/projects/compbio/experiments/protein-predict/casp7/starter-directory/Make.main:725: SECONDARY_TARGET = T0326.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/T0326.} ;\ 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/T0326/ -e s/START_COL/1/ \ -e s/REAL_PDB/2h2wA/ \ -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 1174890181 # 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= 6.03808 sec, elapsed time= 6.14614 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= 6.11507 sec, elapsed time= 6.29221 sec) # command:# Prefix for input files set to # command:# Making conformation for sequence T0326 numbered 1 through 304 Created new target T0326 from T0326.a2m # command:# command:# No conformations to remove in PopConform # command:# cleared Id set # command:# command:2h2wA expands to /projects/compbio/data/pdb/2h2w.pdb.gz 2h2wA: Read 289 residues and 2373 atoms. # WARNING: incomplete conformation T0326 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= 8.59269 sec, elapsed time= 8.86091 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 269 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -82.872 # GDT_score(maxd=8,maxw=2.9)= -84.7847 # GDT_score(maxd=8,maxw=3.2)= -82.7582 # GDT_score(maxd=8,maxw=3.5)= -80.1225 # GDT_score(maxd=10,maxw=3.8)= -81.8846 # GDT_score(maxd=10,maxw=4)= -79.8666 # GDT_score(maxd=10,maxw=4.2)= -77.7333 # GDT_score(maxd=12,maxw=4.3)= -80.7151 # GDT_score(maxd=12,maxw=4.5)= -78.64 # GDT_score(maxd=12,maxw=4.7)= -76.5021 # GDT_score(maxd=14,maxw=5.2)= -74.5996 # GDT_score(maxd=14,maxw=5.5)= -71.3605 # command:# Prefix for output files set to # command:superimposing iter= 0 total_weight= 3.5290000e+03 rmsd (weighted)= 3.4755764e+00 (unweighted)= 1.4332159e+01 superimposing iter= 1 total_weight= 1.3835061e+04 rmsd (weighted)= 1.1254353e+00 (unweighted)= 1.4446860e+01 superimposing iter= 2 total_weight= 6.1021634e+03 rmsd (weighted)= 6.8458418e-01 (unweighted)= 1.4460974e+01 superimposing iter= 3 total_weight= 3.0101968e+03 rmsd (weighted)= 6.0436913e-01 (unweighted)= 1.4466177e+01 superimposing iter= 4 total_weight= 2.4836427e+03 rmsd (weighted)= 5.8868462e-01 (unweighted)= 1.4469254e+01 superimposing iter= 5 total_weight= 2.3965503e+03 rmsd (weighted)= 5.8400610e-01 (unweighted)= 1.4471200e+01 # command:# Prefix for output files set to decoys/ # command:# request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_9174369.pdb -s /var/tmp/to_scwrl_9174369.seq -o /var/tmp/from_scwrl_9174369.pdb > /var/tmp/scwrl_9174369.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_9174369.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 301 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -78.2007 # GDT_score(maxd=8,maxw=2.9)= -79.9737 # GDT_score(maxd=8,maxw=3.2)= -78.1226 # GDT_score(maxd=8,maxw=3.5)= -75.6036 # GDT_score(maxd=10,maxw=3.8)= -76.8991 # GDT_score(maxd=10,maxw=4)= -75.0395 # GDT_score(maxd=10,maxw=4.2)= -73.0481 # GDT_score(maxd=12,maxw=4.3)= -75.6296 # GDT_score(maxd=12,maxw=4.5)= -73.6934 # GDT_score(maxd=12,maxw=4.7)= -71.6814 # GDT_score(maxd=14,maxw=5.2)= -69.785 # GDT_score(maxd=14,maxw=5.5)= -66.9011 # command:# request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_438288618.pdb -s /var/tmp/to_scwrl_438288618.seq -o /var/tmp/from_scwrl_438288618.pdb > /var/tmp/scwrl_438288618.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_438288618.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 301 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -77.8547 # GDT_score(maxd=8,maxw=2.9)= -79.8112 # GDT_score(maxd=8,maxw=3.2)= -77.8741 # GDT_score(maxd=8,maxw=3.5)= -75.1978 # GDT_score(maxd=10,maxw=3.8)= -76.5599 # GDT_score(maxd=10,maxw=4)= -74.603 # GDT_score(maxd=10,maxw=4.2)= -72.4734 # GDT_score(maxd=12,maxw=4.3)= -75.2002 # GDT_score(maxd=12,maxw=4.5)= -73.1393 # GDT_score(maxd=12,maxw=4.7)= -71.0638 # GDT_score(maxd=14,maxw=5.2)= -69.2726 # GDT_score(maxd=14,maxw=5.5)= -66.3275 # command:# request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1219428864.pdb -s /var/tmp/to_scwrl_1219428864.seq -o /var/tmp/from_scwrl_1219428864.pdb > /var/tmp/scwrl_1219428864.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1219428864.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 303 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -78.1142 # GDT_score(maxd=8,maxw=2.9)= -80.3139 # GDT_score(maxd=8,maxw=3.2)= -78.3591 # GDT_score(maxd=8,maxw=3.5)= -75.8594 # GDT_score(maxd=10,maxw=3.8)= -77.1313 # GDT_score(maxd=10,maxw=4)= -75.3408 # GDT_score(maxd=10,maxw=4.2)= -73.4122 # GDT_score(maxd=12,maxw=4.3)= -75.9396 # GDT_score(maxd=12,maxw=4.5)= -74.0571 # GDT_score(maxd=12,maxw=4.7)= -72.0595 # GDT_score(maxd=14,maxw=5.2)= -70.1411 # GDT_score(maxd=14,maxw=5.5)= -67.1417 # command:# request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1852542430.pdb -s /var/tmp/to_scwrl_1852542430.seq -o /var/tmp/from_scwrl_1852542430.pdb > /var/tmp/scwrl_1852542430.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1852542430.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 # WARNING: incomplete conformation T0326 can't currently be optimized by undertaker # command:# fraction of real conformation used = 0.861592 # GDT_score = -78.8062 # GDT_score(maxd=8,maxw=2.9)= -80.5375 # GDT_score(maxd=8,maxw=3.2)= -79.4184 # GDT_score(maxd=8,maxw=3.5)= -77.8835 # GDT_score(maxd=10,maxw=3.8)= -78.4384 # GDT_score(maxd=10,maxw=4)= -77.2414 # GDT_score(maxd=10,maxw=4.2)= -75.6891 # GDT_score(maxd=12,maxw=4.3)= -77.3549 # GDT_score(maxd=12,maxw=4.5)= -75.8138 # GDT_score(maxd=12,maxw=4.7)= -74.032 # GDT_score(maxd=14,maxw=5.2)= -71.8703 # GDT_score(maxd=14,maxw=5.5)= -69.0673 # command:# request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1935766292.pdb -s /var/tmp/to_scwrl_1935766292.seq -o /var/tmp/from_scwrl_1935766292.pdb > /var/tmp/scwrl_1935766292.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1935766292.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 T0326.try1-opt2.pdb looking for model 1 # Found a chain break before 303 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -78.1142 # GDT_score(maxd=8,maxw=2.9)= -80.3065 # GDT_score(maxd=8,maxw=3.2)= -78.3514 # GDT_score(maxd=8,maxw=3.5)= -75.848 # GDT_score(maxd=10,maxw=3.8)= -77.1208 # GDT_score(maxd=10,maxw=4)= -75.3313 # GDT_score(maxd=10,maxw=4.2)= -73.4045 # GDT_score(maxd=12,maxw=4.3)= -75.9299 # GDT_score(maxd=12,maxw=4.5)= -74.0506 # GDT_score(maxd=12,maxw=4.7)= -72.0556 # GDT_score(maxd=14,maxw=5.2)= -70.1405 # GDT_score(maxd=14,maxw=5.5)= -67.1383 # command:# Prefix for output files set to # command:superimposing iter= 0 total_weight= 3.5290000e+03 rmsd (weighted)= 7.9368757e+00 (unweighted)= 1.4753356e+01 superimposing iter= 1 total_weight= 1.1874680e+04 rmsd (weighted)= 2.2114505e+00 (unweighted)= 1.4962219e+01 superimposing iter= 2 total_weight= 1.0427283e+04 rmsd (weighted)= 9.2173948e-01 (unweighted)= 1.5054841e+01 superimposing iter= 3 total_weight= 4.3778989e+03 rmsd (weighted)= 6.6864358e-01 (unweighted)= 1.5066618e+01 superimposing iter= 4 total_weight= 2.6911290e+03 rmsd (weighted)= 6.2490683e-01 (unweighted)= 1.5070365e+01 superimposing iter= 5 total_weight= 2.3953845e+03 rmsd (weighted)= 6.1979140e-01 (unweighted)= 1.5072607e+01 # command:# Prefix for output files set to decoys/ # command:# Prefix for input files set to # command:# ReadConformPDB reading from PDB file T0326.undertaker-align.pdb looking for model 1 # WARNING: incomplete conformation T0326 can't currently be optimized by undertaker # command:# naming current conformation align1 # command:# fraction of real conformation used = 0.878893 # GDT_score = -80.1903 # GDT_score(maxd=8,maxw=2.9)= -81.8955 # GDT_score(maxd=8,maxw=3.2)= -80.7237 # GDT_score(maxd=8,maxw=3.5)= -79.1432 # GDT_score(maxd=10,maxw=3.8)= -79.7401 # GDT_score(maxd=10,maxw=4)= -78.5136 # GDT_score(maxd=10,maxw=4.2)= -76.921 # GDT_score(maxd=12,maxw=4.3)= -78.6502 # GDT_score(maxd=12,maxw=4.5)= -77.0664 # GDT_score(maxd=12,maxw=4.7)= -75.2601 # GDT_score(maxd=14,maxw=5.2)= -73.0697 # GDT_score(maxd=14,maxw=5.5)= -70.1993 # command:# ReadConformPDB reading from PDB file T0326.undertaker-align.pdb looking for model 2 WARNING: atoms too close: (T0326)I85.C and (T0326)L86.C only 0.0000000e+00 apart, marking (T0326)L86.C as missing WARNING: atoms too close: (T0326)L86.N and (T0326)K87.N only 0.0000000e+00 apart, marking (T0326)L86.N as missing WARNING: atoms too close: (T0326)L86.CA and (T0326)K87.CA only 0.0000000e+00 apart, marking (T0326)L86.CA as missing WARNING: atoms too close: (T0326)V110.C and (T0326)P114.C only 0.0000000e+00 apart, marking (T0326)P114.C as missing WARNING: atoms too close: (T0326)E111.N and (T0326)F115.N only 0.0000000e+00 apart, marking (T0326)E111.N as missing WARNING: atoms too close: (T0326)E111.CA and (T0326)F115.CA only 0.0000000e+00 apart, marking (T0326)E111.CA as missing WARNING: atoms too close: (T0326)W121.C and (T0326)M128.C only 0.0000000e+00 apart, marking (T0326)M128.C as missing WARNING: atoms too close: (T0326)E122.N and (T0326)E129.N only 0.0000000e+00 apart, marking (T0326)E122.N as missing WARNING: atoms too close: (T0326)E122.CA and (T0326)E129.CA only 0.0000000e+00 apart, marking (T0326)E122.CA as missing WARNING: atoms too close: (T0326)F152.C and (T0326)Y153.C only 0.0000000e+00 apart, marking (T0326)Y153.C as missing WARNING: atoms too close: (T0326)Y153.N and (T0326)G154.N only 0.0000000e+00 apart, marking (T0326)Y153.N as missing WARNING: atoms too close: (T0326)Y153.CA and (T0326)G154.CA only 0.0000000e+00 apart, marking (T0326)Y153.CA as missing WARNING: atoms too close: (T0326)A188.C and (T0326)R192.C only 0.0000000e+00 apart, marking (T0326)R192.C as missing WARNING: atoms too close: (T0326)P189.N and (T0326)Y193.N only 0.0000000e+00 apart, marking (T0326)P189.N as missing WARNING: atoms too close: (T0326)P189.CA and (T0326)Y193.CA only 0.0000000e+00 apart, marking (T0326)P189.CA as missing WARNING: atoms too close: (T0326)K197.C and (T0326)K198.C only 0.0000000e+00 apart, marking (T0326)K198.C as missing WARNING: atoms too close: (T0326)K198.N and (T0326)E199.N only 0.0000000e+00 apart, marking (T0326)K198.N as missing WARNING: atoms too close: (T0326)K198.CA and (T0326)E199.CA only 0.0000000e+00 apart, marking (T0326)K198.CA as missing # WARNING: incomplete conformation T0326 can't currently be optimized by undertaker # command:# naming current conformation align2 # command:# fraction of real conformation used = 0.605536 # GDT_score = -30.8824 # GDT_score(maxd=8,maxw=2.9)= -31.156 # GDT_score(maxd=8,maxw=3.2)= -29.821 # GDT_score(maxd=8,maxw=3.5)= -28.4352 # GDT_score(maxd=10,maxw=3.8)= -29.9259 # GDT_score(maxd=10,maxw=4)= -29.0034 # GDT_score(maxd=10,maxw=4.2)= -28.0629 # GDT_score(maxd=12,maxw=4.3)= -29.9474 # GDT_score(maxd=12,maxw=4.5)= -29.0141 # GDT_score(maxd=12,maxw=4.7)= -28.0928 # GDT_score(maxd=14,maxw=5.2)= -27.8416 # GDT_score(maxd=14,maxw=5.5)= -26.5796 # command:# ReadConformPDB reading from PDB file T0326.undertaker-align.pdb looking for model 3 WARNING: atoms too close: (T0326)I85.C and (T0326)L86.C only 0.0000000e+00 apart, marking (T0326)L86.C as missing WARNING: atoms too close: (T0326)L86.N and (T0326)K87.N only 0.0000000e+00 apart, marking (T0326)L86.N as missing WARNING: atoms too close: (T0326)L86.CA and (T0326)K87.CA only 0.0000000e+00 apart, marking (T0326)L86.CA as missing WARNING: atoms too close: (T0326)V118.C and (T0326)Y120.C only 0.0000000e+00 apart, marking (T0326)Y120.C as missing WARNING: atoms too close: (T0326)D119.N and (T0326)W121.N only 0.0000000e+00 apart, marking (T0326)D119.N as missing WARNING: atoms too close: (T0326)D119.CA and (T0326)W121.CA only 0.0000000e+00 apart, marking (T0326)D119.CA as missing WARNING: atoms too close: (T0326)W121.C and (T0326)R132.C only 0.0000000e+00 apart, marking (T0326)R132.C as missing WARNING: atoms too close: (T0326)E122.N and (T0326)H133.N only 0.0000000e+00 apart, marking (T0326)E122.N as missing WARNING: atoms too close: (T0326)E122.CA and (T0326)H133.CA only 0.0000000e+00 apart, marking (T0326)E122.CA as missing WARNING: atoms too close: (T0326)F152.C and (T0326)Y153.C only 0.0000000e+00 apart, marking (T0326)Y153.C as missing WARNING: atoms too close: (T0326)Y153.N and (T0326)G154.N only 0.0000000e+00 apart, marking (T0326)Y153.N as missing WARNING: atoms too close: (T0326)Y153.CA and (T0326)G154.CA only 0.0000000e+00 apart, marking (T0326)Y153.CA as missing WARNING: atoms too close: (T0326)A188.C and (T0326)H190.C only 0.0000000e+00 apart, marking (T0326)H190.C as missing WARNING: atoms too close: (T0326)P189.N and (T0326)S191.N only 0.0000000e+00 apart, marking (T0326)P189.N as missing WARNING: atoms too close: (T0326)P189.CA and (T0326)S191.CA only 0.0000000e+00 apart, marking (T0326)P189.CA as missing WARNING: atoms too close: (T0326)K197.C and (T0326)K198.C only 0.0000000e+00 apart, marking (T0326)K198.C as missing WARNING: atoms too close: (T0326)K198.N and (T0326)E199.N only 0.0000000e+00 apart, marking (T0326)K198.N as missing WARNING: atoms too close: (T0326)K198.CA and (T0326)E199.CA only 0.0000000e+00 apart, marking (T0326)K198.CA as missing WARNING: atoms too close: (T0326)P257.C and (T0326)I258.C only 0.0000000e+00 apart, marking (T0326)I258.C as missing WARNING: atoms too close: (T0326)I258.N and (T0326)P259.N only 0.0000000e+00 apart, marking (T0326)I258.N as missing WARNING: atoms too close: (T0326)I258.CA and (T0326)P259.CA only 0.0000000e+00 apart, marking (T0326)I258.CA as missing # WARNING: incomplete conformation T0326 can't currently be optimized by undertaker # command:# naming current conformation align3 # command:# ReadConformPDB reading from PDB file T0326.undertaker-align.pdb looking for model 4 WARNING: atoms too close: (T0326)A94.C and (T0326)K99.C only 0.0000000e+00 apart, marking (T0326)K99.C as missing WARNING: atoms too close: (T0326)V95.N and (T0326)F100.N only 0.0000000e+00 apart, marking (T0326)V95.N as missing WARNING: atoms too close: (T0326)V95.CA and (T0326)F100.CA only 0.0000000e+00 apart, marking (T0326)V95.CA as missing WARNING: atoms too close: (T0326)F152.C and (T0326)Y153.C only 0.0000000e+00 apart, marking (T0326)Y153.C as missing WARNING: atoms too close: (T0326)Y153.N and (T0326)G154.N only 0.0000000e+00 apart, marking (T0326)Y153.N as missing WARNING: atoms too close: (T0326)Y153.CA and (T0326)G154.CA only 0.0000000e+00 apart, marking (T0326)Y153.CA as missing WARNING: atoms too close: (T0326)A188.C and (T0326)R192.C only 0.0000000e+00 apart, marking (T0326)R192.C as missing WARNING: atoms too close: (T0326)P189.N and (T0326)Y193.N only 0.0000000e+00 apart, marking (T0326)P189.N as missing WARNING: atoms too close: (T0326)P189.CA and (T0326)Y193.CA only 0.0000000e+00 apart, marking (T0326)P189.CA as missing WARNING: atoms too close: (T0326)K197.C and (T0326)E199.C only 0.0000000e+00 apart, marking (T0326)E199.C as missing WARNING: atoms too close: (T0326)K198.N and (T0326)D200.N only 0.0000000e+00 apart, marking (T0326)K198.N as missing WARNING: atoms too close: (T0326)K198.CA and (T0326)D200.CA only 0.0000000e+00 apart, marking (T0326)K198.CA as missing WARNING: atoms too close: (T0326)S225.C and (T0326)R227.C only 0.0000000e+00 apart, marking (T0326)R227.C as missing WARNING: atoms too close: (T0326)E226.N and (T0326)Q228.N only 0.0000000e+00 apart, marking (T0326)E226.N as missing WARNING: atoms too close: (T0326)E226.CA and (T0326)Q228.CA only 0.0000000e+00 apart, marking (T0326)E226.CA as missing WARNING: atoms too close: (T0326)N253.C and (T0326)P268.C only 0.0000000e+00 apart, marking (T0326)P268.C as missing WARNING: atoms too close: (T0326)L254.N and (T0326)T269.N only 0.0000000e+00 apart, marking (T0326)L254.N as missing WARNING: atoms too close: (T0326)L254.CA and (T0326)T269.CA only 0.0000000e+00 apart, marking (T0326)L254.CA as missing # WARNING: incomplete conformation T0326 can't currently be optimized by undertaker # command:# naming current conformation align4 # command:# ReadConformPDB reading from PDB file T0326.undertaker-align.pdb looking for model 5 WARNING: atoms too close: (T0326)I85.C and (T0326)L86.C only 0.0000000e+00 apart, marking (T0326)L86.C as missing WARNING: atoms too close: (T0326)L86.N and (T0326)K87.N only 0.0000000e+00 apart, marking (T0326)L86.N as missing WARNING: atoms too close: (T0326)L86.CA and (T0326)K87.CA only 0.0000000e+00 apart, marking (T0326)L86.CA as missing WARNING: atoms too close: (T0326)L112.C and (T0326)F115.C only 0.0000000e+00 apart, marking (T0326)F115.C as missing WARNING: atoms too close: (T0326)L113.N and (T0326)E116.N only 0.0000000e+00 apart, marking (T0326)L113.N as missing WARNING: atoms too close: (T0326)L113.CA and (T0326)E116.CA only 0.0000000e+00 apart, marking (T0326)L113.CA as missing WARNING: atoms too close: (T0326)E117.C and (T0326)Y120.C only 0.0000000e+00 apart, marking (T0326)Y120.C as missing WARNING: atoms too close: (T0326)V118.N and (T0326)W121.N only 0.0000000e+00 apart, marking (T0326)V118.N as missing WARNING: atoms too close: (T0326)V118.CA and (T0326)W121.CA only 0.0000000e+00 apart, marking (T0326)V118.CA as missing WARNING: atoms too close: (T0326)F152.C and (T0326)Y153.C only 0.0000000e+00 apart, marking (T0326)Y153.C as missing WARNING: atoms too close: (T0326)Y153.N and (T0326)G154.N only 0.0000000e+00 apart, marking (T0326)Y153.N as missing WARNING: atoms too close: (T0326)Y153.CA and (T0326)G154.CA only 0.0000000e+00 apart, marking (T0326)Y153.CA as missing WARNING: atoms too close: (T0326)K174.C and (T0326)D183.C only 0.0000000e+00 apart, marking (T0326)D183.C as missing WARNING: atoms too close: (T0326)D175.N and (T0326)D184.N only 0.0000000e+00 apart, marking (T0326)D175.N as missing WARNING: atoms too close: (T0326)D175.CA and (T0326)D184.CA only 0.0000000e+00 apart, marking (T0326)D175.CA as missing WARNING: atoms too close: (T0326)K197.C and (T0326)K198.C only 0.0000000e+00 apart, marking (T0326)K198.C as missing WARNING: atoms too close: (T0326)K198.N and (T0326)E199.N only 0.0000000e+00 apart, marking (T0326)K198.N as missing WARNING: atoms too close: (T0326)K198.CA and (T0326)E199.CA only 0.0000000e+00 apart, marking (T0326)K198.CA as missing # WARNING: incomplete conformation T0326 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 269 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ../model2.ts-submitted looking for model 1 # Found a chain break before 301 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ../model3.ts-submitted looking for model 1 # Found a chain break before 301 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ../model4.ts-submitted looking for model 1 # Found a chain break before 303 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ../model5.ts-submitted looking for model 1 # WARNING: incomplete conformation T0326 can't currently be optimized by undertaker # ReadConformPDB reading from PDB file T0326.try1-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 299 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0326.try1-opt1.pdb.gz looking for model 1 # Found a chain break before 299 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0326.try1-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 303 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0326.try1-opt2.pdb.gz looking for model 1 # Found a chain break before 303 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0326.try1-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 303 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0326.try2-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 282 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0326.try2-opt1.pdb.gz looking for model 1 # Found a chain break before 282 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0326.try2-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 297 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0326.try2-opt2.pdb.gz looking for model 1 # Found a chain break before 294 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0326.try2-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 294 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0326.try3-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 299 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0326.try3-opt1.pdb.gz looking for model 1 # Found a chain break before 299 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0326.try3-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 296 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0326.try3-opt2.pdb.gz looking for model 1 # Found a chain break before 301 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0326.try3-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 301 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0326.try4-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 251 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0326.try4-opt1.pdb.gz looking for model 1 # Found a chain break before 251 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0326.try4-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 237 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0326.try4-opt2.pdb.gz looking for model 1 # Found a chain break before 297 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0326.try4-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 297 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0326.try5-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 297 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0326.try5-opt1.pdb.gz looking for model 1 # Found a chain break before 297 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0326.try5-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 224 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0326.try5-opt2.pdb.gz looking for model 1 # Found a chain break before 297 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0326.try5-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 297 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0326.try6-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 297 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0326.try6-opt1.pdb.gz looking for model 1 # Found a chain break before 297 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0326.try6-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 276 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0326.try6-opt2.pdb.gz looking for model 1 # Found a chain break before 297 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0326.try6-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 297 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0326.try7-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 297 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0326.try7-opt1.pdb.gz looking for model 1 # Found a chain break before 297 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0326.try7-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 225 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0326.try7-opt2.pdb.gz looking for model 1 # Found a chain break before 297 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0326.try7-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 297 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file chimera-dimer2-try4.pdb.gz looking for model 1 # Found a chain break before 297 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ../dimer/decoys/T0326.try1-opt1-scwrl.pdb.gz looking for chain 'A' model 1 # Found a chain break before 301 # copying to AlignedFragments data structure # naming current conformation dimer//try1-opt1-scwrl # ReadConformPDB reading from PDB file ../dimer/decoys/T0326.try1-opt1.pdb.gz looking for chain 'A' model 1 # Found a chain break before 301 # copying to AlignedFragments data structure # naming current conformation dimer//try1-opt1 # ReadConformPDB reading from PDB file ../dimer/decoys/T0326.try1-opt2.gromacs0.pdb.gz looking for chain 'A' model 1 # Found a chain break before 296 # copying to AlignedFragments data structure # naming current conformation dimer//try1-opt2.gromacs0 # ReadConformPDB reading from PDB file ../dimer/decoys/T0326.try1-opt2.pdb.gz looking for chain 'A' model 1 # Found a chain break before 301 # copying to AlignedFragments data structure # naming current conformation dimer//try1-opt2 # ReadConformPDB reading from PDB file ../dimer/decoys/T0326.try1-opt2.repack-nonPC.pdb.gz looking for chain 'A' model 1 # Found a chain break before 301 # copying to AlignedFragments data structure # naming current conformation dimer//try1-opt2.repack-nonPC # ReadConformPDB reading from PDB file ../dimer/decoys/T0326.try1-opt2.unpack.pdb.gz looking for chain 'A' model 1 # Found a chain break before 301 # copying to AlignedFragments data structure # naming current conformation dimer//try1-opt2.unpack # ReadConformPDB reading from PDB file ../dimer/decoys/T0326.try2-opt1-scwrl.pdb.gz looking for chain 'A' model 1 # Found a chain break before 301 # copying to AlignedFragments data structure # naming current conformation dimer//try2-opt1-scwrl # ReadConformPDB reading from PDB file ../dimer/decoys/T0326.try2-opt1.pdb.gz looking for chain 'A' model 1 # Found a chain break before 301 # copying to AlignedFragments data structure # naming current conformation dimer//try2-opt1 # ReadConformPDB reading from PDB file ../dimer/decoys/T0326.try2-opt2.gromacs0.pdb.gz looking for chain 'A' model 1 # Found a chain break before 303 # copying to AlignedFragments data structure # naming current conformation dimer//try2-opt2.gromacs0 # ReadConformPDB reading from PDB file ../dimer/decoys/T0326.try2-opt2.pdb.gz looking for chain 'A' model 1 # Found a chain break before 301 # copying to AlignedFragments data structure # naming current conformation dimer//try2-opt2 # ReadConformPDB reading from PDB file ../dimer/decoys/T0326.try2-opt2.repack-nonPC.pdb.gz looking for chain 'A' model 1 # Found a chain break before 301 # copying to AlignedFragments data structure # naming current conformation dimer//try2-opt2.repack-nonPC # ReadConformPDB reading from PDB file ../dimer/decoys/T0326.try2-opt2.unpack.pdb.gz looking for chain 'A' model 1 # Found a chain break before 301 # copying to AlignedFragments data structure # naming current conformation dimer//try2-opt2.unpack # ReadConformPDB reading from PDB file ../dimer/decoys/T0326.try3-opt1-scwrl.pdb.gz looking for chain 'A' model 1 # Found a chain break before 297 # copying to AlignedFragments data structure # naming current conformation dimer//try3-opt1-scwrl # ReadConformPDB reading from PDB file ../dimer/decoys/T0326.try3-opt1.pdb.gz looking for chain 'A' model 1 # Found a chain break before 297 # copying to AlignedFragments data structure # naming current conformation dimer//try3-opt1 # ReadConformPDB reading from PDB file ../dimer/decoys/T0326.try3-opt2.gromacs0.pdb.gz looking for chain 'A' model 1 # Found a chain break before 303 # copying to AlignedFragments data structure # naming current conformation dimer//try3-opt2.gromacs0 # ReadConformPDB reading from PDB file ../dimer/decoys/T0326.try3-opt2.pdb.gz looking for chain 'A' model 1 # Found a chain break before 297 # copying to AlignedFragments data structure # naming current conformation dimer//try3-opt2 # ReadConformPDB reading from PDB file ../dimer/decoys/T0326.try3-opt2.repack-nonPC.pdb.gz looking for chain 'A' model 1 # Found a chain break before 297 # copying to AlignedFragments data structure # naming current conformation dimer//try3-opt2.repack-nonPC # ReadConformPDB reading from PDB file ../dimer/decoys/T0326.try3-opt2.unpack.pdb.gz looking for chain 'A' model 1 # Found a chain break before 297 # copying to AlignedFragments data structure # naming current conformation dimer//try3-opt2.unpack # ReadConformPDB reading from PDB file ../dimer/decoys/T0326.try4-opt1-scwrl.pdb.gz looking for chain 'A' model 1 # Found a chain break before 297 # copying to AlignedFragments data structure # naming current conformation dimer//try4-opt1-scwrl # ReadConformPDB reading from PDB file ../dimer/decoys/T0326.try4-opt1.pdb.gz looking for chain 'A' model 1 # Found a chain break before 297 # copying to AlignedFragments data structure # naming current conformation dimer//try4-opt1 # ReadConformPDB reading from PDB file ../dimer/decoys/T0326.try4-opt2.gromacs0.pdb.gz looking for chain 'A' model 1 # Found a chain break before 303 # copying to AlignedFragments data structure # naming current conformation dimer//try4-opt2.gromacs0 # ReadConformPDB reading from PDB file ../dimer/decoys/T0326.try4-opt2.pdb.gz looking for chain 'A' model 1 # Found a chain break before 297 # copying to AlignedFragments data structure # naming current conformation dimer//try4-opt2 # ReadConformPDB reading from PDB file ../dimer/decoys/T0326.try4-opt2.repack-nonPC.pdb.gz looking for chain 'A' model 1 # Found a chain break before 297 # copying to AlignedFragments data structure # naming current conformation dimer//try4-opt2.repack-nonPC # ReadConformPDB reading from PDB file ../dimer/decoys/T0326.try4-opt2.unpack.pdb.gz looking for chain 'A' model 1 # Found a chain break before 297 # copying to AlignedFragments data structure # naming current conformation dimer//try4-opt2.unpack # ReadConformPDB reading from PDB file ../dimer/decoys/T0326.try5-opt1-scwrl.pdb.gz looking for chain 'A' model 1 # Found a chain break before 269 # copying to AlignedFragments data structure # naming current conformation dimer//try5-opt1-scwrl # ReadConformPDB reading from PDB file ../dimer/decoys/T0326.try5-opt1.pdb.gz looking for chain 'A' model 1 # Found a chain break before 269 # copying to AlignedFragments data structure # naming current conformation dimer//try5-opt1 # ReadConformPDB reading from PDB file ../dimer/decoys/T0326.try5-opt2.gromacs0.pdb.gz looking for chain 'A' model 1 # Found a chain break before 303 # copying to AlignedFragments data structure # naming current conformation dimer//try5-opt2.gromacs0 # ReadConformPDB reading from PDB file ../dimer/decoys/T0326.try5-opt2.pdb.gz looking for chain 'A' model 1 # Found a chain break before 269 # copying to AlignedFragments data structure # naming current conformation dimer//try5-opt2 # ReadConformPDB reading from PDB file ../dimer/decoys/T0326.try5-opt2.repack-nonPC.pdb.gz looking for chain 'A' model 1 # Found a chain break before 269 # copying to AlignedFragments data structure # naming current conformation dimer//try5-opt2.repack-nonPC # ReadConformPDB reading from PDB file ../dimer/decoys/T0326.try5-opt2.unpack.pdb.gz looking for chain 'A' model 1 # Found a chain break before 269 # copying to AlignedFragments data structure # naming current conformation dimer//try5-opt2.unpack # ReadConformPDB reading from PDB file ../dimer/decoys/dimer-chimera-try4-2ghrA.pdb.gz looking for chain 'A' model 1 # Found a chain break before 297 # copying to AlignedFragments data structure # naming current conformation dimer//dimer-chimera-try4-2ghrA # ReadConformPDB reading from PDB file ../dimer/decoys/dimer-try1-2ghrA.pdb.gz looking for chain 'A' model 1 # Found a chain break before 303 # copying to AlignedFragments data structure # naming current conformation dimer//dimer-try1-2ghrA # ReadConformPDB reading from PDB file ../dimer/decoys/dimer-try3-2ghrA.pdb.gz looking for chain 'A' model 1 # Found a chain break before 301 # copying to AlignedFragments data structure # naming current conformation dimer//dimer-try3-2ghrA # ReadConformPDB reading from PDB file ../dimer/decoys/dimer-try4-2ghrA.pdb.gz looking for chain 'A' model 1 # Found a chain break before 297 # copying to AlignedFragments data structure # naming current conformation dimer//dimer-try4-2ghrA # ReadConformPDB reading from PDB file ../dimer/decoys/dimer-try6-2ghrA.pdb.gz looking for chain 'A' model 1 # Found a chain break before 297 # copying to AlignedFragments data structure # naming current conformation dimer//dimer-try6-2ghrA # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0326 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1536428042.pdb -s /var/tmp/to_scwrl_1536428042.seq -o /var/tmp/from_scwrl_1536428042.pdb > /var/tmp/scwrl_1536428042.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1536428042.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 T0326 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS2 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_361336730.pdb -s /var/tmp/to_scwrl_361336730.seq -o /var/tmp/from_scwrl_361336730.pdb > /var/tmp/scwrl_361336730.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_361336730.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 T0326 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS3 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_2095518312.pdb -s /var/tmp/to_scwrl_2095518312.seq -o /var/tmp/from_scwrl_2095518312.pdb > /var/tmp/scwrl_2095518312.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2095518312.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 T0326 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS4 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_2117261481.pdb -s /var/tmp/to_scwrl_2117261481.seq -o /var/tmp/from_scwrl_2117261481.pdb > /var/tmp/scwrl_2117261481.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2117261481.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 T0326 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS5 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_186260550.pdb -s /var/tmp/to_scwrl_186260550.seq -o /var/tmp/from_scwrl_186260550.pdb > /var/tmp/scwrl_186260550.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_186260550.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 T0326 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_995980171.pdb -s /var/tmp/to_scwrl_995980171.seq -o /var/tmp/from_scwrl_995980171.pdb > /var/tmp/scwrl_995980171.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_995980171.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_RECOM_TS1-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0326 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_311163107.pdb -s /var/tmp/to_scwrl_311163107.seq -o /var/tmp/from_scwrl_311163107.pdb > /var/tmp/scwrl_311163107.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_311163107.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_TS1-scwrl # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1681024488.pdb -s /var/tmp/to_scwrl_1681024488.seq -o /var/tmp/from_scwrl_1681024488.pdb > /var/tmp/scwrl_1681024488.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1681024488.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 275 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS2 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_20257740.pdb -s /var/tmp/to_scwrl_20257740.seq -o /var/tmp/from_scwrl_20257740.pdb > /var/tmp/scwrl_20257740.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_20257740.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 274 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS3 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_552191753.pdb -s /var/tmp/to_scwrl_552191753.seq -o /var/tmp/from_scwrl_552191753.pdb > /var/tmp/scwrl_552191753.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_552191753.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 275 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS4 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1984005272.pdb -s /var/tmp/to_scwrl_1984005272.seq -o /var/tmp/from_scwrl_1984005272.pdb > /var/tmp/scwrl_1984005272.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1984005272.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 290 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS5 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1735306765.pdb -s /var/tmp/to_scwrl_1735306765.seq -o /var/tmp/from_scwrl_1735306765.pdb > /var/tmp/scwrl_1735306765.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1735306765.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 293 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_2033382710.pdb -s /var/tmp/to_scwrl_2033382710.seq -o /var/tmp/from_scwrl_2033382710.pdb > /var/tmp/scwrl_2033382710.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2033382710.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 294 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS2 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_56173230.pdb -s /var/tmp/to_scwrl_56173230.seq -o /var/tmp/from_scwrl_56173230.pdb > /var/tmp/scwrl_56173230.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_56173230.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 266 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS3 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_364129242.pdb -s /var/tmp/to_scwrl_364129242.seq -o /var/tmp/from_scwrl_364129242.pdb > /var/tmp/scwrl_364129242.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_364129242.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 296 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS4 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1620333479.pdb -s /var/tmp/to_scwrl_1620333479.seq -o /var/tmp/from_scwrl_1620333479.pdb > /var/tmp/scwrl_1620333479.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1620333479.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 298 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS5 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_9267407.pdb -s /var/tmp/to_scwrl_9267407.seq -o /var/tmp/from_scwrl_9267407.pdb > /var/tmp/scwrl_9267407.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_9267407.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 275 # copying to AlignedFragments data structure # naming current conformation BayesHH_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_578273132.pdb -s /var/tmp/to_scwrl_578273132.seq -o /var/tmp/from_scwrl_578273132.pdb > /var/tmp/scwrl_578273132.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_578273132.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 240 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_777945481.pdb -s /var/tmp/to_scwrl_777945481.seq -o /var/tmp/from_scwrl_777945481.pdb > /var/tmp/scwrl_777945481.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_777945481.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 240 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS2 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1294259324.pdb -s /var/tmp/to_scwrl_1294259324.seq -o /var/tmp/from_scwrl_1294259324.pdb > /var/tmp/scwrl_1294259324.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1294259324.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 240 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS3 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1574440613.pdb -s /var/tmp/to_scwrl_1574440613.seq -o /var/tmp/from_scwrl_1574440613.pdb > /var/tmp/scwrl_1574440613.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1574440613.pdb # conformation set from SCWRL output # naming current conformation Bilab-ENABLE_TS3-scwrl # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS4.pdb.gz looking for model 1 # Found a chain break before 240 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS4 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1417971310.pdb -s /var/tmp/to_scwrl_1417971310.seq -o /var/tmp/from_scwrl_1417971310.pdb > /var/tmp/scwrl_1417971310.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1417971310.pdb # conformation set from SCWRL output # naming current conformation Bilab-ENABLE_TS4-scwrl # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS5.pdb.gz looking for model 1 # Found a chain break before 240 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS5 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1850974475.pdb -s /var/tmp/to_scwrl_1850974475.seq -o /var/tmp/from_scwrl_1850974475.pdb > /var/tmp/scwrl_1850974475.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1850974475.pdb # conformation set from SCWRL output # naming current conformation Bilab-ENABLE_TS5-scwrl # ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1 # Found a chain break before 303 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_844046042.pdb -s /var/tmp/to_scwrl_844046042.seq -o /var/tmp/from_scwrl_844046042.pdb > /var/tmp/scwrl_844046042.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_844046042.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 T0326 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS2 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1627635062.pdb -s /var/tmp/to_scwrl_1627635062.seq -o /var/tmp/from_scwrl_1627635062.pdb > /var/tmp/scwrl_1627635062.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1627635062.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 T0326 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS3 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_671995303.pdb -s /var/tmp/to_scwrl_671995303.seq -o /var/tmp/from_scwrl_671995303.pdb > /var/tmp/scwrl_671995303.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_671995303.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 T0326 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS4 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_853220411.pdb -s /var/tmp/to_scwrl_853220411.seq -o /var/tmp/from_scwrl_853220411.pdb > /var/tmp/scwrl_853220411.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_853220411.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 # WARNING: incomplete conformation T0326 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS5 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_2065923680.pdb -s /var/tmp/to_scwrl_2065923680.seq -o /var/tmp/from_scwrl_2065923680.pdb > /var/tmp/scwrl_2065923680.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2065923680.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 T0326 can't currently be optimized by undertaker # naming current conformation CPHmodels_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1891424167.pdb -s /var/tmp/to_scwrl_1891424167.seq -o /var/tmp/from_scwrl_1891424167.pdb > /var/tmp/scwrl_1891424167.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1891424167.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 T0326 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_558279194.pdb -s /var/tmp/to_scwrl_558279194.seq -o /var/tmp/from_scwrl_558279194.pdb > /var/tmp/scwrl_558279194.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_558279194.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 T0326 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS2 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1854206325.pdb -s /var/tmp/to_scwrl_1854206325.seq -o /var/tmp/from_scwrl_1854206325.pdb > /var/tmp/scwrl_1854206325.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1854206325.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 T0326 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS3 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1280368562.pdb -s /var/tmp/to_scwrl_1280368562.seq -o /var/tmp/from_scwrl_1280368562.pdb > /var/tmp/scwrl_1280368562.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1280368562.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 T0326 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS4 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_919615924.pdb -s /var/tmp/to_scwrl_919615924.seq -o /var/tmp/from_scwrl_919615924.pdb > /var/tmp/scwrl_919615924.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_919615924.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 T0326 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS5 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1802240990.pdb -s /var/tmp/to_scwrl_1802240990.seq -o /var/tmp/from_scwrl_1802240990.pdb > /var/tmp/scwrl_1802240990.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1802240990.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 T0326 can't currently be optimized by undertaker # naming current conformation Distill_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1250146396.pdb -s /var/tmp/to_scwrl_1250146396.seq -o /var/tmp/from_scwrl_1250146396.pdb > /var/tmp/scwrl_1250146396.log Error: Couldn't open file /var/tmp/from_scwrl_1250146396.pdb or /var/tmp/from_scwrl_1250146396.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1250146396_b.pdb or decoys//var/tmp/from_scwrl_1250146396_b.pdb.gz for input Trying /var/tmp/from_scwrl_1250146396_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_1250146396_b.pdb or /var/tmp/from_scwrl_1250146396_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1250146396_a.pdb or decoys//var/tmp/from_scwrl_1250146396_a.pdb.gz for input Trying /var/tmp/from_scwrl_1250146396_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_1250146396_a.pdb or /var/tmp/from_scwrl_1250146396_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_1250146396.pdb or /var/tmp/from_scwrl_1250146396_b.pdb or /var/tmp/from_scwrl_1250146396_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 T0326 can't currently be optimized by undertaker # naming current conformation Distill_TS2 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1105876473.pdb -s /var/tmp/to_scwrl_1105876473.seq -o /var/tmp/from_scwrl_1105876473.pdb > /var/tmp/scwrl_1105876473.log Error: Couldn't open file /var/tmp/from_scwrl_1105876473.pdb or /var/tmp/from_scwrl_1105876473.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1105876473_b.pdb or decoys//var/tmp/from_scwrl_1105876473_b.pdb.gz for input Trying /var/tmp/from_scwrl_1105876473_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_1105876473_b.pdb or /var/tmp/from_scwrl_1105876473_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1105876473_a.pdb or decoys//var/tmp/from_scwrl_1105876473_a.pdb.gz for input Trying /var/tmp/from_scwrl_1105876473_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_1105876473_a.pdb or /var/tmp/from_scwrl_1105876473_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_1105876473.pdb or /var/tmp/from_scwrl_1105876473_b.pdb or /var/tmp/from_scwrl_1105876473_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 T0326 can't currently be optimized by undertaker # naming current conformation Distill_TS3 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_650737514.pdb -s /var/tmp/to_scwrl_650737514.seq -o /var/tmp/from_scwrl_650737514.pdb > /var/tmp/scwrl_650737514.log Error: Couldn't open file /var/tmp/from_scwrl_650737514.pdb or /var/tmp/from_scwrl_650737514.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_650737514_b.pdb or decoys//var/tmp/from_scwrl_650737514_b.pdb.gz for input Trying /var/tmp/from_scwrl_650737514_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_650737514_b.pdb or /var/tmp/from_scwrl_650737514_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_650737514_a.pdb or decoys//var/tmp/from_scwrl_650737514_a.pdb.gz for input Trying /var/tmp/from_scwrl_650737514_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_650737514_a.pdb or /var/tmp/from_scwrl_650737514_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_650737514.pdb or /var/tmp/from_scwrl_650737514_b.pdb or /var/tmp/from_scwrl_650737514_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 T0326 can't currently be optimized by undertaker # naming current conformation Distill_TS4 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1561309504.pdb -s /var/tmp/to_scwrl_1561309504.seq -o /var/tmp/from_scwrl_1561309504.pdb > /var/tmp/scwrl_1561309504.log Error: Couldn't open file /var/tmp/from_scwrl_1561309504.pdb or /var/tmp/from_scwrl_1561309504.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1561309504_b.pdb or decoys//var/tmp/from_scwrl_1561309504_b.pdb.gz for input Trying /var/tmp/from_scwrl_1561309504_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_1561309504_b.pdb or /var/tmp/from_scwrl_1561309504_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1561309504_a.pdb or decoys//var/tmp/from_scwrl_1561309504_a.pdb.gz for input Trying /var/tmp/from_scwrl_1561309504_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_1561309504_a.pdb or /var/tmp/from_scwrl_1561309504_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_1561309504.pdb or /var/tmp/from_scwrl_1561309504_b.pdb or /var/tmp/from_scwrl_1561309504_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 T0326 can't currently be optimized by undertaker # naming current conformation Distill_TS5 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_639417315.pdb -s /var/tmp/to_scwrl_639417315.seq -o /var/tmp/from_scwrl_639417315.pdb > /var/tmp/scwrl_639417315.log Error: Couldn't open file /var/tmp/from_scwrl_639417315.pdb or /var/tmp/from_scwrl_639417315.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_639417315_b.pdb or decoys//var/tmp/from_scwrl_639417315_b.pdb.gz for input Trying /var/tmp/from_scwrl_639417315_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_639417315_b.pdb or /var/tmp/from_scwrl_639417315_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_639417315_a.pdb or decoys//var/tmp/from_scwrl_639417315_a.pdb.gz for input Trying /var/tmp/from_scwrl_639417315_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_639417315_a.pdb or /var/tmp/from_scwrl_639417315_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_639417315.pdb or /var/tmp/from_scwrl_639417315_b.pdb or /var/tmp/from_scwrl_639417315_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 T0326 can't currently be optimized by undertaker # naming current conformation FAMSD_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_670995254.pdb -s /var/tmp/to_scwrl_670995254.seq -o /var/tmp/from_scwrl_670995254.pdb > /var/tmp/scwrl_670995254.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_670995254.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 T0326 can't currently be optimized by undertaker # naming current conformation FAMSD_TS2 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_2113501257.pdb -s /var/tmp/to_scwrl_2113501257.seq -o /var/tmp/from_scwrl_2113501257.pdb > /var/tmp/scwrl_2113501257.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2113501257.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 T0326 can't currently be optimized by undertaker # naming current conformation FAMSD_TS3 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_475938941.pdb -s /var/tmp/to_scwrl_475938941.seq -o /var/tmp/from_scwrl_475938941.pdb > /var/tmp/scwrl_475938941.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_475938941.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 T0326 can't currently be optimized by undertaker # naming current conformation FAMSD_TS4 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_258818373.pdb -s /var/tmp/to_scwrl_258818373.seq -o /var/tmp/from_scwrl_258818373.pdb > /var/tmp/scwrl_258818373.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_258818373.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 T0326 can't currently be optimized by undertaker # naming current conformation FAMSD_TS5 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1999400320.pdb -s /var/tmp/to_scwrl_1999400320.seq -o /var/tmp/from_scwrl_1999400320.pdb > /var/tmp/scwrl_1999400320.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1999400320.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 # Found a chain break before 301 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_532112171.pdb -s /var/tmp/to_scwrl_532112171.seq -o /var/tmp/from_scwrl_532112171.pdb > /var/tmp/scwrl_532112171.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_532112171.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 T0326 can't currently be optimized by undertaker # naming current conformation FAMS_TS2 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_622947615.pdb -s /var/tmp/to_scwrl_622947615.seq -o /var/tmp/from_scwrl_622947615.pdb > /var/tmp/scwrl_622947615.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_622947615.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 T0326 can't currently be optimized by undertaker # naming current conformation FAMS_TS3 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1472250152.pdb -s /var/tmp/to_scwrl_1472250152.seq -o /var/tmp/from_scwrl_1472250152.pdb > /var/tmp/scwrl_1472250152.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1472250152.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 # Found a chain break before 303 # copying to AlignedFragments data structure # naming current conformation FAMS_TS4 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_541379578.pdb -s /var/tmp/to_scwrl_541379578.seq -o /var/tmp/from_scwrl_541379578.pdb > /var/tmp/scwrl_541379578.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_541379578.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 T0326 can't currently be optimized by undertaker # naming current conformation FAMS_TS5 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1201220746.pdb -s /var/tmp/to_scwrl_1201220746.seq -o /var/tmp/from_scwrl_1201220746.pdb > /var/tmp/scwrl_1201220746.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1201220746.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 297 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_102711986.pdb -s /var/tmp/to_scwrl_102711986.seq -o /var/tmp/from_scwrl_102711986.pdb > /var/tmp/scwrl_102711986.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_102711986.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 275 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS2 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1835638903.pdb -s /var/tmp/to_scwrl_1835638903.seq -o /var/tmp/from_scwrl_1835638903.pdb > /var/tmp/scwrl_1835638903.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1835638903.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 239 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS3 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_628177714.pdb -s /var/tmp/to_scwrl_628177714.seq -o /var/tmp/from_scwrl_628177714.pdb > /var/tmp/scwrl_628177714.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_628177714.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 275 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS4 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1520683296.pdb -s /var/tmp/to_scwrl_1520683296.seq -o /var/tmp/from_scwrl_1520683296.pdb > /var/tmp/scwrl_1520683296.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1520683296.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 275 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS5 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1539129731.pdb -s /var/tmp/to_scwrl_1539129731.seq -o /var/tmp/from_scwrl_1539129731.pdb > /var/tmp/scwrl_1539129731.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1539129731.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 # WARNING: incomplete conformation T0326 can't currently be optimized by undertaker # naming current conformation FORTE1_AL1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1472223755.pdb -s /var/tmp/to_scwrl_1472223755.seq -o /var/tmp/from_scwrl_1472223755.pdb > /var/tmp/scwrl_1472223755.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1472223755.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 T0326 can't currently be optimized by undertaker # naming current conformation FORTE1_AL2 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1000834712.pdb -s /var/tmp/to_scwrl_1000834712.seq -o /var/tmp/from_scwrl_1000834712.pdb > /var/tmp/scwrl_1000834712.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1000834712.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 T0326 can't currently be optimized by undertaker # naming current conformation FORTE1_AL3 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_63641387.pdb -s /var/tmp/to_scwrl_63641387.seq -o /var/tmp/from_scwrl_63641387.pdb > /var/tmp/scwrl_63641387.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_63641387.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 Skipped atom 454, because occupancy 1.0000000e+00 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 456, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 458, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 460, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 1022, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 1024, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 1026, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 1028, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz # WARNING: incomplete conformation T0326 can't currently be optimized by undertaker # naming current conformation FORTE1_AL4 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_177960519.pdb -s /var/tmp/to_scwrl_177960519.seq -o /var/tmp/from_scwrl_177960519.pdb > /var/tmp/scwrl_177960519.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_177960519.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 Skipped atom 670, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz Skipped atom 672, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz Skipped atom 674, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz Skipped atom 676, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz # WARNING: incomplete conformation T0326 can't currently be optimized by undertaker # naming current conformation FORTE1_AL5 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_919274745.pdb -s /var/tmp/to_scwrl_919274745.seq -o /var/tmp/from_scwrl_919274745.pdb > /var/tmp/scwrl_919274745.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_919274745.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 # WARNING: incomplete conformation T0326 can't currently be optimized by undertaker # naming current conformation FORTE2_AL1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1955065554.pdb -s /var/tmp/to_scwrl_1955065554.seq -o /var/tmp/from_scwrl_1955065554.pdb > /var/tmp/scwrl_1955065554.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1955065554.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 T0326 can't currently be optimized by undertaker # naming current conformation FORTE2_AL2 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_736239713.pdb -s /var/tmp/to_scwrl_736239713.seq -o /var/tmp/from_scwrl_736239713.pdb > /var/tmp/scwrl_736239713.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_736239713.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 Skipped atom 454, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 456, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 458, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 460, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 1026, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 1028, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 1030, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 1032, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz # WARNING: incomplete conformation T0326 can't currently be optimized by undertaker # naming current conformation FORTE2_AL3 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_625997423.pdb -s /var/tmp/to_scwrl_625997423.seq -o /var/tmp/from_scwrl_625997423.pdb > /var/tmp/scwrl_625997423.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_625997423.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 Skipped atom 670, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 672, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 674, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 676, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz # WARNING: incomplete conformation T0326 can't currently be optimized by undertaker # naming current conformation FORTE2_AL4 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1087950469.pdb -s /var/tmp/to_scwrl_1087950469.seq -o /var/tmp/from_scwrl_1087950469.pdb > /var/tmp/scwrl_1087950469.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1087950469.pdb # conformation set from SCWRL output # naming current conformation FORTE2_AL4-scwrl # ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0326 can't currently be optimized by undertaker # naming current conformation FORTE2_AL5 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1655855636.pdb -s /var/tmp/to_scwrl_1655855636.seq -o /var/tmp/from_scwrl_1655855636.pdb > /var/tmp/scwrl_1655855636.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1655855636.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 298 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_280754766.pdb -s /var/tmp/to_scwrl_280754766.seq -o /var/tmp/from_scwrl_280754766.pdb > /var/tmp/scwrl_280754766.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_280754766.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 303 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS2 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_190613219.pdb -s /var/tmp/to_scwrl_190613219.seq -o /var/tmp/from_scwrl_190613219.pdb > /var/tmp/scwrl_190613219.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_190613219.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 302 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS3 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_614248463.pdb -s /var/tmp/to_scwrl_614248463.seq -o /var/tmp/from_scwrl_614248463.pdb > /var/tmp/scwrl_614248463.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_614248463.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 303 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS4 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_931492281.pdb -s /var/tmp/to_scwrl_931492281.seq -o /var/tmp/from_scwrl_931492281.pdb > /var/tmp/scwrl_931492281.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_931492281.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 303 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS5 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1751922723.pdb -s /var/tmp/to_scwrl_1751922723.seq -o /var/tmp/from_scwrl_1751922723.pdb > /var/tmp/scwrl_1751922723.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1751922723.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 T0326 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1253665778.pdb -s /var/tmp/to_scwrl_1253665778.seq -o /var/tmp/from_scwrl_1253665778.pdb > /var/tmp/scwrl_1253665778.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1253665778.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 T0326 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS2 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1602487534.pdb -s /var/tmp/to_scwrl_1602487534.seq -o /var/tmp/from_scwrl_1602487534.pdb > /var/tmp/scwrl_1602487534.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1602487534.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 T0326 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS3 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1717940333.pdb -s /var/tmp/to_scwrl_1717940333.seq -o /var/tmp/from_scwrl_1717940333.pdb > /var/tmp/scwrl_1717940333.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1717940333.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 # WARNING: incomplete conformation T0326 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS4 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1729604719.pdb -s /var/tmp/to_scwrl_1729604719.seq -o /var/tmp/from_scwrl_1729604719.pdb > /var/tmp/scwrl_1729604719.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1729604719.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 # Found a chain break before 283 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS5 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1861305907.pdb -s /var/tmp/to_scwrl_1861305907.seq -o /var/tmp/from_scwrl_1861305907.pdb > /var/tmp/scwrl_1861305907.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1861305907.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 T0326 can't currently be optimized by undertaker # naming current conformation FUGUE_AL1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1569857007.pdb -s /var/tmp/to_scwrl_1569857007.seq -o /var/tmp/from_scwrl_1569857007.pdb > /var/tmp/scwrl_1569857007.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1569857007.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 T0326 can't currently be optimized by undertaker # naming current conformation FUGUE_AL2 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_114233243.pdb -s /var/tmp/to_scwrl_114233243.seq -o /var/tmp/from_scwrl_114233243.pdb > /var/tmp/scwrl_114233243.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_114233243.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 Skipped atom 274, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz Skipped atom 276, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz Skipped atom 278, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz Skipped atom 280, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz Skipped atom 334, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz Skipped atom 336, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz Skipped atom 338, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz Skipped atom 340, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz Skipped atom 558, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz Skipped atom 560, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz Skipped atom 562, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz Skipped atom 564, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz Skipped atom 654, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz Skipped atom 656, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz Skipped atom 658, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz Skipped atom 660, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz # WARNING: incomplete conformation T0326 can't currently be optimized by undertaker # naming current conformation FUGUE_AL3 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_336769876.pdb -s /var/tmp/to_scwrl_336769876.seq -o /var/tmp/from_scwrl_336769876.pdb > /var/tmp/scwrl_336769876.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_336769876.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 T0326 can't currently be optimized by undertaker # naming current conformation FUGUE_AL4 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_894623513.pdb -s /var/tmp/to_scwrl_894623513.seq -o /var/tmp/from_scwrl_894623513.pdb > /var/tmp/scwrl_894623513.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_894623513.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 T0326 can't currently be optimized by undertaker # naming current conformation FUGUE_AL5 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_655612821.pdb -s /var/tmp/to_scwrl_655612821.seq -o /var/tmp/from_scwrl_655612821.pdb > /var/tmp/scwrl_655612821.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_655612821.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 # Found a chain break before 296 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1537990622.pdb -s /var/tmp/to_scwrl_1537990622.seq -o /var/tmp/from_scwrl_1537990622.pdb > /var/tmp/scwrl_1537990622.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1537990622.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 300 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS2 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_997335500.pdb -s /var/tmp/to_scwrl_997335500.seq -o /var/tmp/from_scwrl_997335500.pdb > /var/tmp/scwrl_997335500.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_997335500.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 301 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS3 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_343768077.pdb -s /var/tmp/to_scwrl_343768077.seq -o /var/tmp/from_scwrl_343768077.pdb > /var/tmp/scwrl_343768077.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_343768077.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 302 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS4 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_18684689.pdb -s /var/tmp/to_scwrl_18684689.seq -o /var/tmp/from_scwrl_18684689.pdb > /var/tmp/scwrl_18684689.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_18684689.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 300 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_370535149.pdb -s /var/tmp/to_scwrl_370535149.seq -o /var/tmp/from_scwrl_370535149.pdb > /var/tmp/scwrl_370535149.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_370535149.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 T0326 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1882897808.pdb -s /var/tmp/to_scwrl_1882897808.seq -o /var/tmp/from_scwrl_1882897808.pdb > /var/tmp/scwrl_1882897808.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1882897808.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 # WARNING: incomplete conformation T0326 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS2 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1490908444.pdb -s /var/tmp/to_scwrl_1490908444.seq -o /var/tmp/from_scwrl_1490908444.pdb > /var/tmp/scwrl_1490908444.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1490908444.pdb # conformation set from SCWRL output # naming current conformation GeneSilicoMetaServer_TS2-scwrl # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # Found a chain break before 294 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS3 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1371369861.pdb -s /var/tmp/to_scwrl_1371369861.seq -o /var/tmp/from_scwrl_1371369861.pdb > /var/tmp/scwrl_1371369861.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1371369861.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 T0326 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS4 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1946539195.pdb -s /var/tmp/to_scwrl_1946539195.seq -o /var/tmp/from_scwrl_1946539195.pdb > /var/tmp/scwrl_1946539195.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1946539195.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 # WARNING: incomplete conformation T0326 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS5 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1668868963.pdb -s /var/tmp/to_scwrl_1668868963.seq -o /var/tmp/from_scwrl_1668868963.pdb > /var/tmp/scwrl_1668868963.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1668868963.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 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation HHpred1_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_143160959.pdb -s /var/tmp/to_scwrl_143160959.seq -o /var/tmp/from_scwrl_143160959.pdb > /var/tmp/scwrl_143160959.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_143160959.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 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation HHpred2_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1754121102.pdb -s /var/tmp/to_scwrl_1754121102.seq -o /var/tmp/from_scwrl_1754121102.pdb > /var/tmp/scwrl_1754121102.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1754121102.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 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation HHpred3_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_257625029.pdb -s /var/tmp/to_scwrl_257625029.seq -o /var/tmp/from_scwrl_257625029.pdb > /var/tmp/scwrl_257625029.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_257625029.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 T0326 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_769158383.pdb -s /var/tmp/to_scwrl_769158383.seq -o /var/tmp/from_scwrl_769158383.pdb > /var/tmp/scwrl_769158383.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_769158383.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 T0326 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS2 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_694587925.pdb -s /var/tmp/to_scwrl_694587925.seq -o /var/tmp/from_scwrl_694587925.pdb > /var/tmp/scwrl_694587925.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_694587925.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 T0326 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS3 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1913480665.pdb -s /var/tmp/to_scwrl_1913480665.seq -o /var/tmp/from_scwrl_1913480665.pdb > /var/tmp/scwrl_1913480665.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1913480665.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 T0326 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS4 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1049913149.pdb -s /var/tmp/to_scwrl_1049913149.seq -o /var/tmp/from_scwrl_1049913149.pdb > /var/tmp/scwrl_1049913149.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1049913149.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 T0326 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS5 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_885201145.pdb -s /var/tmp/to_scwrl_885201145.seq -o /var/tmp/from_scwrl_885201145.pdb > /var/tmp/scwrl_885201145.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_885201145.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 T0326 can't currently be optimized by undertaker # naming current conformation LOOPP_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_380245482.pdb -s /var/tmp/to_scwrl_380245482.seq -o /var/tmp/from_scwrl_380245482.pdb > /var/tmp/scwrl_380245482.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_380245482.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 T0326 can't currently be optimized by undertaker # naming current conformation LOOPP_TS2 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1981405429.pdb -s /var/tmp/to_scwrl_1981405429.seq -o /var/tmp/from_scwrl_1981405429.pdb > /var/tmp/scwrl_1981405429.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1981405429.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 T0326 can't currently be optimized by undertaker # naming current conformation LOOPP_TS3 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_489640221.pdb -s /var/tmp/to_scwrl_489640221.seq -o /var/tmp/from_scwrl_489640221.pdb > /var/tmp/scwrl_489640221.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_489640221.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 T0326 can't currently be optimized by undertaker # naming current conformation LOOPP_TS4 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1633911260.pdb -s /var/tmp/to_scwrl_1633911260.seq -o /var/tmp/from_scwrl_1633911260.pdb > /var/tmp/scwrl_1633911260.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1633911260.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 T0326 can't currently be optimized by undertaker # naming current conformation LOOPP_TS5 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1436409317.pdb -s /var/tmp/to_scwrl_1436409317.seq -o /var/tmp/from_scwrl_1436409317.pdb > /var/tmp/scwrl_1436409317.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1436409317.pdb # conformation set from SCWRL output # naming current conformation LOOPP_TS5-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS1.pdb.gz looking for model 1 # Found a chain break before 252 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_60096908.pdb -s /var/tmp/to_scwrl_60096908.seq -o /var/tmp/from_scwrl_60096908.pdb > /var/tmp/scwrl_60096908.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_60096908.pdb # conformation set from SCWRL output # naming current conformation Ma-OPUS-server2_TS1-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS2.pdb.gz looking for model 1 # Found a chain break before 302 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS2 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1216032332.pdb -s /var/tmp/to_scwrl_1216032332.seq -o /var/tmp/from_scwrl_1216032332.pdb > /var/tmp/scwrl_1216032332.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1216032332.pdb # conformation set from SCWRL output # naming current conformation Ma-OPUS-server2_TS2-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS3.pdb.gz looking for model 1 # Found a chain break before 302 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS3 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1150231577.pdb -s /var/tmp/to_scwrl_1150231577.seq -o /var/tmp/from_scwrl_1150231577.pdb > /var/tmp/scwrl_1150231577.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1150231577.pdb # conformation set from SCWRL output # naming current conformation Ma-OPUS-server2_TS3-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS4.pdb.gz looking for model 1 # Found a chain break before 301 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS4 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1629953915.pdb -s /var/tmp/to_scwrl_1629953915.seq -o /var/tmp/from_scwrl_1629953915.pdb > /var/tmp/scwrl_1629953915.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1629953915.pdb # conformation set from SCWRL output # naming current conformation Ma-OPUS-server2_TS4-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS5.pdb.gz looking for model 1 # Found a chain break before 227 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS5 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1330265575.pdb -s /var/tmp/to_scwrl_1330265575.seq -o /var/tmp/from_scwrl_1330265575.pdb > /var/tmp/scwrl_1330265575.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1330265575.pdb # conformation set from SCWRL output # naming current conformation Ma-OPUS-server2_TS5-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # Found a chain break before 294 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1487001453.pdb -s /var/tmp/to_scwrl_1487001453.seq -o /var/tmp/from_scwrl_1487001453.pdb > /var/tmp/scwrl_1487001453.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1487001453.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 276 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS2 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_377093781.pdb -s /var/tmp/to_scwrl_377093781.seq -o /var/tmp/from_scwrl_377093781.pdb > /var/tmp/scwrl_377093781.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_377093781.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 301 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS3 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1985878396.pdb -s /var/tmp/to_scwrl_1985878396.seq -o /var/tmp/from_scwrl_1985878396.pdb > /var/tmp/scwrl_1985878396.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1985878396.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 227 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS4 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_877508430.pdb -s /var/tmp/to_scwrl_877508430.seq -o /var/tmp/from_scwrl_877508430.pdb > /var/tmp/scwrl_877508430.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_877508430.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 298 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS5 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1374429280.pdb -s /var/tmp/to_scwrl_1374429280.seq -o /var/tmp/from_scwrl_1374429280.pdb > /var/tmp/scwrl_1374429280.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1374429280.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 303 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_182162827.pdb -s /var/tmp/to_scwrl_182162827.seq -o /var/tmp/from_scwrl_182162827.pdb > /var/tmp/scwrl_182162827.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_182162827.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 302 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS2 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_896193119.pdb -s /var/tmp/to_scwrl_896193119.seq -o /var/tmp/from_scwrl_896193119.pdb > /var/tmp/scwrl_896193119.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_896193119.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 298 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS3 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1744964430.pdb -s /var/tmp/to_scwrl_1744964430.seq -o /var/tmp/from_scwrl_1744964430.pdb > /var/tmp/scwrl_1744964430.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1744964430.pdb # conformation set from SCWRL output # 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 301 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS4 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_2065060635.pdb -s /var/tmp/to_scwrl_2065060635.seq -o /var/tmp/from_scwrl_2065060635.pdb > /var/tmp/scwrl_2065060635.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2065060635.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 303 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS5 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_239617917.pdb -s /var/tmp/to_scwrl_239617917.seq -o /var/tmp/from_scwrl_239617917.pdb > /var/tmp/scwrl_239617917.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_239617917.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 T0326 can't currently be optimized by undertaker # naming current conformation NN_PUT_lab_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_968850645.pdb -s /var/tmp/to_scwrl_968850645.seq -o /var/tmp/from_scwrl_968850645.pdb > /var/tmp/scwrl_968850645.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_968850645.pdb # conformation set from SCWRL output # naming current conformation NN_PUT_lab_TS1-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 274 ; scwrl3 -i /var/tmp/to_scwrl_1864116184.pdb -s /var/tmp/to_scwrl_1864116184.seq -o /var/tmp/from_scwrl_1864116184.pdb > /var/tmp/scwrl_1864116184.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1864116184.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 274 ; scwrl3 -i /var/tmp/to_scwrl_1908486880.pdb -s /var/tmp/to_scwrl_1908486880.seq -o /var/tmp/from_scwrl_1908486880.pdb > /var/tmp/scwrl_1908486880.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1908486880.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 274 ; scwrl3 -i /var/tmp/to_scwrl_1112011603.pdb -s /var/tmp/to_scwrl_1112011603.seq -o /var/tmp/from_scwrl_1112011603.pdb > /var/tmp/scwrl_1112011603.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1112011603.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 274 ; scwrl3 -i /var/tmp/to_scwrl_1470753639.pdb -s /var/tmp/to_scwrl_1470753639.seq -o /var/tmp/from_scwrl_1470753639.pdb > /var/tmp/scwrl_1470753639.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1470753639.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 # WARNING: incomplete conformation T0326 can't currently be optimized by undertaker # naming current conformation PROTINFO-AB_TS5 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_18628263.pdb -s /var/tmp/to_scwrl_18628263.seq -o /var/tmp/from_scwrl_18628263.pdb > /var/tmp/scwrl_18628263.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_18628263.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 288 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1881169986.pdb -s /var/tmp/to_scwrl_1881169986.seq -o /var/tmp/from_scwrl_1881169986.pdb > /var/tmp/scwrl_1881169986.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1881169986.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 # Found a chain break before 175 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS2 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_17857918.pdb -s /var/tmp/to_scwrl_17857918.seq -o /var/tmp/from_scwrl_17857918.pdb > /var/tmp/scwrl_17857918.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_17857918.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 302 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS3 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1932108928.pdb -s /var/tmp/to_scwrl_1932108928.seq -o /var/tmp/from_scwrl_1932108928.pdb > /var/tmp/scwrl_1932108928.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1932108928.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 # WARNING: incomplete conformation T0326 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS4 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_783599489.pdb -s /var/tmp/to_scwrl_783599489.seq -o /var/tmp/from_scwrl_783599489.pdb > /var/tmp/scwrl_783599489.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_783599489.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 # WARNING: incomplete conformation T0326 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS5 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_903059063.pdb -s /var/tmp/to_scwrl_903059063.seq -o /var/tmp/from_scwrl_903059063.pdb > /var/tmp/scwrl_903059063.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_903059063.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 T0326 can't currently be optimized by undertaker # naming current conformation Pcons6_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_164870763.pdb -s /var/tmp/to_scwrl_164870763.seq -o /var/tmp/from_scwrl_164870763.pdb > /var/tmp/scwrl_164870763.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_164870763.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 T0326 can't currently be optimized by undertaker # naming current conformation Pcons6_TS2 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_617521271.pdb -s /var/tmp/to_scwrl_617521271.seq -o /var/tmp/from_scwrl_617521271.pdb > /var/tmp/scwrl_617521271.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_617521271.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 T0326 can't currently be optimized by undertaker # naming current conformation Pcons6_TS3 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1392699283.pdb -s /var/tmp/to_scwrl_1392699283.seq -o /var/tmp/from_scwrl_1392699283.pdb > /var/tmp/scwrl_1392699283.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1392699283.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 T0326 can't currently be optimized by undertaker # naming current conformation Pcons6_TS4 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1798782023.pdb -s /var/tmp/to_scwrl_1798782023.seq -o /var/tmp/from_scwrl_1798782023.pdb > /var/tmp/scwrl_1798782023.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1798782023.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 # WARNING: incomplete conformation T0326 can't currently be optimized by undertaker # naming current conformation Pcons6_TS5 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_2053930588.pdb -s /var/tmp/to_scwrl_2053930588.seq -o /var/tmp/from_scwrl_2053930588.pdb > /var/tmp/scwrl_2053930588.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2053930588.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 T0326 can't currently be optimized by undertaker # naming current conformation Phyre-1_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1452796191.pdb -s /var/tmp/to_scwrl_1452796191.seq -o /var/tmp/from_scwrl_1452796191.pdb > /var/tmp/scwrl_1452796191.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1452796191.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 300 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_867330709.pdb -s /var/tmp/to_scwrl_867330709.seq -o /var/tmp/from_scwrl_867330709.pdb > /var/tmp/scwrl_867330709.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_867330709.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 296 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS2 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1056678520.pdb -s /var/tmp/to_scwrl_1056678520.seq -o /var/tmp/from_scwrl_1056678520.pdb > /var/tmp/scwrl_1056678520.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1056678520.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 296 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS3 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_935266460.pdb -s /var/tmp/to_scwrl_935266460.seq -o /var/tmp/from_scwrl_935266460.pdb > /var/tmp/scwrl_935266460.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_935266460.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 300 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS4 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_50112637.pdb -s /var/tmp/to_scwrl_50112637.seq -o /var/tmp/from_scwrl_50112637.pdb > /var/tmp/scwrl_50112637.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_50112637.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 300 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS5 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_396196326.pdb -s /var/tmp/to_scwrl_396196326.seq -o /var/tmp/from_scwrl_396196326.pdb > /var/tmp/scwrl_396196326.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_396196326.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 # Found a chain break before 195 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1312360241.pdb -s /var/tmp/to_scwrl_1312360241.seq -o /var/tmp/from_scwrl_1312360241.pdb > /var/tmp/scwrl_1312360241.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1312360241.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 # Found a chain break before 195 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS2 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_2035991034.pdb -s /var/tmp/to_scwrl_2035991034.seq -o /var/tmp/from_scwrl_2035991034.pdb > /var/tmp/scwrl_2035991034.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2035991034.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 # Found a chain break before 195 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS3 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1273704755.pdb -s /var/tmp/to_scwrl_1273704755.seq -o /var/tmp/from_scwrl_1273704755.pdb > /var/tmp/scwrl_1273704755.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1273704755.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 # Found a chain break before 195 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS4 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_539305875.pdb -s /var/tmp/to_scwrl_539305875.seq -o /var/tmp/from_scwrl_539305875.pdb > /var/tmp/scwrl_539305875.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_539305875.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 T0326 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS5 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_70670214.pdb -s /var/tmp/to_scwrl_70670214.seq -o /var/tmp/from_scwrl_70670214.pdb > /var/tmp/scwrl_70670214.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_70670214.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 237 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_22414228.pdb -s /var/tmp/to_scwrl_22414228.seq -o /var/tmp/from_scwrl_22414228.pdb > /var/tmp/scwrl_22414228.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_22414228.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 252 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS2 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_136786658.pdb -s /var/tmp/to_scwrl_136786658.seq -o /var/tmp/from_scwrl_136786658.pdb > /var/tmp/scwrl_136786658.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_136786658.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 # WARNING: incomplete conformation T0326 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS3 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_2135730849.pdb -s /var/tmp/to_scwrl_2135730849.seq -o /var/tmp/from_scwrl_2135730849.pdb > /var/tmp/scwrl_2135730849.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2135730849.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 275 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS4 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_262032145.pdb -s /var/tmp/to_scwrl_262032145.seq -o /var/tmp/from_scwrl_262032145.pdb > /var/tmp/scwrl_262032145.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_262032145.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 # WARNING: incomplete conformation T0326 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS5 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1105637302.pdb -s /var/tmp/to_scwrl_1105637302.seq -o /var/tmp/from_scwrl_1105637302.pdb > /var/tmp/scwrl_1105637302.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1105637302.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 300 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1852363386.pdb -s /var/tmp/to_scwrl_1852363386.seq -o /var/tmp/from_scwrl_1852363386.pdb > /var/tmp/scwrl_1852363386.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1852363386.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 300 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS2 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_23035378.pdb -s /var/tmp/to_scwrl_23035378.seq -o /var/tmp/from_scwrl_23035378.pdb > /var/tmp/scwrl_23035378.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_23035378.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 298 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS3 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_70165260.pdb -s /var/tmp/to_scwrl_70165260.seq -o /var/tmp/from_scwrl_70165260.pdb > /var/tmp/scwrl_70165260.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_70165260.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 302 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS4 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1175633379.pdb -s /var/tmp/to_scwrl_1175633379.seq -o /var/tmp/from_scwrl_1175633379.pdb > /var/tmp/scwrl_1175633379.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1175633379.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 300 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS5 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_41663641.pdb -s /var/tmp/to_scwrl_41663641.seq -o /var/tmp/from_scwrl_41663641.pdb > /var/tmp/scwrl_41663641.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_41663641.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 275 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1951335246.pdb -s /var/tmp/to_scwrl_1951335246.seq -o /var/tmp/from_scwrl_1951335246.pdb > /var/tmp/scwrl_1951335246.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1951335246.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 275 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS2 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1193491297.pdb -s /var/tmp/to_scwrl_1193491297.seq -o /var/tmp/from_scwrl_1193491297.pdb > /var/tmp/scwrl_1193491297.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1193491297.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 272 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS3 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1973772570.pdb -s /var/tmp/to_scwrl_1973772570.seq -o /var/tmp/from_scwrl_1973772570.pdb > /var/tmp/scwrl_1973772570.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1973772570.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 205 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS4 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_587451088.pdb -s /var/tmp/to_scwrl_587451088.seq -o /var/tmp/from_scwrl_587451088.pdb > /var/tmp/scwrl_587451088.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_587451088.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 290 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS5 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_2096550360.pdb -s /var/tmp/to_scwrl_2096550360.seq -o /var/tmp/from_scwrl_2096550360.pdb > /var/tmp/scwrl_2096550360.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2096550360.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 195 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_2138643333.pdb -s /var/tmp/to_scwrl_2138643333.seq -o /var/tmp/from_scwrl_2138643333.pdb > /var/tmp/scwrl_2138643333.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2138643333.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 302 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS2 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1204972359.pdb -s /var/tmp/to_scwrl_1204972359.seq -o /var/tmp/from_scwrl_1204972359.pdb > /var/tmp/scwrl_1204972359.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1204972359.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 195 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS3 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1341765996.pdb -s /var/tmp/to_scwrl_1341765996.seq -o /var/tmp/from_scwrl_1341765996.pdb > /var/tmp/scwrl_1341765996.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1341765996.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 195 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS4 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1789941710.pdb -s /var/tmp/to_scwrl_1789941710.seq -o /var/tmp/from_scwrl_1789941710.pdb > /var/tmp/scwrl_1789941710.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1789941710.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 195 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS5 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1111419300.pdb -s /var/tmp/to_scwrl_1111419300.seq -o /var/tmp/from_scwrl_1111419300.pdb > /var/tmp/scwrl_1111419300.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1111419300.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 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_647078542.pdb -s /var/tmp/to_scwrl_647078542.seq -o /var/tmp/from_scwrl_647078542.pdb > /var/tmp/scwrl_647078542.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_647078542.pdb # conformation set from SCWRL output # naming current conformation ROKKY_TS1-scwrl # ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0326 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_509788772.pdb -s /var/tmp/to_scwrl_509788772.seq -o /var/tmp/from_scwrl_509788772.pdb > /var/tmp/scwrl_509788772.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_509788772.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 T0326 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL2 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_20614173.pdb -s /var/tmp/to_scwrl_20614173.seq -o /var/tmp/from_scwrl_20614173.pdb > /var/tmp/scwrl_20614173.log Error: Couldn't open file /var/tmp/from_scwrl_20614173.pdb or /var/tmp/from_scwrl_20614173.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_20614173_b.pdb or decoys//var/tmp/from_scwrl_20614173_b.pdb.gz for input Trying /var/tmp/from_scwrl_20614173_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_20614173_b.pdb or /var/tmp/from_scwrl_20614173_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_20614173_a.pdb or decoys//var/tmp/from_scwrl_20614173_a.pdb.gz for input Trying /var/tmp/from_scwrl_20614173_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_20614173_a.pdb or /var/tmp/from_scwrl_20614173_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_20614173.pdb or /var/tmp/from_scwrl_20614173_b.pdb or /var/tmp/from_scwrl_20614173_a.pdb Error: no new SCWRL conformation added # naming current conformation SAM-T02_AL2-scwrl # ReadConformPDB reading from PDB file servers/SAM-T02_AL3.pdb.gz looking for model 1 Skipped atom 99, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz # WARNING: incomplete conformation T0326 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL3 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1582345001.pdb -s /var/tmp/to_scwrl_1582345001.seq -o /var/tmp/from_scwrl_1582345001.pdb > /var/tmp/scwrl_1582345001.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1582345001.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 T0326 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL4 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_559901410.pdb -s /var/tmp/to_scwrl_559901410.seq -o /var/tmp/from_scwrl_559901410.pdb > /var/tmp/scwrl_559901410.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_559901410.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 T0326 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL5 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_416810500.pdb -s /var/tmp/to_scwrl_416810500.seq -o /var/tmp/from_scwrl_416810500.pdb > /var/tmp/scwrl_416810500.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_416810500.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 T0326 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_747221596.pdb -s /var/tmp/to_scwrl_747221596.seq -o /var/tmp/from_scwrl_747221596.pdb > /var/tmp/scwrl_747221596.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_747221596.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 Skipped atom 99, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL2.pdb.gz # WARNING: incomplete conformation T0326 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL2 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_448408797.pdb -s /var/tmp/to_scwrl_448408797.seq -o /var/tmp/from_scwrl_448408797.pdb > /var/tmp/scwrl_448408797.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_448408797.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 T0326 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL3 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1690515255.pdb -s /var/tmp/to_scwrl_1690515255.seq -o /var/tmp/from_scwrl_1690515255.pdb > /var/tmp/scwrl_1690515255.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1690515255.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 T0326 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL4 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1286527471.pdb -s /var/tmp/to_scwrl_1286527471.seq -o /var/tmp/from_scwrl_1286527471.pdb > /var/tmp/scwrl_1286527471.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1286527471.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 Skipped atom 267, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL5.pdb.gz # WARNING: incomplete conformation T0326 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL5 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_519079011.pdb -s /var/tmp/to_scwrl_519079011.seq -o /var/tmp/from_scwrl_519079011.pdb > /var/tmp/scwrl_519079011.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_519079011.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 294 # copying to AlignedFragments data structure # naming current conformation SAM_T06_server_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1712929483.pdb -s /var/tmp/to_scwrl_1712929483.seq -o /var/tmp/from_scwrl_1712929483.pdb > /var/tmp/scwrl_1712929483.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1712929483.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 T0326 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS2 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1423314129.pdb -s /var/tmp/to_scwrl_1423314129.seq -o /var/tmp/from_scwrl_1423314129.pdb > /var/tmp/scwrl_1423314129.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1423314129.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 T0326 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS3 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_507326213.pdb -s /var/tmp/to_scwrl_507326213.seq -o /var/tmp/from_scwrl_507326213.pdb > /var/tmp/scwrl_507326213.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_507326213.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 T0326 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS4 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1974961628.pdb -s /var/tmp/to_scwrl_1974961628.seq -o /var/tmp/from_scwrl_1974961628.pdb > /var/tmp/scwrl_1974961628.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1974961628.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 T0326 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS5 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_381467786.pdb -s /var/tmp/to_scwrl_381467786.seq -o /var/tmp/from_scwrl_381467786.pdb > /var/tmp/scwrl_381467786.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_381467786.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 275 # copying to AlignedFragments data structure # naming current conformation SP3_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_212205953.pdb -s /var/tmp/to_scwrl_212205953.seq -o /var/tmp/from_scwrl_212205953.pdb > /var/tmp/scwrl_212205953.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_212205953.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 282 # copying to AlignedFragments data structure # naming current conformation SP3_TS2 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1997997007.pdb -s /var/tmp/to_scwrl_1997997007.seq -o /var/tmp/from_scwrl_1997997007.pdb > /var/tmp/scwrl_1997997007.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1997997007.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 251 # copying to AlignedFragments data structure # naming current conformation SP3_TS3 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_451633046.pdb -s /var/tmp/to_scwrl_451633046.seq -o /var/tmp/from_scwrl_451633046.pdb > /var/tmp/scwrl_451633046.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_451633046.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 238 # copying to AlignedFragments data structure # naming current conformation SP3_TS4 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1387839332.pdb -s /var/tmp/to_scwrl_1387839332.seq -o /var/tmp/from_scwrl_1387839332.pdb > /var/tmp/scwrl_1387839332.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1387839332.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 301 # copying to AlignedFragments data structure # naming current conformation SP3_TS5 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_2039660648.pdb -s /var/tmp/to_scwrl_2039660648.seq -o /var/tmp/from_scwrl_2039660648.pdb > /var/tmp/scwrl_2039660648.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2039660648.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 275 # copying to AlignedFragments data structure # naming current conformation SP4_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_255484645.pdb -s /var/tmp/to_scwrl_255484645.seq -o /var/tmp/from_scwrl_255484645.pdb > /var/tmp/scwrl_255484645.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_255484645.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 249 # copying to AlignedFragments data structure # naming current conformation SP4_TS2 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_433846983.pdb -s /var/tmp/to_scwrl_433846983.seq -o /var/tmp/from_scwrl_433846983.pdb > /var/tmp/scwrl_433846983.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_433846983.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 252 # copying to AlignedFragments data structure # naming current conformation SP4_TS3 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1865949571.pdb -s /var/tmp/to_scwrl_1865949571.seq -o /var/tmp/from_scwrl_1865949571.pdb > /var/tmp/scwrl_1865949571.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1865949571.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 251 # copying to AlignedFragments data structure # naming current conformation SP4_TS4 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_842935734.pdb -s /var/tmp/to_scwrl_842935734.seq -o /var/tmp/from_scwrl_842935734.pdb > /var/tmp/scwrl_842935734.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_842935734.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 292 # copying to AlignedFragments data structure # naming current conformation SP4_TS5 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_382913696.pdb -s /var/tmp/to_scwrl_382913696.seq -o /var/tmp/from_scwrl_382913696.pdb > /var/tmp/scwrl_382913696.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_382913696.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 275 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1857109258.pdb -s /var/tmp/to_scwrl_1857109258.seq -o /var/tmp/from_scwrl_1857109258.pdb > /var/tmp/scwrl_1857109258.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1857109258.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 292 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS2 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_2047908093.pdb -s /var/tmp/to_scwrl_2047908093.seq -o /var/tmp/from_scwrl_2047908093.pdb > /var/tmp/scwrl_2047908093.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2047908093.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 299 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS3 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1724679692.pdb -s /var/tmp/to_scwrl_1724679692.seq -o /var/tmp/from_scwrl_1724679692.pdb > /var/tmp/scwrl_1724679692.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1724679692.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 303 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS4 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1499567321.pdb -s /var/tmp/to_scwrl_1499567321.seq -o /var/tmp/from_scwrl_1499567321.pdb > /var/tmp/scwrl_1499567321.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1499567321.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 293 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS5 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1011843747.pdb -s /var/tmp/to_scwrl_1011843747.seq -o /var/tmp/from_scwrl_1011843747.pdb > /var/tmp/scwrl_1011843747.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1011843747.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 T0326 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_224274587.pdb -s /var/tmp/to_scwrl_224274587.seq -o /var/tmp/from_scwrl_224274587.pdb > /var/tmp/scwrl_224274587.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_224274587.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 T0326 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS2 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_2009356093.pdb -s /var/tmp/to_scwrl_2009356093.seq -o /var/tmp/from_scwrl_2009356093.pdb > /var/tmp/scwrl_2009356093.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2009356093.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 T0326 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS3 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1032457921.pdb -s /var/tmp/to_scwrl_1032457921.seq -o /var/tmp/from_scwrl_1032457921.pdb > /var/tmp/scwrl_1032457921.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1032457921.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 T0326 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS4 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1806619589.pdb -s /var/tmp/to_scwrl_1806619589.seq -o /var/tmp/from_scwrl_1806619589.pdb > /var/tmp/scwrl_1806619589.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1806619589.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_bnmx_TS4-scwrl # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0326 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS5 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_421773856.pdb -s /var/tmp/to_scwrl_421773856.seq -o /var/tmp/from_scwrl_421773856.pdb > /var/tmp/scwrl_421773856.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_421773856.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_bnmx_TS5-scwrl # ReadConformPDB reading from PDB file servers/UNI-EID_expm_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0326 can't currently be optimized by undertaker # naming current conformation UNI-EID_expm_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1449268420.pdb -s /var/tmp/to_scwrl_1449268420.seq -o /var/tmp/from_scwrl_1449268420.pdb > /var/tmp/scwrl_1449268420.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1449268420.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 T0326 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_406357538.pdb -s /var/tmp/to_scwrl_406357538.seq -o /var/tmp/from_scwrl_406357538.pdb > /var/tmp/scwrl_406357538.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_406357538.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 T0326 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL2 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_870182653.pdb -s /var/tmp/to_scwrl_870182653.seq -o /var/tmp/from_scwrl_870182653.pdb > /var/tmp/scwrl_870182653.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_870182653.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 T0326 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL3 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_992300029.pdb -s /var/tmp/to_scwrl_992300029.seq -o /var/tmp/from_scwrl_992300029.pdb > /var/tmp/scwrl_992300029.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_992300029.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 Skipped atom 99, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz # WARNING: incomplete conformation T0326 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL4 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1692885009.pdb -s /var/tmp/to_scwrl_1692885009.seq -o /var/tmp/from_scwrl_1692885009.pdb > /var/tmp/scwrl_1692885009.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1692885009.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_sfst_AL4-scwrl # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0326 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL5 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1389261663.pdb -s /var/tmp/to_scwrl_1389261663.seq -o /var/tmp/from_scwrl_1389261663.pdb > /var/tmp/scwrl_1389261663.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1389261663.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_sfst_AL5-scwrl # ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1 # Found a chain break before 289 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_557745866.pdb -s /var/tmp/to_scwrl_557745866.seq -o /var/tmp/from_scwrl_557745866.pdb > /var/tmp/scwrl_557745866.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_557745866.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 300 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS2 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_968715493.pdb -s /var/tmp/to_scwrl_968715493.seq -o /var/tmp/from_scwrl_968715493.pdb > /var/tmp/scwrl_968715493.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_968715493.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 300 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS3 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1896587877.pdb -s /var/tmp/to_scwrl_1896587877.seq -o /var/tmp/from_scwrl_1896587877.pdb > /var/tmp/scwrl_1896587877.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1896587877.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 302 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS4 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_385223847.pdb -s /var/tmp/to_scwrl_385223847.seq -o /var/tmp/from_scwrl_385223847.pdb > /var/tmp/scwrl_385223847.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_385223847.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 302 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS5 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1350183278.pdb -s /var/tmp/to_scwrl_1350183278.seq -o /var/tmp/from_scwrl_1350183278.pdb > /var/tmp/scwrl_1350183278.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1350183278.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 # WARNING: incomplete conformation T0326 can't currently be optimized by undertaker # naming current conformation beautshot_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_2108793830.pdb -s /var/tmp/to_scwrl_2108793830.seq -o /var/tmp/from_scwrl_2108793830.pdb > /var/tmp/scwrl_2108793830.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2108793830.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 T0326 can't currently be optimized by undertaker # naming current conformation beautshotbase_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_235737207.pdb -s /var/tmp/to_scwrl_235737207.seq -o /var/tmp/from_scwrl_235737207.pdb > /var/tmp/scwrl_235737207.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_235737207.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 T0326 can't currently be optimized by undertaker # naming current conformation forecast-s_AL1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1801816324.pdb -s /var/tmp/to_scwrl_1801816324.seq -o /var/tmp/from_scwrl_1801816324.pdb > /var/tmp/scwrl_1801816324.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1801816324.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 T0326 can't currently be optimized by undertaker # naming current conformation forecast-s_AL2 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1349149515.pdb -s /var/tmp/to_scwrl_1349149515.seq -o /var/tmp/from_scwrl_1349149515.pdb > /var/tmp/scwrl_1349149515.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1349149515.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 T0326 can't currently be optimized by undertaker # naming current conformation forecast-s_AL3 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_127914209.pdb -s /var/tmp/to_scwrl_127914209.seq -o /var/tmp/from_scwrl_127914209.pdb > /var/tmp/scwrl_127914209.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_127914209.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 # WARNING: incomplete conformation T0326 can't currently be optimized by undertaker # naming current conformation forecast-s_AL4 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_2057300969.pdb -s /var/tmp/to_scwrl_2057300969.seq -o /var/tmp/from_scwrl_2057300969.pdb > /var/tmp/scwrl_2057300969.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2057300969.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 T0326 can't currently be optimized by undertaker # naming current conformation forecast-s_AL5 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1782996498.pdb -s /var/tmp/to_scwrl_1782996498.seq -o /var/tmp/from_scwrl_1782996498.pdb > /var/tmp/scwrl_1782996498.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1782996498.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 T0326 can't currently be optimized by undertaker # naming current conformation gtg_AL1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1993863780.pdb -s /var/tmp/to_scwrl_1993863780.seq -o /var/tmp/from_scwrl_1993863780.pdb > /var/tmp/scwrl_1993863780.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1993863780.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 # WARNING: incomplete conformation T0326 can't currently be optimized by undertaker # naming current conformation gtg_AL2 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_752753056.pdb -s /var/tmp/to_scwrl_752753056.seq -o /var/tmp/from_scwrl_752753056.pdb > /var/tmp/scwrl_752753056.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_752753056.pdb # conformation set from SCWRL output # naming current conformation gtg_AL2-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # Found a chain break before 262 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_18426547.pdb -s /var/tmp/to_scwrl_18426547.seq -o /var/tmp/from_scwrl_18426547.pdb > /var/tmp/scwrl_18426547.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_18426547.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 252 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS2 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1703489391.pdb -s /var/tmp/to_scwrl_1703489391.seq -o /var/tmp/from_scwrl_1703489391.pdb > /var/tmp/scwrl_1703489391.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1703489391.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 249 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS3 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_653177502.pdb -s /var/tmp/to_scwrl_653177502.seq -o /var/tmp/from_scwrl_653177502.pdb > /var/tmp/scwrl_653177502.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_653177502.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 290 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS4 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1743106239.pdb -s /var/tmp/to_scwrl_1743106239.seq -o /var/tmp/from_scwrl_1743106239.pdb > /var/tmp/scwrl_1743106239.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1743106239.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 291 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS5 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1055573066.pdb -s /var/tmp/to_scwrl_1055573066.seq -o /var/tmp/from_scwrl_1055573066.pdb > /var/tmp/scwrl_1055573066.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1055573066.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: (T0326)K255.O and (T0326)V256.N only 0.000 apart, marking (T0326)V256.N as missing # WARNING: incomplete conformation T0326 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 274 ; scwrl3 -i /var/tmp/to_scwrl_1665021249.pdb -s /var/tmp/to_scwrl_1665021249.seq -o /var/tmp/from_scwrl_1665021249.pdb > /var/tmp/scwrl_1665021249.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1665021249.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 303 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS2 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1967380827.pdb -s /var/tmp/to_scwrl_1967380827.seq -o /var/tmp/from_scwrl_1967380827.pdb > /var/tmp/scwrl_1967380827.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1967380827.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 # Found a chain break before 301 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS3 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_917445513.pdb -s /var/tmp/to_scwrl_917445513.seq -o /var/tmp/from_scwrl_917445513.pdb > /var/tmp/scwrl_917445513.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_917445513.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: (T0326)A108.O and (T0326)P109.N only 0.000 apart, marking (T0326)P109.N as missing # WARNING: incomplete conformation T0326 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 274 ; scwrl3 -i /var/tmp/to_scwrl_549995523.pdb -s /var/tmp/to_scwrl_549995523.seq -o /var/tmp/from_scwrl_549995523.pdb > /var/tmp/scwrl_549995523.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_549995523.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: (T0326)F140.O and (T0326)I141.N only 0.000 apart, marking (T0326)I141.N as missing WARNING: atoms too close: (T0326)K295.O and (T0326)T296.N only 0.000 apart, marking (T0326)T296.N as missing # WARNING: incomplete conformation T0326 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 274 ; scwrl3 -i /var/tmp/to_scwrl_1626516769.pdb -s /var/tmp/to_scwrl_1626516769.seq -o /var/tmp/from_scwrl_1626516769.pdb > /var/tmp/scwrl_1626516769.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1626516769.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 T0326 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1339219368.pdb -s /var/tmp/to_scwrl_1339219368.seq -o /var/tmp/from_scwrl_1339219368.pdb > /var/tmp/scwrl_1339219368.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1339219368.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 T0326 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS2 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1999263943.pdb -s /var/tmp/to_scwrl_1999263943.seq -o /var/tmp/from_scwrl_1999263943.pdb > /var/tmp/scwrl_1999263943.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1999263943.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 T0326 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS3 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_2032874307.pdb -s /var/tmp/to_scwrl_2032874307.seq -o /var/tmp/from_scwrl_2032874307.pdb > /var/tmp/scwrl_2032874307.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2032874307.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 T0326 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS4 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_61918375.pdb -s /var/tmp/to_scwrl_61918375.seq -o /var/tmp/from_scwrl_61918375.pdb > /var/tmp/scwrl_61918375.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_61918375.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 T0326 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS5 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_844080325.pdb -s /var/tmp/to_scwrl_844080325.seq -o /var/tmp/from_scwrl_844080325.pdb > /var/tmp/scwrl_844080325.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_844080325.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 # Found a chain break before 233 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1578275670.pdb -s /var/tmp/to_scwrl_1578275670.seq -o /var/tmp/from_scwrl_1578275670.pdb > /var/tmp/scwrl_1578275670.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1578275670.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 # Found a chain break before 266 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS2 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1451180038.pdb -s /var/tmp/to_scwrl_1451180038.seq -o /var/tmp/from_scwrl_1451180038.pdb > /var/tmp/scwrl_1451180038.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1451180038.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 # WARNING: incomplete conformation T0326 can't currently be optimized by undertaker # naming current conformation keasar-server_TS3 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1401826190.pdb -s /var/tmp/to_scwrl_1401826190.seq -o /var/tmp/from_scwrl_1401826190.pdb > /var/tmp/scwrl_1401826190.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1401826190.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 T0326 can't currently be optimized by undertaker # naming current conformation keasar-server_TS4 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_399507516.pdb -s /var/tmp/to_scwrl_399507516.seq -o /var/tmp/from_scwrl_399507516.pdb > /var/tmp/scwrl_399507516.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_399507516.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 T0326 can't currently be optimized by undertaker # naming current conformation keasar-server_TS5 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1200284268.pdb -s /var/tmp/to_scwrl_1200284268.seq -o /var/tmp/from_scwrl_1200284268.pdb > /var/tmp/scwrl_1200284268.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1200284268.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 T0326 can't currently be optimized by undertaker # naming current conformation mGen-3D_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1787050038.pdb -s /var/tmp/to_scwrl_1787050038.seq -o /var/tmp/from_scwrl_1787050038.pdb > /var/tmp/scwrl_1787050038.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1787050038.pdb # conformation set from SCWRL output # naming current conformation mGen-3D_TS1-scwrl # ReadConformPDB reading from PDB file servers/nFOLD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0326 can't currently be optimized by undertaker # naming current conformation nFOLD_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1749690794.pdb -s /var/tmp/to_scwrl_1749690794.seq -o /var/tmp/from_scwrl_1749690794.pdb > /var/tmp/scwrl_1749690794.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1749690794.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 T0326 can't currently be optimized by undertaker # naming current conformation nFOLD_TS2 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1161594451.pdb -s /var/tmp/to_scwrl_1161594451.seq -o /var/tmp/from_scwrl_1161594451.pdb > /var/tmp/scwrl_1161594451.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1161594451.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 T0326 can't currently be optimized by undertaker # naming current conformation nFOLD_TS3 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_2022787245.pdb -s /var/tmp/to_scwrl_2022787245.seq -o /var/tmp/from_scwrl_2022787245.pdb > /var/tmp/scwrl_2022787245.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2022787245.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: atom 1 has residue number 34 < previous residue 296 in servers/nFOLD_TS4.pdb.gz # WARNING: incomplete conformation T0326 can't currently be optimized by undertaker # naming current conformation nFOLD_TS4 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1404023471.pdb -s /var/tmp/to_scwrl_1404023471.seq -o /var/tmp/from_scwrl_1404023471.pdb > /var/tmp/scwrl_1404023471.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1404023471.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: atom 1 has residue number 35 < previous residue 296 in servers/nFOLD_TS5.pdb.gz # WARNING: incomplete conformation T0326 can't currently be optimized by undertaker # naming current conformation nFOLD_TS5 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_363260320.pdb -s /var/tmp/to_scwrl_363260320.seq -o /var/tmp/from_scwrl_363260320.pdb > /var/tmp/scwrl_363260320.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_363260320.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 T0326 can't currently be optimized by undertaker # naming current conformation panther2_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_3217807.pdb -s /var/tmp/to_scwrl_3217807.seq -o /var/tmp/from_scwrl_3217807.pdb > /var/tmp/scwrl_3217807.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_3217807.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 T0326 can't currently be optimized by undertaker # naming current conformation shub_TS1 # request to SCWRL produces command: ulimit -t 274 ; scwrl3 -i /var/tmp/to_scwrl_1313840793.pdb -s /var/tmp/to_scwrl_1313840793.seq -o /var/tmp/from_scwrl_1313840793.pdb > /var/tmp/scwrl_1313840793.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1313840793.pdb # conformation set from SCWRL output # naming current conformation shub_TS1-scwrl # command:CPU_time= 93.2058 sec, elapsed time= 1107.09 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 = 55.0593 shub_TS1 costs 0 real_cost = 67.0495 panther2_TS1-scwrl costs 0 real_cost = 783.056 panther2_TS1 costs 0 real_cost = 782.867 nFOLD_TS5-scwrl costs 0 real_cost = 368.267 nFOLD_TS5 costs 0 real_cost = 480.496 nFOLD_TS4-scwrl costs 0 real_cost = 381.282 nFOLD_TS4 costs 0 real_cost = 521.369 nFOLD_TS3-scwrl costs 0 real_cost = 239.006 nFOLD_TS3 costs 0 real_cost = 393.729 nFOLD_TS2-scwrl costs 0 real_cost = 249.226 nFOLD_TS2 costs 0 real_cost = 376.77 nFOLD_TS1-scwrl costs 0 real_cost = -94.3233 nFOLD_TS1 costs 0 real_cost = 86.7375 mGen-3D_TS1-scwrl costs 0 real_cost = -60.5193 mGen-3D_TS1 costs 0 real_cost = 120.171 keasar-server_TS5-scwrl costs 0 real_cost = 255.976 keasar-server_TS5 costs 0 real_cost = 252.272 keasar-server_TS4-scwrl costs 0 real_cost = 270.8 keasar-server_TS4 costs 0 real_cost = 286.256 keasar-server_TS3-scwrl costs 0 real_cost = 295.516 keasar-server_TS3 costs 0 real_cost = 305.111 keasar-server_TS2-scwrl costs 0 real_cost = -64.1638 keasar-server_TS2 costs 0 real_cost = -55.6284 keasar-server_TS1-scwrl costs 0 real_cost = -66.1889 keasar-server_TS1 costs 0 real_cost = -64.262 karypis.srv_TS5-scwrl costs 0 real_cost = 307.216 karypis.srv_TS5 costs 0 real_cost = 302.141 karypis.srv_TS4-scwrl costs 0 real_cost = 240.217 karypis.srv_TS4 costs 0 real_cost = 234.756 karypis.srv_TS3-scwrl costs 0 real_cost = 366.291 karypis.srv_TS3 costs 0 real_cost = 363.865 karypis.srv_TS2-scwrl costs 0 real_cost = 307.203 karypis.srv_TS2 costs 0 real_cost = 306.564 karypis.srv_TS1-scwrl costs 0 real_cost = 324.472 karypis.srv_TS1 costs 0 real_cost = 322.675 karypis.srv.4_TS5-scwrl costs 0 real_cost = 380.13 karypis.srv.4_TS5 costs 0 real_cost = 380.141 karypis.srv.4_TS4-scwrl costs 0 real_cost = 352.12 karypis.srv.4_TS4 costs 0 real_cost = 352.523 karypis.srv.4_TS3-scwrl costs 0 real_cost = 352.212 karypis.srv.4_TS3 costs 0 real_cost = 351.807 karypis.srv.4_TS2-scwrl costs 0 real_cost = 327.806 karypis.srv.4_TS2 costs 0 real_cost = 327.519 karypis.srv.4_TS1-scwrl costs 0 real_cost = 368.476 karypis.srv.4_TS1 costs 0 real_cost = 368.456 karypis.srv.2_TS5-scwrl costs 0 real_cost = 168.222 karypis.srv.2_TS5 costs 0 real_cost = 164.144 karypis.srv.2_TS4-scwrl costs 0 real_cost = 162.662 karypis.srv.2_TS4 costs 0 real_cost = 162.662 karypis.srv.2_TS3-scwrl costs 0 real_cost = 237.181 karypis.srv.2_TS3 costs 0 real_cost = 237.181 karypis.srv.2_TS2-scwrl costs 0 real_cost = 250.74 karypis.srv.2_TS2 costs 0 real_cost = 250.74 karypis.srv.2_TS1-scwrl costs 0 real_cost = 326.837 karypis.srv.2_TS1 costs 0 real_cost = 326.88 gtg_AL2-scwrl costs 0 real_cost = 827.197 gtg_AL2 costs 0 real_cost = 844.732 gtg_AL1-scwrl costs 0 real_cost = 713.606 gtg_AL1 costs 0 real_cost = 722.777 forecast-s_AL5-scwrl costs 0 real_cost = 334.557 forecast-s_AL5 costs 0 real_cost = 465.07 forecast-s_AL4-scwrl costs 0 real_cost = 336.857 forecast-s_AL4 costs 0 real_cost = 464.304 forecast-s_AL3-scwrl costs 0 real_cost = 330.319 forecast-s_AL3 costs 0 real_cost = 476.278 forecast-s_AL2-scwrl costs 0 real_cost = 341.914 forecast-s_AL2 costs 0 real_cost = 458.797 forecast-s_AL1-scwrl costs 0 real_cost = 271.639 forecast-s_AL1 costs 0 real_cost = 392.752 beautshotbase_TS1-scwrl costs 0 real_cost = -93.2316 beautshotbase_TS1 costs 0 real_cost = -83.8692 beautshot_TS1-scwrl costs 0 real_cost = 29.9602 beautshot_TS1 costs 0 real_cost = 32.1878 Zhang-Server_TS5-scwrl costs 0 real_cost = -182.705 Zhang-Server_TS5 costs 0 real_cost = -182.595 Zhang-Server_TS4-scwrl costs 0 real_cost = -104.868 Zhang-Server_TS4 costs 0 real_cost = -104.604 Zhang-Server_TS3-scwrl costs 0 real_cost = -100.784 Zhang-Server_TS3 costs 0 real_cost = -100.79 Zhang-Server_TS2-scwrl costs 0 real_cost = -79.3066 Zhang-Server_TS2 costs 0 real_cost = -79.5419 Zhang-Server_TS1-scwrl costs 0 real_cost = -113.206 Zhang-Server_TS1 costs 0 real_cost = -113.206 UNI-EID_sfst_AL5-scwrl costs 0 real_cost = 384.781 UNI-EID_sfst_AL5 costs 0 real_cost = 490.334 UNI-EID_sfst_AL4-scwrl costs 0 real_cost = 343.273 UNI-EID_sfst_AL4 costs 0 real_cost = 448.422 UNI-EID_sfst_AL3-scwrl costs 0 real_cost = 402.513 UNI-EID_sfst_AL3 costs 0 real_cost = 486.39 UNI-EID_sfst_AL2-scwrl costs 0 real_cost = 325.489 UNI-EID_sfst_AL2 costs 0 real_cost = 426.915 UNI-EID_sfst_AL1-scwrl costs 0 real_cost = -90.7666 UNI-EID_sfst_AL1 costs 0 real_cost = 141.303 UNI-EID_expm_TS1-scwrl costs 0 real_cost = -67.4571 UNI-EID_expm_TS1 costs 0 real_cost = 119.372 UNI-EID_bnmx_TS5-scwrl costs 0 real_cost = 343.63 UNI-EID_bnmx_TS5 costs 0 real_cost = 491.413 UNI-EID_bnmx_TS4-scwrl costs 0 real_cost = 367.886 UNI-EID_bnmx_TS4 costs 0 real_cost = 486.277 UNI-EID_bnmx_TS3-scwrl costs 0 real_cost = 392.713 UNI-EID_bnmx_TS3 costs 0 real_cost = 489.284 UNI-EID_bnmx_TS2-scwrl costs 0 real_cost = 180.594 UNI-EID_bnmx_TS2 costs 0 real_cost = 334.311 UNI-EID_bnmx_TS1-scwrl costs 0 real_cost = -90.7666 UNI-EID_bnmx_TS1 costs 0 real_cost = 141.303 SPARKS2_TS5-scwrl costs 0 real_cost = 119.844 SPARKS2_TS5 costs 0 real_cost = 123 SPARKS2_TS4-scwrl costs 0 real_cost = 184.778 SPARKS2_TS4 costs 0 real_cost = 189.63 SPARKS2_TS3-scwrl costs 0 real_cost = 180.238 SPARKS2_TS3 costs 0 real_cost = 186.251 SPARKS2_TS2-scwrl costs 0 real_cost = 135.002 SPARKS2_TS2 costs 0 real_cost = 136.657 SPARKS2_TS1-scwrl costs 0 real_cost = -108.777 SPARKS2_TS1 costs 0 real_cost = -106.328 SP4_TS5-scwrl costs 0 real_cost = 164.59 SP4_TS5 costs 0 real_cost = 170.252 SP4_TS4-scwrl costs 0 real_cost = 177.878 SP4_TS4 costs 0 real_cost = 181.198 SP4_TS3-scwrl costs 0 real_cost = 157.837 SP4_TS3 costs 0 real_cost = 158.055 SP4_TS2-scwrl costs 0 real_cost = 172.649 SP4_TS2 costs 0 real_cost = 178.503 SP4_TS1-scwrl costs 0 real_cost = -99.5144 SP4_TS1 costs 0 real_cost = -98.5533 SP3_TS5-scwrl costs 0 real_cost = 188.838 SP3_TS5 costs 0 real_cost = 198.527 SP3_TS4-scwrl costs 0 real_cost = 186.468 SP3_TS4 costs 0 real_cost = 198.384 SP3_TS3-scwrl costs 0 real_cost = 191.331 SP3_TS3 costs 0 real_cost = 201.411 SP3_TS2-scwrl costs 0 real_cost = 142.59 SP3_TS2 costs 0 real_cost = 149.838 SP3_TS1-scwrl costs 0 real_cost = -99.5144 SP3_TS1 costs 0 real_cost = -98.5533 SAM_T06_server_TS5-scwrl costs 0 real_cost = 364.686 SAM_T06_server_TS5 costs 0 real_cost = 310.087 SAM_T06_server_TS4-scwrl costs 0 real_cost = 393.651 SAM_T06_server_TS4 costs 0 real_cost = 359.855 SAM_T06_server_TS3-scwrl costs 0 real_cost = 446.814 SAM_T06_server_TS3 costs 0 real_cost = 402.983 SAM_T06_server_TS2-scwrl costs 0 real_cost = -39.9439 SAM_T06_server_TS2 costs 0 real_cost = -63.2455 SAM_T06_server_TS1-scwrl costs 0 real_cost = -81.8249 SAM_T06_server_TS1 costs 0 real_cost = -81.3118 SAM-T99_AL5-scwrl costs 0 real_cost = 367.348 SAM-T99_AL5 costs 0 real_cost = 500.865 SAM-T99_AL4-scwrl costs 0 real_cost = 376.425 SAM-T99_AL4 costs 0 real_cost = 505.986 SAM-T99_AL3-scwrl costs 0 real_cost = 379.8 SAM-T99_AL3 costs 0 real_cost = 508.854 SAM-T99_AL2-scwrl costs 0 real_cost = 369.547 SAM-T99_AL2 costs 0 real_cost = 502.55 SAM-T99_AL1-scwrl costs 0 real_cost = -96.3561 SAM-T99_AL1 costs 0 real_cost = 136.516 SAM-T02_AL5-scwrl costs 0 real_cost = 339.073 SAM-T02_AL5 costs 0 real_cost = 479.124 SAM-T02_AL4-scwrl costs 0 real_cost = 316.142 SAM-T02_AL4 costs 0 real_cost = 453.388 SAM-T02_AL3-scwrl costs 0 real_cost = 349.608 SAM-T02_AL3 costs 0 real_cost = 494.584 SAM-T02_AL2-scwrl costs 0 real_cost = 468.834 SAM-T02_AL1-scwrl costs 0 real_cost = -96.3561 SAM-T02_AL1 costs 0 real_cost = 136.516 ROKKY_TS1-scwrl costs 0 real_cost = -96.6815 ROKKY_TS1 costs 0 real_cost = -95.6279 ROBETTA_TS5-scwrl costs 0 real_cost = -127.967 ROBETTA_TS5 costs 0 real_cost = -134.552 ROBETTA_TS4-scwrl costs 0 real_cost = -140.624 ROBETTA_TS4 costs 0 real_cost = -140.404 ROBETTA_TS3-scwrl costs 0 real_cost = -130.58 ROBETTA_TS3 costs 0 real_cost = -132.738 ROBETTA_TS2-scwrl costs 0 real_cost = -120.331 ROBETTA_TS2 costs 0 real_cost = -127.025 ROBETTA_TS1-scwrl costs 0 real_cost = -121.432 ROBETTA_TS1 costs 0 real_cost = -127.419 RAPTOR_TS5-scwrl costs 0 real_cost = 125.46 RAPTOR_TS5 costs 0 real_cost = 126.012 RAPTOR_TS4-scwrl costs 0 real_cost = 195.537 RAPTOR_TS4 costs 0 real_cost = 200.05 RAPTOR_TS3-scwrl costs 0 real_cost = 125.633 RAPTOR_TS3 costs 0 real_cost = 130.114 RAPTOR_TS2-scwrl costs 0 real_cost = -95.6652 RAPTOR_TS2 costs 0 real_cost = -94.125 RAPTOR_TS1-scwrl costs 0 real_cost = -95.6652 RAPTOR_TS1 costs 0 real_cost = -94.125 RAPTORESS_TS5-scwrl costs 0 real_cost = 184.394 RAPTORESS_TS5 costs 0 real_cost = 197.342 RAPTORESS_TS4-scwrl costs 0 real_cost = 94.2727 RAPTORESS_TS4 costs 0 real_cost = 100.067 RAPTORESS_TS3-scwrl costs 0 real_cost = 84.8652 RAPTORESS_TS3 costs 0 real_cost = 93.4119 RAPTORESS_TS2-scwrl costs 0 real_cost = -23.1023 RAPTORESS_TS2 costs 0 real_cost = -20.1616 RAPTORESS_TS1-scwrl costs 0 real_cost = -23.1023 RAPTORESS_TS1 costs 0 real_cost = -20.1616 RAPTOR-ACE_TS5-scwrl costs 0 real_cost = -89.8327 RAPTOR-ACE_TS5 costs 0 real_cost = -92.0197 RAPTOR-ACE_TS4-scwrl costs 0 real_cost = -99.5144 RAPTOR-ACE_TS4 costs 0 real_cost = -98.5533 RAPTOR-ACE_TS3-scwrl costs 0 real_cost = -91.9943 RAPTOR-ACE_TS3 costs 0 real_cost = -92.3313 RAPTOR-ACE_TS2-scwrl costs 0 real_cost = -101.991 RAPTOR-ACE_TS2 costs 0 real_cost = -94.216 RAPTOR-ACE_TS1-scwrl costs 0 real_cost = -90.5275 RAPTOR-ACE_TS1 costs 0 real_cost = -94.626 Pmodeller6_TS5-scwrl costs 0 real_cost = -89.8687 Pmodeller6_TS5 costs 0 real_cost = -91.6019 Pmodeller6_TS4-scwrl costs 0 real_cost = -121.473 Pmodeller6_TS4 costs 0 real_cost = -127.46 Pmodeller6_TS3-scwrl costs 0 real_cost = -130.581 Pmodeller6_TS3 costs 0 real_cost = -132.738 Pmodeller6_TS2-scwrl costs 0 real_cost = -127.971 Pmodeller6_TS2 costs 0 real_cost = -134.556 Pmodeller6_TS1-scwrl costs 0 real_cost = -140.623 Pmodeller6_TS1 costs 0 real_cost = -140.403 Phyre-2_TS5-scwrl costs 0 real_cost = -106.093 Phyre-2_TS5 costs 0 real_cost = -108.127 Phyre-2_TS4-scwrl costs 0 real_cost = -103.577 Phyre-2_TS4 costs 0 real_cost = -105.764 Phyre-2_TS3-scwrl costs 0 real_cost = -106.353 Phyre-2_TS3 costs 0 real_cost = -107.127 Phyre-2_TS2-scwrl costs 0 real_cost = -105.958 Phyre-2_TS2 costs 0 real_cost = -107.354 Phyre-2_TS1-scwrl costs 0 real_cost = -104.508 Phyre-2_TS1 costs 0 real_cost = -105.16 Phyre-1_TS1-scwrl costs 0 real_cost = 195.906 Phyre-1_TS1 costs 0 real_cost = 182.072 Pcons6_TS5-scwrl costs 0 real_cost = -104.224 Pcons6_TS5 costs 0 real_cost = -105.958 Pcons6_TS4-scwrl costs 0 real_cost = -95.1552 Pcons6_TS4 costs 0 real_cost = -96.5123 Pcons6_TS3-scwrl costs 0 real_cost = -89.1654 Pcons6_TS3 costs 0 real_cost = -88.3395 Pcons6_TS2-scwrl costs 0 real_cost = -95.2296 Pcons6_TS2 costs 0 real_cost = -96.6348 Pcons6_TS1-scwrl costs 0 real_cost = -89.8687 Pcons6_TS1 costs 0 real_cost = -91.6019 PROTINFO_TS5-scwrl costs 0 real_cost = -107.434 PROTINFO_TS5 costs 0 real_cost = -107.255 PROTINFO_TS4-scwrl costs 0 real_cost = 304.762 PROTINFO_TS4 costs 0 real_cost = 308.158 PROTINFO_TS3-scwrl costs 0 real_cost = -123.336 PROTINFO_TS3 costs 0 real_cost = -127.551 PROTINFO_TS2-scwrl costs 0 real_cost = -113.842 PROTINFO_TS2 costs 0 real_cost = -113.755 PROTINFO_TS1-scwrl costs 0 real_cost = -104.921 PROTINFO_TS1 costs 0 real_cost = -105.61 PROTINFO-AB_TS5-scwrl costs 0 real_cost = -164.708 PROTINFO-AB_TS5 costs 0 real_cost = -164.973 PROTINFO-AB_TS4-scwrl costs 0 real_cost = -93.6133 PROTINFO-AB_TS4 costs 0 real_cost = -95.0583 PROTINFO-AB_TS3-scwrl costs 0 real_cost = -99.0599 PROTINFO-AB_TS3 costs 0 real_cost = -94.7483 PROTINFO-AB_TS2-scwrl costs 0 real_cost = -93.0924 PROTINFO-AB_TS2 costs 0 real_cost = -93.6024 PROTINFO-AB_TS1-scwrl costs 0 real_cost = -96.791 PROTINFO-AB_TS1 costs 0 real_cost = -94.8648 NN_PUT_lab_TS1-scwrl costs 0 real_cost = 310.801 NN_PUT_lab_TS1 costs 0 real_cost = 314.504 MetaTasser_TS5-scwrl costs 0 real_cost = 51.7026 MetaTasser_TS5 costs 0 real_cost = 47.529 MetaTasser_TS4-scwrl costs 0 real_cost = 50.6627 MetaTasser_TS4 costs 0 real_cost = 53.895 MetaTasser_TS3-scwrl costs 0 real_cost = 23.987 MetaTasser_TS3 costs 0 real_cost = 33.2058 MetaTasser_TS2-scwrl costs 0 real_cost = 46.4532 MetaTasser_TS2 costs 0 real_cost = 55.6767 MetaTasser_TS1-scwrl costs 0 real_cost = 42.5556 MetaTasser_TS1 costs 0 real_cost = 49.4364 Ma-OPUS-server_TS5-scwrl costs 0 real_cost = 285.995 Ma-OPUS-server_TS5 costs 0 real_cost = 288.164 Ma-OPUS-server_TS4-scwrl costs 0 real_cost = 323.094 Ma-OPUS-server_TS4 costs 0 real_cost = 326.421 Ma-OPUS-server_TS3-scwrl costs 0 real_cost = 294.401 Ma-OPUS-server_TS3 costs 0 real_cost = 299.546 Ma-OPUS-server_TS2-scwrl costs 0 real_cost = 107.298 Ma-OPUS-server_TS2 costs 0 real_cost = 115.08 Ma-OPUS-server_TS1-scwrl costs 0 real_cost = -110.875 Ma-OPUS-server_TS1 costs 0 real_cost = -106.219 Ma-OPUS-server2_TS5-scwrl costs 0 real_cost = 323.094 Ma-OPUS-server2_TS5 costs 0 real_cost = 326.421 Ma-OPUS-server2_TS4-scwrl costs 0 real_cost = 294.401 Ma-OPUS-server2_TS4 costs 0 real_cost = 299.546 Ma-OPUS-server2_TS3-scwrl costs 0 real_cost = 287.74 Ma-OPUS-server2_TS3 costs 0 real_cost = 288.542 Ma-OPUS-server2_TS2-scwrl costs 0 real_cost = 89.7114 Ma-OPUS-server2_TS2 costs 0 real_cost = 97.7339 Ma-OPUS-server2_TS1-scwrl costs 0 real_cost = -108.784 Ma-OPUS-server2_TS1 costs 0 real_cost = -111.887 LOOPP_TS5-scwrl costs 0 real_cost = 368.398 LOOPP_TS5 costs 0 real_cost = 370.012 LOOPP_TS4-scwrl costs 0 real_cost = 321.257 LOOPP_TS4 costs 0 real_cost = 323.276 LOOPP_TS3-scwrl costs 0 real_cost = 325.232 LOOPP_TS3 costs 0 real_cost = 323.515 LOOPP_TS2-scwrl costs 0 real_cost = 307.92 LOOPP_TS2 costs 0 real_cost = 311.505 LOOPP_TS1-scwrl costs 0 real_cost = 310.801 LOOPP_TS1 costs 0 real_cost = 314.504 Huber-Torda-Server_TS5-scwrl costs 0 real_cost = 574.077 Huber-Torda-Server_TS5 costs 0 real_cost = 633.047 Huber-Torda-Server_TS4-scwrl costs 0 real_cost = 503.618 Huber-Torda-Server_TS4 costs 0 real_cost = 582.2 Huber-Torda-Server_TS3-scwrl costs 0 real_cost = 519.004 Huber-Torda-Server_TS3 costs 0 real_cost = 586.228 Huber-Torda-Server_TS2-scwrl costs 0 real_cost = 378.13 Huber-Torda-Server_TS2 costs 0 real_cost = 443.591 Huber-Torda-Server_TS1-scwrl costs 0 real_cost = -78.8797 Huber-Torda-Server_TS1 costs 0 real_cost = 93.1573 HHpred3_TS1-scwrl costs 0 real_cost = -75.704 HHpred3_TS1 costs 0 real_cost = -74.5809 HHpred2_TS1-scwrl costs 0 real_cost = -75.704 HHpred2_TS1 costs 0 real_cost = -74.5809 HHpred1_TS1-scwrl costs 0 real_cost = -105.53 HHpred1_TS1 costs 0 real_cost = -104.938 GeneSilicoMetaServer_TS5-scwrl costs 0 real_cost = -117.27 GeneSilicoMetaServer_TS5 costs 0 real_cost = -115.889 GeneSilicoMetaServer_TS4-scwrl costs 0 real_cost = -114.872 GeneSilicoMetaServer_TS4 costs 0 real_cost = -111.396 GeneSilicoMetaServer_TS3-scwrl costs 0 real_cost = -60.8853 GeneSilicoMetaServer_TS3 costs 0 real_cost = -59.3735 GeneSilicoMetaServer_TS2-scwrl costs 0 real_cost = -99.9057 GeneSilicoMetaServer_TS2 costs 0 real_cost = -96.6579 GeneSilicoMetaServer_TS1-scwrl costs 0 real_cost = -101.109 GeneSilicoMetaServer_TS1 costs 0 real_cost = -103.279 FUNCTION_TS5-scwrl costs 0 real_cost = -83.8873 FUNCTION_TS5 costs 0 real_cost = -81.7797 FUNCTION_TS4-scwrl costs 0 real_cost = -105.23 FUNCTION_TS4 costs 0 real_cost = -107.103 FUNCTION_TS3-scwrl costs 0 real_cost = -91.8072 FUNCTION_TS3 costs 0 real_cost = -91.4245 FUNCTION_TS2-scwrl costs 0 real_cost = -91.7227 FUNCTION_TS2 costs 0 real_cost = -93.6358 FUNCTION_TS1-scwrl costs 0 real_cost = -104.887 FUNCTION_TS1 costs 0 real_cost = -101.091 FUGUE_AL5-scwrl costs 0 real_cost = 394.72 FUGUE_AL5 costs 0 real_cost = 639.26 FUGUE_AL4-scwrl costs 0 real_cost = 283.184 FUGUE_AL4 costs 0 real_cost = 432.951 FUGUE_AL3-scwrl costs 0 real_cost = 509.455 FUGUE_AL3 costs 0 real_cost = 667.841 FUGUE_AL2-scwrl costs 0 real_cost = 360.927 FUGUE_AL2 costs 0 real_cost = 478.035 FUGUE_AL1-scwrl costs 0 real_cost = -39.4653 FUGUE_AL1 costs 0 real_cost = 166.448 FUGMOD_TS5-scwrl costs 0 real_cost = 371.012 FUGMOD_TS5 costs 0 real_cost = 372.963 FUGMOD_TS4-scwrl costs 0 real_cost = 200.159 FUGMOD_TS4 costs 0 real_cost = 200.311 FUGMOD_TS3-scwrl costs 0 real_cost = 481.514 FUGMOD_TS3 costs 0 real_cost = 483.149 FUGMOD_TS2-scwrl costs 0 real_cost = 172.948 FUGMOD_TS2 costs 0 real_cost = 177.548 FUGMOD_TS1-scwrl costs 0 real_cost = -91.9877 FUGMOD_TS1 costs 0 real_cost = -91.2603 FPSOLVER-SERVER_TS5-scwrl costs 0 real_cost = 335.942 FPSOLVER-SERVER_TS5 costs 0 real_cost = 339.286 FPSOLVER-SERVER_TS4-scwrl costs 0 real_cost = 347.83 FPSOLVER-SERVER_TS4 costs 0 real_cost = 352.637 FPSOLVER-SERVER_TS3-scwrl costs 0 real_cost = 303.202 FPSOLVER-SERVER_TS3 costs 0 real_cost = 311.013 FPSOLVER-SERVER_TS2-scwrl costs 0 real_cost = 334.739 FPSOLVER-SERVER_TS2 costs 0 real_cost = 337.627 FPSOLVER-SERVER_TS1-scwrl costs 0 real_cost = 343.66 FPSOLVER-SERVER_TS1 costs 0 real_cost = 348.809 FORTE2_AL5-scwrl costs 0 real_cost = 407.746 FORTE2_AL5 costs 0 real_cost = 556.308 FORTE2_AL4-scwrl costs 0 real_cost = 446.642 FORTE2_AL4 costs 0 real_cost = 627.285 FORTE2_AL3-scwrl costs 0 real_cost = 339.961 FORTE2_AL3 costs 0 real_cost = 556.646 FORTE2_AL2-scwrl costs 0 real_cost = 313.572 FORTE2_AL2 costs 0 real_cost = 475.068 FORTE2_AL1-scwrl costs 0 real_cost = -36.3559 FORTE2_AL1 costs 0 real_cost = 184.782 FORTE1_AL5-scwrl costs 0 real_cost = 446.642 FORTE1_AL5 costs 0 real_cost = 627.285 FORTE1_AL4-scwrl costs 0 real_cost = 297.946 FORTE1_AL4 costs 0 real_cost = 519.299 FORTE1_AL3-scwrl costs 0 real_cost = 393.882 FORTE1_AL3 costs 0 real_cost = 549.539 FORTE1_AL2-scwrl costs 0 real_cost = 307.874 FORTE1_AL2 costs 0 real_cost = 466.513 FORTE1_AL1-scwrl costs 0 real_cost = -36.3559 FORTE1_AL1 costs 0 real_cost = 184.782 FOLDpro_TS5-scwrl costs 0 real_cost = -97.7893 FOLDpro_TS5 costs 0 real_cost = -93.2431 FOLDpro_TS4-scwrl costs 0 real_cost = 189.305 FOLDpro_TS4 costs 0 real_cost = 192.607 FOLDpro_TS3-scwrl costs 0 real_cost = -85.6761 FOLDpro_TS3 costs 0 real_cost = -79.5091 FOLDpro_TS2-scwrl costs 0 real_cost = -99.11 FOLDpro_TS2 costs 0 real_cost = -104.98 FOLDpro_TS1-scwrl costs 0 real_cost = -102.084 FOLDpro_TS1 costs 0 real_cost = -105.614 FAMS_TS5-scwrl costs 0 real_cost = -109.209 FAMS_TS5 costs 0 real_cost = -104.474 FAMS_TS4-scwrl costs 0 real_cost = -103.294 FAMS_TS4 costs 0 real_cost = -101.37 FAMS_TS3-scwrl costs 0 real_cost = -106.867 FAMS_TS3 costs 0 real_cost = -102.686 FAMS_TS2-scwrl costs 0 real_cost = -100.12 FAMS_TS2 costs 0 real_cost = -100.393 FAMS_TS1-scwrl costs 0 real_cost = -98.2115 FAMS_TS1 costs 0 real_cost = -96.1607 FAMSD_TS5-scwrl costs 0 real_cost = -109.657 FAMSD_TS5 costs 0 real_cost = -100.904 FAMSD_TS4-scwrl costs 0 real_cost = -105.611 FAMSD_TS4 costs 0 real_cost = -100.817 FAMSD_TS3-scwrl costs 0 real_cost = -111.177 FAMSD_TS3 costs 0 real_cost = -101.088 FAMSD_TS2-scwrl costs 0 real_cost = -109.209 FAMSD_TS2 costs 0 real_cost = -104.474 FAMSD_TS1-scwrl costs 0 real_cost = -106.867 FAMSD_TS1 costs 0 real_cost = -102.686 Distill_TS5-scwrl costs 0 real_cost = 685.228 Distill_TS4-scwrl costs 0 real_cost = 679.774 Distill_TS3-scwrl costs 0 real_cost = 683.883 Distill_TS2-scwrl costs 0 real_cost = 690.266 Distill_TS1-scwrl costs 0 real_cost = 683.24 CaspIta-FOX_TS5-scwrl costs 0 real_cost = 331.663 CaspIta-FOX_TS5 costs 0 real_cost = 317.295 CaspIta-FOX_TS4-scwrl costs 0 real_cost = 396.743 CaspIta-FOX_TS4 costs 0 real_cost = 377.407 CaspIta-FOX_TS3-scwrl costs 0 real_cost = 319.237 CaspIta-FOX_TS3 costs 0 real_cost = 314.207 CaspIta-FOX_TS2-scwrl costs 0 real_cost = 479.095 CaspIta-FOX_TS2 costs 0 real_cost = 473.542 CaspIta-FOX_TS1-scwrl costs 0 real_cost = -89.4556 CaspIta-FOX_TS1 costs 0 real_cost = -89.1258 CPHmodels_TS1-scwrl costs 0 real_cost = -74.1711 CPHmodels_TS1 costs 0 real_cost = -72.5607 CIRCLE_TS5-scwrl costs 0 real_cost = -105.878 CIRCLE_TS5 costs 0 real_cost = -105.614 CIRCLE_TS4-scwrl costs 0 real_cost = -109.209 CIRCLE_TS4 costs 0 real_cost = -104.474 CIRCLE_TS3-scwrl costs 0 real_cost = -99.6574 CIRCLE_TS3 costs 0 real_cost = -98.5656 CIRCLE_TS2-scwrl costs 0 real_cost = -100.12 CIRCLE_TS2 costs 0 real_cost = -100.393 CIRCLE_TS1-scwrl costs 0 real_cost = -103.294 CIRCLE_TS1 costs 0 real_cost = -101.37 Bilab-ENABLE_TS5-scwrl costs 0 real_cost = -162.65 Bilab-ENABLE_TS5 costs 0 real_cost = -162.843 Bilab-ENABLE_TS4-scwrl costs 0 real_cost = -162.787 Bilab-ENABLE_TS4 costs 0 real_cost = -162.989 Bilab-ENABLE_TS3-scwrl costs 0 real_cost = -162.824 Bilab-ENABLE_TS3 costs 0 real_cost = -163.025 Bilab-ENABLE_TS2-scwrl costs 0 real_cost = -163.586 Bilab-ENABLE_TS2 costs 0 real_cost = -163.796 Bilab-ENABLE_TS1-scwrl costs 0 real_cost = -160.469 Bilab-ENABLE_TS1 costs 0 real_cost = -160.352 BayesHH_TS1-scwrl costs 0 real_cost = -75.704 BayesHH_TS1 costs 0 real_cost = -74.5809 ABIpro_TS5-scwrl costs 0 real_cost = 318.387 ABIpro_TS5 costs 0 real_cost = 318.547 ABIpro_TS4-scwrl costs 0 real_cost = 304.744 ABIpro_TS4 costs 0 real_cost = 306.62 ABIpro_TS3-scwrl costs 0 real_cost = 305.335 ABIpro_TS3 costs 0 real_cost = 305.661 ABIpro_TS2-scwrl costs 0 real_cost = 297.31 ABIpro_TS2 costs 0 real_cost = 296.626 ABIpro_TS1-scwrl costs 0 real_cost = 292.778 ABIpro_TS1 costs 0 real_cost = 292.793 3Dpro_TS5-scwrl costs 0 real_cost = 201.817 3Dpro_TS5 costs 0 real_cost = 210.96 3Dpro_TS4-scwrl costs 0 real_cost = -102.643 3Dpro_TS4 costs 0 real_cost = -106.371 3Dpro_TS3-scwrl costs 0 real_cost = -83.1567 3Dpro_TS3 costs 0 real_cost = -82.8627 3Dpro_TS2-scwrl costs 0 real_cost = -82.7035 3Dpro_TS2 costs 0 real_cost = -83.3232 3Dpro_TS1-scwrl costs 0 real_cost = -93.3366 3Dpro_TS1 costs 0 real_cost = -90.8262 3D-JIGSAW_TS1-scwrl costs 0 real_cost = 344.578 3D-JIGSAW_TS1 costs 0 real_cost = 342.303 3D-JIGSAW_RECOM_TS1-scwrl costs 0 real_cost = 344.578 3D-JIGSAW_RECOM_TS1 costs 0 real_cost = 342.303 3D-JIGSAW_POPULUS_TS5-scwrl costs 0 real_cost = 344.578 3D-JIGSAW_POPULUS_TS5 costs 0 real_cost = 342.303 3D-JIGSAW_POPULUS_TS4-scwrl costs 0 real_cost = 344.578 3D-JIGSAW_POPULUS_TS4 costs 0 real_cost = 342.303 3D-JIGSAW_POPULUS_TS3-scwrl costs 0 real_cost = 344.578 3D-JIGSAW_POPULUS_TS3 costs 0 real_cost = 342.303 3D-JIGSAW_POPULUS_TS2-scwrl costs 0 real_cost = 344.578 3D-JIGSAW_POPULUS_TS2 costs 0 real_cost = 342.303 3D-JIGSAW_POPULUS_TS1-scwrl costs 0 real_cost = 344.578 3D-JIGSAW_POPULUS_TS1 costs 0 real_cost = 342.303 dimer//dimer-try6-2ghrA costs 0 real_cost = -183.308 dimer//dimer-try4-2ghrA costs 0 real_cost = -119.925 dimer//dimer-try3-2ghrA costs 0 real_cost = -98.4953 dimer//dimer-try1-2ghrA costs 0 real_cost = -99.7849 dimer//dimer-chimera-try4-2ghrA costs 0 real_cost = -104.242 dimer//try5-opt2.unpack costs 0 real_cost = -182.672 dimer//try5-opt2.repack-nonPC costs 0 real_cost = -184.137 dimer//try5-opt2 costs 0 real_cost = -182.672 dimer//try5-opt2.gromacs0 costs 0 real_cost = -179.22 dimer//try5-opt1 costs 0 real_cost = -182.211 dimer//try5-opt1-scwrl costs 0 real_cost = -189.402 dimer//try4-opt2.unpack costs 0 real_cost = -169.648 dimer//try4-opt2.repack-nonPC costs 0 real_cost = -170.04 dimer//try4-opt2 costs 0 real_cost = -169.648 dimer//try4-opt2.gromacs0 costs 0 real_cost = -164.92 dimer//try4-opt1 costs 0 real_cost = -169.64 dimer//try4-opt1-scwrl costs 0 real_cost = -171.729 dimer//try3-opt2.unpack costs 0 real_cost = -169.684 dimer//try3-opt2.repack-nonPC costs 0 real_cost = -168.557 dimer//try3-opt2 costs 0 real_cost = -169.684 dimer//try3-opt2.gromacs0 costs 0 real_cost = -166.694 dimer//try3-opt1 costs 0 real_cost = -169.28 dimer//try3-opt1-scwrl costs 0 real_cost = -170.112 dimer//try2-opt2.unpack costs 0 real_cost = -94.3983 dimer//try2-opt2.repack-nonPC costs 0 real_cost = -94.8964 dimer//try2-opt2 costs 0 real_cost = -94.3983 dimer//try2-opt2.gromacs0 costs 0 real_cost = -93.7947 dimer//try2-opt1 costs 0 real_cost = -93.9981 dimer//try2-opt1-scwrl costs 0 real_cost = -94.0709 dimer//try1-opt2.unpack costs 0 real_cost = -118.653 dimer//try1-opt2.repack-nonPC costs 0 real_cost = -115.583 dimer//try1-opt2 costs 0 real_cost = -118.653 dimer//try1-opt2.gromacs0 costs 0 real_cost = -117.211 dimer//try1-opt1 costs 0 real_cost = -94.1728 dimer//try1-opt1-scwrl costs 0 real_cost = -93.4098 chimera-dimer2-try4.pdb.gz costs 0 real_cost = -104.419 T0326.try7-opt2.repack-nonPC.pdb.gz costs 0 real_cost = -176.042 T0326.try7-opt2.pdb.gz costs 0 real_cost = -176.359 T0326.try7-opt2.gromacs0.pdb.gz costs 0 real_cost = -175.051 T0326.try7-opt1.pdb.gz costs 0 real_cost = -176.472 T0326.try7-opt1-scwrl.pdb.gz costs 0 real_cost = -183.377 T0326.try6-opt2.repack-nonPC.pdb.gz costs 0 real_cost = -183.883 T0326.try6-opt2.pdb.gz costs 0 real_cost = -183.398 T0326.try6-opt2.gromacs0.pdb.gz costs 0 real_cost = -181.452 T0326.try6-opt1.pdb.gz costs 0 real_cost = -184.676 T0326.try6-opt1-scwrl.pdb.gz costs 0 real_cost = -191.214 T0326.try5-opt2.repack-nonPC.pdb.gz costs 0 real_cost = -178.6 T0326.try5-opt2.pdb.gz costs 0 real_cost = -183.635 T0326.try5-opt2.gromacs0.pdb.gz costs 0 real_cost = -179.359 T0326.try5-opt1.pdb.gz costs 0 real_cost = -183.475 T0326.try5-opt1-scwrl.pdb.gz costs 0 real_cost = -188.594 T0326.try4-opt2.repack-nonPC.pdb.gz costs 0 real_cost = -117.498 T0326.try4-opt2.pdb.gz costs 0 real_cost = -119.964 T0326.try4-opt2.gromacs0.pdb.gz costs 0 real_cost = -117.206 T0326.try4-opt1.pdb.gz costs 0 real_cost = -129.016 T0326.try4-opt1-scwrl.pdb.gz costs 0 real_cost = -133.005 T0326.try3-opt2.repack-nonPC.pdb.gz costs 0 real_cost = -99.4635 T0326.try3-opt2.pdb.gz costs 0 real_cost = -98.5865 T0326.try3-opt2.gromacs0.pdb.gz costs 0 real_cost = -97.2866 T0326.try3-opt1.pdb.gz costs 0 real_cost = -98.5632 T0326.try3-opt1-scwrl.pdb.gz costs 0 real_cost = -99.1554 T0326.try2-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 222.16 T0326.try2-opt2.pdb.gz costs 0 real_cost = 222.658 T0326.try2-opt2.gromacs0.pdb.gz costs 0 real_cost = 220.077 T0326.try2-opt1.pdb.gz costs 0 real_cost = 220.022 T0326.try2-opt1-scwrl.pdb.gz costs 0 real_cost = 221.968 T0326.try1-opt2.repack-nonPC.pdb.gz costs 0 real_cost = -101.093 T0326.try1-opt2.pdb.gz costs 0 real_cost = -99.9007 T0326.try1-opt2.gromacs0.pdb.gz costs 0 real_cost = -101.785 T0326.try1-opt1.pdb.gz costs 0 real_cost = -99.1252 T0326.try1-opt1-scwrl.pdb.gz costs 0 real_cost = -100.79 ../model5.ts-submitted costs 0 real_cost = -53.2758 ../model4.ts-submitted costs 0 real_cost = -99.9286 ../model3.ts-submitted costs 0 real_cost = -118.685 ../model2.ts-submitted costs 0 real_cost = -94.9939 ../model1.ts-submitted costs 0 real_cost = -182.49 align5 costs 0 real_cost = 381.757 align4 costs 0 real_cost = 346.076 align3 costs 0 real_cost = 381.917 align2 costs 0 real_cost = 420.093 align1 costs 0 real_cost = -60.3258 T0326.try1-opt2.pdb costs 0 real_cost = -99.9051 model5-scwrl costs 0 real_cost = -29.9046 model5.ts-submitted costs 0 real_cost = -53.2758 model4-scwrl costs 0 real_cost = -101.383 model4.ts-submitted costs 0 real_cost = -99.9286 model3-scwrl costs 0 real_cost = -119.195 model3.ts-submitted costs 0 real_cost = -118.685 model2-scwrl costs 0 real_cost = -95.855 model2.ts-submitted costs 0 real_cost = -94.9939 model1-scwrl costs 0 real_cost = -189.685 model1.ts-submitted costs 0 real_cost = -182.574 2h2wA costs 0 real_cost = -852.8 # command:CPU_time= 2479.1 sec, elapsed time= 3495.42 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