] w=0.0029 to align
# SetCost created cost = 
#	( 1.0000 * align )
# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0290/
# command:# reading script from file servers-clean.under
# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0290/decoys/
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0290 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 T0290 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 T0290 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 T0290 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 T0290 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 T0290 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 T0290 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 T0290 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 T0290 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 T0290 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 T0290 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 T0290 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
# choosing archetypes in rotamer library
# WARNING: incomplete conformation T0290 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation 3D-JIGSAW_TS3
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0290 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation 3D-JIGSAW_TS4
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0290 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation 3D-JIGSAW_TS5
# ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1
# Found a chain break before 155
# copying to AlignedFragments data structure
# naming current conformation 3Dpro_TS1
# ReadConformPDB reading from PDB file servers/3Dpro_TS2.pdb.gz looking for model 1
# naming current conformation 3Dpro_TS2
# ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1
# Found a chain break before 134
# 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 164
# 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 115
# 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 163
# 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 101
# 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 167
# 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 125
# 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 163
# 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 151
# 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 124
# 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 93
# 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 101
# 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 158
# 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 101
# 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 172
# 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 172
# 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 172
# 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 T0290 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 T0290 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 T0290 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation CaspIta-FOX_TS1
# ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0290 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 T0290 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation CaspIta-FOX_TS3
# ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0290 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 T0290 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 T0290 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 T0290 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 T0290 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 T0290 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 T0290 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 172
# 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 T0290 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 T0290 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 T0290 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FAMSD_TS4
# ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0290 can't currently be optimized by undertaker
# 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 172
# copying to AlignedFragments data structure
# naming current conformation FAMS_TS1
# ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0290 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FAMS_TS2
# ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0290 can't currently be optimized by undertaker
# naming current conformation FAMS_TS3
# ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1
# Found a chain break before 172
# 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 172
# 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 156
# 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 42
# 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 91
# 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 97
# 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 92
# 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 T0290 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 T0290 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 T0290 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 T0290 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 T0290 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 T0290 can't currently be optimized by undertaker
# naming current conformation FORTE2_AL1
# ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0290 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 T0290 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 T0290 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 T0290 can't currently be optimized by undertaker
# naming current conformation FORTE2_AL5
# ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS1.pdb.gz looking for model 1
# Found a chain break before 161
# copying to AlignedFragments data structure
# naming current conformation FPSOLVER-SERVER_TS1
# ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1
# Found a chain break before 93
# copying to AlignedFragments data structure
# naming current conformation FUGMOD_TS1
# ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1
# naming current conformation FUGMOD_TS2
# ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0290 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
# WARNING: incomplete conformation T0290 can't currently be optimized by undertaker
# naming current conformation FUGMOD_TS4
# ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1
# Found a chain break before 93
# 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 T0290 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 T0290 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 T0290 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 T0290 can't currently be optimized by undertaker
# naming current conformation FUGUE_AL4
# ReadConformPDB reading from PDB file servers/FUGUE_AL5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0290 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 172
# 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 171
# 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 171
# 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 172
# 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 172
# copying to AlignedFragments data structure
# naming current conformation FUNCTION_TS5
# ReadConformPDB reading from PDB file servers/Frankenstein_TS1.pdb.gz looking for model 1
# Found a chain break before 157
# copying to AlignedFragments data structure
# naming current conformation Frankenstein_TS1
# ReadConformPDB reading from PDB file servers/Frankenstein_TS2.pdb.gz looking for model 1
# Found a chain break before 170
# copying to AlignedFragments data structure
# naming current conformation Frankenstein_TS2
# ReadConformPDB reading from PDB file servers/Frankenstein_TS3.pdb.gz looking for model 1
# Found a chain break before 156
# copying to AlignedFragments data structure
# naming current conformation Frankenstein_TS3
# ReadConformPDB reading from PDB file servers/Frankenstein_TS4.pdb.gz looking for model 1
# Found a chain break before 157
# copying to AlignedFragments data structure
# naming current conformation Frankenstein_TS4
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1
# Found a chain break before 93
# copying to AlignedFragments data structure
# naming current conformation GeneSilicoMetaServer_TS1
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1
# Found a chain break before 64
# 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 T0290 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation GeneSilicoMetaServer_TS3
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1
# Found a chain break before 154
# copying to AlignedFragments data structure
# naming current conformation GeneSilicoMetaServer_TS4
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1
# Found a chain break before 97
# copying to AlignedFragments data structure
# naming current conformation GeneSilicoMetaServer_TS5
# ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1
# Found a chain break before 97
# copying to AlignedFragments data structure
# naming current conformation HHpred1_TS1
# ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1
# Found a chain break before 171
# copying to AlignedFragments data structure
# naming current conformation HHpred2_TS1
# ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1
# Found a chain break before 171
# copying to AlignedFragments data structure
# naming current conformation HHpred3_TS1
# ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0290 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# 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 T0290 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 T0290 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 T0290 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# 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 T0290 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
# Found a chain break before 161
# copying to AlignedFragments data structure
# naming current conformation LOOPP_TS1
# ReadConformPDB reading from PDB file servers/LOOPP_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0290 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation LOOPP_TS2
# ReadConformPDB reading from PDB file servers/LOOPP_TS3.pdb.gz looking for model 1
# Found a chain break before 119
# copying to AlignedFragments data structure
# naming current conformation LOOPP_TS3
# ReadConformPDB reading from PDB file servers/LOOPP_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0290 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation LOOPP_TS4
# ReadConformPDB reading from PDB file servers/LOOPP_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0290 can't currently be optimized by undertaker
# naming current conformation LOOPP_TS5
# ReadConformPDB reading from PDB file servers/MIG_FROST_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0290 can't currently be optimized by undertaker
# naming current conformation MIG_FROST_AL1
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1
# Found a chain break before 124
# 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 99
# 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 112
# 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 122
# 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 119
# 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 163
# 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 167
# copying to AlignedFragments data structure
# naming current conformation MetaTasser_TS2
# ReadConformPDB reading from PDB file servers/NN_PUT_lab_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0290 can't currently be optimized by undertaker
# naming current conformation NN_PUT_lab_TS1
# ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1
# naming current conformation PROTINFO-AB_TS1
# ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1
# naming current conformation PROTINFO-AB_TS2
# ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1
# naming current conformation PROTINFO-AB_TS3
# ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1
# naming current conformation PROTINFO-AB_TS4
# ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1
# naming current conformation PROTINFO-AB_TS5
# ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1
# naming current conformation PROTINFO_TS1
# ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1
# naming current conformation PROTINFO_TS2
# ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1
# naming current conformation PROTINFO_TS3
# ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1
# Found a chain break before 50
# 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 50
# 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 T0290 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation Pcons6_TS1
# ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0290 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation Pcons6_TS2
# ReadConformPDB reading from PDB file servers/Pcons6_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0290 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation Pcons6_TS3
# ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0290 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation Pcons6_TS4
# ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0290 can't currently be optimized by undertaker
# 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 T0290 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation Phyre-1_TS1
# ReadConformPDB reading from PDB file servers/Phyre-2_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0290 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 T0290 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 T0290 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation Phyre-2_TS3
# ReadConformPDB reading from PDB file servers/Phyre-2_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0290 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 T0290 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 T0290 can't currently be optimized by undertaker
# naming current conformation Pmodeller6_TS1
# ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0290 can't currently be optimized by undertaker
# naming current conformation Pmodeller6_TS2
# ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0290 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 T0290 can't currently be optimized by undertaker
# naming current conformation Pmodeller6_TS4
# ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0290 can't currently be optimized by undertaker
# naming current conformation Pmodeller6_TS5
# ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1
# Found a chain break before 101
# copying to AlignedFragments data structure
# naming current conformation RAPTOR-ACE_TS1
# ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1
# Found a chain break before 154
# copying to AlignedFragments data structure
# naming current conformation RAPTOR-ACE_TS2
# ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1
# Found a chain break before 101
# copying to AlignedFragments data structure
# naming current conformation RAPTOR-ACE_TS3
# ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS4.pdb.gz looking for model 1
# Found a chain break before 140
# copying to AlignedFragments data structure
# naming current conformation RAPTOR-ACE_TS4
# ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1
# Found a chain break before 155
# 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 64
# 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 125
# 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 64
# 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 164
# 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 153
# copying to AlignedFragments data structure
# naming current conformation RAPTORESS_TS5
# ReadConformPDB reading from PDB file servers/RAPTOR_TS1.pdb.gz looking for model 1
# Found a chain break before 64
# copying to AlignedFragments data structure
# naming current conformation RAPTOR_TS1
# ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1
# Found a chain break before 154
# 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 112
# 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 172
# copying to AlignedFragments data structure
# naming current conformation RAPTOR_TS4
# ReadConformPDB reading from PDB file servers/RAPTOR_TS5.pdb.gz looking for model 1
# Found a chain break before 167
# copying to AlignedFragments data structure
# naming current conformation RAPTOR_TS5
# ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1
# naming current conformation ROBETTA_TS1
# ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1
# naming current conformation ROBETTA_TS2
# ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1
# naming current conformation ROBETTA_TS3
# ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1
# naming current conformation ROBETTA_TS4
# ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1
# Found a chain break before 106
# copying to AlignedFragments data structure
# naming current conformation ROBETTA_TS5
# ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1
# Found a chain break before 101
# copying to AlignedFragments data structure
# naming current conformation ROKKY_TS1
# ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1
# Found a chain break before 172
# copying to AlignedFragments data structure
# naming current conformation ROKKY_TS2
# ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1
# Found a chain break before 124
# copying to AlignedFragments data structure
# naming current conformation ROKKY_TS3
# ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1
# Found a chain break before 101
# copying to AlignedFragments data structure
# naming current conformation ROKKY_TS4
# ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1
# Found a chain break before 93
# 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 T0290 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 T0290 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 T0290 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 T0290 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 T0290 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation SAM-T02_AL5
# ReadConformPDB reading from PDB file servers/SAM-T99_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0290 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 T0290 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation SAM-T99_AL2
# ReadConformPDB reading from PDB file servers/SAM-T99_AL3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0290 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 T0290 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 T0290 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 157
# 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 T0290 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 T0290 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 T0290 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 T0290 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 140
# copying to AlignedFragments data structure
# naming current conformation SP3_TS1
# ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1
# Found a chain break before 92
# 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 108
# 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 92
# 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 154
# 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 140
# copying to AlignedFragments data structure
# naming current conformation SP4_TS1
# ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1
# Found a chain break before 92
# copying to AlignedFragments data structure
# naming current conformation SP4_TS2
# ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1
# Found a chain break before 154
# copying to AlignedFragments data structure
# naming current conformation SP4_TS3
# ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1
# Found a chain break before 169
# copying to AlignedFragments data structure
# naming current conformation SP4_TS4
# ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1
# Found a chain break before 92
# 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 97
# 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 92
# 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 170
# 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 92
# 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 124
# 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 T0290 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# 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 T0290 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 T0290 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 T0290 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# 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 T0290 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 T0290 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# 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 T0290 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# 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 T0290 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 T0290 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 T0290 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 T0290 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
# 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 11
# copying to AlignedFragments data structure
# naming current conformation Zhang-Server_TS2
# ReadConformPDB reading from PDB file servers/Zhang-Server_TS3.pdb.gz looking for model 1
# Found a chain break before 64
# copying to AlignedFragments data structure
# naming current conformation Zhang-Server_TS3
# ReadConformPDB reading from PDB file servers/Zhang-Server_TS4.pdb.gz looking for model 1
# 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 11
# 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 172
# 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 T0290 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation beautshotbase_TS1
# ReadConformPDB reading from PDB file servers/forecast-s_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0290 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 T0290 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 T0290 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 T0290 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 T0290 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 T0290 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation gtg_AL1
# ReadConformPDB reading from PDB file servers/gtg_AL2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0290 can't currently be optimized by undertaker
# naming current conformation gtg_AL2
# ReadConformPDB reading from PDB file servers/gtg_AL3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0290 can't currently be optimized by undertaker
# naming current conformation gtg_AL3
# ReadConformPDB reading from PDB file servers/gtg_AL4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0290 can't currently be optimized by undertaker
# naming current conformation gtg_AL4
# ReadConformPDB reading from PDB file servers/gtg_AL5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0290 can't currently be optimized by undertaker
# naming current conformation gtg_AL5
# ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1
# Found a chain break before 93
# 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 124
# 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 93
# 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 155
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.2_TS4
# ReadConformPDB reading from PDB file servers/karypis.srv.2_TS5.pdb.gz looking for model 1
# Found a chain break before 93
# 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 170
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.4_TS1
# ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0290 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 T0290 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation karypis.srv_TS2
# ReadConformPDB reading from PDB file servers/karypis.srv_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0290 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 T0290 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 T0290 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation karypis.srv_TS5
# ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1
# Found a chain break before 68
# 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 125
# 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 68
# 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 169
# 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 T0290 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 T0290 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 T0290 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 T0290 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 T0290 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 T0290 can't currently be optimized by undertaker
# naming current conformation nFOLD_TS5
# ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0290 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation shub_TS1
# command:Using radius: 8.0000
Metaserver mode
NUMB_ALIGNS: 250
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weight: 0.9845 eval: -0.7587 min: -0.8090 max: 2.1084
weight: 0.9874 eval: -0.7681 min: -0.8090 max: 2.1084
weight: 0.9873 eval: -0.7678 min: -0.8090 max: 2.1084
weight: 0.9733 eval: -0.7224 min: -0.8090 max: 2.1084
weight: 0.9747 eval: -0.7271 min: -0.8090 max: 2.1084
weight: 0.3607 eval: 1.2634 min: -0.8090 max: 2.1084
weight: 0.3596 eval: 1.2670 min: -0.8090 max: 2.1084
weight: 0.3553 eval: 1.2807 min: -0.8090 max: 2.1084
weight: 0.3545 eval: 1.2835 min: -0.8090 max: 2.1084
weight: 0.3575 eval: 1.2737 min: -0.8090 max: 2.1084
weight: 0.3606 eval: 1.2635 min: -0.8090 max: 2.1084
weight: 0.3607 eval: 1.2633 min: -0.8090 max: 2.1084
weight: 0.3606 eval: 1.2638 min: -0.8090 max: 2.1084
weight: 0.3607 eval: 1.2632 min: -0.8090 max: 2.1084
weight: 0.3607 eval: 1.2634 min: -0.8090 max: 2.1084
weight: 0.9881 eval: -0.7704 min: -0.8090 max: 2.1084
weight: 0.9831 eval: -0.7543 min: -0.8090 max: 2.1084
weight: 0.9814 eval: -0.7487 min: -0.8090 max: 2.1084
weight: 0.9804 eval: -0.7456 min: -0.8090 max: 2.1084
weight: 0.9881 eval: -0.7704 min: -0.8090 max: 2.1084
weight: 0.1111 eval: 2.0722 min: -0.8090 max: 2.1084
weight: 0.9856 eval: -0.7625 min: -0.8090 max: 2.1084
weight: 0.9923 eval: -0.7841 min: -0.8090 max: 2.1084
weight: 0.9859 eval: -0.7634 min: -0.8090 max: 2.1084
weight: 0.9836 eval: -0.7560 min: -0.8090 max: 2.1084
weight: 0.9837 eval: -0.7564 min: -0.8090 max: 2.1084
weight: 0.9613 eval: -0.6837 min: -0.8090 max: 2.1084
weight: 0.9632 eval: -0.6899 min: -0.8090 max: 2.1084
weight: 0.9613 eval: -0.6837 min: -0.8090 max: 2.1084
weight: 0.9577 eval: -0.6720 min: -0.8090 max: 2.1084
weight: 0.9609 eval: -0.6823 min: -0.8090 max: 2.1084
weight: 0.9900 eval: -0.7766 min: -0.8090 max: 2.1084
weight: 0.9900 eval: -0.7766 min: -0.8090 max: 2.1084
weight: 0.8760 eval: -0.4069 min: -0.8090 max: 2.1084
weight: 0.9134 eval: -0.5285 min: -0.8090 max: 2.1084
weight: 0.2030 eval: 1.7745 min: -0.8090 max: 2.1084
weight: 0.2822 eval: 1.5176 min: -0.8090 max: 2.1084
weight: 0.9806 eval: -0.7461 min: -0.8090 max: 2.1084
Adding 4184 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: -325.8933, CN propb: -325.8933 weights: 0.5574 constraints: 489
# command:Found ConstraintSet
# PrintContacts align.constraints_meta02
Number of constraints in align2.constraints 489
# command:Found ConstraintSet
# PrintContacts align_bonus.constraints_meta02
Number of constraints in align2.constraints.bonus 489
# command:Found ConstraintSet
# PrintContacts rejected.constraints_meta02
Number of constraints in rejected2.constraints 3695
# command:Found ConstraintSet
# PrintContacts rejected_bonus.constraints_meta02
Number of constraints in rejected2.constraints.bonus 3695
# 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 4184
# command: