/projects/compbio/experiments/protein-predict/casp7/starter-directory/Make.main:725: SECONDARY_TARGET = T0316.t06.str2 mkdir -p decoys rm decoys/read-pdb+servers.under cd decoys; shopt -s nullglob ; for x in ../*.ts-submitted* ; do echo ReadConformPDB $x >> read-pdb+servers.under ; done cd decoys; shopt -s nullglob ; for x in *.pdb* ; do echo ReadConformPDB $x >> read-pdb+servers.under ; done cd decoys; shopt -s nullglob ; for x in ../*mer/decoys/*.pdb* ; \ do echo ReadConformPDB $x chain A >> read-pdb+servers.under ; \ y=${x#../} ;\ z=${y/decoys} ;\ a=${z/T0316.} ;\ b=${a%.gz} ;\ c=${b%.pdb} ;\ echo NameConform $c >> read-pdb+servers.under ; \ done cd decoys; shopt -s nullglob ; for x in servers/*.pdb.gz ; do \ echo ReadConformPDB $x >> read-pdb+servers.under ; \ y=${x%.pdb.gz} ; \ z=${y#servers/} ; \ echo NameConform $z >> read-pdb+servers.under ; \ echo SCWRLConform >> read-pdb+servers.under ; \ echo NameConform $z-scwrl >> read-pdb+servers.under ; \ done chgrp protein decoys/read-pdb+servers.under chmod g+w decoys/read-pdb+servers.under rm -f decoys/evaluate.rdb sed -e s/XXX0000/T0316/ -e s/START_COL/1/ \ -e s/REAL_PDB/2hmaA/ \ -e s/_domain// \ -e s/read-pdb/read-pdb+servers/ \ -e 's/include COSTFCN.costfcn//' \ -e s/.COSTFCN// \ < /projects/compbio/experiments/protein-predict/casp7/starter-directory/evaluate.under \ | nice -2 /projects/compbio/programs/undertaker/undertaker # command:# Seed set to 1174993278 # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading monomeric-50pc.atoms # trans (non-proline) backbone unit: # CA= -2.2088 1.0126 -0.0031 # O= -0.1499 2.2440 0.0017 # 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= -0.1462 2.4515 0.0018 # O= -2.0272 0.9713 0.0022 # C= -0.8006 1.0755 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4659 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2099 1.0634 -0.0014 # O= -0.1233 2.2459 0.0075 # C= -0.6871 1.1518 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading monomeric-50pc.atoms have 448 chains in training database # Count of chains,residues,atoms: 448,112605,876684 # 109826 residues have no bad marker # 665 residues lack atoms needed to compute omega # 322 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 6 # HAS_OXT 325 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 523 # HAS_UNKNOWN_ATOMS 2 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 208 # NON_PLANAR_PEPTIDE 143 # BAD_PEPTIDE 1959 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-1332.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:CPU_time= 4.6113 sec, elapsed time= 4.68009 sec) # command:# Reading spots from monomeric-50pc-dry-5.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-5.hist # created burial cost function dry5 with radius 5 with spots at monomeric-50pc-dry-5.spot # command:# Reading spots from monomeric-50pc-wet-6.5.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-wet-6.5.hist # created burial cost function wet6.5 with radius 6.5 with spots at monomeric-50pc-wet-6.5.spot # command:# Reading spots from monomeric-50pc-dry-6.5.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-6.5.hist # created burial cost function dry6.5 with radius 6.5 with spots at monomeric-50pc-dry-6.5.spot # command:# Reading spots from monomeric-50pc-generic-6.5.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-generic-6.5.hist # created burial cost function gen6.5 with radius 6.5 with spots at monomeric-50pc-generic-6.5.spot # command:# Reading spots from near-backbone-center.spot # reading histogram from smoothed-near-backbone-2spot.hist # Reading spots from near-backbone-count.spot # created burial cost function near_backbone with radius 9.65 with spots at near-backbone-center.spot counting only near-backbone-count.spot # command:# Reading spots from way-back-center.spot # reading histogram from smoothed-way-back-2spot.hist # Reading spots from way-back-count.spot # created burial cost function way_back with radius 8.9 with spots at way-back-center.spot counting only way-back-count.spot # command:# Reading spots from monomeric-50pc-dry-8.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-8.hist # created burial cost function dry8 with radius 8 with spots at monomeric-50pc-dry-8.spot # command:# Reading spots from monomeric-50pc-dry-10.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-10.hist # created burial cost function dry10 with radius 10 with spots at monomeric-50pc-dry-10.spot # command:# Reading spots from monomeric-50pc-dry-12.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-12.hist # created burial cost function dry12 with radius 12 with spots at monomeric-50pc-dry-12.spot # command:# reading histogram from dunbrack-2191-alpha.hist # created alpha cost function alpha with offset 0 and 360 bins # command:# reading histogram from dunbrack-2191-alpha-1.hist # created alpha cost function alpha_prev with offset -1 and 360 bins # command:# Prefix for input files set to /projects/compbio/lib/alphabet/ # command:# Read 3 alphabets from alpha.alphabet # command:CPU_time= 4.67429 sec, elapsed time= 4.76331 sec) # command:# Prefix for input files set to # command:# Making conformation for sequence T0316 numbered 1 through 373 Created new target T0316 from T0316.a2m # command:# command:# No conformations to remove in PopConform # command:# cleared Id set # command:# command:2hmaA expands to /projects/compbio/data/pdb/2hma.pdb.gz 2hmaA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 358, because occupancy 3.0000000e-01 <= existing 0.700 in 2hmaA Skipped atom 360, because occupancy 0.300 <= existing 0.700 in 2hmaA Skipped atom 362, because occupancy 0.300 <= existing 0.700 in 2hmaA Skipped atom 364, because occupancy 0.300 <= existing 0.700 in 2hmaA Skipped atom 366, because occupancy 0.300 <= existing 0.700 in 2hmaA Skipped atom 368, because occupancy 0.300 <= existing 0.700 in 2hmaA Skipped atom 370, because occupancy 0.300 <= existing 0.700 in 2hmaA Skipped atom 372, because occupancy 0.300 <= existing 0.700 in 2hmaA Skipped atom 374, because occupancy 0.300 <= existing 0.700 in 2hmaA Skipped atom 396, because occupancy 0.300 <= existing 0.700 in 2hmaA Skipped atom 398, because occupancy 0.300 <= existing 0.700 in 2hmaA Skipped atom 400, because occupancy 0.300 <= existing 0.700 in 2hmaA Skipped atom 402, because occupancy 0.300 <= existing 0.700 in 2hmaA Skipped atom 404, because occupancy 0.300 <= existing 0.700 in 2hmaA Skipped atom 406, because occupancy 0.300 <= existing 0.700 in 2hmaA Skipped atom 408, because occupancy 0.300 <= existing 0.700 in 2hmaA Skipped atom 410, because occupancy 0.300 <= existing 0.700 in 2hmaA Skipped atom 412, because occupancy 0.300 <= existing 0.700 in 2hmaA Skipped atom 461, because occupancy 0.400 <= existing 0.600 in 2hmaA Skipped atom 463, because occupancy 0.400 <= existing 0.600 in 2hmaA Skipped atom 465, because occupancy 0.400 <= existing 0.600 in 2hmaA Skipped atom 467, because occupancy 0.400 <= existing 0.600 in 2hmaA Skipped atom 469, because occupancy 0.400 <= existing 0.600 in 2hmaA Skipped atom 471, because occupancy 0.400 <= existing 0.600 in 2hmaA Skipped atom 473, because occupancy 0.400 <= existing 0.600 in 2hmaA Skipped atom 475, because occupancy 0.400 <= existing 0.600 in 2hmaA Skipped atom 477, because occupancy 0.400 <= existing 0.600 in 2hmaA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1044, because occupancy 0.400 <= existing 0.600 in 2hmaA Skipped atom 1046, because occupancy 0.400 <= existing 0.600 in 2hmaA Skipped atom 1048, because occupancy 0.400 <= existing 0.600 in 2hmaA Skipped atom 1050, because occupancy 0.400 <= existing 0.600 in 2hmaA Skipped atom 1052, because occupancy 0.400 <= existing 0.600 in 2hmaA Skipped atom 1054, because occupancy 0.400 <= existing 0.600 in 2hmaA Skipped atom 1056, because occupancy 0.400 <= existing 0.600 in 2hmaA Skipped atom 1058, because occupancy 0.400 <= existing 0.600 in 2hmaA Skipped atom 1060, because occupancy 0.400 <= existing 0.600 in 2hmaA Skipped atom 1062, because occupancy 0.400 <= existing 0.600 in 2hmaA Skipped atom 1064, because occupancy 0.400 <= existing 0.600 in 2hmaA Skipped atom 1109, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 1111, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 1113, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 1115, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 1117, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 1119, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 1121, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 1123, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 1125, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 1127, because occupancy 0.500 <= existing 0.500 in 2hmaA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1175, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 1177, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 1179, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 1181, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 1183, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 1185, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 1187, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 1189, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 1195, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 1197, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 1199, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 1201, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 1203, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 1205, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 1207, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 1209, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 1211, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 1306, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 1308, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 1310, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 1312, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 1314, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 1316, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 1318, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 1320, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 1322, because occupancy 0.500 <= existing 0.500 in 2hmaA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1463, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 1465, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 1467, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 1469, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 1471, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 1473, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 1475, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 1477, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 1479, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 1481, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 1483, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 1651, because occupancy 0.200 <= existing 0.200 in 2hmaA Skipped atom 1653, because occupancy 0.300 <= existing 0.300 in 2hmaA Skipped atom 1655, because occupancy 0.200 <= existing 0.200 in 2hmaA Skipped atom 1657, because occupancy 0.300 <= existing 0.300 in 2hmaA Skipped atom 1659, because occupancy 0.200 <= existing 0.200 in 2hmaA Skipped atom 1661, because occupancy 0.300 <= existing 0.300 in 2hmaA Skipped atom 1663, because occupancy 0.200 <= existing 0.200 in 2hmaA Skipped atom 1665, because occupancy 0.300 <= existing 0.300 in 2hmaA Skipped atom 1667, because occupancy 0.200 <= existing 0.200 in 2hmaA Skipped atom 1669, because occupancy 0.300 <= existing 0.300 in 2hmaA Skipped atom 1671, because occupancy 0.200 <= existing 0.200 in 2hmaA Skipped atom 1673, because occupancy 0.300 <= existing 0.300 in 2hmaA Skipped atom 1675, because occupancy 0.200 <= existing 0.200 in 2hmaA Skipped atom 1677, because occupancy 0.300 <= existing 0.300 in 2hmaA Skipped atom 1679, because occupancy 0.200 <= existing 0.200 in 2hmaA Skipped atom 1681, because occupancy 0.300 <= existing 0.300 in 2hmaA Skipped atom 1683, because occupancy 0.200 <= existing 0.200 in 2hmaA Skipped atom 1685, because occupancy 0.300 <= existing 0.300 in 2hmaA Skipped atom 1757, because occupancy 0.400 <= existing 0.600 in 2hmaA Skipped atom 1759, because occupancy 0.400 <= existing 0.600 in 2hmaA Skipped atom 1761, because occupancy 0.400 <= existing 0.600 in 2hmaA Skipped atom 1763, because occupancy 0.400 <= existing 0.600 in 2hmaA Skipped atom 1765, because occupancy 0.400 <= existing 0.600 in 2hmaA Skipped atom 1767, because occupancy 0.400 <= existing 0.600 in 2hmaA Skipped atom 1769, because occupancy 0.400 <= existing 0.600 in 2hmaA Skipped atom 1771, because occupancy 0.400 <= existing 0.600 in 2hmaA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1878, because occupancy 0.400 <= existing 0.600 in 2hmaA Skipped atom 1880, because occupancy 0.400 <= existing 0.600 in 2hmaA Skipped atom 1882, because occupancy 0.400 <= existing 0.600 in 2hmaA Skipped atom 1884, because occupancy 0.400 <= existing 0.600 in 2hmaA Skipped atom 1886, because occupancy 0.400 <= existing 0.600 in 2hmaA Skipped atom 1888, because occupancy 0.400 <= existing 0.600 in 2hmaA Skipped atom 1890, because occupancy 0.400 <= existing 0.600 in 2hmaA Skipped atom 1892, because occupancy 0.400 <= existing 0.600 in 2hmaA Skipped atom 1894, because occupancy 0.400 <= existing 0.600 in 2hmaA Skipped atom 1896, because occupancy 0.400 <= existing 0.600 in 2hmaA Skipped atom 1898, because occupancy 0.400 <= existing 0.600 in 2hmaA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1956, because occupancy 0.500 <= existing 0.500 in 2hmaA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1958, because occupancy 0.500 <= existing 0.500 in 2hmaA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1960, because occupancy 0.500 <= existing 0.500 in 2hmaA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1962, because occupancy 0.500 <= existing 0.500 in 2hmaA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1964, because occupancy 0.500 <= existing 0.500 in 2hmaA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1966, because occupancy 0.500 <= existing 0.500 in 2hmaA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1970, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 2275, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 2277, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 2279, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 2281, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 2283, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 2285, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 2287, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 2289, because occupancy 0.500 <= existing 0.500 in 2hmaA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2354, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 2356, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 2358, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 2360, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 2362, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 2364, because occupancy 0.500 <= existing 0.500 in 2hmaA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2559, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 2561, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 2563, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 2565, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 2567, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 2569, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 2571, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 2573, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 2575, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 2577, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 2579, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 2671, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 2673, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 2675, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 2677, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 2679, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 2681, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 2683, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 2685, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 2687, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 2745, because occupancy 0.400 <= existing 0.600 in 2hmaA Skipped atom 2747, because occupancy 0.400 <= existing 0.600 in 2hmaA Skipped atom 2749, because occupancy 0.400 <= existing 0.600 in 2hmaA Skipped atom 2751, because occupancy 0.400 <= existing 0.600 in 2hmaA Skipped atom 2753, because occupancy 0.400 <= existing 0.600 in 2hmaA Skipped atom 2755, because occupancy 0.400 <= existing 0.600 in 2hmaA Skipped atom 2757, because occupancy 0.400 <= existing 0.600 in 2hmaA Skipped atom 2759, because occupancy 0.400 <= existing 0.600 in 2hmaA Skipped atom 2761, because occupancy 0.400 <= existing 0.600 in 2hmaA Skipped atom 2977, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 2979, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 2981, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 2983, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 2985, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 2987, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 2989, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 2991, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 2993, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 2995, because occupancy 0.500 <= existing 0.500 in 2hmaA Skipped atom 2997, because occupancy 0.500 <= existing 0.500 in 2hmaA Read 364 residues and 2867 atoms. # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # command:# Saving current conformation as real # command:# Prefix for output files set to decoys/ # command:# SetRealCost created real_cost = # ( 50 * real_hbond + 50 * real_hbond_u + 50 * decoy_hbond + 50 * decoy_hbond_u + 10 * real_NO_hbond + 10 * real_NO_hbond_u + 10 * decoy_NO_hbond + 10 * decoy_NO_hbond_u + 10 * knot + 200 * clens + 0 * rmsd + 35 * log_rmsd + 0 * rmsd_ca + 30 * log_rmsd_ca + 1 * GDT + 1 * smooth_GDT + 0.2 * missing_atoms ) # command:# SetCost created cost = # ) # command:CPU_time= 6.60999 sec, elapsed time= 6.7534 sec) # command:# Prefix for input files set to # command:# ReadConformPDB reading from PDB file model1.ts-submitted looking for model 1 # choosing archetypes in rotamer library # Found a chain break before 371 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -20.8104 # GDT_score(maxd=8,maxw=2.9)= -20.7943 # GDT_score(maxd=8,maxw=3.2)= -19.6681 # GDT_score(maxd=8,maxw=3.5)= -18.6783 # GDT_score(maxd=10,maxw=3.8)= -20.2315 # GDT_score(maxd=10,maxw=4)= -19.5874 # GDT_score(maxd=10,maxw=4.2)= -18.9582 # GDT_score(maxd=12,maxw=4.3)= -20.7541 # GDT_score(maxd=12,maxw=4.5)= -20.1082 # GDT_score(maxd=12,maxw=4.7)= -19.5007 # GDT_score(maxd=14,maxw=5.2)= -19.7836 # GDT_score(maxd=14,maxw=5.5)= -18.9277 # command:# Prefix for output files set to # command:superimposing iter= 0 total_weight= 4323.000 rmsd (weighted)= 22.746 (unweighted)= 25.865 superimposing iter= 1 total_weight= 5555.537 rmsd (weighted)= 16.037 (unweighted)= 25.848 superimposing iter= 2 total_weight= 3575.248 rmsd (weighted)= 14.147 (unweighted)= 26.030 superimposing iter= 3 total_weight= 3307.666 rmsd (weighted)= 13.030 (unweighted)= 26.264 superimposing iter= 4 total_weight= 3148.302 rmsd (weighted)= 12.330 (unweighted)= 26.490 superimposing iter= 5 total_weight= 3037.636 rmsd (weighted)= 11.889 (unweighted)= 26.689 # command:# Prefix for output files set to decoys/ # command:# request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_52666743.pdb -s /var/tmp/to_scwrl_52666743.seq -o /var/tmp/from_scwrl_52666743.pdb > /var/tmp/scwrl_52666743.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_52666743.pdb # conformation set from SCWRL output # command:# naming current conformation model1-scwrl # command:# ReadConformPDB reading from PDB file model2.ts-submitted looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -20.6731 # GDT_score(maxd=8,maxw=2.9)= -20.4504 # GDT_score(maxd=8,maxw=3.2)= -19.3559 # GDT_score(maxd=8,maxw=3.5)= -18.3772 # GDT_score(maxd=10,maxw=3.8)= -20.0414 # GDT_score(maxd=10,maxw=4)= -19.407 # GDT_score(maxd=10,maxw=4.2)= -18.7891 # GDT_score(maxd=12,maxw=4.3)= -20.6488 # GDT_score(maxd=12,maxw=4.5)= -20.0102 # GDT_score(maxd=12,maxw=4.7)= -19.4052 # GDT_score(maxd=14,maxw=5.2)= -19.761 # GDT_score(maxd=14,maxw=5.5)= -18.908 # command:# request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1969878689.pdb -s /var/tmp/to_scwrl_1969878689.seq -o /var/tmp/from_scwrl_1969878689.pdb > /var/tmp/scwrl_1969878689.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1969878689.pdb # conformation set from SCWRL output # command:# naming current conformation model2-scwrl # command:# ReadConformPDB reading from PDB file model3.ts-submitted looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -17.4451 # GDT_score(maxd=8,maxw=2.9)= -17.1214 # GDT_score(maxd=8,maxw=3.2)= -16.1585 # GDT_score(maxd=8,maxw=3.5)= -15.2451 # GDT_score(maxd=10,maxw=3.8)= -16.7574 # GDT_score(maxd=10,maxw=4)= -16.1532 # GDT_score(maxd=10,maxw=4.2)= -15.5654 # GDT_score(maxd=12,maxw=4.3)= -17.4546 # GDT_score(maxd=12,maxw=4.5)= -16.8438 # GDT_score(maxd=12,maxw=4.7)= -16.279 # GDT_score(maxd=14,maxw=5.2)= -16.8622 # GDT_score(maxd=14,maxw=5.5)= -16.1 # command:# request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_64191715.pdb -s /var/tmp/to_scwrl_64191715.seq -o /var/tmp/from_scwrl_64191715.pdb > /var/tmp/scwrl_64191715.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_64191715.pdb # conformation set from SCWRL output # command:# naming current conformation model3-scwrl # command:# ReadConformPDB reading from PDB file model4.ts-submitted looking for model 1 # Found a chain break before 355 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -28.7775 # GDT_score(maxd=8,maxw=2.9)= -28.8903 # GDT_score(maxd=8,maxw=3.2)= -27.0764 # GDT_score(maxd=8,maxw=3.5)= -25.4539 # GDT_score(maxd=10,maxw=3.8)= -27.7827 # GDT_score(maxd=10,maxw=4)= -26.7563 # GDT_score(maxd=10,maxw=4.2)= -25.7787 # GDT_score(maxd=12,maxw=4.3)= -28.3056 # GDT_score(maxd=12,maxw=4.5)= -27.3148 # GDT_score(maxd=12,maxw=4.7)= -26.3755 # GDT_score(maxd=14,maxw=5.2)= -26.7176 # GDT_score(maxd=14,maxw=5.5)= -25.4694 # command:# request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_129028694.pdb -s /var/tmp/to_scwrl_129028694.seq -o /var/tmp/from_scwrl_129028694.pdb > /var/tmp/scwrl_129028694.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_129028694.pdb # conformation set from SCWRL output # command:# naming current conformation model4-scwrl # command:# ReadConformPDB reading from PDB file model5.ts-submitted looking for model 1 # Found a chain break before 355 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -26.3736 # GDT_score(maxd=8,maxw=2.9)= -26.1572 # GDT_score(maxd=8,maxw=3.2)= -24.806 # GDT_score(maxd=8,maxw=3.5)= -23.5301 # GDT_score(maxd=10,maxw=3.8)= -25.2168 # GDT_score(maxd=10,maxw=4)= -24.398 # GDT_score(maxd=10,maxw=4.2)= -23.5861 # GDT_score(maxd=12,maxw=4.3)= -25.5673 # GDT_score(maxd=12,maxw=4.5)= -24.7448 # GDT_score(maxd=12,maxw=4.7)= -23.9396 # GDT_score(maxd=14,maxw=5.2)= -24.1119 # GDT_score(maxd=14,maxw=5.5)= -23.0054 # command:# request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1986605717.pdb -s /var/tmp/to_scwrl_1986605717.seq -o /var/tmp/from_scwrl_1986605717.pdb > /var/tmp/scwrl_1986605717.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1986605717.pdb # conformation set from SCWRL output # command:# naming current conformation model5-scwrl # command:# Prefix for input files set to decoys/ # command:# ReadConformPDB reading from PDB file T0316.try1-opt2.pdb looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -20.3984 # GDT_score(maxd=8,maxw=2.9)= -20.5014 # GDT_score(maxd=8,maxw=3.2)= -19.4647 # GDT_score(maxd=8,maxw=3.5)= -18.3937 # GDT_score(maxd=10,maxw=3.8)= -19.823 # GDT_score(maxd=10,maxw=4)= -19.1237 # GDT_score(maxd=10,maxw=4.2)= -18.4688 # GDT_score(maxd=12,maxw=4.3)= -20.1734 # GDT_score(maxd=12,maxw=4.5)= -19.5125 # GDT_score(maxd=12,maxw=4.7)= -18.8861 # GDT_score(maxd=14,maxw=5.2)= -19.0994 # GDT_score(maxd=14,maxw=5.5)= -18.2304 # command:# Prefix for output files set to # command:superimposing iter= 0 total_weight= 4323.000 rmsd (weighted)= 22.057 (unweighted)= 25.829 superimposing iter= 1 total_weight= 7632.469 rmsd (weighted)= 12.876 (unweighted)= 26.024 superimposing iter= 2 total_weight= 4490.730 rmsd (weighted)= 10.025 (unweighted)= 26.351 superimposing iter= 3 total_weight= 3663.614 rmsd (weighted)= 8.658 (unweighted)= 26.871 superimposing iter= 4 total_weight= 3531.675 rmsd (weighted)= 7.586 (unweighted)= 27.692 superimposing iter= 5 total_weight= 3680.770 rmsd (weighted)= 6.514 (unweighted)= 28.579 # command:# Prefix for output files set to decoys/ # command:# Prefix for input files set to # command:# ReadConformPDB reading from PDB file T0316.undertaker-align.pdb looking for model 1 WARNING: atoms too close: (T0316)M38.C and (T0316)D45.C only 0.000 apart, marking (T0316)D45.C as missing WARNING: atoms too close: (T0316)K39.N and (T0316)E46.N only 0.000 apart, marking (T0316)K39.N as missing WARNING: atoms too close: (T0316)K39.CA and (T0316)E46.CA only 0.000 apart, marking (T0316)K39.CA as missing WARNING: atoms too close: (T0316)G48.C and (T0316)T51.C only 0.000 apart, marking (T0316)T51.C as missing WARNING: atoms too close: (T0316)V49.N and (T0316)A52.N only 0.000 apart, marking (T0316)V49.N as missing WARNING: atoms too close: (T0316)V49.CA and (T0316)A52.CA only 0.000 apart, marking (T0316)V49.CA as missing WARNING: atoms too close: (T0316)I107.C and (T0316)K108.C only 0.000 apart, marking (T0316)K108.C as missing WARNING: atoms too close: (T0316)K108.N and (T0316)F109.N only 0.000 apart, marking (T0316)K108.N as missing WARNING: atoms too close: (T0316)K108.CA and (T0316)F109.CA only 0.000 apart, marking (T0316)K108.CA as missing WARNING: atoms too close: (T0316)A130.C and (T0316)A133.C only 0.000 apart, marking (T0316)A133.C as missing WARNING: atoms too close: (T0316)R131.N and (T0316)R134.N only 0.000 apart, marking (T0316)R131.N as missing WARNING: atoms too close: (T0316)R131.CA and (T0316)R134.CA only 0.000 apart, marking (T0316)R131.CA as missing WARNING: atoms too close: (T0316)V146.C and (T0316)N148.C only 0.000 apart, marking (T0316)N148.C as missing WARNING: atoms too close: (T0316)D147.N and (T0316)G149.N only 0.000 apart, marking (T0316)D147.N as missing WARNING: atoms too close: (T0316)D147.CA and (T0316)G149.CA only 0.000 apart, marking (T0316)D147.CA as missing WARNING: atoms too close: (T0316)G250.C and (T0316)A258.C only 0.000 apart, marking (T0316)A258.C as missing WARNING: atoms too close: (T0316)G251.N and (T0316)P259.N only 0.000 apart, marking (T0316)G251.N as missing WARNING: atoms too close: (T0316)G251.CA and (T0316)P259.CA only 0.000 apart, marking (T0316)G251.CA as missing WARNING: atoms too close: (T0316)E298.C and (T0316)M299.C only 0.000 apart, marking (T0316)M299.C as missing WARNING: atoms too close: (T0316)M299.N and (T0316)P300.N only 0.000 apart, marking (T0316)M299.N as missing WARNING: atoms too close: (T0316)M299.CA and (T0316)P300.CA only 0.000 apart, marking (T0316)M299.CA as missing # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # command:# naming current conformation align1 # command:# fraction of real conformation used = 0.744505 # GDT_score = -24.2445 # GDT_score(maxd=8,maxw=2.9)= -24.7039 # GDT_score(maxd=8,maxw=3.2)= -23.2658 # GDT_score(maxd=8,maxw=3.5)= -21.9349 # GDT_score(maxd=10,maxw=3.8)= -23.6484 # GDT_score(maxd=10,maxw=4)= -22.8054 # GDT_score(maxd=10,maxw=4.2)= -22.0042 # GDT_score(maxd=12,maxw=4.3)= -24.0581 # GDT_score(maxd=12,maxw=4.5)= -23.2436 # GDT_score(maxd=12,maxw=4.7)= -22.4518 # GDT_score(maxd=14,maxw=5.2)= -22.6283 # GDT_score(maxd=14,maxw=5.5)= -21.5873 # command:# ReadConformPDB reading from PDB file T0316.undertaker-align.pdb looking for model 2 WARNING: atoms too close: (T0316)M38.C and (T0316)D43.C only 0.000 apart, marking (T0316)D43.C as missing WARNING: atoms too close: (T0316)K39.N and (T0316)T44.N only 0.000 apart, marking (T0316)K39.N as missing WARNING: atoms too close: (T0316)K39.CA and (T0316)T44.CA only 0.000 apart, marking (T0316)K39.CA as missing WARNING: atoms too close: (T0316)C50.C and (T0316)T51.C only 0.000 apart, marking (T0316)T51.C as missing WARNING: atoms too close: (T0316)T51.N and (T0316)A52.N only 0.000 apart, marking (T0316)T51.N as missing WARNING: atoms too close: (T0316)T51.CA and (T0316)A52.CA only 0.000 apart, marking (T0316)T51.CA as missing WARNING: atoms too close: (T0316)E76.C and (T0316)F87.C only 0.000 apart, marking (T0316)F87.C as missing WARNING: atoms too close: (T0316)K77.N and (T0316)L88.N only 0.000 apart, marking (T0316)K77.N as missing WARNING: atoms too close: (T0316)K77.CA and (T0316)L88.CA only 0.000 apart, marking (T0316)K77.CA as missing WARNING: atoms too close: (T0316)E106.C and (T0316)I107.C only 0.000 apart, marking (T0316)I107.C as missing WARNING: atoms too close: (T0316)I107.N and (T0316)K108.N only 0.000 apart, marking (T0316)I107.N as missing WARNING: atoms too close: (T0316)I107.CA and (T0316)K108.CA only 0.000 apart, marking (T0316)I107.CA as missing WARNING: atoms too close: (T0316)D135.C and (T0316)Q152.C only 0.000 apart, marking (T0316)Q152.C as missing WARNING: atoms too close: (T0316)E136.N and (T0316)T153.N only 0.000 apart, marking (T0316)E136.N as missing WARNING: atoms too close: (T0316)E136.CA and (T0316)T153.CA only 0.000 apart, marking (T0316)E136.CA as missing WARNING: atoms too close: (T0316)M223.C and (T0316)T286.C only 0.000 apart, marking (T0316)T286.C as missing WARNING: atoms too close: (T0316)T224.N and (T0316)S287.N only 0.000 apart, marking (T0316)T224.N as missing WARNING: atoms too close: (T0316)T224.CA and (T0316)S287.CA only 0.000 apart, marking (T0316)T224.CA as missing WARNING: atoms too close: (T0316)F311.C and (T0316)V324.C only 0.000 apart, marking (T0316)V324.C as missing WARNING: atoms too close: (T0316)R312.N and (T0316)K325.N only 0.000 apart, marking (T0316)R312.N as missing WARNING: atoms too close: (T0316)R312.CA and (T0316)K325.CA only 0.000 apart, marking (T0316)R312.CA as missing # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # command:# naming current conformation align2 # command:# fraction of real conformation used = 0.574176 # GDT_score = -25 # GDT_score(maxd=8,maxw=2.9)= -25.9493 # GDT_score(maxd=8,maxw=3.2)= -24.5633 # GDT_score(maxd=8,maxw=3.5)= -23.1885 # GDT_score(maxd=10,maxw=3.8)= -24.446 # GDT_score(maxd=10,maxw=4)= -23.5796 # GDT_score(maxd=10,maxw=4.2)= -22.7583 # GDT_score(maxd=12,maxw=4.3)= -24.426 # GDT_score(maxd=12,maxw=4.5)= -23.6152 # GDT_score(maxd=12,maxw=4.7)= -22.853 # GDT_score(maxd=14,maxw=5.2)= -22.7551 # GDT_score(maxd=14,maxw=5.5)= -21.7555 # command:# ReadConformPDB reading from PDB file T0316.undertaker-align.pdb looking for model 3 WARNING: atoms too close: (T0316)M38.C and (T0316)D45.C only 0.000 apart, marking (T0316)D45.C as missing WARNING: atoms too close: (T0316)K39.N and (T0316)E46.N only 0.000 apart, marking (T0316)K39.N as missing WARNING: atoms too close: (T0316)K39.CA and (T0316)E46.CA only 0.000 apart, marking (T0316)K39.CA as missing WARNING: atoms too close: (T0316)C50.C and (T0316)T51.C only 0.000 apart, marking (T0316)T51.C as missing WARNING: atoms too close: (T0316)T51.N and (T0316)A52.N only 0.000 apart, marking (T0316)T51.N as missing WARNING: atoms too close: (T0316)T51.CA and (T0316)A52.CA only 0.000 apart, marking (T0316)T51.CA as missing WARNING: atoms too close: (T0316)F87.C and (T0316)C103.C only 0.000 apart, marking (T0316)C103.C as missing WARNING: atoms too close: (T0316)L88.N and (T0316)N104.N only 0.000 apart, marking (T0316)L88.N as missing WARNING: atoms too close: (T0316)L88.CA and (T0316)N104.CA only 0.000 apart, marking (T0316)L88.CA as missing WARNING: atoms too close: (T0316)K108.C and (T0316)F109.C only 0.000 apart, marking (T0316)F109.C as missing WARNING: atoms too close: (T0316)F109.N and (T0316)K110.N only 0.000 apart, marking (T0316)F109.N as missing WARNING: atoms too close: (T0316)F109.CA and (T0316)K110.CA only 0.000 apart, marking (T0316)F109.CA as missing WARNING: atoms too close: (T0316)A130.C and (T0316)A133.C only 0.000 apart, marking (T0316)A133.C as missing WARNING: atoms too close: (T0316)R131.N and (T0316)R134.N only 0.000 apart, marking (T0316)R131.N as missing WARNING: atoms too close: (T0316)R131.CA and (T0316)R134.CA only 0.000 apart, marking (T0316)R131.CA as missing WARNING: atoms too close: (T0316)E162.C and (T0316)Q165.C only 0.000 apart, marking (T0316)Q165.C as missing WARNING: atoms too close: (T0316)Q163.N and (T0316)K166.N only 0.000 apart, marking (T0316)Q163.N as missing WARNING: atoms too close: (T0316)Q163.CA and (T0316)K166.CA only 0.000 apart, marking (T0316)Q163.CA as missing WARNING: atoms too close: (T0316)N206.C and (T0316)F207.C only 0.000 apart, marking (T0316)F207.C as missing WARNING: atoms too close: (T0316)F207.N and (T0316)K208.N only 0.000 apart, marking (T0316)F207.N as missing WARNING: atoms too close: (T0316)F207.CA and (T0316)K208.CA only 0.000 apart, marking (T0316)F207.CA as missing # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # command:# naming current conformation align3 # command:# ReadConformPDB reading from PDB file T0316.undertaker-align.pdb looking for model 4 WARNING: atoms too close: (T0316)M38.C and (T0316)D45.C only 0.000 apart, marking (T0316)D45.C as missing WARNING: atoms too close: (T0316)K39.N and (T0316)E46.N only 0.000 apart, marking (T0316)K39.N as missing WARNING: atoms too close: (T0316)K39.CA and (T0316)E46.CA only 0.000 apart, marking (T0316)K39.CA as missing WARNING: atoms too close: (T0316)C50.C and (T0316)T51.C only 0.000 apart, marking (T0316)T51.C as missing WARNING: atoms too close: (T0316)T51.N and (T0316)A52.N only 0.000 apart, marking (T0316)T51.N as missing WARNING: atoms too close: (T0316)T51.CA and (T0316)A52.CA only 0.000 apart, marking (T0316)T51.CA as missing WARNING: atoms too close: (T0316)Y86.C and (T0316)M102.C only 0.000 apart, marking (T0316)M102.C as missing WARNING: atoms too close: (T0316)F87.N and (T0316)C103.N only 0.000 apart, marking (T0316)F87.N as missing WARNING: atoms too close: (T0316)F87.CA and (T0316)C103.CA only 0.000 apart, marking (T0316)F87.CA as missing WARNING: atoms too close: (T0316)E106.C and (T0316)I107.C only 0.000 apart, marking (T0316)I107.C as missing WARNING: atoms too close: (T0316)I107.N and (T0316)K108.N only 0.000 apart, marking (T0316)I107.N as missing WARNING: atoms too close: (T0316)I107.CA and (T0316)K108.CA only 0.000 apart, marking (T0316)I107.CA as missing WARNING: atoms too close: (T0316)V124.C and (T0316)T126.C only 0.000 apart, marking (T0316)T126.C as missing WARNING: atoms too close: (T0316)A125.N and (T0316)G127.N only 0.000 apart, marking (T0316)A125.N as missing WARNING: atoms too close: (T0316)A125.CA and (T0316)G127.CA only 0.000 apart, marking (T0316)A125.CA as missing WARNING: atoms too close: (T0316)D135.C and (T0316)T139.C only 0.000 apart, marking (T0316)T139.C as missing WARNING: atoms too close: (T0316)E136.N and (T0316)V140.N only 0.000 apart, marking (T0316)E136.N as missing WARNING: atoms too close: (T0316)E136.CA and (T0316)V140.CA only 0.000 apart, marking (T0316)E136.CA as missing WARNING: atoms too close: (T0316)K150.C and (T0316)T167.C only 0.000 apart, marking (T0316)T167.C as missing WARNING: atoms too close: (T0316)D151.N and (T0316)M168.N only 0.000 apart, marking (T0316)D151.N as missing WARNING: atoms too close: (T0316)D151.CA and (T0316)M168.CA only 0.000 apart, marking (T0316)D151.CA as missing WARNING: atoms too close: (T0316)I199.C and (T0316)F201.C only 0.000 apart, marking (T0316)F201.C as missing WARNING: atoms too close: (T0316)C200.N and (T0316)I202.N only 0.000 apart, marking (T0316)C200.N as missing WARNING: atoms too close: (T0316)C200.CA and (T0316)I202.CA only 0.000 apart, marking (T0316)C200.CA as missing WARNING: atoms too close: (T0316)Y214.C and (T0316)S282.C only 0.000 apart, marking (T0316)S282.C as missing WARNING: atoms too close: (T0316)L215.N and (T0316)L283.N only 0.000 apart, marking (T0316)L215.N as missing WARNING: atoms too close: (T0316)L215.CA and (T0316)L283.CA only 0.000 apart, marking (T0316)L215.CA as missing # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # command:# naming current conformation align4 # command:# ReadConformPDB reading from PDB file T0316.undertaker-align.pdb looking for model 5 WARNING: atoms too close: (T0316)M38.C and (T0316)D43.C only 0.000 apart, marking (T0316)D43.C as missing WARNING: atoms too close: (T0316)K39.N and (T0316)T44.N only 0.000 apart, marking (T0316)K39.N as missing WARNING: atoms too close: (T0316)K39.CA and (T0316)T44.CA only 0.000 apart, marking (T0316)K39.CA as missing WARNING: atoms too close: (T0316)C50.C and (T0316)T51.C only 0.000 apart, marking (T0316)T51.C as missing WARNING: atoms too close: (T0316)T51.N and (T0316)A52.N only 0.000 apart, marking (T0316)T51.N as missing WARNING: atoms too close: (T0316)T51.CA and (T0316)A52.CA only 0.000 apart, marking (T0316)T51.CA as missing WARNING: atoms too close: (T0316)E76.C and (T0316)Y91.C only 0.000 apart, marking (T0316)Y91.C as missing WARNING: atoms too close: (T0316)K77.N and (T0316)R92.N only 0.000 apart, marking (T0316)K77.N as missing WARNING: atoms too close: (T0316)K77.CA and (T0316)R92.CA only 0.000 apart, marking (T0316)K77.CA as missing WARNING: atoms too close: (T0316)C103.C and (T0316)K108.C only 0.000 apart, marking (T0316)K108.C as missing WARNING: atoms too close: (T0316)N104.N and (T0316)F109.N only 0.000 apart, marking (T0316)N104.N as missing WARNING: atoms too close: (T0316)N104.CA and (T0316)F109.CA only 0.000 apart, marking (T0316)N104.CA as missing WARNING: atoms too close: (T0316)G120.C and (T0316)A121.C only 0.000 apart, marking (T0316)A121.C as missing WARNING: atoms too close: (T0316)A121.N and (T0316)D122.N only 0.000 apart, marking (T0316)A121.N as missing WARNING: atoms too close: (T0316)A121.CA and (T0316)D122.CA only 0.000 apart, marking (T0316)A121.CA as missing WARNING: atoms too close: (T0316)D135.C and (T0316)E136.C only 0.000 apart, marking (T0316)E136.C as missing WARNING: atoms too close: (T0316)E136.N and (T0316)D137.N only 0.000 apart, marking (T0316)E136.N as missing WARNING: atoms too close: (T0316)E136.CA and (T0316)D137.CA only 0.000 apart, marking (T0316)E136.CA as missing WARNING: atoms too close: (T0316)K150.C and (T0316)Q152.C only 0.000 apart, marking (T0316)Q152.C as missing WARNING: atoms too close: (T0316)D151.N and (T0316)T153.N only 0.000 apart, marking (T0316)D151.N as missing WARNING: atoms too close: (T0316)D151.CA and (T0316)T153.CA only 0.000 apart, marking (T0316)D151.CA as missing WARNING: atoms too close: (T0316)W260.C and (T0316)F311.C only 0.000 apart, marking (T0316)F311.C as missing WARNING: atoms too close: (T0316)F261.N and (T0316)R312.N only 0.000 apart, marking (T0316)F261.N as missing WARNING: atoms too close: (T0316)F261.CA and (T0316)R312.CA only 0.000 apart, marking (T0316)F261.CA as missing # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # command:# naming current conformation align5 # command:# Prefix for input files set to decoys/ # command:# reading script from file read-pdb+servers.under # ReadConformPDB reading from PDB file ../model1.ts-submitted looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ../model2.ts-submitted looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ../model3.ts-submitted looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ../model4.ts-submitted looking for model 1 # Found a chain break before 355 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ../model5.ts-submitted looking for model 1 # Found a chain break before 355 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.M1-A183-try2-opt2-D122-K269-try1-opt2-A130-I373-try4-opt2-proteinshop.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.M1-A183-try2-opt2-D122-K269-try1-opt2-A130-I373-try4-opt2.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try1-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 354 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try1-opt1.pdb.gz looking for model 1 # Found a chain break before 354 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try1-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 362 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try1-opt2.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try1-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try10-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try10-opt1.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try10-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 352 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try10-opt2.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try10-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try11-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 346 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try11-opt1.pdb.gz looking for model 1 # Found a chain break before 346 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try11-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 358 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try11-opt2.pdb.gz looking for model 1 # Found a chain break before 355 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try11-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 355 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try12-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try12-opt1.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try12-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try12-opt2.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try12-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try13-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 349 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try13-opt1.pdb.gz looking for model 1 # Found a chain break before 349 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try13-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 350 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try13-opt2.pdb.gz looking for model 1 # Found a chain break before 349 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try13-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 349 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try14-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try14-opt1.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try14-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 345 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try14-opt2.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try14-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try15-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try15-opt1.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try15-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 369 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try15-opt2.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try15-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try16-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 352 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try16-opt1.pdb.gz looking for model 1 # Found a chain break before 352 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try16-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try16-opt2.pdb.gz looking for model 1 # Found a chain break before 367 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try16-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 367 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try17-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 352 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try17-opt1.pdb.gz looking for model 1 # Found a chain break before 352 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try17-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 352 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try17-opt2.pdb.gz looking for model 1 # Found a chain break before 369 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try17-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 369 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try18-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try18-opt1.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try18-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 343 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try18-opt2.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try18-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try19-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try19-opt1.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try19-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 343 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try19-opt2.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try19-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try2-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 340 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try2-opt1.pdb.gz looking for model 1 # Found a chain break before 340 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try2-opt2-M1-A183-try6-opt2-A130-I373.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try2-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 347 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try2-opt2.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try2-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try20-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try20-opt1.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try20-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 356 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try20-opt2.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try20-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try21-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try21-opt1.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try21-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 356 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try21-opt2.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try21-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try3-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try3-opt1.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try3-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 362 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try3-opt2.pdb.gz looking for model 1 # Found a chain break before 369 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try3-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 369 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try4-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 352 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try4-opt1.pdb.gz looking for model 1 # Found a chain break before 352 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try4-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 347 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try4-opt2.pdb.gz looking for model 1 # Found a chain break before 367 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try4-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 367 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try5-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 363 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try5-opt1.pdb.gz looking for model 1 # Found a chain break before 363 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try5-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 349 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try5-opt2.pdb.gz looking for model 1 # Found a chain break before 363 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try5-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 363 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try6-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 364 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try6-opt1.pdb.gz looking for model 1 # Found a chain break before 364 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try6-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 356 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try6-opt2.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try6-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try7-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 345 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try7-opt1.pdb.gz looking for model 1 # Found a chain break before 345 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try7-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 345 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try7-opt2.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try7-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try8-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try8-opt1.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try8-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 345 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try8-opt2.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try8-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try9-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 349 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try9-opt1.pdb.gz looking for model 1 # Found a chain break before 349 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try9-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 341 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try9-opt2.pdb.gz looking for model 1 # Found a chain break before 355 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try9-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 355 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file chimera1.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file make-chimera.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1233106543.pdb -s /var/tmp/to_scwrl_1233106543.seq -o /var/tmp/from_scwrl_1233106543.pdb > /var/tmp/scwrl_1233106543.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1233106543.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_POPULUS_TS1-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1616837161.pdb -s /var/tmp/to_scwrl_1616837161.seq -o /var/tmp/from_scwrl_1616837161.pdb > /var/tmp/scwrl_1616837161.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1616837161.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_POPULUS_TS2-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_681102730.pdb -s /var/tmp/to_scwrl_681102730.seq -o /var/tmp/from_scwrl_681102730.pdb > /var/tmp/scwrl_681102730.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_681102730.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_POPULUS_TS3-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_126789303.pdb -s /var/tmp/to_scwrl_126789303.seq -o /var/tmp/from_scwrl_126789303.pdb > /var/tmp/scwrl_126789303.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_126789303.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_POPULUS_TS4-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1991021437.pdb -s /var/tmp/to_scwrl_1991021437.seq -o /var/tmp/from_scwrl_1991021437.pdb > /var/tmp/scwrl_1991021437.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1991021437.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_POPULUS_TS5-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1955724168.pdb -s /var/tmp/to_scwrl_1955724168.seq -o /var/tmp/from_scwrl_1955724168.pdb > /var/tmp/scwrl_1955724168.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1955724168.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_RECOM_TS1-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1270610015.pdb -s /var/tmp/to_scwrl_1270610015.seq -o /var/tmp/from_scwrl_1270610015.pdb > /var/tmp/scwrl_1270610015.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1270610015.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_RECOM_TS2-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1519377626.pdb -s /var/tmp/to_scwrl_1519377626.seq -o /var/tmp/from_scwrl_1519377626.pdb > /var/tmp/scwrl_1519377626.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1519377626.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_RECOM_TS3-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_45277594.pdb -s /var/tmp/to_scwrl_45277594.seq -o /var/tmp/from_scwrl_45277594.pdb > /var/tmp/scwrl_45277594.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_45277594.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_RECOM_TS4-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1346066395.pdb -s /var/tmp/to_scwrl_1346066395.seq -o /var/tmp/from_scwrl_1346066395.pdb > /var/tmp/scwrl_1346066395.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1346066395.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_RECOM_TS5-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1560671366.pdb -s /var/tmp/to_scwrl_1560671366.seq -o /var/tmp/from_scwrl_1560671366.pdb > /var/tmp/scwrl_1560671366.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1560671366.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_TS1-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2144295263.pdb -s /var/tmp/to_scwrl_2144295263.seq -o /var/tmp/from_scwrl_2144295263.pdb > /var/tmp/scwrl_2144295263.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2144295263.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_TS2-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1616019698.pdb -s /var/tmp/to_scwrl_1616019698.seq -o /var/tmp/from_scwrl_1616019698.pdb > /var/tmp/scwrl_1616019698.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1616019698.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_TS3-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1865289739.pdb -s /var/tmp/to_scwrl_1865289739.seq -o /var/tmp/from_scwrl_1865289739.pdb > /var/tmp/scwrl_1865289739.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1865289739.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_TS4-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_642744582.pdb -s /var/tmp/to_scwrl_642744582.seq -o /var/tmp/from_scwrl_642744582.pdb > /var/tmp/scwrl_642744582.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_642744582.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_TS5-scwrl # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # Found a chain break before 353 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1779494287.pdb -s /var/tmp/to_scwrl_1779494287.seq -o /var/tmp/from_scwrl_1779494287.pdb > /var/tmp/scwrl_1779494287.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1779494287.pdb # conformation set from SCWRL output # naming current conformation 3Dpro_TS1-scwrl # ReadConformPDB reading from PDB file servers/3Dpro_TS2.pdb.gz looking for model 1 # Found a chain break before 372 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_496969160.pdb -s /var/tmp/to_scwrl_496969160.seq -o /var/tmp/from_scwrl_496969160.pdb > /var/tmp/scwrl_496969160.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_496969160.pdb # conformation set from SCWRL output # naming current conformation 3Dpro_TS2-scwrl # ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1 # Found a chain break before 370 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1476677365.pdb -s /var/tmp/to_scwrl_1476677365.seq -o /var/tmp/from_scwrl_1476677365.pdb > /var/tmp/scwrl_1476677365.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1476677365.pdb # conformation set from SCWRL output # naming current conformation 3Dpro_TS3-scwrl # ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1 # Found a chain break before 338 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1249169449.pdb -s /var/tmp/to_scwrl_1249169449.seq -o /var/tmp/from_scwrl_1249169449.pdb > /var/tmp/scwrl_1249169449.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1249169449.pdb # conformation set from SCWRL output # naming current conformation 3Dpro_TS4-scwrl # ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1 # Found a chain break before 341 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1712000367.pdb -s /var/tmp/to_scwrl_1712000367.seq -o /var/tmp/from_scwrl_1712000367.pdb > /var/tmp/scwrl_1712000367.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1712000367.pdb # conformation set from SCWRL output # naming current conformation 3Dpro_TS5-scwrl # ReadConformPDB reading from PDB file servers/ABIpro_TS1.pdb.gz looking for model 1 # Found a chain break before 369 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1366764485.pdb -s /var/tmp/to_scwrl_1366764485.seq -o /var/tmp/from_scwrl_1366764485.pdb > /var/tmp/scwrl_1366764485.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1366764485.pdb # conformation set from SCWRL output # naming current conformation ABIpro_TS1-scwrl # ReadConformPDB reading from PDB file servers/ABIpro_TS2.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_331945776.pdb -s /var/tmp/to_scwrl_331945776.seq -o /var/tmp/from_scwrl_331945776.pdb > /var/tmp/scwrl_331945776.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_331945776.pdb # conformation set from SCWRL output # naming current conformation ABIpro_TS2-scwrl # ReadConformPDB reading from PDB file servers/ABIpro_TS3.pdb.gz looking for model 1 # Found a chain break before 369 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_41505026.pdb -s /var/tmp/to_scwrl_41505026.seq -o /var/tmp/from_scwrl_41505026.pdb > /var/tmp/scwrl_41505026.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_41505026.pdb # conformation set from SCWRL output # naming current conformation ABIpro_TS3-scwrl # ReadConformPDB reading from PDB file servers/ABIpro_TS4.pdb.gz looking for model 1 # Found a chain break before 369 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1702865762.pdb -s /var/tmp/to_scwrl_1702865762.seq -o /var/tmp/from_scwrl_1702865762.pdb > /var/tmp/scwrl_1702865762.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1702865762.pdb # conformation set from SCWRL output # naming current conformation ABIpro_TS4-scwrl # ReadConformPDB reading from PDB file servers/ABIpro_TS5.pdb.gz looking for model 1 # Found a chain break before 346 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1206194418.pdb -s /var/tmp/to_scwrl_1206194418.seq -o /var/tmp/from_scwrl_1206194418.pdb > /var/tmp/scwrl_1206194418.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1206194418.pdb # conformation set from SCWRL output # naming current conformation ABIpro_TS5-scwrl # ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1 # Found a chain break before 266 # copying to AlignedFragments data structure # naming current conformation BayesHH_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2033867988.pdb -s /var/tmp/to_scwrl_2033867988.seq -o /var/tmp/from_scwrl_2033867988.pdb > /var/tmp/scwrl_2033867988.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2033867988.pdb # conformation set from SCWRL output # naming current conformation BayesHH_TS1-scwrl # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS1.pdb.gz looking for model 1 # Found a chain break before 346 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1755532505.pdb -s /var/tmp/to_scwrl_1755532505.seq -o /var/tmp/from_scwrl_1755532505.pdb > /var/tmp/scwrl_1755532505.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1755532505.pdb # conformation set from SCWRL output # naming current conformation Bilab-ENABLE_TS1-scwrl # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS2.pdb.gz looking for model 1 # Found a chain break before 369 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1028589461.pdb -s /var/tmp/to_scwrl_1028589461.seq -o /var/tmp/from_scwrl_1028589461.pdb > /var/tmp/scwrl_1028589461.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1028589461.pdb # conformation set from SCWRL output # naming current conformation Bilab-ENABLE_TS2-scwrl # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS3.pdb.gz looking for model 1 # Found a chain break before 323 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2098059704.pdb -s /var/tmp/to_scwrl_2098059704.seq -o /var/tmp/from_scwrl_2098059704.pdb > /var/tmp/scwrl_2098059704.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2098059704.pdb # conformation set from SCWRL output # naming current conformation Bilab-ENABLE_TS3-scwrl # ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1884561199.pdb -s /var/tmp/to_scwrl_1884561199.seq -o /var/tmp/from_scwrl_1884561199.pdb > /var/tmp/scwrl_1884561199.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1884561199.pdb # conformation set from SCWRL output # naming current conformation CIRCLE_TS1-scwrl # ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_867711531.pdb -s /var/tmp/to_scwrl_867711531.seq -o /var/tmp/from_scwrl_867711531.pdb > /var/tmp/scwrl_867711531.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_867711531.pdb # conformation set from SCWRL output # naming current conformation CIRCLE_TS2-scwrl # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1183682600.pdb -s /var/tmp/to_scwrl_1183682600.seq -o /var/tmp/from_scwrl_1183682600.pdb > /var/tmp/scwrl_1183682600.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1183682600.pdb # conformation set from SCWRL output # naming current conformation CIRCLE_TS3-scwrl # ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1353914713.pdb -s /var/tmp/to_scwrl_1353914713.seq -o /var/tmp/from_scwrl_1353914713.pdb > /var/tmp/scwrl_1353914713.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1353914713.pdb # conformation set from SCWRL output # naming current conformation CIRCLE_TS4-scwrl # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # Found a chain break before 370 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1548814261.pdb -s /var/tmp/to_scwrl_1548814261.seq -o /var/tmp/from_scwrl_1548814261.pdb > /var/tmp/scwrl_1548814261.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1548814261.pdb # conformation set from SCWRL output # naming current conformation CIRCLE_TS5-scwrl # ReadConformPDB reading from PDB file servers/CPHmodels_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation CPHmodels_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1310471903.pdb -s /var/tmp/to_scwrl_1310471903.seq -o /var/tmp/from_scwrl_1310471903.pdb > /var/tmp/scwrl_1310471903.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1310471903.pdb # conformation set from SCWRL output # naming current conformation CPHmodels_TS1-scwrl # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1197452504.pdb -s /var/tmp/to_scwrl_1197452504.seq -o /var/tmp/from_scwrl_1197452504.pdb > /var/tmp/scwrl_1197452504.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1197452504.pdb # conformation set from SCWRL output # naming current conformation CaspIta-FOX_TS1-scwrl # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1357054782.pdb -s /var/tmp/to_scwrl_1357054782.seq -o /var/tmp/from_scwrl_1357054782.pdb > /var/tmp/scwrl_1357054782.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1357054782.pdb # conformation set from SCWRL output # naming current conformation CaspIta-FOX_TS2-scwrl # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_433598272.pdb -s /var/tmp/to_scwrl_433598272.seq -o /var/tmp/from_scwrl_433598272.pdb > /var/tmp/scwrl_433598272.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_433598272.pdb # conformation set from SCWRL output # naming current conformation CaspIta-FOX_TS3-scwrl # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_569346484.pdb -s /var/tmp/to_scwrl_569346484.seq -o /var/tmp/from_scwrl_569346484.pdb > /var/tmp/scwrl_569346484.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_569346484.pdb # conformation set from SCWRL output # naming current conformation CaspIta-FOX_TS4-scwrl # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1402332376.pdb -s /var/tmp/to_scwrl_1402332376.seq -o /var/tmp/from_scwrl_1402332376.pdb > /var/tmp/scwrl_1402332376.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1402332376.pdb # conformation set from SCWRL output # naming current conformation CaspIta-FOX_TS5-scwrl # ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Distill_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1779664668.pdb -s /var/tmp/to_scwrl_1779664668.seq -o /var/tmp/from_scwrl_1779664668.pdb > /var/tmp/scwrl_1779664668.log Error: Couldn't open file /var/tmp/from_scwrl_1779664668.pdb or /var/tmp/from_scwrl_1779664668.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1779664668_b.pdb or decoys//var/tmp/from_scwrl_1779664668_b.pdb.gz for input Trying /var/tmp/from_scwrl_1779664668_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_1779664668_b.pdb or /var/tmp/from_scwrl_1779664668_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1779664668_a.pdb or decoys//var/tmp/from_scwrl_1779664668_a.pdb.gz for input Trying /var/tmp/from_scwrl_1779664668_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_1779664668_a.pdb or /var/tmp/from_scwrl_1779664668_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_1779664668.pdb or /var/tmp/from_scwrl_1779664668_b.pdb or /var/tmp/from_scwrl_1779664668_a.pdb Error: no new SCWRL conformation added # naming current conformation Distill_TS1-scwrl # ReadConformPDB reading from PDB file servers/Distill_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Distill_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2130017850.pdb -s /var/tmp/to_scwrl_2130017850.seq -o /var/tmp/from_scwrl_2130017850.pdb > /var/tmp/scwrl_2130017850.log Error: Couldn't open file /var/tmp/from_scwrl_2130017850.pdb or /var/tmp/from_scwrl_2130017850.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_2130017850_b.pdb or decoys//var/tmp/from_scwrl_2130017850_b.pdb.gz for input Trying /var/tmp/from_scwrl_2130017850_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_2130017850_b.pdb or /var/tmp/from_scwrl_2130017850_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_2130017850_a.pdb or decoys//var/tmp/from_scwrl_2130017850_a.pdb.gz for input Trying /var/tmp/from_scwrl_2130017850_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_2130017850_a.pdb or /var/tmp/from_scwrl_2130017850_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_2130017850.pdb or /var/tmp/from_scwrl_2130017850_b.pdb or /var/tmp/from_scwrl_2130017850_a.pdb Error: no new SCWRL conformation added # naming current conformation Distill_TS2-scwrl # ReadConformPDB reading from PDB file servers/Distill_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Distill_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1399143993.pdb -s /var/tmp/to_scwrl_1399143993.seq -o /var/tmp/from_scwrl_1399143993.pdb > /var/tmp/scwrl_1399143993.log Error: Couldn't open file /var/tmp/from_scwrl_1399143993.pdb or /var/tmp/from_scwrl_1399143993.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1399143993_b.pdb or decoys//var/tmp/from_scwrl_1399143993_b.pdb.gz for input Trying /var/tmp/from_scwrl_1399143993_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_1399143993_b.pdb or /var/tmp/from_scwrl_1399143993_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1399143993_a.pdb or decoys//var/tmp/from_scwrl_1399143993_a.pdb.gz for input Trying /var/tmp/from_scwrl_1399143993_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_1399143993_a.pdb or /var/tmp/from_scwrl_1399143993_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_1399143993.pdb or /var/tmp/from_scwrl_1399143993_b.pdb or /var/tmp/from_scwrl_1399143993_a.pdb Error: no new SCWRL conformation added # naming current conformation Distill_TS3-scwrl # ReadConformPDB reading from PDB file servers/Distill_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Distill_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1248200719.pdb -s /var/tmp/to_scwrl_1248200719.seq -o /var/tmp/from_scwrl_1248200719.pdb > /var/tmp/scwrl_1248200719.log Error: Couldn't open file /var/tmp/from_scwrl_1248200719.pdb or /var/tmp/from_scwrl_1248200719.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1248200719_b.pdb or decoys//var/tmp/from_scwrl_1248200719_b.pdb.gz for input Trying /var/tmp/from_scwrl_1248200719_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_1248200719_b.pdb or /var/tmp/from_scwrl_1248200719_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1248200719_a.pdb or decoys//var/tmp/from_scwrl_1248200719_a.pdb.gz for input Trying /var/tmp/from_scwrl_1248200719_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_1248200719_a.pdb or /var/tmp/from_scwrl_1248200719_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_1248200719.pdb or /var/tmp/from_scwrl_1248200719_b.pdb or /var/tmp/from_scwrl_1248200719_a.pdb Error: no new SCWRL conformation added # naming current conformation Distill_TS4-scwrl # ReadConformPDB reading from PDB file servers/Distill_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Distill_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1847823943.pdb -s /var/tmp/to_scwrl_1847823943.seq -o /var/tmp/from_scwrl_1847823943.pdb > /var/tmp/scwrl_1847823943.log Error: Couldn't open file /var/tmp/from_scwrl_1847823943.pdb or /var/tmp/from_scwrl_1847823943.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1847823943_b.pdb or decoys//var/tmp/from_scwrl_1847823943_b.pdb.gz for input Trying /var/tmp/from_scwrl_1847823943_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_1847823943_b.pdb or /var/tmp/from_scwrl_1847823943_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1847823943_a.pdb or decoys//var/tmp/from_scwrl_1847823943_a.pdb.gz for input Trying /var/tmp/from_scwrl_1847823943_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_1847823943_a.pdb or /var/tmp/from_scwrl_1847823943_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_1847823943.pdb or /var/tmp/from_scwrl_1847823943_b.pdb or /var/tmp/from_scwrl_1847823943_a.pdb Error: no new SCWRL conformation added # naming current conformation Distill_TS5-scwrl # ReadConformPDB reading from PDB file servers/FAMSD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FAMSD_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2041888575.pdb -s /var/tmp/to_scwrl_2041888575.seq -o /var/tmp/from_scwrl_2041888575.pdb > /var/tmp/scwrl_2041888575.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2041888575.pdb # conformation set from SCWRL output # naming current conformation FAMSD_TS1-scwrl # ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FAMSD_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_880211360.pdb -s /var/tmp/to_scwrl_880211360.seq -o /var/tmp/from_scwrl_880211360.pdb > /var/tmp/scwrl_880211360.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_880211360.pdb # conformation set from SCWRL output # naming current conformation FAMSD_TS2-scwrl # ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FAMSD_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_197309456.pdb -s /var/tmp/to_scwrl_197309456.seq -o /var/tmp/from_scwrl_197309456.pdb > /var/tmp/scwrl_197309456.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_197309456.pdb # conformation set from SCWRL output # naming current conformation FAMSD_TS3-scwrl # ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FAMSD_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1371082293.pdb -s /var/tmp/to_scwrl_1371082293.seq -o /var/tmp/from_scwrl_1371082293.pdb > /var/tmp/scwrl_1371082293.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1371082293.pdb # conformation set from SCWRL output # naming current conformation FAMSD_TS4-scwrl # ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FAMSD_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2129380810.pdb -s /var/tmp/to_scwrl_2129380810.seq -o /var/tmp/from_scwrl_2129380810.pdb > /var/tmp/scwrl_2129380810.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2129380810.pdb # conformation set from SCWRL output # naming current conformation FAMSD_TS5-scwrl # ReadConformPDB reading from PDB file servers/FAMS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FAMS_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1909309823.pdb -s /var/tmp/to_scwrl_1909309823.seq -o /var/tmp/from_scwrl_1909309823.pdb > /var/tmp/scwrl_1909309823.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1909309823.pdb # conformation set from SCWRL output # naming current conformation FAMS_TS1-scwrl # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FAMS_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_590363132.pdb -s /var/tmp/to_scwrl_590363132.seq -o /var/tmp/from_scwrl_590363132.pdb > /var/tmp/scwrl_590363132.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_590363132.pdb # conformation set from SCWRL output # naming current conformation FAMS_TS2-scwrl # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FAMS_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_313842939.pdb -s /var/tmp/to_scwrl_313842939.seq -o /var/tmp/from_scwrl_313842939.pdb > /var/tmp/scwrl_313842939.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_313842939.pdb # conformation set from SCWRL output # naming current conformation FAMS_TS3-scwrl # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FAMS_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1950814850.pdb -s /var/tmp/to_scwrl_1950814850.seq -o /var/tmp/from_scwrl_1950814850.pdb > /var/tmp/scwrl_1950814850.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1950814850.pdb # conformation set from SCWRL output # naming current conformation FAMS_TS4-scwrl # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FAMS_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_145745247.pdb -s /var/tmp/to_scwrl_145745247.seq -o /var/tmp/from_scwrl_145745247.pdb > /var/tmp/scwrl_145745247.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_145745247.pdb # conformation set from SCWRL output # naming current conformation FAMS_TS5-scwrl # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # Found a chain break before 370 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1520037358.pdb -s /var/tmp/to_scwrl_1520037358.seq -o /var/tmp/from_scwrl_1520037358.pdb > /var/tmp/scwrl_1520037358.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1520037358.pdb # conformation set from SCWRL output # naming current conformation FOLDpro_TS1-scwrl # ReadConformPDB reading from PDB file servers/FOLDpro_TS2.pdb.gz looking for model 1 # Found a chain break before 341 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1837199191.pdb -s /var/tmp/to_scwrl_1837199191.seq -o /var/tmp/from_scwrl_1837199191.pdb > /var/tmp/scwrl_1837199191.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1837199191.pdb # conformation set from SCWRL output # naming current conformation FOLDpro_TS2-scwrl # ReadConformPDB reading from PDB file servers/FOLDpro_TS3.pdb.gz looking for model 1 # Found a chain break before 353 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1901277753.pdb -s /var/tmp/to_scwrl_1901277753.seq -o /var/tmp/from_scwrl_1901277753.pdb > /var/tmp/scwrl_1901277753.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1901277753.pdb # conformation set from SCWRL output # naming current conformation FOLDpro_TS3-scwrl # ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1 # Found a chain break before 341 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_401143172.pdb -s /var/tmp/to_scwrl_401143172.seq -o /var/tmp/from_scwrl_401143172.pdb > /var/tmp/scwrl_401143172.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_401143172.pdb # conformation set from SCWRL output # naming current conformation FOLDpro_TS4-scwrl # ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1 # Found a chain break before 335 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1787775248.pdb -s /var/tmp/to_scwrl_1787775248.seq -o /var/tmp/from_scwrl_1787775248.pdb > /var/tmp/scwrl_1787775248.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1787775248.pdb # conformation set from SCWRL output # naming current conformation FOLDpro_TS5-scwrl # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 Skipped atom 526, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 528, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 530, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 532, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 738, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 740, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 742, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 744, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 754, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 756, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 758, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 760, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 842, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 844, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 846, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 848, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 918, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 920, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 922, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 924, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1154, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1156, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1158, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1160, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1230, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1232, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1234, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1236, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1242, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1244, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1246, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1248, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1254, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1256, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1258, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1260, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1342, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1344, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1346, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1348, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FORTE1_AL1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1638355305.pdb -s /var/tmp/to_scwrl_1638355305.seq -o /var/tmp/from_scwrl_1638355305.pdb > /var/tmp/scwrl_1638355305.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1638355305.pdb # conformation set from SCWRL output # naming current conformation FORTE1_AL1-scwrl # ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FORTE1_AL2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1268854703.pdb -s /var/tmp/to_scwrl_1268854703.seq -o /var/tmp/from_scwrl_1268854703.pdb > /var/tmp/scwrl_1268854703.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1268854703.pdb # conformation set from SCWRL output # naming current conformation FORTE1_AL2-scwrl # ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FORTE1_AL3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_823974202.pdb -s /var/tmp/to_scwrl_823974202.seq -o /var/tmp/from_scwrl_823974202.pdb > /var/tmp/scwrl_823974202.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_823974202.pdb # conformation set from SCWRL output # naming current conformation FORTE1_AL3-scwrl # ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FORTE1_AL4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_844786373.pdb -s /var/tmp/to_scwrl_844786373.seq -o /var/tmp/from_scwrl_844786373.pdb > /var/tmp/scwrl_844786373.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_844786373.pdb # conformation set from SCWRL output # naming current conformation FORTE1_AL4-scwrl # ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FORTE1_AL5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_670185318.pdb -s /var/tmp/to_scwrl_670185318.seq -o /var/tmp/from_scwrl_670185318.pdb > /var/tmp/scwrl_670185318.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_670185318.pdb # conformation set from SCWRL output # naming current conformation FORTE1_AL5-scwrl # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 Skipped atom 526, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 528, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 530, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 532, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 738, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 740, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 742, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 744, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 754, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 756, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 758, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 760, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 842, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 844, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 846, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 848, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 918, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 920, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 922, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 924, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1154, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1156, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1158, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1160, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1230, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1232, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1234, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1236, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1242, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1244, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1246, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1248, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1254, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1256, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1258, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1260, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1342, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1344, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1346, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1348, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FORTE2_AL1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2134446105.pdb -s /var/tmp/to_scwrl_2134446105.seq -o /var/tmp/from_scwrl_2134446105.pdb > /var/tmp/scwrl_2134446105.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2134446105.pdb # conformation set from SCWRL output # naming current conformation FORTE2_AL1-scwrl # ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FORTE2_AL2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2042238877.pdb -s /var/tmp/to_scwrl_2042238877.seq -o /var/tmp/from_scwrl_2042238877.pdb > /var/tmp/scwrl_2042238877.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2042238877.pdb # conformation set from SCWRL output # naming current conformation FORTE2_AL2-scwrl # ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FORTE2_AL3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2027240100.pdb -s /var/tmp/to_scwrl_2027240100.seq -o /var/tmp/from_scwrl_2027240100.pdb > /var/tmp/scwrl_2027240100.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2027240100.pdb # conformation set from SCWRL output # naming current conformation FORTE2_AL3-scwrl # ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FORTE2_AL4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_420560731.pdb -s /var/tmp/to_scwrl_420560731.seq -o /var/tmp/from_scwrl_420560731.pdb > /var/tmp/scwrl_420560731.log sh: line 1: 28569 Killed scwrl3 -i /var/tmp/to_scwrl_420560731.pdb -s /var/tmp/to_scwrl_420560731.seq -o /var/tmp/from_scwrl_420560731.pdb >/var/tmp/scwrl_420560731.log Error: Couldn't open file /var/tmp/from_scwrl_420560731.pdb or /var/tmp/from_scwrl_420560731.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_420560731_b.pdb or decoys//var/tmp/from_scwrl_420560731_b.pdb.gz for input Trying /var/tmp/from_scwrl_420560731_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_420560731_b.pdb or /var/tmp/from_scwrl_420560731_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_420560731_a.pdb or decoys//var/tmp/from_scwrl_420560731_a.pdb.gz for input Trying /var/tmp/from_scwrl_420560731_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_420560731_a.pdb or /var/tmp/from_scwrl_420560731_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_420560731.pdb or /var/tmp/from_scwrl_420560731_b.pdb or /var/tmp/from_scwrl_420560731_a.pdb Error: no new SCWRL conformation added # naming current conformation FORTE2_AL4-scwrl # ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FORTE2_AL5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_464101714.pdb -s /var/tmp/to_scwrl_464101714.seq -o /var/tmp/from_scwrl_464101714.pdb > /var/tmp/scwrl_464101714.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_464101714.pdb # conformation set from SCWRL output # naming current conformation FORTE2_AL5-scwrl # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS1.pdb.gz looking for model 1 # Found a chain break before 366 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1282088829.pdb -s /var/tmp/to_scwrl_1282088829.seq -o /var/tmp/from_scwrl_1282088829.pdb > /var/tmp/scwrl_1282088829.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1282088829.pdb # conformation set from SCWRL output # naming current conformation FPSOLVER-SERVER_TS1-scwrl # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS2.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_52741752.pdb -s /var/tmp/to_scwrl_52741752.seq -o /var/tmp/from_scwrl_52741752.pdb > /var/tmp/scwrl_52741752.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_52741752.pdb # conformation set from SCWRL output # naming current conformation FPSOLVER-SERVER_TS2-scwrl # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS3.pdb.gz looking for model 1 # Found a chain break before 372 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_446635918.pdb -s /var/tmp/to_scwrl_446635918.seq -o /var/tmp/from_scwrl_446635918.pdb > /var/tmp/scwrl_446635918.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_446635918.pdb # conformation set from SCWRL output # naming current conformation FPSOLVER-SERVER_TS3-scwrl # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS4.pdb.gz looking for model 1 # Found a chain break before 360 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_533749176.pdb -s /var/tmp/to_scwrl_533749176.seq -o /var/tmp/from_scwrl_533749176.pdb > /var/tmp/scwrl_533749176.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_533749176.pdb # conformation set from SCWRL output # naming current conformation FPSOLVER-SERVER_TS4-scwrl # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS5.pdb.gz looking for model 1 # Found a chain break before 372 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1300942471.pdb -s /var/tmp/to_scwrl_1300942471.seq -o /var/tmp/from_scwrl_1300942471.pdb > /var/tmp/scwrl_1300942471.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1300942471.pdb # conformation set from SCWRL output # naming current conformation FPSOLVER-SERVER_TS5-scwrl # ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_146976214.pdb -s /var/tmp/to_scwrl_146976214.seq -o /var/tmp/from_scwrl_146976214.pdb > /var/tmp/scwrl_146976214.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_146976214.pdb # conformation set from SCWRL output # naming current conformation FUGMOD_TS1-scwrl # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_428154105.pdb -s /var/tmp/to_scwrl_428154105.seq -o /var/tmp/from_scwrl_428154105.pdb > /var/tmp/scwrl_428154105.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_428154105.pdb # conformation set from SCWRL output # naming current conformation FUGMOD_TS2-scwrl # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_33670184.pdb -s /var/tmp/to_scwrl_33670184.seq -o /var/tmp/from_scwrl_33670184.pdb > /var/tmp/scwrl_33670184.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_33670184.pdb # conformation set from SCWRL output # naming current conformation FUGMOD_TS3-scwrl # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # Found a chain break before 348 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_344285670.pdb -s /var/tmp/to_scwrl_344285670.seq -o /var/tmp/from_scwrl_344285670.pdb > /var/tmp/scwrl_344285670.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_344285670.pdb # conformation set from SCWRL output # naming current conformation FUGMOD_TS4-scwrl # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1799236398.pdb -s /var/tmp/to_scwrl_1799236398.seq -o /var/tmp/from_scwrl_1799236398.pdb > /var/tmp/scwrl_1799236398.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1799236398.pdb # conformation set from SCWRL output # naming current conformation FUGMOD_TS5-scwrl # ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FUGUE_AL1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_15567347.pdb -s /var/tmp/to_scwrl_15567347.seq -o /var/tmp/from_scwrl_15567347.pdb > /var/tmp/scwrl_15567347.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_15567347.pdb # conformation set from SCWRL output # naming current conformation FUGUE_AL1-scwrl # ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FUGUE_AL2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_106111846.pdb -s /var/tmp/to_scwrl_106111846.seq -o /var/tmp/from_scwrl_106111846.pdb > /var/tmp/scwrl_106111846.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_106111846.pdb # conformation set from SCWRL output # naming current conformation FUGUE_AL2-scwrl # ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FUGUE_AL3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_242115884.pdb -s /var/tmp/to_scwrl_242115884.seq -o /var/tmp/from_scwrl_242115884.pdb > /var/tmp/scwrl_242115884.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_242115884.pdb # conformation set from SCWRL output # naming current conformation FUGUE_AL3-scwrl # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FUGUE_AL4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_329410287.pdb -s /var/tmp/to_scwrl_329410287.seq -o /var/tmp/from_scwrl_329410287.pdb > /var/tmp/scwrl_329410287.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_329410287.pdb # conformation set from SCWRL output # naming current conformation FUGUE_AL4-scwrl # ReadConformPDB reading from PDB file servers/FUGUE_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FUGUE_AL5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2056926696.pdb -s /var/tmp/to_scwrl_2056926696.seq -o /var/tmp/from_scwrl_2056926696.pdb > /var/tmp/scwrl_2056926696.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2056926696.pdb # conformation set from SCWRL output # naming current conformation FUGUE_AL5-scwrl # ReadConformPDB reading from PDB file servers/FUNCTION_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FUNCTION_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_387861131.pdb -s /var/tmp/to_scwrl_387861131.seq -o /var/tmp/from_scwrl_387861131.pdb > /var/tmp/scwrl_387861131.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_387861131.pdb # conformation set from SCWRL output # naming current conformation FUNCTION_TS1-scwrl # ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1849447645.pdb -s /var/tmp/to_scwrl_1849447645.seq -o /var/tmp/from_scwrl_1849447645.pdb > /var/tmp/scwrl_1849447645.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1849447645.pdb # conformation set from SCWRL output # naming current conformation FUNCTION_TS2-scwrl # ReadConformPDB reading from PDB file servers/FUNCTION_TS3.pdb.gz looking for model 1 # Found a chain break before 366 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1746642241.pdb -s /var/tmp/to_scwrl_1746642241.seq -o /var/tmp/from_scwrl_1746642241.pdb > /var/tmp/scwrl_1746642241.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1746642241.pdb # conformation set from SCWRL output # naming current conformation FUNCTION_TS3-scwrl # ReadConformPDB reading from PDB file servers/FUNCTION_TS4.pdb.gz looking for model 1 # Found a chain break before 367 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_141655237.pdb -s /var/tmp/to_scwrl_141655237.seq -o /var/tmp/from_scwrl_141655237.pdb > /var/tmp/scwrl_141655237.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_141655237.pdb # conformation set from SCWRL output # naming current conformation FUNCTION_TS4-scwrl # ReadConformPDB reading from PDB file servers/FUNCTION_TS5.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_103107170.pdb -s /var/tmp/to_scwrl_103107170.seq -o /var/tmp/from_scwrl_103107170.pdb > /var/tmp/scwrl_103107170.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_103107170.pdb # conformation set from SCWRL output # naming current conformation FUNCTION_TS5-scwrl # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1386933842.pdb -s /var/tmp/to_scwrl_1386933842.seq -o /var/tmp/from_scwrl_1386933842.pdb > /var/tmp/scwrl_1386933842.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1386933842.pdb # conformation set from SCWRL output # naming current conformation GeneSilicoMetaServer_TS1-scwrl # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # Found a chain break before 372 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1780010543.pdb -s /var/tmp/to_scwrl_1780010543.seq -o /var/tmp/from_scwrl_1780010543.pdb > /var/tmp/scwrl_1780010543.log sh: line 1: 28684 Killed scwrl3 -i /var/tmp/to_scwrl_1780010543.pdb -s /var/tmp/to_scwrl_1780010543.seq -o /var/tmp/from_scwrl_1780010543.pdb >/var/tmp/scwrl_1780010543.log Error: Couldn't open file /var/tmp/from_scwrl_1780010543.pdb or /var/tmp/from_scwrl_1780010543.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1780010543_b.pdb or decoys//var/tmp/from_scwrl_1780010543_b.pdb.gz for input Trying /var/tmp/from_scwrl_1780010543_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_1780010543_b.pdb or /var/tmp/from_scwrl_1780010543_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1780010543_a.pdb or decoys//var/tmp/from_scwrl_1780010543_a.pdb.gz for input Trying /var/tmp/from_scwrl_1780010543_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_1780010543_a.pdb or /var/tmp/from_scwrl_1780010543_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_1780010543.pdb or /var/tmp/from_scwrl_1780010543_b.pdb or /var/tmp/from_scwrl_1780010543_a.pdb Error: no new SCWRL conformation added # naming current conformation GeneSilicoMetaServer_TS2-scwrl # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1371961873.pdb -s /var/tmp/to_scwrl_1371961873.seq -o /var/tmp/from_scwrl_1371961873.pdb > /var/tmp/scwrl_1371961873.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1371961873.pdb # conformation set from SCWRL output # naming current conformation GeneSilicoMetaServer_TS3-scwrl # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_63424398.pdb -s /var/tmp/to_scwrl_63424398.seq -o /var/tmp/from_scwrl_63424398.pdb > /var/tmp/scwrl_63424398.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_63424398.pdb # conformation set from SCWRL output # naming current conformation GeneSilicoMetaServer_TS4-scwrl # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1 # Found a chain break before 338 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_477313269.pdb -s /var/tmp/to_scwrl_477313269.seq -o /var/tmp/from_scwrl_477313269.pdb > /var/tmp/scwrl_477313269.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_477313269.pdb # conformation set from SCWRL output # naming current conformation GeneSilicoMetaServer_TS5-scwrl # ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation HHpred1_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2042147191.pdb -s /var/tmp/to_scwrl_2042147191.seq -o /var/tmp/from_scwrl_2042147191.pdb > /var/tmp/scwrl_2042147191.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2042147191.pdb # conformation set from SCWRL output # naming current conformation HHpred1_TS1-scwrl # ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation HHpred2_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_50386856.pdb -s /var/tmp/to_scwrl_50386856.seq -o /var/tmp/from_scwrl_50386856.pdb > /var/tmp/scwrl_50386856.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_50386856.pdb # conformation set from SCWRL output # naming current conformation HHpred2_TS1-scwrl # ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation HHpred3_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_372068499.pdb -s /var/tmp/to_scwrl_372068499.seq -o /var/tmp/from_scwrl_372068499.pdb > /var/tmp/scwrl_372068499.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_372068499.pdb # conformation set from SCWRL output # naming current conformation HHpred3_TS1-scwrl # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1921903644.pdb -s /var/tmp/to_scwrl_1921903644.seq -o /var/tmp/from_scwrl_1921903644.pdb > /var/tmp/scwrl_1921903644.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1921903644.pdb # conformation set from SCWRL output # naming current conformation Huber-Torda-Server_TS1-scwrl # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_470947587.pdb -s /var/tmp/to_scwrl_470947587.seq -o /var/tmp/from_scwrl_470947587.pdb > /var/tmp/scwrl_470947587.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_470947587.pdb # conformation set from SCWRL output # naming current conformation Huber-Torda-Server_TS2-scwrl # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_836170213.pdb -s /var/tmp/to_scwrl_836170213.seq -o /var/tmp/from_scwrl_836170213.pdb > /var/tmp/scwrl_836170213.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_836170213.pdb # conformation set from SCWRL output # naming current conformation Huber-Torda-Server_TS3-scwrl # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1056508828.pdb -s /var/tmp/to_scwrl_1056508828.seq -o /var/tmp/from_scwrl_1056508828.pdb > /var/tmp/scwrl_1056508828.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1056508828.pdb # conformation set from SCWRL output # naming current conformation Huber-Torda-Server_TS4-scwrl # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_523689339.pdb -s /var/tmp/to_scwrl_523689339.seq -o /var/tmp/from_scwrl_523689339.pdb > /var/tmp/scwrl_523689339.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_523689339.pdb # conformation set from SCWRL output # naming current conformation Huber-Torda-Server_TS5-scwrl # ReadConformPDB reading from PDB file servers/LOOPP_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation LOOPP_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1282806130.pdb -s /var/tmp/to_scwrl_1282806130.seq -o /var/tmp/from_scwrl_1282806130.pdb > /var/tmp/scwrl_1282806130.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1282806130.pdb # conformation set from SCWRL output # naming current conformation LOOPP_TS1-scwrl # ReadConformPDB reading from PDB file servers/LOOPP_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation LOOPP_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1590258003.pdb -s /var/tmp/to_scwrl_1590258003.seq -o /var/tmp/from_scwrl_1590258003.pdb > /var/tmp/scwrl_1590258003.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1590258003.pdb # conformation set from SCWRL output # naming current conformation LOOPP_TS2-scwrl # ReadConformPDB reading from PDB file servers/LOOPP_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation LOOPP_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1824631810.pdb -s /var/tmp/to_scwrl_1824631810.seq -o /var/tmp/from_scwrl_1824631810.pdb > /var/tmp/scwrl_1824631810.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1824631810.pdb # conformation set from SCWRL output # naming current conformation LOOPP_TS3-scwrl # ReadConformPDB reading from PDB file servers/LOOPP_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation LOOPP_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1429782344.pdb -s /var/tmp/to_scwrl_1429782344.seq -o /var/tmp/from_scwrl_1429782344.pdb > /var/tmp/scwrl_1429782344.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1429782344.pdb # conformation set from SCWRL output # naming current conformation LOOPP_TS4-scwrl # ReadConformPDB reading from PDB file servers/LOOPP_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation LOOPP_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2018412108.pdb -s /var/tmp/to_scwrl_2018412108.seq -o /var/tmp/from_scwrl_2018412108.pdb > /var/tmp/scwrl_2018412108.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2018412108.pdb # conformation set from SCWRL output # naming current conformation LOOPP_TS5-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # Found a chain break before 332 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1858301995.pdb -s /var/tmp/to_scwrl_1858301995.seq -o /var/tmp/from_scwrl_1858301995.pdb > /var/tmp/scwrl_1858301995.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1858301995.pdb # conformation set from SCWRL output # naming current conformation Ma-OPUS-server_TS1-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS2.pdb.gz looking for model 1 # Found a chain break before 366 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1774068014.pdb -s /var/tmp/to_scwrl_1774068014.seq -o /var/tmp/from_scwrl_1774068014.pdb > /var/tmp/scwrl_1774068014.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1774068014.pdb # conformation set from SCWRL output # naming current conformation Ma-OPUS-server_TS2-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS3.pdb.gz looking for model 1 # Found a chain break before 327 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1670164860.pdb -s /var/tmp/to_scwrl_1670164860.seq -o /var/tmp/from_scwrl_1670164860.pdb > /var/tmp/scwrl_1670164860.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1670164860.pdb # conformation set from SCWRL output # naming current conformation Ma-OPUS-server_TS3-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS4.pdb.gz looking for model 1 # Found a chain break before 364 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1873869342.pdb -s /var/tmp/to_scwrl_1873869342.seq -o /var/tmp/from_scwrl_1873869342.pdb > /var/tmp/scwrl_1873869342.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1873869342.pdb # conformation set from SCWRL output # naming current conformation Ma-OPUS-server_TS4-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS5.pdb.gz looking for model 1 # Found a chain break before 347 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1880179861.pdb -s /var/tmp/to_scwrl_1880179861.seq -o /var/tmp/from_scwrl_1880179861.pdb > /var/tmp/scwrl_1880179861.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1880179861.pdb # conformation set from SCWRL output # naming current conformation Ma-OPUS-server_TS5-scwrl # ReadConformPDB reading from PDB file servers/MetaTasser_TS1.pdb.gz looking for model 1 # Found a chain break before 372 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1912280744.pdb -s /var/tmp/to_scwrl_1912280744.seq -o /var/tmp/from_scwrl_1912280744.pdb > /var/tmp/scwrl_1912280744.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1912280744.pdb # conformation set from SCWRL output # naming current conformation MetaTasser_TS1-scwrl # ReadConformPDB reading from PDB file servers/MetaTasser_TS2.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_55795982.pdb -s /var/tmp/to_scwrl_55795982.seq -o /var/tmp/from_scwrl_55795982.pdb > /var/tmp/scwrl_55795982.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_55795982.pdb # conformation set from SCWRL output # naming current conformation MetaTasser_TS2-scwrl # ReadConformPDB reading from PDB file servers/MetaTasser_TS3.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1789622910.pdb -s /var/tmp/to_scwrl_1789622910.seq -o /var/tmp/from_scwrl_1789622910.pdb > /var/tmp/scwrl_1789622910.log sh: line 1: 28814 Killed scwrl3 -i /var/tmp/to_scwrl_1789622910.pdb -s /var/tmp/to_scwrl_1789622910.seq -o /var/tmp/from_scwrl_1789622910.pdb >/var/tmp/scwrl_1789622910.log Error: Couldn't open file /var/tmp/from_scwrl_1789622910.pdb or /var/tmp/from_scwrl_1789622910.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1789622910_b.pdb or decoys//var/tmp/from_scwrl_1789622910_b.pdb.gz for input Trying /var/tmp/from_scwrl_1789622910_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_1789622910_b.pdb or /var/tmp/from_scwrl_1789622910_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1789622910_a.pdb or decoys//var/tmp/from_scwrl_1789622910_a.pdb.gz for input Trying /var/tmp/from_scwrl_1789622910_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_1789622910_a.pdb or /var/tmp/from_scwrl_1789622910_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_1789622910.pdb or /var/tmp/from_scwrl_1789622910_b.pdb or /var/tmp/from_scwrl_1789622910_a.pdb Error: no new SCWRL conformation added # naming current conformation MetaTasser_TS3-scwrl # ReadConformPDB reading from PDB file servers/MetaTasser_TS4.pdb.gz looking for model 1 # Found a chain break before 372 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_152658228.pdb -s /var/tmp/to_scwrl_152658228.seq -o /var/tmp/from_scwrl_152658228.pdb > /var/tmp/scwrl_152658228.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_152658228.pdb # conformation set from SCWRL output # naming current conformation MetaTasser_TS4-scwrl # ReadConformPDB reading from PDB file servers/MetaTasser_TS5.pdb.gz looking for model 1 # Found a chain break before 372 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1905243627.pdb -s /var/tmp/to_scwrl_1905243627.seq -o /var/tmp/from_scwrl_1905243627.pdb > /var/tmp/scwrl_1905243627.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1905243627.pdb # conformation set from SCWRL output # naming current conformation MetaTasser_TS5-scwrl # ReadConformPDB reading from PDB file servers/NN_PUT_lab_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation NN_PUT_lab_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1388781504.pdb -s /var/tmp/to_scwrl_1388781504.seq -o /var/tmp/from_scwrl_1388781504.pdb > /var/tmp/scwrl_1388781504.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1388781504.pdb # conformation set from SCWRL output # naming current conformation NN_PUT_lab_TS1-scwrl # ReadConformPDB reading from PDB file servers/POMYSL_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation POMYSL_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_294313466.pdb -s /var/tmp/to_scwrl_294313466.seq -o /var/tmp/from_scwrl_294313466.pdb > /var/tmp/scwrl_294313466.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_294313466.pdb # conformation set from SCWRL output # naming current conformation POMYSL_TS1-scwrl # ReadConformPDB reading from PDB file servers/POMYSL_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation POMYSL_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2008350798.pdb -s /var/tmp/to_scwrl_2008350798.seq -o /var/tmp/from_scwrl_2008350798.pdb > /var/tmp/scwrl_2008350798.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2008350798.pdb # conformation set from SCWRL output # naming current conformation POMYSL_TS2-scwrl # ReadConformPDB reading from PDB file servers/POMYSL_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation POMYSL_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_628231701.pdb -s /var/tmp/to_scwrl_628231701.seq -o /var/tmp/from_scwrl_628231701.pdb > /var/tmp/scwrl_628231701.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_628231701.pdb # conformation set from SCWRL output # naming current conformation POMYSL_TS3-scwrl # ReadConformPDB reading from PDB file servers/POMYSL_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation POMYSL_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2074324009.pdb -s /var/tmp/to_scwrl_2074324009.seq -o /var/tmp/from_scwrl_2074324009.pdb > /var/tmp/scwrl_2074324009.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2074324009.pdb # conformation set from SCWRL output # naming current conformation POMYSL_TS4-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1232829024.pdb -s /var/tmp/to_scwrl_1232829024.seq -o /var/tmp/from_scwrl_1232829024.pdb > /var/tmp/scwrl_1232829024.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1232829024.pdb # conformation set from SCWRL output # naming current conformation PROTINFO-AB_TS1-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_691656099.pdb -s /var/tmp/to_scwrl_691656099.seq -o /var/tmp/from_scwrl_691656099.pdb > /var/tmp/scwrl_691656099.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_691656099.pdb # conformation set from SCWRL output # naming current conformation PROTINFO-AB_TS2-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_404153631.pdb -s /var/tmp/to_scwrl_404153631.seq -o /var/tmp/from_scwrl_404153631.pdb > /var/tmp/scwrl_404153631.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_404153631.pdb # conformation set from SCWRL output # naming current conformation PROTINFO-AB_TS3-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1127492569.pdb -s /var/tmp/to_scwrl_1127492569.seq -o /var/tmp/from_scwrl_1127492569.pdb > /var/tmp/scwrl_1127492569.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1127492569.pdb # conformation set from SCWRL output # naming current conformation PROTINFO-AB_TS4-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_742042955.pdb -s /var/tmp/to_scwrl_742042955.seq -o /var/tmp/from_scwrl_742042955.pdb > /var/tmp/scwrl_742042955.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_742042955.pdb # conformation set from SCWRL output # naming current conformation PROTINFO-AB_TS5-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1 # Found a chain break before 338 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_776222130.pdb -s /var/tmp/to_scwrl_776222130.seq -o /var/tmp/from_scwrl_776222130.pdb > /var/tmp/scwrl_776222130.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_776222130.pdb # conformation set from SCWRL output # naming current conformation PROTINFO_TS1-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_901912567.pdb -s /var/tmp/to_scwrl_901912567.seq -o /var/tmp/from_scwrl_901912567.pdb > /var/tmp/scwrl_901912567.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_901912567.pdb # conformation set from SCWRL output # naming current conformation PROTINFO_TS2-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1212990542.pdb -s /var/tmp/to_scwrl_1212990542.seq -o /var/tmp/from_scwrl_1212990542.pdb > /var/tmp/scwrl_1212990542.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1212990542.pdb # conformation set from SCWRL output # naming current conformation PROTINFO_TS3-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # Found a chain break before 369 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1612392342.pdb -s /var/tmp/to_scwrl_1612392342.seq -o /var/tmp/from_scwrl_1612392342.pdb > /var/tmp/scwrl_1612392342.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1612392342.pdb # conformation set from SCWRL output # naming current conformation PROTINFO_TS4-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # Found a chain break before 365 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1958421394.pdb -s /var/tmp/to_scwrl_1958421394.seq -o /var/tmp/from_scwrl_1958421394.pdb > /var/tmp/scwrl_1958421394.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1958421394.pdb # conformation set from SCWRL output # naming current conformation PROTINFO_TS5-scwrl # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Pcons6_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1736679881.pdb -s /var/tmp/to_scwrl_1736679881.seq -o /var/tmp/from_scwrl_1736679881.pdb > /var/tmp/scwrl_1736679881.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1736679881.pdb # conformation set from SCWRL output # naming current conformation Pcons6_TS1-scwrl # ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Pcons6_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_747714827.pdb -s /var/tmp/to_scwrl_747714827.seq -o /var/tmp/from_scwrl_747714827.pdb > /var/tmp/scwrl_747714827.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_747714827.pdb # conformation set from SCWRL output # naming current conformation Pcons6_TS2-scwrl # ReadConformPDB reading from PDB file servers/Pcons6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Pcons6_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1401195751.pdb -s /var/tmp/to_scwrl_1401195751.seq -o /var/tmp/from_scwrl_1401195751.pdb > /var/tmp/scwrl_1401195751.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1401195751.pdb # conformation set from SCWRL output # naming current conformation Pcons6_TS3-scwrl # ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Pcons6_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1413828045.pdb -s /var/tmp/to_scwrl_1413828045.seq -o /var/tmp/from_scwrl_1413828045.pdb > /var/tmp/scwrl_1413828045.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1413828045.pdb # conformation set from SCWRL output # naming current conformation Pcons6_TS4-scwrl # ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1 # Found a chain break before 363 # copying to AlignedFragments data structure # naming current conformation Pcons6_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_30013524.pdb -s /var/tmp/to_scwrl_30013524.seq -o /var/tmp/from_scwrl_30013524.pdb > /var/tmp/scwrl_30013524.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_30013524.pdb # conformation set from SCWRL output # naming current conformation Pcons6_TS5-scwrl # ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Phyre-1_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1272124212.pdb -s /var/tmp/to_scwrl_1272124212.seq -o /var/tmp/from_scwrl_1272124212.pdb > /var/tmp/scwrl_1272124212.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1272124212.pdb # conformation set from SCWRL output # naming current conformation Phyre-1_TS1-scwrl # ReadConformPDB reading from PDB file servers/Phyre-2_TS1.pdb.gz looking for model 1 # Found a chain break before 358 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1124646393.pdb -s /var/tmp/to_scwrl_1124646393.seq -o /var/tmp/from_scwrl_1124646393.pdb > /var/tmp/scwrl_1124646393.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1124646393.pdb # conformation set from SCWRL output # naming current conformation Phyre-2_TS1-scwrl # ReadConformPDB reading from PDB file servers/Phyre-2_TS2.pdb.gz looking for model 1 # Found a chain break before 342 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1804081539.pdb -s /var/tmp/to_scwrl_1804081539.seq -o /var/tmp/from_scwrl_1804081539.pdb > /var/tmp/scwrl_1804081539.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1804081539.pdb # conformation set from SCWRL output # naming current conformation Phyre-2_TS2-scwrl # ReadConformPDB reading from PDB file servers/Phyre-2_TS3.pdb.gz looking for model 1 # Found a chain break before 370 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_794805426.pdb -s /var/tmp/to_scwrl_794805426.seq -o /var/tmp/from_scwrl_794805426.pdb > /var/tmp/scwrl_794805426.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_794805426.pdb # conformation set from SCWRL output # naming current conformation Phyre-2_TS3-scwrl # ReadConformPDB reading from PDB file servers/Phyre-2_TS4.pdb.gz looking for model 1 # Found a chain break before 334 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_851032089.pdb -s /var/tmp/to_scwrl_851032089.seq -o /var/tmp/from_scwrl_851032089.pdb > /var/tmp/scwrl_851032089.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_851032089.pdb # conformation set from SCWRL output # naming current conformation Phyre-2_TS4-scwrl # ReadConformPDB reading from PDB file servers/Phyre-2_TS5.pdb.gz looking for model 1 # Found a chain break before 365 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1536777753.pdb -s /var/tmp/to_scwrl_1536777753.seq -o /var/tmp/from_scwrl_1536777753.pdb > /var/tmp/scwrl_1536777753.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1536777753.pdb # conformation set from SCWRL output # naming current conformation Phyre-2_TS5-scwrl # ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_559602523.pdb -s /var/tmp/to_scwrl_559602523.seq -o /var/tmp/from_scwrl_559602523.pdb > /var/tmp/scwrl_559602523.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_559602523.pdb # conformation set from SCWRL output # naming current conformation Pmodeller6_TS1-scwrl # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_906828072.pdb -s /var/tmp/to_scwrl_906828072.seq -o /var/tmp/from_scwrl_906828072.pdb > /var/tmp/scwrl_906828072.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_906828072.pdb # conformation set from SCWRL output # naming current conformation Pmodeller6_TS2-scwrl # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1178917016.pdb -s /var/tmp/to_scwrl_1178917016.seq -o /var/tmp/from_scwrl_1178917016.pdb > /var/tmp/scwrl_1178917016.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1178917016.pdb # conformation set from SCWRL output # naming current conformation Pmodeller6_TS3-scwrl # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_712260752.pdb -s /var/tmp/to_scwrl_712260752.seq -o /var/tmp/from_scwrl_712260752.pdb > /var/tmp/scwrl_712260752.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_712260752.pdb # conformation set from SCWRL output # naming current conformation Pmodeller6_TS4-scwrl # ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_664588052.pdb -s /var/tmp/to_scwrl_664588052.seq -o /var/tmp/from_scwrl_664588052.pdb > /var/tmp/scwrl_664588052.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_664588052.pdb # conformation set from SCWRL output # naming current conformation Pmodeller6_TS5-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1 # Found a chain break before 340 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_420214875.pdb -s /var/tmp/to_scwrl_420214875.seq -o /var/tmp/from_scwrl_420214875.pdb > /var/tmp/scwrl_420214875.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_420214875.pdb # conformation set from SCWRL output # naming current conformation RAPTOR-ACE_TS1-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1 # Found a chain break before 336 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1006574218.pdb -s /var/tmp/to_scwrl_1006574218.seq -o /var/tmp/from_scwrl_1006574218.pdb > /var/tmp/scwrl_1006574218.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1006574218.pdb # conformation set from SCWRL output # naming current conformation RAPTOR-ACE_TS2-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1 # Found a chain break before 132 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_525455203.pdb -s /var/tmp/to_scwrl_525455203.seq -o /var/tmp/from_scwrl_525455203.pdb > /var/tmp/scwrl_525455203.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_525455203.pdb # conformation set from SCWRL output # naming current conformation RAPTOR-ACE_TS3-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS4.pdb.gz looking for model 1 # Found a chain break before 348 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1048446576.pdb -s /var/tmp/to_scwrl_1048446576.seq -o /var/tmp/from_scwrl_1048446576.pdb > /var/tmp/scwrl_1048446576.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1048446576.pdb # conformation set from SCWRL output # naming current conformation RAPTOR-ACE_TS4-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1 # Found a chain break before 294 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_933414580.pdb -s /var/tmp/to_scwrl_933414580.seq -o /var/tmp/from_scwrl_933414580.pdb > /var/tmp/scwrl_933414580.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_933414580.pdb # conformation set from SCWRL output # naming current conformation RAPTOR-ACE_TS5-scwrl # ReadConformPDB reading from PDB file servers/RAPTORESS_TS1.pdb.gz looking for model 1 # Found a chain break before 372 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1758284228.pdb -s /var/tmp/to_scwrl_1758284228.seq -o /var/tmp/from_scwrl_1758284228.pdb > /var/tmp/scwrl_1758284228.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1758284228.pdb # conformation set from SCWRL output # naming current conformation RAPTORESS_TS1-scwrl # ReadConformPDB reading from PDB file servers/RAPTORESS_TS2.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1740102674.pdb -s /var/tmp/to_scwrl_1740102674.seq -o /var/tmp/from_scwrl_1740102674.pdb > /var/tmp/scwrl_1740102674.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1740102674.pdb # conformation set from SCWRL output # naming current conformation RAPTORESS_TS2-scwrl # ReadConformPDB reading from PDB file servers/RAPTORESS_TS3.pdb.gz looking for model 1 # Found a chain break before 369 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1337568210.pdb -s /var/tmp/to_scwrl_1337568210.seq -o /var/tmp/from_scwrl_1337568210.pdb > /var/tmp/scwrl_1337568210.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1337568210.pdb # conformation set from SCWRL output # naming current conformation RAPTORESS_TS3-scwrl # ReadConformPDB reading from PDB file servers/RAPTORESS_TS4.pdb.gz looking for model 1 # Found a chain break before 365 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_738293151.pdb -s /var/tmp/to_scwrl_738293151.seq -o /var/tmp/from_scwrl_738293151.pdb > /var/tmp/scwrl_738293151.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_738293151.pdb # conformation set from SCWRL output # naming current conformation RAPTORESS_TS4-scwrl # ReadConformPDB reading from PDB file servers/RAPTORESS_TS5.pdb.gz looking for model 1 # Found a chain break before 354 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_334661982.pdb -s /var/tmp/to_scwrl_334661982.seq -o /var/tmp/from_scwrl_334661982.pdb > /var/tmp/scwrl_334661982.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_334661982.pdb # conformation set from SCWRL output # naming current conformation RAPTORESS_TS5-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR_TS1.pdb.gz looking for model 1 # Found a chain break before 372 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2113790340.pdb -s /var/tmp/to_scwrl_2113790340.seq -o /var/tmp/from_scwrl_2113790340.pdb > /var/tmp/scwrl_2113790340.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2113790340.pdb # conformation set from SCWRL output # naming current conformation RAPTOR_TS1-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1 # Found a chain break before 363 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1640205717.pdb -s /var/tmp/to_scwrl_1640205717.seq -o /var/tmp/from_scwrl_1640205717.pdb > /var/tmp/scwrl_1640205717.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1640205717.pdb # conformation set from SCWRL output # naming current conformation RAPTOR_TS2-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR_TS3.pdb.gz looking for model 1 # Found a chain break before 360 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1547652524.pdb -s /var/tmp/to_scwrl_1547652524.seq -o /var/tmp/from_scwrl_1547652524.pdb > /var/tmp/scwrl_1547652524.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1547652524.pdb # conformation set from SCWRL output # naming current conformation RAPTOR_TS3-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR_TS4.pdb.gz looking for model 1 # Found a chain break before 364 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1578699035.pdb -s /var/tmp/to_scwrl_1578699035.seq -o /var/tmp/from_scwrl_1578699035.pdb > /var/tmp/scwrl_1578699035.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1578699035.pdb # conformation set from SCWRL output # naming current conformation RAPTOR_TS4-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR_TS5.pdb.gz looking for model 1 # Found a chain break before 339 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1451143465.pdb -s /var/tmp/to_scwrl_1451143465.seq -o /var/tmp/from_scwrl_1451143465.pdb > /var/tmp/scwrl_1451143465.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1451143465.pdb # conformation set from SCWRL output # naming current conformation RAPTOR_TS5-scwrl # ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1 # Found a chain break before 316 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1136848759.pdb -s /var/tmp/to_scwrl_1136848759.seq -o /var/tmp/from_scwrl_1136848759.pdb > /var/tmp/scwrl_1136848759.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1136848759.pdb # conformation set from SCWRL output # naming current conformation ROBETTA_TS1-scwrl # ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1 # Found a chain break before 339 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_178930215.pdb -s /var/tmp/to_scwrl_178930215.seq -o /var/tmp/from_scwrl_178930215.pdb > /var/tmp/scwrl_178930215.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_178930215.pdb # conformation set from SCWRL output # naming current conformation ROBETTA_TS2-scwrl # ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1 # Found a chain break before 346 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_704855570.pdb -s /var/tmp/to_scwrl_704855570.seq -o /var/tmp/from_scwrl_704855570.pdb > /var/tmp/scwrl_704855570.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_704855570.pdb # conformation set from SCWRL output # naming current conformation ROBETTA_TS3-scwrl # ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1 # Found a chain break before 340 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_403193158.pdb -s /var/tmp/to_scwrl_403193158.seq -o /var/tmp/from_scwrl_403193158.pdb > /var/tmp/scwrl_403193158.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_403193158.pdb # conformation set from SCWRL output # naming current conformation ROBETTA_TS4-scwrl # ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1 # Found a chain break before 305 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_208943740.pdb -s /var/tmp/to_scwrl_208943740.seq -o /var/tmp/from_scwrl_208943740.pdb > /var/tmp/scwrl_208943740.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_208943740.pdb # conformation set from SCWRL output # naming current conformation ROBETTA_TS5-scwrl # ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1976979782.pdb -s /var/tmp/to_scwrl_1976979782.seq -o /var/tmp/from_scwrl_1976979782.pdb > /var/tmp/scwrl_1976979782.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1976979782.pdb # conformation set from SCWRL output # naming current conformation ROKKY_TS1-scwrl # ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1527839551.pdb -s /var/tmp/to_scwrl_1527839551.seq -o /var/tmp/from_scwrl_1527839551.pdb > /var/tmp/scwrl_1527839551.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1527839551.pdb # conformation set from SCWRL output # naming current conformation ROKKY_TS2-scwrl # ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2013025279.pdb -s /var/tmp/to_scwrl_2013025279.seq -o /var/tmp/from_scwrl_2013025279.pdb > /var/tmp/scwrl_2013025279.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2013025279.pdb # conformation set from SCWRL output # naming current conformation ROKKY_TS3-scwrl # ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_624301562.pdb -s /var/tmp/to_scwrl_624301562.seq -o /var/tmp/from_scwrl_624301562.pdb > /var/tmp/scwrl_624301562.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_624301562.pdb # conformation set from SCWRL output # naming current conformation ROKKY_TS4-scwrl # ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_231387993.pdb -s /var/tmp/to_scwrl_231387993.seq -o /var/tmp/from_scwrl_231387993.pdb > /var/tmp/scwrl_231387993.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_231387993.pdb # conformation set from SCWRL output # naming current conformation ROKKY_TS5-scwrl # ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1402319385.pdb -s /var/tmp/to_scwrl_1402319385.seq -o /var/tmp/from_scwrl_1402319385.pdb > /var/tmp/scwrl_1402319385.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1402319385.pdb # conformation set from SCWRL output # naming current conformation SAM-T02_AL1-scwrl # ReadConformPDB reading from PDB file servers/SAM-T02_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1183904084.pdb -s /var/tmp/to_scwrl_1183904084.seq -o /var/tmp/from_scwrl_1183904084.pdb > /var/tmp/scwrl_1183904084.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1183904084.pdb # conformation set from SCWRL output # naming current conformation SAM-T02_AL2-scwrl # ReadConformPDB reading from PDB file servers/SAM-T02_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1138216064.pdb -s /var/tmp/to_scwrl_1138216064.seq -o /var/tmp/from_scwrl_1138216064.pdb > /var/tmp/scwrl_1138216064.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1138216064.pdb # conformation set from SCWRL output # naming current conformation SAM-T02_AL3-scwrl # ReadConformPDB reading from PDB file servers/SAM-T02_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_433752755.pdb -s /var/tmp/to_scwrl_433752755.seq -o /var/tmp/from_scwrl_433752755.pdb > /var/tmp/scwrl_433752755.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_433752755.pdb # conformation set from SCWRL output # naming current conformation SAM-T02_AL4-scwrl # ReadConformPDB reading from PDB file servers/SAM-T02_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1896164836.pdb -s /var/tmp/to_scwrl_1896164836.seq -o /var/tmp/from_scwrl_1896164836.pdb > /var/tmp/scwrl_1896164836.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1896164836.pdb # conformation set from SCWRL output # naming current conformation SAM-T02_AL5-scwrl # ReadConformPDB reading from PDB file servers/SAM-T99_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1802804117.pdb -s /var/tmp/to_scwrl_1802804117.seq -o /var/tmp/from_scwrl_1802804117.pdb > /var/tmp/scwrl_1802804117.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1802804117.pdb # conformation set from SCWRL output # naming current conformation SAM-T99_AL1-scwrl # ReadConformPDB reading from PDB file servers/SAM-T99_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_853967630.pdb -s /var/tmp/to_scwrl_853967630.seq -o /var/tmp/from_scwrl_853967630.pdb > /var/tmp/scwrl_853967630.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_853967630.pdb # conformation set from SCWRL output # naming current conformation SAM-T99_AL2-scwrl # ReadConformPDB reading from PDB file servers/SAM-T99_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_755255407.pdb -s /var/tmp/to_scwrl_755255407.seq -o /var/tmp/from_scwrl_755255407.pdb > /var/tmp/scwrl_755255407.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_755255407.pdb # conformation set from SCWRL output # naming current conformation SAM-T99_AL3-scwrl # ReadConformPDB reading from PDB file servers/SAM-T99_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_180775673.pdb -s /var/tmp/to_scwrl_180775673.seq -o /var/tmp/from_scwrl_180775673.pdb > /var/tmp/scwrl_180775673.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_180775673.pdb # conformation set from SCWRL output # naming current conformation SAM-T99_AL4-scwrl # ReadConformPDB reading from PDB file servers/SAM-T99_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1902414205.pdb -s /var/tmp/to_scwrl_1902414205.seq -o /var/tmp/from_scwrl_1902414205.pdb > /var/tmp/scwrl_1902414205.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1902414205.pdb # conformation set from SCWRL output # naming current conformation SAM-T99_AL5-scwrl # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1 # Found a chain break before 372 # copying to AlignedFragments data structure # naming current conformation SAM_T06_server_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1688669986.pdb -s /var/tmp/to_scwrl_1688669986.seq -o /var/tmp/from_scwrl_1688669986.pdb > /var/tmp/scwrl_1688669986.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1688669986.pdb # conformation set from SCWRL output # naming current conformation SAM_T06_server_TS1-scwrl # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1939059901.pdb -s /var/tmp/to_scwrl_1939059901.seq -o /var/tmp/from_scwrl_1939059901.pdb > /var/tmp/scwrl_1939059901.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1939059901.pdb # conformation set from SCWRL output # naming current conformation SAM_T06_server_TS2-scwrl # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1495033232.pdb -s /var/tmp/to_scwrl_1495033232.seq -o /var/tmp/from_scwrl_1495033232.pdb > /var/tmp/scwrl_1495033232.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1495033232.pdb # conformation set from SCWRL output # naming current conformation SAM_T06_server_TS3-scwrl # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_878754550.pdb -s /var/tmp/to_scwrl_878754550.seq -o /var/tmp/from_scwrl_878754550.pdb > /var/tmp/scwrl_878754550.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_878754550.pdb # conformation set from SCWRL output # naming current conformation SAM_T06_server_TS4-scwrl # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_529869405.pdb -s /var/tmp/to_scwrl_529869405.seq -o /var/tmp/from_scwrl_529869405.pdb > /var/tmp/scwrl_529869405.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_529869405.pdb # conformation set from SCWRL output # naming current conformation SAM_T06_server_TS5-scwrl # ReadConformPDB reading from PDB file servers/SP3_TS1.pdb.gz looking for model 1 # Found a chain break before 173 # copying to AlignedFragments data structure # naming current conformation SP3_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1829695215.pdb -s /var/tmp/to_scwrl_1829695215.seq -o /var/tmp/from_scwrl_1829695215.pdb > /var/tmp/scwrl_1829695215.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1829695215.pdb # conformation set from SCWRL output # naming current conformation SP3_TS1-scwrl # ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1 # Found a chain break before 301 # copying to AlignedFragments data structure # naming current conformation SP3_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_845061243.pdb -s /var/tmp/to_scwrl_845061243.seq -o /var/tmp/from_scwrl_845061243.pdb > /var/tmp/scwrl_845061243.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_845061243.pdb # conformation set from SCWRL output # naming current conformation SP3_TS2-scwrl # ReadConformPDB reading from PDB file servers/SP3_TS3.pdb.gz looking for model 1 # Found a chain break before 288 # copying to AlignedFragments data structure # naming current conformation SP3_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_22591476.pdb -s /var/tmp/to_scwrl_22591476.seq -o /var/tmp/from_scwrl_22591476.pdb > /var/tmp/scwrl_22591476.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_22591476.pdb # conformation set from SCWRL output # naming current conformation SP3_TS3-scwrl # ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1 # Found a chain break before 348 # copying to AlignedFragments data structure # naming current conformation SP3_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1229864092.pdb -s /var/tmp/to_scwrl_1229864092.seq -o /var/tmp/from_scwrl_1229864092.pdb > /var/tmp/scwrl_1229864092.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1229864092.pdb # conformation set from SCWRL output # naming current conformation SP3_TS4-scwrl # ReadConformPDB reading from PDB file servers/SP3_TS5.pdb.gz looking for model 1 # Found a chain break before 212 # copying to AlignedFragments data structure # naming current conformation SP3_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_276276632.pdb -s /var/tmp/to_scwrl_276276632.seq -o /var/tmp/from_scwrl_276276632.pdb > /var/tmp/scwrl_276276632.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_276276632.pdb # conformation set from SCWRL output # naming current conformation SP3_TS5-scwrl # ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1 # Found a chain break before 202 # copying to AlignedFragments data structure # naming current conformation SP4_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1473734941.pdb -s /var/tmp/to_scwrl_1473734941.seq -o /var/tmp/from_scwrl_1473734941.pdb > /var/tmp/scwrl_1473734941.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1473734941.pdb # conformation set from SCWRL output # naming current conformation SP4_TS1-scwrl # ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1 # Found a chain break before 170 # copying to AlignedFragments data structure # naming current conformation SP4_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_219229205.pdb -s /var/tmp/to_scwrl_219229205.seq -o /var/tmp/from_scwrl_219229205.pdb > /var/tmp/scwrl_219229205.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_219229205.pdb # conformation set from SCWRL output # naming current conformation SP4_TS2-scwrl # ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1 # Found a chain break before 259 # copying to AlignedFragments data structure # naming current conformation SP4_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_455206847.pdb -s /var/tmp/to_scwrl_455206847.seq -o /var/tmp/from_scwrl_455206847.pdb > /var/tmp/scwrl_455206847.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_455206847.pdb # conformation set from SCWRL output # naming current conformation SP4_TS3-scwrl # ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1 # Found a chain break before 301 # copying to AlignedFragments data structure # naming current conformation SP4_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_31106864.pdb -s /var/tmp/to_scwrl_31106864.seq -o /var/tmp/from_scwrl_31106864.pdb > /var/tmp/scwrl_31106864.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_31106864.pdb # conformation set from SCWRL output # naming current conformation SP4_TS4-scwrl # ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1 # Found a chain break before 244 # copying to AlignedFragments data structure # naming current conformation SP4_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_622422363.pdb -s /var/tmp/to_scwrl_622422363.seq -o /var/tmp/from_scwrl_622422363.pdb > /var/tmp/scwrl_622422363.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_622422363.pdb # conformation set from SCWRL output # naming current conformation SP4_TS5-scwrl # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # Found a chain break before 162 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_664150587.pdb -s /var/tmp/to_scwrl_664150587.seq -o /var/tmp/from_scwrl_664150587.pdb > /var/tmp/scwrl_664150587.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_664150587.pdb # conformation set from SCWRL output # naming current conformation SPARKS2_TS1-scwrl # ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1 # Found a chain break before 266 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2008086646.pdb -s /var/tmp/to_scwrl_2008086646.seq -o /var/tmp/from_scwrl_2008086646.pdb > /var/tmp/scwrl_2008086646.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2008086646.pdb # conformation set from SCWRL output # naming current conformation SPARKS2_TS2-scwrl # ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1 # Found a chain break before 372 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2778267.pdb -s /var/tmp/to_scwrl_2778267.seq -o /var/tmp/from_scwrl_2778267.pdb > /var/tmp/scwrl_2778267.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2778267.pdb # conformation set from SCWRL output # naming current conformation SPARKS2_TS3-scwrl # ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1 # Found a chain break before 200 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_529692219.pdb -s /var/tmp/to_scwrl_529692219.seq -o /var/tmp/from_scwrl_529692219.pdb > /var/tmp/scwrl_529692219.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_529692219.pdb # conformation set from SCWRL output # naming current conformation SPARKS2_TS4-scwrl # ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1 # Found a chain break before 292 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_484904561.pdb -s /var/tmp/to_scwrl_484904561.seq -o /var/tmp/from_scwrl_484904561.pdb > /var/tmp/scwrl_484904561.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_484904561.pdb # conformation set from SCWRL output # naming current conformation SPARKS2_TS5-scwrl # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_234166261.pdb -s /var/tmp/to_scwrl_234166261.seq -o /var/tmp/from_scwrl_234166261.pdb > /var/tmp/scwrl_234166261.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_234166261.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_bnmx_TS1-scwrl # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1932011604.pdb -s /var/tmp/to_scwrl_1932011604.seq -o /var/tmp/from_scwrl_1932011604.pdb > /var/tmp/scwrl_1932011604.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1932011604.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_bnmx_TS2-scwrl # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1668808646.pdb -s /var/tmp/to_scwrl_1668808646.seq -o /var/tmp/from_scwrl_1668808646.pdb > /var/tmp/scwrl_1668808646.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1668808646.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_bnmx_TS3-scwrl # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1372382325.pdb -s /var/tmp/to_scwrl_1372382325.seq -o /var/tmp/from_scwrl_1372382325.pdb > /var/tmp/scwrl_1372382325.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1372382325.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_bnmx_TS4-scwrl # ReadConformPDB reading from PDB file servers/UNI-EID_expm_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation UNI-EID_expm_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_218280713.pdb -s /var/tmp/to_scwrl_218280713.seq -o /var/tmp/from_scwrl_218280713.pdb > /var/tmp/scwrl_218280713.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_218280713.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_expm_TS1-scwrl # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1417489835.pdb -s /var/tmp/to_scwrl_1417489835.seq -o /var/tmp/from_scwrl_1417489835.pdb > /var/tmp/scwrl_1417489835.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1417489835.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_sfst_AL1-scwrl # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1027702796.pdb -s /var/tmp/to_scwrl_1027702796.seq -o /var/tmp/from_scwrl_1027702796.pdb > /var/tmp/scwrl_1027702796.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1027702796.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_sfst_AL2-scwrl # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1072248343.pdb -s /var/tmp/to_scwrl_1072248343.seq -o /var/tmp/from_scwrl_1072248343.pdb > /var/tmp/scwrl_1072248343.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1072248343.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_sfst_AL3-scwrl # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_25261596.pdb -s /var/tmp/to_scwrl_25261596.seq -o /var/tmp/from_scwrl_25261596.pdb > /var/tmp/scwrl_25261596.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_25261596.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_sfst_AL4-scwrl # ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1208478469.pdb -s /var/tmp/to_scwrl_1208478469.seq -o /var/tmp/from_scwrl_1208478469.pdb > /var/tmp/scwrl_1208478469.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1208478469.pdb # conformation set from SCWRL output # naming current conformation Zhang-Server_TS1-scwrl # ReadConformPDB reading from PDB file servers/Zhang-Server_TS2.pdb.gz looking for model 1 # Found a chain break before 361 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_827178902.pdb -s /var/tmp/to_scwrl_827178902.seq -o /var/tmp/from_scwrl_827178902.pdb > /var/tmp/scwrl_827178902.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_827178902.pdb # conformation set from SCWRL output # naming current conformation Zhang-Server_TS2-scwrl # ReadConformPDB reading from PDB file servers/Zhang-Server_TS3.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1713931582.pdb -s /var/tmp/to_scwrl_1713931582.seq -o /var/tmp/from_scwrl_1713931582.pdb > /var/tmp/scwrl_1713931582.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1713931582.pdb # conformation set from SCWRL output # naming current conformation Zhang-Server_TS3-scwrl # ReadConformPDB reading from PDB file servers/Zhang-Server_TS4.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1000054724.pdb -s /var/tmp/to_scwrl_1000054724.seq -o /var/tmp/from_scwrl_1000054724.pdb > /var/tmp/scwrl_1000054724.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1000054724.pdb # conformation set from SCWRL output # naming current conformation Zhang-Server_TS4-scwrl # ReadConformPDB reading from PDB file servers/Zhang-Server_TS5.pdb.gz looking for model 1 # Found a chain break before 363 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_174728487.pdb -s /var/tmp/to_scwrl_174728487.seq -o /var/tmp/from_scwrl_174728487.pdb > /var/tmp/scwrl_174728487.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_174728487.pdb # conformation set from SCWRL output # naming current conformation Zhang-Server_TS5-scwrl # ReadConformPDB reading from PDB file servers/beautshot_TS1.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # naming current conformation beautshot_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_445202486.pdb -s /var/tmp/to_scwrl_445202486.seq -o /var/tmp/from_scwrl_445202486.pdb > /var/tmp/scwrl_445202486.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_445202486.pdb # conformation set from SCWRL output # naming current conformation beautshot_TS1-scwrl # ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation beautshotbase_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1529924129.pdb -s /var/tmp/to_scwrl_1529924129.seq -o /var/tmp/from_scwrl_1529924129.pdb > /var/tmp/scwrl_1529924129.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1529924129.pdb # conformation set from SCWRL output # naming current conformation beautshotbase_TS1-scwrl # ReadConformPDB reading from PDB file servers/forecast-s_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation forecast-s_AL1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2004423702.pdb -s /var/tmp/to_scwrl_2004423702.seq -o /var/tmp/from_scwrl_2004423702.pdb > /var/tmp/scwrl_2004423702.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2004423702.pdb # conformation set from SCWRL output # naming current conformation forecast-s_AL1-scwrl # ReadConformPDB reading from PDB file servers/forecast-s_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation forecast-s_AL2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1290263728.pdb -s /var/tmp/to_scwrl_1290263728.seq -o /var/tmp/from_scwrl_1290263728.pdb > /var/tmp/scwrl_1290263728.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1290263728.pdb # conformation set from SCWRL output # naming current conformation forecast-s_AL2-scwrl # ReadConformPDB reading from PDB file servers/forecast-s_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation forecast-s_AL3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1552515605.pdb -s /var/tmp/to_scwrl_1552515605.seq -o /var/tmp/from_scwrl_1552515605.pdb > /var/tmp/scwrl_1552515605.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1552515605.pdb # conformation set from SCWRL output # naming current conformation forecast-s_AL3-scwrl # ReadConformPDB reading from PDB file servers/forecast-s_AL4.pdb.gz looking for model 1 Skipped atom 334, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 336, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 338, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 340, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 342, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 344, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 346, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 348, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 350, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 352, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 354, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 356, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation forecast-s_AL4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1086804148.pdb -s /var/tmp/to_scwrl_1086804148.seq -o /var/tmp/from_scwrl_1086804148.pdb > /var/tmp/scwrl_1086804148.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1086804148.pdb # conformation set from SCWRL output # naming current conformation forecast-s_AL4-scwrl # ReadConformPDB reading from PDB file servers/forecast-s_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation forecast-s_AL5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1566540360.pdb -s /var/tmp/to_scwrl_1566540360.seq -o /var/tmp/from_scwrl_1566540360.pdb > /var/tmp/scwrl_1566540360.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1566540360.pdb # conformation set from SCWRL output # naming current conformation forecast-s_AL5-scwrl # ReadConformPDB reading from PDB file servers/gtg_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation gtg_AL1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_878766900.pdb -s /var/tmp/to_scwrl_878766900.seq -o /var/tmp/from_scwrl_878766900.pdb > /var/tmp/scwrl_878766900.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_878766900.pdb # conformation set from SCWRL output # naming current conformation gtg_AL1-scwrl # ReadConformPDB reading from PDB file servers/gtg_AL2.pdb.gz looking for model 1 Skipped atom 278, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 280, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 282, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 284, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 286, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 288, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 290, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 292, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 606, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 608, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 610, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 612, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 622, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 624, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 626, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 628, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 734, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 736, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 738, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 740, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 934, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 936, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 938, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 940, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 1042, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 1044, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 1046, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 1048, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation gtg_AL2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1306033353.pdb -s /var/tmp/to_scwrl_1306033353.seq -o /var/tmp/from_scwrl_1306033353.pdb > /var/tmp/scwrl_1306033353.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1306033353.pdb # conformation set from SCWRL output # naming current conformation gtg_AL2-scwrl # ReadConformPDB reading from PDB file servers/gtg_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation gtg_AL3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2021747208.pdb -s /var/tmp/to_scwrl_2021747208.seq -o /var/tmp/from_scwrl_2021747208.pdb > /var/tmp/scwrl_2021747208.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2021747208.pdb # conformation set from SCWRL output # naming current conformation gtg_AL3-scwrl # ReadConformPDB reading from PDB file servers/gtg_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation gtg_AL4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_909873764.pdb -s /var/tmp/to_scwrl_909873764.seq -o /var/tmp/from_scwrl_909873764.pdb > /var/tmp/scwrl_909873764.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_909873764.pdb # conformation set from SCWRL output # naming current conformation gtg_AL4-scwrl # ReadConformPDB reading from PDB file servers/gtg_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation gtg_AL5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1928455717.pdb -s /var/tmp/to_scwrl_1928455717.seq -o /var/tmp/from_scwrl_1928455717.pdb > /var/tmp/scwrl_1928455717.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1928455717.pdb # conformation set from SCWRL output # naming current conformation gtg_AL5-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # Found a chain break before 363 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_538414148.pdb -s /var/tmp/to_scwrl_538414148.seq -o /var/tmp/from_scwrl_538414148.pdb > /var/tmp/scwrl_538414148.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_538414148.pdb # conformation set from SCWRL output # naming current conformation karypis.srv.2_TS1-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS2.pdb.gz looking for model 1 # Found a chain break before 367 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_770476763.pdb -s /var/tmp/to_scwrl_770476763.seq -o /var/tmp/from_scwrl_770476763.pdb > /var/tmp/scwrl_770476763.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_770476763.pdb # conformation set from SCWRL output # naming current conformation karypis.srv.2_TS2-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS3.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1931233984.pdb -s /var/tmp/to_scwrl_1931233984.seq -o /var/tmp/from_scwrl_1931233984.pdb > /var/tmp/scwrl_1931233984.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1931233984.pdb # conformation set from SCWRL output # naming current conformation karypis.srv.2_TS3-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS4.pdb.gz looking for model 1 # Found a chain break before 358 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1068106368.pdb -s /var/tmp/to_scwrl_1068106368.seq -o /var/tmp/from_scwrl_1068106368.pdb > /var/tmp/scwrl_1068106368.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1068106368.pdb # conformation set from SCWRL output # naming current conformation karypis.srv.2_TS4-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS5.pdb.gz looking for model 1 # Found a chain break before 317 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1255381324.pdb -s /var/tmp/to_scwrl_1255381324.seq -o /var/tmp/from_scwrl_1255381324.pdb > /var/tmp/scwrl_1255381324.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1255381324.pdb # conformation set from SCWRL output # naming current conformation karypis.srv.2_TS5-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS1.pdb.gz looking for model 1 WARNING: atoms too close: (T0316)G172.O and (T0316)H173.N only 0.000 apart, marking (T0316)H173.N as missing WARNING: atoms too close: (T0316)H280.O and (T0316)D281.N only 0.000 apart, marking (T0316)D281.N as missing WARNING: atoms too close: (T0316)Y364.O and (T0316)R365.N only 0.000 apart, marking (T0316)R365.N as missing # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_17916598.pdb -s /var/tmp/to_scwrl_17916598.seq -o /var/tmp/from_scwrl_17916598.pdb > /var/tmp/scwrl_17916598.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_17916598.pdb # conformation set from SCWRL output # naming current conformation karypis.srv.4_TS1-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS2.pdb.gz looking for model 1 # Found a chain break before 370 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_852634325.pdb -s /var/tmp/to_scwrl_852634325.seq -o /var/tmp/from_scwrl_852634325.pdb > /var/tmp/scwrl_852634325.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_852634325.pdb # conformation set from SCWRL output # naming current conformation karypis.srv.4_TS2-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS3.pdb.gz looking for model 1 WARNING: atoms too close: (T0316)I202.O and (T0316)G203.N only 0.000 apart, marking (T0316)G203.N as missing WARNING: atoms too close: (T0316)G264.O and (T0316)K265.N only 0.000 apart, marking (T0316)K265.N as missing # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_776706324.pdb -s /var/tmp/to_scwrl_776706324.seq -o /var/tmp/from_scwrl_776706324.pdb > /var/tmp/scwrl_776706324.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_776706324.pdb # conformation set from SCWRL output # naming current conformation karypis.srv.4_TS3-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS4.pdb.gz looking for model 1 WARNING: atoms too close: (T0316)L143.O and (T0316)R144.N only 0.000 apart, marking (T0316)R144.N as missing WARNING: atoms too close: (T0316)R312.O and (T0316)Y313.N only 0.000 apart, marking (T0316)Y313.N as missing # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1390298924.pdb -s /var/tmp/to_scwrl_1390298924.seq -o /var/tmp/from_scwrl_1390298924.pdb > /var/tmp/scwrl_1390298924.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1390298924.pdb # conformation set from SCWRL output # naming current conformation karypis.srv.4_TS4-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS5.pdb.gz looking for model 1 WARNING: atoms too close: (T0316)C50.O and (T0316)T51.N only 0.000 apart, marking (T0316)T51.N as missing WARNING: atoms too close: (T0316)A186.O and (T0316)G187.N only 0.000 apart, marking (T0316)G187.N as missing WARNING: atoms too close: (T0316)T304.O and (T0316)L305.N only 0.000 apart, marking (T0316)L305.N as missing WARNING: atoms too close: (T0316)Y349.O and (T0316)D350.N only 0.000 apart, marking (T0316)D350.N as missing # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1070915038.pdb -s /var/tmp/to_scwrl_1070915038.seq -o /var/tmp/from_scwrl_1070915038.pdb > /var/tmp/scwrl_1070915038.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1070915038.pdb # conformation set from SCWRL output # naming current conformation karypis.srv.4_TS5-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_46712512.pdb -s /var/tmp/to_scwrl_46712512.seq -o /var/tmp/from_scwrl_46712512.pdb > /var/tmp/scwrl_46712512.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_46712512.pdb # conformation set from SCWRL output # naming current conformation karypis.srv_TS1-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_270518073.pdb -s /var/tmp/to_scwrl_270518073.seq -o /var/tmp/from_scwrl_270518073.pdb > /var/tmp/scwrl_270518073.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_270518073.pdb # conformation set from SCWRL output # naming current conformation karypis.srv_TS2-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2143163381.pdb -s /var/tmp/to_scwrl_2143163381.seq -o /var/tmp/from_scwrl_2143163381.pdb > /var/tmp/scwrl_2143163381.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2143163381.pdb # conformation set from SCWRL output # naming current conformation karypis.srv_TS3-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_71974108.pdb -s /var/tmp/to_scwrl_71974108.seq -o /var/tmp/from_scwrl_71974108.pdb > /var/tmp/scwrl_71974108.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_71974108.pdb # conformation set from SCWRL output # naming current conformation karypis.srv_TS4-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1478996542.pdb -s /var/tmp/to_scwrl_1478996542.seq -o /var/tmp/from_scwrl_1478996542.pdb > /var/tmp/scwrl_1478996542.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1478996542.pdb # conformation set from SCWRL output # naming current conformation karypis.srv_TS5-scwrl # ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation keasar-server_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_822858636.pdb -s /var/tmp/to_scwrl_822858636.seq -o /var/tmp/from_scwrl_822858636.pdb > /var/tmp/scwrl_822858636.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_822858636.pdb # conformation set from SCWRL output # naming current conformation keasar-server_TS1-scwrl # ReadConformPDB reading from PDB file servers/keasar-server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation keasar-server_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1785905691.pdb -s /var/tmp/to_scwrl_1785905691.seq -o /var/tmp/from_scwrl_1785905691.pdb > /var/tmp/scwrl_1785905691.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1785905691.pdb # conformation set from SCWRL output # naming current conformation keasar-server_TS2-scwrl # ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1 # Found a chain break before 310 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_331567620.pdb -s /var/tmp/to_scwrl_331567620.seq -o /var/tmp/from_scwrl_331567620.pdb > /var/tmp/scwrl_331567620.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_331567620.pdb # conformation set from SCWRL output # naming current conformation keasar-server_TS3-scwrl # ReadConformPDB reading from PDB file servers/keasar-server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation keasar-server_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_997587123.pdb -s /var/tmp/to_scwrl_997587123.seq -o /var/tmp/from_scwrl_997587123.pdb > /var/tmp/scwrl_997587123.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_997587123.pdb # conformation set from SCWRL output # naming current conformation keasar-server_TS4-scwrl # ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation keasar-server_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_83624530.pdb -s /var/tmp/to_scwrl_83624530.seq -o /var/tmp/from_scwrl_83624530.pdb > /var/tmp/scwrl_83624530.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_83624530.pdb # conformation set from SCWRL output # naming current conformation keasar-server_TS5-scwrl # ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation mGen-3D_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1861491749.pdb -s /var/tmp/to_scwrl_1861491749.seq -o /var/tmp/from_scwrl_1861491749.pdb > /var/tmp/scwrl_1861491749.log sh: line 1: 29254 Killed scwrl3 -i /var/tmp/to_scwrl_1861491749.pdb -s /var/tmp/to_scwrl_1861491749.seq -o /var/tmp/from_scwrl_1861491749.pdb >/var/tmp/scwrl_1861491749.log Error: Couldn't open file /var/tmp/from_scwrl_1861491749.pdb or /var/tmp/from_scwrl_1861491749.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1861491749_b.pdb or decoys//var/tmp/from_scwrl_1861491749_b.pdb.gz for input Trying /var/tmp/from_scwrl_1861491749_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_1861491749_b.pdb or /var/tmp/from_scwrl_1861491749_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1861491749_a.pdb or decoys//var/tmp/from_scwrl_1861491749_a.pdb.gz for input Trying /var/tmp/from_scwrl_1861491749_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_1861491749_a.pdb or /var/tmp/from_scwrl_1861491749_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_1861491749.pdb or /var/tmp/from_scwrl_1861491749_b.pdb or /var/tmp/from_scwrl_1861491749_a.pdb Error: no new SCWRL conformation added # naming current conformation mGen-3D_TS1-scwrl # ReadConformPDB reading from PDB file servers/nFOLD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation nFOLD_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_854527179.pdb -s /var/tmp/to_scwrl_854527179.seq -o /var/tmp/from_scwrl_854527179.pdb > /var/tmp/scwrl_854527179.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_854527179.pdb # conformation set from SCWRL output # naming current conformation nFOLD_TS1-scwrl # ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation nFOLD_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1373888258.pdb -s /var/tmp/to_scwrl_1373888258.seq -o /var/tmp/from_scwrl_1373888258.pdb > /var/tmp/scwrl_1373888258.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1373888258.pdb # conformation set from SCWRL output # naming current conformation nFOLD_TS2-scwrl # ReadConformPDB reading from PDB file servers/nFOLD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation nFOLD_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1266523707.pdb -s /var/tmp/to_scwrl_1266523707.seq -o /var/tmp/from_scwrl_1266523707.pdb > /var/tmp/scwrl_1266523707.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1266523707.pdb # conformation set from SCWRL output # naming current conformation nFOLD_TS3-scwrl # ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation nFOLD_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1941331327.pdb -s /var/tmp/to_scwrl_1941331327.seq -o /var/tmp/from_scwrl_1941331327.pdb > /var/tmp/scwrl_1941331327.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1941331327.pdb # conformation set from SCWRL output # naming current conformation nFOLD_TS4-scwrl # ReadConformPDB reading from PDB file servers/nFOLD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation nFOLD_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_792944973.pdb -s /var/tmp/to_scwrl_792944973.seq -o /var/tmp/from_scwrl_792944973.pdb > /var/tmp/scwrl_792944973.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_792944973.pdb # conformation set from SCWRL output # naming current conformation nFOLD_TS5-scwrl # ReadConformPDB reading from PDB file servers/panther2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation panther2_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2145290607.pdb -s /var/tmp/to_scwrl_2145290607.seq -o /var/tmp/from_scwrl_2145290607.pdb > /var/tmp/scwrl_2145290607.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2145290607.pdb # conformation set from SCWRL output # naming current conformation panther2_TS1-scwrl # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation shub_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1099881033.pdb -s /var/tmp/to_scwrl_1099881033.seq -o /var/tmp/from_scwrl_1099881033.pdb > /var/tmp/scwrl_1099881033.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1099881033.pdb # conformation set from SCWRL output # naming current conformation shub_TS1-scwrl # command:CPU_time= 90.8922 sec, elapsed time= 2474.91 sec) # command:# Prefix for output files set to decoys/ # command:# Will now start reporting costs to decoys/evaluate.rdb # command:# CostConform Warning: Couldn't open file decoys//projects/compbio/experiments/undertaker/spots/near-backbone-center.spot or decoys//projects/compbio/experiments/undertaker/spots/near-backbone-center.spot.gz for input Trying /projects/compbio/experiments/undertaker/spots/near-backbone-center.spot # Reading spots from /projects/compbio/experiments/undertaker/spots/near-backbone-center.spot shub_TS1-scwrl costs 0 real_cost = 351.572 shub_TS1 costs 0 real_cost = 356.448 panther2_TS1-scwrl costs 0 real_cost = 599.698 panther2_TS1 costs 0 real_cost = 594.611 nFOLD_TS5-scwrl costs 0 real_cost = 392.706 nFOLD_TS5 costs 0 real_cost = 570.1 nFOLD_TS4-scwrl costs 0 real_cost = 378.226 nFOLD_TS4 costs 0 real_cost = 548.663 nFOLD_TS3-scwrl costs 0 real_cost = 342.742 nFOLD_TS3 costs 0 real_cost = 522.253 nFOLD_TS2-scwrl costs 0 real_cost = 318.847 nFOLD_TS2 costs 0 real_cost = 505.467 nFOLD_TS1-scwrl costs 0 real_cost = 303.35 nFOLD_TS1 costs 0 real_cost = 490.43 mGen-3D_TS1-scwrl costs 0 real_cost = 500.457 keasar-server_TS5-scwrl costs 0 real_cost = 409.196 keasar-server_TS5 costs 0 real_cost = 409.766 keasar-server_TS4-scwrl costs 0 real_cost = 409.196 keasar-server_TS4 costs 0 real_cost = 409.766 keasar-server_TS3-scwrl costs 0 real_cost = 287.043 keasar-server_TS3 costs 0 real_cost = 289.567 keasar-server_TS2-scwrl costs 0 real_cost = 370.014 keasar-server_TS2 costs 0 real_cost = 374.074 keasar-server_TS1-scwrl costs 0 real_cost = 356.995 keasar-server_TS1 costs 0 real_cost = 368.606 karypis.srv_TS5-scwrl costs 0 real_cost = 452.218 karypis.srv_TS5 costs 0 real_cost = 445.602 karypis.srv_TS4-scwrl costs 0 real_cost = 324.059 karypis.srv_TS4 costs 0 real_cost = 319.899 karypis.srv_TS3-scwrl costs 0 real_cost = 342.723 karypis.srv_TS3 costs 0 real_cost = 338.645 karypis.srv_TS2-scwrl costs 0 real_cost = 311.468 karypis.srv_TS2 costs 0 real_cost = 306.852 karypis.srv_TS1-scwrl costs 0 real_cost = 305.02 karypis.srv_TS1 costs 0 real_cost = 297.341 karypis.srv.4_TS5-scwrl costs 0 real_cost = 374.218 karypis.srv.4_TS5 costs 0 real_cost = 375.035 karypis.srv.4_TS4-scwrl costs 0 real_cost = 359.956 karypis.srv.4_TS4 costs 0 real_cost = 360.041 karypis.srv.4_TS3-scwrl costs 0 real_cost = 393.531 karypis.srv.4_TS3 costs 0 real_cost = 393.829 karypis.srv.4_TS2-scwrl costs 0 real_cost = 324.063 karypis.srv.4_TS2 costs 0 real_cost = 326.934 karypis.srv.4_TS1-scwrl costs 0 real_cost = 381.77 karypis.srv.4_TS1 costs 0 real_cost = 382.229 karypis.srv.2_TS5-scwrl costs 0 real_cost = 313.149 karypis.srv.2_TS5 costs 0 real_cost = 313.15 karypis.srv.2_TS4-scwrl costs 0 real_cost = 344.544 karypis.srv.2_TS4 costs 0 real_cost = 344.751 karypis.srv.2_TS3-scwrl costs 0 real_cost = 329.215 karypis.srv.2_TS3 costs 0 real_cost = 329.215 karypis.srv.2_TS2-scwrl costs 0 real_cost = 346.356 karypis.srv.2_TS2 costs 0 real_cost = 346.356 karypis.srv.2_TS1-scwrl costs 0 real_cost = 263.88 karypis.srv.2_TS1 costs 0 real_cost = 263.88 gtg_AL5-scwrl costs 0 real_cost = 563.717 gtg_AL5 costs 0 real_cost = 672.185 gtg_AL4-scwrl costs 0 real_cost = 563.631 gtg_AL4 costs 0 real_cost = 660.491 gtg_AL3-scwrl costs 0 real_cost = 582.286 gtg_AL3 costs 0 real_cost = 680.183 gtg_AL2-scwrl costs 0 real_cost = 523.197 gtg_AL2 costs 0 real_cost = 660.79 gtg_AL1-scwrl costs 0 real_cost = 501.887 gtg_AL1 costs 0 real_cost = 643.554 forecast-s_AL5-scwrl costs 0 real_cost = 469.549 forecast-s_AL5 costs 0 real_cost = 618.592 forecast-s_AL4-scwrl costs 0 real_cost = 485.912 forecast-s_AL4 costs 0 real_cost = 601.366 forecast-s_AL3-scwrl costs 0 real_cost = 467.848 forecast-s_AL3 costs 0 real_cost = 578.333 forecast-s_AL2-scwrl costs 0 real_cost = 497.482 forecast-s_AL2 costs 0 real_cost = 642.181 forecast-s_AL1-scwrl costs 0 real_cost = 477.54 forecast-s_AL1 costs 0 real_cost = 581.386 beautshotbase_TS1-scwrl costs 0 real_cost = 442.521 beautshotbase_TS1 costs 0 real_cost = 455.048 beautshot_TS1-scwrl costs 0 real_cost = 252.414 beautshot_TS1 costs 0 real_cost = 262.834 Zhang-Server_TS5-scwrl costs 0 real_cost = 199.088 Zhang-Server_TS5 costs 0 real_cost = 201.342 Zhang-Server_TS4-scwrl costs 0 real_cost = 181.681 Zhang-Server_TS4 costs 0 real_cost = 183.863 Zhang-Server_TS3-scwrl costs 0 real_cost = 180.291 Zhang-Server_TS3 costs 0 real_cost = 185.89 Zhang-Server_TS2-scwrl costs 0 real_cost = 216.718 Zhang-Server_TS2 costs 0 real_cost = 218.861 Zhang-Server_TS1-scwrl costs 0 real_cost = 198.065 Zhang-Server_TS1 costs 0 real_cost = 201.285 UNI-EID_sfst_AL4-scwrl costs 0 real_cost = 546.577 UNI-EID_sfst_AL4 costs 0 real_cost = 632.565 UNI-EID_sfst_AL3-scwrl costs 0 real_cost = 514.906 UNI-EID_sfst_AL3 costs 0 real_cost = 602.94 UNI-EID_sfst_AL2-scwrl costs 0 real_cost = 510.874 UNI-EID_sfst_AL2 costs 0 real_cost = 604.049 UNI-EID_sfst_AL1-scwrl costs 0 real_cost = 518.56 UNI-EID_sfst_AL1 costs 0 real_cost = 614.179 UNI-EID_expm_TS1-scwrl costs 0 real_cost = 269.375 UNI-EID_expm_TS1 costs 0 real_cost = 458.29 UNI-EID_bnmx_TS4-scwrl costs 0 real_cost = 542.141 UNI-EID_bnmx_TS4 costs 0 real_cost = 633.092 UNI-EID_bnmx_TS3-scwrl costs 0 real_cost = 434.149 UNI-EID_bnmx_TS3 costs 0 real_cost = 598.631 UNI-EID_bnmx_TS2-scwrl costs 0 real_cost = 504.407 UNI-EID_bnmx_TS2 costs 0 real_cost = 630.089 UNI-EID_bnmx_TS1-scwrl costs 0 real_cost = 375.763 UNI-EID_bnmx_TS1 costs 0 real_cost = 590.08 SPARKS2_TS5-scwrl costs 0 real_cost = 225.199 SPARKS2_TS5 costs 0 real_cost = 234.912 SPARKS2_TS4-scwrl costs 0 real_cost = 344.531 SPARKS2_TS4 costs 0 real_cost = 350.867 SPARKS2_TS3-scwrl costs 0 real_cost = 265.898 SPARKS2_TS3 costs 0 real_cost = 275.615 SPARKS2_TS2-scwrl costs 0 real_cost = 290.429 SPARKS2_TS2 costs 0 real_cost = 292.927 SPARKS2_TS1-scwrl costs 0 real_cost = 338.49 SPARKS2_TS1 costs 0 real_cost = 351.876 SP4_TS5-scwrl costs 0 real_cost = 339.284 SP4_TS5 costs 0 real_cost = 346.666 SP4_TS4-scwrl costs 0 real_cost = 256.494 SP4_TS4 costs 0 real_cost = 262.097 SP4_TS3-scwrl costs 0 real_cost = 244.71 SP4_TS3 costs 0 real_cost = 254.353 SP4_TS2-scwrl costs 0 real_cost = 296.983 SP4_TS2 costs 0 real_cost = 301.808 SP4_TS1-scwrl costs 0 real_cost = 348.628 SP4_TS1 costs 0 real_cost = 353.091 SP3_TS5-scwrl costs 0 real_cost = 323.182 SP3_TS5 costs 0 real_cost = 324.585 SP3_TS4-scwrl costs 0 real_cost = 235.315 SP3_TS4 costs 0 real_cost = 239.389 SP3_TS3-scwrl costs 0 real_cost = 311.49 SP3_TS3 costs 0 real_cost = 316.925 SP3_TS2-scwrl costs 0 real_cost = 263.699 SP3_TS2 costs 0 real_cost = 264.553 SP3_TS1-scwrl costs 0 real_cost = 347.208 SP3_TS1 costs 0 real_cost = 345.286 SAM_T06_server_TS5-scwrl costs 0 real_cost = 463.89 SAM_T06_server_TS5 costs 0 real_cost = 429.412 SAM_T06_server_TS4-scwrl costs 0 real_cost = 493.461 SAM_T06_server_TS4 costs 0 real_cost = 443.625 SAM_T06_server_TS3-scwrl costs 0 real_cost = 487.684 SAM_T06_server_TS3 costs 0 real_cost = 464.963 SAM_T06_server_TS2-scwrl costs 0 real_cost = 461.123 SAM_T06_server_TS2 costs 0 real_cost = 398.179 SAM_T06_server_TS1-scwrl costs 0 real_cost = 287.843 SAM_T06_server_TS1 costs 0 real_cost = 287.632 SAM-T99_AL5-scwrl costs 0 real_cost = 471.494 SAM-T99_AL5 costs 0 real_cost = 603.219 SAM-T99_AL4-scwrl costs 0 real_cost = 476.655 SAM-T99_AL4 costs 0 real_cost = 612.738 SAM-T99_AL3-scwrl costs 0 real_cost = 485.04 SAM-T99_AL3 costs 0 real_cost = 618.397 SAM-T99_AL2-scwrl costs 0 real_cost = 595.606 SAM-T99_AL2 costs 0 real_cost = 674.384 SAM-T99_AL1-scwrl costs 0 real_cost = 432.274 SAM-T99_AL1 costs 0 real_cost = 571.185 SAM-T02_AL5-scwrl costs 0 real_cost = 446.839 SAM-T02_AL5 costs 0 real_cost = 578.18 SAM-T02_AL4-scwrl costs 0 real_cost = 458.092 SAM-T02_AL4 costs 0 real_cost = 548.725 SAM-T02_AL3-scwrl costs 0 real_cost = 508.212 SAM-T02_AL3 costs 0 real_cost = 593.463 SAM-T02_AL2-scwrl costs 0 real_cost = 499.873 SAM-T02_AL2 costs 0 real_cost = 584.479 SAM-T02_AL1-scwrl costs 0 real_cost = 500.655 SAM-T02_AL1 costs 0 real_cost = 604.894 ROKKY_TS5-scwrl costs 0 real_cost = 253.392 ROKKY_TS5 costs 0 real_cost = 459.997 ROKKY_TS4-scwrl costs 0 real_cost = 255.48 ROKKY_TS4 costs 0 real_cost = 460.073 ROKKY_TS3-scwrl costs 0 real_cost = 248.317 ROKKY_TS3 costs 0 real_cost = 454.746 ROKKY_TS2-scwrl costs 0 real_cost = 257.292 ROKKY_TS2 costs 0 real_cost = 465.209 ROKKY_TS1-scwrl costs 0 real_cost = 243.919 ROKKY_TS1 costs 0 real_cost = 452.893 ROBETTA_TS5-scwrl costs 0 real_cost = 242.553 ROBETTA_TS5 costs 0 real_cost = 246.406 ROBETTA_TS4-scwrl costs 0 real_cost = 232.212 ROBETTA_TS4 costs 0 real_cost = 233.044 ROBETTA_TS3-scwrl costs 0 real_cost = 243.443 ROBETTA_TS3 costs 0 real_cost = 244.535 ROBETTA_TS2-scwrl costs 0 real_cost = 224.982 ROBETTA_TS2 costs 0 real_cost = 227.119 ROBETTA_TS1-scwrl costs 0 real_cost = 229.136 ROBETTA_TS1 costs 0 real_cost = 230.37 RAPTOR_TS5-scwrl costs 0 real_cost = 233.87 RAPTOR_TS5 costs 0 real_cost = 233.281 RAPTOR_TS4-scwrl costs 0 real_cost = 237.786 RAPTOR_TS4 costs 0 real_cost = 241.156 RAPTOR_TS3-scwrl costs 0 real_cost = 227.28 RAPTOR_TS3 costs 0 real_cost = 226.803 RAPTOR_TS2-scwrl costs 0 real_cost = 229.771 RAPTOR_TS2 costs 0 real_cost = 232.927 RAPTOR_TS1-scwrl costs 0 real_cost = 249.717 RAPTOR_TS1 costs 0 real_cost = 256.71 RAPTORESS_TS5-scwrl costs 0 real_cost = 239.391 RAPTORESS_TS5 costs 0 real_cost = 241.137 RAPTORESS_TS4-scwrl costs 0 real_cost = 256.567 RAPTORESS_TS4 costs 0 real_cost = 266.382 RAPTORESS_TS3-scwrl costs 0 real_cost = 239.851 RAPTORESS_TS3 costs 0 real_cost = 246.5 RAPTORESS_TS2-scwrl costs 0 real_cost = 231.998 RAPTORESS_TS2 costs 0 real_cost = 233.805 RAPTORESS_TS1-scwrl costs 0 real_cost = 271.295 RAPTORESS_TS1 costs 0 real_cost = 279.628 RAPTOR-ACE_TS5-scwrl costs 0 real_cost = 232.658 RAPTOR-ACE_TS5 costs 0 real_cost = 232.658 RAPTOR-ACE_TS4-scwrl costs 0 real_cost = 260.218 RAPTOR-ACE_TS4 costs 0 real_cost = 264.191 RAPTOR-ACE_TS3-scwrl costs 0 real_cost = 325.312 RAPTOR-ACE_TS3 costs 0 real_cost = 333.212 RAPTOR-ACE_TS2-scwrl costs 0 real_cost = 287.09 RAPTOR-ACE_TS2 costs 0 real_cost = 284.264 RAPTOR-ACE_TS1-scwrl costs 0 real_cost = 231.249 RAPTOR-ACE_TS1 costs 0 real_cost = 234.067 Pmodeller6_TS5-scwrl costs 0 real_cost = 258.311 Pmodeller6_TS5 costs 0 real_cost = 254.325 Pmodeller6_TS4-scwrl costs 0 real_cost = 274.777 Pmodeller6_TS4 costs 0 real_cost = 274.754 Pmodeller6_TS3-scwrl costs 0 real_cost = 284.447 Pmodeller6_TS3 costs 0 real_cost = 279.955 Pmodeller6_TS2-scwrl costs 0 real_cost = 252.354 Pmodeller6_TS2 costs 0 real_cost = 252.39 Pmodeller6_TS1-scwrl costs 0 real_cost = 272.242 Pmodeller6_TS1 costs 0 real_cost = 267.937 Phyre-2_TS5-scwrl costs 0 real_cost = 208.951 Phyre-2_TS5 costs 0 real_cost = 210.726 Phyre-2_TS4-scwrl costs 0 real_cost = 230.836 Phyre-2_TS4 costs 0 real_cost = 231.939 Phyre-2_TS3-scwrl costs 0 real_cost = 233.838 Phyre-2_TS3 costs 0 real_cost = 235.378 Phyre-2_TS2-scwrl costs 0 real_cost = 237.387 Phyre-2_TS2 costs 0 real_cost = 238.392 Phyre-2_TS1-scwrl costs 0 real_cost = 263.017 Phyre-2_TS1 costs 0 real_cost = 264.394 Phyre-1_TS1-scwrl costs 0 real_cost = 554.134 Phyre-1_TS1 costs 0 real_cost = 542.085 Pcons6_TS5-scwrl costs 0 real_cost = 225.615 Pcons6_TS5 costs 0 real_cost = 228.133 Pcons6_TS4-scwrl costs 0 real_cost = 259.93 Pcons6_TS4 costs 0 real_cost = 254.999 Pcons6_TS3-scwrl costs 0 real_cost = 256.644 Pcons6_TS3 costs 0 real_cost = 253.078 Pcons6_TS2-scwrl costs 0 real_cost = 272.029 Pcons6_TS2 costs 0 real_cost = 267.106 Pcons6_TS1-scwrl costs 0 real_cost = 242.034 Pcons6_TS1 costs 0 real_cost = 243.353 PROTINFO_TS5-scwrl costs 0 real_cost = 250.062 PROTINFO_TS5 costs 0 real_cost = 250.203 PROTINFO_TS4-scwrl costs 0 real_cost = 256.11 PROTINFO_TS4 costs 0 real_cost = 258.902 PROTINFO_TS3-scwrl costs 0 real_cost = 254.898 PROTINFO_TS3 costs 0 real_cost = 256.762 PROTINFO_TS2-scwrl costs 0 real_cost = 327.51 PROTINFO_TS2 costs 0 real_cost = 322.071 PROTINFO_TS1-scwrl costs 0 real_cost = 250.349 PROTINFO_TS1 costs 0 real_cost = 249.838 PROTINFO-AB_TS5-scwrl costs 0 real_cost = 249.626 PROTINFO-AB_TS5 costs 0 real_cost = 250.391 PROTINFO-AB_TS4-scwrl costs 0 real_cost = 239.846 PROTINFO-AB_TS4 costs 0 real_cost = 238.054 PROTINFO-AB_TS3-scwrl costs 0 real_cost = 228.816 PROTINFO-AB_TS3 costs 0 real_cost = 234.922 PROTINFO-AB_TS2-scwrl costs 0 real_cost = 257.827 PROTINFO-AB_TS2 costs 0 real_cost = 255.087 PROTINFO-AB_TS1-scwrl costs 0 real_cost = 257.827 PROTINFO-AB_TS1 costs 0 real_cost = 255.087 POMYSL_TS4-scwrl costs 0 real_cost = 694.492 POMYSL_TS4 costs 0 real_cost = 694.147 POMYSL_TS3-scwrl costs 0 real_cost = 694.177 POMYSL_TS3 costs 0 real_cost = 690.214 POMYSL_TS2-scwrl costs 0 real_cost = 694.288 POMYSL_TS2 costs 0 real_cost = 694.849 POMYSL_TS1-scwrl costs 0 real_cost = 689.728 POMYSL_TS1 costs 0 real_cost = 688.655 NN_PUT_lab_TS1-scwrl costs 0 real_cost = 303.35 NN_PUT_lab_TS1 costs 0 real_cost = 490.43 MetaTasser_TS5-scwrl costs 0 real_cost = 199.665 MetaTasser_TS5 costs 0 real_cost = 202.26 MetaTasser_TS4-scwrl costs 0 real_cost = 217.986 MetaTasser_TS4 costs 0 real_cost = 218.628 MetaTasser_TS3-scwrl costs 0 real_cost = 202.768 MetaTasser_TS2-scwrl costs 0 real_cost = 214.15 MetaTasser_TS2 costs 0 real_cost = 212.494 MetaTasser_TS1-scwrl costs 0 real_cost = 222.496 MetaTasser_TS1 costs 0 real_cost = 227.934 Ma-OPUS-server_TS5-scwrl costs 0 real_cost = 360.378 Ma-OPUS-server_TS5 costs 0 real_cost = 359.869 Ma-OPUS-server_TS4-scwrl costs 0 real_cost = 237.319 Ma-OPUS-server_TS4 costs 0 real_cost = 231.922 Ma-OPUS-server_TS3-scwrl costs 0 real_cost = 235.898 Ma-OPUS-server_TS3 costs 0 real_cost = 240.644 Ma-OPUS-server_TS2-scwrl costs 0 real_cost = 210.911 Ma-OPUS-server_TS2 costs 0 real_cost = 217.207 Ma-OPUS-server_TS1-scwrl costs 0 real_cost = 220.964 Ma-OPUS-server_TS1 costs 0 real_cost = 224.089 LOOPP_TS5-scwrl costs 0 real_cost = 354.11 LOOPP_TS5 costs 0 real_cost = 358.106 LOOPP_TS4-scwrl costs 0 real_cost = 357.293 LOOPP_TS4 costs 0 real_cost = 358.384 LOOPP_TS3-scwrl costs 0 real_cost = 298.494 LOOPP_TS3 costs 0 real_cost = 299.008 LOOPP_TS2-scwrl costs 0 real_cost = 346.832 LOOPP_TS2 costs 0 real_cost = 351.73 LOOPP_TS1-scwrl costs 0 real_cost = 296.122 LOOPP_TS1 costs 0 real_cost = 294.839 Huber-Torda-Server_TS5-scwrl costs 0 real_cost = 703.474 Huber-Torda-Server_TS5 costs 0 real_cost = 737.204 Huber-Torda-Server_TS4-scwrl costs 0 real_cost = 657.993 Huber-Torda-Server_TS4 costs 0 real_cost = 725.489 Huber-Torda-Server_TS3-scwrl costs 0 real_cost = 643.529 Huber-Torda-Server_TS3 costs 0 real_cost = 707.663 Huber-Torda-Server_TS2-scwrl costs 0 real_cost = 625.419 Huber-Torda-Server_TS2 costs 0 real_cost = 689.378 Huber-Torda-Server_TS1-scwrl costs 0 real_cost = 645.801 Huber-Torda-Server_TS1 costs 0 real_cost = 703.663 HHpred3_TS1-scwrl costs 0 real_cost = 260.805 HHpred3_TS1 costs 0 real_cost = 256.29 HHpred2_TS1-scwrl costs 0 real_cost = 260.805 HHpred2_TS1 costs 0 real_cost = 256.29 HHpred1_TS1-scwrl costs 0 real_cost = 247.793 HHpred1_TS1 costs 0 real_cost = 244.487 GeneSilicoMetaServer_TS5-scwrl costs 0 real_cost = 246.18 GeneSilicoMetaServer_TS5 costs 0 real_cost = 244.513 GeneSilicoMetaServer_TS4-scwrl costs 0 real_cost = 417.578 GeneSilicoMetaServer_TS4 costs 0 real_cost = 421.58 GeneSilicoMetaServer_TS3-scwrl costs 0 real_cost = 402.632 GeneSilicoMetaServer_TS3 costs 0 real_cost = 407.983 GeneSilicoMetaServer_TS2-scwrl costs 0 real_cost = 246.291 GeneSilicoMetaServer_TS1-scwrl costs 0 real_cost = 337.565 GeneSilicoMetaServer_TS1 costs 0 real_cost = 336.366 FUNCTION_TS5-scwrl costs 0 real_cost = 261.009 FUNCTION_TS5 costs 0 real_cost = 262.354 FUNCTION_TS4-scwrl costs 0 real_cost = 312.682 FUNCTION_TS4 costs 0 real_cost = 320.73 FUNCTION_TS3-scwrl costs 0 real_cost = 270.84 FUNCTION_TS3 costs 0 real_cost = 286.753 FUNCTION_TS2-scwrl costs 0 real_cost = 258.332 FUNCTION_TS2 costs 0 real_cost = 269.767 FUNCTION_TS1-scwrl costs 0 real_cost = 432.361 FUNCTION_TS1 costs 0 real_cost = 431.807 FUGUE_AL5-scwrl costs 0 real_cost = 418.935 FUGUE_AL5 costs 0 real_cost = 616.201 FUGUE_AL4-scwrl costs 0 real_cost = 339.247 FUGUE_AL4 costs 0 real_cost = 587.118 FUGUE_AL3-scwrl costs 0 real_cost = 559.734 FUGUE_AL3 costs 0 real_cost = 711.4 FUGUE_AL2-scwrl costs 0 real_cost = 571.654 FUGUE_AL2 costs 0 real_cost = 676.592 FUGUE_AL1-scwrl costs 0 real_cost = 436.351 FUGUE_AL1 costs 0 real_cost = 607.921 FUGMOD_TS5-scwrl costs 0 real_cost = 287.765 FUGMOD_TS5 costs 0 real_cost = 289.967 FUGMOD_TS4-scwrl costs 0 real_cost = 269.268 FUGMOD_TS4 costs 0 real_cost = 267.929 FUGMOD_TS3-scwrl costs 0 real_cost = 549.864 FUGMOD_TS3 costs 0 real_cost = 551.546 FUGMOD_TS2-scwrl costs 0 real_cost = 542.787 FUGMOD_TS2 costs 0 real_cost = 540.627 FUGMOD_TS1-scwrl costs 0 real_cost = 277.243 FUGMOD_TS1 costs 0 real_cost = 274.907 FPSOLVER-SERVER_TS5-scwrl costs 0 real_cost = 347.5 FPSOLVER-SERVER_TS5 costs 0 real_cost = 349.513 FPSOLVER-SERVER_TS4-scwrl costs 0 real_cost = 362.431 FPSOLVER-SERVER_TS4 costs 0 real_cost = 365.852 FPSOLVER-SERVER_TS3-scwrl costs 0 real_cost = 356.75 FPSOLVER-SERVER_TS3 costs 0 real_cost = 359.166 FPSOLVER-SERVER_TS2-scwrl costs 0 real_cost = 366.868 FPSOLVER-SERVER_TS2 costs 0 real_cost = 368.915 FPSOLVER-SERVER_TS1-scwrl costs 0 real_cost = 363.952 FPSOLVER-SERVER_TS1 costs 0 real_cost = 368.545 FORTE2_AL5-scwrl costs 0 real_cost = 516.241 FORTE2_AL5 costs 0 real_cost = 672.575 FORTE2_AL4-scwrl costs 0 real_cost = 653.403 FORTE2_AL3-scwrl costs 0 real_cost = 304.557 FORTE2_AL3 costs 0 real_cost = 550.427 FORTE2_AL2-scwrl costs 0 real_cost = 358.545 FORTE2_AL2 costs 0 real_cost = 602.897 FORTE2_AL1-scwrl costs 0 real_cost = 308.508 FORTE2_AL1 costs 0 real_cost = 559.892 FORTE1_AL5-scwrl costs 0 real_cost = 526.146 FORTE1_AL5 costs 0 real_cost = 659.728 FORTE1_AL4-scwrl costs 0 real_cost = 457.709 FORTE1_AL4 costs 0 real_cost = 646.714 FORTE1_AL3-scwrl costs 0 real_cost = 304.557 FORTE1_AL3 costs 0 real_cost = 550.427 FORTE1_AL2-scwrl costs 0 real_cost = 358.545 FORTE1_AL2 costs 0 real_cost = 602.897 FORTE1_AL1-scwrl costs 0 real_cost = 308.508 FORTE1_AL1 costs 0 real_cost = 559.892 FOLDpro_TS5-scwrl costs 0 real_cost = 304.522 FOLDpro_TS5 costs 0 real_cost = 305.097 FOLDpro_TS4-scwrl costs 0 real_cost = 355.922 FOLDpro_TS4 costs 0 real_cost = 358.203 FOLDpro_TS3-scwrl costs 0 real_cost = 228.175 FOLDpro_TS3 costs 0 real_cost = 231.535 FOLDpro_TS2-scwrl costs 0 real_cost = 301.349 FOLDpro_TS2 costs 0 real_cost = 302.495 FOLDpro_TS1-scwrl costs 0 real_cost = 304.693 FOLDpro_TS1 costs 0 real_cost = 305.575 FAMS_TS5-scwrl costs 0 real_cost = 251.482 FAMS_TS5 costs 0 real_cost = 252.198 FAMS_TS4-scwrl costs 0 real_cost = 432.361 FAMS_TS4 costs 0 real_cost = 431.807 FAMS_TS3-scwrl costs 0 real_cost = 454.742 FAMS_TS3 costs 0 real_cost = 454.393 FAMS_TS2-scwrl costs 0 real_cost = 246.816 FAMS_TS2 costs 0 real_cost = 250.192 FAMS_TS1-scwrl costs 0 real_cost = 252.424 FAMS_TS1 costs 0 real_cost = 254.563 FAMSD_TS5-scwrl costs 0 real_cost = 265.384 FAMSD_TS5 costs 0 real_cost = 270.633 FAMSD_TS4-scwrl costs 0 real_cost = 425.45 FAMSD_TS4 costs 0 real_cost = 430.995 FAMSD_TS3-scwrl costs 0 real_cost = 454.742 FAMSD_TS3 costs 0 real_cost = 454.393 FAMSD_TS2-scwrl costs 0 real_cost = 344.456 FAMSD_TS2 costs 0 real_cost = 347.707 FAMSD_TS1-scwrl costs 0 real_cost = 256.392 FAMSD_TS1 costs 0 real_cost = 257.541 Distill_TS5-scwrl costs 0 real_cost = 788.714 Distill_TS4-scwrl costs 0 real_cost = 779.125 Distill_TS3-scwrl costs 0 real_cost = 782.844 Distill_TS2-scwrl costs 0 real_cost = 774.32 Distill_TS1-scwrl costs 0 real_cost = 764.488 CaspIta-FOX_TS5-scwrl costs 0 real_cost = 535.699 CaspIta-FOX_TS5 costs 0 real_cost = 534.235 CaspIta-FOX_TS4-scwrl costs 0 real_cost = 464.774 CaspIta-FOX_TS4 costs 0 real_cost = 456.628 CaspIta-FOX_TS3-scwrl costs 0 real_cost = 437.234 CaspIta-FOX_TS3 costs 0 real_cost = 424.636 CaspIta-FOX_TS2-scwrl costs 0 real_cost = 310.737 CaspIta-FOX_TS2 costs 0 real_cost = 303.398 CaspIta-FOX_TS1-scwrl costs 0 real_cost = 416.986 CaspIta-FOX_TS1 costs 0 real_cost = 401.722 CPHmodels_TS1-scwrl costs 0 real_cost = 663.711 CPHmodels_TS1 costs 0 real_cost = 661.543 CIRCLE_TS5-scwrl costs 0 real_cost = 232.409 CIRCLE_TS5 costs 0 real_cost = 226.845 CIRCLE_TS4-scwrl costs 0 real_cost = 429.753 CIRCLE_TS4 costs 0 real_cost = 428.715 CIRCLE_TS3-scwrl costs 0 real_cost = 438.328 CIRCLE_TS3 costs 0 real_cost = 436.185 CIRCLE_TS2-scwrl costs 0 real_cost = 459.133 CIRCLE_TS2 costs 0 real_cost = 460.361 CIRCLE_TS1-scwrl costs 0 real_cost = 230.486 CIRCLE_TS1 costs 0 real_cost = 235.374 Bilab-ENABLE_TS3-scwrl costs 0 real_cost = 267.805 Bilab-ENABLE_TS3 costs 0 real_cost = 267.747 Bilab-ENABLE_TS2-scwrl costs 0 real_cost = 276.85 Bilab-ENABLE_TS2 costs 0 real_cost = 276.715 Bilab-ENABLE_TS1-scwrl costs 0 real_cost = 341.604 Bilab-ENABLE_TS1 costs 0 real_cost = 341.754 BayesHH_TS1-scwrl costs 0 real_cost = 301.387 BayesHH_TS1 costs 0 real_cost = 311.08 ABIpro_TS5-scwrl costs 0 real_cost = 308.431 ABIpro_TS5 costs 0 real_cost = 309.024 ABIpro_TS4-scwrl costs 0 real_cost = 301.729 ABIpro_TS4 costs 0 real_cost = 301.43 ABIpro_TS3-scwrl costs 0 real_cost = 316.892 ABIpro_TS3 costs 0 real_cost = 317.332 ABIpro_TS2-scwrl costs 0 real_cost = 303.581 ABIpro_TS2 costs 0 real_cost = 303.174 ABIpro_TS1-scwrl costs 0 real_cost = 314.665 ABIpro_TS1 costs 0 real_cost = 315.013 3Dpro_TS5-scwrl costs 0 real_cost = 350.281 3Dpro_TS5 costs 0 real_cost = 356.254 3Dpro_TS4-scwrl costs 0 real_cost = 350.002 3Dpro_TS4 costs 0 real_cost = 350.395 3Dpro_TS3-scwrl costs 0 real_cost = 304.693 3Dpro_TS3 costs 0 real_cost = 305.575 3Dpro_TS2-scwrl costs 0 real_cost = 227.728 3Dpro_TS2 costs 0 real_cost = 239.227 3Dpro_TS1-scwrl costs 0 real_cost = 228.175 3Dpro_TS1 costs 0 real_cost = 231.535 3D-JIGSAW_TS5-scwrl costs 0 real_cost = 436.104 3D-JIGSAW_TS5 costs 0 real_cost = 439.516 3D-JIGSAW_TS4-scwrl costs 0 real_cost = 457.777 3D-JIGSAW_TS4 costs 0 real_cost = 465.552 3D-JIGSAW_TS3-scwrl costs 0 real_cost = 552.277 3D-JIGSAW_TS3 costs 0 real_cost = 558.275 3D-JIGSAW_TS2-scwrl costs 0 real_cost = 559.631 3D-JIGSAW_TS2 costs 0 real_cost = 561.517 3D-JIGSAW_TS1-scwrl costs 0 real_cost = 558.673 3D-JIGSAW_TS1 costs 0 real_cost = 559.519 3D-JIGSAW_RECOM_TS5-scwrl costs 0 real_cost = 488.127 3D-JIGSAW_RECOM_TS5 costs 0 real_cost = 489.169 3D-JIGSAW_RECOM_TS4-scwrl costs 0 real_cost = 488.127 3D-JIGSAW_RECOM_TS4 costs 0 real_cost = 489.169 3D-JIGSAW_RECOM_TS3-scwrl costs 0 real_cost = 487.256 3D-JIGSAW_RECOM_TS3 costs 0 real_cost = 488.765 3D-JIGSAW_RECOM_TS2-scwrl costs 0 real_cost = 480.417 3D-JIGSAW_RECOM_TS2 costs 0 real_cost = 485.534 3D-JIGSAW_RECOM_TS1-scwrl costs 0 real_cost = 483.08 3D-JIGSAW_RECOM_TS1 costs 0 real_cost = 486.772 3D-JIGSAW_POPULUS_TS5-scwrl costs 0 real_cost = 501.334 3D-JIGSAW_POPULUS_TS5 costs 0 real_cost = 497.098 3D-JIGSAW_POPULUS_TS4-scwrl costs 0 real_cost = 498.35 3D-JIGSAW_POPULUS_TS4 costs 0 real_cost = 498.203 3D-JIGSAW_POPULUS_TS3-scwrl costs 0 real_cost = 483.289 3D-JIGSAW_POPULUS_TS3 costs 0 real_cost = 479.036 3D-JIGSAW_POPULUS_TS2-scwrl costs 0 real_cost = 486.376 3D-JIGSAW_POPULUS_TS2 costs 0 real_cost = 481.423 3D-JIGSAW_POPULUS_TS1-scwrl costs 0 real_cost = 477.775 3D-JIGSAW_POPULUS_TS1 costs 0 real_cost = 474.178 make-chimera.pdb.gz costs 0 real_cost = 262.743 chimera1.pdb.gz costs 0 real_cost = 252.925 T0316.try9-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 232.105 T0316.try9-opt2.pdb.gz costs 0 real_cost = 231.83 T0316.try9-opt2.gromacs0.pdb.gz costs 0 real_cost = 232.47 T0316.try9-opt1.pdb.gz costs 0 real_cost = 231.958 T0316.try9-opt1-scwrl.pdb.gz costs 0 real_cost = 230.071 T0316.try8-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 255.441 T0316.try8-opt2.pdb.gz costs 0 real_cost = 255.993 T0316.try8-opt2.gromacs0.pdb.gz costs 0 real_cost = 256.074 T0316.try8-opt1.pdb.gz costs 0 real_cost = 256.007 T0316.try8-opt1-scwrl.pdb.gz costs 0 real_cost = 255.88 T0316.try7-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 252.966 T0316.try7-opt2.pdb.gz costs 0 real_cost = 254.602 T0316.try7-opt2.gromacs0.pdb.gz costs 0 real_cost = 256.47 T0316.try7-opt1.pdb.gz costs 0 real_cost = 252.526 T0316.try7-opt1-scwrl.pdb.gz costs 0 real_cost = 252.744 T0316.try6-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 272.084 T0316.try6-opt2.pdb.gz costs 0 real_cost = 272.286 T0316.try6-opt2.gromacs0.pdb.gz costs 0 real_cost = 271.59 T0316.try6-opt1.pdb.gz costs 0 real_cost = 274.291 T0316.try6-opt1-scwrl.pdb.gz costs 0 real_cost = 272.43 T0316.try5-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 255.061 T0316.try5-opt2.pdb.gz costs 0 real_cost = 257.644 T0316.try5-opt2.gromacs0.pdb.gz costs 0 real_cost = 255.308 T0316.try5-opt1.pdb.gz costs 0 real_cost = 246.287 T0316.try5-opt1-scwrl.pdb.gz costs 0 real_cost = 246.986 T0316.try4-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 263.952 T0316.try4-opt2.pdb.gz costs 0 real_cost = 264.301 T0316.try4-opt2.gromacs0.pdb.gz costs 0 real_cost = 267.806 T0316.try4-opt1.pdb.gz costs 0 real_cost = 266.843 T0316.try4-opt1-scwrl.pdb.gz costs 0 real_cost = 267.149 T0316.try3-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 284.57 T0316.try3-opt2.pdb.gz costs 0 real_cost = 284.958 T0316.try3-opt2.gromacs0.pdb.gz costs 0 real_cost = 285.854 T0316.try3-opt1.pdb.gz costs 0 real_cost = 287.301 T0316.try3-opt1-scwrl.pdb.gz costs 0 real_cost = 287.861 T0316.try21-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 255.801 T0316.try21-opt2.pdb.gz costs 0 real_cost = 253.715 T0316.try21-opt2.gromacs0.pdb.gz costs 0 real_cost = 254.17 T0316.try21-opt1.pdb.gz costs 0 real_cost = 253.647 T0316.try21-opt1-scwrl.pdb.gz costs 0 real_cost = 253.256 T0316.try20-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 271.095 T0316.try20-opt2.pdb.gz costs 0 real_cost = 271.585 T0316.try20-opt2.gromacs0.pdb.gz costs 0 real_cost = 274.747 T0316.try20-opt1.pdb.gz costs 0 real_cost = 272.546 T0316.try20-opt1-scwrl.pdb.gz costs 0 real_cost = 271.48 T0316.try2-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 256.499 T0316.try2-opt2.pdb.gz costs 0 real_cost = 254.314 T0316.try2-opt2.gromacs0.pdb.gz costs 0 real_cost = 255.995 T0316.try2-opt2-M1-A183-try6-opt2-A130-I373.pdb.gz costs 0 real_cost = 265.344 T0316.try2-opt1.pdb.gz costs 0 real_cost = 255.95 T0316.try2-opt1-scwrl.pdb.gz costs 0 real_cost = 255.018 T0316.try19-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 254.874 T0316.try19-opt2.pdb.gz costs 0 real_cost = 252.908 T0316.try19-opt2.gromacs0.pdb.gz costs 0 real_cost = 253.178 T0316.try19-opt1.pdb.gz costs 0 real_cost = 250.843 T0316.try19-opt1-scwrl.pdb.gz costs 0 real_cost = 251.039 T0316.try18-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 274.104 T0316.try18-opt2.pdb.gz costs 0 real_cost = 273.298 T0316.try18-opt2.gromacs0.pdb.gz costs 0 real_cost = 276.663 T0316.try18-opt1.pdb.gz costs 0 real_cost = 272.751 T0316.try18-opt1-scwrl.pdb.gz costs 0 real_cost = 272.786 T0316.try17-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 284.383 T0316.try17-opt2.pdb.gz costs 0 real_cost = 283.937 T0316.try17-opt2.gromacs0.pdb.gz costs 0 real_cost = 287.734 T0316.try17-opt1.pdb.gz costs 0 real_cost = 288.729 T0316.try17-opt1-scwrl.pdb.gz costs 0 real_cost = 289.885 T0316.try16-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 236.578 T0316.try16-opt2.pdb.gz costs 0 real_cost = 236.715 T0316.try16-opt2.gromacs0.pdb.gz costs 0 real_cost = 239.252 T0316.try16-opt1.pdb.gz costs 0 real_cost = 239.077 T0316.try16-opt1-scwrl.pdb.gz costs 0 real_cost = 238.884 T0316.try15-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 253.662 T0316.try15-opt2.pdb.gz costs 0 real_cost = 255.413 T0316.try15-opt2.gromacs0.pdb.gz costs 0 real_cost = 251.859 T0316.try15-opt1.pdb.gz costs 0 real_cost = 248.135 T0316.try15-opt1-scwrl.pdb.gz costs 0 real_cost = 247.563 T0316.try14-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 271.772 T0316.try14-opt2.pdb.gz costs 0 real_cost = 272.18 T0316.try14-opt2.gromacs0.pdb.gz costs 0 real_cost = 272.805 T0316.try14-opt1.pdb.gz costs 0 real_cost = 272.338 T0316.try14-opt1-scwrl.pdb.gz costs 0 real_cost = 270.694 T0316.try13-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 233.655 T0316.try13-opt2.pdb.gz costs 0 real_cost = 233.23 T0316.try13-opt2.gromacs0.pdb.gz costs 0 real_cost = 231.622 T0316.try13-opt1.pdb.gz costs 0 real_cost = 233.459 T0316.try13-opt1-scwrl.pdb.gz costs 0 real_cost = 231.987 T0316.try12-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 252.486 T0316.try12-opt2.pdb.gz costs 0 real_cost = 251.427 T0316.try12-opt2.gromacs0.pdb.gz costs 0 real_cost = 251.436 T0316.try12-opt1.pdb.gz costs 0 real_cost = 251.07 T0316.try12-opt1-scwrl.pdb.gz costs 0 real_cost = 252.28 T0316.try11-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 218.177 T0316.try11-opt2.pdb.gz costs 0 real_cost = 218.936 T0316.try11-opt2.gromacs0.pdb.gz costs 0 real_cost = 220.06 T0316.try11-opt1.pdb.gz costs 0 real_cost = 220.115 T0316.try11-opt1-scwrl.pdb.gz costs 0 real_cost = 221.881 T0316.try10-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 272.997 T0316.try10-opt2.pdb.gz costs 0 real_cost = 272.91 T0316.try10-opt2.gromacs0.pdb.gz costs 0 real_cost = 270.644 T0316.try10-opt1.pdb.gz costs 0 real_cost = 273.187 T0316.try10-opt1-scwrl.pdb.gz costs 0 real_cost = 271.756 T0316.try1-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 261.283 T0316.try1-opt2.pdb.gz costs 0 real_cost = 262.035 T0316.try1-opt2.gromacs0.pdb.gz costs 0 real_cost = 262.888 T0316.try1-opt1.pdb.gz costs 0 real_cost = 265.028 T0316.try1-opt1-scwrl.pdb.gz costs 0 real_cost = 263.792 T0316.M1-A183-try2-opt2-D122-K269-try1-opt2-A130-I373-try4-opt2.pdb.gz costs 0 real_cost = 243.959 T0316.M1-A183-try2-opt2-D122-K269-try1-opt2-A130-I373-try4-opt2-proteinshop.pdb.gz costs 0 real_cost = 257.992 ../model5.ts-submitted costs 0 real_cost = 218.936 ../model4.ts-submitted costs 0 real_cost = 232.175 ../model3.ts-submitted costs 0 real_cost = 271.683 ../model2.ts-submitted costs 0 real_cost = 255.991 ../model1.ts-submitted costs 0 real_cost = 253.971 align5 costs 0 real_cost = 410.283 align4 costs 0 real_cost = 486.665 align3 costs 0 real_cost = 433.537 align2 costs 0 real_cost = 452.497 align1 costs 0 real_cost = 386.437 T0316.try1-opt2.pdb costs 0 real_cost = 262.035 model5-scwrl costs 0 real_cost = 220.93 model5.ts-submitted costs 0 real_cost = 218.936 model4-scwrl costs 0 real_cost = 230.949 model4.ts-submitted costs 0 real_cost = 232.175 model3-scwrl costs 0 real_cost = 270.952 model3.ts-submitted costs 0 real_cost = 271.683 model2-scwrl costs 0 real_cost = 255.865 model2.ts-submitted costs 0 real_cost = 255.991 model1-scwrl costs 0 real_cost = 253.23 model1.ts-submitted costs 0 real_cost = 253.971 2hmaA costs 0 real_cost = -872.4 # command:CPU_time= 2664.85 sec, elapsed time= 5063.22 sec) # command:rm -f sort.tmp /projects/compbio/bin/sorttbl real_cost < decoys/evaluate.rdb > sort.tmp mv -f sort.tmp decoys/evaluate.rdb mv -f decoys/evaluate.pretty decoys/evaluate.pretty.old /projects/compbio/experiments/protein-predict/casp7/scripts/prettyscore -terse -targpfx -decpoint < decoys/evaluate.rdb > decoys/evaluate.pretty rm -f decoys/evaluate_1.rdb sed -e s/XXX0000/T0316/ -e s/START_COL/1/ \ -e s/REAL_PDB/2hmaA/ \ -e s/_domain/_1/ \ -e s/read-pdb/read-pdb+servers/ \ -e 's/ReadConformPDBids/# ReadConformPDBids/' \ -e 's/# ReadConformPDB /ReadConformPDB /' \ -e 's/include COSTFCN.costfcn//' \ -e s/.COSTFCN// \ < /projects/compbio/experiments/protein-predict/casp7/starter-directory/evaluate.under \ | nice -2 /projects/compbio/programs/undertaker/undertaker # command:# Seed set to 1174818593 # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading monomeric-50pc.atoms # trans (non-proline) backbone unit: # CA= -2.2088 1.0126 -0.0031 # O= -0.1499 2.2440 0.0017 # 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= -0.1462 2.4515 0.0018 # O= -2.0272 0.9713 0.0022 # C= -0.8006 1.0755 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4659 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2099 1.0634 -0.0014 # O= -0.1233 2.2459 0.0075 # C= -0.6871 1.1518 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading monomeric-50pc.atoms have 448 chains in training database # Count of chains,residues,atoms: 448,112605,876684 # 109826 residues have no bad marker # 665 residues lack atoms needed to compute omega # 322 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 6 # HAS_OXT 325 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 523 # HAS_UNKNOWN_ATOMS 2 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 208 # NON_PLANAR_PEPTIDE 143 # BAD_PEPTIDE 1959 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-1332.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:CPU_time= 4.65229 sec, elapsed time= 4.72057 sec) # command:# Reading spots from monomeric-50pc-dry-5.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-5.hist # created burial cost function dry5 with radius 5 with spots at monomeric-50pc-dry-5.spot # command:# Reading spots from monomeric-50pc-wet-6.5.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-wet-6.5.hist # created burial cost function wet6.5 with radius 6.5 with spots at monomeric-50pc-wet-6.5.spot # command:# Reading spots from monomeric-50pc-dry-6.5.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-6.5.hist # created burial cost function dry6.5 with radius 6.5 with spots at monomeric-50pc-dry-6.5.spot # command:# Reading spots from monomeric-50pc-generic-6.5.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-generic-6.5.hist # created burial cost function gen6.5 with radius 6.5 with spots at monomeric-50pc-generic-6.5.spot # command:# Reading spots from near-backbone-center.spot # reading histogram from smoothed-near-backbone-2spot.hist # Reading spots from near-backbone-count.spot # created burial cost function near_backbone with radius 9.65 with spots at near-backbone-center.spot counting only near-backbone-count.spot # command:# Reading spots from way-back-center.spot # reading histogram from smoothed-way-back-2spot.hist # Reading spots from way-back-count.spot # created burial cost function way_back with radius 8.9 with spots at way-back-center.spot counting only way-back-count.spot # command:# Reading spots from monomeric-50pc-dry-8.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-8.hist # created burial cost function dry8 with radius 8 with spots at monomeric-50pc-dry-8.spot # command:# Reading spots from monomeric-50pc-dry-10.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-10.hist # created burial cost function dry10 with radius 10 with spots at monomeric-50pc-dry-10.spot # command:# Reading spots from monomeric-50pc-dry-12.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-12.hist # created burial cost function dry12 with radius 12 with spots at monomeric-50pc-dry-12.spot # command:# reading histogram from dunbrack-2191-alpha.hist # created alpha cost function alpha with offset 0 and 360 bins # command:# reading histogram from dunbrack-2191-alpha-1.hist # created alpha cost function alpha_prev with offset -1 and 360 bins # command:# Prefix for input files set to /projects/compbio/lib/alphabet/ # command:# Read 3 alphabets from alpha.alphabet # command:CPU_time= 4.72128 sec, elapsed time= 4.81259 sec) # command:# Prefix for input files set to # command:# Making conformation for sequence T0316 numbered 1 through 373 Created new target T0316 from T0316.a2m # command:# command:# No conformations to remove in PopConform # command:# cleared Id set # command:# command:# ReadConformPDB reading from PDB file T0316_1.real.pdb looking for model 1 Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 358, because occupancy 3.0000000e-01 <= existing 0.700 in T0316_1.real.pdb Skipped atom 360, because occupancy 0.300 <= existing 0.700 in T0316_1.real.pdb Skipped atom 362, because occupancy 0.300 <= existing 0.700 in T0316_1.real.pdb Skipped atom 364, because occupancy 0.300 <= existing 0.700 in T0316_1.real.pdb Skipped atom 366, because occupancy 0.300 <= existing 0.700 in T0316_1.real.pdb Skipped atom 368, because occupancy 0.300 <= existing 0.700 in T0316_1.real.pdb Skipped atom 370, because occupancy 0.300 <= existing 0.700 in T0316_1.real.pdb Skipped atom 372, because occupancy 0.300 <= existing 0.700 in T0316_1.real.pdb Skipped atom 374, because occupancy 0.300 <= existing 0.700 in T0316_1.real.pdb Skipped atom 396, because occupancy 0.300 <= existing 0.700 in T0316_1.real.pdb Skipped atom 398, because occupancy 0.300 <= existing 0.700 in T0316_1.real.pdb Skipped atom 400, because occupancy 0.300 <= existing 0.700 in T0316_1.real.pdb Skipped atom 402, because occupancy 0.300 <= existing 0.700 in T0316_1.real.pdb Skipped atom 404, because occupancy 0.300 <= existing 0.700 in T0316_1.real.pdb Skipped atom 406, because occupancy 0.300 <= existing 0.700 in T0316_1.real.pdb Skipped atom 408, because occupancy 0.300 <= existing 0.700 in T0316_1.real.pdb Skipped atom 410, because occupancy 0.300 <= existing 0.700 in T0316_1.real.pdb Skipped atom 412, because occupancy 0.300 <= existing 0.700 in T0316_1.real.pdb Skipped atom 461, because occupancy 0.400 <= existing 0.600 in T0316_1.real.pdb Skipped atom 463, because occupancy 0.400 <= existing 0.600 in T0316_1.real.pdb Skipped atom 465, because occupancy 0.400 <= existing 0.600 in T0316_1.real.pdb Skipped atom 467, because occupancy 0.400 <= existing 0.600 in T0316_1.real.pdb Skipped atom 469, because occupancy 0.400 <= existing 0.600 in T0316_1.real.pdb Skipped atom 471, because occupancy 0.400 <= existing 0.600 in T0316_1.real.pdb Skipped atom 473, because occupancy 0.400 <= existing 0.600 in T0316_1.real.pdb Skipped atom 475, because occupancy 0.400 <= existing 0.600 in T0316_1.real.pdb Skipped atom 477, because occupancy 0.400 <= existing 0.600 in T0316_1.real.pdb Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1044, because occupancy 0.400 <= existing 0.600 in T0316_1.real.pdb Skipped atom 1046, because occupancy 0.400 <= existing 0.600 in T0316_1.real.pdb Skipped atom 1048, because occupancy 0.400 <= existing 0.600 in T0316_1.real.pdb Skipped atom 1050, because occupancy 0.400 <= existing 0.600 in T0316_1.real.pdb Skipped atom 1052, because occupancy 0.400 <= existing 0.600 in T0316_1.real.pdb Skipped atom 1054, because occupancy 0.400 <= existing 0.600 in T0316_1.real.pdb Skipped atom 1056, because occupancy 0.400 <= existing 0.600 in T0316_1.real.pdb Skipped atom 1058, because occupancy 0.400 <= existing 0.600 in T0316_1.real.pdb Skipped atom 1060, because occupancy 0.400 <= existing 0.600 in T0316_1.real.pdb Skipped atom 1062, because occupancy 0.400 <= existing 0.600 in T0316_1.real.pdb Skipped atom 1064, because occupancy 0.400 <= existing 0.600 in T0316_1.real.pdb Skipped atom 1109, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb Skipped atom 1111, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb Skipped atom 1113, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb Skipped atom 1115, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb Skipped atom 1117, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb Skipped atom 1119, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb Skipped atom 1121, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb Skipped atom 1123, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb Skipped atom 1125, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb Skipped atom 1127, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1175, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb Skipped atom 1177, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb Skipped atom 1179, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb Skipped atom 1181, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb Skipped atom 1183, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb Skipped atom 1185, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb Skipped atom 1187, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb Skipped atom 1189, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb Skipped atom 1195, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb Skipped atom 1197, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb Skipped atom 1199, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb Skipped atom 1201, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb Skipped atom 1203, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb Skipped atom 1205, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb Skipped atom 1207, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb Skipped atom 1209, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb Skipped atom 1211, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb Skipped atom 1306, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb Skipped atom 1308, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb Skipped atom 1310, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb Skipped atom 1312, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb Skipped atom 1314, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb Skipped atom 1316, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb Skipped atom 1318, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb Skipped atom 1320, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb Skipped atom 1322, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1463, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb Skipped atom 1465, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb Skipped atom 1467, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb Skipped atom 1469, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb Skipped atom 1471, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb Skipped atom 1473, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb Skipped atom 1475, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb Skipped atom 1477, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb Skipped atom 1479, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb Skipped atom 1481, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb Skipped atom 1483, because occupancy 0.500 <= existing 0.500 in T0316_1.real.pdb # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # command:# Saving current conformation as real # command:# Prefix for output files set to decoys/ # command:# SetRealCost created real_cost = # ( 50 * real_hbond + 50 * real_hbond_u + 50 * decoy_hbond + 50 * decoy_hbond_u + 10 * real_NO_hbond + 10 * real_NO_hbond_u + 10 * decoy_NO_hbond + 10 * decoy_NO_hbond_u + 10 * knot + 200 * clens + 0 * rmsd + 35 * log_rmsd + 0 * rmsd_ca + 30 * log_rmsd_ca + 1 * GDT + 1 * smooth_GDT + 0.2 * missing_atoms ) # command:# SetCost created cost = # ) # command:CPU_time= 6.604 sec, elapsed time= 6.7137 sec) # command:# Prefix for input files set to # command:# ReadConformPDB reading from PDB file model1.ts-submitted looking for model 1 # choosing archetypes in rotamer library # Found a chain break before 371 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -40.4255 # GDT_score(maxd=8,maxw=2.9)= -40.376 # GDT_score(maxd=8,maxw=3.2)= -38.1761 # GDT_score(maxd=8,maxw=3.5)= -36.2216 # GDT_score(maxd=10,maxw=3.8)= -39.2441 # GDT_score(maxd=10,maxw=4)= -37.9797 # GDT_score(maxd=10,maxw=4.2)= -36.7561 # GDT_score(maxd=12,maxw=4.3)= -40.1851 # GDT_score(maxd=12,maxw=4.5)= -38.9345 # GDT_score(maxd=12,maxw=4.7)= -37.7584 # GDT_score(maxd=14,maxw=5.2)= -38.2087 # GDT_score(maxd=14,maxw=5.5)= -36.5672 # command:# Prefix for output files set to # command:superimposing iter= 0 total_weight= 2245.000 rmsd (weighted)= 10.894 (unweighted)= 55.064 superimposing iter= 1 total_weight= 4888.353 rmsd (weighted)= 5.528 (unweighted)= 55.661 superimposing iter= 2 total_weight= 2598.708 rmsd (weighted)= 3.971 (unweighted)= 55.232 superimposing iter= 3 total_weight= 2149.566 rmsd (weighted)= 3.183 (unweighted)= 54.711 superimposing iter= 4 total_weight= 1951.573 rmsd (weighted)= 2.710 (unweighted)= 54.325 superimposing iter= 5 total_weight= 1797.334 rmsd (weighted)= 2.422 (unweighted)= 54.060 # command:# Prefix for output files set to decoys/ # command:# request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1417783409.pdb -s /var/tmp/to_scwrl_1417783409.seq -o /var/tmp/from_scwrl_1417783409.pdb > /var/tmp/scwrl_1417783409.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1417783409.pdb # conformation set from SCWRL output # command:# naming current conformation model1-scwrl # command:# ReadConformPDB reading from PDB file model2.ts-submitted looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -38.6968 # GDT_score(maxd=8,maxw=2.9)= -38.836 # GDT_score(maxd=8,maxw=3.2)= -36.773 # GDT_score(maxd=8,maxw=3.5)= -34.958 # GDT_score(maxd=10,maxw=3.8)= -37.6136 # GDT_score(maxd=10,maxw=4)= -36.4366 # GDT_score(maxd=10,maxw=4.2)= -35.2962 # GDT_score(maxd=12,maxw=4.3)= -38.2563 # GDT_score(maxd=12,maxw=4.5)= -37.0982 # GDT_score(maxd=12,maxw=4.7)= -35.9966 # GDT_score(maxd=14,maxw=5.2)= -36.1725 # GDT_score(maxd=14,maxw=5.5)= -34.6187 # command:# request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_362912403.pdb -s /var/tmp/to_scwrl_362912403.seq -o /var/tmp/from_scwrl_362912403.pdb > /var/tmp/scwrl_362912403.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_362912403.pdb # conformation set from SCWRL output # command:# naming current conformation model2-scwrl # command:# ReadConformPDB reading from PDB file model3.ts-submitted looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -33.1117 # GDT_score(maxd=8,maxw=2.9)= -32.8699 # GDT_score(maxd=8,maxw=3.2)= -31.0318 # GDT_score(maxd=8,maxw=3.5)= -29.2899 # GDT_score(maxd=10,maxw=3.8)= -31.6005 # GDT_score(maxd=10,maxw=4)= -30.4728 # GDT_score(maxd=10,maxw=4.2)= -29.3812 # GDT_score(maxd=12,maxw=4.3)= -32.0324 # GDT_score(maxd=12,maxw=4.5)= -30.9355 # GDT_score(maxd=12,maxw=4.7)= -29.9134 # GDT_score(maxd=14,maxw=5.2)= -30.0613 # GDT_score(maxd=14,maxw=5.5)= -28.7324 # command:# request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_325482153.pdb -s /var/tmp/to_scwrl_325482153.seq -o /var/tmp/from_scwrl_325482153.pdb > /var/tmp/scwrl_325482153.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_325482153.pdb # conformation set from SCWRL output # command:# naming current conformation model3-scwrl # command:# ReadConformPDB reading from PDB file model4.ts-submitted looking for model 1 # Found a chain break before 355 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -52.7926 # GDT_score(maxd=8,maxw=2.9)= -53.2662 # GDT_score(maxd=8,maxw=3.2)= -50.0034 # GDT_score(maxd=8,maxw=3.5)= -47.075 # GDT_score(maxd=10,maxw=3.8)= -50.92 # GDT_score(maxd=10,maxw=4)= -49.0756 # GDT_score(maxd=10,maxw=4.2)= -47.313 # GDT_score(maxd=12,maxw=4.3)= -51.4458 # GDT_score(maxd=12,maxw=4.5)= -49.6756 # GDT_score(maxd=12,maxw=4.7)= -47.9969 # GDT_score(maxd=14,maxw=5.2)= -47.8751 # GDT_score(maxd=14,maxw=5.5)= -45.6721 # command:# request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1094116598.pdb -s /var/tmp/to_scwrl_1094116598.seq -o /var/tmp/from_scwrl_1094116598.pdb > /var/tmp/scwrl_1094116598.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1094116598.pdb # conformation set from SCWRL output # command:# naming current conformation model4-scwrl # command:# ReadConformPDB reading from PDB file model5.ts-submitted looking for model 1 # Found a chain break before 355 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -48.9362 # GDT_score(maxd=8,maxw=2.9)= -49.6246 # GDT_score(maxd=8,maxw=3.2)= -47.1125 # GDT_score(maxd=8,maxw=3.5)= -44.7153 # GDT_score(maxd=10,maxw=3.8)= -47.5408 # GDT_score(maxd=10,maxw=4)= -46.0197 # GDT_score(maxd=10,maxw=4.2)= -44.5067 # GDT_score(maxd=12,maxw=4.3)= -48.076 # GDT_score(maxd=12,maxw=4.5)= -46.5468 # GDT_score(maxd=12,maxw=4.7)= -45.049 # GDT_score(maxd=14,maxw=5.2)= -45.0937 # GDT_score(maxd=14,maxw=5.5)= -43.0386 # command:# request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1682370198.pdb -s /var/tmp/to_scwrl_1682370198.seq -o /var/tmp/from_scwrl_1682370198.pdb > /var/tmp/scwrl_1682370198.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1682370198.pdb # conformation set from SCWRL output # command:# naming current conformation model5-scwrl # command:# Prefix for input files set to decoys/ # command:# ReadConformPDB reading from PDB file T0316.try1-opt2.pdb looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -39.3617 # GDT_score(maxd=8,maxw=2.9)= -39.6017 # GDT_score(maxd=8,maxw=3.2)= -37.616 # GDT_score(maxd=8,maxw=3.5)= -35.5477 # GDT_score(maxd=10,maxw=3.8)= -38.2028 # GDT_score(maxd=10,maxw=4)= -36.8655 # GDT_score(maxd=10,maxw=4.2)= -35.6083 # GDT_score(maxd=12,maxw=4.3)= -38.8451 # GDT_score(maxd=12,maxw=4.5)= -37.5773 # GDT_score(maxd=12,maxw=4.7)= -36.3741 # GDT_score(maxd=14,maxw=5.2)= -36.6358 # GDT_score(maxd=14,maxw=5.5)= -34.9742 # command:# Prefix for output files set to # command:superimposing iter= 0 total_weight= 2245.000 rmsd (weighted)= 14.657 (unweighted)= 39.480 superimposing iter= 1 total_weight= 6881.232 rmsd (weighted)= 5.793 (unweighted)= 37.519 superimposing iter= 2 total_weight= 3596.883 rmsd (weighted)= 3.513 (unweighted)= 37.067 superimposing iter= 3 total_weight= 2458.451 rmsd (weighted)= 2.654 (unweighted)= 36.927 superimposing iter= 4 total_weight= 2018.235 rmsd (weighted)= 2.246 (unweighted)= 36.865 superimposing iter= 5 total_weight= 1770.740 rmsd (weighted)= 2.044 (unweighted)= 36.819 # command:# Prefix for output files set to decoys/ # command:# Prefix for input files set to # command:# ReadConformPDB reading from PDB file T0316.undertaker-align.pdb looking for model 1 WARNING: atoms too close: (T0316)M38.C and (T0316)D45.C only 0.000 apart, marking (T0316)D45.C as missing WARNING: atoms too close: (T0316)K39.N and (T0316)E46.N only 0.000 apart, marking (T0316)K39.N as missing WARNING: atoms too close: (T0316)K39.CA and (T0316)E46.CA only 0.000 apart, marking (T0316)K39.CA as missing WARNING: atoms too close: (T0316)G48.C and (T0316)T51.C only 0.000 apart, marking (T0316)T51.C as missing WARNING: atoms too close: (T0316)V49.N and (T0316)A52.N only 0.000 apart, marking (T0316)V49.N as missing WARNING: atoms too close: (T0316)V49.CA and (T0316)A52.CA only 0.000 apart, marking (T0316)V49.CA as missing WARNING: atoms too close: (T0316)I107.C and (T0316)K108.C only 0.000 apart, marking (T0316)K108.C as missing WARNING: atoms too close: (T0316)K108.N and (T0316)F109.N only 0.000 apart, marking (T0316)K108.N as missing WARNING: atoms too close: (T0316)K108.CA and (T0316)F109.CA only 0.000 apart, marking (T0316)K108.CA as missing WARNING: atoms too close: (T0316)A130.C and (T0316)A133.C only 0.000 apart, marking (T0316)A133.C as missing WARNING: atoms too close: (T0316)R131.N and (T0316)R134.N only 0.000 apart, marking (T0316)R131.N as missing WARNING: atoms too close: (T0316)R131.CA and (T0316)R134.CA only 0.000 apart, marking (T0316)R131.CA as missing WARNING: atoms too close: (T0316)V146.C and (T0316)N148.C only 0.000 apart, marking (T0316)N148.C as missing WARNING: atoms too close: (T0316)D147.N and (T0316)G149.N only 0.000 apart, marking (T0316)D147.N as missing WARNING: atoms too close: (T0316)D147.CA and (T0316)G149.CA only 0.000 apart, marking (T0316)D147.CA as missing WARNING: atoms too close: (T0316)G250.C and (T0316)A258.C only 0.000 apart, marking (T0316)A258.C as missing WARNING: atoms too close: (T0316)G251.N and (T0316)P259.N only 0.000 apart, marking (T0316)G251.N as missing WARNING: atoms too close: (T0316)G251.CA and (T0316)P259.CA only 0.000 apart, marking (T0316)G251.CA as missing WARNING: atoms too close: (T0316)E298.C and (T0316)M299.C only 0.000 apart, marking (T0316)M299.C as missing WARNING: atoms too close: (T0316)M299.N and (T0316)P300.N only 0.000 apart, marking (T0316)M299.N as missing WARNING: atoms too close: (T0316)M299.CA and (T0316)P300.CA only 0.000 apart, marking (T0316)M299.CA as missing # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # command:# naming current conformation align1 # command:# fraction of real conformation used = 0.803191 # GDT_score = -44.016 # GDT_score(maxd=8,maxw=2.9)= -46.432 # GDT_score(maxd=8,maxw=3.2)= -43.7779 # GDT_score(maxd=8,maxw=3.5)= -41.3098 # GDT_score(maxd=10,maxw=3.8)= -43.3701 # GDT_score(maxd=10,maxw=4)= -41.8586 # GDT_score(maxd=10,maxw=4.2)= -40.4168 # GDT_score(maxd=12,maxw=4.3)= -43.0611 # GDT_score(maxd=12,maxw=4.5)= -41.6404 # GDT_score(maxd=12,maxw=4.7)= -40.2496 # GDT_score(maxd=14,maxw=5.2)= -39.7038 # GDT_score(maxd=14,maxw=5.5)= -37.9123 # command:# ReadConformPDB reading from PDB file T0316.undertaker-align.pdb looking for model 2 WARNING: atoms too close: (T0316)M38.C and (T0316)D43.C only 0.000 apart, marking (T0316)D43.C as missing WARNING: atoms too close: (T0316)K39.N and (T0316)T44.N only 0.000 apart, marking (T0316)K39.N as missing WARNING: atoms too close: (T0316)K39.CA and (T0316)T44.CA only 0.000 apart, marking (T0316)K39.CA as missing WARNING: atoms too close: (T0316)C50.C and (T0316)T51.C only 0.000 apart, marking (T0316)T51.C as missing WARNING: atoms too close: (T0316)T51.N and (T0316)A52.N only 0.000 apart, marking (T0316)T51.N as missing WARNING: atoms too close: (T0316)T51.CA and (T0316)A52.CA only 0.000 apart, marking (T0316)T51.CA as missing WARNING: atoms too close: (T0316)E76.C and (T0316)F87.C only 0.000 apart, marking (T0316)F87.C as missing WARNING: atoms too close: (T0316)K77.N and (T0316)L88.N only 0.000 apart, marking (T0316)K77.N as missing WARNING: atoms too close: (T0316)K77.CA and (T0316)L88.CA only 0.000 apart, marking (T0316)K77.CA as missing WARNING: atoms too close: (T0316)E106.C and (T0316)I107.C only 0.000 apart, marking (T0316)I107.C as missing WARNING: atoms too close: (T0316)I107.N and (T0316)K108.N only 0.000 apart, marking (T0316)I107.N as missing WARNING: atoms too close: (T0316)I107.CA and (T0316)K108.CA only 0.000 apart, marking (T0316)I107.CA as missing WARNING: atoms too close: (T0316)D135.C and (T0316)Q152.C only 0.000 apart, marking (T0316)Q152.C as missing WARNING: atoms too close: (T0316)E136.N and (T0316)T153.N only 0.000 apart, marking (T0316)E136.N as missing WARNING: atoms too close: (T0316)E136.CA and (T0316)T153.CA only 0.000 apart, marking (T0316)E136.CA as missing WARNING: atoms too close: (T0316)M223.C and (T0316)T286.C only 0.000 apart, marking (T0316)T286.C as missing WARNING: atoms too close: (T0316)T224.N and (T0316)S287.N only 0.000 apart, marking (T0316)T224.N as missing WARNING: atoms too close: (T0316)T224.CA and (T0316)S287.CA only 0.000 apart, marking (T0316)T224.CA as missing WARNING: atoms too close: (T0316)F311.C and (T0316)V324.C only 0.000 apart, marking (T0316)V324.C as missing WARNING: atoms too close: (T0316)R312.N and (T0316)K325.N only 0.000 apart, marking (T0316)R312.N as missing WARNING: atoms too close: (T0316)R312.CA and (T0316)K325.CA only 0.000 apart, marking (T0316)R312.CA as missing # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # command:# naming current conformation align2 # command:# fraction of real conformation used = 0.808511 # GDT_score = -47.3404 # GDT_score(maxd=8,maxw=2.9)= -49.4863 # GDT_score(maxd=8,maxw=3.2)= -46.8687 # GDT_score(maxd=8,maxw=3.5)= -44.2705 # GDT_score(maxd=10,maxw=3.8)= -46.5309 # GDT_score(maxd=10,maxw=4)= -44.8918 # GDT_score(maxd=10,maxw=4.2)= -43.3449 # GDT_score(maxd=12,maxw=4.3)= -46.3854 # GDT_score(maxd=12,maxw=4.5)= -44.8644 # GDT_score(maxd=12,maxw=4.7)= -43.4246 # GDT_score(maxd=14,maxw=5.2)= -43.0477 # GDT_score(maxd=14,maxw=5.5)= -41.168 # command:# ReadConformPDB reading from PDB file T0316.undertaker-align.pdb looking for model 3 WARNING: atoms too close: (T0316)M38.C and (T0316)D45.C only 0.000 apart, marking (T0316)D45.C as missing WARNING: atoms too close: (T0316)K39.N and (T0316)E46.N only 0.000 apart, marking (T0316)K39.N as missing WARNING: atoms too close: (T0316)K39.CA and (T0316)E46.CA only 0.000 apart, marking (T0316)K39.CA as missing WARNING: atoms too close: (T0316)C50.C and (T0316)T51.C only 0.000 apart, marking (T0316)T51.C as missing WARNING: atoms too close: (T0316)T51.N and (T0316)A52.N only 0.000 apart, marking (T0316)T51.N as missing WARNING: atoms too close: (T0316)T51.CA and (T0316)A52.CA only 0.000 apart, marking (T0316)T51.CA as missing WARNING: atoms too close: (T0316)F87.C and (T0316)C103.C only 0.000 apart, marking (T0316)C103.C as missing WARNING: atoms too close: (T0316)L88.N and (T0316)N104.N only 0.000 apart, marking (T0316)L88.N as missing WARNING: atoms too close: (T0316)L88.CA and (T0316)N104.CA only 0.000 apart, marking (T0316)L88.CA as missing WARNING: atoms too close: (T0316)K108.C and (T0316)F109.C only 0.000 apart, marking (T0316)F109.C as missing WARNING: atoms too close: (T0316)F109.N and (T0316)K110.N only 0.000 apart, marking (T0316)F109.N as missing WARNING: atoms too close: (T0316)F109.CA and (T0316)K110.CA only 0.000 apart, marking (T0316)F109.CA as missing WARNING: atoms too close: (T0316)A130.C and (T0316)A133.C only 0.000 apart, marking (T0316)A133.C as missing WARNING: atoms too close: (T0316)R131.N and (T0316)R134.N only 0.000 apart, marking (T0316)R131.N as missing WARNING: atoms too close: (T0316)R131.CA and (T0316)R134.CA only 0.000 apart, marking (T0316)R131.CA as missing WARNING: atoms too close: (T0316)E162.C and (T0316)Q165.C only 0.000 apart, marking (T0316)Q165.C as missing WARNING: atoms too close: (T0316)Q163.N and (T0316)K166.N only 0.000 apart, marking (T0316)Q163.N as missing WARNING: atoms too close: (T0316)Q163.CA and (T0316)K166.CA only 0.000 apart, marking (T0316)Q163.CA as missing WARNING: atoms too close: (T0316)N206.C and (T0316)F207.C only 0.000 apart, marking (T0316)F207.C as missing WARNING: atoms too close: (T0316)F207.N and (T0316)K208.N only 0.000 apart, marking (T0316)F207.N as missing WARNING: atoms too close: (T0316)F207.CA and (T0316)K208.CA only 0.000 apart, marking (T0316)F207.CA as missing # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # command:# naming current conformation align3 # command:# ReadConformPDB reading from PDB file T0316.undertaker-align.pdb looking for model 4 WARNING: atoms too close: (T0316)M38.C and (T0316)D45.C only 0.000 apart, marking (T0316)D45.C as missing WARNING: atoms too close: (T0316)K39.N and (T0316)E46.N only 0.000 apart, marking (T0316)K39.N as missing WARNING: atoms too close: (T0316)K39.CA and (T0316)E46.CA only 0.000 apart, marking (T0316)K39.CA as missing WARNING: atoms too close: (T0316)C50.C and (T0316)T51.C only 0.000 apart, marking (T0316)T51.C as missing WARNING: atoms too close: (T0316)T51.N and (T0316)A52.N only 0.000 apart, marking (T0316)T51.N as missing WARNING: atoms too close: (T0316)T51.CA and (T0316)A52.CA only 0.000 apart, marking (T0316)T51.CA as missing WARNING: atoms too close: (T0316)Y86.C and (T0316)M102.C only 0.000 apart, marking (T0316)M102.C as missing WARNING: atoms too close: (T0316)F87.N and (T0316)C103.N only 0.000 apart, marking (T0316)F87.N as missing WARNING: atoms too close: (T0316)F87.CA and (T0316)C103.CA only 0.000 apart, marking (T0316)F87.CA as missing WARNING: atoms too close: (T0316)E106.C and (T0316)I107.C only 0.000 apart, marking (T0316)I107.C as missing WARNING: atoms too close: (T0316)I107.N and (T0316)K108.N only 0.000 apart, marking (T0316)I107.N as missing WARNING: atoms too close: (T0316)I107.CA and (T0316)K108.CA only 0.000 apart, marking (T0316)I107.CA as missing WARNING: atoms too close: (T0316)V124.C and (T0316)T126.C only 0.000 apart, marking (T0316)T126.C as missing WARNING: atoms too close: (T0316)A125.N and (T0316)G127.N only 0.000 apart, marking (T0316)A125.N as missing WARNING: atoms too close: (T0316)A125.CA and (T0316)G127.CA only 0.000 apart, marking (T0316)A125.CA as missing WARNING: atoms too close: (T0316)D135.C and (T0316)T139.C only 0.000 apart, marking (T0316)T139.C as missing WARNING: atoms too close: (T0316)E136.N and (T0316)V140.N only 0.000 apart, marking (T0316)E136.N as missing WARNING: atoms too close: (T0316)E136.CA and (T0316)V140.CA only 0.000 apart, marking (T0316)E136.CA as missing WARNING: atoms too close: (T0316)K150.C and (T0316)T167.C only 0.000 apart, marking (T0316)T167.C as missing WARNING: atoms too close: (T0316)D151.N and (T0316)M168.N only 0.000 apart, marking (T0316)D151.N as missing WARNING: atoms too close: (T0316)D151.CA and (T0316)M168.CA only 0.000 apart, marking (T0316)D151.CA as missing WARNING: atoms too close: (T0316)I199.C and (T0316)F201.C only 0.000 apart, marking (T0316)F201.C as missing WARNING: atoms too close: (T0316)C200.N and (T0316)I202.N only 0.000 apart, marking (T0316)C200.N as missing WARNING: atoms too close: (T0316)C200.CA and (T0316)I202.CA only 0.000 apart, marking (T0316)C200.CA as missing WARNING: atoms too close: (T0316)Y214.C and (T0316)S282.C only 0.000 apart, marking (T0316)S282.C as missing WARNING: atoms too close: (T0316)L215.N and (T0316)L283.N only 0.000 apart, marking (T0316)L215.N as missing WARNING: atoms too close: (T0316)L215.CA and (T0316)L283.CA only 0.000 apart, marking (T0316)L215.CA as missing # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # command:# naming current conformation align4 # command:# ReadConformPDB reading from PDB file T0316.undertaker-align.pdb looking for model 5 WARNING: atoms too close: (T0316)M38.C and (T0316)D43.C only 0.000 apart, marking (T0316)D43.C as missing WARNING: atoms too close: (T0316)K39.N and (T0316)T44.N only 0.000 apart, marking (T0316)K39.N as missing WARNING: atoms too close: (T0316)K39.CA and (T0316)T44.CA only 0.000 apart, marking (T0316)K39.CA as missing WARNING: atoms too close: (T0316)C50.C and (T0316)T51.C only 0.000 apart, marking (T0316)T51.C as missing WARNING: atoms too close: (T0316)T51.N and (T0316)A52.N only 0.000 apart, marking (T0316)T51.N as missing WARNING: atoms too close: (T0316)T51.CA and (T0316)A52.CA only 0.000 apart, marking (T0316)T51.CA as missing WARNING: atoms too close: (T0316)E76.C and (T0316)Y91.C only 0.000 apart, marking (T0316)Y91.C as missing WARNING: atoms too close: (T0316)K77.N and (T0316)R92.N only 0.000 apart, marking (T0316)K77.N as missing WARNING: atoms too close: (T0316)K77.CA and (T0316)R92.CA only 0.000 apart, marking (T0316)K77.CA as missing WARNING: atoms too close: (T0316)C103.C and (T0316)K108.C only 0.000 apart, marking (T0316)K108.C as missing WARNING: atoms too close: (T0316)N104.N and (T0316)F109.N only 0.000 apart, marking (T0316)N104.N as missing WARNING: atoms too close: (T0316)N104.CA and (T0316)F109.CA only 0.000 apart, marking (T0316)N104.CA as missing WARNING: atoms too close: (T0316)G120.C and (T0316)A121.C only 0.000 apart, marking (T0316)A121.C as missing WARNING: atoms too close: (T0316)A121.N and (T0316)D122.N only 0.000 apart, marking (T0316)A121.N as missing WARNING: atoms too close: (T0316)A121.CA and (T0316)D122.CA only 0.000 apart, marking (T0316)A121.CA as missing WARNING: atoms too close: (T0316)D135.C and (T0316)E136.C only 0.000 apart, marking (T0316)E136.C as missing WARNING: atoms too close: (T0316)E136.N and (T0316)D137.N only 0.000 apart, marking (T0316)E136.N as missing WARNING: atoms too close: (T0316)E136.CA and (T0316)D137.CA only 0.000 apart, marking (T0316)E136.CA as missing WARNING: atoms too close: (T0316)K150.C and (T0316)Q152.C only 0.000 apart, marking (T0316)Q152.C as missing WARNING: atoms too close: (T0316)D151.N and (T0316)T153.N only 0.000 apart, marking (T0316)D151.N as missing WARNING: atoms too close: (T0316)D151.CA and (T0316)T153.CA only 0.000 apart, marking (T0316)D151.CA as missing WARNING: atoms too close: (T0316)W260.C and (T0316)F311.C only 0.000 apart, marking (T0316)F311.C as missing WARNING: atoms too close: (T0316)F261.N and (T0316)R312.N only 0.000 apart, marking (T0316)F261.N as missing WARNING: atoms too close: (T0316)F261.CA and (T0316)R312.CA only 0.000 apart, marking (T0316)F261.CA as missing # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # command:# naming current conformation align5 # command:# Prefix for input files set to decoys/ # command:# reading script from file read-pdb+servers.under # ReadConformPDB reading from PDB file ../model1.ts-submitted looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ../model2.ts-submitted looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ../model3.ts-submitted looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ../model4.ts-submitted looking for model 1 # Found a chain break before 355 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ../model5.ts-submitted looking for model 1 # Found a chain break before 355 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.M1-A183-try2-opt2-D122-K269-try1-opt2-A130-I373-try4-opt2-proteinshop.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.M1-A183-try2-opt2-D122-K269-try1-opt2-A130-I373-try4-opt2.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try1-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 354 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try1-opt1.pdb.gz looking for model 1 # Found a chain break before 354 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try1-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 362 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try1-opt2.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try1-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try10-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try10-opt1.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try10-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 352 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try10-opt2.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try10-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try11-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 346 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try11-opt1.pdb.gz looking for model 1 # Found a chain break before 346 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try11-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 358 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try11-opt2.pdb.gz looking for model 1 # Found a chain break before 355 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try11-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 355 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try12-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try12-opt1.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try12-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try12-opt2.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try12-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try13-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 349 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try13-opt1.pdb.gz looking for model 1 # Found a chain break before 349 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try13-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 350 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try13-opt2.pdb.gz looking for model 1 # Found a chain break before 349 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try13-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 349 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try14-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try14-opt1.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try14-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 345 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try14-opt2.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try14-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try15-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try15-opt1.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try15-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 369 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try15-opt2.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try15-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try16-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 352 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try16-opt1.pdb.gz looking for model 1 # Found a chain break before 352 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try16-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try16-opt2.pdb.gz looking for model 1 # Found a chain break before 367 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try16-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 367 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try17-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 352 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try17-opt1.pdb.gz looking for model 1 # Found a chain break before 352 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try17-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 352 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try17-opt2.pdb.gz looking for model 1 # Found a chain break before 369 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try17-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 369 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try18-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try18-opt1.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try18-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 343 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try18-opt2.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try18-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try19-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try19-opt1.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try19-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 343 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try19-opt2.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try19-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try2-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 340 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try2-opt1.pdb.gz looking for model 1 # Found a chain break before 340 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try2-opt2-M1-A183-try6-opt2-A130-I373.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try2-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 347 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try2-opt2.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try2-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try20-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try20-opt1.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try20-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 356 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try20-opt2.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try20-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try21-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try21-opt1.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try21-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 356 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try21-opt2.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try21-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try3-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try3-opt1.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try3-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 362 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try3-opt2.pdb.gz looking for model 1 # Found a chain break before 369 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try3-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 369 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try4-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 352 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try4-opt1.pdb.gz looking for model 1 # Found a chain break before 352 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try4-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 347 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try4-opt2.pdb.gz looking for model 1 # Found a chain break before 367 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try4-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 367 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try5-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 363 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try5-opt1.pdb.gz looking for model 1 # Found a chain break before 363 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try5-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 349 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try5-opt2.pdb.gz looking for model 1 # Found a chain break before 363 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try5-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 363 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try6-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 364 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try6-opt1.pdb.gz looking for model 1 # Found a chain break before 364 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try6-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 356 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try6-opt2.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try6-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try7-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 345 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try7-opt1.pdb.gz looking for model 1 # Found a chain break before 345 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try7-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 345 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try7-opt2.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try7-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try8-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try8-opt1.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try8-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 345 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try8-opt2.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try8-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try9-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 349 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try9-opt1.pdb.gz looking for model 1 # Found a chain break before 349 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try9-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 341 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try9-opt2.pdb.gz looking for model 1 # Found a chain break before 355 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try9-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 355 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file chimera1.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file make-chimera.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1364406966.pdb -s /var/tmp/to_scwrl_1364406966.seq -o /var/tmp/from_scwrl_1364406966.pdb > /var/tmp/scwrl_1364406966.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1364406966.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_POPULUS_TS1-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_143957510.pdb -s /var/tmp/to_scwrl_143957510.seq -o /var/tmp/from_scwrl_143957510.pdb > /var/tmp/scwrl_143957510.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_143957510.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_POPULUS_TS2-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_189608944.pdb -s /var/tmp/to_scwrl_189608944.seq -o /var/tmp/from_scwrl_189608944.pdb > /var/tmp/scwrl_189608944.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_189608944.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_POPULUS_TS3-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2114029991.pdb -s /var/tmp/to_scwrl_2114029991.seq -o /var/tmp/from_scwrl_2114029991.pdb > /var/tmp/scwrl_2114029991.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2114029991.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_POPULUS_TS4-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_110859589.pdb -s /var/tmp/to_scwrl_110859589.seq -o /var/tmp/from_scwrl_110859589.pdb > /var/tmp/scwrl_110859589.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_110859589.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_POPULUS_TS5-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1315990997.pdb -s /var/tmp/to_scwrl_1315990997.seq -o /var/tmp/from_scwrl_1315990997.pdb > /var/tmp/scwrl_1315990997.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1315990997.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_RECOM_TS1-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1979082361.pdb -s /var/tmp/to_scwrl_1979082361.seq -o /var/tmp/from_scwrl_1979082361.pdb > /var/tmp/scwrl_1979082361.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1979082361.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_RECOM_TS2-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1265868091.pdb -s /var/tmp/to_scwrl_1265868091.seq -o /var/tmp/from_scwrl_1265868091.pdb > /var/tmp/scwrl_1265868091.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1265868091.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_RECOM_TS3-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1607280274.pdb -s /var/tmp/to_scwrl_1607280274.seq -o /var/tmp/from_scwrl_1607280274.pdb > /var/tmp/scwrl_1607280274.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1607280274.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_RECOM_TS4-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1152628372.pdb -s /var/tmp/to_scwrl_1152628372.seq -o /var/tmp/from_scwrl_1152628372.pdb > /var/tmp/scwrl_1152628372.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1152628372.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_RECOM_TS5-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1690554879.pdb -s /var/tmp/to_scwrl_1690554879.seq -o /var/tmp/from_scwrl_1690554879.pdb > /var/tmp/scwrl_1690554879.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1690554879.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_TS1-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1941610047.pdb -s /var/tmp/to_scwrl_1941610047.seq -o /var/tmp/from_scwrl_1941610047.pdb > /var/tmp/scwrl_1941610047.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1941610047.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_TS2-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1863789955.pdb -s /var/tmp/to_scwrl_1863789955.seq -o /var/tmp/from_scwrl_1863789955.pdb > /var/tmp/scwrl_1863789955.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1863789955.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_TS3-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1526550045.pdb -s /var/tmp/to_scwrl_1526550045.seq -o /var/tmp/from_scwrl_1526550045.pdb > /var/tmp/scwrl_1526550045.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1526550045.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_TS4-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_628902693.pdb -s /var/tmp/to_scwrl_628902693.seq -o /var/tmp/from_scwrl_628902693.pdb > /var/tmp/scwrl_628902693.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_628902693.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_TS5-scwrl # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # Found a chain break before 353 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2093260959.pdb -s /var/tmp/to_scwrl_2093260959.seq -o /var/tmp/from_scwrl_2093260959.pdb > /var/tmp/scwrl_2093260959.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2093260959.pdb # conformation set from SCWRL output # naming current conformation 3Dpro_TS1-scwrl # ReadConformPDB reading from PDB file servers/3Dpro_TS2.pdb.gz looking for model 1 # Found a chain break before 372 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1035274745.pdb -s /var/tmp/to_scwrl_1035274745.seq -o /var/tmp/from_scwrl_1035274745.pdb > /var/tmp/scwrl_1035274745.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1035274745.pdb # conformation set from SCWRL output # naming current conformation 3Dpro_TS2-scwrl # ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1 # Found a chain break before 370 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1956999147.pdb -s /var/tmp/to_scwrl_1956999147.seq -o /var/tmp/from_scwrl_1956999147.pdb > /var/tmp/scwrl_1956999147.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1956999147.pdb # conformation set from SCWRL output # naming current conformation 3Dpro_TS3-scwrl # ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1 # Found a chain break before 338 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_716283412.pdb -s /var/tmp/to_scwrl_716283412.seq -o /var/tmp/from_scwrl_716283412.pdb > /var/tmp/scwrl_716283412.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_716283412.pdb # conformation set from SCWRL output # naming current conformation 3Dpro_TS4-scwrl # ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1 # Found a chain break before 341 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1438407204.pdb -s /var/tmp/to_scwrl_1438407204.seq -o /var/tmp/from_scwrl_1438407204.pdb > /var/tmp/scwrl_1438407204.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1438407204.pdb # conformation set from SCWRL output # naming current conformation 3Dpro_TS5-scwrl # ReadConformPDB reading from PDB file servers/ABIpro_TS1.pdb.gz looking for model 1 # Found a chain break before 369 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1017071250.pdb -s /var/tmp/to_scwrl_1017071250.seq -o /var/tmp/from_scwrl_1017071250.pdb > /var/tmp/scwrl_1017071250.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1017071250.pdb # conformation set from SCWRL output # naming current conformation ABIpro_TS1-scwrl # ReadConformPDB reading from PDB file servers/ABIpro_TS2.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1238103443.pdb -s /var/tmp/to_scwrl_1238103443.seq -o /var/tmp/from_scwrl_1238103443.pdb > /var/tmp/scwrl_1238103443.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1238103443.pdb # conformation set from SCWRL output # naming current conformation ABIpro_TS2-scwrl # ReadConformPDB reading from PDB file servers/ABIpro_TS3.pdb.gz looking for model 1 # Found a chain break before 369 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2058487206.pdb -s /var/tmp/to_scwrl_2058487206.seq -o /var/tmp/from_scwrl_2058487206.pdb > /var/tmp/scwrl_2058487206.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2058487206.pdb # conformation set from SCWRL output # naming current conformation ABIpro_TS3-scwrl # ReadConformPDB reading from PDB file servers/ABIpro_TS4.pdb.gz looking for model 1 # Found a chain break before 369 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_997825116.pdb -s /var/tmp/to_scwrl_997825116.seq -o /var/tmp/from_scwrl_997825116.pdb > /var/tmp/scwrl_997825116.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_997825116.pdb # conformation set from SCWRL output # naming current conformation ABIpro_TS4-scwrl # ReadConformPDB reading from PDB file servers/ABIpro_TS5.pdb.gz looking for model 1 # Found a chain break before 346 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1882800686.pdb -s /var/tmp/to_scwrl_1882800686.seq -o /var/tmp/from_scwrl_1882800686.pdb > /var/tmp/scwrl_1882800686.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1882800686.pdb # conformation set from SCWRL output # naming current conformation ABIpro_TS5-scwrl # ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1 # Found a chain break before 266 # copying to AlignedFragments data structure # naming current conformation BayesHH_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_62731148.pdb -s /var/tmp/to_scwrl_62731148.seq -o /var/tmp/from_scwrl_62731148.pdb > /var/tmp/scwrl_62731148.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_62731148.pdb # conformation set from SCWRL output # naming current conformation BayesHH_TS1-scwrl # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS1.pdb.gz looking for model 1 # Found a chain break before 346 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_268124879.pdb -s /var/tmp/to_scwrl_268124879.seq -o /var/tmp/from_scwrl_268124879.pdb > /var/tmp/scwrl_268124879.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_268124879.pdb # conformation set from SCWRL output # naming current conformation Bilab-ENABLE_TS1-scwrl # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS2.pdb.gz looking for model 1 # Found a chain break before 369 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_98229442.pdb -s /var/tmp/to_scwrl_98229442.seq -o /var/tmp/from_scwrl_98229442.pdb > /var/tmp/scwrl_98229442.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_98229442.pdb # conformation set from SCWRL output # naming current conformation Bilab-ENABLE_TS2-scwrl # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS3.pdb.gz looking for model 1 # Found a chain break before 323 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_388213301.pdb -s /var/tmp/to_scwrl_388213301.seq -o /var/tmp/from_scwrl_388213301.pdb > /var/tmp/scwrl_388213301.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_388213301.pdb # conformation set from SCWRL output # naming current conformation Bilab-ENABLE_TS3-scwrl # ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1362241477.pdb -s /var/tmp/to_scwrl_1362241477.seq -o /var/tmp/from_scwrl_1362241477.pdb > /var/tmp/scwrl_1362241477.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1362241477.pdb # conformation set from SCWRL output # naming current conformation CIRCLE_TS1-scwrl # ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1780599640.pdb -s /var/tmp/to_scwrl_1780599640.seq -o /var/tmp/from_scwrl_1780599640.pdb > /var/tmp/scwrl_1780599640.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1780599640.pdb # conformation set from SCWRL output # naming current conformation CIRCLE_TS2-scwrl # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1752620267.pdb -s /var/tmp/to_scwrl_1752620267.seq -o /var/tmp/from_scwrl_1752620267.pdb > /var/tmp/scwrl_1752620267.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1752620267.pdb # conformation set from SCWRL output # naming current conformation CIRCLE_TS3-scwrl # ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1506198987.pdb -s /var/tmp/to_scwrl_1506198987.seq -o /var/tmp/from_scwrl_1506198987.pdb > /var/tmp/scwrl_1506198987.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1506198987.pdb # conformation set from SCWRL output # naming current conformation CIRCLE_TS4-scwrl # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # Found a chain break before 370 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1970208584.pdb -s /var/tmp/to_scwrl_1970208584.seq -o /var/tmp/from_scwrl_1970208584.pdb > /var/tmp/scwrl_1970208584.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1970208584.pdb # conformation set from SCWRL output # naming current conformation CIRCLE_TS5-scwrl # ReadConformPDB reading from PDB file servers/CPHmodels_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation CPHmodels_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1719166612.pdb -s /var/tmp/to_scwrl_1719166612.seq -o /var/tmp/from_scwrl_1719166612.pdb > /var/tmp/scwrl_1719166612.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1719166612.pdb # conformation set from SCWRL output # naming current conformation CPHmodels_TS1-scwrl # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1617058576.pdb -s /var/tmp/to_scwrl_1617058576.seq -o /var/tmp/from_scwrl_1617058576.pdb > /var/tmp/scwrl_1617058576.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1617058576.pdb # conformation set from SCWRL output # naming current conformation CaspIta-FOX_TS1-scwrl # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1138715934.pdb -s /var/tmp/to_scwrl_1138715934.seq -o /var/tmp/from_scwrl_1138715934.pdb > /var/tmp/scwrl_1138715934.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1138715934.pdb # conformation set from SCWRL output # naming current conformation CaspIta-FOX_TS2-scwrl # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1550765326.pdb -s /var/tmp/to_scwrl_1550765326.seq -o /var/tmp/from_scwrl_1550765326.pdb > /var/tmp/scwrl_1550765326.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1550765326.pdb # conformation set from SCWRL output # naming current conformation CaspIta-FOX_TS3-scwrl # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_735443021.pdb -s /var/tmp/to_scwrl_735443021.seq -o /var/tmp/from_scwrl_735443021.pdb > /var/tmp/scwrl_735443021.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_735443021.pdb # conformation set from SCWRL output # naming current conformation CaspIta-FOX_TS4-scwrl # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_598512562.pdb -s /var/tmp/to_scwrl_598512562.seq -o /var/tmp/from_scwrl_598512562.pdb > /var/tmp/scwrl_598512562.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_598512562.pdb # conformation set from SCWRL output # naming current conformation CaspIta-FOX_TS5-scwrl # ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Distill_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_555910052.pdb -s /var/tmp/to_scwrl_555910052.seq -o /var/tmp/from_scwrl_555910052.pdb > /var/tmp/scwrl_555910052.log Error: Couldn't open file /var/tmp/from_scwrl_555910052.pdb or /var/tmp/from_scwrl_555910052.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_555910052_b.pdb or decoys//var/tmp/from_scwrl_555910052_b.pdb.gz for input Trying /var/tmp/from_scwrl_555910052_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_555910052_b.pdb or /var/tmp/from_scwrl_555910052_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_555910052_a.pdb or decoys//var/tmp/from_scwrl_555910052_a.pdb.gz for input Trying /var/tmp/from_scwrl_555910052_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_555910052_a.pdb or /var/tmp/from_scwrl_555910052_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_555910052.pdb or /var/tmp/from_scwrl_555910052_b.pdb or /var/tmp/from_scwrl_555910052_a.pdb Error: no new SCWRL conformation added # naming current conformation Distill_TS1-scwrl # ReadConformPDB reading from PDB file servers/Distill_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Distill_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_278514253.pdb -s /var/tmp/to_scwrl_278514253.seq -o /var/tmp/from_scwrl_278514253.pdb > /var/tmp/scwrl_278514253.log Error: Couldn't open file /var/tmp/from_scwrl_278514253.pdb or /var/tmp/from_scwrl_278514253.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_278514253_b.pdb or decoys//var/tmp/from_scwrl_278514253_b.pdb.gz for input Trying /var/tmp/from_scwrl_278514253_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_278514253_b.pdb or /var/tmp/from_scwrl_278514253_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_278514253_a.pdb or decoys//var/tmp/from_scwrl_278514253_a.pdb.gz for input Trying /var/tmp/from_scwrl_278514253_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_278514253_a.pdb or /var/tmp/from_scwrl_278514253_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_278514253.pdb or /var/tmp/from_scwrl_278514253_b.pdb or /var/tmp/from_scwrl_278514253_a.pdb Error: no new SCWRL conformation added # naming current conformation Distill_TS2-scwrl # ReadConformPDB reading from PDB file servers/Distill_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Distill_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_392638962.pdb -s /var/tmp/to_scwrl_392638962.seq -o /var/tmp/from_scwrl_392638962.pdb > /var/tmp/scwrl_392638962.log Error: Couldn't open file /var/tmp/from_scwrl_392638962.pdb or /var/tmp/from_scwrl_392638962.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_392638962_b.pdb or decoys//var/tmp/from_scwrl_392638962_b.pdb.gz for input Trying /var/tmp/from_scwrl_392638962_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_392638962_b.pdb or /var/tmp/from_scwrl_392638962_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_392638962_a.pdb or decoys//var/tmp/from_scwrl_392638962_a.pdb.gz for input Trying /var/tmp/from_scwrl_392638962_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_392638962_a.pdb or /var/tmp/from_scwrl_392638962_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_392638962.pdb or /var/tmp/from_scwrl_392638962_b.pdb or /var/tmp/from_scwrl_392638962_a.pdb Error: no new SCWRL conformation added # naming current conformation Distill_TS3-scwrl # ReadConformPDB reading from PDB file servers/Distill_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Distill_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_272216360.pdb -s /var/tmp/to_scwrl_272216360.seq -o /var/tmp/from_scwrl_272216360.pdb > /var/tmp/scwrl_272216360.log Error: Couldn't open file /var/tmp/from_scwrl_272216360.pdb or /var/tmp/from_scwrl_272216360.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_272216360_b.pdb or decoys//var/tmp/from_scwrl_272216360_b.pdb.gz for input Trying /var/tmp/from_scwrl_272216360_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_272216360_b.pdb or /var/tmp/from_scwrl_272216360_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_272216360_a.pdb or decoys//var/tmp/from_scwrl_272216360_a.pdb.gz for input Trying /var/tmp/from_scwrl_272216360_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_272216360_a.pdb or /var/tmp/from_scwrl_272216360_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_272216360.pdb or /var/tmp/from_scwrl_272216360_b.pdb or /var/tmp/from_scwrl_272216360_a.pdb Error: no new SCWRL conformation added # naming current conformation Distill_TS4-scwrl # ReadConformPDB reading from PDB file servers/Distill_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Distill_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1805064298.pdb -s /var/tmp/to_scwrl_1805064298.seq -o /var/tmp/from_scwrl_1805064298.pdb > /var/tmp/scwrl_1805064298.log Error: Couldn't open file /var/tmp/from_scwrl_1805064298.pdb or /var/tmp/from_scwrl_1805064298.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1805064298_b.pdb or decoys//var/tmp/from_scwrl_1805064298_b.pdb.gz for input Trying /var/tmp/from_scwrl_1805064298_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_1805064298_b.pdb or /var/tmp/from_scwrl_1805064298_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1805064298_a.pdb or decoys//var/tmp/from_scwrl_1805064298_a.pdb.gz for input Trying /var/tmp/from_scwrl_1805064298_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_1805064298_a.pdb or /var/tmp/from_scwrl_1805064298_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_1805064298.pdb or /var/tmp/from_scwrl_1805064298_b.pdb or /var/tmp/from_scwrl_1805064298_a.pdb Error: no new SCWRL conformation added # naming current conformation Distill_TS5-scwrl # ReadConformPDB reading from PDB file servers/FAMSD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FAMSD_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1021541655.pdb -s /var/tmp/to_scwrl_1021541655.seq -o /var/tmp/from_scwrl_1021541655.pdb > /var/tmp/scwrl_1021541655.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1021541655.pdb # conformation set from SCWRL output # naming current conformation FAMSD_TS1-scwrl # ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FAMSD_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_217993672.pdb -s /var/tmp/to_scwrl_217993672.seq -o /var/tmp/from_scwrl_217993672.pdb > /var/tmp/scwrl_217993672.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_217993672.pdb # conformation set from SCWRL output # naming current conformation FAMSD_TS2-scwrl # ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FAMSD_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_692855396.pdb -s /var/tmp/to_scwrl_692855396.seq -o /var/tmp/from_scwrl_692855396.pdb > /var/tmp/scwrl_692855396.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_692855396.pdb # conformation set from SCWRL output # naming current conformation FAMSD_TS3-scwrl # ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FAMSD_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_831057155.pdb -s /var/tmp/to_scwrl_831057155.seq -o /var/tmp/from_scwrl_831057155.pdb > /var/tmp/scwrl_831057155.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_831057155.pdb # conformation set from SCWRL output # naming current conformation FAMSD_TS4-scwrl # ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FAMSD_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_934277085.pdb -s /var/tmp/to_scwrl_934277085.seq -o /var/tmp/from_scwrl_934277085.pdb > /var/tmp/scwrl_934277085.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_934277085.pdb # conformation set from SCWRL output # naming current conformation FAMSD_TS5-scwrl # ReadConformPDB reading from PDB file servers/FAMS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FAMS_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2131262600.pdb -s /var/tmp/to_scwrl_2131262600.seq -o /var/tmp/from_scwrl_2131262600.pdb > /var/tmp/scwrl_2131262600.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2131262600.pdb # conformation set from SCWRL output # naming current conformation FAMS_TS1-scwrl # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FAMS_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1848128405.pdb -s /var/tmp/to_scwrl_1848128405.seq -o /var/tmp/from_scwrl_1848128405.pdb > /var/tmp/scwrl_1848128405.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1848128405.pdb # conformation set from SCWRL output # naming current conformation FAMS_TS2-scwrl # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FAMS_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_24896881.pdb -s /var/tmp/to_scwrl_24896881.seq -o /var/tmp/from_scwrl_24896881.pdb > /var/tmp/scwrl_24896881.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_24896881.pdb # conformation set from SCWRL output # naming current conformation FAMS_TS3-scwrl # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FAMS_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2042266159.pdb -s /var/tmp/to_scwrl_2042266159.seq -o /var/tmp/from_scwrl_2042266159.pdb > /var/tmp/scwrl_2042266159.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2042266159.pdb # conformation set from SCWRL output # naming current conformation FAMS_TS4-scwrl # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FAMS_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_698469874.pdb -s /var/tmp/to_scwrl_698469874.seq -o /var/tmp/from_scwrl_698469874.pdb > /var/tmp/scwrl_698469874.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_698469874.pdb # conformation set from SCWRL output # naming current conformation FAMS_TS5-scwrl # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # Found a chain break before 370 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1907697568.pdb -s /var/tmp/to_scwrl_1907697568.seq -o /var/tmp/from_scwrl_1907697568.pdb > /var/tmp/scwrl_1907697568.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1907697568.pdb # conformation set from SCWRL output # naming current conformation FOLDpro_TS1-scwrl # ReadConformPDB reading from PDB file servers/FOLDpro_TS2.pdb.gz looking for model 1 # Found a chain break before 341 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2104997308.pdb -s /var/tmp/to_scwrl_2104997308.seq -o /var/tmp/from_scwrl_2104997308.pdb > /var/tmp/scwrl_2104997308.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2104997308.pdb # conformation set from SCWRL output # naming current conformation FOLDpro_TS2-scwrl # ReadConformPDB reading from PDB file servers/FOLDpro_TS3.pdb.gz looking for model 1 # Found a chain break before 353 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_966594753.pdb -s /var/tmp/to_scwrl_966594753.seq -o /var/tmp/from_scwrl_966594753.pdb > /var/tmp/scwrl_966594753.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_966594753.pdb # conformation set from SCWRL output # naming current conformation FOLDpro_TS3-scwrl # ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1 # Found a chain break before 341 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2005927010.pdb -s /var/tmp/to_scwrl_2005927010.seq -o /var/tmp/from_scwrl_2005927010.pdb > /var/tmp/scwrl_2005927010.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2005927010.pdb # conformation set from SCWRL output # naming current conformation FOLDpro_TS4-scwrl # ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1 # Found a chain break before 335 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_345726962.pdb -s /var/tmp/to_scwrl_345726962.seq -o /var/tmp/from_scwrl_345726962.pdb > /var/tmp/scwrl_345726962.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_345726962.pdb # conformation set from SCWRL output # naming current conformation FOLDpro_TS5-scwrl # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 Skipped atom 526, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 528, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 530, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 532, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 738, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 740, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 742, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 744, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 754, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 756, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 758, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 760, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 842, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 844, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 846, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 848, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 918, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 920, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 922, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 924, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1154, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1156, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1158, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1160, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1230, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1232, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1234, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1236, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1242, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1244, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1246, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1248, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1254, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1256, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1258, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1260, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1342, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1344, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1346, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1348, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FORTE1_AL1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_181352583.pdb -s /var/tmp/to_scwrl_181352583.seq -o /var/tmp/from_scwrl_181352583.pdb > /var/tmp/scwrl_181352583.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_181352583.pdb # conformation set from SCWRL output # naming current conformation FORTE1_AL1-scwrl # ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FORTE1_AL2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1639043004.pdb -s /var/tmp/to_scwrl_1639043004.seq -o /var/tmp/from_scwrl_1639043004.pdb > /var/tmp/scwrl_1639043004.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1639043004.pdb # conformation set from SCWRL output # naming current conformation FORTE1_AL2-scwrl # ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FORTE1_AL3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2098347230.pdb -s /var/tmp/to_scwrl_2098347230.seq -o /var/tmp/from_scwrl_2098347230.pdb > /var/tmp/scwrl_2098347230.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2098347230.pdb # conformation set from SCWRL output # naming current conformation FORTE1_AL3-scwrl # ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FORTE1_AL4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1687551570.pdb -s /var/tmp/to_scwrl_1687551570.seq -o /var/tmp/from_scwrl_1687551570.pdb > /var/tmp/scwrl_1687551570.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1687551570.pdb # conformation set from SCWRL output # naming current conformation FORTE1_AL4-scwrl # ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FORTE1_AL5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1461767941.pdb -s /var/tmp/to_scwrl_1461767941.seq -o /var/tmp/from_scwrl_1461767941.pdb > /var/tmp/scwrl_1461767941.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1461767941.pdb # conformation set from SCWRL output # naming current conformation FORTE1_AL5-scwrl # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 Skipped atom 526, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 528, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 530, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 532, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 738, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 740, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 742, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 744, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 754, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 756, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 758, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 760, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 842, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 844, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 846, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 848, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 918, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 920, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 922, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 924, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1154, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1156, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1158, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1160, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1230, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1232, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1234, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1236, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1242, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1244, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1246, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1248, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1254, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1256, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1258, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1260, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1342, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1344, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1346, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1348, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FORTE2_AL1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1670030195.pdb -s /var/tmp/to_scwrl_1670030195.seq -o /var/tmp/from_scwrl_1670030195.pdb > /var/tmp/scwrl_1670030195.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1670030195.pdb # conformation set from SCWRL output # naming current conformation FORTE2_AL1-scwrl # ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FORTE2_AL2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1157126499.pdb -s /var/tmp/to_scwrl_1157126499.seq -o /var/tmp/from_scwrl_1157126499.pdb > /var/tmp/scwrl_1157126499.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1157126499.pdb # conformation set from SCWRL output # naming current conformation FORTE2_AL2-scwrl # ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FORTE2_AL3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_453000230.pdb -s /var/tmp/to_scwrl_453000230.seq -o /var/tmp/from_scwrl_453000230.pdb > /var/tmp/scwrl_453000230.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_453000230.pdb # conformation set from SCWRL output # naming current conformation FORTE2_AL3-scwrl # ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FORTE2_AL4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1073311875.pdb -s /var/tmp/to_scwrl_1073311875.seq -o /var/tmp/from_scwrl_1073311875.pdb > /var/tmp/scwrl_1073311875.log sh: line 1: 30018 Killed scwrl3 -i /var/tmp/to_scwrl_1073311875.pdb -s /var/tmp/to_scwrl_1073311875.seq -o /var/tmp/from_scwrl_1073311875.pdb >/var/tmp/scwrl_1073311875.log Error: Couldn't open file /var/tmp/from_scwrl_1073311875.pdb or /var/tmp/from_scwrl_1073311875.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1073311875_b.pdb or decoys//var/tmp/from_scwrl_1073311875_b.pdb.gz for input Trying /var/tmp/from_scwrl_1073311875_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_1073311875_b.pdb or /var/tmp/from_scwrl_1073311875_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1073311875_a.pdb or decoys//var/tmp/from_scwrl_1073311875_a.pdb.gz for input Trying /var/tmp/from_scwrl_1073311875_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_1073311875_a.pdb or /var/tmp/from_scwrl_1073311875_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_1073311875.pdb or /var/tmp/from_scwrl_1073311875_b.pdb or /var/tmp/from_scwrl_1073311875_a.pdb Error: no new SCWRL conformation added # naming current conformation FORTE2_AL4-scwrl # ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FORTE2_AL5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1892569520.pdb -s /var/tmp/to_scwrl_1892569520.seq -o /var/tmp/from_scwrl_1892569520.pdb > /var/tmp/scwrl_1892569520.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1892569520.pdb # conformation set from SCWRL output # naming current conformation FORTE2_AL5-scwrl # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS1.pdb.gz looking for model 1 # Found a chain break before 366 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1051512792.pdb -s /var/tmp/to_scwrl_1051512792.seq -o /var/tmp/from_scwrl_1051512792.pdb > /var/tmp/scwrl_1051512792.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1051512792.pdb # conformation set from SCWRL output # naming current conformation FPSOLVER-SERVER_TS1-scwrl # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS2.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1629221926.pdb -s /var/tmp/to_scwrl_1629221926.seq -o /var/tmp/from_scwrl_1629221926.pdb > /var/tmp/scwrl_1629221926.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1629221926.pdb # conformation set from SCWRL output # naming current conformation FPSOLVER-SERVER_TS2-scwrl # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS3.pdb.gz looking for model 1 # Found a chain break before 372 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_23600126.pdb -s /var/tmp/to_scwrl_23600126.seq -o /var/tmp/from_scwrl_23600126.pdb > /var/tmp/scwrl_23600126.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_23600126.pdb # conformation set from SCWRL output # naming current conformation FPSOLVER-SERVER_TS3-scwrl # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS4.pdb.gz looking for model 1 # Found a chain break before 360 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1444151754.pdb -s /var/tmp/to_scwrl_1444151754.seq -o /var/tmp/from_scwrl_1444151754.pdb > /var/tmp/scwrl_1444151754.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1444151754.pdb # conformation set from SCWRL output # naming current conformation FPSOLVER-SERVER_TS4-scwrl # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS5.pdb.gz looking for model 1 # Found a chain break before 372 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1901438286.pdb -s /var/tmp/to_scwrl_1901438286.seq -o /var/tmp/from_scwrl_1901438286.pdb > /var/tmp/scwrl_1901438286.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1901438286.pdb # conformation set from SCWRL output # naming current conformation FPSOLVER-SERVER_TS5-scwrl # ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1828664424.pdb -s /var/tmp/to_scwrl_1828664424.seq -o /var/tmp/from_scwrl_1828664424.pdb > /var/tmp/scwrl_1828664424.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1828664424.pdb # conformation set from SCWRL output # naming current conformation FUGMOD_TS1-scwrl # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_318209762.pdb -s /var/tmp/to_scwrl_318209762.seq -o /var/tmp/from_scwrl_318209762.pdb > /var/tmp/scwrl_318209762.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_318209762.pdb # conformation set from SCWRL output # naming current conformation FUGMOD_TS2-scwrl # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2119431959.pdb -s /var/tmp/to_scwrl_2119431959.seq -o /var/tmp/from_scwrl_2119431959.pdb > /var/tmp/scwrl_2119431959.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2119431959.pdb # conformation set from SCWRL output # naming current conformation FUGMOD_TS3-scwrl # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # Found a chain break before 348 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_374036174.pdb -s /var/tmp/to_scwrl_374036174.seq -o /var/tmp/from_scwrl_374036174.pdb > /var/tmp/scwrl_374036174.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_374036174.pdb # conformation set from SCWRL output # naming current conformation FUGMOD_TS4-scwrl # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1149266917.pdb -s /var/tmp/to_scwrl_1149266917.seq -o /var/tmp/from_scwrl_1149266917.pdb > /var/tmp/scwrl_1149266917.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1149266917.pdb # conformation set from SCWRL output # naming current conformation FUGMOD_TS5-scwrl # ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FUGUE_AL1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_906225397.pdb -s /var/tmp/to_scwrl_906225397.seq -o /var/tmp/from_scwrl_906225397.pdb > /var/tmp/scwrl_906225397.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_906225397.pdb # conformation set from SCWRL output # naming current conformation FUGUE_AL1-scwrl # ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FUGUE_AL2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_357815127.pdb -s /var/tmp/to_scwrl_357815127.seq -o /var/tmp/from_scwrl_357815127.pdb > /var/tmp/scwrl_357815127.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_357815127.pdb # conformation set from SCWRL output # naming current conformation FUGUE_AL2-scwrl # ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FUGUE_AL3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_849911676.pdb -s /var/tmp/to_scwrl_849911676.seq -o /var/tmp/from_scwrl_849911676.pdb > /var/tmp/scwrl_849911676.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_849911676.pdb # conformation set from SCWRL output # naming current conformation FUGUE_AL3-scwrl # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FUGUE_AL4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_931122278.pdb -s /var/tmp/to_scwrl_931122278.seq -o /var/tmp/from_scwrl_931122278.pdb > /var/tmp/scwrl_931122278.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_931122278.pdb # conformation set from SCWRL output # naming current conformation FUGUE_AL4-scwrl # ReadConformPDB reading from PDB file servers/FUGUE_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FUGUE_AL5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_252597640.pdb -s /var/tmp/to_scwrl_252597640.seq -o /var/tmp/from_scwrl_252597640.pdb > /var/tmp/scwrl_252597640.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_252597640.pdb # conformation set from SCWRL output # naming current conformation FUGUE_AL5-scwrl # ReadConformPDB reading from PDB file servers/FUNCTION_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FUNCTION_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1548381549.pdb -s /var/tmp/to_scwrl_1548381549.seq -o /var/tmp/from_scwrl_1548381549.pdb > /var/tmp/scwrl_1548381549.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1548381549.pdb # conformation set from SCWRL output # naming current conformation FUNCTION_TS1-scwrl # ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_691336199.pdb -s /var/tmp/to_scwrl_691336199.seq -o /var/tmp/from_scwrl_691336199.pdb > /var/tmp/scwrl_691336199.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_691336199.pdb # conformation set from SCWRL output # naming current conformation FUNCTION_TS2-scwrl # ReadConformPDB reading from PDB file servers/FUNCTION_TS3.pdb.gz looking for model 1 # Found a chain break before 366 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_210111301.pdb -s /var/tmp/to_scwrl_210111301.seq -o /var/tmp/from_scwrl_210111301.pdb > /var/tmp/scwrl_210111301.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_210111301.pdb # conformation set from SCWRL output # naming current conformation FUNCTION_TS3-scwrl # ReadConformPDB reading from PDB file servers/FUNCTION_TS4.pdb.gz looking for model 1 # Found a chain break before 367 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_367492656.pdb -s /var/tmp/to_scwrl_367492656.seq -o /var/tmp/from_scwrl_367492656.pdb > /var/tmp/scwrl_367492656.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_367492656.pdb # conformation set from SCWRL output # naming current conformation FUNCTION_TS4-scwrl # ReadConformPDB reading from PDB file servers/FUNCTION_TS5.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_549779563.pdb -s /var/tmp/to_scwrl_549779563.seq -o /var/tmp/from_scwrl_549779563.pdb > /var/tmp/scwrl_549779563.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_549779563.pdb # conformation set from SCWRL output # naming current conformation FUNCTION_TS5-scwrl # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_555838263.pdb -s /var/tmp/to_scwrl_555838263.seq -o /var/tmp/from_scwrl_555838263.pdb > /var/tmp/scwrl_555838263.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_555838263.pdb # conformation set from SCWRL output # naming current conformation GeneSilicoMetaServer_TS1-scwrl # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # Found a chain break before 372 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_548845239.pdb -s /var/tmp/to_scwrl_548845239.seq -o /var/tmp/from_scwrl_548845239.pdb > /var/tmp/scwrl_548845239.log sh: line 1: 30124 Killed scwrl3 -i /var/tmp/to_scwrl_548845239.pdb -s /var/tmp/to_scwrl_548845239.seq -o /var/tmp/from_scwrl_548845239.pdb >/var/tmp/scwrl_548845239.log Error: Couldn't open file /var/tmp/from_scwrl_548845239.pdb or /var/tmp/from_scwrl_548845239.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_548845239_b.pdb or decoys//var/tmp/from_scwrl_548845239_b.pdb.gz for input Trying /var/tmp/from_scwrl_548845239_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_548845239_b.pdb or /var/tmp/from_scwrl_548845239_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_548845239_a.pdb or decoys//var/tmp/from_scwrl_548845239_a.pdb.gz for input Trying /var/tmp/from_scwrl_548845239_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_548845239_a.pdb or /var/tmp/from_scwrl_548845239_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_548845239.pdb or /var/tmp/from_scwrl_548845239_b.pdb or /var/tmp/from_scwrl_548845239_a.pdb Error: no new SCWRL conformation added # naming current conformation GeneSilicoMetaServer_TS2-scwrl # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_41338920.pdb -s /var/tmp/to_scwrl_41338920.seq -o /var/tmp/from_scwrl_41338920.pdb > /var/tmp/scwrl_41338920.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_41338920.pdb # conformation set from SCWRL output # naming current conformation GeneSilicoMetaServer_TS3-scwrl # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_506701846.pdb -s /var/tmp/to_scwrl_506701846.seq -o /var/tmp/from_scwrl_506701846.pdb > /var/tmp/scwrl_506701846.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_506701846.pdb # conformation set from SCWRL output # naming current conformation GeneSilicoMetaServer_TS4-scwrl # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1 # Found a chain break before 338 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_88913163.pdb -s /var/tmp/to_scwrl_88913163.seq -o /var/tmp/from_scwrl_88913163.pdb > /var/tmp/scwrl_88913163.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_88913163.pdb # conformation set from SCWRL output # naming current conformation GeneSilicoMetaServer_TS5-scwrl # ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation HHpred1_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1503106861.pdb -s /var/tmp/to_scwrl_1503106861.seq -o /var/tmp/from_scwrl_1503106861.pdb > /var/tmp/scwrl_1503106861.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1503106861.pdb # conformation set from SCWRL output # naming current conformation HHpred1_TS1-scwrl # ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation HHpred2_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_29248394.pdb -s /var/tmp/to_scwrl_29248394.seq -o /var/tmp/from_scwrl_29248394.pdb > /var/tmp/scwrl_29248394.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_29248394.pdb # conformation set from SCWRL output # naming current conformation HHpred2_TS1-scwrl # ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation HHpred3_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1246039662.pdb -s /var/tmp/to_scwrl_1246039662.seq -o /var/tmp/from_scwrl_1246039662.pdb > /var/tmp/scwrl_1246039662.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1246039662.pdb # conformation set from SCWRL output # naming current conformation HHpred3_TS1-scwrl # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1956107091.pdb -s /var/tmp/to_scwrl_1956107091.seq -o /var/tmp/from_scwrl_1956107091.pdb > /var/tmp/scwrl_1956107091.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1956107091.pdb # conformation set from SCWRL output # naming current conformation Huber-Torda-Server_TS1-scwrl # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1102560268.pdb -s /var/tmp/to_scwrl_1102560268.seq -o /var/tmp/from_scwrl_1102560268.pdb > /var/tmp/scwrl_1102560268.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1102560268.pdb # conformation set from SCWRL output # naming current conformation Huber-Torda-Server_TS2-scwrl # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_991125537.pdb -s /var/tmp/to_scwrl_991125537.seq -o /var/tmp/from_scwrl_991125537.pdb > /var/tmp/scwrl_991125537.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_991125537.pdb # conformation set from SCWRL output # naming current conformation Huber-Torda-Server_TS3-scwrl # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_860136237.pdb -s /var/tmp/to_scwrl_860136237.seq -o /var/tmp/from_scwrl_860136237.pdb > /var/tmp/scwrl_860136237.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_860136237.pdb # conformation set from SCWRL output # naming current conformation Huber-Torda-Server_TS4-scwrl # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_584298548.pdb -s /var/tmp/to_scwrl_584298548.seq -o /var/tmp/from_scwrl_584298548.pdb > /var/tmp/scwrl_584298548.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_584298548.pdb # conformation set from SCWRL output # naming current conformation Huber-Torda-Server_TS5-scwrl # ReadConformPDB reading from PDB file servers/LOOPP_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation LOOPP_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1014725663.pdb -s /var/tmp/to_scwrl_1014725663.seq -o /var/tmp/from_scwrl_1014725663.pdb > /var/tmp/scwrl_1014725663.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1014725663.pdb # conformation set from SCWRL output # naming current conformation LOOPP_TS1-scwrl # ReadConformPDB reading from PDB file servers/LOOPP_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation LOOPP_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_156804344.pdb -s /var/tmp/to_scwrl_156804344.seq -o /var/tmp/from_scwrl_156804344.pdb > /var/tmp/scwrl_156804344.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_156804344.pdb # conformation set from SCWRL output # naming current conformation LOOPP_TS2-scwrl # ReadConformPDB reading from PDB file servers/LOOPP_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation LOOPP_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_338253188.pdb -s /var/tmp/to_scwrl_338253188.seq -o /var/tmp/from_scwrl_338253188.pdb > /var/tmp/scwrl_338253188.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_338253188.pdb # conformation set from SCWRL output # naming current conformation LOOPP_TS3-scwrl # ReadConformPDB reading from PDB file servers/LOOPP_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation LOOPP_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_695906441.pdb -s /var/tmp/to_scwrl_695906441.seq -o /var/tmp/from_scwrl_695906441.pdb > /var/tmp/scwrl_695906441.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_695906441.pdb # conformation set from SCWRL output # naming current conformation LOOPP_TS4-scwrl # ReadConformPDB reading from PDB file servers/LOOPP_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation LOOPP_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_475014106.pdb -s /var/tmp/to_scwrl_475014106.seq -o /var/tmp/from_scwrl_475014106.pdb > /var/tmp/scwrl_475014106.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_475014106.pdb # conformation set from SCWRL output # naming current conformation LOOPP_TS5-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # Found a chain break before 332 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_310201500.pdb -s /var/tmp/to_scwrl_310201500.seq -o /var/tmp/from_scwrl_310201500.pdb > /var/tmp/scwrl_310201500.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_310201500.pdb # conformation set from SCWRL output # naming current conformation Ma-OPUS-server_TS1-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS2.pdb.gz looking for model 1 # Found a chain break before 366 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1069942615.pdb -s /var/tmp/to_scwrl_1069942615.seq -o /var/tmp/from_scwrl_1069942615.pdb > /var/tmp/scwrl_1069942615.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1069942615.pdb # conformation set from SCWRL output # naming current conformation Ma-OPUS-server_TS2-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS3.pdb.gz looking for model 1 # Found a chain break before 327 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1624281023.pdb -s /var/tmp/to_scwrl_1624281023.seq -o /var/tmp/from_scwrl_1624281023.pdb > /var/tmp/scwrl_1624281023.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1624281023.pdb # conformation set from SCWRL output # naming current conformation Ma-OPUS-server_TS3-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS4.pdb.gz looking for model 1 # Found a chain break before 364 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1216426896.pdb -s /var/tmp/to_scwrl_1216426896.seq -o /var/tmp/from_scwrl_1216426896.pdb > /var/tmp/scwrl_1216426896.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1216426896.pdb # conformation set from SCWRL output # naming current conformation Ma-OPUS-server_TS4-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS5.pdb.gz looking for model 1 # Found a chain break before 347 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1427757741.pdb -s /var/tmp/to_scwrl_1427757741.seq -o /var/tmp/from_scwrl_1427757741.pdb > /var/tmp/scwrl_1427757741.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1427757741.pdb # conformation set from SCWRL output # naming current conformation Ma-OPUS-server_TS5-scwrl # ReadConformPDB reading from PDB file servers/MetaTasser_TS1.pdb.gz looking for model 1 # Found a chain break before 372 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_326709052.pdb -s /var/tmp/to_scwrl_326709052.seq -o /var/tmp/from_scwrl_326709052.pdb > /var/tmp/scwrl_326709052.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_326709052.pdb # conformation set from SCWRL output # naming current conformation MetaTasser_TS1-scwrl # ReadConformPDB reading from PDB file servers/MetaTasser_TS2.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_65527.pdb -s /var/tmp/to_scwrl_65527.seq -o /var/tmp/from_scwrl_65527.pdb > /var/tmp/scwrl_65527.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_65527.pdb # conformation set from SCWRL output # naming current conformation MetaTasser_TS2-scwrl # ReadConformPDB reading from PDB file servers/MetaTasser_TS3.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1680355381.pdb -s /var/tmp/to_scwrl_1680355381.seq -o /var/tmp/from_scwrl_1680355381.pdb > /var/tmp/scwrl_1680355381.log sh: line 1: 30234 Killed scwrl3 -i /var/tmp/to_scwrl_1680355381.pdb -s /var/tmp/to_scwrl_1680355381.seq -o /var/tmp/from_scwrl_1680355381.pdb >/var/tmp/scwrl_1680355381.log Error: Couldn't open file /var/tmp/from_scwrl_1680355381.pdb or /var/tmp/from_scwrl_1680355381.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1680355381_b.pdb or decoys//var/tmp/from_scwrl_1680355381_b.pdb.gz for input Trying /var/tmp/from_scwrl_1680355381_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_1680355381_b.pdb or /var/tmp/from_scwrl_1680355381_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1680355381_a.pdb or decoys//var/tmp/from_scwrl_1680355381_a.pdb.gz for input Trying /var/tmp/from_scwrl_1680355381_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_1680355381_a.pdb or /var/tmp/from_scwrl_1680355381_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_1680355381.pdb or /var/tmp/from_scwrl_1680355381_b.pdb or /var/tmp/from_scwrl_1680355381_a.pdb Error: no new SCWRL conformation added # naming current conformation MetaTasser_TS3-scwrl # ReadConformPDB reading from PDB file servers/MetaTasser_TS4.pdb.gz looking for model 1 # Found a chain break before 372 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1875090602.pdb -s /var/tmp/to_scwrl_1875090602.seq -o /var/tmp/from_scwrl_1875090602.pdb > /var/tmp/scwrl_1875090602.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1875090602.pdb # conformation set from SCWRL output # naming current conformation MetaTasser_TS4-scwrl # ReadConformPDB reading from PDB file servers/MetaTasser_TS5.pdb.gz looking for model 1 # Found a chain break before 372 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_691401727.pdb -s /var/tmp/to_scwrl_691401727.seq -o /var/tmp/from_scwrl_691401727.pdb > /var/tmp/scwrl_691401727.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_691401727.pdb # conformation set from SCWRL output # naming current conformation MetaTasser_TS5-scwrl # ReadConformPDB reading from PDB file servers/NN_PUT_lab_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation NN_PUT_lab_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1890466682.pdb -s /var/tmp/to_scwrl_1890466682.seq -o /var/tmp/from_scwrl_1890466682.pdb > /var/tmp/scwrl_1890466682.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1890466682.pdb # conformation set from SCWRL output # naming current conformation NN_PUT_lab_TS1-scwrl # ReadConformPDB reading from PDB file servers/POMYSL_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation POMYSL_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_95099611.pdb -s /var/tmp/to_scwrl_95099611.seq -o /var/tmp/from_scwrl_95099611.pdb > /var/tmp/scwrl_95099611.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_95099611.pdb # conformation set from SCWRL output # naming current conformation POMYSL_TS1-scwrl # ReadConformPDB reading from PDB file servers/POMYSL_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation POMYSL_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1241181289.pdb -s /var/tmp/to_scwrl_1241181289.seq -o /var/tmp/from_scwrl_1241181289.pdb > /var/tmp/scwrl_1241181289.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1241181289.pdb # conformation set from SCWRL output # naming current conformation POMYSL_TS2-scwrl # ReadConformPDB reading from PDB file servers/POMYSL_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation POMYSL_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_298821299.pdb -s /var/tmp/to_scwrl_298821299.seq -o /var/tmp/from_scwrl_298821299.pdb > /var/tmp/scwrl_298821299.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_298821299.pdb # conformation set from SCWRL output # naming current conformation POMYSL_TS3-scwrl # ReadConformPDB reading from PDB file servers/POMYSL_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation POMYSL_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_643944850.pdb -s /var/tmp/to_scwrl_643944850.seq -o /var/tmp/from_scwrl_643944850.pdb > /var/tmp/scwrl_643944850.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_643944850.pdb # conformation set from SCWRL output # naming current conformation POMYSL_TS4-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1282520209.pdb -s /var/tmp/to_scwrl_1282520209.seq -o /var/tmp/from_scwrl_1282520209.pdb > /var/tmp/scwrl_1282520209.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1282520209.pdb # conformation set from SCWRL output # naming current conformation PROTINFO-AB_TS1-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_805523145.pdb -s /var/tmp/to_scwrl_805523145.seq -o /var/tmp/from_scwrl_805523145.pdb > /var/tmp/scwrl_805523145.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_805523145.pdb # conformation set from SCWRL output # naming current conformation PROTINFO-AB_TS2-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_732858013.pdb -s /var/tmp/to_scwrl_732858013.seq -o /var/tmp/from_scwrl_732858013.pdb > /var/tmp/scwrl_732858013.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_732858013.pdb # conformation set from SCWRL output # naming current conformation PROTINFO-AB_TS3-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_638143424.pdb -s /var/tmp/to_scwrl_638143424.seq -o /var/tmp/from_scwrl_638143424.pdb > /var/tmp/scwrl_638143424.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_638143424.pdb # conformation set from SCWRL output # naming current conformation PROTINFO-AB_TS4-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_834771540.pdb -s /var/tmp/to_scwrl_834771540.seq -o /var/tmp/from_scwrl_834771540.pdb > /var/tmp/scwrl_834771540.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_834771540.pdb # conformation set from SCWRL output # naming current conformation PROTINFO-AB_TS5-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1 # Found a chain break before 338 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1978897676.pdb -s /var/tmp/to_scwrl_1978897676.seq -o /var/tmp/from_scwrl_1978897676.pdb > /var/tmp/scwrl_1978897676.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1978897676.pdb # conformation set from SCWRL output # naming current conformation PROTINFO_TS1-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_446766869.pdb -s /var/tmp/to_scwrl_446766869.seq -o /var/tmp/from_scwrl_446766869.pdb > /var/tmp/scwrl_446766869.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_446766869.pdb # conformation set from SCWRL output # naming current conformation PROTINFO_TS2-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1937331808.pdb -s /var/tmp/to_scwrl_1937331808.seq -o /var/tmp/from_scwrl_1937331808.pdb > /var/tmp/scwrl_1937331808.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1937331808.pdb # conformation set from SCWRL output # naming current conformation PROTINFO_TS3-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # Found a chain break before 369 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_822539566.pdb -s /var/tmp/to_scwrl_822539566.seq -o /var/tmp/from_scwrl_822539566.pdb > /var/tmp/scwrl_822539566.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_822539566.pdb # conformation set from SCWRL output # naming current conformation PROTINFO_TS4-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # Found a chain break before 365 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1306903105.pdb -s /var/tmp/to_scwrl_1306903105.seq -o /var/tmp/from_scwrl_1306903105.pdb > /var/tmp/scwrl_1306903105.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1306903105.pdb # conformation set from SCWRL output # naming current conformation PROTINFO_TS5-scwrl # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Pcons6_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_374146710.pdb -s /var/tmp/to_scwrl_374146710.seq -o /var/tmp/from_scwrl_374146710.pdb > /var/tmp/scwrl_374146710.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_374146710.pdb # conformation set from SCWRL output # naming current conformation Pcons6_TS1-scwrl # ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Pcons6_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1837265228.pdb -s /var/tmp/to_scwrl_1837265228.seq -o /var/tmp/from_scwrl_1837265228.pdb > /var/tmp/scwrl_1837265228.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1837265228.pdb # conformation set from SCWRL output # naming current conformation Pcons6_TS2-scwrl # ReadConformPDB reading from PDB file servers/Pcons6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Pcons6_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1463707449.pdb -s /var/tmp/to_scwrl_1463707449.seq -o /var/tmp/from_scwrl_1463707449.pdb > /var/tmp/scwrl_1463707449.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1463707449.pdb # conformation set from SCWRL output # naming current conformation Pcons6_TS3-scwrl # ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Pcons6_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_712399898.pdb -s /var/tmp/to_scwrl_712399898.seq -o /var/tmp/from_scwrl_712399898.pdb > /var/tmp/scwrl_712399898.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_712399898.pdb # conformation set from SCWRL output # naming current conformation Pcons6_TS4-scwrl # ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1 # Found a chain break before 363 # copying to AlignedFragments data structure # naming current conformation Pcons6_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_385688022.pdb -s /var/tmp/to_scwrl_385688022.seq -o /var/tmp/from_scwrl_385688022.pdb > /var/tmp/scwrl_385688022.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_385688022.pdb # conformation set from SCWRL output # naming current conformation Pcons6_TS5-scwrl # ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Phyre-1_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1938721555.pdb -s /var/tmp/to_scwrl_1938721555.seq -o /var/tmp/from_scwrl_1938721555.pdb > /var/tmp/scwrl_1938721555.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1938721555.pdb # conformation set from SCWRL output # naming current conformation Phyre-1_TS1-scwrl # ReadConformPDB reading from PDB file servers/Phyre-2_TS1.pdb.gz looking for model 1 # Found a chain break before 358 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1022601398.pdb -s /var/tmp/to_scwrl_1022601398.seq -o /var/tmp/from_scwrl_1022601398.pdb > /var/tmp/scwrl_1022601398.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1022601398.pdb # conformation set from SCWRL output # naming current conformation Phyre-2_TS1-scwrl # ReadConformPDB reading from PDB file servers/Phyre-2_TS2.pdb.gz looking for model 1 # Found a chain break before 342 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1455630636.pdb -s /var/tmp/to_scwrl_1455630636.seq -o /var/tmp/from_scwrl_1455630636.pdb > /var/tmp/scwrl_1455630636.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1455630636.pdb # conformation set from SCWRL output # naming current conformation Phyre-2_TS2-scwrl # ReadConformPDB reading from PDB file servers/Phyre-2_TS3.pdb.gz looking for model 1 # Found a chain break before 370 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1415518932.pdb -s /var/tmp/to_scwrl_1415518932.seq -o /var/tmp/from_scwrl_1415518932.pdb > /var/tmp/scwrl_1415518932.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1415518932.pdb # conformation set from SCWRL output # naming current conformation Phyre-2_TS3-scwrl # ReadConformPDB reading from PDB file servers/Phyre-2_TS4.pdb.gz looking for model 1 # Found a chain break before 334 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_91544647.pdb -s /var/tmp/to_scwrl_91544647.seq -o /var/tmp/from_scwrl_91544647.pdb > /var/tmp/scwrl_91544647.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_91544647.pdb # conformation set from SCWRL output # naming current conformation Phyre-2_TS4-scwrl # ReadConformPDB reading from PDB file servers/Phyre-2_TS5.pdb.gz looking for model 1 # Found a chain break before 365 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_735904732.pdb -s /var/tmp/to_scwrl_735904732.seq -o /var/tmp/from_scwrl_735904732.pdb > /var/tmp/scwrl_735904732.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_735904732.pdb # conformation set from SCWRL output # naming current conformation Phyre-2_TS5-scwrl # ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1742227984.pdb -s /var/tmp/to_scwrl_1742227984.seq -o /var/tmp/from_scwrl_1742227984.pdb > /var/tmp/scwrl_1742227984.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1742227984.pdb # conformation set from SCWRL output # naming current conformation Pmodeller6_TS1-scwrl # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_91610174.pdb -s /var/tmp/to_scwrl_91610174.seq -o /var/tmp/from_scwrl_91610174.pdb > /var/tmp/scwrl_91610174.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_91610174.pdb # conformation set from SCWRL output # naming current conformation Pmodeller6_TS2-scwrl # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_268776466.pdb -s /var/tmp/to_scwrl_268776466.seq -o /var/tmp/from_scwrl_268776466.pdb > /var/tmp/scwrl_268776466.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_268776466.pdb # conformation set from SCWRL output # naming current conformation Pmodeller6_TS3-scwrl # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1469834939.pdb -s /var/tmp/to_scwrl_1469834939.seq -o /var/tmp/from_scwrl_1469834939.pdb > /var/tmp/scwrl_1469834939.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1469834939.pdb # conformation set from SCWRL output # naming current conformation Pmodeller6_TS4-scwrl # ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_783011901.pdb -s /var/tmp/to_scwrl_783011901.seq -o /var/tmp/from_scwrl_783011901.pdb > /var/tmp/scwrl_783011901.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_783011901.pdb # conformation set from SCWRL output # naming current conformation Pmodeller6_TS5-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1 # Found a chain break before 340 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_11759502.pdb -s /var/tmp/to_scwrl_11759502.seq -o /var/tmp/from_scwrl_11759502.pdb > /var/tmp/scwrl_11759502.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_11759502.pdb # conformation set from SCWRL output # naming current conformation RAPTOR-ACE_TS1-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1 # Found a chain break before 336 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1564934550.pdb -s /var/tmp/to_scwrl_1564934550.seq -o /var/tmp/from_scwrl_1564934550.pdb > /var/tmp/scwrl_1564934550.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1564934550.pdb # conformation set from SCWRL output # naming current conformation RAPTOR-ACE_TS2-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1 # Found a chain break before 132 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2024193190.pdb -s /var/tmp/to_scwrl_2024193190.seq -o /var/tmp/from_scwrl_2024193190.pdb > /var/tmp/scwrl_2024193190.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2024193190.pdb # conformation set from SCWRL output # naming current conformation RAPTOR-ACE_TS3-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS4.pdb.gz looking for model 1 # Found a chain break before 348 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_310580801.pdb -s /var/tmp/to_scwrl_310580801.seq -o /var/tmp/from_scwrl_310580801.pdb > /var/tmp/scwrl_310580801.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_310580801.pdb # conformation set from SCWRL output # naming current conformation RAPTOR-ACE_TS4-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1 # Found a chain break before 294 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_61395754.pdb -s /var/tmp/to_scwrl_61395754.seq -o /var/tmp/from_scwrl_61395754.pdb > /var/tmp/scwrl_61395754.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_61395754.pdb # conformation set from SCWRL output # naming current conformation RAPTOR-ACE_TS5-scwrl # ReadConformPDB reading from PDB file servers/RAPTORESS_TS1.pdb.gz looking for model 1 # Found a chain break before 372 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1159229752.pdb -s /var/tmp/to_scwrl_1159229752.seq -o /var/tmp/from_scwrl_1159229752.pdb > /var/tmp/scwrl_1159229752.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1159229752.pdb # conformation set from SCWRL output # naming current conformation RAPTORESS_TS1-scwrl # ReadConformPDB reading from PDB file servers/RAPTORESS_TS2.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1116103945.pdb -s /var/tmp/to_scwrl_1116103945.seq -o /var/tmp/from_scwrl_1116103945.pdb > /var/tmp/scwrl_1116103945.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1116103945.pdb # conformation set from SCWRL output # naming current conformation RAPTORESS_TS2-scwrl # ReadConformPDB reading from PDB file servers/RAPTORESS_TS3.pdb.gz looking for model 1 # Found a chain break before 369 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_794253767.pdb -s /var/tmp/to_scwrl_794253767.seq -o /var/tmp/from_scwrl_794253767.pdb > /var/tmp/scwrl_794253767.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_794253767.pdb # conformation set from SCWRL output # naming current conformation RAPTORESS_TS3-scwrl # ReadConformPDB reading from PDB file servers/RAPTORESS_TS4.pdb.gz looking for model 1 # Found a chain break before 365 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1797373177.pdb -s /var/tmp/to_scwrl_1797373177.seq -o /var/tmp/from_scwrl_1797373177.pdb > /var/tmp/scwrl_1797373177.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1797373177.pdb # conformation set from SCWRL output # naming current conformation RAPTORESS_TS4-scwrl # ReadConformPDB reading from PDB file servers/RAPTORESS_TS5.pdb.gz looking for model 1 # Found a chain break before 354 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1950875485.pdb -s /var/tmp/to_scwrl_1950875485.seq -o /var/tmp/from_scwrl_1950875485.pdb > /var/tmp/scwrl_1950875485.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1950875485.pdb # conformation set from SCWRL output # naming current conformation RAPTORESS_TS5-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR_TS1.pdb.gz looking for model 1 # Found a chain break before 372 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_625667796.pdb -s /var/tmp/to_scwrl_625667796.seq -o /var/tmp/from_scwrl_625667796.pdb > /var/tmp/scwrl_625667796.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_625667796.pdb # conformation set from SCWRL output # naming current conformation RAPTOR_TS1-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1 # Found a chain break before 363 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_96656399.pdb -s /var/tmp/to_scwrl_96656399.seq -o /var/tmp/from_scwrl_96656399.pdb > /var/tmp/scwrl_96656399.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_96656399.pdb # conformation set from SCWRL output # naming current conformation RAPTOR_TS2-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR_TS3.pdb.gz looking for model 1 # Found a chain break before 360 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1740723647.pdb -s /var/tmp/to_scwrl_1740723647.seq -o /var/tmp/from_scwrl_1740723647.pdb > /var/tmp/scwrl_1740723647.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1740723647.pdb # conformation set from SCWRL output # naming current conformation RAPTOR_TS3-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR_TS4.pdb.gz looking for model 1 # Found a chain break before 364 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1448207361.pdb -s /var/tmp/to_scwrl_1448207361.seq -o /var/tmp/from_scwrl_1448207361.pdb > /var/tmp/scwrl_1448207361.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1448207361.pdb # conformation set from SCWRL output # naming current conformation RAPTOR_TS4-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR_TS5.pdb.gz looking for model 1 # Found a chain break before 339 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1403559504.pdb -s /var/tmp/to_scwrl_1403559504.seq -o /var/tmp/from_scwrl_1403559504.pdb > /var/tmp/scwrl_1403559504.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1403559504.pdb # conformation set from SCWRL output # naming current conformation RAPTOR_TS5-scwrl # ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1 # Found a chain break before 316 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2114870357.pdb -s /var/tmp/to_scwrl_2114870357.seq -o /var/tmp/from_scwrl_2114870357.pdb > /var/tmp/scwrl_2114870357.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2114870357.pdb # conformation set from SCWRL output # naming current conformation ROBETTA_TS1-scwrl # ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1 # Found a chain break before 339 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1137988943.pdb -s /var/tmp/to_scwrl_1137988943.seq -o /var/tmp/from_scwrl_1137988943.pdb > /var/tmp/scwrl_1137988943.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1137988943.pdb # conformation set from SCWRL output # naming current conformation ROBETTA_TS2-scwrl # ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1 # Found a chain break before 346 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_719783307.pdb -s /var/tmp/to_scwrl_719783307.seq -o /var/tmp/from_scwrl_719783307.pdb > /var/tmp/scwrl_719783307.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_719783307.pdb # conformation set from SCWRL output # naming current conformation ROBETTA_TS3-scwrl # ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1 # Found a chain break before 340 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_679786608.pdb -s /var/tmp/to_scwrl_679786608.seq -o /var/tmp/from_scwrl_679786608.pdb > /var/tmp/scwrl_679786608.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_679786608.pdb # conformation set from SCWRL output # naming current conformation ROBETTA_TS4-scwrl # ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1 # Found a chain break before 305 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1523676965.pdb -s /var/tmp/to_scwrl_1523676965.seq -o /var/tmp/from_scwrl_1523676965.pdb > /var/tmp/scwrl_1523676965.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1523676965.pdb # conformation set from SCWRL output # naming current conformation ROBETTA_TS5-scwrl # ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_511021215.pdb -s /var/tmp/to_scwrl_511021215.seq -o /var/tmp/from_scwrl_511021215.pdb > /var/tmp/scwrl_511021215.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_511021215.pdb # conformation set from SCWRL output # naming current conformation ROKKY_TS1-scwrl # ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1702388005.pdb -s /var/tmp/to_scwrl_1702388005.seq -o /var/tmp/from_scwrl_1702388005.pdb > /var/tmp/scwrl_1702388005.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1702388005.pdb # conformation set from SCWRL output # naming current conformation ROKKY_TS2-scwrl # ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_831823956.pdb -s /var/tmp/to_scwrl_831823956.seq -o /var/tmp/from_scwrl_831823956.pdb > /var/tmp/scwrl_831823956.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_831823956.pdb # conformation set from SCWRL output # naming current conformation ROKKY_TS3-scwrl # ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1926540147.pdb -s /var/tmp/to_scwrl_1926540147.seq -o /var/tmp/from_scwrl_1926540147.pdb > /var/tmp/scwrl_1926540147.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1926540147.pdb # conformation set from SCWRL output # naming current conformation ROKKY_TS4-scwrl # ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1793932652.pdb -s /var/tmp/to_scwrl_1793932652.seq -o /var/tmp/from_scwrl_1793932652.pdb > /var/tmp/scwrl_1793932652.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1793932652.pdb # conformation set from SCWRL output # naming current conformation ROKKY_TS5-scwrl # ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1567728687.pdb -s /var/tmp/to_scwrl_1567728687.seq -o /var/tmp/from_scwrl_1567728687.pdb > /var/tmp/scwrl_1567728687.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1567728687.pdb # conformation set from SCWRL output # naming current conformation SAM-T02_AL1-scwrl # ReadConformPDB reading from PDB file servers/SAM-T02_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1521284485.pdb -s /var/tmp/to_scwrl_1521284485.seq -o /var/tmp/from_scwrl_1521284485.pdb > /var/tmp/scwrl_1521284485.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1521284485.pdb # conformation set from SCWRL output # naming current conformation SAM-T02_AL2-scwrl # ReadConformPDB reading from PDB file servers/SAM-T02_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1885542826.pdb -s /var/tmp/to_scwrl_1885542826.seq -o /var/tmp/from_scwrl_1885542826.pdb > /var/tmp/scwrl_1885542826.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1885542826.pdb # conformation set from SCWRL output # naming current conformation SAM-T02_AL3-scwrl # ReadConformPDB reading from PDB file servers/SAM-T02_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1836505153.pdb -s /var/tmp/to_scwrl_1836505153.seq -o /var/tmp/from_scwrl_1836505153.pdb > /var/tmp/scwrl_1836505153.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1836505153.pdb # conformation set from SCWRL output # naming current conformation SAM-T02_AL4-scwrl # ReadConformPDB reading from PDB file servers/SAM-T02_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_843635778.pdb -s /var/tmp/to_scwrl_843635778.seq -o /var/tmp/from_scwrl_843635778.pdb > /var/tmp/scwrl_843635778.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_843635778.pdb # conformation set from SCWRL output # naming current conformation SAM-T02_AL5-scwrl # ReadConformPDB reading from PDB file servers/SAM-T99_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_521071081.pdb -s /var/tmp/to_scwrl_521071081.seq -o /var/tmp/from_scwrl_521071081.pdb > /var/tmp/scwrl_521071081.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_521071081.pdb # conformation set from SCWRL output # naming current conformation SAM-T99_AL1-scwrl # ReadConformPDB reading from PDB file servers/SAM-T99_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1848264655.pdb -s /var/tmp/to_scwrl_1848264655.seq -o /var/tmp/from_scwrl_1848264655.pdb > /var/tmp/scwrl_1848264655.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1848264655.pdb # conformation set from SCWRL output # naming current conformation SAM-T99_AL2-scwrl # ReadConformPDB reading from PDB file servers/SAM-T99_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_261086682.pdb -s /var/tmp/to_scwrl_261086682.seq -o /var/tmp/from_scwrl_261086682.pdb > /var/tmp/scwrl_261086682.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_261086682.pdb # conformation set from SCWRL output # naming current conformation SAM-T99_AL3-scwrl # ReadConformPDB reading from PDB file servers/SAM-T99_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_397780624.pdb -s /var/tmp/to_scwrl_397780624.seq -o /var/tmp/from_scwrl_397780624.pdb > /var/tmp/scwrl_397780624.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_397780624.pdb # conformation set from SCWRL output # naming current conformation SAM-T99_AL4-scwrl # ReadConformPDB reading from PDB file servers/SAM-T99_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_11361809.pdb -s /var/tmp/to_scwrl_11361809.seq -o /var/tmp/from_scwrl_11361809.pdb > /var/tmp/scwrl_11361809.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_11361809.pdb # conformation set from SCWRL output # naming current conformation SAM-T99_AL5-scwrl # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1 # Found a chain break before 372 # copying to AlignedFragments data structure # naming current conformation SAM_T06_server_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_322482436.pdb -s /var/tmp/to_scwrl_322482436.seq -o /var/tmp/from_scwrl_322482436.pdb > /var/tmp/scwrl_322482436.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_322482436.pdb # conformation set from SCWRL output # naming current conformation SAM_T06_server_TS1-scwrl # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1557010377.pdb -s /var/tmp/to_scwrl_1557010377.seq -o /var/tmp/from_scwrl_1557010377.pdb > /var/tmp/scwrl_1557010377.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1557010377.pdb # conformation set from SCWRL output # naming current conformation SAM_T06_server_TS2-scwrl # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1127465755.pdb -s /var/tmp/to_scwrl_1127465755.seq -o /var/tmp/from_scwrl_1127465755.pdb > /var/tmp/scwrl_1127465755.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1127465755.pdb # conformation set from SCWRL output # naming current conformation SAM_T06_server_TS3-scwrl # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1116736202.pdb -s /var/tmp/to_scwrl_1116736202.seq -o /var/tmp/from_scwrl_1116736202.pdb > /var/tmp/scwrl_1116736202.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1116736202.pdb # conformation set from SCWRL output # naming current conformation SAM_T06_server_TS4-scwrl # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1206899907.pdb -s /var/tmp/to_scwrl_1206899907.seq -o /var/tmp/from_scwrl_1206899907.pdb > /var/tmp/scwrl_1206899907.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1206899907.pdb # conformation set from SCWRL output # naming current conformation SAM_T06_server_TS5-scwrl # ReadConformPDB reading from PDB file servers/SP3_TS1.pdb.gz looking for model 1 # Found a chain break before 173 # copying to AlignedFragments data structure # naming current conformation SP3_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_930857594.pdb -s /var/tmp/to_scwrl_930857594.seq -o /var/tmp/from_scwrl_930857594.pdb > /var/tmp/scwrl_930857594.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_930857594.pdb # conformation set from SCWRL output # naming current conformation SP3_TS1-scwrl # ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1 # Found a chain break before 301 # copying to AlignedFragments data structure # naming current conformation SP3_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1742403999.pdb -s /var/tmp/to_scwrl_1742403999.seq -o /var/tmp/from_scwrl_1742403999.pdb > /var/tmp/scwrl_1742403999.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1742403999.pdb # conformation set from SCWRL output # naming current conformation SP3_TS2-scwrl # ReadConformPDB reading from PDB file servers/SP3_TS3.pdb.gz looking for model 1 # Found a chain break before 288 # copying to AlignedFragments data structure # naming current conformation SP3_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1303556306.pdb -s /var/tmp/to_scwrl_1303556306.seq -o /var/tmp/from_scwrl_1303556306.pdb > /var/tmp/scwrl_1303556306.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1303556306.pdb # conformation set from SCWRL output # naming current conformation SP3_TS3-scwrl # ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1 # Found a chain break before 348 # copying to AlignedFragments data structure # naming current conformation SP3_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_524097594.pdb -s /var/tmp/to_scwrl_524097594.seq -o /var/tmp/from_scwrl_524097594.pdb > /var/tmp/scwrl_524097594.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_524097594.pdb # conformation set from SCWRL output # naming current conformation SP3_TS4-scwrl # ReadConformPDB reading from PDB file servers/SP3_TS5.pdb.gz looking for model 1 # Found a chain break before 212 # copying to AlignedFragments data structure # naming current conformation SP3_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1043127714.pdb -s /var/tmp/to_scwrl_1043127714.seq -o /var/tmp/from_scwrl_1043127714.pdb > /var/tmp/scwrl_1043127714.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1043127714.pdb # conformation set from SCWRL output # naming current conformation SP3_TS5-scwrl # ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1 # Found a chain break before 202 # copying to AlignedFragments data structure # naming current conformation SP4_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_559632164.pdb -s /var/tmp/to_scwrl_559632164.seq -o /var/tmp/from_scwrl_559632164.pdb > /var/tmp/scwrl_559632164.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_559632164.pdb # conformation set from SCWRL output # naming current conformation SP4_TS1-scwrl # ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1 # Found a chain break before 170 # copying to AlignedFragments data structure # naming current conformation SP4_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_491484304.pdb -s /var/tmp/to_scwrl_491484304.seq -o /var/tmp/from_scwrl_491484304.pdb > /var/tmp/scwrl_491484304.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_491484304.pdb # conformation set from SCWRL output # naming current conformation SP4_TS2-scwrl # ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1 # Found a chain break before 259 # copying to AlignedFragments data structure # naming current conformation SP4_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_33633010.pdb -s /var/tmp/to_scwrl_33633010.seq -o /var/tmp/from_scwrl_33633010.pdb > /var/tmp/scwrl_33633010.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_33633010.pdb # conformation set from SCWRL output # naming current conformation SP4_TS3-scwrl # ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1 # Found a chain break before 301 # copying to AlignedFragments data structure # naming current conformation SP4_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1279415470.pdb -s /var/tmp/to_scwrl_1279415470.seq -o /var/tmp/from_scwrl_1279415470.pdb > /var/tmp/scwrl_1279415470.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1279415470.pdb # conformation set from SCWRL output # naming current conformation SP4_TS4-scwrl # ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1 # Found a chain break before 244 # copying to AlignedFragments data structure # naming current conformation SP4_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1171270911.pdb -s /var/tmp/to_scwrl_1171270911.seq -o /var/tmp/from_scwrl_1171270911.pdb > /var/tmp/scwrl_1171270911.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1171270911.pdb # conformation set from SCWRL output # naming current conformation SP4_TS5-scwrl # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # Found a chain break before 162 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1557309976.pdb -s /var/tmp/to_scwrl_1557309976.seq -o /var/tmp/from_scwrl_1557309976.pdb > /var/tmp/scwrl_1557309976.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1557309976.pdb # conformation set from SCWRL output # naming current conformation SPARKS2_TS1-scwrl # ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1 # Found a chain break before 266 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1790436685.pdb -s /var/tmp/to_scwrl_1790436685.seq -o /var/tmp/from_scwrl_1790436685.pdb > /var/tmp/scwrl_1790436685.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1790436685.pdb # conformation set from SCWRL output # naming current conformation SPARKS2_TS2-scwrl # ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1 # Found a chain break before 372 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_726175270.pdb -s /var/tmp/to_scwrl_726175270.seq -o /var/tmp/from_scwrl_726175270.pdb > /var/tmp/scwrl_726175270.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_726175270.pdb # conformation set from SCWRL output # naming current conformation SPARKS2_TS3-scwrl # ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1 # Found a chain break before 200 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_241650285.pdb -s /var/tmp/to_scwrl_241650285.seq -o /var/tmp/from_scwrl_241650285.pdb > /var/tmp/scwrl_241650285.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_241650285.pdb # conformation set from SCWRL output # naming current conformation SPARKS2_TS4-scwrl # ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1 # Found a chain break before 292 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1569493186.pdb -s /var/tmp/to_scwrl_1569493186.seq -o /var/tmp/from_scwrl_1569493186.pdb > /var/tmp/scwrl_1569493186.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1569493186.pdb # conformation set from SCWRL output # naming current conformation SPARKS2_TS5-scwrl # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_372624275.pdb -s /var/tmp/to_scwrl_372624275.seq -o /var/tmp/from_scwrl_372624275.pdb > /var/tmp/scwrl_372624275.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_372624275.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_bnmx_TS1-scwrl # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1809378972.pdb -s /var/tmp/to_scwrl_1809378972.seq -o /var/tmp/from_scwrl_1809378972.pdb > /var/tmp/scwrl_1809378972.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1809378972.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_bnmx_TS2-scwrl # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_943294025.pdb -s /var/tmp/to_scwrl_943294025.seq -o /var/tmp/from_scwrl_943294025.pdb > /var/tmp/scwrl_943294025.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_943294025.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_bnmx_TS3-scwrl # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_110683455.pdb -s /var/tmp/to_scwrl_110683455.seq -o /var/tmp/from_scwrl_110683455.pdb > /var/tmp/scwrl_110683455.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_110683455.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_bnmx_TS4-scwrl # ReadConformPDB reading from PDB file servers/UNI-EID_expm_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation UNI-EID_expm_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1498400478.pdb -s /var/tmp/to_scwrl_1498400478.seq -o /var/tmp/from_scwrl_1498400478.pdb > /var/tmp/scwrl_1498400478.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1498400478.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_expm_TS1-scwrl # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1786929802.pdb -s /var/tmp/to_scwrl_1786929802.seq -o /var/tmp/from_scwrl_1786929802.pdb > /var/tmp/scwrl_1786929802.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1786929802.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_sfst_AL1-scwrl # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_631754536.pdb -s /var/tmp/to_scwrl_631754536.seq -o /var/tmp/from_scwrl_631754536.pdb > /var/tmp/scwrl_631754536.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_631754536.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_sfst_AL2-scwrl # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1199181487.pdb -s /var/tmp/to_scwrl_1199181487.seq -o /var/tmp/from_scwrl_1199181487.pdb > /var/tmp/scwrl_1199181487.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1199181487.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_sfst_AL3-scwrl # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2048016484.pdb -s /var/tmp/to_scwrl_2048016484.seq -o /var/tmp/from_scwrl_2048016484.pdb > /var/tmp/scwrl_2048016484.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2048016484.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_sfst_AL4-scwrl # ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1029535160.pdb -s /var/tmp/to_scwrl_1029535160.seq -o /var/tmp/from_scwrl_1029535160.pdb > /var/tmp/scwrl_1029535160.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1029535160.pdb # conformation set from SCWRL output # naming current conformation Zhang-Server_TS1-scwrl # ReadConformPDB reading from PDB file servers/Zhang-Server_TS2.pdb.gz looking for model 1 # Found a chain break before 361 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1210543296.pdb -s /var/tmp/to_scwrl_1210543296.seq -o /var/tmp/from_scwrl_1210543296.pdb > /var/tmp/scwrl_1210543296.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1210543296.pdb # conformation set from SCWRL output # naming current conformation Zhang-Server_TS2-scwrl # ReadConformPDB reading from PDB file servers/Zhang-Server_TS3.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_223015273.pdb -s /var/tmp/to_scwrl_223015273.seq -o /var/tmp/from_scwrl_223015273.pdb > /var/tmp/scwrl_223015273.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_223015273.pdb # conformation set from SCWRL output # naming current conformation Zhang-Server_TS3-scwrl # ReadConformPDB reading from PDB file servers/Zhang-Server_TS4.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_439061890.pdb -s /var/tmp/to_scwrl_439061890.seq -o /var/tmp/from_scwrl_439061890.pdb > /var/tmp/scwrl_439061890.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_439061890.pdb # conformation set from SCWRL output # naming current conformation Zhang-Server_TS4-scwrl # ReadConformPDB reading from PDB file servers/Zhang-Server_TS5.pdb.gz looking for model 1 # Found a chain break before 363 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_190525405.pdb -s /var/tmp/to_scwrl_190525405.seq -o /var/tmp/from_scwrl_190525405.pdb > /var/tmp/scwrl_190525405.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_190525405.pdb # conformation set from SCWRL output # naming current conformation Zhang-Server_TS5-scwrl # ReadConformPDB reading from PDB file servers/beautshot_TS1.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # naming current conformation beautshot_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1339751476.pdb -s /var/tmp/to_scwrl_1339751476.seq -o /var/tmp/from_scwrl_1339751476.pdb > /var/tmp/scwrl_1339751476.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1339751476.pdb # conformation set from SCWRL output # naming current conformation beautshot_TS1-scwrl # ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation beautshotbase_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1645961797.pdb -s /var/tmp/to_scwrl_1645961797.seq -o /var/tmp/from_scwrl_1645961797.pdb > /var/tmp/scwrl_1645961797.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1645961797.pdb # conformation set from SCWRL output # naming current conformation beautshotbase_TS1-scwrl # ReadConformPDB reading from PDB file servers/forecast-s_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation forecast-s_AL1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1121382999.pdb -s /var/tmp/to_scwrl_1121382999.seq -o /var/tmp/from_scwrl_1121382999.pdb > /var/tmp/scwrl_1121382999.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1121382999.pdb # conformation set from SCWRL output # naming current conformation forecast-s_AL1-scwrl # ReadConformPDB reading from PDB file servers/forecast-s_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation forecast-s_AL2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_934671829.pdb -s /var/tmp/to_scwrl_934671829.seq -o /var/tmp/from_scwrl_934671829.pdb > /var/tmp/scwrl_934671829.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_934671829.pdb # conformation set from SCWRL output # naming current conformation forecast-s_AL2-scwrl # ReadConformPDB reading from PDB file servers/forecast-s_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation forecast-s_AL3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_802034457.pdb -s /var/tmp/to_scwrl_802034457.seq -o /var/tmp/from_scwrl_802034457.pdb > /var/tmp/scwrl_802034457.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_802034457.pdb # conformation set from SCWRL output # naming current conformation forecast-s_AL3-scwrl # ReadConformPDB reading from PDB file servers/forecast-s_AL4.pdb.gz looking for model 1 Skipped atom 334, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 336, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 338, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 340, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 342, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 344, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 346, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 348, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 350, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 352, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 354, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 356, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation forecast-s_AL4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1645480593.pdb -s /var/tmp/to_scwrl_1645480593.seq -o /var/tmp/from_scwrl_1645480593.pdb > /var/tmp/scwrl_1645480593.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1645480593.pdb # conformation set from SCWRL output # naming current conformation forecast-s_AL4-scwrl # ReadConformPDB reading from PDB file servers/forecast-s_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation forecast-s_AL5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1977799542.pdb -s /var/tmp/to_scwrl_1977799542.seq -o /var/tmp/from_scwrl_1977799542.pdb > /var/tmp/scwrl_1977799542.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1977799542.pdb # conformation set from SCWRL output # naming current conformation forecast-s_AL5-scwrl # ReadConformPDB reading from PDB file servers/gtg_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation gtg_AL1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1361666620.pdb -s /var/tmp/to_scwrl_1361666620.seq -o /var/tmp/from_scwrl_1361666620.pdb > /var/tmp/scwrl_1361666620.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1361666620.pdb # conformation set from SCWRL output # naming current conformation gtg_AL1-scwrl # ReadConformPDB reading from PDB file servers/gtg_AL2.pdb.gz looking for model 1 Skipped atom 278, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 280, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 282, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 284, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 286, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 288, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 290, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 292, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 606, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 608, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 610, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 612, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 622, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 624, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 626, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 628, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 734, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 736, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 738, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 740, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 934, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 936, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 938, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 940, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 1042, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 1044, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 1046, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 1048, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation gtg_AL2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2136964898.pdb -s /var/tmp/to_scwrl_2136964898.seq -o /var/tmp/from_scwrl_2136964898.pdb > /var/tmp/scwrl_2136964898.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2136964898.pdb # conformation set from SCWRL output # naming current conformation gtg_AL2-scwrl # ReadConformPDB reading from PDB file servers/gtg_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation gtg_AL3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2011432553.pdb -s /var/tmp/to_scwrl_2011432553.seq -o /var/tmp/from_scwrl_2011432553.pdb > /var/tmp/scwrl_2011432553.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2011432553.pdb # conformation set from SCWRL output # naming current conformation gtg_AL3-scwrl # ReadConformPDB reading from PDB file servers/gtg_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation gtg_AL4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_493598444.pdb -s /var/tmp/to_scwrl_493598444.seq -o /var/tmp/from_scwrl_493598444.pdb > /var/tmp/scwrl_493598444.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_493598444.pdb # conformation set from SCWRL output # naming current conformation gtg_AL4-scwrl # ReadConformPDB reading from PDB file servers/gtg_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation gtg_AL5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1160752162.pdb -s /var/tmp/to_scwrl_1160752162.seq -o /var/tmp/from_scwrl_1160752162.pdb > /var/tmp/scwrl_1160752162.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1160752162.pdb # conformation set from SCWRL output # naming current conformation gtg_AL5-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # Found a chain break before 363 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1421258882.pdb -s /var/tmp/to_scwrl_1421258882.seq -o /var/tmp/from_scwrl_1421258882.pdb > /var/tmp/scwrl_1421258882.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1421258882.pdb # conformation set from SCWRL output # naming current conformation karypis.srv.2_TS1-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS2.pdb.gz looking for model 1 # Found a chain break before 367 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_136551483.pdb -s /var/tmp/to_scwrl_136551483.seq -o /var/tmp/from_scwrl_136551483.pdb > /var/tmp/scwrl_136551483.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_136551483.pdb # conformation set from SCWRL output # naming current conformation karypis.srv.2_TS2-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS3.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1886927433.pdb -s /var/tmp/to_scwrl_1886927433.seq -o /var/tmp/from_scwrl_1886927433.pdb > /var/tmp/scwrl_1886927433.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1886927433.pdb # conformation set from SCWRL output # naming current conformation karypis.srv.2_TS3-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS4.pdb.gz looking for model 1 # Found a chain break before 358 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1662909167.pdb -s /var/tmp/to_scwrl_1662909167.seq -o /var/tmp/from_scwrl_1662909167.pdb > /var/tmp/scwrl_1662909167.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1662909167.pdb # conformation set from SCWRL output # naming current conformation karypis.srv.2_TS4-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS5.pdb.gz looking for model 1 # Found a chain break before 317 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1706044669.pdb -s /var/tmp/to_scwrl_1706044669.seq -o /var/tmp/from_scwrl_1706044669.pdb > /var/tmp/scwrl_1706044669.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1706044669.pdb # conformation set from SCWRL output # naming current conformation karypis.srv.2_TS5-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS1.pdb.gz looking for model 1 WARNING: atoms too close: (T0316)G172.O and (T0316)H173.N only 0.000 apart, marking (T0316)H173.N as missing WARNING: atoms too close: (T0316)H280.O and (T0316)D281.N only 0.000 apart, marking (T0316)D281.N as missing WARNING: atoms too close: (T0316)Y364.O and (T0316)R365.N only 0.000 apart, marking (T0316)R365.N as missing # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_112068061.pdb -s /var/tmp/to_scwrl_112068061.seq -o /var/tmp/from_scwrl_112068061.pdb > /var/tmp/scwrl_112068061.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_112068061.pdb # conformation set from SCWRL output # naming current conformation karypis.srv.4_TS1-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS2.pdb.gz looking for model 1 # Found a chain break before 370 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1324804492.pdb -s /var/tmp/to_scwrl_1324804492.seq -o /var/tmp/from_scwrl_1324804492.pdb > /var/tmp/scwrl_1324804492.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1324804492.pdb # conformation set from SCWRL output # naming current conformation karypis.srv.4_TS2-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS3.pdb.gz looking for model 1 WARNING: atoms too close: (T0316)I202.O and (T0316)G203.N only 0.000 apart, marking (T0316)G203.N as missing WARNING: atoms too close: (T0316)G264.O and (T0316)K265.N only 0.000 apart, marking (T0316)K265.N as missing # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_501855047.pdb -s /var/tmp/to_scwrl_501855047.seq -o /var/tmp/from_scwrl_501855047.pdb > /var/tmp/scwrl_501855047.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_501855047.pdb # conformation set from SCWRL output # naming current conformation karypis.srv.4_TS3-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS4.pdb.gz looking for model 1 WARNING: atoms too close: (T0316)L143.O and (T0316)R144.N only 0.000 apart, marking (T0316)R144.N as missing WARNING: atoms too close: (T0316)R312.O and (T0316)Y313.N only 0.000 apart, marking (T0316)Y313.N as missing # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_222751516.pdb -s /var/tmp/to_scwrl_222751516.seq -o /var/tmp/from_scwrl_222751516.pdb > /var/tmp/scwrl_222751516.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_222751516.pdb # conformation set from SCWRL output # naming current conformation karypis.srv.4_TS4-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS5.pdb.gz looking for model 1 WARNING: atoms too close: (T0316)C50.O and (T0316)T51.N only 0.000 apart, marking (T0316)T51.N as missing WARNING: atoms too close: (T0316)A186.O and (T0316)G187.N only 0.000 apart, marking (T0316)G187.N as missing WARNING: atoms too close: (T0316)T304.O and (T0316)L305.N only 0.000 apart, marking (T0316)L305.N as missing WARNING: atoms too close: (T0316)Y349.O and (T0316)D350.N only 0.000 apart, marking (T0316)D350.N as missing # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_675721324.pdb -s /var/tmp/to_scwrl_675721324.seq -o /var/tmp/from_scwrl_675721324.pdb > /var/tmp/scwrl_675721324.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_675721324.pdb # conformation set from SCWRL output # naming current conformation karypis.srv.4_TS5-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_141301202.pdb -s /var/tmp/to_scwrl_141301202.seq -o /var/tmp/from_scwrl_141301202.pdb > /var/tmp/scwrl_141301202.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_141301202.pdb # conformation set from SCWRL output # naming current conformation karypis.srv_TS1-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_854506052.pdb -s /var/tmp/to_scwrl_854506052.seq -o /var/tmp/from_scwrl_854506052.pdb > /var/tmp/scwrl_854506052.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_854506052.pdb # conformation set from SCWRL output # naming current conformation karypis.srv_TS2-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1874902811.pdb -s /var/tmp/to_scwrl_1874902811.seq -o /var/tmp/from_scwrl_1874902811.pdb > /var/tmp/scwrl_1874902811.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1874902811.pdb # conformation set from SCWRL output # naming current conformation karypis.srv_TS3-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_41834040.pdb -s /var/tmp/to_scwrl_41834040.seq -o /var/tmp/from_scwrl_41834040.pdb > /var/tmp/scwrl_41834040.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_41834040.pdb # conformation set from SCWRL output # naming current conformation karypis.srv_TS4-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1884041212.pdb -s /var/tmp/to_scwrl_1884041212.seq -o /var/tmp/from_scwrl_1884041212.pdb > /var/tmp/scwrl_1884041212.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1884041212.pdb # conformation set from SCWRL output # naming current conformation karypis.srv_TS5-scwrl # ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation keasar-server_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_937962462.pdb -s /var/tmp/to_scwrl_937962462.seq -o /var/tmp/from_scwrl_937962462.pdb > /var/tmp/scwrl_937962462.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_937962462.pdb # conformation set from SCWRL output # naming current conformation keasar-server_TS1-scwrl # ReadConformPDB reading from PDB file servers/keasar-server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation keasar-server_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_264849313.pdb -s /var/tmp/to_scwrl_264849313.seq -o /var/tmp/from_scwrl_264849313.pdb > /var/tmp/scwrl_264849313.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_264849313.pdb # conformation set from SCWRL output # naming current conformation keasar-server_TS2-scwrl # ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1 # Found a chain break before 310 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_175619455.pdb -s /var/tmp/to_scwrl_175619455.seq -o /var/tmp/from_scwrl_175619455.pdb > /var/tmp/scwrl_175619455.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_175619455.pdb # conformation set from SCWRL output # naming current conformation keasar-server_TS3-scwrl # ReadConformPDB reading from PDB file servers/keasar-server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation keasar-server_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1128487866.pdb -s /var/tmp/to_scwrl_1128487866.seq -o /var/tmp/from_scwrl_1128487866.pdb > /var/tmp/scwrl_1128487866.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1128487866.pdb # conformation set from SCWRL output # naming current conformation keasar-server_TS4-scwrl # ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation keasar-server_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1604600789.pdb -s /var/tmp/to_scwrl_1604600789.seq -o /var/tmp/from_scwrl_1604600789.pdb > /var/tmp/scwrl_1604600789.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1604600789.pdb # conformation set from SCWRL output # naming current conformation keasar-server_TS5-scwrl # ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation mGen-3D_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1821581253.pdb -s /var/tmp/to_scwrl_1821581253.seq -o /var/tmp/from_scwrl_1821581253.pdb > /var/tmp/scwrl_1821581253.log sh: line 1: 30977 Killed scwrl3 -i /var/tmp/to_scwrl_1821581253.pdb -s /var/tmp/to_scwrl_1821581253.seq -o /var/tmp/from_scwrl_1821581253.pdb >/var/tmp/scwrl_1821581253.log Error: Couldn't open file /var/tmp/from_scwrl_1821581253.pdb or /var/tmp/from_scwrl_1821581253.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1821581253_b.pdb or decoys//var/tmp/from_scwrl_1821581253_b.pdb.gz for input Trying /var/tmp/from_scwrl_1821581253_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_1821581253_b.pdb or /var/tmp/from_scwrl_1821581253_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1821581253_a.pdb or decoys//var/tmp/from_scwrl_1821581253_a.pdb.gz for input Trying /var/tmp/from_scwrl_1821581253_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_1821581253_a.pdb or /var/tmp/from_scwrl_1821581253_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_1821581253.pdb or /var/tmp/from_scwrl_1821581253_b.pdb or /var/tmp/from_scwrl_1821581253_a.pdb Error: no new SCWRL conformation added # naming current conformation mGen-3D_TS1-scwrl # ReadConformPDB reading from PDB file servers/nFOLD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation nFOLD_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_102387219.pdb -s /var/tmp/to_scwrl_102387219.seq -o /var/tmp/from_scwrl_102387219.pdb > /var/tmp/scwrl_102387219.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_102387219.pdb # conformation set from SCWRL output # naming current conformation nFOLD_TS1-scwrl # ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation nFOLD_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_391788971.pdb -s /var/tmp/to_scwrl_391788971.seq -o /var/tmp/from_scwrl_391788971.pdb > /var/tmp/scwrl_391788971.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_391788971.pdb # conformation set from SCWRL output # naming current conformation nFOLD_TS2-scwrl # ReadConformPDB reading from PDB file servers/nFOLD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation nFOLD_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_476132063.pdb -s /var/tmp/to_scwrl_476132063.seq -o /var/tmp/from_scwrl_476132063.pdb > /var/tmp/scwrl_476132063.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_476132063.pdb # conformation set from SCWRL output # naming current conformation nFOLD_TS3-scwrl # ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation nFOLD_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1747867813.pdb -s /var/tmp/to_scwrl_1747867813.seq -o /var/tmp/from_scwrl_1747867813.pdb > /var/tmp/scwrl_1747867813.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1747867813.pdb # conformation set from SCWRL output # naming current conformation nFOLD_TS4-scwrl # ReadConformPDB reading from PDB file servers/nFOLD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation nFOLD_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_222104867.pdb -s /var/tmp/to_scwrl_222104867.seq -o /var/tmp/from_scwrl_222104867.pdb > /var/tmp/scwrl_222104867.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_222104867.pdb # conformation set from SCWRL output # naming current conformation nFOLD_TS5-scwrl # ReadConformPDB reading from PDB file servers/panther2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation panther2_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1837798684.pdb -s /var/tmp/to_scwrl_1837798684.seq -o /var/tmp/from_scwrl_1837798684.pdb > /var/tmp/scwrl_1837798684.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1837798684.pdb # conformation set from SCWRL output # naming current conformation panther2_TS1-scwrl # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation shub_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1737349064.pdb -s /var/tmp/to_scwrl_1737349064.seq -o /var/tmp/from_scwrl_1737349064.pdb > /var/tmp/scwrl_1737349064.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1737349064.pdb # conformation set from SCWRL output # naming current conformation shub_TS1-scwrl # command:CPU_time= 80.0538 sec, elapsed time= 2456.76 sec) # command:# Prefix for output files set to decoys/ # command:# Will now start reporting costs to decoys/evaluate_1.rdb # command:# CostConform Warning: Couldn't open file decoys//projects/compbio/experiments/undertaker/spots/near-backbone-center.spot or decoys//projects/compbio/experiments/undertaker/spots/near-backbone-center.spot.gz for input Trying /projects/compbio/experiments/undertaker/spots/near-backbone-center.spot # Reading spots from /projects/compbio/experiments/undertaker/spots/near-backbone-center.spot shub_TS1-scwrl costs 0 real_cost = 215.663 shub_TS1 costs 0 real_cost = 217.463 panther2_TS1-scwrl costs 0 real_cost = 543.055 panther2_TS1 costs 0 real_cost = 536.459 nFOLD_TS5-scwrl costs 0 real_cost = 160.325 nFOLD_TS5 costs 0 real_cost = 332.626 nFOLD_TS4-scwrl costs 0 real_cost = 144.062 nFOLD_TS4 costs 0 real_cost = 317.035 nFOLD_TS3-scwrl costs 0 real_cost = 166.203 nFOLD_TS3 costs 0 real_cost = 351.348 nFOLD_TS2-scwrl costs 0 real_cost = 116.022 nFOLD_TS2 costs 0 real_cost = 304.308 nFOLD_TS1-scwrl costs 0 real_cost = 118.172 nFOLD_TS1 costs 0 real_cost = 307.205 mGen-3D_TS1-scwrl costs 0 real_cost = 336.68 keasar-server_TS5-scwrl costs 0 real_cost = 272.467 keasar-server_TS5 costs 0 real_cost = 269.111 keasar-server_TS4-scwrl costs 0 real_cost = 272.467 keasar-server_TS4 costs 0 real_cost = 269.111 keasar-server_TS3-scwrl costs 0 real_cost = 126.692 keasar-server_TS3 costs 0 real_cost = 132.348 keasar-server_TS2-scwrl costs 0 real_cost = 246.031 keasar-server_TS2 costs 0 real_cost = 248.953 keasar-server_TS1-scwrl costs 0 real_cost = 226.035 keasar-server_TS1 costs 0 real_cost = 237.706 karypis.srv_TS5-scwrl costs 0 real_cost = 373.061 karypis.srv_TS5 costs 0 real_cost = 366.17 karypis.srv_TS4-scwrl costs 0 real_cost = 167.533 karypis.srv_TS4 costs 0 real_cost = 163.333 karypis.srv_TS3-scwrl costs 0 real_cost = 169.751 karypis.srv_TS3 costs 0 real_cost = 165.177 karypis.srv_TS2-scwrl costs 0 real_cost = 133.932 karypis.srv_TS2 costs 0 real_cost = 129.732 karypis.srv_TS1-scwrl costs 0 real_cost = 98.3468 karypis.srv_TS1 costs 0 real_cost = 89.5889 karypis.srv.4_TS5-scwrl costs 0 real_cost = 319.049 karypis.srv.4_TS5 costs 0 real_cost = 317.264 karypis.srv.4_TS4-scwrl costs 0 real_cost = 311.67 karypis.srv.4_TS4 costs 0 real_cost = 314.209 karypis.srv.4_TS3-scwrl costs 0 real_cost = 338.559 karypis.srv.4_TS3 costs 0 real_cost = 338.559 karypis.srv.4_TS2-scwrl costs 0 real_cost = 272.467 karypis.srv.4_TS2 costs 0 real_cost = 272.467 karypis.srv.4_TS1-scwrl costs 0 real_cost = 316.621 karypis.srv.4_TS1 costs 0 real_cost = 316.624 karypis.srv.2_TS5-scwrl costs 0 real_cost = 29.2669 karypis.srv.2_TS5 costs 0 real_cost = 29.4405 karypis.srv.2_TS4-scwrl costs 0 real_cost = 279.739 karypis.srv.2_TS4 costs 0 real_cost = 279.739 karypis.srv.2_TS3-scwrl costs 0 real_cost = 216.132 karypis.srv.2_TS3 costs 0 real_cost = 216.132 karypis.srv.2_TS2-scwrl costs 0 real_cost = 253.436 karypis.srv.2_TS2 costs 0 real_cost = 253.436 karypis.srv.2_TS1-scwrl costs 0 real_cost = 58.265 karypis.srv.2_TS1 costs 0 real_cost = 58.2661 gtg_AL5-scwrl costs 0 real_cost = 463.932 gtg_AL5 costs 0 real_cost = 567.468 gtg_AL4-scwrl costs 0 real_cost = 432.77 gtg_AL4 costs 0 real_cost = 520.814 gtg_AL3-scwrl costs 0 real_cost = 463.561 gtg_AL3 costs 0 real_cost = 550.135 gtg_AL2-scwrl costs 0 real_cost = 404.033 gtg_AL2 costs 0 real_cost = 533.705 gtg_AL1-scwrl costs 0 real_cost = 364.477 gtg_AL1 costs 0 real_cost = 500.064 forecast-s_AL5-scwrl costs 0 real_cost = 311.974 forecast-s_AL5 costs 0 real_cost = 457.63 forecast-s_AL4-scwrl costs 0 real_cost = 378.023 forecast-s_AL4 costs 0 real_cost = 495.752 forecast-s_AL3-scwrl costs 0 real_cost = 364.993 forecast-s_AL3 costs 0 real_cost = 466.629 forecast-s_AL2-scwrl costs 0 real_cost = 362.226 forecast-s_AL2 costs 0 real_cost = 508.709 forecast-s_AL1-scwrl costs 0 real_cost = 355.871 forecast-s_AL1 costs 0 real_cost = 457.051 beautshotbase_TS1-scwrl costs 0 real_cost = 353.97 beautshotbase_TS1 costs 0 real_cost = 367.572 beautshot_TS1-scwrl costs 0 real_cost = 55.3289 beautshot_TS1 costs 0 real_cost = 68.5049 Zhang-Server_TS5-scwrl costs 0 real_cost = 20.7032 Zhang-Server_TS5 costs 0 real_cost = 22.4861 Zhang-Server_TS4-scwrl costs 0 real_cost = -16.3326 Zhang-Server_TS4 costs 0 real_cost = -12.3291 Zhang-Server_TS3-scwrl costs 0 real_cost = -25.4124 Zhang-Server_TS3 costs 0 real_cost = -17.0163 Zhang-Server_TS2-scwrl costs 0 real_cost = 46.3985 Zhang-Server_TS2 costs 0 real_cost = 44.9616 Zhang-Server_TS1-scwrl costs 0 real_cost = 16.2608 Zhang-Server_TS1 costs 0 real_cost = 20.4425 UNI-EID_sfst_AL4-scwrl costs 0 real_cost = 465.904 UNI-EID_sfst_AL4 costs 0 real_cost = 546.741 UNI-EID_sfst_AL3-scwrl costs 0 real_cost = 413.313 UNI-EID_sfst_AL3 costs 0 real_cost = 501.622 UNI-EID_sfst_AL2-scwrl costs 0 real_cost = 419.1 UNI-EID_sfst_AL2 costs 0 real_cost = 511.782 UNI-EID_sfst_AL1-scwrl costs 0 real_cost = 408.74 UNI-EID_sfst_AL1 costs 0 real_cost = 503.446 UNI-EID_expm_TS1-scwrl costs 0 real_cost = 98.8705 UNI-EID_expm_TS1 costs 0 real_cost = 284.056 UNI-EID_bnmx_TS4-scwrl costs 0 real_cost = 445.774 UNI-EID_bnmx_TS4 costs 0 real_cost = 531.867 UNI-EID_bnmx_TS3-scwrl costs 0 real_cost = 239.826 UNI-EID_bnmx_TS3 costs 0 real_cost = 401.056 UNI-EID_bnmx_TS2-scwrl costs 0 real_cost = 347.149 UNI-EID_bnmx_TS2 costs 0 real_cost = 472.911 UNI-EID_bnmx_TS1-scwrl costs 0 real_cost = 188.801 UNI-EID_bnmx_TS1 costs 0 real_cost = 411.164 SPARKS2_TS5-scwrl costs 0 real_cost = 49.2865 SPARKS2_TS5 costs 0 real_cost = 66.1218 SPARKS2_TS4-scwrl costs 0 real_cost = 97.7922 SPARKS2_TS4 costs 0 real_cost = 101.792 SPARKS2_TS3-scwrl costs 0 real_cost = 101.455 SPARKS2_TS3 costs 0 real_cost = 116.74 SPARKS2_TS2-scwrl costs 0 real_cost = 43.9586 SPARKS2_TS2 costs 0 real_cost = 44.7689 SPARKS2_TS1-scwrl costs 0 real_cost = 80.1405 SPARKS2_TS1 costs 0 real_cost = 95.7306 SP4_TS5-scwrl costs 0 real_cost = 112.279 SP4_TS5 costs 0 real_cost = 118.304 SP4_TS4-scwrl costs 0 real_cost = 81.6908 SP4_TS4 costs 0 real_cost = 87.9114 SP4_TS3-scwrl costs 0 real_cost = 70.9206 SP4_TS3 costs 0 real_cost = 83.0998 SP4_TS2-scwrl costs 0 real_cost = 38.3927 SP4_TS2 costs 0 real_cost = 43.2156 SP4_TS1-scwrl costs 0 real_cost = 116.743 SP4_TS1 costs 0 real_cost = 119.775 SP3_TS5-scwrl costs 0 real_cost = 106.843 SP3_TS5 costs 0 real_cost = 105.545 SP3_TS4-scwrl costs 0 real_cost = 54.7663 SP3_TS4 costs 0 real_cost = 59.5758 SP3_TS3-scwrl costs 0 real_cost = 82.431 SP3_TS3 costs 0 real_cost = 86.4528 SP3_TS2-scwrl costs 0 real_cost = 93.9551 SP3_TS2 costs 0 real_cost = 96.9976 SP3_TS1-scwrl costs 0 real_cost = 102.468 SP3_TS1 costs 0 real_cost = 98.4279 SAM_T06_server_TS5-scwrl costs 0 real_cost = 278.498 SAM_T06_server_TS5 costs 0 real_cost = 253.379 SAM_T06_server_TS4-scwrl costs 0 real_cost = 307.312 SAM_T06_server_TS4 costs 0 real_cost = 261.733 SAM_T06_server_TS3-scwrl costs 0 real_cost = 316.596 SAM_T06_server_TS3 costs 0 real_cost = 293.646 SAM_T06_server_TS2-scwrl costs 0 real_cost = 294.262 SAM_T06_server_TS2 costs 0 real_cost = 225.552 SAM_T06_server_TS1-scwrl costs 0 real_cost = 175.098 SAM_T06_server_TS1 costs 0 real_cost = 174.938 SAM-T99_AL5-scwrl costs 0 real_cost = 326.966 SAM-T99_AL5 costs 0 real_cost = 456.81 SAM-T99_AL4-scwrl costs 0 real_cost = 305.019 SAM-T99_AL4 costs 0 real_cost = 445.035 SAM-T99_AL3-scwrl costs 0 real_cost = 297.668 SAM-T99_AL3 costs 0 real_cost = 432.968 SAM-T99_AL2-scwrl costs 0 real_cost = 525.242 SAM-T99_AL2 costs 0 real_cost = 602.664 SAM-T99_AL1-scwrl costs 0 real_cost = 247.823 SAM-T99_AL1 costs 0 real_cost = 380.535 SAM-T02_AL5-scwrl costs 0 real_cost = 263.678 SAM-T02_AL5 costs 0 real_cost = 379.591 SAM-T02_AL4-scwrl costs 0 real_cost = 346.737 SAM-T02_AL4 costs 0 real_cost = 439.985 SAM-T02_AL3-scwrl costs 0 real_cost = 395.793 SAM-T02_AL3 costs 0 real_cost = 481.377 SAM-T02_AL2-scwrl costs 0 real_cost = 408.979 SAM-T02_AL2 costs 0 real_cost = 493.037 SAM-T02_AL1-scwrl costs 0 real_cost = 392.159 SAM-T02_AL1 costs 0 real_cost = 495.953 ROKKY_TS5-scwrl costs 0 real_cost = 80.589 ROKKY_TS5 costs 0 real_cost = 286.179 ROKKY_TS4-scwrl costs 0 real_cost = 80.5427 ROKKY_TS4 costs 0 real_cost = 286.221 ROKKY_TS3-scwrl costs 0 real_cost = 80.566 ROKKY_TS3 costs 0 real_cost = 286.204 ROKKY_TS2-scwrl costs 0 real_cost = 80.6876 ROKKY_TS2 costs 0 real_cost = 286.327 ROKKY_TS1-scwrl costs 0 real_cost = 80.6316 ROKKY_TS1 costs 0 real_cost = 286.315 ROBETTA_TS5-scwrl costs 0 real_cost = 47.9072 ROBETTA_TS5 costs 0 real_cost = 55.1817 ROBETTA_TS4-scwrl costs 0 real_cost = 51.4853 ROBETTA_TS4 costs 0 real_cost = 52.9082 ROBETTA_TS3-scwrl costs 0 real_cost = 68.64 ROBETTA_TS3 costs 0 real_cost = 73.52 ROBETTA_TS2-scwrl costs 0 real_cost = 26.2674 ROBETTA_TS2 costs 0 real_cost = 29.6706 ROBETTA_TS1-scwrl costs 0 real_cost = 44.3326 ROBETTA_TS1 costs 0 real_cost = 46.0027 RAPTOR_TS5-scwrl costs 0 real_cost = 65.0285 RAPTOR_TS5 costs 0 real_cost = 65.0603 RAPTOR_TS4-scwrl costs 0 real_cost = 61.3938 RAPTOR_TS4 costs 0 real_cost = 66.4195 RAPTOR_TS3-scwrl costs 0 real_cost = 78.8805 RAPTOR_TS3 costs 0 real_cost = 75.6606 RAPTOR_TS2-scwrl costs 0 real_cost = 49.4977 RAPTOR_TS2 costs 0 real_cost = 50.7543 RAPTOR_TS1-scwrl costs 0 real_cost = 83.0668 RAPTOR_TS1 costs 0 real_cost = 90.768 RAPTORESS_TS5-scwrl costs 0 real_cost = 73.3436 RAPTORESS_TS5 costs 0 real_cost = 78.3484 RAPTORESS_TS4-scwrl costs 0 real_cost = 94.6966 RAPTORESS_TS4 costs 0 real_cost = 109.734 RAPTORESS_TS3-scwrl costs 0 real_cost = 92.0954 RAPTORESS_TS3 costs 0 real_cost = 98.5208 RAPTORESS_TS2-scwrl costs 0 real_cost = 51.3287 RAPTORESS_TS2 costs 0 real_cost = 55.0609 RAPTORESS_TS1-scwrl costs 0 real_cost = 112.425 RAPTORESS_TS1 costs 0 real_cost = 127.192 RAPTOR-ACE_TS5-scwrl costs 0 real_cost = 49.1357 RAPTOR-ACE_TS5 costs 0 real_cost = 50.7543 RAPTOR-ACE_TS4-scwrl costs 0 real_cost = 104.854 RAPTOR-ACE_TS4 costs 0 real_cost = 112.494 RAPTOR-ACE_TS3-scwrl costs 0 real_cost = 34.6795 RAPTOR-ACE_TS3 costs 0 real_cost = 44.5093 RAPTOR-ACE_TS2-scwrl costs 0 real_cost = 37.0702 RAPTOR-ACE_TS2 costs 0 real_cost = 36.8809 RAPTOR-ACE_TS1-scwrl costs 0 real_cost = 43.8875 RAPTOR-ACE_TS1 costs 0 real_cost = 45.3657 Pmodeller6_TS5-scwrl costs 0 real_cost = 27.8095 Pmodeller6_TS5 costs 0 real_cost = 24.0348 Pmodeller6_TS4-scwrl costs 0 real_cost = 61.0194 Pmodeller6_TS4 costs 0 real_cost = 61.0194 Pmodeller6_TS3-scwrl costs 0 real_cost = 107.592 Pmodeller6_TS3 costs 0 real_cost = 102.528 Pmodeller6_TS2-scwrl costs 0 real_cost = 18.241 Pmodeller6_TS2 costs 0 real_cost = 18.349 Pmodeller6_TS1-scwrl costs 0 real_cost = 77.0309 Pmodeller6_TS1 costs 0 real_cost = 71.9623 Phyre-2_TS5-scwrl costs 0 real_cost = 48.2768 Phyre-2_TS5 costs 0 real_cost = 50.8396 Phyre-2_TS4-scwrl costs 0 real_cost = 48.3831 Phyre-2_TS4 costs 0 real_cost = 51.2957 Phyre-2_TS3-scwrl costs 0 real_cost = 48.3447 Phyre-2_TS3 costs 0 real_cost = 51.2659 Phyre-2_TS2-scwrl costs 0 real_cost = 51.3071 Phyre-2_TS2 costs 0 real_cost = 53.9468 Phyre-2_TS1-scwrl costs 0 real_cost = 51.1674 Phyre-2_TS1 costs 0 real_cost = 54.0788 Phyre-1_TS1-scwrl costs 0 real_cost = 480.544 Phyre-1_TS1 costs 0 real_cost = 464.72 Pcons6_TS5-scwrl costs 0 real_cost = 70.0049 Pcons6_TS5 costs 0 real_cost = 69.4666 Pcons6_TS4-scwrl costs 0 real_cost = 69.3827 Pcons6_TS4 costs 0 real_cost = 64.0619 Pcons6_TS3-scwrl costs 0 real_cost = 42.7323 Pcons6_TS3 costs 0 real_cost = 40.3129 Pcons6_TS2-scwrl costs 0 real_cost = 29.9731 Pcons6_TS2 costs 0 real_cost = 24.5934 Pcons6_TS1-scwrl costs 0 real_cost = 81.4156 Pcons6_TS1 costs 0 real_cost = 85.9056 PROTINFO_TS5-scwrl costs 0 real_cost = 74.0919 PROTINFO_TS5 costs 0 real_cost = 74.1668 PROTINFO_TS4-scwrl costs 0 real_cost = 99.0001 PROTINFO_TS4 costs 0 real_cost = 103.055 PROTINFO_TS3-scwrl costs 0 real_cost = 85.6784 PROTINFO_TS3 costs 0 real_cost = 85.7157 PROTINFO_TS2-scwrl costs 0 real_cost = 131.772 PROTINFO_TS2 costs 0 real_cost = 124.698 PROTINFO_TS1-scwrl costs 0 real_cost = 65.7804 PROTINFO_TS1 costs 0 real_cost = 65.6305 PROTINFO-AB_TS5-scwrl costs 0 real_cost = 63.4834 PROTINFO-AB_TS5 costs 0 real_cost = 60.4729 PROTINFO-AB_TS4-scwrl costs 0 real_cost = 53.0736 PROTINFO-AB_TS4 costs 0 real_cost = 50.4247 PROTINFO-AB_TS3-scwrl costs 0 real_cost = 53.4816 PROTINFO-AB_TS3 costs 0 real_cost = 57.4097 PROTINFO-AB_TS2-scwrl costs 0 real_cost = 83.2578 PROTINFO-AB_TS2 costs 0 real_cost = 71.0573 PROTINFO-AB_TS1-scwrl costs 0 real_cost = 83.2578 PROTINFO-AB_TS1 costs 0 real_cost = 71.0573 POMYSL_TS4-scwrl costs 0 real_cost = 455.182 POMYSL_TS4 costs 0 real_cost = 459.9 POMYSL_TS3-scwrl costs 0 real_cost = 525.302 POMYSL_TS3 costs 0 real_cost = 549.691 POMYSL_TS2-scwrl costs 0 real_cost = 552.483 POMYSL_TS2 costs 0 real_cost = 548.965 POMYSL_TS1-scwrl costs 0 real_cost = 441.565 POMYSL_TS1 costs 0 real_cost = 447.18 NN_PUT_lab_TS1-scwrl costs 0 real_cost = 118.172 NN_PUT_lab_TS1 costs 0 real_cost = 307.205 MetaTasser_TS5-scwrl costs 0 real_cost = 17.6686 MetaTasser_TS5 costs 0 real_cost = 25.0525 MetaTasser_TS4-scwrl costs 0 real_cost = 41.7115 MetaTasser_TS4 costs 0 real_cost = 41.3805 MetaTasser_TS3-scwrl costs 0 real_cost = 10.4878 MetaTasser_TS2-scwrl costs 0 real_cost = 24.7061 MetaTasser_TS2 costs 0 real_cost = 21.2497 MetaTasser_TS1-scwrl costs 0 real_cost = 41.1715 MetaTasser_TS1 costs 0 real_cost = 48.4018 Ma-OPUS-server_TS5-scwrl costs 0 real_cost = 310.916 Ma-OPUS-server_TS5 costs 0 real_cost = 310.34 Ma-OPUS-server_TS4-scwrl costs 0 real_cost = 85.3821 Ma-OPUS-server_TS4 costs 0 real_cost = 75.1598 Ma-OPUS-server_TS3-scwrl costs 0 real_cost = 37.7561 Ma-OPUS-server_TS3 costs 0 real_cost = 43.3505 Ma-OPUS-server_TS2-scwrl costs 0 real_cost = 49.4768 Ma-OPUS-server_TS2 costs 0 real_cost = 50.2136 Ma-OPUS-server_TS1-scwrl costs 0 real_cost = 16.3015 Ma-OPUS-server_TS1 costs 0 real_cost = 15.5889 LOOPP_TS5-scwrl costs 0 real_cost = 232.471 LOOPP_TS5 costs 0 real_cost = 230.932 LOOPP_TS4-scwrl costs 0 real_cost = 285.826 LOOPP_TS4 costs 0 real_cost = 283.798 LOOPP_TS3-scwrl costs 0 real_cost = 152.792 LOOPP_TS3 costs 0 real_cost = 155.227 LOOPP_TS2-scwrl costs 0 real_cost = 288.184 LOOPP_TS2 costs 0 real_cost = 291.162 LOOPP_TS1-scwrl costs 0 real_cost = 223.509 LOOPP_TS1 costs 0 real_cost = 224.458 Huber-Torda-Server_TS5-scwrl costs 0 real_cost = 648.351 Huber-Torda-Server_TS5 costs 0 real_cost = 672.379 Huber-Torda-Server_TS4-scwrl costs 0 real_cost = 603.219 Huber-Torda-Server_TS4 costs 0 real_cost = 665.628 Huber-Torda-Server_TS3-scwrl costs 0 real_cost = 542.851 Huber-Torda-Server_TS3 costs 0 real_cost = 616.365 Huber-Torda-Server_TS2-scwrl costs 0 real_cost = 549.368 Huber-Torda-Server_TS2 costs 0 real_cost = 614.011 Huber-Torda-Server_TS1-scwrl costs 0 real_cost = 562.034 Huber-Torda-Server_TS1 costs 0 real_cost = 626.145 HHpred3_TS1-scwrl costs 0 real_cost = 61.9149 HHpred3_TS1 costs 0 real_cost = 55.5241 HHpred2_TS1-scwrl costs 0 real_cost = 61.9149 HHpred2_TS1 costs 0 real_cost = 55.5241 HHpred1_TS1-scwrl costs 0 real_cost = 52.4274 HHpred1_TS1 costs 0 real_cost = 52.3542 GeneSilicoMetaServer_TS5-scwrl costs 0 real_cost = 80.1612 GeneSilicoMetaServer_TS5 costs 0 real_cost = 79.969 GeneSilicoMetaServer_TS4-scwrl costs 0 real_cost = 315.356 GeneSilicoMetaServer_TS4 costs 0 real_cost = 320.591 GeneSilicoMetaServer_TS3-scwrl costs 0 real_cost = 259.447 GeneSilicoMetaServer_TS3 costs 0 real_cost = 264.943 GeneSilicoMetaServer_TS2-scwrl costs 0 real_cost = 88.1511 GeneSilicoMetaServer_TS1-scwrl costs 0 real_cost = 162.313 GeneSilicoMetaServer_TS1 costs 0 real_cost = 162.345 FUNCTION_TS5-scwrl costs 0 real_cost = 109.242 FUNCTION_TS5 costs 0 real_cost = 113.625 FUNCTION_TS4-scwrl costs 0 real_cost = 204.492 FUNCTION_TS4 costs 0 real_cost = 210.333 FUNCTION_TS3-scwrl costs 0 real_cost = 84.4509 FUNCTION_TS3 costs 0 real_cost = 95.4822 FUNCTION_TS2-scwrl costs 0 real_cost = 32.506 FUNCTION_TS2 costs 0 real_cost = 40.7181 FUNCTION_TS1-scwrl costs 0 real_cost = 330.424 FUNCTION_TS1 costs 0 real_cost = 328.833 FUGUE_AL5-scwrl costs 0 real_cost = 252.612 FUGUE_AL5 costs 0 real_cost = 442.711 FUGUE_AL4-scwrl costs 0 real_cost = 170.203 FUGUE_AL4 costs 0 real_cost = 415.986 FUGUE_AL3-scwrl costs 0 real_cost = 509.748 FUGUE_AL3 costs 0 real_cost = 660.5 FUGUE_AL2-scwrl costs 0 real_cost = 504.465 FUGUE_AL2 costs 0 real_cost = 609.95 FUGUE_AL1-scwrl costs 0 real_cost = 257.773 FUGUE_AL1 costs 0 real_cost = 426.523 FUGMOD_TS5-scwrl costs 0 real_cost = 133.867 FUGMOD_TS5 costs 0 real_cost = 134.91 FUGMOD_TS4-scwrl costs 0 real_cost = 108.321 FUGMOD_TS4 costs 0 real_cost = 107.703 FUGMOD_TS3-scwrl costs 0 real_cost = 503.097 FUGMOD_TS3 costs 0 real_cost = 505.502 FUGMOD_TS2-scwrl costs 0 real_cost = 479.374 FUGMOD_TS2 costs 0 real_cost = 476.904 FUGMOD_TS1-scwrl costs 0 real_cost = 135.019 FUGMOD_TS1 costs 0 real_cost = 132.121 FPSOLVER-SERVER_TS5-scwrl costs 0 real_cost = 299.588 FPSOLVER-SERVER_TS5 costs 0 real_cost = 300.688 FPSOLVER-SERVER_TS4-scwrl costs 0 real_cost = 325.699 FPSOLVER-SERVER_TS4 costs 0 real_cost = 329.372 FPSOLVER-SERVER_TS3-scwrl costs 0 real_cost = 317.788 FPSOLVER-SERVER_TS3 costs 0 real_cost = 319.53 FPSOLVER-SERVER_TS2-scwrl costs 0 real_cost = 327.703 FPSOLVER-SERVER_TS2 costs 0 real_cost = 329.262 FPSOLVER-SERVER_TS1-scwrl costs 0 real_cost = 325.215 FPSOLVER-SERVER_TS1 costs 0 real_cost = 329.192 FORTE2_AL5-scwrl costs 0 real_cost = 413.705 FORTE2_AL5 costs 0 real_cost = 568.858 FORTE2_AL4-scwrl costs 0 real_cost = 529.867 FORTE2_AL3-scwrl costs 0 real_cost = 118.535 FORTE2_AL3 costs 0 real_cost = 365.074 FORTE2_AL2-scwrl costs 0 real_cost = 184.058 FORTE2_AL2 costs 0 real_cost = 428.533 FORTE2_AL1-scwrl costs 0 real_cost = 124.712 FORTE2_AL1 costs 0 real_cost = 378.881 FORTE1_AL5-scwrl costs 0 real_cost = 386.751 FORTE1_AL5 costs 0 real_cost = 517.631 FORTE1_AL4-scwrl costs 0 real_cost = 357.274 FORTE1_AL4 costs 0 real_cost = 543.893 FORTE1_AL3-scwrl costs 0 real_cost = 118.535 FORTE1_AL3 costs 0 real_cost = 365.074 FORTE1_AL2-scwrl costs 0 real_cost = 184.058 FORTE1_AL2 costs 0 real_cost = 428.533 FORTE1_AL1-scwrl costs 0 real_cost = 124.712 FORTE1_AL1 costs 0 real_cost = 378.881 FOLDpro_TS5-scwrl costs 0 real_cost = 184.76 FOLDpro_TS5 costs 0 real_cost = 189.128 FOLDpro_TS4-scwrl costs 0 real_cost = 296.825 FOLDpro_TS4 costs 0 real_cost = 298.363 FOLDpro_TS3-scwrl costs 0 real_cost = 55.2793 FOLDpro_TS3 costs 0 real_cost = 61.1356 FOLDpro_TS2-scwrl costs 0 real_cost = 197.134 FOLDpro_TS2 costs 0 real_cost = 200.568 FOLDpro_TS1-scwrl costs 0 real_cost = 185.418 FOLDpro_TS1 costs 0 real_cost = 185.351 FAMS_TS5-scwrl costs 0 real_cost = 81.4412 FAMS_TS5 costs 0 real_cost = 80.8513 FAMS_TS4-scwrl costs 0 real_cost = 330.424 FAMS_TS4 costs 0 real_cost = 328.833 FAMS_TS3-scwrl costs 0 real_cost = 355.803 FAMS_TS3 costs 0 real_cost = 354.733 FAMS_TS2-scwrl costs 0 real_cost = 66.6439 FAMS_TS2 costs 0 real_cost = 68.397 FAMS_TS1-scwrl costs 0 real_cost = 31.5763 FAMS_TS1 costs 0 real_cost = 35.5316 FAMSD_TS5-scwrl costs 0 real_cost = 102.032 FAMSD_TS5 costs 0 real_cost = 107.018 FAMSD_TS4-scwrl costs 0 real_cost = 311.435 FAMSD_TS4 costs 0 real_cost = 321.527 FAMSD_TS3-scwrl costs 0 real_cost = 355.803 FAMSD_TS3 costs 0 real_cost = 354.733 FAMSD_TS2-scwrl costs 0 real_cost = 193.006 FAMSD_TS2 costs 0 real_cost = 199.054 FAMSD_TS1-scwrl costs 0 real_cost = 90.2881 FAMSD_TS1 costs 0 real_cost = 92.1324 Distill_TS5-scwrl costs 0 real_cost = 734.96 Distill_TS4-scwrl costs 0 real_cost = 751.055 Distill_TS3-scwrl costs 0 real_cost = 750.799 Distill_TS2-scwrl costs 0 real_cost = 727.806 Distill_TS1-scwrl costs 0 real_cost = 734.057 CaspIta-FOX_TS5-scwrl costs 0 real_cost = 497.194 CaspIta-FOX_TS5 costs 0 real_cost = 496.581 CaspIta-FOX_TS4-scwrl costs 0 real_cost = 393.62 CaspIta-FOX_TS4 costs 0 real_cost = 390.235 CaspIta-FOX_TS3-scwrl costs 0 real_cost = 243.007 CaspIta-FOX_TS3 costs 0 real_cost = 229.547 CaspIta-FOX_TS2-scwrl costs 0 real_cost = 120.239 CaspIta-FOX_TS2 costs 0 real_cost = 112.687 CaspIta-FOX_TS1-scwrl costs 0 real_cost = 231.276 CaspIta-FOX_TS1 costs 0 real_cost = 215.684 CPHmodels_TS1-scwrl costs 0 real_cost = 620.27 CPHmodels_TS1 costs 0 real_cost = 616.867 CIRCLE_TS5-scwrl costs 0 real_cost = 77.3527 CIRCLE_TS5 costs 0 real_cost = 67.6982 CIRCLE_TS4-scwrl costs 0 real_cost = 329.273 CIRCLE_TS4 costs 0 real_cost = 328.562 CIRCLE_TS3-scwrl costs 0 real_cost = 333.473 CIRCLE_TS3 costs 0 real_cost = 331.988 CIRCLE_TS2-scwrl costs 0 real_cost = 368.684 CIRCLE_TS2 costs 0 real_cost = 371.345 CIRCLE_TS1-scwrl costs 0 real_cost = 39.7439 CIRCLE_TS1 costs 0 real_cost = 44.0751 Bilab-ENABLE_TS3-scwrl costs 0 real_cost = 115.574 Bilab-ENABLE_TS3 costs 0 real_cost = 115.646 Bilab-ENABLE_TS2-scwrl costs 0 real_cost = 105.088 Bilab-ENABLE_TS2 costs 0 real_cost = 104.637 Bilab-ENABLE_TS1-scwrl costs 0 real_cost = 252.959 Bilab-ENABLE_TS1 costs 0 real_cost = 253.02 BayesHH_TS1-scwrl costs 0 real_cost = -0.588403 BayesHH_TS1 costs 0 real_cost = 7.0162 ABIpro_TS5-scwrl costs 0 real_cost = 250.983 ABIpro_TS5 costs 0 real_cost = 250.983 ABIpro_TS4-scwrl costs 0 real_cost = 211.951 ABIpro_TS4 costs 0 real_cost = 211.965 ABIpro_TS3-scwrl costs 0 real_cost = 258.518 ABIpro_TS3 costs 0 real_cost = 259.213 ABIpro_TS2-scwrl costs 0 real_cost = 230.362 ABIpro_TS2 costs 0 real_cost = 230.362 ABIpro_TS1-scwrl costs 0 real_cost = 246.108 ABIpro_TS1 costs 0 real_cost = 246.103 3Dpro_TS5-scwrl costs 0 real_cost = 306.709 3Dpro_TS5 costs 0 real_cost = 313.703 3Dpro_TS4-scwrl costs 0 real_cost = 300.374 3Dpro_TS4 costs 0 real_cost = 302.059 3Dpro_TS3-scwrl costs 0 real_cost = 185.418 3Dpro_TS3 costs 0 real_cost = 185.351 3Dpro_TS2-scwrl costs 0 real_cost = 59.864 3Dpro_TS2 costs 0 real_cost = 73.4723 3Dpro_TS1-scwrl costs 0 real_cost = 55.2793 3Dpro_TS1 costs 0 real_cost = 61.1356 3D-JIGSAW_TS5-scwrl costs 0 real_cost = 348.138 3D-JIGSAW_TS5 costs 0 real_cost = 349.247 3D-JIGSAW_TS4-scwrl costs 0 real_cost = 368.229 3D-JIGSAW_TS4 costs 0 real_cost = 376.24 3D-JIGSAW_TS3-scwrl costs 0 real_cost = 488.419 3D-JIGSAW_TS3 costs 0 real_cost = 494.664 3D-JIGSAW_TS2-scwrl costs 0 real_cost = 497.809 3D-JIGSAW_TS2 costs 0 real_cost = 499.898 3D-JIGSAW_TS1-scwrl costs 0 real_cost = 496.002 3D-JIGSAW_TS1 costs 0 real_cost = 496.599 3D-JIGSAW_RECOM_TS5-scwrl costs 0 real_cost = 401.297 3D-JIGSAW_RECOM_TS5 costs 0 real_cost = 401.476 3D-JIGSAW_RECOM_TS4-scwrl costs 0 real_cost = 401.297 3D-JIGSAW_RECOM_TS4 costs 0 real_cost = 401.476 3D-JIGSAW_RECOM_TS3-scwrl costs 0 real_cost = 400.289 3D-JIGSAW_RECOM_TS3 costs 0 real_cost = 400.92 3D-JIGSAW_RECOM_TS2-scwrl costs 0 real_cost = 395.2 3D-JIGSAW_RECOM_TS2 costs 0 real_cost = 400.259 3D-JIGSAW_RECOM_TS1-scwrl costs 0 real_cost = 394.656 3D-JIGSAW_RECOM_TS1 costs 0 real_cost = 397.66 3D-JIGSAW_POPULUS_TS5-scwrl costs 0 real_cost = 407.511 3D-JIGSAW_POPULUS_TS5 costs 0 real_cost = 402.616 3D-JIGSAW_POPULUS_TS4-scwrl costs 0 real_cost = 423.01 3D-JIGSAW_POPULUS_TS4 costs 0 real_cost = 421.81 3D-JIGSAW_POPULUS_TS3-scwrl costs 0 real_cost = 404.855 3D-JIGSAW_POPULUS_TS3 costs 0 real_cost = 399.887 3D-JIGSAW_POPULUS_TS2-scwrl costs 0 real_cost = 409.664 3D-JIGSAW_POPULUS_TS2 costs 0 real_cost = 403.518 3D-JIGSAW_POPULUS_TS1-scwrl costs 0 real_cost = 389.229 3D-JIGSAW_POPULUS_TS1 costs 0 real_cost = 383.918 make-chimera.pdb.gz costs 0 real_cost = 131.189 chimera1.pdb.gz costs 0 real_cost = 123.887 T0316.try9-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 49.7641 T0316.try9-opt2.pdb.gz costs 0 real_cost = 51.0186 T0316.try9-opt2.gromacs0.pdb.gz costs 0 real_cost = 52.7912 T0316.try9-opt1.pdb.gz costs 0 real_cost = 52.3973 T0316.try9-opt1-scwrl.pdb.gz costs 0 real_cost = 49.6326 T0316.try8-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 120.194 T0316.try8-opt2.pdb.gz costs 0 real_cost = 121.834 T0316.try8-opt2.gromacs0.pdb.gz costs 0 real_cost = 119.836 T0316.try8-opt1.pdb.gz costs 0 real_cost = 121.499 T0316.try8-opt1-scwrl.pdb.gz costs 0 real_cost = 120.697 T0316.try7-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 139.73 T0316.try7-opt2.pdb.gz costs 0 real_cost = 142.307 T0316.try7-opt2.gromacs0.pdb.gz costs 0 real_cost = 145.347 T0316.try7-opt1.pdb.gz costs 0 real_cost = 140.274 T0316.try7-opt1-scwrl.pdb.gz costs 0 real_cost = 145.186 T0316.try6-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 157.522 T0316.try6-opt2.pdb.gz costs 0 real_cost = 159.387 T0316.try6-opt2.gromacs0.pdb.gz costs 0 real_cost = 154.477 T0316.try6-opt1.pdb.gz costs 0 real_cost = 161.972 T0316.try6-opt1-scwrl.pdb.gz costs 0 real_cost = 160.88 T0316.try5-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 81.1278 T0316.try5-opt2.pdb.gz costs 0 real_cost = 84.7593 T0316.try5-opt2.gromacs0.pdb.gz costs 0 real_cost = 86.7812 T0316.try5-opt1.pdb.gz costs 0 real_cost = 72.0281 T0316.try5-opt1-scwrl.pdb.gz costs 0 real_cost = 73.6936 T0316.try4-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 120.036 T0316.try4-opt2.pdb.gz costs 0 real_cost = 120.587 T0316.try4-opt2.gromacs0.pdb.gz costs 0 real_cost = 123.64 T0316.try4-opt1.pdb.gz costs 0 real_cost = 120.701 T0316.try4-opt1-scwrl.pdb.gz costs 0 real_cost = 122.54 T0316.try3-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 188.207 T0316.try3-opt2.pdb.gz costs 0 real_cost = 186.661 T0316.try3-opt2.gromacs0.pdb.gz costs 0 real_cost = 190.114 T0316.try3-opt1.pdb.gz costs 0 real_cost = 191.727 T0316.try3-opt1-scwrl.pdb.gz costs 0 real_cost = 191.737 T0316.try21-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 100.646 T0316.try21-opt2.pdb.gz costs 0 real_cost = 97.2968 T0316.try21-opt2.gromacs0.pdb.gz costs 0 real_cost = 97.8754 T0316.try21-opt1.pdb.gz costs 0 real_cost = 97.4607 T0316.try21-opt1-scwrl.pdb.gz costs 0 real_cost = 97.714 T0316.try20-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 148.232 T0316.try20-opt2.pdb.gz costs 0 real_cost = 150.114 T0316.try20-opt2.gromacs0.pdb.gz costs 0 real_cost = 154.084 T0316.try20-opt1.pdb.gz costs 0 real_cost = 151.729 T0316.try20-opt1-scwrl.pdb.gz costs 0 real_cost = 150.572 T0316.try2-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 144.437 T0316.try2-opt2.pdb.gz costs 0 real_cost = 141.803 T0316.try2-opt2.gromacs0.pdb.gz costs 0 real_cost = 143.244 T0316.try2-opt2-M1-A183-try6-opt2-A130-I373.pdb.gz costs 0 real_cost = 128.322 T0316.try2-opt1.pdb.gz costs 0 real_cost = 146.267 T0316.try2-opt1-scwrl.pdb.gz costs 0 real_cost = 145.432 T0316.try19-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 97.3941 T0316.try19-opt2.pdb.gz costs 0 real_cost = 97.0993 T0316.try19-opt2.gromacs0.pdb.gz costs 0 real_cost = 96.2197 T0316.try19-opt1.pdb.gz costs 0 real_cost = 96.7935 T0316.try19-opt1-scwrl.pdb.gz costs 0 real_cost = 97.1408 T0316.try18-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 150.532 T0316.try18-opt2.pdb.gz costs 0 real_cost = 151.759 T0316.try18-opt2.gromacs0.pdb.gz costs 0 real_cost = 154.02 T0316.try18-opt1.pdb.gz costs 0 real_cost = 151.586 T0316.try18-opt1-scwrl.pdb.gz costs 0 real_cost = 151.352 T0316.try17-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 155.898 T0316.try17-opt2.pdb.gz costs 0 real_cost = 156.862 T0316.try17-opt2.gromacs0.pdb.gz costs 0 real_cost = 164.524 T0316.try17-opt1.pdb.gz costs 0 real_cost = 170.658 T0316.try17-opt1-scwrl.pdb.gz costs 0 real_cost = 171.993 T0316.try16-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 102.014 T0316.try16-opt2.pdb.gz costs 0 real_cost = 104.523 T0316.try16-opt2.gromacs0.pdb.gz costs 0 real_cost = 107.969 T0316.try16-opt1.pdb.gz costs 0 real_cost = 109.873 T0316.try16-opt1-scwrl.pdb.gz costs 0 real_cost = 109.979 T0316.try15-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 78.1814 T0316.try15-opt2.pdb.gz costs 0 real_cost = 82.4192 T0316.try15-opt2.gromacs0.pdb.gz costs 0 real_cost = 76.1254 T0316.try15-opt1.pdb.gz costs 0 real_cost = 75.5787 T0316.try15-opt1-scwrl.pdb.gz costs 0 real_cost = 74.202 T0316.try14-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 158.347 T0316.try14-opt2.pdb.gz costs 0 real_cost = 159.12 T0316.try14-opt2.gromacs0.pdb.gz costs 0 real_cost = 158.395 T0316.try14-opt1.pdb.gz costs 0 real_cost = 161.257 T0316.try14-opt1-scwrl.pdb.gz costs 0 real_cost = 157.582 T0316.try13-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 54.9209 T0316.try13-opt2.pdb.gz costs 0 real_cost = 55.9932 T0316.try13-opt2.gromacs0.pdb.gz costs 0 real_cost = 53.7138 T0316.try13-opt1.pdb.gz costs 0 real_cost = 54.2605 T0316.try13-opt1-scwrl.pdb.gz costs 0 real_cost = 51.966 T0316.try12-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 132.22 T0316.try12-opt2.pdb.gz costs 0 real_cost = 127.964 T0316.try12-opt2.gromacs0.pdb.gz costs 0 real_cost = 128.315 T0316.try12-opt1.pdb.gz costs 0 real_cost = 128.355 T0316.try12-opt1-scwrl.pdb.gz costs 0 real_cost = 128.368 T0316.try11-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 57.9117 T0316.try11-opt2.pdb.gz costs 0 real_cost = 59.4279 T0316.try11-opt2.gromacs0.pdb.gz costs 0 real_cost = 62.2695 T0316.try11-opt1.pdb.gz costs 0 real_cost = 60.0672 T0316.try11-opt1-scwrl.pdb.gz costs 0 real_cost = 61.0525 T0316.try10-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 157.91 T0316.try10-opt2.pdb.gz costs 0 real_cost = 160.79 T0316.try10-opt2.gromacs0.pdb.gz costs 0 real_cost = 154.655 T0316.try10-opt1.pdb.gz costs 0 real_cost = 160.83 T0316.try10-opt1-scwrl.pdb.gz costs 0 real_cost = 158.89 T0316.try1-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 128.077 T0316.try1-opt2.pdb.gz costs 0 real_cost = 130.445 T0316.try1-opt2.gromacs0.pdb.gz costs 0 real_cost = 131.289 T0316.try1-opt1.pdb.gz costs 0 real_cost = 131.664 T0316.try1-opt1-scwrl.pdb.gz costs 0 real_cost = 130.215 T0316.M1-A183-try2-opt2-D122-K269-try1-opt2-A130-I373-try4-opt2.pdb.gz costs 0 real_cost = 103.107 T0316.M1-A183-try2-opt2-D122-K269-try1-opt2-A130-I373-try4-opt2-proteinshop.pdb.gz costs 0 real_cost = 103.006 ../model5.ts-submitted costs 0 real_cost = 59.4081 ../model4.ts-submitted costs 0 real_cost = 49.7571 ../model3.ts-submitted costs 0 real_cost = 159.113 ../model2.ts-submitted costs 0 real_cost = 121.848 ../model1.ts-submitted costs 0 real_cost = 97.3169 align5 costs 0 real_cost = 213.792 align4 costs 0 real_cost = 352.42 align3 costs 0 real_cost = 250.368 align2 costs 0 real_cost = 272.286 align1 costs 0 real_cost = 230.649 T0316.try1-opt2.pdb costs 0 real_cost = 130.445 model5-scwrl costs 0 real_cost = 61.7491 model5.ts-submitted costs 0 real_cost = 59.4081 model4-scwrl costs 0 real_cost = 49.2825 model4.ts-submitted costs 0 real_cost = 49.7571 model3-scwrl costs 0 real_cost = 157.308 model3.ts-submitted costs 0 real_cost = 159.113 model2-scwrl costs 0 real_cost = 119.739 model2.ts-submitted costs 0 real_cost = 121.848 model1-scwrl costs 0 real_cost = 98.0752 model1.ts-submitted costs 0 real_cost = 97.3169 T0316_1.real.pdb costs 0 real_cost = -597.6 # command:CPU_time= 726.916 sec, elapsed time= 3105.8 sec) # command:rm -f sort.tmp /projects/compbio/bin/sorttbl real_cost < decoys/evaluate_1.rdb > sort.tmp mv -f sort.tmp decoys/evaluate_1.rdb mv -f decoys/evaluate_1.pretty decoys/evaluate_1.pretty.old mv: cannot stat `decoys/evaluate_1.pretty': No such file or directory make: [decoys/evaluate_1.pretty] Error 1 (ignored) /projects/compbio/experiments/protein-predict/casp7/scripts/prettyscore -terse -targpfx -decpoint < decoys/evaluate_1.rdb > decoys/evaluate_1.pretty rm -f decoys/evaluate_2.rdb sed -e s/XXX0000/T0316/ -e s/START_COL/1/ \ -e s/REAL_PDB/2hmaA/ \ -e s/_domain/_2/ \ -e s/read-pdb/read-pdb+servers/ \ -e 's/ReadConformPDBids/# ReadConformPDBids/' \ -e 's/# ReadConformPDB /ReadConformPDB /' \ -e 's/include COSTFCN.costfcn//' \ -e s/.COSTFCN// \ < /projects/compbio/experiments/protein-predict/casp7/starter-directory/evaluate.under \ | nice -2 /projects/compbio/programs/undertaker/undertaker # command:# Seed set to 1175124094 # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading monomeric-50pc.atoms # trans (non-proline) backbone unit: # CA= -2.2088 1.0126 -0.0031 # O= -0.1499 2.2440 0.0017 # 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= -0.1462 2.4515 0.0018 # O= -2.0272 0.9713 0.0022 # C= -0.8006 1.0755 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4659 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2099 1.0634 -0.0014 # O= -0.1233 2.2459 0.0075 # C= -0.6871 1.1518 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading monomeric-50pc.atoms have 448 chains in training database # Count of chains,residues,atoms: 448,112605,876684 # 109826 residues have no bad marker # 665 residues lack atoms needed to compute omega # 322 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 6 # HAS_OXT 325 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 523 # HAS_UNKNOWN_ATOMS 2 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 208 # NON_PLANAR_PEPTIDE 143 # BAD_PEPTIDE 1959 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-1332.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:CPU_time= 4.5983 sec, elapsed time= 4.64602 sec) # command:# Reading spots from monomeric-50pc-dry-5.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-5.hist # created burial cost function dry5 with radius 5 with spots at monomeric-50pc-dry-5.spot # command:# Reading spots from monomeric-50pc-wet-6.5.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-wet-6.5.hist # created burial cost function wet6.5 with radius 6.5 with spots at monomeric-50pc-wet-6.5.spot # command:# Reading spots from monomeric-50pc-dry-6.5.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-6.5.hist # created burial cost function dry6.5 with radius 6.5 with spots at monomeric-50pc-dry-6.5.spot # command:# Reading spots from monomeric-50pc-generic-6.5.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-generic-6.5.hist # created burial cost function gen6.5 with radius 6.5 with spots at monomeric-50pc-generic-6.5.spot # command:# Reading spots from near-backbone-center.spot # reading histogram from smoothed-near-backbone-2spot.hist # Reading spots from near-backbone-count.spot # created burial cost function near_backbone with radius 9.65 with spots at near-backbone-center.spot counting only near-backbone-count.spot # command:# Reading spots from way-back-center.spot # reading histogram from smoothed-way-back-2spot.hist # Reading spots from way-back-count.spot # created burial cost function way_back with radius 8.9 with spots at way-back-center.spot counting only way-back-count.spot # command:# Reading spots from monomeric-50pc-dry-8.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-8.hist # created burial cost function dry8 with radius 8 with spots at monomeric-50pc-dry-8.spot # command:# Reading spots from monomeric-50pc-dry-10.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-10.hist # created burial cost function dry10 with radius 10 with spots at monomeric-50pc-dry-10.spot # command:# Reading spots from monomeric-50pc-dry-12.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-12.hist # created burial cost function dry12 with radius 12 with spots at monomeric-50pc-dry-12.spot # command:# reading histogram from dunbrack-2191-alpha.hist # created alpha cost function alpha with offset 0 and 360 bins # command:# reading histogram from dunbrack-2191-alpha-1.hist # created alpha cost function alpha_prev with offset -1 and 360 bins # command:# Prefix for input files set to /projects/compbio/lib/alphabet/ # command:# Read 3 alphabets from alpha.alphabet # command:CPU_time= 4.66229 sec, elapsed time= 4.7239 sec) # command:# Prefix for input files set to # command:# Making conformation for sequence T0316 numbered 1 through 373 Created new target T0316 from T0316.a2m # command:# command:# No conformations to remove in PopConform # command:# cleared Id set # command:# command:# ReadConformPDB reading from PDB file T0316_2.real.pdb looking for model 1 Skipped atom 1651, because occupancy 2.0000000e-01 <= existing 0.200 in T0316_2.real.pdb Skipped atom 1653, because occupancy 0.300 <= existing 0.300 in T0316_2.real.pdb Skipped atom 1655, because occupancy 0.200 <= existing 0.200 in T0316_2.real.pdb Skipped atom 1657, because occupancy 0.300 <= existing 0.300 in T0316_2.real.pdb Skipped atom 1659, because occupancy 0.200 <= existing 0.200 in T0316_2.real.pdb Skipped atom 1661, because occupancy 0.300 <= existing 0.300 in T0316_2.real.pdb Skipped atom 1663, because occupancy 0.200 <= existing 0.200 in T0316_2.real.pdb Skipped atom 1665, because occupancy 0.300 <= existing 0.300 in T0316_2.real.pdb Skipped atom 1667, because occupancy 0.200 <= existing 0.200 in T0316_2.real.pdb Skipped atom 1669, because occupancy 0.300 <= existing 0.300 in T0316_2.real.pdb Skipped atom 1671, because occupancy 0.200 <= existing 0.200 in T0316_2.real.pdb Skipped atom 1673, because occupancy 0.300 <= existing 0.300 in T0316_2.real.pdb Skipped atom 1675, because occupancy 0.200 <= existing 0.200 in T0316_2.real.pdb Skipped atom 1677, because occupancy 0.300 <= existing 0.300 in T0316_2.real.pdb Skipped atom 1679, because occupancy 0.200 <= existing 0.200 in T0316_2.real.pdb Skipped atom 1681, because occupancy 0.300 <= existing 0.300 in T0316_2.real.pdb Skipped atom 1683, because occupancy 0.200 <= existing 0.200 in T0316_2.real.pdb Skipped atom 1685, because occupancy 0.300 <= existing 0.300 in T0316_2.real.pdb Skipped atom 1757, because occupancy 0.400 <= existing 0.600 in T0316_2.real.pdb Skipped atom 1759, because occupancy 0.400 <= existing 0.600 in T0316_2.real.pdb Skipped atom 1761, because occupancy 0.400 <= existing 0.600 in T0316_2.real.pdb Skipped atom 1763, because occupancy 0.400 <= existing 0.600 in T0316_2.real.pdb Skipped atom 1765, because occupancy 0.400 <= existing 0.600 in T0316_2.real.pdb Skipped atom 1767, because occupancy 0.400 <= existing 0.600 in T0316_2.real.pdb Skipped atom 1769, because occupancy 0.400 <= existing 0.600 in T0316_2.real.pdb Skipped atom 1771, because occupancy 0.400 <= existing 0.600 in T0316_2.real.pdb Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1878, because occupancy 0.400 <= existing 0.600 in T0316_2.real.pdb Skipped atom 1880, because occupancy 0.400 <= existing 0.600 in T0316_2.real.pdb Skipped atom 1882, because occupancy 0.400 <= existing 0.600 in T0316_2.real.pdb Skipped atom 1884, because occupancy 0.400 <= existing 0.600 in T0316_2.real.pdb Skipped atom 1886, because occupancy 0.400 <= existing 0.600 in T0316_2.real.pdb Skipped atom 1888, because occupancy 0.400 <= existing 0.600 in T0316_2.real.pdb Skipped atom 1890, because occupancy 0.400 <= existing 0.600 in T0316_2.real.pdb Skipped atom 1892, because occupancy 0.400 <= existing 0.600 in T0316_2.real.pdb Skipped atom 1894, because occupancy 0.400 <= existing 0.600 in T0316_2.real.pdb Skipped atom 1896, because occupancy 0.400 <= existing 0.600 in T0316_2.real.pdb Skipped atom 1898, because occupancy 0.400 <= existing 0.600 in T0316_2.real.pdb Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1956, because occupancy 0.500 <= existing 0.500 in T0316_2.real.pdb Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1958, because occupancy 0.500 <= existing 0.500 in T0316_2.real.pdb Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1960, because occupancy 0.500 <= existing 0.500 in T0316_2.real.pdb Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1962, because occupancy 0.500 <= existing 0.500 in T0316_2.real.pdb Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1964, because occupancy 0.500 <= existing 0.500 in T0316_2.real.pdb Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1966, because occupancy 0.500 <= existing 0.500 in T0316_2.real.pdb Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1970, because occupancy 0.500 <= existing 0.500 in T0316_2.real.pdb Skipped atom 2275, because occupancy 0.500 <= existing 0.500 in T0316_2.real.pdb Skipped atom 2277, because occupancy 0.500 <= existing 0.500 in T0316_2.real.pdb Skipped atom 2279, because occupancy 0.500 <= existing 0.500 in T0316_2.real.pdb Skipped atom 2281, because occupancy 0.500 <= existing 0.500 in T0316_2.real.pdb Skipped atom 2283, because occupancy 0.500 <= existing 0.500 in T0316_2.real.pdb Skipped atom 2285, because occupancy 0.500 <= existing 0.500 in T0316_2.real.pdb Skipped atom 2287, because occupancy 0.500 <= existing 0.500 in T0316_2.real.pdb Skipped atom 2289, because occupancy 0.500 <= existing 0.500 in T0316_2.real.pdb # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # command:# Saving current conformation as real # command:# Prefix for output files set to decoys/ # command:# SetRealCost created real_cost = # ( 50 * real_hbond + 50 * real_hbond_u + 50 * decoy_hbond + 50 * decoy_hbond_u + 10 * real_NO_hbond + 10 * real_NO_hbond_u + 10 * decoy_NO_hbond + 10 * decoy_NO_hbond_u + 10 * knot + 200 * clens + 0 * rmsd + 35 * log_rmsd + 0 * rmsd_ca + 30 * log_rmsd_ca + 1 * GDT + 1 * smooth_GDT + 0.2 * missing_atoms ) # command:# SetCost created cost = # ) # command:CPU_time= 6.52301 sec, elapsed time= 6.59858 sec) # command:# Prefix for input files set to # command:# ReadConformPDB reading from PDB file model1.ts-submitted looking for model 1 # choosing archetypes in rotamer library # Found a chain break before 371 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -22.5 # GDT_score(maxd=8,maxw=2.9)= -20.3659 # GDT_score(maxd=8,maxw=3.2)= -19.5692 # GDT_score(maxd=8,maxw=3.5)= -18.8562 # GDT_score(maxd=10,maxw=3.8)= -21.394 # GDT_score(maxd=10,maxw=4)= -20.8777 # GDT_score(maxd=10,maxw=4.2)= -20.3597 # GDT_score(maxd=12,maxw=4.3)= -22.9785 # GDT_score(maxd=12,maxw=4.5)= -22.4017 # GDT_score(maxd=12,maxw=4.7)= -21.874 # GDT_score(maxd=14,maxw=5.2)= -23.0584 # GDT_score(maxd=14,maxw=5.5)= -22.2252 # command:# Prefix for output files set to # command:superimposing iter= 0 total_weight= 941.000 rmsd (weighted)= 15.883 (unweighted)= 47.503 superimposing iter= 1 total_weight= 1261.830 rmsd (weighted)= 10.880 (unweighted)= 45.907 superimposing iter= 2 total_weight= 722.969 rmsd (weighted)= 10.005 (unweighted)= 45.230 superimposing iter= 3 total_weight= 639.846 rmsd (weighted)= 9.791 (unweighted)= 44.751 superimposing iter= 4 total_weight= 634.497 rmsd (weighted)= 9.617 (unweighted)= 44.445 superimposing iter= 5 total_weight= 643.101 rmsd (weighted)= 9.372 (unweighted)= 44.401 # command:# Prefix for output files set to decoys/ # command:# request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_625556474.pdb -s /var/tmp/to_scwrl_625556474.seq -o /var/tmp/from_scwrl_625556474.pdb > /var/tmp/scwrl_625556474.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_625556474.pdb # conformation set from SCWRL output # command:# naming current conformation model1-scwrl # command:# ReadConformPDB reading from PDB file model2.ts-submitted looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -19.375 # GDT_score(maxd=8,maxw=2.9)= -16.187 # GDT_score(maxd=8,maxw=3.2)= -15.6069 # GDT_score(maxd=8,maxw=3.5)= -15.1263 # GDT_score(maxd=10,maxw=3.8)= -18.0077 # GDT_score(maxd=10,maxw=4)= -17.6073 # GDT_score(maxd=10,maxw=4.2)= -17.2451 # GDT_score(maxd=12,maxw=4.3)= -20.1621 # GDT_score(maxd=12,maxw=4.5)= -19.7105 # GDT_score(maxd=12,maxw=4.7)= -19.269 # GDT_score(maxd=14,maxw=5.2)= -20.946 # GDT_score(maxd=14,maxw=5.5)= -20.2718 # command:# request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1614679195.pdb -s /var/tmp/to_scwrl_1614679195.seq -o /var/tmp/from_scwrl_1614679195.pdb > /var/tmp/scwrl_1614679195.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1614679195.pdb # conformation set from SCWRL output # command:# naming current conformation model2-scwrl # command:# ReadConformPDB reading from PDB file model3.ts-submitted looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -19.0625 # GDT_score(maxd=8,maxw=2.9)= -16.3637 # GDT_score(maxd=8,maxw=3.2)= -15.7671 # GDT_score(maxd=8,maxw=3.5)= -15.2728 # GDT_score(maxd=10,maxw=3.8)= -18.1082 # GDT_score(maxd=10,maxw=4)= -17.7028 # GDT_score(maxd=10,maxw=4.2)= -17.336 # GDT_score(maxd=12,maxw=4.3)= -20.2875 # GDT_score(maxd=12,maxw=4.5)= -19.8303 # GDT_score(maxd=12,maxw=4.7)= -19.3976 # GDT_score(maxd=14,maxw=5.2)= -21.0541 # GDT_score(maxd=14,maxw=5.5)= -20.3779 # command:# request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2087782780.pdb -s /var/tmp/to_scwrl_2087782780.seq -o /var/tmp/from_scwrl_2087782780.pdb > /var/tmp/scwrl_2087782780.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2087782780.pdb # conformation set from SCWRL output # command:# naming current conformation model3-scwrl # command:# ReadConformPDB reading from PDB file model4.ts-submitted looking for model 1 # Found a chain break before 355 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -19.0625 # GDT_score(maxd=8,maxw=2.9)= -17.909 # GDT_score(maxd=8,maxw=3.2)= -16.816 # GDT_score(maxd=8,maxw=3.5)= -15.8378 # GDT_score(maxd=10,maxw=3.8)= -17.9104 # GDT_score(maxd=10,maxw=4)= -17.2649 # GDT_score(maxd=10,maxw=4.2)= -16.6808 # GDT_score(maxd=12,maxw=4.3)= -19.0008 # GDT_score(maxd=12,maxw=4.5)= -18.3786 # GDT_score(maxd=12,maxw=4.7)= -17.8093 # GDT_score(maxd=14,maxw=5.2)= -18.763 # GDT_score(maxd=14,maxw=5.5)= -18.0123 # command:# request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_68504077.pdb -s /var/tmp/to_scwrl_68504077.seq -o /var/tmp/from_scwrl_68504077.pdb > /var/tmp/scwrl_68504077.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_68504077.pdb # conformation set from SCWRL output # command:# naming current conformation model4-scwrl # command:# ReadConformPDB reading from PDB file model5.ts-submitted looking for model 1 # Found a chain break before 355 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -21.875 # GDT_score(maxd=8,maxw=2.9)= -19.3049 # GDT_score(maxd=8,maxw=3.2)= -18.3946 # GDT_score(maxd=8,maxw=3.5)= -17.5204 # GDT_score(maxd=10,maxw=3.8)= -19.7981 # GDT_score(maxd=10,maxw=4)= -19.1506 # GDT_score(maxd=10,maxw=4.2)= -18.5362 # GDT_score(maxd=12,maxw=4.3)= -20.8911 # GDT_score(maxd=12,maxw=4.5)= -20.2404 # GDT_score(maxd=12,maxw=4.7)= -19.6005 # GDT_score(maxd=14,maxw=5.2)= -20.5009 # GDT_score(maxd=14,maxw=5.5)= -19.6554 # command:# request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_724379441.pdb -s /var/tmp/to_scwrl_724379441.seq -o /var/tmp/from_scwrl_724379441.pdb > /var/tmp/scwrl_724379441.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_724379441.pdb # conformation set from SCWRL output # command:# naming current conformation model5-scwrl # command:# Prefix for input files set to decoys/ # command:# ReadConformPDB reading from PDB file T0316.try1-opt2.pdb looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -16.25 # GDT_score(maxd=8,maxw=2.9)= -14.575 # GDT_score(maxd=8,maxw=3.2)= -13.7945 # GDT_score(maxd=8,maxw=3.5)= -13.1479 # GDT_score(maxd=10,maxw=3.8)= -15.3658 # GDT_score(maxd=10,maxw=4)= -14.8561 # GDT_score(maxd=10,maxw=4.2)= -14.3868 # GDT_score(maxd=12,maxw=4.3)= -17.0351 # GDT_score(maxd=12,maxw=4.5)= -16.5002 # GDT_score(maxd=12,maxw=4.7)= -16.0108 # GDT_score(maxd=14,maxw=5.2)= -17.4677 # GDT_score(maxd=14,maxw=5.5)= -16.7876 # command:# Prefix for output files set to # command:superimposing iter= 0 total_weight= 941.000 rmsd (weighted)= 15.165 (unweighted)= 64.802 superimposing iter= 1 total_weight= 1217.123 rmsd (weighted)= 10.574 (unweighted)= 63.155 superimposing iter= 2 total_weight= 749.825 rmsd (weighted)= 9.489 (unweighted)= 62.021 superimposing iter= 3 total_weight= 676.412 rmsd (weighted)= 8.999 (unweighted)= 61.303 superimposing iter= 4 total_weight= 654.079 rmsd (weighted)= 8.699 (unweighted)= 60.920 superimposing iter= 5 total_weight= 645.390 rmsd (weighted)= 8.481 (unweighted)= 60.762 # command:# Prefix for output files set to decoys/ # command:# Prefix for input files set to # command:# ReadConformPDB reading from PDB file T0316.undertaker-align.pdb looking for model 1 WARNING: atoms too close: (T0316)M38.C and (T0316)D45.C only 0.000 apart, marking (T0316)D45.C as missing WARNING: atoms too close: (T0316)K39.N and (T0316)E46.N only 0.000 apart, marking (T0316)K39.N as missing WARNING: atoms too close: (T0316)K39.CA and (T0316)E46.CA only 0.000 apart, marking (T0316)K39.CA as missing WARNING: atoms too close: (T0316)G48.C and (T0316)T51.C only 0.000 apart, marking (T0316)T51.C as missing WARNING: atoms too close: (T0316)V49.N and (T0316)A52.N only 0.000 apart, marking (T0316)V49.N as missing WARNING: atoms too close: (T0316)V49.CA and (T0316)A52.CA only 0.000 apart, marking (T0316)V49.CA as missing WARNING: atoms too close: (T0316)I107.C and (T0316)K108.C only 0.000 apart, marking (T0316)K108.C as missing WARNING: atoms too close: (T0316)K108.N and (T0316)F109.N only 0.000 apart, marking (T0316)K108.N as missing WARNING: atoms too close: (T0316)K108.CA and (T0316)F109.CA only 0.000 apart, marking (T0316)K108.CA as missing WARNING: atoms too close: (T0316)A130.C and (T0316)A133.C only 0.000 apart, marking (T0316)A133.C as missing WARNING: atoms too close: (T0316)R131.N and (T0316)R134.N only 0.000 apart, marking (T0316)R131.N as missing WARNING: atoms too close: (T0316)R131.CA and (T0316)R134.CA only 0.000 apart, marking (T0316)R131.CA as missing WARNING: atoms too close: (T0316)V146.C and (T0316)N148.C only 0.000 apart, marking (T0316)N148.C as missing WARNING: atoms too close: (T0316)D147.N and (T0316)G149.N only 0.000 apart, marking (T0316)D147.N as missing WARNING: atoms too close: (T0316)D147.CA and (T0316)G149.CA only 0.000 apart, marking (T0316)D147.CA as missing WARNING: atoms too close: (T0316)G250.C and (T0316)A258.C only 0.000 apart, marking (T0316)A258.C as missing WARNING: atoms too close: (T0316)G251.N and (T0316)P259.N only 0.000 apart, marking (T0316)G251.N as missing WARNING: atoms too close: (T0316)G251.CA and (T0316)P259.CA only 0.000 apart, marking (T0316)G251.CA as missing WARNING: atoms too close: (T0316)E298.C and (T0316)M299.C only 0.000 apart, marking (T0316)M299.C as missing WARNING: atoms too close: (T0316)M299.N and (T0316)P300.N only 0.000 apart, marking (T0316)M299.N as missing WARNING: atoms too close: (T0316)M299.CA and (T0316)P300.CA only 0.000 apart, marking (T0316)M299.CA as missing # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # command:# naming current conformation align1 # command:# fraction of real conformation used = 0.8 # GDT_score = -17.8125 # GDT_score(maxd=8,maxw=2.9)= -15.8635 # GDT_score(maxd=8,maxw=3.2)= -15.0047 # GDT_score(maxd=8,maxw=3.5)= -14.2543 # GDT_score(maxd=10,maxw=3.8)= -16.5351 # GDT_score(maxd=10,maxw=4)= -16.0208 # GDT_score(maxd=10,maxw=4.2)= -15.504 # GDT_score(maxd=12,maxw=4.3)= -18.1267 # GDT_score(maxd=12,maxw=4.5)= -17.5433 # GDT_score(maxd=12,maxw=4.7)= -17.0095 # GDT_score(maxd=14,maxw=5.2)= -18.306 # GDT_score(maxd=14,maxw=5.5)= -17.512 # command:# ReadConformPDB reading from PDB file T0316.undertaker-align.pdb looking for model 2 WARNING: atoms too close: (T0316)M38.C and (T0316)D43.C only 0.000 apart, marking (T0316)D43.C as missing WARNING: atoms too close: (T0316)K39.N and (T0316)T44.N only 0.000 apart, marking (T0316)K39.N as missing WARNING: atoms too close: (T0316)K39.CA and (T0316)T44.CA only 0.000 apart, marking (T0316)K39.CA as missing WARNING: atoms too close: (T0316)C50.C and (T0316)T51.C only 0.000 apart, marking (T0316)T51.C as missing WARNING: atoms too close: (T0316)T51.N and (T0316)A52.N only 0.000 apart, marking (T0316)T51.N as missing WARNING: atoms too close: (T0316)T51.CA and (T0316)A52.CA only 0.000 apart, marking (T0316)T51.CA as missing WARNING: atoms too close: (T0316)E76.C and (T0316)F87.C only 0.000 apart, marking (T0316)F87.C as missing WARNING: atoms too close: (T0316)K77.N and (T0316)L88.N only 0.000 apart, marking (T0316)K77.N as missing WARNING: atoms too close: (T0316)K77.CA and (T0316)L88.CA only 0.000 apart, marking (T0316)K77.CA as missing WARNING: atoms too close: (T0316)E106.C and (T0316)I107.C only 0.000 apart, marking (T0316)I107.C as missing WARNING: atoms too close: (T0316)I107.N and (T0316)K108.N only 0.000 apart, marking (T0316)I107.N as missing WARNING: atoms too close: (T0316)I107.CA and (T0316)K108.CA only 0.000 apart, marking (T0316)I107.CA as missing WARNING: atoms too close: (T0316)D135.C and (T0316)Q152.C only 0.000 apart, marking (T0316)Q152.C as missing WARNING: atoms too close: (T0316)E136.N and (T0316)T153.N only 0.000 apart, marking (T0316)E136.N as missing WARNING: atoms too close: (T0316)E136.CA and (T0316)T153.CA only 0.000 apart, marking (T0316)E136.CA as missing WARNING: atoms too close: (T0316)M223.C and (T0316)T286.C only 0.000 apart, marking (T0316)T286.C as missing WARNING: atoms too close: (T0316)T224.N and (T0316)S287.N only 0.000 apart, marking (T0316)T224.N as missing WARNING: atoms too close: (T0316)T224.CA and (T0316)S287.CA only 0.000 apart, marking (T0316)T224.CA as missing WARNING: atoms too close: (T0316)F311.C and (T0316)V324.C only 0.000 apart, marking (T0316)V324.C as missing WARNING: atoms too close: (T0316)R312.N and (T0316)K325.N only 0.000 apart, marking (T0316)R312.N as missing WARNING: atoms too close: (T0316)R312.CA and (T0316)K325.CA only 0.000 apart, marking (T0316)R312.CA as missing # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # command:# naming current conformation align2 # command:# fraction of real conformation used = 0.3 # GDT_score = -16.5625 # GDT_score(maxd=8,maxw=2.9)= -16.4858 # GDT_score(maxd=8,maxw=3.2)= -15.8175 # GDT_score(maxd=8,maxw=3.5)= -15.1653 # GDT_score(maxd=10,maxw=3.8)= -16.0427 # GDT_score(maxd=10,maxw=4)= -15.6111 # GDT_score(maxd=10,maxw=4.2)= -15.1653 # GDT_score(maxd=12,maxw=4.3)= -16.1183 # GDT_score(maxd=12,maxw=4.5)= -15.6797 # GDT_score(maxd=12,maxw=4.7)= -15.2785 # GDT_score(maxd=14,maxw=5.2)= -15.2657 # GDT_score(maxd=14,maxw=5.5)= -14.7739 # command:# ReadConformPDB reading from PDB file T0316.undertaker-align.pdb looking for model 3 WARNING: atoms too close: (T0316)M38.C and (T0316)D45.C only 0.000 apart, marking (T0316)D45.C as missing WARNING: atoms too close: (T0316)K39.N and (T0316)E46.N only 0.000 apart, marking (T0316)K39.N as missing WARNING: atoms too close: (T0316)K39.CA and (T0316)E46.CA only 0.000 apart, marking (T0316)K39.CA as missing WARNING: atoms too close: (T0316)C50.C and (T0316)T51.C only 0.000 apart, marking (T0316)T51.C as missing WARNING: atoms too close: (T0316)T51.N and (T0316)A52.N only 0.000 apart, marking (T0316)T51.N as missing WARNING: atoms too close: (T0316)T51.CA and (T0316)A52.CA only 0.000 apart, marking (T0316)T51.CA as missing WARNING: atoms too close: (T0316)F87.C and (T0316)C103.C only 0.000 apart, marking (T0316)C103.C as missing WARNING: atoms too close: (T0316)L88.N and (T0316)N104.N only 0.000 apart, marking (T0316)L88.N as missing WARNING: atoms too close: (T0316)L88.CA and (T0316)N104.CA only 0.000 apart, marking (T0316)L88.CA as missing WARNING: atoms too close: (T0316)K108.C and (T0316)F109.C only 0.000 apart, marking (T0316)F109.C as missing WARNING: atoms too close: (T0316)F109.N and (T0316)K110.N only 0.000 apart, marking (T0316)F109.N as missing WARNING: atoms too close: (T0316)F109.CA and (T0316)K110.CA only 0.000 apart, marking (T0316)F109.CA as missing WARNING: atoms too close: (T0316)A130.C and (T0316)A133.C only 0.000 apart, marking (T0316)A133.C as missing WARNING: atoms too close: (T0316)R131.N and (T0316)R134.N only 0.000 apart, marking (T0316)R131.N as missing WARNING: atoms too close: (T0316)R131.CA and (T0316)R134.CA only 0.000 apart, marking (T0316)R131.CA as missing WARNING: atoms too close: (T0316)E162.C and (T0316)Q165.C only 0.000 apart, marking (T0316)Q165.C as missing WARNING: atoms too close: (T0316)Q163.N and (T0316)K166.N only 0.000 apart, marking (T0316)Q163.N as missing WARNING: atoms too close: (T0316)Q163.CA and (T0316)K166.CA only 0.000 apart, marking (T0316)Q163.CA as missing WARNING: atoms too close: (T0316)N206.C and (T0316)F207.C only 0.000 apart, marking (T0316)F207.C as missing WARNING: atoms too close: (T0316)F207.N and (T0316)K208.N only 0.000 apart, marking (T0316)F207.N as missing WARNING: atoms too close: (T0316)F207.CA and (T0316)K208.CA only 0.000 apart, marking (T0316)F207.CA as missing # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # command:# naming current conformation align3 # command:# ReadConformPDB reading from PDB file T0316.undertaker-align.pdb looking for model 4 WARNING: atoms too close: (T0316)M38.C and (T0316)D45.C only 0.000 apart, marking (T0316)D45.C as missing WARNING: atoms too close: (T0316)K39.N and (T0316)E46.N only 0.000 apart, marking (T0316)K39.N as missing WARNING: atoms too close: (T0316)K39.CA and (T0316)E46.CA only 0.000 apart, marking (T0316)K39.CA as missing WARNING: atoms too close: (T0316)C50.C and (T0316)T51.C only 0.000 apart, marking (T0316)T51.C as missing WARNING: atoms too close: (T0316)T51.N and (T0316)A52.N only 0.000 apart, marking (T0316)T51.N as missing WARNING: atoms too close: (T0316)T51.CA and (T0316)A52.CA only 0.000 apart, marking (T0316)T51.CA as missing WARNING: atoms too close: (T0316)Y86.C and (T0316)M102.C only 0.000 apart, marking (T0316)M102.C as missing WARNING: atoms too close: (T0316)F87.N and (T0316)C103.N only 0.000 apart, marking (T0316)F87.N as missing WARNING: atoms too close: (T0316)F87.CA and (T0316)C103.CA only 0.000 apart, marking (T0316)F87.CA as missing WARNING: atoms too close: (T0316)E106.C and (T0316)I107.C only 0.000 apart, marking (T0316)I107.C as missing WARNING: atoms too close: (T0316)I107.N and (T0316)K108.N only 0.000 apart, marking (T0316)I107.N as missing WARNING: atoms too close: (T0316)I107.CA and (T0316)K108.CA only 0.000 apart, marking (T0316)I107.CA as missing WARNING: atoms too close: (T0316)V124.C and (T0316)T126.C only 0.000 apart, marking (T0316)T126.C as missing WARNING: atoms too close: (T0316)A125.N and (T0316)G127.N only 0.000 apart, marking (T0316)A125.N as missing WARNING: atoms too close: (T0316)A125.CA and (T0316)G127.CA only 0.000 apart, marking (T0316)A125.CA as missing WARNING: atoms too close: (T0316)D135.C and (T0316)T139.C only 0.000 apart, marking (T0316)T139.C as missing WARNING: atoms too close: (T0316)E136.N and (T0316)V140.N only 0.000 apart, marking (T0316)E136.N as missing WARNING: atoms too close: (T0316)E136.CA and (T0316)V140.CA only 0.000 apart, marking (T0316)E136.CA as missing WARNING: atoms too close: (T0316)K150.C and (T0316)T167.C only 0.000 apart, marking (T0316)T167.C as missing WARNING: atoms too close: (T0316)D151.N and (T0316)M168.N only 0.000 apart, marking (T0316)D151.N as missing WARNING: atoms too close: (T0316)D151.CA and (T0316)M168.CA only 0.000 apart, marking (T0316)D151.CA as missing WARNING: atoms too close: (T0316)I199.C and (T0316)F201.C only 0.000 apart, marking (T0316)F201.C as missing WARNING: atoms too close: (T0316)C200.N and (T0316)I202.N only 0.000 apart, marking (T0316)C200.N as missing WARNING: atoms too close: (T0316)C200.CA and (T0316)I202.CA only 0.000 apart, marking (T0316)C200.CA as missing WARNING: atoms too close: (T0316)Y214.C and (T0316)S282.C only 0.000 apart, marking (T0316)S282.C as missing WARNING: atoms too close: (T0316)L215.N and (T0316)L283.N only 0.000 apart, marking (T0316)L215.N as missing WARNING: atoms too close: (T0316)L215.CA and (T0316)L283.CA only 0.000 apart, marking (T0316)L215.CA as missing # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # command:# naming current conformation align4 # command:# ReadConformPDB reading from PDB file T0316.undertaker-align.pdb looking for model 5 WARNING: atoms too close: (T0316)M38.C and (T0316)D43.C only 0.000 apart, marking (T0316)D43.C as missing WARNING: atoms too close: (T0316)K39.N and (T0316)T44.N only 0.000 apart, marking (T0316)K39.N as missing WARNING: atoms too close: (T0316)K39.CA and (T0316)T44.CA only 0.000 apart, marking (T0316)K39.CA as missing WARNING: atoms too close: (T0316)C50.C and (T0316)T51.C only 0.000 apart, marking (T0316)T51.C as missing WARNING: atoms too close: (T0316)T51.N and (T0316)A52.N only 0.000 apart, marking (T0316)T51.N as missing WARNING: atoms too close: (T0316)T51.CA and (T0316)A52.CA only 0.000 apart, marking (T0316)T51.CA as missing WARNING: atoms too close: (T0316)E76.C and (T0316)Y91.C only 0.000 apart, marking (T0316)Y91.C as missing WARNING: atoms too close: (T0316)K77.N and (T0316)R92.N only 0.000 apart, marking (T0316)K77.N as missing WARNING: atoms too close: (T0316)K77.CA and (T0316)R92.CA only 0.000 apart, marking (T0316)K77.CA as missing WARNING: atoms too close: (T0316)C103.C and (T0316)K108.C only 0.000 apart, marking (T0316)K108.C as missing WARNING: atoms too close: (T0316)N104.N and (T0316)F109.N only 0.000 apart, marking (T0316)N104.N as missing WARNING: atoms too close: (T0316)N104.CA and (T0316)F109.CA only 0.000 apart, marking (T0316)N104.CA as missing WARNING: atoms too close: (T0316)G120.C and (T0316)A121.C only 0.000 apart, marking (T0316)A121.C as missing WARNING: atoms too close: (T0316)A121.N and (T0316)D122.N only 0.000 apart, marking (T0316)A121.N as missing WARNING: atoms too close: (T0316)A121.CA and (T0316)D122.CA only 0.000 apart, marking (T0316)A121.CA as missing WARNING: atoms too close: (T0316)D135.C and (T0316)E136.C only 0.000 apart, marking (T0316)E136.C as missing WARNING: atoms too close: (T0316)E136.N and (T0316)D137.N only 0.000 apart, marking (T0316)E136.N as missing WARNING: atoms too close: (T0316)E136.CA and (T0316)D137.CA only 0.000 apart, marking (T0316)E136.CA as missing WARNING: atoms too close: (T0316)K150.C and (T0316)Q152.C only 0.000 apart, marking (T0316)Q152.C as missing WARNING: atoms too close: (T0316)D151.N and (T0316)T153.N only 0.000 apart, marking (T0316)D151.N as missing WARNING: atoms too close: (T0316)D151.CA and (T0316)T153.CA only 0.000 apart, marking (T0316)D151.CA as missing WARNING: atoms too close: (T0316)W260.C and (T0316)F311.C only 0.000 apart, marking (T0316)F311.C as missing WARNING: atoms too close: (T0316)F261.N and (T0316)R312.N only 0.000 apart, marking (T0316)F261.N as missing WARNING: atoms too close: (T0316)F261.CA and (T0316)R312.CA only 0.000 apart, marking (T0316)F261.CA as missing # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # command:# naming current conformation align5 # command:# Prefix for input files set to decoys/ # command:# reading script from file read-pdb+servers.under # ReadConformPDB reading from PDB file ../model1.ts-submitted looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ../model2.ts-submitted looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ../model3.ts-submitted looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ../model4.ts-submitted looking for model 1 # Found a chain break before 355 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ../model5.ts-submitted looking for model 1 # Found a chain break before 355 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.M1-A183-try2-opt2-D122-K269-try1-opt2-A130-I373-try4-opt2-proteinshop.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.M1-A183-try2-opt2-D122-K269-try1-opt2-A130-I373-try4-opt2.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try1-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 354 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try1-opt1.pdb.gz looking for model 1 # Found a chain break before 354 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try1-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 362 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try1-opt2.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try1-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try10-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try10-opt1.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try10-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 352 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try10-opt2.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try10-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try11-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 346 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try11-opt1.pdb.gz looking for model 1 # Found a chain break before 346 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try11-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 358 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try11-opt2.pdb.gz looking for model 1 # Found a chain break before 355 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try11-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 355 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try12-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try12-opt1.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try12-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try12-opt2.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try12-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try13-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 349 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try13-opt1.pdb.gz looking for model 1 # Found a chain break before 349 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try13-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 350 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try13-opt2.pdb.gz looking for model 1 # Found a chain break before 349 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try13-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 349 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try14-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try14-opt1.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try14-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 345 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try14-opt2.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try14-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try15-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try15-opt1.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try15-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 369 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try15-opt2.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try15-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try16-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 352 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try16-opt1.pdb.gz looking for model 1 # Found a chain break before 352 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try16-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try16-opt2.pdb.gz looking for model 1 # Found a chain break before 367 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try16-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 367 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try17-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 352 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try17-opt1.pdb.gz looking for model 1 # Found a chain break before 352 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try17-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 352 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try17-opt2.pdb.gz looking for model 1 # Found a chain break before 369 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try17-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 369 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try18-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try18-opt1.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try18-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 343 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try18-opt2.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try18-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try19-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try19-opt1.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try19-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 343 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try19-opt2.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try19-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try2-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 340 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try2-opt1.pdb.gz looking for model 1 # Found a chain break before 340 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try2-opt2-M1-A183-try6-opt2-A130-I373.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try2-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 347 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try2-opt2.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try2-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try20-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try20-opt1.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try20-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 356 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try20-opt2.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try20-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try21-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try21-opt1.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try21-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 356 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try21-opt2.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try21-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try3-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try3-opt1.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try3-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 362 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try3-opt2.pdb.gz looking for model 1 # Found a chain break before 369 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try3-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 369 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try4-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 352 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try4-opt1.pdb.gz looking for model 1 # Found a chain break before 352 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try4-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 347 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try4-opt2.pdb.gz looking for model 1 # Found a chain break before 367 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try4-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 367 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try5-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 363 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try5-opt1.pdb.gz looking for model 1 # Found a chain break before 363 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try5-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 349 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try5-opt2.pdb.gz looking for model 1 # Found a chain break before 363 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try5-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 363 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try6-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 364 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try6-opt1.pdb.gz looking for model 1 # Found a chain break before 364 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try6-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 356 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try6-opt2.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try6-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try7-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 345 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try7-opt1.pdb.gz looking for model 1 # Found a chain break before 345 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try7-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 345 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try7-opt2.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try7-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try8-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try8-opt1.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try8-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 345 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try8-opt2.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try8-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try9-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 349 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try9-opt1.pdb.gz looking for model 1 # Found a chain break before 349 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try9-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 341 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try9-opt2.pdb.gz looking for model 1 # Found a chain break before 355 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try9-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 355 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file chimera1.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file make-chimera.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_259791001.pdb -s /var/tmp/to_scwrl_259791001.seq -o /var/tmp/from_scwrl_259791001.pdb > /var/tmp/scwrl_259791001.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_259791001.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_POPULUS_TS1-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_956033340.pdb -s /var/tmp/to_scwrl_956033340.seq -o /var/tmp/from_scwrl_956033340.pdb > /var/tmp/scwrl_956033340.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_956033340.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_POPULUS_TS2-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1901652369.pdb -s /var/tmp/to_scwrl_1901652369.seq -o /var/tmp/from_scwrl_1901652369.pdb > /var/tmp/scwrl_1901652369.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1901652369.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_POPULUS_TS3-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1691887398.pdb -s /var/tmp/to_scwrl_1691887398.seq -o /var/tmp/from_scwrl_1691887398.pdb > /var/tmp/scwrl_1691887398.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1691887398.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_POPULUS_TS4-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_327667519.pdb -s /var/tmp/to_scwrl_327667519.seq -o /var/tmp/from_scwrl_327667519.pdb > /var/tmp/scwrl_327667519.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_327667519.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_POPULUS_TS5-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_168862666.pdb -s /var/tmp/to_scwrl_168862666.seq -o /var/tmp/from_scwrl_168862666.pdb > /var/tmp/scwrl_168862666.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_168862666.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_RECOM_TS1-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1220246746.pdb -s /var/tmp/to_scwrl_1220246746.seq -o /var/tmp/from_scwrl_1220246746.pdb > /var/tmp/scwrl_1220246746.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1220246746.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_RECOM_TS2-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1320721107.pdb -s /var/tmp/to_scwrl_1320721107.seq -o /var/tmp/from_scwrl_1320721107.pdb > /var/tmp/scwrl_1320721107.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1320721107.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_RECOM_TS3-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1207110143.pdb -s /var/tmp/to_scwrl_1207110143.seq -o /var/tmp/from_scwrl_1207110143.pdb > /var/tmp/scwrl_1207110143.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1207110143.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_RECOM_TS4-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_469047413.pdb -s /var/tmp/to_scwrl_469047413.seq -o /var/tmp/from_scwrl_469047413.pdb > /var/tmp/scwrl_469047413.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_469047413.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_RECOM_TS5-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_731568774.pdb -s /var/tmp/to_scwrl_731568774.seq -o /var/tmp/from_scwrl_731568774.pdb > /var/tmp/scwrl_731568774.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_731568774.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_TS1-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_817871562.pdb -s /var/tmp/to_scwrl_817871562.seq -o /var/tmp/from_scwrl_817871562.pdb > /var/tmp/scwrl_817871562.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_817871562.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_TS2-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1091225774.pdb -s /var/tmp/to_scwrl_1091225774.seq -o /var/tmp/from_scwrl_1091225774.pdb > /var/tmp/scwrl_1091225774.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1091225774.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_TS3-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_146152994.pdb -s /var/tmp/to_scwrl_146152994.seq -o /var/tmp/from_scwrl_146152994.pdb > /var/tmp/scwrl_146152994.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_146152994.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_TS4-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_891501276.pdb -s /var/tmp/to_scwrl_891501276.seq -o /var/tmp/from_scwrl_891501276.pdb > /var/tmp/scwrl_891501276.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_891501276.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_TS5-scwrl # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # Found a chain break before 353 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1073801282.pdb -s /var/tmp/to_scwrl_1073801282.seq -o /var/tmp/from_scwrl_1073801282.pdb > /var/tmp/scwrl_1073801282.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1073801282.pdb # conformation set from SCWRL output # naming current conformation 3Dpro_TS1-scwrl # ReadConformPDB reading from PDB file servers/3Dpro_TS2.pdb.gz looking for model 1 # Found a chain break before 372 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1176416733.pdb -s /var/tmp/to_scwrl_1176416733.seq -o /var/tmp/from_scwrl_1176416733.pdb > /var/tmp/scwrl_1176416733.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1176416733.pdb # conformation set from SCWRL output # naming current conformation 3Dpro_TS2-scwrl # ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1 # Found a chain break before 370 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1493389902.pdb -s /var/tmp/to_scwrl_1493389902.seq -o /var/tmp/from_scwrl_1493389902.pdb > /var/tmp/scwrl_1493389902.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1493389902.pdb # conformation set from SCWRL output # naming current conformation 3Dpro_TS3-scwrl # ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1 # Found a chain break before 338 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_18830371.pdb -s /var/tmp/to_scwrl_18830371.seq -o /var/tmp/from_scwrl_18830371.pdb > /var/tmp/scwrl_18830371.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_18830371.pdb # conformation set from SCWRL output # naming current conformation 3Dpro_TS4-scwrl # ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1 # Found a chain break before 341 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_301277107.pdb -s /var/tmp/to_scwrl_301277107.seq -o /var/tmp/from_scwrl_301277107.pdb > /var/tmp/scwrl_301277107.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_301277107.pdb # conformation set from SCWRL output # naming current conformation 3Dpro_TS5-scwrl # ReadConformPDB reading from PDB file servers/ABIpro_TS1.pdb.gz looking for model 1 # Found a chain break before 369 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1953660434.pdb -s /var/tmp/to_scwrl_1953660434.seq -o /var/tmp/from_scwrl_1953660434.pdb > /var/tmp/scwrl_1953660434.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1953660434.pdb # conformation set from SCWRL output # naming current conformation ABIpro_TS1-scwrl # ReadConformPDB reading from PDB file servers/ABIpro_TS2.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1357895024.pdb -s /var/tmp/to_scwrl_1357895024.seq -o /var/tmp/from_scwrl_1357895024.pdb > /var/tmp/scwrl_1357895024.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1357895024.pdb # conformation set from SCWRL output # naming current conformation ABIpro_TS2-scwrl # ReadConformPDB reading from PDB file servers/ABIpro_TS3.pdb.gz looking for model 1 # Found a chain break before 369 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1428909713.pdb -s /var/tmp/to_scwrl_1428909713.seq -o /var/tmp/from_scwrl_1428909713.pdb > /var/tmp/scwrl_1428909713.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1428909713.pdb # conformation set from SCWRL output # naming current conformation ABIpro_TS3-scwrl # ReadConformPDB reading from PDB file servers/ABIpro_TS4.pdb.gz looking for model 1 # Found a chain break before 369 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1015743356.pdb -s /var/tmp/to_scwrl_1015743356.seq -o /var/tmp/from_scwrl_1015743356.pdb > /var/tmp/scwrl_1015743356.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1015743356.pdb # conformation set from SCWRL output # naming current conformation ABIpro_TS4-scwrl # ReadConformPDB reading from PDB file servers/ABIpro_TS5.pdb.gz looking for model 1 # Found a chain break before 346 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_408306663.pdb -s /var/tmp/to_scwrl_408306663.seq -o /var/tmp/from_scwrl_408306663.pdb > /var/tmp/scwrl_408306663.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_408306663.pdb # conformation set from SCWRL output # naming current conformation ABIpro_TS5-scwrl # ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1 # Found a chain break before 266 # copying to AlignedFragments data structure # naming current conformation BayesHH_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_282899942.pdb -s /var/tmp/to_scwrl_282899942.seq -o /var/tmp/from_scwrl_282899942.pdb > /var/tmp/scwrl_282899942.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_282899942.pdb # conformation set from SCWRL output # naming current conformation BayesHH_TS1-scwrl # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS1.pdb.gz looking for model 1 # Found a chain break before 346 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1641299829.pdb -s /var/tmp/to_scwrl_1641299829.seq -o /var/tmp/from_scwrl_1641299829.pdb > /var/tmp/scwrl_1641299829.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1641299829.pdb # conformation set from SCWRL output # naming current conformation Bilab-ENABLE_TS1-scwrl # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS2.pdb.gz looking for model 1 # Found a chain break before 369 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2022985858.pdb -s /var/tmp/to_scwrl_2022985858.seq -o /var/tmp/from_scwrl_2022985858.pdb > /var/tmp/scwrl_2022985858.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2022985858.pdb # conformation set from SCWRL output # naming current conformation Bilab-ENABLE_TS2-scwrl # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS3.pdb.gz looking for model 1 # Found a chain break before 323 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_223199075.pdb -s /var/tmp/to_scwrl_223199075.seq -o /var/tmp/from_scwrl_223199075.pdb > /var/tmp/scwrl_223199075.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_223199075.pdb # conformation set from SCWRL output # naming current conformation Bilab-ENABLE_TS3-scwrl # ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1709803907.pdb -s /var/tmp/to_scwrl_1709803907.seq -o /var/tmp/from_scwrl_1709803907.pdb > /var/tmp/scwrl_1709803907.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1709803907.pdb # conformation set from SCWRL output # naming current conformation CIRCLE_TS1-scwrl # ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_599881652.pdb -s /var/tmp/to_scwrl_599881652.seq -o /var/tmp/from_scwrl_599881652.pdb > /var/tmp/scwrl_599881652.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_599881652.pdb # conformation set from SCWRL output # naming current conformation CIRCLE_TS2-scwrl # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_482990076.pdb -s /var/tmp/to_scwrl_482990076.seq -o /var/tmp/from_scwrl_482990076.pdb > /var/tmp/scwrl_482990076.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_482990076.pdb # conformation set from SCWRL output # naming current conformation CIRCLE_TS3-scwrl # ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_518353600.pdb -s /var/tmp/to_scwrl_518353600.seq -o /var/tmp/from_scwrl_518353600.pdb > /var/tmp/scwrl_518353600.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_518353600.pdb # conformation set from SCWRL output # naming current conformation CIRCLE_TS4-scwrl # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # Found a chain break before 370 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_354050374.pdb -s /var/tmp/to_scwrl_354050374.seq -o /var/tmp/from_scwrl_354050374.pdb > /var/tmp/scwrl_354050374.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_354050374.pdb # conformation set from SCWRL output # naming current conformation CIRCLE_TS5-scwrl # ReadConformPDB reading from PDB file servers/CPHmodels_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation CPHmodels_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_27393827.pdb -s /var/tmp/to_scwrl_27393827.seq -o /var/tmp/from_scwrl_27393827.pdb > /var/tmp/scwrl_27393827.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_27393827.pdb # conformation set from SCWRL output # naming current conformation CPHmodels_TS1-scwrl # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_846021119.pdb -s /var/tmp/to_scwrl_846021119.seq -o /var/tmp/from_scwrl_846021119.pdb > /var/tmp/scwrl_846021119.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_846021119.pdb # conformation set from SCWRL output # naming current conformation CaspIta-FOX_TS1-scwrl # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_522913041.pdb -s /var/tmp/to_scwrl_522913041.seq -o /var/tmp/from_scwrl_522913041.pdb > /var/tmp/scwrl_522913041.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_522913041.pdb # conformation set from SCWRL output # naming current conformation CaspIta-FOX_TS2-scwrl # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1247640574.pdb -s /var/tmp/to_scwrl_1247640574.seq -o /var/tmp/from_scwrl_1247640574.pdb > /var/tmp/scwrl_1247640574.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1247640574.pdb # conformation set from SCWRL output # naming current conformation CaspIta-FOX_TS3-scwrl # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_19258579.pdb -s /var/tmp/to_scwrl_19258579.seq -o /var/tmp/from_scwrl_19258579.pdb > /var/tmp/scwrl_19258579.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_19258579.pdb # conformation set from SCWRL output # naming current conformation CaspIta-FOX_TS4-scwrl # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1730023184.pdb -s /var/tmp/to_scwrl_1730023184.seq -o /var/tmp/from_scwrl_1730023184.pdb > /var/tmp/scwrl_1730023184.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1730023184.pdb # conformation set from SCWRL output # naming current conformation CaspIta-FOX_TS5-scwrl # ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Distill_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1716687987.pdb -s /var/tmp/to_scwrl_1716687987.seq -o /var/tmp/from_scwrl_1716687987.pdb > /var/tmp/scwrl_1716687987.log Error: Couldn't open file /var/tmp/from_scwrl_1716687987.pdb or /var/tmp/from_scwrl_1716687987.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1716687987_b.pdb or decoys//var/tmp/from_scwrl_1716687987_b.pdb.gz for input Trying /var/tmp/from_scwrl_1716687987_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_1716687987_b.pdb or /var/tmp/from_scwrl_1716687987_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1716687987_a.pdb or decoys//var/tmp/from_scwrl_1716687987_a.pdb.gz for input Trying /var/tmp/from_scwrl_1716687987_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_1716687987_a.pdb or /var/tmp/from_scwrl_1716687987_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_1716687987.pdb or /var/tmp/from_scwrl_1716687987_b.pdb or /var/tmp/from_scwrl_1716687987_a.pdb Error: no new SCWRL conformation added # naming current conformation Distill_TS1-scwrl # ReadConformPDB reading from PDB file servers/Distill_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Distill_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_750827354.pdb -s /var/tmp/to_scwrl_750827354.seq -o /var/tmp/from_scwrl_750827354.pdb > /var/tmp/scwrl_750827354.log Error: Couldn't open file /var/tmp/from_scwrl_750827354.pdb or /var/tmp/from_scwrl_750827354.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_750827354_b.pdb or decoys//var/tmp/from_scwrl_750827354_b.pdb.gz for input Trying /var/tmp/from_scwrl_750827354_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_750827354_b.pdb or /var/tmp/from_scwrl_750827354_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_750827354_a.pdb or decoys//var/tmp/from_scwrl_750827354_a.pdb.gz for input Trying /var/tmp/from_scwrl_750827354_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_750827354_a.pdb or /var/tmp/from_scwrl_750827354_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_750827354.pdb or /var/tmp/from_scwrl_750827354_b.pdb or /var/tmp/from_scwrl_750827354_a.pdb Error: no new SCWRL conformation added # naming current conformation Distill_TS2-scwrl # ReadConformPDB reading from PDB file servers/Distill_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Distill_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_400411099.pdb -s /var/tmp/to_scwrl_400411099.seq -o /var/tmp/from_scwrl_400411099.pdb > /var/tmp/scwrl_400411099.log Error: Couldn't open file /var/tmp/from_scwrl_400411099.pdb or /var/tmp/from_scwrl_400411099.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_400411099_b.pdb or decoys//var/tmp/from_scwrl_400411099_b.pdb.gz for input Trying /var/tmp/from_scwrl_400411099_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_400411099_b.pdb or /var/tmp/from_scwrl_400411099_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_400411099_a.pdb or decoys//var/tmp/from_scwrl_400411099_a.pdb.gz for input Trying /var/tmp/from_scwrl_400411099_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_400411099_a.pdb or /var/tmp/from_scwrl_400411099_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_400411099.pdb or /var/tmp/from_scwrl_400411099_b.pdb or /var/tmp/from_scwrl_400411099_a.pdb Error: no new SCWRL conformation added # naming current conformation Distill_TS3-scwrl # ReadConformPDB reading from PDB file servers/Distill_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Distill_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_660430115.pdb -s /var/tmp/to_scwrl_660430115.seq -o /var/tmp/from_scwrl_660430115.pdb > /var/tmp/scwrl_660430115.log Error: Couldn't open file /var/tmp/from_scwrl_660430115.pdb or /var/tmp/from_scwrl_660430115.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_660430115_b.pdb or decoys//var/tmp/from_scwrl_660430115_b.pdb.gz for input Trying /var/tmp/from_scwrl_660430115_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_660430115_b.pdb or /var/tmp/from_scwrl_660430115_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_660430115_a.pdb or decoys//var/tmp/from_scwrl_660430115_a.pdb.gz for input Trying /var/tmp/from_scwrl_660430115_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_660430115_a.pdb or /var/tmp/from_scwrl_660430115_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_660430115.pdb or /var/tmp/from_scwrl_660430115_b.pdb or /var/tmp/from_scwrl_660430115_a.pdb Error: no new SCWRL conformation added # naming current conformation Distill_TS4-scwrl # ReadConformPDB reading from PDB file servers/Distill_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Distill_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_896980348.pdb -s /var/tmp/to_scwrl_896980348.seq -o /var/tmp/from_scwrl_896980348.pdb > /var/tmp/scwrl_896980348.log Error: Couldn't open file /var/tmp/from_scwrl_896980348.pdb or /var/tmp/from_scwrl_896980348.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_896980348_b.pdb or decoys//var/tmp/from_scwrl_896980348_b.pdb.gz for input Trying /var/tmp/from_scwrl_896980348_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_896980348_b.pdb or /var/tmp/from_scwrl_896980348_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_896980348_a.pdb or decoys//var/tmp/from_scwrl_896980348_a.pdb.gz for input Trying /var/tmp/from_scwrl_896980348_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_896980348_a.pdb or /var/tmp/from_scwrl_896980348_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_896980348.pdb or /var/tmp/from_scwrl_896980348_b.pdb or /var/tmp/from_scwrl_896980348_a.pdb Error: no new SCWRL conformation added # naming current conformation Distill_TS5-scwrl # ReadConformPDB reading from PDB file servers/FAMSD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FAMSD_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1291912375.pdb -s /var/tmp/to_scwrl_1291912375.seq -o /var/tmp/from_scwrl_1291912375.pdb > /var/tmp/scwrl_1291912375.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1291912375.pdb # conformation set from SCWRL output # naming current conformation FAMSD_TS1-scwrl # ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FAMSD_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1734231397.pdb -s /var/tmp/to_scwrl_1734231397.seq -o /var/tmp/from_scwrl_1734231397.pdb > /var/tmp/scwrl_1734231397.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1734231397.pdb # conformation set from SCWRL output # naming current conformation FAMSD_TS2-scwrl # ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FAMSD_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2073397082.pdb -s /var/tmp/to_scwrl_2073397082.seq -o /var/tmp/from_scwrl_2073397082.pdb > /var/tmp/scwrl_2073397082.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2073397082.pdb # conformation set from SCWRL output # naming current conformation FAMSD_TS3-scwrl # ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FAMSD_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_637818631.pdb -s /var/tmp/to_scwrl_637818631.seq -o /var/tmp/from_scwrl_637818631.pdb > /var/tmp/scwrl_637818631.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_637818631.pdb # conformation set from SCWRL output # naming current conformation FAMSD_TS4-scwrl # ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FAMSD_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1753061769.pdb -s /var/tmp/to_scwrl_1753061769.seq -o /var/tmp/from_scwrl_1753061769.pdb > /var/tmp/scwrl_1753061769.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1753061769.pdb # conformation set from SCWRL output # naming current conformation FAMSD_TS5-scwrl # ReadConformPDB reading from PDB file servers/FAMS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FAMS_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_227190542.pdb -s /var/tmp/to_scwrl_227190542.seq -o /var/tmp/from_scwrl_227190542.pdb > /var/tmp/scwrl_227190542.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_227190542.pdb # conformation set from SCWRL output # naming current conformation FAMS_TS1-scwrl # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FAMS_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_443995418.pdb -s /var/tmp/to_scwrl_443995418.seq -o /var/tmp/from_scwrl_443995418.pdb > /var/tmp/scwrl_443995418.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_443995418.pdb # conformation set from SCWRL output # naming current conformation FAMS_TS2-scwrl # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FAMS_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_963473147.pdb -s /var/tmp/to_scwrl_963473147.seq -o /var/tmp/from_scwrl_963473147.pdb > /var/tmp/scwrl_963473147.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_963473147.pdb # conformation set from SCWRL output # naming current conformation FAMS_TS3-scwrl # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FAMS_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1656100255.pdb -s /var/tmp/to_scwrl_1656100255.seq -o /var/tmp/from_scwrl_1656100255.pdb > /var/tmp/scwrl_1656100255.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1656100255.pdb # conformation set from SCWRL output # naming current conformation FAMS_TS4-scwrl # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FAMS_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1459738774.pdb -s /var/tmp/to_scwrl_1459738774.seq -o /var/tmp/from_scwrl_1459738774.pdb > /var/tmp/scwrl_1459738774.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1459738774.pdb # conformation set from SCWRL output # naming current conformation FAMS_TS5-scwrl # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # Found a chain break before 370 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1371779809.pdb -s /var/tmp/to_scwrl_1371779809.seq -o /var/tmp/from_scwrl_1371779809.pdb > /var/tmp/scwrl_1371779809.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1371779809.pdb # conformation set from SCWRL output # naming current conformation FOLDpro_TS1-scwrl # ReadConformPDB reading from PDB file servers/FOLDpro_TS2.pdb.gz looking for model 1 # Found a chain break before 341 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1939000198.pdb -s /var/tmp/to_scwrl_1939000198.seq -o /var/tmp/from_scwrl_1939000198.pdb > /var/tmp/scwrl_1939000198.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1939000198.pdb # conformation set from SCWRL output # naming current conformation FOLDpro_TS2-scwrl # ReadConformPDB reading from PDB file servers/FOLDpro_TS3.pdb.gz looking for model 1 # Found a chain break before 353 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_953554957.pdb -s /var/tmp/to_scwrl_953554957.seq -o /var/tmp/from_scwrl_953554957.pdb > /var/tmp/scwrl_953554957.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_953554957.pdb # conformation set from SCWRL output # naming current conformation FOLDpro_TS3-scwrl # ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1 # Found a chain break before 341 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1247282020.pdb -s /var/tmp/to_scwrl_1247282020.seq -o /var/tmp/from_scwrl_1247282020.pdb > /var/tmp/scwrl_1247282020.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1247282020.pdb # conformation set from SCWRL output # naming current conformation FOLDpro_TS4-scwrl # ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1 # Found a chain break before 335 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_14715626.pdb -s /var/tmp/to_scwrl_14715626.seq -o /var/tmp/from_scwrl_14715626.pdb > /var/tmp/scwrl_14715626.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_14715626.pdb # conformation set from SCWRL output # naming current conformation FOLDpro_TS5-scwrl # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 Skipped atom 526, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 528, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 530, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 532, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 738, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 740, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 742, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 744, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 754, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 756, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 758, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 760, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 842, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 844, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 846, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 848, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 918, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 920, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 922, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 924, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1154, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1156, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1158, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1160, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1230, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1232, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1234, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1236, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1242, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1244, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1246, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1248, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1254, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1256, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1258, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1260, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1342, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1344, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1346, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1348, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FORTE1_AL1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_515875217.pdb -s /var/tmp/to_scwrl_515875217.seq -o /var/tmp/from_scwrl_515875217.pdb > /var/tmp/scwrl_515875217.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_515875217.pdb # conformation set from SCWRL output # naming current conformation FORTE1_AL1-scwrl # ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FORTE1_AL2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1847163673.pdb -s /var/tmp/to_scwrl_1847163673.seq -o /var/tmp/from_scwrl_1847163673.pdb > /var/tmp/scwrl_1847163673.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1847163673.pdb # conformation set from SCWRL output # naming current conformation FORTE1_AL2-scwrl # ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FORTE1_AL3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_497705703.pdb -s /var/tmp/to_scwrl_497705703.seq -o /var/tmp/from_scwrl_497705703.pdb > /var/tmp/scwrl_497705703.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_497705703.pdb # conformation set from SCWRL output # naming current conformation FORTE1_AL3-scwrl # ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FORTE1_AL4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1034228818.pdb -s /var/tmp/to_scwrl_1034228818.seq -o /var/tmp/from_scwrl_1034228818.pdb > /var/tmp/scwrl_1034228818.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1034228818.pdb # conformation set from SCWRL output # naming current conformation FORTE1_AL4-scwrl # ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FORTE1_AL5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_53730400.pdb -s /var/tmp/to_scwrl_53730400.seq -o /var/tmp/from_scwrl_53730400.pdb > /var/tmp/scwrl_53730400.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_53730400.pdb # conformation set from SCWRL output # naming current conformation FORTE1_AL5-scwrl # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 Skipped atom 526, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 528, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 530, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 532, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 738, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 740, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 742, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 744, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 754, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 756, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 758, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 760, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 842, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 844, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 846, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 848, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 918, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 920, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 922, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 924, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1154, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1156, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1158, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1160, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1230, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1232, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1234, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1236, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1242, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1244, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1246, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1248, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1254, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1256, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1258, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1260, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1342, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1344, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1346, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1348, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FORTE2_AL1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_525099530.pdb -s /var/tmp/to_scwrl_525099530.seq -o /var/tmp/from_scwrl_525099530.pdb > /var/tmp/scwrl_525099530.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_525099530.pdb # conformation set from SCWRL output # naming current conformation FORTE2_AL1-scwrl # ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FORTE2_AL2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1880249936.pdb -s /var/tmp/to_scwrl_1880249936.seq -o /var/tmp/from_scwrl_1880249936.pdb > /var/tmp/scwrl_1880249936.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1880249936.pdb # conformation set from SCWRL output # naming current conformation FORTE2_AL2-scwrl # ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FORTE2_AL3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_576643441.pdb -s /var/tmp/to_scwrl_576643441.seq -o /var/tmp/from_scwrl_576643441.pdb > /var/tmp/scwrl_576643441.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_576643441.pdb # conformation set from SCWRL output # naming current conformation FORTE2_AL3-scwrl # ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FORTE2_AL4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1772740104.pdb -s /var/tmp/to_scwrl_1772740104.seq -o /var/tmp/from_scwrl_1772740104.pdb > /var/tmp/scwrl_1772740104.log sh: line 1: 31358 Killed scwrl3 -i /var/tmp/to_scwrl_1772740104.pdb -s /var/tmp/to_scwrl_1772740104.seq -o /var/tmp/from_scwrl_1772740104.pdb >/var/tmp/scwrl_1772740104.log Error: Couldn't open file /var/tmp/from_scwrl_1772740104.pdb or /var/tmp/from_scwrl_1772740104.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1772740104_b.pdb or decoys//var/tmp/from_scwrl_1772740104_b.pdb.gz for input Trying /var/tmp/from_scwrl_1772740104_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_1772740104_b.pdb or /var/tmp/from_scwrl_1772740104_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1772740104_a.pdb or decoys//var/tmp/from_scwrl_1772740104_a.pdb.gz for input Trying /var/tmp/from_scwrl_1772740104_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_1772740104_a.pdb or /var/tmp/from_scwrl_1772740104_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_1772740104.pdb or /var/tmp/from_scwrl_1772740104_b.pdb or /var/tmp/from_scwrl_1772740104_a.pdb Error: no new SCWRL conformation added # naming current conformation FORTE2_AL4-scwrl # ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FORTE2_AL5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1899508516.pdb -s /var/tmp/to_scwrl_1899508516.seq -o /var/tmp/from_scwrl_1899508516.pdb > /var/tmp/scwrl_1899508516.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1899508516.pdb # conformation set from SCWRL output # naming current conformation FORTE2_AL5-scwrl # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS1.pdb.gz looking for model 1 # Found a chain break before 366 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_159182979.pdb -s /var/tmp/to_scwrl_159182979.seq -o /var/tmp/from_scwrl_159182979.pdb > /var/tmp/scwrl_159182979.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_159182979.pdb # conformation set from SCWRL output # naming current conformation FPSOLVER-SERVER_TS1-scwrl # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS2.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1341944445.pdb -s /var/tmp/to_scwrl_1341944445.seq -o /var/tmp/from_scwrl_1341944445.pdb > /var/tmp/scwrl_1341944445.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1341944445.pdb # conformation set from SCWRL output # naming current conformation FPSOLVER-SERVER_TS2-scwrl # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS3.pdb.gz looking for model 1 # Found a chain break before 372 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_502852223.pdb -s /var/tmp/to_scwrl_502852223.seq -o /var/tmp/from_scwrl_502852223.pdb > /var/tmp/scwrl_502852223.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_502852223.pdb # conformation set from SCWRL output # naming current conformation FPSOLVER-SERVER_TS3-scwrl # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS4.pdb.gz looking for model 1 # Found a chain break before 360 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_559594078.pdb -s /var/tmp/to_scwrl_559594078.seq -o /var/tmp/from_scwrl_559594078.pdb > /var/tmp/scwrl_559594078.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_559594078.pdb # conformation set from SCWRL output # naming current conformation FPSOLVER-SERVER_TS4-scwrl # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS5.pdb.gz looking for model 1 # Found a chain break before 372 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2002374560.pdb -s /var/tmp/to_scwrl_2002374560.seq -o /var/tmp/from_scwrl_2002374560.pdb > /var/tmp/scwrl_2002374560.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2002374560.pdb # conformation set from SCWRL output # naming current conformation FPSOLVER-SERVER_TS5-scwrl # ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1399832570.pdb -s /var/tmp/to_scwrl_1399832570.seq -o /var/tmp/from_scwrl_1399832570.pdb > /var/tmp/scwrl_1399832570.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1399832570.pdb # conformation set from SCWRL output # naming current conformation FUGMOD_TS1-scwrl # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1851506453.pdb -s /var/tmp/to_scwrl_1851506453.seq -o /var/tmp/from_scwrl_1851506453.pdb > /var/tmp/scwrl_1851506453.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1851506453.pdb # conformation set from SCWRL output # naming current conformation FUGMOD_TS2-scwrl # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1589122311.pdb -s /var/tmp/to_scwrl_1589122311.seq -o /var/tmp/from_scwrl_1589122311.pdb > /var/tmp/scwrl_1589122311.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1589122311.pdb # conformation set from SCWRL output # naming current conformation FUGMOD_TS3-scwrl # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # Found a chain break before 348 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1325746005.pdb -s /var/tmp/to_scwrl_1325746005.seq -o /var/tmp/from_scwrl_1325746005.pdb > /var/tmp/scwrl_1325746005.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1325746005.pdb # conformation set from SCWRL output # naming current conformation FUGMOD_TS4-scwrl # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_341841437.pdb -s /var/tmp/to_scwrl_341841437.seq -o /var/tmp/from_scwrl_341841437.pdb > /var/tmp/scwrl_341841437.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_341841437.pdb # conformation set from SCWRL output # naming current conformation FUGMOD_TS5-scwrl # ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FUGUE_AL1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1194700433.pdb -s /var/tmp/to_scwrl_1194700433.seq -o /var/tmp/from_scwrl_1194700433.pdb > /var/tmp/scwrl_1194700433.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1194700433.pdb # conformation set from SCWRL output # naming current conformation FUGUE_AL1-scwrl # ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FUGUE_AL2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1552936548.pdb -s /var/tmp/to_scwrl_1552936548.seq -o /var/tmp/from_scwrl_1552936548.pdb > /var/tmp/scwrl_1552936548.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1552936548.pdb # conformation set from SCWRL output # naming current conformation FUGUE_AL2-scwrl # ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FUGUE_AL3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_785836856.pdb -s /var/tmp/to_scwrl_785836856.seq -o /var/tmp/from_scwrl_785836856.pdb > /var/tmp/scwrl_785836856.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_785836856.pdb # conformation set from SCWRL output # naming current conformation FUGUE_AL3-scwrl # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FUGUE_AL4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_10689933.pdb -s /var/tmp/to_scwrl_10689933.seq -o /var/tmp/from_scwrl_10689933.pdb > /var/tmp/scwrl_10689933.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_10689933.pdb # conformation set from SCWRL output # naming current conformation FUGUE_AL4-scwrl # ReadConformPDB reading from PDB file servers/FUGUE_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FUGUE_AL5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1061553157.pdb -s /var/tmp/to_scwrl_1061553157.seq -o /var/tmp/from_scwrl_1061553157.pdb > /var/tmp/scwrl_1061553157.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1061553157.pdb # conformation set from SCWRL output # naming current conformation FUGUE_AL5-scwrl # ReadConformPDB reading from PDB file servers/FUNCTION_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FUNCTION_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_98091983.pdb -s /var/tmp/to_scwrl_98091983.seq -o /var/tmp/from_scwrl_98091983.pdb > /var/tmp/scwrl_98091983.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_98091983.pdb # conformation set from SCWRL output # naming current conformation FUNCTION_TS1-scwrl # ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1382469743.pdb -s /var/tmp/to_scwrl_1382469743.seq -o /var/tmp/from_scwrl_1382469743.pdb > /var/tmp/scwrl_1382469743.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1382469743.pdb # conformation set from SCWRL output # naming current conformation FUNCTION_TS2-scwrl # ReadConformPDB reading from PDB file servers/FUNCTION_TS3.pdb.gz looking for model 1 # Found a chain break before 366 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_853069708.pdb -s /var/tmp/to_scwrl_853069708.seq -o /var/tmp/from_scwrl_853069708.pdb > /var/tmp/scwrl_853069708.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_853069708.pdb # conformation set from SCWRL output # naming current conformation FUNCTION_TS3-scwrl # ReadConformPDB reading from PDB file servers/FUNCTION_TS4.pdb.gz looking for model 1 # Found a chain break before 367 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1051646940.pdb -s /var/tmp/to_scwrl_1051646940.seq -o /var/tmp/from_scwrl_1051646940.pdb > /var/tmp/scwrl_1051646940.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1051646940.pdb # conformation set from SCWRL output # naming current conformation FUNCTION_TS4-scwrl # ReadConformPDB reading from PDB file servers/FUNCTION_TS5.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_482268117.pdb -s /var/tmp/to_scwrl_482268117.seq -o /var/tmp/from_scwrl_482268117.pdb > /var/tmp/scwrl_482268117.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_482268117.pdb # conformation set from SCWRL output # naming current conformation FUNCTION_TS5-scwrl # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_867785335.pdb -s /var/tmp/to_scwrl_867785335.seq -o /var/tmp/from_scwrl_867785335.pdb > /var/tmp/scwrl_867785335.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_867785335.pdb # conformation set from SCWRL output # naming current conformation GeneSilicoMetaServer_TS1-scwrl # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # Found a chain break before 372 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1567522157.pdb -s /var/tmp/to_scwrl_1567522157.seq -o /var/tmp/from_scwrl_1567522157.pdb > /var/tmp/scwrl_1567522157.log sh: line 1: 31465 Killed scwrl3 -i /var/tmp/to_scwrl_1567522157.pdb -s /var/tmp/to_scwrl_1567522157.seq -o /var/tmp/from_scwrl_1567522157.pdb >/var/tmp/scwrl_1567522157.log Error: Couldn't open file /var/tmp/from_scwrl_1567522157.pdb or /var/tmp/from_scwrl_1567522157.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1567522157_b.pdb or decoys//var/tmp/from_scwrl_1567522157_b.pdb.gz for input Trying /var/tmp/from_scwrl_1567522157_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_1567522157_b.pdb or /var/tmp/from_scwrl_1567522157_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1567522157_a.pdb or decoys//var/tmp/from_scwrl_1567522157_a.pdb.gz for input Trying /var/tmp/from_scwrl_1567522157_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_1567522157_a.pdb or /var/tmp/from_scwrl_1567522157_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_1567522157.pdb or /var/tmp/from_scwrl_1567522157_b.pdb or /var/tmp/from_scwrl_1567522157_a.pdb Error: no new SCWRL conformation added # naming current conformation GeneSilicoMetaServer_TS2-scwrl # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_181948143.pdb -s /var/tmp/to_scwrl_181948143.seq -o /var/tmp/from_scwrl_181948143.pdb > /var/tmp/scwrl_181948143.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_181948143.pdb # conformation set from SCWRL output # naming current conformation GeneSilicoMetaServer_TS3-scwrl # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1365491037.pdb -s /var/tmp/to_scwrl_1365491037.seq -o /var/tmp/from_scwrl_1365491037.pdb > /var/tmp/scwrl_1365491037.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1365491037.pdb # conformation set from SCWRL output # naming current conformation GeneSilicoMetaServer_TS4-scwrl # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1 # Found a chain break before 338 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_454267328.pdb -s /var/tmp/to_scwrl_454267328.seq -o /var/tmp/from_scwrl_454267328.pdb > /var/tmp/scwrl_454267328.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_454267328.pdb # conformation set from SCWRL output # naming current conformation GeneSilicoMetaServer_TS5-scwrl # ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation HHpred1_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_235678544.pdb -s /var/tmp/to_scwrl_235678544.seq -o /var/tmp/from_scwrl_235678544.pdb > /var/tmp/scwrl_235678544.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_235678544.pdb # conformation set from SCWRL output # naming current conformation HHpred1_TS1-scwrl # ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation HHpred2_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1890590567.pdb -s /var/tmp/to_scwrl_1890590567.seq -o /var/tmp/from_scwrl_1890590567.pdb > /var/tmp/scwrl_1890590567.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1890590567.pdb # conformation set from SCWRL output # naming current conformation HHpred2_TS1-scwrl # ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation HHpred3_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_187033617.pdb -s /var/tmp/to_scwrl_187033617.seq -o /var/tmp/from_scwrl_187033617.pdb > /var/tmp/scwrl_187033617.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_187033617.pdb # conformation set from SCWRL output # naming current conformation HHpred3_TS1-scwrl # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_812321985.pdb -s /var/tmp/to_scwrl_812321985.seq -o /var/tmp/from_scwrl_812321985.pdb > /var/tmp/scwrl_812321985.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_812321985.pdb # conformation set from SCWRL output # naming current conformation Huber-Torda-Server_TS1-scwrl # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1515847025.pdb -s /var/tmp/to_scwrl_1515847025.seq -o /var/tmp/from_scwrl_1515847025.pdb > /var/tmp/scwrl_1515847025.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1515847025.pdb # conformation set from SCWRL output # naming current conformation Huber-Torda-Server_TS2-scwrl # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2086542133.pdb -s /var/tmp/to_scwrl_2086542133.seq -o /var/tmp/from_scwrl_2086542133.pdb > /var/tmp/scwrl_2086542133.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2086542133.pdb # conformation set from SCWRL output # naming current conformation Huber-Torda-Server_TS3-scwrl # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_971504964.pdb -s /var/tmp/to_scwrl_971504964.seq -o /var/tmp/from_scwrl_971504964.pdb > /var/tmp/scwrl_971504964.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_971504964.pdb # conformation set from SCWRL output # naming current conformation Huber-Torda-Server_TS4-scwrl # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_710307824.pdb -s /var/tmp/to_scwrl_710307824.seq -o /var/tmp/from_scwrl_710307824.pdb > /var/tmp/scwrl_710307824.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_710307824.pdb # conformation set from SCWRL output # naming current conformation Huber-Torda-Server_TS5-scwrl # ReadConformPDB reading from PDB file servers/LOOPP_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation LOOPP_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_441910709.pdb -s /var/tmp/to_scwrl_441910709.seq -o /var/tmp/from_scwrl_441910709.pdb > /var/tmp/scwrl_441910709.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_441910709.pdb # conformation set from SCWRL output # naming current conformation LOOPP_TS1-scwrl # ReadConformPDB reading from PDB file servers/LOOPP_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation LOOPP_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1531099042.pdb -s /var/tmp/to_scwrl_1531099042.seq -o /var/tmp/from_scwrl_1531099042.pdb > /var/tmp/scwrl_1531099042.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1531099042.pdb # conformation set from SCWRL output # naming current conformation LOOPP_TS2-scwrl # ReadConformPDB reading from PDB file servers/LOOPP_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation LOOPP_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_565198737.pdb -s /var/tmp/to_scwrl_565198737.seq -o /var/tmp/from_scwrl_565198737.pdb > /var/tmp/scwrl_565198737.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_565198737.pdb # conformation set from SCWRL output # naming current conformation LOOPP_TS3-scwrl # ReadConformPDB reading from PDB file servers/LOOPP_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation LOOPP_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1841743280.pdb -s /var/tmp/to_scwrl_1841743280.seq -o /var/tmp/from_scwrl_1841743280.pdb > /var/tmp/scwrl_1841743280.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1841743280.pdb # conformation set from SCWRL output # naming current conformation LOOPP_TS4-scwrl # ReadConformPDB reading from PDB file servers/LOOPP_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation LOOPP_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1235121848.pdb -s /var/tmp/to_scwrl_1235121848.seq -o /var/tmp/from_scwrl_1235121848.pdb > /var/tmp/scwrl_1235121848.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1235121848.pdb # conformation set from SCWRL output # naming current conformation LOOPP_TS5-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # Found a chain break before 332 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_6837401.pdb -s /var/tmp/to_scwrl_6837401.seq -o /var/tmp/from_scwrl_6837401.pdb > /var/tmp/scwrl_6837401.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_6837401.pdb # conformation set from SCWRL output # naming current conformation Ma-OPUS-server_TS1-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS2.pdb.gz looking for model 1 # Found a chain break before 366 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1020005639.pdb -s /var/tmp/to_scwrl_1020005639.seq -o /var/tmp/from_scwrl_1020005639.pdb > /var/tmp/scwrl_1020005639.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1020005639.pdb # conformation set from SCWRL output # naming current conformation Ma-OPUS-server_TS2-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS3.pdb.gz looking for model 1 # Found a chain break before 327 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1576963286.pdb -s /var/tmp/to_scwrl_1576963286.seq -o /var/tmp/from_scwrl_1576963286.pdb > /var/tmp/scwrl_1576963286.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1576963286.pdb # conformation set from SCWRL output # naming current conformation Ma-OPUS-server_TS3-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS4.pdb.gz looking for model 1 # Found a chain break before 364 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1201537834.pdb -s /var/tmp/to_scwrl_1201537834.seq -o /var/tmp/from_scwrl_1201537834.pdb > /var/tmp/scwrl_1201537834.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1201537834.pdb # conformation set from SCWRL output # naming current conformation Ma-OPUS-server_TS4-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS5.pdb.gz looking for model 1 # Found a chain break before 347 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_425458540.pdb -s /var/tmp/to_scwrl_425458540.seq -o /var/tmp/from_scwrl_425458540.pdb > /var/tmp/scwrl_425458540.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_425458540.pdb # conformation set from SCWRL output # naming current conformation Ma-OPUS-server_TS5-scwrl # ReadConformPDB reading from PDB file servers/MetaTasser_TS1.pdb.gz looking for model 1 # Found a chain break before 372 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_215316495.pdb -s /var/tmp/to_scwrl_215316495.seq -o /var/tmp/from_scwrl_215316495.pdb > /var/tmp/scwrl_215316495.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_215316495.pdb # conformation set from SCWRL output # naming current conformation MetaTasser_TS1-scwrl # ReadConformPDB reading from PDB file servers/MetaTasser_TS2.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1212227768.pdb -s /var/tmp/to_scwrl_1212227768.seq -o /var/tmp/from_scwrl_1212227768.pdb > /var/tmp/scwrl_1212227768.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1212227768.pdb # conformation set from SCWRL output # naming current conformation MetaTasser_TS2-scwrl # ReadConformPDB reading from PDB file servers/MetaTasser_TS3.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1487011697.pdb -s /var/tmp/to_scwrl_1487011697.seq -o /var/tmp/from_scwrl_1487011697.pdb > /var/tmp/scwrl_1487011697.log sh: line 1: 31578 Killed scwrl3 -i /var/tmp/to_scwrl_1487011697.pdb -s /var/tmp/to_scwrl_1487011697.seq -o /var/tmp/from_scwrl_1487011697.pdb >/var/tmp/scwrl_1487011697.log Error: Couldn't open file /var/tmp/from_scwrl_1487011697.pdb or /var/tmp/from_scwrl_1487011697.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1487011697_b.pdb or decoys//var/tmp/from_scwrl_1487011697_b.pdb.gz for input Trying /var/tmp/from_scwrl_1487011697_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_1487011697_b.pdb or /var/tmp/from_scwrl_1487011697_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1487011697_a.pdb or decoys//var/tmp/from_scwrl_1487011697_a.pdb.gz for input Trying /var/tmp/from_scwrl_1487011697_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_1487011697_a.pdb or /var/tmp/from_scwrl_1487011697_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_1487011697.pdb or /var/tmp/from_scwrl_1487011697_b.pdb or /var/tmp/from_scwrl_1487011697_a.pdb Error: no new SCWRL conformation added # naming current conformation MetaTasser_TS3-scwrl # ReadConformPDB reading from PDB file servers/MetaTasser_TS4.pdb.gz looking for model 1 # Found a chain break before 372 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_313408478.pdb -s /var/tmp/to_scwrl_313408478.seq -o /var/tmp/from_scwrl_313408478.pdb > /var/tmp/scwrl_313408478.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_313408478.pdb # conformation set from SCWRL output # naming current conformation MetaTasser_TS4-scwrl # ReadConformPDB reading from PDB file servers/MetaTasser_TS5.pdb.gz looking for model 1 # Found a chain break before 372 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_447213865.pdb -s /var/tmp/to_scwrl_447213865.seq -o /var/tmp/from_scwrl_447213865.pdb > /var/tmp/scwrl_447213865.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_447213865.pdb # conformation set from SCWRL output # naming current conformation MetaTasser_TS5-scwrl # ReadConformPDB reading from PDB file servers/NN_PUT_lab_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation NN_PUT_lab_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_192597758.pdb -s /var/tmp/to_scwrl_192597758.seq -o /var/tmp/from_scwrl_192597758.pdb > /var/tmp/scwrl_192597758.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_192597758.pdb # conformation set from SCWRL output # naming current conformation NN_PUT_lab_TS1-scwrl # ReadConformPDB reading from PDB file servers/POMYSL_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation POMYSL_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1365055417.pdb -s /var/tmp/to_scwrl_1365055417.seq -o /var/tmp/from_scwrl_1365055417.pdb > /var/tmp/scwrl_1365055417.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1365055417.pdb # conformation set from SCWRL output # naming current conformation POMYSL_TS1-scwrl # ReadConformPDB reading from PDB file servers/POMYSL_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation POMYSL_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_929481982.pdb -s /var/tmp/to_scwrl_929481982.seq -o /var/tmp/from_scwrl_929481982.pdb > /var/tmp/scwrl_929481982.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_929481982.pdb # conformation set from SCWRL output # naming current conformation POMYSL_TS2-scwrl # ReadConformPDB reading from PDB file servers/POMYSL_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation POMYSL_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1060383093.pdb -s /var/tmp/to_scwrl_1060383093.seq -o /var/tmp/from_scwrl_1060383093.pdb > /var/tmp/scwrl_1060383093.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1060383093.pdb # conformation set from SCWRL output # naming current conformation POMYSL_TS3-scwrl # ReadConformPDB reading from PDB file servers/POMYSL_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation POMYSL_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_785093928.pdb -s /var/tmp/to_scwrl_785093928.seq -o /var/tmp/from_scwrl_785093928.pdb > /var/tmp/scwrl_785093928.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_785093928.pdb # conformation set from SCWRL output # naming current conformation POMYSL_TS4-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1111430125.pdb -s /var/tmp/to_scwrl_1111430125.seq -o /var/tmp/from_scwrl_1111430125.pdb > /var/tmp/scwrl_1111430125.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1111430125.pdb # conformation set from SCWRL output # naming current conformation PROTINFO-AB_TS1-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_278390483.pdb -s /var/tmp/to_scwrl_278390483.seq -o /var/tmp/from_scwrl_278390483.pdb > /var/tmp/scwrl_278390483.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_278390483.pdb # conformation set from SCWRL output # naming current conformation PROTINFO-AB_TS2-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1239361255.pdb -s /var/tmp/to_scwrl_1239361255.seq -o /var/tmp/from_scwrl_1239361255.pdb > /var/tmp/scwrl_1239361255.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1239361255.pdb # conformation set from SCWRL output # naming current conformation PROTINFO-AB_TS3-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1347108669.pdb -s /var/tmp/to_scwrl_1347108669.seq -o /var/tmp/from_scwrl_1347108669.pdb > /var/tmp/scwrl_1347108669.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1347108669.pdb # conformation set from SCWRL output # naming current conformation PROTINFO-AB_TS4-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_21497404.pdb -s /var/tmp/to_scwrl_21497404.seq -o /var/tmp/from_scwrl_21497404.pdb > /var/tmp/scwrl_21497404.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_21497404.pdb # conformation set from SCWRL output # naming current conformation PROTINFO-AB_TS5-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1 # Found a chain break before 338 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1426394873.pdb -s /var/tmp/to_scwrl_1426394873.seq -o /var/tmp/from_scwrl_1426394873.pdb > /var/tmp/scwrl_1426394873.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1426394873.pdb # conformation set from SCWRL output # naming current conformation PROTINFO_TS1-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_11947007.pdb -s /var/tmp/to_scwrl_11947007.seq -o /var/tmp/from_scwrl_11947007.pdb > /var/tmp/scwrl_11947007.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_11947007.pdb # conformation set from SCWRL output # naming current conformation PROTINFO_TS2-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1537344429.pdb -s /var/tmp/to_scwrl_1537344429.seq -o /var/tmp/from_scwrl_1537344429.pdb > /var/tmp/scwrl_1537344429.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1537344429.pdb # conformation set from SCWRL output # naming current conformation PROTINFO_TS3-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # Found a chain break before 369 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1365453359.pdb -s /var/tmp/to_scwrl_1365453359.seq -o /var/tmp/from_scwrl_1365453359.pdb > /var/tmp/scwrl_1365453359.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1365453359.pdb # conformation set from SCWRL output # naming current conformation PROTINFO_TS4-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # Found a chain break before 365 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_983451972.pdb -s /var/tmp/to_scwrl_983451972.seq -o /var/tmp/from_scwrl_983451972.pdb > /var/tmp/scwrl_983451972.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_983451972.pdb # conformation set from SCWRL output # naming current conformation PROTINFO_TS5-scwrl # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Pcons6_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_100168606.pdb -s /var/tmp/to_scwrl_100168606.seq -o /var/tmp/from_scwrl_100168606.pdb > /var/tmp/scwrl_100168606.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_100168606.pdb # conformation set from SCWRL output # naming current conformation Pcons6_TS1-scwrl # ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Pcons6_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1807364069.pdb -s /var/tmp/to_scwrl_1807364069.seq -o /var/tmp/from_scwrl_1807364069.pdb > /var/tmp/scwrl_1807364069.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1807364069.pdb # conformation set from SCWRL output # naming current conformation Pcons6_TS2-scwrl # ReadConformPDB reading from PDB file servers/Pcons6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Pcons6_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_367067367.pdb -s /var/tmp/to_scwrl_367067367.seq -o /var/tmp/from_scwrl_367067367.pdb > /var/tmp/scwrl_367067367.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_367067367.pdb # conformation set from SCWRL output # naming current conformation Pcons6_TS3-scwrl # ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Pcons6_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_665367343.pdb -s /var/tmp/to_scwrl_665367343.seq -o /var/tmp/from_scwrl_665367343.pdb > /var/tmp/scwrl_665367343.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_665367343.pdb # conformation set from SCWRL output # naming current conformation Pcons6_TS4-scwrl # ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1 # Found a chain break before 363 # copying to AlignedFragments data structure # naming current conformation Pcons6_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1501623702.pdb -s /var/tmp/to_scwrl_1501623702.seq -o /var/tmp/from_scwrl_1501623702.pdb > /var/tmp/scwrl_1501623702.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1501623702.pdb # conformation set from SCWRL output # naming current conformation Pcons6_TS5-scwrl # ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Phyre-1_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1602189215.pdb -s /var/tmp/to_scwrl_1602189215.seq -o /var/tmp/from_scwrl_1602189215.pdb > /var/tmp/scwrl_1602189215.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1602189215.pdb # conformation set from SCWRL output # naming current conformation Phyre-1_TS1-scwrl # ReadConformPDB reading from PDB file servers/Phyre-2_TS1.pdb.gz looking for model 1 # Found a chain break before 358 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_672204745.pdb -s /var/tmp/to_scwrl_672204745.seq -o /var/tmp/from_scwrl_672204745.pdb > /var/tmp/scwrl_672204745.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_672204745.pdb # conformation set from SCWRL output # naming current conformation Phyre-2_TS1-scwrl # ReadConformPDB reading from PDB file servers/Phyre-2_TS2.pdb.gz looking for model 1 # Found a chain break before 342 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_374145694.pdb -s /var/tmp/to_scwrl_374145694.seq -o /var/tmp/from_scwrl_374145694.pdb > /var/tmp/scwrl_374145694.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_374145694.pdb # conformation set from SCWRL output # naming current conformation Phyre-2_TS2-scwrl # ReadConformPDB reading from PDB file servers/Phyre-2_TS3.pdb.gz looking for model 1 # Found a chain break before 370 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1031668855.pdb -s /var/tmp/to_scwrl_1031668855.seq -o /var/tmp/from_scwrl_1031668855.pdb > /var/tmp/scwrl_1031668855.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1031668855.pdb # conformation set from SCWRL output # naming current conformation Phyre-2_TS3-scwrl # ReadConformPDB reading from PDB file servers/Phyre-2_TS4.pdb.gz looking for model 1 # Found a chain break before 334 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1873742579.pdb -s /var/tmp/to_scwrl_1873742579.seq -o /var/tmp/from_scwrl_1873742579.pdb > /var/tmp/scwrl_1873742579.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1873742579.pdb # conformation set from SCWRL output # naming current conformation Phyre-2_TS4-scwrl # ReadConformPDB reading from PDB file servers/Phyre-2_TS5.pdb.gz looking for model 1 # Found a chain break before 365 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_799604235.pdb -s /var/tmp/to_scwrl_799604235.seq -o /var/tmp/from_scwrl_799604235.pdb > /var/tmp/scwrl_799604235.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_799604235.pdb # conformation set from SCWRL output # naming current conformation Phyre-2_TS5-scwrl # ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1246985349.pdb -s /var/tmp/to_scwrl_1246985349.seq -o /var/tmp/from_scwrl_1246985349.pdb > /var/tmp/scwrl_1246985349.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1246985349.pdb # conformation set from SCWRL output # naming current conformation Pmodeller6_TS1-scwrl # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_938486701.pdb -s /var/tmp/to_scwrl_938486701.seq -o /var/tmp/from_scwrl_938486701.pdb > /var/tmp/scwrl_938486701.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_938486701.pdb # conformation set from SCWRL output # naming current conformation Pmodeller6_TS2-scwrl # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_139132285.pdb -s /var/tmp/to_scwrl_139132285.seq -o /var/tmp/from_scwrl_139132285.pdb > /var/tmp/scwrl_139132285.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_139132285.pdb # conformation set from SCWRL output # naming current conformation Pmodeller6_TS3-scwrl # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1560393827.pdb -s /var/tmp/to_scwrl_1560393827.seq -o /var/tmp/from_scwrl_1560393827.pdb > /var/tmp/scwrl_1560393827.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1560393827.pdb # conformation set from SCWRL output # naming current conformation Pmodeller6_TS4-scwrl # ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1385700565.pdb -s /var/tmp/to_scwrl_1385700565.seq -o /var/tmp/from_scwrl_1385700565.pdb > /var/tmp/scwrl_1385700565.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1385700565.pdb # conformation set from SCWRL output # naming current conformation Pmodeller6_TS5-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1 # Found a chain break before 340 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_331730043.pdb -s /var/tmp/to_scwrl_331730043.seq -o /var/tmp/from_scwrl_331730043.pdb > /var/tmp/scwrl_331730043.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_331730043.pdb # conformation set from SCWRL output # naming current conformation RAPTOR-ACE_TS1-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1 # Found a chain break before 336 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_777965599.pdb -s /var/tmp/to_scwrl_777965599.seq -o /var/tmp/from_scwrl_777965599.pdb > /var/tmp/scwrl_777965599.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_777965599.pdb # conformation set from SCWRL output # naming current conformation RAPTOR-ACE_TS2-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1 # Found a chain break before 132 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_167698901.pdb -s /var/tmp/to_scwrl_167698901.seq -o /var/tmp/from_scwrl_167698901.pdb > /var/tmp/scwrl_167698901.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_167698901.pdb # conformation set from SCWRL output # naming current conformation RAPTOR-ACE_TS3-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS4.pdb.gz looking for model 1 # Found a chain break before 348 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1392113136.pdb -s /var/tmp/to_scwrl_1392113136.seq -o /var/tmp/from_scwrl_1392113136.pdb > /var/tmp/scwrl_1392113136.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1392113136.pdb # conformation set from SCWRL output # naming current conformation RAPTOR-ACE_TS4-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1 # Found a chain break before 294 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1563059526.pdb -s /var/tmp/to_scwrl_1563059526.seq -o /var/tmp/from_scwrl_1563059526.pdb > /var/tmp/scwrl_1563059526.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1563059526.pdb # conformation set from SCWRL output # naming current conformation RAPTOR-ACE_TS5-scwrl # ReadConformPDB reading from PDB file servers/RAPTORESS_TS1.pdb.gz looking for model 1 # Found a chain break before 372 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1279129026.pdb -s /var/tmp/to_scwrl_1279129026.seq -o /var/tmp/from_scwrl_1279129026.pdb > /var/tmp/scwrl_1279129026.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1279129026.pdb # conformation set from SCWRL output # naming current conformation RAPTORESS_TS1-scwrl # ReadConformPDB reading from PDB file servers/RAPTORESS_TS2.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1670503619.pdb -s /var/tmp/to_scwrl_1670503619.seq -o /var/tmp/from_scwrl_1670503619.pdb > /var/tmp/scwrl_1670503619.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1670503619.pdb # conformation set from SCWRL output # naming current conformation RAPTORESS_TS2-scwrl # ReadConformPDB reading from PDB file servers/RAPTORESS_TS3.pdb.gz looking for model 1 # Found a chain break before 369 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_654937136.pdb -s /var/tmp/to_scwrl_654937136.seq -o /var/tmp/from_scwrl_654937136.pdb > /var/tmp/scwrl_654937136.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_654937136.pdb # conformation set from SCWRL output # naming current conformation RAPTORESS_TS3-scwrl # ReadConformPDB reading from PDB file servers/RAPTORESS_TS4.pdb.gz looking for model 1 # Found a chain break before 365 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_478754049.pdb -s /var/tmp/to_scwrl_478754049.seq -o /var/tmp/from_scwrl_478754049.pdb > /var/tmp/scwrl_478754049.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_478754049.pdb # conformation set from SCWRL output # naming current conformation RAPTORESS_TS4-scwrl # ReadConformPDB reading from PDB file servers/RAPTORESS_TS5.pdb.gz looking for model 1 # Found a chain break before 354 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1692001023.pdb -s /var/tmp/to_scwrl_1692001023.seq -o /var/tmp/from_scwrl_1692001023.pdb > /var/tmp/scwrl_1692001023.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1692001023.pdb # conformation set from SCWRL output # naming current conformation RAPTORESS_TS5-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR_TS1.pdb.gz looking for model 1 # Found a chain break before 372 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2081332009.pdb -s /var/tmp/to_scwrl_2081332009.seq -o /var/tmp/from_scwrl_2081332009.pdb > /var/tmp/scwrl_2081332009.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2081332009.pdb # conformation set from SCWRL output # naming current conformation RAPTOR_TS1-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1 # Found a chain break before 363 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_490701056.pdb -s /var/tmp/to_scwrl_490701056.seq -o /var/tmp/from_scwrl_490701056.pdb > /var/tmp/scwrl_490701056.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_490701056.pdb # conformation set from SCWRL output # naming current conformation RAPTOR_TS2-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR_TS3.pdb.gz looking for model 1 # Found a chain break before 360 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1081861805.pdb -s /var/tmp/to_scwrl_1081861805.seq -o /var/tmp/from_scwrl_1081861805.pdb > /var/tmp/scwrl_1081861805.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1081861805.pdb # conformation set from SCWRL output # naming current conformation RAPTOR_TS3-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR_TS4.pdb.gz looking for model 1 # Found a chain break before 364 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1299301721.pdb -s /var/tmp/to_scwrl_1299301721.seq -o /var/tmp/from_scwrl_1299301721.pdb > /var/tmp/scwrl_1299301721.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1299301721.pdb # conformation set from SCWRL output # naming current conformation RAPTOR_TS4-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR_TS5.pdb.gz looking for model 1 # Found a chain break before 339 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1474153027.pdb -s /var/tmp/to_scwrl_1474153027.seq -o /var/tmp/from_scwrl_1474153027.pdb > /var/tmp/scwrl_1474153027.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1474153027.pdb # conformation set from SCWRL output # naming current conformation RAPTOR_TS5-scwrl # ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1 # Found a chain break before 316 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1182030411.pdb -s /var/tmp/to_scwrl_1182030411.seq -o /var/tmp/from_scwrl_1182030411.pdb > /var/tmp/scwrl_1182030411.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1182030411.pdb # conformation set from SCWRL output # naming current conformation ROBETTA_TS1-scwrl # ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1 # Found a chain break before 339 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_959182144.pdb -s /var/tmp/to_scwrl_959182144.seq -o /var/tmp/from_scwrl_959182144.pdb > /var/tmp/scwrl_959182144.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_959182144.pdb # conformation set from SCWRL output # naming current conformation ROBETTA_TS2-scwrl # ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1 # Found a chain break before 346 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1841220394.pdb -s /var/tmp/to_scwrl_1841220394.seq -o /var/tmp/from_scwrl_1841220394.pdb > /var/tmp/scwrl_1841220394.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1841220394.pdb # conformation set from SCWRL output # naming current conformation ROBETTA_TS3-scwrl # ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1 # Found a chain break before 340 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1847397755.pdb -s /var/tmp/to_scwrl_1847397755.seq -o /var/tmp/from_scwrl_1847397755.pdb > /var/tmp/scwrl_1847397755.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1847397755.pdb # conformation set from SCWRL output # naming current conformation ROBETTA_TS4-scwrl # ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1 # Found a chain break before 305 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_313322199.pdb -s /var/tmp/to_scwrl_313322199.seq -o /var/tmp/from_scwrl_313322199.pdb > /var/tmp/scwrl_313322199.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_313322199.pdb # conformation set from SCWRL output # naming current conformation ROBETTA_TS5-scwrl # ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1295925963.pdb -s /var/tmp/to_scwrl_1295925963.seq -o /var/tmp/from_scwrl_1295925963.pdb > /var/tmp/scwrl_1295925963.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1295925963.pdb # conformation set from SCWRL output # naming current conformation ROKKY_TS1-scwrl # ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_372118853.pdb -s /var/tmp/to_scwrl_372118853.seq -o /var/tmp/from_scwrl_372118853.pdb > /var/tmp/scwrl_372118853.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_372118853.pdb # conformation set from SCWRL output # naming current conformation ROKKY_TS2-scwrl # ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_687467894.pdb -s /var/tmp/to_scwrl_687467894.seq -o /var/tmp/from_scwrl_687467894.pdb > /var/tmp/scwrl_687467894.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_687467894.pdb # conformation set from SCWRL output # naming current conformation ROKKY_TS3-scwrl # ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_180111171.pdb -s /var/tmp/to_scwrl_180111171.seq -o /var/tmp/from_scwrl_180111171.pdb > /var/tmp/scwrl_180111171.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_180111171.pdb # conformation set from SCWRL output # naming current conformation ROKKY_TS4-scwrl # ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_98377785.pdb -s /var/tmp/to_scwrl_98377785.seq -o /var/tmp/from_scwrl_98377785.pdb > /var/tmp/scwrl_98377785.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_98377785.pdb # conformation set from SCWRL output # naming current conformation ROKKY_TS5-scwrl # ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1487072128.pdb -s /var/tmp/to_scwrl_1487072128.seq -o /var/tmp/from_scwrl_1487072128.pdb > /var/tmp/scwrl_1487072128.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1487072128.pdb # conformation set from SCWRL output # naming current conformation SAM-T02_AL1-scwrl # ReadConformPDB reading from PDB file servers/SAM-T02_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1427096521.pdb -s /var/tmp/to_scwrl_1427096521.seq -o /var/tmp/from_scwrl_1427096521.pdb > /var/tmp/scwrl_1427096521.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1427096521.pdb # conformation set from SCWRL output # naming current conformation SAM-T02_AL2-scwrl # ReadConformPDB reading from PDB file servers/SAM-T02_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1036864487.pdb -s /var/tmp/to_scwrl_1036864487.seq -o /var/tmp/from_scwrl_1036864487.pdb > /var/tmp/scwrl_1036864487.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1036864487.pdb # conformation set from SCWRL output # naming current conformation SAM-T02_AL3-scwrl # ReadConformPDB reading from PDB file servers/SAM-T02_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1626204413.pdb -s /var/tmp/to_scwrl_1626204413.seq -o /var/tmp/from_scwrl_1626204413.pdb > /var/tmp/scwrl_1626204413.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1626204413.pdb # conformation set from SCWRL output # naming current conformation SAM-T02_AL4-scwrl # ReadConformPDB reading from PDB file servers/SAM-T02_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_840006702.pdb -s /var/tmp/to_scwrl_840006702.seq -o /var/tmp/from_scwrl_840006702.pdb > /var/tmp/scwrl_840006702.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_840006702.pdb # conformation set from SCWRL output # naming current conformation SAM-T02_AL5-scwrl # ReadConformPDB reading from PDB file servers/SAM-T99_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_275081405.pdb -s /var/tmp/to_scwrl_275081405.seq -o /var/tmp/from_scwrl_275081405.pdb > /var/tmp/scwrl_275081405.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_275081405.pdb # conformation set from SCWRL output # naming current conformation SAM-T99_AL1-scwrl # ReadConformPDB reading from PDB file servers/SAM-T99_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1957934456.pdb -s /var/tmp/to_scwrl_1957934456.seq -o /var/tmp/from_scwrl_1957934456.pdb > /var/tmp/scwrl_1957934456.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1957934456.pdb # conformation set from SCWRL output # naming current conformation SAM-T99_AL2-scwrl # ReadConformPDB reading from PDB file servers/SAM-T99_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1617972300.pdb -s /var/tmp/to_scwrl_1617972300.seq -o /var/tmp/from_scwrl_1617972300.pdb > /var/tmp/scwrl_1617972300.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1617972300.pdb # conformation set from SCWRL output # naming current conformation SAM-T99_AL3-scwrl # ReadConformPDB reading from PDB file servers/SAM-T99_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_442780306.pdb -s /var/tmp/to_scwrl_442780306.seq -o /var/tmp/from_scwrl_442780306.pdb > /var/tmp/scwrl_442780306.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_442780306.pdb # conformation set from SCWRL output # naming current conformation SAM-T99_AL4-scwrl # ReadConformPDB reading from PDB file servers/SAM-T99_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1202563945.pdb -s /var/tmp/to_scwrl_1202563945.seq -o /var/tmp/from_scwrl_1202563945.pdb > /var/tmp/scwrl_1202563945.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1202563945.pdb # conformation set from SCWRL output # naming current conformation SAM-T99_AL5-scwrl # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1 # Found a chain break before 372 # copying to AlignedFragments data structure # naming current conformation SAM_T06_server_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1033548181.pdb -s /var/tmp/to_scwrl_1033548181.seq -o /var/tmp/from_scwrl_1033548181.pdb > /var/tmp/scwrl_1033548181.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1033548181.pdb # conformation set from SCWRL output # naming current conformation SAM_T06_server_TS1-scwrl # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1721909332.pdb -s /var/tmp/to_scwrl_1721909332.seq -o /var/tmp/from_scwrl_1721909332.pdb > /var/tmp/scwrl_1721909332.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1721909332.pdb # conformation set from SCWRL output # naming current conformation SAM_T06_server_TS2-scwrl # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_725583919.pdb -s /var/tmp/to_scwrl_725583919.seq -o /var/tmp/from_scwrl_725583919.pdb > /var/tmp/scwrl_725583919.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_725583919.pdb # conformation set from SCWRL output # naming current conformation SAM_T06_server_TS3-scwrl # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1688485316.pdb -s /var/tmp/to_scwrl_1688485316.seq -o /var/tmp/from_scwrl_1688485316.pdb > /var/tmp/scwrl_1688485316.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1688485316.pdb # conformation set from SCWRL output # naming current conformation SAM_T06_server_TS4-scwrl # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_53179734.pdb -s /var/tmp/to_scwrl_53179734.seq -o /var/tmp/from_scwrl_53179734.pdb > /var/tmp/scwrl_53179734.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_53179734.pdb # conformation set from SCWRL output # naming current conformation SAM_T06_server_TS5-scwrl # ReadConformPDB reading from PDB file servers/SP3_TS1.pdb.gz looking for model 1 # Found a chain break before 173 # copying to AlignedFragments data structure # naming current conformation SP3_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_270101295.pdb -s /var/tmp/to_scwrl_270101295.seq -o /var/tmp/from_scwrl_270101295.pdb > /var/tmp/scwrl_270101295.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_270101295.pdb # conformation set from SCWRL output # naming current conformation SP3_TS1-scwrl # ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1 # Found a chain break before 301 # copying to AlignedFragments data structure # naming current conformation SP3_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1622333678.pdb -s /var/tmp/to_scwrl_1622333678.seq -o /var/tmp/from_scwrl_1622333678.pdb > /var/tmp/scwrl_1622333678.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1622333678.pdb # conformation set from SCWRL output # naming current conformation SP3_TS2-scwrl # ReadConformPDB reading from PDB file servers/SP3_TS3.pdb.gz looking for model 1 # Found a chain break before 288 # copying to AlignedFragments data structure # naming current conformation SP3_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_543880791.pdb -s /var/tmp/to_scwrl_543880791.seq -o /var/tmp/from_scwrl_543880791.pdb > /var/tmp/scwrl_543880791.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_543880791.pdb # conformation set from SCWRL output # naming current conformation SP3_TS3-scwrl # ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1 # Found a chain break before 348 # copying to AlignedFragments data structure # naming current conformation SP3_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1351963101.pdb -s /var/tmp/to_scwrl_1351963101.seq -o /var/tmp/from_scwrl_1351963101.pdb > /var/tmp/scwrl_1351963101.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1351963101.pdb # conformation set from SCWRL output # naming current conformation SP3_TS4-scwrl # ReadConformPDB reading from PDB file servers/SP3_TS5.pdb.gz looking for model 1 # Found a chain break before 212 # copying to AlignedFragments data structure # naming current conformation SP3_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_774151753.pdb -s /var/tmp/to_scwrl_774151753.seq -o /var/tmp/from_scwrl_774151753.pdb > /var/tmp/scwrl_774151753.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_774151753.pdb # conformation set from SCWRL output # naming current conformation SP3_TS5-scwrl # ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1 # Found a chain break before 202 # copying to AlignedFragments data structure # naming current conformation SP4_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2018033818.pdb -s /var/tmp/to_scwrl_2018033818.seq -o /var/tmp/from_scwrl_2018033818.pdb > /var/tmp/scwrl_2018033818.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2018033818.pdb # conformation set from SCWRL output # naming current conformation SP4_TS1-scwrl # ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1 # Found a chain break before 170 # copying to AlignedFragments data structure # naming current conformation SP4_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_386509866.pdb -s /var/tmp/to_scwrl_386509866.seq -o /var/tmp/from_scwrl_386509866.pdb > /var/tmp/scwrl_386509866.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_386509866.pdb # conformation set from SCWRL output # naming current conformation SP4_TS2-scwrl # ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1 # Found a chain break before 259 # copying to AlignedFragments data structure # naming current conformation SP4_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1733333897.pdb -s /var/tmp/to_scwrl_1733333897.seq -o /var/tmp/from_scwrl_1733333897.pdb > /var/tmp/scwrl_1733333897.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1733333897.pdb # conformation set from SCWRL output # naming current conformation SP4_TS3-scwrl # ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1 # Found a chain break before 301 # copying to AlignedFragments data structure # naming current conformation SP4_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1711770566.pdb -s /var/tmp/to_scwrl_1711770566.seq -o /var/tmp/from_scwrl_1711770566.pdb > /var/tmp/scwrl_1711770566.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1711770566.pdb # conformation set from SCWRL output # naming current conformation SP4_TS4-scwrl # ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1 # Found a chain break before 244 # copying to AlignedFragments data structure # naming current conformation SP4_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_86423974.pdb -s /var/tmp/to_scwrl_86423974.seq -o /var/tmp/from_scwrl_86423974.pdb > /var/tmp/scwrl_86423974.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_86423974.pdb # conformation set from SCWRL output # naming current conformation SP4_TS5-scwrl # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # Found a chain break before 162 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2046656096.pdb -s /var/tmp/to_scwrl_2046656096.seq -o /var/tmp/from_scwrl_2046656096.pdb > /var/tmp/scwrl_2046656096.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2046656096.pdb # conformation set from SCWRL output # naming current conformation SPARKS2_TS1-scwrl # ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1 # Found a chain break before 266 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_860212883.pdb -s /var/tmp/to_scwrl_860212883.seq -o /var/tmp/from_scwrl_860212883.pdb > /var/tmp/scwrl_860212883.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_860212883.pdb # conformation set from SCWRL output # naming current conformation SPARKS2_TS2-scwrl # ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1 # Found a chain break before 372 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_458542827.pdb -s /var/tmp/to_scwrl_458542827.seq -o /var/tmp/from_scwrl_458542827.pdb > /var/tmp/scwrl_458542827.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_458542827.pdb # conformation set from SCWRL output # naming current conformation SPARKS2_TS3-scwrl # ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1 # Found a chain break before 200 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_586640343.pdb -s /var/tmp/to_scwrl_586640343.seq -o /var/tmp/from_scwrl_586640343.pdb > /var/tmp/scwrl_586640343.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_586640343.pdb # conformation set from SCWRL output # naming current conformation SPARKS2_TS4-scwrl # ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1 # Found a chain break before 292 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1040324054.pdb -s /var/tmp/to_scwrl_1040324054.seq -o /var/tmp/from_scwrl_1040324054.pdb > /var/tmp/scwrl_1040324054.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1040324054.pdb # conformation set from SCWRL output # naming current conformation SPARKS2_TS5-scwrl # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_556920613.pdb -s /var/tmp/to_scwrl_556920613.seq -o /var/tmp/from_scwrl_556920613.pdb > /var/tmp/scwrl_556920613.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_556920613.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_bnmx_TS1-scwrl # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2073712471.pdb -s /var/tmp/to_scwrl_2073712471.seq -o /var/tmp/from_scwrl_2073712471.pdb > /var/tmp/scwrl_2073712471.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2073712471.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_bnmx_TS2-scwrl # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_319936928.pdb -s /var/tmp/to_scwrl_319936928.seq -o /var/tmp/from_scwrl_319936928.pdb > /var/tmp/scwrl_319936928.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_319936928.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_bnmx_TS3-scwrl # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1593785099.pdb -s /var/tmp/to_scwrl_1593785099.seq -o /var/tmp/from_scwrl_1593785099.pdb > /var/tmp/scwrl_1593785099.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1593785099.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_bnmx_TS4-scwrl # ReadConformPDB reading from PDB file servers/UNI-EID_expm_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation UNI-EID_expm_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1552433237.pdb -s /var/tmp/to_scwrl_1552433237.seq -o /var/tmp/from_scwrl_1552433237.pdb > /var/tmp/scwrl_1552433237.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1552433237.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_expm_TS1-scwrl # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1159943630.pdb -s /var/tmp/to_scwrl_1159943630.seq -o /var/tmp/from_scwrl_1159943630.pdb > /var/tmp/scwrl_1159943630.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1159943630.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_sfst_AL1-scwrl # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1868866504.pdb -s /var/tmp/to_scwrl_1868866504.seq -o /var/tmp/from_scwrl_1868866504.pdb > /var/tmp/scwrl_1868866504.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1868866504.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_sfst_AL2-scwrl # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1362884047.pdb -s /var/tmp/to_scwrl_1362884047.seq -o /var/tmp/from_scwrl_1362884047.pdb > /var/tmp/scwrl_1362884047.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1362884047.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_sfst_AL3-scwrl # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_630432284.pdb -s /var/tmp/to_scwrl_630432284.seq -o /var/tmp/from_scwrl_630432284.pdb > /var/tmp/scwrl_630432284.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_630432284.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_sfst_AL4-scwrl # ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_164163164.pdb -s /var/tmp/to_scwrl_164163164.seq -o /var/tmp/from_scwrl_164163164.pdb > /var/tmp/scwrl_164163164.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_164163164.pdb # conformation set from SCWRL output # naming current conformation Zhang-Server_TS1-scwrl # ReadConformPDB reading from PDB file servers/Zhang-Server_TS2.pdb.gz looking for model 1 # Found a chain break before 361 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_417964346.pdb -s /var/tmp/to_scwrl_417964346.seq -o /var/tmp/from_scwrl_417964346.pdb > /var/tmp/scwrl_417964346.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_417964346.pdb # conformation set from SCWRL output # naming current conformation Zhang-Server_TS2-scwrl # ReadConformPDB reading from PDB file servers/Zhang-Server_TS3.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1663980464.pdb -s /var/tmp/to_scwrl_1663980464.seq -o /var/tmp/from_scwrl_1663980464.pdb > /var/tmp/scwrl_1663980464.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1663980464.pdb # conformation set from SCWRL output # naming current conformation Zhang-Server_TS3-scwrl # ReadConformPDB reading from PDB file servers/Zhang-Server_TS4.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1886072496.pdb -s /var/tmp/to_scwrl_1886072496.seq -o /var/tmp/from_scwrl_1886072496.pdb > /var/tmp/scwrl_1886072496.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1886072496.pdb # conformation set from SCWRL output # naming current conformation Zhang-Server_TS4-scwrl # ReadConformPDB reading from PDB file servers/Zhang-Server_TS5.pdb.gz looking for model 1 # Found a chain break before 363 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1143548264.pdb -s /var/tmp/to_scwrl_1143548264.seq -o /var/tmp/from_scwrl_1143548264.pdb > /var/tmp/scwrl_1143548264.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1143548264.pdb # conformation set from SCWRL output # naming current conformation Zhang-Server_TS5-scwrl # ReadConformPDB reading from PDB file servers/beautshot_TS1.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # naming current conformation beautshot_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1204982133.pdb -s /var/tmp/to_scwrl_1204982133.seq -o /var/tmp/from_scwrl_1204982133.pdb > /var/tmp/scwrl_1204982133.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1204982133.pdb # conformation set from SCWRL output # naming current conformation beautshot_TS1-scwrl # ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation beautshotbase_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1939252231.pdb -s /var/tmp/to_scwrl_1939252231.seq -o /var/tmp/from_scwrl_1939252231.pdb > /var/tmp/scwrl_1939252231.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1939252231.pdb # conformation set from SCWRL output # naming current conformation beautshotbase_TS1-scwrl # ReadConformPDB reading from PDB file servers/forecast-s_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation forecast-s_AL1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1413649560.pdb -s /var/tmp/to_scwrl_1413649560.seq -o /var/tmp/from_scwrl_1413649560.pdb > /var/tmp/scwrl_1413649560.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1413649560.pdb # conformation set from SCWRL output # naming current conformation forecast-s_AL1-scwrl # ReadConformPDB reading from PDB file servers/forecast-s_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation forecast-s_AL2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_679832165.pdb -s /var/tmp/to_scwrl_679832165.seq -o /var/tmp/from_scwrl_679832165.pdb > /var/tmp/scwrl_679832165.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_679832165.pdb # conformation set from SCWRL output # naming current conformation forecast-s_AL2-scwrl # ReadConformPDB reading from PDB file servers/forecast-s_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation forecast-s_AL3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_335649375.pdb -s /var/tmp/to_scwrl_335649375.seq -o /var/tmp/from_scwrl_335649375.pdb > /var/tmp/scwrl_335649375.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_335649375.pdb # conformation set from SCWRL output # naming current conformation forecast-s_AL3-scwrl # ReadConformPDB reading from PDB file servers/forecast-s_AL4.pdb.gz looking for model 1 Skipped atom 334, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 336, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 338, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 340, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 342, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 344, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 346, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 348, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 350, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 352, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 354, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 356, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation forecast-s_AL4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_618129015.pdb -s /var/tmp/to_scwrl_618129015.seq -o /var/tmp/from_scwrl_618129015.pdb > /var/tmp/scwrl_618129015.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_618129015.pdb # conformation set from SCWRL output # naming current conformation forecast-s_AL4-scwrl # ReadConformPDB reading from PDB file servers/forecast-s_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation forecast-s_AL5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1453983918.pdb -s /var/tmp/to_scwrl_1453983918.seq -o /var/tmp/from_scwrl_1453983918.pdb > /var/tmp/scwrl_1453983918.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1453983918.pdb # conformation set from SCWRL output # naming current conformation forecast-s_AL5-scwrl # ReadConformPDB reading from PDB file servers/gtg_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation gtg_AL1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_206199546.pdb -s /var/tmp/to_scwrl_206199546.seq -o /var/tmp/from_scwrl_206199546.pdb > /var/tmp/scwrl_206199546.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_206199546.pdb # conformation set from SCWRL output # naming current conformation gtg_AL1-scwrl # ReadConformPDB reading from PDB file servers/gtg_AL2.pdb.gz looking for model 1 Skipped atom 278, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 280, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 282, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 284, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 286, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 288, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 290, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 292, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 606, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 608, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 610, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 612, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 622, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 624, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 626, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 628, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 734, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 736, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 738, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 740, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 934, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 936, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 938, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 940, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 1042, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 1044, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 1046, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 1048, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation gtg_AL2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1004638881.pdb -s /var/tmp/to_scwrl_1004638881.seq -o /var/tmp/from_scwrl_1004638881.pdb > /var/tmp/scwrl_1004638881.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1004638881.pdb # conformation set from SCWRL output # naming current conformation gtg_AL2-scwrl # ReadConformPDB reading from PDB file servers/gtg_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation gtg_AL3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1039834169.pdb -s /var/tmp/to_scwrl_1039834169.seq -o /var/tmp/from_scwrl_1039834169.pdb > /var/tmp/scwrl_1039834169.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1039834169.pdb # conformation set from SCWRL output # naming current conformation gtg_AL3-scwrl # ReadConformPDB reading from PDB file servers/gtg_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation gtg_AL4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1917970112.pdb -s /var/tmp/to_scwrl_1917970112.seq -o /var/tmp/from_scwrl_1917970112.pdb > /var/tmp/scwrl_1917970112.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1917970112.pdb # conformation set from SCWRL output # naming current conformation gtg_AL4-scwrl # ReadConformPDB reading from PDB file servers/gtg_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation gtg_AL5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1091062855.pdb -s /var/tmp/to_scwrl_1091062855.seq -o /var/tmp/from_scwrl_1091062855.pdb > /var/tmp/scwrl_1091062855.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1091062855.pdb # conformation set from SCWRL output # naming current conformation gtg_AL5-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # Found a chain break before 363 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_939006618.pdb -s /var/tmp/to_scwrl_939006618.seq -o /var/tmp/from_scwrl_939006618.pdb > /var/tmp/scwrl_939006618.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_939006618.pdb # conformation set from SCWRL output # naming current conformation karypis.srv.2_TS1-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS2.pdb.gz looking for model 1 # Found a chain break before 367 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_630699348.pdb -s /var/tmp/to_scwrl_630699348.seq -o /var/tmp/from_scwrl_630699348.pdb > /var/tmp/scwrl_630699348.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_630699348.pdb # conformation set from SCWRL output # naming current conformation karypis.srv.2_TS2-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS3.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1549605682.pdb -s /var/tmp/to_scwrl_1549605682.seq -o /var/tmp/from_scwrl_1549605682.pdb > /var/tmp/scwrl_1549605682.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1549605682.pdb # conformation set from SCWRL output # naming current conformation karypis.srv.2_TS3-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS4.pdb.gz looking for model 1 # Found a chain break before 358 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1525646961.pdb -s /var/tmp/to_scwrl_1525646961.seq -o /var/tmp/from_scwrl_1525646961.pdb > /var/tmp/scwrl_1525646961.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1525646961.pdb # conformation set from SCWRL output # naming current conformation karypis.srv.2_TS4-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS5.pdb.gz looking for model 1 # Found a chain break before 317 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1671023402.pdb -s /var/tmp/to_scwrl_1671023402.seq -o /var/tmp/from_scwrl_1671023402.pdb > /var/tmp/scwrl_1671023402.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1671023402.pdb # conformation set from SCWRL output # naming current conformation karypis.srv.2_TS5-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS1.pdb.gz looking for model 1 WARNING: atoms too close: (T0316)G172.O and (T0316)H173.N only 0.000 apart, marking (T0316)H173.N as missing WARNING: atoms too close: (T0316)H280.O and (T0316)D281.N only 0.000 apart, marking (T0316)D281.N as missing WARNING: atoms too close: (T0316)Y364.O and (T0316)R365.N only 0.000 apart, marking (T0316)R365.N as missing # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2106526295.pdb -s /var/tmp/to_scwrl_2106526295.seq -o /var/tmp/from_scwrl_2106526295.pdb > /var/tmp/scwrl_2106526295.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2106526295.pdb # conformation set from SCWRL output # naming current conformation karypis.srv.4_TS1-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS2.pdb.gz looking for model 1 # Found a chain break before 370 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1451875785.pdb -s /var/tmp/to_scwrl_1451875785.seq -o /var/tmp/from_scwrl_1451875785.pdb > /var/tmp/scwrl_1451875785.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1451875785.pdb # conformation set from SCWRL output # naming current conformation karypis.srv.4_TS2-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS3.pdb.gz looking for model 1 WARNING: atoms too close: (T0316)I202.O and (T0316)G203.N only 0.000 apart, marking (T0316)G203.N as missing WARNING: atoms too close: (T0316)G264.O and (T0316)K265.N only 0.000 apart, marking (T0316)K265.N as missing # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1990960330.pdb -s /var/tmp/to_scwrl_1990960330.seq -o /var/tmp/from_scwrl_1990960330.pdb > /var/tmp/scwrl_1990960330.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1990960330.pdb # conformation set from SCWRL output # naming current conformation karypis.srv.4_TS3-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS4.pdb.gz looking for model 1 WARNING: atoms too close: (T0316)L143.O and (T0316)R144.N only 0.000 apart, marking (T0316)R144.N as missing WARNING: atoms too close: (T0316)R312.O and (T0316)Y313.N only 0.000 apart, marking (T0316)Y313.N as missing # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1552827747.pdb -s /var/tmp/to_scwrl_1552827747.seq -o /var/tmp/from_scwrl_1552827747.pdb > /var/tmp/scwrl_1552827747.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1552827747.pdb # conformation set from SCWRL output # naming current conformation karypis.srv.4_TS4-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS5.pdb.gz looking for model 1 WARNING: atoms too close: (T0316)C50.O and (T0316)T51.N only 0.000 apart, marking (T0316)T51.N as missing WARNING: atoms too close: (T0316)A186.O and (T0316)G187.N only 0.000 apart, marking (T0316)G187.N as missing WARNING: atoms too close: (T0316)T304.O and (T0316)L305.N only 0.000 apart, marking (T0316)L305.N as missing WARNING: atoms too close: (T0316)Y349.O and (T0316)D350.N only 0.000 apart, marking (T0316)D350.N as missing # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_856825377.pdb -s /var/tmp/to_scwrl_856825377.seq -o /var/tmp/from_scwrl_856825377.pdb > /var/tmp/scwrl_856825377.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_856825377.pdb # conformation set from SCWRL output # naming current conformation karypis.srv.4_TS5-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1003420314.pdb -s /var/tmp/to_scwrl_1003420314.seq -o /var/tmp/from_scwrl_1003420314.pdb > /var/tmp/scwrl_1003420314.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1003420314.pdb # conformation set from SCWRL output # naming current conformation karypis.srv_TS1-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1274210605.pdb -s /var/tmp/to_scwrl_1274210605.seq -o /var/tmp/from_scwrl_1274210605.pdb > /var/tmp/scwrl_1274210605.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1274210605.pdb # conformation set from SCWRL output # naming current conformation karypis.srv_TS2-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_72225777.pdb -s /var/tmp/to_scwrl_72225777.seq -o /var/tmp/from_scwrl_72225777.pdb > /var/tmp/scwrl_72225777.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_72225777.pdb # conformation set from SCWRL output # naming current conformation karypis.srv_TS3-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1633852598.pdb -s /var/tmp/to_scwrl_1633852598.seq -o /var/tmp/from_scwrl_1633852598.pdb > /var/tmp/scwrl_1633852598.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1633852598.pdb # conformation set from SCWRL output # naming current conformation karypis.srv_TS4-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1438373769.pdb -s /var/tmp/to_scwrl_1438373769.seq -o /var/tmp/from_scwrl_1438373769.pdb > /var/tmp/scwrl_1438373769.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1438373769.pdb # conformation set from SCWRL output # naming current conformation karypis.srv_TS5-scwrl # ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation keasar-server_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_490190123.pdb -s /var/tmp/to_scwrl_490190123.seq -o /var/tmp/from_scwrl_490190123.pdb > /var/tmp/scwrl_490190123.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_490190123.pdb # conformation set from SCWRL output # naming current conformation keasar-server_TS1-scwrl # ReadConformPDB reading from PDB file servers/keasar-server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation keasar-server_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1150349415.pdb -s /var/tmp/to_scwrl_1150349415.seq -o /var/tmp/from_scwrl_1150349415.pdb > /var/tmp/scwrl_1150349415.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1150349415.pdb # conformation set from SCWRL output # naming current conformation keasar-server_TS2-scwrl # ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1 # Found a chain break before 310 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1176962618.pdb -s /var/tmp/to_scwrl_1176962618.seq -o /var/tmp/from_scwrl_1176962618.pdb > /var/tmp/scwrl_1176962618.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1176962618.pdb # conformation set from SCWRL output # naming current conformation keasar-server_TS3-scwrl # ReadConformPDB reading from PDB file servers/keasar-server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation keasar-server_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1633738388.pdb -s /var/tmp/to_scwrl_1633738388.seq -o /var/tmp/from_scwrl_1633738388.pdb > /var/tmp/scwrl_1633738388.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1633738388.pdb # conformation set from SCWRL output # naming current conformation keasar-server_TS4-scwrl # ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation keasar-server_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_207847903.pdb -s /var/tmp/to_scwrl_207847903.seq -o /var/tmp/from_scwrl_207847903.pdb > /var/tmp/scwrl_207847903.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_207847903.pdb # conformation set from SCWRL output # naming current conformation keasar-server_TS5-scwrl # ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation mGen-3D_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_968731203.pdb -s /var/tmp/to_scwrl_968731203.seq -o /var/tmp/from_scwrl_968731203.pdb > /var/tmp/scwrl_968731203.log sh: line 1: 31981 Killed scwrl3 -i /var/tmp/to_scwrl_968731203.pdb -s /var/tmp/to_scwrl_968731203.seq -o /var/tmp/from_scwrl_968731203.pdb >/var/tmp/scwrl_968731203.log Error: Couldn't open file /var/tmp/from_scwrl_968731203.pdb or /var/tmp/from_scwrl_968731203.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_968731203_b.pdb or decoys//var/tmp/from_scwrl_968731203_b.pdb.gz for input Trying /var/tmp/from_scwrl_968731203_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_968731203_b.pdb or /var/tmp/from_scwrl_968731203_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_968731203_a.pdb or decoys//var/tmp/from_scwrl_968731203_a.pdb.gz for input Trying /var/tmp/from_scwrl_968731203_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_968731203_a.pdb or /var/tmp/from_scwrl_968731203_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_968731203.pdb or /var/tmp/from_scwrl_968731203_b.pdb or /var/tmp/from_scwrl_968731203_a.pdb Error: no new SCWRL conformation added # naming current conformation mGen-3D_TS1-scwrl # ReadConformPDB reading from PDB file servers/nFOLD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation nFOLD_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_899904302.pdb -s /var/tmp/to_scwrl_899904302.seq -o /var/tmp/from_scwrl_899904302.pdb > /var/tmp/scwrl_899904302.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_899904302.pdb # conformation set from SCWRL output # naming current conformation nFOLD_TS1-scwrl # ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation nFOLD_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_887680068.pdb -s /var/tmp/to_scwrl_887680068.seq -o /var/tmp/from_scwrl_887680068.pdb > /var/tmp/scwrl_887680068.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_887680068.pdb # conformation set from SCWRL output # naming current conformation nFOLD_TS2-scwrl # ReadConformPDB reading from PDB file servers/nFOLD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation nFOLD_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1304380577.pdb -s /var/tmp/to_scwrl_1304380577.seq -o /var/tmp/from_scwrl_1304380577.pdb > /var/tmp/scwrl_1304380577.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1304380577.pdb # conformation set from SCWRL output # naming current conformation nFOLD_TS3-scwrl # ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation nFOLD_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1518033316.pdb -s /var/tmp/to_scwrl_1518033316.seq -o /var/tmp/from_scwrl_1518033316.pdb > /var/tmp/scwrl_1518033316.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1518033316.pdb # conformation set from SCWRL output # naming current conformation nFOLD_TS4-scwrl # ReadConformPDB reading from PDB file servers/nFOLD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation nFOLD_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_194180339.pdb -s /var/tmp/to_scwrl_194180339.seq -o /var/tmp/from_scwrl_194180339.pdb > /var/tmp/scwrl_194180339.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_194180339.pdb # conformation set from SCWRL output # naming current conformation nFOLD_TS5-scwrl # ReadConformPDB reading from PDB file servers/panther2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation panther2_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1510580124.pdb -s /var/tmp/to_scwrl_1510580124.seq -o /var/tmp/from_scwrl_1510580124.pdb > /var/tmp/scwrl_1510580124.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1510580124.pdb # conformation set from SCWRL output # naming current conformation panther2_TS1-scwrl # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation shub_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_375188550.pdb -s /var/tmp/to_scwrl_375188550.seq -o /var/tmp/from_scwrl_375188550.pdb > /var/tmp/scwrl_375188550.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_375188550.pdb # conformation set from SCWRL output # naming current conformation shub_TS1-scwrl # command:CPU_time= 75.4485 sec, elapsed time= 2442.76 sec) # command:# Prefix for output files set to decoys/ # command:# Will now start reporting costs to decoys/evaluate_2.rdb # command:# CostConform Warning: Couldn't open file decoys//projects/compbio/experiments/undertaker/spots/near-backbone-center.spot or decoys//projects/compbio/experiments/undertaker/spots/near-backbone-center.spot.gz for input Trying /projects/compbio/experiments/undertaker/spots/near-backbone-center.spot # Reading spots from /projects/compbio/experiments/undertaker/spots/near-backbone-center.spot shub_TS1-scwrl costs 0 real_cost = 406.674 shub_TS1 costs 0 real_cost = 414.031 panther2_TS1-scwrl costs 0 real_cost = 1057.67 panther2_TS1 costs 0 real_cost = 1054.07 nFOLD_TS5-scwrl costs 0 real_cost = 407.498 nFOLD_TS5 costs 0 real_cost = 586.075 nFOLD_TS4-scwrl costs 0 real_cost = 430.76 nFOLD_TS4 costs 0 real_cost = 606.509 nFOLD_TS3-scwrl costs 0 real_cost = 401.934 nFOLD_TS3 costs 0 real_cost = 580.863 nFOLD_TS2-scwrl costs 0 real_cost = 404.692 nFOLD_TS2 costs 0 real_cost = 594.368 nFOLD_TS1-scwrl costs 0 real_cost = 391.739 nFOLD_TS1 costs 0 real_cost = 579.72 mGen-3D_TS1-scwrl costs 0 real_cost = 589.818 keasar-server_TS5-scwrl costs 0 real_cost = 483.948 keasar-server_TS5 costs 0 real_cost = 489.342 keasar-server_TS4-scwrl costs 0 real_cost = 483.948 keasar-server_TS4 costs 0 real_cost = 489.342 keasar-server_TS3-scwrl costs 0 real_cost = 321.319 keasar-server_TS3 costs 0 real_cost = 321.766 keasar-server_TS2-scwrl costs 0 real_cost = 445.704 keasar-server_TS2 costs 0 real_cost = 449.34 keasar-server_TS1-scwrl costs 0 real_cost = 468.283 keasar-server_TS1 costs 0 real_cost = 466.919 karypis.srv_TS5-scwrl costs 0 real_cost = 397.152 karypis.srv_TS5 costs 0 real_cost = 391.903 karypis.srv_TS4-scwrl costs 0 real_cost = 387.29 karypis.srv_TS4 costs 0 real_cost = 384.978 karypis.srv_TS3-scwrl costs 0 real_cost = 394.446 karypis.srv_TS3 costs 0 real_cost = 393.415 karypis.srv_TS2-scwrl costs 0 real_cost = 361.039 karypis.srv_TS2 costs 0 real_cost = 359.362 karypis.srv_TS1-scwrl costs 0 real_cost = 403.488 karypis.srv_TS1 costs 0 real_cost = 395.996 karypis.srv.4_TS5-scwrl costs 0 real_cost = 337.103 karypis.srv.4_TS5 costs 0 real_cost = 334.936 karypis.srv.4_TS4-scwrl costs 0 real_cost = 317.865 karypis.srv.4_TS4 costs 0 real_cost = 317.857 karypis.srv.4_TS3-scwrl costs 0 real_cost = 339.557 karypis.srv.4_TS3 costs 0 real_cost = 339.52 karypis.srv.4_TS2-scwrl costs 0 real_cost = 301.407 karypis.srv.4_TS2 costs 0 real_cost = 312.34 karypis.srv.4_TS1-scwrl costs 0 real_cost = 335.207 karypis.srv.4_TS1 costs 0 real_cost = 335.337 karypis.srv.2_TS5-scwrl costs 0 real_cost = 321.253 karypis.srv.2_TS5 costs 0 real_cost = 321.253 karypis.srv.2_TS4-scwrl costs 0 real_cost = 243.716 karypis.srv.2_TS4 costs 0 real_cost = 244.112 karypis.srv.2_TS3-scwrl costs 0 real_cost = 312.199 karypis.srv.2_TS3 costs 0 real_cost = 312.199 karypis.srv.2_TS2-scwrl costs 0 real_cost = 266.59 karypis.srv.2_TS2 costs 0 real_cost = 266.59 karypis.srv.2_TS1-scwrl costs 0 real_cost = 369.543 karypis.srv.2_TS1 costs 0 real_cost = 369.543 gtg_AL5-scwrl costs 0 real_cost = 650.344 gtg_AL5 costs 0 real_cost = 744.723 gtg_AL4-scwrl costs 0 real_cost = 668.034 gtg_AL4 costs 0 real_cost = 758.388 gtg_AL3-scwrl costs 0 real_cost = 639.071 gtg_AL3 costs 0 real_cost = 719.817 gtg_AL2-scwrl costs 0 real_cost = 586.504 gtg_AL2 costs 0 real_cost = 728.335 gtg_AL1-scwrl costs 0 real_cost = 579.557 gtg_AL1 costs 0 real_cost = 725.148 forecast-s_AL5-scwrl costs 0 real_cost = 596.216 forecast-s_AL5 costs 0 real_cost = 745.157 forecast-s_AL4-scwrl costs 0 real_cost = 1012.87 forecast-s_AL4 costs 0 real_cost = 1137.07 forecast-s_AL3-scwrl costs 0 real_cost = 1033.27 forecast-s_AL3 costs 0 real_cost = 1146.67 forecast-s_AL2-scwrl costs 0 real_cost = 549.492 forecast-s_AL2 costs 0 real_cost = 685.016 forecast-s_AL1-scwrl costs 0 real_cost = 510.372 forecast-s_AL1 costs 0 real_cost = 590.838 beautshotbase_TS1-scwrl costs 0 real_cost = 530.994 beautshotbase_TS1 costs 0 real_cost = 521.464 beautshot_TS1-scwrl costs 0 real_cost = 334.219 beautshot_TS1 costs 0 real_cost = 334.123 Zhang-Server_TS5-scwrl costs 0 real_cost = 287.812 Zhang-Server_TS5 costs 0 real_cost = 275.317 Zhang-Server_TS4-scwrl costs 0 real_cost = 253.395 Zhang-Server_TS4 costs 0 real_cost = 245.198 Zhang-Server_TS3-scwrl costs 0 real_cost = 200.433 Zhang-Server_TS3 costs 0 real_cost = 207.82 Zhang-Server_TS2-scwrl costs 0 real_cost = 332.174 Zhang-Server_TS2 costs 0 real_cost = 333.085 Zhang-Server_TS1-scwrl costs 0 real_cost = 222.308 Zhang-Server_TS1 costs 0 real_cost = 229.574 UNI-EID_sfst_AL4-scwrl costs 0 real_cost = 1047.67 UNI-EID_sfst_AL4 costs 0 real_cost = 1146.27 UNI-EID_sfst_AL3-scwrl costs 0 real_cost = 1074.67 UNI-EID_sfst_AL3 costs 0 real_cost = 1164.27 UNI-EID_sfst_AL2-scwrl costs 0 real_cost = 1059.47 UNI-EID_sfst_AL2 costs 0 real_cost = 1153.87 UNI-EID_sfst_AL1-scwrl costs 0 real_cost = 1057.47 UNI-EID_sfst_AL1 costs 0 real_cost = 1150.67 UNI-EID_expm_TS1-scwrl costs 0 real_cost = 341.569 UNI-EID_expm_TS1 costs 0 real_cost = 535.173 UNI-EID_bnmx_TS4-scwrl costs 0 real_cost = 479.145 UNI-EID_bnmx_TS4 costs 0 real_cost = 646.14 UNI-EID_bnmx_TS3-scwrl costs 0 real_cost = 507.958 UNI-EID_bnmx_TS3 costs 0 real_cost = 678.597 UNI-EID_bnmx_TS2-scwrl costs 0 real_cost = 596.165 UNI-EID_bnmx_TS2 costs 0 real_cost = 723.433 UNI-EID_bnmx_TS1-scwrl costs 0 real_cost = 396.331 UNI-EID_bnmx_TS1 costs 0 real_cost = 595.441 SPARKS2_TS5-scwrl costs 0 real_cost = 262.154 SPARKS2_TS5 costs 0 real_cost = 264.516 SPARKS2_TS4-scwrl costs 0 real_cost = 353.335 SPARKS2_TS4 costs 0 real_cost = 356.426 SPARKS2_TS3-scwrl costs 0 real_cost = 308.6 SPARKS2_TS3 costs 0 real_cost = 320.078 SPARKS2_TS2-scwrl costs 0 real_cost = 324.075 SPARKS2_TS2 costs 0 real_cost = 324.724 SPARKS2_TS1-scwrl costs 0 real_cost = 412.646 SPARKS2_TS1 costs 0 real_cost = 412.794 SP4_TS5-scwrl costs 0 real_cost = 349.185 SP4_TS5 costs 0 real_cost = 350.742 SP4_TS4-scwrl costs 0 real_cost = 296.565 SP4_TS4 costs 0 real_cost = 304.479 SP4_TS3-scwrl costs 0 real_cost = 285.979 SP4_TS3 costs 0 real_cost = 285.969 SP4_TS2-scwrl costs 0 real_cost = 356.705 SP4_TS2 costs 0 real_cost = 348.076 SP4_TS1-scwrl costs 0 real_cost = 414.061 SP4_TS1 costs 0 real_cost = 414.228 SP3_TS5-scwrl costs 0 real_cost = 368.773 SP3_TS5 costs 0 real_cost = 368.937 SP3_TS4-scwrl costs 0 real_cost = 279.623 SP3_TS4 costs 0 real_cost = 285.959 SP3_TS3-scwrl costs 0 real_cost = 312.054 SP3_TS3 costs 0 real_cost = 323.987 SP3_TS2-scwrl costs 0 real_cost = 318.289 SP3_TS2 costs 0 real_cost = 318.402 SP3_TS1-scwrl costs 0 real_cost = 415.508 SP3_TS1 costs 0 real_cost = 415.557 SAM_T06_server_TS5-scwrl costs 0 real_cost = 580.617 SAM_T06_server_TS5 costs 0 real_cost = 535.781 SAM_T06_server_TS4-scwrl costs 0 real_cost = 594.053 SAM_T06_server_TS4 costs 0 real_cost = 548.867 SAM_T06_server_TS3-scwrl costs 0 real_cost = 565.24 SAM_T06_server_TS3 costs 0 real_cost = 543.796 SAM_T06_server_TS2-scwrl costs 0 real_cost = 576.204 SAM_T06_server_TS2 costs 0 real_cost = 516.127 SAM_T06_server_TS1-scwrl costs 0 real_cost = 323.865 SAM_T06_server_TS1 costs 0 real_cost = 323.437 SAM-T99_AL5-scwrl costs 0 real_cost = 552.909 SAM-T99_AL5 costs 0 real_cost = 698.676 SAM-T99_AL4-scwrl costs 0 real_cost = 563.835 SAM-T99_AL4 costs 0 real_cost = 702.746 SAM-T99_AL3-scwrl costs 0 real_cost = 623.655 SAM-T99_AL3 costs 0 real_cost = 746.544 SAM-T99_AL2-scwrl costs 0 real_cost = 1096.47 SAM-T99_AL2 costs 0 real_cost = 1177.07 SAM-T99_AL1-scwrl costs 0 real_cost = 601.979 SAM-T99_AL1 costs 0 real_cost = 750.439 SAM-T02_AL5-scwrl costs 0 real_cost = 626.276 SAM-T02_AL5 costs 0 real_cost = 762.766 SAM-T02_AL4-scwrl costs 0 real_cost = 1044.07 SAM-T02_AL4 costs 0 real_cost = 1149.07 SAM-T02_AL3-scwrl costs 0 real_cost = 1080.87 SAM-T02_AL3 costs 0 real_cost = 1168.27 SAM-T02_AL2-scwrl costs 0 real_cost = 1064.27 SAM-T02_AL2 costs 0 real_cost = 1161.87 SAM-T02_AL1-scwrl costs 0 real_cost = 524.472 SAM-T02_AL1 costs 0 real_cost = 734.98 ROKKY_TS5-scwrl costs 0 real_cost = 260.472 ROKKY_TS5 costs 0 real_cost = 487.42 ROKKY_TS4-scwrl costs 0 real_cost = 344.892 ROKKY_TS4 costs 0 real_cost = 564.666 ROKKY_TS3-scwrl costs 0 real_cost = 287.457 ROKKY_TS3 costs 0 real_cost = 506.618 ROKKY_TS2-scwrl costs 0 real_cost = 270.395 ROKKY_TS2 costs 0 real_cost = 503.022 ROKKY_TS1-scwrl costs 0 real_cost = 313.927 ROKKY_TS1 costs 0 real_cost = 529.292 ROBETTA_TS5-scwrl costs 0 real_cost = 336.347 ROBETTA_TS5 costs 0 real_cost = 336.244 ROBETTA_TS4-scwrl costs 0 real_cost = 326.171 ROBETTA_TS4 costs 0 real_cost = 325.442 ROBETTA_TS3-scwrl costs 0 real_cost = 337.232 ROBETTA_TS3 costs 0 real_cost = 337.292 ROBETTA_TS2-scwrl costs 0 real_cost = 335.576 ROBETTA_TS2 costs 0 real_cost = 336.323 ROBETTA_TS1-scwrl costs 0 real_cost = 318.833 ROBETTA_TS1 costs 0 real_cost = 320.648 RAPTOR_TS5-scwrl costs 0 real_cost = 313.414 RAPTOR_TS5 costs 0 real_cost = 313.243 RAPTOR_TS4-scwrl costs 0 real_cost = 330.838 RAPTOR_TS4 costs 0 real_cost = 330.926 RAPTOR_TS3-scwrl costs 0 real_cost = 307.648 RAPTOR_TS3 costs 0 real_cost = 321.722 RAPTOR_TS2-scwrl costs 0 real_cost = 338.562 RAPTOR_TS2 costs 0 real_cost = 335.759 RAPTOR_TS1-scwrl costs 0 real_cost = 336.357 RAPTOR_TS1 costs 0 real_cost = 333.19 RAPTORESS_TS5-scwrl costs 0 real_cost = 312.138 RAPTORESS_TS5 costs 0 real_cost = 313.279 RAPTORESS_TS4-scwrl costs 0 real_cost = 324.165 RAPTORESS_TS4 costs 0 real_cost = 327.36 RAPTORESS_TS3-scwrl costs 0 real_cost = 316.959 RAPTORESS_TS3 costs 0 real_cost = 326.267 RAPTORESS_TS2-scwrl costs 0 real_cost = 332.965 RAPTORESS_TS2 costs 0 real_cost = 333.792 RAPTORESS_TS1-scwrl costs 0 real_cost = 327.092 RAPTORESS_TS1 costs 0 real_cost = 330.905 RAPTOR-ACE_TS5-scwrl costs 0 real_cost = 324.062 RAPTOR-ACE_TS5 costs 0 real_cost = 332.023 RAPTOR-ACE_TS4-scwrl costs 0 real_cost = 309.874 RAPTOR-ACE_TS4 costs 0 real_cost = 313.609 RAPTOR-ACE_TS3-scwrl costs 0 real_cost = 435.932 RAPTOR-ACE_TS3 costs 0 real_cost = 436.029 RAPTOR-ACE_TS2-scwrl costs 0 real_cost = 308.052 RAPTOR-ACE_TS2 costs 0 real_cost = 301.979 RAPTOR-ACE_TS1-scwrl costs 0 real_cost = 339.406 RAPTOR-ACE_TS1 costs 0 real_cost = 336.358 Pmodeller6_TS5-scwrl costs 0 real_cost = 343.117 Pmodeller6_TS5 costs 0 real_cost = 338.697 Pmodeller6_TS4-scwrl costs 0 real_cost = 352.14 Pmodeller6_TS4 costs 0 real_cost = 351.698 Pmodeller6_TS3-scwrl costs 0 real_cost = 341.697 Pmodeller6_TS3 costs 0 real_cost = 337.352 Pmodeller6_TS2-scwrl costs 0 real_cost = 337.812 Pmodeller6_TS2 costs 0 real_cost = 337.266 Pmodeller6_TS1-scwrl costs 0 real_cost = 342.578 Pmodeller6_TS1 costs 0 real_cost = 338.632 Phyre-2_TS5-scwrl costs 0 real_cost = 180.266 Phyre-2_TS5 costs 0 real_cost = 178.801 Phyre-2_TS4-scwrl costs 0 real_cost = 236.1 Phyre-2_TS4 costs 0 real_cost = 224.504 Phyre-2_TS3-scwrl costs 0 real_cost = 342.225 Phyre-2_TS3 costs 0 real_cost = 342.206 Phyre-2_TS2-scwrl costs 0 real_cost = 302.789 Phyre-2_TS2 costs 0 real_cost = 296.358 Phyre-2_TS1-scwrl costs 0 real_cost = 304.708 Phyre-2_TS1 costs 0 real_cost = 304.548 Phyre-1_TS1-scwrl costs 0 real_cost = 1052.87 Phyre-1_TS1 costs 0 real_cost = 1043.07 Pcons6_TS5-scwrl costs 0 real_cost = 308.062 Pcons6_TS5 costs 0 real_cost = 312.921 Pcons6_TS4-scwrl costs 0 real_cost = 355.137 Pcons6_TS4 costs 0 real_cost = 350.537 Pcons6_TS3-scwrl costs 0 real_cost = 313.164 Pcons6_TS3 costs 0 real_cost = 308.97 Pcons6_TS2-scwrl costs 0 real_cost = 304.329 Pcons6_TS2 costs 0 real_cost = 300.543 Pcons6_TS1-scwrl costs 0 real_cost = 315.441 Pcons6_TS1 costs 0 real_cost = 316.438 PROTINFO_TS5-scwrl costs 0 real_cost = 311.521 PROTINFO_TS5 costs 0 real_cost = 308.236 PROTINFO_TS4-scwrl costs 0 real_cost = 323.685 PROTINFO_TS4 costs 0 real_cost = 323.941 PROTINFO_TS3-scwrl costs 0 real_cost = 334.143 PROTINFO_TS3 costs 0 real_cost = 334.671 PROTINFO_TS2-scwrl costs 0 real_cost = 399.288 PROTINFO_TS2 costs 0 real_cost = 395.27 PROTINFO_TS1-scwrl costs 0 real_cost = 330.566 PROTINFO_TS1 costs 0 real_cost = 326.365 PROTINFO-AB_TS5-scwrl costs 0 real_cost = 286.533 PROTINFO-AB_TS5 costs 0 real_cost = 294.795 PROTINFO-AB_TS4-scwrl costs 0 real_cost = 298.217 PROTINFO-AB_TS4 costs 0 real_cost = 301.938 PROTINFO-AB_TS3-scwrl costs 0 real_cost = 269.068 PROTINFO-AB_TS3 costs 0 real_cost = 273.492 PROTINFO-AB_TS2-scwrl costs 0 real_cost = 266.834 PROTINFO-AB_TS2 costs 0 real_cost = 275.047 PROTINFO-AB_TS1-scwrl costs 0 real_cost = 266.834 PROTINFO-AB_TS1 costs 0 real_cost = 275.047 POMYSL_TS4-scwrl costs 0 real_cost = 644.633 POMYSL_TS4 costs 0 real_cost = 643.141 POMYSL_TS3-scwrl costs 0 real_cost = 615.5 POMYSL_TS3 costs 0 real_cost = 602.779 POMYSL_TS2-scwrl costs 0 real_cost = 641.781 POMYSL_TS2 costs 0 real_cost = 648.844 POMYSL_TS1-scwrl costs 0 real_cost = 644.098 POMYSL_TS1 costs 0 real_cost = 643.07 NN_PUT_lab_TS1-scwrl costs 0 real_cost = 391.739 NN_PUT_lab_TS1 costs 0 real_cost = 579.72 MetaTasser_TS5-scwrl costs 0 real_cost = 306.577 MetaTasser_TS5 costs 0 real_cost = 306.332 MetaTasser_TS4-scwrl costs 0 real_cost = 293.754 MetaTasser_TS4 costs 0 real_cost = 298.22 MetaTasser_TS3-scwrl costs 0 real_cost = 285.344 MetaTasser_TS2-scwrl costs 0 real_cost = 312.103 MetaTasser_TS2 costs 0 real_cost = 312.228 MetaTasser_TS1-scwrl costs 0 real_cost = 319.562 MetaTasser_TS1 costs 0 real_cost = 318.479 Ma-OPUS-server_TS5-scwrl costs 0 real_cost = 260.798 Ma-OPUS-server_TS5 costs 0 real_cost = 252.84 Ma-OPUS-server_TS4-scwrl costs 0 real_cost = 296.18 Ma-OPUS-server_TS4 costs 0 real_cost = 296.704 Ma-OPUS-server_TS3-scwrl costs 0 real_cost = 355.22 Ma-OPUS-server_TS3 costs 0 real_cost = 355.566 Ma-OPUS-server_TS2-scwrl costs 0 real_cost = 247.258 Ma-OPUS-server_TS2 costs 0 real_cost = 268.168 Ma-OPUS-server_TS1-scwrl costs 0 real_cost = 336.359 Ma-OPUS-server_TS1 costs 0 real_cost = 347.167 LOOPP_TS5-scwrl costs 0 real_cost = 406.294 LOOPP_TS5 costs 0 real_cost = 415.673 LOOPP_TS4-scwrl costs 0 real_cost = 340.12 LOOPP_TS4 costs 0 real_cost = 337.248 LOOPP_TS3-scwrl costs 0 real_cost = 335.65 LOOPP_TS3 costs 0 real_cost = 328.619 LOOPP_TS2-scwrl costs 0 real_cost = 286.993 LOOPP_TS2 costs 0 real_cost = 300.12 LOOPP_TS1-scwrl costs 0 real_cost = 278.472 LOOPP_TS1 costs 0 real_cost = 270.209 Huber-Torda-Server_TS5-scwrl costs 0 real_cost = 699.71 Huber-Torda-Server_TS5 costs 0 real_cost = 704.125 Huber-Torda-Server_TS4-scwrl costs 0 real_cost = 552.826 Huber-Torda-Server_TS4 costs 0 real_cost = 615.513 Huber-Torda-Server_TS3-scwrl costs 0 real_cost = 610.112 Huber-Torda-Server_TS3 costs 0 real_cost = 663.077 Huber-Torda-Server_TS2-scwrl costs 0 real_cost = 655.685 Huber-Torda-Server_TS2 costs 0 real_cost = 688.897 Huber-Torda-Server_TS1-scwrl costs 0 real_cost = 611.639 Huber-Torda-Server_TS1 costs 0 real_cost = 662.445 HHpred3_TS1-scwrl costs 0 real_cost = 386.252 HHpred3_TS1 costs 0 real_cost = 385.09 HHpred2_TS1-scwrl costs 0 real_cost = 386.252 HHpred2_TS1 costs 0 real_cost = 385.09 HHpred1_TS1-scwrl costs 0 real_cost = 325.781 HHpred1_TS1 costs 0 real_cost = 321.876 GeneSilicoMetaServer_TS5-scwrl costs 0 real_cost = 334.193 GeneSilicoMetaServer_TS5 costs 0 real_cost = 334.105 GeneSilicoMetaServer_TS4-scwrl costs 0 real_cost = 950.466 GeneSilicoMetaServer_TS4 costs 0 real_cost = 617.52 GeneSilicoMetaServer_TS3-scwrl costs 0 real_cost = 518.192 GeneSilicoMetaServer_TS3 costs 0 real_cost = 515.358 GeneSilicoMetaServer_TS2-scwrl costs 0 real_cost = 337.116 GeneSilicoMetaServer_TS1-scwrl costs 0 real_cost = 431.308 GeneSilicoMetaServer_TS1 costs 0 real_cost = 428.439 FUNCTION_TS5-scwrl costs 0 real_cost = 309.275 FUNCTION_TS5 costs 0 real_cost = 308.954 FUNCTION_TS4-scwrl costs 0 real_cost = 292.369 FUNCTION_TS4 costs 0 real_cost = 306.941 FUNCTION_TS3-scwrl costs 0 real_cost = 359.599 FUNCTION_TS3 costs 0 real_cost = 380.378 FUNCTION_TS2-scwrl costs 0 real_cost = 325.368 FUNCTION_TS2 costs 0 real_cost = 353.903 FUNCTION_TS1-scwrl costs 0 real_cost = 973.866 FUNCTION_TS1 costs 0 real_cost = 970.666 FUGUE_AL5-scwrl costs 0 real_cost = 487.059 FUGUE_AL5 costs 0 real_cost = 690.083 FUGUE_AL4-scwrl costs 0 real_cost = 390.21 FUGUE_AL4 costs 0 real_cost = 637.826 FUGUE_AL3-scwrl costs 0 real_cost = 462.908 FUGUE_AL3 costs 0 real_cost = 615.74 FUGUE_AL2-scwrl costs 0 real_cost = 1026.07 FUGUE_AL2 costs 0 real_cost = 1139.87 FUGUE_AL1-scwrl costs 0 real_cost = 490.09 FUGUE_AL1 costs 0 real_cost = 663.546 FUGMOD_TS5-scwrl costs 0 real_cost = 354.17 FUGMOD_TS5 costs 0 real_cost = 358.176 FUGMOD_TS4-scwrl costs 0 real_cost = 319.187 FUGMOD_TS4 costs 0 real_cost = 315.937 FUGMOD_TS3-scwrl costs 0 real_cost = 440.468 FUGMOD_TS3 costs 0 real_cost = 441.303 FUGMOD_TS2-scwrl costs 0 real_cost = 995.666 FUGMOD_TS2 costs 0 real_cost = 994.266 FUGMOD_TS1-scwrl costs 0 real_cost = 353.807 FUGMOD_TS1 costs 0 real_cost = 366.221 FPSOLVER-SERVER_TS5-scwrl costs 0 real_cost = 316.104 FPSOLVER-SERVER_TS5 costs 0 real_cost = 321.549 FPSOLVER-SERVER_TS4-scwrl costs 0 real_cost = 312.847 FPSOLVER-SERVER_TS4 costs 0 real_cost = 310.671 FPSOLVER-SERVER_TS3-scwrl costs 0 real_cost = 292.966 FPSOLVER-SERVER_TS3 costs 0 real_cost = 291.641 FPSOLVER-SERVER_TS2-scwrl costs 0 real_cost = 308.538 FPSOLVER-SERVER_TS2 costs 0 real_cost = 308.441 FPSOLVER-SERVER_TS1-scwrl costs 0 real_cost = 328.513 FPSOLVER-SERVER_TS1 costs 0 real_cost = 329.693 FORTE2_AL5-scwrl costs 0 real_cost = 578.026 FORTE2_AL5 costs 0 real_cost = 730.605 FORTE2_AL4-scwrl costs 0 real_cost = 730.981 FORTE2_AL3-scwrl costs 0 real_cost = 415.452 FORTE2_AL3 costs 0 real_cost = 665.469 FORTE2_AL2-scwrl costs 0 real_cost = 400.995 FORTE2_AL2 costs 0 real_cost = 648.001 FORTE2_AL1-scwrl costs 0 real_cost = 377.457 FORTE2_AL1 costs 0 real_cost = 629.309 FORTE1_AL5-scwrl costs 0 real_cost = 574.133 FORTE1_AL5 costs 0 real_cost = 707.762 FORTE1_AL4-scwrl costs 0 real_cost = 543.964 FORTE1_AL4 costs 0 real_cost = 731.749 FORTE1_AL3-scwrl costs 0 real_cost = 415.452 FORTE1_AL3 costs 0 real_cost = 665.469 FORTE1_AL2-scwrl costs 0 real_cost = 400.995 FORTE1_AL2 costs 0 real_cost = 648.001 FORTE1_AL1-scwrl costs 0 real_cost = 377.457 FORTE1_AL1 costs 0 real_cost = 629.309 FOLDpro_TS5-scwrl costs 0 real_cost = 331.087 FOLDpro_TS5 costs 0 real_cost = 328.049 FOLDpro_TS4-scwrl costs 0 real_cost = 342.751 FOLDpro_TS4 costs 0 real_cost = 342.669 FOLDpro_TS3-scwrl costs 0 real_cost = 300.5 FOLDpro_TS3 costs 0 real_cost = 305.129 FOLDpro_TS2-scwrl costs 0 real_cost = 334.744 FOLDpro_TS2 costs 0 real_cost = 335.13 FOLDpro_TS1-scwrl costs 0 real_cost = 342.461 FOLDpro_TS1 costs 0 real_cost = 342.431 FAMS_TS5-scwrl costs 0 real_cost = 347.431 FAMS_TS5 costs 0 real_cost = 343.72 FAMS_TS4-scwrl costs 0 real_cost = 973.866 FAMS_TS4 costs 0 real_cost = 970.666 FAMS_TS3-scwrl costs 0 real_cost = 973.866 FAMS_TS3 costs 0 real_cost = 970.666 FAMS_TS2-scwrl costs 0 real_cost = 333.164 FAMS_TS2 costs 0 real_cost = 340.309 FAMS_TS1-scwrl costs 0 real_cost = 266.559 FAMS_TS1 costs 0 real_cost = 269.324 FAMSD_TS5-scwrl costs 0 real_cost = 325.214 FAMSD_TS5 costs 0 real_cost = 329.311 FAMSD_TS4-scwrl costs 0 real_cost = 538.721 FAMSD_TS4 costs 0 real_cost = 529.714 FAMSD_TS3-scwrl costs 0 real_cost = 973.866 FAMSD_TS3 costs 0 real_cost = 970.666 FAMSD_TS2-scwrl costs 0 real_cost = 459.368 FAMSD_TS2 costs 0 real_cost = 455.765 FAMSD_TS1-scwrl costs 0 real_cost = 265.129 FAMSD_TS1 costs 0 real_cost = 267.532 Distill_TS5-scwrl costs 0 real_cost = 712.72 Distill_TS4-scwrl costs 0 real_cost = 712.334 Distill_TS3-scwrl costs 0 real_cost = 732.28 Distill_TS2-scwrl costs 0 real_cost = 699.621 Distill_TS1-scwrl costs 0 real_cost = 687.248 CaspIta-FOX_TS5-scwrl costs 0 real_cost = 514.357 CaspIta-FOX_TS5 costs 0 real_cost = 509.639 CaspIta-FOX_TS4-scwrl costs 0 real_cost = 474.512 CaspIta-FOX_TS4 costs 0 real_cost = 464.871 CaspIta-FOX_TS3-scwrl costs 0 real_cost = 400.235 CaspIta-FOX_TS3 costs 0 real_cost = 396.711 CaspIta-FOX_TS2-scwrl costs 0 real_cost = 400.537 CaspIta-FOX_TS2 costs 0 real_cost = 392.722 CaspIta-FOX_TS1-scwrl costs 0 real_cost = 479.011 CaspIta-FOX_TS1 costs 0 real_cost = 472.692 CPHmodels_TS1-scwrl costs 0 real_cost = 1158.07 CPHmodels_TS1 costs 0 real_cost = 1153.47 CIRCLE_TS5-scwrl costs 0 real_cost = 326.664 CIRCLE_TS5 costs 0 real_cost = 326.495 CIRCLE_TS4-scwrl costs 0 real_cost = 965.466 CIRCLE_TS4 costs 0 real_cost = 964.266 CIRCLE_TS3-scwrl costs 0 real_cost = 973.866 CIRCLE_TS3 costs 0 real_cost = 971.466 CIRCLE_TS2-scwrl costs 0 real_cost = 965.466 CIRCLE_TS2 costs 0 real_cost = 964.266 CIRCLE_TS1-scwrl costs 0 real_cost = 278.698 CIRCLE_TS1 costs 0 real_cost = 271.028 Bilab-ENABLE_TS3-scwrl costs 0 real_cost = 310.538 Bilab-ENABLE_TS3 costs 0 real_cost = 310.538 Bilab-ENABLE_TS2-scwrl costs 0 real_cost = 320.782 Bilab-ENABLE_TS2 costs 0 real_cost = 320.823 Bilab-ENABLE_TS1-scwrl costs 0 real_cost = 328.979 Bilab-ENABLE_TS1 costs 0 real_cost = 328.979 BayesHH_TS1-scwrl costs 0 real_cost = 328.073 BayesHH_TS1 costs 0 real_cost = 330.893 ABIpro_TS5-scwrl costs 0 real_cost = 243.281 ABIpro_TS5 costs 0 real_cost = 243.3 ABIpro_TS4-scwrl costs 0 real_cost = 287.229 ABIpro_TS4 costs 0 real_cost = 287.277 ABIpro_TS3-scwrl costs 0 real_cost = 277.166 ABIpro_TS3 costs 0 real_cost = 277.183 ABIpro_TS2-scwrl costs 0 real_cost = 262.142 ABIpro_TS2 costs 0 real_cost = 262.142 ABIpro_TS1-scwrl costs 0 real_cost = 258.998 ABIpro_TS1 costs 0 real_cost = 258.997 3Dpro_TS5-scwrl costs 0 real_cost = 291.976 3Dpro_TS5 costs 0 real_cost = 306.388 3Dpro_TS4-scwrl costs 0 real_cost = 329.612 3Dpro_TS4 costs 0 real_cost = 329.324 3Dpro_TS3-scwrl costs 0 real_cost = 342.461 3Dpro_TS3 costs 0 real_cost = 342.431 3Dpro_TS2-scwrl costs 0 real_cost = 351.642 3Dpro_TS2 costs 0 real_cost = 351.538 3Dpro_TS1-scwrl costs 0 real_cost = 300.5 3Dpro_TS1 costs 0 real_cost = 305.129 3D-JIGSAW_TS5-scwrl costs 0 real_cost = 416.509 3D-JIGSAW_TS5 costs 0 real_cost = 522.015 3D-JIGSAW_TS4-scwrl costs 0 real_cost = 499.516 3D-JIGSAW_TS4 costs 0 real_cost = 498.348 3D-JIGSAW_TS3-scwrl costs 0 real_cost = 1004.27 3D-JIGSAW_TS3 costs 0 real_cost = 999.866 3D-JIGSAW_TS2-scwrl costs 0 real_cost = 1006.47 3D-JIGSAW_TS2 costs 0 real_cost = 1001.47 3D-JIGSAW_TS1-scwrl costs 0 real_cost = 1014.67 3D-JIGSAW_TS1 costs 0 real_cost = 1011.47 3D-JIGSAW_RECOM_TS5-scwrl costs 0 real_cost = 973.866 3D-JIGSAW_RECOM_TS5 costs 0 real_cost = 971.466 3D-JIGSAW_RECOM_TS4-scwrl costs 0 real_cost = 973.866 3D-JIGSAW_RECOM_TS4 costs 0 real_cost = 971.466 3D-JIGSAW_RECOM_TS3-scwrl costs 0 real_cost = 983.866 3D-JIGSAW_RECOM_TS3 costs 0 real_cost = 981.466 3D-JIGSAW_RECOM_TS2-scwrl costs 0 real_cost = 973.466 3D-JIGSAW_RECOM_TS2 costs 0 real_cost = 972.466 3D-JIGSAW_RECOM_TS1-scwrl costs 0 real_cost = 973.866 3D-JIGSAW_RECOM_TS1 costs 0 real_cost = 971.466 3D-JIGSAW_POPULUS_TS5-scwrl costs 0 real_cost = 986.066 3D-JIGSAW_POPULUS_TS5 costs 0 real_cost = 982.866 3D-JIGSAW_POPULUS_TS4-scwrl costs 0 real_cost = 955.466 3D-JIGSAW_POPULUS_TS4 costs 0 real_cost = 954.266 3D-JIGSAW_POPULUS_TS3-scwrl costs 0 real_cost = 983.866 3D-JIGSAW_POPULUS_TS3 costs 0 real_cost = 981.466 3D-JIGSAW_POPULUS_TS2-scwrl costs 0 real_cost = 983.866 3D-JIGSAW_POPULUS_TS2 costs 0 real_cost = 981.466 3D-JIGSAW_POPULUS_TS1-scwrl costs 0 real_cost = 965.866 3D-JIGSAW_POPULUS_TS1 costs 0 real_cost = 963.266 make-chimera.pdb.gz costs 0 real_cost = 290.858 chimera1.pdb.gz costs 0 real_cost = 280.85 T0316.try9-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 326.261 T0316.try9-opt2.pdb.gz costs 0 real_cost = 324.516 T0316.try9-opt2.gromacs0.pdb.gz costs 0 real_cost = 326.296 T0316.try9-opt1.pdb.gz costs 0 real_cost = 324.853 T0316.try9-opt1-scwrl.pdb.gz costs 0 real_cost = 324.133 T0316.try8-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 275.98 T0316.try8-opt2.pdb.gz costs 0 real_cost = 281.875 T0316.try8-opt2.gromacs0.pdb.gz costs 0 real_cost = 281.28 T0316.try8-opt1.pdb.gz costs 0 real_cost = 280.533 T0316.try8-opt1-scwrl.pdb.gz costs 0 real_cost = 276.108 T0316.try7-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 299.212 T0316.try7-opt2.pdb.gz costs 0 real_cost = 299.542 T0316.try7-opt2.gromacs0.pdb.gz costs 0 real_cost = 309.296 T0316.try7-opt1.pdb.gz costs 0 real_cost = 301.469 T0316.try7-opt1-scwrl.pdb.gz costs 0 real_cost = 301.466 T0316.try6-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 282.226 T0316.try6-opt2.pdb.gz costs 0 real_cost = 281.217 T0316.try6-opt2.gromacs0.pdb.gz costs 0 real_cost = 287.705 T0316.try6-opt1.pdb.gz costs 0 real_cost = 283.118 T0316.try6-opt1-scwrl.pdb.gz costs 0 real_cost = 279.373 T0316.try5-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 296.601 T0316.try5-opt2.pdb.gz costs 0 real_cost = 296.491 T0316.try5-opt2.gromacs0.pdb.gz costs 0 real_cost = 283.99 T0316.try5-opt1.pdb.gz costs 0 real_cost = 288.556 T0316.try5-opt1-scwrl.pdb.gz costs 0 real_cost = 288.261 T0316.try4-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 280.587 T0316.try4-opt2.pdb.gz costs 0 real_cost = 277.702 T0316.try4-opt2.gromacs0.pdb.gz costs 0 real_cost = 281.458 T0316.try4-opt1.pdb.gz costs 0 real_cost = 280.763 T0316.try4-opt1-scwrl.pdb.gz costs 0 real_cost = 280.975 T0316.try3-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 271.874 T0316.try3-opt2.pdb.gz costs 0 real_cost = 273.309 T0316.try3-opt2.gromacs0.pdb.gz costs 0 real_cost = 262.111 T0316.try3-opt1.pdb.gz costs 0 real_cost = 280.349 T0316.try3-opt1-scwrl.pdb.gz costs 0 real_cost = 281.596 T0316.try21-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 280.645 T0316.try21-opt2.pdb.gz costs 0 real_cost = 282.285 T0316.try21-opt2.gromacs0.pdb.gz costs 0 real_cost = 291.1 T0316.try21-opt1.pdb.gz costs 0 real_cost = 281.493 T0316.try21-opt1-scwrl.pdb.gz costs 0 real_cost = 279.503 T0316.try20-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 256.883 T0316.try20-opt2.pdb.gz costs 0 real_cost = 253.258 T0316.try20-opt2.gromacs0.pdb.gz costs 0 real_cost = 259.107 T0316.try20-opt1.pdb.gz costs 0 real_cost = 254.421 T0316.try20-opt1-scwrl.pdb.gz costs 0 real_cost = 252.21 T0316.try2-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 280.644 T0316.try2-opt2.pdb.gz costs 0 real_cost = 279.075 T0316.try2-opt2.gromacs0.pdb.gz costs 0 real_cost = 281.453 T0316.try2-opt2-M1-A183-try6-opt2-A130-I373.pdb.gz costs 0 real_cost = 268.724 T0316.try2-opt1.pdb.gz costs 0 real_cost = 282.881 T0316.try2-opt1-scwrl.pdb.gz costs 0 real_cost = 281.674 T0316.try19-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 279.799 T0316.try19-opt2.pdb.gz costs 0 real_cost = 280.268 T0316.try19-opt2.gromacs0.pdb.gz costs 0 real_cost = 286.68 T0316.try19-opt1.pdb.gz costs 0 real_cost = 273.778 T0316.try19-opt1-scwrl.pdb.gz costs 0 real_cost = 272.587 T0316.try18-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 260.263 T0316.try18-opt2.pdb.gz costs 0 real_cost = 252.152 T0316.try18-opt2.gromacs0.pdb.gz costs 0 real_cost = 265.85 T0316.try18-opt1.pdb.gz costs 0 real_cost = 254.962 T0316.try18-opt1-scwrl.pdb.gz costs 0 real_cost = 255.934 T0316.try17-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 317.05 T0316.try17-opt2.pdb.gz costs 0 real_cost = 317.161 T0316.try17-opt2.gromacs0.pdb.gz costs 0 real_cost = 317.032 T0316.try17-opt1.pdb.gz costs 0 real_cost = 316.318 T0316.try17-opt1-scwrl.pdb.gz costs 0 real_cost = 316.362 T0316.try16-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 292.773 T0316.try16-opt2.pdb.gz costs 0 real_cost = 292.559 T0316.try16-opt2.gromacs0.pdb.gz costs 0 real_cost = 292.429 T0316.try16-opt1.pdb.gz costs 0 real_cost = 292.148 T0316.try16-opt1-scwrl.pdb.gz costs 0 real_cost = 292.247 T0316.try15-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 293.493 T0316.try15-opt2.pdb.gz costs 0 real_cost = 293.16 T0316.try15-opt2.gromacs0.pdb.gz costs 0 real_cost = 298.255 T0316.try15-opt1.pdb.gz costs 0 real_cost = 281.817 T0316.try15-opt1-scwrl.pdb.gz costs 0 real_cost = 280.789 T0316.try14-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 278.718 T0316.try14-opt2.pdb.gz costs 0 real_cost = 277.565 T0316.try14-opt2.gromacs0.pdb.gz costs 0 real_cost = 277.327 T0316.try14-opt1.pdb.gz costs 0 real_cost = 279.685 T0316.try14-opt1-scwrl.pdb.gz costs 0 real_cost = 276.795 T0316.try13-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 326.851 T0316.try13-opt2.pdb.gz costs 0 real_cost = 324.992 T0316.try13-opt2.gromacs0.pdb.gz costs 0 real_cost = 326.437 T0316.try13-opt1.pdb.gz costs 0 real_cost = 324.45 T0316.try13-opt1-scwrl.pdb.gz costs 0 real_cost = 323.756 T0316.try12-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 263.652 T0316.try12-opt2.pdb.gz costs 0 real_cost = 267.634 T0316.try12-opt2.gromacs0.pdb.gz costs 0 real_cost = 266.957 T0316.try12-opt1.pdb.gz costs 0 real_cost = 265.831 T0316.try12-opt1-scwrl.pdb.gz costs 0 real_cost = 271.669 T0316.try11-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 290.023 T0316.try11-opt2.pdb.gz costs 0 real_cost = 306.925 T0316.try11-opt2.gromacs0.pdb.gz costs 0 real_cost = 307.313 T0316.try11-opt1.pdb.gz costs 0 real_cost = 308.323 T0316.try11-opt1-scwrl.pdb.gz costs 0 real_cost = 308.808 T0316.try10-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 281.468 T0316.try10-opt2.pdb.gz costs 0 real_cost = 280.711 T0316.try10-opt2.gromacs0.pdb.gz costs 0 real_cost = 281.91 T0316.try10-opt1.pdb.gz costs 0 real_cost = 281.273 T0316.try10-opt1-scwrl.pdb.gz costs 0 real_cost = 276.757 T0316.try1-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 325.418 T0316.try1-opt2.pdb.gz costs 0 real_cost = 325.138 T0316.try1-opt2.gromacs0.pdb.gz costs 0 real_cost = 326.806 T0316.try1-opt1.pdb.gz costs 0 real_cost = 332.776 T0316.try1-opt1-scwrl.pdb.gz costs 0 real_cost = 332.603 T0316.M1-A183-try2-opt2-D122-K269-try1-opt2-A130-I373-try4-opt2.pdb.gz costs 0 real_cost = 253.23 T0316.M1-A183-try2-opt2-D122-K269-try1-opt2-A130-I373-try4-opt2-proteinshop.pdb.gz costs 0 real_cost = 265.872 ../model5.ts-submitted costs 0 real_cost = 306.919 ../model4.ts-submitted costs 0 real_cost = 326.978 ../model3.ts-submitted costs 0 real_cost = 277.585 ../model2.ts-submitted costs 0 real_cost = 281.877 ../model1.ts-submitted costs 0 real_cost = 282.602 align5 costs 0 real_cost = 494.906 align4 costs 0 real_cost = 517.49 align3 costs 0 real_cost = 513.653 align2 costs 0 real_cost = 557.751 align1 costs 0 real_cost = 489.307 T0316.try1-opt2.pdb costs 0 real_cost = 325.138 model5-scwrl costs 0 real_cost = 307.184 model5.ts-submitted costs 0 real_cost = 306.919 model4-scwrl costs 0 real_cost = 326.554 model4.ts-submitted costs 0 real_cost = 326.978 model3-scwrl costs 0 real_cost = 279.011 model3.ts-submitted costs 0 real_cost = 277.585 model2-scwrl costs 0 real_cost = 281.658 model2.ts-submitted costs 0 real_cost = 281.877 model1-scwrl costs 0 real_cost = 278.798 model1.ts-submitted costs 0 real_cost = 282.602 T0316_2.real.pdb costs 0 real_cost = -433.2 # command:CPU_time= 143.564 sec, elapsed time= 2511.14 sec) # command:rm -f sort.tmp /projects/compbio/bin/sorttbl real_cost < decoys/evaluate_2.rdb > sort.tmp mv -f sort.tmp decoys/evaluate_2.rdb mv -f decoys/evaluate_2.pretty decoys/evaluate_2.pretty.old mv: cannot stat `decoys/evaluate_2.pretty': No such file or directory make: [decoys/evaluate_2.pretty] Error 1 (ignored) /projects/compbio/experiments/protein-predict/casp7/scripts/prettyscore -terse -targpfx -decpoint < decoys/evaluate_2.rdb > decoys/evaluate_2.pretty rm -f decoys/evaluate_3.rdb sed -e s/XXX0000/T0316/ -e s/START_COL/1/ \ -e s/REAL_PDB/2hmaA/ \ -e s/_domain/_3/ \ -e s/read-pdb/read-pdb+servers/ \ -e 's/ReadConformPDBids/# ReadConformPDBids/' \ -e 's/# ReadConformPDB /ReadConformPDB /' \ -e 's/include COSTFCN.costfcn//' \ -e s/.COSTFCN// \ < /projects/compbio/experiments/protein-predict/casp7/starter-directory/evaluate.under \ | nice -2 /projects/compbio/programs/undertaker/undertaker # command:# Seed set to 1174700121 # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading monomeric-50pc.atoms # trans (non-proline) backbone unit: # CA= -2.2088 1.0126 -0.0031 # O= -0.1499 2.2440 0.0017 # 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= -0.1462 2.4515 0.0018 # O= -2.0272 0.9713 0.0022 # C= -0.8006 1.0755 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4659 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2099 1.0634 -0.0014 # O= -0.1233 2.2459 0.0075 # C= -0.6871 1.1518 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading monomeric-50pc.atoms have 448 chains in training database # Count of chains,residues,atoms: 448,112605,876684 # 109826 residues have no bad marker # 665 residues lack atoms needed to compute omega # 322 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 6 # HAS_OXT 325 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 523 # HAS_UNKNOWN_ATOMS 2 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 208 # NON_PLANAR_PEPTIDE 143 # BAD_PEPTIDE 1959 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-1332.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:CPU_time= 4.6333 sec, elapsed time= 4.68911 sec) # command:# Reading spots from monomeric-50pc-dry-5.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-5.hist # created burial cost function dry5 with radius 5 with spots at monomeric-50pc-dry-5.spot # command:# Reading spots from monomeric-50pc-wet-6.5.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-wet-6.5.hist # created burial cost function wet6.5 with radius 6.5 with spots at monomeric-50pc-wet-6.5.spot # command:# Reading spots from monomeric-50pc-dry-6.5.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-6.5.hist # created burial cost function dry6.5 with radius 6.5 with spots at monomeric-50pc-dry-6.5.spot # command:# Reading spots from monomeric-50pc-generic-6.5.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-generic-6.5.hist # created burial cost function gen6.5 with radius 6.5 with spots at monomeric-50pc-generic-6.5.spot # command:# Reading spots from near-backbone-center.spot # reading histogram from smoothed-near-backbone-2spot.hist # Reading spots from near-backbone-count.spot # created burial cost function near_backbone with radius 9.65 with spots at near-backbone-center.spot counting only near-backbone-count.spot # command:# Reading spots from way-back-center.spot # reading histogram from smoothed-way-back-2spot.hist # Reading spots from way-back-count.spot # created burial cost function way_back with radius 8.9 with spots at way-back-center.spot counting only way-back-count.spot # command:# Reading spots from monomeric-50pc-dry-8.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-8.hist # created burial cost function dry8 with radius 8 with spots at monomeric-50pc-dry-8.spot # command:# Reading spots from monomeric-50pc-dry-10.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-10.hist # created burial cost function dry10 with radius 10 with spots at monomeric-50pc-dry-10.spot # command:# Reading spots from monomeric-50pc-dry-12.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-12.hist # created burial cost function dry12 with radius 12 with spots at monomeric-50pc-dry-12.spot # command:# reading histogram from dunbrack-2191-alpha.hist # created alpha cost function alpha with offset 0 and 360 bins # command:# reading histogram from dunbrack-2191-alpha-1.hist # created alpha cost function alpha_prev with offset -1 and 360 bins # command:# Prefix for input files set to /projects/compbio/lib/alphabet/ # command:# Read 3 alphabets from alpha.alphabet # command:CPU_time= 4.69629 sec, elapsed time= 4.76625 sec) # command:# Prefix for input files set to # command:# Making conformation for sequence T0316 numbered 1 through 373 Created new target T0316 from T0316.a2m # command:# command:# No conformations to remove in PopConform # command:# cleared Id set # command:# command:# ReadConformPDB reading from PDB file T0316_3.real.pdb looking for model 1 Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2354, because occupancy 5.0000000e-01 <= existing 0.500 in T0316_3.real.pdb Skipped atom 2356, because occupancy 0.500 <= existing 0.500 in T0316_3.real.pdb Skipped atom 2358, because occupancy 0.500 <= existing 0.500 in T0316_3.real.pdb Skipped atom 2360, because occupancy 0.500 <= existing 0.500 in T0316_3.real.pdb Skipped atom 2362, because occupancy 0.500 <= existing 0.500 in T0316_3.real.pdb Skipped atom 2364, because occupancy 0.500 <= existing 0.500 in T0316_3.real.pdb Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2559, because occupancy 0.500 <= existing 0.500 in T0316_3.real.pdb Skipped atom 2561, because occupancy 0.500 <= existing 0.500 in T0316_3.real.pdb Skipped atom 2563, because occupancy 0.500 <= existing 0.500 in T0316_3.real.pdb Skipped atom 2565, because occupancy 0.500 <= existing 0.500 in T0316_3.real.pdb Skipped atom 2567, because occupancy 0.500 <= existing 0.500 in T0316_3.real.pdb Skipped atom 2569, because occupancy 0.500 <= existing 0.500 in T0316_3.real.pdb Skipped atom 2571, because occupancy 0.500 <= existing 0.500 in T0316_3.real.pdb Skipped atom 2573, because occupancy 0.500 <= existing 0.500 in T0316_3.real.pdb Skipped atom 2575, because occupancy 0.500 <= existing 0.500 in T0316_3.real.pdb Skipped atom 2577, because occupancy 0.500 <= existing 0.500 in T0316_3.real.pdb Skipped atom 2579, because occupancy 0.500 <= existing 0.500 in T0316_3.real.pdb Skipped atom 2671, because occupancy 0.500 <= existing 0.500 in T0316_3.real.pdb Skipped atom 2673, because occupancy 0.500 <= existing 0.500 in T0316_3.real.pdb Skipped atom 2675, because occupancy 0.500 <= existing 0.500 in T0316_3.real.pdb Skipped atom 2677, because occupancy 0.500 <= existing 0.500 in T0316_3.real.pdb Skipped atom 2679, because occupancy 0.500 <= existing 0.500 in T0316_3.real.pdb Skipped atom 2681, because occupancy 0.500 <= existing 0.500 in T0316_3.real.pdb Skipped atom 2683, because occupancy 0.500 <= existing 0.500 in T0316_3.real.pdb Skipped atom 2685, because occupancy 0.500 <= existing 0.500 in T0316_3.real.pdb Skipped atom 2687, because occupancy 0.500 <= existing 0.500 in T0316_3.real.pdb Skipped atom 2745, because occupancy 0.400 <= existing 0.600 in T0316_3.real.pdb Skipped atom 2747, because occupancy 0.400 <= existing 0.600 in T0316_3.real.pdb Skipped atom 2749, because occupancy 0.400 <= existing 0.600 in T0316_3.real.pdb Skipped atom 2751, because occupancy 0.400 <= existing 0.600 in T0316_3.real.pdb Skipped atom 2753, because occupancy 0.400 <= existing 0.600 in T0316_3.real.pdb Skipped atom 2755, because occupancy 0.400 <= existing 0.600 in T0316_3.real.pdb Skipped atom 2757, because occupancy 0.400 <= existing 0.600 in T0316_3.real.pdb Skipped atom 2759, because occupancy 0.400 <= existing 0.600 in T0316_3.real.pdb Skipped atom 2761, because occupancy 0.400 <= existing 0.600 in T0316_3.real.pdb Skipped atom 2977, because occupancy 0.500 <= existing 0.500 in T0316_3.real.pdb Skipped atom 2979, because occupancy 0.500 <= existing 0.500 in T0316_3.real.pdb Skipped atom 2981, because occupancy 0.500 <= existing 0.500 in T0316_3.real.pdb Skipped atom 2983, because occupancy 0.500 <= existing 0.500 in T0316_3.real.pdb Skipped atom 2985, because occupancy 0.500 <= existing 0.500 in T0316_3.real.pdb Skipped atom 2987, because occupancy 0.500 <= existing 0.500 in T0316_3.real.pdb Skipped atom 2989, because occupancy 0.500 <= existing 0.500 in T0316_3.real.pdb Skipped atom 2991, because occupancy 0.500 <= existing 0.500 in T0316_3.real.pdb Skipped atom 2993, because occupancy 0.500 <= existing 0.500 in T0316_3.real.pdb Skipped atom 2995, because occupancy 0.500 <= existing 0.500 in T0316_3.real.pdb Skipped atom 2997, because occupancy 0.500 <= existing 0.500 in T0316_3.real.pdb # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # command:# Saving current conformation as real # command:# Prefix for output files set to decoys/ # command:# SetRealCost created real_cost = # ( 50 * real_hbond + 50 * real_hbond_u + 50 * decoy_hbond + 50 * decoy_hbond_u + 10 * real_NO_hbond + 10 * real_NO_hbond_u + 10 * decoy_NO_hbond + 10 * decoy_NO_hbond_u + 10 * knot + 200 * clens + 0 * rmsd + 35 * log_rmsd + 0 * rmsd_ca + 30 * log_rmsd_ca + 1 * GDT + 1 * smooth_GDT + 0.2 * missing_atoms ) # command:# SetCost created cost = # ) # command:CPU_time= 6.559 sec, elapsed time= 6.64472 sec) # command:# Prefix for input files set to # command:# ReadConformPDB reading from PDB file model1.ts-submitted looking for model 1 # choosing archetypes in rotamer library # Found a chain break before 371 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -31.9444 # GDT_score(maxd=8,maxw=2.9)= -31.9423 # GDT_score(maxd=8,maxw=3.2)= -30.1875 # GDT_score(maxd=8,maxw=3.5)= -28.5543 # GDT_score(maxd=10,maxw=3.8)= -31.0928 # GDT_score(maxd=10,maxw=4)= -30.0937 # GDT_score(maxd=10,maxw=4.2)= -29.1548 # GDT_score(maxd=12,maxw=4.3)= -32.0091 # GDT_score(maxd=12,maxw=4.5)= -31.0385 # GDT_score(maxd=12,maxw=4.7)= -30.1108 # GDT_score(maxd=14,maxw=5.2)= -30.6696 # GDT_score(maxd=14,maxw=5.5)= -29.3668 # command:# Prefix for output files set to # command:superimposing iter= 0 total_weight= 1071.000 rmsd (weighted)= 13.449 (unweighted)= 66.173 superimposing iter= 1 total_weight= 2505.590 rmsd (weighted)= 6.706 (unweighted)= 67.488 superimposing iter= 2 total_weight= 1229.652 rmsd (weighted)= 4.922 (unweighted)= 68.018 superimposing iter= 3 total_weight= 1088.426 rmsd (weighted)= 3.894 (unweighted)= 67.947 superimposing iter= 4 total_weight= 911.921 rmsd (weighted)= 3.389 (unweighted)= 67.641 superimposing iter= 5 total_weight= 828.952 rmsd (weighted)= 3.102 (unweighted)= 67.338 # command:# Prefix for output files set to decoys/ # command:# request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1162900524.pdb -s /var/tmp/to_scwrl_1162900524.seq -o /var/tmp/from_scwrl_1162900524.pdb > /var/tmp/scwrl_1162900524.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1162900524.pdb # conformation set from SCWRL output # command:# naming current conformation model1-scwrl # command:# ReadConformPDB reading from PDB file model2.ts-submitted looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -31.6667 # GDT_score(maxd=8,maxw=2.9)= -32.2871 # GDT_score(maxd=8,maxw=3.2)= -30.4557 # GDT_score(maxd=8,maxw=3.5)= -28.7999 # GDT_score(maxd=10,maxw=3.8)= -31.167 # GDT_score(maxd=10,maxw=4)= -30.1087 # GDT_score(maxd=10,maxw=4.2)= -29.1511 # GDT_score(maxd=12,maxw=4.3)= -31.8688 # GDT_score(maxd=12,maxw=4.5)= -30.8898 # GDT_score(maxd=12,maxw=4.7)= -29.9536 # GDT_score(maxd=14,maxw=5.2)= -30.4661 # GDT_score(maxd=14,maxw=5.5)= -29.2286 # command:# request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1047714357.pdb -s /var/tmp/to_scwrl_1047714357.seq -o /var/tmp/from_scwrl_1047714357.pdb > /var/tmp/scwrl_1047714357.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1047714357.pdb # conformation set from SCWRL output # command:# naming current conformation model2-scwrl # command:# ReadConformPDB reading from PDB file model3.ts-submitted looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -33.6111 # GDT_score(maxd=8,maxw=2.9)= -33.8722 # GDT_score(maxd=8,maxw=3.2)= -31.847 # GDT_score(maxd=8,maxw=3.5)= -30.0696 # GDT_score(maxd=10,maxw=3.8)= -32.7462 # GDT_score(maxd=10,maxw=4)= -31.6645 # GDT_score(maxd=10,maxw=4.2)= -30.6696 # GDT_score(maxd=12,maxw=4.3)= -33.5819 # GDT_score(maxd=12,maxw=4.5)= -32.5591 # GDT_score(maxd=12,maxw=4.7)= -31.5526 # GDT_score(maxd=14,maxw=5.2)= -32.0144 # GDT_score(maxd=14,maxw=5.5)= -30.6536 # command:# request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2062816518.pdb -s /var/tmp/to_scwrl_2062816518.seq -o /var/tmp/from_scwrl_2062816518.pdb > /var/tmp/scwrl_2062816518.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2062816518.pdb # conformation set from SCWRL output # command:# naming current conformation model3-scwrl # command:# ReadConformPDB reading from PDB file model4.ts-submitted looking for model 1 # Found a chain break before 355 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -15 # GDT_score(maxd=8,maxw=2.9)= -13.5683 # GDT_score(maxd=8,maxw=3.2)= -12.8397 # GDT_score(maxd=8,maxw=3.5)= -12.2154 # GDT_score(maxd=10,maxw=3.8)= -14.2687 # GDT_score(maxd=10,maxw=4)= -13.8065 # GDT_score(maxd=10,maxw=4.2)= -13.3607 # GDT_score(maxd=12,maxw=4.3)= -15.5395 # GDT_score(maxd=12,maxw=4.5)= -15.0464 # GDT_score(maxd=12,maxw=4.7)= -14.5953 # GDT_score(maxd=14,maxw=5.2)= -15.5962 # GDT_score(maxd=14,maxw=5.5)= -14.9879 # command:# request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1476195371.pdb -s /var/tmp/to_scwrl_1476195371.seq -o /var/tmp/from_scwrl_1476195371.pdb > /var/tmp/scwrl_1476195371.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1476195371.pdb # conformation set from SCWRL output # command:# naming current conformation model4-scwrl # command:# ReadConformPDB reading from PDB file model5.ts-submitted looking for model 1 # Found a chain break before 355 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -48.6111 # GDT_score(maxd=8,maxw=2.9)= -47.5379 # GDT_score(maxd=8,maxw=3.2)= -45.3372 # GDT_score(maxd=8,maxw=3.5)= -43.3753 # GDT_score(maxd=10,maxw=3.8)= -46.9666 # GDT_score(maxd=10,maxw=4)= -45.6085 # GDT_score(maxd=10,maxw=4.2)= -44.3312 # GDT_score(maxd=12,maxw=4.3)= -47.9693 # GDT_score(maxd=12,maxw=4.5)= -46.6631 # GDT_score(maxd=12,maxw=4.7)= -45.3604 # GDT_score(maxd=14,maxw=5.2)= -45.5992 # GDT_score(maxd=14,maxw=5.5)= -43.7112 # command:# request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_710122684.pdb -s /var/tmp/to_scwrl_710122684.seq -o /var/tmp/from_scwrl_710122684.pdb > /var/tmp/scwrl_710122684.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_710122684.pdb # conformation set from SCWRL output # command:# naming current conformation model5-scwrl # command:# Prefix for input files set to decoys/ # command:# ReadConformPDB reading from PDB file T0316.try1-opt2.pdb looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -23.3333 # GDT_score(maxd=8,maxw=2.9)= -22.4971 # GDT_score(maxd=8,maxw=3.2)= -21.4297 # GDT_score(maxd=8,maxw=3.5)= -20.4428 # GDT_score(maxd=10,maxw=3.8)= -22.4675 # GDT_score(maxd=10,maxw=4)= -21.7871 # GDT_score(maxd=10,maxw=4.2)= -21.12 # GDT_score(maxd=12,maxw=4.3)= -23.4376 # GDT_score(maxd=12,maxw=4.5)= -22.7417 # GDT_score(maxd=12,maxw=4.7)= -22.0705 # GDT_score(maxd=14,maxw=5.2)= -22.7798 # GDT_score(maxd=14,maxw=5.5)= -21.8258 # command:# Prefix for output files set to # command:superimposing iter= 0 total_weight= 1071.000 rmsd (weighted)= 15.429 (unweighted)= 64.935 superimposing iter= 1 total_weight= 1647.575 rmsd (weighted)= 9.707 (unweighted)= 69.696 superimposing iter= 2 total_weight= 1065.740 rmsd (weighted)= 7.617 (unweighted)= 73.100 superimposing iter= 3 total_weight= 942.673 rmsd (weighted)= 6.471 (unweighted)= 74.607 superimposing iter= 4 total_weight= 807.818 rmsd (weighted)= 5.989 (unweighted)= 75.413 superimposing iter= 5 total_weight= 747.198 rmsd (weighted)= 5.764 (unweighted)= 76.145 # command:# Prefix for output files set to decoys/ # command:# Prefix for input files set to # command:# ReadConformPDB reading from PDB file T0316.undertaker-align.pdb looking for model 1 WARNING: atoms too close: (T0316)M38.C and (T0316)D45.C only 0.000 apart, marking (T0316)D45.C as missing WARNING: atoms too close: (T0316)K39.N and (T0316)E46.N only 0.000 apart, marking (T0316)K39.N as missing WARNING: atoms too close: (T0316)K39.CA and (T0316)E46.CA only 0.000 apart, marking (T0316)K39.CA as missing WARNING: atoms too close: (T0316)G48.C and (T0316)T51.C only 0.000 apart, marking (T0316)T51.C as missing WARNING: atoms too close: (T0316)V49.N and (T0316)A52.N only 0.000 apart, marking (T0316)V49.N as missing WARNING: atoms too close: (T0316)V49.CA and (T0316)A52.CA only 0.000 apart, marking (T0316)V49.CA as missing WARNING: atoms too close: (T0316)I107.C and (T0316)K108.C only 0.000 apart, marking (T0316)K108.C as missing WARNING: atoms too close: (T0316)K108.N and (T0316)F109.N only 0.000 apart, marking (T0316)K108.N as missing WARNING: atoms too close: (T0316)K108.CA and (T0316)F109.CA only 0.000 apart, marking (T0316)K108.CA as missing WARNING: atoms too close: (T0316)A130.C and (T0316)A133.C only 0.000 apart, marking (T0316)A133.C as missing WARNING: atoms too close: (T0316)R131.N and (T0316)R134.N only 0.000 apart, marking (T0316)R131.N as missing WARNING: atoms too close: (T0316)R131.CA and (T0316)R134.CA only 0.000 apart, marking (T0316)R131.CA as missing WARNING: atoms too close: (T0316)V146.C and (T0316)N148.C only 0.000 apart, marking (T0316)N148.C as missing WARNING: atoms too close: (T0316)D147.N and (T0316)G149.N only 0.000 apart, marking (T0316)D147.N as missing WARNING: atoms too close: (T0316)D147.CA and (T0316)G149.CA only 0.000 apart, marking (T0316)D147.CA as missing WARNING: atoms too close: (T0316)G250.C and (T0316)A258.C only 0.000 apart, marking (T0316)A258.C as missing WARNING: atoms too close: (T0316)G251.N and (T0316)P259.N only 0.000 apart, marking (T0316)G251.N as missing WARNING: atoms too close: (T0316)G251.CA and (T0316)P259.CA only 0.000 apart, marking (T0316)G251.CA as missing WARNING: atoms too close: (T0316)E298.C and (T0316)M299.C only 0.000 apart, marking (T0316)M299.C as missing WARNING: atoms too close: (T0316)M299.N and (T0316)P300.N only 0.000 apart, marking (T0316)M299.N as missing WARNING: atoms too close: (T0316)M299.CA and (T0316)P300.CA only 0.000 apart, marking (T0316)M299.CA as missing # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # command:# naming current conformation align1 # command:# fraction of real conformation used = 0.555556 # GDT_score = -19.7222 # GDT_score(maxd=8,maxw=2.9)= -19.8496 # GDT_score(maxd=8,maxw=3.2)= -19.1325 # GDT_score(maxd=8,maxw=3.5)= -18.3686 # GDT_score(maxd=10,maxw=3.8)= -19.313 # GDT_score(maxd=10,maxw=4)= -18.7918 # GDT_score(maxd=10,maxw=4.2)= -18.2712 # GDT_score(maxd=12,maxw=4.3)= -19.4047 # GDT_score(maxd=12,maxw=4.5)= -18.888 # GDT_score(maxd=12,maxw=4.7)= -18.4152 # GDT_score(maxd=14,maxw=5.2)= -18.4379 # GDT_score(maxd=14,maxw=5.5)= -17.7958 # command:# ReadConformPDB reading from PDB file T0316.undertaker-align.pdb looking for model 2 WARNING: atoms too close: (T0316)M38.C and (T0316)D43.C only 0.000 apart, marking (T0316)D43.C as missing WARNING: atoms too close: (T0316)K39.N and (T0316)T44.N only 0.000 apart, marking (T0316)K39.N as missing WARNING: atoms too close: (T0316)K39.CA and (T0316)T44.CA only 0.000 apart, marking (T0316)K39.CA as missing WARNING: atoms too close: (T0316)C50.C and (T0316)T51.C only 0.000 apart, marking (T0316)T51.C as missing WARNING: atoms too close: (T0316)T51.N and (T0316)A52.N only 0.000 apart, marking (T0316)T51.N as missing WARNING: atoms too close: (T0316)T51.CA and (T0316)A52.CA only 0.000 apart, marking (T0316)T51.CA as missing WARNING: atoms too close: (T0316)E76.C and (T0316)F87.C only 0.000 apart, marking (T0316)F87.C as missing WARNING: atoms too close: (T0316)K77.N and (T0316)L88.N only 0.000 apart, marking (T0316)K77.N as missing WARNING: atoms too close: (T0316)K77.CA and (T0316)L88.CA only 0.000 apart, marking (T0316)K77.CA as missing WARNING: atoms too close: (T0316)E106.C and (T0316)I107.C only 0.000 apart, marking (T0316)I107.C as missing WARNING: atoms too close: (T0316)I107.N and (T0316)K108.N only 0.000 apart, marking (T0316)I107.N as missing WARNING: atoms too close: (T0316)I107.CA and (T0316)K108.CA only 0.000 apart, marking (T0316)I107.CA as missing WARNING: atoms too close: (T0316)D135.C and (T0316)Q152.C only 0.000 apart, marking (T0316)Q152.C as missing WARNING: atoms too close: (T0316)E136.N and (T0316)T153.N only 0.000 apart, marking (T0316)E136.N as missing WARNING: atoms too close: (T0316)E136.CA and (T0316)T153.CA only 0.000 apart, marking (T0316)E136.CA as missing WARNING: atoms too close: (T0316)M223.C and (T0316)T286.C only 0.000 apart, marking (T0316)T286.C as missing WARNING: atoms too close: (T0316)T224.N and (T0316)S287.N only 0.000 apart, marking (T0316)T224.N as missing WARNING: atoms too close: (T0316)T224.CA and (T0316)S287.CA only 0.000 apart, marking (T0316)T224.CA as missing WARNING: atoms too close: (T0316)F311.C and (T0316)V324.C only 0.000 apart, marking (T0316)V324.C as missing WARNING: atoms too close: (T0316)R312.N and (T0316)K325.N only 0.000 apart, marking (T0316)R312.N as missing WARNING: atoms too close: (T0316)R312.CA and (T0316)K325.CA only 0.000 apart, marking (T0316)R312.CA as missing # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # command:# naming current conformation align2 # command:# fraction of real conformation used = 0.3 # GDT_score = -11.1111 # GDT_score(maxd=8,maxw=2.9)= -10.4179 # GDT_score(maxd=8,maxw=3.2)= -9.80998 # GDT_score(maxd=8,maxw=3.5)= -9.25483 # GDT_score(maxd=10,maxw=3.8)= -10.3653 # GDT_score(maxd=10,maxw=4)= -10.0137 # GDT_score(maxd=10,maxw=4.2)= -9.69562 # GDT_score(maxd=12,maxw=4.3)= -10.9262 # GDT_score(maxd=12,maxw=4.5)= -10.5887 # GDT_score(maxd=12,maxw=4.7)= -10.28 # GDT_score(maxd=14,maxw=5.2)= -10.6673 # GDT_score(maxd=14,maxw=5.5)= -10.2673 # command:# ReadConformPDB reading from PDB file T0316.undertaker-align.pdb looking for model 3 WARNING: atoms too close: (T0316)M38.C and (T0316)D45.C only 0.000 apart, marking (T0316)D45.C as missing WARNING: atoms too close: (T0316)K39.N and (T0316)E46.N only 0.000 apart, marking (T0316)K39.N as missing WARNING: atoms too close: (T0316)K39.CA and (T0316)E46.CA only 0.000 apart, marking (T0316)K39.CA as missing WARNING: atoms too close: (T0316)C50.C and (T0316)T51.C only 0.000 apart, marking (T0316)T51.C as missing WARNING: atoms too close: (T0316)T51.N and (T0316)A52.N only 0.000 apart, marking (T0316)T51.N as missing WARNING: atoms too close: (T0316)T51.CA and (T0316)A52.CA only 0.000 apart, marking (T0316)T51.CA as missing WARNING: atoms too close: (T0316)F87.C and (T0316)C103.C only 0.000 apart, marking (T0316)C103.C as missing WARNING: atoms too close: (T0316)L88.N and (T0316)N104.N only 0.000 apart, marking (T0316)L88.N as missing WARNING: atoms too close: (T0316)L88.CA and (T0316)N104.CA only 0.000 apart, marking (T0316)L88.CA as missing WARNING: atoms too close: (T0316)K108.C and (T0316)F109.C only 0.000 apart, marking (T0316)F109.C as missing WARNING: atoms too close: (T0316)F109.N and (T0316)K110.N only 0.000 apart, marking (T0316)F109.N as missing WARNING: atoms too close: (T0316)F109.CA and (T0316)K110.CA only 0.000 apart, marking (T0316)F109.CA as missing WARNING: atoms too close: (T0316)A130.C and (T0316)A133.C only 0.000 apart, marking (T0316)A133.C as missing WARNING: atoms too close: (T0316)R131.N and (T0316)R134.N only 0.000 apart, marking (T0316)R131.N as missing WARNING: atoms too close: (T0316)R131.CA and (T0316)R134.CA only 0.000 apart, marking (T0316)R131.CA as missing WARNING: atoms too close: (T0316)E162.C and (T0316)Q165.C only 0.000 apart, marking (T0316)Q165.C as missing WARNING: atoms too close: (T0316)Q163.N and (T0316)K166.N only 0.000 apart, marking (T0316)Q163.N as missing WARNING: atoms too close: (T0316)Q163.CA and (T0316)K166.CA only 0.000 apart, marking (T0316)Q163.CA as missing WARNING: atoms too close: (T0316)N206.C and (T0316)F207.C only 0.000 apart, marking (T0316)F207.C as missing WARNING: atoms too close: (T0316)F207.N and (T0316)K208.N only 0.000 apart, marking (T0316)F207.N as missing WARNING: atoms too close: (T0316)F207.CA and (T0316)K208.CA only 0.000 apart, marking (T0316)F207.CA as missing # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # command:# naming current conformation align3 # command:# ReadConformPDB reading from PDB file T0316.undertaker-align.pdb looking for model 4 WARNING: atoms too close: (T0316)M38.C and (T0316)D45.C only 0.000 apart, marking (T0316)D45.C as missing WARNING: atoms too close: (T0316)K39.N and (T0316)E46.N only 0.000 apart, marking (T0316)K39.N as missing WARNING: atoms too close: (T0316)K39.CA and (T0316)E46.CA only 0.000 apart, marking (T0316)K39.CA as missing WARNING: atoms too close: (T0316)C50.C and (T0316)T51.C only 0.000 apart, marking (T0316)T51.C as missing WARNING: atoms too close: (T0316)T51.N and (T0316)A52.N only 0.000 apart, marking (T0316)T51.N as missing WARNING: atoms too close: (T0316)T51.CA and (T0316)A52.CA only 0.000 apart, marking (T0316)T51.CA as missing WARNING: atoms too close: (T0316)Y86.C and (T0316)M102.C only 0.000 apart, marking (T0316)M102.C as missing WARNING: atoms too close: (T0316)F87.N and (T0316)C103.N only 0.000 apart, marking (T0316)F87.N as missing WARNING: atoms too close: (T0316)F87.CA and (T0316)C103.CA only 0.000 apart, marking (T0316)F87.CA as missing WARNING: atoms too close: (T0316)E106.C and (T0316)I107.C only 0.000 apart, marking (T0316)I107.C as missing WARNING: atoms too close: (T0316)I107.N and (T0316)K108.N only 0.000 apart, marking (T0316)I107.N as missing WARNING: atoms too close: (T0316)I107.CA and (T0316)K108.CA only 0.000 apart, marking (T0316)I107.CA as missing WARNING: atoms too close: (T0316)V124.C and (T0316)T126.C only 0.000 apart, marking (T0316)T126.C as missing WARNING: atoms too close: (T0316)A125.N and (T0316)G127.N only 0.000 apart, marking (T0316)A125.N as missing WARNING: atoms too close: (T0316)A125.CA and (T0316)G127.CA only 0.000 apart, marking (T0316)A125.CA as missing WARNING: atoms too close: (T0316)D135.C and (T0316)T139.C only 0.000 apart, marking (T0316)T139.C as missing WARNING: atoms too close: (T0316)E136.N and (T0316)V140.N only 0.000 apart, marking (T0316)E136.N as missing WARNING: atoms too close: (T0316)E136.CA and (T0316)V140.CA only 0.000 apart, marking (T0316)E136.CA as missing WARNING: atoms too close: (T0316)K150.C and (T0316)T167.C only 0.000 apart, marking (T0316)T167.C as missing WARNING: atoms too close: (T0316)D151.N and (T0316)M168.N only 0.000 apart, marking (T0316)D151.N as missing WARNING: atoms too close: (T0316)D151.CA and (T0316)M168.CA only 0.000 apart, marking (T0316)D151.CA as missing WARNING: atoms too close: (T0316)I199.C and (T0316)F201.C only 0.000 apart, marking (T0316)F201.C as missing WARNING: atoms too close: (T0316)C200.N and (T0316)I202.N only 0.000 apart, marking (T0316)C200.N as missing WARNING: atoms too close: (T0316)C200.CA and (T0316)I202.CA only 0.000 apart, marking (T0316)C200.CA as missing WARNING: atoms too close: (T0316)Y214.C and (T0316)S282.C only 0.000 apart, marking (T0316)S282.C as missing WARNING: atoms too close: (T0316)L215.N and (T0316)L283.N only 0.000 apart, marking (T0316)L215.N as missing WARNING: atoms too close: (T0316)L215.CA and (T0316)L283.CA only 0.000 apart, marking (T0316)L215.CA as missing # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # command:# naming current conformation align4 # command:# ReadConformPDB reading from PDB file T0316.undertaker-align.pdb looking for model 5 WARNING: atoms too close: (T0316)M38.C and (T0316)D43.C only 0.000 apart, marking (T0316)D43.C as missing WARNING: atoms too close: (T0316)K39.N and (T0316)T44.N only 0.000 apart, marking (T0316)K39.N as missing WARNING: atoms too close: (T0316)K39.CA and (T0316)T44.CA only 0.000 apart, marking (T0316)K39.CA as missing WARNING: atoms too close: (T0316)C50.C and (T0316)T51.C only 0.000 apart, marking (T0316)T51.C as missing WARNING: atoms too close: (T0316)T51.N and (T0316)A52.N only 0.000 apart, marking (T0316)T51.N as missing WARNING: atoms too close: (T0316)T51.CA and (T0316)A52.CA only 0.000 apart, marking (T0316)T51.CA as missing WARNING: atoms too close: (T0316)E76.C and (T0316)Y91.C only 0.000 apart, marking (T0316)Y91.C as missing WARNING: atoms too close: (T0316)K77.N and (T0316)R92.N only 0.000 apart, marking (T0316)K77.N as missing WARNING: atoms too close: (T0316)K77.CA and (T0316)R92.CA only 0.000 apart, marking (T0316)K77.CA as missing WARNING: atoms too close: (T0316)C103.C and (T0316)K108.C only 0.000 apart, marking (T0316)K108.C as missing WARNING: atoms too close: (T0316)N104.N and (T0316)F109.N only 0.000 apart, marking (T0316)N104.N as missing WARNING: atoms too close: (T0316)N104.CA and (T0316)F109.CA only 0.000 apart, marking (T0316)N104.CA as missing WARNING: atoms too close: (T0316)G120.C and (T0316)A121.C only 0.000 apart, marking (T0316)A121.C as missing WARNING: atoms too close: (T0316)A121.N and (T0316)D122.N only 0.000 apart, marking (T0316)A121.N as missing WARNING: atoms too close: (T0316)A121.CA and (T0316)D122.CA only 0.000 apart, marking (T0316)A121.CA as missing WARNING: atoms too close: (T0316)D135.C and (T0316)E136.C only 0.000 apart, marking (T0316)E136.C as missing WARNING: atoms too close: (T0316)E136.N and (T0316)D137.N only 0.000 apart, marking (T0316)E136.N as missing WARNING: atoms too close: (T0316)E136.CA and (T0316)D137.CA only 0.000 apart, marking (T0316)E136.CA as missing WARNING: atoms too close: (T0316)K150.C and (T0316)Q152.C only 0.000 apart, marking (T0316)Q152.C as missing WARNING: atoms too close: (T0316)D151.N and (T0316)T153.N only 0.000 apart, marking (T0316)D151.N as missing WARNING: atoms too close: (T0316)D151.CA and (T0316)T153.CA only 0.000 apart, marking (T0316)D151.CA as missing WARNING: atoms too close: (T0316)W260.C and (T0316)F311.C only 0.000 apart, marking (T0316)F311.C as missing WARNING: atoms too close: (T0316)F261.N and (T0316)R312.N only 0.000 apart, marking (T0316)F261.N as missing WARNING: atoms too close: (T0316)F261.CA and (T0316)R312.CA only 0.000 apart, marking (T0316)F261.CA as missing # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # command:# naming current conformation align5 # command:# Prefix for input files set to decoys/ # command:# reading script from file read-pdb+servers.under # ReadConformPDB reading from PDB file ../model1.ts-submitted looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ../model2.ts-submitted looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ../model3.ts-submitted looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ../model4.ts-submitted looking for model 1 # Found a chain break before 355 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ../model5.ts-submitted looking for model 1 # Found a chain break before 355 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.M1-A183-try2-opt2-D122-K269-try1-opt2-A130-I373-try4-opt2-proteinshop.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.M1-A183-try2-opt2-D122-K269-try1-opt2-A130-I373-try4-opt2.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try1-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 354 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try1-opt1.pdb.gz looking for model 1 # Found a chain break before 354 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try1-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 362 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try1-opt2.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try1-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try10-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try10-opt1.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try10-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 352 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try10-opt2.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try10-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try11-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 346 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try11-opt1.pdb.gz looking for model 1 # Found a chain break before 346 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try11-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 358 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try11-opt2.pdb.gz looking for model 1 # Found a chain break before 355 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try11-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 355 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try12-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try12-opt1.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try12-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try12-opt2.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try12-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try13-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 349 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try13-opt1.pdb.gz looking for model 1 # Found a chain break before 349 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try13-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 350 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try13-opt2.pdb.gz looking for model 1 # Found a chain break before 349 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try13-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 349 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try14-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try14-opt1.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try14-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 345 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try14-opt2.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try14-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try15-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try15-opt1.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try15-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 369 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try15-opt2.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try15-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try16-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 352 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try16-opt1.pdb.gz looking for model 1 # Found a chain break before 352 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try16-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try16-opt2.pdb.gz looking for model 1 # Found a chain break before 367 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try16-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 367 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try17-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 352 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try17-opt1.pdb.gz looking for model 1 # Found a chain break before 352 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try17-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 352 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try17-opt2.pdb.gz looking for model 1 # Found a chain break before 369 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try17-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 369 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try18-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try18-opt1.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try18-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 343 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try18-opt2.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try18-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try19-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try19-opt1.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try19-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 343 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try19-opt2.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try19-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try2-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 340 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try2-opt1.pdb.gz looking for model 1 # Found a chain break before 340 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try2-opt2-M1-A183-try6-opt2-A130-I373.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try2-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 347 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try2-opt2.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try2-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try20-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try20-opt1.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try20-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 356 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try20-opt2.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try20-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try21-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try21-opt1.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try21-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 356 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try21-opt2.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try21-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try3-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try3-opt1.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try3-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 362 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try3-opt2.pdb.gz looking for model 1 # Found a chain break before 369 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try3-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 369 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try4-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 352 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try4-opt1.pdb.gz looking for model 1 # Found a chain break before 352 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try4-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 347 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try4-opt2.pdb.gz looking for model 1 # Found a chain break before 367 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try4-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 367 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try5-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 363 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try5-opt1.pdb.gz looking for model 1 # Found a chain break before 363 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try5-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 349 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try5-opt2.pdb.gz looking for model 1 # Found a chain break before 363 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try5-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 363 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try6-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 364 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try6-opt1.pdb.gz looking for model 1 # Found a chain break before 364 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try6-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 356 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try6-opt2.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try6-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try7-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 345 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try7-opt1.pdb.gz looking for model 1 # Found a chain break before 345 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try7-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 345 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try7-opt2.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try7-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try8-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try8-opt1.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try8-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 345 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try8-opt2.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try8-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try9-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 349 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try9-opt1.pdb.gz looking for model 1 # Found a chain break before 349 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try9-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 341 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try9-opt2.pdb.gz looking for model 1 # Found a chain break before 355 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0316.try9-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 355 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file chimera1.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file make-chimera.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_743312197.pdb -s /var/tmp/to_scwrl_743312197.seq -o /var/tmp/from_scwrl_743312197.pdb > /var/tmp/scwrl_743312197.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_743312197.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_POPULUS_TS1-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1405918144.pdb -s /var/tmp/to_scwrl_1405918144.seq -o /var/tmp/from_scwrl_1405918144.pdb > /var/tmp/scwrl_1405918144.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1405918144.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_POPULUS_TS2-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1075909769.pdb -s /var/tmp/to_scwrl_1075909769.seq -o /var/tmp/from_scwrl_1075909769.pdb > /var/tmp/scwrl_1075909769.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1075909769.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_POPULUS_TS3-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_238639115.pdb -s /var/tmp/to_scwrl_238639115.seq -o /var/tmp/from_scwrl_238639115.pdb > /var/tmp/scwrl_238639115.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_238639115.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_POPULUS_TS4-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_652199320.pdb -s /var/tmp/to_scwrl_652199320.seq -o /var/tmp/from_scwrl_652199320.pdb > /var/tmp/scwrl_652199320.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_652199320.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_POPULUS_TS5-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1034188440.pdb -s /var/tmp/to_scwrl_1034188440.seq -o /var/tmp/from_scwrl_1034188440.pdb > /var/tmp/scwrl_1034188440.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1034188440.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_RECOM_TS1-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_270150894.pdb -s /var/tmp/to_scwrl_270150894.seq -o /var/tmp/from_scwrl_270150894.pdb > /var/tmp/scwrl_270150894.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_270150894.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_RECOM_TS2-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1705057715.pdb -s /var/tmp/to_scwrl_1705057715.seq -o /var/tmp/from_scwrl_1705057715.pdb > /var/tmp/scwrl_1705057715.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1705057715.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_RECOM_TS3-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_833416309.pdb -s /var/tmp/to_scwrl_833416309.seq -o /var/tmp/from_scwrl_833416309.pdb > /var/tmp/scwrl_833416309.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_833416309.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_RECOM_TS4-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_83606619.pdb -s /var/tmp/to_scwrl_83606619.seq -o /var/tmp/from_scwrl_83606619.pdb > /var/tmp/scwrl_83606619.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_83606619.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_RECOM_TS5-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_59803136.pdb -s /var/tmp/to_scwrl_59803136.seq -o /var/tmp/from_scwrl_59803136.pdb > /var/tmp/scwrl_59803136.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_59803136.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_TS1-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_354169035.pdb -s /var/tmp/to_scwrl_354169035.seq -o /var/tmp/from_scwrl_354169035.pdb > /var/tmp/scwrl_354169035.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_354169035.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_TS2-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_742837928.pdb -s /var/tmp/to_scwrl_742837928.seq -o /var/tmp/from_scwrl_742837928.pdb > /var/tmp/scwrl_742837928.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_742837928.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_TS3-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1277007904.pdb -s /var/tmp/to_scwrl_1277007904.seq -o /var/tmp/from_scwrl_1277007904.pdb > /var/tmp/scwrl_1277007904.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1277007904.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_TS4-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2054112442.pdb -s /var/tmp/to_scwrl_2054112442.seq -o /var/tmp/from_scwrl_2054112442.pdb > /var/tmp/scwrl_2054112442.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2054112442.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_TS5-scwrl # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # Found a chain break before 353 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1057801588.pdb -s /var/tmp/to_scwrl_1057801588.seq -o /var/tmp/from_scwrl_1057801588.pdb > /var/tmp/scwrl_1057801588.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1057801588.pdb # conformation set from SCWRL output # naming current conformation 3Dpro_TS1-scwrl # ReadConformPDB reading from PDB file servers/3Dpro_TS2.pdb.gz looking for model 1 # Found a chain break before 372 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1445481751.pdb -s /var/tmp/to_scwrl_1445481751.seq -o /var/tmp/from_scwrl_1445481751.pdb > /var/tmp/scwrl_1445481751.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1445481751.pdb # conformation set from SCWRL output # naming current conformation 3Dpro_TS2-scwrl # ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1 # Found a chain break before 370 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1431564713.pdb -s /var/tmp/to_scwrl_1431564713.seq -o /var/tmp/from_scwrl_1431564713.pdb > /var/tmp/scwrl_1431564713.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1431564713.pdb # conformation set from SCWRL output # naming current conformation 3Dpro_TS3-scwrl # ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1 # Found a chain break before 338 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1146556695.pdb -s /var/tmp/to_scwrl_1146556695.seq -o /var/tmp/from_scwrl_1146556695.pdb > /var/tmp/scwrl_1146556695.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1146556695.pdb # conformation set from SCWRL output # naming current conformation 3Dpro_TS4-scwrl # ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1 # Found a chain break before 341 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1226474115.pdb -s /var/tmp/to_scwrl_1226474115.seq -o /var/tmp/from_scwrl_1226474115.pdb > /var/tmp/scwrl_1226474115.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1226474115.pdb # conformation set from SCWRL output # naming current conformation 3Dpro_TS5-scwrl # ReadConformPDB reading from PDB file servers/ABIpro_TS1.pdb.gz looking for model 1 # Found a chain break before 369 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1119227198.pdb -s /var/tmp/to_scwrl_1119227198.seq -o /var/tmp/from_scwrl_1119227198.pdb > /var/tmp/scwrl_1119227198.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1119227198.pdb # conformation set from SCWRL output # naming current conformation ABIpro_TS1-scwrl # ReadConformPDB reading from PDB file servers/ABIpro_TS2.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1101574986.pdb -s /var/tmp/to_scwrl_1101574986.seq -o /var/tmp/from_scwrl_1101574986.pdb > /var/tmp/scwrl_1101574986.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1101574986.pdb # conformation set from SCWRL output # naming current conformation ABIpro_TS2-scwrl # ReadConformPDB reading from PDB file servers/ABIpro_TS3.pdb.gz looking for model 1 # Found a chain break before 369 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1530139955.pdb -s /var/tmp/to_scwrl_1530139955.seq -o /var/tmp/from_scwrl_1530139955.pdb > /var/tmp/scwrl_1530139955.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1530139955.pdb # conformation set from SCWRL output # naming current conformation ABIpro_TS3-scwrl # ReadConformPDB reading from PDB file servers/ABIpro_TS4.pdb.gz looking for model 1 # Found a chain break before 369 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1230811679.pdb -s /var/tmp/to_scwrl_1230811679.seq -o /var/tmp/from_scwrl_1230811679.pdb > /var/tmp/scwrl_1230811679.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1230811679.pdb # conformation set from SCWRL output # naming current conformation ABIpro_TS4-scwrl # ReadConformPDB reading from PDB file servers/ABIpro_TS5.pdb.gz looking for model 1 # Found a chain break before 346 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_591264307.pdb -s /var/tmp/to_scwrl_591264307.seq -o /var/tmp/from_scwrl_591264307.pdb > /var/tmp/scwrl_591264307.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_591264307.pdb # conformation set from SCWRL output # naming current conformation ABIpro_TS5-scwrl # ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1 # Found a chain break before 266 # copying to AlignedFragments data structure # naming current conformation BayesHH_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_317522442.pdb -s /var/tmp/to_scwrl_317522442.seq -o /var/tmp/from_scwrl_317522442.pdb > /var/tmp/scwrl_317522442.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_317522442.pdb # conformation set from SCWRL output # naming current conformation BayesHH_TS1-scwrl # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS1.pdb.gz looking for model 1 # Found a chain break before 346 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_246228557.pdb -s /var/tmp/to_scwrl_246228557.seq -o /var/tmp/from_scwrl_246228557.pdb > /var/tmp/scwrl_246228557.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_246228557.pdb # conformation set from SCWRL output # naming current conformation Bilab-ENABLE_TS1-scwrl # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS2.pdb.gz looking for model 1 # Found a chain break before 369 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1638978663.pdb -s /var/tmp/to_scwrl_1638978663.seq -o /var/tmp/from_scwrl_1638978663.pdb > /var/tmp/scwrl_1638978663.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1638978663.pdb # conformation set from SCWRL output # naming current conformation Bilab-ENABLE_TS2-scwrl # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS3.pdb.gz looking for model 1 # Found a chain break before 323 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_232855313.pdb -s /var/tmp/to_scwrl_232855313.seq -o /var/tmp/from_scwrl_232855313.pdb > /var/tmp/scwrl_232855313.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_232855313.pdb # conformation set from SCWRL output # naming current conformation Bilab-ENABLE_TS3-scwrl # ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1722423928.pdb -s /var/tmp/to_scwrl_1722423928.seq -o /var/tmp/from_scwrl_1722423928.pdb > /var/tmp/scwrl_1722423928.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1722423928.pdb # conformation set from SCWRL output # naming current conformation CIRCLE_TS1-scwrl # ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_201617700.pdb -s /var/tmp/to_scwrl_201617700.seq -o /var/tmp/from_scwrl_201617700.pdb > /var/tmp/scwrl_201617700.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_201617700.pdb # conformation set from SCWRL output # naming current conformation CIRCLE_TS2-scwrl # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_976167511.pdb -s /var/tmp/to_scwrl_976167511.seq -o /var/tmp/from_scwrl_976167511.pdb > /var/tmp/scwrl_976167511.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_976167511.pdb # conformation set from SCWRL output # naming current conformation CIRCLE_TS3-scwrl # ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_980858426.pdb -s /var/tmp/to_scwrl_980858426.seq -o /var/tmp/from_scwrl_980858426.pdb > /var/tmp/scwrl_980858426.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_980858426.pdb # conformation set from SCWRL output # naming current conformation CIRCLE_TS4-scwrl # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # Found a chain break before 370 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1277527469.pdb -s /var/tmp/to_scwrl_1277527469.seq -o /var/tmp/from_scwrl_1277527469.pdb > /var/tmp/scwrl_1277527469.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1277527469.pdb # conformation set from SCWRL output # naming current conformation CIRCLE_TS5-scwrl # ReadConformPDB reading from PDB file servers/CPHmodels_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation CPHmodels_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1214806625.pdb -s /var/tmp/to_scwrl_1214806625.seq -o /var/tmp/from_scwrl_1214806625.pdb > /var/tmp/scwrl_1214806625.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1214806625.pdb # conformation set from SCWRL output # naming current conformation CPHmodels_TS1-scwrl # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1633057746.pdb -s /var/tmp/to_scwrl_1633057746.seq -o /var/tmp/from_scwrl_1633057746.pdb > /var/tmp/scwrl_1633057746.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1633057746.pdb # conformation set from SCWRL output # naming current conformation CaspIta-FOX_TS1-scwrl # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_164232263.pdb -s /var/tmp/to_scwrl_164232263.seq -o /var/tmp/from_scwrl_164232263.pdb > /var/tmp/scwrl_164232263.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_164232263.pdb # conformation set from SCWRL output # naming current conformation CaspIta-FOX_TS2-scwrl # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1484957519.pdb -s /var/tmp/to_scwrl_1484957519.seq -o /var/tmp/from_scwrl_1484957519.pdb > /var/tmp/scwrl_1484957519.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1484957519.pdb # conformation set from SCWRL output # naming current conformation CaspIta-FOX_TS3-scwrl # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1190631814.pdb -s /var/tmp/to_scwrl_1190631814.seq -o /var/tmp/from_scwrl_1190631814.pdb > /var/tmp/scwrl_1190631814.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1190631814.pdb # conformation set from SCWRL output # naming current conformation CaspIta-FOX_TS4-scwrl # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_997648572.pdb -s /var/tmp/to_scwrl_997648572.seq -o /var/tmp/from_scwrl_997648572.pdb > /var/tmp/scwrl_997648572.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_997648572.pdb # conformation set from SCWRL output # naming current conformation CaspIta-FOX_TS5-scwrl # ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Distill_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1568564138.pdb -s /var/tmp/to_scwrl_1568564138.seq -o /var/tmp/from_scwrl_1568564138.pdb > /var/tmp/scwrl_1568564138.log Error: Couldn't open file /var/tmp/from_scwrl_1568564138.pdb or /var/tmp/from_scwrl_1568564138.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1568564138_b.pdb or decoys//var/tmp/from_scwrl_1568564138_b.pdb.gz for input Trying /var/tmp/from_scwrl_1568564138_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_1568564138_b.pdb or /var/tmp/from_scwrl_1568564138_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1568564138_a.pdb or decoys//var/tmp/from_scwrl_1568564138_a.pdb.gz for input Trying /var/tmp/from_scwrl_1568564138_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_1568564138_a.pdb or /var/tmp/from_scwrl_1568564138_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_1568564138.pdb or /var/tmp/from_scwrl_1568564138_b.pdb or /var/tmp/from_scwrl_1568564138_a.pdb Error: no new SCWRL conformation added # naming current conformation Distill_TS1-scwrl # ReadConformPDB reading from PDB file servers/Distill_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Distill_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1250434950.pdb -s /var/tmp/to_scwrl_1250434950.seq -o /var/tmp/from_scwrl_1250434950.pdb > /var/tmp/scwrl_1250434950.log Error: Couldn't open file /var/tmp/from_scwrl_1250434950.pdb or /var/tmp/from_scwrl_1250434950.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1250434950_b.pdb or decoys//var/tmp/from_scwrl_1250434950_b.pdb.gz for input Trying /var/tmp/from_scwrl_1250434950_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_1250434950_b.pdb or /var/tmp/from_scwrl_1250434950_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1250434950_a.pdb or decoys//var/tmp/from_scwrl_1250434950_a.pdb.gz for input Trying /var/tmp/from_scwrl_1250434950_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_1250434950_a.pdb or /var/tmp/from_scwrl_1250434950_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_1250434950.pdb or /var/tmp/from_scwrl_1250434950_b.pdb or /var/tmp/from_scwrl_1250434950_a.pdb Error: no new SCWRL conformation added # naming current conformation Distill_TS2-scwrl # ReadConformPDB reading from PDB file servers/Distill_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Distill_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1351817607.pdb -s /var/tmp/to_scwrl_1351817607.seq -o /var/tmp/from_scwrl_1351817607.pdb > /var/tmp/scwrl_1351817607.log Error: Couldn't open file /var/tmp/from_scwrl_1351817607.pdb or /var/tmp/from_scwrl_1351817607.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1351817607_b.pdb or decoys//var/tmp/from_scwrl_1351817607_b.pdb.gz for input Trying /var/tmp/from_scwrl_1351817607_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_1351817607_b.pdb or /var/tmp/from_scwrl_1351817607_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1351817607_a.pdb or decoys//var/tmp/from_scwrl_1351817607_a.pdb.gz for input Trying /var/tmp/from_scwrl_1351817607_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_1351817607_a.pdb or /var/tmp/from_scwrl_1351817607_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_1351817607.pdb or /var/tmp/from_scwrl_1351817607_b.pdb or /var/tmp/from_scwrl_1351817607_a.pdb Error: no new SCWRL conformation added # naming current conformation Distill_TS3-scwrl # ReadConformPDB reading from PDB file servers/Distill_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Distill_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_163918419.pdb -s /var/tmp/to_scwrl_163918419.seq -o /var/tmp/from_scwrl_163918419.pdb > /var/tmp/scwrl_163918419.log Error: Couldn't open file /var/tmp/from_scwrl_163918419.pdb or /var/tmp/from_scwrl_163918419.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_163918419_b.pdb or decoys//var/tmp/from_scwrl_163918419_b.pdb.gz for input Trying /var/tmp/from_scwrl_163918419_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_163918419_b.pdb or /var/tmp/from_scwrl_163918419_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_163918419_a.pdb or decoys//var/tmp/from_scwrl_163918419_a.pdb.gz for input Trying /var/tmp/from_scwrl_163918419_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_163918419_a.pdb or /var/tmp/from_scwrl_163918419_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_163918419.pdb or /var/tmp/from_scwrl_163918419_b.pdb or /var/tmp/from_scwrl_163918419_a.pdb Error: no new SCWRL conformation added # naming current conformation Distill_TS4-scwrl # ReadConformPDB reading from PDB file servers/Distill_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Distill_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_379959209.pdb -s /var/tmp/to_scwrl_379959209.seq -o /var/tmp/from_scwrl_379959209.pdb > /var/tmp/scwrl_379959209.log Error: Couldn't open file /var/tmp/from_scwrl_379959209.pdb or /var/tmp/from_scwrl_379959209.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_379959209_b.pdb or decoys//var/tmp/from_scwrl_379959209_b.pdb.gz for input Trying /var/tmp/from_scwrl_379959209_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_379959209_b.pdb or /var/tmp/from_scwrl_379959209_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_379959209_a.pdb or decoys//var/tmp/from_scwrl_379959209_a.pdb.gz for input Trying /var/tmp/from_scwrl_379959209_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_379959209_a.pdb or /var/tmp/from_scwrl_379959209_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_379959209.pdb or /var/tmp/from_scwrl_379959209_b.pdb or /var/tmp/from_scwrl_379959209_a.pdb Error: no new SCWRL conformation added # naming current conformation Distill_TS5-scwrl # ReadConformPDB reading from PDB file servers/FAMSD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FAMSD_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1258446402.pdb -s /var/tmp/to_scwrl_1258446402.seq -o /var/tmp/from_scwrl_1258446402.pdb > /var/tmp/scwrl_1258446402.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1258446402.pdb # conformation set from SCWRL output # naming current conformation FAMSD_TS1-scwrl # ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FAMSD_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1221720006.pdb -s /var/tmp/to_scwrl_1221720006.seq -o /var/tmp/from_scwrl_1221720006.pdb > /var/tmp/scwrl_1221720006.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1221720006.pdb # conformation set from SCWRL output # naming current conformation FAMSD_TS2-scwrl # ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FAMSD_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1825440960.pdb -s /var/tmp/to_scwrl_1825440960.seq -o /var/tmp/from_scwrl_1825440960.pdb > /var/tmp/scwrl_1825440960.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1825440960.pdb # conformation set from SCWRL output # naming current conformation FAMSD_TS3-scwrl # ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FAMSD_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_542527469.pdb -s /var/tmp/to_scwrl_542527469.seq -o /var/tmp/from_scwrl_542527469.pdb > /var/tmp/scwrl_542527469.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_542527469.pdb # conformation set from SCWRL output # naming current conformation FAMSD_TS4-scwrl # ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FAMSD_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_220793055.pdb -s /var/tmp/to_scwrl_220793055.seq -o /var/tmp/from_scwrl_220793055.pdb > /var/tmp/scwrl_220793055.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_220793055.pdb # conformation set from SCWRL output # naming current conformation FAMSD_TS5-scwrl # ReadConformPDB reading from PDB file servers/FAMS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FAMS_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_904431429.pdb -s /var/tmp/to_scwrl_904431429.seq -o /var/tmp/from_scwrl_904431429.pdb > /var/tmp/scwrl_904431429.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_904431429.pdb # conformation set from SCWRL output # naming current conformation FAMS_TS1-scwrl # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FAMS_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1661754667.pdb -s /var/tmp/to_scwrl_1661754667.seq -o /var/tmp/from_scwrl_1661754667.pdb > /var/tmp/scwrl_1661754667.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1661754667.pdb # conformation set from SCWRL output # naming current conformation FAMS_TS2-scwrl # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FAMS_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1322368042.pdb -s /var/tmp/to_scwrl_1322368042.seq -o /var/tmp/from_scwrl_1322368042.pdb > /var/tmp/scwrl_1322368042.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1322368042.pdb # conformation set from SCWRL output # naming current conformation FAMS_TS3-scwrl # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FAMS_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_287087737.pdb -s /var/tmp/to_scwrl_287087737.seq -o /var/tmp/from_scwrl_287087737.pdb > /var/tmp/scwrl_287087737.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_287087737.pdb # conformation set from SCWRL output # naming current conformation FAMS_TS4-scwrl # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FAMS_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_745082700.pdb -s /var/tmp/to_scwrl_745082700.seq -o /var/tmp/from_scwrl_745082700.pdb > /var/tmp/scwrl_745082700.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_745082700.pdb # conformation set from SCWRL output # naming current conformation FAMS_TS5-scwrl # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # Found a chain break before 370 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1913632349.pdb -s /var/tmp/to_scwrl_1913632349.seq -o /var/tmp/from_scwrl_1913632349.pdb > /var/tmp/scwrl_1913632349.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1913632349.pdb # conformation set from SCWRL output # naming current conformation FOLDpro_TS1-scwrl # ReadConformPDB reading from PDB file servers/FOLDpro_TS2.pdb.gz looking for model 1 # Found a chain break before 341 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_604610180.pdb -s /var/tmp/to_scwrl_604610180.seq -o /var/tmp/from_scwrl_604610180.pdb > /var/tmp/scwrl_604610180.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_604610180.pdb # conformation set from SCWRL output # naming current conformation FOLDpro_TS2-scwrl # ReadConformPDB reading from PDB file servers/FOLDpro_TS3.pdb.gz looking for model 1 # Found a chain break before 353 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_991311258.pdb -s /var/tmp/to_scwrl_991311258.seq -o /var/tmp/from_scwrl_991311258.pdb > /var/tmp/scwrl_991311258.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_991311258.pdb # conformation set from SCWRL output # naming current conformation FOLDpro_TS3-scwrl # ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1 # Found a chain break before 341 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1405127365.pdb -s /var/tmp/to_scwrl_1405127365.seq -o /var/tmp/from_scwrl_1405127365.pdb > /var/tmp/scwrl_1405127365.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1405127365.pdb # conformation set from SCWRL output # naming current conformation FOLDpro_TS4-scwrl # ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1 # Found a chain break before 335 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_837465493.pdb -s /var/tmp/to_scwrl_837465493.seq -o /var/tmp/from_scwrl_837465493.pdb > /var/tmp/scwrl_837465493.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_837465493.pdb # conformation set from SCWRL output # naming current conformation FOLDpro_TS5-scwrl # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 Skipped atom 526, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 528, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 530, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 532, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 738, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 740, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 742, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 744, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 754, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 756, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 758, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 760, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 842, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 844, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 846, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 848, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 918, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 920, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 922, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 924, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1154, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1156, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1158, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1160, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1230, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1232, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1234, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1236, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1242, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1244, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1246, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1248, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1254, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1256, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1258, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1260, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1342, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1344, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1346, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 1348, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FORTE1_AL1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_566251539.pdb -s /var/tmp/to_scwrl_566251539.seq -o /var/tmp/from_scwrl_566251539.pdb > /var/tmp/scwrl_566251539.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_566251539.pdb # conformation set from SCWRL output # naming current conformation FORTE1_AL1-scwrl # ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FORTE1_AL2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1606745065.pdb -s /var/tmp/to_scwrl_1606745065.seq -o /var/tmp/from_scwrl_1606745065.pdb > /var/tmp/scwrl_1606745065.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1606745065.pdb # conformation set from SCWRL output # naming current conformation FORTE1_AL2-scwrl # ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FORTE1_AL3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1813633003.pdb -s /var/tmp/to_scwrl_1813633003.seq -o /var/tmp/from_scwrl_1813633003.pdb > /var/tmp/scwrl_1813633003.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1813633003.pdb # conformation set from SCWRL output # naming current conformation FORTE1_AL3-scwrl # ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FORTE1_AL4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1547109965.pdb -s /var/tmp/to_scwrl_1547109965.seq -o /var/tmp/from_scwrl_1547109965.pdb > /var/tmp/scwrl_1547109965.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1547109965.pdb # conformation set from SCWRL output # naming current conformation FORTE1_AL4-scwrl # ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FORTE1_AL5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_736788888.pdb -s /var/tmp/to_scwrl_736788888.seq -o /var/tmp/from_scwrl_736788888.pdb > /var/tmp/scwrl_736788888.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_736788888.pdb # conformation set from SCWRL output # naming current conformation FORTE1_AL5-scwrl # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 Skipped atom 526, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 528, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 530, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 532, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 738, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 740, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 742, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 744, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 754, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 756, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 758, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 760, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 842, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 844, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 846, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 848, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 918, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 920, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 922, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 924, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1154, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1156, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1158, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1160, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1230, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1232, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1234, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1236, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1242, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1244, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1246, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1248, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1254, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1256, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1258, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1260, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1342, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1344, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1346, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 1348, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FORTE2_AL1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_880955982.pdb -s /var/tmp/to_scwrl_880955982.seq -o /var/tmp/from_scwrl_880955982.pdb > /var/tmp/scwrl_880955982.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_880955982.pdb # conformation set from SCWRL output # naming current conformation FORTE2_AL1-scwrl # ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FORTE2_AL2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1032684065.pdb -s /var/tmp/to_scwrl_1032684065.seq -o /var/tmp/from_scwrl_1032684065.pdb > /var/tmp/scwrl_1032684065.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1032684065.pdb # conformation set from SCWRL output # naming current conformation FORTE2_AL2-scwrl # ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FORTE2_AL3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_901021151.pdb -s /var/tmp/to_scwrl_901021151.seq -o /var/tmp/from_scwrl_901021151.pdb > /var/tmp/scwrl_901021151.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_901021151.pdb # conformation set from SCWRL output # naming current conformation FORTE2_AL3-scwrl # ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FORTE2_AL4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_218429854.pdb -s /var/tmp/to_scwrl_218429854.seq -o /var/tmp/from_scwrl_218429854.pdb > /var/tmp/scwrl_218429854.log sh: line 1: 32277 Killed scwrl3 -i /var/tmp/to_scwrl_218429854.pdb -s /var/tmp/to_scwrl_218429854.seq -o /var/tmp/from_scwrl_218429854.pdb >/var/tmp/scwrl_218429854.log Error: Couldn't open file /var/tmp/from_scwrl_218429854.pdb or /var/tmp/from_scwrl_218429854.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_218429854_b.pdb or decoys//var/tmp/from_scwrl_218429854_b.pdb.gz for input Trying /var/tmp/from_scwrl_218429854_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_218429854_b.pdb or /var/tmp/from_scwrl_218429854_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_218429854_a.pdb or decoys//var/tmp/from_scwrl_218429854_a.pdb.gz for input Trying /var/tmp/from_scwrl_218429854_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_218429854_a.pdb or /var/tmp/from_scwrl_218429854_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_218429854.pdb or /var/tmp/from_scwrl_218429854_b.pdb or /var/tmp/from_scwrl_218429854_a.pdb Error: no new SCWRL conformation added # naming current conformation FORTE2_AL4-scwrl # ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FORTE2_AL5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_75832232.pdb -s /var/tmp/to_scwrl_75832232.seq -o /var/tmp/from_scwrl_75832232.pdb > /var/tmp/scwrl_75832232.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_75832232.pdb # conformation set from SCWRL output # naming current conformation FORTE2_AL5-scwrl # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS1.pdb.gz looking for model 1 # Found a chain break before 366 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1898669723.pdb -s /var/tmp/to_scwrl_1898669723.seq -o /var/tmp/from_scwrl_1898669723.pdb > /var/tmp/scwrl_1898669723.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1898669723.pdb # conformation set from SCWRL output # naming current conformation FPSOLVER-SERVER_TS1-scwrl # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS2.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1786993992.pdb -s /var/tmp/to_scwrl_1786993992.seq -o /var/tmp/from_scwrl_1786993992.pdb > /var/tmp/scwrl_1786993992.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1786993992.pdb # conformation set from SCWRL output # naming current conformation FPSOLVER-SERVER_TS2-scwrl # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS3.pdb.gz looking for model 1 # Found a chain break before 372 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1326267182.pdb -s /var/tmp/to_scwrl_1326267182.seq -o /var/tmp/from_scwrl_1326267182.pdb > /var/tmp/scwrl_1326267182.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1326267182.pdb # conformation set from SCWRL output # naming current conformation FPSOLVER-SERVER_TS3-scwrl # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS4.pdb.gz looking for model 1 # Found a chain break before 360 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1103003683.pdb -s /var/tmp/to_scwrl_1103003683.seq -o /var/tmp/from_scwrl_1103003683.pdb > /var/tmp/scwrl_1103003683.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1103003683.pdb # conformation set from SCWRL output # naming current conformation FPSOLVER-SERVER_TS4-scwrl # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS5.pdb.gz looking for model 1 # Found a chain break before 372 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1950912412.pdb -s /var/tmp/to_scwrl_1950912412.seq -o /var/tmp/from_scwrl_1950912412.pdb > /var/tmp/scwrl_1950912412.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1950912412.pdb # conformation set from SCWRL output # naming current conformation FPSOLVER-SERVER_TS5-scwrl # ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1706226391.pdb -s /var/tmp/to_scwrl_1706226391.seq -o /var/tmp/from_scwrl_1706226391.pdb > /var/tmp/scwrl_1706226391.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1706226391.pdb # conformation set from SCWRL output # naming current conformation FUGMOD_TS1-scwrl # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_213966439.pdb -s /var/tmp/to_scwrl_213966439.seq -o /var/tmp/from_scwrl_213966439.pdb > /var/tmp/scwrl_213966439.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_213966439.pdb # conformation set from SCWRL output # naming current conformation FUGMOD_TS2-scwrl # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1025148772.pdb -s /var/tmp/to_scwrl_1025148772.seq -o /var/tmp/from_scwrl_1025148772.pdb > /var/tmp/scwrl_1025148772.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1025148772.pdb # conformation set from SCWRL output # naming current conformation FUGMOD_TS3-scwrl # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # Found a chain break before 348 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1384183704.pdb -s /var/tmp/to_scwrl_1384183704.seq -o /var/tmp/from_scwrl_1384183704.pdb > /var/tmp/scwrl_1384183704.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1384183704.pdb # conformation set from SCWRL output # naming current conformation FUGMOD_TS4-scwrl # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_756493908.pdb -s /var/tmp/to_scwrl_756493908.seq -o /var/tmp/from_scwrl_756493908.pdb > /var/tmp/scwrl_756493908.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_756493908.pdb # conformation set from SCWRL output # naming current conformation FUGMOD_TS5-scwrl # ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FUGUE_AL1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1245941827.pdb -s /var/tmp/to_scwrl_1245941827.seq -o /var/tmp/from_scwrl_1245941827.pdb > /var/tmp/scwrl_1245941827.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1245941827.pdb # conformation set from SCWRL output # naming current conformation FUGUE_AL1-scwrl # ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FUGUE_AL2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_141131487.pdb -s /var/tmp/to_scwrl_141131487.seq -o /var/tmp/from_scwrl_141131487.pdb > /var/tmp/scwrl_141131487.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_141131487.pdb # conformation set from SCWRL output # naming current conformation FUGUE_AL2-scwrl # ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FUGUE_AL3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_270764928.pdb -s /var/tmp/to_scwrl_270764928.seq -o /var/tmp/from_scwrl_270764928.pdb > /var/tmp/scwrl_270764928.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_270764928.pdb # conformation set from SCWRL output # naming current conformation FUGUE_AL3-scwrl # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FUGUE_AL4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_420826223.pdb -s /var/tmp/to_scwrl_420826223.seq -o /var/tmp/from_scwrl_420826223.pdb > /var/tmp/scwrl_420826223.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_420826223.pdb # conformation set from SCWRL output # naming current conformation FUGUE_AL4-scwrl # ReadConformPDB reading from PDB file servers/FUGUE_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FUGUE_AL5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_428219224.pdb -s /var/tmp/to_scwrl_428219224.seq -o /var/tmp/from_scwrl_428219224.pdb > /var/tmp/scwrl_428219224.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_428219224.pdb # conformation set from SCWRL output # naming current conformation FUGUE_AL5-scwrl # ReadConformPDB reading from PDB file servers/FUNCTION_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation FUNCTION_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1015847628.pdb -s /var/tmp/to_scwrl_1015847628.seq -o /var/tmp/from_scwrl_1015847628.pdb > /var/tmp/scwrl_1015847628.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1015847628.pdb # conformation set from SCWRL output # naming current conformation FUNCTION_TS1-scwrl # ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_186974925.pdb -s /var/tmp/to_scwrl_186974925.seq -o /var/tmp/from_scwrl_186974925.pdb > /var/tmp/scwrl_186974925.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_186974925.pdb # conformation set from SCWRL output # naming current conformation FUNCTION_TS2-scwrl # ReadConformPDB reading from PDB file servers/FUNCTION_TS3.pdb.gz looking for model 1 # Found a chain break before 366 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1032829404.pdb -s /var/tmp/to_scwrl_1032829404.seq -o /var/tmp/from_scwrl_1032829404.pdb > /var/tmp/scwrl_1032829404.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1032829404.pdb # conformation set from SCWRL output # naming current conformation FUNCTION_TS3-scwrl # ReadConformPDB reading from PDB file servers/FUNCTION_TS4.pdb.gz looking for model 1 # Found a chain break before 367 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2007158885.pdb -s /var/tmp/to_scwrl_2007158885.seq -o /var/tmp/from_scwrl_2007158885.pdb > /var/tmp/scwrl_2007158885.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2007158885.pdb # conformation set from SCWRL output # naming current conformation FUNCTION_TS4-scwrl # ReadConformPDB reading from PDB file servers/FUNCTION_TS5.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1592102290.pdb -s /var/tmp/to_scwrl_1592102290.seq -o /var/tmp/from_scwrl_1592102290.pdb > /var/tmp/scwrl_1592102290.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1592102290.pdb # conformation set from SCWRL output # naming current conformation FUNCTION_TS5-scwrl # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1870294897.pdb -s /var/tmp/to_scwrl_1870294897.seq -o /var/tmp/from_scwrl_1870294897.pdb > /var/tmp/scwrl_1870294897.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1870294897.pdb # conformation set from SCWRL output # naming current conformation GeneSilicoMetaServer_TS1-scwrl # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # Found a chain break before 372 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_425926778.pdb -s /var/tmp/to_scwrl_425926778.seq -o /var/tmp/from_scwrl_425926778.pdb > /var/tmp/scwrl_425926778.log sh: line 1: 32428 Killed scwrl3 -i /var/tmp/to_scwrl_425926778.pdb -s /var/tmp/to_scwrl_425926778.seq -o /var/tmp/from_scwrl_425926778.pdb >/var/tmp/scwrl_425926778.log Error: Couldn't open file /var/tmp/from_scwrl_425926778.pdb or /var/tmp/from_scwrl_425926778.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_425926778_b.pdb or decoys//var/tmp/from_scwrl_425926778_b.pdb.gz for input Trying /var/tmp/from_scwrl_425926778_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_425926778_b.pdb or /var/tmp/from_scwrl_425926778_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_425926778_a.pdb or decoys//var/tmp/from_scwrl_425926778_a.pdb.gz for input Trying /var/tmp/from_scwrl_425926778_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_425926778_a.pdb or /var/tmp/from_scwrl_425926778_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_425926778.pdb or /var/tmp/from_scwrl_425926778_b.pdb or /var/tmp/from_scwrl_425926778_a.pdb Error: no new SCWRL conformation added # naming current conformation GeneSilicoMetaServer_TS2-scwrl # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1051363709.pdb -s /var/tmp/to_scwrl_1051363709.seq -o /var/tmp/from_scwrl_1051363709.pdb > /var/tmp/scwrl_1051363709.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1051363709.pdb # conformation set from SCWRL output # naming current conformation GeneSilicoMetaServer_TS3-scwrl # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1536444253.pdb -s /var/tmp/to_scwrl_1536444253.seq -o /var/tmp/from_scwrl_1536444253.pdb > /var/tmp/scwrl_1536444253.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1536444253.pdb # conformation set from SCWRL output # naming current conformation GeneSilicoMetaServer_TS4-scwrl # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1 # Found a chain break before 338 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1973036743.pdb -s /var/tmp/to_scwrl_1973036743.seq -o /var/tmp/from_scwrl_1973036743.pdb > /var/tmp/scwrl_1973036743.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1973036743.pdb # conformation set from SCWRL output # naming current conformation GeneSilicoMetaServer_TS5-scwrl # ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation HHpred1_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1788152596.pdb -s /var/tmp/to_scwrl_1788152596.seq -o /var/tmp/from_scwrl_1788152596.pdb > /var/tmp/scwrl_1788152596.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1788152596.pdb # conformation set from SCWRL output # naming current conformation HHpred1_TS1-scwrl # ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation HHpred2_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_269916589.pdb -s /var/tmp/to_scwrl_269916589.seq -o /var/tmp/from_scwrl_269916589.pdb > /var/tmp/scwrl_269916589.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_269916589.pdb # conformation set from SCWRL output # naming current conformation HHpred2_TS1-scwrl # ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation HHpred3_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_858237161.pdb -s /var/tmp/to_scwrl_858237161.seq -o /var/tmp/from_scwrl_858237161.pdb > /var/tmp/scwrl_858237161.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_858237161.pdb # conformation set from SCWRL output # naming current conformation HHpred3_TS1-scwrl # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_541690101.pdb -s /var/tmp/to_scwrl_541690101.seq -o /var/tmp/from_scwrl_541690101.pdb > /var/tmp/scwrl_541690101.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_541690101.pdb # conformation set from SCWRL output # naming current conformation Huber-Torda-Server_TS1-scwrl # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_488346443.pdb -s /var/tmp/to_scwrl_488346443.seq -o /var/tmp/from_scwrl_488346443.pdb > /var/tmp/scwrl_488346443.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_488346443.pdb # conformation set from SCWRL output # naming current conformation Huber-Torda-Server_TS2-scwrl # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_934069393.pdb -s /var/tmp/to_scwrl_934069393.seq -o /var/tmp/from_scwrl_934069393.pdb > /var/tmp/scwrl_934069393.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_934069393.pdb # conformation set from SCWRL output # naming current conformation Huber-Torda-Server_TS3-scwrl # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_292876177.pdb -s /var/tmp/to_scwrl_292876177.seq -o /var/tmp/from_scwrl_292876177.pdb > /var/tmp/scwrl_292876177.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_292876177.pdb # conformation set from SCWRL output # naming current conformation Huber-Torda-Server_TS4-scwrl # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_127856789.pdb -s /var/tmp/to_scwrl_127856789.seq -o /var/tmp/from_scwrl_127856789.pdb > /var/tmp/scwrl_127856789.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_127856789.pdb # conformation set from SCWRL output # naming current conformation Huber-Torda-Server_TS5-scwrl # ReadConformPDB reading from PDB file servers/LOOPP_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation LOOPP_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_112852928.pdb -s /var/tmp/to_scwrl_112852928.seq -o /var/tmp/from_scwrl_112852928.pdb > /var/tmp/scwrl_112852928.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_112852928.pdb # conformation set from SCWRL output # naming current conformation LOOPP_TS1-scwrl # ReadConformPDB reading from PDB file servers/LOOPP_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation LOOPP_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1395879860.pdb -s /var/tmp/to_scwrl_1395879860.seq -o /var/tmp/from_scwrl_1395879860.pdb > /var/tmp/scwrl_1395879860.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1395879860.pdb # conformation set from SCWRL output # naming current conformation LOOPP_TS2-scwrl # ReadConformPDB reading from PDB file servers/LOOPP_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation LOOPP_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2078769201.pdb -s /var/tmp/to_scwrl_2078769201.seq -o /var/tmp/from_scwrl_2078769201.pdb > /var/tmp/scwrl_2078769201.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2078769201.pdb # conformation set from SCWRL output # naming current conformation LOOPP_TS3-scwrl # ReadConformPDB reading from PDB file servers/LOOPP_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation LOOPP_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1819079320.pdb -s /var/tmp/to_scwrl_1819079320.seq -o /var/tmp/from_scwrl_1819079320.pdb > /var/tmp/scwrl_1819079320.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1819079320.pdb # conformation set from SCWRL output # naming current conformation LOOPP_TS4-scwrl # ReadConformPDB reading from PDB file servers/LOOPP_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation LOOPP_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1609846299.pdb -s /var/tmp/to_scwrl_1609846299.seq -o /var/tmp/from_scwrl_1609846299.pdb > /var/tmp/scwrl_1609846299.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1609846299.pdb # conformation set from SCWRL output # naming current conformation LOOPP_TS5-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # Found a chain break before 332 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_956434326.pdb -s /var/tmp/to_scwrl_956434326.seq -o /var/tmp/from_scwrl_956434326.pdb > /var/tmp/scwrl_956434326.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_956434326.pdb # conformation set from SCWRL output # naming current conformation Ma-OPUS-server_TS1-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS2.pdb.gz looking for model 1 # Found a chain break before 366 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1055779378.pdb -s /var/tmp/to_scwrl_1055779378.seq -o /var/tmp/from_scwrl_1055779378.pdb > /var/tmp/scwrl_1055779378.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1055779378.pdb # conformation set from SCWRL output # naming current conformation Ma-OPUS-server_TS2-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS3.pdb.gz looking for model 1 # Found a chain break before 327 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_218856560.pdb -s /var/tmp/to_scwrl_218856560.seq -o /var/tmp/from_scwrl_218856560.pdb > /var/tmp/scwrl_218856560.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_218856560.pdb # conformation set from SCWRL output # naming current conformation Ma-OPUS-server_TS3-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS4.pdb.gz looking for model 1 # Found a chain break before 364 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_54892506.pdb -s /var/tmp/to_scwrl_54892506.seq -o /var/tmp/from_scwrl_54892506.pdb > /var/tmp/scwrl_54892506.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_54892506.pdb # conformation set from SCWRL output # naming current conformation Ma-OPUS-server_TS4-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS5.pdb.gz looking for model 1 # Found a chain break before 347 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1196910864.pdb -s /var/tmp/to_scwrl_1196910864.seq -o /var/tmp/from_scwrl_1196910864.pdb > /var/tmp/scwrl_1196910864.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1196910864.pdb # conformation set from SCWRL output # naming current conformation Ma-OPUS-server_TS5-scwrl # ReadConformPDB reading from PDB file servers/MetaTasser_TS1.pdb.gz looking for model 1 # Found a chain break before 372 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_489621488.pdb -s /var/tmp/to_scwrl_489621488.seq -o /var/tmp/from_scwrl_489621488.pdb > /var/tmp/scwrl_489621488.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_489621488.pdb # conformation set from SCWRL output # naming current conformation MetaTasser_TS1-scwrl # ReadConformPDB reading from PDB file servers/MetaTasser_TS2.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_475718729.pdb -s /var/tmp/to_scwrl_475718729.seq -o /var/tmp/from_scwrl_475718729.pdb > /var/tmp/scwrl_475718729.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_475718729.pdb # conformation set from SCWRL output # naming current conformation MetaTasser_TS2-scwrl # ReadConformPDB reading from PDB file servers/MetaTasser_TS3.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1625130089.pdb -s /var/tmp/to_scwrl_1625130089.seq -o /var/tmp/from_scwrl_1625130089.pdb > /var/tmp/scwrl_1625130089.log sh: line 1: 32540 Killed scwrl3 -i /var/tmp/to_scwrl_1625130089.pdb -s /var/tmp/to_scwrl_1625130089.seq -o /var/tmp/from_scwrl_1625130089.pdb >/var/tmp/scwrl_1625130089.log Error: Couldn't open file /var/tmp/from_scwrl_1625130089.pdb or /var/tmp/from_scwrl_1625130089.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1625130089_b.pdb or decoys//var/tmp/from_scwrl_1625130089_b.pdb.gz for input Trying /var/tmp/from_scwrl_1625130089_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_1625130089_b.pdb or /var/tmp/from_scwrl_1625130089_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1625130089_a.pdb or decoys//var/tmp/from_scwrl_1625130089_a.pdb.gz for input Trying /var/tmp/from_scwrl_1625130089_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_1625130089_a.pdb or /var/tmp/from_scwrl_1625130089_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_1625130089.pdb or /var/tmp/from_scwrl_1625130089_b.pdb or /var/tmp/from_scwrl_1625130089_a.pdb Error: no new SCWRL conformation added # naming current conformation MetaTasser_TS3-scwrl # ReadConformPDB reading from PDB file servers/MetaTasser_TS4.pdb.gz looking for model 1 # Found a chain break before 372 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1505469115.pdb -s /var/tmp/to_scwrl_1505469115.seq -o /var/tmp/from_scwrl_1505469115.pdb > /var/tmp/scwrl_1505469115.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1505469115.pdb # conformation set from SCWRL output # naming current conformation MetaTasser_TS4-scwrl # ReadConformPDB reading from PDB file servers/MetaTasser_TS5.pdb.gz looking for model 1 # Found a chain break before 372 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_662693654.pdb -s /var/tmp/to_scwrl_662693654.seq -o /var/tmp/from_scwrl_662693654.pdb > /var/tmp/scwrl_662693654.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_662693654.pdb # conformation set from SCWRL output # naming current conformation MetaTasser_TS5-scwrl # ReadConformPDB reading from PDB file servers/NN_PUT_lab_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation NN_PUT_lab_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_510475846.pdb -s /var/tmp/to_scwrl_510475846.seq -o /var/tmp/from_scwrl_510475846.pdb > /var/tmp/scwrl_510475846.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_510475846.pdb # conformation set from SCWRL output # naming current conformation NN_PUT_lab_TS1-scwrl # ReadConformPDB reading from PDB file servers/POMYSL_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation POMYSL_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1365144354.pdb -s /var/tmp/to_scwrl_1365144354.seq -o /var/tmp/from_scwrl_1365144354.pdb > /var/tmp/scwrl_1365144354.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1365144354.pdb # conformation set from SCWRL output # naming current conformation POMYSL_TS1-scwrl # ReadConformPDB reading from PDB file servers/POMYSL_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation POMYSL_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_107312297.pdb -s /var/tmp/to_scwrl_107312297.seq -o /var/tmp/from_scwrl_107312297.pdb > /var/tmp/scwrl_107312297.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_107312297.pdb # conformation set from SCWRL output # naming current conformation POMYSL_TS2-scwrl # ReadConformPDB reading from PDB file servers/POMYSL_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation POMYSL_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_233287096.pdb -s /var/tmp/to_scwrl_233287096.seq -o /var/tmp/from_scwrl_233287096.pdb > /var/tmp/scwrl_233287096.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_233287096.pdb # conformation set from SCWRL output # naming current conformation POMYSL_TS3-scwrl # ReadConformPDB reading from PDB file servers/POMYSL_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation POMYSL_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1791071132.pdb -s /var/tmp/to_scwrl_1791071132.seq -o /var/tmp/from_scwrl_1791071132.pdb > /var/tmp/scwrl_1791071132.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1791071132.pdb # conformation set from SCWRL output # naming current conformation POMYSL_TS4-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1158676005.pdb -s /var/tmp/to_scwrl_1158676005.seq -o /var/tmp/from_scwrl_1158676005.pdb > /var/tmp/scwrl_1158676005.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1158676005.pdb # conformation set from SCWRL output # naming current conformation PROTINFO-AB_TS1-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1769731350.pdb -s /var/tmp/to_scwrl_1769731350.seq -o /var/tmp/from_scwrl_1769731350.pdb > /var/tmp/scwrl_1769731350.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1769731350.pdb # conformation set from SCWRL output # naming current conformation PROTINFO-AB_TS2-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1616624228.pdb -s /var/tmp/to_scwrl_1616624228.seq -o /var/tmp/from_scwrl_1616624228.pdb > /var/tmp/scwrl_1616624228.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1616624228.pdb # conformation set from SCWRL output # naming current conformation PROTINFO-AB_TS3-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_799344956.pdb -s /var/tmp/to_scwrl_799344956.seq -o /var/tmp/from_scwrl_799344956.pdb > /var/tmp/scwrl_799344956.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_799344956.pdb # conformation set from SCWRL output # naming current conformation PROTINFO-AB_TS4-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2039647939.pdb -s /var/tmp/to_scwrl_2039647939.seq -o /var/tmp/from_scwrl_2039647939.pdb > /var/tmp/scwrl_2039647939.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2039647939.pdb # conformation set from SCWRL output # naming current conformation PROTINFO-AB_TS5-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1 # Found a chain break before 338 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_327377742.pdb -s /var/tmp/to_scwrl_327377742.seq -o /var/tmp/from_scwrl_327377742.pdb > /var/tmp/scwrl_327377742.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_327377742.pdb # conformation set from SCWRL output # naming current conformation PROTINFO_TS1-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1341035056.pdb -s /var/tmp/to_scwrl_1341035056.seq -o /var/tmp/from_scwrl_1341035056.pdb > /var/tmp/scwrl_1341035056.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1341035056.pdb # conformation set from SCWRL output # naming current conformation PROTINFO_TS2-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # Found a chain break before 368 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_380510735.pdb -s /var/tmp/to_scwrl_380510735.seq -o /var/tmp/from_scwrl_380510735.pdb > /var/tmp/scwrl_380510735.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_380510735.pdb # conformation set from SCWRL output # naming current conformation PROTINFO_TS3-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # Found a chain break before 369 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1261447134.pdb -s /var/tmp/to_scwrl_1261447134.seq -o /var/tmp/from_scwrl_1261447134.pdb > /var/tmp/scwrl_1261447134.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1261447134.pdb # conformation set from SCWRL output # naming current conformation PROTINFO_TS4-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # Found a chain break before 365 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1633911233.pdb -s /var/tmp/to_scwrl_1633911233.seq -o /var/tmp/from_scwrl_1633911233.pdb > /var/tmp/scwrl_1633911233.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1633911233.pdb # conformation set from SCWRL output # naming current conformation PROTINFO_TS5-scwrl # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Pcons6_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_508367524.pdb -s /var/tmp/to_scwrl_508367524.seq -o /var/tmp/from_scwrl_508367524.pdb > /var/tmp/scwrl_508367524.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_508367524.pdb # conformation set from SCWRL output # naming current conformation Pcons6_TS1-scwrl # ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Pcons6_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1374300062.pdb -s /var/tmp/to_scwrl_1374300062.seq -o /var/tmp/from_scwrl_1374300062.pdb > /var/tmp/scwrl_1374300062.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1374300062.pdb # conformation set from SCWRL output # naming current conformation Pcons6_TS2-scwrl # ReadConformPDB reading from PDB file servers/Pcons6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Pcons6_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_882307447.pdb -s /var/tmp/to_scwrl_882307447.seq -o /var/tmp/from_scwrl_882307447.pdb > /var/tmp/scwrl_882307447.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_882307447.pdb # conformation set from SCWRL output # naming current conformation Pcons6_TS3-scwrl # ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Pcons6_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_439653078.pdb -s /var/tmp/to_scwrl_439653078.seq -o /var/tmp/from_scwrl_439653078.pdb > /var/tmp/scwrl_439653078.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_439653078.pdb # conformation set from SCWRL output # naming current conformation Pcons6_TS4-scwrl # ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1 # Found a chain break before 363 # copying to AlignedFragments data structure # naming current conformation Pcons6_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1045895736.pdb -s /var/tmp/to_scwrl_1045895736.seq -o /var/tmp/from_scwrl_1045895736.pdb > /var/tmp/scwrl_1045895736.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1045895736.pdb # conformation set from SCWRL output # naming current conformation Pcons6_TS5-scwrl # ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Phyre-1_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_344670099.pdb -s /var/tmp/to_scwrl_344670099.seq -o /var/tmp/from_scwrl_344670099.pdb > /var/tmp/scwrl_344670099.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_344670099.pdb # conformation set from SCWRL output # naming current conformation Phyre-1_TS1-scwrl # ReadConformPDB reading from PDB file servers/Phyre-2_TS1.pdb.gz looking for model 1 # Found a chain break before 358 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1396087404.pdb -s /var/tmp/to_scwrl_1396087404.seq -o /var/tmp/from_scwrl_1396087404.pdb > /var/tmp/scwrl_1396087404.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1396087404.pdb # conformation set from SCWRL output # naming current conformation Phyre-2_TS1-scwrl # ReadConformPDB reading from PDB file servers/Phyre-2_TS2.pdb.gz looking for model 1 # Found a chain break before 342 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2101675114.pdb -s /var/tmp/to_scwrl_2101675114.seq -o /var/tmp/from_scwrl_2101675114.pdb > /var/tmp/scwrl_2101675114.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2101675114.pdb # conformation set from SCWRL output # naming current conformation Phyre-2_TS2-scwrl # ReadConformPDB reading from PDB file servers/Phyre-2_TS3.pdb.gz looking for model 1 # Found a chain break before 370 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_563526659.pdb -s /var/tmp/to_scwrl_563526659.seq -o /var/tmp/from_scwrl_563526659.pdb > /var/tmp/scwrl_563526659.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_563526659.pdb # conformation set from SCWRL output # naming current conformation Phyre-2_TS3-scwrl # ReadConformPDB reading from PDB file servers/Phyre-2_TS4.pdb.gz looking for model 1 # Found a chain break before 334 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1450979910.pdb -s /var/tmp/to_scwrl_1450979910.seq -o /var/tmp/from_scwrl_1450979910.pdb > /var/tmp/scwrl_1450979910.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1450979910.pdb # conformation set from SCWRL output # naming current conformation Phyre-2_TS4-scwrl # ReadConformPDB reading from PDB file servers/Phyre-2_TS5.pdb.gz looking for model 1 # Found a chain break before 365 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1151102331.pdb -s /var/tmp/to_scwrl_1151102331.seq -o /var/tmp/from_scwrl_1151102331.pdb > /var/tmp/scwrl_1151102331.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1151102331.pdb # conformation set from SCWRL output # naming current conformation Phyre-2_TS5-scwrl # ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1053148147.pdb -s /var/tmp/to_scwrl_1053148147.seq -o /var/tmp/from_scwrl_1053148147.pdb > /var/tmp/scwrl_1053148147.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1053148147.pdb # conformation set from SCWRL output # naming current conformation Pmodeller6_TS1-scwrl # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1926698640.pdb -s /var/tmp/to_scwrl_1926698640.seq -o /var/tmp/from_scwrl_1926698640.pdb > /var/tmp/scwrl_1926698640.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1926698640.pdb # conformation set from SCWRL output # naming current conformation Pmodeller6_TS2-scwrl # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_628748774.pdb -s /var/tmp/to_scwrl_628748774.seq -o /var/tmp/from_scwrl_628748774.pdb > /var/tmp/scwrl_628748774.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_628748774.pdb # conformation set from SCWRL output # naming current conformation Pmodeller6_TS3-scwrl # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_411133615.pdb -s /var/tmp/to_scwrl_411133615.seq -o /var/tmp/from_scwrl_411133615.pdb > /var/tmp/scwrl_411133615.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_411133615.pdb # conformation set from SCWRL output # naming current conformation Pmodeller6_TS4-scwrl # ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_441908647.pdb -s /var/tmp/to_scwrl_441908647.seq -o /var/tmp/from_scwrl_441908647.pdb > /var/tmp/scwrl_441908647.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_441908647.pdb # conformation set from SCWRL output # naming current conformation Pmodeller6_TS5-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1 # Found a chain break before 340 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1139224620.pdb -s /var/tmp/to_scwrl_1139224620.seq -o /var/tmp/from_scwrl_1139224620.pdb > /var/tmp/scwrl_1139224620.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1139224620.pdb # conformation set from SCWRL output # naming current conformation RAPTOR-ACE_TS1-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1 # Found a chain break before 336 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1776277969.pdb -s /var/tmp/to_scwrl_1776277969.seq -o /var/tmp/from_scwrl_1776277969.pdb > /var/tmp/scwrl_1776277969.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1776277969.pdb # conformation set from SCWRL output # naming current conformation RAPTOR-ACE_TS2-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1 # Found a chain break before 132 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_549220945.pdb -s /var/tmp/to_scwrl_549220945.seq -o /var/tmp/from_scwrl_549220945.pdb > /var/tmp/scwrl_549220945.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_549220945.pdb # conformation set from SCWRL output # naming current conformation RAPTOR-ACE_TS3-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS4.pdb.gz looking for model 1 # Found a chain break before 348 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1372511716.pdb -s /var/tmp/to_scwrl_1372511716.seq -o /var/tmp/from_scwrl_1372511716.pdb > /var/tmp/scwrl_1372511716.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1372511716.pdb # conformation set from SCWRL output # naming current conformation RAPTOR-ACE_TS4-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1 # Found a chain break before 294 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1419865454.pdb -s /var/tmp/to_scwrl_1419865454.seq -o /var/tmp/from_scwrl_1419865454.pdb > /var/tmp/scwrl_1419865454.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1419865454.pdb # conformation set from SCWRL output # naming current conformation RAPTOR-ACE_TS5-scwrl # ReadConformPDB reading from PDB file servers/RAPTORESS_TS1.pdb.gz looking for model 1 # Found a chain break before 372 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1707896950.pdb -s /var/tmp/to_scwrl_1707896950.seq -o /var/tmp/from_scwrl_1707896950.pdb > /var/tmp/scwrl_1707896950.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1707896950.pdb # conformation set from SCWRL output # naming current conformation RAPTORESS_TS1-scwrl # ReadConformPDB reading from PDB file servers/RAPTORESS_TS2.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_994759420.pdb -s /var/tmp/to_scwrl_994759420.seq -o /var/tmp/from_scwrl_994759420.pdb > /var/tmp/scwrl_994759420.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_994759420.pdb # conformation set from SCWRL output # naming current conformation RAPTORESS_TS2-scwrl # ReadConformPDB reading from PDB file servers/RAPTORESS_TS3.pdb.gz looking for model 1 # Found a chain break before 369 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_889006036.pdb -s /var/tmp/to_scwrl_889006036.seq -o /var/tmp/from_scwrl_889006036.pdb > /var/tmp/scwrl_889006036.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_889006036.pdb # conformation set from SCWRL output # naming current conformation RAPTORESS_TS3-scwrl # ReadConformPDB reading from PDB file servers/RAPTORESS_TS4.pdb.gz looking for model 1 # Found a chain break before 365 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_359758259.pdb -s /var/tmp/to_scwrl_359758259.seq -o /var/tmp/from_scwrl_359758259.pdb > /var/tmp/scwrl_359758259.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_359758259.pdb # conformation set from SCWRL output # naming current conformation RAPTORESS_TS4-scwrl # ReadConformPDB reading from PDB file servers/RAPTORESS_TS5.pdb.gz looking for model 1 # Found a chain break before 354 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_886923712.pdb -s /var/tmp/to_scwrl_886923712.seq -o /var/tmp/from_scwrl_886923712.pdb > /var/tmp/scwrl_886923712.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_886923712.pdb # conformation set from SCWRL output # naming current conformation RAPTORESS_TS5-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR_TS1.pdb.gz looking for model 1 # Found a chain break before 372 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1216383777.pdb -s /var/tmp/to_scwrl_1216383777.seq -o /var/tmp/from_scwrl_1216383777.pdb > /var/tmp/scwrl_1216383777.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1216383777.pdb # conformation set from SCWRL output # naming current conformation RAPTOR_TS1-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1 # Found a chain break before 363 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1700793315.pdb -s /var/tmp/to_scwrl_1700793315.seq -o /var/tmp/from_scwrl_1700793315.pdb > /var/tmp/scwrl_1700793315.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1700793315.pdb # conformation set from SCWRL output # naming current conformation RAPTOR_TS2-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR_TS3.pdb.gz looking for model 1 # Found a chain break before 360 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1267434447.pdb -s /var/tmp/to_scwrl_1267434447.seq -o /var/tmp/from_scwrl_1267434447.pdb > /var/tmp/scwrl_1267434447.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1267434447.pdb # conformation set from SCWRL output # naming current conformation RAPTOR_TS3-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR_TS4.pdb.gz looking for model 1 # Found a chain break before 364 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_330347265.pdb -s /var/tmp/to_scwrl_330347265.seq -o /var/tmp/from_scwrl_330347265.pdb > /var/tmp/scwrl_330347265.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_330347265.pdb # conformation set from SCWRL output # naming current conformation RAPTOR_TS4-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR_TS5.pdb.gz looking for model 1 # Found a chain break before 339 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1187220901.pdb -s /var/tmp/to_scwrl_1187220901.seq -o /var/tmp/from_scwrl_1187220901.pdb > /var/tmp/scwrl_1187220901.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1187220901.pdb # conformation set from SCWRL output # naming current conformation RAPTOR_TS5-scwrl # ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1 # Found a chain break before 316 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1775801971.pdb -s /var/tmp/to_scwrl_1775801971.seq -o /var/tmp/from_scwrl_1775801971.pdb > /var/tmp/scwrl_1775801971.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1775801971.pdb # conformation set from SCWRL output # naming current conformation ROBETTA_TS1-scwrl # ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1 # Found a chain break before 339 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1704647328.pdb -s /var/tmp/to_scwrl_1704647328.seq -o /var/tmp/from_scwrl_1704647328.pdb > /var/tmp/scwrl_1704647328.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1704647328.pdb # conformation set from SCWRL output # naming current conformation ROBETTA_TS2-scwrl # ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1 # Found a chain break before 346 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2069528348.pdb -s /var/tmp/to_scwrl_2069528348.seq -o /var/tmp/from_scwrl_2069528348.pdb > /var/tmp/scwrl_2069528348.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2069528348.pdb # conformation set from SCWRL output # naming current conformation ROBETTA_TS3-scwrl # ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1 # Found a chain break before 340 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_67971403.pdb -s /var/tmp/to_scwrl_67971403.seq -o /var/tmp/from_scwrl_67971403.pdb > /var/tmp/scwrl_67971403.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_67971403.pdb # conformation set from SCWRL output # naming current conformation ROBETTA_TS4-scwrl # ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1 # Found a chain break before 305 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_603059417.pdb -s /var/tmp/to_scwrl_603059417.seq -o /var/tmp/from_scwrl_603059417.pdb > /var/tmp/scwrl_603059417.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_603059417.pdb # conformation set from SCWRL output # naming current conformation ROBETTA_TS5-scwrl # ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_266714800.pdb -s /var/tmp/to_scwrl_266714800.seq -o /var/tmp/from_scwrl_266714800.pdb > /var/tmp/scwrl_266714800.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_266714800.pdb # conformation set from SCWRL output # naming current conformation ROKKY_TS1-scwrl # ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1464058807.pdb -s /var/tmp/to_scwrl_1464058807.seq -o /var/tmp/from_scwrl_1464058807.pdb > /var/tmp/scwrl_1464058807.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1464058807.pdb # conformation set from SCWRL output # naming current conformation ROKKY_TS2-scwrl # ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_557250884.pdb -s /var/tmp/to_scwrl_557250884.seq -o /var/tmp/from_scwrl_557250884.pdb > /var/tmp/scwrl_557250884.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_557250884.pdb # conformation set from SCWRL output # naming current conformation ROKKY_TS3-scwrl # ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_830241459.pdb -s /var/tmp/to_scwrl_830241459.seq -o /var/tmp/from_scwrl_830241459.pdb > /var/tmp/scwrl_830241459.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_830241459.pdb # conformation set from SCWRL output # naming current conformation ROKKY_TS4-scwrl # ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_767555071.pdb -s /var/tmp/to_scwrl_767555071.seq -o /var/tmp/from_scwrl_767555071.pdb > /var/tmp/scwrl_767555071.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_767555071.pdb # conformation set from SCWRL output # naming current conformation ROKKY_TS5-scwrl # ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1708353216.pdb -s /var/tmp/to_scwrl_1708353216.seq -o /var/tmp/from_scwrl_1708353216.pdb > /var/tmp/scwrl_1708353216.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1708353216.pdb # conformation set from SCWRL output # naming current conformation SAM-T02_AL1-scwrl # ReadConformPDB reading from PDB file servers/SAM-T02_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1883389605.pdb -s /var/tmp/to_scwrl_1883389605.seq -o /var/tmp/from_scwrl_1883389605.pdb > /var/tmp/scwrl_1883389605.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1883389605.pdb # conformation set from SCWRL output # naming current conformation SAM-T02_AL2-scwrl # ReadConformPDB reading from PDB file servers/SAM-T02_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_546770064.pdb -s /var/tmp/to_scwrl_546770064.seq -o /var/tmp/from_scwrl_546770064.pdb > /var/tmp/scwrl_546770064.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_546770064.pdb # conformation set from SCWRL output # naming current conformation SAM-T02_AL3-scwrl # ReadConformPDB reading from PDB file servers/SAM-T02_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_189618343.pdb -s /var/tmp/to_scwrl_189618343.seq -o /var/tmp/from_scwrl_189618343.pdb > /var/tmp/scwrl_189618343.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_189618343.pdb # conformation set from SCWRL output # naming current conformation SAM-T02_AL4-scwrl # ReadConformPDB reading from PDB file servers/SAM-T02_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_147039574.pdb -s /var/tmp/to_scwrl_147039574.seq -o /var/tmp/from_scwrl_147039574.pdb > /var/tmp/scwrl_147039574.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_147039574.pdb # conformation set from SCWRL output # naming current conformation SAM-T02_AL5-scwrl # ReadConformPDB reading from PDB file servers/SAM-T99_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_988678712.pdb -s /var/tmp/to_scwrl_988678712.seq -o /var/tmp/from_scwrl_988678712.pdb > /var/tmp/scwrl_988678712.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_988678712.pdb # conformation set from SCWRL output # naming current conformation SAM-T99_AL1-scwrl # ReadConformPDB reading from PDB file servers/SAM-T99_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1328842963.pdb -s /var/tmp/to_scwrl_1328842963.seq -o /var/tmp/from_scwrl_1328842963.pdb > /var/tmp/scwrl_1328842963.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1328842963.pdb # conformation set from SCWRL output # naming current conformation SAM-T99_AL2-scwrl # ReadConformPDB reading from PDB file servers/SAM-T99_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1923317543.pdb -s /var/tmp/to_scwrl_1923317543.seq -o /var/tmp/from_scwrl_1923317543.pdb > /var/tmp/scwrl_1923317543.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1923317543.pdb # conformation set from SCWRL output # naming current conformation SAM-T99_AL3-scwrl # ReadConformPDB reading from PDB file servers/SAM-T99_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1537899656.pdb -s /var/tmp/to_scwrl_1537899656.seq -o /var/tmp/from_scwrl_1537899656.pdb > /var/tmp/scwrl_1537899656.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1537899656.pdb # conformation set from SCWRL output # naming current conformation SAM-T99_AL4-scwrl # ReadConformPDB reading from PDB file servers/SAM-T99_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_553871034.pdb -s /var/tmp/to_scwrl_553871034.seq -o /var/tmp/from_scwrl_553871034.pdb > /var/tmp/scwrl_553871034.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_553871034.pdb # conformation set from SCWRL output # naming current conformation SAM-T99_AL5-scwrl # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1 # Found a chain break before 372 # copying to AlignedFragments data structure # naming current conformation SAM_T06_server_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1195699351.pdb -s /var/tmp/to_scwrl_1195699351.seq -o /var/tmp/from_scwrl_1195699351.pdb > /var/tmp/scwrl_1195699351.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1195699351.pdb # conformation set from SCWRL output # naming current conformation SAM_T06_server_TS1-scwrl # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1098312959.pdb -s /var/tmp/to_scwrl_1098312959.seq -o /var/tmp/from_scwrl_1098312959.pdb > /var/tmp/scwrl_1098312959.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1098312959.pdb # conformation set from SCWRL output # naming current conformation SAM_T06_server_TS2-scwrl # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1548630453.pdb -s /var/tmp/to_scwrl_1548630453.seq -o /var/tmp/from_scwrl_1548630453.pdb > /var/tmp/scwrl_1548630453.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1548630453.pdb # conformation set from SCWRL output # naming current conformation SAM_T06_server_TS3-scwrl # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2084705387.pdb -s /var/tmp/to_scwrl_2084705387.seq -o /var/tmp/from_scwrl_2084705387.pdb > /var/tmp/scwrl_2084705387.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2084705387.pdb # conformation set from SCWRL output # naming current conformation SAM_T06_server_TS4-scwrl # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1458071219.pdb -s /var/tmp/to_scwrl_1458071219.seq -o /var/tmp/from_scwrl_1458071219.pdb > /var/tmp/scwrl_1458071219.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1458071219.pdb # conformation set from SCWRL output # naming current conformation SAM_T06_server_TS5-scwrl # ReadConformPDB reading from PDB file servers/SP3_TS1.pdb.gz looking for model 1 # Found a chain break before 173 # copying to AlignedFragments data structure # naming current conformation SP3_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_288070519.pdb -s /var/tmp/to_scwrl_288070519.seq -o /var/tmp/from_scwrl_288070519.pdb > /var/tmp/scwrl_288070519.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_288070519.pdb # conformation set from SCWRL output # naming current conformation SP3_TS1-scwrl # ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1 # Found a chain break before 301 # copying to AlignedFragments data structure # naming current conformation SP3_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1153605518.pdb -s /var/tmp/to_scwrl_1153605518.seq -o /var/tmp/from_scwrl_1153605518.pdb > /var/tmp/scwrl_1153605518.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1153605518.pdb # conformation set from SCWRL output # naming current conformation SP3_TS2-scwrl # ReadConformPDB reading from PDB file servers/SP3_TS3.pdb.gz looking for model 1 # Found a chain break before 288 # copying to AlignedFragments data structure # naming current conformation SP3_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1011380888.pdb -s /var/tmp/to_scwrl_1011380888.seq -o /var/tmp/from_scwrl_1011380888.pdb > /var/tmp/scwrl_1011380888.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1011380888.pdb # conformation set from SCWRL output # naming current conformation SP3_TS3-scwrl # ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1 # Found a chain break before 348 # copying to AlignedFragments data structure # naming current conformation SP3_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1555504966.pdb -s /var/tmp/to_scwrl_1555504966.seq -o /var/tmp/from_scwrl_1555504966.pdb > /var/tmp/scwrl_1555504966.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1555504966.pdb # conformation set from SCWRL output # naming current conformation SP3_TS4-scwrl # ReadConformPDB reading from PDB file servers/SP3_TS5.pdb.gz looking for model 1 # Found a chain break before 212 # copying to AlignedFragments data structure # naming current conformation SP3_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1483952783.pdb -s /var/tmp/to_scwrl_1483952783.seq -o /var/tmp/from_scwrl_1483952783.pdb > /var/tmp/scwrl_1483952783.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1483952783.pdb # conformation set from SCWRL output # naming current conformation SP3_TS5-scwrl # ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1 # Found a chain break before 202 # copying to AlignedFragments data structure # naming current conformation SP4_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_51118143.pdb -s /var/tmp/to_scwrl_51118143.seq -o /var/tmp/from_scwrl_51118143.pdb > /var/tmp/scwrl_51118143.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_51118143.pdb # conformation set from SCWRL output # naming current conformation SP4_TS1-scwrl # ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1 # Found a chain break before 170 # copying to AlignedFragments data structure # naming current conformation SP4_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1183823290.pdb -s /var/tmp/to_scwrl_1183823290.seq -o /var/tmp/from_scwrl_1183823290.pdb > /var/tmp/scwrl_1183823290.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1183823290.pdb # conformation set from SCWRL output # naming current conformation SP4_TS2-scwrl # ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1 # Found a chain break before 259 # copying to AlignedFragments data structure # naming current conformation SP4_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1041116465.pdb -s /var/tmp/to_scwrl_1041116465.seq -o /var/tmp/from_scwrl_1041116465.pdb > /var/tmp/scwrl_1041116465.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1041116465.pdb # conformation set from SCWRL output # naming current conformation SP4_TS3-scwrl # ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1 # Found a chain break before 301 # copying to AlignedFragments data structure # naming current conformation SP4_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_2120646491.pdb -s /var/tmp/to_scwrl_2120646491.seq -o /var/tmp/from_scwrl_2120646491.pdb > /var/tmp/scwrl_2120646491.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2120646491.pdb # conformation set from SCWRL output # naming current conformation SP4_TS4-scwrl # ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1 # Found a chain break before 244 # copying to AlignedFragments data structure # naming current conformation SP4_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1251794693.pdb -s /var/tmp/to_scwrl_1251794693.seq -o /var/tmp/from_scwrl_1251794693.pdb > /var/tmp/scwrl_1251794693.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1251794693.pdb # conformation set from SCWRL output # naming current conformation SP4_TS5-scwrl # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # Found a chain break before 162 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1644175882.pdb -s /var/tmp/to_scwrl_1644175882.seq -o /var/tmp/from_scwrl_1644175882.pdb > /var/tmp/scwrl_1644175882.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1644175882.pdb # conformation set from SCWRL output # naming current conformation SPARKS2_TS1-scwrl # ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1 # Found a chain break before 266 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_239877645.pdb -s /var/tmp/to_scwrl_239877645.seq -o /var/tmp/from_scwrl_239877645.pdb > /var/tmp/scwrl_239877645.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_239877645.pdb # conformation set from SCWRL output # naming current conformation SPARKS2_TS2-scwrl # ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1 # Found a chain break before 372 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_568369854.pdb -s /var/tmp/to_scwrl_568369854.seq -o /var/tmp/from_scwrl_568369854.pdb > /var/tmp/scwrl_568369854.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_568369854.pdb # conformation set from SCWRL output # naming current conformation SPARKS2_TS3-scwrl # ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1 # Found a chain break before 200 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_53943119.pdb -s /var/tmp/to_scwrl_53943119.seq -o /var/tmp/from_scwrl_53943119.pdb > /var/tmp/scwrl_53943119.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_53943119.pdb # conformation set from SCWRL output # naming current conformation SPARKS2_TS4-scwrl # ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1 # Found a chain break before 292 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1070119104.pdb -s /var/tmp/to_scwrl_1070119104.seq -o /var/tmp/from_scwrl_1070119104.pdb > /var/tmp/scwrl_1070119104.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1070119104.pdb # conformation set from SCWRL output # naming current conformation SPARKS2_TS5-scwrl # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1335924925.pdb -s /var/tmp/to_scwrl_1335924925.seq -o /var/tmp/from_scwrl_1335924925.pdb > /var/tmp/scwrl_1335924925.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1335924925.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_bnmx_TS1-scwrl # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1762296335.pdb -s /var/tmp/to_scwrl_1762296335.seq -o /var/tmp/from_scwrl_1762296335.pdb > /var/tmp/scwrl_1762296335.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1762296335.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_bnmx_TS2-scwrl # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_806025063.pdb -s /var/tmp/to_scwrl_806025063.seq -o /var/tmp/from_scwrl_806025063.pdb > /var/tmp/scwrl_806025063.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_806025063.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_bnmx_TS3-scwrl # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1882694989.pdb -s /var/tmp/to_scwrl_1882694989.seq -o /var/tmp/from_scwrl_1882694989.pdb > /var/tmp/scwrl_1882694989.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1882694989.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_bnmx_TS4-scwrl # ReadConformPDB reading from PDB file servers/UNI-EID_expm_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation UNI-EID_expm_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1951914679.pdb -s /var/tmp/to_scwrl_1951914679.seq -o /var/tmp/from_scwrl_1951914679.pdb > /var/tmp/scwrl_1951914679.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1951914679.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_expm_TS1-scwrl # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_953064637.pdb -s /var/tmp/to_scwrl_953064637.seq -o /var/tmp/from_scwrl_953064637.pdb > /var/tmp/scwrl_953064637.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_953064637.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_sfst_AL1-scwrl # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_723890054.pdb -s /var/tmp/to_scwrl_723890054.seq -o /var/tmp/from_scwrl_723890054.pdb > /var/tmp/scwrl_723890054.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_723890054.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_sfst_AL2-scwrl # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1133273995.pdb -s /var/tmp/to_scwrl_1133273995.seq -o /var/tmp/from_scwrl_1133273995.pdb > /var/tmp/scwrl_1133273995.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1133273995.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_sfst_AL3-scwrl # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_728898533.pdb -s /var/tmp/to_scwrl_728898533.seq -o /var/tmp/from_scwrl_728898533.pdb > /var/tmp/scwrl_728898533.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_728898533.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_sfst_AL4-scwrl # ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_114306063.pdb -s /var/tmp/to_scwrl_114306063.seq -o /var/tmp/from_scwrl_114306063.pdb > /var/tmp/scwrl_114306063.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_114306063.pdb # conformation set from SCWRL output # naming current conformation Zhang-Server_TS1-scwrl # ReadConformPDB reading from PDB file servers/Zhang-Server_TS2.pdb.gz looking for model 1 # Found a chain break before 361 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1687145029.pdb -s /var/tmp/to_scwrl_1687145029.seq -o /var/tmp/from_scwrl_1687145029.pdb > /var/tmp/scwrl_1687145029.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1687145029.pdb # conformation set from SCWRL output # naming current conformation Zhang-Server_TS2-scwrl # ReadConformPDB reading from PDB file servers/Zhang-Server_TS3.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1924597884.pdb -s /var/tmp/to_scwrl_1924597884.seq -o /var/tmp/from_scwrl_1924597884.pdb > /var/tmp/scwrl_1924597884.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1924597884.pdb # conformation set from SCWRL output # naming current conformation Zhang-Server_TS3-scwrl # ReadConformPDB reading from PDB file servers/Zhang-Server_TS4.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1212619023.pdb -s /var/tmp/to_scwrl_1212619023.seq -o /var/tmp/from_scwrl_1212619023.pdb > /var/tmp/scwrl_1212619023.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1212619023.pdb # conformation set from SCWRL output # naming current conformation Zhang-Server_TS4-scwrl # ReadConformPDB reading from PDB file servers/Zhang-Server_TS5.pdb.gz looking for model 1 # Found a chain break before 363 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1088291836.pdb -s /var/tmp/to_scwrl_1088291836.seq -o /var/tmp/from_scwrl_1088291836.pdb > /var/tmp/scwrl_1088291836.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1088291836.pdb # conformation set from SCWRL output # naming current conformation Zhang-Server_TS5-scwrl # ReadConformPDB reading from PDB file servers/beautshot_TS1.pdb.gz looking for model 1 # Found a chain break before 371 # copying to AlignedFragments data structure # naming current conformation beautshot_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1861819625.pdb -s /var/tmp/to_scwrl_1861819625.seq -o /var/tmp/from_scwrl_1861819625.pdb > /var/tmp/scwrl_1861819625.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1861819625.pdb # conformation set from SCWRL output # naming current conformation beautshot_TS1-scwrl # ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation beautshotbase_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_523206596.pdb -s /var/tmp/to_scwrl_523206596.seq -o /var/tmp/from_scwrl_523206596.pdb > /var/tmp/scwrl_523206596.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_523206596.pdb # conformation set from SCWRL output # naming current conformation beautshotbase_TS1-scwrl # ReadConformPDB reading from PDB file servers/forecast-s_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation forecast-s_AL1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1376362355.pdb -s /var/tmp/to_scwrl_1376362355.seq -o /var/tmp/from_scwrl_1376362355.pdb > /var/tmp/scwrl_1376362355.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1376362355.pdb # conformation set from SCWRL output # naming current conformation forecast-s_AL1-scwrl # ReadConformPDB reading from PDB file servers/forecast-s_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation forecast-s_AL2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_867941497.pdb -s /var/tmp/to_scwrl_867941497.seq -o /var/tmp/from_scwrl_867941497.pdb > /var/tmp/scwrl_867941497.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_867941497.pdb # conformation set from SCWRL output # naming current conformation forecast-s_AL2-scwrl # ReadConformPDB reading from PDB file servers/forecast-s_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation forecast-s_AL3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1534587483.pdb -s /var/tmp/to_scwrl_1534587483.seq -o /var/tmp/from_scwrl_1534587483.pdb > /var/tmp/scwrl_1534587483.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1534587483.pdb # conformation set from SCWRL output # naming current conformation forecast-s_AL3-scwrl # ReadConformPDB reading from PDB file servers/forecast-s_AL4.pdb.gz looking for model 1 Skipped atom 334, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 336, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 338, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 340, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 342, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 344, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 346, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 348, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 350, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 352, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 354, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 356, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation forecast-s_AL4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_784383675.pdb -s /var/tmp/to_scwrl_784383675.seq -o /var/tmp/from_scwrl_784383675.pdb > /var/tmp/scwrl_784383675.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_784383675.pdb # conformation set from SCWRL output # naming current conformation forecast-s_AL4-scwrl # ReadConformPDB reading from PDB file servers/forecast-s_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation forecast-s_AL5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_204410633.pdb -s /var/tmp/to_scwrl_204410633.seq -o /var/tmp/from_scwrl_204410633.pdb > /var/tmp/scwrl_204410633.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_204410633.pdb # conformation set from SCWRL output # naming current conformation forecast-s_AL5-scwrl # ReadConformPDB reading from PDB file servers/gtg_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation gtg_AL1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1585705626.pdb -s /var/tmp/to_scwrl_1585705626.seq -o /var/tmp/from_scwrl_1585705626.pdb > /var/tmp/scwrl_1585705626.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1585705626.pdb # conformation set from SCWRL output # naming current conformation gtg_AL1-scwrl # ReadConformPDB reading from PDB file servers/gtg_AL2.pdb.gz looking for model 1 Skipped atom 278, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 280, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 282, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 284, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 286, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 288, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 290, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 292, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 606, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 608, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 610, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 612, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 622, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 624, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 626, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 628, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 734, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 736, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 738, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 740, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 934, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 936, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 938, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 940, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 1042, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 1044, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 1046, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 1048, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation gtg_AL2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1968206965.pdb -s /var/tmp/to_scwrl_1968206965.seq -o /var/tmp/from_scwrl_1968206965.pdb > /var/tmp/scwrl_1968206965.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1968206965.pdb # conformation set from SCWRL output # naming current conformation gtg_AL2-scwrl # ReadConformPDB reading from PDB file servers/gtg_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation gtg_AL3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1245527098.pdb -s /var/tmp/to_scwrl_1245527098.seq -o /var/tmp/from_scwrl_1245527098.pdb > /var/tmp/scwrl_1245527098.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1245527098.pdb # conformation set from SCWRL output # naming current conformation gtg_AL3-scwrl # ReadConformPDB reading from PDB file servers/gtg_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation gtg_AL4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1558868471.pdb -s /var/tmp/to_scwrl_1558868471.seq -o /var/tmp/from_scwrl_1558868471.pdb > /var/tmp/scwrl_1558868471.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1558868471.pdb # conformation set from SCWRL output # naming current conformation gtg_AL4-scwrl # ReadConformPDB reading from PDB file servers/gtg_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation gtg_AL5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1072518013.pdb -s /var/tmp/to_scwrl_1072518013.seq -o /var/tmp/from_scwrl_1072518013.pdb > /var/tmp/scwrl_1072518013.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1072518013.pdb # conformation set from SCWRL output # naming current conformation gtg_AL5-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # Found a chain break before 363 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_742219334.pdb -s /var/tmp/to_scwrl_742219334.seq -o /var/tmp/from_scwrl_742219334.pdb > /var/tmp/scwrl_742219334.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_742219334.pdb # conformation set from SCWRL output # naming current conformation karypis.srv.2_TS1-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS2.pdb.gz looking for model 1 # Found a chain break before 367 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1798746116.pdb -s /var/tmp/to_scwrl_1798746116.seq -o /var/tmp/from_scwrl_1798746116.pdb > /var/tmp/scwrl_1798746116.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1798746116.pdb # conformation set from SCWRL output # naming current conformation karypis.srv.2_TS2-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS3.pdb.gz looking for model 1 # Found a chain break before 359 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1640887866.pdb -s /var/tmp/to_scwrl_1640887866.seq -o /var/tmp/from_scwrl_1640887866.pdb > /var/tmp/scwrl_1640887866.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1640887866.pdb # conformation set from SCWRL output # naming current conformation karypis.srv.2_TS3-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS4.pdb.gz looking for model 1 # Found a chain break before 358 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_796162453.pdb -s /var/tmp/to_scwrl_796162453.seq -o /var/tmp/from_scwrl_796162453.pdb > /var/tmp/scwrl_796162453.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_796162453.pdb # conformation set from SCWRL output # naming current conformation karypis.srv.2_TS4-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS5.pdb.gz looking for model 1 # Found a chain break before 317 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_721381573.pdb -s /var/tmp/to_scwrl_721381573.seq -o /var/tmp/from_scwrl_721381573.pdb > /var/tmp/scwrl_721381573.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_721381573.pdb # conformation set from SCWRL output # naming current conformation karypis.srv.2_TS5-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS1.pdb.gz looking for model 1 WARNING: atoms too close: (T0316)G172.O and (T0316)H173.N only 0.000 apart, marking (T0316)H173.N as missing WARNING: atoms too close: (T0316)H280.O and (T0316)D281.N only 0.000 apart, marking (T0316)D281.N as missing WARNING: atoms too close: (T0316)Y364.O and (T0316)R365.N only 0.000 apart, marking (T0316)R365.N as missing # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_829329145.pdb -s /var/tmp/to_scwrl_829329145.seq -o /var/tmp/from_scwrl_829329145.pdb > /var/tmp/scwrl_829329145.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_829329145.pdb # conformation set from SCWRL output # naming current conformation karypis.srv.4_TS1-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS2.pdb.gz looking for model 1 # Found a chain break before 370 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_410975142.pdb -s /var/tmp/to_scwrl_410975142.seq -o /var/tmp/from_scwrl_410975142.pdb > /var/tmp/scwrl_410975142.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_410975142.pdb # conformation set from SCWRL output # naming current conformation karypis.srv.4_TS2-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS3.pdb.gz looking for model 1 WARNING: atoms too close: (T0316)I202.O and (T0316)G203.N only 0.000 apart, marking (T0316)G203.N as missing WARNING: atoms too close: (T0316)G264.O and (T0316)K265.N only 0.000 apart, marking (T0316)K265.N as missing # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1527406635.pdb -s /var/tmp/to_scwrl_1527406635.seq -o /var/tmp/from_scwrl_1527406635.pdb > /var/tmp/scwrl_1527406635.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1527406635.pdb # conformation set from SCWRL output # naming current conformation karypis.srv.4_TS3-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS4.pdb.gz looking for model 1 WARNING: atoms too close: (T0316)L143.O and (T0316)R144.N only 0.000 apart, marking (T0316)R144.N as missing WARNING: atoms too close: (T0316)R312.O and (T0316)Y313.N only 0.000 apart, marking (T0316)Y313.N as missing # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_564540488.pdb -s /var/tmp/to_scwrl_564540488.seq -o /var/tmp/from_scwrl_564540488.pdb > /var/tmp/scwrl_564540488.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_564540488.pdb # conformation set from SCWRL output # naming current conformation karypis.srv.4_TS4-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS5.pdb.gz looking for model 1 WARNING: atoms too close: (T0316)C50.O and (T0316)T51.N only 0.000 apart, marking (T0316)T51.N as missing WARNING: atoms too close: (T0316)A186.O and (T0316)G187.N only 0.000 apart, marking (T0316)G187.N as missing WARNING: atoms too close: (T0316)T304.O and (T0316)L305.N only 0.000 apart, marking (T0316)L305.N as missing WARNING: atoms too close: (T0316)Y349.O and (T0316)D350.N only 0.000 apart, marking (T0316)D350.N as missing # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_215406174.pdb -s /var/tmp/to_scwrl_215406174.seq -o /var/tmp/from_scwrl_215406174.pdb > /var/tmp/scwrl_215406174.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_215406174.pdb # conformation set from SCWRL output # naming current conformation karypis.srv.4_TS5-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_332987625.pdb -s /var/tmp/to_scwrl_332987625.seq -o /var/tmp/from_scwrl_332987625.pdb > /var/tmp/scwrl_332987625.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_332987625.pdb # conformation set from SCWRL output # naming current conformation karypis.srv_TS1-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1288430541.pdb -s /var/tmp/to_scwrl_1288430541.seq -o /var/tmp/from_scwrl_1288430541.pdb > /var/tmp/scwrl_1288430541.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1288430541.pdb # conformation set from SCWRL output # naming current conformation karypis.srv_TS2-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1348680169.pdb -s /var/tmp/to_scwrl_1348680169.seq -o /var/tmp/from_scwrl_1348680169.pdb > /var/tmp/scwrl_1348680169.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1348680169.pdb # conformation set from SCWRL output # naming current conformation karypis.srv_TS3-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1061886159.pdb -s /var/tmp/to_scwrl_1061886159.seq -o /var/tmp/from_scwrl_1061886159.pdb > /var/tmp/scwrl_1061886159.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1061886159.pdb # conformation set from SCWRL output # naming current conformation karypis.srv_TS4-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1402736605.pdb -s /var/tmp/to_scwrl_1402736605.seq -o /var/tmp/from_scwrl_1402736605.pdb > /var/tmp/scwrl_1402736605.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1402736605.pdb # conformation set from SCWRL output # naming current conformation karypis.srv_TS5-scwrl # ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation keasar-server_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_888341553.pdb -s /var/tmp/to_scwrl_888341553.seq -o /var/tmp/from_scwrl_888341553.pdb > /var/tmp/scwrl_888341553.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_888341553.pdb # conformation set from SCWRL output # naming current conformation keasar-server_TS1-scwrl # ReadConformPDB reading from PDB file servers/keasar-server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation keasar-server_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_839000396.pdb -s /var/tmp/to_scwrl_839000396.seq -o /var/tmp/from_scwrl_839000396.pdb > /var/tmp/scwrl_839000396.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_839000396.pdb # conformation set from SCWRL output # naming current conformation keasar-server_TS2-scwrl # ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1 # Found a chain break before 310 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_467871982.pdb -s /var/tmp/to_scwrl_467871982.seq -o /var/tmp/from_scwrl_467871982.pdb > /var/tmp/scwrl_467871982.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_467871982.pdb # conformation set from SCWRL output # naming current conformation keasar-server_TS3-scwrl # ReadConformPDB reading from PDB file servers/keasar-server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation keasar-server_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1976633389.pdb -s /var/tmp/to_scwrl_1976633389.seq -o /var/tmp/from_scwrl_1976633389.pdb > /var/tmp/scwrl_1976633389.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1976633389.pdb # conformation set from SCWRL output # naming current conformation keasar-server_TS4-scwrl # ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation keasar-server_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_553336374.pdb -s /var/tmp/to_scwrl_553336374.seq -o /var/tmp/from_scwrl_553336374.pdb > /var/tmp/scwrl_553336374.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_553336374.pdb # conformation set from SCWRL output # naming current conformation keasar-server_TS5-scwrl # ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation mGen-3D_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_991078578.pdb -s /var/tmp/to_scwrl_991078578.seq -o /var/tmp/from_scwrl_991078578.pdb > /var/tmp/scwrl_991078578.log sh: line 1: 556 Killed scwrl3 -i /var/tmp/to_scwrl_991078578.pdb -s /var/tmp/to_scwrl_991078578.seq -o /var/tmp/from_scwrl_991078578.pdb >/var/tmp/scwrl_991078578.log Error: Couldn't open file /var/tmp/from_scwrl_991078578.pdb or /var/tmp/from_scwrl_991078578.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_991078578_b.pdb or decoys//var/tmp/from_scwrl_991078578_b.pdb.gz for input Trying /var/tmp/from_scwrl_991078578_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_991078578_b.pdb or /var/tmp/from_scwrl_991078578_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_991078578_a.pdb or decoys//var/tmp/from_scwrl_991078578_a.pdb.gz for input Trying /var/tmp/from_scwrl_991078578_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_991078578_a.pdb or /var/tmp/from_scwrl_991078578_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_991078578.pdb or /var/tmp/from_scwrl_991078578_b.pdb or /var/tmp/from_scwrl_991078578_a.pdb Error: no new SCWRL conformation added # naming current conformation mGen-3D_TS1-scwrl # ReadConformPDB reading from PDB file servers/nFOLD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation nFOLD_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1205512097.pdb -s /var/tmp/to_scwrl_1205512097.seq -o /var/tmp/from_scwrl_1205512097.pdb > /var/tmp/scwrl_1205512097.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1205512097.pdb # conformation set from SCWRL output # naming current conformation nFOLD_TS1-scwrl # ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation nFOLD_TS2 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1421277870.pdb -s /var/tmp/to_scwrl_1421277870.seq -o /var/tmp/from_scwrl_1421277870.pdb > /var/tmp/scwrl_1421277870.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1421277870.pdb # conformation set from SCWRL output # naming current conformation nFOLD_TS2-scwrl # ReadConformPDB reading from PDB file servers/nFOLD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation nFOLD_TS3 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_378182414.pdb -s /var/tmp/to_scwrl_378182414.seq -o /var/tmp/from_scwrl_378182414.pdb > /var/tmp/scwrl_378182414.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_378182414.pdb # conformation set from SCWRL output # naming current conformation nFOLD_TS3-scwrl # ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation nFOLD_TS4 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1989895772.pdb -s /var/tmp/to_scwrl_1989895772.seq -o /var/tmp/from_scwrl_1989895772.pdb > /var/tmp/scwrl_1989895772.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1989895772.pdb # conformation set from SCWRL output # naming current conformation nFOLD_TS4-scwrl # ReadConformPDB reading from PDB file servers/nFOLD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation nFOLD_TS5 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1625688504.pdb -s /var/tmp/to_scwrl_1625688504.seq -o /var/tmp/from_scwrl_1625688504.pdb > /var/tmp/scwrl_1625688504.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1625688504.pdb # conformation set from SCWRL output # naming current conformation nFOLD_TS5-scwrl # ReadConformPDB reading from PDB file servers/panther2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation panther2_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1963888041.pdb -s /var/tmp/to_scwrl_1963888041.seq -o /var/tmp/from_scwrl_1963888041.pdb > /var/tmp/scwrl_1963888041.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1963888041.pdb # conformation set from SCWRL output # naming current conformation panther2_TS1-scwrl # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0316 can't currently be optimized by undertaker # naming current conformation shub_TS1 # request to SCWRL produces command: ulimit -t 336 ; scwrl3 -i /var/tmp/to_scwrl_1810619090.pdb -s /var/tmp/to_scwrl_1810619090.seq -o /var/tmp/from_scwrl_1810619090.pdb > /var/tmp/scwrl_1810619090.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1810619090.pdb # conformation set from SCWRL output # naming current conformation shub_TS1-scwrl # command:CPU_time= 76.3744 sec, elapsed time= 2454.95 sec) # command:# Prefix for output files set to decoys/ # command:# Will now start reporting costs to decoys/evaluate_3.rdb # command:# CostConform Warning: Couldn't open file decoys//projects/compbio/experiments/undertaker/spots/near-backbone-center.spot or decoys//projects/compbio/experiments/undertaker/spots/near-backbone-center.spot.gz for input Trying /projects/compbio/experiments/undertaker/spots/near-backbone-center.spot # Reading spots from /projects/compbio/experiments/undertaker/spots/near-backbone-center.spot shub_TS1-scwrl costs 0 real_cost = 216.428 shub_TS1 costs 0 real_cost = 334.858 panther2_TS1-scwrl costs 0 real_cost = 1057.67 panther2_TS1 costs 0 real_cost = 1054.07 nFOLD_TS5-scwrl costs 0 real_cost = 522.404 nFOLD_TS5 costs 0 real_cost = 702.679 nFOLD_TS4-scwrl costs 0 real_cost = 443.361 nFOLD_TS4 costs 0 real_cost = 621.43 nFOLD_TS3-scwrl costs 0 real_cost = 431.227 nFOLD_TS3 costs 0 real_cost = 611.155 nFOLD_TS2-scwrl costs 0 real_cost = 413.742 nFOLD_TS2 costs 0 real_cost = 605.491 nFOLD_TS1-scwrl costs 0 real_cost = 408.321 nFOLD_TS1 costs 0 real_cost = 598.63 mGen-3D_TS1-scwrl costs 0 real_cost = 613.884 keasar-server_TS5-scwrl costs 0 real_cost = 886.466 keasar-server_TS5 costs 0 real_cost = 885.066 keasar-server_TS4-scwrl costs 0 real_cost = 886.466 keasar-server_TS4 costs 0 real_cost = 885.066 keasar-server_TS3-scwrl costs 0 real_cost = 348.347 keasar-server_TS3 costs 0 real_cost = 348.26 keasar-server_TS2-scwrl costs 0 real_cost = 330.136 keasar-server_TS2 costs 0 real_cost = 335.659 keasar-server_TS1-scwrl costs 0 real_cost = 235.204 keasar-server_TS1 costs 0 real_cost = 252.038 karypis.srv_TS5-scwrl costs 0 real_cost = 346.645 karypis.srv_TS5 costs 0 real_cost = 341.519 karypis.srv_TS4-scwrl costs 0 real_cost = 344.096 karypis.srv_TS4 costs 0 real_cost = 340.199 karypis.srv_TS3-scwrl costs 0 real_cost = 366.843 karypis.srv_TS3 costs 0 real_cost = 363.701 karypis.srv_TS2-scwrl costs 0 real_cost = 355.911 karypis.srv_TS2 costs 0 real_cost = 351.569 karypis.srv_TS1-scwrl costs 0 real_cost = 396.983 karypis.srv_TS1 costs 0 real_cost = 390.276 karypis.srv.4_TS5-scwrl costs 0 real_cost = 346.693 karypis.srv.4_TS5 costs 0 real_cost = 346.556 karypis.srv.4_TS4-scwrl costs 0 real_cost = 330.016 karypis.srv.4_TS4 costs 0 real_cost = 330.006 karypis.srv.4_TS3-scwrl costs 0 real_cost = 383.023 karypis.srv.4_TS3 costs 0 real_cost = 383.029 karypis.srv.4_TS2-scwrl costs 0 real_cost = 297.025 karypis.srv.4_TS2 costs 0 real_cost = 297.009 karypis.srv.4_TS1-scwrl costs 0 real_cost = 399.389 karypis.srv.4_TS1 costs 0 real_cost = 399.389 karypis.srv.2_TS5-scwrl costs 0 real_cost = 504.744 karypis.srv.2_TS5 costs 0 real_cost = 504.744 karypis.srv.2_TS4-scwrl costs 0 real_cost = 368.059 karypis.srv.2_TS4 costs 0 real_cost = 367.308 karypis.srv.2_TS3-scwrl costs 0 real_cost = 380.748 karypis.srv.2_TS3 costs 0 real_cost = 380.748 karypis.srv.2_TS2-scwrl costs 0 real_cost = 377.88 karypis.srv.2_TS2 costs 0 real_cost = 377.88 karypis.srv.2_TS1-scwrl costs 0 real_cost = 378.374 karypis.srv.2_TS1 costs 0 real_cost = 378.374 gtg_AL5-scwrl costs 0 real_cost = 652.901 gtg_AL5 costs 0 real_cost = 751.239 gtg_AL4-scwrl costs 0 real_cost = 640.887 gtg_AL4 costs 0 real_cost = 738.455 gtg_AL3-scwrl costs 0 real_cost = 622.661 gtg_AL3 costs 0 real_cost = 742.556 gtg_AL2-scwrl costs 0 real_cost = 579.882 gtg_AL2 costs 0 real_cost = 726.939 gtg_AL1-scwrl costs 0 real_cost = 578.358 gtg_AL1 costs 0 real_cost = 725.353 forecast-s_AL5-scwrl costs 0 real_cost = 592.075 forecast-s_AL5 costs 0 real_cost = 747.806 forecast-s_AL4-scwrl costs 0 real_cost = 1012.87 forecast-s_AL4 costs 0 real_cost = 1137.07 forecast-s_AL3-scwrl costs 0 real_cost = 1023.27 forecast-s_AL3 costs 0 real_cost = 793.075 forecast-s_AL2-scwrl costs 0 real_cost = 578.338 forecast-s_AL2 costs 0 real_cost = 705.868 forecast-s_AL1-scwrl costs 0 real_cost = 1035.27 forecast-s_AL1 costs 0 real_cost = 707.853 beautshotbase_TS1-scwrl costs 0 real_cost = 930.066 beautshotbase_TS1 costs 0 real_cost = 926.466 beautshot_TS1-scwrl costs 0 real_cost = 370.566 beautshot_TS1 costs 0 real_cost = 370.484 Zhang-Server_TS5-scwrl costs 0 real_cost = 323.245 Zhang-Server_TS5 costs 0 real_cost = 323.344 Zhang-Server_TS4-scwrl costs 0 real_cost = 327.438 Zhang-Server_TS4 costs 0 real_cost = 327.434 Zhang-Server_TS3-scwrl costs 0 real_cost = 287.015 Zhang-Server_TS3 costs 0 real_cost = 286.338 Zhang-Server_TS2-scwrl costs 0 real_cost = 337.348 Zhang-Server_TS2 costs 0 real_cost = 337.357 Zhang-Server_TS1-scwrl costs 0 real_cost = 223.249 Zhang-Server_TS1 costs 0 real_cost = 235.315 UNI-EID_sfst_AL4-scwrl costs 0 real_cost = 1047.67 UNI-EID_sfst_AL4 costs 0 real_cost = 1146.27 UNI-EID_sfst_AL3-scwrl costs 0 real_cost = 1064.67 UNI-EID_sfst_AL3 costs 0 real_cost = 1154.27 UNI-EID_sfst_AL2-scwrl costs 0 real_cost = 1049.47 UNI-EID_sfst_AL2 costs 0 real_cost = 1143.87 UNI-EID_sfst_AL1-scwrl costs 0 real_cost = 1057.47 UNI-EID_sfst_AL1 costs 0 real_cost = 1150.67 UNI-EID_expm_TS1-scwrl costs 0 real_cost = 367.362 UNI-EID_expm_TS1 costs 0 real_cost = 568.625 UNI-EID_bnmx_TS4-scwrl costs 0 real_cost = 1031.07 UNI-EID_bnmx_TS4 costs 0 real_cost = 1131.87 UNI-EID_bnmx_TS3-scwrl costs 0 real_cost = 561.795 UNI-EID_bnmx_TS3 costs 0 real_cost = 722.22 UNI-EID_bnmx_TS2-scwrl costs 0 real_cost = 975.866 UNI-EID_bnmx_TS2 costs 0 real_cost = 1101.47 UNI-EID_bnmx_TS1-scwrl costs 0 real_cost = 423.071 UNI-EID_bnmx_TS1 costs 0 real_cost = 636.625 SPARKS2_TS5-scwrl costs 0 real_cost = 328.885 SPARKS2_TS5 costs 0 real_cost = 325.982 SPARKS2_TS4-scwrl costs 0 real_cost = 325.64 SPARKS2_TS4 costs 0 real_cost = 425.67 SPARKS2_TS3-scwrl costs 0 real_cost = 342.171 SPARKS2_TS3 costs 0 real_cost = 344.21 SPARKS2_TS2-scwrl costs 0 real_cost = 400.663 SPARKS2_TS2 costs 0 real_cost = 400.667 SPARKS2_TS1-scwrl costs 0 real_cost = 419.064 SPARKS2_TS1 costs 0 real_cost = 419.073 SP4_TS5-scwrl costs 0 real_cost = 431.605 SP4_TS5 costs 0 real_cost = 431.578 SP4_TS4-scwrl costs 0 real_cost = 374.848 SP4_TS4 costs 0 real_cost = 373.121 SP4_TS3-scwrl costs 0 real_cost = 345.032 SP4_TS3 costs 0 real_cost = 345.082 SP4_TS2-scwrl costs 0 real_cost = 398.378 SP4_TS2 costs 0 real_cost = 398.24 SP4_TS1-scwrl costs 0 real_cost = 406.504 SP4_TS1 costs 0 real_cost = 406.483 SP3_TS5-scwrl costs 0 real_cost = 294.119 SP3_TS5 costs 0 real_cost = 393.942 SP3_TS4-scwrl costs 0 real_cost = 332.771 SP3_TS4 costs 0 real_cost = 332.535 SP3_TS3-scwrl costs 0 real_cost = 404.528 SP3_TS3 costs 0 real_cost = 404.412 SP3_TS2-scwrl costs 0 real_cost = 370.618 SP3_TS2 costs 0 real_cost = 363.134 SP3_TS1-scwrl costs 0 real_cost = 419.032 SP3_TS1 costs 0 real_cost = 419.126 SAM_T06_server_TS5-scwrl costs 0 real_cost = 568.533 SAM_T06_server_TS5 costs 0 real_cost = 536.319 SAM_T06_server_TS4-scwrl costs 0 real_cost = 570.354 SAM_T06_server_TS4 costs 0 real_cost = 529.34 SAM_T06_server_TS3-scwrl costs 0 real_cost = 998.266 SAM_T06_server_TS3 costs 0 real_cost = 976.466 SAM_T06_server_TS2-scwrl costs 0 real_cost = 546.938 SAM_T06_server_TS2 costs 0 real_cost = 489.056 SAM_T06_server_TS1-scwrl costs 0 real_cost = 296.935 SAM_T06_server_TS1 costs 0 real_cost = 297.18 SAM-T99_AL5-scwrl costs 0 real_cost = 983.066 SAM-T99_AL5 costs 0 real_cost = 1117.47 SAM-T99_AL4-scwrl costs 0 real_cost = 983.466 SAM-T99_AL4 costs 0 real_cost = 1117.47 SAM-T99_AL3-scwrl costs 0 real_cost = 966.066 SAM-T99_AL3 costs 0 real_cost = 1101.47 SAM-T99_AL2-scwrl costs 0 real_cost = 1086.47 SAM-T99_AL2 costs 0 real_cost = 1167.07 SAM-T99_AL1-scwrl costs 0 real_cost = 940.066 SAM-T99_AL1 costs 0 real_cost = 1089.47 SAM-T02_AL5-scwrl costs 0 real_cost = 964.666 SAM-T02_AL5 costs 0 real_cost = 1105.07 SAM-T02_AL4-scwrl costs 0 real_cost = 1034.07 SAM-T02_AL4 costs 0 real_cost = 1139.07 SAM-T02_AL3-scwrl costs 0 real_cost = 1080.87 SAM-T02_AL3 costs 0 real_cost = 1168.27 SAM-T02_AL2-scwrl costs 0 real_cost = 1054.27 SAM-T02_AL2 costs 0 real_cost = 1151.87 SAM-T02_AL1-scwrl costs 0 real_cost = 1041.27 SAM-T02_AL1 costs 0 real_cost = 1143.47 ROKKY_TS5-scwrl costs 0 real_cost = 284.545 ROKKY_TS5 costs 0 real_cost = 496.566 ROKKY_TS4-scwrl costs 0 real_cost = 250.281 ROKKY_TS4 costs 0 real_cost = 459.616 ROKKY_TS3-scwrl costs 0 real_cost = 268.339 ROKKY_TS3 costs 0 real_cost = 477.326 ROKKY_TS2-scwrl costs 0 real_cost = 300.485 ROKKY_TS2 costs 0 real_cost = 514.694 ROKKY_TS1-scwrl costs 0 real_cost = 283.438 ROKKY_TS1 costs 0 real_cost = 499.21 ROBETTA_TS5-scwrl costs 0 real_cost = 319.886 ROBETTA_TS5 costs 0 real_cost = 319.794 ROBETTA_TS4-scwrl costs 0 real_cost = 336.516 ROBETTA_TS4 costs 0 real_cost = 336.47 ROBETTA_TS3-scwrl costs 0 real_cost = 311.504 ROBETTA_TS3 costs 0 real_cost = 311.628 ROBETTA_TS2-scwrl costs 0 real_cost = 317.538 ROBETTA_TS2 costs 0 real_cost = 318.466 ROBETTA_TS1-scwrl costs 0 real_cost = 308.342 ROBETTA_TS1 costs 0 real_cost = 304.015 RAPTOR_TS5-scwrl costs 0 real_cost = 340.252 RAPTOR_TS5 costs 0 real_cost = 340.137 RAPTOR_TS4-scwrl costs 0 real_cost = 332.686 RAPTOR_TS4 costs 0 real_cost = 336.452 RAPTOR_TS3-scwrl costs 0 real_cost = 336.846 RAPTOR_TS3 costs 0 real_cost = 328.984 RAPTOR_TS2-scwrl costs 0 real_cost = 340.042 RAPTOR_TS2 costs 0 real_cost = 339.845 RAPTOR_TS1-scwrl costs 0 real_cost = 362.281 RAPTOR_TS1 costs 0 real_cost = 362.46 RAPTORESS_TS5-scwrl costs 0 real_cost = 340.323 RAPTORESS_TS5 costs 0 real_cost = 340.436 RAPTORESS_TS4-scwrl costs 0 real_cost = 331.443 RAPTORESS_TS4 costs 0 real_cost = 337.085 RAPTORESS_TS3-scwrl costs 0 real_cost = 332.452 RAPTORESS_TS3 costs 0 real_cost = 332.346 RAPTORESS_TS2-scwrl costs 0 real_cost = 338.671 RAPTORESS_TS2 costs 0 real_cost = 338.689 RAPTORESS_TS1-scwrl costs 0 real_cost = 356.199 RAPTORESS_TS1 costs 0 real_cost = 356.251 RAPTOR-ACE_TS5-scwrl costs 0 real_cost = 345.937 RAPTOR-ACE_TS5 costs 0 real_cost = 345.674 RAPTOR-ACE_TS4-scwrl costs 0 real_cost = 331.793 RAPTOR-ACE_TS4 costs 0 real_cost = 332.017 RAPTOR-ACE_TS3-scwrl costs 0 real_cost = 441.441 RAPTOR-ACE_TS3 costs 0 real_cost = 441.486 RAPTOR-ACE_TS2-scwrl costs 0 real_cost = 425.492 RAPTOR-ACE_TS2 costs 0 real_cost = 425.506 RAPTOR-ACE_TS1-scwrl costs 0 real_cost = 340.52 RAPTOR-ACE_TS1 costs 0 real_cost = 340.46 Pmodeller6_TS5-scwrl costs 0 real_cost = 345.322 Pmodeller6_TS5 costs 0 real_cost = 339.866 Pmodeller6_TS4-scwrl costs 0 real_cost = 349.341 Pmodeller6_TS4 costs 0 real_cost = 349.352 Pmodeller6_TS3-scwrl costs 0 real_cost = 348.322 Pmodeller6_TS3 costs 0 real_cost = 342.66 Pmodeller6_TS2-scwrl costs 0 real_cost = 339.341 Pmodeller6_TS2 costs 0 real_cost = 339.352 Pmodeller6_TS1-scwrl costs 0 real_cost = 349.722 Pmodeller6_TS1 costs 0 real_cost = 344.469 Phyre-2_TS5-scwrl costs 0 real_cost = 363.036 Phyre-2_TS5 costs 0 real_cost = 361.925 Phyre-2_TS4-scwrl costs 0 real_cost = 334.445 Phyre-2_TS4 costs 0 real_cost = 333.686 Phyre-2_TS3-scwrl costs 0 real_cost = 320.618 Phyre-2_TS3 costs 0 real_cost = 319.421 Phyre-2_TS2-scwrl costs 0 real_cost = 306.974 Phyre-2_TS2 costs 0 real_cost = 307.565 Phyre-2_TS1-scwrl costs 0 real_cost = 326.164 Phyre-2_TS1 costs 0 real_cost = 328.335 Phyre-1_TS1-scwrl costs 0 real_cost = 1052.87 Phyre-1_TS1 costs 0 real_cost = 1043.07 Pcons6_TS5-scwrl costs 0 real_cost = 334.986 Pcons6_TS5 costs 0 real_cost = 335.282 Pcons6_TS4-scwrl costs 0 real_cost = 361.914 Pcons6_TS4 costs 0 real_cost = 355.882 Pcons6_TS3-scwrl costs 0 real_cost = 400.767 Pcons6_TS3 costs 0 real_cost = 395.954 Pcons6_TS2-scwrl costs 0 real_cost = 413.311 Pcons6_TS2 costs 0 real_cost = 409.098 Pcons6_TS1-scwrl costs 0 real_cost = 343.844 Pcons6_TS1 costs 0 real_cost = 342.149 PROTINFO_TS5-scwrl costs 0 real_cost = 346.159 PROTINFO_TS5 costs 0 real_cost = 346.095 PROTINFO_TS4-scwrl costs 0 real_cost = 349.211 PROTINFO_TS4 costs 0 real_cost = 349.262 PROTINFO_TS3-scwrl costs 0 real_cost = 356.108 PROTINFO_TS3 costs 0 real_cost = 359.968 PROTINFO_TS2-scwrl costs 0 real_cost = 429.357 PROTINFO_TS2 costs 0 real_cost = 428.809 PROTINFO_TS1-scwrl costs 0 real_cost = 341.388 PROTINFO_TS1 costs 0 real_cost = 341.329 PROTINFO-AB_TS5-scwrl costs 0 real_cost = 324.411 PROTINFO-AB_TS5 costs 0 real_cost = 324.255 PROTINFO-AB_TS4-scwrl costs 0 real_cost = 323.218 PROTINFO-AB_TS4 costs 0 real_cost = 316.965 PROTINFO-AB_TS3-scwrl costs 0 real_cost = 323.174 PROTINFO-AB_TS3 costs 0 real_cost = 322.658 PROTINFO-AB_TS2-scwrl costs 0 real_cost = 324.665 PROTINFO-AB_TS2 costs 0 real_cost = 324.47 PROTINFO-AB_TS1-scwrl costs 0 real_cost = 324.665 PROTINFO-AB_TS1 costs 0 real_cost = 324.47 POMYSL_TS4-scwrl costs 0 real_cost = 640.422 POMYSL_TS4 costs 0 real_cost = 638.922 POMYSL_TS3-scwrl costs 0 real_cost = 655.846 POMYSL_TS3 costs 0 real_cost = 654.912 POMYSL_TS2-scwrl costs 0 real_cost = 645.939 POMYSL_TS2 costs 0 real_cost = 645.868 POMYSL_TS1-scwrl costs 0 real_cost = 647.284 POMYSL_TS1 costs 0 real_cost = 646.051 NN_PUT_lab_TS1-scwrl costs 0 real_cost = 408.321 NN_PUT_lab_TS1 costs 0 real_cost = 598.63 MetaTasser_TS5-scwrl costs 0 real_cost = 350.442 MetaTasser_TS5 costs 0 real_cost = 350.347 MetaTasser_TS4-scwrl costs 0 real_cost = 337.888 MetaTasser_TS4 costs 0 real_cost = 337.604 MetaTasser_TS3-scwrl costs 0 real_cost = 322.832 MetaTasser_TS2-scwrl costs 0 real_cost = 330.061 MetaTasser_TS2 costs 0 real_cost = 324.319 MetaTasser_TS1-scwrl costs 0 real_cost = 342.195 MetaTasser_TS1 costs 0 real_cost = 342.111 Ma-OPUS-server_TS5-scwrl costs 0 real_cost = 339.01 Ma-OPUS-server_TS5 costs 0 real_cost = 342.627 Ma-OPUS-server_TS4-scwrl costs 0 real_cost = 355.519 Ma-OPUS-server_TS4 costs 0 real_cost = 355.72 Ma-OPUS-server_TS3-scwrl costs 0 real_cost = 349.895 Ma-OPUS-server_TS3 costs 0 real_cost = 344.884 Ma-OPUS-server_TS2-scwrl costs 0 real_cost = 299.611 Ma-OPUS-server_TS2 costs 0 real_cost = 300.046 Ma-OPUS-server_TS1-scwrl costs 0 real_cost = 331.551 Ma-OPUS-server_TS1 costs 0 real_cost = 331.706 LOOPP_TS5-scwrl costs 0 real_cost = 404.514 LOOPP_TS5 costs 0 real_cost = 399.26 LOOPP_TS4-scwrl costs 0 real_cost = 375.272 LOOPP_TS4 costs 0 real_cost = 376.197 LOOPP_TS3-scwrl costs 0 real_cost = 416.726 LOOPP_TS3 costs 0 real_cost = 404.961 LOOPP_TS2-scwrl costs 0 real_cost = 346.937 LOOPP_TS2 costs 0 real_cost = 348.9 LOOPP_TS1-scwrl costs 0 real_cost = 315.135 LOOPP_TS1 costs 0 real_cost = 313.699 Huber-Torda-Server_TS5-scwrl costs 0 real_cost = 709.986 Huber-Torda-Server_TS5 costs 0 real_cost = 761.63 Huber-Torda-Server_TS4-scwrl costs 0 real_cost = 656.255 Huber-Torda-Server_TS4 costs 0 real_cost = 725.584 Huber-Torda-Server_TS3-scwrl costs 0 real_cost = 653.202 Huber-Torda-Server_TS3 costs 0 real_cost = 722.905 Huber-Torda-Server_TS2-scwrl costs 0 real_cost = 646.489 Huber-Torda-Server_TS2 costs 0 real_cost = 704.336 Huber-Torda-Server_TS1-scwrl costs 0 real_cost = 674.24 Huber-Torda-Server_TS1 costs 0 real_cost = 733.264 HHpred3_TS1-scwrl costs 0 real_cost = 106.75 HHpred3_TS1 costs 0 real_cost = 97.9731 HHpred2_TS1-scwrl costs 0 real_cost = 106.75 HHpred2_TS1 costs 0 real_cost = 97.9731 HHpred1_TS1-scwrl costs 0 real_cost = 106.75 HHpred1_TS1 costs 0 real_cost = 97.9731 GeneSilicoMetaServer_TS5-scwrl costs 0 real_cost = 333.715 GeneSilicoMetaServer_TS5 costs 0 real_cost = 333.878 GeneSilicoMetaServer_TS4-scwrl costs 0 real_cost = 950.466 GeneSilicoMetaServer_TS4 costs 0 real_cost = 949.266 GeneSilicoMetaServer_TS3-scwrl costs 0 real_cost = 888.866 GeneSilicoMetaServer_TS3 costs 0 real_cost = 886.466 GeneSilicoMetaServer_TS2-scwrl costs 0 real_cost = 346.379 GeneSilicoMetaServer_TS1-scwrl costs 0 real_cost = 440.612 GeneSilicoMetaServer_TS1 costs 0 real_cost = 440.059 FUNCTION_TS5-scwrl costs 0 real_cost = 311.867 FUNCTION_TS5 costs 0 real_cost = 311.33 FUNCTION_TS4-scwrl costs 0 real_cost = 369.405 FUNCTION_TS4 costs 0 real_cost = 369.317 FUNCTION_TS3-scwrl costs 0 real_cost = 264.894 FUNCTION_TS3 costs 0 real_cost = 364.81 FUNCTION_TS2-scwrl costs 0 real_cost = 345.4 FUNCTION_TS2 costs 0 real_cost = 345.299 FUNCTION_TS1-scwrl costs 0 real_cost = 973.866 FUNCTION_TS1 costs 0 real_cost = 970.666 FUGUE_AL5-scwrl costs 0 real_cost = 470.545 FUGUE_AL5 costs 0 real_cost = 668.458 FUGUE_AL4-scwrl costs 0 real_cost = 415.229 FUGUE_AL4 costs 0 real_cost = 663.846 FUGUE_AL3-scwrl costs 0 real_cost = 945.066 FUGUE_AL3 costs 0 real_cost = 1101.47 FUGUE_AL2-scwrl costs 0 real_cost = 1026.07 FUGUE_AL2 costs 0 real_cost = 1139.87 FUGUE_AL1-scwrl costs 0 real_cost = 589.259 FUGUE_AL1 costs 0 real_cost = 765.745 FUGMOD_TS5-scwrl costs 0 real_cost = 370.555 FUGMOD_TS5 costs 0 real_cost = 369.438 FUGMOD_TS4-scwrl costs 0 real_cost = 350.5 FUGMOD_TS4 costs 0 real_cost = 350.506 FUGMOD_TS3-scwrl costs 0 real_cost = 936.066 FUGMOD_TS3 costs 0 real_cost = 933.266 FUGMOD_TS2-scwrl costs 0 real_cost = 995.666 FUGMOD_TS2 costs 0 real_cost = 994.266 FUGMOD_TS1-scwrl costs 0 real_cost = 424.371 FUGMOD_TS1 costs 0 real_cost = 424.903 FPSOLVER-SERVER_TS5-scwrl costs 0 real_cost = 352.404 FPSOLVER-SERVER_TS5 costs 0 real_cost = 352.461 FPSOLVER-SERVER_TS4-scwrl costs 0 real_cost = 365.823 FPSOLVER-SERVER_TS4 costs 0 real_cost = 366.138 FPSOLVER-SERVER_TS3-scwrl costs 0 real_cost = 345.013 FPSOLVER-SERVER_TS3 costs 0 real_cost = 346.322 FPSOLVER-SERVER_TS2-scwrl costs 0 real_cost = 383.08 FPSOLVER-SERVER_TS2 costs 0 real_cost = 383.104 FPSOLVER-SERVER_TS1-scwrl costs 0 real_cost = 364.227 FPSOLVER-SERVER_TS1 costs 0 real_cost = 364.28 FORTE2_AL5-scwrl costs 0 real_cost = 596.012 FORTE2_AL5 costs 0 real_cost = 490.325 FORTE2_AL4-scwrl costs 0 real_cost = 678.492 FORTE2_AL3-scwrl costs 0 real_cost = 405.76 FORTE2_AL3 costs 0 real_cost = 653.93 FORTE2_AL2-scwrl costs 0 real_cost = 415.769 FORTE2_AL2 costs 0 real_cost = 662.736 FORTE2_AL1-scwrl costs 0 real_cost = 384.935 FORTE2_AL1 costs 0 real_cost = 637.555 FORTE1_AL5-scwrl costs 0 real_cost = 372.385 FORTE1_AL5 costs 0 real_cost = 544.616 FORTE1_AL4-scwrl costs 0 real_cost = 487.004 FORTE1_AL4 costs 0 real_cost = 671.427 FORTE1_AL3-scwrl costs 0 real_cost = 405.76 FORTE1_AL3 costs 0 real_cost = 653.93 FORTE1_AL2-scwrl costs 0 real_cost = 415.769 FORTE1_AL2 costs 0 real_cost = 662.736 FORTE1_AL1-scwrl costs 0 real_cost = 384.935 FORTE1_AL1 costs 0 real_cost = 637.555 FOLDpro_TS5-scwrl costs 0 real_cost = 371.437 FOLDpro_TS5 costs 0 real_cost = 368.34 FOLDpro_TS4-scwrl costs 0 real_cost = 346.162 FOLDpro_TS4 costs 0 real_cost = 346.226 FOLDpro_TS3-scwrl costs 0 real_cost = 308.515 FOLDpro_TS3 costs 0 real_cost = 308.197 FOLDpro_TS2-scwrl costs 0 real_cost = 357.088 FOLDpro_TS2 costs 0 real_cost = 357.213 FOLDpro_TS1-scwrl costs 0 real_cost = 307.835 FOLDpro_TS1 costs 0 real_cost = 307.497 FAMS_TS5-scwrl costs 0 real_cost = 353.447 FAMS_TS5 costs 0 real_cost = 350.825 FAMS_TS4-scwrl costs 0 real_cost = 973.866 FAMS_TS4 costs 0 real_cost = 970.666 FAMS_TS3-scwrl costs 0 real_cost = 973.866 FAMS_TS3 costs 0 real_cost = 970.666 FAMS_TS2-scwrl costs 0 real_cost = 353.118 FAMS_TS2 costs 0 real_cost = 351.472 FAMS_TS1-scwrl costs 0 real_cost = 338.443 FAMS_TS1 costs 0 real_cost = 337.069 FAMSD_TS5-scwrl costs 0 real_cost = 310.764 FAMSD_TS5 costs 0 real_cost = 313.408 FAMSD_TS4-scwrl costs 0 real_cost = 880.866 FAMSD_TS4 costs 0 real_cost = 878.666 FAMSD_TS3-scwrl costs 0 real_cost = 973.866 FAMSD_TS3 costs 0 real_cost = 970.666 FAMSD_TS2-scwrl costs 0 real_cost = 414.156 FAMSD_TS2 costs 0 real_cost = 414.191 FAMSD_TS1-scwrl costs 0 real_cost = 337.044 FAMSD_TS1 costs 0 real_cost = 335.27 Distill_TS5-scwrl costs 0 real_cost = 757.207 Distill_TS4-scwrl costs 0 real_cost = 743.658 Distill_TS3-scwrl costs 0 real_cost = 750.566 Distill_TS2-scwrl costs 0 real_cost = 729.452 Distill_TS1-scwrl costs 0 real_cost = 727.3 CaspIta-FOX_TS5-scwrl costs 0 real_cost = 398.192 CaspIta-FOX_TS5 costs 0 real_cost = 398.696 CaspIta-FOX_TS4-scwrl costs 0 real_cost = 447.049 CaspIta-FOX_TS4 costs 0 real_cost = 435.79 CaspIta-FOX_TS3-scwrl costs 0 real_cost = 584.333 CaspIta-FOX_TS3 costs 0 real_cost = 571.533 CaspIta-FOX_TS2-scwrl costs 0 real_cost = 417.025 CaspIta-FOX_TS2 costs 0 real_cost = 409.508 CaspIta-FOX_TS1-scwrl costs 0 real_cost = 551.241 CaspIta-FOX_TS1 costs 0 real_cost = 536.142 CPHmodels_TS1-scwrl costs 0 real_cost = 1158.07 CPHmodels_TS1 costs 0 real_cost = 1153.47 CIRCLE_TS5-scwrl costs 0 real_cost = 345.398 CIRCLE_TS5 costs 0 real_cost = 345.454 CIRCLE_TS4-scwrl costs 0 real_cost = 955.466 CIRCLE_TS4 costs 0 real_cost = 954.266 CIRCLE_TS3-scwrl costs 0 real_cost = 973.866 CIRCLE_TS3 costs 0 real_cost = 971.466 CIRCLE_TS2-scwrl costs 0 real_cost = 955.466 CIRCLE_TS2 costs 0 real_cost = 954.266 CIRCLE_TS1-scwrl costs 0 real_cost = 293.813 CIRCLE_TS1 costs 0 real_cost = 294.426 Bilab-ENABLE_TS3-scwrl costs 0 real_cost = 334.035 Bilab-ENABLE_TS3 costs 0 real_cost = 334.035 Bilab-ENABLE_TS2-scwrl costs 0 real_cost = 348.247 Bilab-ENABLE_TS2 costs 0 real_cost = 348.253 Bilab-ENABLE_TS1-scwrl costs 0 real_cost = 337.928 Bilab-ENABLE_TS1 costs 0 real_cost = 337.928 BayesHH_TS1-scwrl costs 0 real_cost = 431.583 BayesHH_TS1 costs 0 real_cost = 431.57 ABIpro_TS5-scwrl costs 0 real_cost = 269.872 ABIpro_TS5 costs 0 real_cost = 269.895 ABIpro_TS4-scwrl costs 0 real_cost = 298.175 ABIpro_TS4 costs 0 real_cost = 297.898 ABIpro_TS3-scwrl costs 0 real_cost = 309.001 ABIpro_TS3 costs 0 real_cost = 309.001 ABIpro_TS2-scwrl costs 0 real_cost = 325.847 ABIpro_TS2 costs 0 real_cost = 325.905 ABIpro_TS1-scwrl costs 0 real_cost = 306.361 ABIpro_TS1 costs 0 real_cost = 306.678 3Dpro_TS5-scwrl costs 0 real_cost = 351.678 3Dpro_TS5 costs 0 real_cost = 352.141 3Dpro_TS4-scwrl costs 0 real_cost = 345.686 3Dpro_TS4 costs 0 real_cost = 346.015 3Dpro_TS3-scwrl costs 0 real_cost = 307.835 3Dpro_TS3 costs 0 real_cost = 307.497 3Dpro_TS2-scwrl costs 0 real_cost = 292.498 3Dpro_TS2 costs 0 real_cost = 293.811 3Dpro_TS1-scwrl costs 0 real_cost = 308.515 3Dpro_TS1 costs 0 real_cost = 308.197 3D-JIGSAW_TS5-scwrl costs 0 real_cost = 949.866 3D-JIGSAW_TS5 costs 0 real_cost = 945.866 3D-JIGSAW_TS4-scwrl costs 0 real_cost = 864.466 3D-JIGSAW_TS4 costs 0 real_cost = 862.866 3D-JIGSAW_TS3-scwrl costs 0 real_cost = 1004.27 3D-JIGSAW_TS3 costs 0 real_cost = 999.866 3D-JIGSAW_TS2-scwrl costs 0 real_cost = 1006.47 3D-JIGSAW_TS2 costs 0 real_cost = 1001.47 3D-JIGSAW_TS1-scwrl costs 0 real_cost = 1004.67 3D-JIGSAW_TS1 costs 0 real_cost = 1001.47 3D-JIGSAW_RECOM_TS5-scwrl costs 0 real_cost = 973.866 3D-JIGSAW_RECOM_TS5 costs 0 real_cost = 971.466 3D-JIGSAW_RECOM_TS4-scwrl costs 0 real_cost = 973.866 3D-JIGSAW_RECOM_TS4 costs 0 real_cost = 971.466 3D-JIGSAW_RECOM_TS3-scwrl costs 0 real_cost = 973.866 3D-JIGSAW_RECOM_TS3 costs 0 real_cost = 971.466 3D-JIGSAW_RECOM_TS2-scwrl costs 0 real_cost = 963.466 3D-JIGSAW_RECOM_TS2 costs 0 real_cost = 962.466 3D-JIGSAW_RECOM_TS1-scwrl costs 0 real_cost = 973.866 3D-JIGSAW_RECOM_TS1 costs 0 real_cost = 971.466 3D-JIGSAW_POPULUS_TS5-scwrl costs 0 real_cost = 976.066 3D-JIGSAW_POPULUS_TS5 costs 0 real_cost = 972.866 3D-JIGSAW_POPULUS_TS4-scwrl costs 0 real_cost = 955.466 3D-JIGSAW_POPULUS_TS4 costs 0 real_cost = 954.266 3D-JIGSAW_POPULUS_TS3-scwrl costs 0 real_cost = 973.866 3D-JIGSAW_POPULUS_TS3 costs 0 real_cost = 971.466 3D-JIGSAW_POPULUS_TS2-scwrl costs 0 real_cost = 973.866 3D-JIGSAW_POPULUS_TS2 costs 0 real_cost = 971.466 3D-JIGSAW_POPULUS_TS1-scwrl costs 0 real_cost = 965.866 3D-JIGSAW_POPULUS_TS1 costs 0 real_cost = 963.266 make-chimera.pdb.gz costs 0 real_cost = 262.418 chimera1.pdb.gz costs 0 real_cost = 252.401 T0316.try9-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 338.441 T0316.try9-opt2.pdb.gz costs 0 real_cost = 338.434 T0316.try9-opt2.gromacs0.pdb.gz costs 0 real_cost = 337.967 T0316.try9-opt1.pdb.gz costs 0 real_cost = 336.848 T0316.try9-opt1-scwrl.pdb.gz costs 0 real_cost = 336.82 T0316.try8-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 256.073 T0316.try8-opt2.pdb.gz costs 0 real_cost = 254.179 T0316.try8-opt2.gromacs0.pdb.gz costs 0 real_cost = 258.09 T0316.try8-opt1.pdb.gz costs 0 real_cost = 252.905 T0316.try8-opt1-scwrl.pdb.gz costs 0 real_cost = 256.024 T0316.try7-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 103.451 T0316.try7-opt2.pdb.gz costs 0 real_cost = 98.4356 T0316.try7-opt2.gromacs0.pdb.gz costs 0 real_cost = 93.0422 T0316.try7-opt1.pdb.gz costs 0 real_cost = 82.8475 T0316.try7-opt1-scwrl.pdb.gz costs 0 real_cost = 79.2994 T0316.try6-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 248.191 T0316.try6-opt2.pdb.gz costs 0 real_cost = 248.057 T0316.try6-opt2.gromacs0.pdb.gz costs 0 real_cost = 251.711 T0316.try6-opt1.pdb.gz costs 0 real_cost = 247.702 T0316.try6-opt1-scwrl.pdb.gz costs 0 real_cost = 248.463 T0316.try5-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 335.791 T0316.try5-opt2.pdb.gz costs 0 real_cost = 335.739 T0316.try5-opt2.gromacs0.pdb.gz costs 0 real_cost = 326.526 T0316.try5-opt1.pdb.gz costs 0 real_cost = 328.811 T0316.try5-opt1-scwrl.pdb.gz costs 0 real_cost = 328.928 T0316.try4-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 285.436 T0316.try4-opt2.pdb.gz costs 0 real_cost = 285.623 T0316.try4-opt2.gromacs0.pdb.gz costs 0 real_cost = 288.579 T0316.try4-opt1.pdb.gz costs 0 real_cost = 290.715 T0316.try4-opt1-scwrl.pdb.gz costs 0 real_cost = 290.194 T0316.try3-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 316.94 T0316.try3-opt2.pdb.gz costs 0 real_cost = 317.097 T0316.try3-opt2.gromacs0.pdb.gz costs 0 real_cost = 319.932 T0316.try3-opt1.pdb.gz costs 0 real_cost = 316.855 T0316.try3-opt1-scwrl.pdb.gz costs 0 real_cost = 316.831 T0316.try21-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 245.132 T0316.try21-opt2.pdb.gz costs 0 real_cost = 246.279 T0316.try21-opt2.gromacs0.pdb.gz costs 0 real_cost = 244.667 T0316.try21-opt1.pdb.gz costs 0 real_cost = 250.008 T0316.try21-opt1-scwrl.pdb.gz costs 0 real_cost = 249.324 T0316.try20-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 255.395 T0316.try20-opt2.pdb.gz costs 0 real_cost = 256.895 T0316.try20-opt2.gromacs0.pdb.gz costs 0 real_cost = 256.766 T0316.try20-opt1.pdb.gz costs 0 real_cost = 257.217 T0316.try20-opt1-scwrl.pdb.gz costs 0 real_cost = 257.189 T0316.try2-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 176.1 T0316.try2-opt2.pdb.gz costs 0 real_cost = 176.507 T0316.try2-opt2.gromacs0.pdb.gz costs 0 real_cost = 182.725 T0316.try2-opt2-M1-A183-try6-opt2-A130-I373.pdb.gz costs 0 real_cost = 249.748 T0316.try2-opt1.pdb.gz costs 0 real_cost = 179.004 T0316.try2-opt1-scwrl.pdb.gz costs 0 real_cost = 178.47 T0316.try19-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 252.278 T0316.try19-opt2.pdb.gz costs 0 real_cost = 250.19 T0316.try19-opt2.gromacs0.pdb.gz costs 0 real_cost = 249.73 T0316.try19-opt1.pdb.gz costs 0 real_cost = 250.761 T0316.try19-opt1-scwrl.pdb.gz costs 0 real_cost = 250.879 T0316.try18-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 256.138 T0316.try18-opt2.pdb.gz costs 0 real_cost = 256.825 T0316.try18-opt2.gromacs0.pdb.gz costs 0 real_cost = 256.717 T0316.try18-opt1.pdb.gz costs 0 real_cost = 256.5 T0316.try18-opt1-scwrl.pdb.gz costs 0 real_cost = 256.566 T0316.try17-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 338.299 T0316.try17-opt2.pdb.gz costs 0 real_cost = 338.164 T0316.try17-opt2.gromacs0.pdb.gz costs 0 real_cost = 335.65 T0316.try17-opt1.pdb.gz costs 0 real_cost = 340.573 T0316.try17-opt1-scwrl.pdb.gz costs 0 real_cost = 341.019 T0316.try16-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 285.456 T0316.try16-opt2.pdb.gz costs 0 real_cost = 285.685 T0316.try16-opt2.gromacs0.pdb.gz costs 0 real_cost = 279.553 T0316.try16-opt1.pdb.gz costs 0 real_cost = 285.775 T0316.try16-opt1-scwrl.pdb.gz costs 0 real_cost = 284.935 T0316.try15-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 333.298 T0316.try15-opt2.pdb.gz costs 0 real_cost = 333.404 T0316.try15-opt2.gromacs0.pdb.gz costs 0 real_cost = 335.22 T0316.try15-opt1.pdb.gz costs 0 real_cost = 332.777 T0316.try15-opt1-scwrl.pdb.gz costs 0 real_cost = 332.764 T0316.try14-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 247.689 T0316.try14-opt2.pdb.gz costs 0 real_cost = 251.503 T0316.try14-opt2.gromacs0.pdb.gz costs 0 real_cost = 252.588 T0316.try14-opt1.pdb.gz costs 0 real_cost = 249.561 T0316.try14-opt1-scwrl.pdb.gz costs 0 real_cost = 252.357 T0316.try13-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 337.789 T0316.try13-opt2.pdb.gz costs 0 real_cost = 337.691 T0316.try13-opt2.gromacs0.pdb.gz costs 0 real_cost = 336.946 T0316.try13-opt1.pdb.gz costs 0 real_cost = 337.286 T0316.try13-opt1-scwrl.pdb.gz costs 0 real_cost = 337.271 T0316.try12-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 247.924 T0316.try12-opt2.pdb.gz costs 0 real_cost = 247.192 T0316.try12-opt2.gromacs0.pdb.gz costs 0 real_cost = 249.231 T0316.try12-opt1.pdb.gz costs 0 real_cost = 249.114 T0316.try12-opt1-scwrl.pdb.gz costs 0 real_cost = 253.068 T0316.try11-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 158.775 T0316.try11-opt2.pdb.gz costs 0 real_cost = 154.164 T0316.try11-opt2.gromacs0.pdb.gz costs 0 real_cost = 151.308 T0316.try11-opt1.pdb.gz costs 0 real_cost = 145.271 T0316.try11-opt1-scwrl.pdb.gz costs 0 real_cost = 146.599 T0316.try10-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 251.268 T0316.try10-opt2.pdb.gz costs 0 real_cost = 250.195 T0316.try10-opt2.gromacs0.pdb.gz costs 0 real_cost = 251.902 T0316.try10-opt1.pdb.gz costs 0 real_cost = 251.359 T0316.try10-opt1-scwrl.pdb.gz costs 0 real_cost = 252.469 T0316.try1-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 282.61 T0316.try1-opt2.pdb.gz costs 0 real_cost = 283.554 T0316.try1-opt2.gromacs0.pdb.gz costs 0 real_cost = 288.196 T0316.try1-opt1.pdb.gz costs 0 real_cost = 284.379 T0316.try1-opt1-scwrl.pdb.gz costs 0 real_cost = 284.201 T0316.M1-A183-try2-opt2-D122-K269-try1-opt2-A130-I373-try4-opt2.pdb.gz costs 0 real_cost = 252.539 T0316.M1-A183-try2-opt2-D122-K269-try1-opt2-A130-I373-try4-opt2-proteinshop.pdb.gz costs 0 real_cost = 252.815 ../model5.ts-submitted costs 0 real_cost = 153.859 ../model4.ts-submitted costs 0 real_cost = 338.43 ../model3.ts-submitted costs 0 real_cost = 248.554 ../model2.ts-submitted costs 0 real_cost = 254.564 ../model1.ts-submitted costs 0 real_cost = 246.279 align5 costs 0 real_cost = 491.407 align4 costs 0 real_cost = 614.003 align3 costs 0 real_cost = 544.701 align2 costs 0 real_cost = 579.415 align1 costs 0 real_cost = 470.215 T0316.try1-opt2.pdb costs 0 real_cost = 283.554 model5-scwrl costs 0 real_cost = 155.765 model5.ts-submitted costs 0 real_cost = 153.859 model4-scwrl costs 0 real_cost = 338.38 model4.ts-submitted costs 0 real_cost = 338.43 model3-scwrl costs 0 real_cost = 251.351 model3.ts-submitted costs 0 real_cost = 248.554 model2-scwrl costs 0 real_cost = 256.755 model2.ts-submitted costs 0 real_cost = 254.564 model1-scwrl costs 0 real_cost = 244.628 model1.ts-submitted costs 0 real_cost = 246.279 T0316_3.real.pdb costs 0 real_cost = -451.2 # command:CPU_time= 164.658 sec, elapsed time= 2543.71 sec) # command:rm -f sort.tmp /projects/compbio/bin/sorttbl real_cost < decoys/evaluate_3.rdb > sort.tmp mv -f sort.tmp decoys/evaluate_3.rdb mv -f decoys/evaluate_3.pretty decoys/evaluate_3.pretty.old mv: cannot stat `decoys/evaluate_3.pretty': No such file or directory make: [decoys/evaluate_3.pretty] Error 1 (ignored) /projects/compbio/experiments/protein-predict/casp7/scripts/prettyscore -terse -targpfx -decpoint < decoys/evaluate_3.rdb > decoys/evaluate_3.pretty