# 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/T0300/ # command:# Making conformation for sequence T0300 numbered 1 through 102 Created new target T0300 from T0300.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0300/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0300//projects/compbio/experiments/protein-predict/casp7/T0300/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0300//projects/compbio/experiments/protein-predict/casp7/T0300/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0300/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0300/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((T0300)V17.CB, (T0300)L60.CB) [> 3.4292 = 5.7153 < 7.4298] w=1.0000 to align # Constraint # added constraint: constraint((T0300)L44.CB, (T0300)I53.CB) [> 3.8918 = 6.4864 < 8.4323] w=0.8407 to align # Constraint # added constraint: constraint((T0300)I53.CB, (T0300)L88.CB) [> 3.7819 = 6.3031 < 8.1940] w=0.6483 to align # Constraint # added constraint: constraint((T0300)V31.CB, (T0300)S56.CB) [> 3.4218 = 5.7030 < 7.4139] w=0.6444 to align # Constraint # added constraint: constraint((T0300)S34.CB, (T0300)L44.CB) [> 3.5043 = 5.8406 < 7.5928] w=0.6196 to align # Constraint # added constraint: constraint((T0300)V31.CB, (T0300)S57.CB) [> 3.9125 = 6.5209 < 8.4772] w=0.6146 to align # Constraint # added constraint: constraint((T0300)Y10.CB, (T0300)S55.CB) [> 3.3816 = 5.6360 < 7.3268] w=0.5872 to align # Constraint # added constraint: constraint((T0300)Y10.CB, (T0300)S56.CB) [> 2.9580 = 4.9300 < 6.4090] w=0.5872 to align # Constraint # added constraint: constraint((T0300)Y10.CB, (T0300)A59.CB) [> 3.5831 = 5.9717 < 7.7633] w=0.5872 to align # Constraint # added constraint: constraint((T0300)M13.CB, (T0300)S56.CB) [> 3.2457 = 5.4095 < 7.0324] w=0.5872 to align # Constraint # added constraint: constraint((T0300)V14.CB, (T0300)L60.CB) [> 3.6590 = 6.0984 < 7.9279] w=0.5872 to align # Constraint # added constraint: constraint((T0300)M13.CB, (T0300)L60.CB) [> 4.4009 = 7.3348 < 9.5352] w=0.5571 to align # Constraint # added constraint: constraint((T0300)K30.CB, (T0300)S56.CB) [> 3.6936 = 6.1559 < 8.0027] w=0.5458 to align # Constraint # added constraint: constraint((T0300)L27.CB, (T0300)L60.CB) [> 3.6141 = 6.0235 < 7.8306] w=0.5318 to align # Constraint # added constraint: constraint((T0300)S34.CB, (T0300)R49.CB) [> 3.4049 = 5.6749 < 7.3773] w=0.5273 to align # Constraint # added constraint: constraint((T0300)S57.CB, (T0300)L92.CB) [> 3.7933 = 6.3221 < 8.2188] w=0.4983 to align # Constraint # added constraint: constraint((T0300)V54.CB, (T0300)L88.CB) [> 4.0618 = 6.7697 < 8.8006] w=0.4983 to align # Constraint # added constraint: constraint((T0300)N24.CB, (T0300)A46.CB) [> 3.9724 = 6.6206 < 8.6068] w=0.4846 to align # Constraint # added constraint: constraint((T0300)L27.CB, (T0300)V72.CB) [> 4.1893 = 6.9822 < 9.0768] w=0.4822 to align # Constraint # added constraint: constraint((T0300)N24.CB, (T0300)E50.CB) [> 4.0175 = 6.6958 < 8.7045] w=0.4663 to align # Constraint # added constraint: constraint((T0300)K28.CB, (T0300)L44.CB) [> 4.2191 = 7.0318 < 9.1413] w=0.4645 to align # Constraint # added constraint: constraint((T0300)L20.CB, (T0300)V63.CB) [> 3.6801 = 6.1335 < 7.9736] w=0.4633 to align # Constraint # added constraint: constraint((T0300)M13.CB, (T0300)L85.CB) [> 3.8173 = 6.3622 < 8.2708] w=0.4456 to align # Constraint # added constraint: constraint((T0300)S57.CB, (T0300)V96.CB) [> 3.2430 = 5.4050 < 7.0265] w=0.4429 to align # Constraint # added constraint: constraint((T0300)L60.CB, (T0300)L94.CB) [> 3.7368 = 6.2280 < 8.0964] w=0.4429 to align # Constraint # added constraint: constraint((T0300)G61.CA, (T0300)L94.CB) [> 3.6779 = 6.1298 < 7.9687] w=0.4429 to align # Constraint # added constraint: constraint((T0300)A64.CB, (T0300)L92.CB) [> 3.2273 = 5.3788 < 6.9925] w=0.4429 to align # Constraint # added constraint: constraint((T0300)A64.CB, (T0300)T93.CB) [> 4.3765 = 7.2942 < 9.4825] w=0.4429 to align # Constraint # added constraint: constraint((T0300)A64.CB, (T0300)L94.CB) [> 3.3956 = 5.6594 < 7.3572] w=0.4429 to align # Constraint # added constraint: constraint((T0300)K67.CB, (T0300)L92.CB) [> 3.9189 = 6.5316 < 8.4910] w=0.4429 to align # Constraint # added constraint: constraint((T0300)I68.CB, (T0300)L92.CB) [> 3.8580 = 6.4300 < 8.3590] w=0.4429 to align # Constraint # added constraint: constraint((T0300)M13.CB, (T0300)L92.CB) [> 4.1383 = 6.8972 < 8.9663] w=0.4131 to align # Constraint # added constraint: constraint((T0300)N24.CB, (T0300)I53.CB) [> 4.3712 = 7.2853 < 9.4710] w=0.4128 to align # Constraint # added constraint: constraint((T0300)V31.CB, (T0300)L44.CB) [> 4.2114 = 7.0190 < 9.1247] w=0.4030 to align # Constraint # added constraint: constraint((T0300)M13.CB, (T0300)I53.CB) [> 3.5888 = 5.9813 < 7.7758] w=0.4003 to align # Constraint # added constraint: constraint((T0300)K28.CB, (T0300)E50.CB) [> 4.3775 = 7.2958 < 9.4846] w=0.3833 to align # Constraint # added constraint: constraint((T0300)I53.CB, (T0300)V72.CB) [> 4.2354 = 7.0589 < 9.1766] w=0.3688 to align # Constraint # added constraint: constraint((T0300)V31.CB, (T0300)I53.CB) [> 3.5217 = 5.8696 < 7.6304] w=0.3682 to align # Constraint # added constraint: constraint((T0300)S34.CB, (T0300)I53.CB) [> 3.2863 = 5.4771 < 7.1203] w=0.3543 to align # Constraint # added constraint: constraint((T0300)V14.CB, (T0300)K28.CB) [> 3.7859 = 6.3098 < 8.2027] w=0.3477 to align # Constraint # added constraint: constraint((T0300)L20.CB, (T0300)K71.CB) [> 4.2965 = 7.1609 < 9.3091] w=0.3459 to align # Constraint # added constraint: constraint((T0300)R49.CB, (T0300)E84.CB) [> 3.1969 = 5.3281 < 6.9266] w=0.3439 to align # Constraint # added constraint: constraint((T0300)V31.CB, (T0300)V72.CB) [> 4.0732 = 6.7887 < 8.8253] w=0.3342 to align # Constraint # added constraint: constraint((T0300)A64.CB, (T0300)L88.CB) [> 3.1052 = 5.1753 < 6.7279] w=0.3305 to align # Constraint # added constraint: constraint((T0300)L27.CB, (T0300)L89.CB) [> 3.5589 = 5.9314 < 7.7109] w=0.3136 to align # Constraint # added constraint: constraint((T0300)A76.CB, (T0300)L89.CB) [> 3.5250 = 5.8749 < 7.6374] w=0.3074 to align # Constraint # added constraint: constraint((T0300)I53.CB, (T0300)A76.CB) [> 4.2365 = 7.0608 < 9.1791] w=0.3048 to align # Constraint # added constraint: constraint((T0300)I52.CB, (T0300)A76.CB) [> 3.9379 = 6.5632 < 8.5322] w=0.3029 to align # Constraint # added constraint: constraint((T0300)S55.CB, (T0300)K71.CB) [> 3.4044 = 5.6741 < 7.3763] w=0.2958 to align # Constraint # added constraint: constraint((T0300)M13.CB, (T0300)L88.CB) [> 3.6346 = 6.0577 < 7.8750] w=0.2956 to align # Constraint # added constraint: constraint((T0300)E23.CB, (T0300)K71.CB) [> 3.4920 = 5.8200 < 7.5661] w=0.2956 to align # Constraint # added constraint: constraint((T0300)K32.CB, (T0300)S56.CB) [> 4.1817 = 6.9696 < 9.0604] w=0.2762 to align # Constraint # added constraint: constraint((T0300)D41.CB, (T0300)I52.CB) [> 4.0779 = 6.7965 < 8.8354] w=0.2726 to align # Constraint # added constraint: constraint((T0300)N24.CB, (T0300)I52.CB) [> 2.9368 = 4.8947 < 6.3631] w=0.2652 to align # Constraint # added constraint: constraint((T0300)E23.CB, (T0300)A59.CB) [> 4.6255 = 7.7091 < 10.0219] w=0.2652 to align # Constraint # added constraint: constraint((T0300)M13.CB, (T0300)K67.CB) [> 3.1425 = 5.2375 < 6.8088] w=0.2652 to align # Constraint # added constraint: constraint((T0300)M13.CB, (T0300)A64.CB) [> 4.0022 = 6.6704 < 8.6715] w=0.2652 to align # Constraint # added constraint: constraint((T0300)M13.CB, (T0300)V63.CB) [> 4.1095 = 6.8492 < 8.9040] w=0.2652 to align # Constraint # added constraint: constraint((T0300)E12.CB, (T0300)K67.CB) [> 3.5236 = 5.8728 < 7.6346] w=0.2652 to align # Constraint # added constraint: constraint((T0300)I68.CB, (T0300)T93.CB) [> 4.6554 = 7.7590 < 10.0867] w=0.2652 to align # Constraint # added constraint: constraint((T0300)G61.CA, (T0300)V96.CB) [> 4.3971 = 7.3286 < 9.5271] w=0.2652 to align # Constraint # added constraint: constraint((T0300)L60.CB, (T0300)V96.CB) [> 3.9256 = 6.5427 < 8.5055] w=0.2652 to align # Constraint # added constraint: constraint((T0300)S57.CB, (T0300)V98.CB) [> 4.0120 = 6.6867 < 8.6928] w=0.2652 to align # Constraint # added constraint: constraint((T0300)V54.CB, (T0300)V98.CB) [> 3.9835 = 6.6391 < 8.6308] w=0.2652 to align # Constraint # added constraint: constraint((T0300)I53.CB, (T0300)V98.CB) [> 3.0963 = 5.1606 < 6.7087] w=0.2652 to align # Constraint # added constraint: constraint((T0300)E50.CB, (T0300)V98.CB) [> 4.5962 = 7.6603 < 9.9584] w=0.2652 to align # Constraint # added constraint: constraint((T0300)N24.CB, (T0300)S56.CB) [> 2.5821 = 4.3036 < 5.5947] w=0.2652 to align # Constraint # added constraint: constraint((T0300)N24.CB, (T0300)S55.CB) [> 2.9039 = 4.8398 < 6.2917] w=0.2652 to align # Constraint # added constraint: constraint((T0300)N24.CB, (T0300)T45.CB) [> 4.1286 = 6.8810 < 8.9453] w=0.2490 to align # Constraint # added constraint: constraint((T0300)L20.CB, (T0300)E82.CB) [> 3.7970 = 6.3283 < 8.2268] w=0.2479 to align # Constraint # added constraint: constraint((T0300)K21.CB, (T0300)V37.CB) [> 3.7720 = 6.2867 < 8.1727] w=0.2303 to align # Constraint # added constraint: constraint((T0300)Y10.CB, (T0300)K48.CB) [> 2.7223 = 4.5372 < 5.8984] w=0.2303 to align # Constraint # added constraint: constraint((T0300)A46.CB, (T0300)Q90.CB) [> 4.0068 = 6.6780 < 8.6814] w=0.2303 to align # Constraint # added constraint: constraint((T0300)V54.CB, (T0300)S91.CB) [> 2.1252 = 3.5421 < 4.6047] w=0.2303 to align # Constraint # added constraint: constraint((T0300)R58.CB, (T0300)T93.CB) [> 4.3849 = 7.3081 < 9.5006] w=0.2303 to align # Constraint # added constraint: constraint((T0300)L85.CB, (T0300)L94.CB) [> 3.4514 = 5.7523 < 7.4780] w=0.2303 to align # Constraint # added constraint: constraint((T0300)I52.CB, (T0300)V72.CB) [> 3.7421 = 6.2369 < 8.1079] w=0.2244 to align # Constraint # added constraint: constraint((T0300)V17.CB, (T0300)I68.CB) [> 4.0833 = 6.8056 < 8.8472] w=0.1982 to align # Constraint # added constraint: constraint((T0300)V17.CB, (T0300)V72.CB) [> 4.0727 = 6.7878 < 8.8241] w=0.1982 to align # Constraint # added constraint: constraint((T0300)N24.CB, (T0300)M65.CB) [> 3.8038 = 6.3397 < 8.2417] w=0.1982 to align # Constraint # added constraint: constraint((T0300)M13.CB, (T0300)A36.CB) [> 3.7789 = 6.2981 < 8.1876] w=0.1855 to align # Constraint # added constraint: constraint((T0300)V17.CB, (T0300)L27.CB) [> 4.4491 = 7.4152 < 9.6397] w=0.1855 to align # Constraint # added constraint: constraint((T0300)I43.CB, (T0300)I52.CB) [> 3.9487 = 6.5811 < 8.5555] w=0.1855 to align # Constraint # added constraint: constraint((T0300)I43.CB, (T0300)I53.CB) [> 3.4234 = 5.7057 < 7.4174] w=0.1855 to align # Constraint # added constraint: constraint((T0300)L44.CB, (T0300)V54.CB) [> 3.5455 = 5.9092 < 7.6819] w=0.1855 to align # Constraint # added constraint: constraint((T0300)G61.CA, (T0300)A76.CB) [> 3.6334 = 6.0557 < 7.8724] w=0.1855 to align # Constraint # added constraint: constraint((T0300)A64.CB, (T0300)A77.CB) [> 4.1078 = 6.8464 < 8.9003] w=0.1855 to align # Constraint # added constraint: constraint((T0300)V37.CB, (T0300)R49.CB) [> 3.8543 = 6.4239 < 8.3511] w=0.1820 to align # Constraint # added constraint: constraint((T0300)V37.CB, (T0300)V80.CB) [> 3.7672 = 6.2786 < 8.1622] w=0.1791 to align # Constraint # added constraint: constraint((T0300)A79.CB, (T0300)R95.CB) [> 3.9073 = 6.5122 < 8.4658] w=0.1791 to align # Constraint # added constraint: constraint((T0300)A79.CB, (T0300)V96.CB) [> 4.4776 = 7.4627 < 9.7015] w=0.1791 to align # Constraint # added constraint: constraint((T0300)L85.CB, (T0300)R95.CB) [> 2.8774 = 4.7956 < 6.2343] w=0.1791 to align # Constraint # added constraint: constraint((T0300)S57.CB, (T0300)L94.CB) [> 4.3813 = 7.3022 < 9.4929] w=0.1777 to align # Constraint # added constraint: constraint((T0300)M13.CB, (T0300)E50.CB) [> 3.2873 = 5.4789 < 7.1226] w=0.1700 to align # Constraint # added constraint: constraint((T0300)I68.CB, (T0300)L89.CB) [> 4.1934 = 6.9890 < 9.0856] w=0.1700 to align # Constraint # added constraint: constraint((T0300)V14.CB, (T0300)A46.CB) [> 4.4879 = 7.4798 < 9.7237] w=0.1660 to align # Constraint # added constraint: constraint((T0300)V31.CB, (T0300)L89.CB) [> 2.8090 = 4.6817 < 6.0862] w=0.1636 to align # Constraint # added constraint: constraint((T0300)M13.CB, (T0300)E23.CB) [> 3.4651 = 5.7752 < 7.5078] w=0.1636 to align # Constraint # added constraint: constraint((T0300)T26.CB, (T0300)L94.CB) [> 4.2754 = 7.1257 < 9.2635] w=0.1500 to align # Constraint # added constraint: constraint((T0300)M13.CB, (T0300)V80.CB) [> 4.3376 = 7.2294 < 9.3982] w=0.1500 to align # Constraint # added constraint: constraint((T0300)T86.CB, (T0300)V96.CB) [> 3.2796 = 5.4659 < 7.1057] w=0.1500 to align # Constraint # added constraint: constraint((T0300)S57.CB, (T0300)R73.CB) [> 3.7470 = 6.2449 < 8.1184] w=0.1500 to align # Constraint # added constraint: constraint((T0300)I52.CB, (T0300)S91.CB) [> 3.9922 = 6.6537 < 8.6499] w=0.1500 to align # Constraint # added constraint: constraint((T0300)K32.CB, (T0300)R73.CB) [> 4.5878 = 7.6464 < 9.9403] w=0.1500 to align # Constraint # added constraint: constraint((T0300)K30.CB, (T0300)L94.CB) [> 4.3085 = 7.1807 < 9.3350] w=0.1500 to align # Constraint # added constraint: constraint((T0300)L27.CB, (T0300)E69.CB) [> 4.0626 = 6.7710 < 8.8023] w=0.1480 to align # Constraint # added constraint: constraint((T0300)K21.CB, (T0300)V54.CB) [> 4.3453 = 7.2422 < 9.4149] w=0.1477 to align # Constraint # added constraint: constraint((T0300)S51.CB, (T0300)A76.CB) [> 3.4011 = 5.6686 < 7.3691] w=0.1458 to align # Constraint # added constraint: constraint((T0300)S51.CB, (T0300)R75.CB) [> 3.0492 = 5.0820 < 6.6066] w=0.1458 to align # Constraint # added constraint: constraint((T0300)S51.CB, (T0300)V72.CB) [> 4.6125 = 7.6874 < 9.9937] w=0.1458 to align # Constraint # added constraint: constraint((T0300)S51.CB, (T0300)K71.CB) [> 4.5592 = 7.5987 < 9.8783] w=0.1458 to align # Constraint # added constraint: constraint((T0300)E69.CB, (T0300)L85.CB) [> 4.2046 = 7.0077 < 9.1100] w=0.1458 to align # Constraint # added constraint: constraint((T0300)V37.CB, (T0300)I52.CB) [> 4.7810 = 7.9684 < 10.3589] w=0.1426 to align # Constraint # added constraint: constraint((T0300)A36.CB, (T0300)G61.CA) [> 3.9196 = 6.5327 < 8.4925] w=0.1228 to align # Constraint # added constraint: constraint((T0300)L85.CB, (T0300)D97.CB) [> 4.6879 = 7.8131 < 10.1570] w=0.1194 to align # Constraint # added constraint: constraint((T0300)V80.CB, (T0300)D97.CB) [> 3.0774 = 5.1290 < 6.6677] w=0.1194 to align # Constraint # added constraint: constraint((T0300)A79.CB, (T0300)D97.CB) [> 4.1710 = 6.9516 < 9.0371] w=0.1194 to align # Constraint # added constraint: constraint((T0300)L20.CB, (T0300)V96.CB) [> 4.6252 = 7.7087 < 10.0213] w=0.1000 to align # Constraint # added constraint: constraint((T0300)S42.CB, (T0300)S51.CB) [> 3.5864 = 5.9774 < 7.7706] w=0.0985 to align # Constraint # added constraint: constraint((T0300)S51.CB, (T0300)A79.CB) [> 4.6849 = 7.8081 < 10.1505] w=0.0545 to align # Constraint # added constraint: constraint((T0300)E16.CB, (T0300)V96.CB) [> 4.6095 = 7.6824 < 9.9872] w=0.0500 to align # Constraint # added constraint: constraint((T0300)K30.CB, (T0300)M65.CB) [> 2.7688 = 4.6147 < 5.9991] w=0.0493 to align # Constraint # added constraint: constraint((T0300)K30.CB, (T0300)I68.CB) [> 3.8631 = 6.4385 < 8.3700] w=0.0493 to align # Constraint # added constraint: constraint((T0300)S38.CB, (T0300)S51.CB) [> 3.5864 = 5.9774 < 7.7706] w=0.0492 to align # SetCost created cost = # ( 1.0000 * align ) # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0300/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0300/decoys/ # ReadConformPDB reading from PDB file georgesuggestion.renum.pdb.gz looking for model 1 # choosing archetypes in rotamer library # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file rotate5monomer.renum.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file rotate5monomerFixed2.renum.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file rotateFromTry2attempt1.renum.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file rotateFromTry2attempt2.renum.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file rotateFromTry3attempt1.renum.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file rotateFromTry3attempt2.renum.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file rotateFromTry3attempt3.fix.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file rotateFromTry3attempt3.renum.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file rotateNterm2FromTry3.renum.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ../dimer/decoys/dimer-rotate5.pdb.gz looking for chain 'A' model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # naming current conformation dimer//dimer-rotate5 # ReadConformPDB reading from PDB file ../dimer/decoys/dimer-rotate5fixed.pdb.gz looking for chain 'A' model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # naming current conformation dimer//dimer-rotate5fixed # ReadConformPDB reading from PDB file ../dimer/decoys/dimer-rotateNterm2.pdb.gz looking for chain 'A' model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # naming current conformation dimer//dimer-rotateNterm2 # ReadConformPDB reading from PDB file ../dimer/decoys/dimer.flipped180.renum.pdb.gz looking for chain 'A' model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # naming current conformation dimer//dimer.flipped180.renum # ReadConformPDB reading from PDB file ../dimer/decoys/dimer.rot5.renum.pdb.gz looking for chain 'A' model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # naming current conformation dimer//dimer.rot5.renum # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 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 T0300 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS1 # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # naming current conformation 3Dpro_TS1 # ReadConformPDB reading from PDB file servers/3Dpro_TS2.pdb.gz looking for model 1 # Found a chain break before 93 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS2 # ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1 # Found a chain break before 94 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS3 # ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1 # naming current conformation 3Dpro_TS4 # ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1 # naming current conformation 3Dpro_TS5 # ReadConformPDB reading from PDB file servers/ABIpro_TS1.pdb.gz looking for model 1 # Found a chain break before 93 # 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 94 # 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 92 # 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 96 # 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 93 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS5 # ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1 # Found a chain break before 67 # copying to AlignedFragments data structure # naming current conformation BayesHH_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS1.pdb.gz looking for model 1 # Found a chain break before 41 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS1 # ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1 # Found a chain break before 100 # 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 T0300 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 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 T0300 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS4 # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # Found a chain break before 93 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS5 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS2.pdb.gz looking for model 1 # Found a chain break before 10 # 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 T0300 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS3 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 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 T0300 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 T0300 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 T0300 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 T0300 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 T0300 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 T0300 can't currently be optimized by undertaker # naming current conformation Distill_TS5 # ReadConformPDB reading from PDB file servers/FAMSD_TS1.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS1 # ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 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 T0300 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 T0300 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 T0300 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 96 # 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 T0300 can't currently be optimized by undertaker # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 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 T0300 can't currently be optimized by undertaker # naming current conformation FAMS_TS4 # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # Found a chain break before 99 # copying to AlignedFragments data structure # naming current conformation FAMS_TS5 # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # naming current conformation FOLDpro_TS1 # ReadConformPDB reading from PDB file servers/FOLDpro_TS2.pdb.gz looking for model 1 # naming current conformation FOLDpro_TS2 # ReadConformPDB reading from PDB file servers/FOLDpro_TS3.pdb.gz looking for model 1 # naming current conformation FOLDpro_TS3 # ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1 # naming current conformation FOLDpro_TS4 # ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1 # naming current conformation FOLDpro_TS5 # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # naming current conformation FORTE1_AL1 # ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 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 T0300 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 T0300 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 T0300 can't currently be optimized by undertaker # naming current conformation FORTE1_AL5 # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # naming current conformation FORTE2_AL1 # ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 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 T0300 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 T0300 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 T0300 can't currently be optimized by undertaker # naming current conformation FORTE2_AL5 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS1.pdb.gz looking for model 1 # Found a chain break before 91 # 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 # naming current conformation FPSOLVER-SERVER_TS2 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS3.pdb.gz looking for model 1 # 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 100 # 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 94 # 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 # naming current conformation FUGMOD_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS2 # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS3 # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # naming current conformation FUGMOD_TS4 # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 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 T0300 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL1 # ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 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 T0300 can't currently be optimized by undertaker # naming current conformation FUGUE_AL3 # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 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 T0300 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 90 # 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 80 # 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 96 # 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 83 # 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 97 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # naming current conformation GeneSilicoMetaServer_TS1 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # naming current conformation GeneSilicoMetaServer_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # naming current conformation GeneSilicoMetaServer_TS3 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS4 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1 # Found a chain break before 78 # 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 30 # copying to AlignedFragments data structure # naming current conformation HHpred2_TS1 # ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1 # naming current conformation HHpred3_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS2 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS3 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS4 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS5 # ReadConformPDB reading from PDB file servers/LOOPP_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # naming current conformation LOOPP_TS1 # ReadConformPDB reading from PDB file servers/LOOPP_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # naming current conformation LOOPP_TS2 # ReadConformPDB reading from PDB file servers/LOOPP_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # naming current conformation LOOPP_TS3 # ReadConformPDB reading from PDB file servers/LOOPP_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # naming current conformation LOOPP_TS4 # ReadConformPDB reading from PDB file servers/LOOPP_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # naming current conformation LOOPP_TS5 # ReadConformPDB reading from PDB file servers/MIG_FROST_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # naming current conformation MIG_FROST_AL1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # naming current conformation Ma-OPUS-server_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS2.pdb.gz looking for model 1 # naming current conformation Ma-OPUS-server_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS3.pdb.gz looking for model 1 # 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 101 # 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 101 # 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 101 # 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 101 # 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 101 # 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 T0300 can't currently be optimized by undertaker # naming current conformation NN_PUT_lab_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS1.pdb.gz looking for model 1 # Found a chain break before 98 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS2.pdb.gz looking for model 1 # Found a chain break before 92 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS2 # ReadConformPDB reading from PDB file servers/POMYSL_TS3.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS3 # ReadConformPDB reading from PDB file servers/POMYSL_TS4.pdb.gz looking for model 1 # Found a chain break before 66 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS4 # ReadConformPDB reading from PDB file servers/POMYSL_TS5.pdb.gz looking for model 1 # Found a chain break before 99 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # naming current conformation PROTINFO-AB_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # Found a chain break before 82 # 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 # naming current conformation PROTINFO_TS5 # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # naming current conformation Pcons6_TS1 # ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1 # naming current conformation Pcons6_TS2 # ReadConformPDB reading from PDB file servers/Pcons6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # naming current conformation Pcons6_TS3 # ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # naming current conformation Pcons6_TS4 # ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1 # Found a chain break before 90 # copying to AlignedFragments data structure # naming current conformation Pcons6_TS5 # ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 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 T0300 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 T0300 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 # naming current conformation Phyre-2_TS3 # ReadConformPDB reading from PDB file servers/Phyre-2_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS4 # ReadConformPDB reading from PDB file servers/Phyre-2_TS5.pdb.gz looking for model 1 # Found a chain break before 97 # 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 # naming current conformation Pmodeller6_TS1 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 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 T0300 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS3 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # naming current conformation Pmodeller6_TS4 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1 # 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 # naming current conformation RAPTORESS_TS1 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS2.pdb.gz looking for model 1 # Found a chain break before 5 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS2 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS3.pdb.gz looking for model 1 # naming current conformation RAPTORESS_TS3 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS4.pdb.gz looking for model 1 # naming current conformation RAPTORESS_TS4 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS5.pdb.gz looking for model 1 # Found a chain break before 5 # 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 46 # 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 # 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 # 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 # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS1 # ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS2 # ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS3 # ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS4 # ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS5 # ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL1 # ReadConformPDB reading from PDB file servers/SAM-T02_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 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 T0300 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 T0300 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL4 # ReadConformPDB reading from PDB file servers/SAM-T02_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 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 T0300 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 T0300 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL2 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1 # Found a chain break before 100 # 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 T0300 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 T0300 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 T0300 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 T0300 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS5 # ReadConformPDB reading from PDB file servers/SP3_TS1.pdb.gz looking for model 1 # naming current conformation SP3_TS1 # ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1 # Found a chain break before 51 # copying to AlignedFragments data structure # naming current conformation SP3_TS2 # ReadConformPDB reading from PDB file servers/SP3_TS3.pdb.gz looking for model 1 # naming current conformation SP3_TS3 # ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1 # 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 51 # copying to AlignedFragments data structure # naming current conformation SP4_TS2 # ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1 # naming current conformation SP4_TS3 # ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1 # Found a chain break before 26 # copying to AlignedFragments data structure # naming current conformation SP4_TS4 # ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1 # Found a chain break before 23 # copying to AlignedFragments data structure # naming current conformation SP4_TS5 # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS1 # ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS2 # ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS3 # ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS4 # ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 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 T0300 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS3 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 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 T0300 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 T0300 can't currently be optimized by undertaker # naming current conformation UNI-EID_expm_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 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 T0300 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 T0300 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL4 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 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 95 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS1 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS2.pdb.gz looking for model 1 # Found a chain break before 93 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS2 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS3.pdb.gz looking for model 1 # Found a chain break before 99 # 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 92 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS4 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS5.pdb.gz looking for model 1 # Found a chain break before 91 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS5 # ReadConformPDB reading from PDB file servers/beautshot_TS1.pdb.gz looking for model 1 # Found a chain break before 101 # 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 T0300 can't currently be optimized by undertaker # naming current conformation beautshotbase_TS1 # ReadConformPDB reading from PDB file servers/forecast-s_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 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 T0300 can't currently be optimized by undertaker # naming current conformation forecast-s_AL2 # ReadConformPDB reading from PDB file servers/forecast-s_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 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 T0300 can't currently be optimized by undertaker # naming current conformation forecast-s_AL4 # ReadConformPDB reading from PDB file servers/forecast-s_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # naming current conformation forecast-s_AL5 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # 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 # Found a chain break before 18 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS4.pdb.gz looking for model 1 # Found a chain break before 82 # 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 # 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 99 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS2.pdb.gz looking for model 1 WARNING: atoms too close: (T0300)S3.O and (T0300)K4.N only 0 apart, marking (T0300)K4.N as missing WARNING: atoms too close: (T0300)L27.O and (T0300)K28.N only 0 apart, marking (T0300)K28.N as missing # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS3.pdb.gz looking for model 1 WARNING: atoms too close: (T0300)K30.O and (T0300)V31.N only 0 apart, marking (T0300)V31.N as missing WARNING: atoms too close: (T0300)E82.O and (T0300)Q83.N only 0 apart, marking (T0300)Q83.N as missing # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS4.pdb.gz looking for model 1 # Found a chain break before 99 # 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 99 # 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 T0300 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 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 T0300 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 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 94 # 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 94 # 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 # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # naming current conformation keasar-server_TS3 # ReadConformPDB reading from PDB file servers/keasar-server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # naming current conformation keasar-server_TS4 # ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # naming current conformation keasar-server_TS5 # ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # naming current conformation mGen-3D_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # naming current conformation nFOLD_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 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 T0300 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 T0300 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 T0300 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation nFOLD_TS5 # ReadConformPDB reading from PDB file servers/panther2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # naming current conformation panther2_TS1 # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0300 can't currently be optimized by undertaker # naming current conformation shub_TS1 # command:Using radius: 8.0000 Metaserver mode NUMB_ALIGNS: 258 model score 1.7480 model score 2.0326 model score 1.9603 model score 1.9662 model score 1.9325 model score 1.8870 model score 1.8203 model score 1.9616 model score 1.9616 model score 2.0364 model score 2.0326 model score 1.9603 model score 2.0364 model score 2.0364 model score 1.9603 model score 2.3275 model score 2.3275 model score 2.3275 model score 2.3275 model score 2.3275 model score 2.3275 model score 2.3275 model score 2.6873 model score 1.5394 model score 1.4044 model score 1.8600 model score 2.1434 model score 1.5394 model score 1.4044 model score 1.4308 model score 1.6501 model score 1.4009 model score 2.2109 model score 1.8838 model score 2.0451 model score 1.7599 model score 1.7792 model score 1.7540 model score 2.0575 model score 1.9555 model score 2.4835 model score 2.5222 model score 2.4499 model score 2.0394 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 2.0771 model score 1.7540 model score 1.4267 model score 1.3405 model score 1.3412 model score 1.6970 model score 1.7599 model score 1.7792 model score 1.7792 model score 1.5834 model score 2.6557 model score 2.0882 model score 2.8962 model score 2.3402 model score 2.6425 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.9259 model score 2.1103 model score 1.9034 model score 2.1640 model score 2.0740 model score 1.9619 model score 1.8590 model score 2.0021 model score 1.6541 model score 1.3059 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 2.0689 model score 3.0580 model score 1.6970 model score 2.2200 model score 1.6502 model score 2.4558 model score 1.8466 model score 2.3928 model score 1.9617 model score 2.7386 model score 2.2562 model score 1.9334 model score 2.9292 model score 1.7077 model score 1.7015 model score 1.4523 model score 1.4031 model score 1.5618 model score 1.9499 model score 1.7625 model score 1.3905 model score 1.3899 model score 1.8830 model score 1.2771 model score 1.8723 model score 1.8149 model score 2.0122 model score 2.2991 model score 2.2338 model score 1.1871 model score 1.2296 model score 1.3220 model score 1.2425 model score 1.5407 model score 1.9499 model score 2.2551 model score 1.7372 model score 1.7219 model score 1.5879 model score 2.3111 model score 1.6725 model score 1.6739 model score 1.5185 model score 1.4518 model score 2.1194 model score 1.6591 model score 1.9794 model score 1.9551 model score 1.6725 model score 1.6742 model score 1.9810 model score 1.5729 model score 1.8676 model score 2.7287 model score 2.4181 model score 1.8025 model score 1.4931 model score 1.9652 model score 1.8596 model score 1.8619 model score 1.5856 model score 1.5876 model score 1.6488 model score 2.9400 model score 1.5469 model score 2.2206 model score 1.7352 model score 1.4291 model score 1.6841 model score 2.4428 model score 2.4383 model score 1.3176 model score 1.6928 model score 1.5776 model score 2.4774 model score 1.7564 model score 1.2097 model score 1.7479 model score 2.3679 model score 1.4451 model score 1.7868 model score 1.8247 model score 1.5729 model score 1.8153 model score 1.4999 model score 1.7081 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.8356 model score 1.5716 model score 1.2905 model score 1.5485 model score 1.5015 model score 2.2303 model score 1.6441 model score 1.4476 model score 1.6826 model score 1.6841 model score 1.7683 model score 1.5900 model score 2.1464 model score 1.5371 model score 1.7632 model score 2.9266 model score 1.8112 model score 1.6559 model score 2.2303 model score 2.7311 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.8868 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.3175 model score 1.3410 model score 1.3131 model score 1.3450 model score 1.5888 model score 1.6099 model score 1.7464 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.7599 model score 1.9700 model score 2.1683 model score 1.8194 model score 2.5691 model score 3.0111 model score 2.2523 model score 2.3076 model score 1.9285 model score 1.8656 model score 1.7880 model score 1.5754 model score 1.5564 model score 1.6753 model score 1.9840 model score 1.8956 model score 1.9704 model score 2.3147 model score 2.2391 model score 2.1016 model score 1.4220 model score 1.8560 model score 2.1867 model score 2.3852 model score 2.1377 model score 1.9834 model score 1.2782 model score 2.0382 weight: 0.7302 eval: 1.7480 min: 1.1871 max: 3.0580 weight: 0.5933 eval: 2.0326 min: 1.1871 max: 3.0580 weight: 0.6281 eval: 1.9603 min: 1.1871 max: 3.0580 weight: 0.6252 eval: 1.9662 min: 1.1871 max: 3.0580 weight: 0.6414 eval: 1.9325 min: 1.1871 max: 3.0580 weight: 0.6633 eval: 1.8870 min: 1.1871 max: 3.0580 weight: 0.6954 eval: 1.8203 min: 1.1871 max: 3.0580 weight: 0.6274 eval: 1.9616 min: 1.1871 max: 3.0580 weight: 0.6274 eval: 1.9616 min: 1.1871 max: 3.0580 weight: 0.5914 eval: 2.0364 min: 1.1871 max: 3.0580 weight: 0.5933 eval: 2.0326 min: 1.1871 max: 3.0580 weight: 0.6281 eval: 1.9603 min: 1.1871 max: 3.0580 weight: 0.5914 eval: 2.0364 min: 1.1871 max: 3.0580 weight: 0.5914 eval: 2.0364 min: 1.1871 max: 3.0580 weight: 0.6280 eval: 1.9603 min: 1.1871 max: 3.0580 weight: 0.4514 eval: 2.3275 min: 1.1871 max: 3.0580 weight: 0.4514 eval: 2.3275 min: 1.1871 max: 3.0580 weight: 0.4514 eval: 2.3275 min: 1.1871 max: 3.0580 weight: 0.4514 eval: 2.3275 min: 1.1871 max: 3.0580 weight: 0.4514 eval: 2.3275 min: 1.1871 max: 3.0580 weight: 0.4514 eval: 2.3275 min: 1.1871 max: 3.0580 weight: 0.4514 eval: 2.3275 min: 1.1871 max: 3.0580 weight: 0.2783 eval: 2.6873 min: 1.1871 max: 3.0580 weight: 0.8305 eval: 1.5394 min: 1.1871 max: 3.0580 weight: 0.8955 eval: 1.4044 min: 1.1871 max: 3.0580 weight: 0.6763 eval: 1.8600 min: 1.1871 max: 3.0580 weight: 0.5400 eval: 2.1434 min: 1.1871 max: 3.0580 weight: 0.8305 eval: 1.5394 min: 1.1871 max: 3.0580 weight: 0.8955 eval: 1.4044 min: 1.1871 max: 3.0580 weight: 0.8828 eval: 1.4308 min: 1.1871 max: 3.0580 weight: 0.7773 eval: 1.6501 min: 1.1871 max: 3.0580 weight: 0.8971 eval: 1.4009 min: 1.1871 max: 3.0580 weight: 0.5075 eval: 2.2109 min: 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weight: 0.9567 eval: 1.2771 min: 1.1871 max: 3.0580 weight: 0.9567 eval: 1.2771 min: 1.1871 max: 3.0580 weight: 0.9567 eval: 1.2771 min: 1.1871 max: 3.0580 weight: 0.6446 eval: 1.9259 min: 1.1871 max: 3.0580 weight: 0.5559 eval: 2.1103 min: 1.1871 max: 3.0580 weight: 0.6554 eval: 1.9034 min: 1.1871 max: 3.0580 weight: 0.5301 eval: 2.1640 min: 1.1871 max: 3.0580 weight: 0.5733 eval: 2.0740 min: 1.1871 max: 3.0580 weight: 0.6273 eval: 1.9619 min: 1.1871 max: 3.0580 weight: 0.6768 eval: 1.8590 min: 1.1871 max: 3.0580 weight: 0.6079 eval: 2.0021 min: 1.1871 max: 3.0580 weight: 0.7754 eval: 1.6541 min: 1.1871 max: 3.0580 weight: 0.9429 eval: 1.3059 min: 1.1871 max: 3.0580 weight: 0.9567 eval: 1.2771 min: 1.1871 max: 3.0580 weight: 0.9567 eval: 1.2771 min: 1.1871 max: 3.0580 weight: 0.9567 eval: 1.2771 min: 1.1871 max: 3.0580 weight: 0.9567 eval: 1.2771 min: 1.1871 max: 3.0580 weight: 0.9567 eval: 1.2771 min: 1.1871 max: 3.0580 weight: 0.5758 eval: 2.0689 min: 1.1871 max: 3.0580 weight: 0.1000 eval: 3.0580 min: 1.1871 max: 3.0580 weight: 0.7547 eval: 1.6970 min: 1.1871 max: 3.0580 weight: 0.5031 eval: 2.2200 min: 1.1871 max: 3.0580 weight: 0.7772 eval: 1.6502 min: 1.1871 max: 3.0580 weight: 0.3897 eval: 2.4558 min: 1.1871 max: 3.0580 weight: 0.6828 eval: 1.8466 min: 1.1871 max: 3.0580 weight: 0.4200 eval: 2.3928 min: 1.1871 max: 3.0580 weight: 0.6274 eval: 1.9617 min: 1.1871 max: 3.0580 weight: 0.2537 eval: 2.7386 min: 1.1871 max: 3.0580 weight: 0.4857 eval: 2.2562 min: 1.1871 max: 3.0580 weight: 0.6410 eval: 1.9334 min: 1.1871 max: 3.0580 weight: 0.1620 eval: 2.9292 min: 1.1871 max: 3.0580 weight: 0.7496 eval: 1.7077 min: 1.1871 max: 3.0580 weight: 0.7525 eval: 1.7015 min: 1.1871 max: 3.0580 weight: 0.8724 eval: 1.4523 min: 1.1871 max: 3.0580 weight: 0.8961 eval: 1.4031 min: 1.1871 max: 3.0580 weight: 0.8198 eval: 1.5618 min: 1.1871 max: 3.0580 weight: 0.6330 eval: 1.9499 min: 1.1871 max: 3.0580 weight: 0.7232 eval: 1.7625 min: 1.1871 max: 3.0580 weight: 0.9021 eval: 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1.1871 max: 3.0580 weight: 0.7665 eval: 1.6725 min: 1.1871 max: 3.0580 weight: 0.7659 eval: 1.6739 min: 1.1871 max: 3.0580 weight: 0.8406 eval: 1.5185 min: 1.1871 max: 3.0580 weight: 0.8727 eval: 1.4518 min: 1.1871 max: 3.0580 weight: 0.5515 eval: 2.1194 min: 1.1871 max: 3.0580 weight: 0.7730 eval: 1.6591 min: 1.1871 max: 3.0580 weight: 0.6189 eval: 1.9794 min: 1.1871 max: 3.0580 weight: 0.6306 eval: 1.9551 min: 1.1871 max: 3.0580 weight: 0.7665 eval: 1.6725 min: 1.1871 max: 3.0580 weight: 0.7657 eval: 1.6742 min: 1.1871 max: 3.0580 weight: 0.6181 eval: 1.9810 min: 1.1871 max: 3.0580 weight: 0.8144 eval: 1.5729 min: 1.1871 max: 3.0580 weight: 0.6727 eval: 1.8676 min: 1.1871 max: 3.0580 weight: 0.2584 eval: 2.7287 min: 1.1871 max: 3.0580 weight: 0.4079 eval: 2.4181 min: 1.1871 max: 3.0580 weight: 0.7039 eval: 1.8025 min: 1.1871 max: 3.0580 weight: 0.8528 eval: 1.4931 min: 1.1871 max: 3.0580 weight: 0.6257 eval: 1.9652 min: 1.1871 max: 3.0580 weight: 0.6765 eval: 1.8596 min: 1.1871 max: 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weight: 0.4320 eval: 2.3679 min: 1.1871 max: 3.0580 weight: 0.8759 eval: 1.4451 min: 1.1871 max: 3.0580 weight: 0.7115 eval: 1.7868 min: 1.1871 max: 3.0580 weight: 0.6933 eval: 1.8247 min: 1.1871 max: 3.0580 weight: 0.8144 eval: 1.5729 min: 1.1871 max: 3.0580 weight: 0.6978 eval: 1.8153 min: 1.1871 max: 3.0580 weight: 0.8495 eval: 1.4999 min: 1.1871 max: 3.0580 weight: 0.7494 eval: 1.7081 min: 1.1871 max: 3.0580 weight: 0.9567 eval: 1.2771 min: 1.1871 max: 3.0580 weight: 0.9567 eval: 1.2771 min: 1.1871 max: 3.0580 weight: 0.9567 eval: 1.2771 min: 1.1871 max: 3.0580 weight: 0.9567 eval: 1.2771 min: 1.1871 max: 3.0580 weight: 0.9567 eval: 1.2771 min: 1.1871 max: 3.0580 weight: 0.9567 eval: 1.2771 min: 1.1871 max: 3.0580 weight: 0.9567 eval: 1.2771 min: 1.1871 max: 3.0580 weight: 0.9567 eval: 1.2771 min: 1.1871 max: 3.0580 weight: 0.9567 eval: 1.2771 min: 1.1871 max: 3.0580 weight: 0.9567 eval: 1.2771 min: 1.1871 max: 3.0580 weight: 0.9567 eval: 1.2771 min: 1.1871 max: 3.0580 weight: 0.9567 eval: 1.2771 min: 1.1871 max: 3.0580 weight: 0.6881 eval: 1.8356 min: 1.1871 max: 3.0580 weight: 0.8150 eval: 1.5716 min: 1.1871 max: 3.0580 weight: 0.9503 eval: 1.2905 min: 1.1871 max: 3.0580 weight: 0.8262 eval: 1.5485 min: 1.1871 max: 3.0580 weight: 0.8488 eval: 1.5015 min: 1.1871 max: 3.0580 weight: 0.4982 eval: 2.2303 min: 1.1871 max: 3.0580 weight: 0.7801 eval: 1.6441 min: 1.1871 max: 3.0580 weight: 0.8747 eval: 1.4476 min: 1.1871 max: 3.0580 weight: 0.7616 eval: 1.6826 min: 1.1871 max: 3.0580 weight: 0.7609 eval: 1.6841 min: 1.1871 max: 3.0580 weight: 0.7204 eval: 1.7683 min: 1.1871 max: 3.0580 weight: 0.8062 eval: 1.5900 min: 1.1871 max: 3.0580 weight: 0.5385 eval: 2.1464 min: 1.1871 max: 3.0580 weight: 0.8316 eval: 1.5371 min: 1.1871 max: 3.0580 weight: 0.7229 eval: 1.7632 min: 1.1871 max: 3.0580 weight: 0.1632 eval: 2.9266 min: 1.1871 max: 3.0580 weight: 0.6998 eval: 1.8112 min: 1.1871 max: 3.0580 weight: 0.7745 eval: 1.6559 min: 1.1871 max: 3.0580 weight: 0.4982 eval: 2.2303 min: 1.1871 max: 3.0580 weight: 0.2573 eval: 2.7311 min: 1.1871 max: 3.0580 weight: 0.9567 eval: 1.2771 min: 1.1871 max: 3.0580 weight: 0.9567 eval: 1.2771 min: 1.1871 max: 3.0580 weight: 0.9567 eval: 1.2771 min: 1.1871 max: 3.0580 weight: 0.9567 eval: 1.2771 min: 1.1871 max: 3.0580 weight: 0.9567 eval: 1.2771 min: 1.1871 max: 3.0580 weight: 0.6634 eval: 1.8868 min: 1.1871 max: 3.0580 weight: 0.9567 eval: 1.2771 min: 1.1871 max: 3.0580 weight: 0.9567 eval: 1.2771 min: 1.1871 max: 3.0580 weight: 0.9567 eval: 1.2771 min: 1.1871 max: 3.0580 weight: 0.9567 eval: 1.2771 min: 1.1871 max: 3.0580 weight: 0.9567 eval: 1.2771 min: 1.1871 max: 3.0580 weight: 0.9373 eval: 1.3175 min: 1.1871 max: 3.0580 weight: 0.9260 eval: 1.3410 min: 1.1871 max: 3.0580 weight: 0.9394 eval: 1.3131 min: 1.1871 max: 3.0580 weight: 0.9240 eval: 1.3450 min: 1.1871 max: 3.0580 weight: 0.8068 eval: 1.5888 min: 1.1871 max: 3.0580 weight: 0.7966 eval: 1.6099 min: 1.1871 max: 3.0580 weight: 0.7310 eval: 1.7464 min: 1.1871 max: 3.0580 weight: 0.9567 eval: 1.2771 min: 1.1871 max: 3.0580 weight: 0.9567 eval: 1.2771 min: 1.1871 max: 3.0580 weight: 0.9567 eval: 1.2771 min: 1.1871 max: 3.0580 weight: 0.9567 eval: 1.2771 min: 1.1871 max: 3.0580 weight: 0.9567 eval: 1.2771 min: 1.1871 max: 3.0580 weight: 0.7245 eval: 1.7599 min: 1.1871 max: 3.0580 weight: 0.6234 eval: 1.9700 min: 1.1871 max: 3.0580 weight: 0.5280 eval: 2.1683 min: 1.1871 max: 3.0580 weight: 0.6958 eval: 1.8194 min: 1.1871 max: 3.0580 weight: 0.3352 eval: 2.5691 min: 1.1871 max: 3.0580 weight: 0.1226 eval: 3.0111 min: 1.1871 max: 3.0580 weight: 0.4876 eval: 2.2523 min: 1.1871 max: 3.0580 weight: 0.4610 eval: 2.3076 min: 1.1871 max: 3.0580 weight: 0.6434 eval: 1.9285 min: 1.1871 max: 3.0580 weight: 0.6736 eval: 1.8656 min: 1.1871 max: 3.0580 weight: 0.7109 eval: 1.7880 min: 1.1871 max: 3.0580 weight: 0.8132 eval: 1.5754 min: 1.1871 max: 3.0580 weight: 0.8223 eval: 1.5564 min: 1.1871 max: 3.0580 weight: 0.7651 eval: 1.6753 min: 1.1871 max: 3.0580 weight: 0.6166 eval: 1.9840 min: 1.1871 max: 3.0580 weight: 0.6592 eval: 1.8956 min: 1.1871 max: 3.0580 weight: 0.6232 eval: 1.9704 min: 1.1871 max: 3.0580 weight: 0.4576 eval: 2.3147 min: 1.1871 max: 3.0580 weight: 0.4939 eval: 2.2391 min: 1.1871 max: 3.0580 weight: 0.5601 eval: 2.1016 min: 1.1871 max: 3.0580 weight: 0.8870 eval: 1.4220 min: 1.1871 max: 3.0580 weight: 0.6782 eval: 1.8560 min: 1.1871 max: 3.0580 weight: 0.5191 eval: 2.1867 min: 1.1871 max: 3.0580 weight: 0.4237 eval: 2.3852 min: 1.1871 max: 3.0580 weight: 0.5427 eval: 2.1377 min: 1.1871 max: 3.0580 weight: 0.6169 eval: 1.9834 min: 1.1871 max: 3.0580 weight: 0.9562 eval: 1.2782 min: 1.1871 max: 3.0580 weight: 0.5906 eval: 2.0382 min: 1.1871 max: 3.0580 Adding 3448 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: -177.1916, CN propb: -177.1916 weights: 0.2810 constraints: 218 # command:Found ConstraintSet # PrintContacts align.constraints_meta02 Number of constraints in align2.constraints 218 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta02 Number of constraints in align2.constraints.bonus 218 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta02 Number of constraints in rejected2.constraints 3230 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta02 Number of constraints in rejected2.constraints.bonus 3230 # 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 3448 # command: