# 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/T0349/ # command:# Making conformation for sequence T0349 numbered 1 through 75 Created new target T0349 from T0349.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0349/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0349//projects/compbio/experiments/protein-predict/casp7/T0349/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0349//projects/compbio/experiments/protein-predict/casp7/T0349/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0349/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0349/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((T0349)G17.CA, (T0349)H27.CB) [> 3.5414 = 5.9023 < 7.6730] w=1.0000 to align # Constraint # added constraint: constraint((T0349)V16.CB, (T0349)H27.CB) [> 3.7183 = 6.1972 < 8.0564] w=0.8185 to align # Constraint # added constraint: constraint((T0349)L30.CB, (T0349)R46.CB) [> 4.0889 = 6.8148 < 8.8593] w=0.7176 to align # Constraint # added constraint: constraint((T0349)V29.CB, (T0349)R47.CB) [> 3.3590 = 5.5983 < 7.2778] w=0.7158 to align # Constraint # added constraint: constraint((T0349)L13.CB, (T0349)L61.CB) [> 4.0370 = 6.7283 < 8.7468] w=0.7042 to align # Constraint # added constraint: constraint((T0349)I25.CB, (T0349)A58.CB) [> 3.4836 = 5.8060 < 7.5478] w=0.6821 to align # Constraint # added constraint: constraint((T0349)L19.CB, (T0349)L61.CB) [> 3.3579 = 5.5965 < 7.2755] w=0.6821 to align # Constraint # added constraint: constraint((T0349)L30.CB, (T0349)R47.CB) [> 4.1664 = 6.9439 < 9.0271] w=0.6800 to align # Constraint # added constraint: constraint((T0349)V29.CB, (T0349)R46.CB) [> 4.2531 = 7.0885 < 9.2150] w=0.6451 to align # Constraint # added constraint: constraint((T0349)V16.CB, (T0349)L67.CB) [> 3.8496 = 6.4160 < 8.3408] w=0.6091 to align # Constraint # added constraint: constraint((T0349)I25.CB, (T0349)V50.CB) [> 3.5717 = 5.9529 < 7.7387] w=0.5778 to align # Constraint # added constraint: constraint((T0349)L20.CB, (T0349)L61.CB) [> 3.9624 = 6.6040 < 8.5852] w=0.5752 to align # Constraint # added constraint: constraint((T0349)L13.CB, (T0349)V29.CB) [> 4.1312 = 6.8853 < 8.9508] w=0.5743 to align # Constraint # added constraint: constraint((T0349)L28.CB, (T0349)R47.CB) [> 3.7685 = 6.2809 < 8.1652] w=0.5692 to align # Constraint # added constraint: constraint((T0349)V48.CB, (T0349)A58.CB) [> 4.0251 = 6.7086 < 8.7211] w=0.5661 to align # Constraint # added constraint: constraint((T0349)G26.CA, (T0349)V50.CB) [> 3.8662 = 6.4436 < 8.3767] w=0.5425 to align # Constraint # added constraint: constraint((T0349)A15.CB, (T0349)L67.CB) [> 4.1636 = 6.9393 < 9.0211] w=0.5407 to align # Constraint # added constraint: constraint((T0349)A15.CB, (T0349)A65.CB) [> 3.9622 = 6.6036 < 8.5847] w=0.5397 to align # Constraint # added constraint: constraint((T0349)V16.CB, (T0349)L62.CB) [> 3.9759 = 6.6264 < 8.6143] w=0.5381 to align # Constraint # added constraint: constraint((T0349)L28.CB, (T0349)V48.CB) [> 3.8027 = 6.3378 < 8.2392] w=0.5380 to align # Constraint # added constraint: constraint((T0349)G26.CA, (T0349)H51.CB) [> 3.9488 = 6.5813 < 8.5558] w=0.5380 to align # Constraint # added constraint: constraint((T0349)V29.CB, (T0349)L49.CB) [> 4.0512 = 6.7519 < 8.7775] w=0.5379 to align # Constraint # added constraint: constraint((T0349)L30.CB, (T0349)V48.CB) [> 3.6073 = 6.0122 < 7.8158] w=0.5352 to align # Constraint # added constraint: constraint((T0349)L13.CB, (T0349)L62.CB) [> 3.5658 = 5.9431 < 7.7260] w=0.5285 to align # Constraint # added constraint: constraint((T0349)H27.CB, (T0349)L49.CB) [> 4.5167 = 7.5279 < 9.7862] w=0.5057 to align # Constraint # added constraint: constraint((T0349)Q32.CB, (T0349)D54.CB) [> 4.1551 = 6.9252 < 9.0028] w=0.4997 to align # Constraint # added constraint: constraint((T0349)Q32.CB, (T0349)V50.CB) [> 3.4871 = 5.8119 < 7.5554] w=0.4989 to align # Constraint # added constraint: constraint((T0349)L28.CB, (T0349)L49.CB) [> 3.1529 = 5.2548 < 6.8312] w=0.4690 to align # Constraint # added constraint: constraint((T0349)A23.CB, (T0349)L61.CB) [> 3.1349 = 5.2248 < 6.7922] w=0.4688 to align # Constraint # added constraint: constraint((T0349)L20.CB, (T0349)A58.CB) [> 3.6287 = 6.0478 < 7.8622] w=0.4688 to align # Constraint # added constraint: constraint((T0349)L19.CB, (T0349)L62.CB) [> 3.8683 = 6.4472 < 8.3813] w=0.4688 to align # Constraint # added constraint: constraint((T0349)H27.CB, (T0349)V48.CB) [> 3.5715 = 5.9526 < 7.7384] w=0.4672 to align # Constraint # added constraint: constraint((T0349)V16.CB, (T0349)R46.CB) [> 4.0202 = 6.7004 < 8.7105] w=0.4666 to align # Constraint # added constraint: constraint((T0349)L30.CB, (T0349)L49.CB) [> 4.0844 = 6.8073 < 8.8495] w=0.4653 to align # Constraint # added constraint: constraint((T0349)D31.CB, (T0349)L49.CB) [> 3.5160 = 5.8600 < 7.6180] w=0.4599 to align # Constraint # added constraint: constraint((T0349)G17.CA, (T0349)G26.CA) [> 4.1165 = 6.8608 < 8.9191] w=0.4595 to align # Constraint # added constraint: constraint((T0349)L20.CB, (T0349)V50.CB) [> 4.1459 = 6.9099 < 8.9829] w=0.4336 to align # Constraint # added constraint: constraint((T0349)I25.CB, (T0349)H51.CB) [> 4.0315 = 6.7191 < 8.7348] w=0.4290 to align # Constraint # added constraint: constraint((T0349)V29.CB, (T0349)V48.CB) [> 4.0623 = 6.7706 < 8.8017] w=0.4286 to align # Constraint # added constraint: constraint((T0349)H27.CB, (T0349)R47.CB) [> 4.5089 = 7.5148 < 9.7693] w=0.4267 to align # Constraint # added constraint: constraint((T0349)L28.CB, (T0349)R46.CB) [> 3.1377 = 5.2295 < 6.7984] w=0.4251 to align # Constraint # added constraint: constraint((T0349)V16.CB, (T0349)A65.CB) [> 4.4190 = 7.3650 < 9.5745] w=0.4219 to align # Constraint # added constraint: constraint((T0349)L12.CB, (T0349)L67.CB) [> 3.6755 = 6.1259 < 7.9636] w=0.3950 to align # Constraint # added constraint: constraint((T0349)Q32.CB, (T0349)L49.CB) [> 3.1092 = 5.1821 < 6.7367] w=0.3908 to align # Constraint # added constraint: constraint((T0349)D31.CB, (T0349)R47.CB) [> 3.4694 = 5.7822 < 7.5169] w=0.3907 to align # Constraint # added constraint: constraint((T0349)L19.CB, (T0349)A65.CB) [> 2.9040 = 4.8400 < 6.2920] w=0.3616 to align # Constraint # added constraint: constraint((T0349)H27.CB, (T0349)V50.CB) [> 3.6115 = 6.0192 < 7.8249] w=0.3615 to align # Constraint # added constraint: constraint((T0349)A23.CB, (T0349)A58.CB) [> 4.1132 = 6.8554 < 8.9120] w=0.3595 to align # Constraint # added constraint: constraint((T0349)A23.CB, (T0349)G57.CA) [> 4.1296 = 6.8826 < 8.9474] w=0.3595 to align # Constraint # added constraint: constraint((T0349)D31.CB, (T0349)R46.CB) [> 4.0178 = 6.6963 < 8.7052] w=0.3587 to align # Constraint # added constraint: constraint((T0349)V29.CB, (T0349)A58.CB) [> 4.0670 = 6.7783 < 8.8118] w=0.3564 to align # Constraint # added constraint: constraint((T0349)E38.CB, (T0349)R47.CB) [> 3.8982 = 6.4970 < 8.4461] w=0.3564 to align # Constraint # added constraint: constraint((T0349)Q32.CB, (T0349)H51.CB) [> 3.9952 = 6.6586 < 8.6562] w=0.3558 to align # Constraint # added constraint: constraint((T0349)G26.CA, (T0349)P45.CB) [> 3.5760 = 5.9601 < 7.7481] w=0.3539 to align # Constraint # added constraint: constraint((T0349)H27.CB, (T0349)P45.CB) [> 2.8698 = 4.7829 < 6.2178] w=0.3539 to align # Constraint # added constraint: constraint((T0349)L28.CB, (T0349)P45.CB) [> 3.9805 = 6.6341 < 8.6244] w=0.3539 to align # Constraint # added constraint: constraint((T0349)R59.CB, (T0349)H69.CB) [> 3.8920 = 6.4867 < 8.4327] w=0.3362 to align # Constraint # added constraint: constraint((T0349)L13.CB, (T0349)R46.CB) [> 3.2510 = 5.4183 < 7.0437] w=0.3261 to align # Constraint # added constraint: constraint((T0349)V16.CB, (T0349)V48.CB) [> 3.9062 = 6.5103 < 8.4634] w=0.3256 to align # Constraint # added constraint: constraint((T0349)H27.CB, (T0349)R46.CB) [> 4.0616 = 6.7693 < 8.8001] w=0.3210 to align # Constraint # added constraint: constraint((T0349)N33.CB, (T0349)V50.CB) [> 4.1652 = 6.9420 < 9.0246] w=0.3208 to align # Constraint # added constraint: constraint((T0349)N33.CB, (T0349)L55.CB) [> 2.6259 = 4.3765 < 5.6895] w=0.3206 to align # Constraint # added constraint: constraint((T0349)R47.CB, (T0349)A58.CB) [> 3.7575 = 6.2625 < 8.1412] w=0.3204 to align # Constraint # added constraint: constraint((T0349)L28.CB, (T0349)I44.CB) [> 3.7890 = 6.3149 < 8.2094] w=0.3184 to align # Constraint # added constraint: constraint((T0349)H27.CB, (T0349)I44.CB) [> 3.8518 = 6.4197 < 8.3456] w=0.3184 to align # Constraint # added constraint: constraint((T0349)L19.CB, (T0349)L67.CB) [> 4.2102 = 7.0170 < 9.1220] w=0.2863 to align # Constraint # added constraint: constraint((T0349)N33.CB, (T0349)A58.CB) [> 4.1620 = 6.9367 < 9.0177] w=0.2851 to align # Constraint # added constraint: constraint((T0349)S35.CB, (T0349)L55.CB) [> 4.0982 = 6.8304 < 8.8795] w=0.2850 to align # Constraint # added constraint: constraint((T0349)Q32.CB, (T0349)L55.CB) [> 2.3947 = 3.9912 < 5.1885] w=0.2850 to align # Constraint # added constraint: constraint((T0349)L49.CB, (T0349)A58.CB) [> 3.6379 = 6.0632 < 7.8821] w=0.2804 to align # Constraint # added constraint: constraint((T0349)L28.CB, (T0349)V50.CB) [> 4.1950 = 6.9916 < 9.0891] w=0.2534 to align # Constraint # added constraint: constraint((T0349)L20.CB, (T0349)V48.CB) [> 4.5425 = 7.5708 < 9.8421] w=0.2515 to align # Constraint # added constraint: constraint((T0349)R6.CB, (T0349)A68.CB) [> 2.9067 = 4.8445 < 6.2979] w=0.2513 to align # Constraint # added constraint: constraint((T0349)L5.CB, (T0349)V48.CB) [> 4.2755 = 7.1258 < 9.2635] w=0.2513 to align # Constraint # added constraint: constraint((T0349)L5.CB, (T0349)V16.CB) [> 4.0936 = 6.8227 < 8.8695] w=0.2513 to align # Constraint # added constraint: constraint((T0349)L30.CB, (T0349)A58.CB) [> 3.9724 = 6.6207 < 8.6069] w=0.2512 to align # Constraint # added constraint: constraint((T0349)L13.CB, (T0349)L37.CB) [> 4.5159 = 7.5264 < 9.7844] w=0.2504 to align # Constraint # added constraint: constraint((T0349)S14.CB, (T0349)A65.CB) [> 3.8438 = 6.4063 < 8.3282] w=0.2494 to align # Constraint # added constraint: constraint((T0349)D31.CB, (T0349)L55.CB) [> 2.4011 = 4.0018 < 5.2024] w=0.2494 to align # Constraint # added constraint: constraint((T0349)N33.CB, (T0349)G57.CA) [> 4.5097 = 7.5162 < 9.7711] w=0.2494 to align # Constraint # added constraint: constraint((T0349)M34.CB, (T0349)R46.CB) [> 3.3977 = 5.6628 < 7.3616] w=0.2494 to align # Constraint # added constraint: constraint((T0349)L20.CB, (T0349)I44.CB) [> 4.4745 = 7.4575 < 9.6948] w=0.2482 to align # Constraint # added constraint: constraint((T0349)G17.CA, (T0349)V48.CB) [> 4.1496 = 6.9160 < 8.9909] w=0.2183 to align # Constraint # added constraint: constraint((T0349)I36.CB, (T0349)R46.CB) [> 3.5360 = 5.8934 < 7.6613] w=0.2165 to align # Constraint # added constraint: constraint((T0349)L5.CB, (T0349)A68.CB) [> 4.1577 = 6.9295 < 9.0084] w=0.2149 to align # Constraint # added constraint: constraint((T0349)L5.CB, (T0349)R46.CB) [> 2.9759 = 4.9599 < 6.4478] w=0.2149 to align # Constraint # added constraint: constraint((T0349)S35.CB, (T0349)R47.CB) [> 4.3252 = 7.2086 < 9.3712] w=0.2139 to align # Constraint # added constraint: constraint((T0349)S35.CB, (T0349)E52.CB) [> 2.9571 = 4.9284 < 6.4069] w=0.2137 to align # Constraint # added constraint: constraint((T0349)Q32.CB, (T0349)E52.CB) [> 3.0183 = 5.0304 < 6.5396] w=0.2137 to align # Constraint # added constraint: constraint((T0349)N33.CB, (T0349)H51.CB) [> 4.2547 = 7.0911 < 9.2184] w=0.2136 to align # Constraint # added constraint: constraint((T0349)L37.CB, (T0349)R47.CB) [> 2.9464 = 4.9107 < 6.3839] w=0.2136 to align # Constraint # added constraint: constraint((T0349)L19.CB, (T0349)A58.CB) [> 4.2812 = 7.1353 < 9.2759] w=0.2133 to align # Constraint # added constraint: constraint((T0349)Q32.CB, (T0349)A58.CB) [> 4.1086 = 6.8477 < 8.9020] w=0.2123 to align # Constraint # added constraint: constraint((T0349)L19.CB, (T0349)D64.CB) [> 4.2569 = 7.0948 < 9.2233] w=0.1803 to align # Constraint # added constraint: constraint((T0349)R6.CB, (T0349)P45.CB) [> 3.1467 = 5.2445 < 6.8179] w=0.1801 to align # Constraint # added constraint: constraint((T0349)L30.CB, (T0349)L61.CB) [> 3.9714 = 6.6190 < 8.6047] w=0.1801 to align # Constraint # added constraint: constraint((T0349)L41.CB, (T0349)V50.CB) [> 4.1263 = 6.8771 < 8.9403] w=0.1790 to align # Constraint # added constraint: constraint((T0349)L37.CB, (T0349)V48.CB) [> 4.4217 = 7.3696 < 9.5805] w=0.1789 to align # Constraint # added constraint: constraint((T0349)M34.CB, (T0349)L49.CB) [> 3.4845 = 5.8075 < 7.5498] w=0.1788 to align # Constraint # added constraint: constraint((T0349)T7.CB, (T0349)S40.CB) [> 3.5147 = 5.8579 < 7.6153] w=0.1786 to align # Constraint # added constraint: constraint((T0349)S35.CB, (T0349)V50.CB) [> 4.2332 = 7.0554 < 9.1720] w=0.1785 to align # Constraint # added constraint: constraint((T0349)S35.CB, (T0349)V48.CB) [> 3.4317 = 5.7195 < 7.4354] w=0.1785 to align # Constraint # added constraint: constraint((T0349)M34.CB, (T0349)V50.CB) [> 3.3245 = 5.5409 < 7.2032] w=0.1783 to align # Constraint # added constraint: constraint((T0349)M34.CB, (T0349)V48.CB) [> 2.2562 = 3.7603 < 4.8884] w=0.1783 to align # Constraint # added constraint: constraint((T0349)I36.CB, (T0349)R59.CB) [> 3.0901 = 5.1502 < 6.6953] w=0.1774 to align # Constraint # added constraint: constraint((T0349)G17.CA, (T0349)L61.CB) [> 4.3884 = 7.3140 < 9.5082] w=0.1774 to align # Constraint # added constraint: constraint((T0349)D9.CB, (T0349)A58.CB) [> 3.3472 = 5.5788 < 7.2524] w=0.1733 to align # Constraint # added constraint: constraint((T0349)P45.CB, (T0349)L61.CB) [> 3.7511 = 6.2519 < 8.1275] w=0.1470 to align # Constraint # added constraint: constraint((T0349)N33.CB, (T0349)P45.CB) [> 4.2026 = 7.0043 < 9.1056] w=0.1456 to align # Constraint # added constraint: constraint((T0349)L12.CB, (T0349)R46.CB) [> 4.5182 = 7.5303 < 9.7894] w=0.1455 to align # Constraint # added constraint: constraint((T0349)L13.CB, (T0349)G42.CA) [> 3.8925 = 6.4875 < 8.4338] w=0.1453 to align # Constraint # added constraint: constraint((T0349)L12.CB, (T0349)G42.CA) [> 4.5555 = 7.5925 < 9.8702] w=0.1453 to align # Constraint # added constraint: constraint((T0349)A10.CB, (T0349)G42.CA) [> 4.3488 = 7.2480 < 9.4224] w=0.1453 to align # Constraint # added constraint: constraint((T0349)L28.CB, (T0349)L61.CB) [> 2.9088 = 4.8480 < 6.3024] w=0.1445 to align # Constraint # added constraint: constraint((T0349)S14.CB, (T0349)S40.CB) [> 4.5130 = 7.5217 < 9.7782] w=0.1434 to align # Constraint # added constraint: constraint((T0349)L20.CB, (T0349)L41.CB) [> 4.1800 = 6.9667 < 9.0567] w=0.1425 to align # Constraint # added constraint: constraint((T0349)D21.CB, (T0349)L41.CB) [> 4.2182 = 7.0303 < 9.1393] w=0.1425 to align # Constraint # added constraint: constraint((T0349)V29.CB, (T0349)L61.CB) [> 3.9689 = 6.6148 < 8.5992] w=0.1425 to align # Constraint # added constraint: constraint((T0349)R6.CB, (T0349)H69.CB) [> 4.3052 = 7.1754 < 9.3279] w=0.1422 to align # Constraint # added constraint: constraint((T0349)I36.CB, (T0349)A58.CB) [> 3.0317 = 5.0529 < 6.5688] w=0.1420 to align # Constraint # added constraint: constraint((T0349)A10.CB, (T0349)L61.CB) [> 3.4190 = 5.6984 < 7.4079] w=0.1387 to align # Constraint # added constraint: constraint((T0349)D31.CB, (T0349)P45.CB) [> 3.9593 = 6.5988 < 8.5784] w=0.1092 to align # Constraint # added constraint: constraint((T0349)L12.CB, (T0349)G66.CA) [> 4.6536 = 7.7559 < 10.0827] w=0.1091 to align # Constraint # added constraint: constraint((T0349)T7.CB, (T0349)G42.CA) [> 3.3489 = 5.5815 < 7.2560] w=0.1090 to align # Constraint # added constraint: constraint((T0349)T7.CB, (T0349)V43.CB) [> 4.5684 = 7.6140 < 9.8982] w=0.1090 to align # Constraint # added constraint: constraint((T0349)T7.CB, (T0349)I44.CB) [> 3.6697 = 6.1161 < 7.9509] w=0.1090 to align # Constraint # added constraint: constraint((T0349)N8.CB, (T0349)G42.CA) [> 3.8100 = 6.3500 < 8.2549] w=0.1090 to align # Constraint # added constraint: constraint((T0349)N8.CB, (T0349)V43.CB) [> 3.6838 = 6.1397 < 7.9816] w=0.1090 to align # Constraint # added constraint: constraint((T0349)I44.CB, (T0349)H69.CB) [> 4.4895 = 7.4824 < 9.7272] w=0.1090 to align # Constraint # added constraint: constraint((T0349)L28.CB, (T0349)A58.CB) [> 4.0846 = 6.8077 < 8.8499] w=0.1090 to align # Constraint # added constraint: constraint((T0349)D9.CB, (T0349)V43.CB) [> 4.7220 = 7.8701 < 10.2311] w=0.1089 to align # Constraint # added constraint: constraint((T0349)A15.CB, (T0349)L61.CB) [> 4.0662 = 6.7771 < 8.8102] w=0.1089 to align # Constraint # added constraint: constraint((T0349)D24.CB, (T0349)H51.CB) [> 3.4114 = 5.6857 < 7.3914] w=0.1089 to align # Constraint # added constraint: constraint((T0349)L20.CB, (T0349)M34.CB) [> 3.4260 = 5.7101 < 7.4231] w=0.1085 to align # Constraint # added constraint: constraint((T0349)I36.CB, (T0349)R47.CB) [> 4.3534 = 7.2557 < 9.4324] w=0.1079 to align # Constraint # added constraint: constraint((T0349)I36.CB, (T0349)V48.CB) [> 3.2493 = 5.4155 < 7.0401] w=0.1079 to align # Constraint # added constraint: constraint((T0349)L37.CB, (T0349)L49.CB) [> 4.2252 = 7.0420 < 9.1546] w=0.1079 to align # Constraint # added constraint: constraint((T0349)L37.CB, (T0349)L67.CB) [> 4.3922 = 7.3204 < 9.5165] w=0.1075 to align # Constraint # added constraint: constraint((T0349)I25.CB, (T0349)L41.CB) [> 4.0116 = 6.6859 < 8.6917] w=0.1070 to align # Constraint # added constraint: constraint((T0349)L28.CB, (T0349)L37.CB) [> 4.6413 = 7.7355 < 10.0562] w=0.1070 to align # Constraint # added constraint: constraint((T0349)L28.CB, (T0349)E38.CB) [> 4.2996 = 7.1660 < 9.3158] w=0.1070 to align # Constraint # added constraint: constraint((T0349)L28.CB, (T0349)L41.CB) [> 4.2811 = 7.1351 < 9.2757] w=0.1070 to align # Constraint # added constraint: constraint((T0349)M34.CB, (T0349)R47.CB) [> 4.5219 = 7.5365 < 9.7974] w=0.1070 to align # Constraint # added constraint: constraint((T0349)E38.CB, (T0349)V48.CB) [> 2.4730 = 4.1217 < 5.3583] w=0.1070 to align # Constraint # added constraint: constraint((T0349)G39.CA, (T0349)V48.CB) [> 4.7785 = 7.9641 < 10.3534] w=0.1070 to align # Constraint # added constraint: constraint((T0349)R47.CB, (T0349)L61.CB) [> 3.2738 = 5.4564 < 7.0933] w=0.1070 to align # Constraint # added constraint: constraint((T0349)N33.CB, (T0349)I44.CB) [> 4.3232 = 7.2053 < 9.3669] w=0.1065 to align # Constraint # added constraint: constraint((T0349)I36.CB, (T0349)L62.CB) [> 4.7728 = 7.9546 < 10.3410] w=0.1064 to align # Constraint # added constraint: constraint((T0349)L37.CB, (T0349)R59.CB) [> 4.3404 = 7.2340 < 9.4042] w=0.1064 to align # Constraint # added constraint: constraint((T0349)L37.CB, (T0349)L62.CB) [> 4.5981 = 7.6636 < 9.9627] w=0.1064 to align # Constraint # added constraint: constraint((T0349)L12.CB, (T0349)V29.CB) [> 4.0055 = 6.6758 < 8.6786] w=0.1060 to align # Constraint # added constraint: constraint((T0349)N8.CB, (T0349)G39.CA) [> 3.3340 = 5.5566 < 7.2236] w=0.1059 to align # Constraint # added constraint: constraint((T0349)V29.CB, (T0349)I44.CB) [> 3.1225 = 5.2042 < 6.7654] w=0.1058 to align # Constraint # added constraint: constraint((T0349)L20.CB, (T0349)S40.CB) [> 4.1186 = 6.8644 < 8.9237] w=0.1057 to align # Constraint # added constraint: constraint((T0349)L20.CB, (T0349)L37.CB) [> 3.5633 = 5.9388 < 7.7204] w=0.1057 to align # Constraint # added constraint: constraint((T0349)D9.CB, (T0349)G39.CA) [> 4.1981 = 6.9968 < 9.0958] w=0.1044 to align # Constraint # added constraint: constraint((T0349)A10.CB, (T0349)E38.CB) [> 4.0540 = 6.7567 < 8.7838] w=0.0727 to align # Constraint # added constraint: constraint((T0349)L20.CB, (T0349)L30.CB) [> 2.9340 = 4.8900 < 6.3570] w=0.0727 to align # Constraint # added constraint: constraint((T0349)L4.CB, (T0349)R47.CB) [> 3.6117 = 6.0195 < 7.8254] w=0.0727 to align # Constraint # added constraint: constraint((T0349)L13.CB, (T0349)S40.CB) [> 3.0361 = 5.0602 < 6.5782] w=0.0727 to align # Constraint # added constraint: constraint((T0349)A10.CB, (T0349)R46.CB) [> 3.4982 = 5.8304 < 7.5795] w=0.0727 to align # Constraint # added constraint: constraint((T0349)I36.CB, (T0349)L49.CB) [> 4.6492 = 7.7487 < 10.0733] w=0.0715 to align # Constraint # added constraint: constraint((T0349)I36.CB, (T0349)D53.CB) [> 3.3241 = 5.5402 < 7.2022] w=0.0713 to align # Constraint # added constraint: constraint((T0349)V43.CB, (T0349)L71.CB) [> 3.9064 = 6.5107 < 8.4639] w=0.0712 to align # Constraint # added constraint: constraint((T0349)L41.CB, (T0349)L71.CB) [> 4.7035 = 7.8392 < 10.1910] w=0.0712 to align # Constraint # added constraint: constraint((T0349)L37.CB, (T0349)L71.CB) [> 3.7103 = 6.1839 < 8.0391] w=0.0712 to align # Constraint # added constraint: constraint((T0349)M34.CB, (T0349)V43.CB) [> 4.1676 = 6.9461 < 9.0299] w=0.0712 to align # Constraint # added constraint: constraint((T0349)L20.CB, (T0349)G39.CA) [> 4.0012 = 6.6686 < 8.6692] w=0.0711 to align # Constraint # added constraint: constraint((T0349)S14.CB, (T0349)L61.CB) [> 3.2244 = 5.3740 < 6.9862] w=0.0711 to align # Constraint # added constraint: constraint((T0349)A18.CB, (T0349)V43.CB) [> 4.2759 = 7.1265 < 9.2644] w=0.0708 to align # Constraint # added constraint: constraint((T0349)L12.CB, (T0349)V43.CB) [> 4.2450 = 7.0750 < 9.1975] w=0.0705 to align # Constraint # added constraint: constraint((T0349)L5.CB, (T0349)S40.CB) [> 4.7346 = 7.8910 < 10.2583] w=0.0696 to align # Constraint # added constraint: constraint((T0349)I25.CB, (T0349)G39.CA) [> 3.6470 = 6.0783 < 7.9017] w=0.0693 to align # Constraint # added constraint: constraint((T0349)G26.CA, (T0349)L37.CB) [> 2.9155 = 4.8592 < 6.3170] w=0.0693 to align # Constraint # added constraint: constraint((T0349)G26.CA, (T0349)G39.CA) [> 3.2200 = 5.3667 < 6.9767] w=0.0693 to align # Constraint # added constraint: constraint((T0349)A15.CB, (T0349)R46.CB) [> 2.5539 = 4.2565 < 5.5335] w=0.0693 to align # Constraint # added constraint: constraint((T0349)A15.CB, (T0349)V48.CB) [> 3.7338 = 6.2230 < 8.0899] w=0.0693 to align # Constraint # added constraint: constraint((T0349)A18.CB, (T0349)R46.CB) [> 4.0776 = 6.7961 < 8.8349] w=0.0693 to align # Constraint # added constraint: constraint((T0349)G22.CA, (T0349)S40.CB) [> 4.6508 = 7.7513 < 10.0767] w=0.0693 to align # Constraint # added constraint: constraint((T0349)E38.CB, (T0349)A58.CB) [> 3.9779 = 6.6298 < 8.6187] w=0.0399 to align # Constraint # added constraint: constraint((T0349)E38.CB, (T0349)L61.CB) [> 3.3762 = 5.6270 < 7.3151] w=0.0399 to align # Constraint # added constraint: constraint((T0349)G39.CA, (T0349)A58.CB) [> 4.0175 = 6.6958 < 8.7046] w=0.0399 to align # Constraint # added constraint: constraint((T0349)P45.CB, (T0349)A58.CB) [> 4.0631 = 6.7719 < 8.8034] w=0.0399 to align # Constraint # added constraint: constraint((T0349)P45.CB, (T0349)L62.CB) [> 2.7375 = 4.5625 < 5.9313] w=0.0399 to align # Constraint # added constraint: constraint((T0349)A10.CB, (T0349)L41.CB) [> 4.6659 = 7.7765 < 10.1095] w=0.0364 to align # Constraint # added constraint: constraint((T0349)A10.CB, (T0349)L37.CB) [> 4.6986 = 7.8310 < 10.1803] w=0.0364 to align # Constraint # added constraint: constraint((T0349)L4.CB, (T0349)R46.CB) [> 4.3854 = 7.3090 < 9.5016] w=0.0364 to align # Constraint # added constraint: constraint((T0349)L4.CB, (T0349)P45.CB) [> 3.1994 = 5.3323 < 6.9320] w=0.0364 to align # Constraint # added constraint: constraint((T0349)L13.CB, (T0349)L41.CB) [> 3.8691 = 6.4484 < 8.3829] w=0.0364 to align # Constraint # added constraint: constraint((T0349)S14.CB, (T0349)M34.CB) [> 4.7072 = 7.8454 < 10.1990] w=0.0364 to align # Constraint # added constraint: constraint((T0349)S14.CB, (T0349)S35.CB) [> 4.7838 = 7.9730 < 10.3649] w=0.0364 to align # Constraint # added constraint: constraint((T0349)L4.CB, (T0349)L49.CB) [> 3.1598 = 5.2663 < 6.8463] w=0.0363 to align # Constraint # added constraint: constraint((T0349)L4.CB, (T0349)V48.CB) [> 4.6687 = 7.7812 < 10.1156] w=0.0363 to align # Constraint # added constraint: constraint((T0349)R2.CB, (T0349)H51.CB) [> 3.8890 = 6.4816 < 8.4261] w=0.0363 to align # Constraint # added constraint: constraint((T0349)R2.CB, (T0349)L49.CB) [> 2.9534 = 4.9223 < 6.3990] w=0.0363 to align # Constraint # added constraint: constraint((T0349)M1.CB, (T0349)E52.CB) [> 2.4749 = 4.1248 < 5.3622] w=0.0363 to align # Constraint # added constraint: constraint((T0349)M1.CB, (T0349)H51.CB) [> 4.3668 = 7.2780 < 9.4614] w=0.0363 to align # Constraint # added constraint: constraint((T0349)L30.CB, (T0349)G39.CA) [> 3.1554 = 5.2590 < 6.8367] w=0.0363 to align # Constraint # added constraint: constraint((T0349)N8.CB, (T0349)R47.CB) [> 4.6977 = 7.8294 < 10.1783] w=0.0363 to align # Constraint # added constraint: constraint((T0349)D31.CB, (T0349)I44.CB) [> 4.0093 = 6.6821 < 8.6868] w=0.0360 to align # Constraint # added constraint: constraint((T0349)D31.CB, (T0349)V43.CB) [> 3.5015 = 5.8359 < 7.5867] w=0.0360 to align # Constraint # added constraint: constraint((T0349)I44.CB, (T0349)A58.CB) [> 3.2181 = 5.3634 < 6.9725] w=0.0356 to align # Constraint # added constraint: constraint((T0349)L4.CB, (T0349)L30.CB) [> 4.7972 = 7.9953 < 10.3938] w=0.0355 to align # Constraint # added constraint: constraint((T0349)L4.CB, (T0349)A15.CB) [> 3.7346 = 6.2243 < 8.0917] w=0.0355 to align # Constraint # added constraint: constraint((T0349)H51.CB, (T0349)R60.CB) [> 4.1973 = 6.9955 < 9.0942] w=0.0355 to align # Constraint # added constraint: constraint((T0349)L20.CB, (T0349)R46.CB) [> 4.5731 = 7.6218 < 9.9083] w=0.0355 to align # Constraint # added constraint: constraint((T0349)S14.CB, (T0349)V43.CB) [> 3.6430 = 6.0716 < 7.8931] w=0.0353 to align # Constraint # added constraint: constraint((T0349)T7.CB, (T0349)A18.CB) [> 4.6184 = 7.6972 < 10.0064] w=0.0352 to align # Constraint # added constraint: constraint((T0349)L5.CB, (T0349)L41.CB) [> 4.2968 = 7.1614 < 9.3098] w=0.0348 to align # Constraint # added constraint: constraint((T0349)L20.CB, (T0349)G42.CA) [> 4.5832 = 7.6386 < 9.9302] w=0.0347 to align # Constraint # added constraint: constraint((T0349)R46.CB, (T0349)A58.CB) [> 4.7732 = 7.9554 < 10.3420] w=0.0036 to align # SetCost created cost = # ( 1.0000 * align ) # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0349/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0349/decoys/ # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # choosing archetypes in rotamer library # Found a chain break before 74 # copying to AlignedFragments data structure # 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 T0349 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 # Found a chain break before 43 # copying to AlignedFragments data structure # 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 T0349 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 T0349 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 T0349 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 T0349 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 T0349 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 T0349 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 T0349 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 # Found a chain break before 74 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 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 T0349 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS5 # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # Found a chain break before 62 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS1 # ReadConformPDB reading from PDB file servers/3Dpro_TS2.pdb.gz looking for model 1 # naming current conformation 3Dpro_TS2 # ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1 # Found a chain break before 54 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS3 # ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1 # naming current conformation 3Dpro_TS4 # ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1 # Found a chain break before 31 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS5 # ReadConformPDB reading from PDB file servers/ABIpro_TS1.pdb.gz looking for model 1 # Found a chain break before 62 # 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 54 # 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 49 # 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 3 # 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 48 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS5 # ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1 # Found a chain break before 48 # copying to AlignedFragments data structure # naming current conformation BayesHH_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS1.pdb.gz looking for model 1 # 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 67 # 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 # naming current conformation Bilab-ENABLE_TS3 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS4.pdb.gz looking for model 1 # naming current conformation Bilab-ENABLE_TS4 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS5.pdb.gz looking for model 1 # naming current conformation Bilab-ENABLE_TS5 # ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1 # Found a chain break before 74 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS1 # ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1 # Found a chain break before 67 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # Found a chain break before 66 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS3 # ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1 # Found a chain break before 44 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS4 # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # Found a chain break before 50 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS5 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 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 T0349 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 # Found a chain break before 71 # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS3 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 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 # Found a chain break before 60 # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS5 # ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 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 T0349 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 T0349 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 T0349 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 T0349 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 72 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS1 # ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1 # Found a chain break before 74 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS2 # ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1 # Found a chain break before 74 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS3 # ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1 # Found a chain break before 73 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS4 # ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1 # Found a chain break before 73 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS5 # ReadConformPDB reading from PDB file servers/FAMS_TS1.pdb.gz looking for model 1 # Found a chain break before 67 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # Found a chain break before 50 # copying to AlignedFragments data structure # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # Found a chain break before 66 # 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 T0349 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 # Found a chain break before 44 # copying to AlignedFragments data structure # naming current conformation FAMS_TS5 # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # naming current conformation FOLDpro_TS1 # ReadConformPDB reading from PDB file servers/FOLDpro_TS2.pdb.gz looking for model 1 # naming current conformation FOLDpro_TS2 # ReadConformPDB reading from PDB file servers/FOLDpro_TS3.pdb.gz looking for model 1 # naming current conformation FOLDpro_TS3 # ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1 # 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 T0349 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 T0349 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL2 # ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1 Skipped atom 10, because occupancy 1 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 12, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 14, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 16, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 114, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 116, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 118, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 120, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 202, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 204, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 206, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 208, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 230, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 232, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 234, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 236, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz # WARNING: incomplete conformation T0349 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 Skipped atom 271, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz # WARNING: incomplete conformation T0349 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL4 # ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL5 # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL1 # ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL2 # ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1 Skipped atom 10, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 12, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 14, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 16, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 114, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 116, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 118, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 120, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 202, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 204, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 206, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 208, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 230, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 232, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 234, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 236, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz # WARNING: incomplete conformation T0349 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 Skipped atom 271, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz # WARNING: incomplete conformation T0349 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL4 # ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL5 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS1.pdb.gz looking for model 1 # Found a chain break before 73 # 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 73 # 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 16 # 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 11 # 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 74 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS5 # ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1 # Found a chain break before 51 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # naming current conformation FUGMOD_TS2 # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # Found a chain break before 22 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS3 # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # naming current conformation FUGMOD_TS4 # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 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 T0349 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 T0349 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 T0349 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 T0349 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 T0349 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 73 # 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 70 # 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 73 # 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 72 # 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 74 # 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 33 # 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/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # Found a chain break before 67 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS1 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # Found a chain break before 45 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # naming current conformation GeneSilicoMetaServer_TS3 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1 # Found a chain break before 70 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS4 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1 # Found a chain break before 22 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS5 # ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1 # Found a chain break before 67 # copying to AlignedFragments data structure # naming current conformation HHpred1_TS1 # ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1 # Found a chain break before 67 # copying to AlignedFragments data structure # naming current conformation HHpred2_TS1 # ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1 # Found a chain break before 67 # 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 T0349 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 T0349 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 T0349 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 T0349 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 T0349 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 T0349 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 T0349 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 T0349 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 T0349 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 T0349 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 T0349 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 67 # 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 # 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 42 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS4.pdb.gz looking for model 1 # naming current conformation Ma-OPUS-server2_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS5.pdb.gz looking for model 1 # Found a chain break before 67 # 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 46 # 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 # 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 67 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS4.pdb.gz looking for model 1 # naming current conformation Ma-OPUS-server_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS5.pdb.gz looking for model 1 # Found a chain break before 25 # 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 74 # 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 72 # 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 73 # 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 70 # 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 71 # 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 T0349 can't currently be optimized by undertaker # naming current conformation NN_PUT_lab_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS1.pdb.gz looking for model 1 # Found a chain break before 47 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS2.pdb.gz looking for model 1 # Found a chain break before 10 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS2 # ReadConformPDB reading from PDB file servers/POMYSL_TS3.pdb.gz looking for model 1 # Found a chain break before 71 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS3 # ReadConformPDB reading from PDB file servers/POMYSL_TS4.pdb.gz looking for model 1 # Found a chain break before 69 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS4 # ReadConformPDB reading from PDB file servers/POMYSL_TS5.pdb.gz looking for model 1 # Found a chain break before 70 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # Found a chain break before 49 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # Found a chain break before 49 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # Found a chain break before 39 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # Found a chain break before 67 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS5 # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pcons6_TS1 # ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pcons6_TS2 # ReadConformPDB reading from PDB file servers/Pcons6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pcons6_TS3 # ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1 # Found a chain break before 44 # copying to AlignedFragments data structure # naming current conformation Pcons6_TS4 # ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1 # Found a chain break before 46 # copying to AlignedFragments data structure # naming current conformation Pcons6_TS5 # ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 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 # Found a chain break before 36 # 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 # naming current conformation Phyre-2_TS2 # ReadConformPDB reading from PDB file servers/Phyre-2_TS3.pdb.gz looking for model 1 # Found a chain break before 35 # 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 # Found a chain break before 32 # 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 # Found a chain break before 8 # 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 67 # 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 46 # 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 6 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS3 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # Found a chain break before 24 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS4 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1 # Found a chain break before 46 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1 # Found a chain break before 67 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1 # Found a chain break before 47 # 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 29 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1 # Found a chain break before 29 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS5 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS1.pdb.gz looking for model 1 # naming current conformation RAPTORESS_TS1 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS2.pdb.gz looking for model 1 # Found a chain break before 71 # 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 44 # 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 5 # 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 72 # 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 16 # 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 44 # 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 24 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR_TS4.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR_TS5.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS5 # ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1 # Found a chain break before 6 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS1 # ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS2 # ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1 # Found a chain break before 67 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS3 # ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS4 # ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1 # Found a chain break before 46 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS5 # ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS1 # ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS2 # ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS3 # ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS4 # ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS5 # ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 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 T0349 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 T0349 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL3 # ReadConformPDB reading from PDB file servers/SAM-T02_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 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 T0349 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL5 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1 # Found a chain break before 72 # 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 T0349 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 T0349 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 T0349 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 T0349 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 67 # copying to AlignedFragments data structure # naming current conformation SP3_TS1 # ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1 # naming current conformation SP3_TS2 # ReadConformPDB reading from PDB file servers/SP3_TS3.pdb.gz looking for model 1 # Found a chain break before 67 # 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 54 # copying to AlignedFragments data structure # naming current conformation SP3_TS4 # ReadConformPDB reading from PDB file servers/SP3_TS5.pdb.gz looking for model 1 # Found a chain break before 29 # copying to AlignedFragments data structure # naming current conformation SP3_TS5 # ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1 # Found a chain break before 67 # copying to AlignedFragments data structure # naming current conformation SP4_TS1 # ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1 # naming current conformation SP4_TS2 # ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1 # Found a chain break before 43 # 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 69 # copying to AlignedFragments data structure # naming current conformation SP4_TS5 # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS1 # ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS2 # ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS3 # ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS4 # ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 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 T0349 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 T0349 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 T0349 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 T0349 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 T0349 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 T0349 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL2.pdb.gz looking for model 1 Skipped atom 119, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 124, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz # WARNING: incomplete conformation T0349 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 T0349 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 T0349 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 T0349 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 45 # 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 39 # 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 70 # 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 69 # 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 46 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS5 # ReadConformPDB reading from PDB file servers/beautshot_TS1.pdb.gz looking for model 1 # Found a chain break before 74 # copying to AlignedFragments data structure # naming current conformation beautshot_TS1 # ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 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 T0349 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 Skipped atom 50, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 52, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 54, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 56, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 102, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 104, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 106, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 108, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 114, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 116, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 118, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 120, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 126, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 128, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 130, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 132, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 238, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 240, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 242, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 244, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz # WARNING: incomplete conformation T0349 can't currently be optimized by undertaker # naming current conformation forecast-s_AL2 # ReadConformPDB reading from PDB file servers/forecast-s_AL3.pdb.gz looking for model 1 Skipped atom 154, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 156, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 158, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 160, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 162, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 164, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 166, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 168, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 170, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 172, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 174, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 176, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 178, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 180, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 182, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 184, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz # WARNING: incomplete conformation T0349 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 T0349 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation forecast-s_AL4 # ReadConformPDB reading from PDB file servers/forecast-s_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 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 50 # 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 47 # 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 7 # 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 64 # 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 46 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS1.pdb.gz looking for model 1 WARNING: atoms too close: (T0349)L41.O and (T0349)G42.N only 0.000 apart, marking (T0349)G42.N as missing # WARNING: incomplete conformation T0349 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 # Found a chain break before 74 # 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: (T0349)V43.O and (T0349)I44.N only 0.000 apart, marking (T0349)I44.N as missing # WARNING: incomplete conformation T0349 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 # Found a chain break before 72 # 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: (T0349)L4.O and (T0349)L5.N only 0.000 apart, marking (T0349)L5.N as missing # WARNING: incomplete conformation T0349 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 T0349 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 T0349 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 T0349 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 T0349 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS4 # 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 # naming current conformation keasar-server_TS2 # ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1 # naming current conformation keasar-server_TS3 # ReadConformPDB reading from PDB file servers/keasar-server_TS4.pdb.gz looking for model 1 # naming current conformation keasar-server_TS4 # ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1 # naming current conformation keasar-server_TS5 # ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 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 T0349 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 T0349 can't currently be optimized by undertaker # naming current conformation nFOLD_TS2 # ReadConformPDB reading from PDB file servers/nFOLD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 can't currently be optimized by undertaker # naming current conformation nFOLD_TS3 # ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 can't currently be optimized by undertaker # naming current conformation nFOLD_TS4 # ReadConformPDB reading from PDB file servers/nFOLD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation nFOLD_TS5 # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # Found a chain break before 71 # copying to AlignedFragments data structure # naming current conformation shub_TS1 # command:Using radius: 8.0000 Metaserver mode NUMB_ALIGNS: 258 model score 2.5950 model score 2.3789 model score 1.4581 model score 1.3090 model score 2.2559 model score 1.2418 model score 1.1791 model score 1.1761 model score 1.4065 model score 1.1791 model score 1.1164 model score 1.6934 model score 1.7141 model score 1.8297 model score 1.9950 model score 0.9198 model score 1.5635 model score 0.6842 model score 1.3248 model score 0.9025 model score 0.9198 model score 0.6842 model score 1.2494 model score 0.7606 model score 0.9370 model score 0.3822 model score 1.0871 model score 0.5739 model score 1.1234 model score 1.1510 model score 1.1750 model score 0.4641 model score 0.5459 model score 0.8387 model score 0.6506 model score 0.4784 model score 1.8478 model score 1.2063 model score 1.2724 model score 1.3961 model score 1.4660 model score 1.2625 model score 1.2727 model score 1.2635 model score 1.2724 model score 1.2742 model score 0.7663 model score 1.0527 model score 0.7931 model score 0.9591 model score 0.9881 model score 0.5609 model score 0.4784 model score 0.8387 model score 0.7682 model score 0.6506 model score 1.3248 model score 1.6822 model score 2.6030 model score 1.5635 model score 1.3248 model score 1.2772 model score 1.2723 model score 1.2733 model score 1.2697 model score 1.2675 model score 1.2723 model score 1.2787 model score 1.2733 model score 1.2697 model score 1.2879 model score 2.1006 model score 1.9695 model score 1.7099 model score 1.5387 model score 1.9473 model score 0.7749 model score 1.7949 model score 0.5673 model score 1.3474 model score 0.9068 model score 1.2758 model score 1.2654 model score 1.2655 model score 1.2603 model score 1.2768 model score 0.9731 model score 1.2289 model score 0.9335 model score 0.6463 model score 1.2374 model score 1.5030 model score 1.4727 model score 0.5809 model score 0.5051 model score 0.6044 model score 0.5216 model score 0.7005 model score 0.5556 model score 0.5556 model score 0.6136 model score 1.1727 model score 1.2391 model score 1.3572 model score 1.6440 model score 0.6855 model score 1.5515 model score 0.7955 model score 1.1233 model score 1.2012 model score 1.1741 model score 1.2756 model score 0.6300 model score 1.6413 model score 0.7074 model score 0.9406 model score 0.8671 model score 1.2174 model score 0.9406 model score 0.8671 model score 0.8171 model score 1.6735 model score 0.4691 model score 0.4752 model score 0.4411 model score 0.4895 model score 0.3924 model score 1.2758 model score 1.6688 model score 2.0995 model score 1.5132 model score 2.1480 model score 1.6779 model score 1.3061 model score 1.3052 model score 1.3213 model score 1.3112 model score 1.3213 model score 1.3087 model score 0.8504 model score 0.9063 model score 1.2948 model score 0.6397 model score 0.6201 model score 0.6201 model score 0.6201 model score 0.5201 model score 0.6157 model score 1.0581 model score 1.5906 model score 1.5651 model score 1.5514 model score 1.7668 model score 1.3497 model score 0.5742 model score 0.6258 model score 0.5381 model score 0.6911 model score 0.6157 model score 0.7196 model score 0.5848 model score 0.5928 model score 0.7756 model score 0.7756 model score 1.3174 model score 1.0582 model score 0.8596 model score 0.8976 model score 0.6823 model score 1.0171 model score 1.3128 model score 0.8379 model score 0.7816 model score 0.6956 model score 0.5381 model score 1.4023 model score 0.5742 model score 1.5077 model score 0.6258 model score 1.2638 model score 1.2676 model score 1.2661 model score 1.2707 model score 1.2761 model score 1.2835 model score 1.2741 model score 1.2637 model score 1.2588 model score 1.2672 model score 0.7466 model score 0.4513 model score 0.7748 model score 1.0580 model score 1.3690 model score 0.4520 model score 0.9247 model score 1.0102 model score 1.3112 model score 0.6758 model score 0.4520 model score 1.0732 model score 1.5951 model score 1.1631 model score 1.1961 model score 1.0122 model score 0.8352 model score 1.8718 model score 1.9104 model score 1.6093 model score 1.2657 model score 1.2750 model score 1.2737 model score 1.2675 model score 1.2623 model score 0.4317 model score 1.2657 model score 1.2771 model score 1.2750 model score 1.2697 model score 1.2641 model score 0.4765 model score 0.4257 model score 0.4189 model score 0.4010 model score 0.5059 model score 0.4806 model score 0.7504 model score 1.2714 model score 1.2594 model score 1.2749 model score 1.2755 model score 1.2692 model score 1.5496 model score 1.6301 model score 1.7306 model score 1.6310 model score 2.0921 model score 1.6858 model score 1.7691 model score 1.8303 model score 1.5820 model score 1.3823 model score 0.8133 model score 0.6226 model score 0.7173 model score 0.7942 model score 1.2769 model score 1.3137 model score 2.1035 model score 2.0402 model score 1.2010 model score 0.4800 model score 0.4865 model score 1.4275 model score 1.3578 model score 1.3883 model score 1.6910 model score 0.8560 weight: 0.1033 eval: 2.5950 min: 0.3822 max: 2.6030 weight: 0.1908 eval: 2.3789 min: 0.3822 max: 2.6030 weight: 0.5640 eval: 1.4581 min: 0.3822 max: 2.6030 weight: 0.6244 eval: 1.3090 min: 0.3822 max: 2.6030 weight: 0.2407 eval: 2.2559 min: 0.3822 max: 2.6030 weight: 0.6517 eval: 1.2418 min: 0.3822 max: 2.6030 weight: 0.6771 eval: 1.1791 min: 0.3822 max: 2.6030 weight: 0.6783 eval: 1.1761 min: 0.3822 max: 2.6030 weight: 0.5849 eval: 1.4065 min: 0.3822 max: 2.6030 weight: 0.6771 eval: 1.1791 min: 0.3822 max: 2.6030 weight: 0.7025 eval: 1.1164 min: 0.3822 max: 2.6030 weight: 0.4686 eval: 1.6934 min: 0.3822 max: 2.6030 weight: 0.4602 eval: 1.7141 min: 0.3822 max: 2.6030 weight: 0.4134 eval: 1.8297 min: 0.3822 max: 2.6030 weight: 0.3464 eval: 1.9950 min: 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weight: 0.5103 eval: 1.5906 min: 0.3822 max: 2.6030 weight: 0.5206 eval: 1.5651 min: 0.3822 max: 2.6030 weight: 0.5262 eval: 1.5514 min: 0.3822 max: 2.6030 weight: 0.4389 eval: 1.7668 min: 0.3822 max: 2.6030 weight: 0.6079 eval: 1.3497 min: 0.3822 max: 2.6030 weight: 0.9222 eval: 0.5742 min: 0.3822 max: 2.6030 weight: 0.9013 eval: 0.6258 min: 0.3822 max: 2.6030 weight: 0.9368 eval: 0.5381 min: 0.3822 max: 2.6030 weight: 0.8748 eval: 0.6911 min: 0.3822 max: 2.6030 weight: 0.9054 eval: 0.6157 min: 0.3822 max: 2.6030 weight: 0.8633 eval: 0.7196 min: 0.3822 max: 2.6030 weight: 0.9179 eval: 0.5848 min: 0.3822 max: 2.6030 weight: 0.9146 eval: 0.5928 min: 0.3822 max: 2.6030 weight: 0.8405 eval: 0.7756 min: 0.3822 max: 2.6030 weight: 0.8405 eval: 0.7756 min: 0.3822 max: 2.6030 weight: 0.6210 eval: 1.3174 min: 0.3822 max: 2.6030 weight: 0.7261 eval: 1.0582 min: 0.3822 max: 2.6030 weight: 0.8065 eval: 0.8596 min: 0.3822 max: 2.6030 weight: 0.7911 eval: 0.8976 min: 0.3822 max: 2.6030 weight: 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weight: 0.8330 eval: 0.7942 min: 0.3822 max: 2.6030 weight: 0.6374 eval: 1.2769 min: 0.3822 max: 2.6030 weight: 0.6225 eval: 1.3137 min: 0.3822 max: 2.6030 weight: 0.3024 eval: 2.1035 min: 0.3822 max: 2.6030 weight: 0.3281 eval: 2.0402 min: 0.3822 max: 2.6030 weight: 0.6682 eval: 1.2010 min: 0.3822 max: 2.6030 weight: 0.9604 eval: 0.4800 min: 0.3822 max: 2.6030 weight: 0.9577 eval: 0.4865 min: 0.3822 max: 2.6030 weight: 0.5764 eval: 1.4275 min: 0.3822 max: 2.6030 weight: 0.6046 eval: 1.3578 min: 0.3822 max: 2.6030 weight: 0.5923 eval: 1.3883 min: 0.3822 max: 2.6030 weight: 0.4696 eval: 1.6910 min: 0.3822 max: 2.6030 weight: 0.8080 eval: 0.8560 min: 0.3822 max: 2.6030 Adding 1971 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: -133.9731, CN propb: -133.9731 weights: 0.3222 constraints: 196 # command:Found ConstraintSet # PrintContacts align.constraints_meta02 Number of constraints in align2.constraints 196 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta02 Number of constraints in align2.constraints.bonus 196 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta02 Number of constraints in rejected2.constraints 1775 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta02 Number of constraints in rejected2.constraints.bonus 1775 # 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 1971 # command: