# 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/T0359/ # command:# Making conformation for sequence T0359 numbered 1 through 97 Created new target T0359 from T0359.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0359/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0359//projects/compbio/experiments/protein-predict/casp7/T0359/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0359//projects/compbio/experiments/protein-predict/casp7/T0359/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0359/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0359/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((T0359)I40.CB, (T0359)I54.CB) [> 3.8128 = 6.3546 < 8.2610] w=1.0000 to align # Constraint # added constraint: constraint((T0359)V37.CB, (T0359)I58.CB) [> 4.0667 = 6.7779 < 8.8112] w=1.0000 to align # Constraint # added constraint: constraint((T0359)V37.CB, (T0359)G55.CA) [> 3.2234 = 5.3724 < 6.9841] w=1.0000 to align # Constraint # added constraint: constraint((T0359)V37.CB, (T0359)I54.CB) [> 3.3422 = 5.5703 < 7.2414] w=1.0000 to align # Constraint # added constraint: constraint((T0359)F36.CB, (T0359)G55.CA) [> 3.1447 = 5.2412 < 6.8135] w=1.0000 to align # Constraint # added constraint: constraint((T0359)I59.CB, (T0359)M90.CB) [> 3.3862 = 5.6437 < 7.3368] w=0.9893 to align # Constraint # added constraint: constraint((T0359)V37.CB, (T0359)Q53.CB) [> 4.1440 = 6.9067 < 8.9788] w=0.9870 to align # Constraint # added constraint: constraint((T0359)F36.CB, (T0359)Q57.CB) [> 3.2411 = 5.4018 < 7.0223] w=0.9822 to align # Constraint # added constraint: constraint((T0359)V37.CB, (T0359)D56.CB) [> 2.8107 = 4.6845 < 6.0898] w=0.9822 to align # Constraint # added constraint: constraint((T0359)D62.CB, (T0359)L86.CB) [> 3.2976 = 5.4961 < 7.1449] w=0.9813 to align # Constraint # added constraint: constraint((T0359)D62.CB, (T0359)V85.CB) [> 3.7632 = 6.2720 < 8.1536] w=0.9813 to align # Constraint # added constraint: constraint((T0359)I40.CB, (T0359)I52.CB) [> 3.4721 = 5.7868 < 7.5228] w=0.9733 to align # Constraint # added constraint: constraint((T0359)V37.CB, (T0359)I52.CB) [> 3.6575 = 6.0959 < 7.9246] w=0.9733 to align # Constraint # added constraint: constraint((T0359)V61.CB, (T0359)L78.CB) [> 3.8130 = 6.3551 < 8.2616] w=0.9733 to align # Constraint # added constraint: constraint((T0359)V61.CB, (T0359)V77.CB) [> 3.1786 = 5.2976 < 6.8869] w=0.9733 to align # Constraint # added constraint: constraint((T0359)V61.CB, (T0359)V85.CB) [> 3.9060 = 6.5099 < 8.4629] w=0.9635 to align # Constraint # added constraint: constraint((T0359)I58.CB, (T0359)L89.CB) [> 3.4502 = 5.7504 < 7.4755] w=0.9626 to align # Constraint # added constraint: constraint((T0359)I59.CB, (T0359)L89.CB) [> 3.8937 = 6.4895 < 8.4364] w=0.9617 to align # Constraint # added constraint: constraint((T0359)Q57.CB, (T0359)M90.CB) [> 2.8432 = 4.7386 < 6.1602] w=0.9617 to align # Constraint # added constraint: constraint((T0359)S39.CB, (T0359)I54.CB) [> 3.7260 = 6.2099 < 8.0729] w=0.9555 to align # Constraint # added constraint: constraint((T0359)K38.CB, (T0359)I54.CB) [> 3.7066 = 6.1776 < 8.0309] w=0.9528 to align # Constraint # added constraint: constraint((T0359)G18.CA, (T0359)T41.CB) [> 2.5735 = 4.2892 < 5.5760] w=0.9517 to align # Constraint # added constraint: constraint((T0359)G18.CA, (T0359)I40.CB) [> 3.9276 = 6.5461 < 8.5099] w=0.9517 to align # Constraint # added constraint: constraint((T0359)I35.CB, (T0359)I58.CB) [> 2.9077 = 4.8462 < 6.3001] w=0.9465 to align # Constraint # added constraint: constraint((T0359)I21.CB, (T0359)F36.CB) [> 3.9966 = 6.6609 < 8.6592] w=0.9443 to align # Constraint # added constraint: constraint((T0359)I21.CB, (T0359)V37.CB) [> 3.6823 = 6.1371 < 7.9783] w=0.9443 to align # Constraint # added constraint: constraint((T0359)I21.CB, (T0359)I58.CB) [> 4.1553 = 6.9254 < 9.0030] w=0.9443 to align # Constraint # added constraint: constraint((T0359)A22.CB, (T0359)F36.CB) [> 3.3060 = 5.5100 < 7.1631] w=0.9443 to align # Constraint # added constraint: constraint((T0359)F36.CB, (T0359)I58.CB) [> 4.3397 = 7.2328 < 9.4026] w=0.9354 to align # Constraint # added constraint: constraint((T0359)T20.CB, (T0359)V37.CB) [> 4.3685 = 7.2809 < 9.4652] w=0.9353 to align # Constraint # added constraint: constraint((T0359)I19.CB, (T0359)T41.CB) [> 4.1296 = 6.8827 < 8.9475] w=0.9353 to align # Constraint # added constraint: constraint((T0359)I19.CB, (T0359)I40.CB) [> 3.1090 = 5.1816 < 6.7361] w=0.9353 to align # Constraint # added constraint: constraint((T0359)I19.CB, (T0359)V37.CB) [> 3.2789 = 5.4649 < 7.1044] w=0.9353 to align # Constraint # added constraint: constraint((T0359)F36.CB, (T0359)D56.CB) [> 4.0819 = 6.8031 < 8.8440] w=0.9332 to align # Constraint # added constraint: constraint((T0359)I58.CB, (T0359)L87.CB) [> 3.5141 = 5.8568 < 7.6139] w=0.9278 to align # Constraint # added constraint: constraint((T0359)A22.CB, (T0359)K38.CB) [> 2.7483 = 4.5806 < 5.9548] w=0.9264 to align # Constraint # added constraint: constraint((T0359)I21.CB, (T0359)K38.CB) [> 3.9337 = 6.5562 < 8.5231] w=0.9264 to align # Constraint # added constraint: constraint((T0359)T64.CB, (T0359)V77.CB) [> 3.6028 = 6.0046 < 7.8060] w=0.9216 to align # Constraint # added constraint: constraint((T0359)I35.CB, (T0359)L66.CB) [> 3.2564 = 5.4272 < 7.0554] w=0.9198 to align # Constraint # added constraint: constraint((T0359)I35.CB, (T0359)A74.CB) [> 3.0702 = 5.1170 < 6.6521] w=0.9198 to align # Constraint # added constraint: constraint((T0359)T20.CB, (T0359)K38.CB) [> 3.0521 = 5.0869 < 6.6129] w=0.9175 to align # Constraint # added constraint: constraint((T0359)T20.CB, (T0359)S39.CB) [> 2.7226 = 4.5377 < 5.8991] w=0.9175 to align # Constraint # added constraint: constraint((T0359)D56.CB, (T0359)L89.CB) [> 2.5916 = 4.3193 < 5.6151] w=0.9172 to align # Constraint # added constraint: constraint((T0359)D56.CB, (T0359)M90.CB) [> 4.0713 = 6.7856 < 8.8212] w=0.9172 to align # Constraint # added constraint: constraint((T0359)I19.CB, (T0359)V46.CB) [> 2.7043 = 4.5072 < 5.8593] w=0.9161 to align # Constraint # added constraint: constraint((T0359)G18.CA, (T0359)V46.CB) [> 2.8640 = 4.7734 < 6.2054] w=0.9161 to align # Constraint # added constraint: constraint((T0359)I19.CB, (T0359)I52.CB) [> 3.7706 = 6.2843 < 8.1696] w=0.9087 to align # Constraint # added constraint: constraint((T0359)G18.CA, (T0359)S44.CB) [> 2.2411 = 3.7351 < 4.8556] w=0.9072 to align # Constraint # added constraint: constraint((T0359)I35.CB, (T0359)Q57.CB) [> 4.0802 = 6.8003 < 8.8404] w=0.9020 to align # Constraint # added constraint: constraint((T0359)K38.CB, (T0359)G55.CA) [> 4.2869 = 7.1449 < 9.2884] w=0.9020 to align # Constraint # added constraint: constraint((T0359)G63.CA, (T0359)L86.CB) [> 4.2040 = 7.0067 < 9.1088] w=0.9012 to align # Constraint # added constraint: constraint((T0359)A60.CB, (T0359)T88.CB) [> 2.5650 = 4.2751 < 5.5576] w=0.9011 to align # Constraint # added constraint: constraint((T0359)A60.CB, (T0359)L87.CB) [> 4.2150 = 7.0250 < 9.1325] w=0.9011 to align # Constraint # added constraint: constraint((T0359)I59.CB, (T0359)T88.CB) [> 2.8563 = 4.7606 < 6.1887] w=0.9002 to align # Constraint # added constraint: constraint((T0359)L17.CB, (T0359)V46.CB) [> 3.3201 = 5.5334 < 7.1935] w=0.8997 to align # Constraint # added constraint: constraint((T0359)D56.CB, (T0359)R91.CB) [> 3.4088 = 5.6814 < 7.3858] w=0.8994 to align # Constraint # added constraint: constraint((T0359)G18.CA, (T0359)A45.CB) [> 3.4904 = 5.8173 < 7.5626] w=0.8983 to align # Constraint # added constraint: constraint((T0359)A22.CB, (T0359)I35.CB) [> 4.4066 = 7.3444 < 9.5477] w=0.8908 to align # Constraint # added constraint: constraint((T0359)I21.CB, (T0359)I35.CB) [> 3.1665 = 5.2775 < 6.8608] w=0.8908 to align # Constraint # added constraint: constraint((T0359)V61.CB, (T0359)L86.CB) [> 4.3618 = 7.2698 < 9.4507] w=0.8904 to align # Constraint # added constraint: constraint((T0359)L17.CB, (T0359)A45.CB) [> 3.2324 = 5.3873 < 7.0034] w=0.8730 to align # Constraint # added constraint: constraint((T0359)I58.CB, (T0359)A74.CB) [> 4.1636 = 6.9394 < 9.0212] w=0.8664 to align # Constraint # added constraint: constraint((T0359)I40.CB, (T0359)Q53.CB) [> 4.1267 = 6.8778 < 8.9412] w=0.8664 to align # Constraint # added constraint: constraint((T0359)G23.CA, (T0359)N71.CB) [> 3.2868 = 5.4780 < 7.1214] w=0.8641 to align # Constraint # added constraint: constraint((T0359)G23.CA, (T0359)F36.CB) [> 3.7113 = 6.1855 < 8.0411] w=0.8641 to align # Constraint # added constraint: constraint((T0359)I19.CB, (T0359)S39.CB) [> 3.9936 = 6.6560 < 8.6528] w=0.8641 to align # Constraint # added constraint: constraint((T0359)I52.CB, (T0359)L89.CB) [> 4.1186 = 6.8644 < 8.9237] w=0.8557 to align # Constraint # added constraint: constraint((T0359)I58.CB, (T0359)T88.CB) [> 4.4526 = 7.4210 < 9.6473] w=0.8557 to align # Constraint # added constraint: constraint((T0359)L10.CB, (T0359)V85.CB) [> 2.8925 = 4.8208 < 6.2670] w=0.8463 to align # Constraint # added constraint: constraint((T0359)E9.CB, (T0359)L86.CB) [> 3.0157 = 5.0261 < 6.5340] w=0.8463 to align # Constraint # added constraint: constraint((T0359)I19.CB, (T0359)S44.CB) [> 4.2825 = 7.1375 < 9.2788] w=0.8448 to align # Constraint # added constraint: constraint((T0359)D7.CB, (T0359)L86.CB) [> 3.9066 = 6.5111 < 8.4644] w=0.8374 to align # Constraint # added constraint: constraint((T0359)V8.CB, (T0359)L86.CB) [> 4.3390 = 7.2316 < 9.4011] w=0.8374 to align # Constraint # added constraint: constraint((T0359)E9.CB, (T0359)V85.CB) [> 4.2571 = 7.0952 < 9.2237] w=0.8374 to align # Constraint # added constraint: constraint((T0359)G23.CA, (T0359)I35.CB) [> 3.3299 = 5.5499 < 7.2148] w=0.8285 to align # Constraint # added constraint: constraint((T0359)G34.CA, (T0359)Q57.CB) [> 3.6820 = 6.1367 < 7.9777] w=0.8281 to align # Constraint # added constraint: constraint((T0359)V37.CB, (T0359)Q57.CB) [> 4.5982 = 7.6636 < 9.9627] w=0.8218 to align # Constraint # added constraint: constraint((T0359)L17.CB, (T0359)V85.CB) [> 3.7485 = 6.2476 < 8.1219] w=0.8196 to align # Constraint # added constraint: constraint((T0359)L17.CB, (T0359)L78.CB) [> 3.9873 = 6.6455 < 8.6392] w=0.8195 to align # Constraint # added constraint: constraint((T0359)F6.CB, (T0359)L89.CB) [> 3.3949 = 5.6582 < 7.3557] w=0.8107 to align # Constraint # added constraint: constraint((T0359)V8.CB, (T0359)L89.CB) [> 3.7699 = 6.2831 < 8.1681] w=0.8107 to align # Constraint # added constraint: constraint((T0359)V61.CB, (T0359)T81.CB) [> 4.0831 = 6.8052 < 8.8468] w=0.8107 to align # Constraint # added constraint: constraint((T0359)L10.CB, (T0359)T84.CB) [> 4.2494 = 7.0824 < 9.2071] w=0.8107 to align # Constraint # added constraint: constraint((T0359)V8.CB, (T0359)I52.CB) [> 3.7231 = 6.2051 < 8.0667] w=0.8107 to align # Constraint # added constraint: constraint((T0359)I21.CB, (T0359)A74.CB) [> 3.6974 = 6.1623 < 8.0109] w=0.8106 to align # Constraint # added constraint: constraint((T0359)I21.CB, (T0359)V75.CB) [> 4.1252 = 6.8753 < 8.9379] w=0.8106 to align # Constraint # added constraint: constraint((T0359)E9.CB, (T0359)T84.CB) [> 3.6216 = 6.0360 < 7.8467] w=0.7928 to align # Constraint # added constraint: constraint((T0359)T11.CB, (T0359)T84.CB) [> 3.3314 = 5.5523 < 7.2180] w=0.7928 to align # Constraint # added constraint: constraint((T0359)L17.CB, (T0359)S44.CB) [> 4.1292 = 6.8820 < 8.9466] w=0.7839 to align # Constraint # added constraint: constraint((T0359)V8.CB, (T0359)L87.CB) [> 2.9889 = 4.9815 < 6.4760] w=0.7839 to align # Constraint # added constraint: constraint((T0359)I21.CB, (T0359)N71.CB) [> 3.9251 = 6.5418 < 8.5043] w=0.7750 to align # Constraint # added constraint: constraint((T0359)G23.CA, (T0359)G34.CA) [> 3.4955 = 5.8259 < 7.5736] w=0.7661 to align # Constraint # added constraint: constraint((T0359)T5.CB, (T0359)I59.CB) [> 4.0636 = 6.7726 < 8.8044] w=0.7661 to align # Constraint # added constraint: constraint((T0359)T5.CB, (T0359)M90.CB) [> 3.1820 = 5.3034 < 6.8944] w=0.7661 to align # Constraint # added constraint: constraint((T0359)D7.CB, (T0359)T88.CB) [> 3.1683 = 5.2805 < 6.8646] w=0.7661 to align # Constraint # added constraint: constraint((T0359)G18.CA, (T0359)E47.CB) [> 4.2680 = 7.1133 < 9.2473] w=0.7646 to align # Constraint # added constraint: constraint((T0359)T5.CB, (T0359)L89.CB) [> 4.2011 = 7.0019 < 9.1025] w=0.7572 to align # Constraint # added constraint: constraint((T0359)F6.CB, (T0359)T88.CB) [> 4.3296 = 7.2161 < 9.3809] w=0.7572 to align # Constraint # added constraint: constraint((T0359)L10.CB, (T0359)D49.CB) [> 3.5150 = 5.8584 < 7.6159] w=0.7483 to align # Constraint # added constraint: constraint((T0359)A22.CB, (T0359)N71.CB) [> 4.2325 = 7.0541 < 9.1703] w=0.7483 to align # Constraint # added constraint: constraint((T0359)D7.CB, (T0359)L87.CB) [> 4.3462 = 7.2437 < 9.4168] w=0.7305 to align # Constraint # added constraint: constraint((T0359)V61.CB, (T0359)A74.CB) [> 4.1406 = 6.9010 < 8.9713] w=0.7238 to align # Constraint # added constraint: constraint((T0359)T5.CB, (T0359)T88.CB) [> 3.5712 = 5.9520 < 7.7376] w=0.7216 to align # Constraint # added constraint: constraint((T0359)T11.CB, (T0359)Q83.CB) [> 3.8205 = 6.3675 < 8.2777] w=0.7216 to align # Constraint # added constraint: constraint((T0359)D62.CB, (T0359)V77.CB) [> 4.1469 = 6.9116 < 8.9850] w=0.7153 to align # Constraint # added constraint: constraint((T0359)L10.CB, (T0359)L87.CB) [> 4.0205 = 6.7008 < 8.7111] w=0.7038 to align # Constraint # added constraint: constraint((T0359)Y24.CB, (T0359)G34.CA) [> 3.5940 = 5.9900 < 7.7871] w=0.7038 to align # Constraint # added constraint: constraint((T0359)G34.CA, (T0359)L66.CB) [> 4.1941 = 6.9902 < 9.0872] w=0.6944 to align # Constraint # added constraint: constraint((T0359)I35.CB, (T0359)F69.CB) [> 4.0265 = 6.7108 < 8.7240] w=0.6811 to align # Constraint # added constraint: constraint((T0359)L66.CB, (T0359)V77.CB) [> 4.1141 = 6.8568 < 8.9139] w=0.6793 to align # Constraint # added constraint: constraint((T0359)G34.CA, (T0359)Q67.CB) [> 3.8447 = 6.4078 < 8.3302] w=0.6677 to align # Constraint # added constraint: constraint((T0359)L10.CB, (T0359)L86.CB) [> 4.6157 = 7.6929 < 10.0008] w=0.6592 to align # Constraint # added constraint: constraint((T0359)Y24.CB, (T0359)S33.CB) [> 3.9508 = 6.5846 < 8.5600] w=0.6503 to align # Constraint # added constraint: constraint((T0359)I21.CB, (T0359)L78.CB) [> 4.4511 = 7.4185 < 9.6441] w=0.6503 to align # Constraint # added constraint: constraint((T0359)V8.CB, (T0359)D49.CB) [> 3.4486 = 5.7476 < 7.4719] w=0.6503 to align # Constraint # added constraint: constraint((T0359)K12.CB, (T0359)V85.CB) [> 3.8897 = 6.4829 < 8.4278] w=0.6147 to align # Constraint # added constraint: constraint((T0359)G63.CA, (T0359)T88.CB) [> 4.3748 = 7.2914 < 9.4788] w=0.5974 to align # Constraint # added constraint: constraint((T0359)T11.CB, (T0359)V85.CB) [> 4.4653 = 7.4422 < 9.6748] w=0.5969 to align # Constraint # added constraint: constraint((T0359)F6.CB, (T0359)R91.CB) [> 3.8948 = 6.4914 < 8.4388] w=0.5969 to align # Constraint # added constraint: constraint((T0359)Y24.CB, (T0359)N71.CB) [> 2.7944 = 4.6574 < 6.0546] w=0.5939 to align # Constraint # added constraint: constraint((T0359)E9.CB, (T0359)L87.CB) [> 4.5057 = 7.5094 < 9.7623] w=0.5880 to align # Constraint # added constraint: constraint((T0359)V8.CB, (T0359)R51.CB) [> 2.9416 = 4.9026 < 6.3734] w=0.5880 to align # Constraint # added constraint: constraint((T0359)V37.CB, (T0359)V46.CB) [> 4.5914 = 7.6523 < 9.9480] w=0.5701 to align # Constraint # added constraint: constraint((T0359)G23.CA, (T0359)S33.CB) [> 3.6613 = 6.1022 < 7.9329] w=0.5612 to align # Constraint # added constraint: constraint((T0359)L10.CB, (T0359)I52.CB) [> 4.5408 = 7.5680 < 9.8384] w=0.5256 to align # Constraint # added constraint: constraint((T0359)V8.CB, (T0359)T88.CB) [> 4.4791 = 7.4653 < 9.7048] w=0.5256 to align # Constraint # added constraint: constraint((T0359)G55.CA, (T0359)R91.CB) [> 4.1755 = 6.9592 < 9.0470] w=0.5163 to align # Constraint # added constraint: constraint((T0359)V61.CB, (T0359)T88.CB) [> 4.6976 = 7.8293 < 10.1781] w=0.5077 to align # Constraint # added constraint: constraint((T0359)A60.CB, (T0359)L86.CB) [> 4.6289 = 7.7149 < 10.0294] w=0.5047 to align # Constraint # added constraint: constraint((T0359)D56.CB, (T0359)R92.CB) [> 4.1265 = 6.8775 < 8.9407] w=0.4900 to align # Constraint # added constraint: constraint((T0359)K12.CB, (T0359)T84.CB) [> 4.3729 = 7.2882 < 9.4747] w=0.4811 to align # Constraint # added constraint: constraint((T0359)G34.CA, (T0359)I58.CB) [> 4.4150 = 7.3583 < 9.5658] w=0.4806 to align # Constraint # added constraint: constraint((T0359)K12.CB, (T0359)T81.CB) [> 4.0860 = 6.8101 < 8.8531] w=0.4632 to align # Constraint # added constraint: constraint((T0359)F6.CB, (T0359)M90.CB) [> 4.4776 = 7.4626 < 9.7014] w=0.4632 to align # Constraint # added constraint: constraint((T0359)T20.CB, (T0359)T41.CB) [> 4.5209 = 7.5348 < 9.7952] w=0.4617 to align # Constraint # added constraint: constraint((T0359)E4.CB, (T0359)M90.CB) [> 4.1308 = 6.8847 < 8.9501] w=0.4454 to align # Constraint # added constraint: constraint((T0359)D7.CB, (T0359)L89.CB) [> 4.6019 = 7.6699 < 9.9708] w=0.4454 to align # Constraint # added constraint: constraint((T0359)N13.CB, (T0359)A45.CB) [> 3.3978 = 5.6630 < 7.3619] w=0.4365 to align # Constraint # added constraint: constraint((T0359)S33.CB, (T0359)Q67.CB) [> 3.7701 = 6.2835 < 8.1686] w=0.4287 to align # Constraint # added constraint: constraint((T0359)Y24.CB, (T0359)T70.CB) [> 3.0279 = 5.0465 < 6.5604] w=0.4276 to align # Constraint # added constraint: constraint((T0359)G34.CA, (T0359)F69.CB) [> 4.3204 = 7.2007 < 9.3608] w=0.4138 to align # Constraint # added constraint: constraint((T0359)T20.CB, (T0359)I40.CB) [> 4.5735 = 7.6225 < 9.9092] w=0.4083 to align # Constraint # added constraint: constraint((T0359)T5.CB, (T0359)R91.CB) [> 4.4455 = 7.4092 < 9.6320] w=0.3920 to align # Constraint # added constraint: constraint((T0359)S3.CB, (T0359)R91.CB) [> 3.7689 = 6.2815 < 8.1660] w=0.3831 to align # Constraint # added constraint: constraint((T0359)I59.CB, (T0359)L87.CB) [> 4.7194 = 7.8656 < 10.2253] w=0.3608 to align # Constraint # added constraint: constraint((T0359)F6.CB, (T0359)R51.CB) [> 4.1305 = 6.8842 < 8.9495] w=0.3563 to align # Constraint # added constraint: constraint((T0359)Y24.CB, (T0359)F36.CB) [> 3.2994 = 5.4990 < 7.1487] w=0.3356 to align # Constraint # added constraint: constraint((T0359)Y24.CB, (T0359)Q73.CB) [> 4.3947 = 7.3246 < 9.5219] w=0.3207 to align # Constraint # added constraint: constraint((T0359)A22.CB, (T0359)V37.CB) [> 4.5855 = 7.6424 < 9.9352] w=0.3029 to align # Constraint # added constraint: constraint((T0359)I19.CB, (T0359)K38.CB) [> 4.6185 = 7.6975 < 10.0067] w=0.2940 to align # Constraint # added constraint: constraint((T0359)G23.CA, (T0359)A74.CB) [> 4.6152 = 7.6919 < 9.9995] w=0.2940 to align # Constraint # added constraint: constraint((T0359)I25.CB, (T0359)G34.CA) [> 4.1087 = 6.8478 < 8.9021] w=0.2851 to align # Constraint # added constraint: constraint((T0359)Q15.CB, (T0359)A45.CB) [> 3.9234 = 6.5390 < 8.5007] w=0.2762 to align # Constraint # added constraint: constraint((T0359)L10.CB, (T0359)R51.CB) [> 3.9435 = 6.5725 < 8.5443] w=0.2405 to align # Constraint # added constraint: constraint((T0359)I25.CB, (T0359)F69.CB) [> 4.1561 = 6.9269 < 9.0049] w=0.2316 to align # Constraint # added constraint: constraint((T0359)I58.CB, (T0359)L78.CB) [> 4.6742 = 7.7904 < 10.1275] w=0.2227 to align # Constraint # added constraint: constraint((T0359)L17.CB, (T0359)T81.CB) [> 4.5365 = 7.5608 < 9.8291] w=0.2138 to align # Constraint # added constraint: constraint((T0359)F6.CB, (T0359)D56.CB) [> 4.6017 = 7.6696 < 9.9705] w=0.2138 to align # Constraint # added constraint: constraint((T0359)V14.CB, (T0359)Q83.CB) [> 4.2215 = 7.0358 < 9.1465] w=0.2049 to align # Constraint # added constraint: constraint((T0359)F36.CB, (T0359)R92.CB) [> 4.4299 = 7.3832 < 9.5982] w=0.2049 to align # Constraint # added constraint: constraint((T0359)G16.CA, (T0359)R79.CB) [> 4.1725 = 6.9541 < 9.0404] w=0.1871 to align # Constraint # added constraint: constraint((T0359)L10.CB, (T0359)H48.CB) [> 4.6360 = 7.7266 < 10.0446] w=0.1871 to align # Constraint # added constraint: constraint((T0359)G23.CA, (T0359)P32.CB) [> 4.3109 = 7.1848 < 9.3403] w=0.1782 to align # Constraint # added constraint: constraint((T0359)L10.CB, (T0359)I19.CB) [> 4.4681 = 7.4467 < 9.6808] w=0.1693 to align # Constraint # added constraint: constraint((T0359)F36.CB, (T0359)I54.CB) [> 4.3704 = 7.2840 < 9.4691] w=0.1693 to align # Constraint # added constraint: constraint((T0359)G34.CA, (T0359)I59.CB) [> 3.7713 = 6.2855 < 8.1712] w=0.1599 to align # Constraint # added constraint: constraint((T0359)G34.CA, (T0359)A74.CB) [> 4.2050 = 7.0083 < 9.1108] w=0.1559 to align # Constraint # added constraint: constraint((T0359)D7.CB, (T0359)A60.CB) [> 4.6210 = 7.7017 < 10.0122] w=0.1514 to align # Constraint # added constraint: constraint((T0359)I35.CB, (T0359)I59.CB) [> 4.3852 = 7.3086 < 9.5012] w=0.1493 to align # Constraint # added constraint: constraint((T0359)S33.CB, (T0359)L66.CB) [> 3.9684 = 6.6141 < 8.5983] w=0.1247 to align # Constraint # added constraint: constraint((T0359)I35.CB, (T0359)V75.CB) [> 4.3653 = 7.2755 < 9.4581] w=0.1158 to align # Constraint # added constraint: constraint((T0359)G16.CA, (T0359)L78.CB) [> 3.6316 = 6.0526 < 7.8684] w=0.1158 to align # Constraint # added constraint: constraint((T0359)A22.CB, (T0359)S33.CB) [> 4.5617 = 7.6029 < 9.8838] w=0.1069 to align # Constraint # added constraint: constraint((T0359)E9.CB, (T0359)R51.CB) [> 4.4523 = 7.4205 < 9.6466] w=0.1069 to align # Constraint # added constraint: constraint((T0359)G18.CA, (T0359)I52.CB) [> 4.6595 = 7.7658 < 10.0956] w=0.1069 to align # Constraint # added constraint: constraint((T0359)F6.CB, (T0359)Q53.CB) [> 4.4939 = 7.4899 < 9.7369] w=0.1069 to align # Constraint # added constraint: constraint((T0359)T11.CB, (T0359)D49.CB) [> 4.6039 = 7.6732 < 9.9751] w=0.0980 to align # Constraint # added constraint: constraint((T0359)T11.CB, (T0359)H48.CB) [> 4.5244 = 7.5407 < 9.8029] w=0.0980 to align # Constraint # added constraint: constraint((T0359)I19.CB, (T0359)I58.CB) [> 4.6378 = 7.7296 < 10.0485] w=0.0980 to align # Constraint # added constraint: constraint((T0359)L78.CB, (T0359)L87.CB) [> 4.4949 = 7.4915 < 9.7390] w=0.0891 to align # Constraint # added constraint: constraint((T0359)G18.CA, (T0359)S43.CB) [> 4.1198 = 6.8663 < 8.9262] w=0.0891 to align # Constraint # added constraint: constraint((T0359)G55.CA, (T0359)G93.CA) [> 4.2113 = 7.0189 < 9.1245] w=0.0891 to align # Constraint # added constraint: constraint((T0359)G23.CA, (T0359)K38.CB) [> 4.7364 = 7.8939 < 10.2621] w=0.0802 to align # Constraint # added constraint: constraint((T0359)T20.CB, (T0359)I54.CB) [> 4.4396 = 7.3994 < 9.6192] w=0.0802 to align # Constraint # added constraint: constraint((T0359)D56.CB, (T0359)L87.CB) [> 4.7177 = 7.8628 < 10.2216] w=0.0802 to align # Constraint # added constraint: constraint((T0359)S33.CB, (T0359)I58.CB) [> 3.8871 = 6.4784 < 8.4220] w=0.0713 to align # Constraint # added constraint: constraint((T0359)V8.CB, (T0359)V85.CB) [> 4.7102 = 7.8503 < 10.2054] w=0.0713 to align # Constraint # added constraint: constraint((T0359)T11.CB, (T0359)G82.CA) [> 4.1744 = 6.9573 < 9.0444] w=0.0713 to align # Constraint # added constraint: constraint((T0359)T64.CB, (T0359)A74.CB) [> 3.3075 = 5.5125 < 7.1663] w=0.0713 to align # Constraint # added constraint: constraint((T0359)E31.CB, (T0359)M90.CB) [> 3.6825 = 6.1375 < 7.9787] w=0.0577 to align # Constraint # added constraint: constraint((T0359)N65.CB, (T0359)T88.CB) [> 4.7713 = 7.9522 < 10.3379] w=0.0535 to align # Constraint # added constraint: constraint((T0359)I35.CB, (T0359)V61.CB) [> 4.7129 = 7.8549 < 10.2114] w=0.0535 to align # Constraint # added constraint: constraint((T0359)L17.CB, (T0359)I52.CB) [> 4.7351 = 7.8918 < 10.2594] w=0.0535 to align # Constraint # added constraint: constraint((T0359)A22.CB, (T0359)S39.CB) [> 4.6092 = 7.6819 < 9.9865] w=0.0535 to align # Constraint # added constraint: constraint((T0359)G63.CA, (T0359)L87.CB) [> 4.5559 = 7.5931 < 9.8710] w=0.0535 to align # Constraint # added constraint: constraint((T0359)V8.CB, (T0359)D56.CB) [> 4.5105 = 7.5175 < 9.7728] w=0.0535 to align # Constraint # added constraint: constraint((T0359)I21.CB, (T0359)L66.CB) [> 3.9796 = 6.6327 < 8.6225] w=0.0535 to align # Constraint # added constraint: constraint((T0359)G18.CA, (T0359)S39.CB) [> 4.7443 = 7.9072 < 10.2794] w=0.0534 to align # Constraint # added constraint: constraint((T0359)T20.CB, (T0359)V75.CB) [> 4.0010 = 6.6683 < 8.6688] w=0.0534 to align # Constraint # added constraint: constraint((T0359)L30.CB, (T0359)G55.CA) [> 4.5076 = 7.5128 < 9.7666] w=0.0505 to align # Constraint # added constraint: constraint((T0359)F36.CB, (T0359)N71.CB) [> 4.3468 = 7.2447 < 9.4181] w=0.0490 to align # Constraint # added constraint: constraint((T0359)L17.CB, (T0359)L87.CB) [> 4.2509 = 7.0849 < 9.2104] w=0.0445 to align # Constraint # added constraint: constraint((T0359)Y24.CB, (T0359)K38.CB) [> 4.3798 = 7.2996 < 9.4895] w=0.0416 to align # Constraint # added constraint: constraint((T0359)F6.CB, (T0359)I52.CB) [> 4.4437 = 7.4062 < 9.6281] w=0.0356 to align # Constraint # added constraint: constraint((T0359)I25.CB, (T0359)Q72.CB) [> 3.7741 = 6.2902 < 8.1772] w=0.0356 to align # Constraint # added constraint: constraint((T0359)D27.CB, (T0359)K38.CB) [> 4.2568 = 7.0947 < 9.2231] w=0.0356 to align # Constraint # added constraint: constraint((T0359)L17.CB, (T0359)V61.CB) [> 4.6397 = 7.7328 < 10.0526] w=0.0356 to align # Constraint # added constraint: constraint((T0359)T5.CB, (T0359)A60.CB) [> 4.2458 = 7.0764 < 9.1993] w=0.0267 to align # Constraint # added constraint: constraint((T0359)L10.CB, (T0359)D62.CB) [> 4.1016 = 6.8360 < 8.8868] w=0.0267 to align # Constraint # added constraint: constraint((T0359)V8.CB, (T0359)V61.CB) [> 4.7243 = 7.8738 < 10.2360] w=0.0267 to align # Constraint # added constraint: constraint((T0359)G18.CA, (T0359)K42.CB) [> 2.6638 = 4.4397 < 5.7716] w=0.0267 to align # Constraint # added constraint: constraint((T0359)I54.CB, (T0359)R91.CB) [> 4.1377 = 6.8962 < 8.9651] w=0.0267 to align # Constraint # added constraint: constraint((T0359)G26.CA, (T0359)Q57.CB) [> 4.4326 = 7.3877 < 9.6040] w=0.0252 to align # Constraint # added constraint: constraint((T0359)A60.CB, (T0359)L89.CB) [> 4.0547 = 6.7578 < 8.7852] w=0.0228 to align # Constraint # added constraint: constraint((T0359)D7.CB, (T0359)G63.CA) [> 4.6470 = 7.7450 < 10.0685] w=0.0178 to align # Constraint # added constraint: constraint((T0359)I21.CB, (T0359)P32.CB) [> 4.7516 = 7.9193 < 10.2951] w=0.0178 to align # Constraint # added constraint: constraint((T0359)E9.CB, (T0359)T88.CB) [> 3.8129 = 6.3549 < 8.2613] w=0.0178 to align # Constraint # added constraint: constraint((T0359)E9.CB, (T0359)L89.CB) [> 3.8983 = 6.4971 < 8.4463] w=0.0178 to align # Constraint # added constraint: constraint((T0359)T11.CB, (T0359)L87.CB) [> 4.2036 = 7.0060 < 9.1078] w=0.0178 to align # Constraint # added constraint: constraint((T0359)I59.CB, (T0359)S96.CB) [> 4.5015 = 7.5024 < 9.7532] w=0.0178 to align # Constraint # added constraint: constraint((T0359)L30.CB, (T0359)Q57.CB) [> 3.6827 = 6.1378 < 7.9792] w=0.0149 to align # Constraint # added constraint: constraint((T0359)A22.CB, (T0359)G55.CA) [> 4.7204 = 7.8674 < 10.2276] w=0.0089 to align # Constraint # added constraint: constraint((T0359)F6.CB, (T0359)I59.CB) [> 4.2937 = 7.1561 < 9.3030] w=0.0089 to align # Constraint # added constraint: constraint((T0359)D7.CB, (T0359)R91.CB) [> 4.7083 = 7.8472 < 10.2014] w=0.0089 to align # Constraint # added constraint: constraint((T0359)V8.CB, (T0359)M90.CB) [> 3.6625 = 6.1042 < 7.9355] w=0.0089 to align # Constraint # added constraint: constraint((T0359)V8.CB, (T0359)R91.CB) [> 3.4826 = 5.8043 < 7.5456] w=0.0089 to align # Constraint # added constraint: constraint((T0359)T11.CB, (T0359)L86.CB) [> 3.5381 = 5.8969 < 7.6659] w=0.0089 to align # Constraint # added constraint: constraint((T0359)I59.CB, (T0359)R91.CB) [> 3.9654 = 6.6090 < 8.5917] w=0.0089 to align # Constraint # added constraint: constraint((T0359)I19.CB, (T0359)V85.CB) [> 4.7261 = 7.8768 < 10.2399] w=0.0074 to align # Constraint # added constraint: constraint((T0359)T20.CB, (T0359)K42.CB) [> 4.7692 = 7.9487 < 10.3334] w=0.0074 to align # Constraint # added constraint: constraint((T0359)T20.CB, (T0359)S44.CB) [> 1.7046 = 2.8410 < 3.6933] w=0.0074 to align # Constraint # added constraint: constraint((T0359)T20.CB, (T0359)V46.CB) [> 2.5401 = 4.2334 < 5.5034] w=0.0074 to align # Constraint # added constraint: constraint((T0359)I40.CB, (T0359)G55.CA) [> 4.2144 = 7.0241 < 9.1313] w=0.0027 to align # SetCost created cost = # ( 1.0000 * align ) # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0359/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0359/decoys/ # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 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 # choosing archetypes in rotamer library # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 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 T0359 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 T0359 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 T0359 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 T0359 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 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 T0359 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 T0359 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 T0359 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS5 # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # naming current conformation 3Dpro_TS1 # ReadConformPDB reading from PDB file servers/3Dpro_TS2.pdb.gz looking for model 1 # Found a chain break before 65 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS2 # ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1 # Found a chain break before 23 # 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 # naming current conformation 3Dpro_TS5 # ReadConformPDB reading from PDB file servers/ABIpro_TS1.pdb.gz looking for model 1 # Found a chain break before 9 # 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 83 # 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 86 # 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 84 # 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 41 # 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 33 # copying to AlignedFragments data structure # naming current conformation BayesHH_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS1.pdb.gz looking for model 1 # Found a chain break before 31 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS2.pdb.gz looking for model 1 # naming current conformation Bilab-ENABLE_TS2 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS3.pdb.gz looking for model 1 # naming current conformation Bilab-ENABLE_TS3 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS4.pdb.gz looking for model 1 # Found a chain break before 26 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS4 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS5.pdb.gz looking for model 1 # 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 93 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS1 # ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # Found a chain break before 88 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS3 # ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS4 # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # Found a chain break before 88 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS5 # ReadConformPDB reading from PDB file servers/CPHmodels_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # naming current conformation CPHmodels_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 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 T0359 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 30 # 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 T0359 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS4 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS5 # ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 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 T0359 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 T0359 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 T0359 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 T0359 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 61 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS1 # ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # naming current conformation FAMSD_TS2 # ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # naming current conformation FAMSD_TS3 # ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # naming current conformation FAMSD_TS4 # ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # naming current conformation FAMSD_TS5 # ReadConformPDB reading from PDB file servers/FAMS_TS1.pdb.gz looking for model 1 # Found a chain break before 95 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # naming current conformation FAMS_TS3 # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # Found a chain break before 93 # copying to AlignedFragments data structure # naming current conformation FAMS_TS4 # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # naming current conformation FAMS_TS5 # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # 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 # Found a chain break before 65 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS4 # ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1 # Found a chain break before 23 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS5 # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL1 # ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # naming current conformation FORTE1_AL2 # ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL3 # ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # naming current conformation FORTE1_AL4 # ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 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 T0359 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 T0359 can't currently be optimized by undertaker # naming current conformation FORTE2_AL2 # ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # naming current conformation FORTE2_AL3 # ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 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 T0359 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 82 # 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 96 # 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 80 # 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 61 # 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 76 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS5 # ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # naming current conformation FUGMOD_TS2 # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS3 # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS4 # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # naming current conformation FUGMOD_TS5 # ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 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 T0359 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 Skipped atom 211, because occupancy 1 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz # WARNING: incomplete conformation T0359 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 T0359 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 T0359 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 82 # 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 65 # 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 75 # 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 74 # 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 93 # 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 30 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS1 # ReadConformPDB reading from PDB file servers/Frankenstein_TS2.pdb.gz looking for model 1 # Found a chain break before 31 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS2 # ReadConformPDB reading from PDB file servers/Frankenstein_TS3.pdb.gz looking for model 1 # Found a chain break before 34 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS3 # ReadConformPDB reading from PDB file servers/Frankenstein_TS4.pdb.gz looking for model 1 # Found a chain break before 29 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS4 # ReadConformPDB reading from PDB file servers/Frankenstein_TS5.pdb.gz looking for model 1 # naming current conformation Frankenstein_TS5 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # naming current conformation GeneSilicoMetaServer_TS1 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # 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 # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS4 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1 # Found a chain break before 65 # 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 65 # copying to AlignedFragments data structure # naming current conformation HHpred1_TS1 # ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1 # naming current conformation HHpred2_TS1 # ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1 # naming current conformation HHpred3_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Huber-Torda-Server_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 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 T0359 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 T0359 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 # naming current conformation LOOPP_TS1 # ReadConformPDB reading from PDB file servers/LOOPP_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 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 T0359 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 T0359 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 T0359 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 T0359 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 34 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS2.pdb.gz looking for model 1 # Found a chain break before 34 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS3.pdb.gz looking for model 1 # Found a chain break before 82 # 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 # 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 34 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS2.pdb.gz looking for model 1 # Found a chain break before 67 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS3.pdb.gz looking for model 1 # Found a chain break before 26 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS4.pdb.gz looking for model 1 # Found a chain break before 29 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS5.pdb.gz looking for model 1 # Found a chain break before 65 # 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 94 # 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 94 # 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 91 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS3 # ReadConformPDB reading from PDB file servers/NN_PUT_lab_TS1.pdb.gz looking for model 1 # naming current conformation NN_PUT_lab_TS1 # ReadConformPDB reading from PDB file servers/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 32 # 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 32 # 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 42 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS5 # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 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 T0359 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 T0359 can't currently be optimized by undertaker # naming current conformation Pcons6_TS3 # ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # naming current conformation Pcons6_TS4 # ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pcons6_TS5 # ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # naming current conformation Phyre-1_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS2 # ReadConformPDB reading from PDB file servers/Phyre-2_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS3 # ReadConformPDB reading from PDB file servers/Phyre-2_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS4 # ReadConformPDB reading from PDB file servers/Phyre-2_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS5 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1 # Found a chain break before 31 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS1 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # naming current conformation Pmodeller6_TS2 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # naming current conformation Pmodeller6_TS3 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS4 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # 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 65 # 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 65 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS5 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS1.pdb.gz looking for model 1 # Found a chain break before 31 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS1 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS2.pdb.gz looking for model 1 # naming current conformation RAPTORESS_TS2 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS3.pdb.gz looking for model 1 # naming current conformation RAPTORESS_TS3 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS4.pdb.gz looking for model 1 # naming current conformation RAPTORESS_TS4 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS5.pdb.gz looking for model 1 # naming current conformation RAPTORESS_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR_TS1.pdb.gz looking for model 1 # Found a chain break before 67 # 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 67 # 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 67 # 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 # 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 31 # 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 # naming current conformation ROBETTA_TS5 # ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1 # Found a chain break before 31 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS1 # ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1 # Found a chain break before 43 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS2 # ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1 # Found a chain break before 66 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS3 # ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1 # Found a chain break before 65 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS4 # ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1 # naming current conformation ROKKY_TS5 # ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 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 Skipped atom 15, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 296, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 308, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 310, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 312, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 314, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 316, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 318, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 320, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 322, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 324, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 326, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 328, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 330, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 332, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 334, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz # WARNING: incomplete conformation T0359 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 T0359 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 T0359 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 T0359 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL5 # ReadConformPDB reading from PDB file servers/SAM-T99_AL1.pdb.gz looking for model 1 Skipped atom 7, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 320, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL1 # ReadConformPDB reading from PDB file servers/SAM-T99_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL2 # ReadConformPDB reading from PDB file servers/SAM-T99_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL3 # ReadConformPDB reading from PDB file servers/SAM-T99_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL4 # ReadConformPDB reading from PDB file servers/SAM-T99_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL5 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1 # Found a chain break before 95 # 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 T0359 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 T0359 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 T0359 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 T0359 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS5 # ReadConformPDB reading from PDB file servers/SP3_TS1.pdb.gz looking for model 1 # naming current conformation SP3_TS1 # ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1 # Found a chain break before 33 # copying to AlignedFragments data structure # naming current conformation SP3_TS2 # ReadConformPDB reading from PDB file servers/SP3_TS3.pdb.gz looking for model 1 # naming current conformation SP3_TS3 # ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1 # Found a chain break before 84 # 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 80 # copying to AlignedFragments data structure # naming current conformation SP3_TS5 # ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1 # naming current conformation SP4_TS1 # ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1 # Found a chain break before 84 # copying to AlignedFragments data structure # naming current conformation SP4_TS2 # ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1 # Found a chain break before 65 # copying to AlignedFragments data structure # naming current conformation SP4_TS3 # ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1 # Found a chain break before 80 # copying to AlignedFragments data structure # naming current conformation SP4_TS4 # ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1 # naming current conformation SP4_TS5 # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # Found a chain break before 31 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS1 # ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1 # Found a chain break before 84 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS2 # ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1 # Found a chain break before 65 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS3 # ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS4 # ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1 # Found a chain break before 65 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation UNI-EID_bnmx_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # copying to AlignedFragments data structure # 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 T0359 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 T0359 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation UNI-EID_bnmx_TS4 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 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 T0359 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation UNI-EID_expm_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL1.pdb.gz looking for model 1 Skipped atom 11, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 364, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation UNI-EID_sfst_AL1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # copying to AlignedFragments data structure # 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 T0359 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 T0359 can't currently be optimized by undertaker # copying to AlignedFragments data structure # 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 T0359 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 32 # 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 93 # 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 66 # 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 42 # 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 51 # 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 95 # 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 T0359 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 T0359 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation forecast-s_AL1 # ReadConformPDB reading from PDB file servers/forecast-s_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation forecast-s_AL2 # ReadConformPDB reading from PDB file servers/forecast-s_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 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 T0359 can't currently be optimized by undertaker # naming current conformation forecast-s_AL4 # ReadConformPDB reading from PDB file servers/forecast-s_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 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 23 # 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 24 # 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 24 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS4.pdb.gz looking for model 1 # naming current conformation karypis.srv.2_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS5.pdb.gz looking for model 1 # Found a chain break before 31 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS1.pdb.gz looking for model 1 # Found a chain break before 95 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS2.pdb.gz looking for model 1 WARNING: atoms too close: (T0359)M90.O and (T0359)R91.N only 0.000 apart, marking (T0359)R91.N as missing # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS3.pdb.gz looking for model 1 # Found a chain break before 94 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS4.pdb.gz looking for model 1 WARNING: atoms too close: (T0359)T11.O and (T0359)K12.N only 0.000 apart, marking (T0359)K12.N as missing # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS5.pdb.gz looking for model 1 # Found a chain break before 95 # 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 T0359 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 T0359 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 T0359 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS5 # ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1 # Found a chain break before 87 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS1 # ReadConformPDB reading from PDB file servers/keasar-server_TS2.pdb.gz looking for model 1 # Found a chain break before 87 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS2 # ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1 # Found a chain break before 87 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS3 # ReadConformPDB reading from PDB file servers/keasar-server_TS4.pdb.gz looking for model 1 # Found a chain break before 89 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS4 # ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1 # Found a chain break before 89 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS5 # ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 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 T0359 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 T0359 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 T0359 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation nFOLD_TS3 # ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 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 T0359 can't currently be optimized by undertaker # naming current conformation nFOLD_TS5 # ReadConformPDB reading from PDB file servers/panther2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0359 can't currently be optimized by undertaker # naming current conformation panther2_TS1 # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # Found a chain break before 95 # copying to AlignedFragments data structure # naming current conformation shub_TS1 # command:Using radius: 8.0000 Metaserver mode NUMB_ALIGNS: 261 model score -0.5419 model score -0.6722 model score -0.5419 model score -0.5479 model score -0.5124 model score -0.6045 model score -0.6088 model score -0.5576 model score -0.6605 model score -0.6000 model score -0.6664 model score -0.5445 model score -0.6400 model score -0.4876 model score -0.4068 model score -0.7724 model score -0.7459 model score -0.7373 model score -0.7530 model score -0.7505 model score 1.1031 model score 1.1883 model score 1.0316 model score 1.5331 model score 1.3460 model score -0.6852 model score -0.6371 model score -0.7644 model score -0.7023 model score -0.7650 model score -0.6138 model score -0.5982 model score -0.5684 model score -0.6329 model 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2.3460 weight: 0.9720 eval: -0.6886 min: -0.7862 max: 2.3460 weight: 0.9721 eval: -0.6891 min: -0.7862 max: 2.3460 weight: 0.9728 eval: -0.6915 min: -0.7862 max: 2.3460 weight: 0.9663 eval: -0.6688 min: -0.7862 max: 2.3460 weight: 0.9684 eval: -0.6761 min: -0.7862 max: 2.3460 weight: 0.9167 eval: -0.4964 min: -0.7862 max: 2.3460 weight: 0.9269 eval: -0.5317 min: -0.7862 max: 2.3460 weight: 0.9747 eval: -0.6980 min: -0.7862 max: 2.3460 weight: 0.9282 eval: -0.5364 min: -0.7862 max: 2.3460 weight: 0.9853 eval: -0.7349 min: -0.7862 max: 2.3460 Adding 1779 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: -168.4698, CN propb: -168.4698 weights: 0.5180 constraints: 272 # command:Found ConstraintSet # PrintContacts align.constraints_meta02 Number of constraints in align2.constraints 272 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta02 Number of constraints in align2.constraints.bonus 272 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta02 Number of constraints in rejected2.constraints 1507 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta02 Number of constraints in rejected2.constraints.bonus 1507 # 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 1779 # command: