# 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/T0340/ # command:# Making conformation for sequence T0340 numbered 1 through 90 Created new target T0340 from T0340.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0340/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0340//projects/compbio/experiments/protein-predict/casp7/T0340/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0340//projects/compbio/experiments/protein-predict/casp7/T0340/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0340/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0340/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((T0340)V35.CB, (T0340)A48.CB) [> 3.7441 = 6.2402 < 8.1123] w=1.0000 to align # Constraint # added constraint: constraint((T0340)I32.CB, (T0340)L52.CB) [> 4.0464 = 6.7440 < 8.7671] w=1.0000 to align # Constraint # added constraint: constraint((T0340)I32.CB, (T0340)Q49.CB) [> 4.0879 = 6.8131 < 8.8570] w=1.0000 to align # Constraint # added constraint: constraint((T0340)I32.CB, (T0340)A48.CB) [> 3.4278 = 5.7130 < 7.4268] w=1.0000 to align # Constraint # added constraint: constraint((T0340)I32.CB, (T0340)D50.CB) [> 2.8679 = 4.7799 < 6.2138] w=0.9907 to align # Constraint # added constraint: constraint((T0340)Y31.CB, (T0340)R51.CB) [> 3.3006 = 5.5011 < 7.1514] w=0.9907 to align # Constraint # added constraint: constraint((T0340)Y31.CB, (T0340)Q49.CB) [> 3.9972 = 6.6620 < 8.6606] w=0.9774 to align # Constraint # added constraint: constraint((T0340)V55.CB, (T0340)S71.CB) [> 3.1874 = 5.3123 < 6.9060] w=0.9720 to align # Constraint # added constraint: constraint((T0340)V35.CB, (T0340)L46.CB) [> 3.5887 = 5.9812 < 7.7755] w=0.9720 to align # Constraint # added constraint: constraint((T0340)I32.CB, (T0340)L46.CB) [> 3.6783 = 6.1304 < 7.9696] w=0.9720 to align # Constraint # added constraint: constraint((T0340)V55.CB, (T0340)I72.CB) [> 3.8262 = 6.3769 < 8.2900] w=0.9720 to align # Constraint # added constraint: constraint((T0340)N56.CB, (T0340)R80.CB) [> 3.3058 = 5.5097 < 7.1626] w=0.9629 to align # Constraint # added constraint: constraint((T0340)S34.CB, (T0340)A48.CB) [> 3.6777 = 6.1296 < 7.9684] w=0.9626 to align # Constraint # added constraint: constraint((T0340)I53.CB, (T0340)V84.CB) [> 3.4769 = 5.7949 < 7.5333] w=0.9610 to align # Constraint # added constraint: constraint((T0340)R33.CB, (T0340)A48.CB) [> 3.8557 = 6.4262 < 8.3540] w=0.9598 to align # Constraint # added constraint: constraint((T0340)N56.CB, (T0340)A79.CB) [> 3.7155 = 6.1925 < 8.0502] w=0.9535 to align # Constraint # added constraint: constraint((T0340)I32.CB, (T0340)R47.CB) [> 4.1836 = 6.9726 < 9.0644] w=0.9521 to align # Constraint # added constraint: constraint((T0340)R51.CB, (T0340)G85.CA) [> 3.9265 = 6.5442 < 8.5074] w=0.9517 to align # Constraint # added constraint: constraint((T0340)V55.CB, (T0340)A79.CB) [> 3.9317 = 6.5529 < 8.5187] w=0.9442 to align # Constraint # added constraint: constraint((T0340)Q30.CB, (T0340)L52.CB) [> 2.8466 = 4.7444 < 6.1677] w=0.9439 to align # Constraint # added constraint: constraint((T0340)I53.CB, (T0340)V83.CB) [> 4.0699 = 6.7831 < 8.8181] w=0.9423 to align # Constraint # added constraint: constraint((T0340)L52.CB, (T0340)V83.CB) [> 3.5291 = 5.8818 < 7.6464] w=0.9423 to align # Constraint # added constraint: constraint((T0340)R51.CB, (T0340)V84.CB) [> 2.8560 = 4.7600 < 6.1880] w=0.9423 to align # Constraint # added constraint: constraint((T0340)Y31.CB, (T0340)D50.CB) [> 4.1397 = 6.8996 < 8.9694] w=0.9381 to align # Constraint # added constraint: constraint((T0340)Y31.CB, (T0340)L52.CB) [> 4.3347 = 7.2245 < 9.3918] w=0.9249 to align # Constraint # added constraint: constraint((T0340)R51.CB, (T0340)V83.CB) [> 3.8528 = 6.4213 < 8.3477] w=0.9236 to align # Constraint # added constraint: constraint((T0340)V55.CB, (T0340)L81.CB) [> 3.5004 = 5.8340 < 7.5842] w=0.9171 to align # Constraint # added constraint: constraint((T0340)Q30.CB, (T0340)V68.CB) [> 3.0842 = 5.1403 < 6.6824] w=0.9159 to align # Constraint # added constraint: constraint((T0340)H22.CB, (T0340)R33.CB) [> 2.6417 = 4.4029 < 5.7237] w=0.9155 to align # Constraint # added constraint: constraint((T0340)E54.CB, (T0340)L81.CB) [> 4.1877 = 6.9796 < 9.0735] w=0.9068 to align # Constraint # added constraint: constraint((T0340)Q30.CB, (T0340)R51.CB) [> 4.0549 = 6.7581 < 8.7855] w=0.9066 to align # Constraint # added constraint: constraint((T0340)G18.CA, (T0340)D36.CB) [> 2.5384 = 4.2307 < 5.4999] w=0.9062 to align # Constraint # added constraint: constraint((T0340)G18.CA, (T0340)V35.CB) [> 3.9604 = 6.6008 < 8.5810] w=0.9062 to align # Constraint # added constraint: constraint((T0340)L21.CB, (T0340)I32.CB) [> 3.5891 = 5.9818 < 7.7764] w=0.9062 to align # Constraint # added constraint: constraint((T0340)D50.CB, (T0340)V83.CB) [> 2.6049 = 4.3415 < 5.6439] w=0.9050 to align # Constraint # added constraint: constraint((T0340)L52.CB, (T0340)L81.CB) [> 3.5744 = 5.9574 < 7.7446] w=0.8975 to align # Constraint # added constraint: constraint((T0340)E54.CB, (T0340)L82.CB) [> 2.4659 = 4.1099 < 5.3428] w=0.8975 to align # Constraint # added constraint: constraint((T0340)H22.CB, (T0340)Y31.CB) [> 3.0865 = 5.1442 < 6.6875] w=0.8968 to align # Constraint # added constraint: constraint((T0340)L21.CB, (T0340)L52.CB) [> 4.0816 = 6.8027 < 8.8435] w=0.8968 to align # Constraint # added constraint: constraint((T0340)L21.CB, (T0340)R33.CB) [> 3.7164 = 6.1940 < 8.0521] w=0.8968 to align # Constraint # added constraint: constraint((T0340)L21.CB, (T0340)Y31.CB) [> 3.9226 = 6.5377 < 8.4990] w=0.8968 to align # Constraint # added constraint: constraint((T0340)Q58.CB, (T0340)S71.CB) [> 3.7104 = 6.1841 < 8.0393] w=0.8961 to align # Constraint # added constraint: constraint((T0340)D50.CB, (T0340)V84.CB) [> 4.0638 = 6.7730 < 8.8049] w=0.8956 to align # Constraint # added constraint: constraint((T0340)D50.CB, (T0340)G85.CA) [> 3.0836 = 5.1394 < 6.6812] w=0.8956 to align # Constraint # added constraint: constraint((T0340)L52.CB, (T0340)V68.CB) [> 4.0814 = 6.8023 < 8.8429] w=0.8880 to align # Constraint # added constraint: constraint((T0340)Q30.CB, (T0340)V60.CB) [> 3.2459 = 5.4098 < 7.0327] w=0.8879 to align # Constraint # added constraint: constraint((T0340)F19.CB, (T0340)D36.CB) [> 4.0304 = 6.7172 < 8.7324] w=0.8875 to align # Constraint # added constraint: constraint((T0340)F19.CB, (T0340)V35.CB) [> 3.0889 = 5.1482 < 6.6926] w=0.8875 to align # Constraint # added constraint: constraint((T0340)F19.CB, (T0340)I32.CB) [> 3.2121 = 5.3534 < 6.9595] w=0.8875 to align # Constraint # added constraint: constraint((T0340)I53.CB, (T0340)L82.CB) [> 2.9280 = 4.8800 < 6.3440] w=0.8788 to align # Constraint # added constraint: constraint((T0340)G18.CA, (T0340)P40.CB) [> 3.5211 = 5.8684 < 7.6290] w=0.8781 to align # Constraint # added constraint: constraint((T0340)G18.CA, (T0340)S39.CB) [> 2.2305 = 3.7175 < 4.8328] w=0.8781 to align # Constraint # added constraint: constraint((T0340)N20.CB, (T0340)S34.CB) [> 2.6752 = 4.4587 < 5.7963] w=0.8781 to align # Constraint # added constraint: constraint((T0340)N20.CB, (T0340)R33.CB) [> 2.7926 = 4.6543 < 6.0506] w=0.8781 to align # Constraint # added constraint: constraint((T0340)N20.CB, (T0340)I32.CB) [> 4.2429 = 7.0714 < 9.1929] w=0.8781 to align # Constraint # added constraint: constraint((T0340)V55.CB, (T0340)R80.CB) [> 4.3651 = 7.2752 < 9.4577] w=0.8699 to align # Constraint # added constraint: constraint((T0340)F19.CB, (T0340)A41.CB) [> 2.6630 = 4.4383 < 5.7698] w=0.8688 to align # Constraint # added constraint: constraint((T0340)N56.CB, (T0340)R75.CB) [> 3.5929 = 5.9882 < 7.7846] w=0.8604 to align # Constraint # added constraint: constraint((T0340)V35.CB, (T0340)R47.CB) [> 4.0810 = 6.8016 < 8.8421] w=0.8599 to align # Constraint # added constraint: constraint((T0340)G18.CA, (T0340)A41.CB) [> 2.8686 = 4.7810 < 6.2153] w=0.8595 to align # Constraint # added constraint: constraint((T0340)Y17.CB, (T0340)A41.CB) [> 3.2295 = 5.3824 < 6.9972] w=0.8595 to align # Constraint # added constraint: constraint((T0340)F19.CB, (T0340)L46.CB) [> 3.7780 = 6.2967 < 8.1857] w=0.8595 to align # Constraint # added constraint: constraint((T0340)L21.CB, (T0340)Q30.CB) [> 3.1671 = 5.2786 < 6.8622] w=0.8501 to align # Constraint # added constraint: constraint((T0340)G57.CA, (T0340)R80.CB) [> 4.2286 = 7.0477 < 9.1620] w=0.8414 to align # Constraint # added constraint: constraint((T0340)L52.CB, (T0340)L82.CB) [> 4.4303 = 7.3838 < 9.5989] w=0.8414 to align # Constraint # added constraint: constraint((T0340)L10.CB, (T0340)A79.CB) [> 2.9172 = 4.8621 < 6.3207] w=0.8314 to align # Constraint # added constraint: constraint((T0340)F19.CB, (T0340)S34.CB) [> 3.9961 = 6.6602 < 8.6582] w=0.8314 to align # Constraint # added constraint: constraint((T0340)L46.CB, (T0340)V83.CB) [> 4.0198 = 6.6996 < 8.7095] w=0.8302 to align # Constraint # added constraint: constraint((T0340)G29.CA, (T0340)R51.CB) [> 3.6859 = 6.1432 < 7.9862] w=0.8290 to align # Constraint # added constraint: constraint((T0340)I32.CB, (T0340)R51.CB) [> 4.6136 = 7.6893 < 9.9961] w=0.8225 to align # Constraint # added constraint: constraint((T0340)H9.CB, (T0340)R80.CB) [> 3.0357 = 5.0596 < 6.5774] w=0.8221 to align # Constraint # added constraint: constraint((T0340)F19.CB, (T0340)S39.CB) [> 4.2216 = 7.0360 < 9.1468] w=0.8128 to align # Constraint # added constraint: constraint((T0340)H9.CB, (T0340)A79.CB) [> 4.2975 = 7.1625 < 9.3112] w=0.8127 to align # Constraint # added constraint: constraint((T0340)L10.CB, (T0340)P40.CB) [> 3.0474 = 5.0789 < 6.6026] w=0.8035 to align # Constraint # added constraint: constraint((T0340)C8.CB, (T0340)R80.CB) [> 4.2663 = 7.1105 < 9.2437] w=0.8034 to align # Constraint # added constraint: constraint((T0340)L7.CB, (T0340)R80.CB) [> 3.8451 = 6.4085 < 8.3311] w=0.8034 to align # Constraint # added constraint: constraint((T0340)Y17.CB, (T0340)A79.CB) [> 3.7311 = 6.2185 < 8.0840] w=0.7941 to align # Constraint # added constraint: constraint((T0340)C8.CB, (T0340)V83.CB) [> 3.7324 = 6.2207 < 8.0869] w=0.7941 to align # Constraint # added constraint: constraint((T0340)L10.CB, (T0340)E78.CB) [> 4.2595 = 7.0992 < 9.2290] w=0.7941 to align # Constraint # added constraint: constraint((T0340)V55.CB, (T0340)V68.CB) [> 4.1606 = 6.9343 < 9.0146] w=0.7851 to align # Constraint # added constraint: constraint((T0340)L10.CB, (T0340)A41.CB) [> 3.7587 = 6.2645 < 8.1439] w=0.7847 to align # Constraint # added constraint: constraint((T0340)C8.CB, (T0340)L46.CB) [> 3.6440 = 6.0734 < 7.8954] w=0.7847 to align # Constraint # added constraint: constraint((T0340)R11.CB, (T0340)E78.CB) [> 3.3097 = 5.5161 < 7.1710] w=0.7847 to align # Constraint # added constraint: constraint((T0340)G18.CA, (T0340)A42.CB) [> 4.2497 = 7.0828 < 9.2076] w=0.7754 to align # Constraint # added constraint: constraint((T0340)Y17.CB, (T0340)S39.CB) [> 4.0529 = 6.7549 < 8.7814] w=0.7754 to align # Constraint # added constraint: constraint((T0340)L21.CB, (T0340)V68.CB) [> 3.7527 = 6.2546 < 8.1310] w=0.7661 to align # Constraint # added constraint: constraint((T0340)R6.CB, (T0340)V83.CB) [> 3.3003 = 5.5004 < 7.1505] w=0.7660 to align # Constraint # added constraint: constraint((T0340)H9.CB, (T0340)E78.CB) [> 3.7296 = 6.2159 < 8.0807] w=0.7660 to align # Constraint # added constraint: constraint((T0340)L21.CB, (T0340)V69.CB) [> 4.1807 = 6.9678 < 9.0581] w=0.7660 to align # Constraint # added constraint: constraint((T0340)C8.CB, (T0340)L81.CB) [> 2.9848 = 4.9747 < 6.4671] w=0.7567 to align # Constraint # added constraint: constraint((T0340)Y17.CB, (T0340)I72.CB) [> 4.0979 = 6.8298 < 8.8788] w=0.7474 to align # Constraint # added constraint: constraint((T0340)P5.CB, (T0340)V84.CB) [> 3.1755 = 5.2924 < 6.8802] w=0.7287 to align # Constraint # added constraint: constraint((T0340)V55.CB, (T0340)R75.CB) [> 3.9922 = 6.6536 < 8.6497] w=0.7287 to align # Constraint # added constraint: constraint((T0340)L7.CB, (T0340)L82.CB) [> 3.2658 = 5.4429 < 7.0758] w=0.7287 to align # Constraint # added constraint: constraint((T0340)L7.CB, (T0340)L81.CB) [> 4.3499 = 7.2498 < 9.4247] w=0.7287 to align # Constraint # added constraint: constraint((T0340)L10.CB, (T0340)R80.CB) [> 4.5775 = 7.6292 < 9.9180] w=0.7287 to align # Constraint # added constraint: constraint((T0340)P5.CB, (T0340)I53.CB) [> 4.1841 = 6.9735 < 9.0655] w=0.7193 to align # Constraint # added constraint: constraint((T0340)P5.CB, (T0340)V83.CB) [> 4.2422 = 7.0704 < 9.1915] w=0.7193 to align # Constraint # added constraint: constraint((T0340)V60.CB, (T0340)S71.CB) [> 4.0520 = 6.7533 < 8.7793] w=0.7170 to align # Constraint # added constraint: constraint((T0340)L21.CB, (T0340)H65.CB) [> 4.0760 = 6.7933 < 8.8313] w=0.7100 to align # Constraint # added constraint: constraint((T0340)R6.CB, (T0340)L82.CB) [> 4.3823 = 7.3039 < 9.4951] w=0.7100 to align # Constraint # added constraint: constraint((T0340)R11.CB, (T0340)D77.CB) [> 3.8279 = 6.3799 < 8.2938] w=0.7100 to align # Constraint # added constraint: constraint((T0340)L10.CB, (T0340)L81.CB) [> 4.0588 = 6.7646 < 8.7940] w=0.6727 to align # Constraint # added constraint: constraint((T0340)C8.CB, (T0340)S44.CB) [> 3.4492 = 5.7486 < 7.4732] w=0.6726 to align # Constraint # added constraint: constraint((T0340)P5.CB, (T0340)L82.CB) [> 3.6972 = 6.1620 < 8.0106] w=0.6726 to align # Constraint # added constraint: constraint((T0340)K12.CB, (T0340)A79.CB) [> 3.9013 = 6.5021 < 8.4527] w=0.6726 to align # Constraint # added constraint: constraint((T0340)G29.CA, (T0340)E61.CB) [> 3.8521 = 6.4201 < 8.3461] w=0.6702 to align # Constraint # added constraint: constraint((T0340)L21.CB, (T0340)I72.CB) [> 4.4411 = 7.4018 < 9.6223] w=0.6633 to align # Constraint # added constraint: constraint((T0340)L46.CB, (T0340)L81.CB) [> 4.3724 = 7.2874 < 9.4736] w=0.6558 to align # Constraint # added constraint: constraint((T0340)G29.CA, (T0340)V60.CB) [> 4.1853 = 6.9755 < 9.0682] w=0.6515 to align # Constraint # added constraint: constraint((T0340)V55.CB, (T0340)L82.CB) [> 4.6508 = 7.7514 < 10.0768] w=0.6457 to align # Constraint # added constraint: constraint((T0340)Q30.CB, (T0340)L63.CB) [> 4.0019 = 6.6697 < 8.6707] w=0.6364 to align # Constraint # added constraint: constraint((T0340)F19.CB, (T0340)R33.CB) [> 4.6353 = 7.7255 < 10.0432] w=0.6166 to align # Constraint # added constraint: constraint((T0340)H22.CB, (T0340)I32.CB) [> 4.5742 = 7.6236 < 9.9107] w=0.5885 to align # Constraint # added constraint: constraint((T0340)G57.CA, (T0340)L82.CB) [> 4.3077 = 7.1795 < 9.3333] w=0.5873 to align # Constraint # added constraint: constraint((T0340)G29.CA, (T0340)G62.CA) [> 3.6374 = 6.0624 < 7.8811] w=0.5862 to align # Constraint # added constraint: constraint((T0340)H9.CB, (T0340)L81.CB) [> 4.5342 = 7.5569 < 9.8240] w=0.5792 to align # Constraint # added constraint: constraint((T0340)N56.CB, (T0340)S71.CB) [> 4.1907 = 6.9845 < 9.0798] w=0.5727 to align # Constraint # added constraint: constraint((T0340)G29.CA, (T0340)L52.CB) [> 4.3976 = 7.3294 < 9.5282] w=0.5582 to align # Constraint # added constraint: constraint((T0340)R11.CB, (T0340)A79.CB) [> 4.3670 = 7.2783 < 9.4618] w=0.5512 to align # Constraint # added constraint: constraint((T0340)H22.CB, (T0340)H65.CB) [> 4.2245 = 7.0408 < 9.1531] w=0.5419 to align # Constraint # added constraint: constraint((T0340)C8.CB, (T0340)L82.CB) [> 4.5005 = 7.5008 < 9.7511] w=0.5231 to align # Constraint # added constraint: constraint((T0340)N20.CB, (T0340)V35.CB) [> 4.6157 = 7.6928 < 10.0006] w=0.5138 to align # Constraint # added constraint: constraint((T0340)G13.CA, (T0340)P40.CB) [> 3.8176 = 6.3627 < 8.2715] w=0.5045 to align # Constraint # added constraint: constraint((T0340)R6.CB, (T0340)G85.CA) [> 4.1899 = 6.9833 < 9.0782] w=0.5044 to align # Constraint # added constraint: constraint((T0340)R6.CB, (T0340)V84.CB) [> 4.4829 = 7.4714 < 9.7128] w=0.4952 to align # Constraint # added constraint: constraint((T0340)L10.CB, (T0340)L46.CB) [> 4.5409 = 7.5681 < 9.8385] w=0.4951 to align # Constraint # added constraint: constraint((T0340)E54.CB, (T0340)R80.CB) [> 4.6243 = 7.7072 < 10.0193] w=0.4888 to align # Constraint # added constraint: constraint((T0340)H9.CB, (T0340)S44.CB) [> 4.1069 = 6.8448 < 8.8982] w=0.4671 to align # Constraint # added constraint: constraint((T0340)N20.CB, (T0340)D36.CB) [> 4.4157 = 7.3596 < 9.5674] w=0.4577 to align # Constraint # added constraint: constraint((T0340)P28.CB, (T0340)E61.CB) [> 3.7737 = 6.2894 < 8.1763] w=0.4460 to align # Constraint # added constraint: constraint((T0340)L7.CB, (T0340)V83.CB) [> 4.6095 = 7.6824 < 9.9872] w=0.4390 to align # Constraint # added constraint: constraint((T0340)R4.CB, (T0340)V84.CB) [> 4.0868 = 6.8113 < 8.8547] w=0.4298 to align # Constraint # added constraint: constraint((T0340)S23.CB, (T0340)V68.CB) [> 4.2484 = 7.0807 < 9.2049] w=0.4297 to align # Constraint # added constraint: constraint((T0340)L3.CB, (T0340)V84.CB) [> 3.8156 = 6.3593 < 8.2671] w=0.4111 to align # Constraint # added constraint: constraint((T0340)L3.CB, (T0340)G85.CA) [> 3.6806 = 6.1343 < 7.9745] w=0.4111 to align # Constraint # added constraint: constraint((T0340)K12.CB, (T0340)E76.CB) [> 4.0542 = 6.7571 < 8.7842] w=0.4110 to align # Constraint # added constraint: constraint((T0340)P28.CB, (T0340)G62.CA) [> 3.6300 = 6.0499 < 7.8649] w=0.4075 to align # Constraint # added constraint: constraint((T0340)G29.CA, (T0340)L63.CB) [> 4.3226 = 7.2043 < 9.3656] w=0.3935 to align # Constraint # added constraint: constraint((T0340)K12.CB, (T0340)R75.CB) [> 4.0459 = 6.7432 < 8.7661] w=0.3923 to align # Constraint # added constraint: constraint((T0340)P5.CB, (T0340)G85.CA) [> 4.3969 = 7.3282 < 9.5266] w=0.3830 to align # Constraint # added constraint: constraint((T0340)K25.CB, (T0340)R64.CB) [> 3.4928 = 5.8214 < 7.5678] w=0.3737 to align # Constraint # added constraint: constraint((T0340)G18.CA, (T0340)G38.CA) [> 4.4578 = 7.4297 < 9.6587] w=0.3550 to align # Constraint # added constraint: constraint((T0340)D24.CB, (T0340)E67.CB) [> 4.3802 = 7.3004 < 9.4905] w=0.2803 to align # Constraint # added constraint: constraint((T0340)V35.CB, (T0340)G45.CA) [> 4.6921 = 7.8201 < 10.1662] w=0.2767 to align # Constraint # added constraint: constraint((T0340)L52.CB, (T0340)I72.CB) [> 4.6727 = 7.7879 < 10.1242] w=0.2709 to align # Constraint # added constraint: constraint((T0340)C8.CB, (T0340)G45.CA) [> 3.7797 = 6.2995 < 8.1894] w=0.2709 to align # Constraint # added constraint: constraint((T0340)Q15.CB, (T0340)P40.CB) [> 3.9126 = 6.5210 < 8.4772] w=0.2709 to align # Constraint # added constraint: constraint((T0340)P14.CB, (T0340)D77.CB) [> 4.1128 = 6.8547 < 8.9112] w=0.2429 to align # Constraint # added constraint: constraint((T0340)R6.CB, (T0340)D50.CB) [> 4.6332 = 7.7221 < 10.0387] w=0.2242 to align # Constraint # added constraint: constraint((T0340)G29.CA, (T0340)I53.CB) [> 3.9506 = 6.5844 < 8.5597] w=0.2218 to align # Constraint # added constraint: constraint((T0340)C8.CB, (T0340)A41.CB) [> 4.5861 = 7.6435 < 9.9365] w=0.2149 to align # Constraint # added constraint: constraint((T0340)N56.CB, (T0340)E78.CB) [> 4.4987 = 7.4978 < 9.7472] w=0.1962 to align # Constraint # added constraint: constraint((T0340)Q30.CB, (T0340)I53.CB) [> 4.3976 = 7.3293 < 9.5281] w=0.1907 to align # Constraint # added constraint: constraint((T0340)G16.CA, (T0340)K73.CB) [> 4.0704 = 6.7840 < 8.8192] w=0.1868 to align # Constraint # added constraint: constraint((T0340)Y31.CB, (T0340)P86.CB) [> 4.4501 = 7.4168 < 9.6419] w=0.1868 to align # Constraint # added constraint: constraint((T0340)S23.CB, (T0340)R51.CB) [> 4.7498 = 7.9163 < 10.2912] w=0.1682 to align # Constraint # added constraint: constraint((T0340)G29.CA, (T0340)V68.CB) [> 4.2037 = 7.0061 < 9.1079] w=0.1646 to align # Constraint # added constraint: constraint((T0340)S26.CB, (T0340)H65.CB) [> 3.8216 = 6.3693 < 8.2801] w=0.1588 to align # Constraint # added constraint: constraint((T0340)L10.CB, (T0340)R43.CB) [> 4.6360 = 7.7267 < 10.0447] w=0.1588 to align # Constraint # added constraint: constraint((T0340)P28.CB, (T0340)I53.CB) [> 3.8679 = 6.4465 < 8.3805] w=0.1471 to align # Constraint # added constraint: constraint((T0340)G29.CA, (T0340)H65.CB) [> 3.9988 = 6.6647 < 8.6641] w=0.1366 to align # Constraint # added constraint: constraint((T0340)Y31.CB, (T0340)A48.CB) [> 4.5974 = 7.6623 < 9.9610] w=0.1308 to align # Constraint # added constraint: constraint((T0340)I53.CB, (T0340)L81.CB) [> 4.7465 = 7.9108 < 10.2840] w=0.1308 to align # Constraint # added constraint: constraint((T0340)Q30.CB, (T0340)V69.CB) [> 4.3985 = 7.3308 < 9.5301] w=0.1308 to align # Constraint # added constraint: constraint((T0340)L7.CB, (T0340)E54.CB) [> 4.6420 = 7.7366 < 10.0576] w=0.1215 to align # Constraint # added constraint: constraint((T0340)P28.CB, (T0340)V60.CB) [> 4.0192 = 6.6988 < 8.7084] w=0.1214 to align # Constraint # added constraint: constraint((T0340)L10.CB, (T0340)F19.CB) [> 4.3257 = 7.2095 < 9.3723] w=0.1214 to align # Constraint # added constraint: constraint((T0340)M2.CB, (T0340)G85.CA) [> 4.6573 = 7.7621 < 10.0908] w=0.1121 to align # Constraint # added constraint: constraint((T0340)G18.CA, (T0340)L46.CB) [> 4.6855 = 7.8091 < 10.1519] w=0.1121 to align # Constraint # added constraint: constraint((T0340)R6.CB, (T0340)R47.CB) [> 4.5596 = 7.5993 < 9.8790] w=0.1121 to align # Constraint # added constraint: constraint((T0340)G16.CA, (T0340)I72.CB) [> 3.5989 = 5.9981 < 7.7975] w=0.1121 to align # Constraint # added constraint: constraint((T0340)R33.CB, (T0340)Q49.CB) [> 4.3425 = 7.2375 < 9.4088] w=0.1039 to align # Constraint # added constraint: constraint((T0340)Y17.CB, (T0340)L46.CB) [> 4.7556 = 7.9260 < 10.3037] w=0.0841 to align # Constraint # added constraint: constraint((T0340)N59.CB, (T0340)L82.CB) [> 4.7038 = 7.8397 < 10.1916] w=0.0841 to align # Constraint # added constraint: constraint((T0340)S23.CB, (T0340)V69.CB) [> 4.4824 = 7.4706 < 9.7118] w=0.0841 to align # Constraint # added constraint: constraint((T0340)R11.CB, (T0340)R43.CB) [> 4.4669 = 7.4448 < 9.6783] w=0.0747 to align # Constraint # added constraint: constraint((T0340)H22.CB, (T0340)S34.CB) [> 4.1462 = 6.9103 < 8.9834] w=0.0747 to align # Constraint # added constraint: constraint((T0340)G57.CA, (T0340)L81.CB) [> 4.4833 = 7.4721 < 9.7137] w=0.0654 to align # Constraint # added constraint: constraint((T0340)Q58.CB, (T0340)V68.CB) [> 3.1520 = 5.2533 < 6.8292] w=0.0654 to align # Constraint # added constraint: constraint((T0340)Q30.CB, (T0340)V55.CB) [> 4.7228 = 7.8713 < 10.2327] w=0.0561 to align # Constraint # added constraint: constraint((T0340)C8.CB, (T0340)D50.CB) [> 4.5135 = 7.5225 < 9.7793] w=0.0561 to align # Constraint # added constraint: constraint((T0340)C8.CB, (T0340)A79.CB) [> 4.5572 = 7.5953 < 9.8740] w=0.0561 to align # Constraint # added constraint: constraint((T0340)Q30.CB, (T0340)I72.CB) [> 4.3334 = 7.2224 < 9.3891] w=0.0561 to align # Constraint # added constraint: constraint((T0340)F19.CB, (T0340)L52.CB) [> 4.5395 = 7.5658 < 9.8355] w=0.0561 to align # Constraint # added constraint: constraint((T0340)N20.CB, (T0340)A48.CB) [> 4.2503 = 7.0838 < 9.2089] w=0.0561 to align # Constraint # added constraint: constraint((T0340)Y17.CB, (T0340)D36.CB) [> 4.7230 = 7.8717 < 10.2332] w=0.0561 to align # Constraint # added constraint: constraint((T0340)S23.CB, (T0340)V60.CB) [> 3.3363 = 5.5605 < 7.2286] w=0.0560 to align # Constraint # added constraint: constraint((T0340)D24.CB, (T0340)R33.CB) [> 3.6942 = 6.1570 < 8.0041] w=0.0537 to align # Constraint # added constraint: constraint((T0340)Y31.CB, (T0340)H65.CB) [> 4.3822 = 7.3037 < 9.4948] w=0.0525 to align # Constraint # added constraint: constraint((T0340)N20.CB, (T0340)V69.CB) [> 3.9169 = 6.5281 < 8.4865] w=0.0467 to align # Constraint # added constraint: constraint((T0340)L3.CB, (T0340)R51.CB) [> 3.6462 = 6.0770 < 7.9002] w=0.0374 to align # Constraint # added constraint: constraint((T0340)E54.CB, (T0340)V83.CB) [> 4.1641 = 6.9402 < 9.0222] w=0.0292 to align # Constraint # added constraint: constraint((T0340)P5.CB, (T0340)E54.CB) [> 4.3195 = 7.1991 < 9.3588] w=0.0280 to align # Constraint # added constraint: constraint((T0340)Q49.CB, (T0340)T88.CB) [> 4.5719 = 7.6199 < 9.9059] w=0.0280 to align # Constraint # added constraint: constraint((T0340)H9.CB, (T0340)L82.CB) [> 4.2182 = 7.0303 < 9.1394] w=0.0280 to align # Constraint # added constraint: constraint((T0340)C8.CB, (T0340)L52.CB) [> 4.7673 = 7.9456 < 10.3292] w=0.0280 to align # Constraint # added constraint: constraint((T0340)L10.CB, (T0340)V55.CB) [> 4.3456 = 7.2427 < 9.4155] w=0.0280 to align # Constraint # added constraint: constraint((T0340)G18.CA, (T0340)P37.CB) [> 2.4418 = 4.0697 < 5.2906] w=0.0280 to align # Constraint # added constraint: constraint((T0340)E54.CB, (T0340)V84.CB) [> 3.8384 = 6.3973 < 8.3165] w=0.0280 to align # Constraint # added constraint: constraint((T0340)H9.CB, (T0340)N56.CB) [> 4.2806 = 7.1344 < 9.2747] w=0.0280 to align # Constraint # added constraint: constraint((T0340)R6.CB, (T0340)L81.CB) [> 4.7723 = 7.9538 < 10.3399] w=0.0280 to align # Constraint # added constraint: constraint((T0340)Y17.CB, (T0340)N56.CB) [> 4.5457 = 7.5761 < 9.8490] w=0.0280 to align # Constraint # added constraint: constraint((T0340)V35.CB, (T0340)D50.CB) [> 4.6856 = 7.8094 < 10.1522] w=0.0198 to align # Constraint # added constraint: constraint((T0340)Y31.CB, (T0340)L63.CB) [> 3.7304 = 6.2173 < 8.0825] w=0.0198 to align # Constraint # added constraint: constraint((T0340)L7.CB, (T0340)G57.CA) [> 4.7915 = 7.9858 < 10.3815] w=0.0187 to align # Constraint # added constraint: constraint((T0340)H9.CB, (T0340)V83.CB) [> 3.8810 = 6.4684 < 8.4089] w=0.0187 to align # Constraint # added constraint: constraint((T0340)G18.CA, (T0340)S34.CB) [> 4.7387 = 7.8979 < 10.2673] w=0.0187 to align # Constraint # added constraint: constraint((T0340)I53.CB, (T0340)G85.CA) [> 3.4925 = 5.8208 < 7.5671] w=0.0187 to align # Constraint # added constraint: constraint((T0340)C8.CB, (T0340)E54.CB) [> 4.5829 = 7.6381 < 9.9296] w=0.0093 to align # Constraint # added constraint: constraint((T0340)R27.CB, (T0340)I53.CB) [> 4.1923 = 6.9872 < 9.0834] w=0.0093 to align # Constraint # added constraint: constraint((T0340)H22.CB, (T0340)D36.CB) [> 4.7964 = 7.9939 < 10.3921] w=0.0093 to align # Constraint # added constraint: constraint((T0340)F19.CB, (T0340)R80.CB) [> 3.9022 = 6.5036 < 8.4547] w=0.0093 to align # Constraint # added constraint: constraint((T0340)N20.CB, (T0340)P37.CB) [> 4.6514 = 7.7524 < 10.0781] w=0.0093 to align # Constraint # added constraint: constraint((T0340)N20.CB, (T0340)G38.CA) [> 4.1652 = 6.9420 < 9.0246] w=0.0093 to align # Constraint # added constraint: constraint((T0340)N20.CB, (T0340)S39.CB) [> 1.5547 = 2.5912 < 3.3686] w=0.0093 to align # Constraint # added constraint: constraint((T0340)L21.CB, (T0340)V35.CB) [> 3.7579 = 6.2632 < 8.1421] w=0.0093 to align # Constraint # added constraint: constraint((T0340)L21.CB, (T0340)S34.CB) [> 4.3704 = 7.2840 < 9.4692] w=0.0093 to align # Constraint # added constraint: constraint((T0340)L7.CB, (T0340)G85.CA) [> 4.6757 = 7.7928 < 10.1307] w=0.0093 to align # Constraint # added constraint: constraint((T0340)E54.CB, (T0340)G85.CA) [> 4.2110 = 7.0184 < 9.1239] w=0.0093 to align # Constraint # added constraint: constraint((T0340)E54.CB, (T0340)P86.CB) [> 4.5604 = 7.6006 < 9.8808] w=0.0093 to align # Constraint # added constraint: constraint((T0340)Y31.CB, (T0340)S87.CB) [> 4.3998 = 7.3330 < 9.5329] w=0.0093 to align # Constraint # added constraint: constraint((T0340)A79.CB, (T0340)T88.CB) [> 3.1318 = 5.2197 < 6.7856] w=0.0066 to align # SetCost created cost = # ( 1.0000 * align ) # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0340/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0340/decoys/ # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # choosing archetypes in rotamer library # WARNING: incomplete conformation T0340 can't currently be optimized by undertaker # 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 T0340 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 can't currently be optimized by undertaker # 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 T0340 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 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 T0340 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 T0340 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 T0340 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 T0340 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 T0340 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 T0340 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 T0340 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 T0340 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 T0340 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 # Found a chain break before 89 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_TS5 # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # 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 # naming current conformation 3Dpro_TS3 # ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1 # Found a chain break before 59 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS4 # ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1 # Found a chain break before 74 # 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 51 # 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 80 # 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 80 # 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 89 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS5 # ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1 # naming current conformation BayesHH_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS1.pdb.gz looking for model 1 # Found a chain break before 10 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS2.pdb.gz looking for model 1 # Found a chain break before 62 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS2 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS3.pdb.gz looking for model 1 # Found a chain break before 84 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS3 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS4.pdb.gz looking for model 1 # 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 39 # 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 T0340 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS3 # ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS4 # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS5 # ReadConformPDB reading from PDB file servers/CPHmodels_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 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 T0340 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS2 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS3 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS4 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS5 # ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 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 T0340 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 T0340 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 T0340 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 T0340 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 # naming current conformation FAMSD_TS1 # ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 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 T0340 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 T0340 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 T0340 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 86 # 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 T0340 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 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 # WARNING: incomplete conformation T0340 can't currently be optimized by undertaker # naming current conformation FAMS_TS4 # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 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 # Found a chain break before 74 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS3 # ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1 # Found a chain break before 59 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS4 # ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1 # naming current conformation FOLDpro_TS5 # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 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 Skipped atom 211, because occupancy 1 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz # WARNING: incomplete conformation T0340 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 T0340 can't currently be optimized by undertaker # naming current conformation FORTE1_AL3 # ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 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 T0340 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 T0340 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 Skipped atom 211, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz # WARNING: incomplete conformation T0340 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 T0340 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 T0340 can't currently be optimized by undertaker # naming current conformation FORTE2_AL4 # ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 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 89 # 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 75 # 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 89 # 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 48 # 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 89 # 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 T0340 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS2 # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # naming current conformation FUGMOD_TS3 # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # Found a chain break before 26 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS4 # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 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 T0340 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL1 # ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1 Skipped atom 211, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL2.pdb.gz # WARNING: incomplete conformation T0340 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 T0340 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL3 # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL4 # ReadConformPDB reading from PDB file servers/FUGUE_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 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 88 # 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 89 # 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 87 # 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 84 # 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 85 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # Found a chain break before 59 # 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 59 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # Found a chain break before 61 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS3 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1 # Found a chain break before 26 # 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 11 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS5 # ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1 # naming current conformation HHpred1_TS1 # ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1 # Found a chain break before 26 # 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 59 # 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 T0340 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Huber-Torda-Server_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 can't currently be optimized by undertaker # copying to AlignedFragments data structure # 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 T0340 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Huber-Torda-Server_TS3 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Huber-Torda-Server_TS4 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Huber-Torda-Server_TS5 # ReadConformPDB reading from PDB file servers/LOOPP_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation LOOPP_TS1 # ReadConformPDB reading from PDB file servers/LOOPP_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation LOOPP_TS2 # ReadConformPDB reading from PDB file servers/LOOPP_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation LOOPP_TS3 # ReadConformPDB reading from PDB file servers/LOOPP_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation LOOPP_TS4 # ReadConformPDB reading from PDB file servers/LOOPP_TS5.pdb.gz looking for model 1 # Found a chain break before 77 # copying to AlignedFragments data structure # naming current conformation LOOPP_TS5 # ReadConformPDB reading from PDB file servers/MIG_FROST_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 can't currently be optimized by undertaker # copying to AlignedFragments data structure # 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 59 # 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 # 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 38 # 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 59 # 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 59 # 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 89 # 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 # 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 89 # 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 89 # 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 89 # 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 89 # 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 89 # 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 T0340 can't currently be optimized by undertaker # copying to AlignedFragments data structure # 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 # Found a chain break before 75 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # Found a chain break before 25 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # Found a chain break before 86 # 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 T0340 can't currently be optimized by undertaker # naming current conformation Pcons6_TS1 # ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 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 T0340 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pcons6_TS3 # ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pcons6_TS4 # ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 can't currently be optimized by undertaker # naming current conformation Pcons6_TS5 # ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 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 T0340 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 T0340 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 T0340 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_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS5 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS1 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS2 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS3 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # naming current conformation Pmodeller6_TS4 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1 # Found a chain break before 25 # 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 59 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1 # Found a chain break before 59 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1 # Found a chain break before 59 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS4.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1 # 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 4 # 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 # Found a chain break before 82 # 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 58 # 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 89 # 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 84 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR_TS3.pdb.gz looking for model 1 # Found a chain break before 86 # 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 22 # 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 49 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS1 # ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1 # naming current conformation ROKKY_TS2 # ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1 # Found a chain break before 74 # 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 76 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS4 # ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1 # Found a chain break before 59 # 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 T0340 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation SAM-T02_AL1 # ReadConformPDB reading from PDB file servers/SAM-T02_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 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 T0340 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 T0340 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 Skipped atom 15, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 272, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 284, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 286, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 288, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 290, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 292, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 294, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 296, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 298, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 300, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 302, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 304, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 306, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 308, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 310, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz # WARNING: incomplete conformation T0340 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL5 # ReadConformPDB reading from PDB file servers/SAM-T99_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 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 T0340 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 T0340 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 T0340 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 T0340 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 87 # 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 T0340 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 T0340 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 T0340 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 T0340 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 59 # copying to AlignedFragments data structure # naming current conformation SP3_TS1 # ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1 # Found a chain break before 38 # copying to AlignedFragments data structure # naming current conformation SP3_TS2 # ReadConformPDB reading from PDB file servers/SP3_TS3.pdb.gz looking for model 1 # Found a chain break before 77 # copying to AlignedFragments data structure # naming current conformation SP3_TS3 # ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1 # naming current conformation SP3_TS4 # ReadConformPDB reading from PDB file servers/SP3_TS5.pdb.gz looking for model 1 # 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 11 # 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 77 # 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 28 # copying to AlignedFragments data structure # naming current conformation SP4_TS5 # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # Found a chain break before 59 # 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 77 # 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 38 # 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 # naming current conformation SPARKS2_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 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 T0340 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 T0340 can't currently be optimized by undertaker # copying to AlignedFragments data structure # 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 T0340 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 T0340 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 T0340 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation UNI-EID_expm_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 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 T0340 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 T0340 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 T0340 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 Skipped atom 211, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz # WARNING: incomplete conformation T0340 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 48 # 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 48 # 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 48 # 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 48 # 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 # 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 89 # 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 T0340 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation beautshotbase_TS1 # ReadConformPDB reading from PDB file servers/forecast-s_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 can't currently be optimized by undertaker # naming current conformation forecast-s_AL1 # ReadConformPDB reading from PDB file servers/forecast-s_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 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 T0340 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation forecast-s_AL3 # ReadConformPDB reading from PDB file servers/forecast-s_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 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 T0340 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation forecast-s_AL5 # ReadConformPDB reading from PDB file servers/gtg_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 can't currently be optimized by undertaker # naming current conformation gtg_AL1 # ReadConformPDB reading from PDB file servers/gtg_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 can't currently be optimized by undertaker # naming current conformation gtg_AL2 # ReadConformPDB reading from PDB file servers/gtg_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 can't currently be optimized by undertaker # naming current conformation gtg_AL3 # ReadConformPDB reading from PDB file servers/gtg_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 can't currently be optimized by undertaker # naming current conformation gtg_AL4 # ReadConformPDB reading from PDB file servers/gtg_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 can't currently be optimized by undertaker # naming current conformation gtg_AL5 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # Found a chain break before 59 # 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 # naming current conformation karypis.srv.2_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS3.pdb.gz looking for model 1 # 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 75 # 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 75 # 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 84 # 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 87 # 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 89 # 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: (T0340)H22.O and (T0340)S23.N only 0.000 apart, marking (T0340)S23.N as missing # WARNING: incomplete conformation T0340 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 87 # 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 T0340 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 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 T0340 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 T0340 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS5 # ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1 # Found a chain break before 84 # 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 84 # 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 83 # 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 51 # 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 79 # 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 T0340 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation mGen-3D_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation nFOLD_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 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 T0340 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 T0340 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 T0340 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 T0340 can't currently be optimized by undertaker # naming current conformation panther2_TS1 # ReadConformPDB reading from PDB file servers/panther3_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0340 can't currently be optimized by undertaker # naming current conformation panther3_TS1 # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # Found a chain break before 89 # copying to AlignedFragments data structure # naming current conformation shub_TS1 # command:Using radius: 8.0000 Metaserver mode NUMB_ALIGNS: 264 model score -0.6554 model score -0.6601 model score -0.6387 model score -0.6712 model score -0.5897 model score -0.4849 model score -0.6226 model score -0.6521 model score -0.5572 model score -0.6237 model score -0.6489 model score -0.6439 model score -0.6109 model score -0.6200 model score -0.4842 model score -0.7010 model score -0.7216 model score -0.6688 model score -0.6672 model score -0.7074 model score 0.8933 model score 1.0718 model score 1.0196 model score 0.8636 model score 0.9896 model score -0.7364 model score -0.6502 model score -0.7202 model score -0.7512 model score -0.7472 model score -0.7550 model score -0.6218 model score -0.7091 model score -0.7136 model score -0.6457 model score -0.7007 model score -0.6753 model score -0.7289 model score -0.6963 model score -0.6806 model score -0.5474 model score -0.7298 model score 1.2678 model score 1.2639 model score 1.2645 model score 1.2645 model score 1.2667 model score -0.7120 model score -0.6935 model score -0.6977 model score -0.6569 model score -0.6378 model score -0.7590 model score -0.7091 model score -0.6457 model score -0.6935 model score -0.7136 model score -0.7216 model score -0.6688 model score -0.7074 model score -0.6672 model score -0.6991 model score 1.2612 model score 1.2616 model score 1.2616 model score 1.2640 model score 1.2604 model score 1.2612 model score 1.2616 model score 1.2616 model score 1.2640 model score 1.2628 model score 1.8616 model score 2.0826 model score 2.0554 model score 2.0850 model score 2.2199 model score -0.7036 model score -0.7098 model score -0.6506 model score -0.0830 model score -0.4788 model score 1.2719 model score 1.2616 model score 1.2599 model score 1.2693 model score 1.2600 model score -0.7164 model score -0.6256 model score -0.6855 model score -0.6900 model score -0.6719 model score -0.7003 model score -0.6924 model score -0.7105 model score -0.6647 model score -0.6597 model score -0.7174 model score -0.7265 model score -0.7175 model score -0.7145 model score -0.6180 model score -0.6873 model score -0.7127 model score -0.1808 model score -0.6696 model score -0.6684 model score -0.3952 model score -0.3759 model score -0.5821 model score 1.2612 model score -0.7082 model score -0.7435 model score -0.6813 model score -0.6802 model score -0.6133 model score -0.7099 model score -0.7082 model score -0.6784 model score -0.7120 model score -0.7328 model score -0.7247 model score -0.7185 model score -0.7151 model score -0.7186 model score -0.5900 model score -0.6696 model score -0.6976 model score -0.6994 model score -0.6976 model score -0.6966 model score -0.6967 model score -0.6873 model score -0.6789 model score -0.6727 model score -0.7055 model score -0.7057 model score -0.6926 model score -0.7235 model score -0.7253 model score -0.7208 model score -0.6926 model score -0.6215 model score -0.7324 model score -0.6630 model score -0.7302 model score 0.3156 model score -0.6703 model score -0.4602 model score -0.6835 model score -0.6845 model score -0.7420 model score -0.6895 model score -0.6895 model score -0.7190 model score -0.7275 model score -0.7275 model score -0.6763 model score -0.6720 model score -0.4482 model score -0.6211 model score -0.6799 model score -0.6973 model score -0.6936 model score -0.6247 model score -0.6214 model score -0.7433 model score -0.7102 model score -0.6845 model score -0.7164 model score -0.7224 model score -0.7326 model score -0.6858 model score -0.7213 model score -0.6991 model score -0.6703 model score -0.6540 model score 1.2612 model score 1.2603 model score 1.2690 model score 1.2616 model score 1.2597 model score 1.2603 model score 1.2604 model score 1.2610 model score 1.2597 model score 1.2612 model score -0.7215 model score -0.7154 model score -0.5448 model score -0.5320 model score -0.6834 model score -0.7114 model score -0.6208 model score -0.6890 model score -0.7171 model score -0.7636 model score -0.7190 model score -0.5968 model score -0.5560 model score -0.7636 model score -0.7312 model score -0.7114 model score -0.6890 model score -0.6208 model score -0.7176 model score -0.7158 model score 1.2612 model score 1.2599 model score 1.2643 model score 1.2625 model score 1.2616 model 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1.2597 min: -0.7636 max: 2.2199 weight: 0.3892 eval: 1.2612 min: -0.7636 max: 2.2199 weight: 0.9873 eval: -0.7215 min: -0.7636 max: 2.2199 weight: 0.9854 eval: -0.7154 min: -0.7636 max: 2.2199 weight: 0.9340 eval: -0.5448 min: -0.7636 max: 2.2199 weight: 0.9301 eval: -0.5320 min: -0.7636 max: 2.2199 weight: 0.9758 eval: -0.6834 min: -0.7636 max: 2.2199 weight: 0.9842 eval: -0.7114 min: -0.7636 max: 2.2199 weight: 0.9569 eval: -0.6208 min: -0.7636 max: 2.2199 weight: 0.9775 eval: -0.6890 min: -0.7636 max: 2.2199 weight: 0.9860 eval: -0.7171 min: -0.7636 max: 2.2199 weight: 1.0000 eval: -0.7636 min: -0.7636 max: 2.2199 weight: 0.9865 eval: -0.7190 min: -0.7636 max: 2.2199 weight: 0.9497 eval: -0.5968 min: -0.7636 max: 2.2199 weight: 0.9374 eval: -0.5560 min: -0.7636 max: 2.2199 weight: 1.0000 eval: -0.7636 min: -0.7636 max: 2.2199 weight: 0.9902 eval: -0.7312 min: -0.7636 max: 2.2199 weight: 0.9842 eval: -0.7114 min: -0.7636 max: 2.2199 weight: 0.9775 eval: -0.6890 min: -0.7636 max: 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min: -0.7636 max: 2.2199 weight: 0.9916 eval: -0.7356 min: -0.7636 max: 2.2199 weight: 0.9828 eval: -0.7065 min: -0.7636 max: 2.2199 weight: 0.3883 eval: 1.2640 min: -0.7636 max: 2.2199 weight: 0.3869 eval: 1.2688 min: -0.7636 max: 2.2199 weight: 0.3869 eval: 1.2689 min: -0.7636 max: 2.2199 weight: 0.3894 eval: 1.2604 min: -0.7636 max: 2.2199 weight: 0.3859 eval: 1.2723 min: -0.7636 max: 2.2199 weight: 0.3896 eval: 1.2597 min: -0.7636 max: 2.2199 weight: 0.3892 eval: 1.2612 min: -0.7636 max: 2.2199 weight: 0.3895 eval: 1.2602 min: -0.7636 max: 2.2199 weight: 0.3883 eval: 1.2643 min: -0.7636 max: 2.2199 weight: 0.3882 eval: 1.2644 min: -0.7636 max: 2.2199 weight: 0.9767 eval: -0.6864 min: -0.7636 max: 2.2199 weight: 0.9718 eval: -0.6702 min: -0.7636 max: 2.2199 weight: 0.9924 eval: -0.7383 min: -0.7636 max: 2.2199 weight: 0.9850 eval: -0.7140 min: -0.7636 max: 2.2199 weight: 0.9855 eval: -0.7156 min: -0.7636 max: 2.2199 weight: 0.1731 eval: 1.9776 min: -0.7636 max: 2.2199 weight: 0.2323 eval: 1.7814 min: -0.7636 max: 2.2199 weight: 0.1892 eval: 1.9243 min: -0.7636 max: 2.2199 weight: 0.3580 eval: 1.3645 min: -0.7636 max: 2.2199 weight: 0.3149 eval: 1.5076 min: -0.7636 max: 2.2199 weight: 0.9892 eval: -0.7277 min: -0.7636 max: 2.2199 weight: 0.9543 eval: -0.6122 min: -0.7636 max: 2.2199 weight: 0.9901 eval: -0.7309 min: -0.7636 max: 2.2199 weight: 0.9789 eval: -0.6935 min: -0.7636 max: 2.2199 weight: 0.9873 eval: -0.7217 min: -0.7636 max: 2.2199 weight: 0.9752 eval: -0.6814 min: -0.7636 max: 2.2199 weight: 0.9752 eval: -0.6814 min: -0.7636 max: 2.2199 weight: 0.9648 eval: -0.6469 min: -0.7636 max: 2.2199 weight: 0.9569 eval: -0.6207 min: -0.7636 max: 2.2199 weight: 0.9480 eval: -0.5913 min: -0.7636 max: 2.2199 weight: 0.9891 eval: -0.7273 min: -0.7636 max: 2.2199 weight: 0.9891 eval: -0.7273 min: -0.7636 max: 2.2199 weight: 0.9522 eval: -0.6052 min: -0.7636 max: 2.2199 weight: 0.9660 eval: -0.6508 min: -0.7636 max: 2.2199 weight: 0.9875 eval: -0.7223 min: -0.7636 max: 2.2199 weight: 0.9782 eval: -0.6913 min: -0.7636 max: 2.2199 weight: 0.9852 eval: -0.7146 min: -0.7636 max: 2.2199 weight: 0.9893 eval: -0.7281 min: -0.7636 max: 2.2199 weight: 0.9896 eval: -0.7293 min: -0.7636 max: 2.2199 Adding 1373 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: -153.4331, CN propb: -153.4331 weights: 0.5544 constraints: 225 # command:Found ConstraintSet # PrintContacts align.constraints_meta02 Number of constraints in align2.constraints 225 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta02 Number of constraints in align2.constraints.bonus 225 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta02 Number of constraints in rejected2.constraints 1148 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta02 Number of constraints in rejected2.constraints.bonus 1148 # 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 1373 # command: