# 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/T0381/
# command:# Making conformation for sequence T0381 numbered 1 through 265
Created new target T0381 from T0381.a2m
# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0381/
# command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0381//projects/compbio/experiments/protein-predict/casp7/T0381/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0381//projects/compbio/experiments/protein-predict/casp7/T0381/align.constraints_v3.costfcn.gz for input
Trying /projects/compbio/experiments/protein-predict/casp7/T0381/align.constraints_v3.costfcn
# reading script from file /projects/compbio/experiments/protein-predict/casp7/T0381/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((T0381)A43.CB, (T0381)A53.CB) [> 2.8330 = 4.7217 < 6.1382] w=1.0000 to align
# Constraint # added constraint: constraint((T0381)V42.CB, (T0381)A53.CB) [> 3.1410 = 5.2350 < 6.8055] w=1.0000 to align
# Constraint # added constraint: constraint((T0381)L39.CB, (T0381)A53.CB) [> 3.2080 = 5.3467 < 6.9507] w=1.0000 to align
# Constraint # added constraint: constraint((T0381)L39.CB, (T0381)R54.CB) [> 3.5813 = 5.9689 < 7.7596] w=0.9825 to align
# Constraint # added constraint: constraint((T0381)L57.CB, (T0381)V66.CB) [> 3.9009 = 6.5015 < 8.4519] w=0.9796 to align
# Constraint # added constraint: constraint((T0381)V26.CB, (T0381)V42.CB) [> 3.6389 = 6.0649 < 7.8844] w=0.9521 to align
# Constraint # added constraint: constraint((T0381)L39.CB, (T0381)L57.CB) [> 4.0127 = 6.6878 < 8.6941] w=0.9482 to align
# Constraint # added constraint: constraint((T0381)L39.CB, (T0381)R50.CB) [> 3.5814 = 5.9690 < 7.7597] w=0.9441 to align
# Constraint # added constraint: constraint((T0381)S40.CB, (T0381)R50.CB) [> 3.8680 = 6.4467 < 8.3807] w=0.9195 to align
# Constraint # added constraint: constraint((T0381)V26.CB, (T0381)T46.CB) [> 3.8831 = 6.4719 < 8.4134] w=0.8378 to align
# Constraint # added constraint: constraint((T0381)C29.CB, (T0381)A45.CB) [> 3.6150 = 6.0250 < 7.8325] w=0.7939 to align
# Constraint # added constraint: constraint((T0381)R37.CB, (T0381)F73.CB) [> 3.4100 = 5.6833 < 7.3884] w=0.7823 to align
# Constraint # added constraint: constraint((T0381)G23.CA, (T0381)F56.CB) [> 3.7594 = 6.2657 < 8.1455] w=0.7754 to align
# Constraint # added constraint: constraint((T0381)V66.CB, (T0381)L75.CB) [> 3.5552 = 5.9253 < 7.7028] w=0.7717 to align
# Constraint # added constraint: constraint((T0381)L57.CB, (T0381)F73.CB) [> 3.8008 = 6.3347 < 8.2351] w=0.7512 to align
# Constraint # added constraint: constraint((T0381)Y65.CB, (T0381)L75.CB) [> 4.1299 = 6.8832 < 8.9481] w=0.7478 to align
# Constraint # added constraint: constraint((T0381)G23.CA, (T0381)L60.CB) [> 4.2087 = 7.0145 < 9.1188] w=0.7471 to align
# Constraint # added constraint: constraint((T0381)I27.CB, (T0381)V66.CB) [> 4.4152 = 7.3586 < 9.5662] w=0.7324 to align
# Constraint # added constraint: constraint((T0381)T38.CB, (T0381)F73.CB) [> 4.3271 = 7.2119 < 9.3754] w=0.7303 to align
# Constraint # added constraint: constraint((T0381)T38.CB, (T0381)A72.CB) [> 3.4084 = 5.6806 < 7.3848] w=0.7233 to align
# Constraint # added constraint: constraint((T0381)L39.CB, (T0381)F73.CB) [> 4.2217 = 7.0362 < 9.1471] w=0.7188 to align
# Constraint # added constraint: constraint((T0381)V42.CB, (T0381)L57.CB) [> 4.4209 = 7.3682 < 9.5787] w=0.7174 to align
# Constraint # added constraint: constraint((T0381)C29.CB, (T0381)V42.CB) [> 3.6794 = 6.1323 < 7.9719] w=0.7006 to align
# Constraint # added constraint: constraint((T0381)V26.CB, (T0381)L60.CB) [> 4.1241 = 6.8736 < 8.9357] w=0.6941 to align
# Constraint # added constraint: constraint((T0381)A43.CB, (T0381)T52.CB) [> 4.4582 = 7.4303 < 9.6594] w=0.6917 to align
# Constraint # added constraint: constraint((T0381)A25.CB, (T0381)T46.CB) [> 3.5116 = 5.8527 < 7.6085] w=0.6744 to align
# Constraint # added constraint: constraint((T0381)Y65.CB, (T0381)T76.CB) [> 3.5093 = 5.8489 < 7.6035] w=0.6725 to align
# Constraint # added constraint: constraint((T0381)I27.CB, (T0381)L60.CB) [> 4.2303 = 7.0505 < 9.1657] w=0.6719 to align
# Constraint # added constraint: constraint((T0381)A67.CB, (T0381)T76.CB) [> 3.4109 = 5.6849 < 7.3904] w=0.6602 to align
# Constraint # added constraint: constraint((T0381)G64.CA, (T0381)T76.CB) [> 3.2309 = 5.3848 < 7.0002] w=0.6600 to align
# Constraint # added constraint: constraint((T0381)R37.CB, (T0381)A72.CB) [> 3.7032 = 6.1720 < 8.0237] w=0.6502 to align
# Constraint # added constraint: constraint((T0381)I27.CB, (T0381)L75.CB) [> 3.8414 = 6.4024 < 8.3231] w=0.6491 to align
# Constraint # added constraint: constraint((T0381)V26.CB, (T0381)L57.CB) [> 4.1937 = 6.9894 < 9.0863] w=0.6483 to align
# Constraint # added constraint: constraint((T0381)R22.CB, (T0381)T46.CB) [> 3.6682 = 6.1137 < 7.9478] w=0.6446 to align
# Constraint # added constraint: constraint((T0381)V66.CB, (T0381)T76.CB) [> 3.7072 = 6.1787 < 8.0323] w=0.6384 to align
# Constraint # added constraint: constraint((T0381)F30.CB, (T0381)V66.CB) [> 3.9667 = 6.6112 < 8.5946] w=0.6350 to align
# Constraint # added constraint: constraint((T0381)V26.CB, (T0381)F56.CB) [> 3.4002 = 5.6670 < 7.3671] w=0.6300 to align
# Constraint # added constraint: constraint((T0381)V26.CB, (T0381)A53.CB) [> 4.2714 = 7.1190 < 9.2547] w=0.5982 to align
# Constraint # added constraint: constraint((T0381)F30.CB, (T0381)V42.CB) [> 4.4312 = 7.3853 < 9.6009] w=0.5915 to align
# Constraint # added constraint: constraint((T0381)R36.CB, (T0381)A72.CB) [> 2.8210 = 4.7016 < 6.1121] w=0.5731 to align
# Constraint # added constraint: constraint((T0381)F30.CB, (T0381)L75.CB) [> 3.2443 = 5.4071 < 7.0293] w=0.5542 to align
# Constraint # added constraint: constraint((T0381)F30.CB, (T0381)W74.CB) [> 3.8541 = 6.4235 < 8.3506] w=0.5482 to align
# Constraint # added constraint: constraint((T0381)R22.CB, (T0381)F56.CB) [> 3.6175 = 6.0292 < 7.8380] w=0.5070 to align
# Constraint # added constraint: constraint((T0381)R36.CB, (T0381)W74.CB) [> 2.8329 = 4.7215 < 6.1380] w=0.4967 to align
# Constraint # added constraint: constraint((T0381)C29.CB, (T0381)T46.CB) [> 4.0290 = 6.7150 < 8.7295] w=0.4862 to align
# Constraint # added constraint: constraint((T0381)Y65.CB, (T0381)V79.CB) [> 2.3720 = 3.9533 < 5.1393] w=0.4801 to align
# Constraint # added constraint: constraint((T0381)Y65.CB, (T0381)R78.CB) [> 3.4715 = 5.7857 < 7.5215] w=0.4413 to align
# Constraint # added constraint: constraint((T0381)G64.CA, (T0381)R78.CB) [> 3.5031 = 5.8385 < 7.5900] w=0.4340 to align
# Constraint # added constraint: constraint((T0381)D31.CB, (T0381)L75.CB) [> 3.6732 = 6.1221 < 7.9587] w=0.4323 to align
# Constraint # added constraint: constraint((T0381)G64.CA, (T0381)V79.CB) [> 4.1490 = 6.9151 < 8.9896] w=0.4104 to align
# Constraint # added constraint: constraint((T0381)R22.CB, (T0381)L48.CB) [> 4.0519 = 6.7531 < 8.7790] w=0.3946 to align
# Constraint # added constraint: constraint((T0381)V66.CB, (T0381)V79.CB) [> 3.2316 = 5.3859 < 7.0017] w=0.3922 to align
# Constraint # added constraint: constraint((T0381)Y65.CB, (T0381)L82.CB) [> 3.8867 = 6.4778 < 8.4211] w=0.3848 to align
# Constraint # added constraint: constraint((T0381)L60.CB, (T0381)V79.CB) [> 4.3524 = 7.2541 < 9.4303] w=0.3684 to align
# Constraint # added constraint: constraint((T0381)I27.CB, (T0381)V79.CB) [> 4.0830 = 6.8049 < 8.8464] w=0.3585 to align
# Constraint # added constraint: constraint((T0381)R37.CB, (T0381)W74.CB) [> 4.4648 = 7.4414 < 9.6738] w=0.3573 to align
# Constraint # added constraint: constraint((T0381)L20.CB, (T0381)L60.CB) [> 4.0092 = 6.6820 < 8.6866] w=0.3333 to align
# Constraint # added constraint: constraint((T0381)L24.CB, (T0381)Y86.CB) [> 3.6775 = 6.1291 < 7.9678] w=0.3216 to align
# Constraint # added constraint: constraint((T0381)S19.CB, (T0381)F56.CB) [> 3.6133 = 6.0221 < 7.8287] w=0.3210 to align
# Constraint # added constraint: constraint((T0381)L24.CB, (T0381)G83.CA) [> 3.2827 = 5.4712 < 7.1126] w=0.3203 to align
# Constraint # added constraint: constraint((T0381)R28.CB, (T0381)G83.CA) [> 3.7164 = 6.1940 < 8.0522] w=0.3106 to align
# Constraint # added constraint: constraint((T0381)G23.CA, (T0381)T46.CB) [> 3.8200 = 6.3667 < 8.2767] w=0.2773 to align
# Constraint # added constraint: constraint((T0381)L20.CB, (T0381)Y65.CB) [> 3.9681 = 6.6135 < 8.5976] w=0.2593 to align
# Constraint # added constraint: constraint((T0381)L167.CB, (T0381)R183.CB) [> 3.5448 = 5.9079 < 7.6803] w=0.2564 to align
# Constraint # added constraint: constraint((T0381)L167.CB, (T0381)L186.CB) [> 4.1426 = 6.9043 < 8.9756] w=0.2560 to align
# Constraint # added constraint: constraint((T0381)L20.CB, (T0381)F56.CB) [> 3.9685 = 6.6142 < 8.5984] w=0.2242 to align
# Constraint # added constraint: constraint((T0381)S114.CB, (T0381)Y123.CB) [> 3.7220 = 6.2034 < 8.0644] w=0.2184 to align
# Constraint # added constraint: constraint((T0381)L24.CB, (T0381)L75.CB) [> 4.0426 = 6.7376 < 8.7589] w=0.2086 to align
# Constraint # added constraint: constraint((T0381)L24.CB, (T0381)L82.CB) [> 3.5980 = 5.9967 < 7.7957] w=0.2051 to align
# Constraint # added constraint: constraint((T0381)L24.CB, (T0381)L60.CB) [> 4.4225 = 7.3708 < 9.5820] w=0.2047 to align
# Constraint # added constraint: constraint((T0381)C29.CB, (T0381)D41.CB) [> 4.0838 = 6.8063 < 8.8482] w=0.2029 to align
# Constraint # added constraint: constraint((T0381)L24.CB, (T0381)V66.CB) [> 4.6299 = 7.7166 < 10.0315] w=0.2015 to align
# Constraint # added constraint: constraint((T0381)L20.CB, (T0381)L63.CB) [> 4.4164 = 7.3607 < 9.5689] w=0.2003 to align
# Constraint # added constraint: constraint((T0381)S112.CB, (T0381)Y123.CB) [> 3.4605 = 5.7675 < 7.4977] w=0.2001 to align
# Constraint # added constraint: constraint((T0381)V113.CB, (T0381)Y123.CB) [> 3.9344 = 6.5573 < 8.5245] w=0.2001 to align
# Constraint # added constraint: constraint((T0381)L100.CB, (T0381)V113.CB) [> 3.6571 = 6.0952 < 7.9238] w=0.2000 to align
# Constraint # added constraint: constraint((T0381)R28.CB, (T0381)L75.CB) [> 4.2755 = 7.1258 < 9.2635] w=0.1941 to align
# Constraint # added constraint: constraint((T0381)L103.CB, (T0381)S248.CB) [> 3.6890 = 6.1484 < 7.9929] w=0.1928 to align
# Constraint # added constraint: constraint((T0381)R22.CB, (T0381)T52.CB) [> 4.1838 = 6.9729 < 9.0648] w=0.1923 to align
# Constraint # added constraint: constraint((T0381)I172.CB, (T0381)R183.CB) [> 4.2030 = 7.0050 < 9.1065] w=0.1920 to align
# Constraint # added constraint: constraint((T0381)G23.CA, (T0381)T59.CB) [> 4.3679 = 7.2798 < 9.4638] w=0.1855 to align
# Constraint # added constraint: constraint((T0381)S111.CB, (T0381)N228.CB) [> 4.1079 = 6.8465 < 8.9004] w=0.1791 to align
# Constraint # added constraint: constraint((T0381)I216.CB, (T0381)A225.CB) [> 2.7187 = 4.5311 < 5.8904] w=0.1790 to align
# Constraint # added constraint: constraint((T0381)D31.CB, (T0381)L80.CB) [> 4.1362 = 6.8937 < 8.9619] w=0.1771 to align
# Constraint # added constraint: constraint((T0381)S111.CB, (T0381)R126.CB) [> 4.0581 = 6.7636 < 8.7927] w=0.1768 to align
# Constraint # added constraint: constraint((T0381)P215.CB, (T0381)A226.CB) [> 3.4175 = 5.6958 < 7.4046] w=0.1759 to align
# Constraint # added constraint: constraint((T0381)A213.CB, (T0381)N228.CB) [> 2.5174 = 4.1957 < 5.4543] w=0.1759 to align
# Constraint # added constraint: constraint((T0381)A213.CB, (T0381)V227.CB) [> 3.9423 = 6.5705 < 8.5416] w=0.1759 to align
# Constraint # added constraint: constraint((T0381)M212.CB, (T0381)I229.CB) [> 3.0026 = 5.0043 < 6.5056] w=0.1759 to align
# Constraint # added constraint: constraint((T0381)A96.CB, (T0381)V113.CB) [> 3.4258 = 5.7096 < 7.4225] w=0.1759 to align
# Constraint # added constraint: constraint((T0381)V107.CB, (T0381)I229.CB) [> 3.3417 = 5.5694 < 7.2403] w=0.1742 to align
# Constraint # added constraint: constraint((T0381)S111.CB, (T0381)V227.CB) [> 4.1996 = 6.9994 < 9.0992] w=0.1742 to align
# Constraint # added constraint: constraint((T0381)V113.CB, (T0381)A225.CB) [> 3.6605 = 6.1009 < 7.9311] w=0.1742 to align
# Constraint # added constraint: constraint((T0381)V227.CB, (T0381)T252.CB) [> 3.5709 = 5.9515 < 7.7369] w=0.1741 to align
# Constraint # added constraint: constraint((T0381)V113.CB, (T0381)V124.CB) [> 3.4828 = 5.8047 < 7.5462] w=0.1719 to align
# Constraint # added constraint: constraint((T0381)S112.CB, (T0381)A125.CB) [> 4.2762 = 7.1271 < 9.2652] w=0.1715 to align
# Constraint # added constraint: constraint((T0381)S110.CB, (T0381)I229.CB) [> 4.3007 = 7.1678 < 9.3181] w=0.1710 to align
# Constraint # added constraint: constraint((T0381)S110.CB, (T0381)S230.CB) [> 3.0564 = 5.0940 < 6.6223] w=0.1710 to align
# Constraint # added constraint: constraint((T0381)S111.CB, (T0381)I229.CB) [> 3.4271 = 5.7119 < 7.4255] w=0.1710 to align
# Constraint # added constraint: constraint((T0381)S112.CB, (T0381)V227.CB) [> 4.3987 = 7.3313 < 9.5306] w=0.1710 to align
# Constraint # added constraint: constraint((T0381)S112.CB, (T0381)N228.CB) [> 2.7516 = 4.5859 < 5.9617] w=0.1710 to align
# Constraint # added constraint: constraint((T0381)V113.CB, (T0381)A226.CB) [> 4.5220 = 7.5367 < 9.7976] w=0.1710 to align
# Constraint # added constraint: constraint((T0381)V113.CB, (T0381)V227.CB) [> 3.4459 = 5.7432 < 7.4661] w=0.1710 to align
# Constraint # added constraint: constraint((T0381)I198.CB, (T0381)M212.CB) [> 3.7247 = 6.2079 < 8.0702] w=0.1710 to align
# Constraint # added constraint: constraint((T0381)I198.CB, (T0381)A213.CB) [> 3.9309 = 6.5515 < 8.5169] w=0.1710 to align
# Constraint # added constraint: constraint((T0381)C199.CB, (T0381)A213.CB) [> 3.2411 = 5.4019 < 7.0224] w=0.1710 to align
# Constraint # added constraint: constraint((T0381)S211.CB, (T0381)I229.CB) [> 3.9993 = 6.6654 < 8.6651] w=0.1710 to align
# Constraint # added constraint: constraint((T0381)S211.CB, (T0381)S230.CB) [> 2.8215 = 4.7026 < 6.1134] w=0.1710 to align
# Constraint # added constraint: constraint((T0381)M212.CB, (T0381)N228.CB) [> 3.9474 = 6.5791 < 8.5528] w=0.1710 to align
# Constraint # added constraint: constraint((T0381)A213.CB, (T0381)I229.CB) [> 4.5333 = 7.5555 < 9.8222] w=0.1710 to align
# Constraint # added constraint: constraint((T0381)A214.CB, (T0381)A226.CB) [> 3.9969 = 6.6615 < 8.6600] w=0.1710 to align
# Constraint # added constraint: constraint((T0381)A214.CB, (T0381)V227.CB) [> 3.4765 = 5.7941 < 7.5324] w=0.1710 to align
# Constraint # added constraint: constraint((T0381)I216.CB, (T0381)V227.CB) [> 3.7489 = 6.2482 < 8.1226] w=0.1710 to align
# Constraint # added constraint: constraint((T0381)L103.CB, (T0381)L249.CB) [> 4.0633 = 6.7722 < 8.8039] w=0.1703 to align
# Constraint # added constraint: constraint((T0381)A21.CB, (T0381)G83.CA) [> 4.2553 = 7.0921 < 9.2198] w=0.1696 to align
# Constraint # added constraint: constraint((T0381)A21.CB, (T0381)L82.CB) [> 4.0882 = 6.8136 < 8.8577] w=0.1691 to align
# Constraint # added constraint: constraint((T0381)L163.CB, (T0381)L186.CB) [> 3.8933 = 6.4889 < 8.4355] w=0.1672 to align
# Constraint # added constraint: constraint((T0381)L100.CB, (T0381)S111.CB) [> 2.8183 = 4.6971 < 6.1062] w=0.1661 to align
# Constraint # added constraint: constraint((T0381)L103.CB, (T0381)I229.CB) [> 3.9936 = 6.6560 < 8.6528] w=0.1661 to align
# Constraint # added constraint: constraint((T0381)S114.CB, (T0381)V124.CB) [> 4.0620 = 6.7700 < 8.8010] w=0.1661 to align
# Constraint # added constraint: constraint((T0381)I115.CB, (T0381)V124.CB) [> 3.0079 = 5.0132 < 6.5171] w=0.1661 to align
# Constraint # added constraint: constraint((T0381)C199.CB, (T0381)M212.CB) [> 4.2073 = 7.0121 < 9.1157] w=0.1661 to align
# Constraint # added constraint: constraint((T0381)S211.CB, (T0381)N228.CB) [> 3.2207 = 5.3678 < 6.9782] w=0.1661 to align
# Constraint # added constraint: constraint((T0381)A213.CB, (T0381)A226.CB) [> 3.0060 = 5.0099 < 6.5129] w=0.1661 to align
# Constraint # added constraint: constraint((T0381)I216.CB, (T0381)A253.CB) [> 3.0915 = 5.1525 < 6.6982] w=0.1661 to align
# Constraint # added constraint: constraint((T0381)V227.CB, (T0381)L249.CB) [> 3.6377 = 6.0628 < 7.8817] w=0.1661 to align
# Constraint # added constraint: constraint((T0381)S110.CB, (T0381)R126.CB) [> 4.0891 = 6.8151 < 8.8597] w=0.1647 to align
# Constraint # added constraint: constraint((T0381)L155.CB, (T0381)Y166.CB) [> 4.1968 = 6.9946 < 9.0930] w=0.1638 to align
# Constraint # added constraint: constraint((T0381)A25.CB, (T0381)G83.CA) [> 3.3775 = 5.6293 < 7.3180] w=0.1623 to align
# Constraint # added constraint: constraint((T0381)A25.CB, (T0381)Y86.CB) [> 2.8139 = 4.6899 < 6.0969] w=0.1623 to align
# Constraint # added constraint: constraint((T0381)A25.CB, (T0381)L87.CB) [> 3.5054 = 5.8423 < 7.5950] w=0.1623 to align
# Constraint # added constraint: constraint((T0381)R28.CB, (T0381)L80.CB) [> 4.6504 = 7.7507 < 10.0759] w=0.1623 to align
# Constraint # added constraint: constraint((T0381)R28.CB, (T0381)Y84.CB) [> 4.2431 = 7.0718 < 9.1934] w=0.1623 to align
# Constraint # added constraint: constraint((T0381)S88.CB, (T0381)L163.CB) [> 4.0572 = 6.7621 < 8.7907] w=0.1623 to align
# Constraint # added constraint: constraint((T0381)I229.CB, (T0381)L245.CB) [> 3.3905 = 5.6508 < 7.3461] w=0.1621 to align
# Constraint # added constraint: constraint((T0381)V107.CB, (T0381)L245.CB) [> 3.7442 = 6.2403 < 8.1124] w=0.1621 to align
# Constraint # added constraint: constraint((T0381)I115.CB, (T0381)V224.CB) [> 4.3130 = 7.1883 < 9.3447] w=0.1609 to align
# Constraint # added constraint: constraint((T0381)S114.CB, (T0381)A226.CB) [> 3.0838 = 5.1398 < 6.6817] w=0.1609 to align
# Constraint # added constraint: constraint((T0381)S114.CB, (T0381)A225.CB) [> 3.8746 = 6.4576 < 8.3949] w=0.1609 to align
# Constraint # added constraint: constraint((T0381)I216.CB, (T0381)I256.CB) [> 3.1327 = 5.2212 < 6.7876] w=0.1600 to align
# Constraint # added constraint: constraint((T0381)A214.CB, (T0381)L249.CB) [> 2.8449 = 4.7414 < 6.1639] w=0.1600 to align
# Constraint # added constraint: constraint((T0381)H99.CB, (T0381)T252.CB) [> 2.8965 = 4.8274 < 6.2757] w=0.1600 to align
# Constraint # added constraint: constraint((T0381)V227.CB, (T0381)A253.CB) [> 3.1800 = 5.2999 < 6.8899] w=0.1598 to align
# Constraint # added constraint: constraint((T0381)I229.CB, (T0381)L249.CB) [> 3.6759 = 6.1265 < 7.9645] w=0.1598 to align
# Constraint # added constraint: constraint((T0381)I121.CB, (T0381)A145.CB) [> 3.6224 = 6.0373 < 7.8485] w=0.1588 to align
# Constraint # added constraint: constraint((T0381)M212.CB, (T0381)L241.CB) [> 3.9479 = 6.5799 < 8.5539] w=0.1579 to align
# Constraint # added constraint: constraint((T0381)Y123.CB, (T0381)I137.CB) [> 3.3982 = 5.6637 < 7.3629] w=0.1578 to align
# Constraint # added constraint: constraint((T0381)S19.CB, (T0381)T46.CB) [> 4.2928 = 7.1547 < 9.3011] w=0.1565 to align
# Constraint # added constraint: constraint((T0381)S104.CB, (T0381)V127.CB) [> 2.7310 = 4.5517 < 5.9172] w=0.1558 to align
# Constraint # added constraint: constraint((T0381)L163.CB, (T0381)I190.CB) [> 4.2349 = 7.0581 < 9.1755] w=0.1553 to align
# Constraint # added constraint: constraint((T0381)L100.CB, (T0381)V227.CB) [> 4.2529 = 7.0881 < 9.2146] w=0.1553 to align
# Constraint # added constraint: constraint((T0381)H99.CB, (T0381)D255.CB) [> 3.4091 = 5.6819 < 7.3864] w=0.1539 to align
# Constraint # added constraint: constraint((T0381)M212.CB, (T0381)L245.CB) [> 3.1313 = 5.2189 < 6.7846] w=0.1539 to align
# Constraint # added constraint: constraint((T0381)I216.CB, (T0381)A226.CB) [> 3.7420 = 6.2367 < 8.1077] w=0.1527 to align
# Constraint # added constraint: constraint((T0381)R210.CB, (T0381)S230.CB) [> 4.2695 = 7.1158 < 9.2505] w=0.1527 to align
# Constraint # added constraint: constraint((T0381)T176.CB, (T0381)E204.CB) [> 3.5899 = 5.9831 < 7.7781] w=0.1527 to align
# Constraint # added constraint: constraint((T0381)L175.CB, (T0381)L205.CB) [> 3.3842 = 5.6404 < 7.3326] w=0.1527 to align
# Constraint # added constraint: constraint((T0381)Y123.CB, (T0381)L143.CB) [> 4.1765 = 6.9608 < 9.0490] w=0.1527 to align
# Constraint # added constraint: constraint((T0381)I115.CB, (T0381)A225.CB) [> 3.2372 = 5.3954 < 7.0140] w=0.1527 to align
# Constraint # added constraint: constraint((T0381)L100.CB, (T0381)A125.CB) [> 3.8976 = 6.4960 < 8.4447] w=0.1527 to align
# Constraint # added constraint: constraint((T0381)R217.CB, (T0381)E257.CB) [> 2.7623 = 4.6039 < 5.9851] w=0.1518 to align
# Constraint # added constraint: constraint((T0381)M212.CB, (T0381)L249.CB) [> 3.4308 = 5.7180 < 7.4334] w=0.1506 to align
# Constraint # added constraint: constraint((T0381)L103.CB, (T0381)V227.CB) [> 4.2758 = 7.1263 < 9.2642] w=0.1496 to align
# Constraint # added constraint: constraint((T0381)D120.CB, (T0381)R142.CB) [> 2.8430 = 4.7383 < 6.1598] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)D120.CB, (T0381)L143.CB) [> 3.9937 = 6.6562 < 8.6531] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)D120.CB, (T0381)A145.CB) [> 3.9593 = 6.5989 < 8.5786] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)I121.CB, (T0381)R142.CB) [> 4.1523 = 6.9206 < 8.9967] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)I121.CB, (T0381)L143.CB) [> 2.5169 = 4.1948 < 5.4532] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)I121.CB, (T0381)P144.CB) [> 4.5001 = 7.5002 < 9.7503] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)I121.CB, (T0381)T148.CB) [> 3.6095 = 6.0158 < 7.8205] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)I121.CB, (T0381)G151.CA) [> 2.8119 = 4.6865 < 6.0925] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)I121.CB, (T0381)L154.CB) [> 3.8357 = 6.3928 < 8.3106] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)V122.CB, (T0381)T141.CB) [> 4.3169 = 7.1948 < 9.3532] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)V122.CB, (T0381)R142.CB) [> 3.4860 = 5.8100 < 7.5530] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)Y123.CB, (T0381)T141.CB) [> 2.6733 = 4.4555 < 5.7921] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)A145.CB, (T0381)L154.CB) [> 3.8200 = 6.3667 < 8.2767] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)A145.CB, (T0381)L155.CB) [> 3.4245 = 5.7075 < 7.4197] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)A145.CB, (T0381)Y166.CB) [> 3.9128 = 6.5214 < 8.4778] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)Y146.CB, (T0381)I180.CB) [> 3.7548 = 6.2581 < 8.1355] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)Y146.CB, (T0381)L186.CB) [> 3.4688 = 5.7813 < 7.5157] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)A147.CB, (T0381)L175.CB) [> 3.3692 = 5.6154 < 7.3000] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)A147.CB, (T0381)T179.CB) [> 3.0925 = 5.1542 < 6.7005] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)A147.CB, (T0381)I180.CB) [> 4.2980 = 7.1633 < 9.3122] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)P93.CB, (T0381)A125.CB) [> 3.2276 = 5.3793 < 6.9931] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)L100.CB, (T0381)V127.CB) [> 2.8966 = 4.8277 < 6.2761] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)E101.CB, (T0381)V127.CB) [> 3.4098 = 5.6830 < 7.3879] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)S104.CB, (T0381)V129.CB) [> 3.8980 = 6.4967 < 8.4457] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)S110.CB, (T0381)P128.CB) [> 3.0357 = 5.0594 < 6.5773] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)S110.CB, (T0381)V129.CB) [> 3.1472 = 5.2454 < 6.8190] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)S111.CB, (T0381)V127.CB) [> 2.8358 = 4.7263 < 6.1441] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)S112.CB, (T0381)R126.CB) [> 3.0517 = 5.0862 < 6.6120] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)S112.CB, (T0381)M150.CB) [> 4.1357 = 6.8929 < 8.9607] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)V113.CB, (T0381)R126.CB) [> 4.3069 = 7.1782 < 9.3316] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)S114.CB, (T0381)M150.CB) [> 2.4584 = 4.0973 < 5.3264] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)S114.CB, (T0381)G151.CA) [> 4.1651 = 6.9419 < 9.0244] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)S114.CB, (T0381)N228.CB) [> 4.0182 = 6.6971 < 8.7062] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)L116.CB, (T0381)L154.CB) [> 3.0037 = 5.0062 < 6.5081] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)A119.CB, (T0381)A145.CB) [> 3.6784 = 6.1307 < 7.9699] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)A119.CB, (T0381)K169.CB) [> 3.6614 = 6.1024 < 7.9331] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)A119.CB, (T0381)L170.CB) [> 3.3839 = 5.6399 < 7.3318] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)L154.CB, (T0381)A226.CB) [> 3.4502 = 5.7504 < 7.4755] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)L155.CB, (T0381)I190.CB) [> 3.3835 = 5.6392 < 7.3309] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)A156.CB, (T0381)I190.CB) [> 2.6903 = 4.4838 < 5.8289] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)A156.CB, (T0381)L191.CB) [> 4.6067 = 7.6778 < 9.9812] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)A156.CB, (T0381)R194.CB) [> 2.7792 = 4.6320 < 6.0216] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)G157.CA, (T0381)P215.CB) [> 4.3164 = 7.1939 < 9.3521] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)G157.CA, (T0381)T223.CB) [> 3.6576 = 6.0960 < 7.9248] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)T176.CB, (T0381)A207.CB) [> 3.3777 = 5.6296 < 7.3184] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)R178.CB, (T0381)D202.CB) [> 3.7772 = 6.2954 < 8.1840] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)I180.CB, (T0381)A189.CB) [> 3.5814 = 5.9690 < 7.7597] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)I180.CB, (T0381)E204.CB) [> 3.9602 = 6.6004 < 8.5805] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)G197.CA, (T0381)A214.CB) [> 3.9262 = 6.5437 < 8.5069] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)I198.CB, (T0381)I246.CB) [> 3.0076 = 5.0128 < 6.5166] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)C199.CB, (T0381)A214.CB) [> 4.5582 = 7.5970 < 9.8761] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)L209.CB, (T0381)S230.CB) [> 3.8290 = 6.3816 < 8.2961] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)G218.CA, (T0381)E257.CB) [> 3.6991 = 6.1652 < 8.0147] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)A147.CB, (T0381)L205.CB) [> 2.9527 = 4.9211 < 6.3975] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)T148.CB, (T0381)L205.CB) [> 3.4265 = 5.7109 < 7.4241] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)T148.CB, (T0381)A213.CB) [> 4.5646 = 7.6077 < 9.8900] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)S149.CB, (T0381)C199.CB) [> 2.7195 = 4.5324 < 5.8922] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)S149.CB, (T0381)S211.CB) [> 2.3686 = 3.9477 < 5.1320] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)S149.CB, (T0381)M212.CB) [> 3.5055 = 5.8426 < 7.5953] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)S149.CB, (T0381)A213.CB) [> 2.1430 = 3.5717 < 4.6432] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)S149.CB, (T0381)N228.CB) [> 3.2516 = 5.4193 < 7.0451] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)M150.CB, (T0381)A213.CB) [> 2.6810 = 4.4683 < 5.8088] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)M150.CB, (T0381)A226.CB) [> 2.4189 = 4.0315 < 5.2410] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)G151.CA, (T0381)A213.CB) [> 4.3159 = 7.1932 < 9.3512] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)G151.CA, (T0381)A226.CB) [> 3.9557 = 6.5928 < 8.5707] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)L154.CB, (T0381)T223.CB) [> 3.6967 = 6.1611 < 8.0094] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)V153.CB, (T0381)A226.CB) [> 2.6971 = 4.4952 < 5.8437] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)V153.CB, (T0381)P215.CB) [> 2.9077 = 4.8462 < 6.3000] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)V153.CB, (T0381)A214.CB) [> 3.6300 = 6.0501 < 7.8651] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)V153.CB, (T0381)A213.CB) [> 2.7258 = 4.5431 < 5.9060] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)V153.CB, (T0381)C199.CB) [> 2.7217 = 4.5361 < 5.8970] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)V153.CB, (T0381)V193.CB) [> 3.7998 = 6.3331 < 8.2330] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)R152.CB, (T0381)A213.CB) [> 4.3195 = 7.1991 < 9.3588] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)R152.CB, (T0381)C199.CB) [> 2.4824 = 4.1374 < 5.3786] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)R152.CB, (T0381)V193.CB) [> 3.3817 = 5.6362 < 7.3271] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)R152.CB, (T0381)I190.CB) [> 3.9126 = 6.5210 < 8.4773] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)R152.CB, (T0381)A189.CB) [> 3.9486 = 6.5810 < 8.5553] w=0.1478 to align
# Constraint # added constraint: constraint((T0381)L20.CB, (T0381)T59.CB) [> 4.4473 = 7.4122 < 9.6359] w=0.1476 to align
# Constraint # added constraint: constraint((T0381)V95.CB, (T0381)D259.CB) [> 2.9683 = 4.9472 < 6.4314] w=0.1457 to align
# Constraint # added constraint: constraint((T0381)A96.CB, (T0381)I256.CB) [> 3.1644 = 5.2741 < 6.8563] w=0.1457 to align
# Constraint # added constraint: constraint((T0381)H99.CB, (T0381)I256.CB) [> 3.2003 = 5.3338 < 6.9340] w=0.1457 to align
# Constraint # added constraint: constraint((T0381)K102.CB, (T0381)T252.CB) [> 3.9687 = 6.6145 < 8.5989] w=0.1457 to align
# Constraint # added constraint: constraint((T0381)L103.CB, (T0381)T252.CB) [> 2.9344 = 4.8906 < 6.3578] w=0.1457 to align
# Constraint # added constraint: constraint((T0381)M212.CB, (T0381)I246.CB) [> 3.4466 = 5.7443 < 7.4676] w=0.1457 to align
# Constraint # added constraint: constraint((T0381)A214.CB, (T0381)R250.CB) [> 3.1347 = 5.2245 < 6.7918] w=0.1457 to align
# Constraint # added constraint: constraint((T0381)A214.CB, (T0381)A253.CB) [> 2.5754 = 4.2923 < 5.5799] w=0.1457 to align
# Constraint # added constraint: constraint((T0381)P215.CB, (T0381)A253.CB) [> 3.9481 = 6.5802 < 8.5543] w=0.1457 to align
# Constraint # added constraint: constraint((T0381)I216.CB, (T0381)L260.CB) [> 4.2463 = 7.0773 < 9.2004] w=0.1457 to align
# Constraint # added constraint: constraint((T0381)V227.CB, (T0381)I256.CB) [> 4.0866 = 6.8110 < 8.8544] w=0.1457 to align
# Constraint # added constraint: constraint((T0381)F30.CB, (T0381)V79.CB) [> 4.5483 = 7.5805 < 9.8546] w=0.1431 to align
# Constraint # added constraint: constraint((T0381)V200.CB, (T0381)S211.CB) [> 4.1782 = 6.9637 < 9.0528] w=0.1414 to align
# Constraint # added constraint: constraint((T0381)S112.CB, (T0381)S230.CB) [> 4.0969 = 6.8281 < 8.8766] w=0.1414 to align
# Constraint # added constraint: constraint((T0381)I198.CB, (T0381)R250.CB) [> 3.9115 = 6.5192 < 8.4749] w=0.1396 to align
# Constraint # added constraint: constraint((T0381)Y123.CB, (T0381)T138.CB) [> 4.2737 = 7.1229 < 9.2597] w=0.1395 to align
# Constraint # added constraint: constraint((T0381)S112.CB, (T0381)I137.CB) [> 3.8969 = 6.4948 < 8.4432] w=0.1389 to align
# Constraint # added constraint: constraint((T0381)A214.CB, (T0381)I246.CB) [> 4.1998 = 6.9996 < 9.0995] w=0.1353 to align
# Constraint # added constraint: constraint((T0381)G208.CA, (T0381)A233.CB) [> 2.6587 = 4.4312 < 5.7605] w=0.1332 to align
# Constraint # added constraint: constraint((T0381)V95.CB, (T0381)I256.CB) [> 3.5674 = 5.9456 < 7.7293] w=0.1293 to align
# Constraint # added constraint: constraint((T0381)F30.CB, (T0381)A45.CB) [> 4.4945 = 7.4909 < 9.7381] w=0.1291 to align
# Constraint # added constraint: constraint((T0381)E109.CB, (T0381)T231.CB) [> 2.5491 = 4.2485 < 5.5231] w=0.1281 to align
# Constraint # added constraint: constraint((T0381)A125.CB, (T0381)I139.CB) [> 3.8825 = 6.4708 < 8.4121] w=0.1281 to align
# Constraint # added constraint: constraint((T0381)R126.CB, (T0381)I139.CB) [> 3.4981 = 5.8302 < 7.5793] w=0.1281 to align
# Constraint # added constraint: constraint((T0381)T148.CB, (T0381)L201.CB) [> 3.3649 = 5.6081 < 7.2905] w=0.1281 to align
# Constraint # added constraint: constraint((T0381)S149.CB, (T0381)V200.CB) [> 3.6698 = 6.1163 < 7.9511] w=0.1281 to align
# Constraint # added constraint: constraint((T0381)V153.CB, (T0381)I198.CB) [> 3.9938 = 6.6564 < 8.6533] w=0.1281 to align
# Constraint # added constraint: constraint((T0381)L154.CB, (T0381)P215.CB) [> 4.2240 = 7.0399 < 9.1519] w=0.1281 to align
# Constraint # added constraint: constraint((T0381)L175.CB, (T0381)E206.CB) [> 4.1221 = 6.8703 < 8.9313] w=0.1281 to align
# Constraint # added constraint: constraint((T0381)V200.CB, (T0381)R210.CB) [> 4.3408 = 7.2347 < 9.4051] w=0.1281 to align
# Constraint # added constraint: constraint((T0381)L201.CB, (T0381)R210.CB) [> 3.9114 = 6.5191 < 8.4748] w=0.1281 to align
# Constraint # added constraint: constraint((T0381)L201.CB, (T0381)S211.CB) [> 2.7011 = 4.5018 < 5.8524] w=0.1281 to align
# Constraint # added constraint: constraint((T0381)V61.CB, (T0381)F73.CB) [> 4.4365 = 7.3942 < 9.6125] w=0.1239 to align
# Constraint # added constraint: constraint((T0381)Y123.CB, (T0381)I139.CB) [> 3.0463 = 5.0772 < 6.6003] w=0.1232 to align
# Constraint # added constraint: constraint((T0381)Y123.CB, (T0381)G140.CA) [> 3.1462 = 5.2436 < 6.8167] w=0.1232 to align
# Constraint # added constraint: constraint((T0381)Y123.CB, (T0381)R142.CB) [> 4.6810 = 7.8016 < 10.1420] w=0.1232 to align
# Constraint # added constraint: constraint((T0381)V124.CB, (T0381)I139.CB) [> 3.7505 = 6.2509 < 8.1262] w=0.1232 to align
# Constraint # added constraint: constraint((T0381)V124.CB, (T0381)G140.CA) [> 4.1422 = 6.9036 < 8.9747] w=0.1232 to align
# Constraint # added constraint: constraint((T0381)R126.CB, (T0381)I137.CB) [> 4.0206 = 6.7010 < 8.7113] w=0.1232 to align
# Constraint # added constraint: constraint((T0381)M133.CB, (T0381)P232.CB) [> 3.5875 = 5.9792 < 7.7730] w=0.1232 to align
# Constraint # added constraint: constraint((T0381)V135.CB, (T0381)L209.CB) [> 4.2174 = 7.0290 < 9.1376] w=0.1232 to align
# Constraint # added constraint: constraint((T0381)V135.CB, (T0381)S230.CB) [> 2.9919 = 4.9865 < 6.4824] w=0.1232 to align
# Constraint # added constraint: constraint((T0381)P144.CB, (T0381)L205.CB) [> 4.1421 = 6.9035 < 8.9745] w=0.1232 to align
# Constraint # added constraint: constraint((T0381)V122.CB, (T0381)G140.CA) [> 3.3225 = 5.5374 < 7.1987] w=0.1232 to align
# Constraint # added constraint: constraint((T0381)I121.CB, (T0381)A226.CB) [> 4.3309 = 7.2181 < 9.3836] w=0.1232 to align
# Constraint # added constraint: constraint((T0381)D120.CB, (T0381)P144.CB) [> 4.1281 = 6.8802 < 8.9443] w=0.1232 to align
# Constraint # added constraint: constraint((T0381)S114.CB, (T0381)A213.CB) [> 4.5202 = 7.5336 < 9.7937] w=0.1232 to align
# Constraint # added constraint: constraint((T0381)S114.CB, (T0381)L143.CB) [> 3.9155 = 6.5258 < 8.4835] w=0.1232 to align
# Constraint # added constraint: constraint((T0381)S104.CB, (T0381)P128.CB) [> 4.5237 = 7.5394 < 9.8013] w=0.1232 to align
# Constraint # added constraint: constraint((T0381)H99.CB, (T0381)V227.CB) [> 4.5003 = 7.5005 < 9.7506] w=0.1232 to align
# Constraint # added constraint: constraint((T0381)Q97.CB, (T0381)A125.CB) [> 3.9415 = 6.5691 < 8.5398] w=0.1232 to align
# Constraint # added constraint: constraint((T0381)A96.CB, (T0381)A125.CB) [> 3.7575 = 6.2625 < 8.1412] w=0.1232 to align
# Constraint # added constraint: constraint((T0381)L92.CB, (T0381)V224.CB) [> 4.0645 = 6.7741 < 8.8064] w=0.1232 to align
# Constraint # added constraint: constraint((T0381)N228.CB, (T0381)L249.CB) [> 4.4288 = 7.3814 < 9.5958] w=0.1232 to align
# Constraint # added constraint: constraint((T0381)R210.CB, (T0381)P232.CB) [> 4.4549 = 7.4248 < 9.6523] w=0.1232 to align
# Constraint # added constraint: constraint((T0381)R210.CB, (T0381)T231.CB) [> 3.8036 = 6.3394 < 8.2412] w=0.1232 to align
# Constraint # added constraint: constraint((T0381)L209.CB, (T0381)P232.CB) [> 4.1511 = 6.9184 < 8.9939] w=0.1232 to align
# Constraint # added constraint: constraint((T0381)G208.CA, (T0381)P232.CB) [> 3.7220 = 6.2034 < 8.0644] w=0.1232 to align
# Constraint # added constraint: constraint((T0381)V200.CB, (T0381)M212.CB) [> 3.4057 = 5.6761 < 7.3789] w=0.1232 to align
# Constraint # added constraint: constraint((T0381)I198.CB, (T0381)L249.CB) [> 3.6363 = 6.0604 < 7.8785] w=0.1232 to align
# Constraint # added constraint: constraint((T0381)G157.CA, (T0381)I190.CB) [> 4.6511 = 7.7519 < 10.0775] w=0.1232 to align
# Constraint # added constraint: constraint((T0381)R152.CB, (T0381)L201.CB) [> 4.1840 = 6.9734 < 9.0654] w=0.1232 to align
# Constraint # added constraint: constraint((T0381)G151.CA, (T0381)C199.CB) [> 4.3801 = 7.3003 < 9.4903] w=0.1232 to align
# Constraint # added constraint: constraint((T0381)M150.CB, (T0381)S211.CB) [> 4.3661 = 7.2768 < 9.4599] w=0.1232 to align
# Constraint # added constraint: constraint((T0381)S149.CB, (T0381)L201.CB) [> 2.6203 = 4.3671 < 5.6773] w=0.1232 to align
# Constraint # added constraint: constraint((T0381)T148.CB, (T0381)S211.CB) [> 3.8242 = 6.3736 < 8.2857] w=0.1232 to align
# Constraint # added constraint: constraint((T0381)T148.CB, (T0381)E204.CB) [> 4.3958 = 7.3263 < 9.5242] w=0.1232 to align
# Constraint # added constraint: constraint((T0381)A147.CB, (T0381)L201.CB) [> 4.1526 = 6.9210 < 8.9972] w=0.1232 to align
# Constraint # added constraint: constraint((T0381)Y146.CB, (T0381)T179.CB) [> 4.6213 = 7.7021 < 10.0128] w=0.1232 to align
# Constraint # added constraint: constraint((T0381)Y146.CB, (T0381)L170.CB) [> 3.8904 = 6.4840 < 8.4292] w=0.1232 to align
# Constraint # added constraint: constraint((T0381)A145.CB, (T0381)L170.CB) [> 4.0791 = 6.7986 < 8.8382] w=0.1232 to align
# Constraint # added constraint: constraint((T0381)Q203.CB, (T0381)A233.CB) [> 3.8576 = 6.4294 < 8.3582] w=0.1232 to align
# Constraint # added constraint: constraint((T0381)P215.CB, (T0381)A225.CB) [> 4.4822 = 7.4703 < 9.7114] w=0.1217 to align
# Constraint # added constraint: constraint((T0381)I27.CB, (T0381)A96.CB) [> 3.7849 = 6.3082 < 8.2007] w=0.1188 to align
# Constraint # added constraint: constraint((T0381)V42.CB, (T0381)F56.CB) [> 4.5949 = 7.6582 < 9.9557] w=0.1152 to align
# Constraint # added constraint: constraint((T0381)S85.CB, (T0381)D160.CB) [> 4.6487 = 7.7478 < 10.0722] w=0.1150 to align
# Constraint # added constraint: constraint((T0381)A225.CB, (T0381)I256.CB) [> 4.5741 = 7.6235 < 9.9106] w=0.1150 to align
# Constraint # added constraint: constraint((T0381)R210.CB, (T0381)A233.CB) [> 3.0791 = 5.1318 < 6.6714] w=0.1150 to align
# Constraint # added constraint: constraint((T0381)L209.CB, (T0381)A233.CB) [> 4.1314 = 6.8856 < 8.9513] w=0.1150 to align
# Constraint # added constraint: constraint((T0381)V95.CB, (T0381)L260.CB) [> 3.8656 = 6.4427 < 8.3755] w=0.1150 to align
# Constraint # added constraint: constraint((T0381)C29.CB, (T0381)L87.CB) [> 4.5631 = 7.6051 < 9.8866] w=0.1140 to align
# Constraint # added constraint: constraint((T0381)V200.CB, (T0381)L241.CB) [> 3.7812 = 6.3021 < 8.1927] w=0.1136 to align
# Constraint # added constraint: constraint((T0381)L63.CB, (T0381)R78.CB) [> 4.3535 = 7.2559 < 9.4326] w=0.1083 to align
# Constraint # added constraint: constraint((T0381)Q18.CB, (T0381)A156.CB) [> 2.5753 = 4.2921 < 5.5798] w=0.1081 to align
# Constraint # added constraint: constraint((T0381)Y86.CB, (T0381)L155.CB) [> 3.2044 = 5.3407 < 6.9429] w=0.1078 to align
# Constraint # added constraint: constraint((T0381)V95.CB, (T0381)Y166.CB) [> 3.8472 = 6.4120 < 8.3355] w=0.1067 to align
# Constraint # added constraint: constraint((T0381)A96.CB, (T0381)V227.CB) [> 4.3431 = 7.2386 < 9.4101] w=0.1061 to align
# Constraint # added constraint: constraint((T0381)S19.CB, (T0381)L48.CB) [> 3.9833 = 6.6389 < 8.6305] w=0.1052 to align
# Constraint # added constraint: constraint((T0381)V224.CB, (T0381)L260.CB) [> 4.2529 = 7.0882 < 9.2147] w=0.1046 to align
# Constraint # added constraint: constraint((T0381)R217.CB, (T0381)L260.CB) [> 4.3489 = 7.2481 < 9.4226] w=0.1046 to align
# Constraint # added constraint: constraint((T0381)L116.CB, (T0381)A145.CB) [> 4.3930 = 7.3216 < 9.5181] w=0.1046 to align
# Constraint # added constraint: constraint((T0381)L92.CB, (T0381)I115.CB) [> 4.5487 = 7.5812 < 9.8555] w=0.1034 to align
# Constraint # added constraint: constraint((T0381)L100.CB, (T0381)R126.CB) [> 4.4782 = 7.4636 < 9.7027] w=0.1034 to align
# Constraint # added constraint: constraint((T0381)S110.CB, (T0381)T231.CB) [> 3.8389 = 6.3982 < 8.3177] w=0.1034 to align
# Constraint # added constraint: constraint((T0381)L143.CB, (T0381)L205.CB) [> 4.1276 = 6.8794 < 8.9432] w=0.0985 to align
# Constraint # added constraint: constraint((T0381)V122.CB, (T0381)L143.CB) [> 4.3563 = 7.2605 < 9.4387] w=0.0985 to align
# Constraint # added constraint: constraint((T0381)D117.CB, (T0381)R142.CB) [> 4.3731 = 7.2884 < 9.4750] w=0.0985 to align
# Constraint # added constraint: constraint((T0381)L116.CB, (T0381)G151.CA) [> 4.5824 = 7.6373 < 9.9284] w=0.0985 to align
# Constraint # added constraint: constraint((T0381)S114.CB, (T0381)L154.CB) [> 4.1557 = 6.9261 < 9.0039] w=0.0985 to align
# Constraint # added constraint: constraint((T0381)V107.CB, (T0381)T231.CB) [> 4.7035 = 7.8392 < 10.1910] w=0.0985 to align
# Constraint # added constraint: constraint((T0381)Q97.CB, (T0381)V127.CB) [> 4.5829 = 7.6382 < 9.9296] w=0.0985 to align
# Constraint # added constraint: constraint((T0381)L92.CB, (T0381)I216.CB) [> 4.2698 = 7.1164 < 9.2514] w=0.0985 to align
# Constraint # added constraint: constraint((T0381)L92.CB, (T0381)V124.CB) [> 4.4234 = 7.3723 < 9.5839] w=0.0985 to align
# Constraint # added constraint: constraint((T0381)G197.CA, (T0381)I246.CB) [> 4.5482 = 7.5804 < 9.8545] w=0.0985 to align
# Constraint # added constraint: constraint((T0381)G197.CA, (T0381)P215.CB) [> 4.1554 = 6.9257 < 9.0035] w=0.0985 to align
# Constraint # added constraint: constraint((T0381)A189.CB, (T0381)C199.CB) [> 4.5978 = 7.6629 < 9.9618] w=0.0985 to align
# Constraint # added constraint: constraint((T0381)D164.CB, (T0381)R183.CB) [> 4.2713 = 7.1189 < 9.2546] w=0.0985 to align
# Constraint # added constraint: constraint((T0381)L158.CB, (T0381)T223.CB) [> 4.2194 = 7.0324 < 9.1421] w=0.0985 to align
# Constraint # added constraint: constraint((T0381)A156.CB, (T0381)P215.CB) [> 4.2727 = 7.1211 < 9.2575] w=0.0985 to align
# Constraint # added constraint: constraint((T0381)L155.CB, (T0381)L186.CB) [> 4.6937 = 7.8228 < 10.1697] w=0.0985 to align
# Constraint # added constraint: constraint((T0381)L154.CB, (T0381)A225.CB) [> 4.5051 = 7.5085 < 9.7611] w=0.0985 to align
# Constraint # added constraint: constraint((T0381)V153.CB, (T0381)G197.CA) [> 4.6053 = 7.6755 < 9.9782] w=0.0985 to align
# Constraint # added constraint: constraint((T0381)Y146.CB, (T0381)L155.CB) [> 4.1809 = 6.9681 < 9.0585] w=0.0985 to align
# Constraint # added constraint: constraint((T0381)P144.CB, (T0381)L175.CB) [> 4.2198 = 7.0330 < 9.1429] w=0.0985 to align
# Constraint # added constraint: constraint((T0381)Y236.CB, (T0381)L245.CB) [> 4.2488 = 7.0813 < 9.2057] w=0.0972 to align
# Constraint # added constraint: constraint((T0381)A219.CB, (T0381)L260.CB) [> 3.8250 = 6.3750 < 8.2875] w=0.0964 to align
# Constraint # added constraint: constraint((T0381)S85.CB, (T0381)V95.CB) [> 3.8606 = 6.4343 < 8.3646] w=0.0961 to align
# Constraint # added constraint: constraint((T0381)V107.CB, (T0381)L158.CB) [> 4.0206 = 6.7011 < 8.7114] w=0.0955 to align
# Constraint # added constraint: constraint((T0381)S110.CB, (T0381)I137.CB) [> 4.3041 = 7.1736 < 9.3256] w=0.0946 to align
# Constraint # added constraint: constraint((T0381)L75.CB, (T0381)P93.CB) [> 3.4064 = 5.6773 < 7.3804] w=0.0944 to align
# Constraint # added constraint: constraint((T0381)L167.CB, (T0381)K187.CB) [> 3.6028 = 6.0047 < 7.8061] w=0.0940 to align
# Constraint # added constraint: constraint((T0381)Y84.CB, (T0381)T181.CB) [> 2.9001 = 4.8335 < 6.2836] w=0.0933 to align
# Constraint # added constraint: constraint((T0381)Y84.CB, (T0381)A182.CB) [> 2.4899 = 4.1498 < 5.3948] w=0.0933 to align
# Constraint # added constraint: constraint((T0381)S85.CB, (T0381)E185.CB) [> 4.4452 = 7.4087 < 9.6313] w=0.0933 to align
# Constraint # added constraint: constraint((T0381)L87.CB, (T0381)T181.CB) [> 3.1886 = 5.3144 < 6.9087] w=0.0933 to align
# Constraint # added constraint: constraint((T0381)S110.CB, (T0381)G136.CA) [> 3.8763 = 6.4605 < 8.3987] w=0.0927 to align
# Constraint # added constraint: constraint((T0381)S111.CB, (T0381)S230.CB) [> 4.6212 = 7.7020 < 10.0127] w=0.0922 to align
# Constraint # added constraint: constraint((T0381)R210.CB, (T0381)Y236.CB) [> 2.6158 = 4.3596 < 5.6675] w=0.0903 to align
# Constraint # added constraint: constraint((T0381)S19.CB, (T0381)T59.CB) [> 3.3680 = 5.6133 < 7.2972] w=0.0902 to align
# Constraint # added constraint: constraint((T0381)S112.CB, (T0381)V124.CB) [> 3.4443 = 5.7405 < 7.4627] w=0.0895 to align
# Constraint # added constraint: constraint((T0381)I229.CB, (T0381)S248.CB) [> 4.4858 = 7.4763 < 9.7192] w=0.0880 to align
# Constraint # added constraint: constraint((T0381)L75.CB, (T0381)L92.CB) [> 2.9752 = 4.9587 < 6.4463] w=0.0867 to align
# Constraint # added constraint: constraint((T0381)L92.CB, (T0381)L167.CB) [> 4.4424 = 7.4039 < 9.6251] w=0.0858 to align
# Constraint # added constraint: constraint((T0381)M212.CB, (T0381)S230.CB) [> 4.5015 = 7.5025 < 9.7533] w=0.0837 to align
# Constraint # added constraint: constraint((T0381)I172.CB, (T0381)L186.CB) [> 3.9842 = 6.6403 < 8.6324] w=0.0814 to align
# Constraint # added constraint: constraint((T0381)H108.CB, (T0381)S130.CB) [> 4.1553 = 6.9254 < 9.0030] w=0.0814 to align
# Constraint # added constraint: constraint((T0381)I137.CB, (T0381)S230.CB) [> 4.5668 = 7.6113 < 9.8947] w=0.0809 to align
# Constraint # added constraint: constraint((T0381)L100.CB, (T0381)S112.CB) [> 4.4254 = 7.3756 < 9.5883] w=0.0800 to align
# Constraint # added constraint: constraint((T0381)Y16.CB, (T0381)F56.CB) [> 4.0698 = 6.7830 < 8.8179] w=0.0792 to align
# Constraint # added constraint: constraint((T0381)S112.CB, (T0381)I229.CB) [> 4.6166 = 7.6943 < 10.0026] w=0.0788 to align
# Constraint # added constraint: constraint((T0381)L116.CB, (T0381)T223.CB) [> 4.1924 = 6.9873 < 9.0835] w=0.0788 to align
# Constraint # added constraint: constraint((T0381)L116.CB, (T0381)V224.CB) [> 3.5248 = 5.8747 < 7.6371] w=0.0788 to align
# Constraint # added constraint: constraint((T0381)L116.CB, (T0381)A225.CB) [> 4.0849 = 6.8082 < 8.8507] w=0.0788 to align
# Constraint # added constraint: constraint((T0381)V124.CB, (T0381)A225.CB) [> 4.2762 = 7.1270 < 9.2651] w=0.0788 to align
# Constraint # added constraint: constraint((T0381)A96.CB, (T0381)L170.CB) [> 4.1440 = 6.9067 < 8.9787] w=0.0784 to align
# Constraint # added constraint: constraint((T0381)L100.CB, (T0381)L154.CB) [> 3.6460 = 6.0767 < 7.8998] w=0.0774 to align
# Constraint # added constraint: constraint((T0381)G23.CA, (T0381)A53.CB) [> 4.7056 = 7.8426 < 10.1953] w=0.0753 to align
# Constraint # added constraint: constraint((T0381)E109.CB, (T0381)R235.CB) [> 4.3752 = 7.2921 < 9.4797] w=0.0739 to align
# Constraint # added constraint: constraint((T0381)S110.CB, (T0381)T134.CB) [> 3.5541 = 5.9236 < 7.7006] w=0.0739 to align
# Constraint # added constraint: constraint((T0381)I115.CB, (T0381)L154.CB) [> 4.5178 = 7.5297 < 9.7887] w=0.0739 to align
# Constraint # added constraint: constraint((T0381)I115.CB, (T0381)A226.CB) [> 4.7255 = 7.8758 < 10.2385] w=0.0739 to align
# Constraint # added constraint: constraint((T0381)V129.CB, (T0381)T231.CB) [> 4.2245 = 7.0409 < 9.1531] w=0.0739 to align
# Constraint # added constraint: constraint((T0381)V135.CB, (T0381)T231.CB) [> 3.7426 = 6.2376 < 8.1089] w=0.0739 to align
# Constraint # added constraint: constraint((T0381)V135.CB, (T0381)P232.CB) [> 4.4308 = 7.3847 < 9.6001] w=0.0739 to align
# Constraint # added constraint: constraint((T0381)A214.CB, (T0381)T252.CB) [> 4.4996 = 7.4993 < 9.7491] w=0.0739 to align
# Constraint # added constraint: constraint((T0381)L209.CB, (T0381)T231.CB) [> 4.4057 = 7.3428 < 9.5456] w=0.0739 to align
# Constraint # added constraint: constraint((T0381)L201.CB, (T0381)M212.CB) [> 4.5925 = 7.6542 < 9.9504] w=0.0739 to align
# Constraint # added constraint: constraint((T0381)C199.CB, (T0381)S211.CB) [> 4.3206 = 7.2009 < 9.3612] w=0.0724 to align
# Constraint # added constraint: constraint((T0381)L58.CB, (T0381)T68.CB) [> 4.4596 = 7.4327 < 9.6625] w=0.0719 to align
# Constraint # added constraint: constraint((T0381)L90.CB, (T0381)L155.CB) [> 2.3609 = 3.9349 < 5.1154] w=0.0696 to align
# Constraint # added constraint: constraint((T0381)G23.CA, (T0381)L75.CB) [> 4.5119 = 7.5198 < 9.7758] w=0.0685 to align
# Constraint # added constraint: constraint((T0381)V200.CB, (T0381)A213.CB) [> 4.5862 = 7.6437 < 9.9368] w=0.0675 to align
# Constraint # added constraint: constraint((T0381)G208.CA, (T0381)A234.CB) [> 4.4030 = 7.3384 < 9.5399] w=0.0657 to align
# Constraint # added constraint: constraint((T0381)I190.CB, (T0381)C199.CB) [> 4.2227 = 7.0378 < 9.1491] w=0.0636 to align
# Constraint # added constraint: constraint((T0381)T76.CB, (T0381)S89.CB) [> 2.7911 = 4.6519 < 6.0475] w=0.0627 to align
# Constraint # added constraint: constraint((T0381)I139.CB, (T0381)Y166.CB) [> 3.6888 = 6.1480 < 7.9924] w=0.0604 to align
# Constraint # added constraint: constraint((T0381)I139.CB, (T0381)L163.CB) [> 2.8855 = 4.8092 < 6.2520] w=0.0604 to align
# Constraint # added constraint: constraint((T0381)I139.CB, (T0381)E162.CB) [> 2.4570 = 4.0949 < 5.3234] w=0.0604 to align
# Constraint # added constraint: constraint((T0381)I139.CB, (T0381)P159.CB) [> 3.6811 = 6.1352 < 7.9758] w=0.0604 to align
# Constraint # added constraint: constraint((T0381)S110.CB, (T0381)V124.CB) [> 4.1016 = 6.8360 < 8.8868] w=0.0600 to align
# Constraint # added constraint: constraint((T0381)S19.CB, (T0381)T52.CB) [> 3.8229 = 6.3716 < 8.2830] w=0.0597 to align
# Constraint # added constraint: constraint((T0381)R210.CB, (T0381)L241.CB) [> 3.7923 = 6.3205 < 8.2166] w=0.0575 to align
# Constraint # added constraint: constraint((T0381)R131.CB, (T0381)R235.CB) [> 4.5565 = 7.5942 < 9.8724] w=0.0575 to align
# Constraint # added constraint: constraint((T0381)R131.CB, (T0381)T231.CB) [> 4.4011 = 7.3351 < 9.5356] w=0.0575 to align
# Constraint # added constraint: constraint((T0381)S19.CB, (T0381)A53.CB) [> 4.3385 = 7.2309 < 9.4001] w=0.0569 to align
# Constraint # added constraint: constraint((T0381)T38.CB, (T0381)T134.CB) [> 4.1102 = 6.8503 < 8.9054] w=0.0551 to align
# Constraint # added constraint: constraint((T0381)V66.CB, (T0381)G136.CA) [> 3.3639 = 5.6065 < 7.2885] w=0.0551 to align
# Constraint # added constraint: constraint((T0381)V66.CB, (T0381)I137.CB) [> 3.8451 = 6.4085 < 8.3311] w=0.0551 to align
# Constraint # added constraint: constraint((T0381)A67.CB, (T0381)G136.CA) [> 3.6823 = 6.1372 < 7.9784] w=0.0551 to align
# Constraint # added constraint: constraint((T0381)T68.CB, (T0381)T134.CB) [> 3.4458 = 5.7431 < 7.4660] w=0.0551 to align
# Constraint # added constraint: constraint((T0381)T68.CB, (T0381)G136.CA) [> 3.8185 = 6.3642 < 8.2734] w=0.0551 to align
# Constraint # added constraint: constraint((T0381)V124.CB, (T0381)V135.CB) [> 3.6809 = 6.1348 < 7.9752] w=0.0544 to align
# Constraint # added constraint: constraint((T0381)A214.CB, (T0381)N228.CB) [> 4.5742 = 7.6236 < 9.9107] w=0.0542 to align
# Constraint # added constraint: constraint((T0381)S114.CB, (T0381)V227.CB) [> 4.6347 = 7.7246 < 10.0419] w=0.0542 to align
# Constraint # added constraint: constraint((T0381)M212.CB, (T0381)H242.CB) [> 3.8384 = 6.3973 < 8.3164] w=0.0532 to align
# Constraint # added constraint: constraint((T0381)V113.CB, (T0381)V122.CB) [> 4.5367 = 7.5611 < 9.8294] w=0.0523 to align
# Constraint # added constraint: constraint((T0381)S111.CB, (T0381)V124.CB) [> 2.6621 = 4.4369 < 5.7680] w=0.0523 to align
# Constraint # added constraint: constraint((T0381)M133.CB, (T0381)L209.CB) [> 4.0911 = 6.8184 < 8.8640] w=0.0493 to align
# Constraint # added constraint: constraint((T0381)R126.CB, (T0381)G136.CA) [> 4.4369 = 7.3948 < 9.6133] w=0.0493 to align
# Constraint # added constraint: constraint((T0381)V122.CB, (T0381)I139.CB) [> 4.1600 = 6.9334 < 9.0134] w=0.0493 to align
# Constraint # added constraint: constraint((T0381)G118.CA, (T0381)A145.CB) [> 4.6307 = 7.7179 < 10.0332] w=0.0493 to align
# Constraint # added constraint: constraint((T0381)L116.CB, (T0381)A226.CB) [> 4.4036 = 7.3393 < 9.5411] w=0.0493 to align
# Constraint # added constraint: constraint((T0381)S112.CB, (T0381)S211.CB) [> 4.5960 = 7.6601 < 9.9581] w=0.0493 to align
# Constraint # added constraint: constraint((T0381)S110.CB, (T0381)M133.CB) [> 3.9315 = 6.5525 < 8.5183] w=0.0493 to align
# Constraint # added constraint: constraint((T0381)S211.CB, (T0381)T231.CB) [> 4.6492 = 7.7487 < 10.0733] w=0.0493 to align
# Constraint # added constraint: constraint((T0381)D202.CB, (T0381)L238.CB) [> 3.6686 = 6.1143 < 7.9485] w=0.0493 to align
# Constraint # added constraint: constraint((T0381)A156.CB, (T0381)T223.CB) [> 4.5898 = 7.6497 < 9.9446] w=0.0493 to align
# Constraint # added constraint: constraint((T0381)Y146.CB, (T0381)T181.CB) [> 4.4683 = 7.4472 < 9.6814] w=0.0493 to align
# Constraint # added constraint: constraint((T0381)G136.CA, (T0381)S230.CB) [> 4.7544 = 7.9240 < 10.3013] w=0.0493 to align
# Constraint # added constraint: constraint((T0381)V135.CB, (T0381)S211.CB) [> 4.7584 = 7.9307 < 10.3099] w=0.0493 to align
# Constraint # added constraint: constraint((T0381)T134.CB, (T0381)P232.CB) [> 4.1134 = 6.8557 < 8.9124] w=0.0493 to align
# Constraint # added constraint: constraint((T0381)T134.CB, (T0381)T231.CB) [> 3.4623 = 5.7706 < 7.5018] w=0.0493 to align
# Constraint # added constraint: constraint((T0381)M133.CB, (T0381)T231.CB) [> 3.2908 = 5.4847 < 7.1302] w=0.0493 to align
# Constraint # added constraint: constraint((T0381)M133.CB, (T0381)S230.CB) [> 4.0164 = 6.6940 < 8.7022] w=0.0493 to align
# Constraint # added constraint: constraint((T0381)V124.CB, (T0381)T134.CB) [> 3.7175 = 6.1959 < 8.0547] w=0.0488 to align
# Constraint # added constraint: constraint((T0381)P215.CB, (T0381)V227.CB) [> 4.3808 = 7.3014 < 9.4918] w=0.0478 to align
# Constraint # added constraint: constraint((T0381)Y16.CB, (T0381)G64.CA) [> 4.2666 = 7.1109 < 9.2442] w=0.0475 to align
# Constraint # added constraint: constraint((T0381)S110.CB, (T0381)Y123.CB) [> 3.4859 = 5.8098 < 7.5528] w=0.0474 to align
# Constraint # added constraint: constraint((T0381)A67.CB, (T0381)P77.CB) [> 3.6694 = 6.1156 < 7.9503] w=0.0472 to align
# Constraint # added constraint: constraint((T0381)G64.CA, (T0381)P77.CB) [> 3.9244 = 6.5408 < 8.5030] w=0.0472 to align
# Constraint # added constraint: constraint((T0381)V107.CB, (T0381)D244.CB) [> 4.0361 = 6.7269 < 8.7449] w=0.0471 to align
# Constraint # added constraint: constraint((T0381)S91.CB, (T0381)R174.CB) [> 4.6501 = 7.7502 < 10.0752] w=0.0466 to align
# Constraint # added constraint: constraint((T0381)L57.CB, (T0381)A72.CB) [> 4.2076 = 7.0127 < 9.1165] w=0.0459 to align
# Constraint # added constraint: constraint((T0381)R217.CB, (T0381)A253.CB) [> 4.0283 = 6.7138 < 8.7280] w=0.0450 to align
# Constraint # added constraint: constraint((T0381)L100.CB, (T0381)S110.CB) [> 3.2683 = 5.4472 < 7.0813] w=0.0440 to align
# Constraint # added constraint: constraint((T0381)A43.CB, (T0381)R54.CB) [> 4.7319 = 7.8865 < 10.2524] w=0.0435 to align
# Constraint # added constraint: constraint((T0381)S114.CB, (T0381)A125.CB) [> 4.1370 = 6.8950 < 8.9635] w=0.0429 to align
# Constraint # added constraint: constraint((T0381)G23.CA, (T0381)L82.CB) [> 4.4182 = 7.3637 < 9.5728] w=0.0429 to align
# Constraint # added constraint: constraint((T0381)Y123.CB, (T0381)G136.CA) [> 3.2204 = 5.3673 < 6.9775] w=0.0419 to align
# Constraint # added constraint: constraint((T0381)Y123.CB, (T0381)V135.CB) [> 3.5630 = 5.9384 < 7.7199] w=0.0419 to align
# Constraint # added constraint: constraint((T0381)V122.CB, (T0381)I137.CB) [> 4.1362 = 6.8937 < 8.9618] w=0.0419 to align
# Constraint # added constraint: constraint((T0381)V122.CB, (T0381)G136.CA) [> 3.5205 = 5.8674 < 7.6276] w=0.0419 to align
# Constraint # added constraint: constraint((T0381)D120.CB, (T0381)T138.CB) [> 4.2125 = 7.0208 < 9.1270] w=0.0419 to align
# Constraint # added constraint: constraint((T0381)L75.CB, (T0381)L90.CB) [> 4.7304 = 7.8840 < 10.2492] w=0.0412 to align
# Constraint # added constraint: constraint((T0381)T231.CB, (T0381)L245.CB) [> 4.5697 = 7.6162 < 9.9010] w=0.0411 to align
# Constraint # added constraint: constraint((T0381)D120.CB, (T0381)I137.CB) [> 3.8135 = 6.3558 < 8.2625] w=0.0406 to align
# Constraint # added constraint: constraint((T0381)S111.CB, (T0381)Y123.CB) [> 4.5309 = 7.5515 < 9.8170] w=0.0402 to align
# Constraint # added constraint: constraint((T0381)V66.CB, (T0381)T138.CB) [> 3.6833 = 6.1389 < 7.9805] w=0.0389 to align
# Constraint # added constraint: constraint((T0381)L90.CB, (T0381)K106.CB) [> 4.5023 = 7.5039 < 9.7550] w=0.0387 to align
# Constraint # added constraint: constraint((T0381)Y65.CB, (T0381)G83.CA) [> 4.6814 = 7.8023 < 10.1430] w=0.0368 to align
# Constraint # added constraint: constraint((T0381)V17.CB, (T0381)R55.CB) [> 3.7895 = 6.3158 < 8.2105] w=0.0334 to align
# Constraint # added constraint: constraint((T0381)V17.CB, (T0381)T52.CB) [> 4.2945 = 7.1575 < 9.3048] w=0.0334 to align
# Constraint # added constraint: constraint((T0381)R210.CB, (T0381)L238.CB) [> 3.0416 = 5.0693 < 6.5901] w=0.0328 to align
# Constraint # added constraint: constraint((T0381)I132.CB, (T0381)T231.CB) [> 4.0290 = 6.7149 < 8.7294] w=0.0328 to align
# Constraint # added constraint: constraint((T0381)S110.CB, (T0381)I132.CB) [> 2.8189 = 4.6981 < 6.1075] w=0.0328 to align
# Constraint # added constraint: constraint((T0381)E109.CB, (T0381)I132.CB) [> 3.2696 = 5.4493 < 7.0841] w=0.0328 to align
# Constraint # added constraint: constraint((T0381)H108.CB, (T0381)I132.CB) [> 3.6356 = 6.0593 < 7.8770] w=0.0328 to align
# Constraint # added constraint: constraint((T0381)V17.CB, (T0381)L82.CB) [> 4.5530 = 7.5883 < 9.8648] w=0.0327 to align
# Constraint # added constraint: constraint((T0381)V17.CB, (T0381)Y86.CB) [> 3.6001 = 6.0002 < 7.8002] w=0.0327 to align
# Constraint # added constraint: constraint((T0381)L63.CB, (T0381)V79.CB) [> 4.3315 = 7.2191 < 9.3849] w=0.0322 to align
# Constraint # added constraint: constraint((T0381)L100.CB, (T0381)I137.CB) [> 4.3254 = 7.2090 < 9.3717] w=0.0321 to align
# Constraint # added constraint: constraint((T0381)D196.CB, (T0381)A233.CB) [> 4.1141 = 6.8569 < 8.9139] w=0.0320 to align
# Constraint # added constraint: constraint((T0381)W74.CB, (T0381)V127.CB) [> 3.4161 = 5.6936 < 7.4016] w=0.0319 to align
# Constraint # added constraint: constraint((T0381)V66.CB, (T0381)V135.CB) [> 3.2265 = 5.3775 < 6.9907] w=0.0310 to align
# Constraint # added constraint: constraint((T0381)D69.CB, (T0381)M133.CB) [> 3.9621 = 6.6034 < 8.5844] w=0.0310 to align
# Constraint # added constraint: constraint((T0381)V66.CB, (T0381)P77.CB) [> 3.6985 = 6.1642 < 8.0134] w=0.0308 to align
# Constraint # added constraint: constraint((T0381)L154.CB, (T0381)A213.CB) [> 4.4794 = 7.4657 < 9.7054] w=0.0295 to align
# Constraint # added constraint: constraint((T0381)M150.CB, (T0381)P215.CB) [> 4.4091 = 7.3485 < 9.5531] w=0.0295 to align
# Constraint # added constraint: constraint((T0381)L20.CB, (T0381)V79.CB) [> 3.8910 = 6.4850 < 8.4305] w=0.0293 to align
# Constraint # added constraint: constraint((T0381)S111.CB, (T0381)I137.CB) [> 3.8455 = 6.4092 < 8.3319] w=0.0282 to align
# Constraint # added constraint: constraint((T0381)A189.CB, (T0381)L245.CB) [> 3.5257 = 5.8761 < 7.6389] w=0.0280 to align
# Constraint # added constraint: constraint((T0381)G64.CA, (T0381)T138.CB) [> 3.1062 = 5.1770 < 6.7301] w=0.0277 to align
# Constraint # added constraint: constraint((T0381)Y16.CB, (T0381)L48.CB) [> 3.6827 = 6.1377 < 7.9791] w=0.0272 to align
# Constraint # added constraint: constraint((T0381)L63.CB, (T0381)L82.CB) [> 4.7345 = 7.8908 < 10.2580] w=0.0250 to align
# Constraint # added constraint: constraint((T0381)S112.CB, (T0381)A213.CB) [> 4.7857 = 7.9762 < 10.3691] w=0.0246 to align
# Constraint # added constraint: constraint((T0381)V113.CB, (T0381)I216.CB) [> 4.7804 = 7.9673 < 10.3574] w=0.0246 to align
# Constraint # added constraint: constraint((T0381)V129.CB, (T0381)S230.CB) [> 4.0891 = 6.8152 < 8.8598] w=0.0246 to align
# Constraint # added constraint: constraint((T0381)R131.CB, (T0381)P232.CB) [> 4.7407 = 7.9012 < 10.2716] w=0.0246 to align
# Constraint # added constraint: constraint((T0381)M133.CB, (T0381)A234.CB) [> 4.7418 = 7.9030 < 10.2739] w=0.0246 to align
# Constraint # added constraint: constraint((T0381)V61.CB, (T0381)T76.CB) [> 4.4419 = 7.4032 < 9.6242] w=0.0246 to align
# Constraint # added constraint: constraint((T0381)S89.CB, (T0381)I115.CB) [> 3.8861 = 6.4768 < 8.4199] w=0.0246 to align
# Constraint # added constraint: constraint((T0381)D196.CB, (T0381)R250.CB) [> 4.4336 = 7.3894 < 9.6062] w=0.0246 to align
# Constraint # added constraint: constraint((T0381)I198.CB, (T0381)P215.CB) [> 4.6353 = 7.7254 < 10.0431] w=0.0246 to align
# Constraint # added constraint: constraint((T0381)M212.CB, (T0381)S248.CB) [> 4.7957 = 7.9928 < 10.3907] w=0.0246 to align
# Constraint # added constraint: constraint((T0381)L158.CB, (T0381)L222.CB) [> 4.7664 = 7.9440 < 10.3272] w=0.0246 to align
# Constraint # added constraint: constraint((T0381)G157.CA, (T0381)L222.CB) [> 4.7859 = 7.9764 < 10.3694] w=0.0246 to align
# Constraint # added constraint: constraint((T0381)L155.CB, (T0381)T223.CB) [> 4.6867 = 7.8111 < 10.1545] w=0.0246 to align
# Constraint # added constraint: constraint((T0381)L155.CB, (T0381)V193.CB) [> 4.6282 = 7.7137 < 10.0278] w=0.0246 to align
# Constraint # added constraint: constraint((T0381)C29.CB, (T0381)F73.CB) [> 4.5791 = 7.6318 < 9.9213] w=0.0246 to align
# Constraint # added constraint: constraint((T0381)M133.CB, (T0381)R178.CB) [> 4.0585 = 6.7641 < 8.7934] w=0.0245 to align
# Constraint # added constraint: constraint((T0381)Y166.CB, (T0381)K187.CB) [> 3.7743 = 6.2905 < 8.1777] w=0.0245 to align
# Constraint # added constraint: constraint((T0381)V122.CB, (T0381)T138.CB) [> 3.5193 = 5.8655 < 7.6252] w=0.0236 to align
# Constraint # added constraint: constraint((T0381)S112.CB, (T0381)V122.CB) [> 4.5083 = 7.5139 < 9.7681] w=0.0233 to align
# Constraint # added constraint: constraint((T0381)P215.CB, (T0381)V224.CB) [> 4.1575 = 6.9291 < 9.0078] w=0.0232 to align
# Constraint # added constraint: constraint((T0381)A219.CB, (T0381)L241.CB) [> 4.0803 = 6.8006 < 8.8408] w=0.0230 to align
# Constraint # added constraint: constraint((T0381)L39.CB, (T0381)W74.CB) [> 4.4507 = 7.4178 < 9.6432] w=0.0226 to align
# Constraint # added constraint: constraint((T0381)S111.CB, (T0381)T138.CB) [> 3.4463 = 5.7438 < 7.4669] w=0.0207 to align
# Constraint # added constraint: constraint((T0381)L80.CB, (T0381)L238.CB) [> 4.5951 = 7.6585 < 9.9561] w=0.0183 to align
# Constraint # added constraint: constraint((T0381)L80.CB, (T0381)D202.CB) [> 4.6227 = 7.7046 < 10.0160] w=0.0183 to align
# Constraint # added constraint: constraint((T0381)P77.CB, (T0381)L201.CB) [> 3.3438 = 5.5731 < 7.2450] w=0.0183 to align
# Constraint # added constraint: constraint((T0381)V129.CB, (T0381)V224.CB) [> 4.7480 = 7.9133 < 10.2873] w=0.0183 to align
# Constraint # added constraint: constraint((T0381)G118.CA, (T0381)G140.CA) [> 4.5625 = 7.6042 < 9.8855] w=0.0183 to align
# Constraint # added constraint: constraint((T0381)A119.CB, (T0381)G140.CA) [> 3.9230 = 6.5384 < 8.4999] w=0.0183 to align
# Constraint # added constraint: constraint((T0381)V122.CB, (T0381)T134.CB) [> 3.9569 = 6.5948 < 8.5733] w=0.0183 to align
# Constraint # added constraint: constraint((T0381)V122.CB, (T0381)V135.CB) [> 4.4495 = 7.4158 < 9.6405] w=0.0183 to align
# Constraint # added constraint: constraint((T0381)Y16.CB, (T0381)T52.CB) [> 3.7845 = 6.3075 < 8.1997] w=0.0171 to align
# Constraint # added constraint: constraint((T0381)I132.CB, (T0381)P232.CB) [> 4.0729 = 6.7882 < 8.8247] w=0.0164 to align
# Constraint # added constraint: constraint((T0381)A207.CB, (T0381)A233.CB) [> 4.5228 = 7.5381 < 9.7995] w=0.0164 to align
# Constraint # added constraint: constraint((T0381)Y16.CB, (T0381)L82.CB) [> 3.2680 = 5.4466 < 7.0806] w=0.0163 to align
# Constraint # added constraint: constraint((T0381)P77.CB, (T0381)L92.CB) [> 4.3745 = 7.2908 < 9.4780] w=0.0156 to align
# Constraint # added constraint: constraint((T0381)R194.CB, (T0381)A219.CB) [> 3.6309 = 6.0514 < 7.8669] w=0.0154 to align
# Constraint # added constraint: constraint((T0381)D196.CB, (T0381)A219.CB) [> 4.5108 = 7.5180 < 9.7734] w=0.0154 to align
# Constraint # added constraint: constraint((T0381)G197.CA, (T0381)S220.CB) [> 3.5095 = 5.8491 < 7.6039] w=0.0154 to align
# Constraint # added constraint: constraint((T0381)S220.CB, (T0381)Y236.CB) [> 4.3149 = 7.1915 < 9.3489] w=0.0154 to align
# Constraint # added constraint: constraint((T0381)G221.CA, (T0381)Y236.CB) [> 2.8825 = 4.8041 < 6.2454] w=0.0154 to align
# Constraint # added constraint: constraint((T0381)G221.CA, (T0381)S237.CB) [> 4.3801 = 7.3002 < 9.4903] w=0.0154 to align
# Constraint # added constraint: constraint((T0381)A125.CB, (T0381)V135.CB) [> 4.1542 = 6.9237 < 9.0009] w=0.0153 to align
# Constraint # added constraint: constraint((T0381)L143.CB, (T0381)A192.CB) [> 4.4950 = 7.4916 < 9.7391] w=0.0151 to align
# Constraint # added constraint: constraint((T0381)L100.CB, (T0381)G140.CA) [> 4.0650 = 6.7750 < 8.8074] w=0.0150 to align
# Constraint # added constraint: constraint((T0381)E81.CB, (T0381)P93.CB) [> 3.9079 = 6.5131 < 8.4670] w=0.0148 to align
# Constraint # added constraint: constraint((T0381)Y86.CB, (T0381)H242.CB) [> 3.1578 = 5.2631 < 6.8420] w=0.0147 to align
# Constraint # added constraint: constraint((T0381)L80.CB, (T0381)K106.CB) [> 4.5232 = 7.5387 < 9.8003] w=0.0141 to align
# Constraint # added constraint: constraint((T0381)L209.CB, (T0381)T254.CB) [> 4.1615 = 6.9358 < 9.0166] w=0.0141 to align
# Constraint # added constraint: constraint((T0381)L209.CB, (T0381)V251.CB) [> 3.4097 = 5.6828 < 7.3876] w=0.0141 to align
# Constraint # added constraint: constraint((T0381)E206.CB, (T0381)S248.CB) [> 4.2277 = 7.0462 < 9.1600] w=0.0141 to align
# Constraint # added constraint: constraint((T0381)V17.CB, (T0381)R78.CB) [> 2.8291 = 4.7151 < 6.1297] w=0.0136 to align
# Constraint # added constraint: constraint((T0381)L116.CB, (T0381)L222.CB) [> 4.3976 = 7.3293 < 9.5281] w=0.0131 to align
# Constraint # added constraint: constraint((T0381)S114.CB, (T0381)V224.CB) [> 2.9629 = 4.9381 < 6.4196] w=0.0131 to align
# Constraint # added constraint: constraint((T0381)S112.CB, (T0381)A226.CB) [> 3.4698 = 5.7829 < 7.5178] w=0.0131 to align
# Constraint # added constraint: constraint((T0381)S110.CB, (T0381)N228.CB) [> 4.0915 = 6.8192 < 8.8650] w=0.0131 to align
# Constraint # added constraint: constraint((T0381)W74.CB, (T0381)G140.CA) [> 3.2897 = 5.4829 < 7.1277] w=0.0125 to align
# Constraint # added constraint: constraint((T0381)L100.CB, (T0381)S114.CB) [> 4.1551 = 6.9252 < 9.0027] w=0.0124 to align
# Constraint # added constraint: constraint((T0381)A219.CB, (T0381)A253.CB) [> 3.7346 = 6.2243 < 8.0916] w=0.0122 to align
# Constraint # added constraint: constraint((T0381)L100.CB, (T0381)Y123.CB) [> 3.7040 = 6.1734 < 8.0254] w=0.0121 to align
# Constraint # added constraint: constraint((T0381)L80.CB, (T0381)V95.CB) [> 4.4722 = 7.4536 < 9.6897] w=0.0102 to align
# Constraint # added constraint: constraint((T0381)A147.CB, (T0381)T223.CB) [> 4.1966 = 6.9943 < 9.0926] w=0.0098 to align
# Constraint # added constraint: constraint((T0381)P144.CB, (T0381)T223.CB) [> 4.7850 = 7.9750 < 10.3674] w=0.0098 to align
# Constraint # added constraint: constraint((T0381)P144.CB, (T0381)I216.CB) [> 4.5164 = 7.5274 < 9.7856] w=0.0098 to align
# Constraint # added constraint: constraint((T0381)P144.CB, (T0381)A214.CB) [> 3.9196 = 6.5327 < 8.4926] w=0.0098 to align
# Constraint # added constraint: constraint((T0381)A125.CB, (T0381)A225.CB) [> 3.4622 = 5.7703 < 7.5014] w=0.0098 to align
# Constraint # added constraint: constraint((T0381)A125.CB, (T0381)V224.CB) [> 4.5692 = 7.6153 < 9.8999] w=0.0098 to align
# Constraint # added constraint: constraint((T0381)L100.CB, (T0381)V224.CB) [> 2.9134 = 4.8557 < 6.3124] w=0.0098 to align
# Constraint # added constraint: constraint((T0381)L154.CB, (T0381)I229.CB) [> 4.6977 = 7.8295 < 10.1784] w=0.0098 to align
# Constraint # added constraint: constraint((T0381)S110.CB, (T0381)A225.CB) [> 3.2208 = 5.3680 < 6.9784] w=0.0082 to align
# Constraint # added constraint: constraint((T0381)S110.CB, (T0381)A226.CB) [> 4.3771 = 7.2952 < 9.4837] w=0.0082 to align
# Constraint # added constraint: constraint((T0381)S110.CB, (T0381)V227.CB) [> 3.5391 = 5.8985 < 7.6680] w=0.0082 to align
# Constraint # added constraint: constraint((T0381)S111.CB, (T0381)A225.CB) [> 4.4161 = 7.3602 < 9.5682] w=0.0082 to align
# Constraint # added constraint: constraint((T0381)S112.CB, (T0381)A225.CB) [> 4.0586 = 6.7643 < 8.7936] w=0.0082 to align
# Constraint # added constraint: constraint((T0381)V113.CB, (T0381)T223.CB) [> 3.3899 = 5.6498 < 7.3447] w=0.0082 to align
# Constraint # added constraint: constraint((T0381)D117.CB, (T0381)I132.CB) [> 3.4278 = 5.7130 < 7.4269] w=0.0082 to align
# Constraint # added constraint: constraint((T0381)D117.CB, (T0381)M133.CB) [> 2.9217 = 4.8695 < 6.3303] w=0.0082 to align
# Constraint # added constraint: constraint((T0381)V113.CB, (T0381)V224.CB) [> 4.2267 = 7.0445 < 9.1579] w=0.0082 to align
# Constraint # added constraint: constraint((T0381)S114.CB, (T0381)T223.CB) [> 4.0192 = 6.6986 < 8.7082] w=0.0082 to align
# Constraint # added constraint: constraint((T0381)I115.CB, (T0381)L222.CB) [> 4.2661 = 7.1102 < 9.2432] w=0.0082 to align
# Constraint # added constraint: constraint((T0381)M212.CB, (T0381)A225.CB) [> 4.3777 = 7.2961 < 9.4850] w=0.0080 to align
# Constraint # added constraint: constraint((T0381)S211.CB, (T0381)A225.CB) [> 3.1954 = 5.3257 < 6.9234] w=0.0080 to align
# Constraint # added constraint: constraint((T0381)S110.CB, (T0381)V193.CB) [> 4.2711 = 7.1185 < 9.2540] w=0.0080 to align
# Constraint # added constraint: constraint((T0381)L100.CB, (T0381)I229.CB) [> 2.8471 = 4.7452 < 6.1688] w=0.0075 to align
# Constraint # added constraint: constraint((T0381)L100.CB, (T0381)N228.CB) [> 4.0341 = 6.7235 < 8.7406] w=0.0075 to align
# Constraint # added constraint: constraint((T0381)G83.CA, (T0381)L100.CB) [> 4.7955 = 7.9926 < 10.3903] w=0.0075 to align
# Constraint # added constraint: constraint((T0381)I172.CB, (T0381)L222.CB) [> 3.3689 = 5.6148 < 7.2992] w=0.0075 to align
# Constraint # added constraint: constraint((T0381)L222.CB, (T0381)A234.CB) [> 2.9445 = 4.9075 < 6.3797] w=0.0075 to align
# Constraint # added constraint: constraint((T0381)V200.CB, (T0381)I229.CB) [> 4.3302 = 7.2170 < 9.3820] w=0.0075 to align
# Constraint # added constraint: constraint((T0381)V200.CB, (T0381)N228.CB) [> 2.5442 = 4.2403 < 5.5123] w=0.0075 to align
# Constraint # added constraint: constraint((T0381)I132.CB, (T0381)N228.CB) [> 2.4431 = 4.0719 < 5.2934] w=0.0075 to align
# Constraint # added constraint: constraint((T0381)R78.CB, (T0381)H99.CB) [> 3.7444 = 6.2406 < 8.1128] w=0.0074 to align
# Constraint # added constraint: constraint((T0381)R54.CB, (T0381)M133.CB) [> 4.7753 = 7.9589 < 10.3466] w=0.0074 to align
# Constraint # added constraint: constraint((T0381)V135.CB, (T0381)N228.CB) [> 3.3044 = 5.5073 < 7.1595] w=0.0070 to align
# Constraint # added constraint: constraint((T0381)I10.CB, (T0381)P77.CB) [> 4.6699 = 7.7832 < 10.1182] w=0.0068 to align
# Constraint # added constraint: constraint((T0381)I10.CB, (T0381)R78.CB) [> 3.5246 = 5.8743 < 7.6365] w=0.0068 to align
# Constraint # added constraint: constraint((T0381)S114.CB, (T0381)A145.CB) [> 3.1576 = 5.2626 < 6.8414] w=0.0061 to align
# Constraint # added constraint: constraint((T0381)V107.CB, (T0381)V224.CB) [> 4.6097 = 7.6828 < 9.9876] w=0.0049 to align
# Constraint # added constraint: constraint((T0381)Y123.CB, (T0381)A145.CB) [> 3.2750 = 5.4584 < 7.0959] w=0.0049 to align
# Constraint # added constraint: constraint((T0381)Y123.CB, (T0381)A226.CB) [> 4.2394 = 7.0658 < 9.1855] w=0.0049 to align
# Constraint # added constraint: constraint((T0381)Y123.CB, (T0381)V227.CB) [> 2.9941 = 4.9901 < 6.4872] w=0.0049 to align
# Constraint # added constraint: constraint((T0381)Y123.CB, (T0381)N228.CB) [> 4.5711 = 7.6185 < 9.9041] w=0.0049 to align
# Constraint # added constraint: constraint((T0381)Y123.CB, (T0381)I229.CB) [> 4.6661 = 7.7768 < 10.1099] w=0.0049 to align
# Constraint # added constraint: constraint((T0381)P77.CB, (T0381)Y86.CB) [> 4.4186 = 7.3643 < 9.5735] w=0.0049 to align
# Constraint # added constraint: constraint((T0381)P77.CB, (T0381)L87.CB) [> 3.9039 = 6.5065 < 8.4584] w=0.0049 to align
# Constraint # added constraint: constraint((T0381)L100.CB, (T0381)S211.CB) [> 2.9151 = 4.8585 < 6.3160] w=0.0049 to align
# Constraint # added constraint: constraint((T0381)M212.CB, (T0381)V227.CB) [> 3.6734 = 6.1224 < 7.9591] w=0.0049 to align
# Constraint # added constraint: constraint((T0381)A213.CB, (T0381)S230.CB) [> 3.8001 = 6.3334 < 8.2335] w=0.0049 to align
# Constraint # added constraint: constraint((T0381)A214.CB, (T0381)V224.CB) [> 4.6717 = 7.7861 < 10.1220] w=0.0049 to align
# Constraint # added constraint: constraint((T0381)A214.CB, (T0381)A225.CB) [> 3.5867 = 5.9778 < 7.7712] w=0.0049 to align
# Constraint # added constraint: constraint((T0381)R217.CB, (T0381)A226.CB) [> 4.5773 = 7.6289 < 9.9175] w=0.0049 to align
# Constraint # added constraint: constraint((T0381)R217.CB, (T0381)A234.CB) [> 2.4339 = 4.0564 < 5.2733] w=0.0049 to align
# Constraint # added constraint: constraint((T0381)G218.CA, (T0381)A234.CB) [> 2.8951 = 4.8252 < 6.2727] w=0.0049 to align
# Constraint # added constraint: constraint((T0381)R174.CB, (T0381)A207.CB) [> 3.9987 = 6.6644 < 8.6638] w=0.0049 to align
# Constraint # added constraint: constraint((T0381)V127.CB, (T0381)V224.CB) [> 4.6946 = 7.8243 < 10.1715] w=0.0049 to align
# Constraint # added constraint: constraint((T0381)A145.CB, (T0381)A213.CB) [> 4.3291 = 7.2152 < 9.3798] w=0.0049 to align
# Constraint # added constraint: constraint((T0381)T141.CB, (T0381)G218.CA) [> 3.8612 = 6.4353 < 8.3659] w=0.0049 to align
# Constraint # added constraint: constraint((T0381)R142.CB, (T0381)P215.CB) [> 3.1686 = 5.2810 < 6.8653] w=0.0049 to align
# Constraint # added constraint: constraint((T0381)R142.CB, (T0381)G218.CA) [> 3.7497 = 6.2496 < 8.1245] w=0.0049 to align
# Constraint # added constraint: constraint((T0381)Y123.CB, (T0381)V193.CB) [> 4.7733 = 7.9555 < 10.3422] w=0.0040 to align
# SetCost created cost = 
#	( 1.0000 * align )
# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0381/
# command:# reading script from file servers-clean.under
Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/chimera-4-6.pdb.gz or /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/chimera-4-6.pdb.gz.gz for input
Trying chimera-4-6.pdb.gz
Error: Couldn't open file chimera-4-6.pdb.gz or chimera-4-6.pdb.gz.gz for input
Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/chimera-4-8.pdb.gz or /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/chimera-4-8.pdb.gz.gz for input
Trying chimera-4-8.pdb.gz
Error: Couldn't open file chimera-4-8.pdb.gz or chimera-4-8.pdb.gz.gz for input
Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/tr380.gromacs0.pdb.gz or /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/tr380.gromacs0.pdb.gz.gz for input
Trying tr380.gromacs0.pdb.gz
Error: Couldn't open file tr380.gromacs0.pdb.gz or tr380.gromacs0.pdb.gz.gz for input
Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/tr380.gromacs0.repack-nonPC.pdb.gz or /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/tr380.gromacs0.repack-nonPC.pdb.gz.gz for input
Trying tr380.gromacs0.repack-nonPC.pdb.gz
Error: Couldn't open file tr380.gromacs0.repack-nonPC.pdb.gz or tr380.gromacs0.repack-nonPC.pdb.gz.gz for input
Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/tr380.pdb.gz or /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/tr380.pdb.gz.gz for input
Trying tr380.pdb.gz
Error: Couldn't open file tr380.pdb.gz or tr380.pdb.gz.gz for input
Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/tr380.repack-nonPC.pdb.gz or /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/tr380.repack-nonPC.pdb.gz.gz for input
Trying tr380.repack-nonPC.pdb.gz
Error: Couldn't open file tr380.repack-nonPC.pdb.gz or tr380.repack-nonPC.pdb.gz.gz for input
# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/
Error: can't open file chimera-4-6.pdb.gz in ReadConformPDB
Error: can't open file chimera-4-8.pdb.gz in ReadConformPDB
Error: can't open file tr380.gromacs0.pdb.gz in ReadConformPDB
Error: can't open file tr380.gromacs0.repack-nonPC.pdb.gz in ReadConformPDB
Error: can't open file tr380.pdb.gz in ReadConformPDB
Error: can't open file tr380.repack-nonPC.pdb.gz in ReadConformPDB
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 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 T0381 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 T0381 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 T0381 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 T0381 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 T0381 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 T0381 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 T0381 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 T0381 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 T0381 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 T0381 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 T0381 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_TS2
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_TS3
Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/servers/3D-JIGSAW_TS4.pdb.gz or /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/servers/3D-JIGSAW_TS4.pdb.gz.gz for input
Trying servers/3D-JIGSAW_TS4.pdb.gz
Error: Couldn't open file servers/3D-JIGSAW_TS4.pdb.gz or servers/3D-JIGSAW_TS4.pdb.gz.gz for input
Error: can't open file servers/3D-JIGSAW_TS4.pdb.gz in ReadConformPDB
# naming current conformation 3D-JIGSAW_TS4
Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/servers/3D-JIGSAW_TS5.pdb.gz or /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/servers/3D-JIGSAW_TS5.pdb.gz.gz for input
Trying servers/3D-JIGSAW_TS5.pdb.gz
Error: Couldn't open file servers/3D-JIGSAW_TS5.pdb.gz or servers/3D-JIGSAW_TS5.pdb.gz.gz for input
Error: can't open file servers/3D-JIGSAW_TS5.pdb.gz in ReadConformPDB
# naming current conformation 3D-JIGSAW_TS5
# ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1
# choosing archetypes in rotamer library
# Found a chain break before 66
# copying to AlignedFragments data structure
# naming current conformation 3Dpro_TS1
# ReadConformPDB reading from PDB file servers/3Dpro_TS2.pdb.gz looking for model 1
# Found a chain break before 73
# copying to AlignedFragments data structure
# naming current conformation 3Dpro_TS2
# ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1
# Found a chain break before 172
# 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 133
# copying to AlignedFragments data structure
# naming current conformation 3Dpro_TS4
# ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1
# naming current conformation 3Dpro_TS5
# ReadConformPDB reading from PDB file servers/ABIpro_TS1.pdb.gz looking for model 1
# Found a chain break before 224
# 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 243
# 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 200
# 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 228
# 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 256
# copying to AlignedFragments data structure
# naming current conformation ABIpro_TS5
# ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1
# naming current conformation BayesHH_TS1
# ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS1.pdb.gz looking for model 1
# Found a chain break before 173
# 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 243
# 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 264
# 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 264
# 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 264
# 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 246
# copying to AlignedFragments data structure
# naming current conformation CIRCLE_TS1
# ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# naming current conformation CIRCLE_TS2
# ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1
# Found a chain break before 254
# 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 T0381 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 T0381 can't currently be optimized by undertaker
# naming current conformation CIRCLE_TS5
# ReadConformPDB reading from PDB file servers/CPHmodels_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# naming current conformation CPHmodels_TS1
# ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# naming current conformation CaspIta-FOX_TS1
# ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 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 T0381 can't currently be optimized by undertaker
# naming current conformation CaspIta-FOX_TS3
# ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 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 T0381 can't currently be optimized by undertaker
# naming current conformation CaspIta-FOX_TS5
# ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 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 T0381 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 T0381 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 T0381 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 T0381 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 264
# 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 T0381 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 T0381 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 T0381 can't currently be optimized by undertaker
# naming current conformation FAMSD_TS4
# ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# naming current conformation FAMSD_TS5
# ReadConformPDB reading from PDB file servers/FAMS_TS1.pdb.gz looking for model 1
# Found a chain break before 231
# 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 T0381 can't currently be optimized by undertaker
# naming current conformation FAMS_TS2
# ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1
# Found a chain break before 246
# copying to AlignedFragments data structure
# naming current conformation FAMS_TS3
# ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# naming current conformation FAMS_TS4
# ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# naming current conformation FAMS_TS5
# ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1
# Found a chain break before 172
# 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 66
# 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 66
# 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 133
# copying to AlignedFragments data structure
# naming current conformation FOLDpro_TS4
# ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1
# naming current conformation FOLDpro_TS5
# ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 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 T0381 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 T0381 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 T0381 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 T0381 can't currently be optimized by undertaker
# naming current conformation FORTE1_AL5
# ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 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 T0381 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 T0381 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 T0381 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
Skipped atom 50, because occupancy 1 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz
Skipped atom 52, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz
Skipped atom 54, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz
Skipped atom 56, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz
Skipped atom 118, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz
Skipped atom 120, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz
Skipped atom 122, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz
Skipped atom 124, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz
Skipped atom 346, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz
Skipped atom 348, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz
Skipped atom 350, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz
Skipped atom 352, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz
Skipped atom 390, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz
Skipped atom 392, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz
Skipped atom 394, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz
Skipped atom 396, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz
Skipped atom 418, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz
Skipped atom 420, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz
Skipped atom 422, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz
Skipped atom 424, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz
Skipped atom 486, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz
Skipped atom 488, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz
Skipped atom 490, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz
Skipped atom 492, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz
# WARNING: incomplete conformation T0381 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 175
# copying to AlignedFragments data structure
# naming current conformation FPSOLVER-SERVER_TS1
# ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS2.pdb.gz looking for model 1
# Found a chain break before 259
# copying to AlignedFragments data structure
# naming current conformation FPSOLVER-SERVER_TS2
# ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS3.pdb.gz looking for model 1
# Found a chain break before 261
# copying to AlignedFragments data structure
# naming current conformation FPSOLVER-SERVER_TS3
# ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS4.pdb.gz looking for model 1
# Found a chain break before 238
# copying to AlignedFragments data structure
# naming current conformation FPSOLVER-SERVER_TS4
# ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS5.pdb.gz looking for model 1
# Found a chain break before 253
# copying to AlignedFragments data structure
# naming current conformation FPSOLVER-SERVER_TS5
# ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# naming current conformation FUGMOD_TS1
# ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# naming current conformation FUGMOD_TS2
# ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 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 T0381 can't currently be optimized by undertaker
# naming current conformation FUGMOD_TS4
# ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# naming current conformation FUGMOD_TS5
# ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# naming current conformation FUGUE_AL1
# ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# naming current conformation FUGUE_AL2
# ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 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 T0381 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 T0381 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 232
# 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 246
# 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 261
# 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 260
# 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 257
# 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 22
# copying to AlignedFragments data structure
# naming current conformation Frankenstein_TS1
# ReadConformPDB reading from PDB file servers/Frankenstein_TS2.pdb.gz looking for model 1
# naming current conformation Frankenstein_TS2
# ReadConformPDB reading from PDB file servers/Frankenstein_TS3.pdb.gz looking for model 1
# Found a chain break before 168
# copying to AlignedFragments data structure
# naming current conformation Frankenstein_TS3
# ReadConformPDB reading from PDB file servers/Frankenstein_TS4.pdb.gz looking for model 1
Faking rotamer for incomplete or colinear backbone at (T0381)K102
Faking rotamer for incomplete or colinear backbone at (T0381)K102
# Found a chain break before 257
# copying to AlignedFragments data structure
# naming current conformation Frankenstein_TS4
Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/servers/Frankenstein_TS5.pdb.gz or /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/servers/Frankenstein_TS5.pdb.gz.gz for input
Trying servers/Frankenstein_TS5.pdb.gz
Error: Couldn't open file servers/Frankenstein_TS5.pdb.gz or servers/Frankenstein_TS5.pdb.gz.gz for input
Error: can't open file servers/Frankenstein_TS5.pdb.gz in ReadConformPDB
# naming current conformation Frankenstein_TS5
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# naming current conformation GeneSilicoMetaServer_TS1
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# naming current conformation GeneSilicoMetaServer_TS2
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# naming current conformation GeneSilicoMetaServer_TS3
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# naming current conformation GeneSilicoMetaServer_TS4
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# naming current conformation GeneSilicoMetaServer_TS5
# ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1
# Found a chain break before 173
# copying to AlignedFragments data structure
# naming current conformation HHpred1_TS1
# ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1
# naming current conformation HHpred2_TS1
# ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1
# Found a chain break before 36
# 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 T0381 can't currently be optimized by undertaker
# naming current conformation Huber-Torda-Server_TS1
# ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 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 T0381 can't currently be optimized by undertaker
# naming current conformation Huber-Torda-Server_TS3
# ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# naming current conformation Huber-Torda-Server_TS4
# ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# naming current conformation Huber-Torda-Server_TS5
# ReadConformPDB reading from PDB file servers/LOOPP_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# naming current conformation LOOPP_TS1
# ReadConformPDB reading from PDB file servers/LOOPP_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# naming current conformation LOOPP_TS2
# ReadConformPDB reading from PDB file servers/LOOPP_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# naming current conformation LOOPP_TS3
# ReadConformPDB reading from PDB file servers/LOOPP_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# naming current conformation LOOPP_TS4
# ReadConformPDB reading from PDB file servers/LOOPP_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 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 T0381 can't currently be optimized by undertaker
# naming current conformation MIG_FROST_AL1
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS1.pdb.gz looking for model 1
# Found a chain break before 240
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server2_TS1
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS2.pdb.gz looking for model 1
# Found a chain break before 173
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server2_TS2
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS3.pdb.gz looking for model 1
# Found a chain break before 78
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server2_TS3
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS4.pdb.gz looking for model 1
# Found a chain break before 243
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server2_TS4
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS5.pdb.gz looking for model 1
# Found a chain break before 132
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server2_TS5
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1
# Found a chain break before 173
# 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 173
# 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 243
# 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 243
# 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 132
# 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 264
# 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 263
# copying to AlignedFragments data structure
# naming current conformation MetaTasser_TS2
# ReadConformPDB reading from PDB file servers/MetaTasser_TS3.pdb.gz looking for model 1
# Found a chain break before 264
# copying to AlignedFragments data structure
# naming current conformation MetaTasser_TS3
# ReadConformPDB reading from PDB file servers/MetaTasser_TS4.pdb.gz looking for model 1
# Found a chain break before 264
# copying to AlignedFragments data structure
# naming current conformation MetaTasser_TS4
# ReadConformPDB reading from PDB file servers/MetaTasser_TS5.pdb.gz looking for model 1
# Found a chain break before 263
# copying to AlignedFragments data structure
# naming current conformation MetaTasser_TS5
# ReadConformPDB reading from PDB file servers/NN_PUT_lab_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 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
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# naming current conformation PROTINFO_TS1
# ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# naming current conformation PROTINFO_TS2
# ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1
# naming current conformation PROTINFO_TS3
# ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# naming current conformation PROTINFO_TS4
# ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1
# naming current conformation PROTINFO_TS5
# ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# naming current conformation Pcons6_TS1
# ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# naming current conformation Pcons6_TS2
# ReadConformPDB reading from PDB file servers/Pcons6_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# naming current conformation Pcons6_TS3
# ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# naming current conformation Pcons6_TS4
# ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# naming current conformation Pcons6_TS5
# ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# naming current conformation Phyre-1_TS1
# ReadConformPDB reading from PDB file servers/Phyre-2_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 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 T0381 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 T0381 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 T0381 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 T0381 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation Phyre-2_TS5
# ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1
# Found a chain break before 236
# copying to AlignedFragments data structure
# naming current conformation Pmodeller6_TS1
# ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1
# Found a chain break before 236
# copying to AlignedFragments data structure
# naming current conformation Pmodeller6_TS2
# ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1
# Found a chain break before 236
# copying to AlignedFragments data structure
# naming current conformation Pmodeller6_TS3
# ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 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 T0381 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 173
# 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 243
# 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 74
# 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 241
# 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
# 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 242
# 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 176
# 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 262
# 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 176
# 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 260
# 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 173
# 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 169
# 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 243
# 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 243
# 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 120
# copying to AlignedFragments data structure
# naming current conformation RAPTOR_TS5
# ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1
# Found a chain break before 236
# copying to AlignedFragments data structure
# naming current conformation ROBETTA_TS1
# ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1
# Found a chain break before 236
# copying to AlignedFragments data structure
# naming current conformation ROBETTA_TS2
# ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1
# Found a chain break before 236
# copying to AlignedFragments data structure
# naming current conformation ROBETTA_TS3
# ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1
# Found a chain break before 236
# copying to AlignedFragments data structure
# naming current conformation ROBETTA_TS4
# ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1
# Found a chain break before 236
# 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 96
# 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 156
# copying to AlignedFragments data structure
# naming current conformation ROKKY_TS2
Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/servers/ROKKY_TS3.pdb.gz or /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/servers/ROKKY_TS3.pdb.gz.gz for input
Trying servers/ROKKY_TS3.pdb.gz
Error: Couldn't open file servers/ROKKY_TS3.pdb.gz or servers/ROKKY_TS3.pdb.gz.gz for input
Error: can't open file servers/ROKKY_TS3.pdb.gz in ReadConformPDB
# naming current conformation ROKKY_TS3
Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/servers/ROKKY_TS4.pdb.gz or /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/servers/ROKKY_TS4.pdb.gz.gz for input
Trying servers/ROKKY_TS4.pdb.gz
Error: Couldn't open file servers/ROKKY_TS4.pdb.gz or servers/ROKKY_TS4.pdb.gz.gz for input
Error: can't open file servers/ROKKY_TS4.pdb.gz in ReadConformPDB
# naming current conformation ROKKY_TS4
Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/servers/ROKKY_TS5.pdb.gz or /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/servers/ROKKY_TS5.pdb.gz.gz for input
Trying servers/ROKKY_TS5.pdb.gz
Error: Couldn't open file servers/ROKKY_TS5.pdb.gz or servers/ROKKY_TS5.pdb.gz.gz for input
Error: can't open file servers/ROKKY_TS5.pdb.gz in ReadConformPDB
# naming current conformation ROKKY_TS5
# ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 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 T0381 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 T0381 can't currently be optimized by undertaker
# naming current conformation SAM-T02_AL3
# ReadConformPDB reading from PDB file servers/SAM-T02_AL4.pdb.gz looking for model 1
Skipped atom 307, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 320, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 528, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 530, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 532, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 534, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 536, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 538, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 540, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 542, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 544, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 546, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 548, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 550, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 552, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 554, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 556, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 558, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 560, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 562, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 564, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 566, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 568, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 570, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 572, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 574, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 576, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 578, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 580, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 582, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 584, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 586, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 588, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 590, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 657, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
# WARNING: incomplete conformation T0381 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 T0381 can't currently be optimized by undertaker
# naming current conformation SAM-T02_AL5
# ReadConformPDB reading from PDB file servers/SAM-T99_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 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 T0381 can't currently be optimized by undertaker
# naming current conformation SAM-T99_AL2
# ReadConformPDB reading from PDB file servers/SAM-T99_AL3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 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 T0381 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 T0381 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 231
# 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 T0381 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 T0381 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 T0381 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 T0381 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 149
# 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 173
# 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 241
# 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 240
# 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 137
# 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 173
# 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 149
# 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 240
# copying to AlignedFragments data structure
# naming current conformation SP4_TS3
# ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1
# naming current conformation SP4_TS4
# ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1
# Found a chain break before 137
# 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 149
# 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 173
# 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 240
# copying to AlignedFragments data structure
# naming current conformation SPARKS2_TS3
# ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1
# naming current conformation SPARKS2_TS4
# ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1
# Found a chain break before 137
# 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 T0381 can't currently be optimized by undertaker
# naming current conformation UNI-EID_bnmx_TS1
# ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 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 T0381 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 T0381 can't currently be optimized by undertaker
# naming current conformation UNI-EID_bnmx_TS4
# ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 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 T0381 can't currently be optimized by undertaker
# naming current conformation UNI-EID_expm_TS1
# ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# naming current conformation UNI-EID_sfst_AL1
# ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 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 T0381 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 T0381 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 T0381 can't currently be optimized by undertaker
# naming current conformation UNI-EID_sfst_AL5
# ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1
# Found a chain break before 260
# copying to AlignedFragments data structure
# naming current conformation Zhang-Server_TS1
# ReadConformPDB reading from PDB file servers/Zhang-Server_TS2.pdb.gz looking for model 1
# Found a chain break before 262
# 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 260
# copying to AlignedFragments data structure
# naming current conformation Zhang-Server_TS3
# ReadConformPDB reading from PDB file servers/Zhang-Server_TS4.pdb.gz looking for model 1
# Found a chain break before 260
# copying to AlignedFragments data structure
# naming current conformation Zhang-Server_TS4
# ReadConformPDB reading from PDB file servers/Zhang-Server_TS5.pdb.gz looking for model 1
# Found a chain break before 262
# copying to AlignedFragments data structure
# naming current conformation Zhang-Server_TS5
# ReadConformPDB reading from PDB file servers/beautshot_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# naming current conformation beautshot_TS1
# ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# naming current conformation beautshotbase_TS1
# ReadConformPDB reading from PDB file servers/forecast-s_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 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 T0381 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 T0381 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 T0381 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 T0381 can't currently be optimized by undertaker
# naming current conformation forecast-s_AL5
# ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1
# Found a chain break before 70
# 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 70
# 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 180
# 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 118
# 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 243
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.2_TS5
# ReadConformPDB reading from PDB file servers/karypis.srv.4_TS1.pdb.gz looking for model 1
WARNING: atoms too close: (T0381)L11.O and (T0381)P12.N only 0.000 apart, marking (T0381)P12.N as missing
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.4_TS1
# ReadConformPDB reading from PDB file servers/karypis.srv.4_TS2.pdb.gz looking for model 1
WARNING: atoms too close: (T0381)K9.O and (T0381)I10.N only 0.000 apart, marking (T0381)I10.N as missing
WARNING: atoms too close: (T0381)Q35.O and (T0381)R36.N only 0.000 apart, marking (T0381)R36.N as missing
WARNING: atoms too close: (T0381)V129.O and (T0381)S130.N only 0.000 apart, marking (T0381)S130.N as missing
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.4_TS2
# ReadConformPDB reading from PDB file servers/karypis.srv.4_TS3.pdb.gz looking for model 1
WARNING: atoms too close: (T0381)T254.O and (T0381)D255.N only 0.000 apart, marking (T0381)D255.N as missing
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.4_TS3
# ReadConformPDB reading from PDB file servers/karypis.srv.4_TS4.pdb.gz looking for model 1
WARNING: atoms too close: (T0381)V153.O and (T0381)L154.N only 0.000 apart, marking (T0381)L154.N as missing
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.4_TS4
# ReadConformPDB reading from PDB file servers/karypis.srv.4_TS5.pdb.gz looking for model 1
WARNING: atoms too close: (T0381)E206.O and (T0381)A207.N only 0.000 apart, marking (T0381)A207.N as missing
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.4_TS5
# ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# naming current conformation karypis.srv_TS1
# ReadConformPDB reading from PDB file servers/karypis.srv_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# naming current conformation karypis.srv_TS2
# ReadConformPDB reading from PDB file servers/karypis.srv_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 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 T0381 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 T0381 can't currently be optimized by undertaker
# naming current conformation karypis.srv_TS5
# ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1
# naming current conformation keasar-server_TS1
# ReadConformPDB reading from PDB file servers/keasar-server_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# naming current conformation keasar-server_TS2
# ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# naming current conformation keasar-server_TS3
# ReadConformPDB reading from PDB file servers/keasar-server_TS4.pdb.gz looking for model 1
# Found a chain break before 229
# copying to AlignedFragments data structure
# naming current conformation keasar-server_TS4
# ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1
# Found a chain break before 229
# 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 T0381 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 T0381 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 T0381 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: atom 1 has residue number 13  < previous residue 263  in servers/nFOLD_TS3.pdb.gz
# WARNING: incomplete conformation T0381 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: atom 1 has residue number 13  < previous residue 263  in servers/nFOLD_TS4.pdb.gz
# WARNING: incomplete conformation T0381 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: atom 1 has residue number 54  < previous residue 263  in servers/nFOLD_TS5.pdb.gz
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# naming current conformation nFOLD_TS5
# ReadConformPDB reading from PDB file servers/panther2_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# naming current conformation panther2_TS1
Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/servers/panther3_TS1.pdb.gz or /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/servers/panther3_TS1.pdb.gz.gz for input
Trying servers/panther3_TS1.pdb.gz
Error: Couldn't open file servers/panther3_TS1.pdb.gz or servers/panther3_TS1.pdb.gz.gz for input
Error: can't open file servers/panther3_TS1.pdb.gz in ReadConformPDB
# naming current conformation panther3_TS1
# ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0381 can't currently be optimized by undertaker
# naming current conformation shub_TS1
# command:Using radius: 8.0000
Metaserver mode
NUMB_ALIGNS: 258
model score -0.3363
model score -0.3404
model score -0.2958
model score -0.3232
model score -0.3252
model score -0.3268
model score -0.3268
model score -0.3285
model score -0.3283
model score -0.3264
model score -0.3283
model score -0.3283
model score 0.6154
model score -0.4096
model score -0.3730
model score -0.3655
model score -0.2920
model score -0.3154
model score 1.4138
model score 1.3968
model score 1.7226
model score 1.4850
model score 1.5821
model score -0.4194
model score -0.3716
model score -0.3740
model score -0.3783
model score -0.3817
model score -0.3782
model score -0.3553
model score -0.3657
model score -0.3616
model score -0.3643
model score -0.3739
model score -0.3612
model score -0.3197
model score -0.3506
model score 0.4120
model score 0.3771
model score 0.4671
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
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weight: 0.7156 eval: 0.4489 min: -0.4613 max: 2.4194
weight: 0.7311 eval: 0.3993 min: -0.4613 max: 2.4194
weight: 0.7158 eval: 0.4485 min: -0.4613 max: 2.4194
weight: 0.7267 eval: 0.4134 min: -0.4613 max: 2.4194
weight: 0.7295 eval: 0.4046 min: -0.4613 max: 2.4194
weight: 0.2557 eval: 1.9210 min: -0.4613 max: 2.4194
weight: 0.2665 eval: 1.8864 min: -0.4613 max: 2.4194
weight: 0.1152 eval: 2.3709 min: -0.4613 max: 2.4194
weight: 0.1000 eval: 2.4194 min: -0.4613 max: 2.4194
weight: 0.1566 eval: 2.2384 min: -0.4613 max: 2.4194
weight: 0.9783 eval: -0.3920 min: -0.4613 max: 2.4194
weight: 0.9809 eval: -0.4003 min: -0.4613 max: 2.4194
weight: 0.7479 eval: 0.3455 min: -0.4613 max: 2.4194
weight: 0.7025 eval: 0.4908 min: -0.4613 max: 2.4194
weight: 0.7641 eval: 0.2938 min: -0.4613 max: 2.4194
weight: 0.9628 eval: -0.3421 min: -0.4613 max: 2.4194
weight: 0.7430 eval: 0.3613 min: -0.4613 max: 2.4194
weight: 0.7430 eval: 0.3613 min: -0.4613 max: 2.4194
weight: 0.9609 eval: -0.3362 min: -0.4613 max: 2.4194
weight: 0.9609 eval: -0.3362 min: -0.4613 max: 2.4194
weight: 0.9786 eval: -0.3929 min: -0.4613 max: 2.4194
weight: 0.9786 eval: -0.3929 min: -0.4613 max: 2.4194
weight: 0.9746 eval: -0.3801 min: -0.4613 max: 2.4194
weight: 0.7315 eval: 0.3981 min: -0.4613 max: 2.4194
weight: 0.7290 eval: 0.4062 min: -0.4613 max: 2.4194
weight: 0.3869 eval: 1.5010 min: -0.4613 max: 2.4194
weight: 0.7223 eval: 0.4275 min: -0.4613 max: 2.4194
weight: 0.9754 eval: -0.3827 min: -0.4613 max: 2.4194
Adding 7462 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: -444.3811, CN propb: -444.3811 weights: 0.4513 constraints: 752
# command:Found ConstraintSet
# PrintContacts align.constraints_meta02
Number of constraints in align2.constraints 752
# command:Found ConstraintSet
# PrintContacts align_bonus.constraints_meta02
Number of constraints in align2.constraints.bonus 752
# command:Found ConstraintSet
# PrintContacts rejected.constraints_meta02
Number of constraints in rejected2.constraints 6710
# command:Found ConstraintSet
# PrintContacts rejected_bonus.constraints_meta02
Number of constraints in rejected2.constraints.bonus 6710
# 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 7462
# command: