/projects/compbio/experiments/protein-predict/casp7/starter-directory/Make.main:725: SECONDARY_TARGET = T0334.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/T0334.} ;\ 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/T0334/ -e s/START_COL/1/ \ -e s/REAL_PDB/2oalA/ \ -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 1175061510 # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading monomeric-50pc.atoms # trans (non-proline) backbone unit: # CA= -2.2088 1.0126 -0.0031 # O= -0.1499 2.2440 0.0017 # C= -0.6889 1.1368 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4581 0.0000 0.0000 # cis backbone unit: # CA= -0.1462 2.4515 0.0018 # O= -2.0272 0.9713 0.0022 # C= -0.8006 1.0755 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4659 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2099 1.0634 -0.0014 # O= -0.1233 2.2459 0.0075 # C= -0.6871 1.1518 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading monomeric-50pc.atoms have 448 chains in training database # Count of chains,residues,atoms: 448,112605,876684 # 109826 residues have no bad marker # 665 residues lack atoms needed to compute omega # 322 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 6 # HAS_OXT 325 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 523 # HAS_UNKNOWN_ATOMS 2 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 208 # NON_PLANAR_PEPTIDE 143 # BAD_PEPTIDE 1959 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-1332.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:CPU_time= 4.5993 sec, elapsed time= 4.71633 sec) # command:# Reading spots from monomeric-50pc-dry-5.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-5.hist # created burial cost function dry5 with radius 5 with spots at monomeric-50pc-dry-5.spot # command:# Reading spots from monomeric-50pc-wet-6.5.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-wet-6.5.hist # created burial cost function wet6.5 with radius 6.5 with spots at monomeric-50pc-wet-6.5.spot # command:# Reading spots from monomeric-50pc-dry-6.5.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-6.5.hist # created burial cost function dry6.5 with radius 6.5 with spots at monomeric-50pc-dry-6.5.spot # command:# Reading spots from monomeric-50pc-generic-6.5.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-generic-6.5.hist # created burial cost function gen6.5 with radius 6.5 with spots at monomeric-50pc-generic-6.5.spot # command:# Reading spots from near-backbone-center.spot # reading histogram from smoothed-near-backbone-2spot.hist # Reading spots from near-backbone-count.spot # created burial cost function near_backbone with radius 9.65 with spots at near-backbone-center.spot counting only near-backbone-count.spot # command:# Reading spots from way-back-center.spot # reading histogram from smoothed-way-back-2spot.hist # Reading spots from way-back-count.spot # created burial cost function way_back with radius 8.9 with spots at way-back-center.spot counting only way-back-count.spot # command:# Reading spots from monomeric-50pc-dry-8.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-8.hist # created burial cost function dry8 with radius 8 with spots at monomeric-50pc-dry-8.spot # command:# Reading spots from monomeric-50pc-dry-10.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-10.hist # created burial cost function dry10 with radius 10 with spots at monomeric-50pc-dry-10.spot # command:# Reading spots from monomeric-50pc-dry-12.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-12.hist # created burial cost function dry12 with radius 12 with spots at monomeric-50pc-dry-12.spot # command:# reading histogram from dunbrack-2191-alpha.hist # created alpha cost function alpha with offset 0 and 360 bins # command:# reading histogram from dunbrack-2191-alpha-1.hist # created alpha cost function alpha_prev with offset -1 and 360 bins # command:# Prefix for input files set to /projects/compbio/lib/alphabet/ # command:# Read 3 alphabets from alpha.alphabet # command:CPU_time= 4.66429 sec, elapsed time= 4.79787 sec) # command:# Prefix for input files set to # command:# Making conformation for sequence T0334 numbered 1 through 530 Created new target T0334 from T0334.a2m # command:# command:# No conformations to remove in PopConform # command:# cleared Id set # command:# command:2oalA expands to /projects/compbio/data/pdb/2oal.pdb.gz 2oalA: Read 527 residues and 4224 atoms. # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # command:# Saving current conformation as real # command:# Prefix for output files set to decoys/ # command:# SetRealCost created real_cost = # ( 50 * real_hbond + 50 * real_hbond_u + 50 * decoy_hbond + 50 * decoy_hbond_u + 10 * real_NO_hbond + 10 * real_NO_hbond_u + 10 * decoy_NO_hbond + 10 * decoy_NO_hbond_u + 10 * knot + 200 * clens + 0 * rmsd + 35 * log_rmsd + 0 * rmsd_ca + 30 * log_rmsd_ca + 1 * GDT + 1 * smooth_GDT + 0.2 * missing_atoms ) # command:# SetCost created cost = # ) # command:CPU_time= 6.69098 sec, elapsed time= 6.87596 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 451 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -84.3454 # GDT_score(maxd=8,maxw=2.9)= -87.0258 # GDT_score(maxd=8,maxw=3.2)= -84.6143 # GDT_score(maxd=8,maxw=3.5)= -81.7517 # GDT_score(maxd=10,maxw=3.8)= -83.3502 # GDT_score(maxd=10,maxw=4)= -81.3527 # GDT_score(maxd=10,maxw=4.2)= -79.2208 # GDT_score(maxd=12,maxw=4.3)= -82.0611 # GDT_score(maxd=12,maxw=4.5)= -79.9893 # GDT_score(maxd=12,maxw=4.7)= -77.8535 # GDT_score(maxd=14,maxw=5.2)= -75.8937 # GDT_score(maxd=14,maxw=5.5)= -72.7803 # command:# Prefix for output files set to # command:superimposing iter= 0 total_weight= 6.3320000e+03 rmsd (weighted)= 3.4802476e+00 (unweighted)= 1.5181530e+01 superimposing iter= 1 total_weight= 2.8210732e+04 rmsd (weighted)= 1.0910240e+00 (unweighted)= 1.5172288e+01 superimposing iter= 2 total_weight= 1.0945790e+04 rmsd (weighted)= 6.5620913e-01 (unweighted)= 1.5174170e+01 superimposing iter= 3 total_weight= 5.8131255e+03 rmsd (weighted)= 5.5468426e-01 (unweighted)= 1.5174556e+01 superimposing iter= 4 total_weight= 4.5477820e+03 rmsd (weighted)= 5.3196178e-01 (unweighted)= 1.5174640e+01 superimposing iter= 5 total_weight= 4.2789488e+03 rmsd (weighted)= 5.2630258e-01 (unweighted)= 1.5174661e+01 # command:# Prefix for output files set to decoys/ # command:# request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1957011966.pdb -s /var/tmp/to_scwrl_1957011966.seq -o /var/tmp/from_scwrl_1957011966.pdb > /var/tmp/scwrl_1957011966.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1957011966.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 473 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -84.6774 # GDT_score(maxd=8,maxw=2.9)= -87.3441 # GDT_score(maxd=8,maxw=3.2)= -84.9683 # GDT_score(maxd=8,maxw=3.5)= -81.9537 # GDT_score(maxd=10,maxw=3.8)= -83.5459 # GDT_score(maxd=10,maxw=4)= -81.4455 # GDT_score(maxd=10,maxw=4.2)= -79.2388 # GDT_score(maxd=12,maxw=4.3)= -82.1301 # GDT_score(maxd=12,maxw=4.5)= -79.9901 # GDT_score(maxd=12,maxw=4.7)= -77.7731 # GDT_score(maxd=14,maxw=5.2)= -75.6958 # GDT_score(maxd=14,maxw=5.5)= -72.4771 # command:# request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_2042967217.pdb -s /var/tmp/to_scwrl_2042967217.seq -o /var/tmp/from_scwrl_2042967217.pdb > /var/tmp/scwrl_2042967217.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2042967217.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 479 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -82.7799 # GDT_score(maxd=8,maxw=2.9)= -86.7969 # GDT_score(maxd=8,maxw=3.2)= -83.4944 # GDT_score(maxd=8,maxw=3.5)= -79.7846 # GDT_score(maxd=10,maxw=3.8)= -81.625 # GDT_score(maxd=10,maxw=4)= -79.07 # GDT_score(maxd=10,maxw=4.2)= -76.4032 # GDT_score(maxd=12,maxw=4.3)= -79.8521 # GDT_score(maxd=12,maxw=4.5)= -77.2781 # GDT_score(maxd=12,maxw=4.7)= -74.72 # GDT_score(maxd=14,maxw=5.2)= -72.5545 # GDT_score(maxd=14,maxw=5.5)= -69.1734 # command:# request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_971472055.pdb -s /var/tmp/to_scwrl_971472055.seq -o /var/tmp/from_scwrl_971472055.pdb > /var/tmp/scwrl_971472055.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_971472055.pdb # conformation set from SCWRL output # command:# naming current conformation model3-scwrl # command:# ReadConformPDB reading from PDB file model4.ts-submitted looking for model 1 # Found a chain break before 468 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -84.4877 # GDT_score(maxd=8,maxw=2.9)= -86.9754 # GDT_score(maxd=8,maxw=3.2)= -84.4665 # GDT_score(maxd=8,maxw=3.5)= -81.6441 # GDT_score(maxd=10,maxw=3.8)= -83.3388 # GDT_score(maxd=10,maxw=4)= -81.4008 # GDT_score(maxd=10,maxw=4.2)= -79.265 # GDT_score(maxd=12,maxw=4.3)= -82.1733 # GDT_score(maxd=12,maxw=4.5)= -80.0879 # GDT_score(maxd=12,maxw=4.7)= -77.9245 # GDT_score(maxd=14,maxw=5.2)= -76.0198 # GDT_score(maxd=14,maxw=5.5)= -72.8834 # command:# request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1403097679.pdb -s /var/tmp/to_scwrl_1403097679.seq -o /var/tmp/from_scwrl_1403097679.pdb > /var/tmp/scwrl_1403097679.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1403097679.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 T0334 can't currently be optimized by undertaker # command:# fraction of real conformation used = 0.893738 # GDT_score = -65.8444 # GDT_score(maxd=8,maxw=2.9)= -66.6868 # GDT_score(maxd=8,maxw=3.2)= -65.9214 # GDT_score(maxd=8,maxw=3.5)= -64.9384 # GDT_score(maxd=10,maxw=3.8)= -65.5318 # GDT_score(maxd=10,maxw=4)= -64.7451 # GDT_score(maxd=10,maxw=4.2)= -63.8204 # GDT_score(maxd=12,maxw=4.3)= -65.0982 # GDT_score(maxd=12,maxw=4.5)= -64.1793 # GDT_score(maxd=12,maxw=4.7)= -63.1259 # GDT_score(maxd=14,maxw=5.2)= -62.0682 # GDT_score(maxd=14,maxw=5.5)= -60.0818 # command:# request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_2072957298.pdb -s /var/tmp/to_scwrl_2072957298.seq -o /var/tmp/from_scwrl_2072957298.pdb > /var/tmp/scwrl_2072957298.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2072957298.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 T0334.try1-opt2.pdb looking for model 1 # Found a chain break before 488 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -82.6376 # GDT_score(maxd=8,maxw=2.9)= -86.546 # GDT_score(maxd=8,maxw=3.2)= -83.3997 # GDT_score(maxd=8,maxw=3.5)= -79.7464 # GDT_score(maxd=10,maxw=3.8)= -81.5722 # GDT_score(maxd=10,maxw=4)= -79.0429 # GDT_score(maxd=10,maxw=4.2)= -76.4591 # GDT_score(maxd=12,maxw=4.3)= -79.8314 # GDT_score(maxd=12,maxw=4.5)= -77.343 # GDT_score(maxd=12,maxw=4.7)= -74.8682 # GDT_score(maxd=14,maxw=5.2)= -72.7701 # GDT_score(maxd=14,maxw=5.5)= -69.4532 # command:# Prefix for output files set to # command:superimposing iter= 0 total_weight= 6.3320000e+03 rmsd (weighted)= 2.8202080e+00 (unweighted)= 1.5090632e+01 superimposing iter= 1 total_weight= 2.2823386e+04 rmsd (weighted)= 1.1113323e+00 (unweighted)= 1.5101999e+01 superimposing iter= 2 total_weight= 7.4965956e+03 rmsd (weighted)= 8.1854910e-01 (unweighted)= 1.5114844e+01 superimposing iter= 3 total_weight= 5.1651992e+03 rmsd (weighted)= 7.3168748e-01 (unweighted)= 1.5123240e+01 superimposing iter= 4 total_weight= 4.5915666e+03 rmsd (weighted)= 6.9597464e-01 (unweighted)= 1.5127719e+01 superimposing iter= 5 total_weight= 4.3674539e+03 rmsd (weighted)= 6.7984038e-01 (unweighted)= 1.5130088e+01 # command:# Prefix for output files set to decoys/ # command:# Prefix for input files set to # command:# ReadConformPDB reading from PDB file T0334.undertaker-align.pdb looking for model 1 WARNING: atoms too close: (T0334)V136.C and (T0334)I149.C only 0.0000000e+00 apart, marking (T0334)I149.C as missing WARNING: atoms too close: (T0334)E137.N and (T0334)L150.N only 0.0000000e+00 apart, marking (T0334)E137.N as missing WARNING: atoms too close: (T0334)E137.CA and (T0334)L150.CA only 0.0000000e+00 apart, marking (T0334)E137.CA as missing WARNING: atoms too close: (T0334)E194.C and (T0334)D195.C only 0.0000000e+00 apart, marking (T0334)D195.C as missing WARNING: atoms too close: (T0334)D195.N and (T0334)R196.N only 0.0000000e+00 apart, marking (T0334)D195.N as missing WARNING: atoms too close: (T0334)D195.CA and (T0334)R196.CA only 0.0000000e+00 apart, marking (T0334)D195.CA as missing WARNING: atoms too close: (T0334)P320.C and (T0334)E321.C only 0.0000000e+00 apart, marking (T0334)E321.C as missing WARNING: atoms too close: (T0334)E321.N and (T0334)T322.N only 0.0000000e+00 apart, marking (T0334)E321.N as missing WARNING: atoms too close: (T0334)E321.CA and (T0334)T322.CA only 0.0000000e+00 apart, marking (T0334)E321.CA as missing # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # command:# naming current conformation align1 # command:# fraction of real conformation used = 0.918406 # GDT_score = -67.5996 # GDT_score(maxd=8,maxw=2.9)= -68.4089 # GDT_score(maxd=8,maxw=3.2)= -67.6266 # GDT_score(maxd=8,maxw=3.5)= -66.6283 # GDT_score(maxd=10,maxw=3.8)= -67.2744 # GDT_score(maxd=10,maxw=4)= -66.4829 # GDT_score(maxd=10,maxw=4.2)= -65.5432 # GDT_score(maxd=12,maxw=4.3)= -66.8614 # GDT_score(maxd=12,maxw=4.5)= -65.9271 # GDT_score(maxd=12,maxw=4.7)= -64.8497 # GDT_score(maxd=14,maxw=5.2)= -63.7899 # GDT_score(maxd=14,maxw=5.5)= -61.7638 # command:# ReadConformPDB reading from PDB file T0334.undertaker-align.pdb looking for model 2 WARNING: atoms too close: (T0334)F59.C and (T0334)F60.C only 0.0000000e+00 apart, marking (T0334)F60.C as missing WARNING: atoms too close: (T0334)F60.N and (T0334)D61.N only 0.0000000e+00 apart, marking (T0334)F60.N as missing WARNING: atoms too close: (T0334)F60.CA and (T0334)D61.CA only 0.0000000e+00 apart, marking (T0334)F60.CA as missing WARNING: atoms too close: (T0334)I65.C and (T0334)L122.C only 0.0000000e+00 apart, marking (T0334)L122.C as missing WARNING: atoms too close: (T0334)P66.N and (T0334)S123.N only 0.0000000e+00 apart, marking (T0334)P66.N as missing WARNING: atoms too close: (T0334)P66.CA and (T0334)S123.CA only 0.0000000e+00 apart, marking (T0334)P66.CA as missing WARNING: atoms too close: (T0334)R132.C and (T0334)T135.C only 0.0000000e+00 apart, marking (T0334)T135.C as missing WARNING: atoms too close: (T0334)G133.N and (T0334)V136.N only 0.0000000e+00 apart, marking (T0334)G133.N as missing WARNING: atoms too close: (T0334)G133.CA and (T0334)V136.CA only 0.0000000e+00 apart, marking (T0334)G133.CA as missing WARNING: atoms too close: (T0334)D151.C and (T0334)N153.C only 0.0000000e+00 apart, marking (T0334)N153.C as missing WARNING: atoms too close: (T0334)A152.N and (T0334)R154.N only 0.0000000e+00 apart, marking (T0334)A152.N as missing WARNING: atoms too close: (T0334)A152.CA and (T0334)R154.CA only 0.0000000e+00 apart, marking (T0334)A152.CA as missing WARNING: atoms too close: (T0334)W169.C and (T0334)H170.C only 0.0000000e+00 apart, marking (T0334)H170.C as missing WARNING: atoms too close: (T0334)H170.N and (T0334)F171.N only 0.0000000e+00 apart, marking (T0334)H170.N as missing WARNING: atoms too close: (T0334)H170.CA and (T0334)F171.CA only 0.0000000e+00 apart, marking (T0334)H170.CA as missing WARNING: atoms too close: (T0334)L234.C and (T0334)I235.C only 0.0000000e+00 apart, marking (T0334)I235.C as missing WARNING: atoms too close: (T0334)I235.N and (T0334)N236.N only 0.0000000e+00 apart, marking (T0334)I235.N as missing WARNING: atoms too close: (T0334)I235.CA and (T0334)N236.CA only 0.0000000e+00 apart, marking (T0334)I235.CA as missing WARNING: atoms too close: (T0334)H249.C and (T0334)N252.C only 0.0000000e+00 apart, marking (T0334)N252.C as missing WARNING: atoms too close: (T0334)L250.N and (T0334)D253.N only 0.0000000e+00 apart, marking (T0334)L250.N as missing WARNING: atoms too close: (T0334)L250.CA and (T0334)D253.CA only 0.0000000e+00 apart, marking (T0334)L250.CA as missing WARNING: atoms too close: (T0334)L318.C and (T0334)E321.C only 0.0000000e+00 apart, marking (T0334)E321.C as missing WARNING: atoms too close: (T0334)D319.N and (T0334)T322.N only 0.0000000e+00 apart, marking (T0334)D319.N as missing WARNING: atoms too close: (T0334)D319.CA and (T0334)T322.CA only 0.0000000e+00 apart, marking (T0334)D319.CA as missing WARNING: atoms too close: (T0334)D414.C and (T0334)L480.C only 0.0000000e+00 apart, marking (T0334)L480.C as missing WARNING: atoms too close: (T0334)T415.N and (T0334)V481.N only 0.0000000e+00 apart, marking (T0334)T415.N as missing WARNING: atoms too close: (T0334)T415.CA and (T0334)V481.CA only 0.0000000e+00 apart, marking (T0334)T415.CA as missing # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # command:# naming current conformation align2 # command:# fraction of real conformation used = 0.677419 # GDT_score = -31.167 # GDT_score(maxd=8,maxw=2.9)= -32.1343 # GDT_score(maxd=8,maxw=3.2)= -29.9586 # GDT_score(maxd=8,maxw=3.5)= -28.0253 # GDT_score(maxd=10,maxw=3.8)= -30.2569 # GDT_score(maxd=10,maxw=4)= -29.0419 # GDT_score(maxd=10,maxw=4.2)= -27.909 # GDT_score(maxd=12,maxw=4.3)= -30.4587 # GDT_score(maxd=12,maxw=4.5)= -29.3355 # GDT_score(maxd=12,maxw=4.7)= -28.2902 # GDT_score(maxd=14,maxw=5.2)= -28.2425 # GDT_score(maxd=14,maxw=5.5)= -26.8849 # command:# ReadConformPDB reading from PDB file T0334.undertaker-align.pdb looking for model 3 WARNING: atoms too close: (T0334)G3.C and (T0334)K4.C only 0.0000000e+00 apart, marking (T0334)K4.C as missing WARNING: atoms too close: (T0334)K4.N and (T0334)I5.N only 0.0000000e+00 apart, marking (T0334)K4.N as missing WARNING: atoms too close: (T0334)K4.CA and (T0334)I5.CA only 0.0000000e+00 apart, marking (T0334)K4.CA as missing WARNING: atoms too close: (T0334)K26.C and (T0334)Q29.C only 0.0000000e+00 apart, marking (T0334)Q29.C as missing WARNING: atoms too close: (T0334)A27.N and (T0334)G30.N only 0.0000000e+00 apart, marking (T0334)A27.N as missing WARNING: atoms too close: (T0334)A27.CA and (T0334)G30.CA only 0.0000000e+00 apart, marking (T0334)A27.CA as missing WARNING: atoms too close: (T0334)K115.C and (T0334)L122.C only 0.0000000e+00 apart, marking (T0334)L122.C as missing WARNING: atoms too close: (T0334)Y116.N and (T0334)S123.N only 0.0000000e+00 apart, marking (T0334)Y116.N as missing WARNING: atoms too close: (T0334)Y116.CA and (T0334)S123.CA only 0.0000000e+00 apart, marking (T0334)Y116.CA as missing WARNING: atoms too close: (T0334)S130.C and (T0334)Y131.C only 0.0000000e+00 apart, marking (T0334)Y131.C as missing WARNING: atoms too close: (T0334)Y131.N and (T0334)R132.N only 0.0000000e+00 apart, marking (T0334)Y131.N as missing WARNING: atoms too close: (T0334)Y131.CA and (T0334)R132.CA only 0.0000000e+00 apart, marking (T0334)Y131.CA as missing WARNING: atoms too close: (T0334)P147.C and (T0334)R154.C only 0.0000000e+00 apart, marking (T0334)R154.C as missing WARNING: atoms too close: (T0334)V148.N and (T0334)S155.N only 0.0000000e+00 apart, marking (T0334)V148.N as missing WARNING: atoms too close: (T0334)V148.CA and (T0334)S155.CA only 0.0000000e+00 apart, marking (T0334)V148.CA as missing WARNING: atoms too close: (T0334)K163.C and (T0334)T165.C only 0.0000000e+00 apart, marking (T0334)T165.C as missing WARNING: atoms too close: (T0334)V164.N and (T0334)N166.N only 0.0000000e+00 apart, marking (T0334)V164.N as missing WARNING: atoms too close: (T0334)V164.CA and (T0334)N166.CA only 0.0000000e+00 apart, marking (T0334)V164.CA as missing WARNING: atoms too close: (T0334)A184.C and (T0334)T185.C only 0.0000000e+00 apart, marking (T0334)T185.C as missing WARNING: atoms too close: (T0334)T185.N and (T0334)E186.N only 0.0000000e+00 apart, marking (T0334)T185.N as missing WARNING: atoms too close: (T0334)T185.CA and (T0334)E186.CA only 0.0000000e+00 apart, marking (T0334)T185.CA as missing WARNING: atoms too close: (T0334)R217.C and (T0334)V218.C only 0.0000000e+00 apart, marking (T0334)V218.C as missing WARNING: atoms too close: (T0334)V218.N and (T0334)F219.N only 0.0000000e+00 apart, marking (T0334)V218.N as missing WARNING: atoms too close: (T0334)V218.CA and (T0334)F219.CA only 0.0000000e+00 apart, marking (T0334)V218.CA as missing WARNING: atoms too close: (T0334)H249.C and (T0334)N252.C only 0.0000000e+00 apart, marking (T0334)N252.C as missing WARNING: atoms too close: (T0334)L250.N and (T0334)D253.N only 0.0000000e+00 apart, marking (T0334)L250.N as missing WARNING: atoms too close: (T0334)L250.CA and (T0334)D253.CA only 0.0000000e+00 apart, marking (T0334)L250.CA as missing WARNING: atoms too close: (T0334)H262.C and (T0334)D265.C only 0.0000000e+00 apart, marking (T0334)D265.C as missing WARNING: atoms too close: (T0334)D263.N and (T0334)A266.N only 0.0000000e+00 apart, marking (T0334)D263.N as missing WARNING: atoms too close: (T0334)D263.CA and (T0334)A266.CA only 0.0000000e+00 apart, marking (T0334)D263.CA as missing WARNING: atoms too close: (T0334)A266.C and (T0334)N267.C only 0.0000000e+00 apart, marking (T0334)N267.C as missing WARNING: atoms too close: (T0334)N267.N and (T0334)G268.N only 0.0000000e+00 apart, marking (T0334)N267.N as missing WARNING: atoms too close: (T0334)N267.CA and (T0334)G268.CA only 0.0000000e+00 apart, marking (T0334)N267.CA as missing WARNING: atoms too close: (T0334)A275.C and (T0334)M278.C only 0.0000000e+00 apart, marking (T0334)M278.C as missing WARNING: atoms too close: (T0334)I276.N and (T0334)K279.N only 0.0000000e+00 apart, marking (T0334)I276.N as missing WARNING: atoms too close: (T0334)I276.CA and (T0334)K279.CA only 0.0000000e+00 apart, marking (T0334)I276.CA as missing WARNING: atoms too close: (T0334)R336.C and (T0334)R337.C only 0.0000000e+00 apart, marking (T0334)R337.C as missing WARNING: atoms too close: (T0334)R337.N and (T0334)A338.N only 0.0000000e+00 apart, marking (T0334)R337.N as missing WARNING: atoms too close: (T0334)R337.CA and (T0334)A338.CA only 0.0000000e+00 apart, marking (T0334)R337.CA as missing # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # command:# naming current conformation align3 # command:# ReadConformPDB reading from PDB file T0334.undertaker-align.pdb looking for model 4 WARNING: atoms too close: (T0334)K26.C and (T0334)Q29.C only 0.0000000e+00 apart, marking (T0334)Q29.C as missing WARNING: atoms too close: (T0334)A27.N and (T0334)G30.N only 0.0000000e+00 apart, marking (T0334)A27.N as missing WARNING: atoms too close: (T0334)A27.CA and (T0334)G30.CA only 0.0000000e+00 apart, marking (T0334)A27.CA as missing WARNING: atoms too close: (T0334)F59.C and (T0334)F60.C only 0.0000000e+00 apart, marking (T0334)F60.C as missing WARNING: atoms too close: (T0334)F60.N and (T0334)D61.N only 0.0000000e+00 apart, marking (T0334)F60.N as missing WARNING: atoms too close: (T0334)F60.CA and (T0334)D61.CA only 0.0000000e+00 apart, marking (T0334)F60.CA as missing WARNING: atoms too close: (T0334)I65.C and (T0334)L122.C only 0.0000000e+00 apart, marking (T0334)L122.C as missing WARNING: atoms too close: (T0334)P66.N and (T0334)S123.N only 0.0000000e+00 apart, marking (T0334)P66.N as missing WARNING: atoms too close: (T0334)P66.CA and (T0334)S123.CA only 0.0000000e+00 apart, marking (T0334)P66.CA as missing WARNING: atoms too close: (T0334)R132.C and (T0334)T135.C only 0.0000000e+00 apart, marking (T0334)T135.C as missing WARNING: atoms too close: (T0334)G133.N and (T0334)V136.N only 0.0000000e+00 apart, marking (T0334)G133.N as missing WARNING: atoms too close: (T0334)G133.CA and (T0334)V136.CA only 0.0000000e+00 apart, marking (T0334)G133.CA as missing WARNING: atoms too close: (T0334)L150.C and (T0334)N153.C only 0.0000000e+00 apart, marking (T0334)N153.C as missing WARNING: atoms too close: (T0334)D151.N and (T0334)R154.N only 0.0000000e+00 apart, marking (T0334)D151.N as missing WARNING: atoms too close: (T0334)D151.CA and (T0334)R154.CA only 0.0000000e+00 apart, marking (T0334)D151.CA as missing WARNING: atoms too close: (T0334)G161.C and (T0334)T165.C only 0.0000000e+00 apart, marking (T0334)T165.C as missing WARNING: atoms too close: (T0334)S162.N and (T0334)N166.N only 0.0000000e+00 apart, marking (T0334)S162.N as missing WARNING: atoms too close: (T0334)S162.CA and (T0334)N166.CA only 0.0000000e+00 apart, marking (T0334)S162.CA as missing WARNING: atoms too close: (T0334)A184.C and (T0334)T185.C only 0.0000000e+00 apart, marking (T0334)T185.C as missing WARNING: atoms too close: (T0334)T185.N and (T0334)E186.N only 0.0000000e+00 apart, marking (T0334)T185.N as missing WARNING: atoms too close: (T0334)T185.CA and (T0334)E186.CA only 0.0000000e+00 apart, marking (T0334)T185.CA as missing WARNING: atoms too close: (T0334)G206.C and (T0334)I208.C only 0.0000000e+00 apart, marking (T0334)I208.C as missing WARNING: atoms too close: (T0334)N207.N and (T0334)E209.N only 0.0000000e+00 apart, marking (T0334)N207.N as missing WARNING: atoms too close: (T0334)N207.CA and (T0334)E209.CA only 0.0000000e+00 apart, marking (T0334)N207.CA as missing WARNING: atoms too close: (T0334)L234.C and (T0334)I235.C only 0.0000000e+00 apart, marking (T0334)I235.C as missing WARNING: atoms too close: (T0334)I235.N and (T0334)N236.N only 0.0000000e+00 apart, marking (T0334)I235.N as missing WARNING: atoms too close: (T0334)I235.CA and (T0334)N236.CA only 0.0000000e+00 apart, marking (T0334)I235.CA as missing WARNING: atoms too close: (T0334)T258.C and (T0334)D263.C only 0.0000000e+00 apart, marking (T0334)D263.C as missing WARNING: atoms too close: (T0334)Q259.N and (T0334)D264.N only 0.0000000e+00 apart, marking (T0334)Q259.N as missing WARNING: atoms too close: (T0334)Q259.CA and (T0334)D264.CA only 0.0000000e+00 apart, marking (T0334)Q259.CA as missing WARNING: atoms too close: (T0334)R419.C and (T0334)F503.C only 0.0000000e+00 apart, marking (T0334)F503.C as missing WARNING: atoms too close: (T0334)A420.N and (T0334)G504.N only 0.0000000e+00 apart, marking (T0334)A420.N as missing WARNING: atoms too close: (T0334)A420.CA and (T0334)G504.CA only 0.0000000e+00 apart, marking (T0334)A420.CA as missing # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # command:# naming current conformation align4 # command:# ReadConformPDB reading from PDB file T0334.undertaker-align.pdb looking for model 5 WARNING: atoms too close: (T0334)A27.C and (T0334)G30.C only 0.0000000e+00 apart, marking (T0334)G30.C as missing WARNING: atoms too close: (T0334)L28.N and (T0334)T31.N only 0.0000000e+00 apart, marking (T0334)L28.N as missing WARNING: atoms too close: (T0334)L28.CA and (T0334)T31.CA only 0.0000000e+00 apart, marking (T0334)L28.CA as missing WARNING: atoms too close: (T0334)F59.C and (T0334)F60.C only 0.0000000e+00 apart, marking (T0334)F60.C as missing WARNING: atoms too close: (T0334)F60.N and (T0334)D61.N only 0.0000000e+00 apart, marking (T0334)F60.N as missing WARNING: atoms too close: (T0334)F60.CA and (T0334)D61.CA only 0.0000000e+00 apart, marking (T0334)F60.CA as missing WARNING: atoms too close: (T0334)I65.C and (T0334)L122.C only 0.0000000e+00 apart, marking (T0334)L122.C as missing WARNING: atoms too close: (T0334)P66.N and (T0334)S123.N only 0.0000000e+00 apart, marking (T0334)P66.N as missing WARNING: atoms too close: (T0334)P66.CA and (T0334)S123.CA only 0.0000000e+00 apart, marking (T0334)P66.CA as missing WARNING: atoms too close: (T0334)R132.C and (T0334)T135.C only 0.0000000e+00 apart, marking (T0334)T135.C as missing WARNING: atoms too close: (T0334)G133.N and (T0334)V136.N only 0.0000000e+00 apart, marking (T0334)G133.N as missing WARNING: atoms too close: (T0334)G133.CA and (T0334)V136.CA only 0.0000000e+00 apart, marking (T0334)G133.CA as missing WARNING: atoms too close: (T0334)D151.C and (T0334)R154.C only 0.0000000e+00 apart, marking (T0334)R154.C as missing WARNING: atoms too close: (T0334)A152.N and (T0334)S155.N only 0.0000000e+00 apart, marking (T0334)A152.N as missing WARNING: atoms too close: (T0334)A152.CA and (T0334)S155.CA only 0.0000000e+00 apart, marking (T0334)A152.CA as missing WARNING: atoms too close: (T0334)G161.C and (T0334)T165.C only 0.0000000e+00 apart, marking (T0334)T165.C as missing WARNING: atoms too close: (T0334)S162.N and (T0334)N166.N only 0.0000000e+00 apart, marking (T0334)S162.N as missing WARNING: atoms too close: (T0334)S162.CA and (T0334)N166.CA only 0.0000000e+00 apart, marking (T0334)S162.CA as missing WARNING: atoms too close: (T0334)A184.C and (T0334)T185.C only 0.0000000e+00 apart, marking (T0334)T185.C as missing WARNING: atoms too close: (T0334)T185.N and (T0334)E186.N only 0.0000000e+00 apart, marking (T0334)T185.N as missing WARNING: atoms too close: (T0334)T185.CA and (T0334)E186.CA only 0.0000000e+00 apart, marking (T0334)T185.CA as missing WARNING: atoms too close: (T0334)G206.C and (T0334)I208.C only 0.0000000e+00 apart, marking (T0334)I208.C as missing WARNING: atoms too close: (T0334)N207.N and (T0334)E209.N only 0.0000000e+00 apart, marking (T0334)N207.N as missing WARNING: atoms too close: (T0334)N207.CA and (T0334)E209.CA only 0.0000000e+00 apart, marking (T0334)N207.CA as missing WARNING: atoms too close: (T0334)L234.C and (T0334)I235.C only 0.0000000e+00 apart, marking (T0334)I235.C as missing WARNING: atoms too close: (T0334)I235.N and (T0334)N236.N only 0.0000000e+00 apart, marking (T0334)I235.N as missing WARNING: atoms too close: (T0334)I235.CA and (T0334)N236.CA only 0.0000000e+00 apart, marking (T0334)I235.CA as missing WARNING: atoms too close: (T0334)T258.C and (T0334)D263.C only 0.0000000e+00 apart, marking (T0334)D263.C as missing WARNING: atoms too close: (T0334)Q259.N and (T0334)D264.N only 0.0000000e+00 apart, marking (T0334)Q259.N as missing WARNING: atoms too close: (T0334)Q259.CA and (T0334)D264.CA only 0.0000000e+00 apart, marking (T0334)Q259.CA as missing WARNING: atoms too close: (T0334)R419.C and (T0334)F503.C only 0.0000000e+00 apart, marking (T0334)F503.C as missing WARNING: atoms too close: (T0334)A420.N and (T0334)G504.N only 0.0000000e+00 apart, marking (T0334)A420.N as missing WARNING: atoms too close: (T0334)A420.CA and (T0334)G504.CA only 0.0000000e+00 apart, marking (T0334)A420.CA as missing # WARNING: incomplete conformation T0334 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 451 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ../model2.ts-submitted looking for model 1 # Found a chain break before 473 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ../model3.ts-submitted looking for model 1 # Found a chain break before 479 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ../model4.ts-submitted looking for model 1 # Found a chain break before 468 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ../model5.ts-submitted looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # ReadConformPDB reading from PDB file T0334.try1-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 488 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try1-opt1.pdb.gz looking for model 1 # Found a chain break before 488 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try1-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 518 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try1-opt2.gromacs0.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 518 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try1-opt2.pdb.gz looking for model 1 # Found a chain break before 488 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try1-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 488 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try10-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 450 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try10-opt1.pdb.gz looking for model 1 # Found a chain break before 450 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try10-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 477 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try10-opt2.gromacs0.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 477 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try10-opt2.pdb.gz looking for model 1 # Found a chain break before 451 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try10-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 451 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try11-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 451 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try11-opt1.pdb.gz looking for model 1 # Found a chain break before 451 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try11-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 478 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try11-opt2.gromacs0.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 478 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try11-opt2.pdb.gz looking for model 1 # Found a chain break before 451 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try11-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 451 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try12-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 477 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try12-opt1.pdb.gz looking for model 1 # Found a chain break before 477 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try12-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 473 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try12-opt2.gromacs0.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 473 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try12-opt2.pdb.gz looking for model 1 # Found a chain break before 477 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try12-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 477 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try13-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 451 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try13-opt1.pdb.gz looking for model 1 # Found a chain break before 451 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try13-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 487 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try13-opt2.gromacs0.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 487 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try13-opt2.pdb.gz looking for model 1 # Found a chain break before 451 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try13-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 451 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try14-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 451 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try14-opt1.pdb.gz looking for model 1 # Found a chain break before 451 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try14-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 487 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try14-opt2.gromacs0.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 487 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try14-opt2.pdb.gz looking for model 1 # Found a chain break before 451 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try14-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 451 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try15-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 468 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try15-opt1.pdb.gz looking for model 1 # Found a chain break before 468 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try15-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 464 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try15-opt2.gromacs0.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 464 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try15-opt2.pdb.gz looking for model 1 # Found a chain break before 468 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try15-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 468 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try16-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 455 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try16-opt1.pdb.gz looking for model 1 # Found a chain break before 455 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try16-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 456 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try16-opt2.gromacs0.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 456 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try16-opt2.pdb.gz looking for model 1 # Found a chain break before 479 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try16-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 479 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try17-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 526 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try17-opt1.pdb.gz looking for model 1 # Found a chain break before 526 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try17-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 450 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try17-opt2.gromacs0.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 450 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try17-opt2.pdb.gz looking for model 1 # Found a chain break before 526 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try17-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 526 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try2-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 450 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try2-opt1.pdb.gz looking for model 1 # Found a chain break before 450 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try2-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 477 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try2-opt2.gromacs0.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 477 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try2-opt2.pdb.gz looking for model 1 # Found a chain break before 456 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try2-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 456 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try3-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 493 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try3-opt1.pdb.gz looking for model 1 # Found a chain break before 493 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try3-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 526 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try3-opt2.gromacs0.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 526 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try3-opt2.pdb.gz looking for model 1 # Found a chain break before 459 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try3-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 459 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try6-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 456 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try6-opt1.pdb.gz looking for model 1 # Found a chain break before 456 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try6-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 477 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try6-opt2.gromacs0.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 477 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try6-opt2.pdb.gz looking for model 1 # Found a chain break before 456 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try6-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 456 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try7-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 456 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try7-opt1.pdb.gz looking for model 1 # Found a chain break before 456 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try7-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 528 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try7-opt2.gromacs0.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 528 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try7-opt2.pdb.gz looking for model 1 # Found a chain break before 456 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try7-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 456 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try8-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 451 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try8-opt1.pdb.gz looking for model 1 # Found a chain break before 451 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try8-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 514 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try8-opt2.gromacs0.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 514 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try8-opt2.pdb.gz looking for model 1 # Found a chain break before 451 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try8-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 451 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try9-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 445 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try9-opt1.pdb.gz looking for model 1 # Found a chain break before 445 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try9-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 449 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try9-opt2.gromacs0.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 449 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try9-opt2.pdb.gz looking for model 1 # Found a chain break before 448 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try9-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 448 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ../dimer/decoys/T0334.try1-opt1-scwrl.pdb.gz looking for chain 'A' model 1 # Found a chain break before 520 # copying to AlignedFragments data structure # naming current conformation dimer//try1-opt1-scwrl # ReadConformPDB reading from PDB file ../dimer/decoys/T0334.try1-opt1.pdb.gz looking for chain 'A' model 1 # Found a chain break before 520 # copying to AlignedFragments data structure # naming current conformation dimer//try1-opt1 # ReadConformPDB reading from PDB file ../dimer/decoys/T0334.try1-opt2.pdb.gz looking for chain 'A' model 1 # Found a chain break before 526 # copying to AlignedFragments data structure # naming current conformation dimer//try1-opt2 # ReadConformPDB reading from PDB file ../dimer/decoys/T0334.try1-opt2.repack-nonPC.pdb.gz looking for chain 'A' model 1 # Found a chain break before 526 # copying to AlignedFragments data structure # naming current conformation dimer//try1-opt2.repack-nonPC # ReadConformPDB reading from PDB file ../dimer/decoys/T0334.try1-opt2.unpack.gromacs0.pdb.gz looking for chain 'A' model 1 # Found a chain break before 524 # copying to AlignedFragments data structure # naming current conformation dimer//try1-opt2.unpack.gromacs0 # ReadConformPDB reading from PDB file ../dimer/decoys/T0334.try1-opt2.unpack.gromacs0.repack-nonPC.pdb.gz looking for chain 'A' model 1 # Found a chain break before 524 # copying to AlignedFragments data structure # naming current conformation dimer//try1-opt2.unpack.gromacs0.repack-nonPC # ReadConformPDB reading from PDB file ../dimer/decoys/T0334.try1-opt2.unpack.pdb.gz looking for chain 'A' model 1 # Found a chain break before 526 # copying to AlignedFragments data structure # naming current conformation dimer//try1-opt2.unpack # ReadConformPDB reading from PDB file ../dimer/decoys/dimer-2aqj-from-T0334.try6-opt2.pdb.gz looking for chain 'A' model 1 # Found a chain break before 456 # copying to AlignedFragments data structure # naming current conformation dimer//dimer-2aqj-from-try6-opt2 # ReadConformPDB reading from PDB file ../dimer/decoys/dimer-2aqj-from-T0334.try7-opt2.pdb.gz looking for chain 'A' model 1 # Found a chain break before 456 # copying to AlignedFragments data structure # naming current conformation dimer//dimer-2aqj-from-try7-opt2 # ReadConformPDB reading from PDB file ../dimer/decoys/dimer-2aqj-from-T0334.try8-opt2.pdb.gz looking for chain 'A' model 1 # Found a chain break before 451 # copying to AlignedFragments data structure # naming current conformation dimer//dimer-2aqj-from-try8-opt2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_669798299.pdb -s /var/tmp/to_scwrl_669798299.seq -o /var/tmp/from_scwrl_669798299.pdb > /var/tmp/scwrl_669798299.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_669798299.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 T0334 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_371364323.pdb -s /var/tmp/to_scwrl_371364323.seq -o /var/tmp/from_scwrl_371364323.pdb > /var/tmp/scwrl_371364323.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_371364323.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 T0334 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1969277577.pdb -s /var/tmp/to_scwrl_1969277577.seq -o /var/tmp/from_scwrl_1969277577.pdb > /var/tmp/scwrl_1969277577.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1969277577.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 T0334 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_2012531187.pdb -s /var/tmp/to_scwrl_2012531187.seq -o /var/tmp/from_scwrl_2012531187.pdb > /var/tmp/scwrl_2012531187.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2012531187.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 T0334 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_2016132580.pdb -s /var/tmp/to_scwrl_2016132580.seq -o /var/tmp/from_scwrl_2016132580.pdb > /var/tmp/scwrl_2016132580.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2016132580.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 T0334 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_381488441.pdb -s /var/tmp/to_scwrl_381488441.seq -o /var/tmp/from_scwrl_381488441.pdb > /var/tmp/scwrl_381488441.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_381488441.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 T0334 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_532709368.pdb -s /var/tmp/to_scwrl_532709368.seq -o /var/tmp/from_scwrl_532709368.pdb > /var/tmp/scwrl_532709368.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_532709368.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 T0334 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_2060867357.pdb -s /var/tmp/to_scwrl_2060867357.seq -o /var/tmp/from_scwrl_2060867357.pdb > /var/tmp/scwrl_2060867357.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2060867357.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 T0334 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_2055949024.pdb -s /var/tmp/to_scwrl_2055949024.seq -o /var/tmp/from_scwrl_2055949024.pdb > /var/tmp/scwrl_2055949024.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2055949024.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 T0334 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_985522196.pdb -s /var/tmp/to_scwrl_985522196.seq -o /var/tmp/from_scwrl_985522196.pdb > /var/tmp/scwrl_985522196.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_985522196.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 T0334 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_912194836.pdb -s /var/tmp/to_scwrl_912194836.seq -o /var/tmp/from_scwrl_912194836.pdb > /var/tmp/scwrl_912194836.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_912194836.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 T0334 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_16991062.pdb -s /var/tmp/to_scwrl_16991062.seq -o /var/tmp/from_scwrl_16991062.pdb > /var/tmp/scwrl_16991062.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_16991062.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 T0334 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1971596344.pdb -s /var/tmp/to_scwrl_1971596344.seq -o /var/tmp/from_scwrl_1971596344.pdb > /var/tmp/scwrl_1971596344.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1971596344.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 T0334 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1634448900.pdb -s /var/tmp/to_scwrl_1634448900.seq -o /var/tmp/from_scwrl_1634448900.pdb > /var/tmp/scwrl_1634448900.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1634448900.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_TS4-scwrl # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # Found a chain break before 491 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_834576945.pdb -s /var/tmp/to_scwrl_834576945.seq -o /var/tmp/from_scwrl_834576945.pdb > /var/tmp/scwrl_834576945.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_834576945.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 491 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_636118462.pdb -s /var/tmp/to_scwrl_636118462.seq -o /var/tmp/from_scwrl_636118462.pdb > /var/tmp/scwrl_636118462.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_636118462.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 453 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_659234991.pdb -s /var/tmp/to_scwrl_659234991.seq -o /var/tmp/from_scwrl_659234991.pdb > /var/tmp/scwrl_659234991.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_659234991.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 519 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_77783891.pdb -s /var/tmp/to_scwrl_77783891.seq -o /var/tmp/from_scwrl_77783891.pdb > /var/tmp/scwrl_77783891.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_77783891.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 464 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_704144275.pdb -s /var/tmp/to_scwrl_704144275.seq -o /var/tmp/from_scwrl_704144275.pdb > /var/tmp/scwrl_704144275.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_704144275.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 491 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_446663333.pdb -s /var/tmp/to_scwrl_446663333.seq -o /var/tmp/from_scwrl_446663333.pdb > /var/tmp/scwrl_446663333.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_446663333.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 491 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_2045907780.pdb -s /var/tmp/to_scwrl_2045907780.seq -o /var/tmp/from_scwrl_2045907780.pdb > /var/tmp/scwrl_2045907780.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2045907780.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 501 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1618669443.pdb -s /var/tmp/to_scwrl_1618669443.seq -o /var/tmp/from_scwrl_1618669443.pdb > /var/tmp/scwrl_1618669443.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1618669443.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 525 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1159014366.pdb -s /var/tmp/to_scwrl_1159014366.seq -o /var/tmp/from_scwrl_1159014366.pdb > /var/tmp/scwrl_1159014366.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1159014366.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 472 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_187503063.pdb -s /var/tmp/to_scwrl_187503063.seq -o /var/tmp/from_scwrl_187503063.pdb > /var/tmp/scwrl_187503063.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_187503063.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 519 # copying to AlignedFragments data structure # naming current conformation BayesHH_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_814287457.pdb -s /var/tmp/to_scwrl_814287457.seq -o /var/tmp/from_scwrl_814287457.pdb > /var/tmp/scwrl_814287457.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_814287457.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 463 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1290463542.pdb -s /var/tmp/to_scwrl_1290463542.seq -o /var/tmp/from_scwrl_1290463542.pdb > /var/tmp/scwrl_1290463542.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1290463542.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 446 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_2144515029.pdb -s /var/tmp/to_scwrl_2144515029.seq -o /var/tmp/from_scwrl_2144515029.pdb > /var/tmp/scwrl_2144515029.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2144515029.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 491 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_709771027.pdb -s /var/tmp/to_scwrl_709771027.seq -o /var/tmp/from_scwrl_709771027.pdb > /var/tmp/scwrl_709771027.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_709771027.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 422 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_114451950.pdb -s /var/tmp/to_scwrl_114451950.seq -o /var/tmp/from_scwrl_114451950.pdb > /var/tmp/scwrl_114451950.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_114451950.pdb # conformation set from SCWRL output # naming current conformation Bilab-ENABLE_TS4-scwrl # ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1 # Found a chain break before 528 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1400129061.pdb -s /var/tmp/to_scwrl_1400129061.seq -o /var/tmp/from_scwrl_1400129061.pdb > /var/tmp/scwrl_1400129061.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1400129061.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 T0334 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_635244679.pdb -s /var/tmp/to_scwrl_635244679.seq -o /var/tmp/from_scwrl_635244679.pdb > /var/tmp/scwrl_635244679.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_635244679.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 529 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_784250249.pdb -s /var/tmp/to_scwrl_784250249.seq -o /var/tmp/from_scwrl_784250249.pdb > /var/tmp/scwrl_784250249.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_784250249.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 T0334 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1771493385.pdb -s /var/tmp/to_scwrl_1771493385.seq -o /var/tmp/from_scwrl_1771493385.pdb > /var/tmp/scwrl_1771493385.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1771493385.pdb # conformation set from SCWRL output # naming current conformation CIRCLE_TS4-scwrl # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # Found a chain break before 526 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_457038609.pdb -s /var/tmp/to_scwrl_457038609.seq -o /var/tmp/from_scwrl_457038609.pdb > /var/tmp/scwrl_457038609.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_457038609.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 T0334 can't currently be optimized by undertaker # naming current conformation CPHmodels_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_649297789.pdb -s /var/tmp/to_scwrl_649297789.seq -o /var/tmp/from_scwrl_649297789.pdb > /var/tmp/scwrl_649297789.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_649297789.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 T0334 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1640142318.pdb -s /var/tmp/to_scwrl_1640142318.seq -o /var/tmp/from_scwrl_1640142318.pdb > /var/tmp/scwrl_1640142318.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1640142318.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 T0334 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_838527050.pdb -s /var/tmp/to_scwrl_838527050.seq -o /var/tmp/from_scwrl_838527050.pdb > /var/tmp/scwrl_838527050.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_838527050.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 T0334 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1182007157.pdb -s /var/tmp/to_scwrl_1182007157.seq -o /var/tmp/from_scwrl_1182007157.pdb > /var/tmp/scwrl_1182007157.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1182007157.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 T0334 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1553526028.pdb -s /var/tmp/to_scwrl_1553526028.seq -o /var/tmp/from_scwrl_1553526028.pdb > /var/tmp/scwrl_1553526028.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1553526028.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 T0334 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_746992427.pdb -s /var/tmp/to_scwrl_746992427.seq -o /var/tmp/from_scwrl_746992427.pdb > /var/tmp/scwrl_746992427.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_746992427.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 T0334 can't currently be optimized by undertaker # naming current conformation Distill_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_20045706.pdb -s /var/tmp/to_scwrl_20045706.seq -o /var/tmp/from_scwrl_20045706.pdb > /var/tmp/scwrl_20045706.log Error: Couldn't open file /var/tmp/from_scwrl_20045706.pdb or /var/tmp/from_scwrl_20045706.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_20045706_b.pdb or decoys//var/tmp/from_scwrl_20045706_b.pdb.gz for input Trying /var/tmp/from_scwrl_20045706_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_20045706_b.pdb or /var/tmp/from_scwrl_20045706_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_20045706_a.pdb or decoys//var/tmp/from_scwrl_20045706_a.pdb.gz for input Trying /var/tmp/from_scwrl_20045706_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_20045706_a.pdb or /var/tmp/from_scwrl_20045706_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_20045706.pdb or /var/tmp/from_scwrl_20045706_b.pdb or /var/tmp/from_scwrl_20045706_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 T0334 can't currently be optimized by undertaker # naming current conformation Distill_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_318237217.pdb -s /var/tmp/to_scwrl_318237217.seq -o /var/tmp/from_scwrl_318237217.pdb > /var/tmp/scwrl_318237217.log Error: Couldn't open file /var/tmp/from_scwrl_318237217.pdb or /var/tmp/from_scwrl_318237217.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_318237217_b.pdb or decoys//var/tmp/from_scwrl_318237217_b.pdb.gz for input Trying /var/tmp/from_scwrl_318237217_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_318237217_b.pdb or /var/tmp/from_scwrl_318237217_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_318237217_a.pdb or decoys//var/tmp/from_scwrl_318237217_a.pdb.gz for input Trying /var/tmp/from_scwrl_318237217_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_318237217_a.pdb or /var/tmp/from_scwrl_318237217_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_318237217.pdb or /var/tmp/from_scwrl_318237217_b.pdb or /var/tmp/from_scwrl_318237217_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 T0334 can't currently be optimized by undertaker # naming current conformation Distill_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_763983490.pdb -s /var/tmp/to_scwrl_763983490.seq -o /var/tmp/from_scwrl_763983490.pdb > /var/tmp/scwrl_763983490.log Error: Couldn't open file /var/tmp/from_scwrl_763983490.pdb or /var/tmp/from_scwrl_763983490.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_763983490_b.pdb or decoys//var/tmp/from_scwrl_763983490_b.pdb.gz for input Trying /var/tmp/from_scwrl_763983490_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_763983490_b.pdb or /var/tmp/from_scwrl_763983490_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_763983490_a.pdb or decoys//var/tmp/from_scwrl_763983490_a.pdb.gz for input Trying /var/tmp/from_scwrl_763983490_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_763983490_a.pdb or /var/tmp/from_scwrl_763983490_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_763983490.pdb or /var/tmp/from_scwrl_763983490_b.pdb or /var/tmp/from_scwrl_763983490_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 T0334 can't currently be optimized by undertaker # naming current conformation Distill_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1991642051.pdb -s /var/tmp/to_scwrl_1991642051.seq -o /var/tmp/from_scwrl_1991642051.pdb > /var/tmp/scwrl_1991642051.log Error: Couldn't open file /var/tmp/from_scwrl_1991642051.pdb or /var/tmp/from_scwrl_1991642051.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1991642051_b.pdb or decoys//var/tmp/from_scwrl_1991642051_b.pdb.gz for input Trying /var/tmp/from_scwrl_1991642051_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_1991642051_b.pdb or /var/tmp/from_scwrl_1991642051_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1991642051_a.pdb or decoys//var/tmp/from_scwrl_1991642051_a.pdb.gz for input Trying /var/tmp/from_scwrl_1991642051_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_1991642051_a.pdb or /var/tmp/from_scwrl_1991642051_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_1991642051.pdb or /var/tmp/from_scwrl_1991642051_b.pdb or /var/tmp/from_scwrl_1991642051_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 T0334 can't currently be optimized by undertaker # naming current conformation Distill_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1952686117.pdb -s /var/tmp/to_scwrl_1952686117.seq -o /var/tmp/from_scwrl_1952686117.pdb > /var/tmp/scwrl_1952686117.log Error: Couldn't open file /var/tmp/from_scwrl_1952686117.pdb or /var/tmp/from_scwrl_1952686117.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1952686117_b.pdb or decoys//var/tmp/from_scwrl_1952686117_b.pdb.gz for input Trying /var/tmp/from_scwrl_1952686117_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_1952686117_b.pdb or /var/tmp/from_scwrl_1952686117_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1952686117_a.pdb or decoys//var/tmp/from_scwrl_1952686117_a.pdb.gz for input Trying /var/tmp/from_scwrl_1952686117_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_1952686117_a.pdb or /var/tmp/from_scwrl_1952686117_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_1952686117.pdb or /var/tmp/from_scwrl_1952686117_b.pdb or /var/tmp/from_scwrl_1952686117_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 529 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1598560434.pdb -s /var/tmp/to_scwrl_1598560434.seq -o /var/tmp/from_scwrl_1598560434.pdb > /var/tmp/scwrl_1598560434.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1598560434.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 T0334 can't currently be optimized by undertaker # naming current conformation FAMSD_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_480276866.pdb -s /var/tmp/to_scwrl_480276866.seq -o /var/tmp/from_scwrl_480276866.pdb > /var/tmp/scwrl_480276866.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_480276866.pdb # conformation set from SCWRL output # naming current conformation FAMSD_TS2-scwrl # ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation FAMSD_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_464437462.pdb -s /var/tmp/to_scwrl_464437462.seq -o /var/tmp/from_scwrl_464437462.pdb > /var/tmp/scwrl_464437462.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_464437462.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 T0334 can't currently be optimized by undertaker # naming current conformation FAMSD_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1676344325.pdb -s /var/tmp/to_scwrl_1676344325.seq -o /var/tmp/from_scwrl_1676344325.pdb > /var/tmp/scwrl_1676344325.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1676344325.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 T0334 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FAMSD_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1184421140.pdb -s /var/tmp/to_scwrl_1184421140.seq -o /var/tmp/from_scwrl_1184421140.pdb > /var/tmp/scwrl_1184421140.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1184421140.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 529 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_911100795.pdb -s /var/tmp/to_scwrl_911100795.seq -o /var/tmp/from_scwrl_911100795.pdb > /var/tmp/scwrl_911100795.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_911100795.pdb # conformation set from SCWRL output # naming current conformation FAMS_TS1-scwrl # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation FAMS_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1574768459.pdb -s /var/tmp/to_scwrl_1574768459.seq -o /var/tmp/from_scwrl_1574768459.pdb > /var/tmp/scwrl_1574768459.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1574768459.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 # Found a chain break before 528 # copying to AlignedFragments data structure # naming current conformation FAMS_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_655606937.pdb -s /var/tmp/to_scwrl_655606937.seq -o /var/tmp/from_scwrl_655606937.pdb > /var/tmp/scwrl_655606937.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_655606937.pdb # conformation set from SCWRL output # naming current conformation FAMS_TS3-scwrl # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation FAMS_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_2070115161.pdb -s /var/tmp/to_scwrl_2070115161.seq -o /var/tmp/from_scwrl_2070115161.pdb > /var/tmp/scwrl_2070115161.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2070115161.pdb # conformation set from SCWRL output # naming current conformation FAMS_TS4-scwrl # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation FAMS_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1762271522.pdb -s /var/tmp/to_scwrl_1762271522.seq -o /var/tmp/from_scwrl_1762271522.pdb > /var/tmp/scwrl_1762271522.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1762271522.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 491 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1469894393.pdb -s /var/tmp/to_scwrl_1469894393.seq -o /var/tmp/from_scwrl_1469894393.pdb > /var/tmp/scwrl_1469894393.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1469894393.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 453 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1213095056.pdb -s /var/tmp/to_scwrl_1213095056.seq -o /var/tmp/from_scwrl_1213095056.pdb > /var/tmp/scwrl_1213095056.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1213095056.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 453 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1759302904.pdb -s /var/tmp/to_scwrl_1759302904.seq -o /var/tmp/from_scwrl_1759302904.pdb > /var/tmp/scwrl_1759302904.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1759302904.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 453 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_32181774.pdb -s /var/tmp/to_scwrl_32181774.seq -o /var/tmp/from_scwrl_32181774.pdb > /var/tmp/scwrl_32181774.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_32181774.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 460 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1327547006.pdb -s /var/tmp/to_scwrl_1327547006.seq -o /var/tmp/from_scwrl_1327547006.pdb > /var/tmp/scwrl_1327547006.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1327547006.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 T0334 can't currently be optimized by undertaker # naming current conformation FORTE1_AL1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1011948320.pdb -s /var/tmp/to_scwrl_1011948320.seq -o /var/tmp/from_scwrl_1011948320.pdb > /var/tmp/scwrl_1011948320.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1011948320.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 Skipped atom 762, because occupancy 1.0000000e+00 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 764, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 766, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 768, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 1386, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 1388, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 1390, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 1392, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation FORTE1_AL2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_667426453.pdb -s /var/tmp/to_scwrl_667426453.seq -o /var/tmp/from_scwrl_667426453.pdb > /var/tmp/scwrl_667426453.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_667426453.pdb # conformation set from SCWRL output # naming current conformation FORTE1_AL2-scwrl # ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation FORTE1_AL3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_2111797256.pdb -s /var/tmp/to_scwrl_2111797256.seq -o /var/tmp/from_scwrl_2111797256.pdb > /var/tmp/scwrl_2111797256.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2111797256.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 T0334 can't currently be optimized by undertaker # naming current conformation FORTE1_AL4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_635958058.pdb -s /var/tmp/to_scwrl_635958058.seq -o /var/tmp/from_scwrl_635958058.pdb > /var/tmp/scwrl_635958058.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_635958058.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 T0334 can't currently be optimized by undertaker # naming current conformation FORTE1_AL5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1124465061.pdb -s /var/tmp/to_scwrl_1124465061.seq -o /var/tmp/from_scwrl_1124465061.pdb > /var/tmp/scwrl_1124465061.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1124465061.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 T0334 can't currently be optimized by undertaker # naming current conformation FORTE2_AL1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_613611398.pdb -s /var/tmp/to_scwrl_613611398.seq -o /var/tmp/from_scwrl_613611398.pdb > /var/tmp/scwrl_613611398.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_613611398.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 T0334 can't currently be optimized by undertaker # naming current conformation FORTE2_AL2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_128616729.pdb -s /var/tmp/to_scwrl_128616729.seq -o /var/tmp/from_scwrl_128616729.pdb > /var/tmp/scwrl_128616729.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_128616729.pdb # conformation set from SCWRL output # naming current conformation FORTE2_AL2-scwrl # ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1 Skipped atom 762, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 764, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 766, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 768, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 1386, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 1388, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 1390, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 1392, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation FORTE2_AL3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1962992111.pdb -s /var/tmp/to_scwrl_1962992111.seq -o /var/tmp/from_scwrl_1962992111.pdb > /var/tmp/scwrl_1962992111.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1962992111.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 T0334 can't currently be optimized by undertaker # naming current conformation FORTE2_AL4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1795618555.pdb -s /var/tmp/to_scwrl_1795618555.seq -o /var/tmp/from_scwrl_1795618555.pdb > /var/tmp/scwrl_1795618555.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1795618555.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 T0334 can't currently be optimized by undertaker # naming current conformation FORTE2_AL5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1682142757.pdb -s /var/tmp/to_scwrl_1682142757.seq -o /var/tmp/from_scwrl_1682142757.pdb > /var/tmp/scwrl_1682142757.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1682142757.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 529 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_562500891.pdb -s /var/tmp/to_scwrl_562500891.seq -o /var/tmp/from_scwrl_562500891.pdb > /var/tmp/scwrl_562500891.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_562500891.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 522 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1815664262.pdb -s /var/tmp/to_scwrl_1815664262.seq -o /var/tmp/from_scwrl_1815664262.pdb > /var/tmp/scwrl_1815664262.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1815664262.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 529 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_2000379975.pdb -s /var/tmp/to_scwrl_2000379975.seq -o /var/tmp/from_scwrl_2000379975.pdb > /var/tmp/scwrl_2000379975.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2000379975.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 529 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1326484380.pdb -s /var/tmp/to_scwrl_1326484380.seq -o /var/tmp/from_scwrl_1326484380.pdb > /var/tmp/scwrl_1326484380.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1326484380.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 521 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1659822666.pdb -s /var/tmp/to_scwrl_1659822666.seq -o /var/tmp/from_scwrl_1659822666.pdb > /var/tmp/scwrl_1659822666.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1659822666.pdb # conformation set from SCWRL output # naming current conformation FPSOLVER-SERVER_TS5-scwrl # ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1805582445.pdb -s /var/tmp/to_scwrl_1805582445.seq -o /var/tmp/from_scwrl_1805582445.pdb > /var/tmp/scwrl_1805582445.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1805582445.pdb # conformation set from SCWRL output # naming current conformation FUGMOD_TS1-scwrl # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_777561168.pdb -s /var/tmp/to_scwrl_777561168.seq -o /var/tmp/from_scwrl_777561168.pdb > /var/tmp/scwrl_777561168.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_777561168.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 T0334 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_2140099532.pdb -s /var/tmp/to_scwrl_2140099532.seq -o /var/tmp/from_scwrl_2140099532.pdb > /var/tmp/scwrl_2140099532.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2140099532.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 T0334 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_122536260.pdb -s /var/tmp/to_scwrl_122536260.seq -o /var/tmp/from_scwrl_122536260.pdb > /var/tmp/scwrl_122536260.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_122536260.pdb Faking rotamer for incomplete or colinear backbone at (T0334)C343 Faking rotamer for incomplete or colinear backbone at (T0334)C343 # conformation set from SCWRL output # naming current conformation FUGMOD_TS4-scwrl # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_306421847.pdb -s /var/tmp/to_scwrl_306421847.seq -o /var/tmp/from_scwrl_306421847.pdb > /var/tmp/scwrl_306421847.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_306421847.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 T0334 can't currently be optimized by undertaker # naming current conformation FUGUE_AL1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1177037025.pdb -s /var/tmp/to_scwrl_1177037025.seq -o /var/tmp/from_scwrl_1177037025.pdb > /var/tmp/scwrl_1177037025.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1177037025.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 T0334 can't currently be optimized by undertaker # naming current conformation FUGUE_AL2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1033637055.pdb -s /var/tmp/to_scwrl_1033637055.seq -o /var/tmp/from_scwrl_1033637055.pdb > /var/tmp/scwrl_1033637055.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1033637055.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 T0334 can't currently be optimized by undertaker # naming current conformation FUGUE_AL3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1881190306.pdb -s /var/tmp/to_scwrl_1881190306.seq -o /var/tmp/from_scwrl_1881190306.pdb > /var/tmp/scwrl_1881190306.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1881190306.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 T0334 can't currently be optimized by undertaker # naming current conformation FUGUE_AL4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1832643962.pdb -s /var/tmp/to_scwrl_1832643962.seq -o /var/tmp/from_scwrl_1832643962.pdb > /var/tmp/scwrl_1832643962.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1832643962.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 T0334 can't currently be optimized by undertaker # naming current conformation FUGUE_AL5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_956268570.pdb -s /var/tmp/to_scwrl_956268570.seq -o /var/tmp/from_scwrl_956268570.pdb > /var/tmp/scwrl_956268570.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_956268570.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 529 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1495978181.pdb -s /var/tmp/to_scwrl_1495978181.seq -o /var/tmp/from_scwrl_1495978181.pdb > /var/tmp/scwrl_1495978181.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1495978181.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 529 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1155054709.pdb -s /var/tmp/to_scwrl_1155054709.seq -o /var/tmp/from_scwrl_1155054709.pdb > /var/tmp/scwrl_1155054709.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1155054709.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 529 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_21879979.pdb -s /var/tmp/to_scwrl_21879979.seq -o /var/tmp/from_scwrl_21879979.pdb > /var/tmp/scwrl_21879979.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_21879979.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 528 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1107797438.pdb -s /var/tmp/to_scwrl_1107797438.seq -o /var/tmp/from_scwrl_1107797438.pdb > /var/tmp/scwrl_1107797438.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1107797438.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 529 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1187236483.pdb -s /var/tmp/to_scwrl_1187236483.seq -o /var/tmp/from_scwrl_1187236483.pdb > /var/tmp/scwrl_1187236483.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1187236483.pdb # conformation set from SCWRL output # naming current conformation FUNCTION_TS5-scwrl # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1349426986.pdb -s /var/tmp/to_scwrl_1349426986.seq -o /var/tmp/from_scwrl_1349426986.pdb > /var/tmp/scwrl_1349426986.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1349426986.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 527 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_2119745758.pdb -s /var/tmp/to_scwrl_2119745758.seq -o /var/tmp/from_scwrl_2119745758.pdb > /var/tmp/scwrl_2119745758.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2119745758.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 447 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1854662936.pdb -s /var/tmp/to_scwrl_1854662936.seq -o /var/tmp/from_scwrl_1854662936.pdb > /var/tmp/scwrl_1854662936.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1854662936.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 T0334 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1313740595.pdb -s /var/tmp/to_scwrl_1313740595.seq -o /var/tmp/from_scwrl_1313740595.pdb > /var/tmp/scwrl_1313740595.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1313740595.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 502 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_608220169.pdb -s /var/tmp/to_scwrl_608220169.seq -o /var/tmp/from_scwrl_608220169.pdb > /var/tmp/scwrl_608220169.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_608220169.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 519 # copying to AlignedFragments data structure # naming current conformation HHpred1_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_831644351.pdb -s /var/tmp/to_scwrl_831644351.seq -o /var/tmp/from_scwrl_831644351.pdb > /var/tmp/scwrl_831644351.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_831644351.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 519 # copying to AlignedFragments data structure # naming current conformation HHpred2_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1927351993.pdb -s /var/tmp/to_scwrl_1927351993.seq -o /var/tmp/from_scwrl_1927351993.pdb > /var/tmp/scwrl_1927351993.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1927351993.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 519 # copying to AlignedFragments data structure # naming current conformation HHpred3_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_736836898.pdb -s /var/tmp/to_scwrl_736836898.seq -o /var/tmp/from_scwrl_736836898.pdb > /var/tmp/scwrl_736836898.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_736836898.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 T0334 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_647152815.pdb -s /var/tmp/to_scwrl_647152815.seq -o /var/tmp/from_scwrl_647152815.pdb > /var/tmp/scwrl_647152815.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_647152815.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 T0334 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1575486902.pdb -s /var/tmp/to_scwrl_1575486902.seq -o /var/tmp/from_scwrl_1575486902.pdb > /var/tmp/scwrl_1575486902.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1575486902.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 T0334 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_271496009.pdb -s /var/tmp/to_scwrl_271496009.seq -o /var/tmp/from_scwrl_271496009.pdb > /var/tmp/scwrl_271496009.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_271496009.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 T0334 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1209653705.pdb -s /var/tmp/to_scwrl_1209653705.seq -o /var/tmp/from_scwrl_1209653705.pdb > /var/tmp/scwrl_1209653705.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1209653705.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 T0334 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1243667517.pdb -s /var/tmp/to_scwrl_1243667517.seq -o /var/tmp/from_scwrl_1243667517.pdb > /var/tmp/scwrl_1243667517.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1243667517.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 T0334 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation LOOPP_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_124392337.pdb -s /var/tmp/to_scwrl_124392337.seq -o /var/tmp/from_scwrl_124392337.pdb > /var/tmp/scwrl_124392337.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_124392337.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 T0334 can't currently be optimized by undertaker # naming current conformation LOOPP_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_388654440.pdb -s /var/tmp/to_scwrl_388654440.seq -o /var/tmp/from_scwrl_388654440.pdb > /var/tmp/scwrl_388654440.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_388654440.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 T0334 can't currently be optimized by undertaker # naming current conformation LOOPP_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_756006537.pdb -s /var/tmp/to_scwrl_756006537.seq -o /var/tmp/from_scwrl_756006537.pdb > /var/tmp/scwrl_756006537.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_756006537.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 T0334 can't currently be optimized by undertaker # naming current conformation LOOPP_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1929974782.pdb -s /var/tmp/to_scwrl_1929974782.seq -o /var/tmp/from_scwrl_1929974782.pdb > /var/tmp/scwrl_1929974782.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1929974782.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 T0334 can't currently be optimized by undertaker # naming current conformation LOOPP_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1166215607.pdb -s /var/tmp/to_scwrl_1166215607.seq -o /var/tmp/from_scwrl_1166215607.pdb > /var/tmp/scwrl_1166215607.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1166215607.pdb # conformation set from SCWRL output # naming current conformation LOOPP_TS5-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS1.pdb.gz looking for model 1 # Found a chain break before 519 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_748622422.pdb -s /var/tmp/to_scwrl_748622422.seq -o /var/tmp/from_scwrl_748622422.pdb > /var/tmp/scwrl_748622422.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_748622422.pdb # conformation set from SCWRL output # naming current conformation Ma-OPUS-server2_TS1-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS2.pdb.gz looking for model 1 # Found a chain break before 517 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_2052511043.pdb -s /var/tmp/to_scwrl_2052511043.seq -o /var/tmp/from_scwrl_2052511043.pdb > /var/tmp/scwrl_2052511043.log sh: line 1: 24421 Killed scwrl3 -i /var/tmp/to_scwrl_2052511043.pdb -s /var/tmp/to_scwrl_2052511043.seq -o /var/tmp/from_scwrl_2052511043.pdb >/var/tmp/scwrl_2052511043.log Error: Couldn't open file /var/tmp/from_scwrl_2052511043.pdb or /var/tmp/from_scwrl_2052511043.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_2052511043_b.pdb or decoys//var/tmp/from_scwrl_2052511043_b.pdb.gz for input Trying /var/tmp/from_scwrl_2052511043_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_2052511043_b.pdb or /var/tmp/from_scwrl_2052511043_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_2052511043_a.pdb or decoys//var/tmp/from_scwrl_2052511043_a.pdb.gz for input Trying /var/tmp/from_scwrl_2052511043_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_2052511043_a.pdb or /var/tmp/from_scwrl_2052511043_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_2052511043.pdb or /var/tmp/from_scwrl_2052511043_b.pdb or /var/tmp/from_scwrl_2052511043_a.pdb Error: no new SCWRL conformation added # naming current conformation Ma-OPUS-server2_TS2-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS3.pdb.gz looking for model 1 # Found a chain break before 527 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1472637454.pdb -s /var/tmp/to_scwrl_1472637454.seq -o /var/tmp/from_scwrl_1472637454.pdb > /var/tmp/scwrl_1472637454.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1472637454.pdb # conformation set from SCWRL output # naming current conformation Ma-OPUS-server2_TS3-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS4.pdb.gz looking for model 1 # Found a chain break before 529 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1925659447.pdb -s /var/tmp/to_scwrl_1925659447.seq -o /var/tmp/from_scwrl_1925659447.pdb > /var/tmp/scwrl_1925659447.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1925659447.pdb # conformation set from SCWRL output # naming current conformation Ma-OPUS-server2_TS4-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS5.pdb.gz looking for model 1 # Found a chain break before 520 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_938664451.pdb -s /var/tmp/to_scwrl_938664451.seq -o /var/tmp/from_scwrl_938664451.pdb > /var/tmp/scwrl_938664451.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_938664451.pdb # conformation set from SCWRL output # naming current conformation Ma-OPUS-server2_TS5-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # Found a chain break before 519 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1206344113.pdb -s /var/tmp/to_scwrl_1206344113.seq -o /var/tmp/from_scwrl_1206344113.pdb > /var/tmp/scwrl_1206344113.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1206344113.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 446 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1610819762.pdb -s /var/tmp/to_scwrl_1610819762.seq -o /var/tmp/from_scwrl_1610819762.pdb > /var/tmp/scwrl_1610819762.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1610819762.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 522 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1894933020.pdb -s /var/tmp/to_scwrl_1894933020.seq -o /var/tmp/from_scwrl_1894933020.pdb > /var/tmp/scwrl_1894933020.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1894933020.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 525 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_554838648.pdb -s /var/tmp/to_scwrl_554838648.seq -o /var/tmp/from_scwrl_554838648.pdb > /var/tmp/scwrl_554838648.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_554838648.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 519 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_618390825.pdb -s /var/tmp/to_scwrl_618390825.seq -o /var/tmp/from_scwrl_618390825.pdb > /var/tmp/scwrl_618390825.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_618390825.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 528 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1916813000.pdb -s /var/tmp/to_scwrl_1916813000.seq -o /var/tmp/from_scwrl_1916813000.pdb > /var/tmp/scwrl_1916813000.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1916813000.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 529 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1662636087.pdb -s /var/tmp/to_scwrl_1662636087.seq -o /var/tmp/from_scwrl_1662636087.pdb > /var/tmp/scwrl_1662636087.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1662636087.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 529 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1805627308.pdb -s /var/tmp/to_scwrl_1805627308.seq -o /var/tmp/from_scwrl_1805627308.pdb > /var/tmp/scwrl_1805627308.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1805627308.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 529 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1118756339.pdb -s /var/tmp/to_scwrl_1118756339.seq -o /var/tmp/from_scwrl_1118756339.pdb > /var/tmp/scwrl_1118756339.log sh: line 1: 24536 Killed scwrl3 -i /var/tmp/to_scwrl_1118756339.pdb -s /var/tmp/to_scwrl_1118756339.seq -o /var/tmp/from_scwrl_1118756339.pdb >/var/tmp/scwrl_1118756339.log Error: Couldn't open file /var/tmp/from_scwrl_1118756339.pdb or /var/tmp/from_scwrl_1118756339.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1118756339_b.pdb or decoys//var/tmp/from_scwrl_1118756339_b.pdb.gz for input Trying /var/tmp/from_scwrl_1118756339_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_1118756339_b.pdb or /var/tmp/from_scwrl_1118756339_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1118756339_a.pdb or decoys//var/tmp/from_scwrl_1118756339_a.pdb.gz for input Trying /var/tmp/from_scwrl_1118756339_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_1118756339_a.pdb or /var/tmp/from_scwrl_1118756339_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_1118756339.pdb or /var/tmp/from_scwrl_1118756339_b.pdb or /var/tmp/from_scwrl_1118756339_a.pdb Error: no new SCWRL conformation added # 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 529 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1634898198.pdb -s /var/tmp/to_scwrl_1634898198.seq -o /var/tmp/from_scwrl_1634898198.pdb > /var/tmp/scwrl_1634898198.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1634898198.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 # Found a chain break before 479 # copying to AlignedFragments data structure # naming current conformation NN_PUT_lab_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1512806597.pdb -s /var/tmp/to_scwrl_1512806597.seq -o /var/tmp/from_scwrl_1512806597.pdb > /var/tmp/scwrl_1512806597.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1512806597.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 477 ; scwrl3 -i /var/tmp/to_scwrl_285013288.pdb -s /var/tmp/to_scwrl_285013288.seq -o /var/tmp/from_scwrl_285013288.pdb > /var/tmp/scwrl_285013288.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_285013288.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 477 ; scwrl3 -i /var/tmp/to_scwrl_95634721.pdb -s /var/tmp/to_scwrl_95634721.seq -o /var/tmp/from_scwrl_95634721.pdb > /var/tmp/scwrl_95634721.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_95634721.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 477 ; scwrl3 -i /var/tmp/to_scwrl_196967301.pdb -s /var/tmp/to_scwrl_196967301.seq -o /var/tmp/from_scwrl_196967301.pdb > /var/tmp/scwrl_196967301.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_196967301.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 477 ; scwrl3 -i /var/tmp/to_scwrl_64881634.pdb -s /var/tmp/to_scwrl_64881634.seq -o /var/tmp/from_scwrl_64881634.pdb > /var/tmp/scwrl_64881634.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_64881634.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 477 ; scwrl3 -i /var/tmp/to_scwrl_832471619.pdb -s /var/tmp/to_scwrl_832471619.seq -o /var/tmp/from_scwrl_832471619.pdb > /var/tmp/scwrl_832471619.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_832471619.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 517 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_844120116.pdb -s /var/tmp/to_scwrl_844120116.seq -o /var/tmp/from_scwrl_844120116.pdb > /var/tmp/scwrl_844120116.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_844120116.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 517 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1640368536.pdb -s /var/tmp/to_scwrl_1640368536.seq -o /var/tmp/from_scwrl_1640368536.pdb > /var/tmp/scwrl_1640368536.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1640368536.pdb # conformation set from SCWRL output # naming current conformation PROTINFO_TS2-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # Found a chain break before 449 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1103967627.pdb -s /var/tmp/to_scwrl_1103967627.seq -o /var/tmp/from_scwrl_1103967627.pdb > /var/tmp/scwrl_1103967627.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1103967627.pdb # conformation set from SCWRL output # naming current conformation PROTINFO_TS3-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # Found a chain break before 484 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_2053773822.pdb -s /var/tmp/to_scwrl_2053773822.seq -o /var/tmp/from_scwrl_2053773822.pdb > /var/tmp/scwrl_2053773822.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2053773822.pdb # conformation set from SCWRL output # naming current conformation PROTINFO_TS4-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # Found a chain break before 517 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_736552407.pdb -s /var/tmp/to_scwrl_736552407.seq -o /var/tmp/from_scwrl_736552407.pdb > /var/tmp/scwrl_736552407.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_736552407.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 T0334 can't currently be optimized by undertaker # naming current conformation Pcons6_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1228359964.pdb -s /var/tmp/to_scwrl_1228359964.seq -o /var/tmp/from_scwrl_1228359964.pdb > /var/tmp/scwrl_1228359964.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1228359964.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 T0334 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pcons6_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_294944615.pdb -s /var/tmp/to_scwrl_294944615.seq -o /var/tmp/from_scwrl_294944615.pdb > /var/tmp/scwrl_294944615.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_294944615.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 T0334 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pcons6_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1492558943.pdb -s /var/tmp/to_scwrl_1492558943.seq -o /var/tmp/from_scwrl_1492558943.pdb > /var/tmp/scwrl_1492558943.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1492558943.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 T0334 can't currently be optimized by undertaker # naming current conformation Pcons6_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1010851101.pdb -s /var/tmp/to_scwrl_1010851101.seq -o /var/tmp/from_scwrl_1010851101.pdb > /var/tmp/scwrl_1010851101.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1010851101.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 T0334 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pcons6_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1461160222.pdb -s /var/tmp/to_scwrl_1461160222.seq -o /var/tmp/from_scwrl_1461160222.pdb > /var/tmp/scwrl_1461160222.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1461160222.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 T0334 can't currently be optimized by undertaker # naming current conformation Phyre-1_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_93697718.pdb -s /var/tmp/to_scwrl_93697718.seq -o /var/tmp/from_scwrl_93697718.pdb > /var/tmp/scwrl_93697718.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_93697718.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 527 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_915878497.pdb -s /var/tmp/to_scwrl_915878497.seq -o /var/tmp/from_scwrl_915878497.pdb > /var/tmp/scwrl_915878497.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_915878497.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 527 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_786314031.pdb -s /var/tmp/to_scwrl_786314031.seq -o /var/tmp/from_scwrl_786314031.pdb > /var/tmp/scwrl_786314031.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_786314031.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 529 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_2019357165.pdb -s /var/tmp/to_scwrl_2019357165.seq -o /var/tmp/from_scwrl_2019357165.pdb > /var/tmp/scwrl_2019357165.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2019357165.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 529 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1854542947.pdb -s /var/tmp/to_scwrl_1854542947.seq -o /var/tmp/from_scwrl_1854542947.pdb > /var/tmp/scwrl_1854542947.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1854542947.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 529 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1992658144.pdb -s /var/tmp/to_scwrl_1992658144.seq -o /var/tmp/from_scwrl_1992658144.pdb > /var/tmp/scwrl_1992658144.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1992658144.pdb # conformation set from SCWRL output # naming current conformation Phyre-2_TS5-scwrl # ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1 # Found a chain break before 527 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1482693281.pdb -s /var/tmp/to_scwrl_1482693281.seq -o /var/tmp/from_scwrl_1482693281.pdb > /var/tmp/scwrl_1482693281.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1482693281.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 T0334 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1601992321.pdb -s /var/tmp/to_scwrl_1601992321.seq -o /var/tmp/from_scwrl_1601992321.pdb > /var/tmp/scwrl_1601992321.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1601992321.pdb # conformation set from SCWRL output # naming current conformation Pmodeller6_TS2-scwrl # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # Found a chain break before 527 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_400013146.pdb -s /var/tmp/to_scwrl_400013146.seq -o /var/tmp/from_scwrl_400013146.pdb > /var/tmp/scwrl_400013146.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_400013146.pdb # conformation set from SCWRL output # naming current conformation Pmodeller6_TS3-scwrl # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # Found a chain break before 457 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_2101084106.pdb -s /var/tmp/to_scwrl_2101084106.seq -o /var/tmp/from_scwrl_2101084106.pdb > /var/tmp/scwrl_2101084106.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2101084106.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 # Found a chain break before 457 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1371321674.pdb -s /var/tmp/to_scwrl_1371321674.seq -o /var/tmp/from_scwrl_1371321674.pdb > /var/tmp/scwrl_1371321674.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1371321674.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 423 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_2062649233.pdb -s /var/tmp/to_scwrl_2062649233.seq -o /var/tmp/from_scwrl_2062649233.pdb > /var/tmp/scwrl_2062649233.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2062649233.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 446 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1759227768.pdb -s /var/tmp/to_scwrl_1759227768.seq -o /var/tmp/from_scwrl_1759227768.pdb > /var/tmp/scwrl_1759227768.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1759227768.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 447 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_342594367.pdb -s /var/tmp/to_scwrl_342594367.seq -o /var/tmp/from_scwrl_342594367.pdb > /var/tmp/scwrl_342594367.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_342594367.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 447 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1550063784.pdb -s /var/tmp/to_scwrl_1550063784.seq -o /var/tmp/from_scwrl_1550063784.pdb > /var/tmp/scwrl_1550063784.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1550063784.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 466 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1124550718.pdb -s /var/tmp/to_scwrl_1124550718.seq -o /var/tmp/from_scwrl_1124550718.pdb > /var/tmp/scwrl_1124550718.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1124550718.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 484 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_627607655.pdb -s /var/tmp/to_scwrl_627607655.seq -o /var/tmp/from_scwrl_627607655.pdb > /var/tmp/scwrl_627607655.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_627607655.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 484 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1645698505.pdb -s /var/tmp/to_scwrl_1645698505.seq -o /var/tmp/from_scwrl_1645698505.pdb > /var/tmp/scwrl_1645698505.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1645698505.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 522 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1321518020.pdb -s /var/tmp/to_scwrl_1321518020.seq -o /var/tmp/from_scwrl_1321518020.pdb > /var/tmp/scwrl_1321518020.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1321518020.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 526 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_692489289.pdb -s /var/tmp/to_scwrl_692489289.seq -o /var/tmp/from_scwrl_692489289.pdb > /var/tmp/scwrl_692489289.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_692489289.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 524 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_330686478.pdb -s /var/tmp/to_scwrl_330686478.seq -o /var/tmp/from_scwrl_330686478.pdb > /var/tmp/scwrl_330686478.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_330686478.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 491 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_18154489.pdb -s /var/tmp/to_scwrl_18154489.seq -o /var/tmp/from_scwrl_18154489.pdb > /var/tmp/scwrl_18154489.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_18154489.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 521 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_185374179.pdb -s /var/tmp/to_scwrl_185374179.seq -o /var/tmp/from_scwrl_185374179.pdb > /var/tmp/scwrl_185374179.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_185374179.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 359 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1434654105.pdb -s /var/tmp/to_scwrl_1434654105.seq -o /var/tmp/from_scwrl_1434654105.pdb > /var/tmp/scwrl_1434654105.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1434654105.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 519 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_2071928311.pdb -s /var/tmp/to_scwrl_2071928311.seq -o /var/tmp/from_scwrl_2071928311.pdb > /var/tmp/scwrl_2071928311.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2071928311.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 Faking rotamer for incomplete or colinear backbone at (T0334)Y125 Faking rotamer for incomplete or colinear backbone at (T0334)Y125 # Found a chain break before 519 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_921926586.pdb -s /var/tmp/to_scwrl_921926586.seq -o /var/tmp/from_scwrl_921926586.pdb > /var/tmp/scwrl_921926586.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_921926586.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 527 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_515530424.pdb -s /var/tmp/to_scwrl_515530424.seq -o /var/tmp/from_scwrl_515530424.pdb > /var/tmp/scwrl_515530424.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_515530424.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 527 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_219389279.pdb -s /var/tmp/to_scwrl_219389279.seq -o /var/tmp/from_scwrl_219389279.pdb > /var/tmp/scwrl_219389279.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_219389279.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 527 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_267001883.pdb -s /var/tmp/to_scwrl_267001883.seq -o /var/tmp/from_scwrl_267001883.pdb > /var/tmp/scwrl_267001883.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_267001883.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 457 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1526381524.pdb -s /var/tmp/to_scwrl_1526381524.seq -o /var/tmp/from_scwrl_1526381524.pdb > /var/tmp/scwrl_1526381524.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1526381524.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 457 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1680549502.pdb -s /var/tmp/to_scwrl_1680549502.seq -o /var/tmp/from_scwrl_1680549502.pdb > /var/tmp/scwrl_1680549502.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1680549502.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 527 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_360699601.pdb -s /var/tmp/to_scwrl_360699601.seq -o /var/tmp/from_scwrl_360699601.pdb > /var/tmp/scwrl_360699601.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_360699601.pdb # conformation set from SCWRL output # naming current conformation ROKKY_TS1-scwrl # ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_294776374.pdb -s /var/tmp/to_scwrl_294776374.seq -o /var/tmp/from_scwrl_294776374.pdb > /var/tmp/scwrl_294776374.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_294776374.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 T0334 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_319379886.pdb -s /var/tmp/to_scwrl_319379886.seq -o /var/tmp/from_scwrl_319379886.pdb > /var/tmp/scwrl_319379886.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_319379886.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 Skipped atom 626, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 628, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 630, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 632, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 846, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 848, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 850, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 852, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 1274, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 1276, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 1278, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 1280, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 1286, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 1288, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 1290, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 1292, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_232573120.pdb -s /var/tmp/to_scwrl_232573120.seq -o /var/tmp/from_scwrl_232573120.pdb > /var/tmp/scwrl_232573120.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_232573120.pdb # conformation set from SCWRL output # naming current conformation SAM-T02_AL3-scwrl # ReadConformPDB reading from PDB file servers/SAM-T02_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1835674.pdb -s /var/tmp/to_scwrl_1835674.seq -o /var/tmp/from_scwrl_1835674.pdb > /var/tmp/scwrl_1835674.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1835674.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 Skipped atom 694, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 696, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 698, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 700, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 1098, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 1100, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 1102, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 1104, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_164554383.pdb -s /var/tmp/to_scwrl_164554383.seq -o /var/tmp/from_scwrl_164554383.pdb > /var/tmp/scwrl_164554383.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_164554383.pdb # conformation set from SCWRL output # naming current conformation SAM-T02_AL5-scwrl # ReadConformPDB reading from PDB file servers/SAM-T99_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1715266401.pdb -s /var/tmp/to_scwrl_1715266401.seq -o /var/tmp/from_scwrl_1715266401.pdb > /var/tmp/scwrl_1715266401.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1715266401.pdb # conformation set from SCWRL output # naming current conformation SAM-T99_AL1-scwrl # ReadConformPDB reading from PDB file servers/SAM-T99_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1603827995.pdb -s /var/tmp/to_scwrl_1603827995.seq -o /var/tmp/from_scwrl_1603827995.pdb > /var/tmp/scwrl_1603827995.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1603827995.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 T0334 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_564567529.pdb -s /var/tmp/to_scwrl_564567529.seq -o /var/tmp/from_scwrl_564567529.pdb > /var/tmp/scwrl_564567529.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_564567529.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 T0334 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1668866860.pdb -s /var/tmp/to_scwrl_1668866860.seq -o /var/tmp/from_scwrl_1668866860.pdb > /var/tmp/scwrl_1668866860.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1668866860.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 T0334 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_827666023.pdb -s /var/tmp/to_scwrl_827666023.seq -o /var/tmp/from_scwrl_827666023.pdb > /var/tmp/scwrl_827666023.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_827666023.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 513 # copying to AlignedFragments data structure # naming current conformation SAM_T06_server_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_479733115.pdb -s /var/tmp/to_scwrl_479733115.seq -o /var/tmp/from_scwrl_479733115.pdb > /var/tmp/scwrl_479733115.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_479733115.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 T0334 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1280610981.pdb -s /var/tmp/to_scwrl_1280610981.seq -o /var/tmp/from_scwrl_1280610981.pdb > /var/tmp/scwrl_1280610981.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1280610981.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 T0334 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1170260389.pdb -s /var/tmp/to_scwrl_1170260389.seq -o /var/tmp/from_scwrl_1170260389.pdb > /var/tmp/scwrl_1170260389.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1170260389.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 T0334 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_2029796900.pdb -s /var/tmp/to_scwrl_2029796900.seq -o /var/tmp/from_scwrl_2029796900.pdb > /var/tmp/scwrl_2029796900.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2029796900.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 T0334 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_257678054.pdb -s /var/tmp/to_scwrl_257678054.seq -o /var/tmp/from_scwrl_257678054.pdb > /var/tmp/scwrl_257678054.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_257678054.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 447 # copying to AlignedFragments data structure # naming current conformation SP3_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1797868044.pdb -s /var/tmp/to_scwrl_1797868044.seq -o /var/tmp/from_scwrl_1797868044.pdb > /var/tmp/scwrl_1797868044.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1797868044.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 Faking rotamer for incomplete or colinear backbone at (T0334)A173 Faking rotamer for incomplete or colinear backbone at (T0334)A173 # Found a chain break before 517 # copying to AlignedFragments data structure # naming current conformation SP3_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1528011758.pdb -s /var/tmp/to_scwrl_1528011758.seq -o /var/tmp/from_scwrl_1528011758.pdb > /var/tmp/scwrl_1528011758.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1528011758.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 505 # copying to AlignedFragments data structure # naming current conformation SP3_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1579196074.pdb -s /var/tmp/to_scwrl_1579196074.seq -o /var/tmp/from_scwrl_1579196074.pdb > /var/tmp/scwrl_1579196074.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1579196074.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 360 # copying to AlignedFragments data structure # naming current conformation SP3_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_342873687.pdb -s /var/tmp/to_scwrl_342873687.seq -o /var/tmp/from_scwrl_342873687.pdb > /var/tmp/scwrl_342873687.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_342873687.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 507 # copying to AlignedFragments data structure # naming current conformation SP3_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1858698236.pdb -s /var/tmp/to_scwrl_1858698236.seq -o /var/tmp/from_scwrl_1858698236.pdb > /var/tmp/scwrl_1858698236.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1858698236.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 491 # copying to AlignedFragments data structure # naming current conformation SP4_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1597350563.pdb -s /var/tmp/to_scwrl_1597350563.seq -o /var/tmp/from_scwrl_1597350563.pdb > /var/tmp/scwrl_1597350563.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1597350563.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 471 # copying to AlignedFragments data structure # naming current conformation SP4_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_528247866.pdb -s /var/tmp/to_scwrl_528247866.seq -o /var/tmp/from_scwrl_528247866.pdb > /var/tmp/scwrl_528247866.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_528247866.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 Faking rotamer for incomplete or colinear backbone at (T0334)A173 Faking rotamer for incomplete or colinear backbone at (T0334)A173 # Found a chain break before 517 # copying to AlignedFragments data structure # naming current conformation SP4_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1145868695.pdb -s /var/tmp/to_scwrl_1145868695.seq -o /var/tmp/from_scwrl_1145868695.pdb > /var/tmp/scwrl_1145868695.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1145868695.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 527 # copying to AlignedFragments data structure # naming current conformation SP4_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1521795228.pdb -s /var/tmp/to_scwrl_1521795228.seq -o /var/tmp/from_scwrl_1521795228.pdb > /var/tmp/scwrl_1521795228.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1521795228.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 368 # copying to AlignedFragments data structure # naming current conformation SP4_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1450174451.pdb -s /var/tmp/to_scwrl_1450174451.seq -o /var/tmp/from_scwrl_1450174451.pdb > /var/tmp/scwrl_1450174451.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1450174451.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 479 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1661399119.pdb -s /var/tmp/to_scwrl_1661399119.seq -o /var/tmp/from_scwrl_1661399119.pdb > /var/tmp/scwrl_1661399119.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1661399119.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 444 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1741184507.pdb -s /var/tmp/to_scwrl_1741184507.seq -o /var/tmp/from_scwrl_1741184507.pdb > /var/tmp/scwrl_1741184507.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1741184507.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 376 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1717176334.pdb -s /var/tmp/to_scwrl_1717176334.seq -o /var/tmp/from_scwrl_1717176334.pdb > /var/tmp/scwrl_1717176334.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1717176334.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 Faking rotamer for incomplete or colinear backbone at (T0334)A173 Faking rotamer for incomplete or colinear backbone at (T0334)A173 # Found a chain break before 517 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1040296997.pdb -s /var/tmp/to_scwrl_1040296997.seq -o /var/tmp/from_scwrl_1040296997.pdb > /var/tmp/scwrl_1040296997.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1040296997.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 391 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1274250362.pdb -s /var/tmp/to_scwrl_1274250362.seq -o /var/tmp/from_scwrl_1274250362.pdb > /var/tmp/scwrl_1274250362.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1274250362.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 T0334 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_2077875936.pdb -s /var/tmp/to_scwrl_2077875936.seq -o /var/tmp/from_scwrl_2077875936.pdb > /var/tmp/scwrl_2077875936.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2077875936.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_bnmx_TS1-scwrl # ReadConformPDB reading from PDB file servers/UNI-EID_expm_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation UNI-EID_expm_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1335073370.pdb -s /var/tmp/to_scwrl_1335073370.seq -o /var/tmp/from_scwrl_1335073370.pdb > /var/tmp/scwrl_1335073370.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1335073370.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_expm_TS1-scwrl # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1593630248.pdb -s /var/tmp/to_scwrl_1593630248.seq -o /var/tmp/from_scwrl_1593630248.pdb > /var/tmp/scwrl_1593630248.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1593630248.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_sfst_AL1-scwrl # ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1 # Found a chain break before 502 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_162965409.pdb -s /var/tmp/to_scwrl_162965409.seq -o /var/tmp/from_scwrl_162965409.pdb > /var/tmp/scwrl_162965409.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_162965409.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 491 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1336909044.pdb -s /var/tmp/to_scwrl_1336909044.seq -o /var/tmp/from_scwrl_1336909044.pdb > /var/tmp/scwrl_1336909044.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1336909044.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 528 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1758184632.pdb -s /var/tmp/to_scwrl_1758184632.seq -o /var/tmp/from_scwrl_1758184632.pdb > /var/tmp/scwrl_1758184632.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1758184632.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 527 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1878231810.pdb -s /var/tmp/to_scwrl_1878231810.seq -o /var/tmp/from_scwrl_1878231810.pdb > /var/tmp/scwrl_1878231810.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1878231810.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 491 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_793253394.pdb -s /var/tmp/to_scwrl_793253394.seq -o /var/tmp/from_scwrl_793253394.pdb > /var/tmp/scwrl_793253394.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_793253394.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 529 # copying to AlignedFragments data structure # naming current conformation beautshot_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_175268514.pdb -s /var/tmp/to_scwrl_175268514.seq -o /var/tmp/from_scwrl_175268514.pdb > /var/tmp/scwrl_175268514.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_175268514.pdb # conformation set from SCWRL output # naming current conformation beautshot_TS1-scwrl # ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation beautshotbase_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1399615023.pdb -s /var/tmp/to_scwrl_1399615023.seq -o /var/tmp/from_scwrl_1399615023.pdb > /var/tmp/scwrl_1399615023.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1399615023.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 111, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 113, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 115, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 117, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 119, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 121, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 123, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 125, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 127, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 129, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 131, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 133, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 135, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 137, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 139, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 141, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 143, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 145, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 147, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation forecast-s_AL1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1620919416.pdb -s /var/tmp/to_scwrl_1620919416.seq -o /var/tmp/from_scwrl_1620919416.pdb > /var/tmp/scwrl_1620919416.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1620919416.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 T0334 can't currently be optimized by undertaker # naming current conformation forecast-s_AL2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_655001630.pdb -s /var/tmp/to_scwrl_655001630.seq -o /var/tmp/from_scwrl_655001630.pdb > /var/tmp/scwrl_655001630.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_655001630.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 T0334 can't currently be optimized by undertaker # naming current conformation forecast-s_AL3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_532742359.pdb -s /var/tmp/to_scwrl_532742359.seq -o /var/tmp/from_scwrl_532742359.pdb > /var/tmp/scwrl_532742359.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_532742359.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 T0334 can't currently be optimized by undertaker # naming current conformation forecast-s_AL4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_643696160.pdb -s /var/tmp/to_scwrl_643696160.seq -o /var/tmp/from_scwrl_643696160.pdb > /var/tmp/scwrl_643696160.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_643696160.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 T0334 can't currently be optimized by undertaker # naming current conformation forecast-s_AL5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_537314883.pdb -s /var/tmp/to_scwrl_537314883.seq -o /var/tmp/from_scwrl_537314883.pdb > /var/tmp/scwrl_537314883.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_537314883.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 T0334 can't currently be optimized by undertaker # naming current conformation gtg_AL1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_790420413.pdb -s /var/tmp/to_scwrl_790420413.seq -o /var/tmp/from_scwrl_790420413.pdb > /var/tmp/scwrl_790420413.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_790420413.pdb # conformation set from SCWRL output # naming current conformation gtg_AL1-scwrl # ReadConformPDB reading from PDB file servers/gtg_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation gtg_AL2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_294080557.pdb -s /var/tmp/to_scwrl_294080557.seq -o /var/tmp/from_scwrl_294080557.pdb > /var/tmp/scwrl_294080557.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_294080557.pdb # conformation set from SCWRL output # naming current conformation gtg_AL2-scwrl # ReadConformPDB reading from PDB file servers/gtg_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation gtg_AL3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_2065326641.pdb -s /var/tmp/to_scwrl_2065326641.seq -o /var/tmp/from_scwrl_2065326641.pdb > /var/tmp/scwrl_2065326641.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2065326641.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 T0334 can't currently be optimized by undertaker # naming current conformation gtg_AL4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_222132840.pdb -s /var/tmp/to_scwrl_222132840.seq -o /var/tmp/from_scwrl_222132840.pdb > /var/tmp/scwrl_222132840.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_222132840.pdb # conformation set from SCWRL output # naming current conformation gtg_AL4-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # Found a chain break before 464 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_636954244.pdb -s /var/tmp/to_scwrl_636954244.seq -o /var/tmp/from_scwrl_636954244.pdb > /var/tmp/scwrl_636954244.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_636954244.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 479 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1776541231.pdb -s /var/tmp/to_scwrl_1776541231.seq -o /var/tmp/from_scwrl_1776541231.pdb > /var/tmp/scwrl_1776541231.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1776541231.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 456 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1819483403.pdb -s /var/tmp/to_scwrl_1819483403.seq -o /var/tmp/from_scwrl_1819483403.pdb > /var/tmp/scwrl_1819483403.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1819483403.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 519 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1165202109.pdb -s /var/tmp/to_scwrl_1165202109.seq -o /var/tmp/from_scwrl_1165202109.pdb > /var/tmp/scwrl_1165202109.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1165202109.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 519 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_774926280.pdb -s /var/tmp/to_scwrl_774926280.seq -o /var/tmp/from_scwrl_774926280.pdb > /var/tmp/scwrl_774926280.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_774926280.pdb # conformation set from SCWRL output # naming current conformation karypis.srv.2_TS5-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1193794984.pdb -s /var/tmp/to_scwrl_1193794984.seq -o /var/tmp/from_scwrl_1193794984.pdb > /var/tmp/scwrl_1193794984.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1193794984.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 T0334 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_467892915.pdb -s /var/tmp/to_scwrl_467892915.seq -o /var/tmp/from_scwrl_467892915.pdb > /var/tmp/scwrl_467892915.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_467892915.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 T0334 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_288841752.pdb -s /var/tmp/to_scwrl_288841752.seq -o /var/tmp/from_scwrl_288841752.pdb > /var/tmp/scwrl_288841752.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_288841752.pdb # conformation set from SCWRL output # naming current conformation karypis.srv_TS3-scwrl # ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1 # Found a chain break before 517 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_787495846.pdb -s /var/tmp/to_scwrl_787495846.seq -o /var/tmp/from_scwrl_787495846.pdb > /var/tmp/scwrl_787495846.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_787495846.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 519 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_37585602.pdb -s /var/tmp/to_scwrl_37585602.seq -o /var/tmp/from_scwrl_37585602.pdb > /var/tmp/scwrl_37585602.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_37585602.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 328 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1329138748.pdb -s /var/tmp/to_scwrl_1329138748.seq -o /var/tmp/from_scwrl_1329138748.pdb > /var/tmp/scwrl_1329138748.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1329138748.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 524 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_2061746208.pdb -s /var/tmp/to_scwrl_2061746208.seq -o /var/tmp/from_scwrl_2061746208.pdb > /var/tmp/scwrl_2061746208.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2061746208.pdb # conformation set from SCWRL output # naming current conformation keasar-server_TS4-scwrl # ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation keasar-server_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_2115461538.pdb -s /var/tmp/to_scwrl_2115461538.seq -o /var/tmp/from_scwrl_2115461538.pdb > /var/tmp/scwrl_2115461538.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2115461538.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 T0334 can't currently be optimized by undertaker # naming current conformation mGen-3D_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_516728472.pdb -s /var/tmp/to_scwrl_516728472.seq -o /var/tmp/from_scwrl_516728472.pdb > /var/tmp/scwrl_516728472.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_516728472.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 T0334 can't currently be optimized by undertaker # naming current conformation nFOLD_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1507892810.pdb -s /var/tmp/to_scwrl_1507892810.seq -o /var/tmp/from_scwrl_1507892810.pdb > /var/tmp/scwrl_1507892810.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1507892810.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: atom 1 has residue number 1 < previous residue 529 in servers/nFOLD_TS2.pdb.gz # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation nFOLD_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_130943300.pdb -s /var/tmp/to_scwrl_130943300.seq -o /var/tmp/from_scwrl_130943300.pdb > /var/tmp/scwrl_130943300.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_130943300.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: atom 1 has residue number 4 < previous residue 529 in servers/nFOLD_TS3.pdb.gz # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation nFOLD_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1853637516.pdb -s /var/tmp/to_scwrl_1853637516.seq -o /var/tmp/from_scwrl_1853637516.pdb > /var/tmp/scwrl_1853637516.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1853637516.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 T0334 can't currently be optimized by undertaker # naming current conformation nFOLD_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1118593795.pdb -s /var/tmp/to_scwrl_1118593795.seq -o /var/tmp/from_scwrl_1118593795.pdb > /var/tmp/scwrl_1118593795.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1118593795.pdb # conformation set from SCWRL output # naming current conformation nFOLD_TS4-scwrl # ReadConformPDB reading from PDB file servers/nFOLD_TS5.pdb.gz looking for model 1 WARNING: atom 1 has residue number 2 < previous residue 381 in servers/nFOLD_TS5.pdb.gz # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation nFOLD_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_2009175110.pdb -s /var/tmp/to_scwrl_2009175110.seq -o /var/tmp/from_scwrl_2009175110.pdb > /var/tmp/scwrl_2009175110.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2009175110.pdb # conformation set from SCWRL output # naming current conformation nFOLD_TS5-scwrl # ReadConformPDB reading from PDB file servers/panther2_TS1.pdb.gz looking for model 1 WARNING: atoms too close: (T0334)I5.N and (T0334)L55.N only 0.000 apart, marking (T0334)L55.N as missing WARNING: atoms too close: (T0334)I5.CA and (T0334)L55.CA only 0.000 apart, marking (T0334)L55.CA as missing WARNING: atoms too close: (T0334)I5.CB and (T0334)L55.CB only 0.000 apart, marking (T0334)L55.CB as missing WARNING: atoms too close: (T0334)I5.CG1 and (T0334)L55.CG only 0.000 apart, marking (T0334)L55.CG as missing WARNING: atoms too close: (T0334)I5.O and (T0334)L55.O only 0.000 apart, marking (T0334)L55.O as missing WARNING: atoms too close: (T0334)I5.C and (T0334)L55.C only 0.000 apart, marking (T0334)L55.C as missing WARNING: atoms too close: (T0334)L55.N and (T0334)Q56.N only 0.000 apart, marking (T0334)L55.N as missing WARNING: atoms too close: (T0334)I5.N and (T0334)Q56.N only 0.000 apart, marking (T0334)Q56.N as missing WARNING: atoms too close: (T0334)L55.CA and (T0334)Q56.CA only 0.000 apart, marking (T0334)Q56.CA as missing WARNING: atoms too close: (T0334)I5.CA and (T0334)Q56.CA only 0.000 apart, marking (T0334)Q56.CA as missing WARNING: atoms too close: (T0334)L55.CB and (T0334)Q56.CB only 0.000 apart, marking (T0334)Q56.CB as missing WARNING: atoms too close: (T0334)I5.CB and (T0334)Q56.CB only 0.000 apart, marking (T0334)Q56.CB as missing WARNING: atoms too close: (T0334)L55.CG and (T0334)Q56.CG only 0.000 apart, marking (T0334)Q56.CG as missing WARNING: atoms too close: (T0334)I5.CG1 and (T0334)Q56.CG only 0.000 apart, marking (T0334)Q56.CG as missing WARNING: atoms too close: (T0334)L55.O and (T0334)Q56.O only 0.000 apart, marking (T0334)Q56.O as missing WARNING: atoms too close: (T0334)I5.O and (T0334)Q56.O only 0.000 apart, marking (T0334)Q56.O as missing WARNING: atoms too close: (T0334)L55.C and (T0334)Q56.C only 0.000 apart, marking (T0334)Q56.C as missing WARNING: atoms too close: (T0334)I5.C and (T0334)Q56.C only 0.000 apart, marking (T0334)Q56.C as missing WARNING: atoms too close: (T0334)Q56.N and (T0334)P66.N only 0.000 apart, marking (T0334)Q56.N as missing WARNING: atoms too close: (T0334)L55.N and (T0334)P66.N only 0.000 apart, marking (T0334)L55.N as missing WARNING: atoms too close: (T0334)I5.N and (T0334)P66.N only 0.000 apart, marking (T0334)P66.N as missing WARNING: atoms too close: (T0334)Q56.CA and (T0334)P66.CA only 0.000 apart, marking (T0334)P66.CA as missing WARNING: atoms too close: (T0334)L55.CA and (T0334)P66.CA only 0.000 apart, marking (T0334)P66.CA as missing WARNING: atoms too close: (T0334)I5.CA and (T0334)P66.CA only 0.000 apart, marking (T0334)P66.CA as missing WARNING: atoms too close: (T0334)Q56.CB and (T0334)P66.CB only 0.000 apart, marking (T0334)P66.CB as missing WARNING: atoms too close: (T0334)L55.CB and (T0334)P66.CB only 0.000 apart, marking (T0334)P66.CB as missing WARNING: atoms too close: (T0334)I5.CB and (T0334)P66.CB only 0.000 apart, marking (T0334)P66.CB as missing WARNING: atoms too close: (T0334)Q56.O and (T0334)P66.O only 0.000 apart, marking (T0334)P66.O as missing WARNING: atoms too close: (T0334)L55.O and (T0334)P66.O only 0.000 apart, marking (T0334)P66.O as missing WARNING: atoms too close: (T0334)I5.O and (T0334)P66.O only 0.000 apart, marking (T0334)P66.O as missing WARNING: atoms too close: (T0334)Q56.C and (T0334)P66.C only 0.000 apart, marking (T0334)P66.C as missing WARNING: atoms too close: (T0334)L55.C and (T0334)P66.C only 0.000 apart, marking (T0334)P66.C as missing WARNING: atoms too close: (T0334)I5.C and (T0334)P66.C only 0.000 apart, marking (T0334)P66.C as missing WARNING: atoms too close: (T0334)P66.N and (T0334)V80.N only 0.000 apart, marking (T0334)P66.N as missing WARNING: atoms too close: (T0334)Q56.N and (T0334)V80.N only 0.000 apart, marking (T0334)Q56.N as missing WARNING: atoms too close: (T0334)L55.N and (T0334)V80.N only 0.000 apart, marking (T0334)L55.N as missing WARNING: atoms too close: (T0334)I5.N and (T0334)V80.N only 0.000 apart, marking (T0334)V80.N as missing WARNING: atoms too close: (T0334)P66.CA and (T0334)V80.CA only 0.000 apart, marking (T0334)V80.CA as missing WARNING: atoms too close: (T0334)Q56.CA and (T0334)V80.CA only 0.000 apart, marking (T0334)V80.CA as missing WARNING: atoms too close: (T0334)L55.CA and (T0334)V80.CA only 0.000 apart, marking (T0334)V80.CA as missing WARNING: atoms too close: (T0334)I5.CA and (T0334)V80.CA only 0.000 apart, marking (T0334)V80.CA as missing WARNING: atoms too close: (T0334)P66.CB and (T0334)V80.CB only 0.000 apart, marking (T0334)V80.CB as missing WARNING: atoms too close: (T0334)Q56.CB and (T0334)V80.CB only 0.000 apart, marking (T0334)V80.CB as missing WARNING: atoms too close: (T0334)L55.CB and (T0334)V80.CB only 0.000 apart, marking (T0334)V80.CB as missing WARNING: atoms too close: (T0334)I5.CB and (T0334)V80.CB only 0.000 apart, marking (T0334)V80.CB as missing WARNING: atoms too close: (T0334)Q56.CG and (T0334)V80.CG1 only 0.000 apart, marking (T0334)V80.CG1 as missing WARNING: atoms too close: (T0334)L55.CG and (T0334)V80.CG1 only 0.000 apart, marking (T0334)V80.CG1 as missing WARNING: atoms too close: (T0334)I5.CG1 and (T0334)V80.CG1 only 0.000 apart, marking (T0334)V80.CG1 as missing WARNING: atoms too close: (T0334)P66.O and (T0334)V80.O only 0.000 apart, marking (T0334)V80.O as missing WARNING: atoms too close: (T0334)Q56.O and (T0334)V80.O only 0.000 apart, marking (T0334)V80.O as missing WARNING: atoms too close: (T0334)L55.O and (T0334)V80.O only 0.000 apart, marking (T0334)V80.O as missing WARNING: atoms too close: (T0334)I5.O and (T0334)V80.O only 0.000 apart, marking (T0334)V80.O as missing WARNING: atoms too close: (T0334)P66.C and (T0334)V80.C only 0.000 apart, marking (T0334)V80.C as missing WARNING: atoms too close: (T0334)Q56.C and (T0334)V80.C only 0.000 apart, marking (T0334)V80.C as missing WARNING: atoms too close: (T0334)L55.C and (T0334)V80.C only 0.000 apart, marking (T0334)V80.C as missing WARNING: atoms too close: (T0334)I5.C and (T0334)V80.C only 0.000 apart, marking (T0334)V80.C as missing WARNING: atoms too close: (T0334)V80.N and (T0334)A81.N only 0.000 apart, marking (T0334)V80.N as missing WARNING: atoms too close: (T0334)P66.N and (T0334)A81.N only 0.000 apart, marking (T0334)P66.N as missing WARNING: atoms too close: (T0334)Q56.N and (T0334)A81.N only 0.000 apart, marking (T0334)Q56.N as missing WARNING: atoms too close: (T0334)L55.N and (T0334)A81.N only 0.000 apart, marking (T0334)L55.N as missing WARNING: atoms too close: (T0334)I5.N and (T0334)A81.N only 0.000 apart, marking (T0334)A81.N as missing WARNING: atoms too close: (T0334)V80.CA and (T0334)A81.CA only 0.000 apart, marking (T0334)A81.CA as missing WARNING: atoms too close: (T0334)P66.CA and (T0334)A81.CA only 0.000 apart, marking (T0334)A81.CA as missing WARNING: atoms too close: (T0334)Q56.CA and (T0334)A81.CA only 0.000 apart, marking (T0334)A81.CA as missing WARNING: atoms too close: (T0334)L55.CA and (T0334)A81.CA only 0.000 apart, marking (T0334)A81.CA as missing WARNING: atoms too close: (T0334)I5.CA and (T0334)A81.CA only 0.000 apart, marking (T0334)A81.CA as missing WARNING: atoms too close: (T0334)V80.CB and (T0334)A81.CB only 0.000 apart, marking (T0334)A81.CB as missing WARNING: atoms too close: (T0334)P66.CB and (T0334)A81.CB only 0.000 apart, marking (T0334)A81.CB as missing WARNING: atoms too close: (T0334)Q56.CB and (T0334)A81.CB only 0.000 apart, marking (T0334)A81.CB as missing WARNING: atoms too close: (T0334)L55.CB and (T0334)A81.CB only 0.000 apart, marking (T0334)A81.CB as missing WARNING: atoms too close: (T0334)I5.CB and (T0334)A81.CB only 0.000 apart, marking (T0334)A81.CB as missing WARNING: atoms too close: (T0334)V80.O and (T0334)A81.O only 0.000 apart, marking (T0334)A81.O as missing WARNING: atoms too close: (T0334)P66.O and (T0334)A81.O only 0.000 apart, marking (T0334)A81.O as missing WARNING: atoms too close: (T0334)Q56.O and (T0334)A81.O only 0.000 apart, marking (T0334)A81.O as missing WARNING: atoms too close: (T0334)L55.O and (T0334)A81.O only 0.000 apart, marking (T0334)A81.O as missing WARNING: atoms too close: (T0334)I5.O and (T0334)A81.O only 0.000 apart, marking (T0334)A81.O as missing WARNING: atoms too close: (T0334)V80.C and (T0334)A81.C only 0.000 apart, marking (T0334)A81.C as missing WARNING: atoms too close: (T0334)P66.C and (T0334)A81.C only 0.000 apart, marking (T0334)A81.C as missing WARNING: atoms too close: (T0334)Q56.C and (T0334)A81.C only 0.000 apart, marking (T0334)A81.C as missing WARNING: atoms too close: (T0334)L55.C and (T0334)A81.C only 0.000 apart, marking (T0334)A81.C as missing WARNING: atoms too close: (T0334)I5.C and (T0334)A81.C only 0.000 apart, marking (T0334)A81.C as missing # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation panther2_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_499407263.pdb -s /var/tmp/to_scwrl_499407263.seq -o /var/tmp/from_scwrl_499407263.pdb > /var/tmp/scwrl_499407263.log Error: Couldn't open file /var/tmp/from_scwrl_499407263.pdb or /var/tmp/from_scwrl_499407263.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_499407263_b.pdb or decoys//var/tmp/from_scwrl_499407263_b.pdb.gz for input Trying /var/tmp/from_scwrl_499407263_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_499407263_b.pdb or /var/tmp/from_scwrl_499407263_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_499407263_a.pdb or decoys//var/tmp/from_scwrl_499407263_a.pdb.gz for input Trying /var/tmp/from_scwrl_499407263_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_499407263_a.pdb or /var/tmp/from_scwrl_499407263_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_499407263.pdb or /var/tmp/from_scwrl_499407263_b.pdb or /var/tmp/from_scwrl_499407263_a.pdb Error: no new SCWRL conformation added # naming current conformation panther2_TS1-scwrl # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # Found a chain break before 529 # copying to AlignedFragments data structure # naming current conformation shub_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1293862309.pdb -s /var/tmp/to_scwrl_1293862309.seq -o /var/tmp/from_scwrl_1293862309.pdb > /var/tmp/scwrl_1293862309.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1293862309.pdb # conformation set from SCWRL output # naming current conformation shub_TS1-scwrl # command:CPU_time= 172.645 sec, elapsed time= 3853.58 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 = -38.9317 shub_TS1 costs 0 real_cost = -31.2881 panther2_TS1-scwrl costs 0 real_cost = 1046.58 nFOLD_TS5-scwrl costs 0 real_cost = 364.36 nFOLD_TS5 costs 0 real_cost = 646.129 nFOLD_TS4-scwrl costs 0 real_cost = 417.503 nFOLD_TS4 costs 0 real_cost = 680.246 nFOLD_TS3-scwrl costs 0 real_cost = 485.658 nFOLD_TS3 costs 0 real_cost = 708.862 nFOLD_TS2-scwrl costs 0 real_cost = 575.336 nFOLD_TS2 costs 0 real_cost = 756.65 nFOLD_TS1-scwrl costs 0 real_cost = -222.543 nFOLD_TS1 costs 0 real_cost = 78.0029 mGen-3D_TS1-scwrl costs 0 real_cost = -194.72 mGen-3D_TS1 costs 0 real_cost = 97.7428 keasar-server_TS5-scwrl costs 0 real_cost = 460.991 keasar-server_TS5 costs 0 real_cost = 466.268 keasar-server_TS4-scwrl costs 0 real_cost = -201.357 keasar-server_TS4 costs 0 real_cost = -191.252 keasar-server_TS3-scwrl costs 0 real_cost = -205.329 keasar-server_TS3 costs 0 real_cost = -197.656 keasar-server_TS2-scwrl costs 0 real_cost = -211.184 keasar-server_TS2 costs 0 real_cost = -207.792 keasar-server_TS1-scwrl costs 0 real_cost = -231.133 keasar-server_TS1 costs 0 real_cost = -225.628 karypis.srv_TS3-scwrl costs 0 real_cost = 772.414 karypis.srv_TS3 costs 0 real_cost = 770.012 karypis.srv_TS2-scwrl costs 0 real_cost = -255.941 karypis.srv_TS2 costs 0 real_cost = -255.968 karypis.srv_TS1-scwrl costs 0 real_cost = -252.344 karypis.srv_TS1 costs 0 real_cost = -251.434 karypis.srv.2_TS5-scwrl costs 0 real_cost = -163.629 karypis.srv.2_TS5 costs 0 real_cost = -163.043 karypis.srv.2_TS4-scwrl costs 0 real_cost = -217.825 karypis.srv.2_TS4 costs 0 real_cost = -218.556 karypis.srv.2_TS3-scwrl costs 0 real_cost = -241.169 karypis.srv.2_TS3 costs 0 real_cost = -240.931 karypis.srv.2_TS2-scwrl costs 0 real_cost = -203.267 karypis.srv.2_TS2 costs 0 real_cost = -203.618 karypis.srv.2_TS1-scwrl costs 0 real_cost = -149.525 karypis.srv.2_TS1 costs 0 real_cost = -149.323 gtg_AL4-scwrl costs 0 real_cost = 688.868 gtg_AL4 costs 0 real_cost = 875.551 gtg_AL3-scwrl costs 0 real_cost = 600.353 gtg_AL3 costs 0 real_cost = 816.018 gtg_AL2-scwrl costs 0 real_cost = 603.951 gtg_AL2 costs 0 real_cost = 811.414 gtg_AL1-scwrl costs 0 real_cost = 441.022 gtg_AL1 costs 0 real_cost = 701.505 forecast-s_AL5-scwrl costs 0 real_cost = 915.755 forecast-s_AL5 costs 0 real_cost = 967.548 forecast-s_AL4-scwrl costs 0 real_cost = 943.034 forecast-s_AL4 costs 0 real_cost = 999.622 forecast-s_AL3-scwrl costs 0 real_cost = 1017.12 forecast-s_AL3 costs 0 real_cost = 1084.1 forecast-s_AL2-scwrl costs 0 real_cost = 876.098 forecast-s_AL2 costs 0 real_cost = 944.32 forecast-s_AL1-scwrl costs 0 real_cost = 887.579 forecast-s_AL1 costs 0 real_cost = 945.739 beautshotbase_TS1-scwrl costs 0 real_cost = -247.128 beautshotbase_TS1 costs 0 real_cost = -233.855 beautshot_TS1-scwrl costs 0 real_cost = -90.3875 beautshot_TS1 costs 0 real_cost = -79.539 Zhang-Server_TS5-scwrl costs 0 real_cost = -278.725 Zhang-Server_TS5 costs 0 real_cost = -278.868 Zhang-Server_TS4-scwrl costs 0 real_cost = -277.247 Zhang-Server_TS4 costs 0 real_cost = -277.149 Zhang-Server_TS3-scwrl costs 0 real_cost = -267.78 Zhang-Server_TS3 costs 0 real_cost = -267.877 Zhang-Server_TS2-scwrl costs 0 real_cost = -260.131 Zhang-Server_TS2 costs 0 real_cost = -260.127 Zhang-Server_TS1-scwrl costs 0 real_cost = -284.254 Zhang-Server_TS1 costs 0 real_cost = -283.797 UNI-EID_sfst_AL1-scwrl costs 0 real_cost = -241.385 UNI-EID_sfst_AL1 costs 0 real_cost = 150.978 UNI-EID_expm_TS1-scwrl costs 0 real_cost = -221.632 UNI-EID_expm_TS1 costs 0 real_cost = 67.0848 UNI-EID_bnmx_TS1-scwrl costs 0 real_cost = -256.635 UNI-EID_bnmx_TS1 costs 0 real_cost = 139.255 SPARKS2_TS5-scwrl costs 0 real_cost = 341.114 SPARKS2_TS5 costs 0 real_cost = 346.918 SPARKS2_TS4-scwrl costs 0 real_cost = 371.527 SPARKS2_TS4 costs 0 real_cost = 372.266 SPARKS2_TS3-scwrl costs 0 real_cost = 234.114 SPARKS2_TS3 costs 0 real_cost = 238.856 SPARKS2_TS2-scwrl costs 0 real_cost = 236.857 SPARKS2_TS2 costs 0 real_cost = 241.597 SPARKS2_TS1-scwrl costs 0 real_cost = -282.877 SPARKS2_TS1 costs 0 real_cost = -284.58 SP4_TS5-scwrl costs 0 real_cost = 346.451 SP4_TS5 costs 0 real_cost = 353.102 SP4_TS4-scwrl costs 0 real_cost = 261.407 SP4_TS4 costs 0 real_cost = 263.848 SP4_TS3-scwrl costs 0 real_cost = 343.852 SP4_TS3 costs 0 real_cost = 349.221 SP4_TS2-scwrl costs 0 real_cost = 233.381 SP4_TS2 costs 0 real_cost = 238.133 SP4_TS1-scwrl costs 0 real_cost = -256.121 SP4_TS1 costs 0 real_cost = -259.956 SP3_TS5-scwrl costs 0 real_cost = 261.909 SP3_TS5 costs 0 real_cost = 266.412 SP3_TS4-scwrl costs 0 real_cost = 340.169 SP3_TS4 costs 0 real_cost = 342.166 SP3_TS3-scwrl costs 0 real_cost = 232.926 SP3_TS3 costs 0 real_cost = 238.677 SP3_TS2-scwrl costs 0 real_cost = 299.589 SP3_TS2 costs 0 real_cost = 301.885 SP3_TS1-scwrl costs 0 real_cost = -275.668 SP3_TS1 costs 0 real_cost = -274.493 SAM_T06_server_TS5-scwrl costs 0 real_cost = 663.364 SAM_T06_server_TS5 costs 0 real_cost = 598.947 SAM_T06_server_TS4-scwrl costs 0 real_cost = 585.38 SAM_T06_server_TS4 costs 0 real_cost = 520.808 SAM_T06_server_TS3-scwrl costs 0 real_cost = 487.401 SAM_T06_server_TS3 costs 0 real_cost = 439.522 SAM_T06_server_TS2-scwrl costs 0 real_cost = 153.036 SAM_T06_server_TS2 costs 0 real_cost = 86.734 SAM_T06_server_TS1-scwrl costs 0 real_cost = -97.2857 SAM_T06_server_TS1 costs 0 real_cost = -98.561 SAM-T99_AL5-scwrl costs 0 real_cost = 601.396 SAM-T99_AL5 costs 0 real_cost = 811.812 SAM-T99_AL4-scwrl costs 0 real_cost = -178.694 SAM-T99_AL4 costs 0 real_cost = 190.96 SAM-T99_AL3-scwrl costs 0 real_cost = -227.413 SAM-T99_AL3 costs 0 real_cost = 164.319 SAM-T99_AL2-scwrl costs 0 real_cost = -231.058 SAM-T99_AL2 costs 0 real_cost = 161.146 SAM-T99_AL1-scwrl costs 0 real_cost = -230.131 SAM-T99_AL1 costs 0 real_cost = 163.419 SAM-T02_AL5-scwrl costs 0 real_cost = 715.735 SAM-T02_AL5 costs 0 real_cost = 897.497 SAM-T02_AL4-scwrl costs 0 real_cost = 477.712 SAM-T02_AL4 costs 0 real_cost = 716.725 SAM-T02_AL3-scwrl costs 0 real_cost = 498.106 SAM-T02_AL3 costs 0 real_cost = 735.767 SAM-T02_AL2-scwrl costs 0 real_cost = 456.36 SAM-T02_AL2 costs 0 real_cost = 720.654 SAM-T02_AL1-scwrl costs 0 real_cost = 22.1955 SAM-T02_AL1 costs 0 real_cost = 413.459 ROKKY_TS1-scwrl costs 0 real_cost = -239.396 ROKKY_TS1 costs 0 real_cost = -243.103 ROBETTA_TS5-scwrl costs 0 real_cost = -265.395 ROBETTA_TS5 costs 0 real_cost = -270.465 ROBETTA_TS4-scwrl costs 0 real_cost = -269.432 ROBETTA_TS4 costs 0 real_cost = -274.285 ROBETTA_TS3-scwrl costs 0 real_cost = -257.255 ROBETTA_TS3 costs 0 real_cost = -260.972 ROBETTA_TS2-scwrl costs 0 real_cost = -256.259 ROBETTA_TS2 costs 0 real_cost = -261.29 ROBETTA_TS1-scwrl costs 0 real_cost = -261.213 ROBETTA_TS1 costs 0 real_cost = -268.094 RAPTOR_TS5-scwrl costs 0 real_cost = 416.22 RAPTOR_TS5 costs 0 real_cost = 416.054 RAPTOR_TS4-scwrl costs 0 real_cost = 224.778 RAPTOR_TS4 costs 0 real_cost = 228.48 RAPTOR_TS3-scwrl costs 0 real_cost = 362.981 RAPTOR_TS3 costs 0 real_cost = 366.171 RAPTOR_TS2-scwrl costs 0 real_cost = 210.139 RAPTOR_TS2 costs 0 real_cost = 215.361 RAPTOR_TS1-scwrl costs 0 real_cost = -246.94 RAPTOR_TS1 costs 0 real_cost = -249.391 RAPTORESS_TS5-scwrl costs 0 real_cost = 238.07 RAPTORESS_TS5 costs 0 real_cost = 246.859 RAPTORESS_TS4-scwrl costs 0 real_cost = 331.469 RAPTORESS_TS4 costs 0 real_cost = 334.933 RAPTORESS_TS3-scwrl costs 0 real_cost = 220.587 RAPTORESS_TS3 costs 0 real_cost = 226.076 RAPTORESS_TS2-scwrl costs 0 real_cost = -221.997 RAPTORESS_TS2 costs 0 real_cost = -220.195 RAPTORESS_TS1-scwrl costs 0 real_cost = -221.997 RAPTORESS_TS1 costs 0 real_cost = -220.195 RAPTOR-ACE_TS5-scwrl costs 0 real_cost = -29.6743 RAPTOR-ACE_TS5 costs 0 real_cost = -34.1388 RAPTOR-ACE_TS4-scwrl costs 0 real_cost = -275.668 RAPTOR-ACE_TS4 costs 0 real_cost = -274.493 RAPTOR-ACE_TS3-scwrl costs 0 real_cost = -243.149 RAPTOR-ACE_TS3 costs 0 real_cost = -238.649 RAPTOR-ACE_TS2-scwrl costs 0 real_cost = -282.96 RAPTOR-ACE_TS2 costs 0 real_cost = -281.361 RAPTOR-ACE_TS1-scwrl costs 0 real_cost = -249.442 RAPTOR-ACE_TS1 costs 0 real_cost = -249.094 Pmodeller6_TS5-scwrl costs 0 real_cost = -269.432 Pmodeller6_TS5 costs 0 real_cost = -274.285 Pmodeller6_TS4-scwrl costs 0 real_cost = -265.395 Pmodeller6_TS4 costs 0 real_cost = -270.465 Pmodeller6_TS3-scwrl costs 0 real_cost = -261.213 Pmodeller6_TS3 costs 0 real_cost = -268.094 Pmodeller6_TS2-scwrl costs 0 real_cost = -211.248 Pmodeller6_TS2 costs 0 real_cost = -220.087 Pmodeller6_TS1-scwrl costs 0 real_cost = -257.255 Pmodeller6_TS1 costs 0 real_cost = -260.972 Phyre-2_TS5-scwrl costs 0 real_cost = -208.4 Phyre-2_TS5 costs 0 real_cost = -207.66 Phyre-2_TS4-scwrl costs 0 real_cost = -207.99 Phyre-2_TS4 costs 0 real_cost = -207.25 Phyre-2_TS3-scwrl costs 0 real_cost = -208.217 Phyre-2_TS3 costs 0 real_cost = -207.395 Phyre-2_TS2-scwrl costs 0 real_cost = -204.031 Phyre-2_TS2 costs 0 real_cost = -203.765 Phyre-2_TS1-scwrl costs 0 real_cost = -203.656 Phyre-2_TS1 costs 0 real_cost = -203.273 Phyre-1_TS1-scwrl costs 0 real_cost = 447.17 Phyre-1_TS1 costs 0 real_cost = 440.525 Pcons6_TS5-scwrl costs 0 real_cost = -200.696 Pcons6_TS5 costs 0 real_cost = -204.4 Pcons6_TS4-scwrl costs 0 real_cost = -211.248 Pcons6_TS4 costs 0 real_cost = -220.087 Pcons6_TS3-scwrl costs 0 real_cost = -199.726 Pcons6_TS3 costs 0 real_cost = -200.082 Pcons6_TS2-scwrl costs 0 real_cost = -208.215 Pcons6_TS2 costs 0 real_cost = -208.087 Pcons6_TS1-scwrl costs 0 real_cost = -200.264 Pcons6_TS1 costs 0 real_cost = -204.276 PROTINFO_TS5-scwrl costs 0 real_cost = -256.916 PROTINFO_TS5 costs 0 real_cost = -255.835 PROTINFO_TS4-scwrl costs 0 real_cost = -257.612 PROTINFO_TS4 costs 0 real_cost = -258.545 PROTINFO_TS3-scwrl costs 0 real_cost = -248.757 PROTINFO_TS3 costs 0 real_cost = -255.711 PROTINFO_TS2-scwrl costs 0 real_cost = -242.514 PROTINFO_TS2 costs 0 real_cost = -251.922 PROTINFO_TS1-scwrl costs 0 real_cost = -272.713 PROTINFO_TS1 costs 0 real_cost = -276.883 PROTINFO-AB_TS5-scwrl costs 0 real_cost = -234.133 PROTINFO-AB_TS5 costs 0 real_cost = -237.474 PROTINFO-AB_TS4-scwrl costs 0 real_cost = -241.794 PROTINFO-AB_TS4 costs 0 real_cost = -245.024 PROTINFO-AB_TS3-scwrl costs 0 real_cost = -238.966 PROTINFO-AB_TS3 costs 0 real_cost = -244.055 PROTINFO-AB_TS2-scwrl costs 0 real_cost = -241.312 PROTINFO-AB_TS2 costs 0 real_cost = -243.066 PROTINFO-AB_TS1-scwrl costs 0 real_cost = -244.313 PROTINFO-AB_TS1 costs 0 real_cost = -246.873 NN_PUT_lab_TS1-scwrl costs 0 real_cost = -282.877 NN_PUT_lab_TS1 costs 0 real_cost = -284.58 MetaTasser_TS5-scwrl costs 0 real_cost = 131.473 MetaTasser_TS5 costs 0 real_cost = 137.457 MetaTasser_TS4-scwrl costs 0 real_cost = 180.144 MetaTasser_TS3-scwrl costs 0 real_cost = 201.958 MetaTasser_TS3 costs 0 real_cost = 204.286 MetaTasser_TS2-scwrl costs 0 real_cost = -148.819 MetaTasser_TS2 costs 0 real_cost = -144.897 MetaTasser_TS1-scwrl costs 0 real_cost = -236.153 MetaTasser_TS1 costs 0 real_cost = -229.393 Ma-OPUS-server_TS5-scwrl costs 0 real_cost = 322.542 Ma-OPUS-server_TS5 costs 0 real_cost = 327.404 Ma-OPUS-server_TS4-scwrl costs 0 real_cost = 308.971 Ma-OPUS-server_TS4 costs 0 real_cost = 311.296 Ma-OPUS-server_TS3-scwrl costs 0 real_cost = 215.212 Ma-OPUS-server_TS3 costs 0 real_cost = 219.118 Ma-OPUS-server_TS2-scwrl costs 0 real_cost = 244.254 Ma-OPUS-server_TS2 costs 0 real_cost = 248.178 Ma-OPUS-server_TS1-scwrl costs 0 real_cost = -272.361 Ma-OPUS-server_TS1 costs 0 real_cost = -270.347 Ma-OPUS-server2_TS5-scwrl costs 0 real_cost = 260.329 Ma-OPUS-server2_TS5 costs 0 real_cost = 261.539 Ma-OPUS-server2_TS4-scwrl costs 0 real_cost = 297.82 Ma-OPUS-server2_TS4 costs 0 real_cost = 301.796 Ma-OPUS-server2_TS3-scwrl costs 0 real_cost = 242.201 Ma-OPUS-server2_TS3 costs 0 real_cost = 246.31 Ma-OPUS-server2_TS2-scwrl costs 0 real_cost = 356.835 Ma-OPUS-server2_TS1-scwrl costs 0 real_cost = -272.361 Ma-OPUS-server2_TS1 costs 0 real_cost = -270.347 LOOPP_TS5-scwrl costs 0 real_cost = 468.782 LOOPP_TS5 costs 0 real_cost = 473.555 LOOPP_TS4-scwrl costs 0 real_cost = 274.882 LOOPP_TS4 costs 0 real_cost = 276.874 LOOPP_TS3-scwrl costs 0 real_cost = 261.611 LOOPP_TS3 costs 0 real_cost = 259.836 LOOPP_TS2-scwrl costs 0 real_cost = 273.93 LOOPP_TS2 costs 0 real_cost = 277.175 LOOPP_TS1-scwrl costs 0 real_cost = -183.334 LOOPP_TS1 costs 0 real_cost = -185.393 Huber-Torda-Server_TS5-scwrl costs 0 real_cost = 710.026 Huber-Torda-Server_TS5 costs 0 real_cost = 842.194 Huber-Torda-Server_TS4-scwrl costs 0 real_cost = 705.534 Huber-Torda-Server_TS4 costs 0 real_cost = 830.642 Huber-Torda-Server_TS3-scwrl costs 0 real_cost = 593.348 Huber-Torda-Server_TS3 costs 0 real_cost = 781.777 Huber-Torda-Server_TS2-scwrl costs 0 real_cost = 648.591 Huber-Torda-Server_TS2 costs 0 real_cost = 821.431 Huber-Torda-Server_TS1-scwrl costs 0 real_cost = -235.511 Huber-Torda-Server_TS1 costs 0 real_cost = 62.5535 HHpred3_TS1-scwrl costs 0 real_cost = -242.021 HHpred3_TS1 costs 0 real_cost = -246.216 HHpred2_TS1-scwrl costs 0 real_cost = -242.021 HHpred2_TS1 costs 0 real_cost = -246.216 HHpred1_TS1-scwrl costs 0 real_cost = -242.021 HHpred1_TS1 costs 0 real_cost = -246.216 GeneSilicoMetaServer_TS5-scwrl costs 0 real_cost = -32.2595 GeneSilicoMetaServer_TS5 costs 0 real_cost = -33.3203 GeneSilicoMetaServer_TS4-scwrl costs 0 real_cost = -239.052 GeneSilicoMetaServer_TS4 costs 0 real_cost = -240.85 GeneSilicoMetaServer_TS3-scwrl costs 0 real_cost = -280.192 GeneSilicoMetaServer_TS3 costs 0 real_cost = -279.437 GeneSilicoMetaServer_TS2-scwrl costs 0 real_cost = -277.945 GeneSilicoMetaServer_TS2 costs 0 real_cost = -279.103 GeneSilicoMetaServer_TS1-scwrl costs 0 real_cost = -243.054 GeneSilicoMetaServer_TS1 costs 0 real_cost = -244.056 FUNCTION_TS5-scwrl costs 0 real_cost = -231.043 FUNCTION_TS5 costs 0 real_cost = -239.425 FUNCTION_TS4-scwrl costs 0 real_cost = -250.679 FUNCTION_TS4 costs 0 real_cost = -258.428 FUNCTION_TS3-scwrl costs 0 real_cost = -253.362 FUNCTION_TS3 costs 0 real_cost = -259.66 FUNCTION_TS2-scwrl costs 0 real_cost = -252.613 FUNCTION_TS2 costs 0 real_cost = -250.999 FUNCTION_TS1-scwrl costs 0 real_cost = -242.938 FUNCTION_TS1 costs 0 real_cost = -251.948 FUGUE_AL5-scwrl costs 0 real_cost = 569.102 FUGUE_AL5 costs 0 real_cost = 840.792 FUGUE_AL4-scwrl costs 0 real_cost = 625.927 FUGUE_AL4 costs 0 real_cost = 881.674 FUGUE_AL3-scwrl costs 0 real_cost = 635.218 FUGUE_AL3 costs 0 real_cost = 892.974 FUGUE_AL2-scwrl costs 0 real_cost = 917.55 FUGUE_AL2 costs 0 real_cost = 1041.62 FUGUE_AL1-scwrl costs 0 real_cost = -245.614 FUGUE_AL1 costs 0 real_cost = 152.053 FUGMOD_TS5-scwrl costs 0 real_cost = 386.912 FUGMOD_TS5 costs 0 real_cost = 388.549 FUGMOD_TS4-scwrl costs 0 real_cost = 423.215 FUGMOD_TS4 costs 0 real_cost = 430.179 FUGMOD_TS3-scwrl costs 0 real_cost = 368.896 FUGMOD_TS3 costs 0 real_cost = 372.581 FUGMOD_TS2-scwrl costs 0 real_cost = 893.275 FUGMOD_TS2 costs 0 real_cost = 893.665 FUGMOD_TS1-scwrl costs 0 real_cost = -265.455 FUGMOD_TS1 costs 0 real_cost = -269.296 FPSOLVER-SERVER_TS5-scwrl costs 0 real_cost = 376.087 FPSOLVER-SERVER_TS5 costs 0 real_cost = 380.187 FPSOLVER-SERVER_TS4-scwrl costs 0 real_cost = 410.244 FPSOLVER-SERVER_TS4 costs 0 real_cost = 409.877 FPSOLVER-SERVER_TS3-scwrl costs 0 real_cost = 372.96 FPSOLVER-SERVER_TS3 costs 0 real_cost = 377.509 FPSOLVER-SERVER_TS2-scwrl costs 0 real_cost = 390.715 FPSOLVER-SERVER_TS2 costs 0 real_cost = 391.437 FPSOLVER-SERVER_TS1-scwrl costs 0 real_cost = 381.385 FPSOLVER-SERVER_TS1 costs 0 real_cost = 386.602 FORTE2_AL5-scwrl costs 0 real_cost = 368.904 FORTE2_AL5 costs 0 real_cost = 751.22 FORTE2_AL4-scwrl costs 0 real_cost = 367.942 FORTE2_AL4 costs 0 real_cost = 766.233 FORTE2_AL3-scwrl costs 0 real_cost = 566.412 FORTE2_AL3 costs 0 real_cost = 845.77 FORTE2_AL2-scwrl costs 0 real_cost = 361.673 FORTE2_AL2 costs 0 real_cost = 750.333 FORTE2_AL1-scwrl costs 0 real_cost = 110.282 FORTE2_AL1 costs 0 real_cost = 496.805 FORTE1_AL5-scwrl costs 0 real_cost = 355.911 FORTE1_AL5 costs 0 real_cost = 736.058 FORTE1_AL4-scwrl costs 0 real_cost = 567.298 FORTE1_AL4 costs 0 real_cost = 824.923 FORTE1_AL3-scwrl costs 0 real_cost = 372.417 FORTE1_AL3 costs 0 real_cost = 759.42 FORTE1_AL2-scwrl costs 0 real_cost = 570.19 FORTE1_AL2 costs 0 real_cost = 849.572 FORTE1_AL1-scwrl costs 0 real_cost = 81.7163 FORTE1_AL1 costs 0 real_cost = 472.336 FOLDpro_TS5-scwrl costs 0 real_cost = -240.795 FOLDpro_TS5 costs 0 real_cost = -248 FOLDpro_TS4-scwrl costs 0 real_cost = -278.241 FOLDpro_TS4 costs 0 real_cost = -281.069 FOLDpro_TS3-scwrl costs 0 real_cost = -278.241 FOLDpro_TS3 costs 0 real_cost = -281.069 FOLDpro_TS2-scwrl costs 0 real_cost = -275.106 FOLDpro_TS2 costs 0 real_cost = -279.567 FOLDpro_TS1-scwrl costs 0 real_cost = -273.761 FOLDpro_TS1 costs 0 real_cost = -277.605 FAMS_TS5-scwrl costs 0 real_cost = -238.873 FAMS_TS5 costs 0 real_cost = -243.75 FAMS_TS4-scwrl costs 0 real_cost = -238.873 FAMS_TS4 costs 0 real_cost = -243.75 FAMS_TS3-scwrl costs 0 real_cost = -252.278 FAMS_TS3 costs 0 real_cost = -251.577 FAMS_TS2-scwrl costs 0 real_cost = -241.268 FAMS_TS2 costs 0 real_cost = -245.522 FAMS_TS1-scwrl costs 0 real_cost = -248.259 FAMS_TS1 costs 0 real_cost = -252.606 FAMSD_TS5-scwrl costs 0 real_cost = -243.056 FAMSD_TS5 costs 0 real_cost = -247.841 FAMSD_TS4-scwrl costs 0 real_cost = -202.1 FAMSD_TS4 costs 0 real_cost = -210.271 FAMSD_TS3-scwrl costs 0 real_cost = -234.031 FAMSD_TS3 costs 0 real_cost = -242.568 FAMSD_TS2-scwrl costs 0 real_cost = -237.038 FAMSD_TS2 costs 0 real_cost = -243.741 FAMSD_TS1-scwrl costs 0 real_cost = -265.615 FAMSD_TS1 costs 0 real_cost = -264.292 Distill_TS5-scwrl costs 0 real_cost = 1034.43 Distill_TS4-scwrl costs 0 real_cost = 1036.3 Distill_TS3-scwrl costs 0 real_cost = 1033.68 Distill_TS2-scwrl costs 0 real_cost = 1033.02 Distill_TS1-scwrl costs 0 real_cost = 1020.21 CaspIta-FOX_TS5-scwrl costs 0 real_cost = 465.197 CaspIta-FOX_TS5 costs 0 real_cost = 459.816 CaspIta-FOX_TS4-scwrl costs 0 real_cost = 523.094 CaspIta-FOX_TS4 costs 0 real_cost = 513.632 CaspIta-FOX_TS3-scwrl costs 0 real_cost = 458.881 CaspIta-FOX_TS3 costs 0 real_cost = 439.55 CaspIta-FOX_TS2-scwrl costs 0 real_cost = 406.527 CaspIta-FOX_TS2 costs 0 real_cost = 402.724 CaspIta-FOX_TS1-scwrl costs 0 real_cost = -246.42 CaspIta-FOX_TS1 costs 0 real_cost = -256.41 CPHmodels_TS1-scwrl costs 0 real_cost = -226.374 CPHmodels_TS1 costs 0 real_cost = -232.966 CIRCLE_TS5-scwrl costs 0 real_cost = -268.579 CIRCLE_TS5 costs 0 real_cost = -273.277 CIRCLE_TS4-scwrl costs 0 real_cost = -238.873 CIRCLE_TS4 costs 0 real_cost = -243.75 CIRCLE_TS3-scwrl costs 0 real_cost = -255.295 CIRCLE_TS3 costs 0 real_cost = -258.64 CIRCLE_TS2-scwrl costs 0 real_cost = -241.268 CIRCLE_TS2 costs 0 real_cost = -245.522 CIRCLE_TS1-scwrl costs 0 real_cost = -252.278 CIRCLE_TS1 costs 0 real_cost = -251.577 Bilab-ENABLE_TS4-scwrl costs 0 real_cost = -222.927 Bilab-ENABLE_TS4 costs 0 real_cost = -223.136 Bilab-ENABLE_TS3-scwrl costs 0 real_cost = -214.27 Bilab-ENABLE_TS3 costs 0 real_cost = -214.27 Bilab-ENABLE_TS2-scwrl costs 0 real_cost = -285.301 Bilab-ENABLE_TS2 costs 0 real_cost = -285.282 Bilab-ENABLE_TS1-scwrl costs 0 real_cost = -228.854 Bilab-ENABLE_TS1 costs 0 real_cost = -228.457 BayesHH_TS1-scwrl costs 0 real_cost = -242.021 BayesHH_TS1 costs 0 real_cost = -246.216 ABIpro_TS5-scwrl costs 0 real_cost = 332.594 ABIpro_TS5 costs 0 real_cost = 332.598 ABIpro_TS4-scwrl costs 0 real_cost = 330.7 ABIpro_TS4 costs 0 real_cost = 329.646 ABIpro_TS3-scwrl costs 0 real_cost = 319.963 ABIpro_TS3 costs 0 real_cost = 319.038 ABIpro_TS2-scwrl costs 0 real_cost = 324.344 ABIpro_TS2 costs 0 real_cost = 323.864 ABIpro_TS1-scwrl costs 0 real_cost = 324.881 ABIpro_TS1 costs 0 real_cost = 324.87 3Dpro_TS5-scwrl costs 0 real_cost = -227.271 3Dpro_TS5 costs 0 real_cost = -235.383 3Dpro_TS4-scwrl costs 0 real_cost = -269.149 3Dpro_TS4 costs 0 real_cost = -275.304 3Dpro_TS3-scwrl costs 0 real_cost = -275.55 3Dpro_TS3 costs 0 real_cost = -277.382 3Dpro_TS2-scwrl costs 0 real_cost = -275.624 3Dpro_TS2 costs 0 real_cost = -275.54 3Dpro_TS1-scwrl costs 0 real_cost = -273.761 3Dpro_TS1 costs 0 real_cost = -277.605 3D-JIGSAW_TS4-scwrl costs 0 real_cost = -224.156 3D-JIGSAW_TS4 costs 0 real_cost = -220.013 3D-JIGSAW_TS3-scwrl costs 0 real_cost = -222.013 3D-JIGSAW_TS3 costs 0 real_cost = -221.646 3D-JIGSAW_TS2-scwrl costs 0 real_cost = -222.094 3D-JIGSAW_TS2 costs 0 real_cost = -220.704 3D-JIGSAW_TS1-scwrl costs 0 real_cost = -154.465 3D-JIGSAW_TS1 costs 0 real_cost = -156.821 3D-JIGSAW_RECOM_TS5-scwrl costs 0 real_cost = -228.455 3D-JIGSAW_RECOM_TS5 costs 0 real_cost = -235.287 3D-JIGSAW_RECOM_TS4-scwrl costs 0 real_cost = -222.033 3D-JIGSAW_RECOM_TS4 costs 0 real_cost = -225.565 3D-JIGSAW_RECOM_TS3-scwrl costs 0 real_cost = -223.313 3D-JIGSAW_RECOM_TS3 costs 0 real_cost = -229.202 3D-JIGSAW_RECOM_TS2-scwrl costs 0 real_cost = -224.629 3D-JIGSAW_RECOM_TS2 costs 0 real_cost = -231.05 3D-JIGSAW_RECOM_TS1-scwrl costs 0 real_cost = -229.145 3D-JIGSAW_RECOM_TS1 costs 0 real_cost = -234.305 3D-JIGSAW_POPULUS_TS5-scwrl costs 0 real_cost = -219.265 3D-JIGSAW_POPULUS_TS5 costs 0 real_cost = -225.438 3D-JIGSAW_POPULUS_TS4-scwrl costs 0 real_cost = -206.374 3D-JIGSAW_POPULUS_TS4 costs 0 real_cost = -212.624 3D-JIGSAW_POPULUS_TS3-scwrl costs 0 real_cost = -222.003 3D-JIGSAW_POPULUS_TS3 costs 0 real_cost = -227.777 3D-JIGSAW_POPULUS_TS2-scwrl costs 0 real_cost = -221.907 3D-JIGSAW_POPULUS_TS2 costs 0 real_cost = -227.937 3D-JIGSAW_POPULUS_TS1-scwrl costs 0 real_cost = -219.495 3D-JIGSAW_POPULUS_TS1 costs 0 real_cost = -226.378 dimer//dimer-2aqj-from-try8-opt2 costs 0 real_cost = -189.763 dimer//dimer-2aqj-from-try7-opt2 costs 0 real_cost = -189.66 dimer//dimer-2aqj-from-try6-opt2 costs 0 real_cost = -189.178 dimer//try1-opt2.unpack costs 0 real_cost = 395.948 dimer//try1-opt2.unpack.gromacs0.repack-nonPC costs 0 real_cost = 395.869 dimer//try1-opt2.unpack.gromacs0 costs 0 real_cost = 396.392 dimer//try1-opt2.repack-nonPC costs 0 real_cost = 396.087 dimer//try1-opt2 costs 0 real_cost = 395.948 dimer//try1-opt1 costs 0 real_cost = 398.205 dimer//try1-opt1-scwrl costs 0 real_cost = 398.456 T0334.try9-opt2.repack-nonPC.pdb.gz costs 0 real_cost = -189.675 T0334.try9-opt2.pdb.gz costs 0 real_cost = -187.665 T0334.try9-opt2.gromacs0.repack-nonPC.pdb.gz costs 0 real_cost = -189.803 T0334.try9-opt2.gromacs0.pdb.gz costs 0 real_cost = -188.585 T0334.try9-opt1.pdb.gz costs 0 real_cost = -187.408 T0334.try9-opt1-scwrl.pdb.gz costs 0 real_cost = -189.116 T0334.try8-opt2.repack-nonPC.pdb.gz costs 0 real_cost = -189.762 T0334.try8-opt2.pdb.gz costs 0 real_cost = -189.809 T0334.try8-opt2.gromacs0.repack-nonPC.pdb.gz costs 0 real_cost = -187.575 T0334.try8-opt2.gromacs0.pdb.gz costs 0 real_cost = -189.056 T0334.try8-opt1.pdb.gz costs 0 real_cost = -189.393 T0334.try8-opt1-scwrl.pdb.gz costs 0 real_cost = -190.528 T0334.try7-opt2.repack-nonPC.pdb.gz costs 0 real_cost = -188.252 T0334.try7-opt2.pdb.gz costs 0 real_cost = -189.671 T0334.try7-opt2.gromacs0.repack-nonPC.pdb.gz costs 0 real_cost = -188.11 T0334.try7-opt2.gromacs0.pdb.gz costs 0 real_cost = -190.065 T0334.try7-opt1.pdb.gz costs 0 real_cost = -190.641 T0334.try7-opt1-scwrl.pdb.gz costs 0 real_cost = -189.488 T0334.try6-opt2.repack-nonPC.pdb.gz costs 0 real_cost = -187.65 T0334.try6-opt2.pdb.gz costs 0 real_cost = -189.226 T0334.try6-opt2.gromacs0.repack-nonPC.pdb.gz costs 0 real_cost = -188.878 T0334.try6-opt2.gromacs0.pdb.gz costs 0 real_cost = -190.141 T0334.try6-opt1.pdb.gz costs 0 real_cost = -189.764 T0334.try6-opt1-scwrl.pdb.gz costs 0 real_cost = -188.073 T0334.try3-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 7.79645 T0334.try3-opt2.pdb.gz costs 0 real_cost = 5.94242 T0334.try3-opt2.gromacs0.repack-nonPC.pdb.gz costs 0 real_cost = 5.60245 T0334.try3-opt2.gromacs0.pdb.gz costs 0 real_cost = 7.22814 T0334.try3-opt1.pdb.gz costs 0 real_cost = 3.78513 T0334.try3-opt1-scwrl.pdb.gz costs 0 real_cost = 5.09765 T0334.try2-opt2.repack-nonPC.pdb.gz costs 0 real_cost = -192.036 T0334.try2-opt2.pdb.gz costs 0 real_cost = -188.088 T0334.try2-opt2.gromacs0.repack-nonPC.pdb.gz costs 0 real_cost = -186.739 T0334.try2-opt2.gromacs0.pdb.gz costs 0 real_cost = -186.841 T0334.try2-opt1.pdb.gz costs 0 real_cost = -185.827 T0334.try2-opt1-scwrl.pdb.gz costs 0 real_cost = -187.016 T0334.try17-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 7.03322 T0334.try17-opt2.pdb.gz costs 0 real_cost = 6.46623 T0334.try17-opt2.gromacs0.repack-nonPC.pdb.gz costs 0 real_cost = 7.15849 T0334.try17-opt2.gromacs0.pdb.gz costs 0 real_cost = 6.09993 T0334.try17-opt1.pdb.gz costs 0 real_cost = 4.74915 T0334.try17-opt1-scwrl.pdb.gz costs 0 real_cost = 7.43635 T0334.try16-opt2.repack-nonPC.pdb.gz costs 0 real_cost = -220.453 T0334.try16-opt2.pdb.gz costs 0 real_cost = -220.64 T0334.try16-opt2.gromacs0.repack-nonPC.pdb.gz costs 0 real_cost = -220.838 T0334.try16-opt2.gromacs0.pdb.gz costs 0 real_cost = -218.7 T0334.try16-opt1.pdb.gz costs 0 real_cost = -217.878 T0334.try16-opt1-scwrl.pdb.gz costs 0 real_cost = -216.553 T0334.try15-opt2.repack-nonPC.pdb.gz costs 0 real_cost = -207.578 T0334.try15-opt2.pdb.gz costs 0 real_cost = -205.149 T0334.try15-opt2.gromacs0.repack-nonPC.pdb.gz costs 0 real_cost = -208.341 T0334.try15-opt2.gromacs0.pdb.gz costs 0 real_cost = -203.115 T0334.try15-opt1.pdb.gz costs 0 real_cost = -203.009 T0334.try15-opt1-scwrl.pdb.gz costs 0 real_cost = -202.707 T0334.try14-opt2.repack-nonPC.pdb.gz costs 0 real_cost = -188.852 T0334.try14-opt2.pdb.gz costs 0 real_cost = -188.724 T0334.try14-opt2.gromacs0.repack-nonPC.pdb.gz costs 0 real_cost = -188.026 T0334.try14-opt2.gromacs0.pdb.gz costs 0 real_cost = -188.6 T0334.try14-opt1.pdb.gz costs 0 real_cost = -189.806 T0334.try14-opt1-scwrl.pdb.gz costs 0 real_cost = -190.153 T0334.try13-opt2.repack-nonPC.pdb.gz costs 0 real_cost = -191.159 T0334.try13-opt2.pdb.gz costs 0 real_cost = -189.771 T0334.try13-opt2.gromacs0.repack-nonPC.pdb.gz costs 0 real_cost = -189.751 T0334.try13-opt2.gromacs0.pdb.gz costs 0 real_cost = -188.209 T0334.try13-opt1.pdb.gz costs 0 real_cost = -189.379 T0334.try13-opt1-scwrl.pdb.gz costs 0 real_cost = -189.837 T0334.try12-opt2.repack-nonPC.pdb.gz costs 0 real_cost = -188.136 T0334.try12-opt2.pdb.gz costs 0 real_cost = -189.551 T0334.try12-opt2.gromacs0.repack-nonPC.pdb.gz costs 0 real_cost = -187.843 T0334.try12-opt2.gromacs0.pdb.gz costs 0 real_cost = -188.324 T0334.try12-opt1.pdb.gz costs 0 real_cost = -189.39 T0334.try12-opt1-scwrl.pdb.gz costs 0 real_cost = -186.41 T0334.try11-opt2.repack-nonPC.pdb.gz costs 0 real_cost = -191.759 T0334.try11-opt2.pdb.gz costs 0 real_cost = -189.265 T0334.try11-opt2.gromacs0.repack-nonPC.pdb.gz costs 0 real_cost = -185.748 T0334.try11-opt2.gromacs0.pdb.gz costs 0 real_cost = -188.796 T0334.try11-opt1.pdb.gz costs 0 real_cost = -189.813 T0334.try11-opt1-scwrl.pdb.gz costs 0 real_cost = -189.921 T0334.try10-opt2.repack-nonPC.pdb.gz costs 0 real_cost = -190.748 T0334.try10-opt2.pdb.gz costs 0 real_cost = -189.828 T0334.try10-opt2.gromacs0.repack-nonPC.pdb.gz costs 0 real_cost = -188.875 T0334.try10-opt2.gromacs0.pdb.gz costs 0 real_cost = -188.858 T0334.try10-opt1.pdb.gz costs 0 real_cost = -189.884 T0334.try10-opt1-scwrl.pdb.gz costs 0 real_cost = -190.945 T0334.try1-opt2.repack-nonPC.pdb.gz costs 0 real_cost = -217.427 T0334.try1-opt2.pdb.gz costs 0 real_cost = -218.082 T0334.try1-opt2.gromacs0.repack-nonPC.pdb.gz costs 0 real_cost = -218.514 T0334.try1-opt2.gromacs0.pdb.gz costs 0 real_cost = -218.805 T0334.try1-opt1.pdb.gz costs 0 real_cost = -224.613 T0334.try1-opt1-scwrl.pdb.gz costs 0 real_cost = -225.538 ../model5.ts-submitted costs 0 real_cost = 84.5057 ../model4.ts-submitted costs 0 real_cost = -205.17 ../model3.ts-submitted costs 0 real_cost = -220.533 ../model2.ts-submitted costs 0 real_cost = -187.905 ../model1.ts-submitted costs 0 real_cost = -188.686 align5 costs 0 real_cost = 439.781 align4 costs 0 real_cost = 425.23 align3 costs 0 real_cost = 605.268 align2 costs 0 real_cost = 444.289 align1 costs 0 real_cost = 71.0469 T0334.try1-opt2.pdb costs 0 real_cost = -218.083 model5-scwrl costs 0 real_cost = 148.688 model5.ts-submitted costs 0 real_cost = 84.5057 model4-scwrl costs 0 real_cost = -206.168 model4.ts-submitted costs 0 real_cost = -205.17 model3-scwrl costs 0 real_cost = -218.791 model3.ts-submitted costs 0 real_cost = -220.533 model2-scwrl costs 0 real_cost = -188.768 model2.ts-submitted costs 0 real_cost = -187.905 model1-scwrl costs 0 real_cost = -188.863 model1.ts-submitted costs 0 real_cost = -188.683 2oalA costs 0 real_cost = -878.4 # command:CPU_time= 8473.13 sec, elapsed time= 12214.6 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 mv: cannot stat `decoys/evaluate.pretty': No such file or directory make: [decoys/evaluate.pretty] Error 1 (ignored) /projects/compbio/experiments/protein-predict/casp7/scripts/prettyscore -terse -targpfx -decpoint < decoys/evaluate.rdb > decoys/evaluate.pretty make: *** No rule to make target `decoys/evaluate_1.rdb'. make: Target `decoys/evaluate_1.pretty' not remade because of errors. /projects/compbio/experiments/protein-predict/casp7/starter-directory/Make.main:725: SECONDARY_TARGET = T0334.t06.str2 make: *** No rule to make target `decoys/evaluate_1.rdb'. make: Target `decoys/evaluate_1.pretty' not remade because of errors. /projects/compbio/experiments/protein-predict/casp7/starter-directory/Make.main:725: SECONDARY_TARGET = T0334.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/T0334.} ;\ 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_1.rdb sed -e s/XXX0000/T0334/ -e s/START_COL/1/ \ -e s/REAL_PDB/2oalA/ \ -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 1175489110 # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading monomeric-50pc.atoms # trans (non-proline) backbone unit: # CA= -2.2088 1.0126 -0.0031 # O= -0.1499 2.2440 0.0017 # C= -0.6889 1.1368 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4581 0.0000 0.0000 # cis backbone unit: # CA= -0.1462 2.4515 0.0018 # O= -2.0272 0.9713 0.0022 # C= -0.8006 1.0755 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4659 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2099 1.0634 -0.0014 # O= -0.1233 2.2459 0.0075 # C= -0.6871 1.1518 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading monomeric-50pc.atoms have 448 chains in training database # Count of chains,residues,atoms: 448,112605,876684 # 109826 residues have no bad marker # 665 residues lack atoms needed to compute omega # 322 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 6 # HAS_OXT 325 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 523 # HAS_UNKNOWN_ATOMS 2 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 208 # NON_PLANAR_PEPTIDE 143 # BAD_PEPTIDE 1959 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-1332.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:CPU_time= 4.6253 sec, elapsed time= 4.77701 sec) # command:# Reading spots from monomeric-50pc-dry-5.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-5.hist # created burial cost function dry5 with radius 5 with spots at monomeric-50pc-dry-5.spot # command:# Reading spots from monomeric-50pc-wet-6.5.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-wet-6.5.hist # created burial cost function wet6.5 with radius 6.5 with spots at monomeric-50pc-wet-6.5.spot # command:# Reading spots from monomeric-50pc-dry-6.5.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-6.5.hist # created burial cost function dry6.5 with radius 6.5 with spots at monomeric-50pc-dry-6.5.spot # command:# Reading spots from monomeric-50pc-generic-6.5.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-generic-6.5.hist # created burial cost function gen6.5 with radius 6.5 with spots at monomeric-50pc-generic-6.5.spot # command:# Reading spots from near-backbone-center.spot # reading histogram from smoothed-near-backbone-2spot.hist # Reading spots from near-backbone-count.spot # created burial cost function near_backbone with radius 9.65 with spots at near-backbone-center.spot counting only near-backbone-count.spot # command:# Reading spots from way-back-center.spot # reading histogram from smoothed-way-back-2spot.hist # Reading spots from way-back-count.spot # created burial cost function way_back with radius 8.9 with spots at way-back-center.spot counting only way-back-count.spot # command:# Reading spots from monomeric-50pc-dry-8.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-8.hist # created burial cost function dry8 with radius 8 with spots at monomeric-50pc-dry-8.spot # command:# Reading spots from monomeric-50pc-dry-10.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-10.hist # created burial cost function dry10 with radius 10 with spots at monomeric-50pc-dry-10.spot # command:# Reading spots from monomeric-50pc-dry-12.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-12.hist # created burial cost function dry12 with radius 12 with spots at monomeric-50pc-dry-12.spot # command:# reading histogram from dunbrack-2191-alpha.hist # created alpha cost function alpha with offset 0 and 360 bins # command:# reading histogram from dunbrack-2191-alpha-1.hist # created alpha cost function alpha_prev with offset -1 and 360 bins # command:# Prefix for input files set to /projects/compbio/lib/alphabet/ # command:# Read 3 alphabets from alpha.alphabet # command:CPU_time= 4.68529 sec, elapsed time= 4.91094 sec) # command:# Prefix for input files set to # command:# Making conformation for sequence T0334 numbered 1 through 530 Created new target T0334 from T0334.a2m # command:# command:# No conformations to remove in PopConform # command:# cleared Id set # command:# command:# ReadConformPDB reading from PDB file T0334_1.real.pdb looking for model 1 WARNING: atom 4226 has residue number 2 < previous residue 527 in T0334_1.real.pdb # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # command:# Saving current conformation as real # command:# Prefix for output files set to decoys/ # command:# SetRealCost created real_cost = # ( 50 * real_hbond + 50 * real_hbond_u + 50 * decoy_hbond + 50 * decoy_hbond_u + 10 * real_NO_hbond + 10 * real_NO_hbond_u + 10 * decoy_NO_hbond + 10 * decoy_NO_hbond_u + 10 * knot + 200 * clens + 0 * rmsd + 35 * log_rmsd + 0 * rmsd_ca + 30 * log_rmsd_ca + 1 * GDT + 1 * smooth_GDT + 0.2 * missing_atoms ) # command:# SetCost created cost = # ) # command:CPU_time= 6.72198 sec, elapsed time= 7.00178 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 451 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -85.2273 # GDT_score(maxd=8,maxw=2.9)= -87.6839 # GDT_score(maxd=8,maxw=3.2)= -85.5324 # GDT_score(maxd=8,maxw=3.5)= -83.0655 # GDT_score(maxd=10,maxw=3.8)= -84.5295 # GDT_score(maxd=10,maxw=4)= -82.7456 # GDT_score(maxd=10,maxw=4.2)= -80.8038 # GDT_score(maxd=12,maxw=4.3)= -83.3981 # GDT_score(maxd=12,maxw=4.5)= -81.4987 # GDT_score(maxd=12,maxw=4.7)= -79.4669 # GDT_score(maxd=14,maxw=5.2)= -77.5196 # GDT_score(maxd=14,maxw=5.5)= -74.4158 # command:# Prefix for output files set to # command:superimposing iter= 0 total_weight= 6.3500000e+03 rmsd (weighted)= 3.4839350e+00 (unweighted)= 5.2182769e+00 superimposing iter= 1 total_weight= 2.8787183e+04 rmsd (weighted)= 1.0592798e+00 (unweighted)= 5.2126398e+00 superimposing iter= 2 total_weight= 1.1925552e+04 rmsd (weighted)= 6.0955151e-01 (unweighted)= 5.2144104e+00 superimposing iter= 3 total_weight= 5.9045601e+03 rmsd (weighted)= 5.1243083e-01 (unweighted)= 5.2152507e+00 superimposing iter= 4 total_weight= 4.5305699e+03 rmsd (weighted)= 4.9314007e-01 (unweighted)= 5.2157558e+00 superimposing iter= 5 total_weight= 4.2932817e+03 rmsd (weighted)= 4.8776119e-01 (unweighted)= 5.2160669e+00 # command:# Prefix for output files set to decoys/ # command:# request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1150741999.pdb -s /var/tmp/to_scwrl_1150741999.seq -o /var/tmp/from_scwrl_1150741999.pdb > /var/tmp/scwrl_1150741999.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1150741999.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 473 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -85.7481 # GDT_score(maxd=8,maxw=2.9)= -88.0716 # GDT_score(maxd=8,maxw=3.2)= -85.9579 # GDT_score(maxd=8,maxw=3.5)= -83.2777 # GDT_score(maxd=10,maxw=3.8)= -84.7425 # GDT_score(maxd=10,maxw=4)= -82.8113 # GDT_score(maxd=10,maxw=4.2)= -80.757 # GDT_score(maxd=12,maxw=4.3)= -83.4406 # GDT_score(maxd=12,maxw=4.5)= -81.4384 # GDT_score(maxd=12,maxw=4.7)= -79.349 # GDT_score(maxd=14,maxw=5.2)= -77.3325 # GDT_score(maxd=14,maxw=5.5)= -74.1724 # command:# request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_799162803.pdb -s /var/tmp/to_scwrl_799162803.seq -o /var/tmp/from_scwrl_799162803.pdb > /var/tmp/scwrl_799162803.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_799162803.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 479 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -84.233 # GDT_score(maxd=8,maxw=2.9)= -87.8139 # GDT_score(maxd=8,maxw=3.2)= -84.7549 # GDT_score(maxd=8,maxw=3.5)= -81.2979 # GDT_score(maxd=10,maxw=3.8)= -82.9673 # GDT_score(maxd=10,maxw=4)= -80.6364 # GDT_score(maxd=10,maxw=4.2)= -78.2051 # GDT_score(maxd=12,maxw=4.3)= -81.3592 # GDT_score(maxd=12,maxw=4.5)= -78.9921 # GDT_score(maxd=12,maxw=4.7)= -76.5328 # GDT_score(maxd=14,maxw=5.2)= -74.2543 # GDT_score(maxd=14,maxw=5.5)= -70.8211 # command:# request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_943423057.pdb -s /var/tmp/to_scwrl_943423057.seq -o /var/tmp/from_scwrl_943423057.pdb > /var/tmp/scwrl_943423057.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_943423057.pdb # conformation set from SCWRL output # command:# naming current conformation model3-scwrl # command:# ReadConformPDB reading from PDB file model4.ts-submitted looking for model 1 # Found a chain break before 468 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -85.464 # GDT_score(maxd=8,maxw=2.9)= -87.8773 # GDT_score(maxd=8,maxw=3.2)= -85.6385 # GDT_score(maxd=8,maxw=3.5)= -83.1368 # GDT_score(maxd=10,maxw=3.8)= -84.6933 # GDT_score(maxd=10,maxw=4)= -82.9486 # GDT_score(maxd=10,maxw=4.2)= -81.0259 # GDT_score(maxd=12,maxw=4.3)= -83.6681 # GDT_score(maxd=12,maxw=4.5)= -81.7885 # GDT_score(maxd=12,maxw=4.7)= -79.8139 # GDT_score(maxd=14,maxw=5.2)= -77.92 # GDT_score(maxd=14,maxw=5.5)= -74.8329 # command:# request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_585278775.pdb -s /var/tmp/to_scwrl_585278775.seq -o /var/tmp/from_scwrl_585278775.pdb > /var/tmp/scwrl_585278775.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_585278775.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 T0334 can't currently be optimized by undertaker # command:# fraction of real conformation used = 0.892045 # GDT_score = -66.572 # GDT_score(maxd=8,maxw=2.9)= -67.0618 # GDT_score(maxd=8,maxw=3.2)= -66.5131 # GDT_score(maxd=8,maxw=3.5)= -65.7764 # GDT_score(maxd=10,maxw=3.8)= -66.2842 # GDT_score(maxd=10,maxw=4)= -65.693 # GDT_score(maxd=10,maxw=4.2)= -64.9338 # GDT_score(maxd=12,maxw=4.3)= -66.0195 # GDT_score(maxd=12,maxw=4.5)= -65.2591 # GDT_score(maxd=12,maxw=4.7)= -64.3772 # GDT_score(maxd=14,maxw=5.2)= -63.4891 # GDT_score(maxd=14,maxw=5.5)= -61.687 # command:# request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1416052548.pdb -s /var/tmp/to_scwrl_1416052548.seq -o /var/tmp/from_scwrl_1416052548.pdb > /var/tmp/scwrl_1416052548.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1416052548.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 T0334.try1-opt2.pdb looking for model 1 # Found a chain break before 488 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -83.9962 # GDT_score(maxd=8,maxw=2.9)= -87.5391 # GDT_score(maxd=8,maxw=3.2)= -84.5554 # GDT_score(maxd=8,maxw=3.5)= -81.149 # GDT_score(maxd=10,maxw=3.8)= -82.8026 # GDT_score(maxd=10,maxw=4)= -80.5493 # GDT_score(maxd=10,maxw=4.2)= -78.1633 # GDT_score(maxd=12,maxw=4.3)= -81.2778 # GDT_score(maxd=12,maxw=4.5)= -78.9535 # GDT_score(maxd=12,maxw=4.7)= -76.5735 # GDT_score(maxd=14,maxw=5.2)= -74.4608 # GDT_score(maxd=14,maxw=5.5)= -71.1059 # command:# Prefix for output files set to # command:superimposing iter= 0 total_weight= 6.3500000e+03 rmsd (weighted)= 2.8844923e+00 (unweighted)= 4.7201161e+00 superimposing iter= 1 total_weight= 2.4525163e+04 rmsd (weighted)= 1.0780664e+00 (unweighted)= 4.7297861e+00 superimposing iter= 2 total_weight= 7.8424913e+03 rmsd (weighted)= 7.7761934e-01 (unweighted)= 4.7408266e+00 superimposing iter= 3 total_weight= 5.0881106e+03 rmsd (weighted)= 7.0179215e-01 (unweighted)= 4.7507237e+00 superimposing iter= 4 total_weight= 4.5666693e+03 rmsd (weighted)= 6.7066703e-01 (unweighted)= 4.7580566e+00 superimposing iter= 5 total_weight= 4.3961781e+03 rmsd (weighted)= 6.5428919e-01 (unweighted)= 4.7629863e+00 # command:# Prefix for output files set to decoys/ # command:# Prefix for input files set to # command:# ReadConformPDB reading from PDB file T0334.undertaker-align.pdb looking for model 1 WARNING: atoms too close: (T0334)V136.C and (T0334)I149.C only 0.0000000e+00 apart, marking (T0334)I149.C as missing WARNING: atoms too close: (T0334)E137.N and (T0334)L150.N only 0.0000000e+00 apart, marking (T0334)E137.N as missing WARNING: atoms too close: (T0334)E137.CA and (T0334)L150.CA only 0.0000000e+00 apart, marking (T0334)E137.CA as missing WARNING: atoms too close: (T0334)E194.C and (T0334)D195.C only 0.0000000e+00 apart, marking (T0334)D195.C as missing WARNING: atoms too close: (T0334)D195.N and (T0334)R196.N only 0.0000000e+00 apart, marking (T0334)D195.N as missing WARNING: atoms too close: (T0334)D195.CA and (T0334)R196.CA only 0.0000000e+00 apart, marking (T0334)D195.CA as missing WARNING: atoms too close: (T0334)P320.C and (T0334)E321.C only 0.0000000e+00 apart, marking (T0334)E321.C as missing WARNING: atoms too close: (T0334)E321.N and (T0334)T322.N only 0.0000000e+00 apart, marking (T0334)E321.N as missing WARNING: atoms too close: (T0334)E321.CA and (T0334)T322.CA only 0.0000000e+00 apart, marking (T0334)E321.CA as missing # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # command:# naming current conformation align1 # command:# fraction of real conformation used = 0.916667 # GDT_score = -68.2765 # GDT_score(maxd=8,maxw=2.9)= -68.8445 # GDT_score(maxd=8,maxw=3.2)= -68.2448 # GDT_score(maxd=8,maxw=3.5)= -67.4847 # GDT_score(maxd=10,maxw=3.8)= -67.999 # GDT_score(maxd=10,maxw=4)= -67.3949 # GDT_score(maxd=10,maxw=4.2)= -66.6135 # GDT_score(maxd=12,maxw=4.3)= -67.7568 # GDT_score(maxd=12,maxw=4.5)= -66.9748 # GDT_score(maxd=12,maxw=4.7)= -66.0702 # GDT_score(maxd=14,maxw=5.2)= -65.2091 # GDT_score(maxd=14,maxw=5.5)= -63.353 # command:# ReadConformPDB reading from PDB file T0334.undertaker-align.pdb looking for model 2 WARNING: atoms too close: (T0334)F59.C and (T0334)F60.C only 0.0000000e+00 apart, marking (T0334)F60.C as missing WARNING: atoms too close: (T0334)F60.N and (T0334)D61.N only 0.0000000e+00 apart, marking (T0334)F60.N as missing WARNING: atoms too close: (T0334)F60.CA and (T0334)D61.CA only 0.0000000e+00 apart, marking (T0334)F60.CA as missing WARNING: atoms too close: (T0334)I65.C and (T0334)L122.C only 0.0000000e+00 apart, marking (T0334)L122.C as missing WARNING: atoms too close: (T0334)P66.N and (T0334)S123.N only 0.0000000e+00 apart, marking (T0334)P66.N as missing WARNING: atoms too close: (T0334)P66.CA and (T0334)S123.CA only 0.0000000e+00 apart, marking (T0334)P66.CA as missing WARNING: atoms too close: (T0334)R132.C and (T0334)T135.C only 0.0000000e+00 apart, marking (T0334)T135.C as missing WARNING: atoms too close: (T0334)G133.N and (T0334)V136.N only 0.0000000e+00 apart, marking (T0334)G133.N as missing WARNING: atoms too close: (T0334)G133.CA and (T0334)V136.CA only 0.0000000e+00 apart, marking (T0334)G133.CA as missing WARNING: atoms too close: (T0334)D151.C and (T0334)N153.C only 0.0000000e+00 apart, marking (T0334)N153.C as missing WARNING: atoms too close: (T0334)A152.N and (T0334)R154.N only 0.0000000e+00 apart, marking (T0334)A152.N as missing WARNING: atoms too close: (T0334)A152.CA and (T0334)R154.CA only 0.0000000e+00 apart, marking (T0334)A152.CA as missing WARNING: atoms too close: (T0334)W169.C and (T0334)H170.C only 0.0000000e+00 apart, marking (T0334)H170.C as missing WARNING: atoms too close: (T0334)H170.N and (T0334)F171.N only 0.0000000e+00 apart, marking (T0334)H170.N as missing WARNING: atoms too close: (T0334)H170.CA and (T0334)F171.CA only 0.0000000e+00 apart, marking (T0334)H170.CA as missing WARNING: atoms too close: (T0334)L234.C and (T0334)I235.C only 0.0000000e+00 apart, marking (T0334)I235.C as missing WARNING: atoms too close: (T0334)I235.N and (T0334)N236.N only 0.0000000e+00 apart, marking (T0334)I235.N as missing WARNING: atoms too close: (T0334)I235.CA and (T0334)N236.CA only 0.0000000e+00 apart, marking (T0334)I235.CA as missing WARNING: atoms too close: (T0334)H249.C and (T0334)N252.C only 0.0000000e+00 apart, marking (T0334)N252.C as missing WARNING: atoms too close: (T0334)L250.N and (T0334)D253.N only 0.0000000e+00 apart, marking (T0334)L250.N as missing WARNING: atoms too close: (T0334)L250.CA and (T0334)D253.CA only 0.0000000e+00 apart, marking (T0334)L250.CA as missing WARNING: atoms too close: (T0334)L318.C and (T0334)E321.C only 0.0000000e+00 apart, marking (T0334)E321.C as missing WARNING: atoms too close: (T0334)D319.N and (T0334)T322.N only 0.0000000e+00 apart, marking (T0334)D319.N as missing WARNING: atoms too close: (T0334)D319.CA and (T0334)T322.CA only 0.0000000e+00 apart, marking (T0334)D319.CA as missing WARNING: atoms too close: (T0334)D414.C and (T0334)L480.C only 0.0000000e+00 apart, marking (T0334)L480.C as missing WARNING: atoms too close: (T0334)T415.N and (T0334)V481.N only 0.0000000e+00 apart, marking (T0334)T415.N as missing WARNING: atoms too close: (T0334)T415.CA and (T0334)V481.CA only 0.0000000e+00 apart, marking (T0334)T415.CA as missing # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # command:# naming current conformation align2 # command:# fraction of real conformation used = 0.676136 # GDT_score = -30.9186 # GDT_score(maxd=8,maxw=2.9)= -31.9147 # GDT_score(maxd=8,maxw=3.2)= -29.7631 # GDT_score(maxd=8,maxw=3.5)= -27.8641 # GDT_score(maxd=10,maxw=3.8)= -30.1046 # GDT_score(maxd=10,maxw=4)= -28.9223 # GDT_score(maxd=10,maxw=4.2)= -27.8189 # GDT_score(maxd=12,maxw=4.3)= -30.3464 # GDT_score(maxd=12,maxw=4.5)= -29.2459 # GDT_score(maxd=12,maxw=4.7)= -28.2068 # GDT_score(maxd=14,maxw=5.2)= -28.1794 # GDT_score(maxd=14,maxw=5.5)= -26.8329 # command:# ReadConformPDB reading from PDB file T0334.undertaker-align.pdb looking for model 3 WARNING: atoms too close: (T0334)G3.C and (T0334)K4.C only 0.0000000e+00 apart, marking (T0334)K4.C as missing WARNING: atoms too close: (T0334)K4.N and (T0334)I5.N only 0.0000000e+00 apart, marking (T0334)K4.N as missing WARNING: atoms too close: (T0334)K4.CA and (T0334)I5.CA only 0.0000000e+00 apart, marking (T0334)K4.CA as missing WARNING: atoms too close: (T0334)K26.C and (T0334)Q29.C only 0.0000000e+00 apart, marking (T0334)Q29.C as missing WARNING: atoms too close: (T0334)A27.N and (T0334)G30.N only 0.0000000e+00 apart, marking (T0334)A27.N as missing WARNING: atoms too close: (T0334)A27.CA and (T0334)G30.CA only 0.0000000e+00 apart, marking (T0334)A27.CA as missing WARNING: atoms too close: (T0334)K115.C and (T0334)L122.C only 0.0000000e+00 apart, marking (T0334)L122.C as missing WARNING: atoms too close: (T0334)Y116.N and (T0334)S123.N only 0.0000000e+00 apart, marking (T0334)Y116.N as missing WARNING: atoms too close: (T0334)Y116.CA and (T0334)S123.CA only 0.0000000e+00 apart, marking (T0334)Y116.CA as missing WARNING: atoms too close: (T0334)S130.C and (T0334)Y131.C only 0.0000000e+00 apart, marking (T0334)Y131.C as missing WARNING: atoms too close: (T0334)Y131.N and (T0334)R132.N only 0.0000000e+00 apart, marking (T0334)Y131.N as missing WARNING: atoms too close: (T0334)Y131.CA and (T0334)R132.CA only 0.0000000e+00 apart, marking (T0334)Y131.CA as missing WARNING: atoms too close: (T0334)P147.C and (T0334)R154.C only 0.0000000e+00 apart, marking (T0334)R154.C as missing WARNING: atoms too close: (T0334)V148.N and (T0334)S155.N only 0.0000000e+00 apart, marking (T0334)V148.N as missing WARNING: atoms too close: (T0334)V148.CA and (T0334)S155.CA only 0.0000000e+00 apart, marking (T0334)V148.CA as missing WARNING: atoms too close: (T0334)K163.C and (T0334)T165.C only 0.0000000e+00 apart, marking (T0334)T165.C as missing WARNING: atoms too close: (T0334)V164.N and (T0334)N166.N only 0.0000000e+00 apart, marking (T0334)V164.N as missing WARNING: atoms too close: (T0334)V164.CA and (T0334)N166.CA only 0.0000000e+00 apart, marking (T0334)V164.CA as missing WARNING: atoms too close: (T0334)A184.C and (T0334)T185.C only 0.0000000e+00 apart, marking (T0334)T185.C as missing WARNING: atoms too close: (T0334)T185.N and (T0334)E186.N only 0.0000000e+00 apart, marking (T0334)T185.N as missing WARNING: atoms too close: (T0334)T185.CA and (T0334)E186.CA only 0.0000000e+00 apart, marking (T0334)T185.CA as missing WARNING: atoms too close: (T0334)R217.C and (T0334)V218.C only 0.0000000e+00 apart, marking (T0334)V218.C as missing WARNING: atoms too close: (T0334)V218.N and (T0334)F219.N only 0.0000000e+00 apart, marking (T0334)V218.N as missing WARNING: atoms too close: (T0334)V218.CA and (T0334)F219.CA only 0.0000000e+00 apart, marking (T0334)V218.CA as missing WARNING: atoms too close: (T0334)H249.C and (T0334)N252.C only 0.0000000e+00 apart, marking (T0334)N252.C as missing WARNING: atoms too close: (T0334)L250.N and (T0334)D253.N only 0.0000000e+00 apart, marking (T0334)L250.N as missing WARNING: atoms too close: (T0334)L250.CA and (T0334)D253.CA only 0.0000000e+00 apart, marking (T0334)L250.CA as missing WARNING: atoms too close: (T0334)H262.C and (T0334)D265.C only 0.0000000e+00 apart, marking (T0334)D265.C as missing WARNING: atoms too close: (T0334)D263.N and (T0334)A266.N only 0.0000000e+00 apart, marking (T0334)D263.N as missing WARNING: atoms too close: (T0334)D263.CA and (T0334)A266.CA only 0.0000000e+00 apart, marking (T0334)D263.CA as missing WARNING: atoms too close: (T0334)A266.C and (T0334)N267.C only 0.0000000e+00 apart, marking (T0334)N267.C as missing WARNING: atoms too close: (T0334)N267.N and (T0334)G268.N only 0.0000000e+00 apart, marking (T0334)N267.N as missing WARNING: atoms too close: (T0334)N267.CA and (T0334)G268.CA only 0.0000000e+00 apart, marking (T0334)N267.CA as missing WARNING: atoms too close: (T0334)A275.C and (T0334)M278.C only 0.0000000e+00 apart, marking (T0334)M278.C as missing WARNING: atoms too close: (T0334)I276.N and (T0334)K279.N only 0.0000000e+00 apart, marking (T0334)I276.N as missing WARNING: atoms too close: (T0334)I276.CA and (T0334)K279.CA only 0.0000000e+00 apart, marking (T0334)I276.CA as missing WARNING: atoms too close: (T0334)R336.C and (T0334)R337.C only 0.0000000e+00 apart, marking (T0334)R337.C as missing WARNING: atoms too close: (T0334)R337.N and (T0334)A338.N only 0.0000000e+00 apart, marking (T0334)R337.N as missing WARNING: atoms too close: (T0334)R337.CA and (T0334)A338.CA only 0.0000000e+00 apart, marking (T0334)R337.CA as missing # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # command:# naming current conformation align3 # command:# ReadConformPDB reading from PDB file T0334.undertaker-align.pdb looking for model 4 WARNING: atoms too close: (T0334)K26.C and (T0334)Q29.C only 0.0000000e+00 apart, marking (T0334)Q29.C as missing WARNING: atoms too close: (T0334)A27.N and (T0334)G30.N only 0.0000000e+00 apart, marking (T0334)A27.N as missing WARNING: atoms too close: (T0334)A27.CA and (T0334)G30.CA only 0.0000000e+00 apart, marking (T0334)A27.CA as missing WARNING: atoms too close: (T0334)F59.C and (T0334)F60.C only 0.0000000e+00 apart, marking (T0334)F60.C as missing WARNING: atoms too close: (T0334)F60.N and (T0334)D61.N only 0.0000000e+00 apart, marking (T0334)F60.N as missing WARNING: atoms too close: (T0334)F60.CA and (T0334)D61.CA only 0.0000000e+00 apart, marking (T0334)F60.CA as missing WARNING: atoms too close: (T0334)I65.C and (T0334)L122.C only 0.0000000e+00 apart, marking (T0334)L122.C as missing WARNING: atoms too close: (T0334)P66.N and (T0334)S123.N only 0.0000000e+00 apart, marking (T0334)P66.N as missing WARNING: atoms too close: (T0334)P66.CA and (T0334)S123.CA only 0.0000000e+00 apart, marking (T0334)P66.CA as missing WARNING: atoms too close: (T0334)R132.C and (T0334)T135.C only 0.0000000e+00 apart, marking (T0334)T135.C as missing WARNING: atoms too close: (T0334)G133.N and (T0334)V136.N only 0.0000000e+00 apart, marking (T0334)G133.N as missing WARNING: atoms too close: (T0334)G133.CA and (T0334)V136.CA only 0.0000000e+00 apart, marking (T0334)G133.CA as missing WARNING: atoms too close: (T0334)L150.C and (T0334)N153.C only 0.0000000e+00 apart, marking (T0334)N153.C as missing WARNING: atoms too close: (T0334)D151.N and (T0334)R154.N only 0.0000000e+00 apart, marking (T0334)D151.N as missing WARNING: atoms too close: (T0334)D151.CA and (T0334)R154.CA only 0.0000000e+00 apart, marking (T0334)D151.CA as missing WARNING: atoms too close: (T0334)G161.C and (T0334)T165.C only 0.0000000e+00 apart, marking (T0334)T165.C as missing WARNING: atoms too close: (T0334)S162.N and (T0334)N166.N only 0.0000000e+00 apart, marking (T0334)S162.N as missing WARNING: atoms too close: (T0334)S162.CA and (T0334)N166.CA only 0.0000000e+00 apart, marking (T0334)S162.CA as missing WARNING: atoms too close: (T0334)A184.C and (T0334)T185.C only 0.0000000e+00 apart, marking (T0334)T185.C as missing WARNING: atoms too close: (T0334)T185.N and (T0334)E186.N only 0.0000000e+00 apart, marking (T0334)T185.N as missing WARNING: atoms too close: (T0334)T185.CA and (T0334)E186.CA only 0.0000000e+00 apart, marking (T0334)T185.CA as missing WARNING: atoms too close: (T0334)G206.C and (T0334)I208.C only 0.0000000e+00 apart, marking (T0334)I208.C as missing WARNING: atoms too close: (T0334)N207.N and (T0334)E209.N only 0.0000000e+00 apart, marking (T0334)N207.N as missing WARNING: atoms too close: (T0334)N207.CA and (T0334)E209.CA only 0.0000000e+00 apart, marking (T0334)N207.CA as missing WARNING: atoms too close: (T0334)L234.C and (T0334)I235.C only 0.0000000e+00 apart, marking (T0334)I235.C as missing WARNING: atoms too close: (T0334)I235.N and (T0334)N236.N only 0.0000000e+00 apart, marking (T0334)I235.N as missing WARNING: atoms too close: (T0334)I235.CA and (T0334)N236.CA only 0.0000000e+00 apart, marking (T0334)I235.CA as missing WARNING: atoms too close: (T0334)T258.C and (T0334)D263.C only 0.0000000e+00 apart, marking (T0334)D263.C as missing WARNING: atoms too close: (T0334)Q259.N and (T0334)D264.N only 0.0000000e+00 apart, marking (T0334)Q259.N as missing WARNING: atoms too close: (T0334)Q259.CA and (T0334)D264.CA only 0.0000000e+00 apart, marking (T0334)Q259.CA as missing WARNING: atoms too close: (T0334)R419.C and (T0334)F503.C only 0.0000000e+00 apart, marking (T0334)F503.C as missing WARNING: atoms too close: (T0334)A420.N and (T0334)G504.N only 0.0000000e+00 apart, marking (T0334)A420.N as missing WARNING: atoms too close: (T0334)A420.CA and (T0334)G504.CA only 0.0000000e+00 apart, marking (T0334)A420.CA as missing # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # command:# naming current conformation align4 # command:# ReadConformPDB reading from PDB file T0334.undertaker-align.pdb looking for model 5 WARNING: atoms too close: (T0334)A27.C and (T0334)G30.C only 0.0000000e+00 apart, marking (T0334)G30.C as missing WARNING: atoms too close: (T0334)L28.N and (T0334)T31.N only 0.0000000e+00 apart, marking (T0334)L28.N as missing WARNING: atoms too close: (T0334)L28.CA and (T0334)T31.CA only 0.0000000e+00 apart, marking (T0334)L28.CA as missing WARNING: atoms too close: (T0334)F59.C and (T0334)F60.C only 0.0000000e+00 apart, marking (T0334)F60.C as missing WARNING: atoms too close: (T0334)F60.N and (T0334)D61.N only 0.0000000e+00 apart, marking (T0334)F60.N as missing WARNING: atoms too close: (T0334)F60.CA and (T0334)D61.CA only 0.0000000e+00 apart, marking (T0334)F60.CA as missing WARNING: atoms too close: (T0334)I65.C and (T0334)L122.C only 0.0000000e+00 apart, marking (T0334)L122.C as missing WARNING: atoms too close: (T0334)P66.N and (T0334)S123.N only 0.0000000e+00 apart, marking (T0334)P66.N as missing WARNING: atoms too close: (T0334)P66.CA and (T0334)S123.CA only 0.0000000e+00 apart, marking (T0334)P66.CA as missing WARNING: atoms too close: (T0334)R132.C and (T0334)T135.C only 0.0000000e+00 apart, marking (T0334)T135.C as missing WARNING: atoms too close: (T0334)G133.N and (T0334)V136.N only 0.0000000e+00 apart, marking (T0334)G133.N as missing WARNING: atoms too close: (T0334)G133.CA and (T0334)V136.CA only 0.0000000e+00 apart, marking (T0334)G133.CA as missing WARNING: atoms too close: (T0334)D151.C and (T0334)R154.C only 0.0000000e+00 apart, marking (T0334)R154.C as missing WARNING: atoms too close: (T0334)A152.N and (T0334)S155.N only 0.0000000e+00 apart, marking (T0334)A152.N as missing WARNING: atoms too close: (T0334)A152.CA and (T0334)S155.CA only 0.0000000e+00 apart, marking (T0334)A152.CA as missing WARNING: atoms too close: (T0334)G161.C and (T0334)T165.C only 0.0000000e+00 apart, marking (T0334)T165.C as missing WARNING: atoms too close: (T0334)S162.N and (T0334)N166.N only 0.0000000e+00 apart, marking (T0334)S162.N as missing WARNING: atoms too close: (T0334)S162.CA and (T0334)N166.CA only 0.0000000e+00 apart, marking (T0334)S162.CA as missing WARNING: atoms too close: (T0334)A184.C and (T0334)T185.C only 0.0000000e+00 apart, marking (T0334)T185.C as missing WARNING: atoms too close: (T0334)T185.N and (T0334)E186.N only 0.0000000e+00 apart, marking (T0334)T185.N as missing WARNING: atoms too close: (T0334)T185.CA and (T0334)E186.CA only 0.0000000e+00 apart, marking (T0334)T185.CA as missing WARNING: atoms too close: (T0334)G206.C and (T0334)I208.C only 0.0000000e+00 apart, marking (T0334)I208.C as missing WARNING: atoms too close: (T0334)N207.N and (T0334)E209.N only 0.0000000e+00 apart, marking (T0334)N207.N as missing WARNING: atoms too close: (T0334)N207.CA and (T0334)E209.CA only 0.0000000e+00 apart, marking (T0334)N207.CA as missing WARNING: atoms too close: (T0334)L234.C and (T0334)I235.C only 0.0000000e+00 apart, marking (T0334)I235.C as missing WARNING: atoms too close: (T0334)I235.N and (T0334)N236.N only 0.0000000e+00 apart, marking (T0334)I235.N as missing WARNING: atoms too close: (T0334)I235.CA and (T0334)N236.CA only 0.0000000e+00 apart, marking (T0334)I235.CA as missing WARNING: atoms too close: (T0334)T258.C and (T0334)D263.C only 0.0000000e+00 apart, marking (T0334)D263.C as missing WARNING: atoms too close: (T0334)Q259.N and (T0334)D264.N only 0.0000000e+00 apart, marking (T0334)Q259.N as missing WARNING: atoms too close: (T0334)Q259.CA and (T0334)D264.CA only 0.0000000e+00 apart, marking (T0334)Q259.CA as missing WARNING: atoms too close: (T0334)R419.C and (T0334)F503.C only 0.0000000e+00 apart, marking (T0334)F503.C as missing WARNING: atoms too close: (T0334)A420.N and (T0334)G504.N only 0.0000000e+00 apart, marking (T0334)A420.N as missing WARNING: atoms too close: (T0334)A420.CA and (T0334)G504.CA only 0.0000000e+00 apart, marking (T0334)A420.CA as missing # WARNING: incomplete conformation T0334 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 451 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ../model2.ts-submitted looking for model 1 # Found a chain break before 473 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ../model3.ts-submitted looking for model 1 # Found a chain break before 479 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ../model4.ts-submitted looking for model 1 # Found a chain break before 468 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ../model5.ts-submitted looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # ReadConformPDB reading from PDB file T0334.try1-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 488 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try1-opt1.pdb.gz looking for model 1 # Found a chain break before 488 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try1-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 518 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try1-opt2.gromacs0.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 518 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try1-opt2.pdb.gz looking for model 1 # Found a chain break before 488 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try1-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 488 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try10-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 450 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try10-opt1.pdb.gz looking for model 1 # Found a chain break before 450 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try10-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 477 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try10-opt2.gromacs0.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 477 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try10-opt2.pdb.gz looking for model 1 # Found a chain break before 451 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try10-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 451 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try11-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 451 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try11-opt1.pdb.gz looking for model 1 # Found a chain break before 451 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try11-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 478 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try11-opt2.gromacs0.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 478 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try11-opt2.pdb.gz looking for model 1 # Found a chain break before 451 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try11-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 451 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try12-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 477 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try12-opt1.pdb.gz looking for model 1 # Found a chain break before 477 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try12-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 473 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try12-opt2.gromacs0.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 473 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try12-opt2.pdb.gz looking for model 1 # Found a chain break before 477 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try12-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 477 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try13-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 451 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try13-opt1.pdb.gz looking for model 1 # Found a chain break before 451 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try13-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 487 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try13-opt2.gromacs0.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 487 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try13-opt2.pdb.gz looking for model 1 # Found a chain break before 451 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try13-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 451 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try14-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 451 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try14-opt1.pdb.gz looking for model 1 # Found a chain break before 451 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try14-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 487 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try14-opt2.gromacs0.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 487 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try14-opt2.pdb.gz looking for model 1 # Found a chain break before 451 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try14-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 451 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try15-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 468 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try15-opt1.pdb.gz looking for model 1 # Found a chain break before 468 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try15-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 464 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try15-opt2.gromacs0.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 464 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try15-opt2.pdb.gz looking for model 1 # Found a chain break before 468 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try15-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 468 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try16-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 455 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try16-opt1.pdb.gz looking for model 1 # Found a chain break before 455 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try16-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 456 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try16-opt2.gromacs0.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 456 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try16-opt2.pdb.gz looking for model 1 # Found a chain break before 479 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try16-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 479 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try17-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 526 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try17-opt1.pdb.gz looking for model 1 # Found a chain break before 526 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try17-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 450 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try17-opt2.gromacs0.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 450 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try17-opt2.pdb.gz looking for model 1 # Found a chain break before 526 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try17-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 526 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try2-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 450 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try2-opt1.pdb.gz looking for model 1 # Found a chain break before 450 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try2-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 477 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try2-opt2.gromacs0.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 477 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try2-opt2.pdb.gz looking for model 1 # Found a chain break before 456 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try2-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 456 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try3-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 493 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try3-opt1.pdb.gz looking for model 1 # Found a chain break before 493 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try3-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 526 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try3-opt2.gromacs0.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 526 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try3-opt2.pdb.gz looking for model 1 # Found a chain break before 459 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try3-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 459 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try6-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 456 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try6-opt1.pdb.gz looking for model 1 # Found a chain break before 456 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try6-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 477 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try6-opt2.gromacs0.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 477 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try6-opt2.pdb.gz looking for model 1 # Found a chain break before 456 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try6-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 456 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try7-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 456 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try7-opt1.pdb.gz looking for model 1 # Found a chain break before 456 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try7-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 528 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try7-opt2.gromacs0.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 528 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try7-opt2.pdb.gz looking for model 1 # Found a chain break before 456 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try7-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 456 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try8-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 451 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try8-opt1.pdb.gz looking for model 1 # Found a chain break before 451 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try8-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 514 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try8-opt2.gromacs0.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 514 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try8-opt2.pdb.gz looking for model 1 # Found a chain break before 451 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try8-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 451 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try9-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 445 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try9-opt1.pdb.gz looking for model 1 # Found a chain break before 445 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try9-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 449 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try9-opt2.gromacs0.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 449 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try9-opt2.pdb.gz looking for model 1 # Found a chain break before 448 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0334.try9-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 448 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ../dimer/decoys/T0334.try1-opt1-scwrl.pdb.gz looking for chain 'A' model 1 # Found a chain break before 520 # copying to AlignedFragments data structure # naming current conformation dimer//try1-opt1-scwrl # ReadConformPDB reading from PDB file ../dimer/decoys/T0334.try1-opt1.pdb.gz looking for chain 'A' model 1 # Found a chain break before 520 # copying to AlignedFragments data structure # naming current conformation dimer//try1-opt1 # ReadConformPDB reading from PDB file ../dimer/decoys/T0334.try1-opt2.pdb.gz looking for chain 'A' model 1 # Found a chain break before 526 # copying to AlignedFragments data structure # naming current conformation dimer//try1-opt2 # ReadConformPDB reading from PDB file ../dimer/decoys/T0334.try1-opt2.repack-nonPC.pdb.gz looking for chain 'A' model 1 # Found a chain break before 526 # copying to AlignedFragments data structure # naming current conformation dimer//try1-opt2.repack-nonPC # ReadConformPDB reading from PDB file ../dimer/decoys/T0334.try1-opt2.unpack.gromacs0.pdb.gz looking for chain 'A' model 1 # Found a chain break before 524 # copying to AlignedFragments data structure # naming current conformation dimer//try1-opt2.unpack.gromacs0 # ReadConformPDB reading from PDB file ../dimer/decoys/T0334.try1-opt2.unpack.gromacs0.repack-nonPC.pdb.gz looking for chain 'A' model 1 # Found a chain break before 524 # copying to AlignedFragments data structure # naming current conformation dimer//try1-opt2.unpack.gromacs0.repack-nonPC # ReadConformPDB reading from PDB file ../dimer/decoys/T0334.try1-opt2.unpack.pdb.gz looking for chain 'A' model 1 # Found a chain break before 526 # copying to AlignedFragments data structure # naming current conformation dimer//try1-opt2.unpack # ReadConformPDB reading from PDB file ../dimer/decoys/dimer-2aqj-from-T0334.try6-opt2.pdb.gz looking for chain 'A' model 1 # Found a chain break before 456 # copying to AlignedFragments data structure # naming current conformation dimer//dimer-2aqj-from-try6-opt2 # ReadConformPDB reading from PDB file ../dimer/decoys/dimer-2aqj-from-T0334.try7-opt2.pdb.gz looking for chain 'A' model 1 # Found a chain break before 456 # copying to AlignedFragments data structure # naming current conformation dimer//dimer-2aqj-from-try7-opt2 # ReadConformPDB reading from PDB file ../dimer/decoys/dimer-2aqj-from-T0334.try8-opt2.pdb.gz looking for chain 'A' model 1 # Found a chain break before 451 # copying to AlignedFragments data structure # naming current conformation dimer//dimer-2aqj-from-try8-opt2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1834627386.pdb -s /var/tmp/to_scwrl_1834627386.seq -o /var/tmp/from_scwrl_1834627386.pdb > /var/tmp/scwrl_1834627386.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1834627386.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 T0334 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_344668874.pdb -s /var/tmp/to_scwrl_344668874.seq -o /var/tmp/from_scwrl_344668874.pdb > /var/tmp/scwrl_344668874.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_344668874.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 T0334 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_960650980.pdb -s /var/tmp/to_scwrl_960650980.seq -o /var/tmp/from_scwrl_960650980.pdb > /var/tmp/scwrl_960650980.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_960650980.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 T0334 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1852466496.pdb -s /var/tmp/to_scwrl_1852466496.seq -o /var/tmp/from_scwrl_1852466496.pdb > /var/tmp/scwrl_1852466496.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1852466496.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 T0334 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1310414973.pdb -s /var/tmp/to_scwrl_1310414973.seq -o /var/tmp/from_scwrl_1310414973.pdb > /var/tmp/scwrl_1310414973.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1310414973.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 T0334 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1940649219.pdb -s /var/tmp/to_scwrl_1940649219.seq -o /var/tmp/from_scwrl_1940649219.pdb > /var/tmp/scwrl_1940649219.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1940649219.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 T0334 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_25551987.pdb -s /var/tmp/to_scwrl_25551987.seq -o /var/tmp/from_scwrl_25551987.pdb > /var/tmp/scwrl_25551987.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_25551987.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 T0334 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_855588359.pdb -s /var/tmp/to_scwrl_855588359.seq -o /var/tmp/from_scwrl_855588359.pdb > /var/tmp/scwrl_855588359.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_855588359.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 T0334 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_315051825.pdb -s /var/tmp/to_scwrl_315051825.seq -o /var/tmp/from_scwrl_315051825.pdb > /var/tmp/scwrl_315051825.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_315051825.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 T0334 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_2086597488.pdb -s /var/tmp/to_scwrl_2086597488.seq -o /var/tmp/from_scwrl_2086597488.pdb > /var/tmp/scwrl_2086597488.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2086597488.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 T0334 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_78458487.pdb -s /var/tmp/to_scwrl_78458487.seq -o /var/tmp/from_scwrl_78458487.pdb > /var/tmp/scwrl_78458487.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_78458487.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 T0334 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1293264446.pdb -s /var/tmp/to_scwrl_1293264446.seq -o /var/tmp/from_scwrl_1293264446.pdb > /var/tmp/scwrl_1293264446.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1293264446.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 T0334 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_2102218200.pdb -s /var/tmp/to_scwrl_2102218200.seq -o /var/tmp/from_scwrl_2102218200.pdb > /var/tmp/scwrl_2102218200.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2102218200.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 T0334 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_141528903.pdb -s /var/tmp/to_scwrl_141528903.seq -o /var/tmp/from_scwrl_141528903.pdb > /var/tmp/scwrl_141528903.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_141528903.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_TS4-scwrl # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # Found a chain break before 491 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_889114068.pdb -s /var/tmp/to_scwrl_889114068.seq -o /var/tmp/from_scwrl_889114068.pdb > /var/tmp/scwrl_889114068.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_889114068.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 491 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1885920146.pdb -s /var/tmp/to_scwrl_1885920146.seq -o /var/tmp/from_scwrl_1885920146.pdb > /var/tmp/scwrl_1885920146.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1885920146.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 453 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_377466507.pdb -s /var/tmp/to_scwrl_377466507.seq -o /var/tmp/from_scwrl_377466507.pdb > /var/tmp/scwrl_377466507.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_377466507.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 519 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_357154928.pdb -s /var/tmp/to_scwrl_357154928.seq -o /var/tmp/from_scwrl_357154928.pdb > /var/tmp/scwrl_357154928.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_357154928.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 464 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1206679990.pdb -s /var/tmp/to_scwrl_1206679990.seq -o /var/tmp/from_scwrl_1206679990.pdb > /var/tmp/scwrl_1206679990.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1206679990.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 491 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_948612339.pdb -s /var/tmp/to_scwrl_948612339.seq -o /var/tmp/from_scwrl_948612339.pdb > /var/tmp/scwrl_948612339.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_948612339.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 491 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_528198729.pdb -s /var/tmp/to_scwrl_528198729.seq -o /var/tmp/from_scwrl_528198729.pdb > /var/tmp/scwrl_528198729.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_528198729.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 501 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_804320169.pdb -s /var/tmp/to_scwrl_804320169.seq -o /var/tmp/from_scwrl_804320169.pdb > /var/tmp/scwrl_804320169.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_804320169.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 525 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_2007346562.pdb -s /var/tmp/to_scwrl_2007346562.seq -o /var/tmp/from_scwrl_2007346562.pdb > /var/tmp/scwrl_2007346562.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2007346562.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 472 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_908279948.pdb -s /var/tmp/to_scwrl_908279948.seq -o /var/tmp/from_scwrl_908279948.pdb > /var/tmp/scwrl_908279948.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_908279948.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 519 # copying to AlignedFragments data structure # naming current conformation BayesHH_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_437177188.pdb -s /var/tmp/to_scwrl_437177188.seq -o /var/tmp/from_scwrl_437177188.pdb > /var/tmp/scwrl_437177188.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_437177188.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 463 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_304582439.pdb -s /var/tmp/to_scwrl_304582439.seq -o /var/tmp/from_scwrl_304582439.pdb > /var/tmp/scwrl_304582439.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_304582439.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 446 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_2059021948.pdb -s /var/tmp/to_scwrl_2059021948.seq -o /var/tmp/from_scwrl_2059021948.pdb > /var/tmp/scwrl_2059021948.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2059021948.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 491 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1236339990.pdb -s /var/tmp/to_scwrl_1236339990.seq -o /var/tmp/from_scwrl_1236339990.pdb > /var/tmp/scwrl_1236339990.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1236339990.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 422 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1248005495.pdb -s /var/tmp/to_scwrl_1248005495.seq -o /var/tmp/from_scwrl_1248005495.pdb > /var/tmp/scwrl_1248005495.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1248005495.pdb # conformation set from SCWRL output # naming current conformation Bilab-ENABLE_TS4-scwrl # ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1 # Found a chain break before 528 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_496817076.pdb -s /var/tmp/to_scwrl_496817076.seq -o /var/tmp/from_scwrl_496817076.pdb > /var/tmp/scwrl_496817076.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_496817076.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 T0334 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_504908892.pdb -s /var/tmp/to_scwrl_504908892.seq -o /var/tmp/from_scwrl_504908892.pdb > /var/tmp/scwrl_504908892.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_504908892.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 529 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_935149235.pdb -s /var/tmp/to_scwrl_935149235.seq -o /var/tmp/from_scwrl_935149235.pdb > /var/tmp/scwrl_935149235.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_935149235.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 T0334 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_841485950.pdb -s /var/tmp/to_scwrl_841485950.seq -o /var/tmp/from_scwrl_841485950.pdb > /var/tmp/scwrl_841485950.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_841485950.pdb # conformation set from SCWRL output # naming current conformation CIRCLE_TS4-scwrl # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # Found a chain break before 526 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1465559872.pdb -s /var/tmp/to_scwrl_1465559872.seq -o /var/tmp/from_scwrl_1465559872.pdb > /var/tmp/scwrl_1465559872.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1465559872.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 T0334 can't currently be optimized by undertaker # naming current conformation CPHmodels_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_640132085.pdb -s /var/tmp/to_scwrl_640132085.seq -o /var/tmp/from_scwrl_640132085.pdb > /var/tmp/scwrl_640132085.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_640132085.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 T0334 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_4417277.pdb -s /var/tmp/to_scwrl_4417277.seq -o /var/tmp/from_scwrl_4417277.pdb > /var/tmp/scwrl_4417277.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_4417277.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 T0334 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1258725444.pdb -s /var/tmp/to_scwrl_1258725444.seq -o /var/tmp/from_scwrl_1258725444.pdb > /var/tmp/scwrl_1258725444.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1258725444.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 T0334 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_665684072.pdb -s /var/tmp/to_scwrl_665684072.seq -o /var/tmp/from_scwrl_665684072.pdb > /var/tmp/scwrl_665684072.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_665684072.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 T0334 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_860005636.pdb -s /var/tmp/to_scwrl_860005636.seq -o /var/tmp/from_scwrl_860005636.pdb > /var/tmp/scwrl_860005636.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_860005636.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 T0334 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1573777269.pdb -s /var/tmp/to_scwrl_1573777269.seq -o /var/tmp/from_scwrl_1573777269.pdb > /var/tmp/scwrl_1573777269.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1573777269.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 T0334 can't currently be optimized by undertaker # naming current conformation Distill_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_604797913.pdb -s /var/tmp/to_scwrl_604797913.seq -o /var/tmp/from_scwrl_604797913.pdb > /var/tmp/scwrl_604797913.log Error: Couldn't open file /var/tmp/from_scwrl_604797913.pdb or /var/tmp/from_scwrl_604797913.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_604797913_b.pdb or decoys//var/tmp/from_scwrl_604797913_b.pdb.gz for input Trying /var/tmp/from_scwrl_604797913_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_604797913_b.pdb or /var/tmp/from_scwrl_604797913_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_604797913_a.pdb or decoys//var/tmp/from_scwrl_604797913_a.pdb.gz for input Trying /var/tmp/from_scwrl_604797913_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_604797913_a.pdb or /var/tmp/from_scwrl_604797913_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_604797913.pdb or /var/tmp/from_scwrl_604797913_b.pdb or /var/tmp/from_scwrl_604797913_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 T0334 can't currently be optimized by undertaker # naming current conformation Distill_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_938464123.pdb -s /var/tmp/to_scwrl_938464123.seq -o /var/tmp/from_scwrl_938464123.pdb > /var/tmp/scwrl_938464123.log Error: Couldn't open file /var/tmp/from_scwrl_938464123.pdb or /var/tmp/from_scwrl_938464123.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_938464123_b.pdb or decoys//var/tmp/from_scwrl_938464123_b.pdb.gz for input Trying /var/tmp/from_scwrl_938464123_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_938464123_b.pdb or /var/tmp/from_scwrl_938464123_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_938464123_a.pdb or decoys//var/tmp/from_scwrl_938464123_a.pdb.gz for input Trying /var/tmp/from_scwrl_938464123_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_938464123_a.pdb or /var/tmp/from_scwrl_938464123_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_938464123.pdb or /var/tmp/from_scwrl_938464123_b.pdb or /var/tmp/from_scwrl_938464123_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 T0334 can't currently be optimized by undertaker # naming current conformation Distill_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_719558069.pdb -s /var/tmp/to_scwrl_719558069.seq -o /var/tmp/from_scwrl_719558069.pdb > /var/tmp/scwrl_719558069.log Error: Couldn't open file /var/tmp/from_scwrl_719558069.pdb or /var/tmp/from_scwrl_719558069.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_719558069_b.pdb or decoys//var/tmp/from_scwrl_719558069_b.pdb.gz for input Trying /var/tmp/from_scwrl_719558069_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_719558069_b.pdb or /var/tmp/from_scwrl_719558069_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_719558069_a.pdb or decoys//var/tmp/from_scwrl_719558069_a.pdb.gz for input Trying /var/tmp/from_scwrl_719558069_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_719558069_a.pdb or /var/tmp/from_scwrl_719558069_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_719558069.pdb or /var/tmp/from_scwrl_719558069_b.pdb or /var/tmp/from_scwrl_719558069_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 T0334 can't currently be optimized by undertaker # naming current conformation Distill_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_559532466.pdb -s /var/tmp/to_scwrl_559532466.seq -o /var/tmp/from_scwrl_559532466.pdb > /var/tmp/scwrl_559532466.log Error: Couldn't open file /var/tmp/from_scwrl_559532466.pdb or /var/tmp/from_scwrl_559532466.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_559532466_b.pdb or decoys//var/tmp/from_scwrl_559532466_b.pdb.gz for input Trying /var/tmp/from_scwrl_559532466_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_559532466_b.pdb or /var/tmp/from_scwrl_559532466_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_559532466_a.pdb or decoys//var/tmp/from_scwrl_559532466_a.pdb.gz for input Trying /var/tmp/from_scwrl_559532466_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_559532466_a.pdb or /var/tmp/from_scwrl_559532466_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_559532466.pdb or /var/tmp/from_scwrl_559532466_b.pdb or /var/tmp/from_scwrl_559532466_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 T0334 can't currently be optimized by undertaker # naming current conformation Distill_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1079993025.pdb -s /var/tmp/to_scwrl_1079993025.seq -o /var/tmp/from_scwrl_1079993025.pdb > /var/tmp/scwrl_1079993025.log Error: Couldn't open file /var/tmp/from_scwrl_1079993025.pdb or /var/tmp/from_scwrl_1079993025.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1079993025_b.pdb or decoys//var/tmp/from_scwrl_1079993025_b.pdb.gz for input Trying /var/tmp/from_scwrl_1079993025_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_1079993025_b.pdb or /var/tmp/from_scwrl_1079993025_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1079993025_a.pdb or decoys//var/tmp/from_scwrl_1079993025_a.pdb.gz for input Trying /var/tmp/from_scwrl_1079993025_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_1079993025_a.pdb or /var/tmp/from_scwrl_1079993025_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_1079993025.pdb or /var/tmp/from_scwrl_1079993025_b.pdb or /var/tmp/from_scwrl_1079993025_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 529 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1608672137.pdb -s /var/tmp/to_scwrl_1608672137.seq -o /var/tmp/from_scwrl_1608672137.pdb > /var/tmp/scwrl_1608672137.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1608672137.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 T0334 can't currently be optimized by undertaker # naming current conformation FAMSD_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_297968966.pdb -s /var/tmp/to_scwrl_297968966.seq -o /var/tmp/from_scwrl_297968966.pdb > /var/tmp/scwrl_297968966.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_297968966.pdb # conformation set from SCWRL output # naming current conformation FAMSD_TS2-scwrl # ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation FAMSD_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1457459532.pdb -s /var/tmp/to_scwrl_1457459532.seq -o /var/tmp/from_scwrl_1457459532.pdb > /var/tmp/scwrl_1457459532.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1457459532.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 T0334 can't currently be optimized by undertaker # naming current conformation FAMSD_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1965827065.pdb -s /var/tmp/to_scwrl_1965827065.seq -o /var/tmp/from_scwrl_1965827065.pdb > /var/tmp/scwrl_1965827065.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1965827065.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 T0334 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FAMSD_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1504648956.pdb -s /var/tmp/to_scwrl_1504648956.seq -o /var/tmp/from_scwrl_1504648956.pdb > /var/tmp/scwrl_1504648956.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1504648956.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 529 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_258588224.pdb -s /var/tmp/to_scwrl_258588224.seq -o /var/tmp/from_scwrl_258588224.pdb > /var/tmp/scwrl_258588224.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_258588224.pdb # conformation set from SCWRL output # naming current conformation FAMS_TS1-scwrl # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation FAMS_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_346542147.pdb -s /var/tmp/to_scwrl_346542147.seq -o /var/tmp/from_scwrl_346542147.pdb > /var/tmp/scwrl_346542147.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_346542147.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 # Found a chain break before 528 # copying to AlignedFragments data structure # naming current conformation FAMS_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_161485478.pdb -s /var/tmp/to_scwrl_161485478.seq -o /var/tmp/from_scwrl_161485478.pdb > /var/tmp/scwrl_161485478.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_161485478.pdb # conformation set from SCWRL output # naming current conformation FAMS_TS3-scwrl # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation FAMS_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_118451140.pdb -s /var/tmp/to_scwrl_118451140.seq -o /var/tmp/from_scwrl_118451140.pdb > /var/tmp/scwrl_118451140.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_118451140.pdb # conformation set from SCWRL output # naming current conformation FAMS_TS4-scwrl # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation FAMS_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1254822094.pdb -s /var/tmp/to_scwrl_1254822094.seq -o /var/tmp/from_scwrl_1254822094.pdb > /var/tmp/scwrl_1254822094.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1254822094.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 491 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_598662666.pdb -s /var/tmp/to_scwrl_598662666.seq -o /var/tmp/from_scwrl_598662666.pdb > /var/tmp/scwrl_598662666.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_598662666.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 453 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_423033579.pdb -s /var/tmp/to_scwrl_423033579.seq -o /var/tmp/from_scwrl_423033579.pdb > /var/tmp/scwrl_423033579.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_423033579.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 453 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1166360395.pdb -s /var/tmp/to_scwrl_1166360395.seq -o /var/tmp/from_scwrl_1166360395.pdb > /var/tmp/scwrl_1166360395.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1166360395.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 453 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1835002656.pdb -s /var/tmp/to_scwrl_1835002656.seq -o /var/tmp/from_scwrl_1835002656.pdb > /var/tmp/scwrl_1835002656.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1835002656.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 460 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1671039074.pdb -s /var/tmp/to_scwrl_1671039074.seq -o /var/tmp/from_scwrl_1671039074.pdb > /var/tmp/scwrl_1671039074.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1671039074.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 T0334 can't currently be optimized by undertaker # naming current conformation FORTE1_AL1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1663177472.pdb -s /var/tmp/to_scwrl_1663177472.seq -o /var/tmp/from_scwrl_1663177472.pdb > /var/tmp/scwrl_1663177472.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1663177472.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 Skipped atom 762, because occupancy 1.0000000e+00 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 764, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 766, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 768, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 1386, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 1388, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 1390, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 1392, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation FORTE1_AL2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_192427902.pdb -s /var/tmp/to_scwrl_192427902.seq -o /var/tmp/from_scwrl_192427902.pdb > /var/tmp/scwrl_192427902.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_192427902.pdb # conformation set from SCWRL output # naming current conformation FORTE1_AL2-scwrl # ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation FORTE1_AL3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_458704663.pdb -s /var/tmp/to_scwrl_458704663.seq -o /var/tmp/from_scwrl_458704663.pdb > /var/tmp/scwrl_458704663.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_458704663.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 T0334 can't currently be optimized by undertaker # naming current conformation FORTE1_AL4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_357179775.pdb -s /var/tmp/to_scwrl_357179775.seq -o /var/tmp/from_scwrl_357179775.pdb > /var/tmp/scwrl_357179775.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_357179775.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 T0334 can't currently be optimized by undertaker # naming current conformation FORTE1_AL5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1657987774.pdb -s /var/tmp/to_scwrl_1657987774.seq -o /var/tmp/from_scwrl_1657987774.pdb > /var/tmp/scwrl_1657987774.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1657987774.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 T0334 can't currently be optimized by undertaker # naming current conformation FORTE2_AL1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1098836747.pdb -s /var/tmp/to_scwrl_1098836747.seq -o /var/tmp/from_scwrl_1098836747.pdb > /var/tmp/scwrl_1098836747.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1098836747.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 T0334 can't currently be optimized by undertaker # naming current conformation FORTE2_AL2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_361597052.pdb -s /var/tmp/to_scwrl_361597052.seq -o /var/tmp/from_scwrl_361597052.pdb > /var/tmp/scwrl_361597052.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_361597052.pdb # conformation set from SCWRL output # naming current conformation FORTE2_AL2-scwrl # ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1 Skipped atom 762, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 764, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 766, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 768, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 1386, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 1388, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 1390, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 1392, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation FORTE2_AL3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_769229572.pdb -s /var/tmp/to_scwrl_769229572.seq -o /var/tmp/from_scwrl_769229572.pdb > /var/tmp/scwrl_769229572.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_769229572.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 T0334 can't currently be optimized by undertaker # naming current conformation FORTE2_AL4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1764520819.pdb -s /var/tmp/to_scwrl_1764520819.seq -o /var/tmp/from_scwrl_1764520819.pdb > /var/tmp/scwrl_1764520819.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1764520819.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 T0334 can't currently be optimized by undertaker # naming current conformation FORTE2_AL5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1221602687.pdb -s /var/tmp/to_scwrl_1221602687.seq -o /var/tmp/from_scwrl_1221602687.pdb > /var/tmp/scwrl_1221602687.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1221602687.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 529 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_195523194.pdb -s /var/tmp/to_scwrl_195523194.seq -o /var/tmp/from_scwrl_195523194.pdb > /var/tmp/scwrl_195523194.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_195523194.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 522 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_221835086.pdb -s /var/tmp/to_scwrl_221835086.seq -o /var/tmp/from_scwrl_221835086.pdb > /var/tmp/scwrl_221835086.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_221835086.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 529 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_12583163.pdb -s /var/tmp/to_scwrl_12583163.seq -o /var/tmp/from_scwrl_12583163.pdb > /var/tmp/scwrl_12583163.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_12583163.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 529 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_915081264.pdb -s /var/tmp/to_scwrl_915081264.seq -o /var/tmp/from_scwrl_915081264.pdb > /var/tmp/scwrl_915081264.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_915081264.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 521 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_781367552.pdb -s /var/tmp/to_scwrl_781367552.seq -o /var/tmp/from_scwrl_781367552.pdb > /var/tmp/scwrl_781367552.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_781367552.pdb # conformation set from SCWRL output # naming current conformation FPSOLVER-SERVER_TS5-scwrl # ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1092576188.pdb -s /var/tmp/to_scwrl_1092576188.seq -o /var/tmp/from_scwrl_1092576188.pdb > /var/tmp/scwrl_1092576188.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1092576188.pdb # conformation set from SCWRL output # naming current conformation FUGMOD_TS1-scwrl # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_376269754.pdb -s /var/tmp/to_scwrl_376269754.seq -o /var/tmp/from_scwrl_376269754.pdb > /var/tmp/scwrl_376269754.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_376269754.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 T0334 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1079336517.pdb -s /var/tmp/to_scwrl_1079336517.seq -o /var/tmp/from_scwrl_1079336517.pdb > /var/tmp/scwrl_1079336517.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1079336517.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 T0334 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_402552074.pdb -s /var/tmp/to_scwrl_402552074.seq -o /var/tmp/from_scwrl_402552074.pdb > /var/tmp/scwrl_402552074.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_402552074.pdb Faking rotamer for incomplete or colinear backbone at (T0334)C343 Faking rotamer for incomplete or colinear backbone at (T0334)C343 # conformation set from SCWRL output # naming current conformation FUGMOD_TS4-scwrl # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_194613172.pdb -s /var/tmp/to_scwrl_194613172.seq -o /var/tmp/from_scwrl_194613172.pdb > /var/tmp/scwrl_194613172.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_194613172.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 T0334 can't currently be optimized by undertaker # naming current conformation FUGUE_AL1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_436501827.pdb -s /var/tmp/to_scwrl_436501827.seq -o /var/tmp/from_scwrl_436501827.pdb > /var/tmp/scwrl_436501827.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_436501827.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 T0334 can't currently be optimized by undertaker # naming current conformation FUGUE_AL2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_661140299.pdb -s /var/tmp/to_scwrl_661140299.seq -o /var/tmp/from_scwrl_661140299.pdb > /var/tmp/scwrl_661140299.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_661140299.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 T0334 can't currently be optimized by undertaker # naming current conformation FUGUE_AL3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_541155319.pdb -s /var/tmp/to_scwrl_541155319.seq -o /var/tmp/from_scwrl_541155319.pdb > /var/tmp/scwrl_541155319.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_541155319.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 T0334 can't currently be optimized by undertaker # naming current conformation FUGUE_AL4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_597987305.pdb -s /var/tmp/to_scwrl_597987305.seq -o /var/tmp/from_scwrl_597987305.pdb > /var/tmp/scwrl_597987305.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_597987305.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 T0334 can't currently be optimized by undertaker # naming current conformation FUGUE_AL5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_779591439.pdb -s /var/tmp/to_scwrl_779591439.seq -o /var/tmp/from_scwrl_779591439.pdb > /var/tmp/scwrl_779591439.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_779591439.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 529 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1795977413.pdb -s /var/tmp/to_scwrl_1795977413.seq -o /var/tmp/from_scwrl_1795977413.pdb > /var/tmp/scwrl_1795977413.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1795977413.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 529 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1196649970.pdb -s /var/tmp/to_scwrl_1196649970.seq -o /var/tmp/from_scwrl_1196649970.pdb > /var/tmp/scwrl_1196649970.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1196649970.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 529 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1202625017.pdb -s /var/tmp/to_scwrl_1202625017.seq -o /var/tmp/from_scwrl_1202625017.pdb > /var/tmp/scwrl_1202625017.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1202625017.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 528 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_814854163.pdb -s /var/tmp/to_scwrl_814854163.seq -o /var/tmp/from_scwrl_814854163.pdb > /var/tmp/scwrl_814854163.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_814854163.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 529 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_884168981.pdb -s /var/tmp/to_scwrl_884168981.seq -o /var/tmp/from_scwrl_884168981.pdb > /var/tmp/scwrl_884168981.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_884168981.pdb # conformation set from SCWRL output # naming current conformation FUNCTION_TS5-scwrl # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_726180445.pdb -s /var/tmp/to_scwrl_726180445.seq -o /var/tmp/from_scwrl_726180445.pdb > /var/tmp/scwrl_726180445.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_726180445.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 527 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_330547988.pdb -s /var/tmp/to_scwrl_330547988.seq -o /var/tmp/from_scwrl_330547988.pdb > /var/tmp/scwrl_330547988.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_330547988.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 447 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1076596882.pdb -s /var/tmp/to_scwrl_1076596882.seq -o /var/tmp/from_scwrl_1076596882.pdb > /var/tmp/scwrl_1076596882.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1076596882.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 T0334 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1184885107.pdb -s /var/tmp/to_scwrl_1184885107.seq -o /var/tmp/from_scwrl_1184885107.pdb > /var/tmp/scwrl_1184885107.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1184885107.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 502 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_687727763.pdb -s /var/tmp/to_scwrl_687727763.seq -o /var/tmp/from_scwrl_687727763.pdb > /var/tmp/scwrl_687727763.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_687727763.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 519 # copying to AlignedFragments data structure # naming current conformation HHpred1_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_587101010.pdb -s /var/tmp/to_scwrl_587101010.seq -o /var/tmp/from_scwrl_587101010.pdb > /var/tmp/scwrl_587101010.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_587101010.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 519 # copying to AlignedFragments data structure # naming current conformation HHpred2_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_136238208.pdb -s /var/tmp/to_scwrl_136238208.seq -o /var/tmp/from_scwrl_136238208.pdb > /var/tmp/scwrl_136238208.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_136238208.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 519 # copying to AlignedFragments data structure # naming current conformation HHpred3_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1049324816.pdb -s /var/tmp/to_scwrl_1049324816.seq -o /var/tmp/from_scwrl_1049324816.pdb > /var/tmp/scwrl_1049324816.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1049324816.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 T0334 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1356330581.pdb -s /var/tmp/to_scwrl_1356330581.seq -o /var/tmp/from_scwrl_1356330581.pdb > /var/tmp/scwrl_1356330581.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1356330581.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 T0334 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1900759028.pdb -s /var/tmp/to_scwrl_1900759028.seq -o /var/tmp/from_scwrl_1900759028.pdb > /var/tmp/scwrl_1900759028.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1900759028.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 T0334 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_123443856.pdb -s /var/tmp/to_scwrl_123443856.seq -o /var/tmp/from_scwrl_123443856.pdb > /var/tmp/scwrl_123443856.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_123443856.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 T0334 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1551853775.pdb -s /var/tmp/to_scwrl_1551853775.seq -o /var/tmp/from_scwrl_1551853775.pdb > /var/tmp/scwrl_1551853775.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1551853775.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 T0334 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_2122594114.pdb -s /var/tmp/to_scwrl_2122594114.seq -o /var/tmp/from_scwrl_2122594114.pdb > /var/tmp/scwrl_2122594114.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2122594114.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 T0334 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation LOOPP_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_136027020.pdb -s /var/tmp/to_scwrl_136027020.seq -o /var/tmp/from_scwrl_136027020.pdb > /var/tmp/scwrl_136027020.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_136027020.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 T0334 can't currently be optimized by undertaker # naming current conformation LOOPP_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_319451392.pdb -s /var/tmp/to_scwrl_319451392.seq -o /var/tmp/from_scwrl_319451392.pdb > /var/tmp/scwrl_319451392.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_319451392.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 T0334 can't currently be optimized by undertaker # naming current conformation LOOPP_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_756478019.pdb -s /var/tmp/to_scwrl_756478019.seq -o /var/tmp/from_scwrl_756478019.pdb > /var/tmp/scwrl_756478019.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_756478019.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 T0334 can't currently be optimized by undertaker # naming current conformation LOOPP_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1228603208.pdb -s /var/tmp/to_scwrl_1228603208.seq -o /var/tmp/from_scwrl_1228603208.pdb > /var/tmp/scwrl_1228603208.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1228603208.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 T0334 can't currently be optimized by undertaker # naming current conformation LOOPP_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_695721146.pdb -s /var/tmp/to_scwrl_695721146.seq -o /var/tmp/from_scwrl_695721146.pdb > /var/tmp/scwrl_695721146.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_695721146.pdb # conformation set from SCWRL output # naming current conformation LOOPP_TS5-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS1.pdb.gz looking for model 1 # Found a chain break before 519 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1835814537.pdb -s /var/tmp/to_scwrl_1835814537.seq -o /var/tmp/from_scwrl_1835814537.pdb > /var/tmp/scwrl_1835814537.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1835814537.pdb # conformation set from SCWRL output # naming current conformation Ma-OPUS-server2_TS1-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS2.pdb.gz looking for model 1 # Found a chain break before 517 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1631155283.pdb -s /var/tmp/to_scwrl_1631155283.seq -o /var/tmp/from_scwrl_1631155283.pdb > /var/tmp/scwrl_1631155283.log sh: line 1: 9711 Killed scwrl3 -i /var/tmp/to_scwrl_1631155283.pdb -s /var/tmp/to_scwrl_1631155283.seq -o /var/tmp/from_scwrl_1631155283.pdb >/var/tmp/scwrl_1631155283.log Error: Couldn't open file /var/tmp/from_scwrl_1631155283.pdb or /var/tmp/from_scwrl_1631155283.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1631155283_b.pdb or decoys//var/tmp/from_scwrl_1631155283_b.pdb.gz for input Trying /var/tmp/from_scwrl_1631155283_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_1631155283_b.pdb or /var/tmp/from_scwrl_1631155283_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1631155283_a.pdb or decoys//var/tmp/from_scwrl_1631155283_a.pdb.gz for input Trying /var/tmp/from_scwrl_1631155283_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_1631155283_a.pdb or /var/tmp/from_scwrl_1631155283_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_1631155283.pdb or /var/tmp/from_scwrl_1631155283_b.pdb or /var/tmp/from_scwrl_1631155283_a.pdb Error: no new SCWRL conformation added # naming current conformation Ma-OPUS-server2_TS2-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS3.pdb.gz looking for model 1 # Found a chain break before 527 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_890334318.pdb -s /var/tmp/to_scwrl_890334318.seq -o /var/tmp/from_scwrl_890334318.pdb > /var/tmp/scwrl_890334318.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_890334318.pdb # conformation set from SCWRL output # naming current conformation Ma-OPUS-server2_TS3-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS4.pdb.gz looking for model 1 # Found a chain break before 529 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_124832717.pdb -s /var/tmp/to_scwrl_124832717.seq -o /var/tmp/from_scwrl_124832717.pdb > /var/tmp/scwrl_124832717.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_124832717.pdb # conformation set from SCWRL output # naming current conformation Ma-OPUS-server2_TS4-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS5.pdb.gz looking for model 1 # Found a chain break before 520 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_144811935.pdb -s /var/tmp/to_scwrl_144811935.seq -o /var/tmp/from_scwrl_144811935.pdb > /var/tmp/scwrl_144811935.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_144811935.pdb # conformation set from SCWRL output # naming current conformation Ma-OPUS-server2_TS5-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # Found a chain break before 519 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1431489636.pdb -s /var/tmp/to_scwrl_1431489636.seq -o /var/tmp/from_scwrl_1431489636.pdb > /var/tmp/scwrl_1431489636.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1431489636.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 446 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_722820023.pdb -s /var/tmp/to_scwrl_722820023.seq -o /var/tmp/from_scwrl_722820023.pdb > /var/tmp/scwrl_722820023.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_722820023.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 522 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_924403374.pdb -s /var/tmp/to_scwrl_924403374.seq -o /var/tmp/from_scwrl_924403374.pdb > /var/tmp/scwrl_924403374.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_924403374.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 525 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1079983403.pdb -s /var/tmp/to_scwrl_1079983403.seq -o /var/tmp/from_scwrl_1079983403.pdb > /var/tmp/scwrl_1079983403.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1079983403.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 519 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1919469993.pdb -s /var/tmp/to_scwrl_1919469993.seq -o /var/tmp/from_scwrl_1919469993.pdb > /var/tmp/scwrl_1919469993.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1919469993.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 528 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_2127028391.pdb -s /var/tmp/to_scwrl_2127028391.seq -o /var/tmp/from_scwrl_2127028391.pdb > /var/tmp/scwrl_2127028391.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2127028391.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 529 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1894837566.pdb -s /var/tmp/to_scwrl_1894837566.seq -o /var/tmp/from_scwrl_1894837566.pdb > /var/tmp/scwrl_1894837566.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1894837566.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 529 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_656155327.pdb -s /var/tmp/to_scwrl_656155327.seq -o /var/tmp/from_scwrl_656155327.pdb > /var/tmp/scwrl_656155327.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_656155327.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 529 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_705725189.pdb -s /var/tmp/to_scwrl_705725189.seq -o /var/tmp/from_scwrl_705725189.pdb > /var/tmp/scwrl_705725189.log sh: line 1: 9898 Killed scwrl3 -i /var/tmp/to_scwrl_705725189.pdb -s /var/tmp/to_scwrl_705725189.seq -o /var/tmp/from_scwrl_705725189.pdb >/var/tmp/scwrl_705725189.log Error: Couldn't open file /var/tmp/from_scwrl_705725189.pdb or /var/tmp/from_scwrl_705725189.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_705725189_b.pdb or decoys//var/tmp/from_scwrl_705725189_b.pdb.gz for input Trying /var/tmp/from_scwrl_705725189_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_705725189_b.pdb or /var/tmp/from_scwrl_705725189_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_705725189_a.pdb or decoys//var/tmp/from_scwrl_705725189_a.pdb.gz for input Trying /var/tmp/from_scwrl_705725189_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_705725189_a.pdb or /var/tmp/from_scwrl_705725189_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_705725189.pdb or /var/tmp/from_scwrl_705725189_b.pdb or /var/tmp/from_scwrl_705725189_a.pdb Error: no new SCWRL conformation added # 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 529 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_77901907.pdb -s /var/tmp/to_scwrl_77901907.seq -o /var/tmp/from_scwrl_77901907.pdb > /var/tmp/scwrl_77901907.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_77901907.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 # Found a chain break before 479 # copying to AlignedFragments data structure # naming current conformation NN_PUT_lab_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1732752209.pdb -s /var/tmp/to_scwrl_1732752209.seq -o /var/tmp/from_scwrl_1732752209.pdb > /var/tmp/scwrl_1732752209.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1732752209.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 477 ; scwrl3 -i /var/tmp/to_scwrl_1890610297.pdb -s /var/tmp/to_scwrl_1890610297.seq -o /var/tmp/from_scwrl_1890610297.pdb > /var/tmp/scwrl_1890610297.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1890610297.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 477 ; scwrl3 -i /var/tmp/to_scwrl_765629670.pdb -s /var/tmp/to_scwrl_765629670.seq -o /var/tmp/from_scwrl_765629670.pdb > /var/tmp/scwrl_765629670.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_765629670.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 477 ; scwrl3 -i /var/tmp/to_scwrl_172369572.pdb -s /var/tmp/to_scwrl_172369572.seq -o /var/tmp/from_scwrl_172369572.pdb > /var/tmp/scwrl_172369572.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_172369572.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 477 ; scwrl3 -i /var/tmp/to_scwrl_2026848505.pdb -s /var/tmp/to_scwrl_2026848505.seq -o /var/tmp/from_scwrl_2026848505.pdb > /var/tmp/scwrl_2026848505.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2026848505.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 477 ; scwrl3 -i /var/tmp/to_scwrl_1814954485.pdb -s /var/tmp/to_scwrl_1814954485.seq -o /var/tmp/from_scwrl_1814954485.pdb > /var/tmp/scwrl_1814954485.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1814954485.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 517 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1528700153.pdb -s /var/tmp/to_scwrl_1528700153.seq -o /var/tmp/from_scwrl_1528700153.pdb > /var/tmp/scwrl_1528700153.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1528700153.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 517 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1780123886.pdb -s /var/tmp/to_scwrl_1780123886.seq -o /var/tmp/from_scwrl_1780123886.pdb > /var/tmp/scwrl_1780123886.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1780123886.pdb # conformation set from SCWRL output # naming current conformation PROTINFO_TS2-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # Found a chain break before 449 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1938398342.pdb -s /var/tmp/to_scwrl_1938398342.seq -o /var/tmp/from_scwrl_1938398342.pdb > /var/tmp/scwrl_1938398342.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1938398342.pdb # conformation set from SCWRL output # naming current conformation PROTINFO_TS3-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # Found a chain break before 484 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_933070283.pdb -s /var/tmp/to_scwrl_933070283.seq -o /var/tmp/from_scwrl_933070283.pdb > /var/tmp/scwrl_933070283.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_933070283.pdb # conformation set from SCWRL output # naming current conformation PROTINFO_TS4-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # Found a chain break before 517 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1755234353.pdb -s /var/tmp/to_scwrl_1755234353.seq -o /var/tmp/from_scwrl_1755234353.pdb > /var/tmp/scwrl_1755234353.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1755234353.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 T0334 can't currently be optimized by undertaker # naming current conformation Pcons6_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_2074425362.pdb -s /var/tmp/to_scwrl_2074425362.seq -o /var/tmp/from_scwrl_2074425362.pdb > /var/tmp/scwrl_2074425362.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2074425362.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 T0334 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pcons6_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1252521674.pdb -s /var/tmp/to_scwrl_1252521674.seq -o /var/tmp/from_scwrl_1252521674.pdb > /var/tmp/scwrl_1252521674.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1252521674.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 T0334 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pcons6_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_364228726.pdb -s /var/tmp/to_scwrl_364228726.seq -o /var/tmp/from_scwrl_364228726.pdb > /var/tmp/scwrl_364228726.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_364228726.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 T0334 can't currently be optimized by undertaker # naming current conformation Pcons6_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1155544923.pdb -s /var/tmp/to_scwrl_1155544923.seq -o /var/tmp/from_scwrl_1155544923.pdb > /var/tmp/scwrl_1155544923.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1155544923.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 T0334 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pcons6_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1948242821.pdb -s /var/tmp/to_scwrl_1948242821.seq -o /var/tmp/from_scwrl_1948242821.pdb > /var/tmp/scwrl_1948242821.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1948242821.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 T0334 can't currently be optimized by undertaker # naming current conformation Phyre-1_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_52559616.pdb -s /var/tmp/to_scwrl_52559616.seq -o /var/tmp/from_scwrl_52559616.pdb > /var/tmp/scwrl_52559616.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_52559616.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 527 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_639216560.pdb -s /var/tmp/to_scwrl_639216560.seq -o /var/tmp/from_scwrl_639216560.pdb > /var/tmp/scwrl_639216560.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_639216560.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 527 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_691093492.pdb -s /var/tmp/to_scwrl_691093492.seq -o /var/tmp/from_scwrl_691093492.pdb > /var/tmp/scwrl_691093492.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_691093492.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 529 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_177392333.pdb -s /var/tmp/to_scwrl_177392333.seq -o /var/tmp/from_scwrl_177392333.pdb > /var/tmp/scwrl_177392333.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_177392333.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 529 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_784028495.pdb -s /var/tmp/to_scwrl_784028495.seq -o /var/tmp/from_scwrl_784028495.pdb > /var/tmp/scwrl_784028495.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_784028495.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 529 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_2122583129.pdb -s /var/tmp/to_scwrl_2122583129.seq -o /var/tmp/from_scwrl_2122583129.pdb > /var/tmp/scwrl_2122583129.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2122583129.pdb # conformation set from SCWRL output # naming current conformation Phyre-2_TS5-scwrl # ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1 # Found a chain break before 527 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_900212356.pdb -s /var/tmp/to_scwrl_900212356.seq -o /var/tmp/from_scwrl_900212356.pdb > /var/tmp/scwrl_900212356.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_900212356.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 T0334 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1708431868.pdb -s /var/tmp/to_scwrl_1708431868.seq -o /var/tmp/from_scwrl_1708431868.pdb > /var/tmp/scwrl_1708431868.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1708431868.pdb # conformation set from SCWRL output # naming current conformation Pmodeller6_TS2-scwrl # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # Found a chain break before 527 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1055082886.pdb -s /var/tmp/to_scwrl_1055082886.seq -o /var/tmp/from_scwrl_1055082886.pdb > /var/tmp/scwrl_1055082886.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1055082886.pdb # conformation set from SCWRL output # naming current conformation Pmodeller6_TS3-scwrl # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # Found a chain break before 457 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_672198703.pdb -s /var/tmp/to_scwrl_672198703.seq -o /var/tmp/from_scwrl_672198703.pdb > /var/tmp/scwrl_672198703.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_672198703.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 # Found a chain break before 457 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1687976612.pdb -s /var/tmp/to_scwrl_1687976612.seq -o /var/tmp/from_scwrl_1687976612.pdb > /var/tmp/scwrl_1687976612.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1687976612.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 423 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_802436805.pdb -s /var/tmp/to_scwrl_802436805.seq -o /var/tmp/from_scwrl_802436805.pdb > /var/tmp/scwrl_802436805.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_802436805.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 446 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1328354029.pdb -s /var/tmp/to_scwrl_1328354029.seq -o /var/tmp/from_scwrl_1328354029.pdb > /var/tmp/scwrl_1328354029.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1328354029.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 447 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_246218155.pdb -s /var/tmp/to_scwrl_246218155.seq -o /var/tmp/from_scwrl_246218155.pdb > /var/tmp/scwrl_246218155.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_246218155.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 447 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_880338712.pdb -s /var/tmp/to_scwrl_880338712.seq -o /var/tmp/from_scwrl_880338712.pdb > /var/tmp/scwrl_880338712.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_880338712.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 466 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_913622593.pdb -s /var/tmp/to_scwrl_913622593.seq -o /var/tmp/from_scwrl_913622593.pdb > /var/tmp/scwrl_913622593.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_913622593.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 484 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_2136828452.pdb -s /var/tmp/to_scwrl_2136828452.seq -o /var/tmp/from_scwrl_2136828452.pdb > /var/tmp/scwrl_2136828452.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2136828452.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 484 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1645968381.pdb -s /var/tmp/to_scwrl_1645968381.seq -o /var/tmp/from_scwrl_1645968381.pdb > /var/tmp/scwrl_1645968381.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1645968381.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 522 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1085992164.pdb -s /var/tmp/to_scwrl_1085992164.seq -o /var/tmp/from_scwrl_1085992164.pdb > /var/tmp/scwrl_1085992164.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1085992164.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 526 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_2016193310.pdb -s /var/tmp/to_scwrl_2016193310.seq -o /var/tmp/from_scwrl_2016193310.pdb > /var/tmp/scwrl_2016193310.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2016193310.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 524 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1313439220.pdb -s /var/tmp/to_scwrl_1313439220.seq -o /var/tmp/from_scwrl_1313439220.pdb > /var/tmp/scwrl_1313439220.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1313439220.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 491 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_467208672.pdb -s /var/tmp/to_scwrl_467208672.seq -o /var/tmp/from_scwrl_467208672.pdb > /var/tmp/scwrl_467208672.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_467208672.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 521 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1648833550.pdb -s /var/tmp/to_scwrl_1648833550.seq -o /var/tmp/from_scwrl_1648833550.pdb > /var/tmp/scwrl_1648833550.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1648833550.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 359 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1104353915.pdb -s /var/tmp/to_scwrl_1104353915.seq -o /var/tmp/from_scwrl_1104353915.pdb > /var/tmp/scwrl_1104353915.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1104353915.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 519 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1400278954.pdb -s /var/tmp/to_scwrl_1400278954.seq -o /var/tmp/from_scwrl_1400278954.pdb > /var/tmp/scwrl_1400278954.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1400278954.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 Faking rotamer for incomplete or colinear backbone at (T0334)Y125 Faking rotamer for incomplete or colinear backbone at (T0334)Y125 # Found a chain break before 519 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1256584256.pdb -s /var/tmp/to_scwrl_1256584256.seq -o /var/tmp/from_scwrl_1256584256.pdb > /var/tmp/scwrl_1256584256.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1256584256.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 527 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1031295631.pdb -s /var/tmp/to_scwrl_1031295631.seq -o /var/tmp/from_scwrl_1031295631.pdb > /var/tmp/scwrl_1031295631.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1031295631.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 527 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_505316982.pdb -s /var/tmp/to_scwrl_505316982.seq -o /var/tmp/from_scwrl_505316982.pdb > /var/tmp/scwrl_505316982.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_505316982.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 527 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1620812982.pdb -s /var/tmp/to_scwrl_1620812982.seq -o /var/tmp/from_scwrl_1620812982.pdb > /var/tmp/scwrl_1620812982.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1620812982.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 457 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_39356907.pdb -s /var/tmp/to_scwrl_39356907.seq -o /var/tmp/from_scwrl_39356907.pdb > /var/tmp/scwrl_39356907.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_39356907.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 457 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_306076156.pdb -s /var/tmp/to_scwrl_306076156.seq -o /var/tmp/from_scwrl_306076156.pdb > /var/tmp/scwrl_306076156.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_306076156.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 527 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1673372598.pdb -s /var/tmp/to_scwrl_1673372598.seq -o /var/tmp/from_scwrl_1673372598.pdb > /var/tmp/scwrl_1673372598.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1673372598.pdb # conformation set from SCWRL output # naming current conformation ROKKY_TS1-scwrl # ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_678573468.pdb -s /var/tmp/to_scwrl_678573468.seq -o /var/tmp/from_scwrl_678573468.pdb > /var/tmp/scwrl_678573468.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_678573468.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 T0334 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_997169649.pdb -s /var/tmp/to_scwrl_997169649.seq -o /var/tmp/from_scwrl_997169649.pdb > /var/tmp/scwrl_997169649.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_997169649.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 Skipped atom 626, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 628, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 630, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 632, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 846, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 848, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 850, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 852, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 1274, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 1276, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 1278, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 1280, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 1286, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 1288, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 1290, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 1292, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1850764932.pdb -s /var/tmp/to_scwrl_1850764932.seq -o /var/tmp/from_scwrl_1850764932.pdb > /var/tmp/scwrl_1850764932.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1850764932.pdb # conformation set from SCWRL output # naming current conformation SAM-T02_AL3-scwrl # ReadConformPDB reading from PDB file servers/SAM-T02_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1462601962.pdb -s /var/tmp/to_scwrl_1462601962.seq -o /var/tmp/from_scwrl_1462601962.pdb > /var/tmp/scwrl_1462601962.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1462601962.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 Skipped atom 694, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 696, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 698, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 700, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 1098, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 1100, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 1102, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 1104, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_972269131.pdb -s /var/tmp/to_scwrl_972269131.seq -o /var/tmp/from_scwrl_972269131.pdb > /var/tmp/scwrl_972269131.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_972269131.pdb # conformation set from SCWRL output # naming current conformation SAM-T02_AL5-scwrl # ReadConformPDB reading from PDB file servers/SAM-T99_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_603493641.pdb -s /var/tmp/to_scwrl_603493641.seq -o /var/tmp/from_scwrl_603493641.pdb > /var/tmp/scwrl_603493641.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_603493641.pdb # conformation set from SCWRL output # naming current conformation SAM-T99_AL1-scwrl # ReadConformPDB reading from PDB file servers/SAM-T99_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1023550185.pdb -s /var/tmp/to_scwrl_1023550185.seq -o /var/tmp/from_scwrl_1023550185.pdb > /var/tmp/scwrl_1023550185.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1023550185.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 T0334 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_2027352016.pdb -s /var/tmp/to_scwrl_2027352016.seq -o /var/tmp/from_scwrl_2027352016.pdb > /var/tmp/scwrl_2027352016.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2027352016.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 T0334 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1275692343.pdb -s /var/tmp/to_scwrl_1275692343.seq -o /var/tmp/from_scwrl_1275692343.pdb > /var/tmp/scwrl_1275692343.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1275692343.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 T0334 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_564043150.pdb -s /var/tmp/to_scwrl_564043150.seq -o /var/tmp/from_scwrl_564043150.pdb > /var/tmp/scwrl_564043150.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_564043150.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 513 # copying to AlignedFragments data structure # naming current conformation SAM_T06_server_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_682305174.pdb -s /var/tmp/to_scwrl_682305174.seq -o /var/tmp/from_scwrl_682305174.pdb > /var/tmp/scwrl_682305174.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_682305174.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 T0334 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_456562727.pdb -s /var/tmp/to_scwrl_456562727.seq -o /var/tmp/from_scwrl_456562727.pdb > /var/tmp/scwrl_456562727.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_456562727.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 T0334 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_810261305.pdb -s /var/tmp/to_scwrl_810261305.seq -o /var/tmp/from_scwrl_810261305.pdb > /var/tmp/scwrl_810261305.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_810261305.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 T0334 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1562643885.pdb -s /var/tmp/to_scwrl_1562643885.seq -o /var/tmp/from_scwrl_1562643885.pdb > /var/tmp/scwrl_1562643885.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1562643885.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 T0334 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1370185319.pdb -s /var/tmp/to_scwrl_1370185319.seq -o /var/tmp/from_scwrl_1370185319.pdb > /var/tmp/scwrl_1370185319.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1370185319.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 447 # copying to AlignedFragments data structure # naming current conformation SP3_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_799606110.pdb -s /var/tmp/to_scwrl_799606110.seq -o /var/tmp/from_scwrl_799606110.pdb > /var/tmp/scwrl_799606110.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_799606110.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 Faking rotamer for incomplete or colinear backbone at (T0334)A173 Faking rotamer for incomplete or colinear backbone at (T0334)A173 # Found a chain break before 517 # copying to AlignedFragments data structure # naming current conformation SP3_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1061128620.pdb -s /var/tmp/to_scwrl_1061128620.seq -o /var/tmp/from_scwrl_1061128620.pdb > /var/tmp/scwrl_1061128620.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1061128620.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 505 # copying to AlignedFragments data structure # naming current conformation SP3_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_308693837.pdb -s /var/tmp/to_scwrl_308693837.seq -o /var/tmp/from_scwrl_308693837.pdb > /var/tmp/scwrl_308693837.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_308693837.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 360 # copying to AlignedFragments data structure # naming current conformation SP3_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_668315774.pdb -s /var/tmp/to_scwrl_668315774.seq -o /var/tmp/from_scwrl_668315774.pdb > /var/tmp/scwrl_668315774.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_668315774.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 507 # copying to AlignedFragments data structure # naming current conformation SP3_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_227084193.pdb -s /var/tmp/to_scwrl_227084193.seq -o /var/tmp/from_scwrl_227084193.pdb > /var/tmp/scwrl_227084193.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_227084193.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 491 # copying to AlignedFragments data structure # naming current conformation SP4_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_775902509.pdb -s /var/tmp/to_scwrl_775902509.seq -o /var/tmp/from_scwrl_775902509.pdb > /var/tmp/scwrl_775902509.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_775902509.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 471 # copying to AlignedFragments data structure # naming current conformation SP4_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_169665677.pdb -s /var/tmp/to_scwrl_169665677.seq -o /var/tmp/from_scwrl_169665677.pdb > /var/tmp/scwrl_169665677.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_169665677.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 Faking rotamer for incomplete or colinear backbone at (T0334)A173 Faking rotamer for incomplete or colinear backbone at (T0334)A173 # Found a chain break before 517 # copying to AlignedFragments data structure # naming current conformation SP4_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1331438108.pdb -s /var/tmp/to_scwrl_1331438108.seq -o /var/tmp/from_scwrl_1331438108.pdb > /var/tmp/scwrl_1331438108.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1331438108.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 527 # copying to AlignedFragments data structure # naming current conformation SP4_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_28697816.pdb -s /var/tmp/to_scwrl_28697816.seq -o /var/tmp/from_scwrl_28697816.pdb > /var/tmp/scwrl_28697816.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_28697816.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 368 # copying to AlignedFragments data structure # naming current conformation SP4_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1426249933.pdb -s /var/tmp/to_scwrl_1426249933.seq -o /var/tmp/from_scwrl_1426249933.pdb > /var/tmp/scwrl_1426249933.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1426249933.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 479 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_215250092.pdb -s /var/tmp/to_scwrl_215250092.seq -o /var/tmp/from_scwrl_215250092.pdb > /var/tmp/scwrl_215250092.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_215250092.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 444 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_534014799.pdb -s /var/tmp/to_scwrl_534014799.seq -o /var/tmp/from_scwrl_534014799.pdb > /var/tmp/scwrl_534014799.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_534014799.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 376 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_899579270.pdb -s /var/tmp/to_scwrl_899579270.seq -o /var/tmp/from_scwrl_899579270.pdb > /var/tmp/scwrl_899579270.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_899579270.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 Faking rotamer for incomplete or colinear backbone at (T0334)A173 Faking rotamer for incomplete or colinear backbone at (T0334)A173 # Found a chain break before 517 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_254607000.pdb -s /var/tmp/to_scwrl_254607000.seq -o /var/tmp/from_scwrl_254607000.pdb > /var/tmp/scwrl_254607000.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_254607000.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 391 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_840090955.pdb -s /var/tmp/to_scwrl_840090955.seq -o /var/tmp/from_scwrl_840090955.pdb > /var/tmp/scwrl_840090955.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_840090955.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 T0334 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_425468221.pdb -s /var/tmp/to_scwrl_425468221.seq -o /var/tmp/from_scwrl_425468221.pdb > /var/tmp/scwrl_425468221.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_425468221.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_bnmx_TS1-scwrl # ReadConformPDB reading from PDB file servers/UNI-EID_expm_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation UNI-EID_expm_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_933180468.pdb -s /var/tmp/to_scwrl_933180468.seq -o /var/tmp/from_scwrl_933180468.pdb > /var/tmp/scwrl_933180468.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_933180468.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_expm_TS1-scwrl # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1837260603.pdb -s /var/tmp/to_scwrl_1837260603.seq -o /var/tmp/from_scwrl_1837260603.pdb > /var/tmp/scwrl_1837260603.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1837260603.pdb # conformation set from SCWRL output # naming current conformation UNI-EID_sfst_AL1-scwrl # ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1 # Found a chain break before 502 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_128749506.pdb -s /var/tmp/to_scwrl_128749506.seq -o /var/tmp/from_scwrl_128749506.pdb > /var/tmp/scwrl_128749506.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_128749506.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 491 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_248298783.pdb -s /var/tmp/to_scwrl_248298783.seq -o /var/tmp/from_scwrl_248298783.pdb > /var/tmp/scwrl_248298783.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_248298783.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 528 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_662046087.pdb -s /var/tmp/to_scwrl_662046087.seq -o /var/tmp/from_scwrl_662046087.pdb > /var/tmp/scwrl_662046087.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_662046087.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 527 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_732243148.pdb -s /var/tmp/to_scwrl_732243148.seq -o /var/tmp/from_scwrl_732243148.pdb > /var/tmp/scwrl_732243148.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_732243148.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 491 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1271848967.pdb -s /var/tmp/to_scwrl_1271848967.seq -o /var/tmp/from_scwrl_1271848967.pdb > /var/tmp/scwrl_1271848967.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1271848967.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 529 # copying to AlignedFragments data structure # naming current conformation beautshot_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_541914456.pdb -s /var/tmp/to_scwrl_541914456.seq -o /var/tmp/from_scwrl_541914456.pdb > /var/tmp/scwrl_541914456.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_541914456.pdb # conformation set from SCWRL output # naming current conformation beautshot_TS1-scwrl # ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation beautshotbase_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_2007935491.pdb -s /var/tmp/to_scwrl_2007935491.seq -o /var/tmp/from_scwrl_2007935491.pdb > /var/tmp/scwrl_2007935491.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2007935491.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 111, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 113, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 115, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 117, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 119, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 121, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 123, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 125, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 127, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 129, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 131, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 133, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 135, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 137, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 139, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 141, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 143, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 145, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 147, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation forecast-s_AL1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1835892118.pdb -s /var/tmp/to_scwrl_1835892118.seq -o /var/tmp/from_scwrl_1835892118.pdb > /var/tmp/scwrl_1835892118.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1835892118.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 T0334 can't currently be optimized by undertaker # naming current conformation forecast-s_AL2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1224219629.pdb -s /var/tmp/to_scwrl_1224219629.seq -o /var/tmp/from_scwrl_1224219629.pdb > /var/tmp/scwrl_1224219629.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1224219629.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 T0334 can't currently be optimized by undertaker # naming current conformation forecast-s_AL3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_317014571.pdb -s /var/tmp/to_scwrl_317014571.seq -o /var/tmp/from_scwrl_317014571.pdb > /var/tmp/scwrl_317014571.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_317014571.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 T0334 can't currently be optimized by undertaker # naming current conformation forecast-s_AL4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_498669776.pdb -s /var/tmp/to_scwrl_498669776.seq -o /var/tmp/from_scwrl_498669776.pdb > /var/tmp/scwrl_498669776.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_498669776.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 T0334 can't currently be optimized by undertaker # naming current conformation forecast-s_AL5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_639379868.pdb -s /var/tmp/to_scwrl_639379868.seq -o /var/tmp/from_scwrl_639379868.pdb > /var/tmp/scwrl_639379868.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_639379868.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 T0334 can't currently be optimized by undertaker # naming current conformation gtg_AL1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1687199890.pdb -s /var/tmp/to_scwrl_1687199890.seq -o /var/tmp/from_scwrl_1687199890.pdb > /var/tmp/scwrl_1687199890.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1687199890.pdb # conformation set from SCWRL output # naming current conformation gtg_AL1-scwrl # ReadConformPDB reading from PDB file servers/gtg_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation gtg_AL2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1298275886.pdb -s /var/tmp/to_scwrl_1298275886.seq -o /var/tmp/from_scwrl_1298275886.pdb > /var/tmp/scwrl_1298275886.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1298275886.pdb # conformation set from SCWRL output # naming current conformation gtg_AL2-scwrl # ReadConformPDB reading from PDB file servers/gtg_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation gtg_AL3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1700508488.pdb -s /var/tmp/to_scwrl_1700508488.seq -o /var/tmp/from_scwrl_1700508488.pdb > /var/tmp/scwrl_1700508488.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1700508488.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 T0334 can't currently be optimized by undertaker # naming current conformation gtg_AL4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1995893728.pdb -s /var/tmp/to_scwrl_1995893728.seq -o /var/tmp/from_scwrl_1995893728.pdb > /var/tmp/scwrl_1995893728.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1995893728.pdb # conformation set from SCWRL output # naming current conformation gtg_AL4-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # Found a chain break before 464 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1966591660.pdb -s /var/tmp/to_scwrl_1966591660.seq -o /var/tmp/from_scwrl_1966591660.pdb > /var/tmp/scwrl_1966591660.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1966591660.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 479 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1927592681.pdb -s /var/tmp/to_scwrl_1927592681.seq -o /var/tmp/from_scwrl_1927592681.pdb > /var/tmp/scwrl_1927592681.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1927592681.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 456 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_624312590.pdb -s /var/tmp/to_scwrl_624312590.seq -o /var/tmp/from_scwrl_624312590.pdb > /var/tmp/scwrl_624312590.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_624312590.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 519 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_2136257337.pdb -s /var/tmp/to_scwrl_2136257337.seq -o /var/tmp/from_scwrl_2136257337.pdb > /var/tmp/scwrl_2136257337.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2136257337.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 519 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1111547143.pdb -s /var/tmp/to_scwrl_1111547143.seq -o /var/tmp/from_scwrl_1111547143.pdb > /var/tmp/scwrl_1111547143.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1111547143.pdb # conformation set from SCWRL output # naming current conformation karypis.srv.2_TS5-scwrl # ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_653010407.pdb -s /var/tmp/to_scwrl_653010407.seq -o /var/tmp/from_scwrl_653010407.pdb > /var/tmp/scwrl_653010407.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_653010407.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 T0334 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1415023623.pdb -s /var/tmp/to_scwrl_1415023623.seq -o /var/tmp/from_scwrl_1415023623.pdb > /var/tmp/scwrl_1415023623.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1415023623.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 T0334 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1326797235.pdb -s /var/tmp/to_scwrl_1326797235.seq -o /var/tmp/from_scwrl_1326797235.pdb > /var/tmp/scwrl_1326797235.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1326797235.pdb # conformation set from SCWRL output # naming current conformation karypis.srv_TS3-scwrl # ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1 # Found a chain break before 517 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1187025205.pdb -s /var/tmp/to_scwrl_1187025205.seq -o /var/tmp/from_scwrl_1187025205.pdb > /var/tmp/scwrl_1187025205.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1187025205.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 519 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_167119246.pdb -s /var/tmp/to_scwrl_167119246.seq -o /var/tmp/from_scwrl_167119246.pdb > /var/tmp/scwrl_167119246.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_167119246.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 328 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1581404235.pdb -s /var/tmp/to_scwrl_1581404235.seq -o /var/tmp/from_scwrl_1581404235.pdb > /var/tmp/scwrl_1581404235.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1581404235.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 524 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_2027116160.pdb -s /var/tmp/to_scwrl_2027116160.seq -o /var/tmp/from_scwrl_2027116160.pdb > /var/tmp/scwrl_2027116160.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2027116160.pdb # conformation set from SCWRL output # naming current conformation keasar-server_TS4-scwrl # ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation keasar-server_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_592587468.pdb -s /var/tmp/to_scwrl_592587468.seq -o /var/tmp/from_scwrl_592587468.pdb > /var/tmp/scwrl_592587468.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_592587468.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 T0334 can't currently be optimized by undertaker # naming current conformation mGen-3D_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_367101056.pdb -s /var/tmp/to_scwrl_367101056.seq -o /var/tmp/from_scwrl_367101056.pdb > /var/tmp/scwrl_367101056.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_367101056.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 T0334 can't currently be optimized by undertaker # naming current conformation nFOLD_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1716893117.pdb -s /var/tmp/to_scwrl_1716893117.seq -o /var/tmp/from_scwrl_1716893117.pdb > /var/tmp/scwrl_1716893117.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1716893117.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: atom 1 has residue number 1 < previous residue 529 in servers/nFOLD_TS2.pdb.gz # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation nFOLD_TS2 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_721336974.pdb -s /var/tmp/to_scwrl_721336974.seq -o /var/tmp/from_scwrl_721336974.pdb > /var/tmp/scwrl_721336974.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_721336974.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: atom 1 has residue number 4 < previous residue 529 in servers/nFOLD_TS3.pdb.gz # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation nFOLD_TS3 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_615399840.pdb -s /var/tmp/to_scwrl_615399840.seq -o /var/tmp/from_scwrl_615399840.pdb > /var/tmp/scwrl_615399840.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_615399840.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 T0334 can't currently be optimized by undertaker # naming current conformation nFOLD_TS4 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_231455557.pdb -s /var/tmp/to_scwrl_231455557.seq -o /var/tmp/from_scwrl_231455557.pdb > /var/tmp/scwrl_231455557.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_231455557.pdb # conformation set from SCWRL output # naming current conformation nFOLD_TS4-scwrl # ReadConformPDB reading from PDB file servers/nFOLD_TS5.pdb.gz looking for model 1 WARNING: atom 1 has residue number 2 < previous residue 381 in servers/nFOLD_TS5.pdb.gz # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation nFOLD_TS5 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1453580121.pdb -s /var/tmp/to_scwrl_1453580121.seq -o /var/tmp/from_scwrl_1453580121.pdb > /var/tmp/scwrl_1453580121.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1453580121.pdb # conformation set from SCWRL output # naming current conformation nFOLD_TS5-scwrl # ReadConformPDB reading from PDB file servers/panther2_TS1.pdb.gz looking for model 1 WARNING: atoms too close: (T0334)I5.N and (T0334)L55.N only 0.000 apart, marking (T0334)L55.N as missing WARNING: atoms too close: (T0334)I5.CA and (T0334)L55.CA only 0.000 apart, marking (T0334)L55.CA as missing WARNING: atoms too close: (T0334)I5.CB and (T0334)L55.CB only 0.000 apart, marking (T0334)L55.CB as missing WARNING: atoms too close: (T0334)I5.CG1 and (T0334)L55.CG only 0.000 apart, marking (T0334)L55.CG as missing WARNING: atoms too close: (T0334)I5.O and (T0334)L55.O only 0.000 apart, marking (T0334)L55.O as missing WARNING: atoms too close: (T0334)I5.C and (T0334)L55.C only 0.000 apart, marking (T0334)L55.C as missing WARNING: atoms too close: (T0334)L55.N and (T0334)Q56.N only 0.000 apart, marking (T0334)L55.N as missing WARNING: atoms too close: (T0334)I5.N and (T0334)Q56.N only 0.000 apart, marking (T0334)Q56.N as missing WARNING: atoms too close: (T0334)L55.CA and (T0334)Q56.CA only 0.000 apart, marking (T0334)Q56.CA as missing WARNING: atoms too close: (T0334)I5.CA and (T0334)Q56.CA only 0.000 apart, marking (T0334)Q56.CA as missing WARNING: atoms too close: (T0334)L55.CB and (T0334)Q56.CB only 0.000 apart, marking (T0334)Q56.CB as missing WARNING: atoms too close: (T0334)I5.CB and (T0334)Q56.CB only 0.000 apart, marking (T0334)Q56.CB as missing WARNING: atoms too close: (T0334)L55.CG and (T0334)Q56.CG only 0.000 apart, marking (T0334)Q56.CG as missing WARNING: atoms too close: (T0334)I5.CG1 and (T0334)Q56.CG only 0.000 apart, marking (T0334)Q56.CG as missing WARNING: atoms too close: (T0334)L55.O and (T0334)Q56.O only 0.000 apart, marking (T0334)Q56.O as missing WARNING: atoms too close: (T0334)I5.O and (T0334)Q56.O only 0.000 apart, marking (T0334)Q56.O as missing WARNING: atoms too close: (T0334)L55.C and (T0334)Q56.C only 0.000 apart, marking (T0334)Q56.C as missing WARNING: atoms too close: (T0334)I5.C and (T0334)Q56.C only 0.000 apart, marking (T0334)Q56.C as missing WARNING: atoms too close: (T0334)Q56.N and (T0334)P66.N only 0.000 apart, marking (T0334)Q56.N as missing WARNING: atoms too close: (T0334)L55.N and (T0334)P66.N only 0.000 apart, marking (T0334)L55.N as missing WARNING: atoms too close: (T0334)I5.N and (T0334)P66.N only 0.000 apart, marking (T0334)P66.N as missing WARNING: atoms too close: (T0334)Q56.CA and (T0334)P66.CA only 0.000 apart, marking (T0334)P66.CA as missing WARNING: atoms too close: (T0334)L55.CA and (T0334)P66.CA only 0.000 apart, marking (T0334)P66.CA as missing WARNING: atoms too close: (T0334)I5.CA and (T0334)P66.CA only 0.000 apart, marking (T0334)P66.CA as missing WARNING: atoms too close: (T0334)Q56.CB and (T0334)P66.CB only 0.000 apart, marking (T0334)P66.CB as missing WARNING: atoms too close: (T0334)L55.CB and (T0334)P66.CB only 0.000 apart, marking (T0334)P66.CB as missing WARNING: atoms too close: (T0334)I5.CB and (T0334)P66.CB only 0.000 apart, marking (T0334)P66.CB as missing WARNING: atoms too close: (T0334)Q56.O and (T0334)P66.O only 0.000 apart, marking (T0334)P66.O as missing WARNING: atoms too close: (T0334)L55.O and (T0334)P66.O only 0.000 apart, marking (T0334)P66.O as missing WARNING: atoms too close: (T0334)I5.O and (T0334)P66.O only 0.000 apart, marking (T0334)P66.O as missing WARNING: atoms too close: (T0334)Q56.C and (T0334)P66.C only 0.000 apart, marking (T0334)P66.C as missing WARNING: atoms too close: (T0334)L55.C and (T0334)P66.C only 0.000 apart, marking (T0334)P66.C as missing WARNING: atoms too close: (T0334)I5.C and (T0334)P66.C only 0.000 apart, marking (T0334)P66.C as missing WARNING: atoms too close: (T0334)P66.N and (T0334)V80.N only 0.000 apart, marking (T0334)P66.N as missing WARNING: atoms too close: (T0334)Q56.N and (T0334)V80.N only 0.000 apart, marking (T0334)Q56.N as missing WARNING: atoms too close: (T0334)L55.N and (T0334)V80.N only 0.000 apart, marking (T0334)L55.N as missing WARNING: atoms too close: (T0334)I5.N and (T0334)V80.N only 0.000 apart, marking (T0334)V80.N as missing WARNING: atoms too close: (T0334)P66.CA and (T0334)V80.CA only 0.000 apart, marking (T0334)V80.CA as missing WARNING: atoms too close: (T0334)Q56.CA and (T0334)V80.CA only 0.000 apart, marking (T0334)V80.CA as missing WARNING: atoms too close: (T0334)L55.CA and (T0334)V80.CA only 0.000 apart, marking (T0334)V80.CA as missing WARNING: atoms too close: (T0334)I5.CA and (T0334)V80.CA only 0.000 apart, marking (T0334)V80.CA as missing WARNING: atoms too close: (T0334)P66.CB and (T0334)V80.CB only 0.000 apart, marking (T0334)V80.CB as missing WARNING: atoms too close: (T0334)Q56.CB and (T0334)V80.CB only 0.000 apart, marking (T0334)V80.CB as missing WARNING: atoms too close: (T0334)L55.CB and (T0334)V80.CB only 0.000 apart, marking (T0334)V80.CB as missing WARNING: atoms too close: (T0334)I5.CB and (T0334)V80.CB only 0.000 apart, marking (T0334)V80.CB as missing WARNING: atoms too close: (T0334)Q56.CG and (T0334)V80.CG1 only 0.000 apart, marking (T0334)V80.CG1 as missing WARNING: atoms too close: (T0334)L55.CG and (T0334)V80.CG1 only 0.000 apart, marking (T0334)V80.CG1 as missing WARNING: atoms too close: (T0334)I5.CG1 and (T0334)V80.CG1 only 0.000 apart, marking (T0334)V80.CG1 as missing WARNING: atoms too close: (T0334)P66.O and (T0334)V80.O only 0.000 apart, marking (T0334)V80.O as missing WARNING: atoms too close: (T0334)Q56.O and (T0334)V80.O only 0.000 apart, marking (T0334)V80.O as missing WARNING: atoms too close: (T0334)L55.O and (T0334)V80.O only 0.000 apart, marking (T0334)V80.O as missing WARNING: atoms too close: (T0334)I5.O and (T0334)V80.O only 0.000 apart, marking (T0334)V80.O as missing WARNING: atoms too close: (T0334)P66.C and (T0334)V80.C only 0.000 apart, marking (T0334)V80.C as missing WARNING: atoms too close: (T0334)Q56.C and (T0334)V80.C only 0.000 apart, marking (T0334)V80.C as missing WARNING: atoms too close: (T0334)L55.C and (T0334)V80.C only 0.000 apart, marking (T0334)V80.C as missing WARNING: atoms too close: (T0334)I5.C and (T0334)V80.C only 0.000 apart, marking (T0334)V80.C as missing WARNING: atoms too close: (T0334)V80.N and (T0334)A81.N only 0.000 apart, marking (T0334)V80.N as missing WARNING: atoms too close: (T0334)P66.N and (T0334)A81.N only 0.000 apart, marking (T0334)P66.N as missing WARNING: atoms too close: (T0334)Q56.N and (T0334)A81.N only 0.000 apart, marking (T0334)Q56.N as missing WARNING: atoms too close: (T0334)L55.N and (T0334)A81.N only 0.000 apart, marking (T0334)L55.N as missing WARNING: atoms too close: (T0334)I5.N and (T0334)A81.N only 0.000 apart, marking (T0334)A81.N as missing WARNING: atoms too close: (T0334)V80.CA and (T0334)A81.CA only 0.000 apart, marking (T0334)A81.CA as missing WARNING: atoms too close: (T0334)P66.CA and (T0334)A81.CA only 0.000 apart, marking (T0334)A81.CA as missing WARNING: atoms too close: (T0334)Q56.CA and (T0334)A81.CA only 0.000 apart, marking (T0334)A81.CA as missing WARNING: atoms too close: (T0334)L55.CA and (T0334)A81.CA only 0.000 apart, marking (T0334)A81.CA as missing WARNING: atoms too close: (T0334)I5.CA and (T0334)A81.CA only 0.000 apart, marking (T0334)A81.CA as missing WARNING: atoms too close: (T0334)V80.CB and (T0334)A81.CB only 0.000 apart, marking (T0334)A81.CB as missing WARNING: atoms too close: (T0334)P66.CB and (T0334)A81.CB only 0.000 apart, marking (T0334)A81.CB as missing WARNING: atoms too close: (T0334)Q56.CB and (T0334)A81.CB only 0.000 apart, marking (T0334)A81.CB as missing WARNING: atoms too close: (T0334)L55.CB and (T0334)A81.CB only 0.000 apart, marking (T0334)A81.CB as missing WARNING: atoms too close: (T0334)I5.CB and (T0334)A81.CB only 0.000 apart, marking (T0334)A81.CB as missing WARNING: atoms too close: (T0334)V80.O and (T0334)A81.O only 0.000 apart, marking (T0334)A81.O as missing WARNING: atoms too close: (T0334)P66.O and (T0334)A81.O only 0.000 apart, marking (T0334)A81.O as missing WARNING: atoms too close: (T0334)Q56.O and (T0334)A81.O only 0.000 apart, marking (T0334)A81.O as missing WARNING: atoms too close: (T0334)L55.O and (T0334)A81.O only 0.000 apart, marking (T0334)A81.O as missing WARNING: atoms too close: (T0334)I5.O and (T0334)A81.O only 0.000 apart, marking (T0334)A81.O as missing WARNING: atoms too close: (T0334)V80.C and (T0334)A81.C only 0.000 apart, marking (T0334)A81.C as missing WARNING: atoms too close: (T0334)P66.C and (T0334)A81.C only 0.000 apart, marking (T0334)A81.C as missing WARNING: atoms too close: (T0334)Q56.C and (T0334)A81.C only 0.000 apart, marking (T0334)A81.C as missing WARNING: atoms too close: (T0334)L55.C and (T0334)A81.C only 0.000 apart, marking (T0334)A81.C as missing WARNING: atoms too close: (T0334)I5.C and (T0334)A81.C only 0.000 apart, marking (T0334)A81.C as missing # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation panther2_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_1887248807.pdb -s /var/tmp/to_scwrl_1887248807.seq -o /var/tmp/from_scwrl_1887248807.pdb > /var/tmp/scwrl_1887248807.log Error: Couldn't open file /var/tmp/from_scwrl_1887248807.pdb or /var/tmp/from_scwrl_1887248807.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1887248807_b.pdb or decoys//var/tmp/from_scwrl_1887248807_b.pdb.gz for input Trying /var/tmp/from_scwrl_1887248807_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_1887248807_b.pdb or /var/tmp/from_scwrl_1887248807_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1887248807_a.pdb or decoys//var/tmp/from_scwrl_1887248807_a.pdb.gz for input Trying /var/tmp/from_scwrl_1887248807_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_1887248807_a.pdb or /var/tmp/from_scwrl_1887248807_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_1887248807.pdb or /var/tmp/from_scwrl_1887248807_b.pdb or /var/tmp/from_scwrl_1887248807_a.pdb Error: no new SCWRL conformation added # naming current conformation panther2_TS1-scwrl # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # Found a chain break before 529 # copying to AlignedFragments data structure # naming current conformation shub_TS1 # request to SCWRL produces command: ulimit -t 477 ; scwrl3 -i /var/tmp/to_scwrl_773370014.pdb -s /var/tmp/to_scwrl_773370014.seq -o /var/tmp/from_scwrl_773370014.pdb > /var/tmp/scwrl_773370014.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_773370014.pdb # conformation set from SCWRL output # naming current conformation shub_TS1-scwrl # command:CPU_time= 173.459 sec, elapsed time= 4059.52 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 = -38.5179 shub_TS1 costs 0 real_cost = -30.8666 panther2_TS1-scwrl costs 0 real_cost = 1045.49 nFOLD_TS5-scwrl costs 0 real_cost = 369.043 nFOLD_TS5 costs 0 real_cost = 649.303 nFOLD_TS4-scwrl costs 0 real_cost = 421.316 nFOLD_TS4 costs 0 real_cost = 683.458 nFOLD_TS3-scwrl costs 0 real_cost = 494.064 nFOLD_TS3 costs 0 real_cost = 716.932 nFOLD_TS2-scwrl costs 0 real_cost = 584.708 nFOLD_TS2 costs 0 real_cost = 766.087 nFOLD_TS1-scwrl costs 0 real_cost = -223.921 nFOLD_TS1 costs 0 real_cost = 77.2252 mGen-3D_TS1-scwrl costs 0 real_cost = -197.725 mGen-3D_TS1 costs 0 real_cost = 98.1465 keasar-server_TS5-scwrl costs 0 real_cost = 469.185 keasar-server_TS5 costs 0 real_cost = 473.874 keasar-server_TS4-scwrl costs 0 real_cost = -202.516 keasar-server_TS4 costs 0 real_cost = -194.579 keasar-server_TS3-scwrl costs 0 real_cost = -203.676 keasar-server_TS3 costs 0 real_cost = -199.806 keasar-server_TS2-scwrl costs 0 real_cost = -208.128 keasar-server_TS2 costs 0 real_cost = -208.589 keasar-server_TS1-scwrl costs 0 real_cost = -230.329 keasar-server_TS1 costs 0 real_cost = -224.575 karypis.srv_TS3-scwrl costs 0 real_cost = 780.26 karypis.srv_TS3 costs 0 real_cost = 777.923 karypis.srv_TS2-scwrl costs 0 real_cost = -257.671 karypis.srv_TS2 costs 0 real_cost = -258 karypis.srv_TS1-scwrl costs 0 real_cost = -254.271 karypis.srv_TS1 costs 0 real_cost = -253.244 karypis.srv.2_TS5-scwrl costs 0 real_cost = -165.031 karypis.srv.2_TS5 costs 0 real_cost = -165.176 karypis.srv.2_TS4-scwrl costs 0 real_cost = -217.674 karypis.srv.2_TS4 costs 0 real_cost = -217.868 karypis.srv.2_TS3-scwrl costs 0 real_cost = -240.802 karypis.srv.2_TS3 costs 0 real_cost = -240.872 karypis.srv.2_TS2-scwrl costs 0 real_cost = -201.24 karypis.srv.2_TS2 costs 0 real_cost = -201.662 karypis.srv.2_TS1-scwrl costs 0 real_cost = -146.7 karypis.srv.2_TS1 costs 0 real_cost = -146.511 gtg_AL4-scwrl costs 0 real_cost = 689.275 gtg_AL4 costs 0 real_cost = 875.161 gtg_AL3-scwrl costs 0 real_cost = 598.653 gtg_AL3 costs 0 real_cost = 814.601 gtg_AL2-scwrl costs 0 real_cost = 602.589 gtg_AL2 costs 0 real_cost = 810.401 gtg_AL1-scwrl costs 0 real_cost = 451.197 gtg_AL1 costs 0 real_cost = 711.458 forecast-s_AL5-scwrl costs 0 real_cost = 925.042 forecast-s_AL5 costs 0 real_cost = 976.873 forecast-s_AL4-scwrl costs 0 real_cost = 949.151 forecast-s_AL4 costs 0 real_cost = 1001.06 forecast-s_AL3-scwrl costs 0 real_cost = 1027.57 forecast-s_AL3 costs 0 real_cost = 1094.46 forecast-s_AL2-scwrl costs 0 real_cost = 886.429 forecast-s_AL2 costs 0 real_cost = 954.092 forecast-s_AL1-scwrl costs 0 real_cost = 888.389 forecast-s_AL1 costs 0 real_cost = 946.553 beautshotbase_TS1-scwrl costs 0 real_cost = -249.695 beautshotbase_TS1 costs 0 real_cost = -236.428 beautshot_TS1-scwrl costs 0 real_cost = -90.4292 beautshot_TS1 costs 0 real_cost = -78.9367 Zhang-Server_TS5-scwrl costs 0 real_cost = -277.021 Zhang-Server_TS5 costs 0 real_cost = -277.248 Zhang-Server_TS4-scwrl costs 0 real_cost = -271.666 Zhang-Server_TS4 costs 0 real_cost = -271.571 Zhang-Server_TS3-scwrl costs 0 real_cost = -264.488 Zhang-Server_TS3 costs 0 real_cost = -264.82 Zhang-Server_TS2-scwrl costs 0 real_cost = -258.044 Zhang-Server_TS2 costs 0 real_cost = -258.04 Zhang-Server_TS1-scwrl costs 0 real_cost = -281.578 Zhang-Server_TS1 costs 0 real_cost = -281.445 UNI-EID_sfst_AL1-scwrl costs 0 real_cost = -243.748 UNI-EID_sfst_AL1 costs 0 real_cost = 149.434 UNI-EID_expm_TS1-scwrl costs 0 real_cost = -212.978 UNI-EID_expm_TS1 costs 0 real_cost = 74.5049 UNI-EID_bnmx_TS1-scwrl costs 0 real_cost = -248.816 UNI-EID_bnmx_TS1 costs 0 real_cost = 147.856 SPARKS2_TS5-scwrl costs 0 real_cost = 340.671 SPARKS2_TS5 costs 0 real_cost = 346.435 SPARKS2_TS4-scwrl costs 0 real_cost = 371.256 SPARKS2_TS4 costs 0 real_cost = 371.806 SPARKS2_TS3-scwrl costs 0 real_cost = 235.182 SPARKS2_TS3 costs 0 real_cost = 240.175 SPARKS2_TS2-scwrl costs 0 real_cost = 239.464 SPARKS2_TS2 costs 0 real_cost = 243.965 SPARKS2_TS1-scwrl costs 0 real_cost = -280.682 SPARKS2_TS1 costs 0 real_cost = -285.704 SP4_TS5-scwrl costs 0 real_cost = 347.5 SP4_TS5 costs 0 real_cost = 352.19 SP4_TS4-scwrl costs 0 real_cost = 262.708 SP4_TS4 costs 0 real_cost = 264.166 SP4_TS3-scwrl costs 0 real_cost = 344.315 SP4_TS3 costs 0 real_cost = 348.66 SP4_TS2-scwrl costs 0 real_cost = 234.814 SP4_TS2 costs 0 real_cost = 239.538 SP4_TS1-scwrl costs 0 real_cost = -254.689 SP4_TS1 costs 0 real_cost = -263.463 SP3_TS5-scwrl costs 0 real_cost = 263.74 SP3_TS5 costs 0 real_cost = 267.409 SP3_TS4-scwrl costs 0 real_cost = 342.001 SP3_TS4 costs 0 real_cost = 343.547 SP3_TS3-scwrl costs 0 real_cost = 235.344 SP3_TS3 costs 0 real_cost = 241.184 SP3_TS2-scwrl costs 0 real_cost = 300.584 SP3_TS2 costs 0 real_cost = 301.967 SP3_TS1-scwrl costs 0 real_cost = -275.591 SP3_TS1 costs 0 real_cost = -278.578 SAM_T06_server_TS5-scwrl costs 0 real_cost = 663.761 SAM_T06_server_TS5 costs 0 real_cost = 598.676 SAM_T06_server_TS4-scwrl costs 0 real_cost = 584.064 SAM_T06_server_TS4 costs 0 real_cost = 519.509 SAM_T06_server_TS3-scwrl costs 0 real_cost = 486.754 SAM_T06_server_TS3 costs 0 real_cost = 440.378 SAM_T06_server_TS2-scwrl costs 0 real_cost = 153.843 SAM_T06_server_TS2 costs 0 real_cost = 87.4865 SAM_T06_server_TS1-scwrl costs 0 real_cost = -96.7331 SAM_T06_server_TS1 costs 0 real_cost = -97.3815 SAM-T99_AL5-scwrl costs 0 real_cost = 599.328 SAM-T99_AL5 costs 0 real_cost = 808.592 SAM-T99_AL4-scwrl costs 0 real_cost = -185.568 SAM-T99_AL4 costs 0 real_cost = 184.127 SAM-T99_AL3-scwrl costs 0 real_cost = -227.41 SAM-T99_AL3 costs 0 real_cost = 164.393 SAM-T99_AL2-scwrl costs 0 real_cost = -233.306 SAM-T99_AL2 costs 0 real_cost = 160.605 SAM-T99_AL1-scwrl costs 0 real_cost = -231.087 SAM-T99_AL1 costs 0 real_cost = 162.551 SAM-T02_AL5-scwrl costs 0 real_cost = 713.677 SAM-T02_AL5 costs 0 real_cost = 896.259 SAM-T02_AL4-scwrl costs 0 real_cost = 487.569 SAM-T02_AL4 costs 0 real_cost = 725.682 SAM-T02_AL3-scwrl costs 0 real_cost = 498.119 SAM-T02_AL3 costs 0 real_cost = 735.438 SAM-T02_AL2-scwrl costs 0 real_cost = 456.661 SAM-T02_AL2 costs 0 real_cost = 721.146 SAM-T02_AL1-scwrl costs 0 real_cost = 22.1967 SAM-T02_AL1 costs 0 real_cost = 414.436 ROKKY_TS1-scwrl costs 0 real_cost = -239.64 ROKKY_TS1 costs 0 real_cost = -246.842 ROBETTA_TS5-scwrl costs 0 real_cost = -265.333 ROBETTA_TS5 costs 0 real_cost = -269.542 ROBETTA_TS4-scwrl costs 0 real_cost = -268.299 ROBETTA_TS4 costs 0 real_cost = -273.405 ROBETTA_TS3-scwrl costs 0 real_cost = -260.904 ROBETTA_TS3 costs 0 real_cost = -265.507 ROBETTA_TS2-scwrl costs 0 real_cost = -255.265 ROBETTA_TS2 costs 0 real_cost = -260.957 ROBETTA_TS1-scwrl costs 0 real_cost = -263.835 ROBETTA_TS1 costs 0 real_cost = -272.079 RAPTOR_TS5-scwrl costs 0 real_cost = 415.999 RAPTOR_TS5 costs 0 real_cost = 416.535 RAPTOR_TS4-scwrl costs 0 real_cost = 224.12 RAPTOR_TS4 costs 0 real_cost = 228.318 RAPTOR_TS3-scwrl costs 0 real_cost = 360.968 RAPTOR_TS3 costs 0 real_cost = 364.44 RAPTOR_TS2-scwrl costs 0 real_cost = 209.903 RAPTOR_TS2 costs 0 real_cost = 216.059 RAPTOR_TS1-scwrl costs 0 real_cost = -245.549 RAPTOR_TS1 costs 0 real_cost = -249.934 RAPTORESS_TS5-scwrl costs 0 real_cost = 239.645 RAPTORESS_TS5 costs 0 real_cost = 248.862 RAPTORESS_TS4-scwrl costs 0 real_cost = 332.626 RAPTORESS_TS4 costs 0 real_cost = 336.408 RAPTORESS_TS3-scwrl costs 0 real_cost = 221.387 RAPTORESS_TS3 costs 0 real_cost = 228.645 RAPTORESS_TS2-scwrl costs 0 real_cost = -220.553 RAPTORESS_TS2 costs 0 real_cost = -219.642 RAPTORESS_TS1-scwrl costs 0 real_cost = -220.553 RAPTORESS_TS1 costs 0 real_cost = -219.642 RAPTOR-ACE_TS5-scwrl costs 0 real_cost = -31.7773 RAPTOR-ACE_TS5 costs 0 real_cost = -36.8209 RAPTOR-ACE_TS4-scwrl costs 0 real_cost = -275.591 RAPTOR-ACE_TS4 costs 0 real_cost = -278.578 RAPTOR-ACE_TS3-scwrl costs 0 real_cost = -242.221 RAPTOR-ACE_TS3 costs 0 real_cost = -243.009 RAPTOR-ACE_TS2-scwrl costs 0 real_cost = -282.681 RAPTOR-ACE_TS2 costs 0 real_cost = -281.527 RAPTOR-ACE_TS1-scwrl costs 0 real_cost = -250.969 RAPTOR-ACE_TS1 costs 0 real_cost = -253.647 Pmodeller6_TS5-scwrl costs 0 real_cost = -268.299 Pmodeller6_TS5 costs 0 real_cost = -273.405 Pmodeller6_TS4-scwrl costs 0 real_cost = -265.333 Pmodeller6_TS4 costs 0 real_cost = -269.542 Pmodeller6_TS3-scwrl costs 0 real_cost = -263.835 Pmodeller6_TS3 costs 0 real_cost = -272.079 Pmodeller6_TS2-scwrl costs 0 real_cost = -214.331 Pmodeller6_TS2 costs 0 real_cost = -223.836 Pmodeller6_TS1-scwrl costs 0 real_cost = -260.904 Pmodeller6_TS1 costs 0 real_cost = -265.507 Phyre-2_TS5-scwrl costs 0 real_cost = -207.772 Phyre-2_TS5 costs 0 real_cost = -208.285 Phyre-2_TS4-scwrl costs 0 real_cost = -208.517 Phyre-2_TS4 costs 0 real_cost = -208.922 Phyre-2_TS3-scwrl costs 0 real_cost = -207.988 Phyre-2_TS3 costs 0 real_cost = -208.514 Phyre-2_TS2-scwrl costs 0 real_cost = -203.56 Phyre-2_TS2 costs 0 real_cost = -204.489 Phyre-2_TS1-scwrl costs 0 real_cost = -204.291 Phyre-2_TS1 costs 0 real_cost = -204.992 Phyre-1_TS1-scwrl costs 0 real_cost = 459.274 Phyre-1_TS1 costs 0 real_cost = 452.584 Pcons6_TS5-scwrl costs 0 real_cost = -204.655 Pcons6_TS5 costs 0 real_cost = -210.66 Pcons6_TS4-scwrl costs 0 real_cost = -214.331 Pcons6_TS4 costs 0 real_cost = -223.836 Pcons6_TS3-scwrl costs 0 real_cost = -202.018 Pcons6_TS3 costs 0 real_cost = -201.376 Pcons6_TS2-scwrl costs 0 real_cost = -213.003 Pcons6_TS2 costs 0 real_cost = -211.893 Pcons6_TS1-scwrl costs 0 real_cost = -202.927 Pcons6_TS1 costs 0 real_cost = -206.628 PROTINFO_TS5-scwrl costs 0 real_cost = -255.477 PROTINFO_TS5 costs 0 real_cost = -254.299 PROTINFO_TS4-scwrl costs 0 real_cost = -256.008 PROTINFO_TS4 costs 0 real_cost = -255.21 PROTINFO_TS3-scwrl costs 0 real_cost = -245.255 PROTINFO_TS3 costs 0 real_cost = -251.712 PROTINFO_TS2-scwrl costs 0 real_cost = -240.949 PROTINFO_TS2 costs 0 real_cost = -249.296 PROTINFO_TS1-scwrl costs 0 real_cost = -269.177 PROTINFO_TS1 costs 0 real_cost = -273.381 PROTINFO-AB_TS5-scwrl costs 0 real_cost = -233.449 PROTINFO-AB_TS5 costs 0 real_cost = -236.624 PROTINFO-AB_TS4-scwrl costs 0 real_cost = -241.394 PROTINFO-AB_TS4 costs 0 real_cost = -244.015 PROTINFO-AB_TS3-scwrl costs 0 real_cost = -238.641 PROTINFO-AB_TS3 costs 0 real_cost = -242.558 PROTINFO-AB_TS2-scwrl costs 0 real_cost = -240.008 PROTINFO-AB_TS2 costs 0 real_cost = -241.351 PROTINFO-AB_TS1-scwrl costs 0 real_cost = -243.027 PROTINFO-AB_TS1 costs 0 real_cost = -245.557 NN_PUT_lab_TS1-scwrl costs 0 real_cost = -280.682 NN_PUT_lab_TS1 costs 0 real_cost = -285.704 MetaTasser_TS5-scwrl costs 0 real_cost = 134.339 MetaTasser_TS5 costs 0 real_cost = 136.148 MetaTasser_TS4-scwrl costs 0 real_cost = 179.98 MetaTasser_TS3-scwrl costs 0 real_cost = 202.268 MetaTasser_TS3 costs 0 real_cost = 206.051 MetaTasser_TS2-scwrl costs 0 real_cost = -147.146 MetaTasser_TS2 costs 0 real_cost = -140.716 MetaTasser_TS1-scwrl costs 0 real_cost = -228.06 MetaTasser_TS1 costs 0 real_cost = -222.494 Ma-OPUS-server_TS5-scwrl costs 0 real_cost = 321.339 Ma-OPUS-server_TS5 costs 0 real_cost = 326.511 Ma-OPUS-server_TS4-scwrl costs 0 real_cost = 307.313 Ma-OPUS-server_TS4 costs 0 real_cost = 309.188 Ma-OPUS-server_TS3-scwrl costs 0 real_cost = 218.531 Ma-OPUS-server_TS3 costs 0 real_cost = 220.07 Ma-OPUS-server_TS2-scwrl costs 0 real_cost = 245.015 Ma-OPUS-server_TS2 costs 0 real_cost = 248.85 Ma-OPUS-server_TS1-scwrl costs 0 real_cost = -272.078 Ma-OPUS-server_TS1 costs 0 real_cost = -272.965 Ma-OPUS-server2_TS5-scwrl costs 0 real_cost = 262.89 Ma-OPUS-server2_TS5 costs 0 real_cost = 262.302 Ma-OPUS-server2_TS4-scwrl costs 0 real_cost = 298.65 Ma-OPUS-server2_TS4 costs 0 real_cost = 301.812 Ma-OPUS-server2_TS3-scwrl costs 0 real_cost = 242.561 Ma-OPUS-server2_TS3 costs 0 real_cost = 246.823 Ma-OPUS-server2_TS2-scwrl costs 0 real_cost = 356.1 Ma-OPUS-server2_TS1-scwrl costs 0 real_cost = -272.078 Ma-OPUS-server2_TS1 costs 0 real_cost = -272.965 LOOPP_TS5-scwrl costs 0 real_cost = 468.329 LOOPP_TS5 costs 0 real_cost = 472.297 LOOPP_TS4-scwrl costs 0 real_cost = 270.663 LOOPP_TS4 costs 0 real_cost = 272.958 LOOPP_TS3-scwrl costs 0 real_cost = 261.903 LOOPP_TS3 costs 0 real_cost = 259.917 LOOPP_TS2-scwrl costs 0 real_cost = 273.946 LOOPP_TS2 costs 0 real_cost = 277.614 LOOPP_TS1-scwrl costs 0 real_cost = -182.797 LOOPP_TS1 costs 0 real_cost = -190.179 Huber-Torda-Server_TS5-scwrl costs 0 real_cost = 709.633 Huber-Torda-Server_TS5 costs 0 real_cost = 841.374 Huber-Torda-Server_TS4-scwrl costs 0 real_cost = 704.455 Huber-Torda-Server_TS4 costs 0 real_cost = 828.538 Huber-Torda-Server_TS3-scwrl costs 0 real_cost = 595.913 Huber-Torda-Server_TS3 costs 0 real_cost = 783.212 Huber-Torda-Server_TS2-scwrl costs 0 real_cost = 649.59 Huber-Torda-Server_TS2 costs 0 real_cost = 821.948 Huber-Torda-Server_TS1-scwrl costs 0 real_cost = -237.388 Huber-Torda-Server_TS1 costs 0 real_cost = 60.1413 HHpred3_TS1-scwrl costs 0 real_cost = -242.317 HHpred3_TS1 costs 0 real_cost = -249.559 HHpred2_TS1-scwrl costs 0 real_cost = -242.317 HHpred2_TS1 costs 0 real_cost = -249.559 HHpred1_TS1-scwrl costs 0 real_cost = -242.317 HHpred1_TS1 costs 0 real_cost = -249.559 GeneSilicoMetaServer_TS5-scwrl costs 0 real_cost = -34.7149 GeneSilicoMetaServer_TS5 costs 0 real_cost = -35.9762 GeneSilicoMetaServer_TS4-scwrl costs 0 real_cost = -228.834 GeneSilicoMetaServer_TS4 costs 0 real_cost = -231.475 GeneSilicoMetaServer_TS3-scwrl costs 0 real_cost = -277.591 GeneSilicoMetaServer_TS3 costs 0 real_cost = -280.107 GeneSilicoMetaServer_TS2-scwrl costs 0 real_cost = -275.165 GeneSilicoMetaServer_TS2 costs 0 real_cost = -278.695 GeneSilicoMetaServer_TS1-scwrl costs 0 real_cost = -242.666 GeneSilicoMetaServer_TS1 costs 0 real_cost = -243.58 FUNCTION_TS5-scwrl costs 0 real_cost = -229.933 FUNCTION_TS5 costs 0 real_cost = -238.544 FUNCTION_TS4-scwrl costs 0 real_cost = -250.243 FUNCTION_TS4 costs 0 real_cost = -258.843 FUNCTION_TS3-scwrl costs 0 real_cost = -250.894 FUNCTION_TS3 costs 0 real_cost = -256.549 FUNCTION_TS2-scwrl costs 0 real_cost = -250.49 FUNCTION_TS2 costs 0 real_cost = -251.746 FUNCTION_TS1-scwrl costs 0 real_cost = -244.973 FUNCTION_TS1 costs 0 real_cost = -253.767 FUGUE_AL5-scwrl costs 0 real_cost = 569.662 FUGUE_AL5 costs 0 real_cost = 840.718 FUGUE_AL4-scwrl costs 0 real_cost = 627.112 FUGUE_AL4 costs 0 real_cost = 881.556 FUGUE_AL3-scwrl costs 0 real_cost = 636.061 FUGUE_AL3 costs 0 real_cost = 892.95 FUGUE_AL2-scwrl costs 0 real_cost = 927.209 FUGUE_AL2 costs 0 real_cost = 1051.06 FUGUE_AL1-scwrl costs 0 real_cost = -247.913 FUGUE_AL1 costs 0 real_cost = 151.553 FUGMOD_TS5-scwrl costs 0 real_cost = 388.062 FUGMOD_TS5 costs 0 real_cost = 389.69 FUGMOD_TS4-scwrl costs 0 real_cost = 421.801 FUGMOD_TS4 costs 0 real_cost = 429.451 FUGMOD_TS3-scwrl costs 0 real_cost = 369.284 FUGMOD_TS3 costs 0 real_cost = 372.281 FUGMOD_TS2-scwrl costs 0 real_cost = 903.488 FUGMOD_TS2 costs 0 real_cost = 903.838 FUGMOD_TS1-scwrl costs 0 real_cost = -267.517 FUGMOD_TS1 costs 0 real_cost = -273.16 FPSOLVER-SERVER_TS5-scwrl costs 0 real_cost = 375.706 FPSOLVER-SERVER_TS5 costs 0 real_cost = 380.052 FPSOLVER-SERVER_TS4-scwrl costs 0 real_cost = 412.835 FPSOLVER-SERVER_TS4 costs 0 real_cost = 412.223 FPSOLVER-SERVER_TS3-scwrl costs 0 real_cost = 377.201 FPSOLVER-SERVER_TS3 costs 0 real_cost = 380.699 FPSOLVER-SERVER_TS2-scwrl costs 0 real_cost = 389.864 FPSOLVER-SERVER_TS2 costs 0 real_cost = 390.914 FPSOLVER-SERVER_TS1-scwrl costs 0 real_cost = 383.832 FPSOLVER-SERVER_TS1 costs 0 real_cost = 387.425 FORTE2_AL5-scwrl costs 0 real_cost = 359.081 FORTE2_AL5 costs 0 real_cost = 741.477 FORTE2_AL4-scwrl costs 0 real_cost = 369.184 FORTE2_AL4 costs 0 real_cost = 768.027 FORTE2_AL3-scwrl costs 0 real_cost = 566.809 FORTE2_AL3 costs 0 real_cost = 845.703 FORTE2_AL2-scwrl costs 0 real_cost = 374.38 FORTE2_AL2 costs 0 real_cost = 762.072 FORTE2_AL1-scwrl costs 0 real_cost = 100.386 FORTE2_AL1 costs 0 real_cost = 488.405 FORTE1_AL5-scwrl costs 0 real_cost = 365.753 FORTE1_AL5 costs 0 real_cost = 746.276 FORTE1_AL4-scwrl costs 0 real_cost = 565.898 FORTE1_AL4 costs 0 real_cost = 823.686 FORTE1_AL3-scwrl costs 0 real_cost = 374.477 FORTE1_AL3 costs 0 real_cost = 760.476 FORTE1_AL2-scwrl costs 0 real_cost = 570.786 FORTE1_AL2 costs 0 real_cost = 849.417 FORTE1_AL1-scwrl costs 0 real_cost = 81.3944 FORTE1_AL1 costs 0 real_cost = 473.176 FOLDpro_TS5-scwrl costs 0 real_cost = -242.382 FOLDpro_TS5 costs 0 real_cost = -253.411 FOLDpro_TS4-scwrl costs 0 real_cost = -276.05 FOLDpro_TS4 costs 0 real_cost = -283.131 FOLDpro_TS3-scwrl costs 0 real_cost = -276.05 FOLDpro_TS3 costs 0 real_cost = -283.131 FOLDpro_TS2-scwrl costs 0 real_cost = -274.801 FOLDpro_TS2 costs 0 real_cost = -282.389 FOLDpro_TS1-scwrl costs 0 real_cost = -269.222 FOLDpro_TS1 costs 0 real_cost = -277.546 FAMS_TS5-scwrl costs 0 real_cost = -240.959 FAMS_TS5 costs 0 real_cost = -247.934 FAMS_TS4-scwrl costs 0 real_cost = -240.959 FAMS_TS4 costs 0 real_cost = -247.934 FAMS_TS3-scwrl costs 0 real_cost = -251.134 FAMS_TS3 costs 0 real_cost = -252.548 FAMS_TS2-scwrl costs 0 real_cost = -242.721 FAMS_TS2 costs 0 real_cost = -249.12 FAMS_TS1-scwrl costs 0 real_cost = -249.987 FAMS_TS1 costs 0 real_cost = -255.43 FAMSD_TS5-scwrl costs 0 real_cost = -242.639 FAMSD_TS5 costs 0 real_cost = -247.208 FAMSD_TS4-scwrl costs 0 real_cost = -214.713 FAMSD_TS4 costs 0 real_cost = -221.997 FAMSD_TS3-scwrl costs 0 real_cost = -234.721 FAMSD_TS3 costs 0 real_cost = -246.718 FAMSD_TS2-scwrl costs 0 real_cost = -238.526 FAMSD_TS2 costs 0 real_cost = -246.326 FAMSD_TS1-scwrl costs 0 real_cost = -262.555 FAMSD_TS1 costs 0 real_cost = -263.474 Distill_TS5-scwrl costs 0 real_cost = 1034.46 Distill_TS4-scwrl costs 0 real_cost = 1036.27 Distill_TS3-scwrl costs 0 real_cost = 1034.02 Distill_TS2-scwrl costs 0 real_cost = 1033.29 Distill_TS1-scwrl costs 0 real_cost = 1020.53 CaspIta-FOX_TS5-scwrl costs 0 real_cost = 464.341 CaspIta-FOX_TS5 costs 0 real_cost = 458.846 CaspIta-FOX_TS4-scwrl costs 0 real_cost = 523.135 CaspIta-FOX_TS4 costs 0 real_cost = 513.788 CaspIta-FOX_TS3-scwrl costs 0 real_cost = 460.532 CaspIta-FOX_TS3 costs 0 real_cost = 440.893 CaspIta-FOX_TS2-scwrl costs 0 real_cost = 404.993 CaspIta-FOX_TS2 costs 0 real_cost = 401.251 CaspIta-FOX_TS1-scwrl costs 0 real_cost = -246.827 CaspIta-FOX_TS1 costs 0 real_cost = -255.95 CPHmodels_TS1-scwrl costs 0 real_cost = -228.501 CPHmodels_TS1 costs 0 real_cost = -236.362 CIRCLE_TS5-scwrl costs 0 real_cost = -267.629 CIRCLE_TS5 costs 0 real_cost = -271.78 CIRCLE_TS4-scwrl costs 0 real_cost = -240.959 CIRCLE_TS4 costs 0 real_cost = -247.934 CIRCLE_TS3-scwrl costs 0 real_cost = -254.741 CIRCLE_TS3 costs 0 real_cost = -262.113 CIRCLE_TS2-scwrl costs 0 real_cost = -242.721 CIRCLE_TS2 costs 0 real_cost = -249.12 CIRCLE_TS1-scwrl costs 0 real_cost = -251.134 CIRCLE_TS1 costs 0 real_cost = -252.548 Bilab-ENABLE_TS4-scwrl costs 0 real_cost = -224.093 Bilab-ENABLE_TS4 costs 0 real_cost = -224.29 Bilab-ENABLE_TS3-scwrl costs 0 real_cost = -218.194 Bilab-ENABLE_TS3 costs 0 real_cost = -218.194 Bilab-ENABLE_TS2-scwrl costs 0 real_cost = -284.481 Bilab-ENABLE_TS2 costs 0 real_cost = -284.463 Bilab-ENABLE_TS1-scwrl costs 0 real_cost = -231.217 Bilab-ENABLE_TS1 costs 0 real_cost = -230.803 BayesHH_TS1-scwrl costs 0 real_cost = -242.317 BayesHH_TS1 costs 0 real_cost = -249.559 ABIpro_TS5-scwrl costs 0 real_cost = 334.391 ABIpro_TS5 costs 0 real_cost = 334.395 ABIpro_TS4-scwrl costs 0 real_cost = 335.079 ABIpro_TS4 costs 0 real_cost = 334.227 ABIpro_TS3-scwrl costs 0 real_cost = 326.982 ABIpro_TS3 costs 0 real_cost = 326.195 ABIpro_TS2-scwrl costs 0 real_cost = 327.049 ABIpro_TS2 costs 0 real_cost = 326.582 ABIpro_TS1-scwrl costs 0 real_cost = 328.02 ABIpro_TS1 costs 0 real_cost = 328.011 3Dpro_TS5-scwrl costs 0 real_cost = -228.184 3Dpro_TS5 costs 0 real_cost = -235.584 3Dpro_TS4-scwrl costs 0 real_cost = -270.361 3Dpro_TS4 costs 0 real_cost = -279.602 3Dpro_TS3-scwrl costs 0 real_cost = -274.577 3Dpro_TS3 costs 0 real_cost = -280.003 3Dpro_TS2-scwrl costs 0 real_cost = -273.117 3Dpro_TS2 costs 0 real_cost = -278.253 3Dpro_TS1-scwrl costs 0 real_cost = -269.222 3Dpro_TS1 costs 0 real_cost = -277.546 3D-JIGSAW_TS4-scwrl costs 0 real_cost = -223.473 3D-JIGSAW_TS4 costs 0 real_cost = -219.736 3D-JIGSAW_TS3-scwrl costs 0 real_cost = -220.633 3D-JIGSAW_TS3 costs 0 real_cost = -221.492 3D-JIGSAW_TS2-scwrl costs 0 real_cost = -220.319 3D-JIGSAW_TS2 costs 0 real_cost = -222.33 3D-JIGSAW_TS1-scwrl costs 0 real_cost = -154.095 3D-JIGSAW_TS1 costs 0 real_cost = -159.049 3D-JIGSAW_RECOM_TS5-scwrl costs 0 real_cost = -227.832 3D-JIGSAW_RECOM_TS5 costs 0 real_cost = -234.544 3D-JIGSAW_RECOM_TS4-scwrl costs 0 real_cost = -222.096 3D-JIGSAW_RECOM_TS4 costs 0 real_cost = -226.117 3D-JIGSAW_RECOM_TS3-scwrl costs 0 real_cost = -222.977 3D-JIGSAW_RECOM_TS3 costs 0 real_cost = -229.226 3D-JIGSAW_RECOM_TS2-scwrl costs 0 real_cost = -223.849 3D-JIGSAW_RECOM_TS2 costs 0 real_cost = -230.814 3D-JIGSAW_RECOM_TS1-scwrl costs 0 real_cost = -228.034 3D-JIGSAW_RECOM_TS1 costs 0 real_cost = -233.741 3D-JIGSAW_POPULUS_TS5-scwrl costs 0 real_cost = -209.54 3D-JIGSAW_POPULUS_TS5 costs 0 real_cost = -215.85 3D-JIGSAW_POPULUS_TS4-scwrl costs 0 real_cost = -206.537 3D-JIGSAW_POPULUS_TS4 costs 0 real_cost = -212.868 3D-JIGSAW_POPULUS_TS3-scwrl costs 0 real_cost = -213.239 3D-JIGSAW_POPULUS_TS3 costs 0 real_cost = -219.21 3D-JIGSAW_POPULUS_TS2-scwrl costs 0 real_cost = -211.53 3D-JIGSAW_POPULUS_TS2 costs 0 real_cost = -216.736 3D-JIGSAW_POPULUS_TS1-scwrl costs 0 real_cost = -211.661 3D-JIGSAW_POPULUS_TS1 costs 0 real_cost = -218.656 dimer//dimer-2aqj-from-try8-opt2 costs 0 real_cost = -186.836 dimer//dimer-2aqj-from-try7-opt2 costs 0 real_cost = -185.657 dimer//dimer-2aqj-from-try6-opt2 costs 0 real_cost = -183.172 dimer//try1-opt2.unpack costs 0 real_cost = 398.312 dimer//try1-opt2.unpack.gromacs0.repack-nonPC costs 0 real_cost = 397.215 dimer//try1-opt2.unpack.gromacs0 costs 0 real_cost = 398.972 dimer//try1-opt2.repack-nonPC costs 0 real_cost = 397.492 dimer//try1-opt2 costs 0 real_cost = 398.312 dimer//try1-opt1 costs 0 real_cost = 397.783 dimer//try1-opt1-scwrl costs 0 real_cost = 397.955 T0334.try9-opt2.repack-nonPC.pdb.gz costs 0 real_cost = -186.493 T0334.try9-opt2.pdb.gz costs 0 real_cost = -183.667 T0334.try9-opt2.gromacs0.repack-nonPC.pdb.gz costs 0 real_cost = -186.807 T0334.try9-opt2.gromacs0.pdb.gz costs 0 real_cost = -183.952 T0334.try9-opt1.pdb.gz costs 0 real_cost = -183.572 T0334.try9-opt1-scwrl.pdb.gz costs 0 real_cost = -188.021 T0334.try8-opt2.repack-nonPC.pdb.gz costs 0 real_cost = -186.3 T0334.try8-opt2.pdb.gz costs 0 real_cost = -186.824 T0334.try8-opt2.gromacs0.repack-nonPC.pdb.gz costs 0 real_cost = -187.04 T0334.try8-opt2.gromacs0.pdb.gz costs 0 real_cost = -185.735 T0334.try8-opt1.pdb.gz costs 0 real_cost = -185.489 T0334.try8-opt1-scwrl.pdb.gz costs 0 real_cost = -188.168 T0334.try7-opt2.repack-nonPC.pdb.gz costs 0 real_cost = -184.081 T0334.try7-opt2.pdb.gz costs 0 real_cost = -185.65 T0334.try7-opt2.gromacs0.repack-nonPC.pdb.gz costs 0 real_cost = -184.281 T0334.try7-opt2.gromacs0.pdb.gz costs 0 real_cost = -186.132 T0334.try7-opt1.pdb.gz costs 0 real_cost = -186.729 T0334.try7-opt1-scwrl.pdb.gz costs 0 real_cost = -187.736 T0334.try6-opt2.repack-nonPC.pdb.gz costs 0 real_cost = -181.188 T0334.try6-opt2.pdb.gz costs 0 real_cost = -183.25 T0334.try6-opt2.gromacs0.repack-nonPC.pdb.gz costs 0 real_cost = -184.759 T0334.try6-opt2.gromacs0.pdb.gz costs 0 real_cost = -184.664 T0334.try6-opt1.pdb.gz costs 0 real_cost = -183.771 T0334.try6-opt1-scwrl.pdb.gz costs 0 real_cost = -184.084 T0334.try3-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 10.3238 T0334.try3-opt2.pdb.gz costs 0 real_cost = 7.14232 T0334.try3-opt2.gromacs0.repack-nonPC.pdb.gz costs 0 real_cost = 9.27713 T0334.try3-opt2.gromacs0.pdb.gz costs 0 real_cost = 9.04963 T0334.try3-opt1.pdb.gz costs 0 real_cost = 4.4829 T0334.try3-opt1-scwrl.pdb.gz costs 0 real_cost = 6.21945 T0334.try2-opt2.repack-nonPC.pdb.gz costs 0 real_cost = -185.904 T0334.try2-opt2.pdb.gz costs 0 real_cost = -184.995 T0334.try2-opt2.gromacs0.repack-nonPC.pdb.gz costs 0 real_cost = -183.508 T0334.try2-opt2.gromacs0.pdb.gz costs 0 real_cost = -182.809 T0334.try2-opt1.pdb.gz costs 0 real_cost = -183.247 T0334.try2-opt1-scwrl.pdb.gz costs 0 real_cost = -183.791 T0334.try17-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 9.52432 T0334.try17-opt2.pdb.gz costs 0 real_cost = 9.77948 T0334.try17-opt2.gromacs0.repack-nonPC.pdb.gz costs 0 real_cost = 9.92714 T0334.try17-opt2.gromacs0.pdb.gz costs 0 real_cost = 9.47596 T0334.try17-opt1.pdb.gz costs 0 real_cost = 8.17567 T0334.try17-opt1-scwrl.pdb.gz costs 0 real_cost = 8.19458 T0334.try16-opt2.repack-nonPC.pdb.gz costs 0 real_cost = -218.193 T0334.try16-opt2.pdb.gz costs 0 real_cost = -218.272 T0334.try16-opt2.gromacs0.repack-nonPC.pdb.gz costs 0 real_cost = -218.337 T0334.try16-opt2.gromacs0.pdb.gz costs 0 real_cost = -215.912 T0334.try16-opt1.pdb.gz costs 0 real_cost = -215.307 T0334.try16-opt1-scwrl.pdb.gz costs 0 real_cost = -216.605 T0334.try15-opt2.repack-nonPC.pdb.gz costs 0 real_cost = -208.392 T0334.try15-opt2.pdb.gz costs 0 real_cost = -205.023 T0334.try15-opt2.gromacs0.repack-nonPC.pdb.gz costs 0 real_cost = -207.663 T0334.try15-opt2.gromacs0.pdb.gz costs 0 real_cost = -202.364 T0334.try15-opt1.pdb.gz costs 0 real_cost = -202.25 T0334.try15-opt1-scwrl.pdb.gz costs 0 real_cost = -202.402 T0334.try14-opt2.repack-nonPC.pdb.gz costs 0 real_cost = -186.655 T0334.try14-opt2.pdb.gz costs 0 real_cost = -186.26 T0334.try14-opt2.gromacs0.repack-nonPC.pdb.gz costs 0 real_cost = -185.131 T0334.try14-opt2.gromacs0.pdb.gz costs 0 real_cost = -186.141 T0334.try14-opt1.pdb.gz costs 0 real_cost = -187.38 T0334.try14-opt1-scwrl.pdb.gz costs 0 real_cost = -188.426 T0334.try13-opt2.repack-nonPC.pdb.gz costs 0 real_cost = -188.479 T0334.try13-opt2.pdb.gz costs 0 real_cost = -187.073 T0334.try13-opt2.gromacs0.repack-nonPC.pdb.gz costs 0 real_cost = -188.327 T0334.try13-opt2.gromacs0.pdb.gz costs 0 real_cost = -185.238 T0334.try13-opt1.pdb.gz costs 0 real_cost = -186.714 T0334.try13-opt1-scwrl.pdb.gz costs 0 real_cost = -187.905 T0334.try12-opt2.repack-nonPC.pdb.gz costs 0 real_cost = -187.139 T0334.try12-opt2.pdb.gz costs 0 real_cost = -189.092 T0334.try12-opt2.gromacs0.repack-nonPC.pdb.gz costs 0 real_cost = -187.316 T0334.try12-opt2.gromacs0.pdb.gz costs 0 real_cost = -189.004 T0334.try12-opt1.pdb.gz costs 0 real_cost = -188.692 T0334.try12-opt1-scwrl.pdb.gz costs 0 real_cost = -185.35 T0334.try11-opt2.repack-nonPC.pdb.gz costs 0 real_cost = -188.224 T0334.try11-opt2.pdb.gz costs 0 real_cost = -186.661 T0334.try11-opt2.gromacs0.repack-nonPC.pdb.gz costs 0 real_cost = -185.305 T0334.try11-opt2.gromacs0.pdb.gz costs 0 real_cost = -186.392 T0334.try11-opt1.pdb.gz costs 0 real_cost = -187.14 T0334.try11-opt1-scwrl.pdb.gz costs 0 real_cost = -187.833 T0334.try10-opt2.repack-nonPC.pdb.gz costs 0 real_cost = -186.923 T0334.try10-opt2.pdb.gz costs 0 real_cost = -187.07 T0334.try10-opt2.gromacs0.repack-nonPC.pdb.gz costs 0 real_cost = -187.685 T0334.try10-opt2.gromacs0.pdb.gz costs 0 real_cost = -186.581 T0334.try10-opt1.pdb.gz costs 0 real_cost = -186.302 T0334.try10-opt1-scwrl.pdb.gz costs 0 real_cost = -188.491 T0334.try1-opt2.repack-nonPC.pdb.gz costs 0 real_cost = -214.711 T0334.try1-opt2.pdb.gz costs 0 real_cost = -215.642 T0334.try1-opt2.gromacs0.repack-nonPC.pdb.gz costs 0 real_cost = -215.424 T0334.try1-opt2.gromacs0.pdb.gz costs 0 real_cost = -215.728 T0334.try1-opt1.pdb.gz costs 0 real_cost = -220.483 T0334.try1-opt1-scwrl.pdb.gz costs 0 real_cost = -221.678 ../model5.ts-submitted costs 0 real_cost = 84.9951 ../model4.ts-submitted costs 0 real_cost = -204.927 ../model3.ts-submitted costs 0 real_cost = -218.188 ../model2.ts-submitted costs 0 real_cost = -187.32 ../model1.ts-submitted costs 0 real_cost = -186.286 align5 costs 0 real_cost = 440.848 align4 costs 0 real_cost = 425.763 align3 costs 0 real_cost = 605.111 align2 costs 0 real_cost = 446.268 align1 costs 0 real_cost = 71.6238 T0334.try1-opt2.pdb costs 0 real_cost = -215.641 model5-scwrl costs 0 real_cost = 149.415 model5.ts-submitted costs 0 real_cost = 84.9951 model4-scwrl costs 0 real_cost = -205.645 model4.ts-submitted costs 0 real_cost = -204.927 model3-scwrl costs 0 real_cost = -217.744 model3.ts-submitted costs 0 real_cost = -218.188 model2-scwrl costs 0 real_cost = -188.407 model2.ts-submitted costs 0 real_cost = -187.32 model1-scwrl costs 0 real_cost = -187.562 model1.ts-submitted costs 0 real_cost = -186.237 T0334_1.real.pdb costs 0 real_cost = -881.2 # command:CPU_time= 8614.53 sec, elapsed time= 12774.8 sec) # command:rm -f sort.tmp /projects/compbio/bin/sorttbl real_cost < decoys/evaluate_1.rdb > sort.tmp mv -f sort.tmp decoys/evaluate_1.rdb mv -f decoys/evaluate_1.pretty decoys/evaluate_1.pretty.old mv: cannot stat `decoys/evaluate_1.pretty': No such file or directory make: [decoys/evaluate_1.pretty] Error 1 (ignored) /projects/compbio/experiments/protein-predict/casp7/scripts/prettyscore -terse -targpfx -decpoint < decoys/evaluate_1.rdb > decoys/evaluate_1.pretty