/projects/compbio/experiments/protein-predict/casp7/starter-directory/Make.main:725: SECONDARY_TARGET = T0305.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/T0305.} ;\ 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/T0305/ -e s/START_COL/1/ \ -e s/REAL_PDB/2h4vA/ \ -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 1174583692 # 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= 6.11407 sec, elapsed time= 8.82608 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= 6.19906 sec, elapsed time= 8.98705 sec) # command:# Prefix for input files set to # command:# Making conformation for sequence T0305 numbered 1 through 297 Created new target T0305 from T0305.a2m # command:# command:# No conformations to remove in PopConform # command:# cleared Id set # command:# command:2h4vA expands to /projects/compbio/data/pdb/2h4v.pdb.gz 2h4vA:Skipped atom 698, because occupancy 5.0000000e-01 <= existing 0.500 in 2h4vA Skipped atom 700, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 702, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 704, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 706, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 708, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 710, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 712, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 714, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 716, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 718, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 720, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 722, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 724, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 726, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 728, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 730, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 732, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 734, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 736, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 920, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 922, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 924, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 926, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 928, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 930, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 932, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 934, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 1113, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 1117, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 1119, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 1121, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 1123, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 1175, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 1179, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 1181, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 1183, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 1185, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 1187, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 1254, because occupancy 0.300 <= existing 0.700 in 2h4vA Skipped atom 1258, because occupancy 0.300 <= existing 0.700 in 2h4vA Skipped atom 1260, because occupancy 0.300 <= existing 0.700 in 2h4vA Skipped atom 1262, because occupancy 0.300 <= existing 0.700 in 2h4vA Skipped atom 1264, because occupancy 0.300 <= existing 0.700 in 2h4vA Skipped atom 1343, because occupancy 0.200 <= existing 0.800 in 2h4vA Skipped atom 1347, because occupancy 0.200 <= existing 0.800 in 2h4vA Skipped atom 1349, because occupancy 0.200 <= existing 0.800 in 2h4vA Skipped atom 1661, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 1665, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 1667, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 1669, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 1671, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 1727, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 1731, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 1733, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 1837, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 1841, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 1843, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 1960, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 1964, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 1966, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 1968, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 1970, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 1972, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 2008, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 2010, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 2012, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 2014, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 2016, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 2018, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 2020, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 2022, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 2024, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 2026, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 2028, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 2030, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 2032, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 2034, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 2036, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 2038, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 2040, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 2042, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 2044, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 2046, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 2294, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 2298, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 2300, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 2302, because occupancy 0.500 <= existing 0.500 in 2h4vA Skipped atom 2304, because occupancy 0.500 <= existing 0.500 in 2h4vA Read 278 residues and 2270 atoms. # WARNING: incomplete conformation T0305 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= 8.73767 sec, elapsed time= 11.9293 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 275 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -90.4676 # GDT_score(maxd=8,maxw=2.9)= -93.3264 # GDT_score(maxd=8,maxw=3.2)= -91.4793 # GDT_score(maxd=8,maxw=3.5)= -89.3218 # GDT_score(maxd=10,maxw=3.8)= -90.3288 # GDT_score(maxd=10,maxw=4)= -88.7634 # GDT_score(maxd=10,maxw=4.2)= -86.9598 # GDT_score(maxd=12,maxw=4.3)= -89.1393 # GDT_score(maxd=12,maxw=4.5)= -87.3701 # GDT_score(maxd=12,maxw=4.7)= -85.4628 # GDT_score(maxd=14,maxw=5.2)= -83.4124 # GDT_score(maxd=14,maxw=5.5)= -80.4246 # command:# Prefix for output files set to # command:superimposing iter= 0 total_weight= 3382.000 rmsd (weighted)= 2.422 (unweighted)= 15.604 superimposing iter= 1 total_weight= 13959.153 rmsd (weighted)= 0.821 (unweighted)= 15.608 superimposing iter= 2 total_weight= 5368.895 rmsd (weighted)= 0.519 (unweighted)= 15.614 superimposing iter= 3 total_weight= 2920.223 rmsd (weighted)= 0.453 (unweighted)= 15.618 superimposing iter= 4 total_weight= 2497.906 rmsd (weighted)= 0.428 (unweighted)= 15.622 superimposing iter= 5 total_weight= 2387.397 rmsd (weighted)= 0.415 (unweighted)= 15.625 # command:# Prefix for output files set to decoys/ # command:# request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_827852118.pdb -s /var/tmp/to_scwrl_827852118.seq -o /var/tmp/from_scwrl_827852118.pdb > /var/tmp/scwrl_827852118.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_827852118.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 275 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -87.1403 # GDT_score(maxd=8,maxw=2.9)= -89.0848 # GDT_score(maxd=8,maxw=3.2)= -87.0733 # GDT_score(maxd=8,maxw=3.5)= -84.7132 # GDT_score(maxd=10,maxw=3.8)= -86.1819 # GDT_score(maxd=10,maxw=4)= -84.3845 # GDT_score(maxd=10,maxw=4.2)= -82.433 # GDT_score(maxd=12,maxw=4.3)= -85.0063 # GDT_score(maxd=12,maxw=4.5)= -83.1135 # GDT_score(maxd=12,maxw=4.7)= -81.0798 # GDT_score(maxd=14,maxw=5.2)= -78.9971 # GDT_score(maxd=14,maxw=5.5)= -75.7128 # command:# request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1475095264.pdb -s /var/tmp/to_scwrl_1475095264.seq -o /var/tmp/from_scwrl_1475095264.pdb > /var/tmp/scwrl_1475095264.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1475095264.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 295 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -90.2878 # GDT_score(maxd=8,maxw=2.9)= -93.3846 # GDT_score(maxd=8,maxw=3.2)= -91.4917 # GDT_score(maxd=8,maxw=3.5)= -89.3993 # GDT_score(maxd=10,maxw=3.8)= -90.397 # GDT_score(maxd=10,maxw=4)= -88.8669 # GDT_score(maxd=10,maxw=4.2)= -87.0228 # GDT_score(maxd=12,maxw=4.3)= -89.2447 # GDT_score(maxd=12,maxw=4.5)= -87.4292 # GDT_score(maxd=12,maxw=4.7)= -85.4641 # GDT_score(maxd=14,maxw=5.2)= -83.4086 # GDT_score(maxd=14,maxw=5.5)= -80.4002 # command:# request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1489216859.pdb -s /var/tmp/to_scwrl_1489216859.seq -o /var/tmp/from_scwrl_1489216859.pdb > /var/tmp/scwrl_1489216859.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1489216859.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 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # command:# fraction of real conformation used = 0.92446 # GDT_score = -85.5216 # GDT_score(maxd=8,maxw=2.9)= -87.4855 # GDT_score(maxd=8,maxw=3.2)= -86.0479 # GDT_score(maxd=8,maxw=3.5)= -84.3146 # GDT_score(maxd=10,maxw=3.8)= -85.0597 # GDT_score(maxd=10,maxw=4)= -83.7895 # GDT_score(maxd=10,maxw=4.2)= -82.363 # GDT_score(maxd=12,maxw=4.3)= -84.0518 # GDT_score(maxd=12,maxw=4.5)= -82.6605 # GDT_score(maxd=12,maxw=4.7)= -81.1541 # GDT_score(maxd=14,maxw=5.2)= -79.5095 # GDT_score(maxd=14,maxw=5.5)= -77.0476 # command:# request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_888717523.pdb -s /var/tmp/to_scwrl_888717523.seq -o /var/tmp/from_scwrl_888717523.pdb > /var/tmp/scwrl_888717523.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_888717523.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 T0305 can't currently be optimized by undertaker # command:# fraction of real conformation used = 0.942446 # GDT_score = -81.4748 # GDT_score(maxd=8,maxw=2.9)= -83.3147 # GDT_score(maxd=8,maxw=3.2)= -81.3081 # GDT_score(maxd=8,maxw=3.5)= -79.2557 # GDT_score(maxd=10,maxw=3.8)= -80.6651 # GDT_score(maxd=10,maxw=4)= -79.2376 # GDT_score(maxd=10,maxw=4.2)= -77.6216 # GDT_score(maxd=12,maxw=4.3)= -79.8873 # GDT_score(maxd=12,maxw=4.5)= -78.3065 # GDT_score(maxd=12,maxw=4.7)= -76.6594 # GDT_score(maxd=14,maxw=5.2)= -75.1009 # GDT_score(maxd=14,maxw=5.5)= -72.4468 # command:# request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1046476407.pdb -s /var/tmp/to_scwrl_1046476407.seq -o /var/tmp/from_scwrl_1046476407.pdb > /var/tmp/scwrl_1046476407.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1046476407.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 T0305.try1-opt2.pdb looking for model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -87.5 # GDT_score(maxd=8,maxw=2.9)= -89.2827 # GDT_score(maxd=8,maxw=3.2)= -87.3849 # GDT_score(maxd=8,maxw=3.5)= -85.0464 # GDT_score(maxd=10,maxw=3.8)= -86.488 # GDT_score(maxd=10,maxw=4)= -84.7247 # GDT_score(maxd=10,maxw=4.2)= -82.7733 # GDT_score(maxd=12,maxw=4.3)= -85.3346 # GDT_score(maxd=12,maxw=4.5)= -83.42 # GDT_score(maxd=12,maxw=4.7)= -81.3838 # GDT_score(maxd=14,maxw=5.2)= -79.2883 # GDT_score(maxd=14,maxw=5.5)= -76.0718 # command:# Prefix for output files set to # command:superimposing iter= 0 total_weight= 3382.000 rmsd (weighted)= 2.486 (unweighted)= 15.911 superimposing iter= 1 total_weight= 12570.608 rmsd (weighted)= 0.873 (unweighted)= 15.889 superimposing iter= 2 total_weight= 5282.102 rmsd (weighted)= 0.560 (unweighted)= 15.890 superimposing iter= 3 total_weight= 2812.470 rmsd (weighted)= 0.499 (unweighted)= 15.892 superimposing iter= 4 total_weight= 2368.905 rmsd (weighted)= 0.485 (unweighted)= 15.893 superimposing iter= 5 total_weight= 2276.324 rmsd (weighted)= 0.481 (unweighted)= 15.895 # command:# Prefix for output files set to decoys/ # command:# Prefix for input files set to # command:# ReadConformPDB reading from PDB file T0305.undertaker-align.pdb looking for model 1 WARNING: atoms too close: (T0305)V30.C and (T0305)C33.C only 0.000 apart, marking (T0305)C33.C as missing WARNING: atoms too close: (T0305)Q31.N and (T0305)T34.N only 0.000 apart, marking (T0305)Q31.N as missing WARNING: atoms too close: (T0305)Q31.CA and (T0305)T34.CA only 0.000 apart, marking (T0305)Q31.CA as missing WARNING: atoms too close: (T0305)S76.C and (T0305)H78.C only 0.000 apart, marking (T0305)H78.C as missing WARNING: atoms too close: (T0305)K77.N and (T0305)S79.N only 0.000 apart, marking (T0305)K77.N as missing WARNING: atoms too close: (T0305)K77.CA and (T0305)S79.CA only 0.000 apart, marking (T0305)K77.CA as missing WARNING: atoms too close: (T0305)K175.C and (T0305)G186.C only 0.000 apart, marking (T0305)G186.C as missing WARNING: atoms too close: (T0305)V176.N and (T0305)R187.N only 0.000 apart, marking (T0305)V176.N as missing WARNING: atoms too close: (T0305)V176.CA and (T0305)R187.CA only 0.000 apart, marking (T0305)V176.CA as missing # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # command:# naming current conformation align1 # command:# fraction of real conformation used = 0.956835 # GDT_score = -88.3993 # GDT_score(maxd=8,maxw=2.9)= -90.5553 # GDT_score(maxd=8,maxw=3.2)= -89.0133 # GDT_score(maxd=8,maxw=3.5)= -87.1741 # GDT_score(maxd=10,maxw=3.8)= -87.9578 # GDT_score(maxd=10,maxw=4)= -86.6221 # GDT_score(maxd=10,maxw=4.2)= -85.1387 # GDT_score(maxd=12,maxw=4.3)= -86.9022 # GDT_score(maxd=12,maxw=4.5)= -85.4533 # GDT_score(maxd=12,maxw=4.7)= -83.8754 # GDT_score(maxd=14,maxw=5.2)= -82.1633 # GDT_score(maxd=14,maxw=5.5)= -79.5969 # command:# ReadConformPDB reading from PDB file T0305.undertaker-align.pdb looking for model 2 WARNING: atoms too close: (T0305)Q20.C and (T0305)G22.C only 0.000 apart, marking (T0305)G22.C as missing WARNING: atoms too close: (T0305)H21.N and (T0305)F23.N only 0.000 apart, marking (T0305)H21.N as missing WARNING: atoms too close: (T0305)H21.CA and (T0305)F23.CA only 0.000 apart, marking (T0305)H21.CA as missing WARNING: atoms too close: (T0305)T34.C and (T0305)D36.C only 0.000 apart, marking (T0305)D36.C as missing WARNING: atoms too close: (T0305)A35.N and (T0305)M37.N only 0.000 apart, marking (T0305)A35.N as missing WARNING: atoms too close: (T0305)A35.CA and (T0305)M37.CA only 0.000 apart, marking (T0305)A35.CA as missing WARNING: atoms too close: (T0305)K175.C and (T0305)G186.C only 0.000 apart, marking (T0305)G186.C as missing WARNING: atoms too close: (T0305)V176.N and (T0305)R187.N only 0.000 apart, marking (T0305)V176.N as missing WARNING: atoms too close: (T0305)V176.CA and (T0305)R187.CA only 0.000 apart, marking (T0305)V176.CA as missing # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # command:# naming current conformation align2 # command:# fraction of real conformation used = 0.956835 # GDT_score = -82.3741 # GDT_score(maxd=8,maxw=2.9)= -84.2238 # GDT_score(maxd=8,maxw=3.2)= -82.1899 # GDT_score(maxd=8,maxw=3.5)= -80.0921 # GDT_score(maxd=10,maxw=3.8)= -81.5548 # GDT_score(maxd=10,maxw=4)= -80.0998 # GDT_score(maxd=10,maxw=4.2)= -78.4618 # GDT_score(maxd=12,maxw=4.3)= -80.781 # GDT_score(maxd=12,maxw=4.5)= -79.1765 # GDT_score(maxd=12,maxw=4.7)= -77.5121 # GDT_score(maxd=14,maxw=5.2)= -75.976 # GDT_score(maxd=14,maxw=5.5)= -73.2947 # command:# ReadConformPDB reading from PDB file T0305.undertaker-align.pdb looking for model 3 WARNING: atoms too close: (T0305)A35.C and (T0305)M37.C only 0.000 apart, marking (T0305)M37.C as missing WARNING: atoms too close: (T0305)D36.N and (T0305)N38.N only 0.000 apart, marking (T0305)D36.N as missing WARNING: atoms too close: (T0305)D36.CA and (T0305)N38.CA only 0.000 apart, marking (T0305)D36.CA as missing WARNING: atoms too close: (T0305)K175.C and (T0305)G186.C only 0.000 apart, marking (T0305)G186.C as missing WARNING: atoms too close: (T0305)V176.N and (T0305)R187.N only 0.000 apart, marking (T0305)V176.N as missing WARNING: atoms too close: (T0305)V176.CA and (T0305)R187.CA only 0.000 apart, marking (T0305)V176.CA as missing # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # command:# naming current conformation align3 # command:# ReadConformPDB reading from PDB file T0305.undertaker-align.pdb looking for model 4 WARNING: atoms too close: (T0305)R69.C and (T0305)S76.C only 0.000 apart, marking (T0305)S76.C as missing WARNING: atoms too close: (T0305)P70.N and (T0305)K77.N only 0.000 apart, marking (T0305)P70.N as missing WARNING: atoms too close: (T0305)P70.CA and (T0305)K77.CA only 0.000 apart, marking (T0305)P70.CA as missing WARNING: atoms too close: (T0305)N173.C and (T0305)P184.C only 0.000 apart, marking (T0305)P184.C as missing WARNING: atoms too close: (T0305)T174.N and (T0305)K185.N only 0.000 apart, marking (T0305)T174.N as missing WARNING: atoms too close: (T0305)T174.CA and (T0305)K185.CA only 0.000 apart, marking (T0305)T174.CA as missing WARNING: atoms too close: (T0305)A222.C and (T0305)A223.C only 0.000 apart, marking (T0305)A223.C as missing WARNING: atoms too close: (T0305)A223.N and (T0305)R224.N only 0.000 apart, marking (T0305)A223.N as missing WARNING: atoms too close: (T0305)A223.CA and (T0305)R224.CA only 0.000 apart, marking (T0305)A223.CA as missing # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # command:# naming current conformation align4 # command:# ReadConformPDB reading from PDB file T0305.undertaker-align.pdb looking for model 5 WARNING: atoms too close: (T0305)R69.C and (T0305)P72.C only 0.000 apart, marking (T0305)P72.C as missing WARNING: atoms too close: (T0305)P70.N and (T0305)G73.N only 0.000 apart, marking (T0305)P70.N as missing WARNING: atoms too close: (T0305)P70.CA and (T0305)G73.CA only 0.000 apart, marking (T0305)P70.CA as missing WARNING: atoms too close: (T0305)N173.C and (T0305)P184.C only 0.000 apart, marking (T0305)P184.C as missing WARNING: atoms too close: (T0305)T174.N and (T0305)K185.N only 0.000 apart, marking (T0305)T174.N as missing WARNING: atoms too close: (T0305)T174.CA and (T0305)K185.CA only 0.000 apart, marking (T0305)T174.CA as missing # WARNING: incomplete conformation T0305 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 275 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ../model2.ts-submitted looking for model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ../model3.ts-submitted looking for model 1 # Found a chain break before 295 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ../model4.ts-submitted looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # ReadConformPDB reading from PDB file ../model5.ts-submitted looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # ReadConformPDB reading from PDB file T0305.try1-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 276 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0305.try1-opt1.pdb.gz looking for model 1 # Found a chain break before 276 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0305.try1-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0305.try1-opt2.pdb.gz looking for model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0305.try1-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0305.try2-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0305.try2-opt1.pdb.gz looking for model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0305.try2-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 296 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0305.try2-opt2.pdb.gz looking for model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0305.try2-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0305.try3-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 295 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0305.try3-opt1.pdb.gz looking for model 1 # Found a chain break before 295 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0305.try3-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 277 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0305.try3-opt2.pdb.gz looking for model 1 # Found a chain break before 295 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0305.try3-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 295 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0305.try4-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0305.try4-opt1.pdb.gz looking for model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0305.try4-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 277 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0305.try4-opt2.pdb.gz looking for model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0305.try4-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ../dimer/decoys/T0305.try1-opt1-scwrl.pdb.gz looking for chain 'A' model 1 # Found a chain break before 273 # copying to AlignedFragments data structure # naming current conformation dimer//try1-opt1-scwrl # ReadConformPDB reading from PDB file ../dimer/decoys/T0305.try1-opt1.pdb.gz looking for chain 'A' model 1 # Found a chain break before 273 # copying to AlignedFragments data structure # naming current conformation dimer//try1-opt1 # ReadConformPDB reading from PDB file ../dimer/decoys/T0305.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/T0305.try1-opt2.pdb.gz looking for chain 'A' model 1 # Found a chain break before 273 # copying to AlignedFragments data structure # naming current conformation dimer//try1-opt2 # ReadConformPDB reading from PDB file ../dimer/decoys/T0305.try1-opt2.repack-nonPC.pdb.gz looking for chain 'A' model 1 # Found a chain break before 273 # copying to AlignedFragments data structure # naming current conformation dimer//try1-opt2.repack-nonPC # ReadConformPDB reading from PDB file ../dimer/decoys/T0305.try1-opt2.unpack.pdb.gz looking for chain 'A' model 1 # Found a chain break before 273 # copying to AlignedFragments data structure # naming current conformation dimer//try1-opt2.unpack # ReadConformPDB reading from PDB file ../dimer/decoys/T0305.try2-opt1-scwrl.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation dimer//try2-opt1-scwrl # ReadConformPDB reading from PDB file ../dimer/decoys/T0305.try2-opt1.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation dimer//try2-opt1 # ReadConformPDB reading from PDB file ../dimer/decoys/T0305.try2-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//try2-opt2.gromacs0 # ReadConformPDB reading from PDB file ../dimer/decoys/T0305.try2-opt2.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation dimer//try2-opt2 # ReadConformPDB reading from PDB file ../dimer/decoys/T0305.try2-opt2.repack-nonPC.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation dimer//try2-opt2.repack-nonPC # ReadConformPDB reading from PDB file ../dimer/decoys/T0305.try2-opt2.unpack.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation dimer//try2-opt2.unpack # ReadConformPDB reading from PDB file ../dimer/decoys/dimer-try4-1rpmA.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation dimer//dimer-try4-1rpmA # ReadConformPDB reading from PDB file ../dimer/decoys/dimer-try4-1rpmA.unpack.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation dimer//dimer-try4-1rpmA.unpack # ReadConformPDB reading from PDB file ../dimer/decoys/dimer-try4-2fh7A.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation dimer//dimer-try4-2fh7A # ReadConformPDB reading from PDB file ../dimer/decoys/from-tetramer-try1-opt2.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation dimer//from-tetramer-try1-opt2 # ReadConformPDB reading from PDB file ../dimer/decoys/from-tetramer-try1-opt2.unpack.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation dimer//from-tetramer-try1-opt2.unpack # ReadConformPDB reading from PDB file ../dimer/decoys/from-tetramer-try4-1larA.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation dimer//from-tetramer-try4-1larA # ReadConformPDB reading from PDB file ../dimer/decoys/from-tetramer-try4-1larA.unpack.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation dimer//from-tetramer-try4-1larA.unpack # ReadConformPDB reading from PDB file ../tetramer/decoys/T0305.try1-opt1-scwrl.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation tetramer//try1-opt1-scwrl # ReadConformPDB reading from PDB file ../tetramer/decoys/T0305.try1-opt1.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation tetramer//try1-opt1 # ReadConformPDB reading from PDB file ../tetramer/decoys/T0305.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 tetramer//try1-opt2.gromacs0 # ReadConformPDB reading from PDB file ../tetramer/decoys/T0305.try1-opt2.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation tetramer//try1-opt2 # ReadConformPDB reading from PDB file ../tetramer/decoys/T0305.try2-opt1-scwrl.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation tetramer//try2-opt1-scwrl # ReadConformPDB reading from PDB file ../tetramer/decoys/T0305.try2-opt1.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation tetramer//try2-opt1 # ReadConformPDB reading from PDB file ../tetramer/decoys/T0305.try2-opt2.gromacs0.pdb.gz looking for chain 'A' model 1 Faking rotamer for incomplete or colinear backbone at (T0305)G297 # Found a chain break before 296 # copying to AlignedFragments data structure # naming current conformation tetramer//try2-opt2.gromacs0 # ReadConformPDB reading from PDB file ../tetramer/decoys/T0305.try2-opt2.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation tetramer//try2-opt2 # ReadConformPDB reading from PDB file ../tetramer/decoys/T0305.try3-opt1-scwrl.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation tetramer//try3-opt1-scwrl # ReadConformPDB reading from PDB file ../tetramer/decoys/T0305.try3-opt1.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation tetramer//try3-opt1 # ReadConformPDB reading from PDB file ../tetramer/decoys/T0305.try3-opt2.gromacs0.pdb.gz looking for chain 'A' model 1 # Found a chain break before 296 # copying to AlignedFragments data structure # naming current conformation tetramer//try3-opt2.gromacs0 # ReadConformPDB reading from PDB file ../tetramer/decoys/T0305.try3-opt2.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation tetramer//try3-opt2 # ReadConformPDB reading from PDB file ../tetramer/decoys/T0305.try4-opt1-scwrl.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation tetramer//try4-opt1-scwrl # ReadConformPDB reading from PDB file ../tetramer/decoys/T0305.try4-opt1.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation tetramer//try4-opt1 # ReadConformPDB reading from PDB file ../tetramer/decoys/T0305.try4-opt2.gromacs0.pdb.gz looking for chain 'A' model 1 # Found a chain break before 296 # copying to AlignedFragments data structure # naming current conformation tetramer//try4-opt2.gromacs0 # ReadConformPDB reading from PDB file ../tetramer/decoys/T0305.try4-opt2.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation tetramer//try4-opt2 # ReadConformPDB reading from PDB file ../tetramer/decoys/tetramer-try4-1larA.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation tetramer//tetramer-try4-1larA # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_2126810609.pdb -s /var/tmp/to_scwrl_2126810609.seq -o /var/tmp/from_scwrl_2126810609.pdb > /var/tmp/scwrl_2126810609.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2126810609.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 T0305 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_239284447.pdb -s /var/tmp/to_scwrl_239284447.seq -o /var/tmp/from_scwrl_239284447.pdb > /var/tmp/scwrl_239284447.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_239284447.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 T0305 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_2107176518.pdb -s /var/tmp/to_scwrl_2107176518.seq -o /var/tmp/from_scwrl_2107176518.pdb > /var/tmp/scwrl_2107176518.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2107176518.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 T0305 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_138526348.pdb -s /var/tmp/to_scwrl_138526348.seq -o /var/tmp/from_scwrl_138526348.pdb > /var/tmp/scwrl_138526348.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_138526348.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 T0305 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_2134136188.pdb -s /var/tmp/to_scwrl_2134136188.seq -o /var/tmp/from_scwrl_2134136188.pdb > /var/tmp/scwrl_2134136188.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2134136188.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 T0305 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1879157781.pdb -s /var/tmp/to_scwrl_1879157781.seq -o /var/tmp/from_scwrl_1879157781.pdb > /var/tmp/scwrl_1879157781.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1879157781.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_RECOM_TS1-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_2007600793.pdb -s /var/tmp/to_scwrl_2007600793.seq -o /var/tmp/from_scwrl_2007600793.pdb > /var/tmp/scwrl_2007600793.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2007600793.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_RECOM_TS2-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_473512713.pdb -s /var/tmp/to_scwrl_473512713.seq -o /var/tmp/from_scwrl_473512713.pdb > /var/tmp/scwrl_473512713.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_473512713.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_RECOM_TS3-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1444178654.pdb -s /var/tmp/to_scwrl_1444178654.seq -o /var/tmp/from_scwrl_1444178654.pdb > /var/tmp/scwrl_1444178654.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1444178654.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_RECOM_TS4-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1694572576.pdb -s /var/tmp/to_scwrl_1694572576.seq -o /var/tmp/from_scwrl_1694572576.pdb > /var/tmp/scwrl_1694572576.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1694572576.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_RECOM_TS5-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1073404967.pdb -s /var/tmp/to_scwrl_1073404967.seq -o /var/tmp/from_scwrl_1073404967.pdb > /var/tmp/scwrl_1073404967.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1073404967.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_TS1-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1681207192.pdb -s /var/tmp/to_scwrl_1681207192.seq -o /var/tmp/from_scwrl_1681207192.pdb > /var/tmp/scwrl_1681207192.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1681207192.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_TS2-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_563613411.pdb -s /var/tmp/to_scwrl_563613411.seq -o /var/tmp/from_scwrl_563613411.pdb > /var/tmp/scwrl_563613411.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_563613411.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_TS3-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_659625520.pdb -s /var/tmp/to_scwrl_659625520.seq -o /var/tmp/from_scwrl_659625520.pdb > /var/tmp/scwrl_659625520.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_659625520.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_TS4-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_948491097.pdb -s /var/tmp/to_scwrl_948491097.seq -o /var/tmp/from_scwrl_948491097.pdb > /var/tmp/scwrl_948491097.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_948491097.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_TS5-scwrl # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # Found a chain break before 278 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1864060488.pdb -s /var/tmp/to_scwrl_1864060488.seq -o /var/tmp/from_scwrl_1864060488.pdb > /var/tmp/scwrl_1864060488.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1864060488.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 289 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1822798179.pdb -s /var/tmp/to_scwrl_1822798179.seq -o /var/tmp/from_scwrl_1822798179.pdb > /var/tmp/scwrl_1822798179.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1822798179.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 290 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1374767831.pdb -s /var/tmp/to_scwrl_1374767831.seq -o /var/tmp/from_scwrl_1374767831.pdb > /var/tmp/scwrl_1374767831.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1374767831.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 290 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_96742264.pdb -s /var/tmp/to_scwrl_96742264.seq -o /var/tmp/from_scwrl_96742264.pdb > /var/tmp/scwrl_96742264.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_96742264.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 276 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1871185473.pdb -s /var/tmp/to_scwrl_1871185473.seq -o /var/tmp/from_scwrl_1871185473.pdb > /var/tmp/scwrl_1871185473.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1871185473.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 292 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_2057138589.pdb -s /var/tmp/to_scwrl_2057138589.seq -o /var/tmp/from_scwrl_2057138589.pdb > /var/tmp/scwrl_2057138589.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2057138589.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 281 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_885479382.pdb -s /var/tmp/to_scwrl_885479382.seq -o /var/tmp/from_scwrl_885479382.pdb > /var/tmp/scwrl_885479382.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_885479382.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 292 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1480906006.pdb -s /var/tmp/to_scwrl_1480906006.seq -o /var/tmp/from_scwrl_1480906006.pdb > /var/tmp/scwrl_1480906006.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1480906006.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 266 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_193839549.pdb -s /var/tmp/to_scwrl_193839549.seq -o /var/tmp/from_scwrl_193839549.pdb > /var/tmp/scwrl_193839549.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_193839549.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 290 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_361584446.pdb -s /var/tmp/to_scwrl_361584446.seq -o /var/tmp/from_scwrl_361584446.pdb > /var/tmp/scwrl_361584446.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_361584446.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 278 # copying to AlignedFragments data structure # naming current conformation BayesHH_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1690229500.pdb -s /var/tmp/to_scwrl_1690229500.seq -o /var/tmp/from_scwrl_1690229500.pdb > /var/tmp/scwrl_1690229500.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1690229500.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 279 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1021691667.pdb -s /var/tmp/to_scwrl_1021691667.seq -o /var/tmp/from_scwrl_1021691667.pdb > /var/tmp/scwrl_1021691667.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1021691667.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 279 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1836679710.pdb -s /var/tmp/to_scwrl_1836679710.seq -o /var/tmp/from_scwrl_1836679710.pdb > /var/tmp/scwrl_1836679710.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1836679710.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 278 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1031962714.pdb -s /var/tmp/to_scwrl_1031962714.seq -o /var/tmp/from_scwrl_1031962714.pdb > /var/tmp/scwrl_1031962714.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1031962714.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 278 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1910409189.pdb -s /var/tmp/to_scwrl_1910409189.seq -o /var/tmp/from_scwrl_1910409189.pdb > /var/tmp/scwrl_1910409189.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1910409189.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 294 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_735672471.pdb -s /var/tmp/to_scwrl_735672471.seq -o /var/tmp/from_scwrl_735672471.pdb > /var/tmp/scwrl_735672471.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_735672471.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 294 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1011289676.pdb -s /var/tmp/to_scwrl_1011289676.seq -o /var/tmp/from_scwrl_1011289676.pdb > /var/tmp/scwrl_1011289676.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1011289676.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 T0305 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_2209989.pdb -s /var/tmp/to_scwrl_2209989.seq -o /var/tmp/from_scwrl_2209989.pdb > /var/tmp/scwrl_2209989.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2209989.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 # Found a chain break before 294 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_695365342.pdb -s /var/tmp/to_scwrl_695365342.seq -o /var/tmp/from_scwrl_695365342.pdb > /var/tmp/scwrl_695365342.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_695365342.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 T0305 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1149816023.pdb -s /var/tmp/to_scwrl_1149816023.seq -o /var/tmp/from_scwrl_1149816023.pdb > /var/tmp/scwrl_1149816023.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1149816023.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 T0305 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_2136346177.pdb -s /var/tmp/to_scwrl_2136346177.seq -o /var/tmp/from_scwrl_2136346177.pdb > /var/tmp/scwrl_2136346177.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2136346177.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 T0305 can't currently be optimized by undertaker # naming current conformation CPHmodels_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_427039476.pdb -s /var/tmp/to_scwrl_427039476.seq -o /var/tmp/from_scwrl_427039476.pdb > /var/tmp/scwrl_427039476.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_427039476.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 T0305 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1009933170.pdb -s /var/tmp/to_scwrl_1009933170.seq -o /var/tmp/from_scwrl_1009933170.pdb > /var/tmp/scwrl_1009933170.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1009933170.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 T0305 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_462375243.pdb -s /var/tmp/to_scwrl_462375243.seq -o /var/tmp/from_scwrl_462375243.pdb > /var/tmp/scwrl_462375243.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_462375243.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 T0305 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1871218130.pdb -s /var/tmp/to_scwrl_1871218130.seq -o /var/tmp/from_scwrl_1871218130.pdb > /var/tmp/scwrl_1871218130.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1871218130.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 T0305 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_557022100.pdb -s /var/tmp/to_scwrl_557022100.seq -o /var/tmp/from_scwrl_557022100.pdb > /var/tmp/scwrl_557022100.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_557022100.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 T0305 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1535780209.pdb -s /var/tmp/to_scwrl_1535780209.seq -o /var/tmp/from_scwrl_1535780209.pdb > /var/tmp/scwrl_1535780209.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1535780209.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 T0305 can't currently be optimized by undertaker # naming current conformation Distill_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1404941675.pdb -s /var/tmp/to_scwrl_1404941675.seq -o /var/tmp/from_scwrl_1404941675.pdb > /var/tmp/scwrl_1404941675.log Error: Couldn't open file /var/tmp/from_scwrl_1404941675.pdb or /var/tmp/from_scwrl_1404941675.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1404941675_b.pdb or decoys//var/tmp/from_scwrl_1404941675_b.pdb.gz for input Trying /var/tmp/from_scwrl_1404941675_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_1404941675_b.pdb or /var/tmp/from_scwrl_1404941675_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1404941675_a.pdb or decoys//var/tmp/from_scwrl_1404941675_a.pdb.gz for input Trying /var/tmp/from_scwrl_1404941675_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_1404941675_a.pdb or /var/tmp/from_scwrl_1404941675_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_1404941675.pdb or /var/tmp/from_scwrl_1404941675_b.pdb or /var/tmp/from_scwrl_1404941675_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 T0305 can't currently be optimized by undertaker # naming current conformation Distill_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1120635510.pdb -s /var/tmp/to_scwrl_1120635510.seq -o /var/tmp/from_scwrl_1120635510.pdb > /var/tmp/scwrl_1120635510.log Error: Couldn't open file /var/tmp/from_scwrl_1120635510.pdb or /var/tmp/from_scwrl_1120635510.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1120635510_b.pdb or decoys//var/tmp/from_scwrl_1120635510_b.pdb.gz for input Trying /var/tmp/from_scwrl_1120635510_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_1120635510_b.pdb or /var/tmp/from_scwrl_1120635510_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1120635510_a.pdb or decoys//var/tmp/from_scwrl_1120635510_a.pdb.gz for input Trying /var/tmp/from_scwrl_1120635510_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_1120635510_a.pdb or /var/tmp/from_scwrl_1120635510_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_1120635510.pdb or /var/tmp/from_scwrl_1120635510_b.pdb or /var/tmp/from_scwrl_1120635510_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 T0305 can't currently be optimized by undertaker # naming current conformation Distill_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_47922082.pdb -s /var/tmp/to_scwrl_47922082.seq -o /var/tmp/from_scwrl_47922082.pdb > /var/tmp/scwrl_47922082.log Error: Couldn't open file /var/tmp/from_scwrl_47922082.pdb or /var/tmp/from_scwrl_47922082.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_47922082_b.pdb or decoys//var/tmp/from_scwrl_47922082_b.pdb.gz for input Trying /var/tmp/from_scwrl_47922082_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_47922082_b.pdb or /var/tmp/from_scwrl_47922082_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_47922082_a.pdb or decoys//var/tmp/from_scwrl_47922082_a.pdb.gz for input Trying /var/tmp/from_scwrl_47922082_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_47922082_a.pdb or /var/tmp/from_scwrl_47922082_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_47922082.pdb or /var/tmp/from_scwrl_47922082_b.pdb or /var/tmp/from_scwrl_47922082_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 T0305 can't currently be optimized by undertaker # naming current conformation Distill_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_205949125.pdb -s /var/tmp/to_scwrl_205949125.seq -o /var/tmp/from_scwrl_205949125.pdb > /var/tmp/scwrl_205949125.log Error: Couldn't open file /var/tmp/from_scwrl_205949125.pdb or /var/tmp/from_scwrl_205949125.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_205949125_b.pdb or decoys//var/tmp/from_scwrl_205949125_b.pdb.gz for input Trying /var/tmp/from_scwrl_205949125_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_205949125_b.pdb or /var/tmp/from_scwrl_205949125_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_205949125_a.pdb or decoys//var/tmp/from_scwrl_205949125_a.pdb.gz for input Trying /var/tmp/from_scwrl_205949125_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_205949125_a.pdb or /var/tmp/from_scwrl_205949125_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_205949125.pdb or /var/tmp/from_scwrl_205949125_b.pdb or /var/tmp/from_scwrl_205949125_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 T0305 can't currently be optimized by undertaker # naming current conformation Distill_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_837212352.pdb -s /var/tmp/to_scwrl_837212352.seq -o /var/tmp/from_scwrl_837212352.pdb > /var/tmp/scwrl_837212352.log Error: Couldn't open file /var/tmp/from_scwrl_837212352.pdb or /var/tmp/from_scwrl_837212352.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_837212352_b.pdb or decoys//var/tmp/from_scwrl_837212352_b.pdb.gz for input Trying /var/tmp/from_scwrl_837212352_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_837212352_b.pdb or /var/tmp/from_scwrl_837212352_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_837212352_a.pdb or decoys//var/tmp/from_scwrl_837212352_a.pdb.gz for input Trying /var/tmp/from_scwrl_837212352_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_837212352_a.pdb or /var/tmp/from_scwrl_837212352_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_837212352.pdb or /var/tmp/from_scwrl_837212352_b.pdb or /var/tmp/from_scwrl_837212352_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 # Found a chain break before 277 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1870720261.pdb -s /var/tmp/to_scwrl_1870720261.seq -o /var/tmp/from_scwrl_1870720261.pdb > /var/tmp/scwrl_1870720261.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1870720261.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 T0305 can't currently be optimized by undertaker # naming current conformation FAMSD_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1580716956.pdb -s /var/tmp/to_scwrl_1580716956.seq -o /var/tmp/from_scwrl_1580716956.pdb > /var/tmp/scwrl_1580716956.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1580716956.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 # Found a chain break before 289 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_933954617.pdb -s /var/tmp/to_scwrl_933954617.seq -o /var/tmp/from_scwrl_933954617.pdb > /var/tmp/scwrl_933954617.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_933954617.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 T0305 can't currently be optimized by undertaker # naming current conformation FAMSD_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1594422088.pdb -s /var/tmp/to_scwrl_1594422088.seq -o /var/tmp/from_scwrl_1594422088.pdb > /var/tmp/scwrl_1594422088.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1594422088.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 T0305 can't currently be optimized by undertaker # naming current conformation FAMSD_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1490371899.pdb -s /var/tmp/to_scwrl_1490371899.seq -o /var/tmp/from_scwrl_1490371899.pdb > /var/tmp/scwrl_1490371899.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1490371899.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 291 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1819433998.pdb -s /var/tmp/to_scwrl_1819433998.seq -o /var/tmp/from_scwrl_1819433998.pdb > /var/tmp/scwrl_1819433998.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1819433998.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 # Found a chain break before 295 # copying to AlignedFragments data structure # naming current conformation FAMS_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_927844448.pdb -s /var/tmp/to_scwrl_927844448.seq -o /var/tmp/from_scwrl_927844448.pdb > /var/tmp/scwrl_927844448.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_927844448.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 T0305 can't currently be optimized by undertaker # naming current conformation FAMS_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1684211448.pdb -s /var/tmp/to_scwrl_1684211448.seq -o /var/tmp/from_scwrl_1684211448.pdb > /var/tmp/scwrl_1684211448.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1684211448.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 292 # copying to AlignedFragments data structure # naming current conformation FAMS_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_33534797.pdb -s /var/tmp/to_scwrl_33534797.seq -o /var/tmp/from_scwrl_33534797.pdb > /var/tmp/scwrl_33534797.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_33534797.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 # Found a chain break before 294 # copying to AlignedFragments data structure # naming current conformation FAMS_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_470590302.pdb -s /var/tmp/to_scwrl_470590302.seq -o /var/tmp/from_scwrl_470590302.pdb > /var/tmp/scwrl_470590302.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_470590302.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 275 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_558419468.pdb -s /var/tmp/to_scwrl_558419468.seq -o /var/tmp/from_scwrl_558419468.pdb > /var/tmp/scwrl_558419468.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_558419468.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 279 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1870214508.pdb -s /var/tmp/to_scwrl_1870214508.seq -o /var/tmp/from_scwrl_1870214508.pdb > /var/tmp/scwrl_1870214508.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1870214508.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 266 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1502553015.pdb -s /var/tmp/to_scwrl_1502553015.seq -o /var/tmp/from_scwrl_1502553015.pdb > /var/tmp/scwrl_1502553015.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1502553015.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 265 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_321345011.pdb -s /var/tmp/to_scwrl_321345011.seq -o /var/tmp/from_scwrl_321345011.pdb > /var/tmp/scwrl_321345011.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_321345011.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 273 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_458403332.pdb -s /var/tmp/to_scwrl_458403332.seq -o /var/tmp/from_scwrl_458403332.pdb > /var/tmp/scwrl_458403332.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_458403332.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 T0305 can't currently be optimized by undertaker # naming current conformation FORTE1_AL1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_366359044.pdb -s /var/tmp/to_scwrl_366359044.seq -o /var/tmp/from_scwrl_366359044.pdb > /var/tmp/scwrl_366359044.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_366359044.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 T0305 can't currently be optimized by undertaker # naming current conformation FORTE1_AL2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_323555000.pdb -s /var/tmp/to_scwrl_323555000.seq -o /var/tmp/from_scwrl_323555000.pdb > /var/tmp/scwrl_323555000.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_323555000.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 Skipped atom 26, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 28, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 30, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 32, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 210, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 212, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 214, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 216, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 262, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 264, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 266, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 268, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 270, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 272, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 274, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 276, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 278, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 280, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 282, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 284, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 286, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 288, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 290, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 292, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 386, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 388, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 390, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 392, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 462, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 464, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 466, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 468, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 518, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 520, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 522, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 524, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 526, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 528, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 530, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 532, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 666, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 668, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 670, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 672, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 678, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 680, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 682, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 684, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 754, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 756, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 758, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 760, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 762, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 764, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 766, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 768, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 770, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 772, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 774, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 776, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 778, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 780, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 782, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 784, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 786, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 788, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 790, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 792, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 794, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 796, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 798, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 800, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 802, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 804, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 806, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 808, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 810, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 812, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 814, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 816, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 818, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 820, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 822, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 824, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 826, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 828, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 830, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 832, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 834, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 836, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 838, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 840, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 842, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 844, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 846, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 848, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 854, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 856, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 858, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 860, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 954, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 956, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 958, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 960, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 978, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 980, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 982, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 984, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1002, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1004, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1006, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1008, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1074, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1076, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1078, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1080, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1106, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1107, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1109, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1110, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1112, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1113, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1115, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1116, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation FORTE1_AL3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1153768673.pdb -s /var/tmp/to_scwrl_1153768673.seq -o /var/tmp/from_scwrl_1153768673.pdb > /var/tmp/scwrl_1153768673.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1153768673.pdb # conformation set from SCWRL output # naming current conformation FORTE1_AL3-scwrl # ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation FORTE1_AL4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1516175067.pdb -s /var/tmp/to_scwrl_1516175067.seq -o /var/tmp/from_scwrl_1516175067.pdb > /var/tmp/scwrl_1516175067.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1516175067.pdb # conformation set from SCWRL output # naming current conformation FORTE1_AL4-scwrl # ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation FORTE1_AL5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_312417531.pdb -s /var/tmp/to_scwrl_312417531.seq -o /var/tmp/from_scwrl_312417531.pdb > /var/tmp/scwrl_312417531.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_312417531.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 T0305 can't currently be optimized by undertaker # naming current conformation FORTE2_AL1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1580808149.pdb -s /var/tmp/to_scwrl_1580808149.seq -o /var/tmp/from_scwrl_1580808149.pdb > /var/tmp/scwrl_1580808149.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1580808149.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 T0305 can't currently be optimized by undertaker # naming current conformation FORTE2_AL2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_378624591.pdb -s /var/tmp/to_scwrl_378624591.seq -o /var/tmp/from_scwrl_378624591.pdb > /var/tmp/scwrl_378624591.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_378624591.pdb # conformation set from SCWRL output # naming current conformation FORTE2_AL2-scwrl # ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation FORTE2_AL3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_774792774.pdb -s /var/tmp/to_scwrl_774792774.seq -o /var/tmp/from_scwrl_774792774.pdb > /var/tmp/scwrl_774792774.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_774792774.pdb # conformation set from SCWRL output # naming current conformation FORTE2_AL3-scwrl # ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation FORTE2_AL4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1304542632.pdb -s /var/tmp/to_scwrl_1304542632.seq -o /var/tmp/from_scwrl_1304542632.pdb > /var/tmp/scwrl_1304542632.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1304542632.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 T0305 can't currently be optimized by undertaker # naming current conformation FORTE2_AL5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_935646691.pdb -s /var/tmp/to_scwrl_935646691.seq -o /var/tmp/from_scwrl_935646691.pdb > /var/tmp/scwrl_935646691.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_935646691.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 292 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_163089337.pdb -s /var/tmp/to_scwrl_163089337.seq -o /var/tmp/from_scwrl_163089337.pdb > /var/tmp/scwrl_163089337.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_163089337.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 289 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_562000662.pdb -s /var/tmp/to_scwrl_562000662.seq -o /var/tmp/from_scwrl_562000662.pdb > /var/tmp/scwrl_562000662.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_562000662.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 287 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_2056282201.pdb -s /var/tmp/to_scwrl_2056282201.seq -o /var/tmp/from_scwrl_2056282201.pdb > /var/tmp/scwrl_2056282201.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2056282201.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 296 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_211011419.pdb -s /var/tmp/to_scwrl_211011419.seq -o /var/tmp/from_scwrl_211011419.pdb > /var/tmp/scwrl_211011419.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_211011419.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 296 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_767949787.pdb -s /var/tmp/to_scwrl_767949787.seq -o /var/tmp/from_scwrl_767949787.pdb > /var/tmp/scwrl_767949787.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_767949787.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 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_746010907.pdb -s /var/tmp/to_scwrl_746010907.seq -o /var/tmp/from_scwrl_746010907.pdb > /var/tmp/scwrl_746010907.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_746010907.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 # Found a chain break before 278 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_2081731681.pdb -s /var/tmp/to_scwrl_2081731681.seq -o /var/tmp/from_scwrl_2081731681.pdb > /var/tmp/scwrl_2081731681.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2081731681.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 T0305 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_201183097.pdb -s /var/tmp/to_scwrl_201183097.seq -o /var/tmp/from_scwrl_201183097.pdb > /var/tmp/scwrl_201183097.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_201183097.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 T0305 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1679965523.pdb -s /var/tmp/to_scwrl_1679965523.seq -o /var/tmp/from_scwrl_1679965523.pdb > /var/tmp/scwrl_1679965523.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1679965523.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 293 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1528670122.pdb -s /var/tmp/to_scwrl_1528670122.seq -o /var/tmp/from_scwrl_1528670122.pdb > /var/tmp/scwrl_1528670122.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1528670122.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 T0305 can't currently be optimized by undertaker # naming current conformation FUGUE_AL1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1691554996.pdb -s /var/tmp/to_scwrl_1691554996.seq -o /var/tmp/from_scwrl_1691554996.pdb > /var/tmp/scwrl_1691554996.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1691554996.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 T0305 can't currently be optimized by undertaker # naming current conformation FUGUE_AL2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1351915874.pdb -s /var/tmp/to_scwrl_1351915874.seq -o /var/tmp/from_scwrl_1351915874.pdb > /var/tmp/scwrl_1351915874.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1351915874.pdb # conformation set from SCWRL output # naming current conformation FUGUE_AL2-scwrl # ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation FUGUE_AL3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_309030923.pdb -s /var/tmp/to_scwrl_309030923.seq -o /var/tmp/from_scwrl_309030923.pdb > /var/tmp/scwrl_309030923.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_309030923.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 T0305 can't currently be optimized by undertaker # naming current conformation FUGUE_AL4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1228282797.pdb -s /var/tmp/to_scwrl_1228282797.seq -o /var/tmp/from_scwrl_1228282797.pdb > /var/tmp/scwrl_1228282797.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1228282797.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 T0305 can't currently be optimized by undertaker # naming current conformation FUGUE_AL5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1385450671.pdb -s /var/tmp/to_scwrl_1385450671.seq -o /var/tmp/from_scwrl_1385450671.pdb > /var/tmp/scwrl_1385450671.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1385450671.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 268 ; scwrl3 -i /var/tmp/to_scwrl_779621225.pdb -s /var/tmp/to_scwrl_779621225.seq -o /var/tmp/from_scwrl_779621225.pdb > /var/tmp/scwrl_779621225.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_779621225.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 295 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1786702265.pdb -s /var/tmp/to_scwrl_1786702265.seq -o /var/tmp/from_scwrl_1786702265.pdb > /var/tmp/scwrl_1786702265.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1786702265.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 291 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1108181532.pdb -s /var/tmp/to_scwrl_1108181532.seq -o /var/tmp/from_scwrl_1108181532.pdb > /var/tmp/scwrl_1108181532.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1108181532.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 293 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_134690593.pdb -s /var/tmp/to_scwrl_134690593.seq -o /var/tmp/from_scwrl_134690593.pdb > /var/tmp/scwrl_134690593.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_134690593.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 292 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_2108047276.pdb -s /var/tmp/to_scwrl_2108047276.seq -o /var/tmp/from_scwrl_2108047276.pdb > /var/tmp/scwrl_2108047276.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2108047276.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 # Found a chain break before 278 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1566584864.pdb -s /var/tmp/to_scwrl_1566584864.seq -o /var/tmp/from_scwrl_1566584864.pdb > /var/tmp/scwrl_1566584864.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1566584864.pdb # conformation set from SCWRL output # naming current conformation GeneSilicoMetaServer_TS1-scwrl # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # Found a chain break before 278 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_501049637.pdb -s /var/tmp/to_scwrl_501049637.seq -o /var/tmp/from_scwrl_501049637.pdb > /var/tmp/scwrl_501049637.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_501049637.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 275 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_284118630.pdb -s /var/tmp/to_scwrl_284118630.seq -o /var/tmp/from_scwrl_284118630.pdb > /var/tmp/scwrl_284118630.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_284118630.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 T0305 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_572869891.pdb -s /var/tmp/to_scwrl_572869891.seq -o /var/tmp/from_scwrl_572869891.pdb > /var/tmp/scwrl_572869891.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_572869891.pdb # conformation set from SCWRL output # naming current conformation GeneSilicoMetaServer_TS4-scwrl # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1 # Found a chain break before 276 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_2017224705.pdb -s /var/tmp/to_scwrl_2017224705.seq -o /var/tmp/from_scwrl_2017224705.pdb > /var/tmp/scwrl_2017224705.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2017224705.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 268 ; scwrl3 -i /var/tmp/to_scwrl_596536161.pdb -s /var/tmp/to_scwrl_596536161.seq -o /var/tmp/from_scwrl_596536161.pdb > /var/tmp/scwrl_596536161.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_596536161.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 257 # copying to AlignedFragments data structure # naming current conformation HHpred2_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_6194393.pdb -s /var/tmp/to_scwrl_6194393.seq -o /var/tmp/from_scwrl_6194393.pdb > /var/tmp/scwrl_6194393.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_6194393.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 276 # copying to AlignedFragments data structure # naming current conformation HHpred3_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_248365649.pdb -s /var/tmp/to_scwrl_248365649.seq -o /var/tmp/from_scwrl_248365649.pdb > /var/tmp/scwrl_248365649.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_248365649.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 T0305 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1371328934.pdb -s /var/tmp/to_scwrl_1371328934.seq -o /var/tmp/from_scwrl_1371328934.pdb > /var/tmp/scwrl_1371328934.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1371328934.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 T0305 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1310737026.pdb -s /var/tmp/to_scwrl_1310737026.seq -o /var/tmp/from_scwrl_1310737026.pdb > /var/tmp/scwrl_1310737026.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1310737026.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 T0305 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1184012339.pdb -s /var/tmp/to_scwrl_1184012339.seq -o /var/tmp/from_scwrl_1184012339.pdb > /var/tmp/scwrl_1184012339.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1184012339.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 T0305 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1534418271.pdb -s /var/tmp/to_scwrl_1534418271.seq -o /var/tmp/from_scwrl_1534418271.pdb > /var/tmp/scwrl_1534418271.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1534418271.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 T0305 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1872737688.pdb -s /var/tmp/to_scwrl_1872737688.seq -o /var/tmp/from_scwrl_1872737688.pdb > /var/tmp/scwrl_1872737688.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1872737688.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 T0305 can't currently be optimized by undertaker # naming current conformation LOOPP_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1092810893.pdb -s /var/tmp/to_scwrl_1092810893.seq -o /var/tmp/from_scwrl_1092810893.pdb > /var/tmp/scwrl_1092810893.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1092810893.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 T0305 can't currently be optimized by undertaker # naming current conformation LOOPP_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1745429691.pdb -s /var/tmp/to_scwrl_1745429691.seq -o /var/tmp/from_scwrl_1745429691.pdb > /var/tmp/scwrl_1745429691.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1745429691.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 T0305 can't currently be optimized by undertaker # naming current conformation LOOPP_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_493203828.pdb -s /var/tmp/to_scwrl_493203828.seq -o /var/tmp/from_scwrl_493203828.pdb > /var/tmp/scwrl_493203828.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_493203828.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 T0305 can't currently be optimized by undertaker # naming current conformation LOOPP_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1838821800.pdb -s /var/tmp/to_scwrl_1838821800.seq -o /var/tmp/from_scwrl_1838821800.pdb > /var/tmp/scwrl_1838821800.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1838821800.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 T0305 can't currently be optimized by undertaker # naming current conformation LOOPP_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1679677725.pdb -s /var/tmp/to_scwrl_1679677725.seq -o /var/tmp/from_scwrl_1679677725.pdb > /var/tmp/scwrl_1679677725.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1679677725.pdb # conformation set from SCWRL output # naming current conformation LOOPP_TS5-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # Found a chain break before 257 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_694386925.pdb -s /var/tmp/to_scwrl_694386925.seq -o /var/tmp/from_scwrl_694386925.pdb > /var/tmp/scwrl_694386925.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_694386925.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 275 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1371303676.pdb -s /var/tmp/to_scwrl_1371303676.seq -o /var/tmp/from_scwrl_1371303676.pdb > /var/tmp/scwrl_1371303676.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1371303676.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 224 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1060864201.pdb -s /var/tmp/to_scwrl_1060864201.seq -o /var/tmp/from_scwrl_1060864201.pdb > /var/tmp/scwrl_1060864201.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1060864201.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 279 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_238458274.pdb -s /var/tmp/to_scwrl_238458274.seq -o /var/tmp/from_scwrl_238458274.pdb > /var/tmp/scwrl_238458274.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_238458274.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 279 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_575735904.pdb -s /var/tmp/to_scwrl_575735904.seq -o /var/tmp/from_scwrl_575735904.pdb > /var/tmp/scwrl_575735904.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_575735904.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 296 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1369895123.pdb -s /var/tmp/to_scwrl_1369895123.seq -o /var/tmp/from_scwrl_1369895123.pdb > /var/tmp/scwrl_1369895123.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1369895123.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 290 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1466741071.pdb -s /var/tmp/to_scwrl_1466741071.seq -o /var/tmp/from_scwrl_1466741071.pdb > /var/tmp/scwrl_1466741071.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1466741071.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 284 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1961186576.pdb -s /var/tmp/to_scwrl_1961186576.seq -o /var/tmp/from_scwrl_1961186576.pdb > /var/tmp/scwrl_1961186576.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1961186576.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 278 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_2032702.pdb -s /var/tmp/to_scwrl_2032702.seq -o /var/tmp/from_scwrl_2032702.pdb > /var/tmp/scwrl_2032702.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2032702.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 278 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1105959690.pdb -s /var/tmp/to_scwrl_1105959690.seq -o /var/tmp/from_scwrl_1105959690.pdb > /var/tmp/scwrl_1105959690.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1105959690.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 T0305 can't currently be optimized by undertaker # naming current conformation NN_PUT_lab_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_921884462.pdb -s /var/tmp/to_scwrl_921884462.seq -o /var/tmp/from_scwrl_921884462.pdb > /var/tmp/scwrl_921884462.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_921884462.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 268 ; scwrl3 -i /var/tmp/to_scwrl_136723295.pdb -s /var/tmp/to_scwrl_136723295.seq -o /var/tmp/from_scwrl_136723295.pdb > /var/tmp/scwrl_136723295.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_136723295.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 268 ; scwrl3 -i /var/tmp/to_scwrl_1066523320.pdb -s /var/tmp/to_scwrl_1066523320.seq -o /var/tmp/from_scwrl_1066523320.pdb > /var/tmp/scwrl_1066523320.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1066523320.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 268 ; scwrl3 -i /var/tmp/to_scwrl_340985680.pdb -s /var/tmp/to_scwrl_340985680.seq -o /var/tmp/from_scwrl_340985680.pdb > /var/tmp/scwrl_340985680.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_340985680.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 268 ; scwrl3 -i /var/tmp/to_scwrl_637772933.pdb -s /var/tmp/to_scwrl_637772933.seq -o /var/tmp/from_scwrl_637772933.pdb > /var/tmp/scwrl_637772933.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_637772933.pdb # conformation set from SCWRL output # naming current conformation PROTINFO-AB_TS4-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1350641949.pdb -s /var/tmp/to_scwrl_1350641949.seq -o /var/tmp/from_scwrl_1350641949.pdb > /var/tmp/scwrl_1350641949.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1350641949.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 277 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_913855571.pdb -s /var/tmp/to_scwrl_913855571.seq -o /var/tmp/from_scwrl_913855571.pdb > /var/tmp/scwrl_913855571.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_913855571.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 278 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_507513991.pdb -s /var/tmp/to_scwrl_507513991.seq -o /var/tmp/from_scwrl_507513991.pdb > /var/tmp/scwrl_507513991.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_507513991.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 # naming current conformation PROTINFO_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1947178110.pdb -s /var/tmp/to_scwrl_1947178110.seq -o /var/tmp/from_scwrl_1947178110.pdb > /var/tmp/scwrl_1947178110.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1947178110.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 T0305 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_920049965.pdb -s /var/tmp/to_scwrl_920049965.seq -o /var/tmp/from_scwrl_920049965.pdb > /var/tmp/scwrl_920049965.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_920049965.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 T0305 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_755879640.pdb -s /var/tmp/to_scwrl_755879640.seq -o /var/tmp/from_scwrl_755879640.pdb > /var/tmp/scwrl_755879640.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_755879640.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 T0305 can't currently be optimized by undertaker # naming current conformation Pcons6_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1171023398.pdb -s /var/tmp/to_scwrl_1171023398.seq -o /var/tmp/from_scwrl_1171023398.pdb > /var/tmp/scwrl_1171023398.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1171023398.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 T0305 can't currently be optimized by undertaker # naming current conformation Pcons6_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_83303344.pdb -s /var/tmp/to_scwrl_83303344.seq -o /var/tmp/from_scwrl_83303344.pdb > /var/tmp/scwrl_83303344.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_83303344.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 T0305 can't currently be optimized by undertaker # naming current conformation Pcons6_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1939891979.pdb -s /var/tmp/to_scwrl_1939891979.seq -o /var/tmp/from_scwrl_1939891979.pdb > /var/tmp/scwrl_1939891979.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1939891979.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 T0305 can't currently be optimized by undertaker # naming current conformation Pcons6_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_557958023.pdb -s /var/tmp/to_scwrl_557958023.seq -o /var/tmp/from_scwrl_557958023.pdb > /var/tmp/scwrl_557958023.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_557958023.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 T0305 can't currently be optimized by undertaker # naming current conformation Pcons6_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1956041032.pdb -s /var/tmp/to_scwrl_1956041032.seq -o /var/tmp/from_scwrl_1956041032.pdb > /var/tmp/scwrl_1956041032.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1956041032.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 T0305 can't currently be optimized by undertaker # naming current conformation Phyre-1_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_885219226.pdb -s /var/tmp/to_scwrl_885219226.seq -o /var/tmp/from_scwrl_885219226.pdb > /var/tmp/scwrl_885219226.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_885219226.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 274 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_155904067.pdb -s /var/tmp/to_scwrl_155904067.seq -o /var/tmp/from_scwrl_155904067.pdb > /var/tmp/scwrl_155904067.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_155904067.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 274 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_301761213.pdb -s /var/tmp/to_scwrl_301761213.seq -o /var/tmp/from_scwrl_301761213.pdb > /var/tmp/scwrl_301761213.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_301761213.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 274 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_576557380.pdb -s /var/tmp/to_scwrl_576557380.seq -o /var/tmp/from_scwrl_576557380.pdb > /var/tmp/scwrl_576557380.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_576557380.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 274 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1835581792.pdb -s /var/tmp/to_scwrl_1835581792.seq -o /var/tmp/from_scwrl_1835581792.pdb > /var/tmp/scwrl_1835581792.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1835581792.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 274 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_996148139.pdb -s /var/tmp/to_scwrl_996148139.seq -o /var/tmp/from_scwrl_996148139.pdb > /var/tmp/scwrl_996148139.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_996148139.pdb # conformation set from SCWRL output # naming current conformation Phyre-2_TS5-scwrl # ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1947861056.pdb -s /var/tmp/to_scwrl_1947861056.seq -o /var/tmp/from_scwrl_1947861056.pdb > /var/tmp/scwrl_1947861056.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1947861056.pdb # conformation set from SCWRL output # naming current conformation Pmodeller6_TS1-scwrl # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_748962346.pdb -s /var/tmp/to_scwrl_748962346.seq -o /var/tmp/from_scwrl_748962346.pdb > /var/tmp/scwrl_748962346.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_748962346.pdb # conformation set from SCWRL output # naming current conformation Pmodeller6_TS2-scwrl # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1234606412.pdb -s /var/tmp/to_scwrl_1234606412.seq -o /var/tmp/from_scwrl_1234606412.pdb > /var/tmp/scwrl_1234606412.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1234606412.pdb # conformation set from SCWRL output # naming current conformation Pmodeller6_TS3-scwrl # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_376113314.pdb -s /var/tmp/to_scwrl_376113314.seq -o /var/tmp/from_scwrl_376113314.pdb > /var/tmp/scwrl_376113314.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_376113314.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 T0305 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_2118857470.pdb -s /var/tmp/to_scwrl_2118857470.seq -o /var/tmp/from_scwrl_2118857470.pdb > /var/tmp/scwrl_2118857470.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2118857470.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 279 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_553863838.pdb -s /var/tmp/to_scwrl_553863838.seq -o /var/tmp/from_scwrl_553863838.pdb > /var/tmp/scwrl_553863838.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_553863838.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 278 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_189816243.pdb -s /var/tmp/to_scwrl_189816243.seq -o /var/tmp/from_scwrl_189816243.pdb > /var/tmp/scwrl_189816243.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_189816243.pdb # conformation set from SCWRL output # naming current conformation RAPTOR-ACE_TS2-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1 # Found a chain break before 279 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_2120890172.pdb -s /var/tmp/to_scwrl_2120890172.seq -o /var/tmp/from_scwrl_2120890172.pdb > /var/tmp/scwrl_2120890172.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2120890172.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 276 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1659823528.pdb -s /var/tmp/to_scwrl_1659823528.seq -o /var/tmp/from_scwrl_1659823528.pdb > /var/tmp/scwrl_1659823528.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1659823528.pdb # conformation set from SCWRL output # naming current conformation RAPTOR-ACE_TS4-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1111700704.pdb -s /var/tmp/to_scwrl_1111700704.seq -o /var/tmp/from_scwrl_1111700704.pdb > /var/tmp/scwrl_1111700704.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1111700704.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 277 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_110129820.pdb -s /var/tmp/to_scwrl_110129820.seq -o /var/tmp/from_scwrl_110129820.pdb > /var/tmp/scwrl_110129820.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_110129820.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 275 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_578863201.pdb -s /var/tmp/to_scwrl_578863201.seq -o /var/tmp/from_scwrl_578863201.pdb > /var/tmp/scwrl_578863201.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_578863201.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 271 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1452686384.pdb -s /var/tmp/to_scwrl_1452686384.seq -o /var/tmp/from_scwrl_1452686384.pdb > /var/tmp/scwrl_1452686384.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1452686384.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 278 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_747902753.pdb -s /var/tmp/to_scwrl_747902753.seq -o /var/tmp/from_scwrl_747902753.pdb > /var/tmp/scwrl_747902753.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_747902753.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 277 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1929505151.pdb -s /var/tmp/to_scwrl_1929505151.seq -o /var/tmp/from_scwrl_1929505151.pdb > /var/tmp/scwrl_1929505151.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1929505151.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 278 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_219058309.pdb -s /var/tmp/to_scwrl_219058309.seq -o /var/tmp/from_scwrl_219058309.pdb > /var/tmp/scwrl_219058309.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_219058309.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 278 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1255416743.pdb -s /var/tmp/to_scwrl_1255416743.seq -o /var/tmp/from_scwrl_1255416743.pdb > /var/tmp/scwrl_1255416743.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1255416743.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 276 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1729199614.pdb -s /var/tmp/to_scwrl_1729199614.seq -o /var/tmp/from_scwrl_1729199614.pdb > /var/tmp/scwrl_1729199614.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1729199614.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 276 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1139108273.pdb -s /var/tmp/to_scwrl_1139108273.seq -o /var/tmp/from_scwrl_1139108273.pdb > /var/tmp/scwrl_1139108273.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1139108273.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 276 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_2011296383.pdb -s /var/tmp/to_scwrl_2011296383.seq -o /var/tmp/from_scwrl_2011296383.pdb > /var/tmp/scwrl_2011296383.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2011296383.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 278 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_752739366.pdb -s /var/tmp/to_scwrl_752739366.seq -o /var/tmp/from_scwrl_752739366.pdb > /var/tmp/scwrl_752739366.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_752739366.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 278 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1222411617.pdb -s /var/tmp/to_scwrl_1222411617.seq -o /var/tmp/from_scwrl_1222411617.pdb > /var/tmp/scwrl_1222411617.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1222411617.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 278 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1803704715.pdb -s /var/tmp/to_scwrl_1803704715.seq -o /var/tmp/from_scwrl_1803704715.pdb > /var/tmp/scwrl_1803704715.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1803704715.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 278 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1310697389.pdb -s /var/tmp/to_scwrl_1310697389.seq -o /var/tmp/from_scwrl_1310697389.pdb > /var/tmp/scwrl_1310697389.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1310697389.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 278 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1030969003.pdb -s /var/tmp/to_scwrl_1030969003.seq -o /var/tmp/from_scwrl_1030969003.pdb > /var/tmp/scwrl_1030969003.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1030969003.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 278 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_541440295.pdb -s /var/tmp/to_scwrl_541440295.seq -o /var/tmp/from_scwrl_541440295.pdb > /var/tmp/scwrl_541440295.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_541440295.pdb # conformation set from SCWRL output # naming current conformation ROKKY_TS1-scwrl # ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1 # Found a chain break before 244 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1466601456.pdb -s /var/tmp/to_scwrl_1466601456.seq -o /var/tmp/from_scwrl_1466601456.pdb > /var/tmp/scwrl_1466601456.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1466601456.pdb # conformation set from SCWRL output # naming current conformation ROKKY_TS2-scwrl # ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1 # Found a chain break before 277 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1332730215.pdb -s /var/tmp/to_scwrl_1332730215.seq -o /var/tmp/from_scwrl_1332730215.pdb > /var/tmp/scwrl_1332730215.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1332730215.pdb # conformation set from SCWRL output # naming current conformation ROKKY_TS3-scwrl # ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1117997674.pdb -s /var/tmp/to_scwrl_1117997674.seq -o /var/tmp/from_scwrl_1117997674.pdb > /var/tmp/scwrl_1117997674.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1117997674.pdb # conformation set from SCWRL output # naming current conformation ROKKY_TS4-scwrl # ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1 # Found a chain break before 277 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1154699602.pdb -s /var/tmp/to_scwrl_1154699602.seq -o /var/tmp/from_scwrl_1154699602.pdb > /var/tmp/scwrl_1154699602.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1154699602.pdb # conformation set from SCWRL output # naming current conformation ROKKY_TS5-scwrl # ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_181394707.pdb -s /var/tmp/to_scwrl_181394707.seq -o /var/tmp/from_scwrl_181394707.pdb > /var/tmp/scwrl_181394707.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_181394707.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 T0305 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_918375084.pdb -s /var/tmp/to_scwrl_918375084.seq -o /var/tmp/from_scwrl_918375084.pdb > /var/tmp/scwrl_918375084.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_918375084.pdb # conformation set from SCWRL output # naming current conformation SAM-T02_AL2-scwrl # ReadConformPDB reading from PDB file servers/SAM-T02_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1903661948.pdb -s /var/tmp/to_scwrl_1903661948.seq -o /var/tmp/from_scwrl_1903661948.pdb > /var/tmp/scwrl_1903661948.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1903661948.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 Skipped atom 26, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 28, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 30, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 32, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 162, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 164, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 166, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 168, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 326, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 328, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 330, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 332, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 622, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 624, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 626, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 628, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 830, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 832, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 834, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 836, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 914, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 916, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 918, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 920, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1416001120.pdb -s /var/tmp/to_scwrl_1416001120.seq -o /var/tmp/from_scwrl_1416001120.pdb > /var/tmp/scwrl_1416001120.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1416001120.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 T0305 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1294488397.pdb -s /var/tmp/to_scwrl_1294488397.seq -o /var/tmp/from_scwrl_1294488397.pdb > /var/tmp/scwrl_1294488397.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1294488397.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 Skipped atom 38, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 40, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 42, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 44, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 174, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 176, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 178, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 180, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 338, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 340, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 342, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 344, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 634, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 636, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 638, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 640, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 842, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 844, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 846, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 848, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 926, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 928, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 930, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 932, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1875035771.pdb -s /var/tmp/to_scwrl_1875035771.seq -o /var/tmp/from_scwrl_1875035771.pdb > /var/tmp/scwrl_1875035771.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1875035771.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 585, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL2.pdb.gz Skipped atom 770, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL2.pdb.gz # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1969864958.pdb -s /var/tmp/to_scwrl_1969864958.seq -o /var/tmp/from_scwrl_1969864958.pdb > /var/tmp/scwrl_1969864958.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1969864958.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 T0305 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1484304640.pdb -s /var/tmp/to_scwrl_1484304640.seq -o /var/tmp/from_scwrl_1484304640.pdb > /var/tmp/scwrl_1484304640.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1484304640.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 T0305 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1848442296.pdb -s /var/tmp/to_scwrl_1848442296.seq -o /var/tmp/from_scwrl_1848442296.pdb > /var/tmp/scwrl_1848442296.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1848442296.pdb # conformation set from SCWRL output # naming current conformation SAM-T99_AL4-scwrl # ReadConformPDB reading from PDB file servers/SAM-T99_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1482204839.pdb -s /var/tmp/to_scwrl_1482204839.seq -o /var/tmp/from_scwrl_1482204839.pdb > /var/tmp/scwrl_1482204839.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1482204839.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 279 # copying to AlignedFragments data structure # naming current conformation SAM_T06_server_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_448521699.pdb -s /var/tmp/to_scwrl_448521699.seq -o /var/tmp/from_scwrl_448521699.pdb > /var/tmp/scwrl_448521699.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_448521699.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 T0305 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1958572117.pdb -s /var/tmp/to_scwrl_1958572117.seq -o /var/tmp/from_scwrl_1958572117.pdb > /var/tmp/scwrl_1958572117.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1958572117.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 T0305 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_2061068040.pdb -s /var/tmp/to_scwrl_2061068040.seq -o /var/tmp/from_scwrl_2061068040.pdb > /var/tmp/scwrl_2061068040.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2061068040.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 T0305 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1901208083.pdb -s /var/tmp/to_scwrl_1901208083.seq -o /var/tmp/from_scwrl_1901208083.pdb > /var/tmp/scwrl_1901208083.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1901208083.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 T0305 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_558991223.pdb -s /var/tmp/to_scwrl_558991223.seq -o /var/tmp/from_scwrl_558991223.pdb > /var/tmp/scwrl_558991223.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_558991223.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 268 ; scwrl3 -i /var/tmp/to_scwrl_1843089544.pdb -s /var/tmp/to_scwrl_1843089544.seq -o /var/tmp/from_scwrl_1843089544.pdb > /var/tmp/scwrl_1843089544.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1843089544.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 278 # copying to AlignedFragments data structure # naming current conformation SP3_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_2120266392.pdb -s /var/tmp/to_scwrl_2120266392.seq -o /var/tmp/from_scwrl_2120266392.pdb > /var/tmp/scwrl_2120266392.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2120266392.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 278 # copying to AlignedFragments data structure # naming current conformation SP3_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1814407967.pdb -s /var/tmp/to_scwrl_1814407967.seq -o /var/tmp/from_scwrl_1814407967.pdb > /var/tmp/scwrl_1814407967.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1814407967.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 278 # copying to AlignedFragments data structure # naming current conformation SP3_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1424805512.pdb -s /var/tmp/to_scwrl_1424805512.seq -o /var/tmp/from_scwrl_1424805512.pdb > /var/tmp/scwrl_1424805512.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1424805512.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 295 # copying to AlignedFragments data structure # naming current conformation SP3_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1111891018.pdb -s /var/tmp/to_scwrl_1111891018.seq -o /var/tmp/from_scwrl_1111891018.pdb > /var/tmp/scwrl_1111891018.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1111891018.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 278 # copying to AlignedFragments data structure # naming current conformation SP4_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1678220703.pdb -s /var/tmp/to_scwrl_1678220703.seq -o /var/tmp/from_scwrl_1678220703.pdb > /var/tmp/scwrl_1678220703.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1678220703.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 236 # copying to AlignedFragments data structure # naming current conformation SP4_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_30061231.pdb -s /var/tmp/to_scwrl_30061231.seq -o /var/tmp/from_scwrl_30061231.pdb > /var/tmp/scwrl_30061231.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_30061231.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 236 # copying to AlignedFragments data structure # naming current conformation SP4_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_186818989.pdb -s /var/tmp/to_scwrl_186818989.seq -o /var/tmp/from_scwrl_186818989.pdb > /var/tmp/scwrl_186818989.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_186818989.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 278 # copying to AlignedFragments data structure # naming current conformation SP4_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1334441772.pdb -s /var/tmp/to_scwrl_1334441772.seq -o /var/tmp/from_scwrl_1334441772.pdb > /var/tmp/scwrl_1334441772.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1334441772.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 278 # copying to AlignedFragments data structure # naming current conformation SP4_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1340758620.pdb -s /var/tmp/to_scwrl_1340758620.seq -o /var/tmp/from_scwrl_1340758620.pdb > /var/tmp/scwrl_1340758620.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1340758620.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 268 ; scwrl3 -i /var/tmp/to_scwrl_1217787991.pdb -s /var/tmp/to_scwrl_1217787991.seq -o /var/tmp/from_scwrl_1217787991.pdb > /var/tmp/scwrl_1217787991.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1217787991.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 278 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1875882067.pdb -s /var/tmp/to_scwrl_1875882067.seq -o /var/tmp/from_scwrl_1875882067.pdb > /var/tmp/scwrl_1875882067.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1875882067.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 279 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_659876431.pdb -s /var/tmp/to_scwrl_659876431.seq -o /var/tmp/from_scwrl_659876431.pdb > /var/tmp/scwrl_659876431.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_659876431.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 278 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_403034561.pdb -s /var/tmp/to_scwrl_403034561.seq -o /var/tmp/from_scwrl_403034561.pdb > /var/tmp/scwrl_403034561.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_403034561.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 199 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_846396095.pdb -s /var/tmp/to_scwrl_846396095.seq -o /var/tmp/from_scwrl_846396095.pdb > /var/tmp/scwrl_846396095.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_846396095.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 T0305 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1814576033.pdb -s /var/tmp/to_scwrl_1814576033.seq -o /var/tmp/from_scwrl_1814576033.pdb > /var/tmp/scwrl_1814576033.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1814576033.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 T0305 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_584429268.pdb -s /var/tmp/to_scwrl_584429268.seq -o /var/tmp/from_scwrl_584429268.pdb > /var/tmp/scwrl_584429268.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_584429268.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 T0305 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1764771178.pdb -s /var/tmp/to_scwrl_1764771178.seq -o /var/tmp/from_scwrl_1764771178.pdb > /var/tmp/scwrl_1764771178.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1764771178.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 T0305 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1570754334.pdb -s /var/tmp/to_scwrl_1570754334.seq -o /var/tmp/from_scwrl_1570754334.pdb > /var/tmp/scwrl_1570754334.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1570754334.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 T0305 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_2000430388.pdb -s /var/tmp/to_scwrl_2000430388.seq -o /var/tmp/from_scwrl_2000430388.pdb > /var/tmp/scwrl_2000430388.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2000430388.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: atoms too close: (T0305)T174.CA and (T0305)K185.CA only 0.000 apart, marking (T0305)K185.CA as missing # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation UNI-EID_expm_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_911775930.pdb -s /var/tmp/to_scwrl_911775930.seq -o /var/tmp/from_scwrl_911775930.pdb > /var/tmp/scwrl_911775930.log Error: Couldn't open file /var/tmp/from_scwrl_911775930.pdb or /var/tmp/from_scwrl_911775930.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_911775930_b.pdb or decoys//var/tmp/from_scwrl_911775930_b.pdb.gz for input Trying /var/tmp/from_scwrl_911775930_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_911775930_b.pdb or /var/tmp/from_scwrl_911775930_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_911775930_a.pdb or decoys//var/tmp/from_scwrl_911775930_a.pdb.gz for input Trying /var/tmp/from_scwrl_911775930_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_911775930_a.pdb or /var/tmp/from_scwrl_911775930_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_911775930.pdb or /var/tmp/from_scwrl_911775930_b.pdb or /var/tmp/from_scwrl_911775930_a.pdb Error: no new SCWRL conformation added # 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 T0305 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1298306459.pdb -s /var/tmp/to_scwrl_1298306459.seq -o /var/tmp/from_scwrl_1298306459.pdb > /var/tmp/scwrl_1298306459.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1298306459.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 Skipped atom 131, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 792, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 1049, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1822811699.pdb -s /var/tmp/to_scwrl_1822811699.seq -o /var/tmp/from_scwrl_1822811699.pdb > /var/tmp/scwrl_1822811699.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1822811699.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 Skipped atom 987, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_248596923.pdb -s /var/tmp/to_scwrl_248596923.seq -o /var/tmp/from_scwrl_248596923.pdb > /var/tmp/scwrl_248596923.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_248596923.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_sfst_AL3-scwrl # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_999265109.pdb -s /var/tmp/to_scwrl_999265109.seq -o /var/tmp/from_scwrl_999265109.pdb > /var/tmp/scwrl_999265109.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_999265109.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 Skipped atom 585, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz Skipped atom 770, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1157532891.pdb -s /var/tmp/to_scwrl_1157532891.seq -o /var/tmp/from_scwrl_1157532891.pdb > /var/tmp/scwrl_1157532891.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1157532891.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 279 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_697118622.pdb -s /var/tmp/to_scwrl_697118622.seq -o /var/tmp/from_scwrl_697118622.pdb > /var/tmp/scwrl_697118622.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_697118622.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 279 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_810353579.pdb -s /var/tmp/to_scwrl_810353579.seq -o /var/tmp/from_scwrl_810353579.pdb > /var/tmp/scwrl_810353579.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_810353579.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 279 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1071117286.pdb -s /var/tmp/to_scwrl_1071117286.seq -o /var/tmp/from_scwrl_1071117286.pdb > /var/tmp/scwrl_1071117286.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1071117286.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 278 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_450843059.pdb -s /var/tmp/to_scwrl_450843059.seq -o /var/tmp/from_scwrl_450843059.pdb > /var/tmp/scwrl_450843059.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_450843059.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 279 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1369344802.pdb -s /var/tmp/to_scwrl_1369344802.seq -o /var/tmp/from_scwrl_1369344802.pdb > /var/tmp/scwrl_1369344802.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1369344802.pdb # conformation set from SCWRL output # naming current conformation Zhang-Server_TS5-scwrl # ReadConformPDB reading from PDB file servers/beautshot_TS1.pdb.gz looking for model 1 # Found a chain break before 278 # copying to AlignedFragments data structure # naming current conformation beautshot_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_766723183.pdb -s /var/tmp/to_scwrl_766723183.seq -o /var/tmp/from_scwrl_766723183.pdb > /var/tmp/scwrl_766723183.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_766723183.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 # Found a chain break before 278 # copying to AlignedFragments data structure # naming current conformation beautshotbase_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_423625804.pdb -s /var/tmp/to_scwrl_423625804.seq -o /var/tmp/from_scwrl_423625804.pdb > /var/tmp/scwrl_423625804.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_423625804.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 Skipped atom 18, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 20, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 22, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 24, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 202, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 204, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 206, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 208, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 254, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 256, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 258, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 260, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 262, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 264, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 266, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 268, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 270, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 272, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 274, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 276, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 278, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 280, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 282, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 284, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 378, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 380, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 382, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 384, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 454, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 456, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 458, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 460, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 510, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 512, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 514, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 516, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 518, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 520, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 522, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 524, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 658, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 660, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 662, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 664, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 670, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 672, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 674, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 676, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 746, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 748, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 750, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 752, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 754, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 756, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 758, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 760, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 762, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 764, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 766, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 768, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 770, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 772, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 774, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 776, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 778, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 780, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 782, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 784, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 786, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 788, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 790, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 792, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 794, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 796, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 798, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 800, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 802, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 804, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 806, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 808, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 810, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 812, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 814, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 816, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 818, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 820, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 822, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 824, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 826, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 828, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 830, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 832, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 834, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 836, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 838, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 840, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 846, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 848, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 850, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 852, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 946, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 948, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 950, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 952, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 970, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 972, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 974, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 976, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 994, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 996, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 998, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 1000, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 1066, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 1068, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 1070, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 1072, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 1098, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 1099, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 1101, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 1102, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 1104, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 1105, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 1107, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 1108, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation forecast-s_AL1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1036269123.pdb -s /var/tmp/to_scwrl_1036269123.seq -o /var/tmp/from_scwrl_1036269123.pdb > /var/tmp/scwrl_1036269123.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1036269123.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 T0305 can't currently be optimized by undertaker # naming current conformation forecast-s_AL2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_44045048.pdb -s /var/tmp/to_scwrl_44045048.seq -o /var/tmp/from_scwrl_44045048.pdb > /var/tmp/scwrl_44045048.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_44045048.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 T0305 can't currently be optimized by undertaker # naming current conformation forecast-s_AL3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1535516823.pdb -s /var/tmp/to_scwrl_1535516823.seq -o /var/tmp/from_scwrl_1535516823.pdb > /var/tmp/scwrl_1535516823.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1535516823.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 T0305 can't currently be optimized by undertaker # naming current conformation forecast-s_AL4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_567006179.pdb -s /var/tmp/to_scwrl_567006179.seq -o /var/tmp/from_scwrl_567006179.pdb > /var/tmp/scwrl_567006179.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_567006179.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 T0305 can't currently be optimized by undertaker # naming current conformation forecast-s_AL5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_74106280.pdb -s /var/tmp/to_scwrl_74106280.seq -o /var/tmp/from_scwrl_74106280.pdb > /var/tmp/scwrl_74106280.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_74106280.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 T0305 can't currently be optimized by undertaker # naming current conformation gtg_AL1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1722335812.pdb -s /var/tmp/to_scwrl_1722335812.seq -o /var/tmp/from_scwrl_1722335812.pdb > /var/tmp/scwrl_1722335812.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1722335812.pdb # conformation set from SCWRL output # naming current conformation gtg_AL1-scwrl # ReadConformPDB reading from PDB file servers/gtg_AL2.pdb.gz looking for model 1 Skipped atom 622, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 624, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 626, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 628, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation gtg_AL2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1901447951.pdb -s /var/tmp/to_scwrl_1901447951.seq -o /var/tmp/from_scwrl_1901447951.pdb > /var/tmp/scwrl_1901447951.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1901447951.pdb # conformation set from SCWRL output # naming current conformation gtg_AL2-scwrl # ReadConformPDB reading from PDB file servers/gtg_AL3.pdb.gz looking for model 1 Skipped atom 585, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL3.pdb.gz Skipped atom 770, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL3.pdb.gz # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation gtg_AL3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1414864900.pdb -s /var/tmp/to_scwrl_1414864900.seq -o /var/tmp/from_scwrl_1414864900.pdb > /var/tmp/scwrl_1414864900.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1414864900.pdb # conformation set from SCWRL output # naming current conformation gtg_AL3-scwrl # ReadConformPDB reading from PDB file servers/gtg_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation gtg_AL4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_792640158.pdb -s /var/tmp/to_scwrl_792640158.seq -o /var/tmp/from_scwrl_792640158.pdb > /var/tmp/scwrl_792640158.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_792640158.pdb # conformation set from SCWRL output # naming current conformation gtg_AL4-scwrl # ReadConformPDB reading from PDB file servers/gtg_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation gtg_AL5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1629846371.pdb -s /var/tmp/to_scwrl_1629846371.seq -o /var/tmp/from_scwrl_1629846371.pdb > /var/tmp/scwrl_1629846371.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1629846371.pdb # conformation set from SCWRL output # naming current conformation gtg_AL5-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # Found a chain break before 279 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_2074741331.pdb -s /var/tmp/to_scwrl_2074741331.seq -o /var/tmp/from_scwrl_2074741331.pdb > /var/tmp/scwrl_2074741331.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2074741331.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 275 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1195674718.pdb -s /var/tmp/to_scwrl_1195674718.seq -o /var/tmp/from_scwrl_1195674718.pdb > /var/tmp/scwrl_1195674718.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1195674718.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 278 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_328758819.pdb -s /var/tmp/to_scwrl_328758819.seq -o /var/tmp/from_scwrl_328758819.pdb > /var/tmp/scwrl_328758819.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_328758819.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 278 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1741833717.pdb -s /var/tmp/to_scwrl_1741833717.seq -o /var/tmp/from_scwrl_1741833717.pdb > /var/tmp/scwrl_1741833717.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1741833717.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 277 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1780103986.pdb -s /var/tmp/to_scwrl_1780103986.seq -o /var/tmp/from_scwrl_1780103986.pdb > /var/tmp/scwrl_1780103986.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1780103986.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 # Found a chain break before 294 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_2093529998.pdb -s /var/tmp/to_scwrl_2093529998.seq -o /var/tmp/from_scwrl_2093529998.pdb > /var/tmp/scwrl_2093529998.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2093529998.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 294 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1165104405.pdb -s /var/tmp/to_scwrl_1165104405.seq -o /var/tmp/from_scwrl_1165104405.pdb > /var/tmp/scwrl_1165104405.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1165104405.pdb # conformation set from SCWRL output # naming current conformation karypis.srv.4_TS2-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS3.pdb.gz looking for model 1 WARNING: atoms too close: (T0305)S157.O and (T0305)T158.N only 0.000 apart, marking (T0305)T158.N as missing # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1633050728.pdb -s /var/tmp/to_scwrl_1633050728.seq -o /var/tmp/from_scwrl_1633050728.pdb > /var/tmp/scwrl_1633050728.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1633050728.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: (T0305)V129.O and (T0305)E130.N only 0.000 apart, marking (T0305)E130.N as missing # WARNING: incomplete conformation T0305 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 268 ; scwrl3 -i /var/tmp/to_scwrl_857822281.pdb -s /var/tmp/to_scwrl_857822281.seq -o /var/tmp/from_scwrl_857822281.pdb > /var/tmp/scwrl_857822281.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_857822281.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: (T0305)Q3.O and (T0305)S4.N only 0.000 apart, marking (T0305)S4.N as missing WARNING: atoms too close: (T0305)L68.O and (T0305)R69.N only 0.000 apart, marking (T0305)R69.N as missing # WARNING: incomplete conformation T0305 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 268 ; scwrl3 -i /var/tmp/to_scwrl_315927218.pdb -s /var/tmp/to_scwrl_315927218.seq -o /var/tmp/from_scwrl_315927218.pdb > /var/tmp/scwrl_315927218.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_315927218.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 T0305 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1308378780.pdb -s /var/tmp/to_scwrl_1308378780.seq -o /var/tmp/from_scwrl_1308378780.pdb > /var/tmp/scwrl_1308378780.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1308378780.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 T0305 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1106419203.pdb -s /var/tmp/to_scwrl_1106419203.seq -o /var/tmp/from_scwrl_1106419203.pdb > /var/tmp/scwrl_1106419203.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1106419203.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 T0305 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1315192326.pdb -s /var/tmp/to_scwrl_1315192326.seq -o /var/tmp/from_scwrl_1315192326.pdb > /var/tmp/scwrl_1315192326.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1315192326.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 T0305 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_318428026.pdb -s /var/tmp/to_scwrl_318428026.seq -o /var/tmp/from_scwrl_318428026.pdb > /var/tmp/scwrl_318428026.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_318428026.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 T0305 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1803537826.pdb -s /var/tmp/to_scwrl_1803537826.seq -o /var/tmp/from_scwrl_1803537826.pdb > /var/tmp/scwrl_1803537826.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1803537826.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 268 ; scwrl3 -i /var/tmp/to_scwrl_2125545906.pdb -s /var/tmp/to_scwrl_2125545906.seq -o /var/tmp/from_scwrl_2125545906.pdb > /var/tmp/scwrl_2125545906.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2125545906.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 233 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1389545311.pdb -s /var/tmp/to_scwrl_1389545311.seq -o /var/tmp/from_scwrl_1389545311.pdb > /var/tmp/scwrl_1389545311.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1389545311.pdb # conformation set from SCWRL output # naming current conformation keasar-server_TS2-scwrl # ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1 # Found a chain break before 274 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_106897238.pdb -s /var/tmp/to_scwrl_106897238.seq -o /var/tmp/from_scwrl_106897238.pdb > /var/tmp/scwrl_106897238.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_106897238.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 # Found a chain break before 235 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1347407061.pdb -s /var/tmp/to_scwrl_1347407061.seq -o /var/tmp/from_scwrl_1347407061.pdb > /var/tmp/scwrl_1347407061.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1347407061.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 # Found a chain break before 233 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_8784847.pdb -s /var/tmp/to_scwrl_8784847.seq -o /var/tmp/from_scwrl_8784847.pdb > /var/tmp/scwrl_8784847.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_8784847.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 T0305 can't currently be optimized by undertaker # naming current conformation mGen-3D_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_530523042.pdb -s /var/tmp/to_scwrl_530523042.seq -o /var/tmp/from_scwrl_530523042.pdb > /var/tmp/scwrl_530523042.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_530523042.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 T0305 can't currently be optimized by undertaker # naming current conformation nFOLD_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_236192537.pdb -s /var/tmp/to_scwrl_236192537.seq -o /var/tmp/from_scwrl_236192537.pdb > /var/tmp/scwrl_236192537.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_236192537.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 T0305 can't currently be optimized by undertaker # naming current conformation nFOLD_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_52829896.pdb -s /var/tmp/to_scwrl_52829896.seq -o /var/tmp/from_scwrl_52829896.pdb > /var/tmp/scwrl_52829896.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_52829896.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 T0305 can't currently be optimized by undertaker # naming current conformation nFOLD_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_2066039865.pdb -s /var/tmp/to_scwrl_2066039865.seq -o /var/tmp/from_scwrl_2066039865.pdb > /var/tmp/scwrl_2066039865.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2066039865.pdb # conformation set from SCWRL output # naming current conformation nFOLD_TS3-scwrl # ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation nFOLD_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_803198716.pdb -s /var/tmp/to_scwrl_803198716.seq -o /var/tmp/from_scwrl_803198716.pdb > /var/tmp/scwrl_803198716.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_803198716.pdb # conformation set from SCWRL output # naming current conformation nFOLD_TS4-scwrl # ReadConformPDB reading from PDB file servers/nFOLD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation nFOLD_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_126936176.pdb -s /var/tmp/to_scwrl_126936176.seq -o /var/tmp/from_scwrl_126936176.pdb > /var/tmp/scwrl_126936176.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_126936176.pdb # conformation set from SCWRL output # naming current conformation nFOLD_TS5-scwrl # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # Found a chain break before 278 # copying to AlignedFragments data structure # naming current conformation shub_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1640892031.pdb -s /var/tmp/to_scwrl_1640892031.seq -o /var/tmp/from_scwrl_1640892031.pdb > /var/tmp/scwrl_1640892031.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1640892031.pdb # conformation set from SCWRL output # naming current conformation shub_TS1-scwrl # command:CPU_time= 90.4842 sec, elapsed time= 1550.49 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 = -231.96 shub_TS1 costs 0 real_cost = -228.574 nFOLD_TS5-scwrl costs 0 real_cost = 86.9134 nFOLD_TS5 costs 0 real_cost = 231.092 nFOLD_TS4-scwrl costs 0 real_cost = -50.5623 nFOLD_TS4 costs 0 real_cost = 100.87 nFOLD_TS3-scwrl costs 0 real_cost = -71.4204 nFOLD_TS3 costs 0 real_cost = 78.41 nFOLD_TS2-scwrl costs 0 real_cost = -140.3 nFOLD_TS2 costs 0 real_cost = 12.9677 nFOLD_TS1-scwrl costs 0 real_cost = -131.2 nFOLD_TS1 costs 0 real_cost = 24.2003 mGen-3D_TS1-scwrl costs 0 real_cost = -85.2295 mGen-3D_TS1 costs 0 real_cost = 69.9154 keasar-server_TS5-scwrl costs 0 real_cost = -225.065 keasar-server_TS5 costs 0 real_cost = -218.184 keasar-server_TS4-scwrl costs 0 real_cost = -218.659 keasar-server_TS4 costs 0 real_cost = -205.988 keasar-server_TS3-scwrl costs 0 real_cost = -239.345 keasar-server_TS3 costs 0 real_cost = -240.818 keasar-server_TS2-scwrl costs 0 real_cost = -250.654 keasar-server_TS2 costs 0 real_cost = -243.207 keasar-server_TS1-scwrl costs 0 real_cost = -235.476 keasar-server_TS1 costs 0 real_cost = -227.175 karypis.srv_TS5-scwrl costs 0 real_cost = -162.14 karypis.srv_TS5 costs 0 real_cost = -162.271 karypis.srv_TS4-scwrl costs 0 real_cost = -115.691 karypis.srv_TS4 costs 0 real_cost = -117.18 karypis.srv_TS3-scwrl costs 0 real_cost = -94.1305 karypis.srv_TS3 costs 0 real_cost = -96.3457 karypis.srv_TS2-scwrl costs 0 real_cost = -184.015 karypis.srv_TS2 costs 0 real_cost = -188.729 karypis.srv_TS1-scwrl costs 0 real_cost = -271.681 karypis.srv_TS1 costs 0 real_cost = -275.149 karypis.srv.4_TS5-scwrl costs 0 real_cost = 362.346 karypis.srv.4_TS5 costs 0 real_cost = 362.419 karypis.srv.4_TS4-scwrl costs 0 real_cost = 315.543 karypis.srv.4_TS4 costs 0 real_cost = 314.518 karypis.srv.4_TS3-scwrl costs 0 real_cost = 358.797 karypis.srv.4_TS3 costs 0 real_cost = 358.973 karypis.srv.4_TS2-scwrl costs 0 real_cost = 321.597 karypis.srv.4_TS2 costs 0 real_cost = 323.121 karypis.srv.4_TS1-scwrl costs 0 real_cost = 317.473 karypis.srv.4_TS1 costs 0 real_cost = 317.614 karypis.srv.2_TS5-scwrl costs 0 real_cost = -197.139 karypis.srv.2_TS5 costs 0 real_cost = -197.139 karypis.srv.2_TS4-scwrl costs 0 real_cost = -149.55 karypis.srv.2_TS4 costs 0 real_cost = -149.558 karypis.srv.2_TS3-scwrl costs 0 real_cost = -292.022 karypis.srv.2_TS3 costs 0 real_cost = -291.341 karypis.srv.2_TS2-scwrl costs 0 real_cost = -265.532 karypis.srv.2_TS2 costs 0 real_cost = -264.79 karypis.srv.2_TS1-scwrl costs 0 real_cost = -268.849 karypis.srv.2_TS1 costs 0 real_cost = -267.955 gtg_AL5-scwrl costs 0 real_cost = -154.26 gtg_AL5 costs 0 real_cost = 49.8801 gtg_AL4-scwrl costs 0 real_cost = -135.521 gtg_AL4 costs 0 real_cost = 75.8914 gtg_AL3-scwrl costs 0 real_cost = -230.73 gtg_AL3 costs 0 real_cost = -24.4841 gtg_AL2-scwrl costs 0 real_cost = -187.05 gtg_AL2 costs 0 real_cost = 23.1848 gtg_AL1-scwrl costs 0 real_cost = -234.34 gtg_AL1 costs 0 real_cost = -26.1662 forecast-s_AL5-scwrl costs 0 real_cost = 78.4676 forecast-s_AL5 costs 0 real_cost = 271.651 forecast-s_AL4-scwrl costs 0 real_cost = -83.5779 forecast-s_AL4 costs 0 real_cost = 91.3174 forecast-s_AL3-scwrl costs 0 real_cost = -112.467 forecast-s_AL3 costs 0 real_cost = 95.914 forecast-s_AL2-scwrl costs 0 real_cost = -244.388 forecast-s_AL2 costs 0 real_cost = -27.7895 forecast-s_AL1-scwrl costs 0 real_cost = -154.554 forecast-s_AL1 costs 0 real_cost = 53.5622 beautshotbase_TS1-scwrl costs 0 real_cost = -220.959 beautshotbase_TS1 costs 0 real_cost = -220.797 beautshot_TS1-scwrl costs 0 real_cost = -245.513 beautshot_TS1 costs 0 real_cost = -243.506 Zhang-Server_TS5-scwrl costs 0 real_cost = -270.669 Zhang-Server_TS5 costs 0 real_cost = -262.173 Zhang-Server_TS4-scwrl costs 0 real_cost = -264.33 Zhang-Server_TS4 costs 0 real_cost = -266.934 Zhang-Server_TS3-scwrl costs 0 real_cost = -277.185 Zhang-Server_TS3 costs 0 real_cost = -264.594 Zhang-Server_TS2-scwrl costs 0 real_cost = -280.371 Zhang-Server_TS2 costs 0 real_cost = -284.454 Zhang-Server_TS1-scwrl costs 0 real_cost = -276.672 Zhang-Server_TS1 costs 0 real_cost = -269.874 UNI-EID_sfst_AL5-scwrl costs 0 real_cost = -215.127 UNI-EID_sfst_AL5 costs 0 real_cost = -11.2731 UNI-EID_sfst_AL4-scwrl costs 0 real_cost = -229.533 UNI-EID_sfst_AL4 costs 0 real_cost = -24.2072 UNI-EID_sfst_AL3-scwrl costs 0 real_cost = -213.406 UNI-EID_sfst_AL3 costs 0 real_cost = -5.62001 UNI-EID_sfst_AL2-scwrl costs 0 real_cost = -262.417 UNI-EID_sfst_AL2 costs 0 real_cost = -48.4346 UNI-EID_sfst_AL1-scwrl costs 0 real_cost = -255.124 UNI-EID_sfst_AL1 costs 0 real_cost = -44.9719 UNI-EID_expm_TS1-scwrl costs 0 real_cost = -65.4646 UNI-EID_bnmx_TS5-scwrl costs 0 real_cost = -215.127 UNI-EID_bnmx_TS5 costs 0 real_cost = -11.2731 UNI-EID_bnmx_TS4-scwrl costs 0 real_cost = -229.533 UNI-EID_bnmx_TS4 costs 0 real_cost = -24.2072 UNI-EID_bnmx_TS3-scwrl costs 0 real_cost = -213.406 UNI-EID_bnmx_TS3 costs 0 real_cost = -5.62001 UNI-EID_bnmx_TS2-scwrl costs 0 real_cost = -271.297 UNI-EID_bnmx_TS2 costs 0 real_cost = -52.6641 UNI-EID_bnmx_TS1-scwrl costs 0 real_cost = -255.124 UNI-EID_bnmx_TS1 costs 0 real_cost = -44.9719 SPARKS2_TS5-scwrl costs 0 real_cost = -287.128 SPARKS2_TS5 costs 0 real_cost = -294.16 SPARKS2_TS4-scwrl costs 0 real_cost = -197.884 SPARKS2_TS4 costs 0 real_cost = -199.922 SPARKS2_TS3-scwrl costs 0 real_cost = -117.953 SPARKS2_TS3 costs 0 real_cost = -122.661 SPARKS2_TS2-scwrl costs 0 real_cost = -177.445 SPARKS2_TS2 costs 0 real_cost = -179.327 SPARKS2_TS1-scwrl costs 0 real_cost = -264.791 SPARKS2_TS1 costs 0 real_cost = -270.715 SP4_TS5-scwrl costs 0 real_cost = -203.676 SP4_TS5 costs 0 real_cost = -199.812 SP4_TS4-scwrl costs 0 real_cost = -290.842 SP4_TS4 costs 0 real_cost = -294.811 SP4_TS3-scwrl costs 0 real_cost = -115.313 SP4_TS3 costs 0 real_cost = -115.292 SP4_TS2-scwrl costs 0 real_cost = -164.449 SP4_TS2 costs 0 real_cost = -167.98 SP4_TS1-scwrl costs 0 real_cost = -267.381 SP4_TS1 costs 0 real_cost = -270.934 SP3_TS5-scwrl costs 0 real_cost = -198.568 SP3_TS5 costs 0 real_cost = -199.052 SP3_TS4-scwrl costs 0 real_cost = -290.842 SP3_TS4 costs 0 real_cost = -294.811 SP3_TS3-scwrl costs 0 real_cost = -107.342 SP3_TS3 costs 0 real_cost = -106.346 SP3_TS2-scwrl costs 0 real_cost = -159.566 SP3_TS2 costs 0 real_cost = -156.76 SP3_TS1-scwrl costs 0 real_cost = -264.791 SP3_TS1 costs 0 real_cost = -270.715 SAM_T06_server_TS5-scwrl costs 0 real_cost = -142.846 SAM_T06_server_TS5 costs 0 real_cost = -157.062 SAM_T06_server_TS4-scwrl costs 0 real_cost = -170.692 SAM_T06_server_TS4 costs 0 real_cost = -190.218 SAM_T06_server_TS3-scwrl costs 0 real_cost = -156.101 SAM_T06_server_TS3 costs 0 real_cost = -178.057 SAM_T06_server_TS2-scwrl costs 0 real_cost = -50.6669 SAM_T06_server_TS2 costs 0 real_cost = -125.539 SAM_T06_server_TS1-scwrl costs 0 real_cost = -158.456 SAM_T06_server_TS1 costs 0 real_cost = -158.754 SAM-T99_AL5-scwrl costs 0 real_cost = -149.668 SAM-T99_AL5 costs 0 real_cost = 12.7874 SAM-T99_AL4-scwrl costs 0 real_cost = -254.937 SAM-T99_AL4 costs 0 real_cost = -46.1499 SAM-T99_AL3-scwrl costs 0 real_cost = -103.876 SAM-T99_AL3 costs 0 real_cost = 117.253 SAM-T99_AL2-scwrl costs 0 real_cost = -223.873 SAM-T99_AL2 costs 0 real_cost = -18.7583 SAM-T99_AL1-scwrl costs 0 real_cost = -242.127 SAM-T99_AL1 costs 0 real_cost = -30.3891 SAM-T02_AL5-scwrl costs 0 real_cost = -152.085 SAM-T02_AL5 costs 0 real_cost = 28.3864 SAM-T02_AL4-scwrl costs 0 real_cost = -184.677 SAM-T02_AL4 costs 0 real_cost = 20.8795 SAM-T02_AL3-scwrl costs 0 real_cost = -114.722 SAM-T02_AL3 costs 0 real_cost = 81.683 SAM-T02_AL2-scwrl costs 0 real_cost = -180.814 SAM-T02_AL2 costs 0 real_cost = 25.0353 SAM-T02_AL1-scwrl costs 0 real_cost = -140.946 SAM-T02_AL1 costs 0 real_cost = 57.3933 ROKKY_TS5-scwrl costs 0 real_cost = -185.028 ROKKY_TS5 costs 0 real_cost = -189.607 ROKKY_TS4-scwrl costs 0 real_cost = -279.943 ROKKY_TS4 costs 0 real_cost = -275.571 ROKKY_TS3-scwrl costs 0 real_cost = -290.144 ROKKY_TS3 costs 0 real_cost = -290.203 ROKKY_TS2-scwrl costs 0 real_cost = 353.028 ROKKY_TS2 costs 0 real_cost = 356.917 ROKKY_TS1-scwrl costs 0 real_cost = -277.754 ROKKY_TS1 costs 0 real_cost = -286.775 ROBETTA_TS5-scwrl costs 0 real_cost = -264.542 ROBETTA_TS5 costs 0 real_cost = -271.568 ROBETTA_TS4-scwrl costs 0 real_cost = -271.718 ROBETTA_TS4 costs 0 real_cost = -275.876 ROBETTA_TS3-scwrl costs 0 real_cost = -261.955 ROBETTA_TS3 costs 0 real_cost = -270.537 ROBETTA_TS2-scwrl costs 0 real_cost = -244.724 ROBETTA_TS2 costs 0 real_cost = -250.539 ROBETTA_TS1-scwrl costs 0 real_cost = -262.51 ROBETTA_TS1 costs 0 real_cost = -264.733 RAPTOR_TS5-scwrl costs 0 real_cost = -261.287 RAPTOR_TS5 costs 0 real_cost = -258.978 RAPTOR_TS4-scwrl costs 0 real_cost = -261.287 RAPTOR_TS4 costs 0 real_cost = -258.978 RAPTOR_TS3-scwrl costs 0 real_cost = -231.027 RAPTOR_TS3 costs 0 real_cost = -231.669 RAPTOR_TS2-scwrl costs 0 real_cost = -258.106 RAPTOR_TS2 costs 0 real_cost = -267.985 RAPTOR_TS1-scwrl costs 0 real_cost = -275.445 RAPTOR_TS1 costs 0 real_cost = -281.604 RAPTORESS_TS5-scwrl costs 0 real_cost = -171.323 RAPTORESS_TS5 costs 0 real_cost = -169.326 RAPTORESS_TS4-scwrl costs 0 real_cost = -250.957 RAPTORESS_TS4 costs 0 real_cost = -248.412 RAPTORESS_TS3-scwrl costs 0 real_cost = -202.21 RAPTORESS_TS3 costs 0 real_cost = -209.794 RAPTORESS_TS2-scwrl costs 0 real_cost = -238.896 RAPTORESS_TS2 costs 0 real_cost = -244.498 RAPTORESS_TS1-scwrl costs 0 real_cost = -255.362 RAPTORESS_TS1 costs 0 real_cost = -256.068 RAPTOR-ACE_TS5-scwrl costs 0 real_cost = -270.138 RAPTOR-ACE_TS5 costs 0 real_cost = -264.787 RAPTOR-ACE_TS4-scwrl costs 0 real_cost = -252.781 RAPTOR-ACE_TS4 costs 0 real_cost = -252.344 RAPTOR-ACE_TS3-scwrl costs 0 real_cost = -262.655 RAPTOR-ACE_TS3 costs 0 real_cost = -260.333 RAPTOR-ACE_TS2-scwrl costs 0 real_cost = -289.302 RAPTOR-ACE_TS2 costs 0 real_cost = -296.179 RAPTOR-ACE_TS1-scwrl costs 0 real_cost = -156.017 RAPTOR-ACE_TS1 costs 0 real_cost = -156.77 Pmodeller6_TS5-scwrl costs 0 real_cost = -267.698 Pmodeller6_TS5 costs 0 real_cost = -272.587 Pmodeller6_TS4-scwrl costs 0 real_cost = -286.669 Pmodeller6_TS4 costs 0 real_cost = -293.198 Pmodeller6_TS3-scwrl costs 0 real_cost = -245.334 Pmodeller6_TS3 costs 0 real_cost = -250.572 Pmodeller6_TS2-scwrl costs 0 real_cost = -236.855 Pmodeller6_TS2 costs 0 real_cost = -238.314 Pmodeller6_TS1-scwrl costs 0 real_cost = -236.855 Pmodeller6_TS1 costs 0 real_cost = -238.314 Phyre-2_TS5-scwrl costs 0 real_cost = -277.099 Phyre-2_TS5 costs 0 real_cost = -280.342 Phyre-2_TS4-scwrl costs 0 real_cost = -266.531 Phyre-2_TS4 costs 0 real_cost = -268.95 Phyre-2_TS3-scwrl costs 0 real_cost = -257.926 Phyre-2_TS3 costs 0 real_cost = -260.044 Phyre-2_TS2-scwrl costs 0 real_cost = -257.926 Phyre-2_TS2 costs 0 real_cost = -260.044 Phyre-2_TS1-scwrl costs 0 real_cost = -268.513 Phyre-2_TS1 costs 0 real_cost = -271.543 Phyre-1_TS1-scwrl costs 0 real_cost = -262.784 Phyre-1_TS1 costs 0 real_cost = -267.298 Pcons6_TS5-scwrl costs 0 real_cost = -271.707 Pcons6_TS5 costs 0 real_cost = -276.91 Pcons6_TS4-scwrl costs 0 real_cost = -267.698 Pcons6_TS4 costs 0 real_cost = -272.587 Pcons6_TS3-scwrl costs 0 real_cost = -269.28 Pcons6_TS3 costs 0 real_cost = -274.318 Pcons6_TS2-scwrl costs 0 real_cost = -269.055 Pcons6_TS2 costs 0 real_cost = -275.117 Pcons6_TS1-scwrl costs 0 real_cost = -269.055 Pcons6_TS1 costs 0 real_cost = -275.117 PROTINFO_TS5-scwrl costs 0 real_cost = -247.468 PROTINFO_TS5 costs 0 real_cost = -250.231 PROTINFO_TS4-scwrl costs 0 real_cost = 121.22 PROTINFO_TS4 costs 0 real_cost = 115.089 PROTINFO_TS3-scwrl costs 0 real_cost = -244.105 PROTINFO_TS3 costs 0 real_cost = -254.367 PROTINFO_TS2-scwrl costs 0 real_cost = -262.632 PROTINFO_TS2 costs 0 real_cost = -276.238 PROTINFO_TS1-scwrl costs 0 real_cost = -301.548 PROTINFO_TS1 costs 0 real_cost = -314.417 PROTINFO-AB_TS5-scwrl costs 0 real_cost = -249.322 PROTINFO-AB_TS5 costs 0 real_cost = -255.497 PROTINFO-AB_TS4-scwrl costs 0 real_cost = -245.829 PROTINFO-AB_TS4 costs 0 real_cost = -256.379 PROTINFO-AB_TS3-scwrl costs 0 real_cost = -245.258 PROTINFO-AB_TS3 costs 0 real_cost = -250.163 PROTINFO-AB_TS2-scwrl costs 0 real_cost = -244.105 PROTINFO-AB_TS2 costs 0 real_cost = -254.367 PROTINFO-AB_TS1-scwrl costs 0 real_cost = -244.105 PROTINFO-AB_TS1 costs 0 real_cost = -254.367 NN_PUT_lab_TS1-scwrl costs 0 real_cost = -249.039 NN_PUT_lab_TS1 costs 0 real_cost = -246.331 MetaTasser_TS5-scwrl costs 0 real_cost = -49.072 MetaTasser_TS5 costs 0 real_cost = -54.2013 MetaTasser_TS4-scwrl costs 0 real_cost = -57.585 MetaTasser_TS4 costs 0 real_cost = -54.0255 MetaTasser_TS3-scwrl costs 0 real_cost = -44.9542 MetaTasser_TS3 costs 0 real_cost = -38.2479 MetaTasser_TS2-scwrl costs 0 real_cost = -12.0209 MetaTasser_TS2 costs 0 real_cost = -20.775 MetaTasser_TS1-scwrl costs 0 real_cost = 31.6717 MetaTasser_TS1 costs 0 real_cost = 41.5772 Ma-OPUS-server_TS5-scwrl costs 0 real_cost = -190.384 Ma-OPUS-server_TS5 costs 0 real_cost = -187.099 Ma-OPUS-server_TS4-scwrl costs 0 real_cost = -215.635 Ma-OPUS-server_TS4 costs 0 real_cost = -215.918 Ma-OPUS-server_TS3-scwrl costs 0 real_cost = -158.988 Ma-OPUS-server_TS3 costs 0 real_cost = -160.277 Ma-OPUS-server_TS2-scwrl costs 0 real_cost = -289.691 Ma-OPUS-server_TS2 costs 0 real_cost = -295.166 Ma-OPUS-server_TS1-scwrl costs 0 real_cost = -242.549 Ma-OPUS-server_TS1 costs 0 real_cost = -245.293 LOOPP_TS5-scwrl costs 0 real_cost = -213.833 LOOPP_TS5 costs 0 real_cost = -209.077 LOOPP_TS4-scwrl costs 0 real_cost = -235.688 LOOPP_TS4 costs 0 real_cost = -230.035 LOOPP_TS3-scwrl costs 0 real_cost = -241.44 LOOPP_TS3 costs 0 real_cost = -232.285 LOOPP_TS2-scwrl costs 0 real_cost = -251.458 LOOPP_TS2 costs 0 real_cost = -241.511 LOOPP_TS1-scwrl costs 0 real_cost = -249.039 LOOPP_TS1 costs 0 real_cost = -246.331 Huber-Torda-Server_TS5-scwrl costs 0 real_cost = -177.531 Huber-Torda-Server_TS5 costs 0 real_cost = -36.3263 Huber-Torda-Server_TS4-scwrl costs 0 real_cost = -178.096 Huber-Torda-Server_TS4 costs 0 real_cost = -32.9647 Huber-Torda-Server_TS3-scwrl costs 0 real_cost = -187.575 Huber-Torda-Server_TS3 costs 0 real_cost = -31.0895 Huber-Torda-Server_TS2-scwrl costs 0 real_cost = -162.241 Huber-Torda-Server_TS2 costs 0 real_cost = -15.0163 Huber-Torda-Server_TS1-scwrl costs 0 real_cost = -203.953 Huber-Torda-Server_TS1 costs 0 real_cost = -29.2049 HHpred3_TS1-scwrl costs 0 real_cost = -294.833 HHpred3_TS1 costs 0 real_cost = -299.974 HHpred2_TS1-scwrl costs 0 real_cost = -286.808 HHpred2_TS1 costs 0 real_cost = -294.395 HHpred1_TS1-scwrl costs 0 real_cost = -252.603 HHpred1_TS1 costs 0 real_cost = -254.235 GeneSilicoMetaServer_TS5-scwrl costs 0 real_cost = -272.869 GeneSilicoMetaServer_TS5 costs 0 real_cost = -273.456 GeneSilicoMetaServer_TS4-scwrl costs 0 real_cost = -229.935 GeneSilicoMetaServer_TS4 costs 0 real_cost = -241.99 GeneSilicoMetaServer_TS3-scwrl costs 0 real_cost = -285.569 GeneSilicoMetaServer_TS3 costs 0 real_cost = -285.416 GeneSilicoMetaServer_TS2-scwrl costs 0 real_cost = -148.119 GeneSilicoMetaServer_TS2 costs 0 real_cost = -141.597 GeneSilicoMetaServer_TS1-scwrl costs 0 real_cost = -156.634 GeneSilicoMetaServer_TS1 costs 0 real_cost = -149.936 FUNCTION_TS5-scwrl costs 0 real_cost = -271.751 FUNCTION_TS5 costs 0 real_cost = -285.413 FUNCTION_TS4-scwrl costs 0 real_cost = -236.654 FUNCTION_TS4 costs 0 real_cost = -253.058 FUNCTION_TS3-scwrl costs 0 real_cost = -280.288 FUNCTION_TS3 costs 0 real_cost = -287.211 FUNCTION_TS2-scwrl costs 0 real_cost = -270.016 FUNCTION_TS2 costs 0 real_cost = -280.649 FUNCTION_TS1-scwrl costs 0 real_cost = -244.275 FUNCTION_TS1 costs 0 real_cost = -262.106 FUGUE_AL5-scwrl costs 0 real_cost = 378.061 FUGUE_AL5 costs 0 real_cost = 587.037 FUGUE_AL4-scwrl costs 0 real_cost = 177.248 FUGUE_AL4 costs 0 real_cost = 368.209 FUGUE_AL3-scwrl costs 0 real_cost = 75.9454 FUGUE_AL3 costs 0 real_cost = 271.64 FUGUE_AL2-scwrl costs 0 real_cost = -106.059 FUGUE_AL2 costs 0 real_cost = 101.393 FUGUE_AL1-scwrl costs 0 real_cost = -213.403 FUGUE_AL1 costs 0 real_cost = -3.72196 FUGMOD_TS5-scwrl costs 0 real_cost = 325.83 FUGMOD_TS5 costs 0 real_cost = 329.211 FUGMOD_TS4-scwrl costs 0 real_cost = 98.6588 FUGMOD_TS4 costs 0 real_cost = 101.711 FUGMOD_TS3-scwrl costs 0 real_cost = 33.8578 FUGMOD_TS3 costs 0 real_cost = 39.0079 FUGMOD_TS2-scwrl costs 0 real_cost = -155.43 FUGMOD_TS2 costs 0 real_cost = -157.262 FUGMOD_TS1-scwrl costs 0 real_cost = -245.454 FUGMOD_TS1 costs 0 real_cost = -253.024 FPSOLVER-SERVER_TS5-scwrl costs 0 real_cost = 311.147 FPSOLVER-SERVER_TS5 costs 0 real_cost = 314.417 FPSOLVER-SERVER_TS4-scwrl costs 0 real_cost = 288.284 FPSOLVER-SERVER_TS4 costs 0 real_cost = 300.95 FPSOLVER-SERVER_TS3-scwrl costs 0 real_cost = 297.556 FPSOLVER-SERVER_TS3 costs 0 real_cost = 306.649 FPSOLVER-SERVER_TS2-scwrl costs 0 real_cost = 302.223 FPSOLVER-SERVER_TS2 costs 0 real_cost = 312.429 FPSOLVER-SERVER_TS1-scwrl costs 0 real_cost = 304.898 FPSOLVER-SERVER_TS1 costs 0 real_cost = 307.945 FORTE2_AL5-scwrl costs 0 real_cost = 184.463 FORTE2_AL5 costs 0 real_cost = 375.616 FORTE2_AL4-scwrl costs 0 real_cost = 81.6448 FORTE2_AL4 costs 0 real_cost = 277.105 FORTE2_AL3-scwrl costs 0 real_cost = -240.261 FORTE2_AL3 costs 0 real_cost = -27.0679 FORTE2_AL2-scwrl costs 0 real_cost = 59.7906 FORTE2_AL2 costs 0 real_cost = 291.842 FORTE2_AL1-scwrl costs 0 real_cost = -124.388 FORTE2_AL1 costs 0 real_cost = 76.2481 FORTE1_AL5-scwrl costs 0 real_cost = -58.2101 FORTE1_AL5 costs 0 real_cost = 157.029 FORTE1_AL4-scwrl costs 0 real_cost = -151.371 FORTE1_AL4 costs 0 real_cost = 45.86 FORTE1_AL3-scwrl costs 0 real_cost = -151.886 FORTE1_AL3 costs 0 real_cost = 60.3447 FORTE1_AL2-scwrl costs 0 real_cost = -242.167 FORTE1_AL2 costs 0 real_cost = -30.0681 FORTE1_AL1-scwrl costs 0 real_cost = 59.7906 FORTE1_AL1 costs 0 real_cost = 291.842 FOLDpro_TS5-scwrl costs 0 real_cost = 317.682 FOLDpro_TS5 costs 0 real_cost = 315.647 FOLDpro_TS4-scwrl costs 0 real_cost = 284.814 FOLDpro_TS4 costs 0 real_cost = 291.832 FOLDpro_TS3-scwrl costs 0 real_cost = 304.236 FOLDpro_TS3 costs 0 real_cost = 305.363 FOLDpro_TS2-scwrl costs 0 real_cost = 295.918 FOLDpro_TS2 costs 0 real_cost = 299.582 FOLDpro_TS1-scwrl costs 0 real_cost = -298.603 FOLDpro_TS1 costs 0 real_cost = -310.55 FAMS_TS5-scwrl costs 0 real_cost = -259.054 FAMS_TS5 costs 0 real_cost = -269.925 FAMS_TS4-scwrl costs 0 real_cost = -271.751 FAMS_TS4 costs 0 real_cost = -285.413 FAMS_TS3-scwrl costs 0 real_cost = -264.166 FAMS_TS3 costs 0 real_cost = -267.939 FAMS_TS2-scwrl costs 0 real_cost = -270.016 FAMS_TS2 costs 0 real_cost = -280.649 FAMS_TS1-scwrl costs 0 real_cost = -278.001 FAMS_TS1 costs 0 real_cost = -283.963 FAMSD_TS5-scwrl costs 0 real_cost = -256.987 FAMSD_TS5 costs 0 real_cost = -276.226 FAMSD_TS4-scwrl costs 0 real_cost = -239.912 FAMSD_TS4 costs 0 real_cost = -259.662 FAMSD_TS3-scwrl costs 0 real_cost = -237.114 FAMSD_TS3 costs 0 real_cost = -238.013 FAMSD_TS2-scwrl costs 0 real_cost = -245.087 FAMSD_TS2 costs 0 real_cost = -261.063 FAMSD_TS1-scwrl costs 0 real_cost = -260.919 FAMSD_TS1 costs 0 real_cost = -264.058 Distill_TS5-scwrl costs 0 real_cost = 529.468 Distill_TS4-scwrl costs 0 real_cost = 564.454 Distill_TS3-scwrl costs 0 real_cost = 529.129 Distill_TS2-scwrl costs 0 real_cost = 540.11 Distill_TS1-scwrl costs 0 real_cost = 489.994 CaspIta-FOX_TS5-scwrl costs 0 real_cost = -158.4 CaspIta-FOX_TS5 costs 0 real_cost = -169.69 CaspIta-FOX_TS4-scwrl costs 0 real_cost = -205.588 CaspIta-FOX_TS4 costs 0 real_cost = -222.76 CaspIta-FOX_TS3-scwrl costs 0 real_cost = -236.363 CaspIta-FOX_TS3 costs 0 real_cost = -246.078 CaspIta-FOX_TS2-scwrl costs 0 real_cost = -283.598 CaspIta-FOX_TS2 costs 0 real_cost = -297.124 CaspIta-FOX_TS1-scwrl costs 0 real_cost = -245.747 CaspIta-FOX_TS1 costs 0 real_cost = -260.369 CPHmodels_TS1-scwrl costs 0 real_cost = -243.042 CPHmodels_TS1 costs 0 real_cost = -258.249 CIRCLE_TS5-scwrl costs 0 real_cost = -246.097 CIRCLE_TS5 costs 0 real_cost = -256.57 CIRCLE_TS4-scwrl costs 0 real_cost = -258.699 CIRCLE_TS4 costs 0 real_cost = -270.294 CIRCLE_TS3-scwrl costs 0 real_cost = -259.054 CIRCLE_TS3 costs 0 real_cost = -269.925 CIRCLE_TS2-scwrl costs 0 real_cost = -264.166 CIRCLE_TS2 costs 0 real_cost = -267.939 CIRCLE_TS1-scwrl costs 0 real_cost = -256.623 CIRCLE_TS1 costs 0 real_cost = -265.725 Bilab-ENABLE_TS5-scwrl costs 0 real_cost = -168.354 Bilab-ENABLE_TS5 costs 0 real_cost = -168.194 Bilab-ENABLE_TS4-scwrl costs 0 real_cost = -158.122 Bilab-ENABLE_TS4 costs 0 real_cost = -158.078 Bilab-ENABLE_TS3-scwrl costs 0 real_cost = -254.607 Bilab-ENABLE_TS3 costs 0 real_cost = -255.001 Bilab-ENABLE_TS2-scwrl costs 0 real_cost = -122.005 Bilab-ENABLE_TS2 costs 0 real_cost = -121.124 Bilab-ENABLE_TS1-scwrl costs 0 real_cost = -114.739 Bilab-ENABLE_TS1 costs 0 real_cost = -114.742 BayesHH_TS1-scwrl costs 0 real_cost = -289.286 BayesHH_TS1 costs 0 real_cost = -298.573 ABIpro_TS5-scwrl costs 0 real_cost = 279.665 ABIpro_TS5 costs 0 real_cost = 279.665 ABIpro_TS4-scwrl costs 0 real_cost = 280.819 ABIpro_TS4 costs 0 real_cost = 280.819 ABIpro_TS3-scwrl costs 0 real_cost = 296.536 ABIpro_TS3 costs 0 real_cost = 296.536 ABIpro_TS2-scwrl costs 0 real_cost = 250.765 ABIpro_TS2 costs 0 real_cost = 250.579 ABIpro_TS1-scwrl costs 0 real_cost = 306.017 ABIpro_TS1 costs 0 real_cost = 305.66 3Dpro_TS5-scwrl costs 0 real_cost = 277.026 3Dpro_TS5 costs 0 real_cost = 280.464 3Dpro_TS4-scwrl costs 0 real_cost = 316.604 3Dpro_TS4 costs 0 real_cost = 317.51 3Dpro_TS3-scwrl costs 0 real_cost = 284.189 3Dpro_TS3 costs 0 real_cost = 282.824 3Dpro_TS2-scwrl costs 0 real_cost = 329.83 3Dpro_TS2 costs 0 real_cost = 336.638 3Dpro_TS1-scwrl costs 0 real_cost = -289.232 3Dpro_TS1 costs 0 real_cost = -295.62 3D-JIGSAW_TS5-scwrl costs 0 real_cost = -224.951 3D-JIGSAW_TS5 costs 0 real_cost = -214.505 3D-JIGSAW_TS4-scwrl costs 0 real_cost = -250.23 3D-JIGSAW_TS4 costs 0 real_cost = -247.673 3D-JIGSAW_TS3-scwrl costs 0 real_cost = -214.558 3D-JIGSAW_TS3 costs 0 real_cost = -214.765 3D-JIGSAW_TS2-scwrl costs 0 real_cost = -240.078 3D-JIGSAW_TS2 costs 0 real_cost = -249.899 3D-JIGSAW_TS1-scwrl costs 0 real_cost = -118.878 3D-JIGSAW_TS1 costs 0 real_cost = -132.6 3D-JIGSAW_RECOM_TS5-scwrl costs 0 real_cost = -206.009 3D-JIGSAW_RECOM_TS5 costs 0 real_cost = -206.784 3D-JIGSAW_RECOM_TS4-scwrl costs 0 real_cost = -236.117 3D-JIGSAW_RECOM_TS4 costs 0 real_cost = -226.445 3D-JIGSAW_RECOM_TS3-scwrl costs 0 real_cost = -122.736 3D-JIGSAW_RECOM_TS3 costs 0 real_cost = -136.743 3D-JIGSAW_RECOM_TS2-scwrl costs 0 real_cost = -234.719 3D-JIGSAW_RECOM_TS2 costs 0 real_cost = -230.268 3D-JIGSAW_RECOM_TS1-scwrl costs 0 real_cost = -231.62 3D-JIGSAW_RECOM_TS1 costs 0 real_cost = -237.52 3D-JIGSAW_POPULUS_TS5-scwrl costs 0 real_cost = -208.847 3D-JIGSAW_POPULUS_TS5 costs 0 real_cost = -213.151 3D-JIGSAW_POPULUS_TS4-scwrl costs 0 real_cost = -243.867 3D-JIGSAW_POPULUS_TS4 costs 0 real_cost = -249.823 3D-JIGSAW_POPULUS_TS3-scwrl costs 0 real_cost = -218.445 3D-JIGSAW_POPULUS_TS3 costs 0 real_cost = -224.142 3D-JIGSAW_POPULUS_TS2-scwrl costs 0 real_cost = -222.479 3D-JIGSAW_POPULUS_TS2 costs 0 real_cost = -223.479 3D-JIGSAW_POPULUS_TS1-scwrl costs 0 real_cost = -213.803 3D-JIGSAW_POPULUS_TS1 costs 0 real_cost = -214.616 tetramer//tetramer-try4-1larA costs 0 real_cost = -274.195 tetramer//try4-opt2 costs 0 real_cost = -273.741 tetramer//try4-opt2.gromacs0 costs 0 real_cost = -269.813 tetramer//try4-opt1 costs 0 real_cost = -273.81 tetramer//try4-opt1-scwrl costs 0 real_cost = -271.608 tetramer//try3-opt2 costs 0 real_cost = -274.092 tetramer//try3-opt2.gromacs0 costs 0 real_cost = -250.228 tetramer//try3-opt1 costs 0 real_cost = -274.422 tetramer//try3-opt1-scwrl costs 0 real_cost = -271.928 tetramer//try2-opt2 costs 0 real_cost = -274.229 tetramer//try2-opt2.gromacs0 costs 0 real_cost = -256.616 tetramer//try2-opt1 costs 0 real_cost = -274.026 tetramer//try2-opt1-scwrl costs 0 real_cost = -271.977 tetramer//try1-opt2 costs 0 real_cost = -273.93 tetramer//try1-opt2.gromacs0 costs 0 real_cost = -259.878 tetramer//try1-opt1 costs 0 real_cost = -273.559 tetramer//try1-opt1-scwrl costs 0 real_cost = -271.987 dimer//from-tetramer-try4-1larA.unpack costs 0 real_cost = -274.195 dimer//from-tetramer-try4-1larA costs 0 real_cost = -274.195 dimer//from-tetramer-try1-opt2.unpack costs 0 real_cost = -273.93 dimer//from-tetramer-try1-opt2 costs 0 real_cost = -273.93 dimer//dimer-try4-2fh7A costs 0 real_cost = -273.985 dimer//dimer-try4-1rpmA.unpack costs 0 real_cost = -274.058 dimer//dimer-try4-1rpmA costs 0 real_cost = -274.058 dimer//try2-opt2.unpack costs 0 real_cost = -275.356 dimer//try2-opt2.repack-nonPC costs 0 real_cost = -271.944 dimer//try2-opt2 costs 0 real_cost = -275.356 dimer//try2-opt2.gromacs0 costs 0 real_cost = -259.437 dimer//try2-opt1 costs 0 real_cost = -275.106 dimer//try2-opt1-scwrl costs 0 real_cost = -272.063 dimer//try1-opt2.unpack costs 0 real_cost = -272.216 dimer//try1-opt2.repack-nonPC costs 0 real_cost = -271.683 dimer//try1-opt2 costs 0 real_cost = -272.216 dimer//try1-opt2.gromacs0 costs 0 real_cost = -273.192 dimer//try1-opt1 costs 0 real_cost = -271.73 dimer//try1-opt1-scwrl costs 0 real_cost = -268.022 T0305.try4-opt2.repack-nonPC.pdb.gz costs 0 real_cost = -273.448 T0305.try4-opt2.pdb.gz costs 0 real_cost = -274.332 T0305.try4-opt2.gromacs0.pdb.gz costs 0 real_cost = -274.848 T0305.try4-opt1.pdb.gz costs 0 real_cost = -273.18 T0305.try4-opt1-scwrl.pdb.gz costs 0 real_cost = -271.601 T0305.try3-opt2.repack-nonPC.pdb.gz costs 0 real_cost = -270.447 T0305.try3-opt2.pdb.gz costs 0 real_cost = -271.967 T0305.try3-opt2.gromacs0.pdb.gz costs 0 real_cost = -271.968 T0305.try3-opt1.pdb.gz costs 0 real_cost = -273.608 T0305.try3-opt1-scwrl.pdb.gz costs 0 real_cost = -269.036 T0305.try2-opt2.repack-nonPC.pdb.gz costs 0 real_cost = -233.706 T0305.try2-opt2.pdb.gz costs 0 real_cost = -235.333 T0305.try2-opt2.gromacs0.pdb.gz costs 0 real_cost = -235.569 T0305.try2-opt1.pdb.gz costs 0 real_cost = -238.264 T0305.try2-opt1-scwrl.pdb.gz costs 0 real_cost = -236.157 T0305.try1-opt2.repack-nonPC.pdb.gz costs 0 real_cost = -238.428 T0305.try1-opt2.pdb.gz costs 0 real_cost = -240.447 T0305.try1-opt2.gromacs0.pdb.gz costs 0 real_cost = -237.426 T0305.try1-opt1.pdb.gz costs 0 real_cost = -233.949 T0305.try1-opt1-scwrl.pdb.gz costs 0 real_cost = -233.726 ../model5.ts-submitted costs 0 real_cost = -174.047 ../model4.ts-submitted costs 0 real_cost = -179.666 ../model3.ts-submitted costs 0 real_cost = -270.464 ../model2.ts-submitted costs 0 real_cost = -235.355 ../model1.ts-submitted costs 0 real_cost = -274.145 align5 costs 0 real_cost = -94.6278 align4 costs 0 real_cost = -72.1395 align3 costs 0 real_cost = -142.407 align2 costs 0 real_cost = -179.727 align1 costs 0 real_cost = -193.228 T0305.try1-opt2.pdb costs 0 real_cost = -240.575 model5-scwrl costs 0 real_cost = -142.244 model5.ts-submitted costs 0 real_cost = -174.047 model4-scwrl costs 0 real_cost = -105.245 model4.ts-submitted costs 0 real_cost = -179.666 model3-scwrl costs 0 real_cost = -268.593 model3.ts-submitted costs 0 real_cost = -270.464 model2-scwrl costs 0 real_cost = -235.608 model2.ts-submitted costs 0 real_cost = -235.355 model1-scwrl costs 0 real_cost = -270.174 model1.ts-submitted costs 0 real_cost = -274.138 2h4vA costs 0 real_cost = -863.6 # command:CPU_time= 2906.97 sec, elapsed time= 4752.81 sec) # command:rm -f sort.tmp /projects/compbio/bin/sorttbl real_cost < decoys/evaluate.rdb > sort.tmp mv -f sort.tmp decoys/evaluate.rdb mv -f decoys/evaluate.pretty decoys/evaluate.pretty.old /projects/compbio/experiments/protein-predict/casp7/scripts/prettyscore -terse -targpfx -decpoint < decoys/evaluate.rdb > decoys/evaluate.pretty rm -f decoys/evaluate_1.rdb sed -e s/XXX0000/T0305/ -e s/START_COL/1/ \ -e s/REAL_PDB/2h4vA/ \ -e s/_domain/_1/ \ -e s/read-pdb/read-pdb+servers/ \ -e 's/ReadConformPDBids/# ReadConformPDBids/' \ -e 's/# ReadConformPDB /ReadConformPDB /' \ -e 's/include COSTFCN.costfcn//' \ -e s/.COSTFCN// \ < /projects/compbio/experiments/protein-predict/casp7/starter-directory/evaluate.under \ | nice -2 /projects/compbio/programs/undertaker/undertaker # command:# Seed set to 1175189298 # 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= 6.10007 sec, elapsed time= 7.58916 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= 6.18306 sec, elapsed time= 7.94461 sec) # command:# Prefix for input files set to # command:# Making conformation for sequence T0305 numbered 1 through 297 Created new target T0305 from T0305.a2m # command:# command:# No conformations to remove in PopConform # command:# cleared Id set # command:# command:# ReadConformPDB reading from PDB file T0305_1.real.pdb looking for model 1 Skipped atom 698, because occupancy 5.0000000e-01 <= existing 0.500 in T0305_1.real.pdb Skipped atom 700, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 702, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 704, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 706, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 708, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 710, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 712, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 714, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 716, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 718, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 720, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 722, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 724, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 726, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 728, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 730, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 732, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 734, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 736, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 920, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 922, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 924, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 926, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 928, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 930, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 932, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 934, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 1113, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 1117, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 1119, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 1121, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 1123, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 1175, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 1179, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 1181, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 1183, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 1185, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 1187, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 1254, because occupancy 0.300 <= existing 0.700 in T0305_1.real.pdb Skipped atom 1258, because occupancy 0.300 <= existing 0.700 in T0305_1.real.pdb Skipped atom 1260, because occupancy 0.300 <= existing 0.700 in T0305_1.real.pdb Skipped atom 1262, because occupancy 0.300 <= existing 0.700 in T0305_1.real.pdb Skipped atom 1264, because occupancy 0.300 <= existing 0.700 in T0305_1.real.pdb Skipped atom 1343, because occupancy 0.200 <= existing 0.800 in T0305_1.real.pdb Skipped atom 1347, because occupancy 0.200 <= existing 0.800 in T0305_1.real.pdb Skipped atom 1349, because occupancy 0.200 <= existing 0.800 in T0305_1.real.pdb Skipped atom 1661, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 1665, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 1667, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 1669, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 1671, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 1727, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 1731, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 1733, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 1837, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 1841, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 1843, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 1960, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 1964, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 1966, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 1968, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 1970, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 1972, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 2008, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 2010, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 2012, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 2014, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 2016, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 2018, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 2020, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 2022, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 2024, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 2026, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 2028, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 2030, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 2032, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 2034, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 2036, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 2038, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 2040, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 2042, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 2044, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 2046, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 2294, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 2298, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 2300, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 2302, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb Skipped atom 2304, because occupancy 0.500 <= existing 0.500 in T0305_1.real.pdb # WARNING: incomplete conformation T0305 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= 8.66268 sec, elapsed time= 10.7612 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 275 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -91.1232 # GDT_score(maxd=8,maxw=2.9)= -93.9906 # GDT_score(maxd=8,maxw=3.2)= -92.1353 # GDT_score(maxd=8,maxw=3.5)= -89.9671 # GDT_score(maxd=10,maxw=3.8)= -90.9748 # GDT_score(maxd=10,maxw=4)= -89.3993 # GDT_score(maxd=10,maxw=4.2)= -87.5829 # GDT_score(maxd=12,maxw=4.3)= -89.751 # GDT_score(maxd=12,maxw=4.5)= -87.9712 # GDT_score(maxd=12,maxw=4.7)= -86.0521 # GDT_score(maxd=14,maxw=5.2)= -83.9586 # GDT_score(maxd=14,maxw=5.5)= -80.9519 # command:# Prefix for output files set to # command:superimposing iter= 0 total_weight= 3351.000 rmsd (weighted)= 1.888 (unweighted)= 14.142 superimposing iter= 1 total_weight= 12087.735 rmsd (weighted)= 0.714 (unweighted)= 14.165 superimposing iter= 2 total_weight= 4574.475 rmsd (weighted)= 0.491 (unweighted)= 14.173 superimposing iter= 3 total_weight= 2766.412 rmsd (weighted)= 0.438 (unweighted)= 14.177 superimposing iter= 4 total_weight= 2438.331 rmsd (weighted)= 0.418 (unweighted)= 14.180 superimposing iter= 5 total_weight= 2350.015 rmsd (weighted)= 0.406 (unweighted)= 14.181 # command:# Prefix for output files set to decoys/ # command:# request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1998339410.pdb -s /var/tmp/to_scwrl_1998339410.seq -o /var/tmp/from_scwrl_1998339410.pdb > /var/tmp/scwrl_1998339410.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1998339410.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 275 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -87.4094 # GDT_score(maxd=8,maxw=2.9)= -89.2849 # GDT_score(maxd=8,maxw=3.2)= -87.3105 # GDT_score(maxd=8,maxw=3.5)= -84.9687 # GDT_score(maxd=10,maxw=3.8)= -86.4141 # GDT_score(maxd=10,maxw=4)= -84.6245 # GDT_score(maxd=10,maxw=4.2)= -82.6777 # GDT_score(maxd=12,maxw=4.3)= -85.2328 # GDT_score(maxd=12,maxw=4.5)= -83.3442 # GDT_score(maxd=12,maxw=4.7)= -81.3125 # GDT_score(maxd=14,maxw=5.2)= -79.2169 # GDT_score(maxd=14,maxw=5.5)= -75.9326 # command:# request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1637759969.pdb -s /var/tmp/to_scwrl_1637759969.seq -o /var/tmp/from_scwrl_1637759969.pdb > /var/tmp/scwrl_1637759969.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1637759969.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 295 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -91.0326 # GDT_score(maxd=8,maxw=2.9)= -94.0296 # GDT_score(maxd=8,maxw=3.2)= -92.1277 # GDT_score(maxd=8,maxw=3.5)= -90.0235 # GDT_score(maxd=10,maxw=3.8)= -91.0227 # GDT_score(maxd=10,maxw=4)= -89.4827 # GDT_score(maxd=10,maxw=4.2)= -87.6233 # GDT_score(maxd=12,maxw=4.3)= -89.8285 # GDT_score(maxd=12,maxw=4.5)= -87.999 # GDT_score(maxd=12,maxw=4.7)= -86.0186 # GDT_score(maxd=14,maxw=5.2)= -83.9225 # GDT_score(maxd=14,maxw=5.5)= -80.8943 # command:# request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1747890152.pdb -s /var/tmp/to_scwrl_1747890152.seq -o /var/tmp/from_scwrl_1747890152.pdb > /var/tmp/scwrl_1747890152.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1747890152.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 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # command:# fraction of real conformation used = 0.923913 # GDT_score = -85.9601 # GDT_score(maxd=8,maxw=2.9)= -88.088 # GDT_score(maxd=8,maxw=3.2)= -86.642 # GDT_score(maxd=8,maxw=3.5)= -84.8987 # GDT_score(maxd=10,maxw=3.8)= -85.6513 # GDT_score(maxd=10,maxw=4)= -84.3731 # GDT_score(maxd=10,maxw=4.2)= -82.9374 # GDT_score(maxd=12,maxw=4.3)= -84.6228 # GDT_score(maxd=12,maxw=4.5)= -83.2232 # GDT_score(maxd=12,maxw=4.7)= -81.7073 # GDT_score(maxd=14,maxw=5.2)= -80.0232 # GDT_score(maxd=14,maxw=5.5)= -77.5468 # command:# request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1664043589.pdb -s /var/tmp/to_scwrl_1664043589.seq -o /var/tmp/from_scwrl_1664043589.pdb > /var/tmp/scwrl_1664043589.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1664043589.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 T0305 can't currently be optimized by undertaker # command:# fraction of real conformation used = 0.949275 # GDT_score = -82.0652 # GDT_score(maxd=8,maxw=2.9)= -83.9184 # GDT_score(maxd=8,maxw=3.2)= -81.8972 # GDT_score(maxd=8,maxw=3.5)= -79.83 # GDT_score(maxd=10,maxw=3.8)= -81.2496 # GDT_score(maxd=10,maxw=4)= -79.8118 # GDT_score(maxd=10,maxw=4.2)= -78.1841 # GDT_score(maxd=12,maxw=4.3)= -80.4662 # GDT_score(maxd=12,maxw=4.5)= -78.874 # GDT_score(maxd=12,maxw=4.7)= -77.2149 # GDT_score(maxd=14,maxw=5.2)= -75.6451 # GDT_score(maxd=14,maxw=5.5)= -72.9717 # command:# request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_83511183.pdb -s /var/tmp/to_scwrl_83511183.seq -o /var/tmp/from_scwrl_83511183.pdb > /var/tmp/scwrl_83511183.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_83511183.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 T0305.try1-opt2.pdb looking for model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -87.7717 # GDT_score(maxd=8,maxw=2.9)= -89.575 # GDT_score(maxd=8,maxw=3.2)= -87.6989 # GDT_score(maxd=8,maxw=3.5)= -85.3718 # GDT_score(maxd=10,maxw=3.8)= -86.7847 # GDT_score(maxd=10,maxw=4)= -85.025 # GDT_score(maxd=10,maxw=4.2)= -83.0787 # GDT_score(maxd=12,maxw=4.3)= -85.6169 # GDT_score(maxd=12,maxw=4.5)= -83.7068 # GDT_score(maxd=12,maxw=4.7)= -81.6665 # GDT_score(maxd=14,maxw=5.2)= -79.5578 # GDT_score(maxd=14,maxw=5.5)= -76.3373 # command:# Prefix for output files set to # command:superimposing iter= 0 total_weight= 3351.000 rmsd (weighted)= 2.447 (unweighted)= 14.891 superimposing iter= 1 total_weight= 12407.392 rmsd (weighted)= 0.861 (unweighted)= 14.886 superimposing iter= 2 total_weight= 5176.158 rmsd (weighted)= 0.555 (unweighted)= 14.889 superimposing iter= 3 total_weight= 2770.966 rmsd (weighted)= 0.495 (unweighted)= 14.891 superimposing iter= 4 total_weight= 2342.244 rmsd (weighted)= 0.482 (unweighted)= 14.893 superimposing iter= 5 total_weight= 2252.380 rmsd (weighted)= 0.478 (unweighted)= 14.895 # command:# Prefix for output files set to decoys/ # command:# Prefix for input files set to # command:# ReadConformPDB reading from PDB file T0305.undertaker-align.pdb looking for model 1 WARNING: atoms too close: (T0305)V30.C and (T0305)C33.C only 0.000 apart, marking (T0305)C33.C as missing WARNING: atoms too close: (T0305)Q31.N and (T0305)T34.N only 0.000 apart, marking (T0305)Q31.N as missing WARNING: atoms too close: (T0305)Q31.CA and (T0305)T34.CA only 0.000 apart, marking (T0305)Q31.CA as missing WARNING: atoms too close: (T0305)S76.C and (T0305)H78.C only 0.000 apart, marking (T0305)H78.C as missing WARNING: atoms too close: (T0305)K77.N and (T0305)S79.N only 0.000 apart, marking (T0305)K77.N as missing WARNING: atoms too close: (T0305)K77.CA and (T0305)S79.CA only 0.000 apart, marking (T0305)K77.CA as missing WARNING: atoms too close: (T0305)K175.C and (T0305)G186.C only 0.000 apart, marking (T0305)G186.C as missing WARNING: atoms too close: (T0305)V176.N and (T0305)R187.N only 0.000 apart, marking (T0305)V176.N as missing WARNING: atoms too close: (T0305)V176.CA and (T0305)R187.CA only 0.000 apart, marking (T0305)V176.CA as missing # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # command:# naming current conformation align1 # command:# fraction of real conformation used = 0.956522 # GDT_score = -89.0399 # GDT_score(maxd=8,maxw=2.9)= -91.2088 # GDT_score(maxd=8,maxw=3.2)= -89.6558 # GDT_score(maxd=8,maxw=3.5)= -87.8035 # GDT_score(maxd=10,maxw=3.8)= -88.5931 # GDT_score(maxd=10,maxw=4)= -87.2478 # GDT_score(maxd=10,maxw=4.2)= -85.7538 # GDT_score(maxd=12,maxw=4.3)= -87.5123 # GDT_score(maxd=12,maxw=4.5)= -86.0537 # GDT_score(maxd=12,maxw=4.7)= -84.4653 # GDT_score(maxd=14,maxw=5.2)= -82.7115 # GDT_score(maxd=14,maxw=5.5)= -80.1291 # command:# ReadConformPDB reading from PDB file T0305.undertaker-align.pdb looking for model 2 WARNING: atoms too close: (T0305)Q20.C and (T0305)G22.C only 0.000 apart, marking (T0305)G22.C as missing WARNING: atoms too close: (T0305)H21.N and (T0305)F23.N only 0.000 apart, marking (T0305)H21.N as missing WARNING: atoms too close: (T0305)H21.CA and (T0305)F23.CA only 0.000 apart, marking (T0305)H21.CA as missing WARNING: atoms too close: (T0305)T34.C and (T0305)D36.C only 0.000 apart, marking (T0305)D36.C as missing WARNING: atoms too close: (T0305)A35.N and (T0305)M37.N only 0.000 apart, marking (T0305)A35.N as missing WARNING: atoms too close: (T0305)A35.CA and (T0305)M37.CA only 0.000 apart, marking (T0305)A35.CA as missing WARNING: atoms too close: (T0305)K175.C and (T0305)G186.C only 0.000 apart, marking (T0305)G186.C as missing WARNING: atoms too close: (T0305)V176.N and (T0305)R187.N only 0.000 apart, marking (T0305)V176.N as missing WARNING: atoms too close: (T0305)V176.CA and (T0305)R187.CA only 0.000 apart, marking (T0305)V176.CA as missing # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # command:# naming current conformation align2 # command:# fraction of real conformation used = 0.963768 # GDT_score = -82.971 # GDT_score(maxd=8,maxw=2.9)= -84.8341 # GDT_score(maxd=8,maxw=3.2)= -82.7855 # GDT_score(maxd=8,maxw=3.5)= -80.6725 # GDT_score(maxd=10,maxw=3.8)= -82.1458 # GDT_score(maxd=10,maxw=4)= -80.6803 # GDT_score(maxd=10,maxw=4.2)= -79.0304 # GDT_score(maxd=12,maxw=4.3)= -81.3663 # GDT_score(maxd=12,maxw=4.5)= -79.7502 # GDT_score(maxd=12,maxw=4.7)= -78.0738 # GDT_score(maxd=14,maxw=5.2)= -76.5265 # GDT_score(maxd=14,maxw=5.5)= -73.8258 # command:# ReadConformPDB reading from PDB file T0305.undertaker-align.pdb looking for model 3 WARNING: atoms too close: (T0305)A35.C and (T0305)M37.C only 0.000 apart, marking (T0305)M37.C as missing WARNING: atoms too close: (T0305)D36.N and (T0305)N38.N only 0.000 apart, marking (T0305)D36.N as missing WARNING: atoms too close: (T0305)D36.CA and (T0305)N38.CA only 0.000 apart, marking (T0305)D36.CA as missing WARNING: atoms too close: (T0305)K175.C and (T0305)G186.C only 0.000 apart, marking (T0305)G186.C as missing WARNING: atoms too close: (T0305)V176.N and (T0305)R187.N only 0.000 apart, marking (T0305)V176.N as missing WARNING: atoms too close: (T0305)V176.CA and (T0305)R187.CA only 0.000 apart, marking (T0305)V176.CA as missing # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # command:# naming current conformation align3 # command:# ReadConformPDB reading from PDB file T0305.undertaker-align.pdb looking for model 4 WARNING: atoms too close: (T0305)R69.C and (T0305)S76.C only 0.000 apart, marking (T0305)S76.C as missing WARNING: atoms too close: (T0305)P70.N and (T0305)K77.N only 0.000 apart, marking (T0305)P70.N as missing WARNING: atoms too close: (T0305)P70.CA and (T0305)K77.CA only 0.000 apart, marking (T0305)P70.CA as missing WARNING: atoms too close: (T0305)N173.C and (T0305)P184.C only 0.000 apart, marking (T0305)P184.C as missing WARNING: atoms too close: (T0305)T174.N and (T0305)K185.N only 0.000 apart, marking (T0305)T174.N as missing WARNING: atoms too close: (T0305)T174.CA and (T0305)K185.CA only 0.000 apart, marking (T0305)T174.CA as missing WARNING: atoms too close: (T0305)A222.C and (T0305)A223.C only 0.000 apart, marking (T0305)A223.C as missing WARNING: atoms too close: (T0305)A223.N and (T0305)R224.N only 0.000 apart, marking (T0305)A223.N as missing WARNING: atoms too close: (T0305)A223.CA and (T0305)R224.CA only 0.000 apart, marking (T0305)A223.CA as missing # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # command:# naming current conformation align4 # command:# ReadConformPDB reading from PDB file T0305.undertaker-align.pdb looking for model 5 WARNING: atoms too close: (T0305)R69.C and (T0305)P72.C only 0.000 apart, marking (T0305)P72.C as missing WARNING: atoms too close: (T0305)P70.N and (T0305)G73.N only 0.000 apart, marking (T0305)P70.N as missing WARNING: atoms too close: (T0305)P70.CA and (T0305)G73.CA only 0.000 apart, marking (T0305)P70.CA as missing WARNING: atoms too close: (T0305)N173.C and (T0305)P184.C only 0.000 apart, marking (T0305)P184.C as missing WARNING: atoms too close: (T0305)T174.N and (T0305)K185.N only 0.000 apart, marking (T0305)T174.N as missing WARNING: atoms too close: (T0305)T174.CA and (T0305)K185.CA only 0.000 apart, marking (T0305)T174.CA as missing # WARNING: incomplete conformation T0305 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 275 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ../model2.ts-submitted looking for model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ../model3.ts-submitted looking for model 1 # Found a chain break before 295 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ../model4.ts-submitted looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # ReadConformPDB reading from PDB file ../model5.ts-submitted looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # ReadConformPDB reading from PDB file T0305.try1-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 276 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0305.try1-opt1.pdb.gz looking for model 1 # Found a chain break before 276 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0305.try1-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0305.try1-opt2.pdb.gz looking for model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0305.try1-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0305.try2-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0305.try2-opt1.pdb.gz looking for model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0305.try2-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 296 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0305.try2-opt2.pdb.gz looking for model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0305.try2-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0305.try3-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 295 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0305.try3-opt1.pdb.gz looking for model 1 # Found a chain break before 295 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0305.try3-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 277 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0305.try3-opt2.pdb.gz looking for model 1 # Found a chain break before 295 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0305.try3-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 295 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0305.try4-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0305.try4-opt1.pdb.gz looking for model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0305.try4-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 277 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0305.try4-opt2.pdb.gz looking for model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0305.try4-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ../dimer/decoys/T0305.try1-opt1-scwrl.pdb.gz looking for chain 'A' model 1 # Found a chain break before 273 # copying to AlignedFragments data structure # naming current conformation dimer//try1-opt1-scwrl # ReadConformPDB reading from PDB file ../dimer/decoys/T0305.try1-opt1.pdb.gz looking for chain 'A' model 1 # Found a chain break before 273 # copying to AlignedFragments data structure # naming current conformation dimer//try1-opt1 # ReadConformPDB reading from PDB file ../dimer/decoys/T0305.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/T0305.try1-opt2.pdb.gz looking for chain 'A' model 1 # Found a chain break before 273 # copying to AlignedFragments data structure # naming current conformation dimer//try1-opt2 # ReadConformPDB reading from PDB file ../dimer/decoys/T0305.try1-opt2.repack-nonPC.pdb.gz looking for chain 'A' model 1 # Found a chain break before 273 # copying to AlignedFragments data structure # naming current conformation dimer//try1-opt2.repack-nonPC # ReadConformPDB reading from PDB file ../dimer/decoys/T0305.try1-opt2.unpack.pdb.gz looking for chain 'A' model 1 # Found a chain break before 273 # copying to AlignedFragments data structure # naming current conformation dimer//try1-opt2.unpack # ReadConformPDB reading from PDB file ../dimer/decoys/T0305.try2-opt1-scwrl.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation dimer//try2-opt1-scwrl # ReadConformPDB reading from PDB file ../dimer/decoys/T0305.try2-opt1.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation dimer//try2-opt1 # ReadConformPDB reading from PDB file ../dimer/decoys/T0305.try2-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//try2-opt2.gromacs0 # ReadConformPDB reading from PDB file ../dimer/decoys/T0305.try2-opt2.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation dimer//try2-opt2 # ReadConformPDB reading from PDB file ../dimer/decoys/T0305.try2-opt2.repack-nonPC.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation dimer//try2-opt2.repack-nonPC # ReadConformPDB reading from PDB file ../dimer/decoys/T0305.try2-opt2.unpack.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation dimer//try2-opt2.unpack # ReadConformPDB reading from PDB file ../dimer/decoys/dimer-try4-1rpmA.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation dimer//dimer-try4-1rpmA # ReadConformPDB reading from PDB file ../dimer/decoys/dimer-try4-1rpmA.unpack.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation dimer//dimer-try4-1rpmA.unpack # ReadConformPDB reading from PDB file ../dimer/decoys/dimer-try4-2fh7A.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation dimer//dimer-try4-2fh7A # ReadConformPDB reading from PDB file ../dimer/decoys/from-tetramer-try1-opt2.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation dimer//from-tetramer-try1-opt2 # ReadConformPDB reading from PDB file ../dimer/decoys/from-tetramer-try1-opt2.unpack.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation dimer//from-tetramer-try1-opt2.unpack # ReadConformPDB reading from PDB file ../dimer/decoys/from-tetramer-try4-1larA.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation dimer//from-tetramer-try4-1larA # ReadConformPDB reading from PDB file ../dimer/decoys/from-tetramer-try4-1larA.unpack.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation dimer//from-tetramer-try4-1larA.unpack # ReadConformPDB reading from PDB file ../tetramer/decoys/T0305.try1-opt1-scwrl.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation tetramer//try1-opt1-scwrl # ReadConformPDB reading from PDB file ../tetramer/decoys/T0305.try1-opt1.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation tetramer//try1-opt1 # ReadConformPDB reading from PDB file ../tetramer/decoys/T0305.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 tetramer//try1-opt2.gromacs0 # ReadConformPDB reading from PDB file ../tetramer/decoys/T0305.try1-opt2.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation tetramer//try1-opt2 # ReadConformPDB reading from PDB file ../tetramer/decoys/T0305.try2-opt1-scwrl.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation tetramer//try2-opt1-scwrl # ReadConformPDB reading from PDB file ../tetramer/decoys/T0305.try2-opt1.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation tetramer//try2-opt1 # ReadConformPDB reading from PDB file ../tetramer/decoys/T0305.try2-opt2.gromacs0.pdb.gz looking for chain 'A' model 1 Faking rotamer for incomplete or colinear backbone at (T0305)G297 # Found a chain break before 296 # copying to AlignedFragments data structure # naming current conformation tetramer//try2-opt2.gromacs0 # ReadConformPDB reading from PDB file ../tetramer/decoys/T0305.try2-opt2.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation tetramer//try2-opt2 # ReadConformPDB reading from PDB file ../tetramer/decoys/T0305.try3-opt1-scwrl.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation tetramer//try3-opt1-scwrl # ReadConformPDB reading from PDB file ../tetramer/decoys/T0305.try3-opt1.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation tetramer//try3-opt1 # ReadConformPDB reading from PDB file ../tetramer/decoys/T0305.try3-opt2.gromacs0.pdb.gz looking for chain 'A' model 1 # Found a chain break before 296 # copying to AlignedFragments data structure # naming current conformation tetramer//try3-opt2.gromacs0 # ReadConformPDB reading from PDB file ../tetramer/decoys/T0305.try3-opt2.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation tetramer//try3-opt2 # ReadConformPDB reading from PDB file ../tetramer/decoys/T0305.try4-opt1-scwrl.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation tetramer//try4-opt1-scwrl # ReadConformPDB reading from PDB file ../tetramer/decoys/T0305.try4-opt1.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation tetramer//try4-opt1 # ReadConformPDB reading from PDB file ../tetramer/decoys/T0305.try4-opt2.gromacs0.pdb.gz looking for chain 'A' model 1 # Found a chain break before 296 # copying to AlignedFragments data structure # naming current conformation tetramer//try4-opt2.gromacs0 # ReadConformPDB reading from PDB file ../tetramer/decoys/T0305.try4-opt2.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation tetramer//try4-opt2 # ReadConformPDB reading from PDB file ../tetramer/decoys/tetramer-try4-1larA.pdb.gz looking for chain 'A' model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation tetramer//tetramer-try4-1larA # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_678630481.pdb -s /var/tmp/to_scwrl_678630481.seq -o /var/tmp/from_scwrl_678630481.pdb > /var/tmp/scwrl_678630481.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_678630481.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 T0305 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1111492933.pdb -s /var/tmp/to_scwrl_1111492933.seq -o /var/tmp/from_scwrl_1111492933.pdb > /var/tmp/scwrl_1111492933.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1111492933.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 T0305 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1841929067.pdb -s /var/tmp/to_scwrl_1841929067.seq -o /var/tmp/from_scwrl_1841929067.pdb > /var/tmp/scwrl_1841929067.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1841929067.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 T0305 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_764882093.pdb -s /var/tmp/to_scwrl_764882093.seq -o /var/tmp/from_scwrl_764882093.pdb > /var/tmp/scwrl_764882093.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_764882093.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 T0305 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_623500525.pdb -s /var/tmp/to_scwrl_623500525.seq -o /var/tmp/from_scwrl_623500525.pdb > /var/tmp/scwrl_623500525.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_623500525.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 T0305 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_188234420.pdb -s /var/tmp/to_scwrl_188234420.seq -o /var/tmp/from_scwrl_188234420.pdb > /var/tmp/scwrl_188234420.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_188234420.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_RECOM_TS1-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1080990203.pdb -s /var/tmp/to_scwrl_1080990203.seq -o /var/tmp/from_scwrl_1080990203.pdb > /var/tmp/scwrl_1080990203.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1080990203.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_RECOM_TS2-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_2048168019.pdb -s /var/tmp/to_scwrl_2048168019.seq -o /var/tmp/from_scwrl_2048168019.pdb > /var/tmp/scwrl_2048168019.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2048168019.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_RECOM_TS3-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1663791546.pdb -s /var/tmp/to_scwrl_1663791546.seq -o /var/tmp/from_scwrl_1663791546.pdb > /var/tmp/scwrl_1663791546.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1663791546.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_RECOM_TS4-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1075726250.pdb -s /var/tmp/to_scwrl_1075726250.seq -o /var/tmp/from_scwrl_1075726250.pdb > /var/tmp/scwrl_1075726250.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1075726250.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_RECOM_TS5-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1979594066.pdb -s /var/tmp/to_scwrl_1979594066.seq -o /var/tmp/from_scwrl_1979594066.pdb > /var/tmp/scwrl_1979594066.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1979594066.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_TS1-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_932392952.pdb -s /var/tmp/to_scwrl_932392952.seq -o /var/tmp/from_scwrl_932392952.pdb > /var/tmp/scwrl_932392952.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_932392952.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_TS2-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1624247891.pdb -s /var/tmp/to_scwrl_1624247891.seq -o /var/tmp/from_scwrl_1624247891.pdb > /var/tmp/scwrl_1624247891.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1624247891.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_TS3-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1519088834.pdb -s /var/tmp/to_scwrl_1519088834.seq -o /var/tmp/from_scwrl_1519088834.pdb > /var/tmp/scwrl_1519088834.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1519088834.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_TS4-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_946756262.pdb -s /var/tmp/to_scwrl_946756262.seq -o /var/tmp/from_scwrl_946756262.pdb > /var/tmp/scwrl_946756262.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_946756262.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_TS5-scwrl # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # Found a chain break before 278 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1844680617.pdb -s /var/tmp/to_scwrl_1844680617.seq -o /var/tmp/from_scwrl_1844680617.pdb > /var/tmp/scwrl_1844680617.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1844680617.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 289 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_310897203.pdb -s /var/tmp/to_scwrl_310897203.seq -o /var/tmp/from_scwrl_310897203.pdb > /var/tmp/scwrl_310897203.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_310897203.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 290 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1764729039.pdb -s /var/tmp/to_scwrl_1764729039.seq -o /var/tmp/from_scwrl_1764729039.pdb > /var/tmp/scwrl_1764729039.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1764729039.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 290 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_133319363.pdb -s /var/tmp/to_scwrl_133319363.seq -o /var/tmp/from_scwrl_133319363.pdb > /var/tmp/scwrl_133319363.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_133319363.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 276 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1868689568.pdb -s /var/tmp/to_scwrl_1868689568.seq -o /var/tmp/from_scwrl_1868689568.pdb > /var/tmp/scwrl_1868689568.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1868689568.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 292 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_875224540.pdb -s /var/tmp/to_scwrl_875224540.seq -o /var/tmp/from_scwrl_875224540.pdb > /var/tmp/scwrl_875224540.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_875224540.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 281 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1026971265.pdb -s /var/tmp/to_scwrl_1026971265.seq -o /var/tmp/from_scwrl_1026971265.pdb > /var/tmp/scwrl_1026971265.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1026971265.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 292 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_169296637.pdb -s /var/tmp/to_scwrl_169296637.seq -o /var/tmp/from_scwrl_169296637.pdb > /var/tmp/scwrl_169296637.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_169296637.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 266 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1357680251.pdb -s /var/tmp/to_scwrl_1357680251.seq -o /var/tmp/from_scwrl_1357680251.pdb > /var/tmp/scwrl_1357680251.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1357680251.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 290 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_174324097.pdb -s /var/tmp/to_scwrl_174324097.seq -o /var/tmp/from_scwrl_174324097.pdb > /var/tmp/scwrl_174324097.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_174324097.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 278 # copying to AlignedFragments data structure # naming current conformation BayesHH_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1738565199.pdb -s /var/tmp/to_scwrl_1738565199.seq -o /var/tmp/from_scwrl_1738565199.pdb > /var/tmp/scwrl_1738565199.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1738565199.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 279 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1208536014.pdb -s /var/tmp/to_scwrl_1208536014.seq -o /var/tmp/from_scwrl_1208536014.pdb > /var/tmp/scwrl_1208536014.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1208536014.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 279 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1812084067.pdb -s /var/tmp/to_scwrl_1812084067.seq -o /var/tmp/from_scwrl_1812084067.pdb > /var/tmp/scwrl_1812084067.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1812084067.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 278 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1338971704.pdb -s /var/tmp/to_scwrl_1338971704.seq -o /var/tmp/from_scwrl_1338971704.pdb > /var/tmp/scwrl_1338971704.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1338971704.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 278 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_725095957.pdb -s /var/tmp/to_scwrl_725095957.seq -o /var/tmp/from_scwrl_725095957.pdb > /var/tmp/scwrl_725095957.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_725095957.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 294 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1895595250.pdb -s /var/tmp/to_scwrl_1895595250.seq -o /var/tmp/from_scwrl_1895595250.pdb > /var/tmp/scwrl_1895595250.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1895595250.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 294 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_2017602185.pdb -s /var/tmp/to_scwrl_2017602185.seq -o /var/tmp/from_scwrl_2017602185.pdb > /var/tmp/scwrl_2017602185.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2017602185.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 T0305 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1836588891.pdb -s /var/tmp/to_scwrl_1836588891.seq -o /var/tmp/from_scwrl_1836588891.pdb > /var/tmp/scwrl_1836588891.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1836588891.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 # Found a chain break before 294 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1590040670.pdb -s /var/tmp/to_scwrl_1590040670.seq -o /var/tmp/from_scwrl_1590040670.pdb > /var/tmp/scwrl_1590040670.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1590040670.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 T0305 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_635000632.pdb -s /var/tmp/to_scwrl_635000632.seq -o /var/tmp/from_scwrl_635000632.pdb > /var/tmp/scwrl_635000632.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_635000632.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 T0305 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_312605769.pdb -s /var/tmp/to_scwrl_312605769.seq -o /var/tmp/from_scwrl_312605769.pdb > /var/tmp/scwrl_312605769.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_312605769.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 T0305 can't currently be optimized by undertaker # naming current conformation CPHmodels_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1778275090.pdb -s /var/tmp/to_scwrl_1778275090.seq -o /var/tmp/from_scwrl_1778275090.pdb > /var/tmp/scwrl_1778275090.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1778275090.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 T0305 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1715990835.pdb -s /var/tmp/to_scwrl_1715990835.seq -o /var/tmp/from_scwrl_1715990835.pdb > /var/tmp/scwrl_1715990835.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1715990835.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 T0305 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_213290141.pdb -s /var/tmp/to_scwrl_213290141.seq -o /var/tmp/from_scwrl_213290141.pdb > /var/tmp/scwrl_213290141.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_213290141.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 T0305 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1294582989.pdb -s /var/tmp/to_scwrl_1294582989.seq -o /var/tmp/from_scwrl_1294582989.pdb > /var/tmp/scwrl_1294582989.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1294582989.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 T0305 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_644233439.pdb -s /var/tmp/to_scwrl_644233439.seq -o /var/tmp/from_scwrl_644233439.pdb > /var/tmp/scwrl_644233439.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_644233439.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 T0305 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_45400560.pdb -s /var/tmp/to_scwrl_45400560.seq -o /var/tmp/from_scwrl_45400560.pdb > /var/tmp/scwrl_45400560.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_45400560.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 T0305 can't currently be optimized by undertaker # naming current conformation Distill_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_79492295.pdb -s /var/tmp/to_scwrl_79492295.seq -o /var/tmp/from_scwrl_79492295.pdb > /var/tmp/scwrl_79492295.log Error: Couldn't open file /var/tmp/from_scwrl_79492295.pdb or /var/tmp/from_scwrl_79492295.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_79492295_b.pdb or decoys//var/tmp/from_scwrl_79492295_b.pdb.gz for input Trying /var/tmp/from_scwrl_79492295_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_79492295_b.pdb or /var/tmp/from_scwrl_79492295_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_79492295_a.pdb or decoys//var/tmp/from_scwrl_79492295_a.pdb.gz for input Trying /var/tmp/from_scwrl_79492295_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_79492295_a.pdb or /var/tmp/from_scwrl_79492295_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_79492295.pdb or /var/tmp/from_scwrl_79492295_b.pdb or /var/tmp/from_scwrl_79492295_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 T0305 can't currently be optimized by undertaker # naming current conformation Distill_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_120997683.pdb -s /var/tmp/to_scwrl_120997683.seq -o /var/tmp/from_scwrl_120997683.pdb > /var/tmp/scwrl_120997683.log Error: Couldn't open file /var/tmp/from_scwrl_120997683.pdb or /var/tmp/from_scwrl_120997683.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_120997683_b.pdb or decoys//var/tmp/from_scwrl_120997683_b.pdb.gz for input Trying /var/tmp/from_scwrl_120997683_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_120997683_b.pdb or /var/tmp/from_scwrl_120997683_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_120997683_a.pdb or decoys//var/tmp/from_scwrl_120997683_a.pdb.gz for input Trying /var/tmp/from_scwrl_120997683_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_120997683_a.pdb or /var/tmp/from_scwrl_120997683_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_120997683.pdb or /var/tmp/from_scwrl_120997683_b.pdb or /var/tmp/from_scwrl_120997683_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 T0305 can't currently be optimized by undertaker # naming current conformation Distill_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1564489394.pdb -s /var/tmp/to_scwrl_1564489394.seq -o /var/tmp/from_scwrl_1564489394.pdb > /var/tmp/scwrl_1564489394.log Error: Couldn't open file /var/tmp/from_scwrl_1564489394.pdb or /var/tmp/from_scwrl_1564489394.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1564489394_b.pdb or decoys//var/tmp/from_scwrl_1564489394_b.pdb.gz for input Trying /var/tmp/from_scwrl_1564489394_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_1564489394_b.pdb or /var/tmp/from_scwrl_1564489394_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1564489394_a.pdb or decoys//var/tmp/from_scwrl_1564489394_a.pdb.gz for input Trying /var/tmp/from_scwrl_1564489394_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_1564489394_a.pdb or /var/tmp/from_scwrl_1564489394_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_1564489394.pdb or /var/tmp/from_scwrl_1564489394_b.pdb or /var/tmp/from_scwrl_1564489394_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 T0305 can't currently be optimized by undertaker # naming current conformation Distill_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1026248557.pdb -s /var/tmp/to_scwrl_1026248557.seq -o /var/tmp/from_scwrl_1026248557.pdb > /var/tmp/scwrl_1026248557.log Error: Couldn't open file /var/tmp/from_scwrl_1026248557.pdb or /var/tmp/from_scwrl_1026248557.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1026248557_b.pdb or decoys//var/tmp/from_scwrl_1026248557_b.pdb.gz for input Trying /var/tmp/from_scwrl_1026248557_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_1026248557_b.pdb or /var/tmp/from_scwrl_1026248557_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1026248557_a.pdb or decoys//var/tmp/from_scwrl_1026248557_a.pdb.gz for input Trying /var/tmp/from_scwrl_1026248557_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_1026248557_a.pdb or /var/tmp/from_scwrl_1026248557_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_1026248557.pdb or /var/tmp/from_scwrl_1026248557_b.pdb or /var/tmp/from_scwrl_1026248557_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 T0305 can't currently be optimized by undertaker # naming current conformation Distill_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1965678300.pdb -s /var/tmp/to_scwrl_1965678300.seq -o /var/tmp/from_scwrl_1965678300.pdb > /var/tmp/scwrl_1965678300.log Error: Couldn't open file /var/tmp/from_scwrl_1965678300.pdb or /var/tmp/from_scwrl_1965678300.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1965678300_b.pdb or decoys//var/tmp/from_scwrl_1965678300_b.pdb.gz for input Trying /var/tmp/from_scwrl_1965678300_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_1965678300_b.pdb or /var/tmp/from_scwrl_1965678300_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1965678300_a.pdb or decoys//var/tmp/from_scwrl_1965678300_a.pdb.gz for input Trying /var/tmp/from_scwrl_1965678300_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_1965678300_a.pdb or /var/tmp/from_scwrl_1965678300_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_1965678300.pdb or /var/tmp/from_scwrl_1965678300_b.pdb or /var/tmp/from_scwrl_1965678300_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 # Found a chain break before 277 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1875386598.pdb -s /var/tmp/to_scwrl_1875386598.seq -o /var/tmp/from_scwrl_1875386598.pdb > /var/tmp/scwrl_1875386598.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1875386598.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 T0305 can't currently be optimized by undertaker # naming current conformation FAMSD_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_643493949.pdb -s /var/tmp/to_scwrl_643493949.seq -o /var/tmp/from_scwrl_643493949.pdb > /var/tmp/scwrl_643493949.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_643493949.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 # Found a chain break before 289 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_2098997663.pdb -s /var/tmp/to_scwrl_2098997663.seq -o /var/tmp/from_scwrl_2098997663.pdb > /var/tmp/scwrl_2098997663.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2098997663.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 T0305 can't currently be optimized by undertaker # naming current conformation FAMSD_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1596592519.pdb -s /var/tmp/to_scwrl_1596592519.seq -o /var/tmp/from_scwrl_1596592519.pdb > /var/tmp/scwrl_1596592519.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1596592519.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 T0305 can't currently be optimized by undertaker # naming current conformation FAMSD_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1518718488.pdb -s /var/tmp/to_scwrl_1518718488.seq -o /var/tmp/from_scwrl_1518718488.pdb > /var/tmp/scwrl_1518718488.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1518718488.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 291 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_978485282.pdb -s /var/tmp/to_scwrl_978485282.seq -o /var/tmp/from_scwrl_978485282.pdb > /var/tmp/scwrl_978485282.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_978485282.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 # Found a chain break before 295 # copying to AlignedFragments data structure # naming current conformation FAMS_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1765889156.pdb -s /var/tmp/to_scwrl_1765889156.seq -o /var/tmp/from_scwrl_1765889156.pdb > /var/tmp/scwrl_1765889156.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1765889156.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 T0305 can't currently be optimized by undertaker # naming current conformation FAMS_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_728915094.pdb -s /var/tmp/to_scwrl_728915094.seq -o /var/tmp/from_scwrl_728915094.pdb > /var/tmp/scwrl_728915094.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_728915094.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 292 # copying to AlignedFragments data structure # naming current conformation FAMS_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1152809378.pdb -s /var/tmp/to_scwrl_1152809378.seq -o /var/tmp/from_scwrl_1152809378.pdb > /var/tmp/scwrl_1152809378.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1152809378.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 # Found a chain break before 294 # copying to AlignedFragments data structure # naming current conformation FAMS_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1356970708.pdb -s /var/tmp/to_scwrl_1356970708.seq -o /var/tmp/from_scwrl_1356970708.pdb > /var/tmp/scwrl_1356970708.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1356970708.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 275 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1937451108.pdb -s /var/tmp/to_scwrl_1937451108.seq -o /var/tmp/from_scwrl_1937451108.pdb > /var/tmp/scwrl_1937451108.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1937451108.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 279 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_817409799.pdb -s /var/tmp/to_scwrl_817409799.seq -o /var/tmp/from_scwrl_817409799.pdb > /var/tmp/scwrl_817409799.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_817409799.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 266 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_548458766.pdb -s /var/tmp/to_scwrl_548458766.seq -o /var/tmp/from_scwrl_548458766.pdb > /var/tmp/scwrl_548458766.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_548458766.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 265 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_515063419.pdb -s /var/tmp/to_scwrl_515063419.seq -o /var/tmp/from_scwrl_515063419.pdb > /var/tmp/scwrl_515063419.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_515063419.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 273 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_565521403.pdb -s /var/tmp/to_scwrl_565521403.seq -o /var/tmp/from_scwrl_565521403.pdb > /var/tmp/scwrl_565521403.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_565521403.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 T0305 can't currently be optimized by undertaker # naming current conformation FORTE1_AL1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_418577305.pdb -s /var/tmp/to_scwrl_418577305.seq -o /var/tmp/from_scwrl_418577305.pdb > /var/tmp/scwrl_418577305.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_418577305.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 T0305 can't currently be optimized by undertaker # naming current conformation FORTE1_AL2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_204168663.pdb -s /var/tmp/to_scwrl_204168663.seq -o /var/tmp/from_scwrl_204168663.pdb > /var/tmp/scwrl_204168663.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_204168663.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 Skipped atom 26, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 28, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 30, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 32, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 210, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 212, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 214, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 216, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 262, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 264, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 266, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 268, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 270, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 272, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 274, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 276, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 278, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 280, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 282, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 284, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 286, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 288, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 290, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 292, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 386, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 388, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 390, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 392, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 462, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 464, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 466, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 468, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 518, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 520, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 522, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 524, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 526, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 528, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 530, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 532, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 666, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 668, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 670, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 672, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 678, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 680, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 682, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 684, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 754, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 756, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 758, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 760, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 762, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 764, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 766, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 768, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 770, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 772, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 774, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 776, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 778, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 780, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 782, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 784, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 786, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 788, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 790, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 792, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 794, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 796, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 798, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 800, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 802, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 804, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 806, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 808, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 810, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 812, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 814, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 816, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 818, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 820, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 822, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 824, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 826, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 828, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 830, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 832, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 834, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 836, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 838, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 840, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 842, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 844, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 846, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 848, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 854, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 856, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 858, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 860, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 954, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 956, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 958, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 960, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 978, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 980, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 982, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 984, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1002, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1004, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1006, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1008, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1074, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1076, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1078, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1080, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1106, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1107, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1109, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1110, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1112, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1113, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1115, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1116, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation FORTE1_AL3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_8078426.pdb -s /var/tmp/to_scwrl_8078426.seq -o /var/tmp/from_scwrl_8078426.pdb > /var/tmp/scwrl_8078426.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_8078426.pdb # conformation set from SCWRL output # naming current conformation FORTE1_AL3-scwrl # ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation FORTE1_AL4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1053577937.pdb -s /var/tmp/to_scwrl_1053577937.seq -o /var/tmp/from_scwrl_1053577937.pdb > /var/tmp/scwrl_1053577937.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1053577937.pdb # conformation set from SCWRL output # naming current conformation FORTE1_AL4-scwrl # ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation FORTE1_AL5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_516774432.pdb -s /var/tmp/to_scwrl_516774432.seq -o /var/tmp/from_scwrl_516774432.pdb > /var/tmp/scwrl_516774432.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_516774432.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 T0305 can't currently be optimized by undertaker # naming current conformation FORTE2_AL1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1786353517.pdb -s /var/tmp/to_scwrl_1786353517.seq -o /var/tmp/from_scwrl_1786353517.pdb > /var/tmp/scwrl_1786353517.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1786353517.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 T0305 can't currently be optimized by undertaker # naming current conformation FORTE2_AL2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_622085125.pdb -s /var/tmp/to_scwrl_622085125.seq -o /var/tmp/from_scwrl_622085125.pdb > /var/tmp/scwrl_622085125.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_622085125.pdb # conformation set from SCWRL output # naming current conformation FORTE2_AL2-scwrl # ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation FORTE2_AL3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_730064573.pdb -s /var/tmp/to_scwrl_730064573.seq -o /var/tmp/from_scwrl_730064573.pdb > /var/tmp/scwrl_730064573.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_730064573.pdb # conformation set from SCWRL output # naming current conformation FORTE2_AL3-scwrl # ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation FORTE2_AL4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_933452860.pdb -s /var/tmp/to_scwrl_933452860.seq -o /var/tmp/from_scwrl_933452860.pdb > /var/tmp/scwrl_933452860.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_933452860.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 T0305 can't currently be optimized by undertaker # naming current conformation FORTE2_AL5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1266318563.pdb -s /var/tmp/to_scwrl_1266318563.seq -o /var/tmp/from_scwrl_1266318563.pdb > /var/tmp/scwrl_1266318563.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1266318563.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 292 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_775465134.pdb -s /var/tmp/to_scwrl_775465134.seq -o /var/tmp/from_scwrl_775465134.pdb > /var/tmp/scwrl_775465134.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_775465134.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 289 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1012945155.pdb -s /var/tmp/to_scwrl_1012945155.seq -o /var/tmp/from_scwrl_1012945155.pdb > /var/tmp/scwrl_1012945155.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1012945155.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 287 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1387316246.pdb -s /var/tmp/to_scwrl_1387316246.seq -o /var/tmp/from_scwrl_1387316246.pdb > /var/tmp/scwrl_1387316246.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1387316246.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 296 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_192470881.pdb -s /var/tmp/to_scwrl_192470881.seq -o /var/tmp/from_scwrl_192470881.pdb > /var/tmp/scwrl_192470881.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_192470881.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 296 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_2039193712.pdb -s /var/tmp/to_scwrl_2039193712.seq -o /var/tmp/from_scwrl_2039193712.pdb > /var/tmp/scwrl_2039193712.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2039193712.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 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1205510900.pdb -s /var/tmp/to_scwrl_1205510900.seq -o /var/tmp/from_scwrl_1205510900.pdb > /var/tmp/scwrl_1205510900.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1205510900.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 # Found a chain break before 278 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_2067857479.pdb -s /var/tmp/to_scwrl_2067857479.seq -o /var/tmp/from_scwrl_2067857479.pdb > /var/tmp/scwrl_2067857479.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2067857479.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 T0305 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_535204014.pdb -s /var/tmp/to_scwrl_535204014.seq -o /var/tmp/from_scwrl_535204014.pdb > /var/tmp/scwrl_535204014.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_535204014.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 T0305 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1157024916.pdb -s /var/tmp/to_scwrl_1157024916.seq -o /var/tmp/from_scwrl_1157024916.pdb > /var/tmp/scwrl_1157024916.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1157024916.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 293 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1516966351.pdb -s /var/tmp/to_scwrl_1516966351.seq -o /var/tmp/from_scwrl_1516966351.pdb > /var/tmp/scwrl_1516966351.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1516966351.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 T0305 can't currently be optimized by undertaker # naming current conformation FUGUE_AL1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_2053922503.pdb -s /var/tmp/to_scwrl_2053922503.seq -o /var/tmp/from_scwrl_2053922503.pdb > /var/tmp/scwrl_2053922503.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2053922503.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 T0305 can't currently be optimized by undertaker # naming current conformation FUGUE_AL2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_2135510198.pdb -s /var/tmp/to_scwrl_2135510198.seq -o /var/tmp/from_scwrl_2135510198.pdb > /var/tmp/scwrl_2135510198.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2135510198.pdb # conformation set from SCWRL output # naming current conformation FUGUE_AL2-scwrl # ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation FUGUE_AL3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1135371860.pdb -s /var/tmp/to_scwrl_1135371860.seq -o /var/tmp/from_scwrl_1135371860.pdb > /var/tmp/scwrl_1135371860.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1135371860.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 T0305 can't currently be optimized by undertaker # naming current conformation FUGUE_AL4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_635353950.pdb -s /var/tmp/to_scwrl_635353950.seq -o /var/tmp/from_scwrl_635353950.pdb > /var/tmp/scwrl_635353950.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_635353950.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 T0305 can't currently be optimized by undertaker # naming current conformation FUGUE_AL5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1140835930.pdb -s /var/tmp/to_scwrl_1140835930.seq -o /var/tmp/from_scwrl_1140835930.pdb > /var/tmp/scwrl_1140835930.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1140835930.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 268 ; scwrl3 -i /var/tmp/to_scwrl_344858922.pdb -s /var/tmp/to_scwrl_344858922.seq -o /var/tmp/from_scwrl_344858922.pdb > /var/tmp/scwrl_344858922.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_344858922.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 295 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_425321411.pdb -s /var/tmp/to_scwrl_425321411.seq -o /var/tmp/from_scwrl_425321411.pdb > /var/tmp/scwrl_425321411.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_425321411.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 291 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1958245729.pdb -s /var/tmp/to_scwrl_1958245729.seq -o /var/tmp/from_scwrl_1958245729.pdb > /var/tmp/scwrl_1958245729.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1958245729.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 293 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_893317689.pdb -s /var/tmp/to_scwrl_893317689.seq -o /var/tmp/from_scwrl_893317689.pdb > /var/tmp/scwrl_893317689.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_893317689.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 292 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_940384830.pdb -s /var/tmp/to_scwrl_940384830.seq -o /var/tmp/from_scwrl_940384830.pdb > /var/tmp/scwrl_940384830.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_940384830.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 # Found a chain break before 278 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_376283485.pdb -s /var/tmp/to_scwrl_376283485.seq -o /var/tmp/from_scwrl_376283485.pdb > /var/tmp/scwrl_376283485.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_376283485.pdb # conformation set from SCWRL output # naming current conformation GeneSilicoMetaServer_TS1-scwrl # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # Found a chain break before 278 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1311894993.pdb -s /var/tmp/to_scwrl_1311894993.seq -o /var/tmp/from_scwrl_1311894993.pdb > /var/tmp/scwrl_1311894993.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1311894993.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 275 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1144553492.pdb -s /var/tmp/to_scwrl_1144553492.seq -o /var/tmp/from_scwrl_1144553492.pdb > /var/tmp/scwrl_1144553492.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1144553492.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 T0305 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_384361912.pdb -s /var/tmp/to_scwrl_384361912.seq -o /var/tmp/from_scwrl_384361912.pdb > /var/tmp/scwrl_384361912.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_384361912.pdb # conformation set from SCWRL output # naming current conformation GeneSilicoMetaServer_TS4-scwrl # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1 # Found a chain break before 276 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_217989283.pdb -s /var/tmp/to_scwrl_217989283.seq -o /var/tmp/from_scwrl_217989283.pdb > /var/tmp/scwrl_217989283.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_217989283.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 268 ; scwrl3 -i /var/tmp/to_scwrl_1661327924.pdb -s /var/tmp/to_scwrl_1661327924.seq -o /var/tmp/from_scwrl_1661327924.pdb > /var/tmp/scwrl_1661327924.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1661327924.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 257 # copying to AlignedFragments data structure # naming current conformation HHpred2_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_23231782.pdb -s /var/tmp/to_scwrl_23231782.seq -o /var/tmp/from_scwrl_23231782.pdb > /var/tmp/scwrl_23231782.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_23231782.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 276 # copying to AlignedFragments data structure # naming current conformation HHpred3_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_840074408.pdb -s /var/tmp/to_scwrl_840074408.seq -o /var/tmp/from_scwrl_840074408.pdb > /var/tmp/scwrl_840074408.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_840074408.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 T0305 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_243908851.pdb -s /var/tmp/to_scwrl_243908851.seq -o /var/tmp/from_scwrl_243908851.pdb > /var/tmp/scwrl_243908851.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_243908851.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 T0305 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_956684642.pdb -s /var/tmp/to_scwrl_956684642.seq -o /var/tmp/from_scwrl_956684642.pdb > /var/tmp/scwrl_956684642.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_956684642.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 T0305 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_2106392971.pdb -s /var/tmp/to_scwrl_2106392971.seq -o /var/tmp/from_scwrl_2106392971.pdb > /var/tmp/scwrl_2106392971.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2106392971.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 T0305 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1019373985.pdb -s /var/tmp/to_scwrl_1019373985.seq -o /var/tmp/from_scwrl_1019373985.pdb > /var/tmp/scwrl_1019373985.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1019373985.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 T0305 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1969629797.pdb -s /var/tmp/to_scwrl_1969629797.seq -o /var/tmp/from_scwrl_1969629797.pdb > /var/tmp/scwrl_1969629797.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1969629797.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 T0305 can't currently be optimized by undertaker # naming current conformation LOOPP_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1346225570.pdb -s /var/tmp/to_scwrl_1346225570.seq -o /var/tmp/from_scwrl_1346225570.pdb > /var/tmp/scwrl_1346225570.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1346225570.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 T0305 can't currently be optimized by undertaker # naming current conformation LOOPP_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1211844865.pdb -s /var/tmp/to_scwrl_1211844865.seq -o /var/tmp/from_scwrl_1211844865.pdb > /var/tmp/scwrl_1211844865.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1211844865.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 T0305 can't currently be optimized by undertaker # naming current conformation LOOPP_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1861339862.pdb -s /var/tmp/to_scwrl_1861339862.seq -o /var/tmp/from_scwrl_1861339862.pdb > /var/tmp/scwrl_1861339862.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1861339862.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 T0305 can't currently be optimized by undertaker # naming current conformation LOOPP_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_404252824.pdb -s /var/tmp/to_scwrl_404252824.seq -o /var/tmp/from_scwrl_404252824.pdb > /var/tmp/scwrl_404252824.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_404252824.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 T0305 can't currently be optimized by undertaker # naming current conformation LOOPP_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1132218698.pdb -s /var/tmp/to_scwrl_1132218698.seq -o /var/tmp/from_scwrl_1132218698.pdb > /var/tmp/scwrl_1132218698.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1132218698.pdb # conformation set from SCWRL output # naming current conformation LOOPP_TS5-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # Found a chain break before 257 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_249060229.pdb -s /var/tmp/to_scwrl_249060229.seq -o /var/tmp/from_scwrl_249060229.pdb > /var/tmp/scwrl_249060229.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_249060229.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 275 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1561277741.pdb -s /var/tmp/to_scwrl_1561277741.seq -o /var/tmp/from_scwrl_1561277741.pdb > /var/tmp/scwrl_1561277741.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1561277741.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 224 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_501701403.pdb -s /var/tmp/to_scwrl_501701403.seq -o /var/tmp/from_scwrl_501701403.pdb > /var/tmp/scwrl_501701403.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_501701403.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 279 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_155499085.pdb -s /var/tmp/to_scwrl_155499085.seq -o /var/tmp/from_scwrl_155499085.pdb > /var/tmp/scwrl_155499085.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_155499085.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 279 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1549304292.pdb -s /var/tmp/to_scwrl_1549304292.seq -o /var/tmp/from_scwrl_1549304292.pdb > /var/tmp/scwrl_1549304292.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1549304292.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 296 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1637073264.pdb -s /var/tmp/to_scwrl_1637073264.seq -o /var/tmp/from_scwrl_1637073264.pdb > /var/tmp/scwrl_1637073264.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1637073264.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 290 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_790853035.pdb -s /var/tmp/to_scwrl_790853035.seq -o /var/tmp/from_scwrl_790853035.pdb > /var/tmp/scwrl_790853035.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_790853035.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 284 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_542656576.pdb -s /var/tmp/to_scwrl_542656576.seq -o /var/tmp/from_scwrl_542656576.pdb > /var/tmp/scwrl_542656576.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_542656576.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 278 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1981932186.pdb -s /var/tmp/to_scwrl_1981932186.seq -o /var/tmp/from_scwrl_1981932186.pdb > /var/tmp/scwrl_1981932186.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1981932186.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 278 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1216174446.pdb -s /var/tmp/to_scwrl_1216174446.seq -o /var/tmp/from_scwrl_1216174446.pdb > /var/tmp/scwrl_1216174446.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1216174446.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 T0305 can't currently be optimized by undertaker # naming current conformation NN_PUT_lab_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_353418659.pdb -s /var/tmp/to_scwrl_353418659.seq -o /var/tmp/from_scwrl_353418659.pdb > /var/tmp/scwrl_353418659.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_353418659.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 268 ; scwrl3 -i /var/tmp/to_scwrl_727766228.pdb -s /var/tmp/to_scwrl_727766228.seq -o /var/tmp/from_scwrl_727766228.pdb > /var/tmp/scwrl_727766228.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_727766228.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 268 ; scwrl3 -i /var/tmp/to_scwrl_9075629.pdb -s /var/tmp/to_scwrl_9075629.seq -o /var/tmp/from_scwrl_9075629.pdb > /var/tmp/scwrl_9075629.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_9075629.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 268 ; scwrl3 -i /var/tmp/to_scwrl_729702144.pdb -s /var/tmp/to_scwrl_729702144.seq -o /var/tmp/from_scwrl_729702144.pdb > /var/tmp/scwrl_729702144.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_729702144.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 268 ; scwrl3 -i /var/tmp/to_scwrl_2039661221.pdb -s /var/tmp/to_scwrl_2039661221.seq -o /var/tmp/from_scwrl_2039661221.pdb > /var/tmp/scwrl_2039661221.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2039661221.pdb # conformation set from SCWRL output # naming current conformation PROTINFO-AB_TS4-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1153629122.pdb -s /var/tmp/to_scwrl_1153629122.seq -o /var/tmp/from_scwrl_1153629122.pdb > /var/tmp/scwrl_1153629122.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1153629122.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 277 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1114064055.pdb -s /var/tmp/to_scwrl_1114064055.seq -o /var/tmp/from_scwrl_1114064055.pdb > /var/tmp/scwrl_1114064055.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1114064055.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 278 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_110166857.pdb -s /var/tmp/to_scwrl_110166857.seq -o /var/tmp/from_scwrl_110166857.pdb > /var/tmp/scwrl_110166857.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_110166857.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 # naming current conformation PROTINFO_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_667473400.pdb -s /var/tmp/to_scwrl_667473400.seq -o /var/tmp/from_scwrl_667473400.pdb > /var/tmp/scwrl_667473400.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_667473400.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 T0305 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1137295837.pdb -s /var/tmp/to_scwrl_1137295837.seq -o /var/tmp/from_scwrl_1137295837.pdb > /var/tmp/scwrl_1137295837.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1137295837.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 T0305 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_950241265.pdb -s /var/tmp/to_scwrl_950241265.seq -o /var/tmp/from_scwrl_950241265.pdb > /var/tmp/scwrl_950241265.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_950241265.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 T0305 can't currently be optimized by undertaker # naming current conformation Pcons6_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_911382251.pdb -s /var/tmp/to_scwrl_911382251.seq -o /var/tmp/from_scwrl_911382251.pdb > /var/tmp/scwrl_911382251.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_911382251.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 T0305 can't currently be optimized by undertaker # naming current conformation Pcons6_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_2093980480.pdb -s /var/tmp/to_scwrl_2093980480.seq -o /var/tmp/from_scwrl_2093980480.pdb > /var/tmp/scwrl_2093980480.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2093980480.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 T0305 can't currently be optimized by undertaker # naming current conformation Pcons6_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_909150589.pdb -s /var/tmp/to_scwrl_909150589.seq -o /var/tmp/from_scwrl_909150589.pdb > /var/tmp/scwrl_909150589.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_909150589.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 T0305 can't currently be optimized by undertaker # naming current conformation Pcons6_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1930756235.pdb -s /var/tmp/to_scwrl_1930756235.seq -o /var/tmp/from_scwrl_1930756235.pdb > /var/tmp/scwrl_1930756235.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1930756235.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 T0305 can't currently be optimized by undertaker # naming current conformation Pcons6_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1916126630.pdb -s /var/tmp/to_scwrl_1916126630.seq -o /var/tmp/from_scwrl_1916126630.pdb > /var/tmp/scwrl_1916126630.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1916126630.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 T0305 can't currently be optimized by undertaker # naming current conformation Phyre-1_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_107892513.pdb -s /var/tmp/to_scwrl_107892513.seq -o /var/tmp/from_scwrl_107892513.pdb > /var/tmp/scwrl_107892513.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_107892513.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 274 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_995117455.pdb -s /var/tmp/to_scwrl_995117455.seq -o /var/tmp/from_scwrl_995117455.pdb > /var/tmp/scwrl_995117455.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_995117455.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 274 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1629982845.pdb -s /var/tmp/to_scwrl_1629982845.seq -o /var/tmp/from_scwrl_1629982845.pdb > /var/tmp/scwrl_1629982845.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1629982845.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 274 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_512145337.pdb -s /var/tmp/to_scwrl_512145337.seq -o /var/tmp/from_scwrl_512145337.pdb > /var/tmp/scwrl_512145337.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_512145337.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 274 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_2127336153.pdb -s /var/tmp/to_scwrl_2127336153.seq -o /var/tmp/from_scwrl_2127336153.pdb > /var/tmp/scwrl_2127336153.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2127336153.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 274 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1879043074.pdb -s /var/tmp/to_scwrl_1879043074.seq -o /var/tmp/from_scwrl_1879043074.pdb > /var/tmp/scwrl_1879043074.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1879043074.pdb # conformation set from SCWRL output # naming current conformation Phyre-2_TS5-scwrl # ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_2073423078.pdb -s /var/tmp/to_scwrl_2073423078.seq -o /var/tmp/from_scwrl_2073423078.pdb > /var/tmp/scwrl_2073423078.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2073423078.pdb # conformation set from SCWRL output # naming current conformation Pmodeller6_TS1-scwrl # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_481553909.pdb -s /var/tmp/to_scwrl_481553909.seq -o /var/tmp/from_scwrl_481553909.pdb > /var/tmp/scwrl_481553909.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_481553909.pdb # conformation set from SCWRL output # naming current conformation Pmodeller6_TS2-scwrl # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_2034542160.pdb -s /var/tmp/to_scwrl_2034542160.seq -o /var/tmp/from_scwrl_2034542160.pdb > /var/tmp/scwrl_2034542160.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2034542160.pdb # conformation set from SCWRL output # naming current conformation Pmodeller6_TS3-scwrl # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1475243724.pdb -s /var/tmp/to_scwrl_1475243724.seq -o /var/tmp/from_scwrl_1475243724.pdb > /var/tmp/scwrl_1475243724.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1475243724.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 T0305 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_2118627173.pdb -s /var/tmp/to_scwrl_2118627173.seq -o /var/tmp/from_scwrl_2118627173.pdb > /var/tmp/scwrl_2118627173.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2118627173.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 279 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_677911548.pdb -s /var/tmp/to_scwrl_677911548.seq -o /var/tmp/from_scwrl_677911548.pdb > /var/tmp/scwrl_677911548.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_677911548.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 278 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_2017900300.pdb -s /var/tmp/to_scwrl_2017900300.seq -o /var/tmp/from_scwrl_2017900300.pdb > /var/tmp/scwrl_2017900300.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2017900300.pdb # conformation set from SCWRL output # naming current conformation RAPTOR-ACE_TS2-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1 # Found a chain break before 279 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1953075713.pdb -s /var/tmp/to_scwrl_1953075713.seq -o /var/tmp/from_scwrl_1953075713.pdb > /var/tmp/scwrl_1953075713.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1953075713.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 276 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1894085994.pdb -s /var/tmp/to_scwrl_1894085994.seq -o /var/tmp/from_scwrl_1894085994.pdb > /var/tmp/scwrl_1894085994.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1894085994.pdb # conformation set from SCWRL output # naming current conformation RAPTOR-ACE_TS4-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_223835312.pdb -s /var/tmp/to_scwrl_223835312.seq -o /var/tmp/from_scwrl_223835312.pdb > /var/tmp/scwrl_223835312.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_223835312.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 277 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_533358294.pdb -s /var/tmp/to_scwrl_533358294.seq -o /var/tmp/from_scwrl_533358294.pdb > /var/tmp/scwrl_533358294.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_533358294.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 275 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1903161624.pdb -s /var/tmp/to_scwrl_1903161624.seq -o /var/tmp/from_scwrl_1903161624.pdb > /var/tmp/scwrl_1903161624.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1903161624.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 271 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_953537457.pdb -s /var/tmp/to_scwrl_953537457.seq -o /var/tmp/from_scwrl_953537457.pdb > /var/tmp/scwrl_953537457.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_953537457.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 278 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_425535869.pdb -s /var/tmp/to_scwrl_425535869.seq -o /var/tmp/from_scwrl_425535869.pdb > /var/tmp/scwrl_425535869.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_425535869.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 277 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_909307100.pdb -s /var/tmp/to_scwrl_909307100.seq -o /var/tmp/from_scwrl_909307100.pdb > /var/tmp/scwrl_909307100.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_909307100.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 278 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_2067601512.pdb -s /var/tmp/to_scwrl_2067601512.seq -o /var/tmp/from_scwrl_2067601512.pdb > /var/tmp/scwrl_2067601512.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2067601512.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 278 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_535702726.pdb -s /var/tmp/to_scwrl_535702726.seq -o /var/tmp/from_scwrl_535702726.pdb > /var/tmp/scwrl_535702726.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_535702726.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 276 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1576780499.pdb -s /var/tmp/to_scwrl_1576780499.seq -o /var/tmp/from_scwrl_1576780499.pdb > /var/tmp/scwrl_1576780499.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1576780499.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 276 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1057413704.pdb -s /var/tmp/to_scwrl_1057413704.seq -o /var/tmp/from_scwrl_1057413704.pdb > /var/tmp/scwrl_1057413704.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1057413704.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 276 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1485943991.pdb -s /var/tmp/to_scwrl_1485943991.seq -o /var/tmp/from_scwrl_1485943991.pdb > /var/tmp/scwrl_1485943991.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1485943991.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 278 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_340679104.pdb -s /var/tmp/to_scwrl_340679104.seq -o /var/tmp/from_scwrl_340679104.pdb > /var/tmp/scwrl_340679104.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_340679104.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 278 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1003910537.pdb -s /var/tmp/to_scwrl_1003910537.seq -o /var/tmp/from_scwrl_1003910537.pdb > /var/tmp/scwrl_1003910537.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1003910537.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 278 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_247610933.pdb -s /var/tmp/to_scwrl_247610933.seq -o /var/tmp/from_scwrl_247610933.pdb > /var/tmp/scwrl_247610933.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_247610933.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 278 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_123951692.pdb -s /var/tmp/to_scwrl_123951692.seq -o /var/tmp/from_scwrl_123951692.pdb > /var/tmp/scwrl_123951692.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_123951692.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 278 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_772553520.pdb -s /var/tmp/to_scwrl_772553520.seq -o /var/tmp/from_scwrl_772553520.pdb > /var/tmp/scwrl_772553520.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_772553520.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 278 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_355503446.pdb -s /var/tmp/to_scwrl_355503446.seq -o /var/tmp/from_scwrl_355503446.pdb > /var/tmp/scwrl_355503446.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_355503446.pdb # conformation set from SCWRL output # naming current conformation ROKKY_TS1-scwrl # ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1 # Found a chain break before 244 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1119069146.pdb -s /var/tmp/to_scwrl_1119069146.seq -o /var/tmp/from_scwrl_1119069146.pdb > /var/tmp/scwrl_1119069146.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1119069146.pdb # conformation set from SCWRL output # naming current conformation ROKKY_TS2-scwrl # ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1 # Found a chain break before 277 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_255052718.pdb -s /var/tmp/to_scwrl_255052718.seq -o /var/tmp/from_scwrl_255052718.pdb > /var/tmp/scwrl_255052718.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_255052718.pdb # conformation set from SCWRL output # naming current conformation ROKKY_TS3-scwrl # ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_867648784.pdb -s /var/tmp/to_scwrl_867648784.seq -o /var/tmp/from_scwrl_867648784.pdb > /var/tmp/scwrl_867648784.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_867648784.pdb # conformation set from SCWRL output # naming current conformation ROKKY_TS4-scwrl # ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1 # Found a chain break before 277 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1098921652.pdb -s /var/tmp/to_scwrl_1098921652.seq -o /var/tmp/from_scwrl_1098921652.pdb > /var/tmp/scwrl_1098921652.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1098921652.pdb # conformation set from SCWRL output # naming current conformation ROKKY_TS5-scwrl # ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_2134095792.pdb -s /var/tmp/to_scwrl_2134095792.seq -o /var/tmp/from_scwrl_2134095792.pdb > /var/tmp/scwrl_2134095792.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2134095792.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 T0305 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_793588215.pdb -s /var/tmp/to_scwrl_793588215.seq -o /var/tmp/from_scwrl_793588215.pdb > /var/tmp/scwrl_793588215.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_793588215.pdb # conformation set from SCWRL output # naming current conformation SAM-T02_AL2-scwrl # ReadConformPDB reading from PDB file servers/SAM-T02_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1580475562.pdb -s /var/tmp/to_scwrl_1580475562.seq -o /var/tmp/from_scwrl_1580475562.pdb > /var/tmp/scwrl_1580475562.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1580475562.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 Skipped atom 26, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 28, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 30, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 32, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 162, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 164, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 166, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 168, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 326, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 328, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 330, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 332, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 622, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 624, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 626, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 628, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 830, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 832, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 834, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 836, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 914, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 916, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 918, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 920, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_2021154305.pdb -s /var/tmp/to_scwrl_2021154305.seq -o /var/tmp/from_scwrl_2021154305.pdb > /var/tmp/scwrl_2021154305.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2021154305.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 T0305 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_121348292.pdb -s /var/tmp/to_scwrl_121348292.seq -o /var/tmp/from_scwrl_121348292.pdb > /var/tmp/scwrl_121348292.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_121348292.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 Skipped atom 38, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 40, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 42, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 44, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 174, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 176, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 178, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 180, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 338, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 340, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 342, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 344, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 634, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 636, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 638, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 640, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 842, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 844, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 846, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 848, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 926, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 928, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 930, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 932, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1551619088.pdb -s /var/tmp/to_scwrl_1551619088.seq -o /var/tmp/from_scwrl_1551619088.pdb > /var/tmp/scwrl_1551619088.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1551619088.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 585, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL2.pdb.gz Skipped atom 770, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL2.pdb.gz # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_551582207.pdb -s /var/tmp/to_scwrl_551582207.seq -o /var/tmp/from_scwrl_551582207.pdb > /var/tmp/scwrl_551582207.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_551582207.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 T0305 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_2139248593.pdb -s /var/tmp/to_scwrl_2139248593.seq -o /var/tmp/from_scwrl_2139248593.pdb > /var/tmp/scwrl_2139248593.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2139248593.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 T0305 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1357211154.pdb -s /var/tmp/to_scwrl_1357211154.seq -o /var/tmp/from_scwrl_1357211154.pdb > /var/tmp/scwrl_1357211154.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1357211154.pdb # conformation set from SCWRL output # naming current conformation SAM-T99_AL4-scwrl # ReadConformPDB reading from PDB file servers/SAM-T99_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_298184554.pdb -s /var/tmp/to_scwrl_298184554.seq -o /var/tmp/from_scwrl_298184554.pdb > /var/tmp/scwrl_298184554.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_298184554.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 279 # copying to AlignedFragments data structure # naming current conformation SAM_T06_server_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_215600258.pdb -s /var/tmp/to_scwrl_215600258.seq -o /var/tmp/from_scwrl_215600258.pdb > /var/tmp/scwrl_215600258.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_215600258.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 T0305 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1890569449.pdb -s /var/tmp/to_scwrl_1890569449.seq -o /var/tmp/from_scwrl_1890569449.pdb > /var/tmp/scwrl_1890569449.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1890569449.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 T0305 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_53862531.pdb -s /var/tmp/to_scwrl_53862531.seq -o /var/tmp/from_scwrl_53862531.pdb > /var/tmp/scwrl_53862531.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_53862531.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 T0305 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1169137714.pdb -s /var/tmp/to_scwrl_1169137714.seq -o /var/tmp/from_scwrl_1169137714.pdb > /var/tmp/scwrl_1169137714.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1169137714.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 T0305 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_168621671.pdb -s /var/tmp/to_scwrl_168621671.seq -o /var/tmp/from_scwrl_168621671.pdb > /var/tmp/scwrl_168621671.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_168621671.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 268 ; scwrl3 -i /var/tmp/to_scwrl_963169631.pdb -s /var/tmp/to_scwrl_963169631.seq -o /var/tmp/from_scwrl_963169631.pdb > /var/tmp/scwrl_963169631.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_963169631.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 278 # copying to AlignedFragments data structure # naming current conformation SP3_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1089255580.pdb -s /var/tmp/to_scwrl_1089255580.seq -o /var/tmp/from_scwrl_1089255580.pdb > /var/tmp/scwrl_1089255580.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1089255580.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 278 # copying to AlignedFragments data structure # naming current conformation SP3_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_704324397.pdb -s /var/tmp/to_scwrl_704324397.seq -o /var/tmp/from_scwrl_704324397.pdb > /var/tmp/scwrl_704324397.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_704324397.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 278 # copying to AlignedFragments data structure # naming current conformation SP3_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_392466484.pdb -s /var/tmp/to_scwrl_392466484.seq -o /var/tmp/from_scwrl_392466484.pdb > /var/tmp/scwrl_392466484.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_392466484.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 295 # copying to AlignedFragments data structure # naming current conformation SP3_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_2146669284.pdb -s /var/tmp/to_scwrl_2146669284.seq -o /var/tmp/from_scwrl_2146669284.pdb > /var/tmp/scwrl_2146669284.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2146669284.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 278 # copying to AlignedFragments data structure # naming current conformation SP4_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_42784741.pdb -s /var/tmp/to_scwrl_42784741.seq -o /var/tmp/from_scwrl_42784741.pdb > /var/tmp/scwrl_42784741.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_42784741.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 236 # copying to AlignedFragments data structure # naming current conformation SP4_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_733145588.pdb -s /var/tmp/to_scwrl_733145588.seq -o /var/tmp/from_scwrl_733145588.pdb > /var/tmp/scwrl_733145588.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_733145588.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 236 # copying to AlignedFragments data structure # naming current conformation SP4_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1003096174.pdb -s /var/tmp/to_scwrl_1003096174.seq -o /var/tmp/from_scwrl_1003096174.pdb > /var/tmp/scwrl_1003096174.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1003096174.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 278 # copying to AlignedFragments data structure # naming current conformation SP4_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_290395675.pdb -s /var/tmp/to_scwrl_290395675.seq -o /var/tmp/from_scwrl_290395675.pdb > /var/tmp/scwrl_290395675.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_290395675.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 278 # copying to AlignedFragments data structure # naming current conformation SP4_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_857097280.pdb -s /var/tmp/to_scwrl_857097280.seq -o /var/tmp/from_scwrl_857097280.pdb > /var/tmp/scwrl_857097280.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_857097280.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 268 ; scwrl3 -i /var/tmp/to_scwrl_1775649693.pdb -s /var/tmp/to_scwrl_1775649693.seq -o /var/tmp/from_scwrl_1775649693.pdb > /var/tmp/scwrl_1775649693.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1775649693.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 278 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_645899121.pdb -s /var/tmp/to_scwrl_645899121.seq -o /var/tmp/from_scwrl_645899121.pdb > /var/tmp/scwrl_645899121.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_645899121.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 279 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1976166427.pdb -s /var/tmp/to_scwrl_1976166427.seq -o /var/tmp/from_scwrl_1976166427.pdb > /var/tmp/scwrl_1976166427.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1976166427.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 278 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_2030702411.pdb -s /var/tmp/to_scwrl_2030702411.seq -o /var/tmp/from_scwrl_2030702411.pdb > /var/tmp/scwrl_2030702411.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2030702411.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 199 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1513547904.pdb -s /var/tmp/to_scwrl_1513547904.seq -o /var/tmp/from_scwrl_1513547904.pdb > /var/tmp/scwrl_1513547904.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1513547904.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 T0305 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_927604433.pdb -s /var/tmp/to_scwrl_927604433.seq -o /var/tmp/from_scwrl_927604433.pdb > /var/tmp/scwrl_927604433.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_927604433.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 T0305 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_2017314556.pdb -s /var/tmp/to_scwrl_2017314556.seq -o /var/tmp/from_scwrl_2017314556.pdb > /var/tmp/scwrl_2017314556.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2017314556.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 T0305 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_159652473.pdb -s /var/tmp/to_scwrl_159652473.seq -o /var/tmp/from_scwrl_159652473.pdb > /var/tmp/scwrl_159652473.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_159652473.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 T0305 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_360596348.pdb -s /var/tmp/to_scwrl_360596348.seq -o /var/tmp/from_scwrl_360596348.pdb > /var/tmp/scwrl_360596348.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_360596348.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 T0305 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1890985215.pdb -s /var/tmp/to_scwrl_1890985215.seq -o /var/tmp/from_scwrl_1890985215.pdb > /var/tmp/scwrl_1890985215.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1890985215.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: atoms too close: (T0305)T174.CA and (T0305)K185.CA only 0.000 apart, marking (T0305)K185.CA as missing # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation UNI-EID_expm_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_281000765.pdb -s /var/tmp/to_scwrl_281000765.seq -o /var/tmp/from_scwrl_281000765.pdb > /var/tmp/scwrl_281000765.log Error: Couldn't open file /var/tmp/from_scwrl_281000765.pdb or /var/tmp/from_scwrl_281000765.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_281000765_b.pdb or decoys//var/tmp/from_scwrl_281000765_b.pdb.gz for input Trying /var/tmp/from_scwrl_281000765_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_281000765_b.pdb or /var/tmp/from_scwrl_281000765_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_281000765_a.pdb or decoys//var/tmp/from_scwrl_281000765_a.pdb.gz for input Trying /var/tmp/from_scwrl_281000765_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_281000765_a.pdb or /var/tmp/from_scwrl_281000765_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_281000765.pdb or /var/tmp/from_scwrl_281000765_b.pdb or /var/tmp/from_scwrl_281000765_a.pdb Error: no new SCWRL conformation added # 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 T0305 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1912215437.pdb -s /var/tmp/to_scwrl_1912215437.seq -o /var/tmp/from_scwrl_1912215437.pdb > /var/tmp/scwrl_1912215437.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1912215437.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 Skipped atom 131, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 792, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 1049, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_295083775.pdb -s /var/tmp/to_scwrl_295083775.seq -o /var/tmp/from_scwrl_295083775.pdb > /var/tmp/scwrl_295083775.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_295083775.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 Skipped atom 987, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_272765711.pdb -s /var/tmp/to_scwrl_272765711.seq -o /var/tmp/from_scwrl_272765711.pdb > /var/tmp/scwrl_272765711.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_272765711.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_sfst_AL3-scwrl # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1121942944.pdb -s /var/tmp/to_scwrl_1121942944.seq -o /var/tmp/from_scwrl_1121942944.pdb > /var/tmp/scwrl_1121942944.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1121942944.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 Skipped atom 585, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz Skipped atom 770, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_593268329.pdb -s /var/tmp/to_scwrl_593268329.seq -o /var/tmp/from_scwrl_593268329.pdb > /var/tmp/scwrl_593268329.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_593268329.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 279 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_488365970.pdb -s /var/tmp/to_scwrl_488365970.seq -o /var/tmp/from_scwrl_488365970.pdb > /var/tmp/scwrl_488365970.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_488365970.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 279 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_865028747.pdb -s /var/tmp/to_scwrl_865028747.seq -o /var/tmp/from_scwrl_865028747.pdb > /var/tmp/scwrl_865028747.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_865028747.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 279 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_647130861.pdb -s /var/tmp/to_scwrl_647130861.seq -o /var/tmp/from_scwrl_647130861.pdb > /var/tmp/scwrl_647130861.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_647130861.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 278 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1657503684.pdb -s /var/tmp/to_scwrl_1657503684.seq -o /var/tmp/from_scwrl_1657503684.pdb > /var/tmp/scwrl_1657503684.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1657503684.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 279 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1033650418.pdb -s /var/tmp/to_scwrl_1033650418.seq -o /var/tmp/from_scwrl_1033650418.pdb > /var/tmp/scwrl_1033650418.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1033650418.pdb # conformation set from SCWRL output # naming current conformation Zhang-Server_TS5-scwrl # ReadConformPDB reading from PDB file servers/beautshot_TS1.pdb.gz looking for model 1 # Found a chain break before 278 # copying to AlignedFragments data structure # naming current conformation beautshot_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1610300491.pdb -s /var/tmp/to_scwrl_1610300491.seq -o /var/tmp/from_scwrl_1610300491.pdb > /var/tmp/scwrl_1610300491.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1610300491.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 # Found a chain break before 278 # copying to AlignedFragments data structure # naming current conformation beautshotbase_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_599275618.pdb -s /var/tmp/to_scwrl_599275618.seq -o /var/tmp/from_scwrl_599275618.pdb > /var/tmp/scwrl_599275618.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_599275618.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 Skipped atom 18, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 20, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 22, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 24, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 202, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 204, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 206, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 208, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 254, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 256, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 258, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 260, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 262, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 264, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 266, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 268, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 270, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 272, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 274, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 276, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 278, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 280, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 282, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 284, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 378, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 380, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 382, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 384, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 454, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 456, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 458, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 460, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 510, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 512, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 514, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 516, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 518, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 520, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 522, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 524, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 658, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 660, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 662, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 664, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 670, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 672, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 674, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 676, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 746, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 748, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 750, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 752, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 754, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 756, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 758, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 760, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 762, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 764, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 766, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 768, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 770, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 772, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 774, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 776, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 778, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 780, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 782, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 784, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 786, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 788, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 790, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 792, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 794, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 796, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 798, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 800, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 802, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 804, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 806, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 808, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 810, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 812, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 814, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 816, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 818, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 820, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 822, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 824, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 826, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 828, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 830, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 832, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 834, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 836, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 838, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 840, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 846, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 848, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 850, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 852, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 946, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 948, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 950, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 952, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 970, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 972, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 974, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 976, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 994, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 996, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 998, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 1000, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 1066, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 1068, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 1070, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 1072, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 1098, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 1099, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 1101, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 1102, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 1104, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 1105, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 1107, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 1108, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation forecast-s_AL1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1737974815.pdb -s /var/tmp/to_scwrl_1737974815.seq -o /var/tmp/from_scwrl_1737974815.pdb > /var/tmp/scwrl_1737974815.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1737974815.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 T0305 can't currently be optimized by undertaker # naming current conformation forecast-s_AL2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_2002766975.pdb -s /var/tmp/to_scwrl_2002766975.seq -o /var/tmp/from_scwrl_2002766975.pdb > /var/tmp/scwrl_2002766975.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2002766975.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 T0305 can't currently be optimized by undertaker # naming current conformation forecast-s_AL3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_598461255.pdb -s /var/tmp/to_scwrl_598461255.seq -o /var/tmp/from_scwrl_598461255.pdb > /var/tmp/scwrl_598461255.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_598461255.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 T0305 can't currently be optimized by undertaker # naming current conformation forecast-s_AL4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1780759556.pdb -s /var/tmp/to_scwrl_1780759556.seq -o /var/tmp/from_scwrl_1780759556.pdb > /var/tmp/scwrl_1780759556.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1780759556.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 T0305 can't currently be optimized by undertaker # naming current conformation forecast-s_AL5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_588428916.pdb -s /var/tmp/to_scwrl_588428916.seq -o /var/tmp/from_scwrl_588428916.pdb > /var/tmp/scwrl_588428916.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_588428916.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 T0305 can't currently be optimized by undertaker # naming current conformation gtg_AL1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1601557428.pdb -s /var/tmp/to_scwrl_1601557428.seq -o /var/tmp/from_scwrl_1601557428.pdb > /var/tmp/scwrl_1601557428.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1601557428.pdb # conformation set from SCWRL output # naming current conformation gtg_AL1-scwrl # ReadConformPDB reading from PDB file servers/gtg_AL2.pdb.gz looking for model 1 Skipped atom 622, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 624, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 626, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 628, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation gtg_AL2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_2071155231.pdb -s /var/tmp/to_scwrl_2071155231.seq -o /var/tmp/from_scwrl_2071155231.pdb > /var/tmp/scwrl_2071155231.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2071155231.pdb # conformation set from SCWRL output # naming current conformation gtg_AL2-scwrl # ReadConformPDB reading from PDB file servers/gtg_AL3.pdb.gz looking for model 1 Skipped atom 585, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL3.pdb.gz Skipped atom 770, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL3.pdb.gz # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation gtg_AL3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1445526196.pdb -s /var/tmp/to_scwrl_1445526196.seq -o /var/tmp/from_scwrl_1445526196.pdb > /var/tmp/scwrl_1445526196.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1445526196.pdb # conformation set from SCWRL output # naming current conformation gtg_AL3-scwrl # ReadConformPDB reading from PDB file servers/gtg_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation gtg_AL4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1229723474.pdb -s /var/tmp/to_scwrl_1229723474.seq -o /var/tmp/from_scwrl_1229723474.pdb > /var/tmp/scwrl_1229723474.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1229723474.pdb # conformation set from SCWRL output # naming current conformation gtg_AL4-scwrl # ReadConformPDB reading from PDB file servers/gtg_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation gtg_AL5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_569570706.pdb -s /var/tmp/to_scwrl_569570706.seq -o /var/tmp/from_scwrl_569570706.pdb > /var/tmp/scwrl_569570706.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_569570706.pdb # conformation set from SCWRL output # naming current conformation gtg_AL5-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # Found a chain break before 279 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1274208976.pdb -s /var/tmp/to_scwrl_1274208976.seq -o /var/tmp/from_scwrl_1274208976.pdb > /var/tmp/scwrl_1274208976.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1274208976.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 275 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1112942238.pdb -s /var/tmp/to_scwrl_1112942238.seq -o /var/tmp/from_scwrl_1112942238.pdb > /var/tmp/scwrl_1112942238.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1112942238.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 278 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_2083118610.pdb -s /var/tmp/to_scwrl_2083118610.seq -o /var/tmp/from_scwrl_2083118610.pdb > /var/tmp/scwrl_2083118610.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2083118610.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 278 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_54329762.pdb -s /var/tmp/to_scwrl_54329762.seq -o /var/tmp/from_scwrl_54329762.pdb > /var/tmp/scwrl_54329762.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_54329762.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 277 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_982773149.pdb -s /var/tmp/to_scwrl_982773149.seq -o /var/tmp/from_scwrl_982773149.pdb > /var/tmp/scwrl_982773149.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_982773149.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 # Found a chain break before 294 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_95287436.pdb -s /var/tmp/to_scwrl_95287436.seq -o /var/tmp/from_scwrl_95287436.pdb > /var/tmp/scwrl_95287436.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_95287436.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 294 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_414926111.pdb -s /var/tmp/to_scwrl_414926111.seq -o /var/tmp/from_scwrl_414926111.pdb > /var/tmp/scwrl_414926111.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_414926111.pdb # conformation set from SCWRL output # naming current conformation karypis.srv.4_TS2-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS3.pdb.gz looking for model 1 WARNING: atoms too close: (T0305)S157.O and (T0305)T158.N only 0.000 apart, marking (T0305)T158.N as missing # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_726274717.pdb -s /var/tmp/to_scwrl_726274717.seq -o /var/tmp/from_scwrl_726274717.pdb > /var/tmp/scwrl_726274717.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_726274717.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: (T0305)V129.O and (T0305)E130.N only 0.000 apart, marking (T0305)E130.N as missing # WARNING: incomplete conformation T0305 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 268 ; scwrl3 -i /var/tmp/to_scwrl_376288202.pdb -s /var/tmp/to_scwrl_376288202.seq -o /var/tmp/from_scwrl_376288202.pdb > /var/tmp/scwrl_376288202.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_376288202.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: (T0305)Q3.O and (T0305)S4.N only 0.000 apart, marking (T0305)S4.N as missing WARNING: atoms too close: (T0305)L68.O and (T0305)R69.N only 0.000 apart, marking (T0305)R69.N as missing # WARNING: incomplete conformation T0305 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 268 ; scwrl3 -i /var/tmp/to_scwrl_179657901.pdb -s /var/tmp/to_scwrl_179657901.seq -o /var/tmp/from_scwrl_179657901.pdb > /var/tmp/scwrl_179657901.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_179657901.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 T0305 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1021358492.pdb -s /var/tmp/to_scwrl_1021358492.seq -o /var/tmp/from_scwrl_1021358492.pdb > /var/tmp/scwrl_1021358492.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1021358492.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 T0305 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_649053913.pdb -s /var/tmp/to_scwrl_649053913.seq -o /var/tmp/from_scwrl_649053913.pdb > /var/tmp/scwrl_649053913.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_649053913.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 T0305 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1301600845.pdb -s /var/tmp/to_scwrl_1301600845.seq -o /var/tmp/from_scwrl_1301600845.pdb > /var/tmp/scwrl_1301600845.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1301600845.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 T0305 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1614626820.pdb -s /var/tmp/to_scwrl_1614626820.seq -o /var/tmp/from_scwrl_1614626820.pdb > /var/tmp/scwrl_1614626820.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1614626820.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 T0305 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1137419882.pdb -s /var/tmp/to_scwrl_1137419882.seq -o /var/tmp/from_scwrl_1137419882.pdb > /var/tmp/scwrl_1137419882.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1137419882.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 268 ; scwrl3 -i /var/tmp/to_scwrl_19145946.pdb -s /var/tmp/to_scwrl_19145946.seq -o /var/tmp/from_scwrl_19145946.pdb > /var/tmp/scwrl_19145946.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_19145946.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 233 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_114274034.pdb -s /var/tmp/to_scwrl_114274034.seq -o /var/tmp/from_scwrl_114274034.pdb > /var/tmp/scwrl_114274034.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_114274034.pdb # conformation set from SCWRL output # naming current conformation keasar-server_TS2-scwrl # ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1 # Found a chain break before 274 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_647439921.pdb -s /var/tmp/to_scwrl_647439921.seq -o /var/tmp/from_scwrl_647439921.pdb > /var/tmp/scwrl_647439921.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_647439921.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 # Found a chain break before 235 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1052796364.pdb -s /var/tmp/to_scwrl_1052796364.seq -o /var/tmp/from_scwrl_1052796364.pdb > /var/tmp/scwrl_1052796364.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1052796364.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 # Found a chain break before 233 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1724574526.pdb -s /var/tmp/to_scwrl_1724574526.seq -o /var/tmp/from_scwrl_1724574526.pdb > /var/tmp/scwrl_1724574526.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1724574526.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 T0305 can't currently be optimized by undertaker # naming current conformation mGen-3D_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1246715538.pdb -s /var/tmp/to_scwrl_1246715538.seq -o /var/tmp/from_scwrl_1246715538.pdb > /var/tmp/scwrl_1246715538.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1246715538.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 T0305 can't currently be optimized by undertaker # naming current conformation nFOLD_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_643287532.pdb -s /var/tmp/to_scwrl_643287532.seq -o /var/tmp/from_scwrl_643287532.pdb > /var/tmp/scwrl_643287532.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_643287532.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 T0305 can't currently be optimized by undertaker # naming current conformation nFOLD_TS2 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1579857854.pdb -s /var/tmp/to_scwrl_1579857854.seq -o /var/tmp/from_scwrl_1579857854.pdb > /var/tmp/scwrl_1579857854.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1579857854.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 T0305 can't currently be optimized by undertaker # naming current conformation nFOLD_TS3 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1845176794.pdb -s /var/tmp/to_scwrl_1845176794.seq -o /var/tmp/from_scwrl_1845176794.pdb > /var/tmp/scwrl_1845176794.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1845176794.pdb # conformation set from SCWRL output # naming current conformation nFOLD_TS3-scwrl # ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation nFOLD_TS4 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_276563442.pdb -s /var/tmp/to_scwrl_276563442.seq -o /var/tmp/from_scwrl_276563442.pdb > /var/tmp/scwrl_276563442.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_276563442.pdb # conformation set from SCWRL output # naming current conformation nFOLD_TS4-scwrl # ReadConformPDB reading from PDB file servers/nFOLD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation nFOLD_TS5 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_20803124.pdb -s /var/tmp/to_scwrl_20803124.seq -o /var/tmp/from_scwrl_20803124.pdb > /var/tmp/scwrl_20803124.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_20803124.pdb # conformation set from SCWRL output # naming current conformation nFOLD_TS5-scwrl # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # Found a chain break before 278 # copying to AlignedFragments data structure # naming current conformation shub_TS1 # request to SCWRL produces command: ulimit -t 268 ; scwrl3 -i /var/tmp/to_scwrl_1299250575.pdb -s /var/tmp/to_scwrl_1299250575.seq -o /var/tmp/from_scwrl_1299250575.pdb > /var/tmp/scwrl_1299250575.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1299250575.pdb # conformation set from SCWRL output # naming current conformation shub_TS1-scwrl # command:CPU_time= 90.3563 sec, elapsed time= 1570.74 sec) # command:# Prefix for output files set to decoys/ # command:# Will now start reporting costs to decoys/evaluate_1.rdb # command:# CostConform Warning: Couldn't open file decoys//projects/compbio/experiments/undertaker/spots/near-backbone-center.spot or decoys//projects/compbio/experiments/undertaker/spots/near-backbone-center.spot.gz for input Trying /projects/compbio/experiments/undertaker/spots/near-backbone-center.spot # Reading spots from /projects/compbio/experiments/undertaker/spots/near-backbone-center.spot shub_TS1-scwrl costs 0 real_cost = -251.002 shub_TS1 costs 0 real_cost = -246.911 nFOLD_TS5-scwrl costs 0 real_cost = 85.2654 nFOLD_TS5 costs 0 real_cost = 229.51 nFOLD_TS4-scwrl costs 0 real_cost = -52.7609 nFOLD_TS4 costs 0 real_cost = 98.7874 nFOLD_TS3-scwrl costs 0 real_cost = -72.6664 nFOLD_TS3 costs 0 real_cost = 80.0413 nFOLD_TS2-scwrl costs 0 real_cost = -152.788 nFOLD_TS2 costs 0 real_cost = 0.63216 nFOLD_TS1-scwrl costs 0 real_cost = -143.607 nFOLD_TS1 costs 0 real_cost = 11.9137 mGen-3D_TS1-scwrl costs 0 real_cost = -87.423 mGen-3D_TS1 costs 0 real_cost = 67.814 keasar-server_TS5-scwrl costs 0 real_cost = -229.302 keasar-server_TS5 costs 0 real_cost = -223.606 keasar-server_TS4-scwrl costs 0 real_cost = -225.846 keasar-server_TS4 costs 0 real_cost = -213.573 keasar-server_TS3-scwrl costs 0 real_cost = -250.776 keasar-server_TS3 costs 0 real_cost = -252.247 keasar-server_TS2-scwrl costs 0 real_cost = -252.168 keasar-server_TS2 costs 0 real_cost = -244.672 keasar-server_TS1-scwrl costs 0 real_cost = -236.681 keasar-server_TS1 costs 0 real_cost = -228.429 karypis.srv_TS5-scwrl costs 0 real_cost = -164.513 karypis.srv_TS5 costs 0 real_cost = -164.655 karypis.srv_TS4-scwrl costs 0 real_cost = -117.861 karypis.srv_TS4 costs 0 real_cost = -119.351 karypis.srv_TS3-scwrl costs 0 real_cost = -96.3373 karypis.srv_TS3 costs 0 real_cost = -98.5652 karypis.srv_TS2-scwrl costs 0 real_cost = -186.448 karypis.srv_TS2 costs 0 real_cost = -191.178 karypis.srv_TS1-scwrl costs 0 real_cost = -274.455 karypis.srv_TS1 costs 0 real_cost = -277.939 karypis.srv.4_TS5-scwrl costs 0 real_cost = 361.691 karypis.srv.4_TS5 costs 0 real_cost = 361.765 karypis.srv.4_TS4-scwrl costs 0 real_cost = 315.13 karypis.srv.4_TS4 costs 0 real_cost = 314.104 karypis.srv.4_TS3-scwrl costs 0 real_cost = 358.785 karypis.srv.4_TS3 costs 0 real_cost = 358.96 karypis.srv.4_TS2-scwrl costs 0 real_cost = 320.745 karypis.srv.4_TS2 costs 0 real_cost = 322.269 karypis.srv.4_TS1-scwrl costs 0 real_cost = 316.807 karypis.srv.4_TS1 costs 0 real_cost = 316.948 karypis.srv.2_TS5-scwrl costs 0 real_cost = -203.606 karypis.srv.2_TS5 costs 0 real_cost = -203.606 karypis.srv.2_TS4-scwrl costs 0 real_cost = -165.629 karypis.srv.2_TS4 costs 0 real_cost = -165.638 karypis.srv.2_TS3-scwrl costs 0 real_cost = -302.147 karypis.srv.2_TS3 costs 0 real_cost = -301.448 karypis.srv.2_TS2-scwrl costs 0 real_cost = -280.263 karypis.srv.2_TS2 costs 0 real_cost = -279.368 karypis.srv.2_TS1-scwrl costs 0 real_cost = -279.859 karypis.srv.2_TS1 costs 0 real_cost = -278.814 gtg_AL5-scwrl costs 0 real_cost = -156.761 gtg_AL5 costs 0 real_cost = 47.5165 gtg_AL4-scwrl costs 0 real_cost = -137.919 gtg_AL4 costs 0 real_cost = 73.625 gtg_AL3-scwrl costs 0 real_cost = -223.465 gtg_AL3 costs 0 real_cost = -17.0457 gtg_AL2-scwrl costs 0 real_cost = -179.678 gtg_AL2 costs 0 real_cost = 30.7264 gtg_AL1-scwrl costs 0 real_cost = -247.128 gtg_AL1 costs 0 real_cost = -38.7954 forecast-s_AL5-scwrl costs 0 real_cost = 76.8193 forecast-s_AL5 costs 0 real_cost = 270.092 forecast-s_AL4-scwrl costs 0 real_cost = -85.6881 forecast-s_AL4 costs 0 real_cost = 89.3158 forecast-s_AL3-scwrl costs 0 real_cost = -130.857 forecast-s_AL3 costs 0 real_cost = 79.4683 forecast-s_AL2-scwrl costs 0 real_cost = -247.17 forecast-s_AL2 costs 0 real_cost = -30.4142 forecast-s_AL1-scwrl costs 0 real_cost = -157.083 forecast-s_AL1 costs 0 real_cost = 51.182 beautshotbase_TS1-scwrl costs 0 real_cost = -234.977 beautshotbase_TS1 costs 0 real_cost = -234.73 beautshot_TS1-scwrl costs 0 real_cost = -265.298 beautshot_TS1 costs 0 real_cost = -262.995 Zhang-Server_TS5-scwrl costs 0 real_cost = -296.375 Zhang-Server_TS5 costs 0 real_cost = -287.585 Zhang-Server_TS4-scwrl costs 0 real_cost = -294.167 Zhang-Server_TS4 costs 0 real_cost = -296.964 Zhang-Server_TS3-scwrl costs 0 real_cost = -303.571 Zhang-Server_TS3 costs 0 real_cost = -290.287 Zhang-Server_TS2-scwrl costs 0 real_cost = -307.474 Zhang-Server_TS2 costs 0 real_cost = -311.717 Zhang-Server_TS1-scwrl costs 0 real_cost = -303.502 Zhang-Server_TS1 costs 0 real_cost = -295.005 UNI-EID_sfst_AL5-scwrl costs 0 real_cost = -227.847 UNI-EID_sfst_AL5 costs 0 real_cost = -23.8313 UNI-EID_sfst_AL4-scwrl costs 0 real_cost = -242.296 UNI-EID_sfst_AL4 costs 0 real_cost = -36.8259 UNI-EID_sfst_AL3-scwrl costs 0 real_cost = -216.065 UNI-EID_sfst_AL3 costs 0 real_cost = -8.14135 UNI-EID_sfst_AL2-scwrl costs 0 real_cost = -255.21 UNI-EID_sfst_AL2 costs 0 real_cost = -41.0323 UNI-EID_sfst_AL1-scwrl costs 0 real_cost = -257.926 UNI-EID_sfst_AL1 costs 0 real_cost = -47.5838 UNI-EID_expm_TS1-scwrl costs 0 real_cost = -77.9344 UNI-EID_bnmx_TS5-scwrl costs 0 real_cost = -227.847 UNI-EID_bnmx_TS5 costs 0 real_cost = -23.8313 UNI-EID_bnmx_TS4-scwrl costs 0 real_cost = -242.296 UNI-EID_bnmx_TS4 costs 0 real_cost = -36.8259 UNI-EID_bnmx_TS3-scwrl costs 0 real_cost = -216.065 UNI-EID_bnmx_TS3 costs 0 real_cost = -8.14135 UNI-EID_bnmx_TS2-scwrl costs 0 real_cost = -264.127 UNI-EID_bnmx_TS2 costs 0 real_cost = -45.2844 UNI-EID_bnmx_TS1-scwrl costs 0 real_cost = -257.926 UNI-EID_bnmx_TS1 costs 0 real_cost = -47.5838 SPARKS2_TS5-scwrl costs 0 real_cost = -292.61 SPARKS2_TS5 costs 0 real_cost = -299.736 SPARKS2_TS4-scwrl costs 0 real_cost = -198.95 SPARKS2_TS4 costs 0 real_cost = -201.076 SPARKS2_TS3-scwrl costs 0 real_cost = -128.715 SPARKS2_TS3 costs 0 real_cost = -133.483 SPARKS2_TS2-scwrl costs 0 real_cost = -191.183 SPARKS2_TS2 costs 0 real_cost = -193.424 SPARKS2_TS1-scwrl costs 0 real_cost = -287.267 SPARKS2_TS1 costs 0 real_cost = -292.144 SP4_TS5-scwrl costs 0 real_cost = -205.181 SP4_TS5 costs 0 real_cost = -201.358 SP4_TS4-scwrl costs 0 real_cost = -298.059 SP4_TS4 costs 0 real_cost = -302.802 SP4_TS3-scwrl costs 0 real_cost = -125.801 SP4_TS3 costs 0 real_cost = -125.917 SP4_TS2-scwrl costs 0 real_cost = -177.354 SP4_TS2 costs 0 real_cost = -181.106 SP4_TS1-scwrl costs 0 real_cost = -282.017 SP4_TS1 costs 0 real_cost = -284.518 SP3_TS5-scwrl costs 0 real_cost = -201.602 SP3_TS5 costs 0 real_cost = -202.094 SP3_TS4-scwrl costs 0 real_cost = -298.059 SP3_TS4 costs 0 real_cost = -302.802 SP3_TS3-scwrl costs 0 real_cost = -118.675 SP3_TS3 costs 0 real_cost = -116.287 SP3_TS2-scwrl costs 0 real_cost = -175.792 SP3_TS2 costs 0 real_cost = -172.875 SP3_TS1-scwrl costs 0 real_cost = -287.267 SP3_TS1 costs 0 real_cost = -292.144 SAM_T06_server_TS5-scwrl costs 0 real_cost = -155.269 SAM_T06_server_TS5 costs 0 real_cost = -169.516 SAM_T06_server_TS4-scwrl costs 0 real_cost = -173.235 SAM_T06_server_TS4 costs 0 real_cost = -192.831 SAM_T06_server_TS3-scwrl costs 0 real_cost = -168.622 SAM_T06_server_TS3 costs 0 real_cost = -190.638 SAM_T06_server_TS2-scwrl costs 0 real_cost = -52.8242 SAM_T06_server_TS2 costs 0 real_cost = -127.936 SAM_T06_server_TS1-scwrl costs 0 real_cost = -176.244 SAM_T06_server_TS1 costs 0 real_cost = -176.958 SAM-T99_AL5-scwrl costs 0 real_cost = -152.054 SAM-T99_AL5 costs 0 real_cost = 10.5084 SAM-T99_AL4-scwrl costs 0 real_cost = -247.73 SAM-T99_AL4 costs 0 real_cost = -38.7681 SAM-T99_AL3-scwrl costs 0 real_cost = -110.035 SAM-T99_AL3 costs 0 real_cost = 112.225 SAM-T99_AL2-scwrl costs 0 real_cost = -226.563 SAM-T99_AL2 costs 0 real_cost = -21.2907 SAM-T99_AL1-scwrl costs 0 real_cost = -244.888 SAM-T99_AL1 costs 0 real_cost = -32.9858 SAM-T02_AL5-scwrl costs 0 real_cost = -144.504 SAM-T02_AL5 costs 0 real_cost = 36.0621 SAM-T02_AL4-scwrl costs 0 real_cost = -187.247 SAM-T02_AL4 costs 0 real_cost = 18.4586 SAM-T02_AL3-scwrl costs 0 real_cost = -117.116 SAM-T02_AL3 costs 0 real_cost = 79.4118 SAM-T02_AL2-scwrl costs 0 real_cost = -183.374 SAM-T02_AL2 costs 0 real_cost = 22.6115 SAM-T02_AL1-scwrl costs 0 real_cost = -143.477 SAM-T02_AL1 costs 0 real_cost = 55.0147 ROKKY_TS5-scwrl costs 0 real_cost = -196.239 ROKKY_TS5 costs 0 real_cost = -201.584 ROKKY_TS4-scwrl costs 0 real_cost = -294.692 ROKKY_TS4 costs 0 real_cost = -289.982 ROKKY_TS3-scwrl costs 0 real_cost = -295.98 ROKKY_TS3 costs 0 real_cost = -295.51 ROKKY_TS2-scwrl costs 0 real_cost = 352.513 ROKKY_TS2 costs 0 real_cost = 356.42 ROKKY_TS1-scwrl costs 0 real_cost = -290.779 ROKKY_TS1 costs 0 real_cost = -300.034 ROBETTA_TS5-scwrl costs 0 real_cost = -284.551 ROBETTA_TS5 costs 0 real_cost = -291.211 ROBETTA_TS4-scwrl costs 0 real_cost = -296.709 ROBETTA_TS4 costs 0 real_cost = -301.949 ROBETTA_TS3-scwrl costs 0 real_cost = -282.88 ROBETTA_TS3 costs 0 real_cost = -291.479 ROBETTA_TS2-scwrl costs 0 real_cost = -262.983 ROBETTA_TS2 costs 0 real_cost = -269.021 ROBETTA_TS1-scwrl costs 0 real_cost = -282.966 ROBETTA_TS1 costs 0 real_cost = -285.429 RAPTOR_TS5-scwrl costs 0 real_cost = -282.366 RAPTOR_TS5 costs 0 real_cost = -279.043 RAPTOR_TS4-scwrl costs 0 real_cost = -282.366 RAPTOR_TS4 costs 0 real_cost = -279.043 RAPTOR_TS3-scwrl costs 0 real_cost = -246.793 RAPTOR_TS3 costs 0 real_cost = -248.414 RAPTOR_TS2-scwrl costs 0 real_cost = -270.414 RAPTOR_TS2 costs 0 real_cost = -281.229 RAPTOR_TS1-scwrl costs 0 real_cost = -279.805 RAPTOR_TS1 costs 0 real_cost = -285.595 RAPTORESS_TS5-scwrl costs 0 real_cost = -174.999 RAPTORESS_TS5 costs 0 real_cost = -172.787 RAPTORESS_TS4-scwrl costs 0 real_cost = -269.534 RAPTORESS_TS4 costs 0 real_cost = -267.322 RAPTORESS_TS3-scwrl costs 0 real_cost = -213.622 RAPTORESS_TS3 costs 0 real_cost = -220.718 RAPTORESS_TS2-scwrl costs 0 real_cost = -253.345 RAPTORESS_TS2 costs 0 real_cost = -259.019 RAPTORESS_TS1-scwrl costs 0 real_cost = -258.66 RAPTORESS_TS1 costs 0 real_cost = -259.409 RAPTOR-ACE_TS5-scwrl costs 0 real_cost = -284.845 RAPTOR-ACE_TS5 costs 0 real_cost = -279.73 RAPTOR-ACE_TS4-scwrl costs 0 real_cost = -270.957 RAPTOR-ACE_TS4 costs 0 real_cost = -270.912 RAPTOR-ACE_TS3-scwrl costs 0 real_cost = -280.834 RAPTOR-ACE_TS3 costs 0 real_cost = -279.203 RAPTOR-ACE_TS2-scwrl costs 0 real_cost = -293.816 RAPTOR-ACE_TS2 costs 0 real_cost = -300.828 RAPTOR-ACE_TS1-scwrl costs 0 real_cost = -167.591 RAPTOR-ACE_TS1 costs 0 real_cost = -168.501 Pmodeller6_TS5-scwrl costs 0 real_cost = -270.434 Pmodeller6_TS5 costs 0 real_cost = -275.347 Pmodeller6_TS4-scwrl costs 0 real_cost = -289.472 Pmodeller6_TS4 costs 0 real_cost = -296.03 Pmodeller6_TS3-scwrl costs 0 real_cost = -247.972 Pmodeller6_TS3 costs 0 real_cost = -253.233 Pmodeller6_TS2-scwrl costs 0 real_cost = -239.453 Pmodeller6_TS2 costs 0 real_cost = -240.978 Pmodeller6_TS1-scwrl costs 0 real_cost = -239.453 Pmodeller6_TS1 costs 0 real_cost = -240.978 Phyre-2_TS5-scwrl costs 0 real_cost = -288.143 Phyre-2_TS5 costs 0 real_cost = -290.766 Phyre-2_TS4-scwrl costs 0 real_cost = -275.453 Phyre-2_TS4 costs 0 real_cost = -277.694 Phyre-2_TS3-scwrl costs 0 real_cost = -262.853 Phyre-2_TS3 costs 0 real_cost = -264.879 Phyre-2_TS2-scwrl costs 0 real_cost = -262.853 Phyre-2_TS2 costs 0 real_cost = -264.879 Phyre-2_TS1-scwrl costs 0 real_cost = -273.819 Phyre-2_TS1 costs 0 real_cost = -276.74 Phyre-1_TS1-scwrl costs 0 real_cost = -265.517 Phyre-1_TS1 costs 0 real_cost = -270.048 Pcons6_TS5-scwrl costs 0 real_cost = -274.474 Pcons6_TS5 costs 0 real_cost = -279.701 Pcons6_TS4-scwrl costs 0 real_cost = -270.434 Pcons6_TS4 costs 0 real_cost = -275.347 Pcons6_TS3-scwrl costs 0 real_cost = -272.035 Pcons6_TS3 costs 0 real_cost = -277.099 Pcons6_TS2-scwrl costs 0 real_cost = -271.814 Pcons6_TS2 costs 0 real_cost = -277.901 Pcons6_TS1-scwrl costs 0 real_cost = -271.814 Pcons6_TS1 costs 0 real_cost = -277.901 PROTINFO_TS5-scwrl costs 0 real_cost = -252.984 PROTINFO_TS5 costs 0 real_cost = -255.3 PROTINFO_TS4-scwrl costs 0 real_cost = 118.884 PROTINFO_TS4 costs 0 real_cost = 112.856 PROTINFO_TS3-scwrl costs 0 real_cost = -260.416 PROTINFO_TS3 costs 0 real_cost = -272.369 PROTINFO_TS2-scwrl costs 0 real_cost = -280.855 PROTINFO_TS2 costs 0 real_cost = -296.224 PROTINFO_TS1-scwrl costs 0 real_cost = -307.872 PROTINFO_TS1 costs 0 real_cost = -320.928 PROTINFO-AB_TS5-scwrl costs 0 real_cost = -269.028 PROTINFO-AB_TS5 costs 0 real_cost = -276.33 PROTINFO-AB_TS4-scwrl costs 0 real_cost = -263.16 PROTINFO-AB_TS4 costs 0 real_cost = -275.216 PROTINFO-AB_TS3-scwrl costs 0 real_cost = -264.838 PROTINFO-AB_TS3 costs 0 real_cost = -270.938 PROTINFO-AB_TS2-scwrl costs 0 real_cost = -260.416 PROTINFO-AB_TS2 costs 0 real_cost = -272.369 PROTINFO-AB_TS1-scwrl costs 0 real_cost = -260.416 PROTINFO-AB_TS1 costs 0 real_cost = -272.369 NN_PUT_lab_TS1-scwrl costs 0 real_cost = -251.705 NN_PUT_lab_TS1 costs 0 real_cost = -249.017 MetaTasser_TS5-scwrl costs 0 real_cost = -61.1467 MetaTasser_TS5 costs 0 real_cost = -65.8649 MetaTasser_TS4-scwrl costs 0 real_cost = -66.066 MetaTasser_TS4 costs 0 real_cost = -63.0136 MetaTasser_TS3-scwrl costs 0 real_cost = -55.5204 MetaTasser_TS3 costs 0 real_cost = -49.3073 MetaTasser_TS2-scwrl costs 0 real_cost = -20.3958 MetaTasser_TS2 costs 0 real_cost = -29.75 MetaTasser_TS1-scwrl costs 0 real_cost = 26.8122 MetaTasser_TS1 costs 0 real_cost = 37.0319 Ma-OPUS-server_TS5-scwrl costs 0 real_cost = -192.612 Ma-OPUS-server_TS5 costs 0 real_cost = -189.345 Ma-OPUS-server_TS4-scwrl costs 0 real_cost = -231.126 Ma-OPUS-server_TS4 costs 0 real_cost = -231.595 Ma-OPUS-server_TS3-scwrl costs 0 real_cost = -175.502 Ma-OPUS-server_TS3 costs 0 real_cost = -176.501 Ma-OPUS-server_TS2-scwrl costs 0 real_cost = -295.713 Ma-OPUS-server_TS2 costs 0 real_cost = -301.134 Ma-OPUS-server_TS1-scwrl costs 0 real_cost = -258.41 Ma-OPUS-server_TS1 costs 0 real_cost = -261.269 LOOPP_TS5-scwrl costs 0 real_cost = -216.327 LOOPP_TS5 costs 0 real_cost = -211.585 LOOPP_TS4-scwrl costs 0 real_cost = -238.289 LOOPP_TS4 costs 0 real_cost = -232.656 LOOPP_TS3-scwrl costs 0 real_cost = -244.038 LOOPP_TS3 costs 0 real_cost = -234.892 LOOPP_TS2-scwrl costs 0 real_cost = -254.083 LOOPP_TS2 costs 0 real_cost = -244.142 LOOPP_TS1-scwrl costs 0 real_cost = -251.705 LOOPP_TS1 costs 0 real_cost = -249.017 Huber-Torda-Server_TS5-scwrl costs 0 real_cost = -200.436 Huber-Torda-Server_TS5 costs 0 real_cost = -54.9883 Huber-Torda-Server_TS4-scwrl costs 0 real_cost = -197.097 Huber-Torda-Server_TS4 costs 0 real_cost = -50.5579 Huber-Torda-Server_TS3-scwrl costs 0 real_cost = -211.031 Huber-Torda-Server_TS3 costs 0 real_cost = -52.7878 Huber-Torda-Server_TS2-scwrl costs 0 real_cost = -176.159 Huber-Torda-Server_TS2 costs 0 real_cost = -27.3413 Huber-Torda-Server_TS1-scwrl costs 0 real_cost = -238.236 Huber-Torda-Server_TS1 costs 0 real_cost = -68.4935 HHpred3_TS1-scwrl costs 0 real_cost = -301.105 HHpred3_TS1 costs 0 real_cost = -307.353 HHpred2_TS1-scwrl costs 0 real_cost = -296.717 HHpred2_TS1 costs 0 real_cost = -304.828 HHpred1_TS1-scwrl costs 0 real_cost = -264.555 HHpred1_TS1 costs 0 real_cost = -265.34 GeneSilicoMetaServer_TS5-scwrl costs 0 real_cost = -278.25 GeneSilicoMetaServer_TS5 costs 0 real_cost = -278.834 GeneSilicoMetaServer_TS4-scwrl costs 0 real_cost = -252.374 GeneSilicoMetaServer_TS4 costs 0 real_cost = -263.986 GeneSilicoMetaServer_TS3-scwrl costs 0 real_cost = -295.821 GeneSilicoMetaServer_TS3 costs 0 real_cost = -295.789 GeneSilicoMetaServer_TS2-scwrl costs 0 real_cost = -165.796 GeneSilicoMetaServer_TS2 costs 0 real_cost = -158.828 GeneSilicoMetaServer_TS1-scwrl costs 0 real_cost = -171.325 GeneSilicoMetaServer_TS1 costs 0 real_cost = -165.265 FUNCTION_TS5-scwrl costs 0 real_cost = -281.098 FUNCTION_TS5 costs 0 real_cost = -295.865 FUNCTION_TS4-scwrl costs 0 real_cost = -244.777 FUNCTION_TS4 costs 0 real_cost = -261.554 FUNCTION_TS3-scwrl costs 0 real_cost = -283.975 FUNCTION_TS3 costs 0 real_cost = -292.18 FUNCTION_TS2-scwrl costs 0 real_cost = -281.448 FUNCTION_TS2 costs 0 real_cost = -293.843 FUNCTION_TS1-scwrl costs 0 real_cost = -259.177 FUNCTION_TS1 costs 0 real_cost = -277.382 FUGUE_AL5-scwrl costs 0 real_cost = 387.557 FUGUE_AL5 costs 0 real_cost = 596.477 FUGUE_AL4-scwrl costs 0 real_cost = 176.091 FUGUE_AL4 costs 0 real_cost = 367.154 FUGUE_AL3-scwrl costs 0 real_cost = 74.2719 FUGUE_AL3 costs 0 real_cost = 270.049 FUGUE_AL2-scwrl costs 0 real_cost = -123.337 FUGUE_AL2 costs 0 real_cost = 86.724 FUGUE_AL1-scwrl costs 0 real_cost = -206.058 FUGUE_AL1 costs 0 real_cost = -4.94763 FUGMOD_TS5-scwrl costs 0 real_cost = 325.321 FUGMOD_TS5 costs 0 real_cost = 328.696 FUGMOD_TS4-scwrl costs 0 real_cost = 97.4355 FUGMOD_TS4 costs 0 real_cost = 100.239 FUGMOD_TS3-scwrl costs 0 real_cost = 32.2631 FUGMOD_TS3 costs 0 real_cost = 37.4061 FUGMOD_TS2-scwrl costs 0 real_cost = -169.698 FUGMOD_TS2 costs 0 real_cost = -172.403 FUGMOD_TS1-scwrl costs 0 real_cost = -262.208 FUGMOD_TS1 costs 0 real_cost = -269.419 FPSOLVER-SERVER_TS5-scwrl costs 0 real_cost = 312.672 FPSOLVER-SERVER_TS5 costs 0 real_cost = 315.761 FPSOLVER-SERVER_TS4-scwrl costs 0 real_cost = 290.182 FPSOLVER-SERVER_TS4 costs 0 real_cost = 302.708 FPSOLVER-SERVER_TS3-scwrl costs 0 real_cost = 299.771 FPSOLVER-SERVER_TS3 costs 0 real_cost = 308.631 FPSOLVER-SERVER_TS2-scwrl costs 0 real_cost = 303.334 FPSOLVER-SERVER_TS2 costs 0 real_cost = 313.288 FPSOLVER-SERVER_TS1-scwrl costs 0 real_cost = 307.854 FPSOLVER-SERVER_TS1 costs 0 real_cost = 310.874 FORTE2_AL5-scwrl costs 0 real_cost = 173.032 FORTE2_AL5 costs 0 real_cost = 364.198 FORTE2_AL4-scwrl costs 0 real_cost = 70.0016 FORTE2_AL4 costs 0 real_cost = 265.564 FORTE2_AL3-scwrl costs 0 real_cost = -243.019 FORTE2_AL3 costs 0 real_cost = -29.6724 FORTE2_AL2-scwrl costs 0 real_cost = 57.9267 FORTE2_AL2 costs 0 real_cost = 290.065 FORTE2_AL1-scwrl costs 0 real_cost = -137.887 FORTE2_AL1 costs 0 real_cost = 70.15 FORTE1_AL5-scwrl costs 0 real_cost = -70.9395 FORTE1_AL5 costs 0 real_cost = 145.484 FORTE1_AL4-scwrl costs 0 real_cost = -176.445 FORTE1_AL4 costs 0 real_cost = 22.5294 FORTE1_AL3-scwrl costs 0 real_cost = -154.417 FORTE1_AL3 costs 0 real_cost = 55.8583 FORTE1_AL2-scwrl costs 0 real_cost = -244.931 FORTE1_AL2 costs 0 real_cost = -32.6812 FORTE1_AL1-scwrl costs 0 real_cost = 57.9267 FORTE1_AL1 costs 0 real_cost = 290.065 FOLDpro_TS5-scwrl costs 0 real_cost = 317.239 FOLDpro_TS5 costs 0 real_cost = 314.861 FOLDpro_TS4-scwrl costs 0 real_cost = 283.943 FOLDpro_TS4 costs 0 real_cost = 290.699 FOLDpro_TS3-scwrl costs 0 real_cost = 302.949 FOLDpro_TS3 costs 0 real_cost = 304.11 FOLDpro_TS2-scwrl costs 0 real_cost = 294.605 FOLDpro_TS2 costs 0 real_cost = 298.233 FOLDpro_TS1-scwrl costs 0 real_cost = -305.786 FOLDpro_TS1 costs 0 real_cost = -317.856 FAMS_TS5-scwrl costs 0 real_cost = -275.326 FAMS_TS5 costs 0 real_cost = -286.66 FAMS_TS4-scwrl costs 0 real_cost = -281.098 FAMS_TS4 costs 0 real_cost = -295.865 FAMS_TS3-scwrl costs 0 real_cost = -256.839 FAMS_TS3 costs 0 real_cost = -260.65 FAMS_TS2-scwrl costs 0 real_cost = -281.448 FAMS_TS2 costs 0 real_cost = -293.843 FAMS_TS1-scwrl costs 0 real_cost = -287.239 FAMS_TS1 costs 0 real_cost = -294.18 FAMSD_TS5-scwrl costs 0 real_cost = -259.677 FAMSD_TS5 costs 0 real_cost = -279.033 FAMSD_TS4-scwrl costs 0 real_cost = -242.527 FAMSD_TS4 costs 0 real_cost = -262.443 FAMSD_TS3-scwrl costs 0 real_cost = -258.071 FAMSD_TS3 costs 0 real_cost = -261.546 FAMSD_TS2-scwrl costs 0 real_cost = -247.75 FAMSD_TS2 costs 0 real_cost = -263.866 FAMSD_TS1-scwrl costs 0 real_cost = -284.018 FAMSD_TS1 costs 0 real_cost = -290.415 Distill_TS5-scwrl costs 0 real_cost = 526.737 Distill_TS4-scwrl costs 0 real_cost = 562.341 Distill_TS3-scwrl costs 0 real_cost = 524.818 Distill_TS2-scwrl costs 0 real_cost = 535.893 Distill_TS1-scwrl costs 0 real_cost = 485.904 CaspIta-FOX_TS5-scwrl costs 0 real_cost = -160.881 CaspIta-FOX_TS5 costs 0 real_cost = -172.259 CaspIta-FOX_TS4-scwrl costs 0 real_cost = -223.884 CaspIta-FOX_TS4 costs 0 real_cost = -241.667 CaspIta-FOX_TS3-scwrl costs 0 real_cost = -257.581 CaspIta-FOX_TS3 costs 0 real_cost = -267.939 CaspIta-FOX_TS2-scwrl costs 0 real_cost = -276.413 CaspIta-FOX_TS2 costs 0 real_cost = -290.027 CaspIta-FOX_TS1-scwrl costs 0 real_cost = -248.476 CaspIta-FOX_TS1 costs 0 real_cost = -272.018 CPHmodels_TS1-scwrl costs 0 real_cost = -245.702 CPHmodels_TS1 costs 0 real_cost = -261.089 CIRCLE_TS5-scwrl costs 0 real_cost = -263.568 CIRCLE_TS5 costs 0 real_cost = -273.935 CIRCLE_TS4-scwrl costs 0 real_cost = -261.391 CIRCLE_TS4 costs 0 real_cost = -273.087 CIRCLE_TS3-scwrl costs 0 real_cost = -275.326 CIRCLE_TS3 costs 0 real_cost = -286.66 CIRCLE_TS2-scwrl costs 0 real_cost = -256.839 CIRCLE_TS2 costs 0 real_cost = -260.65 CIRCLE_TS1-scwrl costs 0 real_cost = -269.94 CIRCLE_TS1 costs 0 real_cost = -281.321 Bilab-ENABLE_TS5-scwrl costs 0 real_cost = -173.265 Bilab-ENABLE_TS5 costs 0 real_cost = -173.094 Bilab-ENABLE_TS4-scwrl costs 0 real_cost = -172.293 Bilab-ENABLE_TS4 costs 0 real_cost = -172.227 Bilab-ENABLE_TS3-scwrl costs 0 real_cost = -264.101 Bilab-ENABLE_TS3 costs 0 real_cost = -264.477 Bilab-ENABLE_TS2-scwrl costs 0 real_cost = -134.721 Bilab-ENABLE_TS2 costs 0 real_cost = -133.868 Bilab-ENABLE_TS1-scwrl costs 0 real_cost = -126.676 Bilab-ENABLE_TS1 costs 0 real_cost = -126.68 BayesHH_TS1-scwrl costs 0 real_cost = -306.25 BayesHH_TS1 costs 0 real_cost = -315.457 ABIpro_TS5-scwrl costs 0 real_cost = 277.122 ABIpro_TS5 costs 0 real_cost = 277.122 ABIpro_TS4-scwrl costs 0 real_cost = 280.126 ABIpro_TS4 costs 0 real_cost = 280.126 ABIpro_TS3-scwrl costs 0 real_cost = 295.341 ABIpro_TS3 costs 0 real_cost = 295.341 ABIpro_TS2-scwrl costs 0 real_cost = 249.997 ABIpro_TS2 costs 0 real_cost = 249.811 ABIpro_TS1-scwrl costs 0 real_cost = 305.601 ABIpro_TS1 costs 0 real_cost = 305.244 3Dpro_TS5-scwrl costs 0 real_cost = 275.056 3Dpro_TS5 costs 0 real_cost = 278.486 3Dpro_TS4-scwrl costs 0 real_cost = 315.195 3Dpro_TS4 costs 0 real_cost = 316.097 3Dpro_TS3-scwrl costs 0 real_cost = 282.048 3Dpro_TS3 costs 0 real_cost = 280.66 3Dpro_TS2-scwrl costs 0 real_cost = 325.471 3Dpro_TS2 costs 0 real_cost = 332.321 3Dpro_TS1-scwrl costs 0 real_cost = -307.034 3Dpro_TS1 costs 0 real_cost = -312.908 3D-JIGSAW_TS5-scwrl costs 0 real_cost = -227.54 3D-JIGSAW_TS5 costs 0 real_cost = -217.085 3D-JIGSAW_TS4-scwrl costs 0 real_cost = -252.896 3D-JIGSAW_TS4 costs 0 real_cost = -250.377 3D-JIGSAW_TS3-scwrl costs 0 real_cost = -217.099 3D-JIGSAW_TS3 costs 0 real_cost = -217.376 3D-JIGSAW_TS2-scwrl costs 0 real_cost = -242.723 3D-JIGSAW_TS2 costs 0 real_cost = -252.66 3D-JIGSAW_TS1-scwrl costs 0 real_cost = -121.119 3D-JIGSAW_TS1 costs 0 real_cost = -134.966 3D-JIGSAW_RECOM_TS5-scwrl costs 0 real_cost = -208.486 3D-JIGSAW_RECOM_TS5 costs 0 real_cost = -209.286 3D-JIGSAW_RECOM_TS4-scwrl costs 0 real_cost = -238.718 3D-JIGSAW_RECOM_TS4 costs 0 real_cost = -229.027 3D-JIGSAW_RECOM_TS3-scwrl costs 0 real_cost = -125.024 3D-JIGSAW_RECOM_TS3 costs 0 real_cost = -139.154 3D-JIGSAW_RECOM_TS2-scwrl costs 0 real_cost = -237.332 3D-JIGSAW_RECOM_TS2 costs 0 real_cost = -232.941 3D-JIGSAW_RECOM_TS1-scwrl costs 0 real_cost = -244.251 3D-JIGSAW_RECOM_TS1 costs 0 real_cost = -250.191 3D-JIGSAW_POPULUS_TS5-scwrl costs 0 real_cost = -211.367 3D-JIGSAW_POPULUS_TS5 costs 0 real_cost = -215.686 3D-JIGSAW_POPULUS_TS4-scwrl costs 0 real_cost = -246.505 3D-JIGSAW_POPULUS_TS4 costs 0 real_cost = -252.477 3D-JIGSAW_POPULUS_TS3-scwrl costs 0 real_cost = -221.015 3D-JIGSAW_POPULUS_TS3 costs 0 real_cost = -226.73 3D-JIGSAW_POPULUS_TS2-scwrl costs 0 real_cost = -225.063 3D-JIGSAW_POPULUS_TS2 costs 0 real_cost = -226.072 3D-JIGSAW_POPULUS_TS1-scwrl costs 0 real_cost = -216.336 3D-JIGSAW_POPULUS_TS1 costs 0 real_cost = -217.153 tetramer//tetramer-try4-1larA costs 0 real_cost = -297.298 tetramer//try4-opt2 costs 0 real_cost = -296.83 tetramer//try4-opt2.gromacs0 costs 0 real_cost = -291.738 tetramer//try4-opt1 costs 0 real_cost = -296.835 tetramer//try4-opt1-scwrl costs 0 real_cost = -294.109 tetramer//try3-opt2 costs 0 real_cost = -297.632 tetramer//try3-opt2.gromacs0 costs 0 real_cost = -266.935 tetramer//try3-opt1 costs 0 real_cost = -297.578 tetramer//try3-opt1-scwrl costs 0 real_cost = -294.692 tetramer//try2-opt2 costs 0 real_cost = -297.52 tetramer//try2-opt2.gromacs0 costs 0 real_cost = -274.305 tetramer//try2-opt1 costs 0 real_cost = -297.124 tetramer//try2-opt1-scwrl costs 0 real_cost = -294.527 tetramer//try1-opt2 costs 0 real_cost = -296.726 tetramer//try1-opt2.gromacs0 costs 0 real_cost = -277.818 tetramer//try1-opt1 costs 0 real_cost = -296.375 tetramer//try1-opt1-scwrl costs 0 real_cost = -294.484 dimer//from-tetramer-try4-1larA.unpack costs 0 real_cost = -297.298 dimer//from-tetramer-try4-1larA costs 0 real_cost = -297.298 dimer//from-tetramer-try1-opt2.unpack costs 0 real_cost = -296.726 dimer//from-tetramer-try1-opt2 costs 0 real_cost = -296.726 dimer//dimer-try4-2fh7A costs 0 real_cost = -297.098 dimer//dimer-try4-1rpmA.unpack costs 0 real_cost = -297.111 dimer//dimer-try4-1rpmA costs 0 real_cost = -297.111 dimer//try2-opt2.unpack costs 0 real_cost = -298.29 dimer//try2-opt2.repack-nonPC costs 0 real_cost = -294.916 dimer//try2-opt2 costs 0 real_cost = -298.29 dimer//try2-opt2.gromacs0 costs 0 real_cost = -276.847 dimer//try2-opt1 costs 0 real_cost = -298.071 dimer//try2-opt1-scwrl costs 0 real_cost = -294.539 dimer//try1-opt2.unpack costs 0 real_cost = -295.143 dimer//try1-opt2.repack-nonPC costs 0 real_cost = -294.255 dimer//try1-opt2 costs 0 real_cost = -295.143 dimer//try1-opt2.gromacs0 costs 0 real_cost = -296.112 dimer//try1-opt1 costs 0 real_cost = -294.444 dimer//try1-opt1-scwrl costs 0 real_cost = -289.97 T0305.try4-opt2.repack-nonPC.pdb.gz costs 0 real_cost = -296.536 T0305.try4-opt2.pdb.gz costs 0 real_cost = -297.195 T0305.try4-opt2.gromacs0.pdb.gz costs 0 real_cost = -297.949 T0305.try4-opt1.pdb.gz costs 0 real_cost = -296.249 T0305.try4-opt1-scwrl.pdb.gz costs 0 real_cost = -294.17 T0305.try3-opt2.repack-nonPC.pdb.gz costs 0 real_cost = -293.591 T0305.try3-opt2.pdb.gz costs 0 real_cost = -294.767 T0305.try3-opt2.gromacs0.pdb.gz costs 0 real_cost = -294.673 T0305.try3-opt1.pdb.gz costs 0 real_cost = -296.66 T0305.try3-opt1-scwrl.pdb.gz costs 0 real_cost = -291.64 T0305.try2-opt2.repack-nonPC.pdb.gz costs 0 real_cost = -236.676 T0305.try2-opt2.pdb.gz costs 0 real_cost = -238.339 T0305.try2-opt2.gromacs0.pdb.gz costs 0 real_cost = -238.629 T0305.try2-opt1.pdb.gz costs 0 real_cost = -241.141 T0305.try2-opt1-scwrl.pdb.gz costs 0 real_cost = -238.971 T0305.try1-opt2.repack-nonPC.pdb.gz costs 0 real_cost = -241.421 T0305.try1-opt2.pdb.gz costs 0 real_cost = -243.452 T0305.try1-opt2.gromacs0.pdb.gz costs 0 real_cost = -240.201 T0305.try1-opt1.pdb.gz costs 0 real_cost = -237.084 T0305.try1-opt1-scwrl.pdb.gz costs 0 real_cost = -236.874 ../model5.ts-submitted costs 0 real_cost = -176.585 ../model4.ts-submitted costs 0 real_cost = -203.636 ../model3.ts-submitted costs 0 real_cost = -293.59 ../model2.ts-submitted costs 0 real_cost = -238.467 ../model1.ts-submitted costs 0 real_cost = -297.195 align5 costs 0 real_cost = -96.9019 align4 costs 0 real_cost = -74.4126 align3 costs 0 real_cost = -144.9 align2 costs 0 real_cost = -182.408 align1 costs 0 real_cost = -217.305 T0305.try1-opt2.pdb costs 0 real_cost = -243.44 model5-scwrl costs 0 real_cost = -144.688 model5.ts-submitted costs 0 real_cost = -176.585 model4-scwrl costs 0 real_cost = -130.876 model4.ts-submitted costs 0 real_cost = -203.636 model3-scwrl costs 0 real_cost = -291.064 model3.ts-submitted costs 0 real_cost = -293.59 model2-scwrl costs 0 real_cost = -238.742 model2.ts-submitted costs 0 real_cost = -238.467 model1-scwrl costs 0 real_cost = -293.195 model1.ts-submitted costs 0 real_cost = -297.192 T0305_1.real.pdb costs 0 real_cost = -859 # command:CPU_time= 2883.36 sec, elapsed time= 5448.16 sec) # command:rm -f sort.tmp /projects/compbio/bin/sorttbl real_cost < decoys/evaluate_1.rdb > sort.tmp mv -f sort.tmp decoys/evaluate_1.rdb mv -f decoys/evaluate_1.pretty decoys/evaluate_1.pretty.old mv: cannot stat `decoys/evaluate_1.pretty': No such file or directory make: [decoys/evaluate_1.pretty] Error 1 (ignored) /projects/compbio/experiments/protein-predict/casp7/scripts/prettyscore -terse -targpfx -decpoint < decoys/evaluate_1.rdb > decoys/evaluate_1.pretty