/projects/compbio/experiments/protein-predict/casp7/starter-directory/Make.main:725: SECONDARY_TARGET = T0327.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/T0327.} ;\
		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/T0327/ -e s/START_COL/1/ \
-e s/REAL_PDB/2hgcA/ \
-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 1174742335
# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/
# command:# reading monomeric-50pc.atoms
# trans (non-proline) backbone unit:
#	  CA= -2.2088 1.0126 -0.0031
#	   O= -0.1499 2.2440 0.0017
#	   C= -0.6889 1.1368 0.0000
#	 N+1= 0.0000 0.0000 0.0000
#	CA+1= 1.4581 0.0000 0.0000
# cis backbone unit:
#	  CA= -0.1462 2.4515 0.0018
#	   O= -2.0272 0.9713 0.0022
#	   C= -0.8006 1.0755 0.0000
#	 N+1= 0.0000 0.0000 0.0000
#	CA+1= 1.4659 0.0000 0.0000
# trans backbone unit before proline:
#	  CA= -2.2099 1.0634 -0.0014
#	   O= -0.1233 2.2459 0.0075
#	   C= -0.6871 1.1518 0.0000
#	 N+1= 0.0000 0.0000 0.0000
#	CA+1= 1.4660 0.0000 0.0000


# After reading monomeric-50pc.atoms have 448 chains in training database
#  Count of chains,residues,atoms: 448,112605,876684
#  109826 residues have no bad marker
#  665 residues lack atoms needed to compute omega
#  322 residues have cis peptide
#  number of each bad type:
#	NON_STANDARD_RESIDUE	6
#	HAS_OXT	325
#	TOO_MANY_ATOMS	1
#	TOO_FEW_ATOMS	523
#	HAS_UNKNOWN_ATOMS	2
#	HAS_DUPLICATE_ATOMS	0
#	CHAIN_BREAK_BEFORE	208
#	NON_PLANAR_PEPTIDE	143
#	BAD_PEPTIDE	1959
#  Note: may sum to more than number of residues, 
#    because one residue may have multiple problems
# command:# Reading rotamer library from dunbrack-1332.rot
# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/
# command:# ReadAtomType exp-pdb.types
Read AtomType exp-pdb with 49 types.
# command:# ReadClashTable exp-pdb-2191-2symm.clash
# Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2
# command:# command:CPU_time= 6.13207 sec, elapsed time= 6.16444 sec)
# command:# Reading spots from monomeric-50pc-dry-5.spot
Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes
# reading histogram from smoothed-monomeric-50pc-dry-5.hist
# created burial cost function dry5 with radius 5 with spots at monomeric-50pc-dry-5.spot
# command:# Reading spots from monomeric-50pc-wet-6.5.spot
Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes
# reading histogram from smoothed-monomeric-50pc-wet-6.5.hist
# created burial cost function wet6.5 with radius 6.5 with spots at monomeric-50pc-wet-6.5.spot
# command:# Reading spots from monomeric-50pc-dry-6.5.spot
Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes
# reading histogram from smoothed-monomeric-50pc-dry-6.5.hist
# created burial cost function dry6.5 with radius 6.5 with spots at monomeric-50pc-dry-6.5.spot
# command:# Reading spots from monomeric-50pc-generic-6.5.spot
Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes
# reading histogram from smoothed-monomeric-50pc-generic-6.5.hist
# created burial cost function gen6.5 with radius 6.5 with spots at monomeric-50pc-generic-6.5.spot
# command:# Reading spots from near-backbone-center.spot
# reading histogram from smoothed-near-backbone-2spot.hist
# Reading spots from near-backbone-count.spot
# created burial cost function near_backbone with radius 9.65 with spots at near-backbone-center.spot counting only near-backbone-count.spot
# command:# Reading spots from way-back-center.spot
# reading histogram from smoothed-way-back-2spot.hist
# Reading spots from way-back-count.spot
# created burial cost function way_back with radius 8.9 with spots at way-back-center.spot counting only way-back-count.spot
# command:# Reading spots from monomeric-50pc-dry-8.spot
Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes
# reading histogram from smoothed-monomeric-50pc-dry-8.hist
# created burial cost function dry8 with radius 8 with spots at monomeric-50pc-dry-8.spot
# command:# Reading spots from monomeric-50pc-dry-10.spot
Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes
# reading histogram from smoothed-monomeric-50pc-dry-10.hist
# created burial cost function dry10 with radius 10 with spots at monomeric-50pc-dry-10.spot
# command:# Reading spots from monomeric-50pc-dry-12.spot
Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes
# reading histogram from smoothed-monomeric-50pc-dry-12.hist
# created burial cost function dry12 with radius 12 with spots at monomeric-50pc-dry-12.spot
# command:# reading histogram from dunbrack-2191-alpha.hist
# created alpha cost function alpha with offset 0 and  360 bins
# command:# reading histogram from dunbrack-2191-alpha-1.hist
# created alpha cost function alpha_prev with offset -1 and  360 bins
# command:# Prefix for input files set to /projects/compbio/lib/alphabet/
# command:# Read 3 alphabets from alpha.alphabet
# command:CPU_time= 6.21306 sec, elapsed time= 6.26135 sec)
# command:# Prefix for input files set to 
# command:# Making conformation for sequence T0327 numbered 1 through 102
Created new target T0327 from T0327.a2m
# command:# command:# No conformations to remove in PopConform
# command:# cleared Id set
# command:# command:2hgcA expands to /projects/compbio/data/pdb/2hgc.pdb.gz
2hgcA: Read 78 residues and 636 atoms.
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# command:# Saving current conformation as real
# command:# Prefix for output files set to decoys/
# command:# SetRealCost created real_cost = 
#	( 50 * real_hbond + 50 * real_hbond_u + 50 * decoy_hbond + 50 * decoy_hbond_u + 10 * real_NO_hbond + 10 * real_NO_hbond_u + 10 * decoy_NO_hbond + 10 * decoy_NO_hbond_u + 10 * knot + 200 * clens + 0 * rmsd + 35 * log_rmsd + 0 * rmsd_ca + 30 * log_rmsd_ca + 1 * GDT + 1 * smooth_GDT + 0.2 * missing_atoms )
# command:# SetCost created cost = 
#	)
# command:CPU_time= 8.64769 sec, elapsed time= 8.73951 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 56
# copying to AlignedFragments data structure
# command:# fraction of real conformation used = 1
# GDT_score = -55.4487
# GDT_score(maxd=8,maxw=2.9)= -54.7537
# GDT_score(maxd=8,maxw=3.2)= -52.0205
# GDT_score(maxd=8,maxw=3.5)= -49.4597
# GDT_score(maxd=10,maxw=3.8)= -53.2603
# GDT_score(maxd=10,maxw=4)= -51.6446
# GDT_score(maxd=10,maxw=4.2)= -50.0173
# GDT_score(maxd=12,maxw=4.3)= -54.1332
# GDT_score(maxd=12,maxw=4.5)= -52.476
# GDT_score(maxd=12,maxw=4.7)= -50.8563
# GDT_score(maxd=14,maxw=5.2)= -50.7962
# GDT_score(maxd=14,maxw=5.5)= -48.6549
# command:# Prefix for output files set to 
# command:superimposing iter= 0 total_weight= 9.4800000e+02 rmsd (weighted)= 6.4424782e+00 (unweighted)= 2.1008239e+01
superimposing iter= 1 total_weight= 2.4623192e+03 rmsd (weighted)= 2.8557686e+00 (unweighted)= 2.1353091e+01
superimposing iter= 2 total_weight= 1.4064487e+03 rmsd (weighted)= 1.8493410e+00 (unweighted)= 2.1376567e+01
superimposing iter= 3 total_weight= 9.3679190e+02 rmsd (weighted)= 1.4923636e+00 (unweighted)= 2.1359393e+01
superimposing iter= 4 total_weight= 7.9332951e+02 rmsd (weighted)= 1.3149905e+00 (unweighted)= 2.1352470e+01
superimposing iter= 5 total_weight= 7.2789557e+02 rmsd (weighted)= 1.2128127e+00 (unweighted)= 2.1348734e+01
# command:# Prefix for output files set to decoys/
# command:# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1249929061.pdb -s /var/tmp/to_scwrl_1249929061.seq -o /var/tmp/from_scwrl_1249929061.pdb > /var/tmp/scwrl_1249929061.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1249929061.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 56
# copying to AlignedFragments data structure
# command:# fraction of real conformation used = 1
# GDT_score = -56.7308
# GDT_score(maxd=8,maxw=2.9)= -55.9161
# GDT_score(maxd=8,maxw=3.2)= -53.1135
# GDT_score(maxd=8,maxw=3.5)= -50.4794
# GDT_score(maxd=10,maxw=3.8)= -54.1885
# GDT_score(maxd=10,maxw=4)= -52.4707
# GDT_score(maxd=10,maxw=4.2)= -50.8116
# GDT_score(maxd=12,maxw=4.3)= -54.9129
# GDT_score(maxd=12,maxw=4.5)= -53.2243
# GDT_score(maxd=12,maxw=4.7)= -51.5323
# GDT_score(maxd=14,maxw=5.2)= -51.4104
# GDT_score(maxd=14,maxw=5.5)= -49.2356
# command:# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_226667771.pdb -s /var/tmp/to_scwrl_226667771.seq -o /var/tmp/from_scwrl_226667771.pdb > /var/tmp/scwrl_226667771.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_226667771.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 78
# copying to AlignedFragments data structure
# command:# fraction of real conformation used = 1
# GDT_score = -52.8846
# GDT_score(maxd=8,maxw=2.9)= -51.1101
# GDT_score(maxd=8,maxw=3.2)= -48.5276
# GDT_score(maxd=8,maxw=3.5)= -46.0857
# GDT_score(maxd=10,maxw=3.8)= -50.5693
# GDT_score(maxd=10,maxw=4)= -48.9043
# GDT_score(maxd=10,maxw=4.2)= -47.3078
# GDT_score(maxd=12,maxw=4.3)= -51.7527
# GDT_score(maxd=12,maxw=4.5)= -50.115
# GDT_score(maxd=12,maxw=4.7)= -48.546
# GDT_score(maxd=14,maxw=5.2)= -48.7709
# GDT_score(maxd=14,maxw=5.5)= -46.74
# command:# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_916954303.pdb -s /var/tmp/to_scwrl_916954303.seq -o /var/tmp/from_scwrl_916954303.pdb > /var/tmp/scwrl_916954303.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_916954303.pdb
# conformation set from SCWRL output
# command:# naming current conformation model3-scwrl
# command:# ReadConformPDB reading from PDB file model4.ts-submitted looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# command:# fraction of real conformation used = 0.807692
# GDT_score = -58.9744
# GDT_score(maxd=8,maxw=2.9)= -59.227
# GDT_score(maxd=8,maxw=3.2)= -57.1738
# GDT_score(maxd=8,maxw=3.5)= -55.1172
# GDT_score(maxd=10,maxw=3.8)= -57.3902
# GDT_score(maxd=10,maxw=4)= -56.0663
# GDT_score(maxd=10,maxw=4.2)= -54.621
# GDT_score(maxd=12,maxw=4.3)= -57.3295
# GDT_score(maxd=12,maxw=4.5)= -55.892
# GDT_score(maxd=12,maxw=4.7)= -54.4523
# GDT_score(maxd=14,maxw=5.2)= -53.7439
# GDT_score(maxd=14,maxw=5.5)= -51.6888
# command:# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_13836132.pdb -s /var/tmp/to_scwrl_13836132.seq -o /var/tmp/from_scwrl_13836132.pdb > /var/tmp/scwrl_13836132.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_13836132.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 T0327 can't currently be optimized by undertaker
# command:# fraction of real conformation used = 0.846154
# GDT_score = -57.0513
# GDT_score(maxd=8,maxw=2.9)= -59.5084
# GDT_score(maxd=8,maxw=3.2)= -56.5319
# GDT_score(maxd=8,maxw=3.5)= -53.6098
# GDT_score(maxd=10,maxw=3.8)= -56.1123
# GDT_score(maxd=10,maxw=4)= -54.2544
# GDT_score(maxd=10,maxw=4.2)= -52.5256
# GDT_score(maxd=12,maxw=4.3)= -55.7715
# GDT_score(maxd=12,maxw=4.5)= -54.086
# GDT_score(maxd=12,maxw=4.7)= -52.4135
# GDT_score(maxd=14,maxw=5.2)= -51.684
# GDT_score(maxd=14,maxw=5.5)= -49.468
# command:# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_641101725.pdb -s /var/tmp/to_scwrl_641101725.seq -o /var/tmp/from_scwrl_641101725.pdb > /var/tmp/scwrl_641101725.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_641101725.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 T0327.try1-opt2.pdb looking for model 1
# Found a chain break before 100
# copying to AlignedFragments data structure
# command:# fraction of real conformation used = 1
# GDT_score = -58.0128
# GDT_score(maxd=8,maxw=2.9)= -58.4851
# GDT_score(maxd=8,maxw=3.2)= -55.3115
# GDT_score(maxd=8,maxw=3.5)= -52.397
# GDT_score(maxd=10,maxw=3.8)= -56.3643
# GDT_score(maxd=10,maxw=4)= -54.5112
# GDT_score(maxd=10,maxw=4.2)= -52.7057
# GDT_score(maxd=12,maxw=4.3)= -56.9673
# GDT_score(maxd=12,maxw=4.5)= -55.1414
# GDT_score(maxd=12,maxw=4.7)= -53.3559
# GDT_score(maxd=14,maxw=5.2)= -53.1351
# GDT_score(maxd=14,maxw=5.5)= -50.8662
# command:# Prefix for output files set to 
# command:superimposing iter= 0 total_weight= 9.4800000e+02 rmsd (weighted)= 5.2409560e+00 (unweighted)= 1.6301571e+01
superimposing iter= 1 total_weight= 2.1710197e+03 rmsd (weighted)= 2.5857587e+00 (unweighted)= 1.6848750e+01
superimposing iter= 2 total_weight= 1.1552385e+03 rmsd (weighted)= 1.8652925e+00 (unweighted)= 1.7041748e+01
superimposing iter= 3 total_weight= 8.3779601e+02 rmsd (weighted)= 1.6010521e+00 (unweighted)= 1.7165489e+01
superimposing iter= 4 total_weight= 7.7843313e+02 rmsd (weighted)= 1.4289997e+00 (unweighted)= 1.7260524e+01
superimposing iter= 5 total_weight= 7.4513392e+02 rmsd (weighted)= 1.3047893e+00 (unweighted)= 1.7321343e+01
# command:# Prefix for output files set to decoys/
# command:# Prefix for input files set to 
# command:# ReadConformPDB reading from PDB file T0327.undertaker-align.pdb looking for model 1
WARNING: atoms too close: (T0327)G48.C and (T0327)V49.C only 0.0000000e+00 apart, marking (T0327)V49.C as missing
WARNING: atoms too close: (T0327)V49.N and (T0327)H50.N only 0.0000000e+00 apart, marking (T0327)V49.N as missing
WARNING: atoms too close: (T0327)V49.CA and (T0327)H50.CA only 0.0000000e+00 apart, marking (T0327)V49.CA as missing
WARNING: atoms too close: (T0327)Y59.C and (T0327)E64.C only 0.0000000e+00 apart, marking (T0327)E64.C as missing
WARNING: atoms too close: (T0327)K60.N and (T0327)L65.N only 0.0000000e+00 apart, marking (T0327)K60.N as missing
WARNING: atoms too close: (T0327)K60.CA and (T0327)L65.CA only 0.0000000e+00 apart, marking (T0327)K60.CA as missing
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# command:# naming current conformation align1
# command:# fraction of real conformation used = 0.833333
# GDT_score = -60.2564
# GDT_score(maxd=8,maxw=2.9)= -59.9902
# GDT_score(maxd=8,maxw=3.2)= -57.8723
# GDT_score(maxd=8,maxw=3.5)= -55.7518
# GDT_score(maxd=10,maxw=3.8)= -58.167
# GDT_score(maxd=10,maxw=4)= -56.795
# GDT_score(maxd=10,maxw=4.2)= -55.3155
# GDT_score(maxd=12,maxw=4.3)= -58.1631
# GDT_score(maxd=12,maxw=4.5)= -56.6948
# GDT_score(maxd=12,maxw=4.7)= -55.223
# GDT_score(maxd=14,maxw=5.2)= -54.5498
# GDT_score(maxd=14,maxw=5.5)= -52.4509
# command:# ReadConformPDB reading from PDB file T0327.undertaker-align.pdb looking for model 2
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# command:# naming current conformation align2
# command:# fraction of real conformation used = 0.884615
# GDT_score = -57.6923
# GDT_score(maxd=8,maxw=2.9)= -60.0855
# GDT_score(maxd=8,maxw=3.2)= -56.9621
# GDT_score(maxd=8,maxw=3.5)= -54.0206
# GDT_score(maxd=10,maxw=3.8)= -56.6259
# GDT_score(maxd=10,maxw=4)= -54.7524
# GDT_score(maxd=10,maxw=4.2)= -52.9561
# GDT_score(maxd=12,maxw=4.3)= -56.4204
# GDT_score(maxd=12,maxw=4.5)= -54.6467
# GDT_score(maxd=12,maxw=4.7)= -52.9069
# GDT_score(maxd=14,maxw=5.2)= -52.2875
# GDT_score(maxd=14,maxw=5.5)= -50.0389
# command:# ReadConformPDB reading from PDB file T0327.undertaker-align.pdb looking for model 3
WARNING: atoms too close: (T0327)Y83.C and (T0327)T85.C only 0.0000000e+00 apart, marking (T0327)T85.C as missing
WARNING: atoms too close: (T0327)K84.N and (T0327)I86.N only 0.0000000e+00 apart, marking (T0327)K84.N as missing
WARNING: atoms too close: (T0327)K84.CA and (T0327)I86.CA only 0.0000000e+00 apart, marking (T0327)K84.CA as missing
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# command:# naming current conformation align3
# command:# ReadConformPDB reading from PDB file T0327.undertaker-align.pdb looking for model 4
WARNING: atoms too close: (T0327)K60.C and (T0327)E64.C only 0.0000000e+00 apart, marking (T0327)E64.C as missing
WARNING: atoms too close: (T0327)L61.N and (T0327)L65.N only 0.0000000e+00 apart, marking (T0327)L61.N as missing
WARNING: atoms too close: (T0327)L61.CA and (T0327)L65.CA only 0.0000000e+00 apart, marking (T0327)L61.CA as missing
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# command:# naming current conformation align4
# command:# ReadConformPDB reading from PDB file T0327.undertaker-align.pdb looking for model 5
WARNING: atoms too close: (T0327)L61.C and (T0327)L65.C only 0.0000000e+00 apart, marking (T0327)L65.C as missing
WARNING: atoms too close: (T0327)G62.N and (T0327)T66.N only 0.0000000e+00 apart, marking (T0327)G62.N as missing
WARNING: atoms too close: (T0327)G62.CA and (T0327)T66.CA only 0.0000000e+00 apart, marking (T0327)G62.CA as missing
WARNING: atoms too close: (T0327)G69.C and (T0327)L73.C only 0.0000000e+00 apart, marking (T0327)L73.C as missing
WARNING: atoms too close: (T0327)E70.N and (T0327)K74.N only 0.0000000e+00 apart, marking (T0327)E70.N as missing
WARNING: atoms too close: (T0327)E70.CA and (T0327)K74.CA only 0.0000000e+00 apart, marking (T0327)E70.CA as missing
# WARNING: incomplete conformation T0327 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 56
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file ../model2.ts-submitted looking for model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file ../model3.ts-submitted looking for model 1
# Found a chain break before 78
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file ../model4.ts-submitted looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# ReadConformPDB reading from PDB file ../model5.ts-submitted looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# ReadConformPDB reading from PDB file T0327.try1-opt1-scwrl.pdb.gz looking for model 1
# Found a chain break before 100
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0327.try1-opt1.pdb.gz looking for model 1
# Found a chain break before 100
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0327.try1-opt2-proteinshop-2.pdb.gz looking for model 1
# Found a chain break before 100
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0327.try1-opt2-proteinshop.pdb.gz looking for model 1
# Found a chain break before 100
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0327.try1-opt2.gromacs0.pdb.gz looking for model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0327.try1-opt2.pdb.gz looking for model 1
# Found a chain break before 100
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0327.try1-opt2.repack-nonPC.pdb.gz looking for model 1
# Found a chain break before 100
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0327.try2-opt1-scwrl.pdb.gz looking for model 1
# Found a chain break before 78
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0327.try2-opt1.pdb.gz looking for model 1
# Found a chain break before 78
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0327.try2-opt2.gromacs0.pdb.gz looking for model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0327.try2-opt2.pdb.gz looking for model 1
# Found a chain break before 78
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0327.try2-opt2.repack-nonPC.pdb.gz looking for model 1
# Found a chain break before 78
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0327.try3-opt1-scwrl.pdb.gz looking for model 1
# Found a chain break before 95
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0327.try3-opt1.pdb.gz looking for model 1
# Found a chain break before 95
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0327.try3-opt2.gromacs0.pdb.gz looking for model 1
# Found a chain break before 93
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0327.try3-opt2.pdb.gz looking for model 1
# Found a chain break before 95
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0327.try3-opt2.repack-nonPC.pdb.gz looking for model 1
# Found a chain break before 95
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0327.try4-opt1-scwrl.pdb.gz looking for model 1
# Found a chain break before 76
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0327.try4-opt1.pdb.gz looking for model 1
# Found a chain break before 76
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0327.try4-opt2.gromacs0.pdb.gz looking for model 1
# Found a chain break before 54
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0327.try4-opt2.pdb.gz looking for model 1
# Found a chain break before 78
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0327.try4-opt2.repack-nonPC.pdb.gz looking for model 1
# Found a chain break before 78
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try1-opt1-scwrl.pdb.gz looking for chain 'A' model 1
# Found a chain break before 51
# copying to AlignedFragments data structure
# naming current conformation dimer//try1-opt1-scwrl
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try1-opt1.pdb.gz looking for chain 'A' model 1
# Found a chain break before 51
# copying to AlignedFragments data structure
# naming current conformation dimer//try1-opt1
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try1-opt2.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 26
# copying to AlignedFragments data structure
# naming current conformation dimer//try1-opt2.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try1-opt2.pdb.gz looking for chain 'A' model 1
# Found a chain break before 75
# copying to AlignedFragments data structure
# naming current conformation dimer//try1-opt2
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try1-opt2.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 75
# copying to AlignedFragments data structure
# naming current conformation dimer//try1-opt2.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try1-opt2.unpack.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 26
# copying to AlignedFragments data structure
# naming current conformation dimer//try1-opt2.unpack.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try1-opt2.unpack.gromacs0.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 26
# copying to AlignedFragments data structure
# naming current conformation dimer//try1-opt2.unpack.gromacs0.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try1-opt2.unpack.pdb.gz looking for chain 'A' model 1
# Found a chain break before 75
# copying to AlignedFragments data structure
# naming current conformation dimer//try1-opt2.unpack
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try10-opt1-scwrl.pdb.gz looking for chain 'A' model 1
# Found a chain break before 59
# copying to AlignedFragments data structure
# naming current conformation dimer//try10-opt1-scwrl
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try10-opt1.pdb.gz looking for chain 'A' model 1
# Found a chain break before 59
# copying to AlignedFragments data structure
# naming current conformation dimer//try10-opt1
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try10-opt2.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 101
# copying to AlignedFragments data structure
# naming current conformation dimer//try10-opt2.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try10-opt2.pdb.gz looking for chain 'A' model 1
# Found a chain break before 59
# copying to AlignedFragments data structure
# naming current conformation dimer//try10-opt2
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try10-opt2.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 59
# copying to AlignedFragments data structure
# naming current conformation dimer//try10-opt2.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try10-opt2.unpack.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try10-opt2.unpack.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try10-opt2.unpack.gromacs0.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try10-opt2.unpack.gromacs0.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try10-opt2.unpack.pdb.gz looking for chain 'A' model 1
# Found a chain break before 59
# copying to AlignedFragments data structure
# naming current conformation dimer//try10-opt2.unpack
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try11-opt1-scwrl.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try11-opt1-scwrl
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try11-opt1.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try11-opt1
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try11-opt2.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 101
# copying to AlignedFragments data structure
# naming current conformation dimer//try11-opt2.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try11-opt2.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try11-opt2
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try11-opt2.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try11-opt2.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try11-opt2.unpack.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try11-opt2.unpack.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try11-opt2.unpack.gromacs0.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try11-opt2.unpack.gromacs0.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try11-opt2.unpack.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try11-opt2.unpack
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try12-opt1-scwrl.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try12-opt1-scwrl
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try12-opt1.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try12-opt1
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try12-opt2.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 101
# copying to AlignedFragments data structure
# naming current conformation dimer//try12-opt2.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try12-opt2.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try12-opt2
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try12-opt2.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try12-opt2.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try12-opt2.unpack.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try12-opt2.unpack.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try12-opt2.unpack.gromacs0.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try12-opt2.unpack.gromacs0.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try12-opt2.unpack.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try12-opt2.unpack
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try13-opt1-scwrl.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try13-opt1-scwrl
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try13-opt1.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try13-opt1
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try13-opt2.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 101
# copying to AlignedFragments data structure
# naming current conformation dimer//try13-opt2.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try13-opt2.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try13-opt2
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try13-opt2.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try13-opt2.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try13-opt2.unpack.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try13-opt2.unpack.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try13-opt2.unpack.gromacs0.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try13-opt2.unpack.gromacs0.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try13-opt2.unpack.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try13-opt2.unpack
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try14-opt1-scwrl.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try14-opt1-scwrl
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try14-opt1.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try14-opt1
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try14-opt2.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 101
# copying to AlignedFragments data structure
# naming current conformation dimer//try14-opt2.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try14-opt2.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try14-opt2
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try14-opt2.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try14-opt2.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try14-opt2.unpack.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try14-opt2.unpack.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try14-opt2.unpack.gromacs0.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try14-opt2.unpack.gromacs0.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try14-opt2.unpack.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try14-opt2.unpack
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try15-opt1-scwrl.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try15-opt1-scwrl
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try15-opt1.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try15-opt1
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try15-opt2.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try15-opt2
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try15-opt2.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try15-opt2.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try15-opt2.unpack.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 59
# copying to AlignedFragments data structure
# naming current conformation dimer//try15-opt2.unpack.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try15-opt2.unpack.gromacs0.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 59
# copying to AlignedFragments data structure
# naming current conformation dimer//try15-opt2.unpack.gromacs0.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try15-opt2.unpack.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try15-opt2.unpack
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try2-opt1-scwrl.pdb.gz looking for chain 'A' model 1
# Found a chain break before 100
# copying to AlignedFragments data structure
# naming current conformation dimer//try2-opt1-scwrl
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try2-opt1.pdb.gz looking for chain 'A' model 1
# Found a chain break before 100
# copying to AlignedFragments data structure
# naming current conformation dimer//try2-opt1
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try2-opt2.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 101
# copying to AlignedFragments data structure
# naming current conformation dimer//try2-opt2.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try2-opt2.pdb.gz looking for chain 'A' model 1
# Found a chain break before 100
# copying to AlignedFragments data structure
# naming current conformation dimer//try2-opt2
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try2-opt2.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 100
# copying to AlignedFragments data structure
# naming current conformation dimer//try2-opt2.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try2-opt2.unpack.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try2-opt2.unpack.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try2-opt2.unpack.gromacs0.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try2-opt2.unpack.gromacs0.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try2-opt2.unpack.pdb.gz looking for chain 'A' model 1
# Found a chain break before 100
# copying to AlignedFragments data structure
# naming current conformation dimer//try2-opt2.unpack
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try3-opt1-scwrl.pdb.gz looking for chain 'A' model 1
# Found a chain break before 70
# copying to AlignedFragments data structure
# naming current conformation dimer//try3-opt1-scwrl
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try3-opt1.pdb.gz looking for chain 'A' model 1
# Found a chain break before 70
# copying to AlignedFragments data structure
# naming current conformation dimer//try3-opt1
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try3-opt2.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 101
# copying to AlignedFragments data structure
# naming current conformation dimer//try3-opt2.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try3-opt2.pdb.gz looking for chain 'A' model 1
# Found a chain break before 70
# copying to AlignedFragments data structure
# naming current conformation dimer//try3-opt2
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try3-opt2.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 70
# copying to AlignedFragments data structure
# naming current conformation dimer//try3-opt2.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try3-opt2.unpack.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try3-opt2.unpack.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try3-opt2.unpack.gromacs0.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try3-opt2.unpack.gromacs0.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try3-opt2.unpack.pdb.gz looking for chain 'A' model 1
# Found a chain break before 70
# copying to AlignedFragments data structure
# naming current conformation dimer//try3-opt2.unpack
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try4-opt1-scwrl.pdb.gz looking for chain 'A' model 1
# Found a chain break before 78
# copying to AlignedFragments data structure
# naming current conformation dimer//try4-opt1-scwrl
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try4-opt1.pdb.gz looking for chain 'A' model 1
# Found a chain break before 78
# copying to AlignedFragments data structure
# naming current conformation dimer//try4-opt1
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try4-opt2.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 101
# copying to AlignedFragments data structure
# naming current conformation dimer//try4-opt2.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try4-opt2.pdb.gz looking for chain 'A' model 1
# Found a chain break before 78
# copying to AlignedFragments data structure
# naming current conformation dimer//try4-opt2
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try4-opt2.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 78
# copying to AlignedFragments data structure
# naming current conformation dimer//try4-opt2.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try4-opt2.unpack.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try4-opt2.unpack.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try4-opt2.unpack.gromacs0.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try4-opt2.unpack.gromacs0.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try4-opt2.unpack.pdb.gz looking for chain 'A' model 1
# Found a chain break before 78
# copying to AlignedFragments data structure
# naming current conformation dimer//try4-opt2.unpack
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try5-opt1-scwrl.pdb.gz looking for chain 'A' model 1
# Found a chain break before 75
# copying to AlignedFragments data structure
# naming current conformation dimer//try5-opt1-scwrl
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try5-opt1.pdb.gz looking for chain 'A' model 1
# Found a chain break before 75
# copying to AlignedFragments data structure
# naming current conformation dimer//try5-opt1
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try5-opt2.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 101
# copying to AlignedFragments data structure
# naming current conformation dimer//try5-opt2.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try5-opt2.pdb.gz looking for chain 'A' model 1
# Found a chain break before 75
# copying to AlignedFragments data structure
# naming current conformation dimer//try5-opt2
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try5-opt2.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 75
# copying to AlignedFragments data structure
# naming current conformation dimer//try5-opt2.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try5-opt2.unpack.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try5-opt2.unpack.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try5-opt2.unpack.gromacs0.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try5-opt2.unpack.gromacs0.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try5-opt2.unpack.pdb.gz looking for chain 'A' model 1
# Found a chain break before 75
# copying to AlignedFragments data structure
# naming current conformation dimer//try5-opt2.unpack
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try6-opt1-scwrl.pdb.gz looking for chain 'A' model 1
# Found a chain break before 83
# copying to AlignedFragments data structure
# naming current conformation dimer//try6-opt1-scwrl
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try6-opt1.pdb.gz looking for chain 'A' model 1
# Found a chain break before 83
# copying to AlignedFragments data structure
# naming current conformation dimer//try6-opt1
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try6-opt2.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 101
# copying to AlignedFragments data structure
# naming current conformation dimer//try6-opt2.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try6-opt2.pdb.gz looking for chain 'A' model 1
# Found a chain break before 79
# copying to AlignedFragments data structure
# naming current conformation dimer//try6-opt2
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try6-opt2.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 79
# copying to AlignedFragments data structure
# naming current conformation dimer//try6-opt2.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try6-opt2.unpack.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try6-opt2.unpack.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try6-opt2.unpack.gromacs0.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try6-opt2.unpack.gromacs0.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try6-opt2.unpack.pdb.gz looking for chain 'A' model 1
# Found a chain break before 79
# copying to AlignedFragments data structure
# naming current conformation dimer//try6-opt2.unpack
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try7-opt1-scwrl.pdb.gz looking for chain 'A' model 1
# Found a chain break before 78
# copying to AlignedFragments data structure
# naming current conformation dimer//try7-opt1-scwrl
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try7-opt1.pdb.gz looking for chain 'A' model 1
# Found a chain break before 78
# copying to AlignedFragments data structure
# naming current conformation dimer//try7-opt1
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try7-opt2.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 59
# copying to AlignedFragments data structure
# naming current conformation dimer//try7-opt2.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try7-opt2.pdb.gz looking for chain 'A' model 1
# Found a chain break before 59
# copying to AlignedFragments data structure
# naming current conformation dimer//try7-opt2
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try7-opt2.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 59
# copying to AlignedFragments data structure
# naming current conformation dimer//try7-opt2.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try7-opt2.unpack.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 74
# copying to AlignedFragments data structure
# naming current conformation dimer//try7-opt2.unpack.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try7-opt2.unpack.gromacs0.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 74
# copying to AlignedFragments data structure
# naming current conformation dimer//try7-opt2.unpack.gromacs0.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try7-opt2.unpack.pdb.gz looking for chain 'A' model 1
# Found a chain break before 59
# copying to AlignedFragments data structure
# naming current conformation dimer//try7-opt2.unpack
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try8-opt1-scwrl.pdb.gz looking for chain 'A' model 1
# Found a chain break before 76
# copying to AlignedFragments data structure
# naming current conformation dimer//try8-opt1-scwrl
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try8-opt1.pdb.gz looking for chain 'A' model 1
# Found a chain break before 76
# copying to AlignedFragments data structure
# naming current conformation dimer//try8-opt1
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try8-opt2.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 101
# copying to AlignedFragments data structure
# naming current conformation dimer//try8-opt2.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try8-opt2.pdb.gz looking for chain 'A' model 1
# Found a chain break before 76
# copying to AlignedFragments data structure
# naming current conformation dimer//try8-opt2
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try8-opt2.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 76
# copying to AlignedFragments data structure
# naming current conformation dimer//try8-opt2.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try8-opt2.unpack.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try8-opt2.unpack.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try8-opt2.unpack.gromacs0.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try8-opt2.unpack.gromacs0.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try8-opt2.unpack.pdb.gz looking for chain 'A' model 1
# Found a chain break before 76
# copying to AlignedFragments data structure
# naming current conformation dimer//try8-opt2.unpack
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try9-opt1-scwrl.pdb.gz looking for chain 'A' model 1
# Found a chain break before 59
# copying to AlignedFragments data structure
# naming current conformation dimer//try9-opt1-scwrl
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try9-opt1.pdb.gz looking for chain 'A' model 1
# Found a chain break before 59
# copying to AlignedFragments data structure
# naming current conformation dimer//try9-opt1
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try9-opt2.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 101
# copying to AlignedFragments data structure
# naming current conformation dimer//try9-opt2.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try9-opt2.pdb.gz looking for chain 'A' model 1
# Found a chain break before 59
# copying to AlignedFragments data structure
# naming current conformation dimer//try9-opt2
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try9-opt2.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 59
# copying to AlignedFragments data structure
# naming current conformation dimer//try9-opt2.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try9-opt2.unpack.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try9-opt2.unpack.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try9-opt2.unpack.gromacs0.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try9-opt2.unpack.gromacs0.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try9-opt2.unpack.pdb.gz looking for chain 'A' model 1
# Found a chain break before 59
# copying to AlignedFragments data structure
# naming current conformation dimer//try9-opt2.unpack
# ReadConformPDB reading from PDB file ../dimer/decoys/dimer-1tbxA-try1-opt2-proteinshop.pdb.gz looking for chain 'A' model 1
# Found a chain break before 100
# copying to AlignedFragments data structure
# naming current conformation dimer//dimer-1tbxA-try1-opt2-proteinshop
# ReadConformPDB reading from PDB file ../dimer/decoys/dimer-1tbxA-try1-opt2.pdb.gz looking for chain 'A' model 1
# Found a chain break before 100
# copying to AlignedFragments data structure
# naming current conformation dimer//dimer-1tbxA-try1-opt2
# ReadConformPDB reading from PDB file ../dimer/decoys/dimer-1ub9A-dimer11.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//dimer-1ub9A-dimer11
# ReadConformPDB reading from PDB file ../dimer/decoys/dimer1-1tbxA-dimer6.pdb.gz looking for chain 'A' model 1
# Found a chain break before 79
# copying to AlignedFragments data structure
# naming current conformation dimer//dimer1-1tbxA-dimer6
# ReadConformPDB reading from PDB file ../dimer/decoys/dimer2-1tbxA-dimer6.pdb.gz looking for chain 'A' model 1
# Found a chain break before 79
# copying to AlignedFragments data structure
# naming current conformation dimer//dimer2-1tbxA-dimer6
# ReadConformPDB reading from PDB file ../dimer/decoys/dimer3-1tbxA-dimer6.pdb.gz looking for chain 'A' model 1
# Found a chain break before 79
# copying to AlignedFragments data structure
# naming current conformation dimer//dimer3-1tbxA-dimer6
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_POPULUS_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1403662006.pdb -s /var/tmp/to_scwrl_1403662006.seq -o /var/tmp/from_scwrl_1403662006.pdb > /var/tmp/scwrl_1403662006.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1403662006.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 T0327 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_POPULUS_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1210090542.pdb -s /var/tmp/to_scwrl_1210090542.seq -o /var/tmp/from_scwrl_1210090542.pdb > /var/tmp/scwrl_1210090542.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1210090542.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 T0327 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_POPULUS_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1908559345.pdb -s /var/tmp/to_scwrl_1908559345.seq -o /var/tmp/from_scwrl_1908559345.pdb > /var/tmp/scwrl_1908559345.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1908559345.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 T0327 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_POPULUS_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1053148745.pdb -s /var/tmp/to_scwrl_1053148745.seq -o /var/tmp/from_scwrl_1053148745.pdb > /var/tmp/scwrl_1053148745.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1053148745.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 T0327 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_POPULUS_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_868827109.pdb -s /var/tmp/to_scwrl_868827109.seq -o /var/tmp/from_scwrl_868827109.pdb > /var/tmp/scwrl_868827109.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_868827109.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 T0327 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_RECOM_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1054728845.pdb -s /var/tmp/to_scwrl_1054728845.seq -o /var/tmp/from_scwrl_1054728845.pdb > /var/tmp/scwrl_1054728845.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1054728845.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 T0327 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_RECOM_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_869974829.pdb -s /var/tmp/to_scwrl_869974829.seq -o /var/tmp/from_scwrl_869974829.pdb > /var/tmp/scwrl_869974829.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_869974829.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 T0327 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_RECOM_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_742273320.pdb -s /var/tmp/to_scwrl_742273320.seq -o /var/tmp/from_scwrl_742273320.pdb > /var/tmp/scwrl_742273320.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_742273320.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 T0327 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_RECOM_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1645662136.pdb -s /var/tmp/to_scwrl_1645662136.seq -o /var/tmp/from_scwrl_1645662136.pdb > /var/tmp/scwrl_1645662136.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1645662136.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 T0327 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_RECOM_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_684063752.pdb -s /var/tmp/to_scwrl_684063752.seq -o /var/tmp/from_scwrl_684063752.pdb > /var/tmp/scwrl_684063752.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_684063752.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 T0327 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_334431966.pdb -s /var/tmp/to_scwrl_334431966.seq -o /var/tmp/from_scwrl_334431966.pdb > /var/tmp/scwrl_334431966.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_334431966.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 T0327 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1591230378.pdb -s /var/tmp/to_scwrl_1591230378.seq -o /var/tmp/from_scwrl_1591230378.pdb > /var/tmp/scwrl_1591230378.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1591230378.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
# Found a chain break before 100
# copying to AlignedFragments data structure
# naming current conformation 3D-JIGSAW_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1241124022.pdb -s /var/tmp/to_scwrl_1241124022.seq -o /var/tmp/from_scwrl_1241124022.pdb > /var/tmp/scwrl_1241124022.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1241124022.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 T0327 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1381723674.pdb -s /var/tmp/to_scwrl_1381723674.seq -o /var/tmp/from_scwrl_1381723674.pdb > /var/tmp/scwrl_1381723674.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1381723674.pdb
# conformation set from SCWRL output
# naming current conformation 3D-JIGSAW_TS4-scwrl
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1387404018.pdb -s /var/tmp/to_scwrl_1387404018.seq -o /var/tmp/from_scwrl_1387404018.pdb > /var/tmp/scwrl_1387404018.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1387404018.pdb
# conformation set from SCWRL output
# naming current conformation 3D-JIGSAW_TS5-scwrl
# ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1
# Found a chain break before 59
# copying to AlignedFragments data structure
# naming current conformation 3Dpro_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1339989246.pdb -s /var/tmp/to_scwrl_1339989246.seq -o /var/tmp/from_scwrl_1339989246.pdb > /var/tmp/scwrl_1339989246.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1339989246.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 34
# copying to AlignedFragments data structure
# naming current conformation 3Dpro_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1676334020.pdb -s /var/tmp/to_scwrl_1676334020.seq -o /var/tmp/from_scwrl_1676334020.pdb > /var/tmp/scwrl_1676334020.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1676334020.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 97
# copying to AlignedFragments data structure
# naming current conformation 3Dpro_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_902955398.pdb -s /var/tmp/to_scwrl_902955398.seq -o /var/tmp/from_scwrl_902955398.pdb > /var/tmp/scwrl_902955398.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_902955398.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 97
# copying to AlignedFragments data structure
# naming current conformation 3Dpro_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1025069216.pdb -s /var/tmp/to_scwrl_1025069216.seq -o /var/tmp/from_scwrl_1025069216.pdb > /var/tmp/scwrl_1025069216.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1025069216.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 97
# copying to AlignedFragments data structure
# naming current conformation 3Dpro_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_171309320.pdb -s /var/tmp/to_scwrl_171309320.seq -o /var/tmp/from_scwrl_171309320.pdb > /var/tmp/scwrl_171309320.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_171309320.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 97
# copying to AlignedFragments data structure
# naming current conformation ABIpro_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1330630756.pdb -s /var/tmp/to_scwrl_1330630756.seq -o /var/tmp/from_scwrl_1330630756.pdb > /var/tmp/scwrl_1330630756.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1330630756.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 78
# copying to AlignedFragments data structure
# naming current conformation ABIpro_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_2076700264.pdb -s /var/tmp/to_scwrl_2076700264.seq -o /var/tmp/from_scwrl_2076700264.pdb > /var/tmp/scwrl_2076700264.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2076700264.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 52
# copying to AlignedFragments data structure
# naming current conformation ABIpro_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1052843950.pdb -s /var/tmp/to_scwrl_1052843950.seq -o /var/tmp/from_scwrl_1052843950.pdb > /var/tmp/scwrl_1052843950.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1052843950.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 99
# copying to AlignedFragments data structure
# naming current conformation ABIpro_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1239177807.pdb -s /var/tmp/to_scwrl_1239177807.seq -o /var/tmp/from_scwrl_1239177807.pdb > /var/tmp/scwrl_1239177807.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1239177807.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 89
# copying to AlignedFragments data structure
# naming current conformation ABIpro_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1687334412.pdb -s /var/tmp/to_scwrl_1687334412.seq -o /var/tmp/from_scwrl_1687334412.pdb > /var/tmp/scwrl_1687334412.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1687334412.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 55
# copying to AlignedFragments data structure
# naming current conformation BayesHH_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1826991126.pdb -s /var/tmp/to_scwrl_1826991126.seq -o /var/tmp/from_scwrl_1826991126.pdb > /var/tmp/scwrl_1826991126.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1826991126.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 69
# copying to AlignedFragments data structure
# naming current conformation Bilab-ENABLE_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_341623222.pdb -s /var/tmp/to_scwrl_341623222.seq -o /var/tmp/from_scwrl_341623222.pdb > /var/tmp/scwrl_341623222.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_341623222.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 64
# copying to AlignedFragments data structure
# naming current conformation Bilab-ENABLE_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1914002183.pdb -s /var/tmp/to_scwrl_1914002183.seq -o /var/tmp/from_scwrl_1914002183.pdb > /var/tmp/scwrl_1914002183.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1914002183.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 101
# copying to AlignedFragments data structure
# naming current conformation Bilab-ENABLE_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_596461782.pdb -s /var/tmp/to_scwrl_596461782.seq -o /var/tmp/from_scwrl_596461782.pdb > /var/tmp/scwrl_596461782.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_596461782.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 101
# copying to AlignedFragments data structure
# naming current conformation Bilab-ENABLE_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_355459355.pdb -s /var/tmp/to_scwrl_355459355.seq -o /var/tmp/from_scwrl_355459355.pdb > /var/tmp/scwrl_355459355.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_355459355.pdb
# conformation set from SCWRL output
# naming current conformation Bilab-ENABLE_TS4-scwrl
# ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS5.pdb.gz looking for model 1
# Found a chain break before 101
# copying to AlignedFragments data structure
# naming current conformation Bilab-ENABLE_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_407620262.pdb -s /var/tmp/to_scwrl_407620262.seq -o /var/tmp/from_scwrl_407620262.pdb > /var/tmp/scwrl_407620262.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_407620262.pdb
# conformation set from SCWRL output
# naming current conformation Bilab-ENABLE_TS5-scwrl
# ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1
# Found a chain break before 89
# copying to AlignedFragments data structure
# naming current conformation CIRCLE_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_2000123788.pdb -s /var/tmp/to_scwrl_2000123788.seq -o /var/tmp/from_scwrl_2000123788.pdb > /var/tmp/scwrl_2000123788.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2000123788.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
# Found a chain break before 90
# copying to AlignedFragments data structure
# naming current conformation CIRCLE_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1565549897.pdb -s /var/tmp/to_scwrl_1565549897.seq -o /var/tmp/from_scwrl_1565549897.pdb > /var/tmp/scwrl_1565549897.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1565549897.pdb
# conformation set from SCWRL output
# naming current conformation CIRCLE_TS2-scwrl
# ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation CIRCLE_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_168695960.pdb -s /var/tmp/to_scwrl_168695960.seq -o /var/tmp/from_scwrl_168695960.pdb > /var/tmp/scwrl_168695960.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_168695960.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 T0327 can't currently be optimized by undertaker
# naming current conformation CIRCLE_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_905788886.pdb -s /var/tmp/to_scwrl_905788886.seq -o /var/tmp/from_scwrl_905788886.pdb > /var/tmp/scwrl_905788886.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_905788886.pdb
# conformation set from SCWRL output
# naming current conformation CIRCLE_TS4-scwrl
# ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation CIRCLE_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_286893359.pdb -s /var/tmp/to_scwrl_286893359.seq -o /var/tmp/from_scwrl_286893359.pdb > /var/tmp/scwrl_286893359.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_286893359.pdb
# conformation set from SCWRL output
# naming current conformation CIRCLE_TS5-scwrl
# ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation CaspIta-FOX_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1223424804.pdb -s /var/tmp/to_scwrl_1223424804.seq -o /var/tmp/from_scwrl_1223424804.pdb > /var/tmp/scwrl_1223424804.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1223424804.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 T0327 can't currently be optimized by undertaker
# naming current conformation CaspIta-FOX_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1775763714.pdb -s /var/tmp/to_scwrl_1775763714.seq -o /var/tmp/from_scwrl_1775763714.pdb > /var/tmp/scwrl_1775763714.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1775763714.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 T0327 can't currently be optimized by undertaker
# naming current conformation CaspIta-FOX_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1029166679.pdb -s /var/tmp/to_scwrl_1029166679.seq -o /var/tmp/from_scwrl_1029166679.pdb > /var/tmp/scwrl_1029166679.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1029166679.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 T0327 can't currently be optimized by undertaker
# naming current conformation CaspIta-FOX_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_721603294.pdb -s /var/tmp/to_scwrl_721603294.seq -o /var/tmp/from_scwrl_721603294.pdb > /var/tmp/scwrl_721603294.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_721603294.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 T0327 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation CaspIta-FOX_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_312343820.pdb -s /var/tmp/to_scwrl_312343820.seq -o /var/tmp/from_scwrl_312343820.pdb > /var/tmp/scwrl_312343820.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_312343820.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 T0327 can't currently be optimized by undertaker
# naming current conformation Distill_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1363598645.pdb -s /var/tmp/to_scwrl_1363598645.seq -o /var/tmp/from_scwrl_1363598645.pdb > /var/tmp/scwrl_1363598645.log
Error: Couldn't open file /var/tmp/from_scwrl_1363598645.pdb or /var/tmp/from_scwrl_1363598645.pdb.gz for input
Warning: Couldn't open file decoys//var/tmp/from_scwrl_1363598645_b.pdb or decoys//var/tmp/from_scwrl_1363598645_b.pdb.gz for input
Trying /var/tmp/from_scwrl_1363598645_b.pdb
Error: Couldn't open file /var/tmp/from_scwrl_1363598645_b.pdb or /var/tmp/from_scwrl_1363598645_b.pdb.gz for input
Warning: Couldn't open file decoys//var/tmp/from_scwrl_1363598645_a.pdb or decoys//var/tmp/from_scwrl_1363598645_a.pdb.gz for input
Trying /var/tmp/from_scwrl_1363598645_a.pdb
Error: Couldn't open file /var/tmp/from_scwrl_1363598645_a.pdb or /var/tmp/from_scwrl_1363598645_a.pdb.gz for input
Error: can't open any of /var/tmp/from_scwrl_1363598645.pdb or /var/tmp/from_scwrl_1363598645_b.pdb or /var/tmp/from_scwrl_1363598645_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 T0327 can't currently be optimized by undertaker
# naming current conformation Distill_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_165350025.pdb -s /var/tmp/to_scwrl_165350025.seq -o /var/tmp/from_scwrl_165350025.pdb > /var/tmp/scwrl_165350025.log
Error: Couldn't open file /var/tmp/from_scwrl_165350025.pdb or /var/tmp/from_scwrl_165350025.pdb.gz for input
Warning: Couldn't open file decoys//var/tmp/from_scwrl_165350025_b.pdb or decoys//var/tmp/from_scwrl_165350025_b.pdb.gz for input
Trying /var/tmp/from_scwrl_165350025_b.pdb
Error: Couldn't open file /var/tmp/from_scwrl_165350025_b.pdb or /var/tmp/from_scwrl_165350025_b.pdb.gz for input
Warning: Couldn't open file decoys//var/tmp/from_scwrl_165350025_a.pdb or decoys//var/tmp/from_scwrl_165350025_a.pdb.gz for input
Trying /var/tmp/from_scwrl_165350025_a.pdb
Error: Couldn't open file /var/tmp/from_scwrl_165350025_a.pdb or /var/tmp/from_scwrl_165350025_a.pdb.gz for input
Error: can't open any of /var/tmp/from_scwrl_165350025.pdb or /var/tmp/from_scwrl_165350025_b.pdb or /var/tmp/from_scwrl_165350025_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 T0327 can't currently be optimized by undertaker
# naming current conformation Distill_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1553467842.pdb -s /var/tmp/to_scwrl_1553467842.seq -o /var/tmp/from_scwrl_1553467842.pdb > /var/tmp/scwrl_1553467842.log
Error: Couldn't open file /var/tmp/from_scwrl_1553467842.pdb or /var/tmp/from_scwrl_1553467842.pdb.gz for input
Warning: Couldn't open file decoys//var/tmp/from_scwrl_1553467842_b.pdb or decoys//var/tmp/from_scwrl_1553467842_b.pdb.gz for input
Trying /var/tmp/from_scwrl_1553467842_b.pdb
Error: Couldn't open file /var/tmp/from_scwrl_1553467842_b.pdb or /var/tmp/from_scwrl_1553467842_b.pdb.gz for input
Warning: Couldn't open file decoys//var/tmp/from_scwrl_1553467842_a.pdb or decoys//var/tmp/from_scwrl_1553467842_a.pdb.gz for input
Trying /var/tmp/from_scwrl_1553467842_a.pdb
Error: Couldn't open file /var/tmp/from_scwrl_1553467842_a.pdb or /var/tmp/from_scwrl_1553467842_a.pdb.gz for input
Error: can't open any of /var/tmp/from_scwrl_1553467842.pdb or /var/tmp/from_scwrl_1553467842_b.pdb or /var/tmp/from_scwrl_1553467842_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 T0327 can't currently be optimized by undertaker
# naming current conformation Distill_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_597838673.pdb -s /var/tmp/to_scwrl_597838673.seq -o /var/tmp/from_scwrl_597838673.pdb > /var/tmp/scwrl_597838673.log
Error: Couldn't open file /var/tmp/from_scwrl_597838673.pdb or /var/tmp/from_scwrl_597838673.pdb.gz for input
Warning: Couldn't open file decoys//var/tmp/from_scwrl_597838673_b.pdb or decoys//var/tmp/from_scwrl_597838673_b.pdb.gz for input
Trying /var/tmp/from_scwrl_597838673_b.pdb
Error: Couldn't open file /var/tmp/from_scwrl_597838673_b.pdb or /var/tmp/from_scwrl_597838673_b.pdb.gz for input
Warning: Couldn't open file decoys//var/tmp/from_scwrl_597838673_a.pdb or decoys//var/tmp/from_scwrl_597838673_a.pdb.gz for input
Trying /var/tmp/from_scwrl_597838673_a.pdb
Error: Couldn't open file /var/tmp/from_scwrl_597838673_a.pdb or /var/tmp/from_scwrl_597838673_a.pdb.gz for input
Error: can't open any of /var/tmp/from_scwrl_597838673.pdb or /var/tmp/from_scwrl_597838673_b.pdb or /var/tmp/from_scwrl_597838673_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 T0327 can't currently be optimized by undertaker
# naming current conformation Distill_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1552754043.pdb -s /var/tmp/to_scwrl_1552754043.seq -o /var/tmp/from_scwrl_1552754043.pdb > /var/tmp/scwrl_1552754043.log
Error: Couldn't open file /var/tmp/from_scwrl_1552754043.pdb or /var/tmp/from_scwrl_1552754043.pdb.gz for input
Warning: Couldn't open file decoys//var/tmp/from_scwrl_1552754043_b.pdb or decoys//var/tmp/from_scwrl_1552754043_b.pdb.gz for input
Trying /var/tmp/from_scwrl_1552754043_b.pdb
Error: Couldn't open file /var/tmp/from_scwrl_1552754043_b.pdb or /var/tmp/from_scwrl_1552754043_b.pdb.gz for input
Warning: Couldn't open file decoys//var/tmp/from_scwrl_1552754043_a.pdb or decoys//var/tmp/from_scwrl_1552754043_a.pdb.gz for input
Trying /var/tmp/from_scwrl_1552754043_a.pdb
Error: Couldn't open file /var/tmp/from_scwrl_1552754043_a.pdb or /var/tmp/from_scwrl_1552754043_a.pdb.gz for input
Error: can't open any of /var/tmp/from_scwrl_1552754043.pdb or /var/tmp/from_scwrl_1552754043_b.pdb or /var/tmp/from_scwrl_1552754043_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 100
# copying to AlignedFragments data structure
# naming current conformation FAMSD_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_745973443.pdb -s /var/tmp/to_scwrl_745973443.seq -o /var/tmp/from_scwrl_745973443.pdb > /var/tmp/scwrl_745973443.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_745973443.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 T0327 can't currently be optimized by undertaker
# naming current conformation FAMSD_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_126689047.pdb -s /var/tmp/to_scwrl_126689047.seq -o /var/tmp/from_scwrl_126689047.pdb > /var/tmp/scwrl_126689047.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_126689047.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 T0327 can't currently be optimized by undertaker
# naming current conformation FAMSD_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_308225794.pdb -s /var/tmp/to_scwrl_308225794.seq -o /var/tmp/from_scwrl_308225794.pdb > /var/tmp/scwrl_308225794.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_308225794.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 T0327 can't currently be optimized by undertaker
# naming current conformation FAMSD_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1771042658.pdb -s /var/tmp/to_scwrl_1771042658.seq -o /var/tmp/from_scwrl_1771042658.pdb > /var/tmp/scwrl_1771042658.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1771042658.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 T0327 can't currently be optimized by undertaker
# naming current conformation FAMSD_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_297998367.pdb -s /var/tmp/to_scwrl_297998367.seq -o /var/tmp/from_scwrl_297998367.pdb > /var/tmp/scwrl_297998367.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_297998367.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 98
# copying to AlignedFragments data structure
# naming current conformation FAMS_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1638856550.pdb -s /var/tmp/to_scwrl_1638856550.seq -o /var/tmp/from_scwrl_1638856550.pdb > /var/tmp/scwrl_1638856550.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1638856550.pdb
# conformation set from SCWRL output
# naming current conformation FAMS_TS1-scwrl
# ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1
# Found a chain break before 89
# copying to AlignedFragments data structure
# naming current conformation FAMS_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1700259275.pdb -s /var/tmp/to_scwrl_1700259275.seq -o /var/tmp/from_scwrl_1700259275.pdb > /var/tmp/scwrl_1700259275.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1700259275.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 90
# copying to AlignedFragments data structure
# naming current conformation FAMS_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1350842317.pdb -s /var/tmp/to_scwrl_1350842317.seq -o /var/tmp/from_scwrl_1350842317.pdb > /var/tmp/scwrl_1350842317.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1350842317.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 T0327 can't currently be optimized by undertaker
# naming current conformation FAMS_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_730550711.pdb -s /var/tmp/to_scwrl_730550711.seq -o /var/tmp/from_scwrl_730550711.pdb > /var/tmp/scwrl_730550711.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_730550711.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 T0327 can't currently be optimized by undertaker
# naming current conformation FAMS_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1240110040.pdb -s /var/tmp/to_scwrl_1240110040.seq -o /var/tmp/from_scwrl_1240110040.pdb > /var/tmp/scwrl_1240110040.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1240110040.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 58
# copying to AlignedFragments data structure
# naming current conformation FOLDpro_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1030349797.pdb -s /var/tmp/to_scwrl_1030349797.seq -o /var/tmp/from_scwrl_1030349797.pdb > /var/tmp/scwrl_1030349797.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1030349797.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 63
# copying to AlignedFragments data structure
# naming current conformation FOLDpro_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1072173933.pdb -s /var/tmp/to_scwrl_1072173933.seq -o /var/tmp/from_scwrl_1072173933.pdb > /var/tmp/scwrl_1072173933.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1072173933.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 58
# copying to AlignedFragments data structure
# naming current conformation FOLDpro_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1006628578.pdb -s /var/tmp/to_scwrl_1006628578.seq -o /var/tmp/from_scwrl_1006628578.pdb > /var/tmp/scwrl_1006628578.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1006628578.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 62
# copying to AlignedFragments data structure
# naming current conformation FOLDpro_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1626811578.pdb -s /var/tmp/to_scwrl_1626811578.seq -o /var/tmp/from_scwrl_1626811578.pdb > /var/tmp/scwrl_1626811578.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1626811578.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 61
# copying to AlignedFragments data structure
# naming current conformation FOLDpro_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1427633287.pdb -s /var/tmp/to_scwrl_1427633287.seq -o /var/tmp/from_scwrl_1427633287.pdb > /var/tmp/scwrl_1427633287.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1427633287.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 T0327 can't currently be optimized by undertaker
# naming current conformation FORTE1_AL1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1414248839.pdb -s /var/tmp/to_scwrl_1414248839.seq -o /var/tmp/from_scwrl_1414248839.pdb > /var/tmp/scwrl_1414248839.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1414248839.pdb
# conformation set from SCWRL output
# naming current conformation FORTE1_AL1-scwrl
# ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation FORTE1_AL2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1479451720.pdb -s /var/tmp/to_scwrl_1479451720.seq -o /var/tmp/from_scwrl_1479451720.pdb > /var/tmp/scwrl_1479451720.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1479451720.pdb
# conformation set from SCWRL output
# naming current conformation FORTE1_AL2-scwrl
# ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1
Skipped atom 265, because occupancy 1.0000000e+00 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation FORTE1_AL3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_845699539.pdb -s /var/tmp/to_scwrl_845699539.seq -o /var/tmp/from_scwrl_845699539.pdb > /var/tmp/scwrl_845699539.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_845699539.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 T0327 can't currently be optimized by undertaker
# naming current conformation FORTE1_AL4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1582944799.pdb -s /var/tmp/to_scwrl_1582944799.seq -o /var/tmp/from_scwrl_1582944799.pdb > /var/tmp/scwrl_1582944799.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1582944799.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 T0327 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FORTE1_AL5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_237756959.pdb -s /var/tmp/to_scwrl_237756959.seq -o /var/tmp/from_scwrl_237756959.pdb > /var/tmp/scwrl_237756959.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_237756959.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 T0327 can't currently be optimized by undertaker
# naming current conformation FORTE2_AL1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1132592897.pdb -s /var/tmp/to_scwrl_1132592897.seq -o /var/tmp/from_scwrl_1132592897.pdb > /var/tmp/scwrl_1132592897.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1132592897.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
Skipped atom 265, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation FORTE2_AL2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_658885957.pdb -s /var/tmp/to_scwrl_658885957.seq -o /var/tmp/from_scwrl_658885957.pdb > /var/tmp/scwrl_658885957.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_658885957.pdb
# conformation set from SCWRL output
# naming current conformation FORTE2_AL2-scwrl
# ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation FORTE2_AL3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_2013520674.pdb -s /var/tmp/to_scwrl_2013520674.seq -o /var/tmp/from_scwrl_2013520674.pdb > /var/tmp/scwrl_2013520674.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2013520674.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 T0327 can't currently be optimized by undertaker
# naming current conformation FORTE2_AL4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_14275930.pdb -s /var/tmp/to_scwrl_14275930.seq -o /var/tmp/from_scwrl_14275930.pdb > /var/tmp/scwrl_14275930.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_14275930.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 T0327 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FORTE2_AL5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1380489250.pdb -s /var/tmp/to_scwrl_1380489250.seq -o /var/tmp/from_scwrl_1380489250.pdb > /var/tmp/scwrl_1380489250.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1380489250.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 99
# copying to AlignedFragments data structure
# naming current conformation FPSOLVER-SERVER_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_178380847.pdb -s /var/tmp/to_scwrl_178380847.seq -o /var/tmp/from_scwrl_178380847.pdb > /var/tmp/scwrl_178380847.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_178380847.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 101
# copying to AlignedFragments data structure
# naming current conformation FPSOLVER-SERVER_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1377874575.pdb -s /var/tmp/to_scwrl_1377874575.seq -o /var/tmp/from_scwrl_1377874575.pdb > /var/tmp/scwrl_1377874575.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1377874575.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 101
# copying to AlignedFragments data structure
# naming current conformation FPSOLVER-SERVER_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1545839275.pdb -s /var/tmp/to_scwrl_1545839275.seq -o /var/tmp/from_scwrl_1545839275.pdb > /var/tmp/scwrl_1545839275.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1545839275.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 75
# copying to AlignedFragments data structure
# naming current conformation FPSOLVER-SERVER_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1731848689.pdb -s /var/tmp/to_scwrl_1731848689.seq -o /var/tmp/from_scwrl_1731848689.pdb > /var/tmp/scwrl_1731848689.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1731848689.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 96
# copying to AlignedFragments data structure
# naming current conformation FPSOLVER-SERVER_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1975713248.pdb -s /var/tmp/to_scwrl_1975713248.seq -o /var/tmp/from_scwrl_1975713248.pdb > /var/tmp/scwrl_1975713248.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1975713248.pdb
# conformation set from SCWRL output
# naming current conformation FPSOLVER-SERVER_TS5-scwrl
# ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1
# Found a chain break before 68
# copying to AlignedFragments data structure
# naming current conformation FUGMOD_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_951109672.pdb -s /var/tmp/to_scwrl_951109672.seq -o /var/tmp/from_scwrl_951109672.pdb > /var/tmp/scwrl_951109672.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_951109672.pdb
# conformation set from SCWRL output
# naming current conformation FUGMOD_TS1-scwrl
# ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1
# Found a chain break before 78
# copying to AlignedFragments data structure
# naming current conformation FUGMOD_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_330338485.pdb -s /var/tmp/to_scwrl_330338485.seq -o /var/tmp/from_scwrl_330338485.pdb > /var/tmp/scwrl_330338485.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_330338485.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 T0327 can't currently be optimized by undertaker
# naming current conformation FUGMOD_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_2102402295.pdb -s /var/tmp/to_scwrl_2102402295.seq -o /var/tmp/from_scwrl_2102402295.pdb > /var/tmp/scwrl_2102402295.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2102402295.pdb
# conformation set from SCWRL output
# naming current conformation FUGMOD_TS3-scwrl
# ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1
# Found a chain break before 95
# copying to AlignedFragments data structure
# naming current conformation FUGMOD_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1259335465.pdb -s /var/tmp/to_scwrl_1259335465.seq -o /var/tmp/from_scwrl_1259335465.pdb > /var/tmp/scwrl_1259335465.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1259335465.pdb
# conformation set from SCWRL output
# naming current conformation FUGMOD_TS4-scwrl
# ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1
# Found a chain break before 69
# copying to AlignedFragments data structure
# naming current conformation FUGMOD_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_2101381143.pdb -s /var/tmp/to_scwrl_2101381143.seq -o /var/tmp/from_scwrl_2101381143.pdb > /var/tmp/scwrl_2101381143.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2101381143.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 T0327 can't currently be optimized by undertaker
# naming current conformation FUGUE_AL1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_252917016.pdb -s /var/tmp/to_scwrl_252917016.seq -o /var/tmp/from_scwrl_252917016.pdb > /var/tmp/scwrl_252917016.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_252917016.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 T0327 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FUGUE_AL2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_750708369.pdb -s /var/tmp/to_scwrl_750708369.seq -o /var/tmp/from_scwrl_750708369.pdb > /var/tmp/scwrl_750708369.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_750708369.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 T0327 can't currently be optimized by undertaker
# naming current conformation FUGUE_AL3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1654156772.pdb -s /var/tmp/to_scwrl_1654156772.seq -o /var/tmp/from_scwrl_1654156772.pdb > /var/tmp/scwrl_1654156772.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1654156772.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 T0327 can't currently be optimized by undertaker
# naming current conformation FUGUE_AL4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1603759333.pdb -s /var/tmp/to_scwrl_1603759333.seq -o /var/tmp/from_scwrl_1603759333.pdb > /var/tmp/scwrl_1603759333.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1603759333.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
Skipped atom 323, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL5.pdb.gz
Skipped atom 325, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL5.pdb.gz
Skipped atom 327, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL5.pdb.gz
Skipped atom 329, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL5.pdb.gz
Skipped atom 331, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL5.pdb.gz
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FUGUE_AL5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1481259079.pdb -s /var/tmp/to_scwrl_1481259079.seq -o /var/tmp/from_scwrl_1481259079.pdb > /var/tmp/scwrl_1481259079.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1481259079.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 99
# copying to AlignedFragments data structure
# naming current conformation FUNCTION_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_746783166.pdb -s /var/tmp/to_scwrl_746783166.seq -o /var/tmp/from_scwrl_746783166.pdb > /var/tmp/scwrl_746783166.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_746783166.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 99
# copying to AlignedFragments data structure
# naming current conformation FUNCTION_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_486625483.pdb -s /var/tmp/to_scwrl_486625483.seq -o /var/tmp/from_scwrl_486625483.pdb > /var/tmp/scwrl_486625483.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_486625483.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 97
# copying to AlignedFragments data structure
# naming current conformation FUNCTION_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_405949365.pdb -s /var/tmp/to_scwrl_405949365.seq -o /var/tmp/from_scwrl_405949365.pdb > /var/tmp/scwrl_405949365.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_405949365.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 98
# copying to AlignedFragments data structure
# naming current conformation FUNCTION_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1753411743.pdb -s /var/tmp/to_scwrl_1753411743.seq -o /var/tmp/from_scwrl_1753411743.pdb > /var/tmp/scwrl_1753411743.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1753411743.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 98
# copying to AlignedFragments data structure
# naming current conformation FUNCTION_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_2113437061.pdb -s /var/tmp/to_scwrl_2113437061.seq -o /var/tmp/from_scwrl_2113437061.pdb > /var/tmp/scwrl_2113437061.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2113437061.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
# naming current conformation GeneSilicoMetaServer_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1833582653.pdb -s /var/tmp/to_scwrl_1833582653.seq -o /var/tmp/from_scwrl_1833582653.pdb > /var/tmp/scwrl_1833582653.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1833582653.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 78
# copying to AlignedFragments data structure
# naming current conformation GeneSilicoMetaServer_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1020176936.pdb -s /var/tmp/to_scwrl_1020176936.seq -o /var/tmp/from_scwrl_1020176936.pdb > /var/tmp/scwrl_1020176936.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1020176936.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
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation GeneSilicoMetaServer_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1445405134.pdb -s /var/tmp/to_scwrl_1445405134.seq -o /var/tmp/from_scwrl_1445405134.pdb > /var/tmp/scwrl_1445405134.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1445405134.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
# Found a chain break before 62
# copying to AlignedFragments data structure
# naming current conformation GeneSilicoMetaServer_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_531798545.pdb -s /var/tmp/to_scwrl_531798545.seq -o /var/tmp/from_scwrl_531798545.pdb > /var/tmp/scwrl_531798545.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_531798545.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 64
# copying to AlignedFragments data structure
# naming current conformation GeneSilicoMetaServer_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_455638088.pdb -s /var/tmp/to_scwrl_455638088.seq -o /var/tmp/from_scwrl_455638088.pdb > /var/tmp/scwrl_455638088.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_455638088.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 47
# copying to AlignedFragments data structure
# naming current conformation HHpred1_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1683162094.pdb -s /var/tmp/to_scwrl_1683162094.seq -o /var/tmp/from_scwrl_1683162094.pdb > /var/tmp/scwrl_1683162094.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1683162094.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 55
# copying to AlignedFragments data structure
# naming current conformation HHpred2_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1664391442.pdb -s /var/tmp/to_scwrl_1664391442.seq -o /var/tmp/from_scwrl_1664391442.pdb > /var/tmp/scwrl_1664391442.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1664391442.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 55
# copying to AlignedFragments data structure
# naming current conformation HHpred3_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1114524044.pdb -s /var/tmp/to_scwrl_1114524044.seq -o /var/tmp/from_scwrl_1114524044.pdb > /var/tmp/scwrl_1114524044.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1114524044.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 T0327 can't currently be optimized by undertaker
# naming current conformation Huber-Torda-Server_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1549199121.pdb -s /var/tmp/to_scwrl_1549199121.seq -o /var/tmp/from_scwrl_1549199121.pdb > /var/tmp/scwrl_1549199121.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1549199121.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 T0327 can't currently be optimized by undertaker
# naming current conformation Huber-Torda-Server_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1678667372.pdb -s /var/tmp/to_scwrl_1678667372.seq -o /var/tmp/from_scwrl_1678667372.pdb > /var/tmp/scwrl_1678667372.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1678667372.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 T0327 can't currently be optimized by undertaker
# naming current conformation Huber-Torda-Server_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_347529648.pdb -s /var/tmp/to_scwrl_347529648.seq -o /var/tmp/from_scwrl_347529648.pdb > /var/tmp/scwrl_347529648.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_347529648.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 T0327 can't currently be optimized by undertaker
# naming current conformation Huber-Torda-Server_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1727579968.pdb -s /var/tmp/to_scwrl_1727579968.seq -o /var/tmp/from_scwrl_1727579968.pdb > /var/tmp/scwrl_1727579968.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1727579968.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 T0327 can't currently be optimized by undertaker
# naming current conformation Huber-Torda-Server_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_909058301.pdb -s /var/tmp/to_scwrl_909058301.seq -o /var/tmp/from_scwrl_909058301.pdb > /var/tmp/scwrl_909058301.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_909058301.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 T0327 can't currently be optimized by undertaker
# naming current conformation LOOPP_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1893368923.pdb -s /var/tmp/to_scwrl_1893368923.seq -o /var/tmp/from_scwrl_1893368923.pdb > /var/tmp/scwrl_1893368923.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1893368923.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 T0327 can't currently be optimized by undertaker
# naming current conformation LOOPP_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1311945010.pdb -s /var/tmp/to_scwrl_1311945010.seq -o /var/tmp/from_scwrl_1311945010.pdb > /var/tmp/scwrl_1311945010.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1311945010.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 T0327 can't currently be optimized by undertaker
# naming current conformation LOOPP_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_737287903.pdb -s /var/tmp/to_scwrl_737287903.seq -o /var/tmp/from_scwrl_737287903.pdb > /var/tmp/scwrl_737287903.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_737287903.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 T0327 can't currently be optimized by undertaker
# naming current conformation LOOPP_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_696994948.pdb -s /var/tmp/to_scwrl_696994948.seq -o /var/tmp/from_scwrl_696994948.pdb > /var/tmp/scwrl_696994948.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_696994948.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 T0327 can't currently be optimized by undertaker
# naming current conformation LOOPP_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1642283496.pdb -s /var/tmp/to_scwrl_1642283496.seq -o /var/tmp/from_scwrl_1642283496.pdb > /var/tmp/scwrl_1642283496.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1642283496.pdb
# conformation set from SCWRL output
# naming current conformation LOOPP_TS5-scwrl
# ReadConformPDB reading from PDB file servers/MIG_FROST_AL1.pdb.gz looking for model 1
Error: Reading chain from PDB file servers/MIG_FROST_AL1.pdb.gz failed.
# naming current conformation MIG_FROST_AL1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_692206551.pdb -s /var/tmp/to_scwrl_692206551.seq -o /var/tmp/from_scwrl_692206551.pdb > /var/tmp/scwrl_692206551.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_692206551.pdb
# conformation set from SCWRL output
# naming current conformation MIG_FROST_AL1-scwrl
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS1.pdb.gz looking for model 1
# Found a chain break before 92
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server2_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1956330413.pdb -s /var/tmp/to_scwrl_1956330413.seq -o /var/tmp/from_scwrl_1956330413.pdb > /var/tmp/scwrl_1956330413.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1956330413.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 64
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server2_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1596180992.pdb -s /var/tmp/to_scwrl_1596180992.seq -o /var/tmp/from_scwrl_1596180992.pdb > /var/tmp/scwrl_1596180992.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1596180992.pdb
# conformation set from SCWRL output
# naming current conformation Ma-OPUS-server2_TS2-scwrl
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS3.pdb.gz looking for model 1
# Found a chain break before 92
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server2_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_945123567.pdb -s /var/tmp/to_scwrl_945123567.seq -o /var/tmp/from_scwrl_945123567.pdb > /var/tmp/scwrl_945123567.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_945123567.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 47
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server2_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_559555135.pdb -s /var/tmp/to_scwrl_559555135.seq -o /var/tmp/from_scwrl_559555135.pdb > /var/tmp/scwrl_559555135.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_559555135.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 89
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server2_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1102854117.pdb -s /var/tmp/to_scwrl_1102854117.seq -o /var/tmp/from_scwrl_1102854117.pdb > /var/tmp/scwrl_1102854117.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1102854117.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 88
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_401399253.pdb -s /var/tmp/to_scwrl_401399253.seq -o /var/tmp/from_scwrl_401399253.pdb > /var/tmp/scwrl_401399253.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_401399253.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 63
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_2040814214.pdb -s /var/tmp/to_scwrl_2040814214.seq -o /var/tmp/from_scwrl_2040814214.pdb > /var/tmp/scwrl_2040814214.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2040814214.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 92
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1849637284.pdb -s /var/tmp/to_scwrl_1849637284.seq -o /var/tmp/from_scwrl_1849637284.pdb > /var/tmp/scwrl_1849637284.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1849637284.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 48
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_888024736.pdb -s /var/tmp/to_scwrl_888024736.seq -o /var/tmp/from_scwrl_888024736.pdb > /var/tmp/scwrl_888024736.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_888024736.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 89
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_299279933.pdb -s /var/tmp/to_scwrl_299279933.seq -o /var/tmp/from_scwrl_299279933.pdb > /var/tmp/scwrl_299279933.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_299279933.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 97
# copying to AlignedFragments data structure
# naming current conformation MetaTasser_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1455565380.pdb -s /var/tmp/to_scwrl_1455565380.seq -o /var/tmp/from_scwrl_1455565380.pdb > /var/tmp/scwrl_1455565380.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1455565380.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 99
# copying to AlignedFragments data structure
# naming current conformation MetaTasser_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_853978151.pdb -s /var/tmp/to_scwrl_853978151.seq -o /var/tmp/from_scwrl_853978151.pdb > /var/tmp/scwrl_853978151.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_853978151.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 101
# copying to AlignedFragments data structure
# naming current conformation MetaTasser_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_2132862586.pdb -s /var/tmp/to_scwrl_2132862586.seq -o /var/tmp/from_scwrl_2132862586.pdb > /var/tmp/scwrl_2132862586.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2132862586.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 101
# copying to AlignedFragments data structure
# naming current conformation MetaTasser_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_328258670.pdb -s /var/tmp/to_scwrl_328258670.seq -o /var/tmp/from_scwrl_328258670.pdb > /var/tmp/scwrl_328258670.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_328258670.pdb
# conformation set from SCWRL output
# naming current conformation MetaTasser_TS4-scwrl
# ReadConformPDB reading from PDB file servers/MetaTasser_TS5.pdb.gz looking for model 1
# Found a chain break before 98
# copying to AlignedFragments data structure
# naming current conformation MetaTasser_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_151899638.pdb -s /var/tmp/to_scwrl_151899638.seq -o /var/tmp/from_scwrl_151899638.pdb > /var/tmp/scwrl_151899638.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_151899638.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 77
# copying to AlignedFragments data structure
# naming current conformation NN_PUT_lab_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_517177484.pdb -s /var/tmp/to_scwrl_517177484.seq -o /var/tmp/from_scwrl_517177484.pdb > /var/tmp/scwrl_517177484.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_517177484.pdb
# conformation set from SCWRL output
# naming current conformation NN_PUT_lab_TS1-scwrl
# ReadConformPDB reading from PDB file servers/POMYSL_TS1.pdb.gz looking for model 1
# Found a chain break before 83
# copying to AlignedFragments data structure
# naming current conformation POMYSL_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_783896758.pdb -s /var/tmp/to_scwrl_783896758.seq -o /var/tmp/from_scwrl_783896758.pdb > /var/tmp/scwrl_783896758.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_783896758.pdb
# conformation set from SCWRL output
# naming current conformation POMYSL_TS1-scwrl
# ReadConformPDB reading from PDB file servers/POMYSL_TS2.pdb.gz looking for model 1
# Found a chain break before 101
# copying to AlignedFragments data structure
# naming current conformation POMYSL_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1835061732.pdb -s /var/tmp/to_scwrl_1835061732.seq -o /var/tmp/from_scwrl_1835061732.pdb > /var/tmp/scwrl_1835061732.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1835061732.pdb
# conformation set from SCWRL output
# naming current conformation POMYSL_TS2-scwrl
# ReadConformPDB reading from PDB file servers/POMYSL_TS3.pdb.gz looking for model 1
# Found a chain break before 98
# copying to AlignedFragments data structure
# naming current conformation POMYSL_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_34085279.pdb -s /var/tmp/to_scwrl_34085279.seq -o /var/tmp/from_scwrl_34085279.pdb > /var/tmp/scwrl_34085279.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_34085279.pdb
# conformation set from SCWRL output
# naming current conformation POMYSL_TS3-scwrl
# ReadConformPDB reading from PDB file servers/POMYSL_TS4.pdb.gz looking for model 1
# Found a chain break before 97
# copying to AlignedFragments data structure
# naming current conformation POMYSL_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1898420803.pdb -s /var/tmp/to_scwrl_1898420803.seq -o /var/tmp/from_scwrl_1898420803.pdb > /var/tmp/scwrl_1898420803.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1898420803.pdb
# conformation set from SCWRL output
# naming current conformation POMYSL_TS4-scwrl
# ReadConformPDB reading from PDB file servers/POMYSL_TS5.pdb.gz looking for model 1
# Found a chain break before 100
# copying to AlignedFragments data structure
# naming current conformation POMYSL_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1236777206.pdb -s /var/tmp/to_scwrl_1236777206.seq -o /var/tmp/from_scwrl_1236777206.pdb > /var/tmp/scwrl_1236777206.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1236777206.pdb
# conformation set from SCWRL output
# naming current conformation POMYSL_TS5-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 92 ; scwrl3 -i /var/tmp/to_scwrl_1712752652.pdb -s /var/tmp/to_scwrl_1712752652.seq -o /var/tmp/from_scwrl_1712752652.pdb > /var/tmp/scwrl_1712752652.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1712752652.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 92 ; scwrl3 -i /var/tmp/to_scwrl_98466804.pdb -s /var/tmp/to_scwrl_98466804.seq -o /var/tmp/from_scwrl_98466804.pdb > /var/tmp/scwrl_98466804.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_98466804.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 92 ; scwrl3 -i /var/tmp/to_scwrl_816873528.pdb -s /var/tmp/to_scwrl_816873528.seq -o /var/tmp/from_scwrl_816873528.pdb > /var/tmp/scwrl_816873528.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_816873528.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 92 ; scwrl3 -i /var/tmp/to_scwrl_474327306.pdb -s /var/tmp/to_scwrl_474327306.seq -o /var/tmp/from_scwrl_474327306.pdb > /var/tmp/scwrl_474327306.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_474327306.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 92 ; scwrl3 -i /var/tmp/to_scwrl_1991835728.pdb -s /var/tmp/to_scwrl_1991835728.seq -o /var/tmp/from_scwrl_1991835728.pdb > /var/tmp/scwrl_1991835728.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1991835728.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 65
# copying to AlignedFragments data structure
# naming current conformation PROTINFO_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_2128818539.pdb -s /var/tmp/to_scwrl_2128818539.seq -o /var/tmp/from_scwrl_2128818539.pdb > /var/tmp/scwrl_2128818539.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2128818539.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 65
# copying to AlignedFragments data structure
# naming current conformation PROTINFO_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1211615208.pdb -s /var/tmp/to_scwrl_1211615208.seq -o /var/tmp/from_scwrl_1211615208.pdb > /var/tmp/scwrl_1211615208.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1211615208.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 65
# copying to AlignedFragments data structure
# naming current conformation PROTINFO_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_541347029.pdb -s /var/tmp/to_scwrl_541347029.seq -o /var/tmp/from_scwrl_541347029.pdb > /var/tmp/scwrl_541347029.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_541347029.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 64
# copying to AlignedFragments data structure
# naming current conformation PROTINFO_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1623618388.pdb -s /var/tmp/to_scwrl_1623618388.seq -o /var/tmp/from_scwrl_1623618388.pdb > /var/tmp/scwrl_1623618388.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1623618388.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 81
# copying to AlignedFragments data structure
# naming current conformation PROTINFO_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1903821760.pdb -s /var/tmp/to_scwrl_1903821760.seq -o /var/tmp/from_scwrl_1903821760.pdb > /var/tmp/scwrl_1903821760.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1903821760.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 T0327 can't currently be optimized by undertaker
# naming current conformation Pcons6_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_350193796.pdb -s /var/tmp/to_scwrl_350193796.seq -o /var/tmp/from_scwrl_350193796.pdb > /var/tmp/scwrl_350193796.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_350193796.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 T0327 can't currently be optimized by undertaker
# naming current conformation Pcons6_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1072315734.pdb -s /var/tmp/to_scwrl_1072315734.seq -o /var/tmp/from_scwrl_1072315734.pdb > /var/tmp/scwrl_1072315734.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1072315734.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 T0327 can't currently be optimized by undertaker
# naming current conformation Pcons6_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_701461680.pdb -s /var/tmp/to_scwrl_701461680.seq -o /var/tmp/from_scwrl_701461680.pdb > /var/tmp/scwrl_701461680.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_701461680.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 T0327 can't currently be optimized by undertaker
# naming current conformation Pcons6_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_909748931.pdb -s /var/tmp/to_scwrl_909748931.seq -o /var/tmp/from_scwrl_909748931.pdb > /var/tmp/scwrl_909748931.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_909748931.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 T0327 can't currently be optimized by undertaker
# naming current conformation Pcons6_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_27686205.pdb -s /var/tmp/to_scwrl_27686205.seq -o /var/tmp/from_scwrl_27686205.pdb > /var/tmp/scwrl_27686205.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_27686205.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 T0327 can't currently be optimized by undertaker
# naming current conformation Phyre-1_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1102860933.pdb -s /var/tmp/to_scwrl_1102860933.seq -o /var/tmp/from_scwrl_1102860933.pdb > /var/tmp/scwrl_1102860933.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1102860933.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
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation Phyre-2_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_803079499.pdb -s /var/tmp/to_scwrl_803079499.seq -o /var/tmp/from_scwrl_803079499.pdb > /var/tmp/scwrl_803079499.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_803079499.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
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation Phyre-2_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1877323489.pdb -s /var/tmp/to_scwrl_1877323489.seq -o /var/tmp/from_scwrl_1877323489.pdb > /var/tmp/scwrl_1877323489.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1877323489.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
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation Phyre-2_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1990885669.pdb -s /var/tmp/to_scwrl_1990885669.seq -o /var/tmp/from_scwrl_1990885669.pdb > /var/tmp/scwrl_1990885669.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1990885669.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
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation Phyre-2_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1102359431.pdb -s /var/tmp/to_scwrl_1102359431.seq -o /var/tmp/from_scwrl_1102359431.pdb > /var/tmp/scwrl_1102359431.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1102359431.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
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation Phyre-2_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1185405222.pdb -s /var/tmp/to_scwrl_1185405222.seq -o /var/tmp/from_scwrl_1185405222.pdb > /var/tmp/scwrl_1185405222.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1185405222.pdb
# conformation set from SCWRL output
# naming current conformation Phyre-2_TS5-scwrl
# ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation Pmodeller6_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_697380173.pdb -s /var/tmp/to_scwrl_697380173.seq -o /var/tmp/from_scwrl_697380173.pdb > /var/tmp/scwrl_697380173.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_697380173.pdb
# conformation set from SCWRL output
# naming current conformation Pmodeller6_TS1-scwrl
# ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1
# Found a chain break before 77
# copying to AlignedFragments data structure
# naming current conformation Pmodeller6_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1087738370.pdb -s /var/tmp/to_scwrl_1087738370.seq -o /var/tmp/from_scwrl_1087738370.pdb > /var/tmp/scwrl_1087738370.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1087738370.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 59
# copying to AlignedFragments data structure
# naming current conformation Pmodeller6_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1513663892.pdb -s /var/tmp/to_scwrl_1513663892.seq -o /var/tmp/from_scwrl_1513663892.pdb > /var/tmp/scwrl_1513663892.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1513663892.pdb
# conformation set from SCWRL output
# naming current conformation Pmodeller6_TS3-scwrl
# ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation Pmodeller6_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_849279812.pdb -s /var/tmp/to_scwrl_849279812.seq -o /var/tmp/from_scwrl_849279812.pdb > /var/tmp/scwrl_849279812.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_849279812.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 51
# copying to AlignedFragments data structure
# naming current conformation Pmodeller6_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1604915854.pdb -s /var/tmp/to_scwrl_1604915854.seq -o /var/tmp/from_scwrl_1604915854.pdb > /var/tmp/scwrl_1604915854.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1604915854.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 79
# copying to AlignedFragments data structure
# naming current conformation RAPTOR-ACE_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_150077004.pdb -s /var/tmp/to_scwrl_150077004.seq -o /var/tmp/from_scwrl_150077004.pdb > /var/tmp/scwrl_150077004.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_150077004.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
# naming current conformation RAPTOR-ACE_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_536857897.pdb -s /var/tmp/to_scwrl_536857897.seq -o /var/tmp/from_scwrl_536857897.pdb > /var/tmp/scwrl_536857897.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_536857897.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 77
# copying to AlignedFragments data structure
# naming current conformation RAPTOR-ACE_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1639001133.pdb -s /var/tmp/to_scwrl_1639001133.seq -o /var/tmp/from_scwrl_1639001133.pdb > /var/tmp/scwrl_1639001133.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1639001133.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 18
# copying to AlignedFragments data structure
# naming current conformation RAPTOR-ACE_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_2048497807.pdb -s /var/tmp/to_scwrl_2048497807.seq -o /var/tmp/from_scwrl_2048497807.pdb > /var/tmp/scwrl_2048497807.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2048497807.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 65
# copying to AlignedFragments data structure
# naming current conformation RAPTOR-ACE_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1773635104.pdb -s /var/tmp/to_scwrl_1773635104.seq -o /var/tmp/from_scwrl_1773635104.pdb > /var/tmp/scwrl_1773635104.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1773635104.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 99
# copying to AlignedFragments data structure
# naming current conformation RAPTORESS_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1204270138.pdb -s /var/tmp/to_scwrl_1204270138.seq -o /var/tmp/from_scwrl_1204270138.pdb > /var/tmp/scwrl_1204270138.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1204270138.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 62
# copying to AlignedFragments data structure
# naming current conformation RAPTORESS_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_2146964611.pdb -s /var/tmp/to_scwrl_2146964611.seq -o /var/tmp/from_scwrl_2146964611.pdb > /var/tmp/scwrl_2146964611.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2146964611.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 31
# copying to AlignedFragments data structure
# naming current conformation RAPTORESS_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_443024985.pdb -s /var/tmp/to_scwrl_443024985.seq -o /var/tmp/from_scwrl_443024985.pdb > /var/tmp/scwrl_443024985.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_443024985.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 101
# copying to AlignedFragments data structure
# naming current conformation RAPTORESS_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1678597445.pdb -s /var/tmp/to_scwrl_1678597445.seq -o /var/tmp/from_scwrl_1678597445.pdb > /var/tmp/scwrl_1678597445.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1678597445.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 101
# copying to AlignedFragments data structure
# naming current conformation RAPTORESS_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1991316692.pdb -s /var/tmp/to_scwrl_1991316692.seq -o /var/tmp/from_scwrl_1991316692.pdb > /var/tmp/scwrl_1991316692.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1991316692.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 88
# copying to AlignedFragments data structure
# naming current conformation RAPTOR_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_424359877.pdb -s /var/tmp/to_scwrl_424359877.seq -o /var/tmp/from_scwrl_424359877.pdb > /var/tmp/scwrl_424359877.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_424359877.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 82
# copying to AlignedFragments data structure
# naming current conformation RAPTOR_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_742729007.pdb -s /var/tmp/to_scwrl_742729007.seq -o /var/tmp/from_scwrl_742729007.pdb > /var/tmp/scwrl_742729007.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_742729007.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 96
# copying to AlignedFragments data structure
# naming current conformation RAPTOR_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_385180075.pdb -s /var/tmp/to_scwrl_385180075.seq -o /var/tmp/from_scwrl_385180075.pdb > /var/tmp/scwrl_385180075.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_385180075.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 65
# copying to AlignedFragments data structure
# naming current conformation RAPTOR_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_2047978265.pdb -s /var/tmp/to_scwrl_2047978265.seq -o /var/tmp/from_scwrl_2047978265.pdb > /var/tmp/scwrl_2047978265.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2047978265.pdb
# conformation set from SCWRL output
# naming current conformation RAPTOR_TS4-scwrl
# ReadConformPDB reading from PDB file servers/RAPTOR_TS5.pdb.gz looking for model 1
# Found a chain break before 77
# copying to AlignedFragments data structure
# naming current conformation RAPTOR_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_499067120.pdb -s /var/tmp/to_scwrl_499067120.seq -o /var/tmp/from_scwrl_499067120.pdb > /var/tmp/scwrl_499067120.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_499067120.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 59
# copying to AlignedFragments data structure
# naming current conformation ROBETTA_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_735373871.pdb -s /var/tmp/to_scwrl_735373871.seq -o /var/tmp/from_scwrl_735373871.pdb > /var/tmp/scwrl_735373871.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_735373871.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 59
# copying to AlignedFragments data structure
# naming current conformation ROBETTA_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_972810353.pdb -s /var/tmp/to_scwrl_972810353.seq -o /var/tmp/from_scwrl_972810353.pdb > /var/tmp/scwrl_972810353.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_972810353.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 75
# copying to AlignedFragments data structure
# naming current conformation ROBETTA_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1200528800.pdb -s /var/tmp/to_scwrl_1200528800.seq -o /var/tmp/from_scwrl_1200528800.pdb > /var/tmp/scwrl_1200528800.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1200528800.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 51
# copying to AlignedFragments data structure
# naming current conformation ROBETTA_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1645122801.pdb -s /var/tmp/to_scwrl_1645122801.seq -o /var/tmp/from_scwrl_1645122801.pdb > /var/tmp/scwrl_1645122801.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1645122801.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 77
# copying to AlignedFragments data structure
# naming current conformation ROBETTA_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1000496558.pdb -s /var/tmp/to_scwrl_1000496558.seq -o /var/tmp/from_scwrl_1000496558.pdb > /var/tmp/scwrl_1000496558.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1000496558.pdb
# conformation set from SCWRL output
# naming current conformation ROBETTA_TS5-scwrl
# ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation ROKKY_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_155906087.pdb -s /var/tmp/to_scwrl_155906087.seq -o /var/tmp/from_scwrl_155906087.pdb > /var/tmp/scwrl_155906087.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_155906087.pdb
# conformation set from SCWRL output
# naming current conformation ROKKY_TS1-scwrl
# ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation ROKKY_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_300718653.pdb -s /var/tmp/to_scwrl_300718653.seq -o /var/tmp/from_scwrl_300718653.pdb > /var/tmp/scwrl_300718653.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_300718653.pdb
# conformation set from SCWRL output
# naming current conformation ROKKY_TS2-scwrl
# ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation ROKKY_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_730336400.pdb -s /var/tmp/to_scwrl_730336400.seq -o /var/tmp/from_scwrl_730336400.pdb > /var/tmp/scwrl_730336400.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_730336400.pdb
# conformation set from SCWRL output
# naming current conformation ROKKY_TS3-scwrl
# ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation ROKKY_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_2146791756.pdb -s /var/tmp/to_scwrl_2146791756.seq -o /var/tmp/from_scwrl_2146791756.pdb > /var/tmp/scwrl_2146791756.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2146791756.pdb
# conformation set from SCWRL output
# naming current conformation ROKKY_TS4-scwrl
# ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation ROKKY_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1403078084.pdb -s /var/tmp/to_scwrl_1403078084.seq -o /var/tmp/from_scwrl_1403078084.pdb > /var/tmp/scwrl_1403078084.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1403078084.pdb
# conformation set from SCWRL output
# naming current conformation ROKKY_TS5-scwrl
# ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation SAM-T02_AL1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1915741622.pdb -s /var/tmp/to_scwrl_1915741622.seq -o /var/tmp/from_scwrl_1915741622.pdb > /var/tmp/scwrl_1915741622.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1915741622.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 T0327 can't currently be optimized by undertaker
# naming current conformation SAM-T02_AL2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_696688283.pdb -s /var/tmp/to_scwrl_696688283.seq -o /var/tmp/from_scwrl_696688283.pdb > /var/tmp/scwrl_696688283.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_696688283.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 118, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz
Skipped atom 120, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz
Skipped atom 122, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz
Skipped atom 124, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz
Skipped atom 198, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz
Skipped atom 200, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz
Skipped atom 202, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz
Skipped atom 204, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation SAM-T02_AL3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_343332808.pdb -s /var/tmp/to_scwrl_343332808.seq -o /var/tmp/from_scwrl_343332808.pdb > /var/tmp/scwrl_343332808.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_343332808.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 T0327 can't currently be optimized by undertaker
# naming current conformation SAM-T02_AL4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1281921868.pdb -s /var/tmp/to_scwrl_1281921868.seq -o /var/tmp/from_scwrl_1281921868.pdb > /var/tmp/scwrl_1281921868.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1281921868.pdb
# conformation set from SCWRL output
# naming current conformation SAM-T02_AL4-scwrl
# ReadConformPDB reading from PDB file servers/SAM-T02_AL5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation SAM-T02_AL5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1545968094.pdb -s /var/tmp/to_scwrl_1545968094.seq -o /var/tmp/from_scwrl_1545968094.pdb > /var/tmp/scwrl_1545968094.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1545968094.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 T0327 can't currently be optimized by undertaker
# naming current conformation SAM-T99_AL1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1948248662.pdb -s /var/tmp/to_scwrl_1948248662.seq -o /var/tmp/from_scwrl_1948248662.pdb > /var/tmp/scwrl_1948248662.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1948248662.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 T0327 can't currently be optimized by undertaker
# naming current conformation SAM-T99_AL2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1431998872.pdb -s /var/tmp/to_scwrl_1431998872.seq -o /var/tmp/from_scwrl_1431998872.pdb > /var/tmp/scwrl_1431998872.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1431998872.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
Skipped atom 50, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
Skipped atom 52, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
Skipped atom 54, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
Skipped atom 56, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
Skipped atom 70, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
Skipped atom 72, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
Skipped atom 74, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
Skipped atom 76, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
Skipped atom 202, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
Skipped atom 204, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
Skipped atom 206, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
Skipped atom 208, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
Skipped atom 234, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
Skipped atom 236, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
Skipped atom 238, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
Skipped atom 240, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation SAM-T99_AL3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_2082825991.pdb -s /var/tmp/to_scwrl_2082825991.seq -o /var/tmp/from_scwrl_2082825991.pdb > /var/tmp/scwrl_2082825991.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2082825991.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 T0327 can't currently be optimized by undertaker
# naming current conformation SAM-T99_AL4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1439766149.pdb -s /var/tmp/to_scwrl_1439766149.seq -o /var/tmp/from_scwrl_1439766149.pdb > /var/tmp/scwrl_1439766149.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1439766149.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 T0327 can't currently be optimized by undertaker
# naming current conformation SAM-T99_AL5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1333013032.pdb -s /var/tmp/to_scwrl_1333013032.seq -o /var/tmp/from_scwrl_1333013032.pdb > /var/tmp/scwrl_1333013032.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1333013032.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 100
# copying to AlignedFragments data structure
# naming current conformation SAM_T06_server_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1708977448.pdb -s /var/tmp/to_scwrl_1708977448.seq -o /var/tmp/from_scwrl_1708977448.pdb > /var/tmp/scwrl_1708977448.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1708977448.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 T0327 can't currently be optimized by undertaker
# naming current conformation SAM_T06_server_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_496552641.pdb -s /var/tmp/to_scwrl_496552641.seq -o /var/tmp/from_scwrl_496552641.pdb > /var/tmp/scwrl_496552641.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_496552641.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 T0327 can't currently be optimized by undertaker
# naming current conformation SAM_T06_server_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1332493996.pdb -s /var/tmp/to_scwrl_1332493996.seq -o /var/tmp/from_scwrl_1332493996.pdb > /var/tmp/scwrl_1332493996.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1332493996.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 T0327 can't currently be optimized by undertaker
# naming current conformation SAM_T06_server_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_4518787.pdb -s /var/tmp/to_scwrl_4518787.seq -o /var/tmp/from_scwrl_4518787.pdb > /var/tmp/scwrl_4518787.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_4518787.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 T0327 can't currently be optimized by undertaker
# naming current conformation SAM_T06_server_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_27666439.pdb -s /var/tmp/to_scwrl_27666439.seq -o /var/tmp/from_scwrl_27666439.pdb > /var/tmp/scwrl_27666439.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_27666439.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 77
# copying to AlignedFragments data structure
# naming current conformation SP3_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1176327042.pdb -s /var/tmp/to_scwrl_1176327042.seq -o /var/tmp/from_scwrl_1176327042.pdb > /var/tmp/scwrl_1176327042.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1176327042.pdb
# conformation set from SCWRL output
# naming current conformation SP3_TS1-scwrl
# ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1
# Found a chain break before 66
# copying to AlignedFragments data structure
# naming current conformation SP3_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_428878664.pdb -s /var/tmp/to_scwrl_428878664.seq -o /var/tmp/from_scwrl_428878664.pdb > /var/tmp/scwrl_428878664.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_428878664.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 93
# copying to AlignedFragments data structure
# naming current conformation SP3_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_770395447.pdb -s /var/tmp/to_scwrl_770395447.seq -o /var/tmp/from_scwrl_770395447.pdb > /var/tmp/scwrl_770395447.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_770395447.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 59
# copying to AlignedFragments data structure
# naming current conformation SP3_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1561507117.pdb -s /var/tmp/to_scwrl_1561507117.seq -o /var/tmp/from_scwrl_1561507117.pdb > /var/tmp/scwrl_1561507117.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1561507117.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 79
# copying to AlignedFragments data structure
# naming current conformation SP3_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_329373283.pdb -s /var/tmp/to_scwrl_329373283.seq -o /var/tmp/from_scwrl_329373283.pdb > /var/tmp/scwrl_329373283.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_329373283.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 58
# copying to AlignedFragments data structure
# naming current conformation SP4_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1269462566.pdb -s /var/tmp/to_scwrl_1269462566.seq -o /var/tmp/from_scwrl_1269462566.pdb > /var/tmp/scwrl_1269462566.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1269462566.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 20
# copying to AlignedFragments data structure
# naming current conformation SP4_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_149397341.pdb -s /var/tmp/to_scwrl_149397341.seq -o /var/tmp/from_scwrl_149397341.pdb > /var/tmp/scwrl_149397341.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_149397341.pdb
# conformation set from SCWRL output
# naming current conformation SP4_TS2-scwrl
# ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1
# Found a chain break before 75
# copying to AlignedFragments data structure
# naming current conformation SP4_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1302183635.pdb -s /var/tmp/to_scwrl_1302183635.seq -o /var/tmp/from_scwrl_1302183635.pdb > /var/tmp/scwrl_1302183635.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1302183635.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 82
# copying to AlignedFragments data structure
# naming current conformation SP4_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_322507720.pdb -s /var/tmp/to_scwrl_322507720.seq -o /var/tmp/from_scwrl_322507720.pdb > /var/tmp/scwrl_322507720.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_322507720.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 88
# copying to AlignedFragments data structure
# naming current conformation SP4_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1794520142.pdb -s /var/tmp/to_scwrl_1794520142.seq -o /var/tmp/from_scwrl_1794520142.pdb > /var/tmp/scwrl_1794520142.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1794520142.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 77
# copying to AlignedFragments data structure
# naming current conformation SPARKS2_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_155196546.pdb -s /var/tmp/to_scwrl_155196546.seq -o /var/tmp/from_scwrl_155196546.pdb > /var/tmp/scwrl_155196546.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_155196546.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 22
# copying to AlignedFragments data structure
# naming current conformation SPARKS2_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_478413807.pdb -s /var/tmp/to_scwrl_478413807.seq -o /var/tmp/from_scwrl_478413807.pdb > /var/tmp/scwrl_478413807.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_478413807.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 94
# copying to AlignedFragments data structure
# naming current conformation SPARKS2_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_2095238796.pdb -s /var/tmp/to_scwrl_2095238796.seq -o /var/tmp/from_scwrl_2095238796.pdb > /var/tmp/scwrl_2095238796.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2095238796.pdb
# conformation set from SCWRL output
# naming current conformation SPARKS2_TS3-scwrl
# ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1
# Found a chain break before 99
# copying to AlignedFragments data structure
# naming current conformation SPARKS2_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_885532946.pdb -s /var/tmp/to_scwrl_885532946.seq -o /var/tmp/from_scwrl_885532946.pdb > /var/tmp/scwrl_885532946.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_885532946.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 92
# copying to AlignedFragments data structure
# naming current conformation SPARKS2_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_477721917.pdb -s /var/tmp/to_scwrl_477721917.seq -o /var/tmp/from_scwrl_477721917.pdb > /var/tmp/scwrl_477721917.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_477721917.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 T0327 can't currently be optimized by undertaker
# naming current conformation UNI-EID_bnmx_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1350833233.pdb -s /var/tmp/to_scwrl_1350833233.seq -o /var/tmp/from_scwrl_1350833233.pdb > /var/tmp/scwrl_1350833233.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1350833233.pdb
# conformation set from SCWRL output
# naming current conformation UNI-EID_bnmx_TS1-scwrl
# ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation UNI-EID_bnmx_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_653790921.pdb -s /var/tmp/to_scwrl_653790921.seq -o /var/tmp/from_scwrl_653790921.pdb > /var/tmp/scwrl_653790921.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_653790921.pdb
# conformation set from SCWRL output
# naming current conformation UNI-EID_bnmx_TS2-scwrl
# ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation UNI-EID_bnmx_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1174410199.pdb -s /var/tmp/to_scwrl_1174410199.seq -o /var/tmp/from_scwrl_1174410199.pdb > /var/tmp/scwrl_1174410199.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1174410199.pdb
# conformation set from SCWRL output
# naming current conformation UNI-EID_bnmx_TS3-scwrl
# ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation UNI-EID_bnmx_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1694166042.pdb -s /var/tmp/to_scwrl_1694166042.seq -o /var/tmp/from_scwrl_1694166042.pdb > /var/tmp/scwrl_1694166042.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1694166042.pdb
# conformation set from SCWRL output
# naming current conformation UNI-EID_bnmx_TS4-scwrl
# ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation UNI-EID_bnmx_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1935712789.pdb -s /var/tmp/to_scwrl_1935712789.seq -o /var/tmp/from_scwrl_1935712789.pdb > /var/tmp/scwrl_1935712789.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1935712789.pdb
# conformation set from SCWRL output
# naming current conformation UNI-EID_bnmx_TS5-scwrl
# ReadConformPDB reading from PDB file servers/UNI-EID_expm_TS1.pdb.gz looking for model 1
WARNING: atoms too close: (T0327)N76.CA and (T0327)K87.CA only 0.000 apart, marking (T0327)K87.CA as missing
WARNING: atoms too close: (T0327)G77.CA and (T0327)E88.CA only 0.000 apart, marking (T0327)E88.CA as missing
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation UNI-EID_expm_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_572894647.pdb -s /var/tmp/to_scwrl_572894647.seq -o /var/tmp/from_scwrl_572894647.pdb > /var/tmp/scwrl_572894647.log
Error: Couldn't open file /var/tmp/from_scwrl_572894647.pdb or /var/tmp/from_scwrl_572894647.pdb.gz for input
Warning: Couldn't open file decoys//var/tmp/from_scwrl_572894647_b.pdb or decoys//var/tmp/from_scwrl_572894647_b.pdb.gz for input
Trying /var/tmp/from_scwrl_572894647_b.pdb
Error: Couldn't open file /var/tmp/from_scwrl_572894647_b.pdb or /var/tmp/from_scwrl_572894647_b.pdb.gz for input
Warning: Couldn't open file decoys//var/tmp/from_scwrl_572894647_a.pdb or decoys//var/tmp/from_scwrl_572894647_a.pdb.gz for input
Trying /var/tmp/from_scwrl_572894647_a.pdb
Error: Couldn't open file /var/tmp/from_scwrl_572894647_a.pdb or /var/tmp/from_scwrl_572894647_a.pdb.gz for input
Error: can't open any of /var/tmp/from_scwrl_572894647.pdb or /var/tmp/from_scwrl_572894647_b.pdb or /var/tmp/from_scwrl_572894647_a.pdb
Error: no new SCWRL conformation added
# naming current conformation UNI-EID_expm_TS1-scwrl
# ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation UNI-EID_sfst_AL1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1494931057.pdb -s /var/tmp/to_scwrl_1494931057.seq -o /var/tmp/from_scwrl_1494931057.pdb > /var/tmp/scwrl_1494931057.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1494931057.pdb
# conformation set from SCWRL output
# naming current conformation UNI-EID_sfst_AL1-scwrl
# ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation UNI-EID_sfst_AL2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1220228014.pdb -s /var/tmp/to_scwrl_1220228014.seq -o /var/tmp/from_scwrl_1220228014.pdb > /var/tmp/scwrl_1220228014.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1220228014.pdb
# conformation set from SCWRL output
# naming current conformation UNI-EID_sfst_AL2-scwrl
# ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation UNI-EID_sfst_AL3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_508236991.pdb -s /var/tmp/to_scwrl_508236991.seq -o /var/tmp/from_scwrl_508236991.pdb > /var/tmp/scwrl_508236991.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_508236991.pdb
# conformation set from SCWRL output
# naming current conformation UNI-EID_sfst_AL3-scwrl
# ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL4.pdb.gz looking for model 1
Skipped atom 58, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz
Skipped atom 60, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz
Skipped atom 62, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz
Skipped atom 64, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz
Skipped atom 170, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz
Skipped atom 172, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz
Skipped atom 174, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz
Skipped atom 176, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz
Skipped atom 222, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz
Skipped atom 224, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz
Skipped atom 226, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz
Skipped atom 228, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation UNI-EID_sfst_AL4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_787213560.pdb -s /var/tmp/to_scwrl_787213560.seq -o /var/tmp/from_scwrl_787213560.pdb > /var/tmp/scwrl_787213560.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_787213560.pdb
# conformation set from SCWRL output
# naming current conformation UNI-EID_sfst_AL4-scwrl
# ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation UNI-EID_sfst_AL5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_405757400.pdb -s /var/tmp/to_scwrl_405757400.seq -o /var/tmp/from_scwrl_405757400.pdb > /var/tmp/scwrl_405757400.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_405757400.pdb
# conformation set from SCWRL output
# naming current conformation UNI-EID_sfst_AL5-scwrl
# ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1
# Found a chain break before 97
# copying to AlignedFragments data structure
# naming current conformation Zhang-Server_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_69730793.pdb -s /var/tmp/to_scwrl_69730793.seq -o /var/tmp/from_scwrl_69730793.pdb > /var/tmp/scwrl_69730793.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_69730793.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 65
# copying to AlignedFragments data structure
# naming current conformation Zhang-Server_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1283766201.pdb -s /var/tmp/to_scwrl_1283766201.seq -o /var/tmp/from_scwrl_1283766201.pdb > /var/tmp/scwrl_1283766201.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1283766201.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 79
# copying to AlignedFragments data structure
# naming current conformation Zhang-Server_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1738251397.pdb -s /var/tmp/to_scwrl_1738251397.seq -o /var/tmp/from_scwrl_1738251397.pdb > /var/tmp/scwrl_1738251397.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1738251397.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 100
# copying to AlignedFragments data structure
# naming current conformation Zhang-Server_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_74249580.pdb -s /var/tmp/to_scwrl_74249580.seq -o /var/tmp/from_scwrl_74249580.pdb > /var/tmp/scwrl_74249580.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_74249580.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 98
# copying to AlignedFragments data structure
# naming current conformation Zhang-Server_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1311432640.pdb -s /var/tmp/to_scwrl_1311432640.seq -o /var/tmp/from_scwrl_1311432640.pdb > /var/tmp/scwrl_1311432640.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1311432640.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 101
# copying to AlignedFragments data structure
# naming current conformation beautshot_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_767094793.pdb -s /var/tmp/to_scwrl_767094793.seq -o /var/tmp/from_scwrl_767094793.pdb > /var/tmp/scwrl_767094793.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_767094793.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 T0327 can't currently be optimized by undertaker
# naming current conformation beautshotbase_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_503128244.pdb -s /var/tmp/to_scwrl_503128244.seq -o /var/tmp/from_scwrl_503128244.pdb > /var/tmp/scwrl_503128244.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_503128244.pdb
# conformation set from SCWRL output
# naming current conformation beautshotbase_TS1-scwrl
# ReadConformPDB reading from PDB file servers/forecast-s_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation forecast-s_AL1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_2081828087.pdb -s /var/tmp/to_scwrl_2081828087.seq -o /var/tmp/from_scwrl_2081828087.pdb > /var/tmp/scwrl_2081828087.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2081828087.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 T0327 can't currently be optimized by undertaker
# naming current conformation forecast-s_AL2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_181118263.pdb -s /var/tmp/to_scwrl_181118263.seq -o /var/tmp/from_scwrl_181118263.pdb > /var/tmp/scwrl_181118263.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_181118263.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 T0327 can't currently be optimized by undertaker
# naming current conformation forecast-s_AL3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_832501527.pdb -s /var/tmp/to_scwrl_832501527.seq -o /var/tmp/from_scwrl_832501527.pdb > /var/tmp/scwrl_832501527.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_832501527.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 T0327 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation forecast-s_AL4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1203807007.pdb -s /var/tmp/to_scwrl_1203807007.seq -o /var/tmp/from_scwrl_1203807007.pdb > /var/tmp/scwrl_1203807007.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1203807007.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
Skipped atom 138, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL5.pdb.gz
Skipped atom 140, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL5.pdb.gz
Skipped atom 142, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL5.pdb.gz
Skipped atom 144, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL5.pdb.gz
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation forecast-s_AL5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_330515604.pdb -s /var/tmp/to_scwrl_330515604.seq -o /var/tmp/from_scwrl_330515604.pdb > /var/tmp/scwrl_330515604.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_330515604.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 T0327 can't currently be optimized by undertaker
# naming current conformation gtg_AL1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_2134685162.pdb -s /var/tmp/to_scwrl_2134685162.seq -o /var/tmp/from_scwrl_2134685162.pdb > /var/tmp/scwrl_2134685162.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2134685162.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 T0327 can't currently be optimized by undertaker
# naming current conformation gtg_AL2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1526314727.pdb -s /var/tmp/to_scwrl_1526314727.seq -o /var/tmp/from_scwrl_1526314727.pdb > /var/tmp/scwrl_1526314727.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1526314727.pdb
# conformation set from SCWRL output
# naming current conformation gtg_AL2-scwrl
# ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1
# Found a chain break before 85
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.2_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_2125035746.pdb -s /var/tmp/to_scwrl_2125035746.seq -o /var/tmp/from_scwrl_2125035746.pdb > /var/tmp/scwrl_2125035746.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2125035746.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 92
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.2_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_142398061.pdb -s /var/tmp/to_scwrl_142398061.seq -o /var/tmp/from_scwrl_142398061.pdb > /var/tmp/scwrl_142398061.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_142398061.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 92
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.2_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_2004728535.pdb -s /var/tmp/to_scwrl_2004728535.seq -o /var/tmp/from_scwrl_2004728535.pdb > /var/tmp/scwrl_2004728535.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2004728535.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 91
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.2_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_2072790895.pdb -s /var/tmp/to_scwrl_2072790895.seq -o /var/tmp/from_scwrl_2072790895.pdb > /var/tmp/scwrl_2072790895.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2072790895.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 91
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.2_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1027931007.pdb -s /var/tmp/to_scwrl_1027931007.seq -o /var/tmp/from_scwrl_1027931007.pdb > /var/tmp/scwrl_1027931007.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1027931007.pdb
# conformation set from SCWRL output
# naming current conformation karypis.srv.2_TS5-scwrl
# ReadConformPDB reading from PDB file servers/karypis.srv.4_TS1.pdb.gz looking for model 1
# Found a chain break before 93
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.4_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_334966805.pdb -s /var/tmp/to_scwrl_334966805.seq -o /var/tmp/from_scwrl_334966805.pdb > /var/tmp/scwrl_334966805.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_334966805.pdb
# conformation set from SCWRL output
# naming current conformation karypis.srv.4_TS1-scwrl
# ReadConformPDB reading from PDB file servers/karypis.srv.4_TS2.pdb.gz looking for model 1
# Found a chain break before 99
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.4_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1276140482.pdb -s /var/tmp/to_scwrl_1276140482.seq -o /var/tmp/from_scwrl_1276140482.pdb > /var/tmp/scwrl_1276140482.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1276140482.pdb
# conformation set from SCWRL output
# naming current conformation karypis.srv.4_TS2-scwrl
# ReadConformPDB reading from PDB file servers/karypis.srv.4_TS3.pdb.gz looking for model 1
# Found a chain break before 99
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.4_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1681721928.pdb -s /var/tmp/to_scwrl_1681721928.seq -o /var/tmp/from_scwrl_1681721928.pdb > /var/tmp/scwrl_1681721928.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1681721928.pdb
# conformation set from SCWRL output
# naming current conformation karypis.srv.4_TS3-scwrl
# ReadConformPDB reading from PDB file servers/karypis.srv.4_TS4.pdb.gz looking for model 1
# Found a chain break before 99
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.4_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1509377004.pdb -s /var/tmp/to_scwrl_1509377004.seq -o /var/tmp/from_scwrl_1509377004.pdb > /var/tmp/scwrl_1509377004.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1509377004.pdb
# conformation set from SCWRL output
# naming current conformation karypis.srv.4_TS4-scwrl
# ReadConformPDB reading from PDB file servers/karypis.srv.4_TS5.pdb.gz looking for model 1
# Found a chain break before 99
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.4_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_822822878.pdb -s /var/tmp/to_scwrl_822822878.seq -o /var/tmp/from_scwrl_822822878.pdb > /var/tmp/scwrl_822822878.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_822822878.pdb
# conformation set from SCWRL output
# naming current conformation karypis.srv.4_TS5-scwrl
# ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation karypis.srv_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1469951070.pdb -s /var/tmp/to_scwrl_1469951070.seq -o /var/tmp/from_scwrl_1469951070.pdb > /var/tmp/scwrl_1469951070.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1469951070.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 T0327 can't currently be optimized by undertaker
# naming current conformation karypis.srv_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_2082271651.pdb -s /var/tmp/to_scwrl_2082271651.seq -o /var/tmp/from_scwrl_2082271651.pdb > /var/tmp/scwrl_2082271651.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2082271651.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 T0327 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation karypis.srv_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_170270288.pdb -s /var/tmp/to_scwrl_170270288.seq -o /var/tmp/from_scwrl_170270288.pdb > /var/tmp/scwrl_170270288.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_170270288.pdb
# conformation set from SCWRL output
# naming current conformation karypis.srv_TS3-scwrl
# ReadConformPDB reading from PDB file servers/karypis.srv_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation karypis.srv_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_542695439.pdb -s /var/tmp/to_scwrl_542695439.seq -o /var/tmp/from_scwrl_542695439.pdb > /var/tmp/scwrl_542695439.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_542695439.pdb
# conformation set from SCWRL output
# naming current conformation karypis.srv_TS4-scwrl
# ReadConformPDB reading from PDB file servers/karypis.srv_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation karypis.srv_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_443024995.pdb -s /var/tmp/to_scwrl_443024995.seq -o /var/tmp/from_scwrl_443024995.pdb > /var/tmp/scwrl_443024995.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_443024995.pdb
# conformation set from SCWRL output
# naming current conformation karypis.srv_TS5-scwrl
# ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1
# Found a chain break before 84
# copying to AlignedFragments data structure
# naming current conformation keasar-server_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_957483849.pdb -s /var/tmp/to_scwrl_957483849.seq -o /var/tmp/from_scwrl_957483849.pdb > /var/tmp/scwrl_957483849.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_957483849.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 86
# copying to AlignedFragments data structure
# naming current conformation keasar-server_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_948452839.pdb -s /var/tmp/to_scwrl_948452839.seq -o /var/tmp/from_scwrl_948452839.pdb > /var/tmp/scwrl_948452839.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_948452839.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 73
# copying to AlignedFragments data structure
# naming current conformation keasar-server_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_512755788.pdb -s /var/tmp/to_scwrl_512755788.seq -o /var/tmp/from_scwrl_512755788.pdb > /var/tmp/scwrl_512755788.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_512755788.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
# naming current conformation keasar-server_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_93766403.pdb -s /var/tmp/to_scwrl_93766403.seq -o /var/tmp/from_scwrl_93766403.pdb > /var/tmp/scwrl_93766403.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_93766403.pdb
# conformation set from SCWRL output
# naming current conformation keasar-server_TS4-scwrl
# ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1
# Found a chain break before 19
# copying to AlignedFragments data structure
# naming current conformation keasar-server_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_539220589.pdb -s /var/tmp/to_scwrl_539220589.seq -o /var/tmp/from_scwrl_539220589.pdb > /var/tmp/scwrl_539220589.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_539220589.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 T0327 can't currently be optimized by undertaker
# naming current conformation mGen-3D_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_587005368.pdb -s /var/tmp/to_scwrl_587005368.seq -o /var/tmp/from_scwrl_587005368.pdb > /var/tmp/scwrl_587005368.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_587005368.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 T0327 can't currently be optimized by undertaker
# naming current conformation nFOLD_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1405199043.pdb -s /var/tmp/to_scwrl_1405199043.seq -o /var/tmp/from_scwrl_1405199043.pdb > /var/tmp/scwrl_1405199043.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1405199043.pdb
# conformation set from SCWRL output
# naming current conformation nFOLD_TS1-scwrl
# ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation nFOLD_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1306315381.pdb -s /var/tmp/to_scwrl_1306315381.seq -o /var/tmp/from_scwrl_1306315381.pdb > /var/tmp/scwrl_1306315381.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1306315381.pdb
# conformation set from SCWRL output
# naming current conformation nFOLD_TS2-scwrl
# ReadConformPDB reading from PDB file servers/nFOLD_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation nFOLD_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1090133612.pdb -s /var/tmp/to_scwrl_1090133612.seq -o /var/tmp/from_scwrl_1090133612.pdb > /var/tmp/scwrl_1090133612.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1090133612.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 T0327 can't currently be optimized by undertaker
# naming current conformation nFOLD_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1339543484.pdb -s /var/tmp/to_scwrl_1339543484.seq -o /var/tmp/from_scwrl_1339543484.pdb > /var/tmp/scwrl_1339543484.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1339543484.pdb
# conformation set from SCWRL output
# naming current conformation nFOLD_TS4-scwrl
# ReadConformPDB reading from PDB file servers/nFOLD_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation nFOLD_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1487433644.pdb -s /var/tmp/to_scwrl_1487433644.seq -o /var/tmp/from_scwrl_1487433644.pdb > /var/tmp/scwrl_1487433644.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1487433644.pdb
# conformation set from SCWRL output
# naming current conformation nFOLD_TS5-scwrl
# ReadConformPDB reading from PDB file servers/panther2_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation panther2_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1922635139.pdb -s /var/tmp/to_scwrl_1922635139.seq -o /var/tmp/from_scwrl_1922635139.pdb > /var/tmp/scwrl_1922635139.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1922635139.pdb
# conformation set from SCWRL output
# naming current conformation panther2_TS1-scwrl
# ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation shub_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_395866845.pdb -s /var/tmp/to_scwrl_395866845.seq -o /var/tmp/from_scwrl_395866845.pdb > /var/tmp/scwrl_395866845.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_395866845.pdb
# conformation set from SCWRL output
# naming current conformation shub_TS1-scwrl
# command:CPU_time= 33.099 sec, elapsed time= 227.797 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 = -13.7887
shub_TS1	costs 0	real_cost = -13.5492
panther2_TS1-scwrl	costs 0	real_cost = 303.657
panther2_TS1	costs 0	real_cost = 314.847
nFOLD_TS5-scwrl	costs 0	real_cost = 109.124
nFOLD_TS5	costs 0	real_cost = 148.931
nFOLD_TS4-scwrl	costs 0	real_cost = 40.2332
nFOLD_TS4	costs 0	real_cost = 87.7581
nFOLD_TS3-scwrl	costs 0	real_cost = 66.5104
nFOLD_TS3	costs 0	real_cost = 114.391
nFOLD_TS2-scwrl	costs 0	real_cost = 18.5709
nFOLD_TS2	costs 0	real_cost = 80.8793
nFOLD_TS1-scwrl	costs 0	real_cost = 66.786
nFOLD_TS1	costs 0	real_cost = 129.348
mGen-3D_TS1-scwrl	costs 0	real_cost = 73.3978
mGen-3D_TS1	costs 0	real_cost = 135.203
keasar-server_TS5-scwrl	costs 0	real_cost = 25.4668
keasar-server_TS5	costs 0	real_cost = 36.6854
keasar-server_TS4-scwrl	costs 0	real_cost = 17.2622
keasar-server_TS4	costs 0	real_cost = 25.1175
keasar-server_TS3-scwrl	costs 0	real_cost = 40.1826
keasar-server_TS3	costs 0	real_cost = 45.1482
keasar-server_TS2-scwrl	costs 0	real_cost = 52.5043
keasar-server_TS2	costs 0	real_cost = 66.2698
keasar-server_TS1-scwrl	costs 0	real_cost = 11.7937
keasar-server_TS1	costs 0	real_cost = 56.6357
karypis.srv_TS5-scwrl	costs 0	real_cost = 11.2489
karypis.srv_TS5	costs 0	real_cost = 9.24888
karypis.srv_TS4-scwrl	costs 0	real_cost = 21.2752
karypis.srv_TS4	costs 0	real_cost = 19.2752
karypis.srv_TS3-scwrl	costs 0	real_cost = 24.4015
karypis.srv_TS3	costs 0	real_cost = 24.4015
karypis.srv_TS2-scwrl	costs 0	real_cost = -22.7944
karypis.srv_TS2	costs 0	real_cost = -24.7944
karypis.srv_TS1-scwrl	costs 0	real_cost = -26.8979
karypis.srv_TS1	costs 0	real_cost = -28.8979
karypis.srv.4_TS5-scwrl	costs 0	real_cost = 273.198
karypis.srv.4_TS5	costs 0	real_cost = 273.201
karypis.srv.4_TS4-scwrl	costs 0	real_cost = 279.8
karypis.srv.4_TS4	costs 0	real_cost = 279.877
karypis.srv.4_TS3-scwrl	costs 0	real_cost = 269.038
karypis.srv.4_TS3	costs 0	real_cost = 269.038
karypis.srv.4_TS2-scwrl	costs 0	real_cost = 229.751
karypis.srv.4_TS2	costs 0	real_cost = 229.751
karypis.srv.4_TS1-scwrl	costs 0	real_cost = 211.689
karypis.srv.4_TS1	costs 0	real_cost = 211.689
karypis.srv.2_TS5-scwrl	costs 0	real_cost = 64.0029
karypis.srv.2_TS5	costs 0	real_cost = 64.0029
karypis.srv.2_TS4-scwrl	costs 0	real_cost = 2.47769
karypis.srv.2_TS4	costs 0	real_cost = 2.47769
karypis.srv.2_TS3-scwrl	costs 0	real_cost = -25.1368
karypis.srv.2_TS3	costs 0	real_cost = -25.1368
karypis.srv.2_TS2-scwrl	costs 0	real_cost = 5.61617
karypis.srv.2_TS2	costs 0	real_cost = 5.61617
karypis.srv.2_TS1-scwrl	costs 0	real_cost = -43.4133
karypis.srv.2_TS1	costs 0	real_cost = -43.4133
gtg_AL2-scwrl	costs 0	real_cost = 444.963
gtg_AL2	costs 0	real_cost = 466.378
gtg_AL1-scwrl	costs 0	real_cost = 439.371
gtg_AL1	costs 0	real_cost = 453.467
forecast-s_AL5-scwrl	costs 0	real_cost = 48.4189
forecast-s_AL5	costs 0	real_cost = 88.8653
forecast-s_AL4-scwrl	costs 0	real_cost = 165.197
forecast-s_AL4	costs 0	real_cost = 241.049
forecast-s_AL3-scwrl	costs 0	real_cost = 175.812
forecast-s_AL3	costs 0	real_cost = 238.193
forecast-s_AL2-scwrl	costs 0	real_cost = 147.456
forecast-s_AL2	costs 0	real_cost = 169.117
forecast-s_AL1-scwrl	costs 0	real_cost = 85.2347
forecast-s_AL1	costs 0	real_cost = 141.362
beautshotbase_TS1-scwrl	costs 0	real_cost = 0.0651918
beautshotbase_TS1	costs 0	real_cost = 1.0328
beautshot_TS1-scwrl	costs 0	real_cost = -40.4837
beautshot_TS1	costs 0	real_cost = -29.4434
Zhang-Server_TS5-scwrl	costs 0	real_cost = -80.4555
Zhang-Server_TS5	costs 0	real_cost = -65.2625
Zhang-Server_TS4-scwrl	costs 0	real_cost = -51.9549
Zhang-Server_TS4	costs 0	real_cost = -43.0088
Zhang-Server_TS3-scwrl	costs 0	real_cost = -47.0749
Zhang-Server_TS3	costs 0	real_cost = -34.7148
Zhang-Server_TS2-scwrl	costs 0	real_cost = -83.1783
Zhang-Server_TS2	costs 0	real_cost = -74.7593
Zhang-Server_TS1-scwrl	costs 0	real_cost = -44.8709
Zhang-Server_TS1	costs 0	real_cost = -32.552
UNI-EID_sfst_AL5-scwrl	costs 0	real_cost = 132.685
UNI-EID_sfst_AL5	costs 0	real_cost = 191.601
UNI-EID_sfst_AL4-scwrl	costs 0	real_cost = 176.28
UNI-EID_sfst_AL4	costs 0	real_cost = 213.457
UNI-EID_sfst_AL3-scwrl	costs 0	real_cost = 155.315
UNI-EID_sfst_AL3	costs 0	real_cost = 181.583
UNI-EID_sfst_AL2-scwrl	costs 0	real_cost = 116.476
UNI-EID_sfst_AL2	costs 0	real_cost = 176.01
UNI-EID_sfst_AL1-scwrl	costs 0	real_cost = 199.942
UNI-EID_sfst_AL1	costs 0	real_cost = 218.296
UNI-EID_expm_TS1-scwrl	costs 0	real_cost = 172.335
UNI-EID_bnmx_TS5-scwrl	costs 0	real_cost = 102.682
UNI-EID_bnmx_TS5	costs 0	real_cost = 156.732
UNI-EID_bnmx_TS4-scwrl	costs 0	real_cost = 177.985
UNI-EID_bnmx_TS4	costs 0	real_cost = 220.373
UNI-EID_bnmx_TS3-scwrl	costs 0	real_cost = 123.608
UNI-EID_bnmx_TS3	costs 0	real_cost = 177.367
UNI-EID_bnmx_TS2-scwrl	costs 0	real_cost = 123.52
UNI-EID_bnmx_TS2	costs 0	real_cost = 181.371
UNI-EID_bnmx_TS1-scwrl	costs 0	real_cost = 185.193
UNI-EID_bnmx_TS1	costs 0	real_cost = 206.416
SPARKS2_TS5-scwrl	costs 0	real_cost = 220.925
SPARKS2_TS5	costs 0	real_cost = 219.471
SPARKS2_TS4-scwrl	costs 0	real_cost = 52.9882
SPARKS2_TS4	costs 0	real_cost = 48.9659
SPARKS2_TS3-scwrl	costs 0	real_cost = -20.6178
SPARKS2_TS3	costs 0	real_cost = -18.535
SPARKS2_TS2-scwrl	costs 0	real_cost = -19.291
SPARKS2_TS2	costs 0	real_cost = -25.298
SPARKS2_TS1-scwrl	costs 0	real_cost = -39.4369
SPARKS2_TS1	costs 0	real_cost = -40.4849
SP4_TS5-scwrl	costs 0	real_cost = 95.0946
SP4_TS5	costs 0	real_cost = 101.678
SP4_TS4-scwrl	costs 0	real_cost = 282.459
SP4_TS4	costs 0	real_cost = 280.027
SP4_TS3-scwrl	costs 0	real_cost = 16.1064
SP4_TS3	costs 0	real_cost = 2.38702
SP4_TS2-scwrl	costs 0	real_cost = -23.1023
SP4_TS2	costs 0	real_cost = -16.7833
SP4_TS1-scwrl	costs 0	real_cost = -46.4126
SP4_TS1	costs 0	real_cost = -47.1537
SP3_TS5-scwrl	costs 0	real_cost = -22.443
SP3_TS5	costs 0	real_cost = -21.4051
SP3_TS4-scwrl	costs 0	real_cost = 38.0723
SP3_TS4	costs 0	real_cost = 43.0024
SP3_TS3-scwrl	costs 0	real_cost = -5.69514
SP3_TS3	costs 0	real_cost = -2.99551
SP3_TS2-scwrl	costs 0	real_cost = 11.0336
SP3_TS2	costs 0	real_cost = 21.485
SP3_TS1-scwrl	costs 0	real_cost = -39.4369
SP3_TS1	costs 0	real_cost = -40.4849
SAM_T06_server_TS5-scwrl	costs 0	real_cost = 205.913
SAM_T06_server_TS5	costs 0	real_cost = 170.285
SAM_T06_server_TS4-scwrl	costs 0	real_cost = 10.6982
SAM_T06_server_TS4	costs 0	real_cost = 13.1278
SAM_T06_server_TS3-scwrl	costs 0	real_cost = 144.234
SAM_T06_server_TS3	costs 0	real_cost = 104.345
SAM_T06_server_TS2-scwrl	costs 0	real_cost = 142.936
SAM_T06_server_TS2	costs 0	real_cost = 136.243
SAM_T06_server_TS1-scwrl	costs 0	real_cost = 75.1825
SAM_T06_server_TS1	costs 0	real_cost = 82.0374
SAM-T99_AL5-scwrl	costs 0	real_cost = 51.534
SAM-T99_AL5	costs 0	real_cost = 102.84
SAM-T99_AL4-scwrl	costs 0	real_cost = -17.5795
SAM-T99_AL4	costs 0	real_cost = 52.0625
SAM-T99_AL3-scwrl	costs 0	real_cost = 35.5673
SAM-T99_AL3	costs 0	real_cost = 82.5496
SAM-T99_AL2-scwrl	costs 0	real_cost = 152.108
SAM-T99_AL2	costs 0	real_cost = 200.103
SAM-T99_AL1-scwrl	costs 0	real_cost = 27.2778
SAM-T99_AL1	costs 0	real_cost = 82.8054
SAM-T02_AL5-scwrl	costs 0	real_cost = 142.085
SAM-T02_AL5	costs 0	real_cost = 178.547
SAM-T02_AL4-scwrl	costs 0	real_cost = 99.8131
SAM-T02_AL4	costs 0	real_cost = 137.773
SAM-T02_AL3-scwrl	costs 0	real_cost = 189.2
SAM-T02_AL3	costs 0	real_cost = 219.022
SAM-T02_AL2-scwrl	costs 0	real_cost = 90.9606
SAM-T02_AL2	costs 0	real_cost = 138.415
SAM-T02_AL1-scwrl	costs 0	real_cost = 158.701
SAM-T02_AL1	costs 0	real_cost = 176.49
ROKKY_TS5-scwrl	costs 0	real_cost = 62.3706
ROKKY_TS5	costs 0	real_cost = 142.429
ROKKY_TS4-scwrl	costs 0	real_cost = 60.5225
ROKKY_TS4	costs 0	real_cost = 146.973
ROKKY_TS3-scwrl	costs 0	real_cost = 48.5974
ROKKY_TS3	costs 0	real_cost = 132.009
ROKKY_TS2-scwrl	costs 0	real_cost = 33.8076
ROKKY_TS2	costs 0	real_cost = 113.962
ROKKY_TS1-scwrl	costs 0	real_cost = 78.7513
ROKKY_TS1	costs 0	real_cost = 164.605
ROBETTA_TS5-scwrl	costs 0	real_cost = 13.4437
ROBETTA_TS5	costs 0	real_cost = 23.4657
ROBETTA_TS4-scwrl	costs 0	real_cost = -10.0633
ROBETTA_TS4	costs 0	real_cost = -9.49006
ROBETTA_TS3-scwrl	costs 0	real_cost = 15.4395
ROBETTA_TS3	costs 0	real_cost = 15.3909
ROBETTA_TS2-scwrl	costs 0	real_cost = 28.6262
ROBETTA_TS2	costs 0	real_cost = 34.2437
ROBETTA_TS1-scwrl	costs 0	real_cost = 13.5076
ROBETTA_TS1	costs 0	real_cost = 15.1517
RAPTOR_TS5-scwrl	costs 0	real_cost = 26.5986
RAPTOR_TS5	costs 0	real_cost = 23.7348
RAPTOR_TS4-scwrl	costs 0	real_cost = -18.7104
RAPTOR_TS4	costs 0	real_cost = -2.85846
RAPTOR_TS3-scwrl	costs 0	real_cost = 10.7306
RAPTOR_TS3	costs 0	real_cost = 3.4903
RAPTOR_TS2-scwrl	costs 0	real_cost = -32.1002
RAPTOR_TS2	costs 0	real_cost = -22.379
RAPTOR_TS1-scwrl	costs 0	real_cost = 6.74403
RAPTOR_TS1	costs 0	real_cost = -1.8303
RAPTORESS_TS5-scwrl	costs 0	real_cost = 36.2096
RAPTORESS_TS5	costs 0	real_cost = 31.1237
RAPTORESS_TS4-scwrl	costs 0	real_cost = 24.4233
RAPTORESS_TS4	costs 0	real_cost = 34.568
RAPTORESS_TS3-scwrl	costs 0	real_cost = 34.0111
RAPTORESS_TS3	costs 0	real_cost = 27.6872
RAPTORESS_TS2-scwrl	costs 0	real_cost = 10.6334
RAPTORESS_TS2	costs 0	real_cost = 15.6613
RAPTORESS_TS1-scwrl	costs 0	real_cost = 1.10292
RAPTORESS_TS1	costs 0	real_cost = 14.8278
RAPTOR-ACE_TS5-scwrl	costs 0	real_cost = -18.0537
RAPTOR-ACE_TS5	costs 0	real_cost = -6.37826
RAPTOR-ACE_TS4-scwrl	costs 0	real_cost = -54.8003
RAPTOR-ACE_TS4	costs 0	real_cost = -52.1628
RAPTOR-ACE_TS3-scwrl	costs 0	real_cost = -39.4369
RAPTOR-ACE_TS3	costs 0	real_cost = -40.4849
RAPTOR-ACE_TS2-scwrl	costs 0	real_cost = -34.8791
RAPTOR-ACE_TS2	costs 0	real_cost = -30.29
RAPTOR-ACE_TS1-scwrl	costs 0	real_cost = -22.443
RAPTOR-ACE_TS1	costs 0	real_cost = -21.4051
Pmodeller6_TS5-scwrl	costs 0	real_cost = -10.0633
Pmodeller6_TS5	costs 0	real_cost = -9.49006
Pmodeller6_TS4-scwrl	costs 0	real_cost = -22.8051
Pmodeller6_TS4	costs 0	real_cost = -24.9402
Pmodeller6_TS3-scwrl	costs 0	real_cost = 13.5076
Pmodeller6_TS3	costs 0	real_cost = 15.1517
Pmodeller6_TS2-scwrl	costs 0	real_cost = 13.4437
Pmodeller6_TS2	costs 0	real_cost = 23.4657
Pmodeller6_TS1-scwrl	costs 0	real_cost = -54.9024
Pmodeller6_TS1	costs 0	real_cost = -56.7024
Phyre-2_TS5-scwrl	costs 0	real_cost = 32.4808
Phyre-2_TS5	costs 0	real_cost = 26.8883
Phyre-2_TS4-scwrl	costs 0	real_cost = 34.1395
Phyre-2_TS4	costs 0	real_cost = 36.968
Phyre-2_TS3-scwrl	costs 0	real_cost = 16.7737
Phyre-2_TS3	costs 0	real_cost = 3.64638
Phyre-2_TS2-scwrl	costs 0	real_cost = -14.1915
Phyre-2_TS2	costs 0	real_cost = -18.5071
Phyre-2_TS1-scwrl	costs 0	real_cost = 34.1395
Phyre-2_TS1	costs 0	real_cost = 36.968
Phyre-1_TS1-scwrl	costs 0	real_cost = 128.795
Phyre-1_TS1	costs 0	real_cost = 124.253
Pcons6_TS5-scwrl	costs 0	real_cost = 4.19791
Pcons6_TS5	costs 0	real_cost = -0.202094
Pcons6_TS4-scwrl	costs 0	real_cost = 110.514
Pcons6_TS4	costs 0	real_cost = 106.914
Pcons6_TS3-scwrl	costs 0	real_cost = -55.4246
Pcons6_TS3	costs 0	real_cost = -57.0246
Pcons6_TS2-scwrl	costs 0	real_cost = -34.3713
Pcons6_TS2	costs 0	real_cost = -37.5713
Pcons6_TS1-scwrl	costs 0	real_cost = -38.5911
Pcons6_TS1	costs 0	real_cost = -40.5911
PROTINFO_TS5-scwrl	costs 0	real_cost = -17.4881
PROTINFO_TS5	costs 0	real_cost = -19.7735
PROTINFO_TS4-scwrl	costs 0	real_cost = 6.13751
PROTINFO_TS4	costs 0	real_cost = 7.31934
PROTINFO_TS3-scwrl	costs 0	real_cost = -22.8057
PROTINFO_TS3	costs 0	real_cost = -14.805
PROTINFO_TS2-scwrl	costs 0	real_cost = -21.4808
PROTINFO_TS2	costs 0	real_cost = -17.3758
PROTINFO_TS1-scwrl	costs 0	real_cost = -0.668365
PROTINFO_TS1	costs 0	real_cost = 0.567186
PROTINFO-AB_TS5-scwrl	costs 0	real_cost = -13.5592
PROTINFO-AB_TS5	costs 0	real_cost = -23.3593
PROTINFO-AB_TS4-scwrl	costs 0	real_cost = -18.5018
PROTINFO-AB_TS4	costs 0	real_cost = -22.427
PROTINFO-AB_TS3-scwrl	costs 0	real_cost = -16.8397
PROTINFO-AB_TS3	costs 0	real_cost = -24.4016
PROTINFO-AB_TS2-scwrl	costs 0	real_cost = -14.614
PROTINFO-AB_TS2	costs 0	real_cost = -21.7747
PROTINFO-AB_TS1-scwrl	costs 0	real_cost = -15.9671
PROTINFO-AB_TS1	costs 0	real_cost = -24.1986
POMYSL_TS5-scwrl	costs 0	real_cost = 254.03
POMYSL_TS5	costs 0	real_cost = 261.393
POMYSL_TS4-scwrl	costs 0	real_cost = 198.607
POMYSL_TS4	costs 0	real_cost = 226.267
POMYSL_TS3-scwrl	costs 0	real_cost = 272.018
POMYSL_TS3	costs 0	real_cost = 269.004
POMYSL_TS2-scwrl	costs 0	real_cost = 174.466
POMYSL_TS2	costs 0	real_cost = 196.679
POMYSL_TS1-scwrl	costs 0	real_cost = 225.091
POMYSL_TS1	costs 0	real_cost = 236.907
NN_PUT_lab_TS1-scwrl	costs 0	real_cost = -39.4369
NN_PUT_lab_TS1	costs 0	real_cost = -40.4849
MetaTasser_TS5-scwrl	costs 0	real_cost = -34.0905
MetaTasser_TS5	costs 0	real_cost = -30.6939
MetaTasser_TS4-scwrl	costs 0	real_cost = -18.4883
MetaTasser_TS4	costs 0	real_cost = -15.7032
MetaTasser_TS3-scwrl	costs 0	real_cost = -44.3029
MetaTasser_TS3	costs 0	real_cost = -38.6767
MetaTasser_TS2-scwrl	costs 0	real_cost = -18.6777
MetaTasser_TS2	costs 0	real_cost = -18.4922
MetaTasser_TS1-scwrl	costs 0	real_cost = -40.2236
MetaTasser_TS1	costs 0	real_cost = -34.5219
Ma-OPUS-server_TS5-scwrl	costs 0	real_cost = 271.575
Ma-OPUS-server_TS5	costs 0	real_cost = 275.651
Ma-OPUS-server_TS4-scwrl	costs 0	real_cost = 98.0133
Ma-OPUS-server_TS4	costs 0	real_cost = 101.369
Ma-OPUS-server_TS3-scwrl	costs 0	real_cost = 202.616
Ma-OPUS-server_TS3	costs 0	real_cost = 206.451
Ma-OPUS-server_TS2-scwrl	costs 0	real_cost = 46.7784
Ma-OPUS-server_TS2	costs 0	real_cost = 64.5931
Ma-OPUS-server_TS1-scwrl	costs 0	real_cost = -54.8309
Ma-OPUS-server_TS1	costs 0	real_cost = -53.8083
Ma-OPUS-server2_TS5-scwrl	costs 0	real_cost = 271.575
Ma-OPUS-server2_TS5	costs 0	real_cost = 275.651
Ma-OPUS-server2_TS4-scwrl	costs 0	real_cost = 106.081
Ma-OPUS-server2_TS4	costs 0	real_cost = 114.347
Ma-OPUS-server2_TS3-scwrl	costs 0	real_cost = 202.616
Ma-OPUS-server2_TS3	costs 0	real_cost = 206.451
Ma-OPUS-server2_TS2-scwrl	costs 0	real_cost = -44.5692
Ma-OPUS-server2_TS2	costs 0	real_cost = -35.0576
Ma-OPUS-server2_TS1-scwrl	costs 0	real_cost = -34.7428
Ma-OPUS-server2_TS1	costs 0	real_cost = -27.5631
MIG_FROST_AL1-scwrl	costs 0	real_cost = 220.332
MIG_FROST_AL1	costs 0	real_cost = 220.332
LOOPP_TS5	costs 0	real_cost = 211.515
LOOPP_TS4-scwrl	costs 0	real_cost = 221.517
LOOPP_TS4	costs 0	real_cost = 214.299
LOOPP_TS3-scwrl	costs 0	real_cost = 32.4276
LOOPP_TS3	costs 0	real_cost = 32.9802
LOOPP_TS2-scwrl	costs 0	real_cost = 28.2884
LOOPP_TS2	costs 0	real_cost = 39.7471
LOOPP_TS1-scwrl	costs 0	real_cost = 0.0435013
LOOPP_TS1	costs 0	real_cost = -4.73709
Huber-Torda-Server_TS5-scwrl	costs 0	real_cost = 199.755
Huber-Torda-Server_TS5	costs 0	real_cost = 246.25
Huber-Torda-Server_TS4-scwrl	costs 0	real_cost = 248.605
Huber-Torda-Server_TS4	costs 0	real_cost = 264.286
Huber-Torda-Server_TS3-scwrl	costs 0	real_cost = 226.697
Huber-Torda-Server_TS3	costs 0	real_cost = 278.67
Huber-Torda-Server_TS2-scwrl	costs 0	real_cost = 159.787
Huber-Torda-Server_TS2	costs 0	real_cost = 181.802
Huber-Torda-Server_TS1-scwrl	costs 0	real_cost = 58.7731
Huber-Torda-Server_TS1	costs 0	real_cost = 94.9392
HHpred3_TS1-scwrl	costs 0	real_cost = -22.1623
HHpred3_TS1	costs 0	real_cost = -20.1332
HHpred2_TS1-scwrl	costs 0	real_cost = -22.1623
HHpred2_TS1	costs 0	real_cost = -20.1332
HHpred1_TS1-scwrl	costs 0	real_cost = -40.0292
HHpred1_TS1	costs 0	real_cost = -33.337
GeneSilicoMetaServer_TS5-scwrl	costs 0	real_cost = -35.7415
GeneSilicoMetaServer_TS5	costs 0	real_cost = -32.4271
GeneSilicoMetaServer_TS4-scwrl	costs 0	real_cost = 107.864
GeneSilicoMetaServer_TS4	costs 0	real_cost = 112.862
GeneSilicoMetaServer_TS3-scwrl	costs 0	real_cost = -10.4189
GeneSilicoMetaServer_TS3	costs 0	real_cost = -24.9695
GeneSilicoMetaServer_TS2-scwrl	costs 0	real_cost = 12.2137
GeneSilicoMetaServer_TS2	costs 0	real_cost = 13.045
GeneSilicoMetaServer_TS1-scwrl	costs 0	real_cost = -58.8686
GeneSilicoMetaServer_TS1	costs 0	real_cost = -57.0614
FUNCTION_TS5-scwrl	costs 0	real_cost = 14.3473
FUNCTION_TS5	costs 0	real_cost = 25.2563
FUNCTION_TS4-scwrl	costs 0	real_cost = 38.5951
FUNCTION_TS4	costs 0	real_cost = 41.2254
FUNCTION_TS3-scwrl	costs 0	real_cost = 23.6366
FUNCTION_TS3	costs 0	real_cost = 33.1438
FUNCTION_TS2-scwrl	costs 0	real_cost = 96.0368
FUNCTION_TS2	costs 0	real_cost = 99.2938
FUNCTION_TS1-scwrl	costs 0	real_cost = -0.296538
FUNCTION_TS1	costs 0	real_cost = -4.2943
FUGUE_AL5-scwrl	costs 0	real_cost = 273.078
FUGUE_AL5	costs 0	real_cost = 273.078
FUGUE_AL4-scwrl	costs 0	real_cost = 231.067
FUGUE_AL4	costs 0	real_cost = 294.101
FUGUE_AL3-scwrl	costs 0	real_cost = -37.4077
FUGUE_AL3	costs 0	real_cost = 35.4774
FUGUE_AL2-scwrl	costs 0	real_cost = 184.976
FUGUE_AL2	costs 0	real_cost = 252.381
FUGUE_AL1-scwrl	costs 0	real_cost = 226.61
FUGUE_AL1	costs 0	real_cost = 303.624
FUGMOD_TS5-scwrl	costs 0	real_cost = 176.53
FUGMOD_TS5	costs 0	real_cost = 176.966
FUGMOD_TS4-scwrl	costs 0	real_cost = 196.782
FUGMOD_TS4	costs 0	real_cost = 199.457
FUGMOD_TS3-scwrl	costs 0	real_cost = -26.3545
FUGMOD_TS3	costs 0	real_cost = -14.0746
FUGMOD_TS2-scwrl	costs 0	real_cost = 155.584
FUGMOD_TS2	costs 0	real_cost = 163.413
FUGMOD_TS1-scwrl	costs 0	real_cost = 218.163
FUGMOD_TS1	costs 0	real_cost = 218.302
FPSOLVER-SERVER_TS5-scwrl	costs 0	real_cost = 228.763
FPSOLVER-SERVER_TS5	costs 0	real_cost = 235.753
FPSOLVER-SERVER_TS4-scwrl	costs 0	real_cost = 187.614
FPSOLVER-SERVER_TS4	costs 0	real_cost = 188.008
FPSOLVER-SERVER_TS3-scwrl	costs 0	real_cost = 182.484
FPSOLVER-SERVER_TS3	costs 0	real_cost = 180.533
FPSOLVER-SERVER_TS2-scwrl	costs 0	real_cost = 207.038
FPSOLVER-SERVER_TS2	costs 0	real_cost = 213.516
FPSOLVER-SERVER_TS1-scwrl	costs 0	real_cost = 234.6
FPSOLVER-SERVER_TS1	costs 0	real_cost = 235.071
FORTE2_AL5-scwrl	costs 0	real_cost = 278.241
FORTE2_AL5	costs 0	real_cost = 338.953
FORTE2_AL4-scwrl	costs 0	real_cost = 85.135
FORTE2_AL4	costs 0	real_cost = 175.356
FORTE2_AL3-scwrl	costs 0	real_cost = 47.4632
FORTE2_AL3	costs 0	real_cost = 99.26
FORTE2_AL2-scwrl	costs 0	real_cost = 117.083
FORTE2_AL2	costs 0	real_cost = 165.345
FORTE2_AL1-scwrl	costs 0	real_cost = 324.624
FORTE2_AL1	costs 0	real_cost = 402.018
FORTE1_AL5-scwrl	costs 0	real_cost = 278.241
FORTE1_AL5	costs 0	real_cost = 338.953
FORTE1_AL4-scwrl	costs 0	real_cost = 85.135
FORTE1_AL4	costs 0	real_cost = 175.356
FORTE1_AL3-scwrl	costs 0	real_cost = 117.083
FORTE1_AL3	costs 0	real_cost = 165.345
FORTE1_AL2-scwrl	costs 0	real_cost = 324.624
FORTE1_AL2	costs 0	real_cost = 402.018
FORTE1_AL1-scwrl	costs 0	real_cost = 104.543
FORTE1_AL1	costs 0	real_cost = 154.691
FOLDpro_TS5-scwrl	costs 0	real_cost = 12.3519
FOLDpro_TS5	costs 0	real_cost = 15.463
FOLDpro_TS4-scwrl	costs 0	real_cost = 166.328
FOLDpro_TS4	costs 0	real_cost = 172.424
FOLDpro_TS3-scwrl	costs 0	real_cost = 133.687
FOLDpro_TS3	costs 0	real_cost = 136.15
FOLDpro_TS2-scwrl	costs 0	real_cost = -64.3091
FOLDpro_TS2	costs 0	real_cost = -55.326
FOLDpro_TS1-scwrl	costs 0	real_cost = 0.713474
FOLDpro_TS1	costs 0	real_cost = 7.29928
FAMS_TS5-scwrl	costs 0	real_cost = 8.92163
FAMS_TS5	costs 0	real_cost = 17.752
FAMS_TS4-scwrl	costs 0	real_cost = -34.6199
FAMS_TS4	costs 0	real_cost = -25.0879
FAMS_TS3-scwrl	costs 0	real_cost = -45.7937
FAMS_TS3	costs 0	real_cost = -40.2647
FAMS_TS2-scwrl	costs 0	real_cost = -35.0689
FAMS_TS2	costs 0	real_cost = -41.2881
FAMS_TS1-scwrl	costs 0	real_cost = 29.6408
FAMS_TS1	costs 0	real_cost = 43.4631
FAMSD_TS5-scwrl	costs 0	real_cost = -1.64821
FAMSD_TS5	costs 0	real_cost = -7.02798
FAMSD_TS4-scwrl	costs 0	real_cost = 66.6528
FAMSD_TS4	costs 0	real_cost = 61.7681
FAMSD_TS3-scwrl	costs 0	real_cost = 8.92163
FAMSD_TS3	costs 0	real_cost = 17.752
FAMSD_TS2-scwrl	costs 0	real_cost = 54.1686
FAMSD_TS2	costs 0	real_cost = 59.2443
FAMSD_TS1-scwrl	costs 0	real_cost = 6.27294
FAMSD_TS1	costs 0	real_cost = 22.9723
Distill_TS5-scwrl	costs 0	real_cost = 309.104
Distill_TS4-scwrl	costs 0	real_cost = 315.566
Distill_TS3-scwrl	costs 0	real_cost = 314.921
Distill_TS2-scwrl	costs 0	real_cost = 314.987
Distill_TS1-scwrl	costs 0	real_cost = 316.174
CaspIta-FOX_TS5-scwrl	costs 0	real_cost = 111.017
CaspIta-FOX_TS5	costs 0	real_cost = 108.606
CaspIta-FOX_TS4-scwrl	costs 0	real_cost = 4.35083
CaspIta-FOX_TS4	costs 0	real_cost = -0.265475
CaspIta-FOX_TS3-scwrl	costs 0	real_cost = -35.627
CaspIta-FOX_TS3	costs 0	real_cost = -38.1967
CaspIta-FOX_TS2-scwrl	costs 0	real_cost = 17.8055
CaspIta-FOX_TS2	costs 0	real_cost = 11.3876
CaspIta-FOX_TS1-scwrl	costs 0	real_cost = 55.4187
CaspIta-FOX_TS1	costs 0	real_cost = 44.9844
CIRCLE_TS5-scwrl	costs 0	real_cost = 54.1686
CIRCLE_TS5	costs 0	real_cost = 59.2443
CIRCLE_TS4-scwrl	costs 0	real_cost = -18.747
CIRCLE_TS4	costs 0	real_cost = -16.4005
CIRCLE_TS3-scwrl	costs 0	real_cost = -34.6199
CIRCLE_TS3	costs 0	real_cost = -25.0879
CIRCLE_TS2-scwrl	costs 0	real_cost = -45.7937
CIRCLE_TS2	costs 0	real_cost = -40.2647
CIRCLE_TS1-scwrl	costs 0	real_cost = -35.0689
CIRCLE_TS1	costs 0	real_cost = -41.2881
Bilab-ENABLE_TS5-scwrl	costs 0	real_cost = -42.1086
Bilab-ENABLE_TS5	costs 0	real_cost = -42.1086
Bilab-ENABLE_TS4-scwrl	costs 0	real_cost = -42.1086
Bilab-ENABLE_TS4	costs 0	real_cost = -42.1086
Bilab-ENABLE_TS3-scwrl	costs 0	real_cost = -41.3949
Bilab-ENABLE_TS3	costs 0	real_cost = -41.3949
Bilab-ENABLE_TS2-scwrl	costs 0	real_cost = 156.621
Bilab-ENABLE_TS2	costs 0	real_cost = 158.855
Bilab-ENABLE_TS1-scwrl	costs 0	real_cost = 182.15
Bilab-ENABLE_TS1	costs 0	real_cost = 182.15
BayesHH_TS1-scwrl	costs 0	real_cost = -22.1623
BayesHH_TS1	costs 0	real_cost = -20.1332
ABIpro_TS5-scwrl	costs 0	real_cost = 135.667
ABIpro_TS5	costs 0	real_cost = 135.667
ABIpro_TS4-scwrl	costs 0	real_cost = 181.885
ABIpro_TS4	costs 0	real_cost = 183.7
ABIpro_TS3-scwrl	costs 0	real_cost = 123.288
ABIpro_TS3	costs 0	real_cost = 123.288
ABIpro_TS2-scwrl	costs 0	real_cost = 126.875
ABIpro_TS2	costs 0	real_cost = 126.984
ABIpro_TS1-scwrl	costs 0	real_cost = 142.663
ABIpro_TS1	costs 0	real_cost = 141.402
3Dpro_TS5-scwrl	costs 0	real_cost = 142.663
3Dpro_TS5	costs 0	real_cost = 141.402
3Dpro_TS4-scwrl	costs 0	real_cost = 143.523
3Dpro_TS4	costs 0	real_cost = 140.246
3Dpro_TS3-scwrl	costs 0	real_cost = 71.9768
3Dpro_TS3	costs 0	real_cost = 88.0245
3Dpro_TS2-scwrl	costs 0	real_cost = 142.732
3Dpro_TS2	costs 0	real_cost = 148.496
3Dpro_TS1-scwrl	costs 0	real_cost = -4.23557
3Dpro_TS1	costs 0	real_cost = -4.04952
3D-JIGSAW_TS5-scwrl	costs 0	real_cost = 75.7379
3D-JIGSAW_TS5	costs 0	real_cost = 82.2044
3D-JIGSAW_TS4-scwrl	costs 0	real_cost = 236.372
3D-JIGSAW_TS4	costs 0	real_cost = 238.256
3D-JIGSAW_TS3-scwrl	costs 0	real_cost = 81.7239
3D-JIGSAW_TS3	costs 0	real_cost = 92.0675
3D-JIGSAW_TS2-scwrl	costs 0	real_cost = 113.045
3D-JIGSAW_TS2	costs 0	real_cost = 113.77
3D-JIGSAW_TS1-scwrl	costs 0	real_cost = 115.13
3D-JIGSAW_TS1	costs 0	real_cost = 115.084
3D-JIGSAW_RECOM_TS5-scwrl	costs 0	real_cost = 46.3291
3D-JIGSAW_RECOM_TS5	costs 0	real_cost = 44.4538
3D-JIGSAW_RECOM_TS4-scwrl	costs 0	real_cost = 91.0755
3D-JIGSAW_RECOM_TS4	costs 0	real_cost = 89.754
3D-JIGSAW_RECOM_TS3-scwrl	costs 0	real_cost = 21.5669
3D-JIGSAW_RECOM_TS3	costs 0	real_cost = 21.0082
3D-JIGSAW_RECOM_TS2-scwrl	costs 0	real_cost = 22.9864
3D-JIGSAW_RECOM_TS2	costs 0	real_cost = 20.5678
3D-JIGSAW_RECOM_TS1-scwrl	costs 0	real_cost = 82.6848
3D-JIGSAW_RECOM_TS1	costs 0	real_cost = 85.32
3D-JIGSAW_POPULUS_TS5-scwrl	costs 0	real_cost = 115.585
3D-JIGSAW_POPULUS_TS5	costs 0	real_cost = 113.585
3D-JIGSAW_POPULUS_TS4-scwrl	costs 0	real_cost = 37.4847
3D-JIGSAW_POPULUS_TS4	costs 0	real_cost = 35.4847
3D-JIGSAW_POPULUS_TS3-scwrl	costs 0	real_cost = 36.4777
3D-JIGSAW_POPULUS_TS3	costs 0	real_cost = 34.4777
3D-JIGSAW_POPULUS_TS2-scwrl	costs 0	real_cost = 83.695
3D-JIGSAW_POPULUS_TS2	costs 0	real_cost = 81.695
3D-JIGSAW_POPULUS_TS1-scwrl	costs 0	real_cost = 36.6736
3D-JIGSAW_POPULUS_TS1	costs 0	real_cost = 34.6736
dimer//dimer3-1tbxA-dimer6	costs 0	real_cost = 53.0326
dimer//dimer2-1tbxA-dimer6	costs 0	real_cost = 53.0199
dimer//dimer1-1tbxA-dimer6	costs 0	real_cost = 53.0218
dimer//dimer-1ub9A-dimer11	costs 0	real_cost = 57.427
dimer//dimer-1tbxA-try1-opt2	costs 0	real_cost = 7.58432
dimer//dimer-1tbxA-try1-opt2-proteinshop	costs 0	real_cost = 48.1025
dimer//try9-opt2.unpack	costs 0	real_cost = 58.6523
dimer//try9-opt2.unpack.gromacs0.repack-nonPC	costs 0	real_cost = 50.1646
dimer//try9-opt2.unpack.gromacs0	costs 0	real_cost = 60.188
dimer//try9-opt2.repack-nonPC	costs 0	real_cost = 52.9797
dimer//try9-opt2	costs 0	real_cost = 58.6523
dimer//try9-opt2.gromacs0	costs 0	real_cost = 59.2138
dimer//try9-opt1	costs 0	real_cost = 58.4411
dimer//try9-opt1-scwrl	costs 0	real_cost = 55.1942
dimer//try8-opt2.unpack	costs 0	real_cost = 54.7586
dimer//try8-opt2.unpack.gromacs0.repack-nonPC	costs 0	real_cost = 51.7316
dimer//try8-opt2.unpack.gromacs0	costs 0	real_cost = 54.7006
dimer//try8-opt2.repack-nonPC	costs 0	real_cost = 53.0312
dimer//try8-opt2	costs 0	real_cost = 54.7586
dimer//try8-opt2.gromacs0	costs 0	real_cost = 55.4458
dimer//try8-opt1	costs 0	real_cost = 53.7323
dimer//try8-opt1-scwrl	costs 0	real_cost = 51.8873
dimer//try7-opt2.unpack	costs 0	real_cost = 57.0655
dimer//try7-opt2.unpack.gromacs0.repack-nonPC	costs 0	real_cost = 52.8053
dimer//try7-opt2.unpack.gromacs0	costs 0	real_cost = 55.0259
dimer//try7-opt2.repack-nonPC	costs 0	real_cost = 55.565
dimer//try7-opt2	costs 0	real_cost = 57.0655
dimer//try7-opt2.gromacs0	costs 0	real_cost = 63.2387
dimer//try7-opt1	costs 0	real_cost = 55.321
dimer//try7-opt1-scwrl	costs 0	real_cost = 52.1663
dimer//try6-opt2.unpack	costs 0	real_cost = 53.0205
dimer//try6-opt2.unpack.gromacs0.repack-nonPC	costs 0	real_cost = 49.3705
dimer//try6-opt2.unpack.gromacs0	costs 0	real_cost = 51.2255
dimer//try6-opt2.repack-nonPC	costs 0	real_cost = 51.9131
dimer//try6-opt2	costs 0	real_cost = 53.0205
dimer//try6-opt2.gromacs0	costs 0	real_cost = 52.5725
dimer//try6-opt1	costs 0	real_cost = 53.9945
dimer//try6-opt1-scwrl	costs 0	real_cost = 52.9609
dimer//try5-opt2.unpack	costs 0	real_cost = 44.0341
dimer//try5-opt2.unpack.gromacs0.repack-nonPC	costs 0	real_cost = 44.9131
dimer//try5-opt2.unpack.gromacs0	costs 0	real_cost = 48.2115
dimer//try5-opt2.repack-nonPC	costs 0	real_cost = 46.5371
dimer//try5-opt2	costs 0	real_cost = 44.0341
dimer//try5-opt2.gromacs0	costs 0	real_cost = 48.0559
dimer//try5-opt1	costs 0	real_cost = 43.1647
dimer//try5-opt1-scwrl	costs 0	real_cost = 42.966
dimer//try4-opt2.unpack	costs 0	real_cost = 52.4119
dimer//try4-opt2.unpack.gromacs0.repack-nonPC	costs 0	real_cost = 48.6847
dimer//try4-opt2.unpack.gromacs0	costs 0	real_cost = 48.8594
dimer//try4-opt2.repack-nonPC	costs 0	real_cost = 52.9819
dimer//try4-opt2	costs 0	real_cost = 52.4119
dimer//try4-opt2.gromacs0	costs 0	real_cost = 50.6412
dimer//try4-opt1	costs 0	real_cost = 54.9366
dimer//try4-opt1-scwrl	costs 0	real_cost = 55.2112
dimer//try3-opt2.unpack	costs 0	real_cost = 31.7927
dimer//try3-opt2.unpack.gromacs0.repack-nonPC	costs 0	real_cost = 28.3503
dimer//try3-opt2.unpack.gromacs0	costs 0	real_cost = 27.0797
dimer//try3-opt2.repack-nonPC	costs 0	real_cost = 31.9109
dimer//try3-opt2	costs 0	real_cost = 31.7927
dimer//try3-opt2.gromacs0	costs 0	real_cost = 26.4919
dimer//try3-opt1	costs 0	real_cost = 32.1074
dimer//try3-opt1-scwrl	costs 0	real_cost = 33.667
dimer//try2-opt2.unpack	costs 0	real_cost = 108.489
dimer//try2-opt2.unpack.gromacs0.repack-nonPC	costs 0	real_cost = 108.587
dimer//try2-opt2.unpack.gromacs0	costs 0	real_cost = 105.561
dimer//try2-opt2.repack-nonPC	costs 0	real_cost = 107.818
dimer//try2-opt2	costs 0	real_cost = 108.489
dimer//try2-opt2.gromacs0	costs 0	real_cost = 106.932
dimer//try2-opt1	costs 0	real_cost = 111.414
dimer//try2-opt1-scwrl	costs 0	real_cost = 113.379
dimer//try15-opt2.unpack	costs 0	real_cost = 55.1911
dimer//try15-opt2.unpack.gromacs0.repack-nonPC	costs 0	real_cost = 51.5866
dimer//try15-opt2.unpack.gromacs0	costs 0	real_cost = 54.3568
dimer//try15-opt2.repack-nonPC	costs 0	real_cost = 53.3489
dimer//try15-opt2	costs 0	real_cost = 55.1911
dimer//try15-opt1	costs 0	real_cost = 53.0462
dimer//try15-opt1-scwrl	costs 0	real_cost = 53.5053
dimer//try14-opt2.unpack	costs 0	real_cost = 58.6469
dimer//try14-opt2.unpack.gromacs0.repack-nonPC	costs 0	real_cost = 55.1739
dimer//try14-opt2.unpack.gromacs0	costs 0	real_cost = 57.9452
dimer//try14-opt2.repack-nonPC	costs 0	real_cost = 53.955
dimer//try14-opt2	costs 0	real_cost = 58.6469
dimer//try14-opt2.gromacs0	costs 0	real_cost = 60.3775
dimer//try14-opt1	costs 0	real_cost = 57.3116
dimer//try14-opt1-scwrl	costs 0	real_cost = 54.5154
dimer//try13-opt2.unpack	costs 0	real_cost = 47.2557
dimer//try13-opt2.unpack.gromacs0.repack-nonPC	costs 0	real_cost = 42.6646
dimer//try13-opt2.unpack.gromacs0	costs 0	real_cost = 45.0519
dimer//try13-opt2.repack-nonPC	costs 0	real_cost = 43.4262
dimer//try13-opt2	costs 0	real_cost = 47.2557
dimer//try13-opt2.gromacs0	costs 0	real_cost = 46.7651
dimer//try13-opt1	costs 0	real_cost = 48.4837
dimer//try13-opt1-scwrl	costs 0	real_cost = 45.2124
dimer//try12-opt2.unpack	costs 0	real_cost = 45.7999
dimer//try12-opt2.unpack.gromacs0.repack-nonPC	costs 0	real_cost = 44.7791
dimer//try12-opt2.unpack.gromacs0	costs 0	real_cost = 45.8129
dimer//try12-opt2.repack-nonPC	costs 0	real_cost = 42.6001
dimer//try12-opt2	costs 0	real_cost = 45.7999
dimer//try12-opt2.gromacs0	costs 0	real_cost = 48.5388
dimer//try12-opt1	costs 0	real_cost = 47.6413
dimer//try12-opt1-scwrl	costs 0	real_cost = 45.6246
dimer//try11-opt2.unpack	costs 0	real_cost = 57.4083
dimer//try11-opt2.unpack.gromacs0.repack-nonPC	costs 0	real_cost = 50.9459
dimer//try11-opt2.unpack.gromacs0	costs 0	real_cost = 56.8379
dimer//try11-opt2.repack-nonPC	costs 0	real_cost = 51.0707
dimer//try11-opt2	costs 0	real_cost = 57.4083
dimer//try11-opt2.gromacs0	costs 0	real_cost = 57.8779
dimer//try11-opt1	costs 0	real_cost = 58.3026
dimer//try11-opt1-scwrl	costs 0	real_cost = 52.6365
dimer//try10-opt2.unpack	costs 0	real_cost = 58.8015
dimer//try10-opt2.unpack.gromacs0.repack-nonPC	costs 0	real_cost = 52.397
dimer//try10-opt2.unpack.gromacs0	costs 0	real_cost = 62.5407
dimer//try10-opt2.repack-nonPC	costs 0	real_cost = 50.9278
dimer//try10-opt2	costs 0	real_cost = 58.8015
dimer//try10-opt2.gromacs0	costs 0	real_cost = 63.8054
dimer//try10-opt1	costs 0	real_cost = 57.4451
dimer//try10-opt1-scwrl	costs 0	real_cost = 51.4263
dimer//try1-opt2.unpack	costs 0	real_cost = 101.712
dimer//try1-opt2.unpack.gromacs0.repack-nonPC	costs 0	real_cost = 104.282
dimer//try1-opt2.unpack.gromacs0	costs 0	real_cost = 103.975
dimer//try1-opt2.repack-nonPC	costs 0	real_cost = 104.425
dimer//try1-opt2	costs 0	real_cost = 101.712
dimer//try1-opt2.gromacs0	costs 0	real_cost = 104.879
dimer//try1-opt1	costs 0	real_cost = 110.099
dimer//try1-opt1-scwrl	costs 0	real_cost = 104.712
T0327.try4-opt2.repack-nonPC.pdb.gz	costs 0	real_cost = 61.4282
T0327.try4-opt2.pdb.gz	costs 0	real_cost = 65.0254
T0327.try4-opt2.gromacs0.pdb.gz	costs 0	real_cost = 65.3393
T0327.try4-opt1.pdb.gz	costs 0	real_cost = 59.4491
T0327.try4-opt1-scwrl.pdb.gz	costs 0	real_cost = 60.1191
T0327.try3-opt2.repack-nonPC.pdb.gz	costs 0	real_cost = 108.137
T0327.try3-opt2.pdb.gz	costs 0	real_cost = 105.781
T0327.try3-opt2.gromacs0.pdb.gz	costs 0	real_cost = 103.997
T0327.try3-opt1.pdb.gz	costs 0	real_cost = 105.442
T0327.try3-opt1-scwrl.pdb.gz	costs 0	real_cost = 103.319
T0327.try2-opt2.repack-nonPC.pdb.gz	costs 0	real_cost = 7.25882
T0327.try2-opt2.pdb.gz	costs 0	real_cost = 11.7567
T0327.try2-opt2.gromacs0.pdb.gz	costs 0	real_cost = 12.8434
T0327.try2-opt1.pdb.gz	costs 0	real_cost = 11.884
T0327.try2-opt1-scwrl.pdb.gz	costs 0	real_cost = 11.7898
T0327.try1-opt2.repack-nonPC.pdb.gz	costs 0	real_cost = 10.6616
T0327.try1-opt2.pdb.gz	costs 0	real_cost = 7.60813
T0327.try1-opt2.gromacs0.pdb.gz	costs 0	real_cost = 6.86175
T0327.try1-opt2-proteinshop.pdb.gz	costs 0	real_cost = 48.4317
T0327.try1-opt2-proteinshop-2.pdb.gz	costs 0	real_cost = 48.4317
T0327.try1-opt1.pdb.gz	costs 0	real_cost = 8.67838
T0327.try1-opt1-scwrl.pdb.gz	costs 0	real_cost = 9.11184
../model5.ts-submitted	costs 0	real_cost = 24.1601
../model4.ts-submitted	costs 0	real_cost = 21.498
../model3.ts-submitted	costs 0	real_cost = 65.0146
../model2.ts-submitted	costs 0	real_cost = 47.267
../model1.ts-submitted	costs 0	real_cost = 58.6738
align5	costs 0	real_cost = 87.8309
align4	costs 0	real_cost = 15.1411
align3	costs 0	real_cost = 37.3377
align2	costs 0	real_cost = 20.9858
align1	costs 0	real_cost = 25.4929
T0327.try1-opt2.pdb	costs 0	real_cost = 7.60816
model5-scwrl	costs 0	real_cost = 37.5824
model5.ts-submitted	costs 0	real_cost = 24.1601
model4-scwrl	costs 0	real_cost = 40.0748
model4.ts-submitted	costs 0	real_cost = 21.498
model3-scwrl	costs 0	real_cost = 63.0155
model3.ts-submitted	costs 0	real_cost = 65.0146
model2-scwrl	costs 0	real_cost = 45.8789
model2.ts-submitted	costs 0	real_cost = 47.267
model1-scwrl	costs 0	real_cost = 56.308
model1.ts-submitted	costs 0	real_cost = 58.6738
2hgcA	costs 0	real_cost = -851
# command:CPU_time= 157.252 sec, elapsed time= 352.07 sec)
# command:rm -f sort.tmp
/projects/compbio/bin/sorttbl real_cost < decoys/evaluate.rdb > sort.tmp
mv -f sort.tmp decoys/evaluate.rdb
mv -f decoys/evaluate.pretty decoys/evaluate.pretty.old
/projects/compbio/experiments/protein-predict/casp7/scripts/prettyscore -terse -targpfx -decpoint < decoys/evaluate.rdb > decoys/evaluate.pretty
rm -f decoys/evaluate_1.rdb
sed -e s/XXX0000/T0327/ -e s/START_COL/1/ \
-e s/REAL_PDB/2hgcA/ \
-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 1174837627
# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/
# command:# reading monomeric-50pc.atoms
# trans (non-proline) backbone unit:
#	  CA= -2.2088 1.0126 -0.0031
#	   O= -0.1499 2.2440 0.0017
#	   C= -0.6889 1.1368 0.0000
#	 N+1= 0.0000 0.0000 0.0000
#	CA+1= 1.4581 0.0000 0.0000
# cis backbone unit:
#	  CA= -0.1462 2.4515 0.0018
#	   O= -2.0272 0.9713 0.0022
#	   C= -0.8006 1.0755 0.0000
#	 N+1= 0.0000 0.0000 0.0000
#	CA+1= 1.4659 0.0000 0.0000
# trans backbone unit before proline:
#	  CA= -2.2099 1.0634 -0.0014
#	   O= -0.1233 2.2459 0.0075
#	   C= -0.6871 1.1518 0.0000
#	 N+1= 0.0000 0.0000 0.0000
#	CA+1= 1.4660 0.0000 0.0000


# After reading monomeric-50pc.atoms have 448 chains in training database
#  Count of chains,residues,atoms: 448,112605,876684
#  109826 residues have no bad marker
#  665 residues lack atoms needed to compute omega
#  322 residues have cis peptide
#  number of each bad type:
#	NON_STANDARD_RESIDUE	6
#	HAS_OXT	325
#	TOO_MANY_ATOMS	1
#	TOO_FEW_ATOMS	523
#	HAS_UNKNOWN_ATOMS	2
#	HAS_DUPLICATE_ATOMS	0
#	CHAIN_BREAK_BEFORE	208
#	NON_PLANAR_PEPTIDE	143
#	BAD_PEPTIDE	1959
#  Note: may sum to more than number of residues, 
#    because one residue may have multiple problems
# command:# Reading rotamer library from dunbrack-1332.rot
# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/
# command:# ReadAtomType exp-pdb.types
Read AtomType exp-pdb with 49 types.
# command:# ReadClashTable exp-pdb-2191-2symm.clash
# Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2
# command:# command:CPU_time= 6.08207 sec, elapsed time= 6.1187 sec)
# command:# Reading spots from monomeric-50pc-dry-5.spot
Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes
# reading histogram from smoothed-monomeric-50pc-dry-5.hist
# created burial cost function dry5 with radius 5 with spots at monomeric-50pc-dry-5.spot
# command:# Reading spots from monomeric-50pc-wet-6.5.spot
Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes
# reading histogram from smoothed-monomeric-50pc-wet-6.5.hist
# created burial cost function wet6.5 with radius 6.5 with spots at monomeric-50pc-wet-6.5.spot
# command:# Reading spots from monomeric-50pc-dry-6.5.spot
Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes
# reading histogram from smoothed-monomeric-50pc-dry-6.5.hist
# created burial cost function dry6.5 with radius 6.5 with spots at monomeric-50pc-dry-6.5.spot
# command:# Reading spots from monomeric-50pc-generic-6.5.spot
Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes
# reading histogram from smoothed-monomeric-50pc-generic-6.5.hist
# created burial cost function gen6.5 with radius 6.5 with spots at monomeric-50pc-generic-6.5.spot
# command:# Reading spots from near-backbone-center.spot
# reading histogram from smoothed-near-backbone-2spot.hist
# Reading spots from near-backbone-count.spot
# created burial cost function near_backbone with radius 9.65 with spots at near-backbone-center.spot counting only near-backbone-count.spot
# command:# Reading spots from way-back-center.spot
# reading histogram from smoothed-way-back-2spot.hist
# Reading spots from way-back-count.spot
# created burial cost function way_back with radius 8.9 with spots at way-back-center.spot counting only way-back-count.spot
# command:# Reading spots from monomeric-50pc-dry-8.spot
Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes
# reading histogram from smoothed-monomeric-50pc-dry-8.hist
# created burial cost function dry8 with radius 8 with spots at monomeric-50pc-dry-8.spot
# command:# Reading spots from monomeric-50pc-dry-10.spot
Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes
# reading histogram from smoothed-monomeric-50pc-dry-10.hist
# created burial cost function dry10 with radius 10 with spots at monomeric-50pc-dry-10.spot
# command:# Reading spots from monomeric-50pc-dry-12.spot
Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes
# reading histogram from smoothed-monomeric-50pc-dry-12.hist
# created burial cost function dry12 with radius 12 with spots at monomeric-50pc-dry-12.spot
# command:# reading histogram from dunbrack-2191-alpha.hist
# created alpha cost function alpha with offset 0 and  360 bins
# command:# reading histogram from dunbrack-2191-alpha-1.hist
# created alpha cost function alpha_prev with offset -1 and  360 bins
# command:# Prefix for input files set to /projects/compbio/lib/alphabet/
# command:# Read 3 alphabets from alpha.alphabet
# command:CPU_time= 6.16406 sec, elapsed time= 6.21542 sec)
# command:# Prefix for input files set to 
# command:# Making conformation for sequence T0327 numbered 1 through 102
Created new target T0327 from T0327.a2m
# command:# command:# No conformations to remove in PopConform
# command:# cleared Id set
# command:# command:# ReadConformPDB reading from PDB file T0327_1.real.pdb looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# command:# Saving current conformation as real
# command:# Prefix for output files set to decoys/
# command:# SetRealCost created real_cost = 
#	( 50 * real_hbond + 50 * real_hbond_u + 50 * decoy_hbond + 50 * decoy_hbond_u + 10 * real_NO_hbond + 10 * real_NO_hbond_u + 10 * decoy_NO_hbond + 10 * decoy_NO_hbond_u + 10 * knot + 200 * clens + 0 * rmsd + 35 * log_rmsd + 0 * rmsd_ca + 30 * log_rmsd_ca + 1 * GDT + 1 * smooth_GDT + 0.2 * missing_atoms )
# command:# SetCost created cost = 
#	)
# command:CPU_time= 8.5677 sec, elapsed time= 8.633 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 56
# copying to AlignedFragments data structure
# command:# fraction of real conformation used = 1
# GDT_score = -58.9041
# GDT_score(maxd=8,maxw=2.9)= -58.4207
# GDT_score(maxd=8,maxw=3.2)= -55.4896
# GDT_score(maxd=8,maxw=3.5)= -52.7468
# GDT_score(maxd=10,maxw=3.8)= -56.553
# GDT_score(maxd=10,maxw=4)= -54.7721
# GDT_score(maxd=10,maxw=4.2)= -53.0523
# GDT_score(maxd=12,maxw=4.3)= -57.2445
# GDT_score(maxd=12,maxw=4.5)= -55.4958
# GDT_score(maxd=12,maxw=4.7)= -53.7489
# GDT_score(maxd=14,maxw=5.2)= -53.5396
# GDT_score(maxd=14,maxw=5.5)= -51.2917
# command:# Prefix for output files set to 
# command:superimposing iter= 0 total_weight= 8.8700000e+02 rmsd (weighted)= 5.4819309e+00 (unweighted)= 2.3842934e+01
superimposing iter= 1 total_weight= 2.2698312e+03 rmsd (weighted)= 2.5384598e+00 (unweighted)= 2.3567372e+01
superimposing iter= 2 total_weight= 1.1110819e+03 rmsd (weighted)= 1.8041057e+00 (unweighted)= 2.3275579e+01
superimposing iter= 3 total_weight= 8.1780372e+02 rmsd (weighted)= 1.5083810e+00 (unweighted)= 2.3061315e+01
superimposing iter= 4 total_weight= 7.5553034e+02 rmsd (weighted)= 1.3167848e+00 (unweighted)= 2.2921891e+01
superimposing iter= 5 total_weight= 6.9939956e+02 rmsd (weighted)= 1.1977285e+00 (unweighted)= 2.2841936e+01
# command:# Prefix for output files set to decoys/
# command:# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_568256224.pdb -s /var/tmp/to_scwrl_568256224.seq -o /var/tmp/from_scwrl_568256224.pdb > /var/tmp/scwrl_568256224.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_568256224.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 56
# copying to AlignedFragments data structure
# command:# fraction of real conformation used = 1
# GDT_score = -59.9315
# GDT_score(maxd=8,maxw=2.9)= -59.4789
# GDT_score(maxd=8,maxw=3.2)= -56.4286
# GDT_score(maxd=8,maxw=3.5)= -53.6466
# GDT_score(maxd=10,maxw=3.8)= -57.4959
# GDT_score(maxd=10,maxw=4)= -55.6839
# GDT_score(maxd=10,maxw=4.2)= -53.9297
# GDT_score(maxd=12,maxw=4.3)= -58.0701
# GDT_score(maxd=12,maxw=4.5)= -56.293
# GDT_score(maxd=12,maxw=4.7)= -54.5186
# GDT_score(maxd=14,maxw=5.2)= -54.229
# GDT_score(maxd=14,maxw=5.5)= -51.9436
# command:# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_194812106.pdb -s /var/tmp/to_scwrl_194812106.seq -o /var/tmp/from_scwrl_194812106.pdb > /var/tmp/scwrl_194812106.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_194812106.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 78
# copying to AlignedFragments data structure
# command:# fraction of real conformation used = 1
# GDT_score = -54.7945
# GDT_score(maxd=8,maxw=2.9)= -54.3058
# GDT_score(maxd=8,maxw=3.2)= -51.5751
# GDT_score(maxd=8,maxw=3.5)= -48.9896
# GDT_score(maxd=10,maxw=3.8)= -53.3375
# GDT_score(maxd=10,maxw=4)= -51.5932
# GDT_score(maxd=10,maxw=4.2)= -49.9188
# GDT_score(maxd=12,maxw=4.3)= -54.2639
# GDT_score(maxd=12,maxw=4.5)= -52.5599
# GDT_score(maxd=12,maxw=4.7)= -50.9254
# GDT_score(maxd=14,maxw=5.2)= -50.9637
# GDT_score(maxd=14,maxw=5.5)= -48.8563
# command:# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1491962060.pdb -s /var/tmp/to_scwrl_1491962060.seq -o /var/tmp/from_scwrl_1491962060.pdb > /var/tmp/scwrl_1491962060.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1491962060.pdb
# conformation set from SCWRL output
# command:# naming current conformation model3-scwrl
# command:# ReadConformPDB reading from PDB file model4.ts-submitted looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# command:# fraction of real conformation used = 0.794521
# GDT_score = -59.589
# GDT_score(maxd=8,maxw=2.9)= -60.3269
# GDT_score(maxd=8,maxw=3.2)= -58.3901
# GDT_score(maxd=8,maxw=3.5)= -56.4317
# GDT_score(maxd=10,maxw=3.8)= -58.4874
# GDT_score(maxd=10,maxw=4)= -57.2102
# GDT_score(maxd=10,maxw=4.2)= -55.7795
# GDT_score(maxd=12,maxw=4.3)= -58.3293
# GDT_score(maxd=12,maxw=4.5)= -56.8983
# GDT_score(maxd=12,maxw=4.7)= -55.4681
# GDT_score(maxd=14,maxw=5.2)= -54.6961
# GDT_score(maxd=14,maxw=5.5)= -52.6491
# command:# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1121465540.pdb -s /var/tmp/to_scwrl_1121465540.seq -o /var/tmp/from_scwrl_1121465540.pdb > /var/tmp/scwrl_1121465540.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1121465540.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 T0327 can't currently be optimized by undertaker
# command:# fraction of real conformation used = 0.835616
# GDT_score = -60.274
# GDT_score(maxd=8,maxw=2.9)= -63.0964
# GDT_score(maxd=8,maxw=3.2)= -59.953
# GDT_score(maxd=8,maxw=3.5)= -56.9032
# GDT_score(maxd=10,maxw=3.8)= -59.3099
# GDT_score(maxd=10,maxw=4)= -57.3563
# GDT_score(maxd=10,maxw=4.2)= -55.5382
# GDT_score(maxd=12,maxw=4.3)= -58.6311
# GDT_score(maxd=12,maxw=4.5)= -56.8643
# GDT_score(maxd=12,maxw=4.7)= -55.1198
# GDT_score(maxd=14,maxw=5.2)= -54.1302
# GDT_score(maxd=14,maxw=5.5)= -51.8481
# command:# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_2073245469.pdb -s /var/tmp/to_scwrl_2073245469.seq -o /var/tmp/from_scwrl_2073245469.pdb > /var/tmp/scwrl_2073245469.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2073245469.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 T0327.try1-opt2.pdb looking for model 1
# Found a chain break before 100
# copying to AlignedFragments data structure
# command:# fraction of real conformation used = 1
# GDT_score = -60.9589
# GDT_score(maxd=8,maxw=2.9)= -60.8928
# GDT_score(maxd=8,maxw=3.2)= -57.6451
# GDT_score(maxd=8,maxw=3.5)= -54.6573
# GDT_score(maxd=10,maxw=3.8)= -58.5737
# GDT_score(maxd=10,maxw=4)= -56.6809
# GDT_score(maxd=10,maxw=4.2)= -54.7737
# GDT_score(maxd=12,maxw=4.3)= -58.9982
# GDT_score(maxd=12,maxw=4.5)= -57.0911
# GDT_score(maxd=12,maxw=4.7)= -55.263
# GDT_score(maxd=14,maxw=5.2)= -54.8987
# GDT_score(maxd=14,maxw=5.5)= -52.5767
# command:# Prefix for output files set to 
# command:superimposing iter= 0 total_weight= 8.8700000e+02 rmsd (weighted)= 5.0673541e+00 (unweighted)= 2.8403701e+01
superimposing iter= 1 total_weight= 2.1935205e+03 rmsd (weighted)= 2.3814035e+00 (unweighted)= 2.8645825e+01
superimposing iter= 2 total_weight= 1.1012168e+03 rmsd (weighted)= 1.7053126e+00 (unweighted)= 2.8729677e+01
superimposing iter= 3 total_weight= 7.7868749e+02 rmsd (weighted)= 1.4676733e+00 (unweighted)= 2.8799127e+01
superimposing iter= 4 total_weight= 7.2008099e+02 rmsd (weighted)= 1.3158359e+00 (unweighted)= 2.8839380e+01
superimposing iter= 5 total_weight= 6.8377596e+02 rmsd (weighted)= 1.2131147e+00 (unweighted)= 2.8853294e+01
# command:# Prefix for output files set to decoys/
# command:# Prefix for input files set to 
# command:# ReadConformPDB reading from PDB file T0327.undertaker-align.pdb looking for model 1
WARNING: atoms too close: (T0327)G48.C and (T0327)V49.C only 0.0000000e+00 apart, marking (T0327)V49.C as missing
WARNING: atoms too close: (T0327)V49.N and (T0327)H50.N only 0.0000000e+00 apart, marking (T0327)V49.N as missing
WARNING: atoms too close: (T0327)V49.CA and (T0327)H50.CA only 0.0000000e+00 apart, marking (T0327)V49.CA as missing
WARNING: atoms too close: (T0327)Y59.C and (T0327)E64.C only 0.0000000e+00 apart, marking (T0327)E64.C as missing
WARNING: atoms too close: (T0327)K60.N and (T0327)L65.N only 0.0000000e+00 apart, marking (T0327)K60.N as missing
WARNING: atoms too close: (T0327)K60.CA and (T0327)L65.CA only 0.0000000e+00 apart, marking (T0327)K60.CA as missing
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# command:# naming current conformation align1
# command:# fraction of real conformation used = 0.821918
# GDT_score = -61.3014
# GDT_score(maxd=8,maxw=2.9)= -61.0138
# GDT_score(maxd=8,maxw=3.2)= -59.0227
# GDT_score(maxd=8,maxw=3.5)= -57.0098
# GDT_score(maxd=10,maxw=3.8)= -59.2745
# GDT_score(maxd=10,maxw=4)= -57.958
# GDT_score(maxd=10,maxw=4.2)= -56.4919
# GDT_score(maxd=12,maxw=4.3)= -59.1924
# GDT_score(maxd=12,maxw=4.5)= -57.7234
# GDT_score(maxd=12,maxw=4.7)= -56.258
# GDT_score(maxd=14,maxw=5.2)= -55.5271
# GDT_score(maxd=14,maxw=5.5)= -53.435
# command:# ReadConformPDB reading from PDB file T0327.undertaker-align.pdb looking for model 2
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# command:# naming current conformation align2
# command:# fraction of real conformation used = 0.876712
# GDT_score = -60.9589
# GDT_score(maxd=8,maxw=2.9)= -63.7045
# GDT_score(maxd=8,maxw=3.2)= -60.3887
# GDT_score(maxd=8,maxw=3.5)= -57.2812
# GDT_score(maxd=10,maxw=3.8)= -59.8461
# GDT_score(maxd=10,maxw=4)= -57.8687
# GDT_score(maxd=10,maxw=4.2)= -56.0002
# GDT_score(maxd=12,maxw=4.3)= -59.3216
# GDT_score(maxd=12,maxw=4.5)= -57.5019
# GDT_score(maxd=12,maxw=4.7)= -55.7313
# GDT_score(maxd=14,maxw=5.2)= -54.885
# GDT_score(maxd=14,maxw=5.5)= -52.5774
# command:# ReadConformPDB reading from PDB file T0327.undertaker-align.pdb looking for model 3
WARNING: atoms too close: (T0327)Y83.C and (T0327)T85.C only 0.0000000e+00 apart, marking (T0327)T85.C as missing
WARNING: atoms too close: (T0327)K84.N and (T0327)I86.N only 0.0000000e+00 apart, marking (T0327)K84.N as missing
WARNING: atoms too close: (T0327)K84.CA and (T0327)I86.CA only 0.0000000e+00 apart, marking (T0327)K84.CA as missing
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# command:# naming current conformation align3
# command:# ReadConformPDB reading from PDB file T0327.undertaker-align.pdb looking for model 4
WARNING: atoms too close: (T0327)K60.C and (T0327)E64.C only 0.0000000e+00 apart, marking (T0327)E64.C as missing
WARNING: atoms too close: (T0327)L61.N and (T0327)L65.N only 0.0000000e+00 apart, marking (T0327)L61.N as missing
WARNING: atoms too close: (T0327)L61.CA and (T0327)L65.CA only 0.0000000e+00 apart, marking (T0327)L61.CA as missing
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# command:# naming current conformation align4
# command:# ReadConformPDB reading from PDB file T0327.undertaker-align.pdb looking for model 5
WARNING: atoms too close: (T0327)L61.C and (T0327)L65.C only 0.0000000e+00 apart, marking (T0327)L65.C as missing
WARNING: atoms too close: (T0327)G62.N and (T0327)T66.N only 0.0000000e+00 apart, marking (T0327)G62.N as missing
WARNING: atoms too close: (T0327)G62.CA and (T0327)T66.CA only 0.0000000e+00 apart, marking (T0327)G62.CA as missing
WARNING: atoms too close: (T0327)G69.C and (T0327)L73.C only 0.0000000e+00 apart, marking (T0327)L73.C as missing
WARNING: atoms too close: (T0327)E70.N and (T0327)K74.N only 0.0000000e+00 apart, marking (T0327)E70.N as missing
WARNING: atoms too close: (T0327)E70.CA and (T0327)K74.CA only 0.0000000e+00 apart, marking (T0327)E70.CA as missing
# WARNING: incomplete conformation T0327 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 56
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file ../model2.ts-submitted looking for model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file ../model3.ts-submitted looking for model 1
# Found a chain break before 78
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file ../model4.ts-submitted looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# ReadConformPDB reading from PDB file ../model5.ts-submitted looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# ReadConformPDB reading from PDB file T0327.try1-opt1-scwrl.pdb.gz looking for model 1
# Found a chain break before 100
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0327.try1-opt1.pdb.gz looking for model 1
# Found a chain break before 100
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0327.try1-opt2-proteinshop-2.pdb.gz looking for model 1
# Found a chain break before 100
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0327.try1-opt2-proteinshop.pdb.gz looking for model 1
# Found a chain break before 100
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0327.try1-opt2.gromacs0.pdb.gz looking for model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0327.try1-opt2.pdb.gz looking for model 1
# Found a chain break before 100
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0327.try1-opt2.repack-nonPC.pdb.gz looking for model 1
# Found a chain break before 100
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0327.try2-opt1-scwrl.pdb.gz looking for model 1
# Found a chain break before 78
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0327.try2-opt1.pdb.gz looking for model 1
# Found a chain break before 78
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0327.try2-opt2.gromacs0.pdb.gz looking for model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0327.try2-opt2.pdb.gz looking for model 1
# Found a chain break before 78
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0327.try2-opt2.repack-nonPC.pdb.gz looking for model 1
# Found a chain break before 78
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0327.try3-opt1-scwrl.pdb.gz looking for model 1
# Found a chain break before 95
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0327.try3-opt1.pdb.gz looking for model 1
# Found a chain break before 95
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0327.try3-opt2.gromacs0.pdb.gz looking for model 1
# Found a chain break before 93
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0327.try3-opt2.pdb.gz looking for model 1
# Found a chain break before 95
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0327.try3-opt2.repack-nonPC.pdb.gz looking for model 1
# Found a chain break before 95
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0327.try4-opt1-scwrl.pdb.gz looking for model 1
# Found a chain break before 76
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0327.try4-opt1.pdb.gz looking for model 1
# Found a chain break before 76
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0327.try4-opt2.gromacs0.pdb.gz looking for model 1
# Found a chain break before 54
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0327.try4-opt2.pdb.gz looking for model 1
# Found a chain break before 78
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file T0327.try4-opt2.repack-nonPC.pdb.gz looking for model 1
# Found a chain break before 78
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try1-opt1-scwrl.pdb.gz looking for chain 'A' model 1
# Found a chain break before 51
# copying to AlignedFragments data structure
# naming current conformation dimer//try1-opt1-scwrl
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try1-opt1.pdb.gz looking for chain 'A' model 1
# Found a chain break before 51
# copying to AlignedFragments data structure
# naming current conformation dimer//try1-opt1
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try1-opt2.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 26
# copying to AlignedFragments data structure
# naming current conformation dimer//try1-opt2.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try1-opt2.pdb.gz looking for chain 'A' model 1
# Found a chain break before 75
# copying to AlignedFragments data structure
# naming current conformation dimer//try1-opt2
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try1-opt2.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 75
# copying to AlignedFragments data structure
# naming current conformation dimer//try1-opt2.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try1-opt2.unpack.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 26
# copying to AlignedFragments data structure
# naming current conformation dimer//try1-opt2.unpack.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try1-opt2.unpack.gromacs0.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 26
# copying to AlignedFragments data structure
# naming current conformation dimer//try1-opt2.unpack.gromacs0.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try1-opt2.unpack.pdb.gz looking for chain 'A' model 1
# Found a chain break before 75
# copying to AlignedFragments data structure
# naming current conformation dimer//try1-opt2.unpack
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try10-opt1-scwrl.pdb.gz looking for chain 'A' model 1
# Found a chain break before 59
# copying to AlignedFragments data structure
# naming current conformation dimer//try10-opt1-scwrl
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try10-opt1.pdb.gz looking for chain 'A' model 1
# Found a chain break before 59
# copying to AlignedFragments data structure
# naming current conformation dimer//try10-opt1
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try10-opt2.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 101
# copying to AlignedFragments data structure
# naming current conformation dimer//try10-opt2.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try10-opt2.pdb.gz looking for chain 'A' model 1
# Found a chain break before 59
# copying to AlignedFragments data structure
# naming current conformation dimer//try10-opt2
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try10-opt2.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 59
# copying to AlignedFragments data structure
# naming current conformation dimer//try10-opt2.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try10-opt2.unpack.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try10-opt2.unpack.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try10-opt2.unpack.gromacs0.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try10-opt2.unpack.gromacs0.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try10-opt2.unpack.pdb.gz looking for chain 'A' model 1
# Found a chain break before 59
# copying to AlignedFragments data structure
# naming current conformation dimer//try10-opt2.unpack
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try11-opt1-scwrl.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try11-opt1-scwrl
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try11-opt1.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try11-opt1
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try11-opt2.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 101
# copying to AlignedFragments data structure
# naming current conformation dimer//try11-opt2.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try11-opt2.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try11-opt2
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try11-opt2.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try11-opt2.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try11-opt2.unpack.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try11-opt2.unpack.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try11-opt2.unpack.gromacs0.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try11-opt2.unpack.gromacs0.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try11-opt2.unpack.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try11-opt2.unpack
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try12-opt1-scwrl.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try12-opt1-scwrl
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try12-opt1.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try12-opt1
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try12-opt2.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 101
# copying to AlignedFragments data structure
# naming current conformation dimer//try12-opt2.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try12-opt2.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try12-opt2
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try12-opt2.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try12-opt2.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try12-opt2.unpack.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try12-opt2.unpack.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try12-opt2.unpack.gromacs0.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try12-opt2.unpack.gromacs0.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try12-opt2.unpack.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try12-opt2.unpack
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try13-opt1-scwrl.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try13-opt1-scwrl
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try13-opt1.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try13-opt1
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try13-opt2.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 101
# copying to AlignedFragments data structure
# naming current conformation dimer//try13-opt2.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try13-opt2.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try13-opt2
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try13-opt2.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try13-opt2.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try13-opt2.unpack.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try13-opt2.unpack.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try13-opt2.unpack.gromacs0.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try13-opt2.unpack.gromacs0.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try13-opt2.unpack.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try13-opt2.unpack
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try14-opt1-scwrl.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try14-opt1-scwrl
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try14-opt1.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try14-opt1
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try14-opt2.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 101
# copying to AlignedFragments data structure
# naming current conformation dimer//try14-opt2.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try14-opt2.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try14-opt2
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try14-opt2.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try14-opt2.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try14-opt2.unpack.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try14-opt2.unpack.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try14-opt2.unpack.gromacs0.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try14-opt2.unpack.gromacs0.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try14-opt2.unpack.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try14-opt2.unpack
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try15-opt1-scwrl.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try15-opt1-scwrl
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try15-opt1.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try15-opt1
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try15-opt2.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try15-opt2
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try15-opt2.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try15-opt2.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try15-opt2.unpack.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 59
# copying to AlignedFragments data structure
# naming current conformation dimer//try15-opt2.unpack.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try15-opt2.unpack.gromacs0.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 59
# copying to AlignedFragments data structure
# naming current conformation dimer//try15-opt2.unpack.gromacs0.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try15-opt2.unpack.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try15-opt2.unpack
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try2-opt1-scwrl.pdb.gz looking for chain 'A' model 1
# Found a chain break before 100
# copying to AlignedFragments data structure
# naming current conformation dimer//try2-opt1-scwrl
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try2-opt1.pdb.gz looking for chain 'A' model 1
# Found a chain break before 100
# copying to AlignedFragments data structure
# naming current conformation dimer//try2-opt1
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try2-opt2.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 101
# copying to AlignedFragments data structure
# naming current conformation dimer//try2-opt2.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try2-opt2.pdb.gz looking for chain 'A' model 1
# Found a chain break before 100
# copying to AlignedFragments data structure
# naming current conformation dimer//try2-opt2
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try2-opt2.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 100
# copying to AlignedFragments data structure
# naming current conformation dimer//try2-opt2.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try2-opt2.unpack.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try2-opt2.unpack.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try2-opt2.unpack.gromacs0.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try2-opt2.unpack.gromacs0.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try2-opt2.unpack.pdb.gz looking for chain 'A' model 1
# Found a chain break before 100
# copying to AlignedFragments data structure
# naming current conformation dimer//try2-opt2.unpack
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try3-opt1-scwrl.pdb.gz looking for chain 'A' model 1
# Found a chain break before 70
# copying to AlignedFragments data structure
# naming current conformation dimer//try3-opt1-scwrl
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try3-opt1.pdb.gz looking for chain 'A' model 1
# Found a chain break before 70
# copying to AlignedFragments data structure
# naming current conformation dimer//try3-opt1
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try3-opt2.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 101
# copying to AlignedFragments data structure
# naming current conformation dimer//try3-opt2.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try3-opt2.pdb.gz looking for chain 'A' model 1
# Found a chain break before 70
# copying to AlignedFragments data structure
# naming current conformation dimer//try3-opt2
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try3-opt2.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 70
# copying to AlignedFragments data structure
# naming current conformation dimer//try3-opt2.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try3-opt2.unpack.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try3-opt2.unpack.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try3-opt2.unpack.gromacs0.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try3-opt2.unpack.gromacs0.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try3-opt2.unpack.pdb.gz looking for chain 'A' model 1
# Found a chain break before 70
# copying to AlignedFragments data structure
# naming current conformation dimer//try3-opt2.unpack
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try4-opt1-scwrl.pdb.gz looking for chain 'A' model 1
# Found a chain break before 78
# copying to AlignedFragments data structure
# naming current conformation dimer//try4-opt1-scwrl
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try4-opt1.pdb.gz looking for chain 'A' model 1
# Found a chain break before 78
# copying to AlignedFragments data structure
# naming current conformation dimer//try4-opt1
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try4-opt2.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 101
# copying to AlignedFragments data structure
# naming current conformation dimer//try4-opt2.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try4-opt2.pdb.gz looking for chain 'A' model 1
# Found a chain break before 78
# copying to AlignedFragments data structure
# naming current conformation dimer//try4-opt2
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try4-opt2.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 78
# copying to AlignedFragments data structure
# naming current conformation dimer//try4-opt2.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try4-opt2.unpack.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try4-opt2.unpack.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try4-opt2.unpack.gromacs0.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try4-opt2.unpack.gromacs0.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try4-opt2.unpack.pdb.gz looking for chain 'A' model 1
# Found a chain break before 78
# copying to AlignedFragments data structure
# naming current conformation dimer//try4-opt2.unpack
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try5-opt1-scwrl.pdb.gz looking for chain 'A' model 1
# Found a chain break before 75
# copying to AlignedFragments data structure
# naming current conformation dimer//try5-opt1-scwrl
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try5-opt1.pdb.gz looking for chain 'A' model 1
# Found a chain break before 75
# copying to AlignedFragments data structure
# naming current conformation dimer//try5-opt1
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try5-opt2.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 101
# copying to AlignedFragments data structure
# naming current conformation dimer//try5-opt2.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try5-opt2.pdb.gz looking for chain 'A' model 1
# Found a chain break before 75
# copying to AlignedFragments data structure
# naming current conformation dimer//try5-opt2
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try5-opt2.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 75
# copying to AlignedFragments data structure
# naming current conformation dimer//try5-opt2.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try5-opt2.unpack.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try5-opt2.unpack.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try5-opt2.unpack.gromacs0.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try5-opt2.unpack.gromacs0.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try5-opt2.unpack.pdb.gz looking for chain 'A' model 1
# Found a chain break before 75
# copying to AlignedFragments data structure
# naming current conformation dimer//try5-opt2.unpack
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try6-opt1-scwrl.pdb.gz looking for chain 'A' model 1
# Found a chain break before 83
# copying to AlignedFragments data structure
# naming current conformation dimer//try6-opt1-scwrl
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try6-opt1.pdb.gz looking for chain 'A' model 1
# Found a chain break before 83
# copying to AlignedFragments data structure
# naming current conformation dimer//try6-opt1
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try6-opt2.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 101
# copying to AlignedFragments data structure
# naming current conformation dimer//try6-opt2.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try6-opt2.pdb.gz looking for chain 'A' model 1
# Found a chain break before 79
# copying to AlignedFragments data structure
# naming current conformation dimer//try6-opt2
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try6-opt2.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 79
# copying to AlignedFragments data structure
# naming current conformation dimer//try6-opt2.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try6-opt2.unpack.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try6-opt2.unpack.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try6-opt2.unpack.gromacs0.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try6-opt2.unpack.gromacs0.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try6-opt2.unpack.pdb.gz looking for chain 'A' model 1
# Found a chain break before 79
# copying to AlignedFragments data structure
# naming current conformation dimer//try6-opt2.unpack
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try7-opt1-scwrl.pdb.gz looking for chain 'A' model 1
# Found a chain break before 78
# copying to AlignedFragments data structure
# naming current conformation dimer//try7-opt1-scwrl
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try7-opt1.pdb.gz looking for chain 'A' model 1
# Found a chain break before 78
# copying to AlignedFragments data structure
# naming current conformation dimer//try7-opt1
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try7-opt2.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 59
# copying to AlignedFragments data structure
# naming current conformation dimer//try7-opt2.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try7-opt2.pdb.gz looking for chain 'A' model 1
# Found a chain break before 59
# copying to AlignedFragments data structure
# naming current conformation dimer//try7-opt2
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try7-opt2.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 59
# copying to AlignedFragments data structure
# naming current conformation dimer//try7-opt2.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try7-opt2.unpack.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 74
# copying to AlignedFragments data structure
# naming current conformation dimer//try7-opt2.unpack.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try7-opt2.unpack.gromacs0.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 74
# copying to AlignedFragments data structure
# naming current conformation dimer//try7-opt2.unpack.gromacs0.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try7-opt2.unpack.pdb.gz looking for chain 'A' model 1
# Found a chain break before 59
# copying to AlignedFragments data structure
# naming current conformation dimer//try7-opt2.unpack
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try8-opt1-scwrl.pdb.gz looking for chain 'A' model 1
# Found a chain break before 76
# copying to AlignedFragments data structure
# naming current conformation dimer//try8-opt1-scwrl
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try8-opt1.pdb.gz looking for chain 'A' model 1
# Found a chain break before 76
# copying to AlignedFragments data structure
# naming current conformation dimer//try8-opt1
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try8-opt2.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 101
# copying to AlignedFragments data structure
# naming current conformation dimer//try8-opt2.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try8-opt2.pdb.gz looking for chain 'A' model 1
# Found a chain break before 76
# copying to AlignedFragments data structure
# naming current conformation dimer//try8-opt2
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try8-opt2.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 76
# copying to AlignedFragments data structure
# naming current conformation dimer//try8-opt2.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try8-opt2.unpack.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try8-opt2.unpack.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try8-opt2.unpack.gromacs0.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try8-opt2.unpack.gromacs0.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try8-opt2.unpack.pdb.gz looking for chain 'A' model 1
# Found a chain break before 76
# copying to AlignedFragments data structure
# naming current conformation dimer//try8-opt2.unpack
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try9-opt1-scwrl.pdb.gz looking for chain 'A' model 1
# Found a chain break before 59
# copying to AlignedFragments data structure
# naming current conformation dimer//try9-opt1-scwrl
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try9-opt1.pdb.gz looking for chain 'A' model 1
# Found a chain break before 59
# copying to AlignedFragments data structure
# naming current conformation dimer//try9-opt1
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try9-opt2.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 101
# copying to AlignedFragments data structure
# naming current conformation dimer//try9-opt2.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try9-opt2.pdb.gz looking for chain 'A' model 1
# Found a chain break before 59
# copying to AlignedFragments data structure
# naming current conformation dimer//try9-opt2
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try9-opt2.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 59
# copying to AlignedFragments data structure
# naming current conformation dimer//try9-opt2.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try9-opt2.unpack.gromacs0.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try9-opt2.unpack.gromacs0
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try9-opt2.unpack.gromacs0.repack-nonPC.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//try9-opt2.unpack.gromacs0.repack-nonPC
# ReadConformPDB reading from PDB file ../dimer/decoys/T0327.try9-opt2.unpack.pdb.gz looking for chain 'A' model 1
# Found a chain break before 59
# copying to AlignedFragments data structure
# naming current conformation dimer//try9-opt2.unpack
# ReadConformPDB reading from PDB file ../dimer/decoys/dimer-1tbxA-try1-opt2-proteinshop.pdb.gz looking for chain 'A' model 1
# Found a chain break before 100
# copying to AlignedFragments data structure
# naming current conformation dimer//dimer-1tbxA-try1-opt2-proteinshop
# ReadConformPDB reading from PDB file ../dimer/decoys/dimer-1tbxA-try1-opt2.pdb.gz looking for chain 'A' model 1
# Found a chain break before 100
# copying to AlignedFragments data structure
# naming current conformation dimer//dimer-1tbxA-try1-opt2
# ReadConformPDB reading from PDB file ../dimer/decoys/dimer-1ub9A-dimer11.pdb.gz looking for chain 'A' model 1
# Found a chain break before 56
# copying to AlignedFragments data structure
# naming current conformation dimer//dimer-1ub9A-dimer11
# ReadConformPDB reading from PDB file ../dimer/decoys/dimer1-1tbxA-dimer6.pdb.gz looking for chain 'A' model 1
# Found a chain break before 79
# copying to AlignedFragments data structure
# naming current conformation dimer//dimer1-1tbxA-dimer6
# ReadConformPDB reading from PDB file ../dimer/decoys/dimer2-1tbxA-dimer6.pdb.gz looking for chain 'A' model 1
# Found a chain break before 79
# copying to AlignedFragments data structure
# naming current conformation dimer//dimer2-1tbxA-dimer6
# ReadConformPDB reading from PDB file ../dimer/decoys/dimer3-1tbxA-dimer6.pdb.gz looking for chain 'A' model 1
# Found a chain break before 79
# copying to AlignedFragments data structure
# naming current conformation dimer//dimer3-1tbxA-dimer6
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_POPULUS_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_943051234.pdb -s /var/tmp/to_scwrl_943051234.seq -o /var/tmp/from_scwrl_943051234.pdb > /var/tmp/scwrl_943051234.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_943051234.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 T0327 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_POPULUS_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_228606695.pdb -s /var/tmp/to_scwrl_228606695.seq -o /var/tmp/from_scwrl_228606695.pdb > /var/tmp/scwrl_228606695.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_228606695.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 T0327 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_POPULUS_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_668047358.pdb -s /var/tmp/to_scwrl_668047358.seq -o /var/tmp/from_scwrl_668047358.pdb > /var/tmp/scwrl_668047358.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_668047358.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 T0327 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_POPULUS_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_969670767.pdb -s /var/tmp/to_scwrl_969670767.seq -o /var/tmp/from_scwrl_969670767.pdb > /var/tmp/scwrl_969670767.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_969670767.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 T0327 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_POPULUS_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_164765370.pdb -s /var/tmp/to_scwrl_164765370.seq -o /var/tmp/from_scwrl_164765370.pdb > /var/tmp/scwrl_164765370.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_164765370.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 T0327 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_RECOM_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1339381226.pdb -s /var/tmp/to_scwrl_1339381226.seq -o /var/tmp/from_scwrl_1339381226.pdb > /var/tmp/scwrl_1339381226.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1339381226.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 T0327 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_RECOM_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1902460688.pdb -s /var/tmp/to_scwrl_1902460688.seq -o /var/tmp/from_scwrl_1902460688.pdb > /var/tmp/scwrl_1902460688.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1902460688.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 T0327 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_RECOM_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_376968322.pdb -s /var/tmp/to_scwrl_376968322.seq -o /var/tmp/from_scwrl_376968322.pdb > /var/tmp/scwrl_376968322.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_376968322.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 T0327 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_RECOM_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_504938655.pdb -s /var/tmp/to_scwrl_504938655.seq -o /var/tmp/from_scwrl_504938655.pdb > /var/tmp/scwrl_504938655.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_504938655.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 T0327 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_RECOM_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1851909542.pdb -s /var/tmp/to_scwrl_1851909542.seq -o /var/tmp/from_scwrl_1851909542.pdb > /var/tmp/scwrl_1851909542.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1851909542.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 T0327 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_564159712.pdb -s /var/tmp/to_scwrl_564159712.seq -o /var/tmp/from_scwrl_564159712.pdb > /var/tmp/scwrl_564159712.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_564159712.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 T0327 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_724450604.pdb -s /var/tmp/to_scwrl_724450604.seq -o /var/tmp/from_scwrl_724450604.pdb > /var/tmp/scwrl_724450604.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_724450604.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
# Found a chain break before 100
# copying to AlignedFragments data structure
# naming current conformation 3D-JIGSAW_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1516580103.pdb -s /var/tmp/to_scwrl_1516580103.seq -o /var/tmp/from_scwrl_1516580103.pdb > /var/tmp/scwrl_1516580103.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1516580103.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 T0327 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_432926232.pdb -s /var/tmp/to_scwrl_432926232.seq -o /var/tmp/from_scwrl_432926232.pdb > /var/tmp/scwrl_432926232.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_432926232.pdb
# conformation set from SCWRL output
# naming current conformation 3D-JIGSAW_TS4-scwrl
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_246091169.pdb -s /var/tmp/to_scwrl_246091169.seq -o /var/tmp/from_scwrl_246091169.pdb > /var/tmp/scwrl_246091169.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_246091169.pdb
# conformation set from SCWRL output
# naming current conformation 3D-JIGSAW_TS5-scwrl
# ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1
# Found a chain break before 59
# copying to AlignedFragments data structure
# naming current conformation 3Dpro_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1484288818.pdb -s /var/tmp/to_scwrl_1484288818.seq -o /var/tmp/from_scwrl_1484288818.pdb > /var/tmp/scwrl_1484288818.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1484288818.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 34
# copying to AlignedFragments data structure
# naming current conformation 3Dpro_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1653721731.pdb -s /var/tmp/to_scwrl_1653721731.seq -o /var/tmp/from_scwrl_1653721731.pdb > /var/tmp/scwrl_1653721731.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1653721731.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 97
# copying to AlignedFragments data structure
# naming current conformation 3Dpro_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1948146431.pdb -s /var/tmp/to_scwrl_1948146431.seq -o /var/tmp/from_scwrl_1948146431.pdb > /var/tmp/scwrl_1948146431.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1948146431.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 97
# copying to AlignedFragments data structure
# naming current conformation 3Dpro_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1727163969.pdb -s /var/tmp/to_scwrl_1727163969.seq -o /var/tmp/from_scwrl_1727163969.pdb > /var/tmp/scwrl_1727163969.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1727163969.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 97
# copying to AlignedFragments data structure
# naming current conformation 3Dpro_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1368909345.pdb -s /var/tmp/to_scwrl_1368909345.seq -o /var/tmp/from_scwrl_1368909345.pdb > /var/tmp/scwrl_1368909345.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1368909345.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 97
# copying to AlignedFragments data structure
# naming current conformation ABIpro_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_2070465541.pdb -s /var/tmp/to_scwrl_2070465541.seq -o /var/tmp/from_scwrl_2070465541.pdb > /var/tmp/scwrl_2070465541.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2070465541.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 78
# copying to AlignedFragments data structure
# naming current conformation ABIpro_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1202105193.pdb -s /var/tmp/to_scwrl_1202105193.seq -o /var/tmp/from_scwrl_1202105193.pdb > /var/tmp/scwrl_1202105193.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1202105193.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 52
# copying to AlignedFragments data structure
# naming current conformation ABIpro_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_2120745989.pdb -s /var/tmp/to_scwrl_2120745989.seq -o /var/tmp/from_scwrl_2120745989.pdb > /var/tmp/scwrl_2120745989.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2120745989.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 99
# copying to AlignedFragments data structure
# naming current conformation ABIpro_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1162817453.pdb -s /var/tmp/to_scwrl_1162817453.seq -o /var/tmp/from_scwrl_1162817453.pdb > /var/tmp/scwrl_1162817453.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1162817453.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 89
# copying to AlignedFragments data structure
# naming current conformation ABIpro_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_934634323.pdb -s /var/tmp/to_scwrl_934634323.seq -o /var/tmp/from_scwrl_934634323.pdb > /var/tmp/scwrl_934634323.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_934634323.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 55
# copying to AlignedFragments data structure
# naming current conformation BayesHH_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_288179190.pdb -s /var/tmp/to_scwrl_288179190.seq -o /var/tmp/from_scwrl_288179190.pdb > /var/tmp/scwrl_288179190.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_288179190.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 69
# copying to AlignedFragments data structure
# naming current conformation Bilab-ENABLE_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1731073677.pdb -s /var/tmp/to_scwrl_1731073677.seq -o /var/tmp/from_scwrl_1731073677.pdb > /var/tmp/scwrl_1731073677.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1731073677.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 64
# copying to AlignedFragments data structure
# naming current conformation Bilab-ENABLE_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1129446428.pdb -s /var/tmp/to_scwrl_1129446428.seq -o /var/tmp/from_scwrl_1129446428.pdb > /var/tmp/scwrl_1129446428.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1129446428.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 101
# copying to AlignedFragments data structure
# naming current conformation Bilab-ENABLE_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1780141250.pdb -s /var/tmp/to_scwrl_1780141250.seq -o /var/tmp/from_scwrl_1780141250.pdb > /var/tmp/scwrl_1780141250.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1780141250.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 101
# copying to AlignedFragments data structure
# naming current conformation Bilab-ENABLE_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_705055571.pdb -s /var/tmp/to_scwrl_705055571.seq -o /var/tmp/from_scwrl_705055571.pdb > /var/tmp/scwrl_705055571.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_705055571.pdb
# conformation set from SCWRL output
# naming current conformation Bilab-ENABLE_TS4-scwrl
# ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS5.pdb.gz looking for model 1
# Found a chain break before 101
# copying to AlignedFragments data structure
# naming current conformation Bilab-ENABLE_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1055208251.pdb -s /var/tmp/to_scwrl_1055208251.seq -o /var/tmp/from_scwrl_1055208251.pdb > /var/tmp/scwrl_1055208251.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1055208251.pdb
# conformation set from SCWRL output
# naming current conformation Bilab-ENABLE_TS5-scwrl
# ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1
# Found a chain break before 89
# copying to AlignedFragments data structure
# naming current conformation CIRCLE_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_575708837.pdb -s /var/tmp/to_scwrl_575708837.seq -o /var/tmp/from_scwrl_575708837.pdb > /var/tmp/scwrl_575708837.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_575708837.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
# Found a chain break before 90
# copying to AlignedFragments data structure
# naming current conformation CIRCLE_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_933662266.pdb -s /var/tmp/to_scwrl_933662266.seq -o /var/tmp/from_scwrl_933662266.pdb > /var/tmp/scwrl_933662266.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_933662266.pdb
# conformation set from SCWRL output
# naming current conformation CIRCLE_TS2-scwrl
# ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation CIRCLE_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1723255609.pdb -s /var/tmp/to_scwrl_1723255609.seq -o /var/tmp/from_scwrl_1723255609.pdb > /var/tmp/scwrl_1723255609.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1723255609.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 T0327 can't currently be optimized by undertaker
# naming current conformation CIRCLE_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1545379603.pdb -s /var/tmp/to_scwrl_1545379603.seq -o /var/tmp/from_scwrl_1545379603.pdb > /var/tmp/scwrl_1545379603.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1545379603.pdb
# conformation set from SCWRL output
# naming current conformation CIRCLE_TS4-scwrl
# ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation CIRCLE_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1098427636.pdb -s /var/tmp/to_scwrl_1098427636.seq -o /var/tmp/from_scwrl_1098427636.pdb > /var/tmp/scwrl_1098427636.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1098427636.pdb
# conformation set from SCWRL output
# naming current conformation CIRCLE_TS5-scwrl
# ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation CaspIta-FOX_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_915153189.pdb -s /var/tmp/to_scwrl_915153189.seq -o /var/tmp/from_scwrl_915153189.pdb > /var/tmp/scwrl_915153189.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_915153189.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 T0327 can't currently be optimized by undertaker
# naming current conformation CaspIta-FOX_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1300356645.pdb -s /var/tmp/to_scwrl_1300356645.seq -o /var/tmp/from_scwrl_1300356645.pdb > /var/tmp/scwrl_1300356645.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1300356645.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 T0327 can't currently be optimized by undertaker
# naming current conformation CaspIta-FOX_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1475395958.pdb -s /var/tmp/to_scwrl_1475395958.seq -o /var/tmp/from_scwrl_1475395958.pdb > /var/tmp/scwrl_1475395958.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1475395958.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 T0327 can't currently be optimized by undertaker
# naming current conformation CaspIta-FOX_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1420091843.pdb -s /var/tmp/to_scwrl_1420091843.seq -o /var/tmp/from_scwrl_1420091843.pdb > /var/tmp/scwrl_1420091843.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1420091843.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 T0327 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation CaspIta-FOX_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1004782541.pdb -s /var/tmp/to_scwrl_1004782541.seq -o /var/tmp/from_scwrl_1004782541.pdb > /var/tmp/scwrl_1004782541.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1004782541.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 T0327 can't currently be optimized by undertaker
# naming current conformation Distill_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_2039555670.pdb -s /var/tmp/to_scwrl_2039555670.seq -o /var/tmp/from_scwrl_2039555670.pdb > /var/tmp/scwrl_2039555670.log
Error: Couldn't open file /var/tmp/from_scwrl_2039555670.pdb or /var/tmp/from_scwrl_2039555670.pdb.gz for input
Warning: Couldn't open file decoys//var/tmp/from_scwrl_2039555670_b.pdb or decoys//var/tmp/from_scwrl_2039555670_b.pdb.gz for input
Trying /var/tmp/from_scwrl_2039555670_b.pdb
Error: Couldn't open file /var/tmp/from_scwrl_2039555670_b.pdb or /var/tmp/from_scwrl_2039555670_b.pdb.gz for input
Warning: Couldn't open file decoys//var/tmp/from_scwrl_2039555670_a.pdb or decoys//var/tmp/from_scwrl_2039555670_a.pdb.gz for input
Trying /var/tmp/from_scwrl_2039555670_a.pdb
Error: Couldn't open file /var/tmp/from_scwrl_2039555670_a.pdb or /var/tmp/from_scwrl_2039555670_a.pdb.gz for input
Error: can't open any of /var/tmp/from_scwrl_2039555670.pdb or /var/tmp/from_scwrl_2039555670_b.pdb or /var/tmp/from_scwrl_2039555670_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 T0327 can't currently be optimized by undertaker
# naming current conformation Distill_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_2144542447.pdb -s /var/tmp/to_scwrl_2144542447.seq -o /var/tmp/from_scwrl_2144542447.pdb > /var/tmp/scwrl_2144542447.log
Error: Couldn't open file /var/tmp/from_scwrl_2144542447.pdb or /var/tmp/from_scwrl_2144542447.pdb.gz for input
Warning: Couldn't open file decoys//var/tmp/from_scwrl_2144542447_b.pdb or decoys//var/tmp/from_scwrl_2144542447_b.pdb.gz for input
Trying /var/tmp/from_scwrl_2144542447_b.pdb
Error: Couldn't open file /var/tmp/from_scwrl_2144542447_b.pdb or /var/tmp/from_scwrl_2144542447_b.pdb.gz for input
Warning: Couldn't open file decoys//var/tmp/from_scwrl_2144542447_a.pdb or decoys//var/tmp/from_scwrl_2144542447_a.pdb.gz for input
Trying /var/tmp/from_scwrl_2144542447_a.pdb
Error: Couldn't open file /var/tmp/from_scwrl_2144542447_a.pdb or /var/tmp/from_scwrl_2144542447_a.pdb.gz for input
Error: can't open any of /var/tmp/from_scwrl_2144542447.pdb or /var/tmp/from_scwrl_2144542447_b.pdb or /var/tmp/from_scwrl_2144542447_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 T0327 can't currently be optimized by undertaker
# naming current conformation Distill_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_373878998.pdb -s /var/tmp/to_scwrl_373878998.seq -o /var/tmp/from_scwrl_373878998.pdb > /var/tmp/scwrl_373878998.log
Error: Couldn't open file /var/tmp/from_scwrl_373878998.pdb or /var/tmp/from_scwrl_373878998.pdb.gz for input
Warning: Couldn't open file decoys//var/tmp/from_scwrl_373878998_b.pdb or decoys//var/tmp/from_scwrl_373878998_b.pdb.gz for input
Trying /var/tmp/from_scwrl_373878998_b.pdb
Error: Couldn't open file /var/tmp/from_scwrl_373878998_b.pdb or /var/tmp/from_scwrl_373878998_b.pdb.gz for input
Warning: Couldn't open file decoys//var/tmp/from_scwrl_373878998_a.pdb or decoys//var/tmp/from_scwrl_373878998_a.pdb.gz for input
Trying /var/tmp/from_scwrl_373878998_a.pdb
Error: Couldn't open file /var/tmp/from_scwrl_373878998_a.pdb or /var/tmp/from_scwrl_373878998_a.pdb.gz for input
Error: can't open any of /var/tmp/from_scwrl_373878998.pdb or /var/tmp/from_scwrl_373878998_b.pdb or /var/tmp/from_scwrl_373878998_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 T0327 can't currently be optimized by undertaker
# naming current conformation Distill_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_324998255.pdb -s /var/tmp/to_scwrl_324998255.seq -o /var/tmp/from_scwrl_324998255.pdb > /var/tmp/scwrl_324998255.log
Error: Couldn't open file /var/tmp/from_scwrl_324998255.pdb or /var/tmp/from_scwrl_324998255.pdb.gz for input
Warning: Couldn't open file decoys//var/tmp/from_scwrl_324998255_b.pdb or decoys//var/tmp/from_scwrl_324998255_b.pdb.gz for input
Trying /var/tmp/from_scwrl_324998255_b.pdb
Error: Couldn't open file /var/tmp/from_scwrl_324998255_b.pdb or /var/tmp/from_scwrl_324998255_b.pdb.gz for input
Warning: Couldn't open file decoys//var/tmp/from_scwrl_324998255_a.pdb or decoys//var/tmp/from_scwrl_324998255_a.pdb.gz for input
Trying /var/tmp/from_scwrl_324998255_a.pdb
Error: Couldn't open file /var/tmp/from_scwrl_324998255_a.pdb or /var/tmp/from_scwrl_324998255_a.pdb.gz for input
Error: can't open any of /var/tmp/from_scwrl_324998255.pdb or /var/tmp/from_scwrl_324998255_b.pdb or /var/tmp/from_scwrl_324998255_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 T0327 can't currently be optimized by undertaker
# naming current conformation Distill_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_243149970.pdb -s /var/tmp/to_scwrl_243149970.seq -o /var/tmp/from_scwrl_243149970.pdb > /var/tmp/scwrl_243149970.log
Error: Couldn't open file /var/tmp/from_scwrl_243149970.pdb or /var/tmp/from_scwrl_243149970.pdb.gz for input
Warning: Couldn't open file decoys//var/tmp/from_scwrl_243149970_b.pdb or decoys//var/tmp/from_scwrl_243149970_b.pdb.gz for input
Trying /var/tmp/from_scwrl_243149970_b.pdb
Error: Couldn't open file /var/tmp/from_scwrl_243149970_b.pdb or /var/tmp/from_scwrl_243149970_b.pdb.gz for input
Warning: Couldn't open file decoys//var/tmp/from_scwrl_243149970_a.pdb or decoys//var/tmp/from_scwrl_243149970_a.pdb.gz for input
Trying /var/tmp/from_scwrl_243149970_a.pdb
Error: Couldn't open file /var/tmp/from_scwrl_243149970_a.pdb or /var/tmp/from_scwrl_243149970_a.pdb.gz for input
Error: can't open any of /var/tmp/from_scwrl_243149970.pdb or /var/tmp/from_scwrl_243149970_b.pdb or /var/tmp/from_scwrl_243149970_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 100
# copying to AlignedFragments data structure
# naming current conformation FAMSD_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1858167816.pdb -s /var/tmp/to_scwrl_1858167816.seq -o /var/tmp/from_scwrl_1858167816.pdb > /var/tmp/scwrl_1858167816.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1858167816.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 T0327 can't currently be optimized by undertaker
# naming current conformation FAMSD_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1978719986.pdb -s /var/tmp/to_scwrl_1978719986.seq -o /var/tmp/from_scwrl_1978719986.pdb > /var/tmp/scwrl_1978719986.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1978719986.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 T0327 can't currently be optimized by undertaker
# naming current conformation FAMSD_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_43812754.pdb -s /var/tmp/to_scwrl_43812754.seq -o /var/tmp/from_scwrl_43812754.pdb > /var/tmp/scwrl_43812754.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_43812754.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 T0327 can't currently be optimized by undertaker
# naming current conformation FAMSD_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1437848139.pdb -s /var/tmp/to_scwrl_1437848139.seq -o /var/tmp/from_scwrl_1437848139.pdb > /var/tmp/scwrl_1437848139.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1437848139.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 T0327 can't currently be optimized by undertaker
# naming current conformation FAMSD_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1200145685.pdb -s /var/tmp/to_scwrl_1200145685.seq -o /var/tmp/from_scwrl_1200145685.pdb > /var/tmp/scwrl_1200145685.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1200145685.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 98
# copying to AlignedFragments data structure
# naming current conformation FAMS_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_2114278295.pdb -s /var/tmp/to_scwrl_2114278295.seq -o /var/tmp/from_scwrl_2114278295.pdb > /var/tmp/scwrl_2114278295.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2114278295.pdb
# conformation set from SCWRL output
# naming current conformation FAMS_TS1-scwrl
# ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1
# Found a chain break before 89
# copying to AlignedFragments data structure
# naming current conformation FAMS_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_492469686.pdb -s /var/tmp/to_scwrl_492469686.seq -o /var/tmp/from_scwrl_492469686.pdb > /var/tmp/scwrl_492469686.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_492469686.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 90
# copying to AlignedFragments data structure
# naming current conformation FAMS_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1173408027.pdb -s /var/tmp/to_scwrl_1173408027.seq -o /var/tmp/from_scwrl_1173408027.pdb > /var/tmp/scwrl_1173408027.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1173408027.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 T0327 can't currently be optimized by undertaker
# naming current conformation FAMS_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1129612102.pdb -s /var/tmp/to_scwrl_1129612102.seq -o /var/tmp/from_scwrl_1129612102.pdb > /var/tmp/scwrl_1129612102.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1129612102.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 T0327 can't currently be optimized by undertaker
# naming current conformation FAMS_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1427104008.pdb -s /var/tmp/to_scwrl_1427104008.seq -o /var/tmp/from_scwrl_1427104008.pdb > /var/tmp/scwrl_1427104008.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1427104008.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 58
# copying to AlignedFragments data structure
# naming current conformation FOLDpro_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1461587218.pdb -s /var/tmp/to_scwrl_1461587218.seq -o /var/tmp/from_scwrl_1461587218.pdb > /var/tmp/scwrl_1461587218.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1461587218.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 63
# copying to AlignedFragments data structure
# naming current conformation FOLDpro_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_713202133.pdb -s /var/tmp/to_scwrl_713202133.seq -o /var/tmp/from_scwrl_713202133.pdb > /var/tmp/scwrl_713202133.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_713202133.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 58
# copying to AlignedFragments data structure
# naming current conformation FOLDpro_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_409066791.pdb -s /var/tmp/to_scwrl_409066791.seq -o /var/tmp/from_scwrl_409066791.pdb > /var/tmp/scwrl_409066791.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_409066791.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 62
# copying to AlignedFragments data structure
# naming current conformation FOLDpro_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1094244821.pdb -s /var/tmp/to_scwrl_1094244821.seq -o /var/tmp/from_scwrl_1094244821.pdb > /var/tmp/scwrl_1094244821.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1094244821.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 61
# copying to AlignedFragments data structure
# naming current conformation FOLDpro_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1418257704.pdb -s /var/tmp/to_scwrl_1418257704.seq -o /var/tmp/from_scwrl_1418257704.pdb > /var/tmp/scwrl_1418257704.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1418257704.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 T0327 can't currently be optimized by undertaker
# naming current conformation FORTE1_AL1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1464275041.pdb -s /var/tmp/to_scwrl_1464275041.seq -o /var/tmp/from_scwrl_1464275041.pdb > /var/tmp/scwrl_1464275041.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1464275041.pdb
# conformation set from SCWRL output
# naming current conformation FORTE1_AL1-scwrl
# ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation FORTE1_AL2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1669953659.pdb -s /var/tmp/to_scwrl_1669953659.seq -o /var/tmp/from_scwrl_1669953659.pdb > /var/tmp/scwrl_1669953659.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1669953659.pdb
# conformation set from SCWRL output
# naming current conformation FORTE1_AL2-scwrl
# ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1
Skipped atom 265, because occupancy 1.0000000e+00 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation FORTE1_AL3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_204436323.pdb -s /var/tmp/to_scwrl_204436323.seq -o /var/tmp/from_scwrl_204436323.pdb > /var/tmp/scwrl_204436323.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_204436323.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 T0327 can't currently be optimized by undertaker
# naming current conformation FORTE1_AL4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1040047004.pdb -s /var/tmp/to_scwrl_1040047004.seq -o /var/tmp/from_scwrl_1040047004.pdb > /var/tmp/scwrl_1040047004.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1040047004.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 T0327 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FORTE1_AL5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1067849616.pdb -s /var/tmp/to_scwrl_1067849616.seq -o /var/tmp/from_scwrl_1067849616.pdb > /var/tmp/scwrl_1067849616.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1067849616.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 T0327 can't currently be optimized by undertaker
# naming current conformation FORTE2_AL1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1302863959.pdb -s /var/tmp/to_scwrl_1302863959.seq -o /var/tmp/from_scwrl_1302863959.pdb > /var/tmp/scwrl_1302863959.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1302863959.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
Skipped atom 265, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation FORTE2_AL2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1955200192.pdb -s /var/tmp/to_scwrl_1955200192.seq -o /var/tmp/from_scwrl_1955200192.pdb > /var/tmp/scwrl_1955200192.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1955200192.pdb
# conformation set from SCWRL output
# naming current conformation FORTE2_AL2-scwrl
# ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation FORTE2_AL3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_220722614.pdb -s /var/tmp/to_scwrl_220722614.seq -o /var/tmp/from_scwrl_220722614.pdb > /var/tmp/scwrl_220722614.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_220722614.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 T0327 can't currently be optimized by undertaker
# naming current conformation FORTE2_AL4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_630776272.pdb -s /var/tmp/to_scwrl_630776272.seq -o /var/tmp/from_scwrl_630776272.pdb > /var/tmp/scwrl_630776272.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_630776272.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 T0327 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FORTE2_AL5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1227808388.pdb -s /var/tmp/to_scwrl_1227808388.seq -o /var/tmp/from_scwrl_1227808388.pdb > /var/tmp/scwrl_1227808388.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1227808388.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 99
# copying to AlignedFragments data structure
# naming current conformation FPSOLVER-SERVER_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1225505155.pdb -s /var/tmp/to_scwrl_1225505155.seq -o /var/tmp/from_scwrl_1225505155.pdb > /var/tmp/scwrl_1225505155.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1225505155.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 101
# copying to AlignedFragments data structure
# naming current conformation FPSOLVER-SERVER_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_522848295.pdb -s /var/tmp/to_scwrl_522848295.seq -o /var/tmp/from_scwrl_522848295.pdb > /var/tmp/scwrl_522848295.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_522848295.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 101
# copying to AlignedFragments data structure
# naming current conformation FPSOLVER-SERVER_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1224867189.pdb -s /var/tmp/to_scwrl_1224867189.seq -o /var/tmp/from_scwrl_1224867189.pdb > /var/tmp/scwrl_1224867189.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1224867189.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 75
# copying to AlignedFragments data structure
# naming current conformation FPSOLVER-SERVER_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1599384153.pdb -s /var/tmp/to_scwrl_1599384153.seq -o /var/tmp/from_scwrl_1599384153.pdb > /var/tmp/scwrl_1599384153.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1599384153.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 96
# copying to AlignedFragments data structure
# naming current conformation FPSOLVER-SERVER_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_847846551.pdb -s /var/tmp/to_scwrl_847846551.seq -o /var/tmp/from_scwrl_847846551.pdb > /var/tmp/scwrl_847846551.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_847846551.pdb
# conformation set from SCWRL output
# naming current conformation FPSOLVER-SERVER_TS5-scwrl
# ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1
# Found a chain break before 68
# copying to AlignedFragments data structure
# naming current conformation FUGMOD_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1468017159.pdb -s /var/tmp/to_scwrl_1468017159.seq -o /var/tmp/from_scwrl_1468017159.pdb > /var/tmp/scwrl_1468017159.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1468017159.pdb
# conformation set from SCWRL output
# naming current conformation FUGMOD_TS1-scwrl
# ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1
# Found a chain break before 78
# copying to AlignedFragments data structure
# naming current conformation FUGMOD_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1310068322.pdb -s /var/tmp/to_scwrl_1310068322.seq -o /var/tmp/from_scwrl_1310068322.pdb > /var/tmp/scwrl_1310068322.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1310068322.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 T0327 can't currently be optimized by undertaker
# naming current conformation FUGMOD_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_679082890.pdb -s /var/tmp/to_scwrl_679082890.seq -o /var/tmp/from_scwrl_679082890.pdb > /var/tmp/scwrl_679082890.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_679082890.pdb
# conformation set from SCWRL output
# naming current conformation FUGMOD_TS3-scwrl
# ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1
# Found a chain break before 95
# copying to AlignedFragments data structure
# naming current conformation FUGMOD_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1511829913.pdb -s /var/tmp/to_scwrl_1511829913.seq -o /var/tmp/from_scwrl_1511829913.pdb > /var/tmp/scwrl_1511829913.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1511829913.pdb
# conformation set from SCWRL output
# naming current conformation FUGMOD_TS4-scwrl
# ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1
# Found a chain break before 69
# copying to AlignedFragments data structure
# naming current conformation FUGMOD_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_600432815.pdb -s /var/tmp/to_scwrl_600432815.seq -o /var/tmp/from_scwrl_600432815.pdb > /var/tmp/scwrl_600432815.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_600432815.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 T0327 can't currently be optimized by undertaker
# naming current conformation FUGUE_AL1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1879228575.pdb -s /var/tmp/to_scwrl_1879228575.seq -o /var/tmp/from_scwrl_1879228575.pdb > /var/tmp/scwrl_1879228575.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1879228575.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 T0327 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FUGUE_AL2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1478624561.pdb -s /var/tmp/to_scwrl_1478624561.seq -o /var/tmp/from_scwrl_1478624561.pdb > /var/tmp/scwrl_1478624561.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1478624561.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 T0327 can't currently be optimized by undertaker
# naming current conformation FUGUE_AL3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1092902500.pdb -s /var/tmp/to_scwrl_1092902500.seq -o /var/tmp/from_scwrl_1092902500.pdb > /var/tmp/scwrl_1092902500.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1092902500.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 T0327 can't currently be optimized by undertaker
# naming current conformation FUGUE_AL4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_905152957.pdb -s /var/tmp/to_scwrl_905152957.seq -o /var/tmp/from_scwrl_905152957.pdb > /var/tmp/scwrl_905152957.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_905152957.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
Skipped atom 323, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL5.pdb.gz
Skipped atom 325, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL5.pdb.gz
Skipped atom 327, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL5.pdb.gz
Skipped atom 329, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL5.pdb.gz
Skipped atom 331, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL5.pdb.gz
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FUGUE_AL5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_460753017.pdb -s /var/tmp/to_scwrl_460753017.seq -o /var/tmp/from_scwrl_460753017.pdb > /var/tmp/scwrl_460753017.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_460753017.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 99
# copying to AlignedFragments data structure
# naming current conformation FUNCTION_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_372522863.pdb -s /var/tmp/to_scwrl_372522863.seq -o /var/tmp/from_scwrl_372522863.pdb > /var/tmp/scwrl_372522863.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_372522863.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 99
# copying to AlignedFragments data structure
# naming current conformation FUNCTION_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_219256528.pdb -s /var/tmp/to_scwrl_219256528.seq -o /var/tmp/from_scwrl_219256528.pdb > /var/tmp/scwrl_219256528.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_219256528.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 97
# copying to AlignedFragments data structure
# naming current conformation FUNCTION_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1173955150.pdb -s /var/tmp/to_scwrl_1173955150.seq -o /var/tmp/from_scwrl_1173955150.pdb > /var/tmp/scwrl_1173955150.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1173955150.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 98
# copying to AlignedFragments data structure
# naming current conformation FUNCTION_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_781589654.pdb -s /var/tmp/to_scwrl_781589654.seq -o /var/tmp/from_scwrl_781589654.pdb > /var/tmp/scwrl_781589654.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_781589654.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 98
# copying to AlignedFragments data structure
# naming current conformation FUNCTION_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1313501349.pdb -s /var/tmp/to_scwrl_1313501349.seq -o /var/tmp/from_scwrl_1313501349.pdb > /var/tmp/scwrl_1313501349.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1313501349.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
# naming current conformation GeneSilicoMetaServer_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_444729208.pdb -s /var/tmp/to_scwrl_444729208.seq -o /var/tmp/from_scwrl_444729208.pdb > /var/tmp/scwrl_444729208.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_444729208.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 78
# copying to AlignedFragments data structure
# naming current conformation GeneSilicoMetaServer_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_98381048.pdb -s /var/tmp/to_scwrl_98381048.seq -o /var/tmp/from_scwrl_98381048.pdb > /var/tmp/scwrl_98381048.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_98381048.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
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation GeneSilicoMetaServer_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_835971362.pdb -s /var/tmp/to_scwrl_835971362.seq -o /var/tmp/from_scwrl_835971362.pdb > /var/tmp/scwrl_835971362.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_835971362.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
# Found a chain break before 62
# copying to AlignedFragments data structure
# naming current conformation GeneSilicoMetaServer_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_649165531.pdb -s /var/tmp/to_scwrl_649165531.seq -o /var/tmp/from_scwrl_649165531.pdb > /var/tmp/scwrl_649165531.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_649165531.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 64
# copying to AlignedFragments data structure
# naming current conformation GeneSilicoMetaServer_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1138428052.pdb -s /var/tmp/to_scwrl_1138428052.seq -o /var/tmp/from_scwrl_1138428052.pdb > /var/tmp/scwrl_1138428052.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1138428052.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 47
# copying to AlignedFragments data structure
# naming current conformation HHpred1_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1903820978.pdb -s /var/tmp/to_scwrl_1903820978.seq -o /var/tmp/from_scwrl_1903820978.pdb > /var/tmp/scwrl_1903820978.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1903820978.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 55
# copying to AlignedFragments data structure
# naming current conformation HHpred2_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1952029491.pdb -s /var/tmp/to_scwrl_1952029491.seq -o /var/tmp/from_scwrl_1952029491.pdb > /var/tmp/scwrl_1952029491.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1952029491.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 55
# copying to AlignedFragments data structure
# naming current conformation HHpred3_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_946144598.pdb -s /var/tmp/to_scwrl_946144598.seq -o /var/tmp/from_scwrl_946144598.pdb > /var/tmp/scwrl_946144598.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_946144598.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 T0327 can't currently be optimized by undertaker
# naming current conformation Huber-Torda-Server_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_2124543592.pdb -s /var/tmp/to_scwrl_2124543592.seq -o /var/tmp/from_scwrl_2124543592.pdb > /var/tmp/scwrl_2124543592.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2124543592.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 T0327 can't currently be optimized by undertaker
# naming current conformation Huber-Torda-Server_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_435322116.pdb -s /var/tmp/to_scwrl_435322116.seq -o /var/tmp/from_scwrl_435322116.pdb > /var/tmp/scwrl_435322116.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_435322116.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 T0327 can't currently be optimized by undertaker
# naming current conformation Huber-Torda-Server_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_26469340.pdb -s /var/tmp/to_scwrl_26469340.seq -o /var/tmp/from_scwrl_26469340.pdb > /var/tmp/scwrl_26469340.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_26469340.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 T0327 can't currently be optimized by undertaker
# naming current conformation Huber-Torda-Server_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1202565100.pdb -s /var/tmp/to_scwrl_1202565100.seq -o /var/tmp/from_scwrl_1202565100.pdb > /var/tmp/scwrl_1202565100.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1202565100.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 T0327 can't currently be optimized by undertaker
# naming current conformation Huber-Torda-Server_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_958170411.pdb -s /var/tmp/to_scwrl_958170411.seq -o /var/tmp/from_scwrl_958170411.pdb > /var/tmp/scwrl_958170411.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_958170411.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 T0327 can't currently be optimized by undertaker
# naming current conformation LOOPP_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1251336529.pdb -s /var/tmp/to_scwrl_1251336529.seq -o /var/tmp/from_scwrl_1251336529.pdb > /var/tmp/scwrl_1251336529.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1251336529.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 T0327 can't currently be optimized by undertaker
# naming current conformation LOOPP_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_654465607.pdb -s /var/tmp/to_scwrl_654465607.seq -o /var/tmp/from_scwrl_654465607.pdb > /var/tmp/scwrl_654465607.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_654465607.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 T0327 can't currently be optimized by undertaker
# naming current conformation LOOPP_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1806016961.pdb -s /var/tmp/to_scwrl_1806016961.seq -o /var/tmp/from_scwrl_1806016961.pdb > /var/tmp/scwrl_1806016961.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1806016961.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 T0327 can't currently be optimized by undertaker
# naming current conformation LOOPP_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_571870042.pdb -s /var/tmp/to_scwrl_571870042.seq -o /var/tmp/from_scwrl_571870042.pdb > /var/tmp/scwrl_571870042.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_571870042.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 T0327 can't currently be optimized by undertaker
# naming current conformation LOOPP_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1964533930.pdb -s /var/tmp/to_scwrl_1964533930.seq -o /var/tmp/from_scwrl_1964533930.pdb > /var/tmp/scwrl_1964533930.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1964533930.pdb
# conformation set from SCWRL output
# naming current conformation LOOPP_TS5-scwrl
# ReadConformPDB reading from PDB file servers/MIG_FROST_AL1.pdb.gz looking for model 1
Error: Reading chain from PDB file servers/MIG_FROST_AL1.pdb.gz failed.
# naming current conformation MIG_FROST_AL1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_337616205.pdb -s /var/tmp/to_scwrl_337616205.seq -o /var/tmp/from_scwrl_337616205.pdb > /var/tmp/scwrl_337616205.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_337616205.pdb
# conformation set from SCWRL output
# naming current conformation MIG_FROST_AL1-scwrl
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS1.pdb.gz looking for model 1
# Found a chain break before 92
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server2_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_2083699955.pdb -s /var/tmp/to_scwrl_2083699955.seq -o /var/tmp/from_scwrl_2083699955.pdb > /var/tmp/scwrl_2083699955.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2083699955.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 64
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server2_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_417483098.pdb -s /var/tmp/to_scwrl_417483098.seq -o /var/tmp/from_scwrl_417483098.pdb > /var/tmp/scwrl_417483098.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_417483098.pdb
# conformation set from SCWRL output
# naming current conformation Ma-OPUS-server2_TS2-scwrl
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS3.pdb.gz looking for model 1
# Found a chain break before 92
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server2_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_69361133.pdb -s /var/tmp/to_scwrl_69361133.seq -o /var/tmp/from_scwrl_69361133.pdb > /var/tmp/scwrl_69361133.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_69361133.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 47
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server2_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1414840869.pdb -s /var/tmp/to_scwrl_1414840869.seq -o /var/tmp/from_scwrl_1414840869.pdb > /var/tmp/scwrl_1414840869.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1414840869.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 89
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server2_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1510385599.pdb -s /var/tmp/to_scwrl_1510385599.seq -o /var/tmp/from_scwrl_1510385599.pdb > /var/tmp/scwrl_1510385599.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1510385599.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 88
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_974514090.pdb -s /var/tmp/to_scwrl_974514090.seq -o /var/tmp/from_scwrl_974514090.pdb > /var/tmp/scwrl_974514090.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_974514090.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 63
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1875593887.pdb -s /var/tmp/to_scwrl_1875593887.seq -o /var/tmp/from_scwrl_1875593887.pdb > /var/tmp/scwrl_1875593887.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1875593887.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 92
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1882908462.pdb -s /var/tmp/to_scwrl_1882908462.seq -o /var/tmp/from_scwrl_1882908462.pdb > /var/tmp/scwrl_1882908462.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1882908462.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 48
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1193770617.pdb -s /var/tmp/to_scwrl_1193770617.seq -o /var/tmp/from_scwrl_1193770617.pdb > /var/tmp/scwrl_1193770617.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1193770617.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 89
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_902065391.pdb -s /var/tmp/to_scwrl_902065391.seq -o /var/tmp/from_scwrl_902065391.pdb > /var/tmp/scwrl_902065391.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_902065391.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 97
# copying to AlignedFragments data structure
# naming current conformation MetaTasser_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_517014469.pdb -s /var/tmp/to_scwrl_517014469.seq -o /var/tmp/from_scwrl_517014469.pdb > /var/tmp/scwrl_517014469.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_517014469.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 99
# copying to AlignedFragments data structure
# naming current conformation MetaTasser_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_359788321.pdb -s /var/tmp/to_scwrl_359788321.seq -o /var/tmp/from_scwrl_359788321.pdb > /var/tmp/scwrl_359788321.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_359788321.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 101
# copying to AlignedFragments data structure
# naming current conformation MetaTasser_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1346794598.pdb -s /var/tmp/to_scwrl_1346794598.seq -o /var/tmp/from_scwrl_1346794598.pdb > /var/tmp/scwrl_1346794598.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1346794598.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 101
# copying to AlignedFragments data structure
# naming current conformation MetaTasser_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_615395517.pdb -s /var/tmp/to_scwrl_615395517.seq -o /var/tmp/from_scwrl_615395517.pdb > /var/tmp/scwrl_615395517.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_615395517.pdb
# conformation set from SCWRL output
# naming current conformation MetaTasser_TS4-scwrl
# ReadConformPDB reading from PDB file servers/MetaTasser_TS5.pdb.gz looking for model 1
# Found a chain break before 98
# copying to AlignedFragments data structure
# naming current conformation MetaTasser_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1195759682.pdb -s /var/tmp/to_scwrl_1195759682.seq -o /var/tmp/from_scwrl_1195759682.pdb > /var/tmp/scwrl_1195759682.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1195759682.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 77
# copying to AlignedFragments data structure
# naming current conformation NN_PUT_lab_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1995960129.pdb -s /var/tmp/to_scwrl_1995960129.seq -o /var/tmp/from_scwrl_1995960129.pdb > /var/tmp/scwrl_1995960129.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1995960129.pdb
# conformation set from SCWRL output
# naming current conformation NN_PUT_lab_TS1-scwrl
# ReadConformPDB reading from PDB file servers/POMYSL_TS1.pdb.gz looking for model 1
# Found a chain break before 83
# copying to AlignedFragments data structure
# naming current conformation POMYSL_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1753823569.pdb -s /var/tmp/to_scwrl_1753823569.seq -o /var/tmp/from_scwrl_1753823569.pdb > /var/tmp/scwrl_1753823569.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1753823569.pdb
# conformation set from SCWRL output
# naming current conformation POMYSL_TS1-scwrl
# ReadConformPDB reading from PDB file servers/POMYSL_TS2.pdb.gz looking for model 1
# Found a chain break before 101
# copying to AlignedFragments data structure
# naming current conformation POMYSL_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_952097014.pdb -s /var/tmp/to_scwrl_952097014.seq -o /var/tmp/from_scwrl_952097014.pdb > /var/tmp/scwrl_952097014.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_952097014.pdb
# conformation set from SCWRL output
# naming current conformation POMYSL_TS2-scwrl
# ReadConformPDB reading from PDB file servers/POMYSL_TS3.pdb.gz looking for model 1
# Found a chain break before 98
# copying to AlignedFragments data structure
# naming current conformation POMYSL_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1800505973.pdb -s /var/tmp/to_scwrl_1800505973.seq -o /var/tmp/from_scwrl_1800505973.pdb > /var/tmp/scwrl_1800505973.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1800505973.pdb
# conformation set from SCWRL output
# naming current conformation POMYSL_TS3-scwrl
# ReadConformPDB reading from PDB file servers/POMYSL_TS4.pdb.gz looking for model 1
# Found a chain break before 97
# copying to AlignedFragments data structure
# naming current conformation POMYSL_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_552484521.pdb -s /var/tmp/to_scwrl_552484521.seq -o /var/tmp/from_scwrl_552484521.pdb > /var/tmp/scwrl_552484521.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_552484521.pdb
# conformation set from SCWRL output
# naming current conformation POMYSL_TS4-scwrl
# ReadConformPDB reading from PDB file servers/POMYSL_TS5.pdb.gz looking for model 1
# Found a chain break before 100
# copying to AlignedFragments data structure
# naming current conformation POMYSL_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_929156960.pdb -s /var/tmp/to_scwrl_929156960.seq -o /var/tmp/from_scwrl_929156960.pdb > /var/tmp/scwrl_929156960.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_929156960.pdb
# conformation set from SCWRL output
# naming current conformation POMYSL_TS5-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 92 ; scwrl3 -i /var/tmp/to_scwrl_88344442.pdb -s /var/tmp/to_scwrl_88344442.seq -o /var/tmp/from_scwrl_88344442.pdb > /var/tmp/scwrl_88344442.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_88344442.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 92 ; scwrl3 -i /var/tmp/to_scwrl_578953861.pdb -s /var/tmp/to_scwrl_578953861.seq -o /var/tmp/from_scwrl_578953861.pdb > /var/tmp/scwrl_578953861.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_578953861.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 92 ; scwrl3 -i /var/tmp/to_scwrl_2131722060.pdb -s /var/tmp/to_scwrl_2131722060.seq -o /var/tmp/from_scwrl_2131722060.pdb > /var/tmp/scwrl_2131722060.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2131722060.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 92 ; scwrl3 -i /var/tmp/to_scwrl_1046514854.pdb -s /var/tmp/to_scwrl_1046514854.seq -o /var/tmp/from_scwrl_1046514854.pdb > /var/tmp/scwrl_1046514854.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1046514854.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 92 ; scwrl3 -i /var/tmp/to_scwrl_1830290390.pdb -s /var/tmp/to_scwrl_1830290390.seq -o /var/tmp/from_scwrl_1830290390.pdb > /var/tmp/scwrl_1830290390.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1830290390.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 65
# copying to AlignedFragments data structure
# naming current conformation PROTINFO_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_638704021.pdb -s /var/tmp/to_scwrl_638704021.seq -o /var/tmp/from_scwrl_638704021.pdb > /var/tmp/scwrl_638704021.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_638704021.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 65
# copying to AlignedFragments data structure
# naming current conformation PROTINFO_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_705048168.pdb -s /var/tmp/to_scwrl_705048168.seq -o /var/tmp/from_scwrl_705048168.pdb > /var/tmp/scwrl_705048168.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_705048168.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 65
# copying to AlignedFragments data structure
# naming current conformation PROTINFO_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_254676785.pdb -s /var/tmp/to_scwrl_254676785.seq -o /var/tmp/from_scwrl_254676785.pdb > /var/tmp/scwrl_254676785.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_254676785.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 64
# copying to AlignedFragments data structure
# naming current conformation PROTINFO_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_455754304.pdb -s /var/tmp/to_scwrl_455754304.seq -o /var/tmp/from_scwrl_455754304.pdb > /var/tmp/scwrl_455754304.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_455754304.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 81
# copying to AlignedFragments data structure
# naming current conformation PROTINFO_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1042664373.pdb -s /var/tmp/to_scwrl_1042664373.seq -o /var/tmp/from_scwrl_1042664373.pdb > /var/tmp/scwrl_1042664373.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1042664373.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 T0327 can't currently be optimized by undertaker
# naming current conformation Pcons6_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_190893093.pdb -s /var/tmp/to_scwrl_190893093.seq -o /var/tmp/from_scwrl_190893093.pdb > /var/tmp/scwrl_190893093.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_190893093.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 T0327 can't currently be optimized by undertaker
# naming current conformation Pcons6_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_873237402.pdb -s /var/tmp/to_scwrl_873237402.seq -o /var/tmp/from_scwrl_873237402.pdb > /var/tmp/scwrl_873237402.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_873237402.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 T0327 can't currently be optimized by undertaker
# naming current conformation Pcons6_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1112025506.pdb -s /var/tmp/to_scwrl_1112025506.seq -o /var/tmp/from_scwrl_1112025506.pdb > /var/tmp/scwrl_1112025506.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1112025506.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 T0327 can't currently be optimized by undertaker
# naming current conformation Pcons6_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1605733962.pdb -s /var/tmp/to_scwrl_1605733962.seq -o /var/tmp/from_scwrl_1605733962.pdb > /var/tmp/scwrl_1605733962.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1605733962.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 T0327 can't currently be optimized by undertaker
# naming current conformation Pcons6_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_236139354.pdb -s /var/tmp/to_scwrl_236139354.seq -o /var/tmp/from_scwrl_236139354.pdb > /var/tmp/scwrl_236139354.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_236139354.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 T0327 can't currently be optimized by undertaker
# naming current conformation Phyre-1_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_2086539596.pdb -s /var/tmp/to_scwrl_2086539596.seq -o /var/tmp/from_scwrl_2086539596.pdb > /var/tmp/scwrl_2086539596.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2086539596.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
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation Phyre-2_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1333844202.pdb -s /var/tmp/to_scwrl_1333844202.seq -o /var/tmp/from_scwrl_1333844202.pdb > /var/tmp/scwrl_1333844202.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1333844202.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
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation Phyre-2_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_2119047816.pdb -s /var/tmp/to_scwrl_2119047816.seq -o /var/tmp/from_scwrl_2119047816.pdb > /var/tmp/scwrl_2119047816.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2119047816.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
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation Phyre-2_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1132826567.pdb -s /var/tmp/to_scwrl_1132826567.seq -o /var/tmp/from_scwrl_1132826567.pdb > /var/tmp/scwrl_1132826567.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1132826567.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
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation Phyre-2_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_88425946.pdb -s /var/tmp/to_scwrl_88425946.seq -o /var/tmp/from_scwrl_88425946.pdb > /var/tmp/scwrl_88425946.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_88425946.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
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation Phyre-2_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_488578638.pdb -s /var/tmp/to_scwrl_488578638.seq -o /var/tmp/from_scwrl_488578638.pdb > /var/tmp/scwrl_488578638.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_488578638.pdb
# conformation set from SCWRL output
# naming current conformation Phyre-2_TS5-scwrl
# ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation Pmodeller6_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1492614888.pdb -s /var/tmp/to_scwrl_1492614888.seq -o /var/tmp/from_scwrl_1492614888.pdb > /var/tmp/scwrl_1492614888.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1492614888.pdb
# conformation set from SCWRL output
# naming current conformation Pmodeller6_TS1-scwrl
# ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1
# Found a chain break before 77
# copying to AlignedFragments data structure
# naming current conformation Pmodeller6_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1435220544.pdb -s /var/tmp/to_scwrl_1435220544.seq -o /var/tmp/from_scwrl_1435220544.pdb > /var/tmp/scwrl_1435220544.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1435220544.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 59
# copying to AlignedFragments data structure
# naming current conformation Pmodeller6_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1103974155.pdb -s /var/tmp/to_scwrl_1103974155.seq -o /var/tmp/from_scwrl_1103974155.pdb > /var/tmp/scwrl_1103974155.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1103974155.pdb
# conformation set from SCWRL output
# naming current conformation Pmodeller6_TS3-scwrl
# ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation Pmodeller6_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_540890924.pdb -s /var/tmp/to_scwrl_540890924.seq -o /var/tmp/from_scwrl_540890924.pdb > /var/tmp/scwrl_540890924.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_540890924.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 51
# copying to AlignedFragments data structure
# naming current conformation Pmodeller6_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1283697027.pdb -s /var/tmp/to_scwrl_1283697027.seq -o /var/tmp/from_scwrl_1283697027.pdb > /var/tmp/scwrl_1283697027.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1283697027.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 79
# copying to AlignedFragments data structure
# naming current conformation RAPTOR-ACE_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_710314078.pdb -s /var/tmp/to_scwrl_710314078.seq -o /var/tmp/from_scwrl_710314078.pdb > /var/tmp/scwrl_710314078.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_710314078.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
# naming current conformation RAPTOR-ACE_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1492987938.pdb -s /var/tmp/to_scwrl_1492987938.seq -o /var/tmp/from_scwrl_1492987938.pdb > /var/tmp/scwrl_1492987938.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1492987938.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 77
# copying to AlignedFragments data structure
# naming current conformation RAPTOR-ACE_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_936719354.pdb -s /var/tmp/to_scwrl_936719354.seq -o /var/tmp/from_scwrl_936719354.pdb > /var/tmp/scwrl_936719354.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_936719354.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 18
# copying to AlignedFragments data structure
# naming current conformation RAPTOR-ACE_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1262798598.pdb -s /var/tmp/to_scwrl_1262798598.seq -o /var/tmp/from_scwrl_1262798598.pdb > /var/tmp/scwrl_1262798598.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1262798598.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 65
# copying to AlignedFragments data structure
# naming current conformation RAPTOR-ACE_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_274661251.pdb -s /var/tmp/to_scwrl_274661251.seq -o /var/tmp/from_scwrl_274661251.pdb > /var/tmp/scwrl_274661251.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_274661251.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 99
# copying to AlignedFragments data structure
# naming current conformation RAPTORESS_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1025063797.pdb -s /var/tmp/to_scwrl_1025063797.seq -o /var/tmp/from_scwrl_1025063797.pdb > /var/tmp/scwrl_1025063797.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1025063797.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 62
# copying to AlignedFragments data structure
# naming current conformation RAPTORESS_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1841752459.pdb -s /var/tmp/to_scwrl_1841752459.seq -o /var/tmp/from_scwrl_1841752459.pdb > /var/tmp/scwrl_1841752459.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1841752459.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 31
# copying to AlignedFragments data structure
# naming current conformation RAPTORESS_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_258899664.pdb -s /var/tmp/to_scwrl_258899664.seq -o /var/tmp/from_scwrl_258899664.pdb > /var/tmp/scwrl_258899664.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_258899664.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 101
# copying to AlignedFragments data structure
# naming current conformation RAPTORESS_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_2071578650.pdb -s /var/tmp/to_scwrl_2071578650.seq -o /var/tmp/from_scwrl_2071578650.pdb > /var/tmp/scwrl_2071578650.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2071578650.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 101
# copying to AlignedFragments data structure
# naming current conformation RAPTORESS_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1524559202.pdb -s /var/tmp/to_scwrl_1524559202.seq -o /var/tmp/from_scwrl_1524559202.pdb > /var/tmp/scwrl_1524559202.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1524559202.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 88
# copying to AlignedFragments data structure
# naming current conformation RAPTOR_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_897603685.pdb -s /var/tmp/to_scwrl_897603685.seq -o /var/tmp/from_scwrl_897603685.pdb > /var/tmp/scwrl_897603685.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_897603685.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 82
# copying to AlignedFragments data structure
# naming current conformation RAPTOR_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_629143171.pdb -s /var/tmp/to_scwrl_629143171.seq -o /var/tmp/from_scwrl_629143171.pdb > /var/tmp/scwrl_629143171.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_629143171.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 96
# copying to AlignedFragments data structure
# naming current conformation RAPTOR_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1779235987.pdb -s /var/tmp/to_scwrl_1779235987.seq -o /var/tmp/from_scwrl_1779235987.pdb > /var/tmp/scwrl_1779235987.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1779235987.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 65
# copying to AlignedFragments data structure
# naming current conformation RAPTOR_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1353357988.pdb -s /var/tmp/to_scwrl_1353357988.seq -o /var/tmp/from_scwrl_1353357988.pdb > /var/tmp/scwrl_1353357988.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1353357988.pdb
# conformation set from SCWRL output
# naming current conformation RAPTOR_TS4-scwrl
# ReadConformPDB reading from PDB file servers/RAPTOR_TS5.pdb.gz looking for model 1
# Found a chain break before 77
# copying to AlignedFragments data structure
# naming current conformation RAPTOR_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1671807544.pdb -s /var/tmp/to_scwrl_1671807544.seq -o /var/tmp/from_scwrl_1671807544.pdb > /var/tmp/scwrl_1671807544.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1671807544.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 59
# copying to AlignedFragments data structure
# naming current conformation ROBETTA_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1970129080.pdb -s /var/tmp/to_scwrl_1970129080.seq -o /var/tmp/from_scwrl_1970129080.pdb > /var/tmp/scwrl_1970129080.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1970129080.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 59
# copying to AlignedFragments data structure
# naming current conformation ROBETTA_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_79111744.pdb -s /var/tmp/to_scwrl_79111744.seq -o /var/tmp/from_scwrl_79111744.pdb > /var/tmp/scwrl_79111744.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_79111744.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 75
# copying to AlignedFragments data structure
# naming current conformation ROBETTA_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_636349404.pdb -s /var/tmp/to_scwrl_636349404.seq -o /var/tmp/from_scwrl_636349404.pdb > /var/tmp/scwrl_636349404.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_636349404.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 51
# copying to AlignedFragments data structure
# naming current conformation ROBETTA_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1428379396.pdb -s /var/tmp/to_scwrl_1428379396.seq -o /var/tmp/from_scwrl_1428379396.pdb > /var/tmp/scwrl_1428379396.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1428379396.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 77
# copying to AlignedFragments data structure
# naming current conformation ROBETTA_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_315251098.pdb -s /var/tmp/to_scwrl_315251098.seq -o /var/tmp/from_scwrl_315251098.pdb > /var/tmp/scwrl_315251098.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_315251098.pdb
# conformation set from SCWRL output
# naming current conformation ROBETTA_TS5-scwrl
# ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation ROKKY_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_575405353.pdb -s /var/tmp/to_scwrl_575405353.seq -o /var/tmp/from_scwrl_575405353.pdb > /var/tmp/scwrl_575405353.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_575405353.pdb
# conformation set from SCWRL output
# naming current conformation ROKKY_TS1-scwrl
# ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation ROKKY_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_614739952.pdb -s /var/tmp/to_scwrl_614739952.seq -o /var/tmp/from_scwrl_614739952.pdb > /var/tmp/scwrl_614739952.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_614739952.pdb
# conformation set from SCWRL output
# naming current conformation ROKKY_TS2-scwrl
# ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation ROKKY_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_286815268.pdb -s /var/tmp/to_scwrl_286815268.seq -o /var/tmp/from_scwrl_286815268.pdb > /var/tmp/scwrl_286815268.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_286815268.pdb
# conformation set from SCWRL output
# naming current conformation ROKKY_TS3-scwrl
# ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation ROKKY_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1708231920.pdb -s /var/tmp/to_scwrl_1708231920.seq -o /var/tmp/from_scwrl_1708231920.pdb > /var/tmp/scwrl_1708231920.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1708231920.pdb
# conformation set from SCWRL output
# naming current conformation ROKKY_TS4-scwrl
# ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation ROKKY_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_703165899.pdb -s /var/tmp/to_scwrl_703165899.seq -o /var/tmp/from_scwrl_703165899.pdb > /var/tmp/scwrl_703165899.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_703165899.pdb
# conformation set from SCWRL output
# naming current conformation ROKKY_TS5-scwrl
# ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation SAM-T02_AL1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_775393906.pdb -s /var/tmp/to_scwrl_775393906.seq -o /var/tmp/from_scwrl_775393906.pdb > /var/tmp/scwrl_775393906.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_775393906.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 T0327 can't currently be optimized by undertaker
# naming current conformation SAM-T02_AL2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1053363162.pdb -s /var/tmp/to_scwrl_1053363162.seq -o /var/tmp/from_scwrl_1053363162.pdb > /var/tmp/scwrl_1053363162.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1053363162.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 118, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz
Skipped atom 120, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz
Skipped atom 122, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz
Skipped atom 124, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz
Skipped atom 198, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz
Skipped atom 200, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz
Skipped atom 202, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz
Skipped atom 204, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation SAM-T02_AL3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_2138386443.pdb -s /var/tmp/to_scwrl_2138386443.seq -o /var/tmp/from_scwrl_2138386443.pdb > /var/tmp/scwrl_2138386443.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2138386443.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 T0327 can't currently be optimized by undertaker
# naming current conformation SAM-T02_AL4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1879368061.pdb -s /var/tmp/to_scwrl_1879368061.seq -o /var/tmp/from_scwrl_1879368061.pdb > /var/tmp/scwrl_1879368061.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1879368061.pdb
# conformation set from SCWRL output
# naming current conformation SAM-T02_AL4-scwrl
# ReadConformPDB reading from PDB file servers/SAM-T02_AL5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation SAM-T02_AL5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1594254086.pdb -s /var/tmp/to_scwrl_1594254086.seq -o /var/tmp/from_scwrl_1594254086.pdb > /var/tmp/scwrl_1594254086.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1594254086.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 T0327 can't currently be optimized by undertaker
# naming current conformation SAM-T99_AL1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1274599823.pdb -s /var/tmp/to_scwrl_1274599823.seq -o /var/tmp/from_scwrl_1274599823.pdb > /var/tmp/scwrl_1274599823.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1274599823.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 T0327 can't currently be optimized by undertaker
# naming current conformation SAM-T99_AL2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_442198493.pdb -s /var/tmp/to_scwrl_442198493.seq -o /var/tmp/from_scwrl_442198493.pdb > /var/tmp/scwrl_442198493.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_442198493.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
Skipped atom 50, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
Skipped atom 52, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
Skipped atom 54, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
Skipped atom 56, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
Skipped atom 70, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
Skipped atom 72, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
Skipped atom 74, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
Skipped atom 76, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
Skipped atom 202, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
Skipped atom 204, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
Skipped atom 206, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
Skipped atom 208, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
Skipped atom 234, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
Skipped atom 236, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
Skipped atom 238, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
Skipped atom 240, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation SAM-T99_AL3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_939758378.pdb -s /var/tmp/to_scwrl_939758378.seq -o /var/tmp/from_scwrl_939758378.pdb > /var/tmp/scwrl_939758378.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_939758378.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 T0327 can't currently be optimized by undertaker
# naming current conformation SAM-T99_AL4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_63835531.pdb -s /var/tmp/to_scwrl_63835531.seq -o /var/tmp/from_scwrl_63835531.pdb > /var/tmp/scwrl_63835531.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_63835531.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 T0327 can't currently be optimized by undertaker
# naming current conformation SAM-T99_AL5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1704997091.pdb -s /var/tmp/to_scwrl_1704997091.seq -o /var/tmp/from_scwrl_1704997091.pdb > /var/tmp/scwrl_1704997091.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1704997091.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 100
# copying to AlignedFragments data structure
# naming current conformation SAM_T06_server_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1214419628.pdb -s /var/tmp/to_scwrl_1214419628.seq -o /var/tmp/from_scwrl_1214419628.pdb > /var/tmp/scwrl_1214419628.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1214419628.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 T0327 can't currently be optimized by undertaker
# naming current conformation SAM_T06_server_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1088899327.pdb -s /var/tmp/to_scwrl_1088899327.seq -o /var/tmp/from_scwrl_1088899327.pdb > /var/tmp/scwrl_1088899327.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1088899327.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 T0327 can't currently be optimized by undertaker
# naming current conformation SAM_T06_server_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1399265904.pdb -s /var/tmp/to_scwrl_1399265904.seq -o /var/tmp/from_scwrl_1399265904.pdb > /var/tmp/scwrl_1399265904.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1399265904.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 T0327 can't currently be optimized by undertaker
# naming current conformation SAM_T06_server_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1473319292.pdb -s /var/tmp/to_scwrl_1473319292.seq -o /var/tmp/from_scwrl_1473319292.pdb > /var/tmp/scwrl_1473319292.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1473319292.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 T0327 can't currently be optimized by undertaker
# naming current conformation SAM_T06_server_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1012994331.pdb -s /var/tmp/to_scwrl_1012994331.seq -o /var/tmp/from_scwrl_1012994331.pdb > /var/tmp/scwrl_1012994331.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1012994331.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 77
# copying to AlignedFragments data structure
# naming current conformation SP3_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_776341460.pdb -s /var/tmp/to_scwrl_776341460.seq -o /var/tmp/from_scwrl_776341460.pdb > /var/tmp/scwrl_776341460.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_776341460.pdb
# conformation set from SCWRL output
# naming current conformation SP3_TS1-scwrl
# ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1
# Found a chain break before 66
# copying to AlignedFragments data structure
# naming current conformation SP3_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_223439331.pdb -s /var/tmp/to_scwrl_223439331.seq -o /var/tmp/from_scwrl_223439331.pdb > /var/tmp/scwrl_223439331.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_223439331.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 93
# copying to AlignedFragments data structure
# naming current conformation SP3_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1642137501.pdb -s /var/tmp/to_scwrl_1642137501.seq -o /var/tmp/from_scwrl_1642137501.pdb > /var/tmp/scwrl_1642137501.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1642137501.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 59
# copying to AlignedFragments data structure
# naming current conformation SP3_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_408093801.pdb -s /var/tmp/to_scwrl_408093801.seq -o /var/tmp/from_scwrl_408093801.pdb > /var/tmp/scwrl_408093801.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_408093801.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 79
# copying to AlignedFragments data structure
# naming current conformation SP3_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1576797319.pdb -s /var/tmp/to_scwrl_1576797319.seq -o /var/tmp/from_scwrl_1576797319.pdb > /var/tmp/scwrl_1576797319.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1576797319.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 58
# copying to AlignedFragments data structure
# naming current conformation SP4_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1166461398.pdb -s /var/tmp/to_scwrl_1166461398.seq -o /var/tmp/from_scwrl_1166461398.pdb > /var/tmp/scwrl_1166461398.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1166461398.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 20
# copying to AlignedFragments data structure
# naming current conformation SP4_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_230739234.pdb -s /var/tmp/to_scwrl_230739234.seq -o /var/tmp/from_scwrl_230739234.pdb > /var/tmp/scwrl_230739234.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_230739234.pdb
# conformation set from SCWRL output
# naming current conformation SP4_TS2-scwrl
# ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1
# Found a chain break before 75
# copying to AlignedFragments data structure
# naming current conformation SP4_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1655909063.pdb -s /var/tmp/to_scwrl_1655909063.seq -o /var/tmp/from_scwrl_1655909063.pdb > /var/tmp/scwrl_1655909063.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1655909063.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 82
# copying to AlignedFragments data structure
# naming current conformation SP4_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1802810802.pdb -s /var/tmp/to_scwrl_1802810802.seq -o /var/tmp/from_scwrl_1802810802.pdb > /var/tmp/scwrl_1802810802.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1802810802.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 88
# copying to AlignedFragments data structure
# naming current conformation SP4_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1659118630.pdb -s /var/tmp/to_scwrl_1659118630.seq -o /var/tmp/from_scwrl_1659118630.pdb > /var/tmp/scwrl_1659118630.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1659118630.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 77
# copying to AlignedFragments data structure
# naming current conformation SPARKS2_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1971160162.pdb -s /var/tmp/to_scwrl_1971160162.seq -o /var/tmp/from_scwrl_1971160162.pdb > /var/tmp/scwrl_1971160162.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1971160162.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 22
# copying to AlignedFragments data structure
# naming current conformation SPARKS2_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_230732509.pdb -s /var/tmp/to_scwrl_230732509.seq -o /var/tmp/from_scwrl_230732509.pdb > /var/tmp/scwrl_230732509.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_230732509.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 94
# copying to AlignedFragments data structure
# naming current conformation SPARKS2_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_126374936.pdb -s /var/tmp/to_scwrl_126374936.seq -o /var/tmp/from_scwrl_126374936.pdb > /var/tmp/scwrl_126374936.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_126374936.pdb
# conformation set from SCWRL output
# naming current conformation SPARKS2_TS3-scwrl
# ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1
# Found a chain break before 99
# copying to AlignedFragments data structure
# naming current conformation SPARKS2_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_110491783.pdb -s /var/tmp/to_scwrl_110491783.seq -o /var/tmp/from_scwrl_110491783.pdb > /var/tmp/scwrl_110491783.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_110491783.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 92
# copying to AlignedFragments data structure
# naming current conformation SPARKS2_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1938964429.pdb -s /var/tmp/to_scwrl_1938964429.seq -o /var/tmp/from_scwrl_1938964429.pdb > /var/tmp/scwrl_1938964429.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1938964429.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 T0327 can't currently be optimized by undertaker
# naming current conformation UNI-EID_bnmx_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_829540835.pdb -s /var/tmp/to_scwrl_829540835.seq -o /var/tmp/from_scwrl_829540835.pdb > /var/tmp/scwrl_829540835.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_829540835.pdb
# conformation set from SCWRL output
# naming current conformation UNI-EID_bnmx_TS1-scwrl
# ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation UNI-EID_bnmx_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_885885689.pdb -s /var/tmp/to_scwrl_885885689.seq -o /var/tmp/from_scwrl_885885689.pdb > /var/tmp/scwrl_885885689.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_885885689.pdb
# conformation set from SCWRL output
# naming current conformation UNI-EID_bnmx_TS2-scwrl
# ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation UNI-EID_bnmx_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_844843945.pdb -s /var/tmp/to_scwrl_844843945.seq -o /var/tmp/from_scwrl_844843945.pdb > /var/tmp/scwrl_844843945.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_844843945.pdb
# conformation set from SCWRL output
# naming current conformation UNI-EID_bnmx_TS3-scwrl
# ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation UNI-EID_bnmx_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_820443631.pdb -s /var/tmp/to_scwrl_820443631.seq -o /var/tmp/from_scwrl_820443631.pdb > /var/tmp/scwrl_820443631.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_820443631.pdb
# conformation set from SCWRL output
# naming current conformation UNI-EID_bnmx_TS4-scwrl
# ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation UNI-EID_bnmx_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_617770104.pdb -s /var/tmp/to_scwrl_617770104.seq -o /var/tmp/from_scwrl_617770104.pdb > /var/tmp/scwrl_617770104.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_617770104.pdb
# conformation set from SCWRL output
# naming current conformation UNI-EID_bnmx_TS5-scwrl
# ReadConformPDB reading from PDB file servers/UNI-EID_expm_TS1.pdb.gz looking for model 1
WARNING: atoms too close: (T0327)N76.CA and (T0327)K87.CA only 0.000 apart, marking (T0327)K87.CA as missing
WARNING: atoms too close: (T0327)G77.CA and (T0327)E88.CA only 0.000 apart, marking (T0327)E88.CA as missing
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation UNI-EID_expm_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_291614384.pdb -s /var/tmp/to_scwrl_291614384.seq -o /var/tmp/from_scwrl_291614384.pdb > /var/tmp/scwrl_291614384.log
Error: Couldn't open file /var/tmp/from_scwrl_291614384.pdb or /var/tmp/from_scwrl_291614384.pdb.gz for input
Warning: Couldn't open file decoys//var/tmp/from_scwrl_291614384_b.pdb or decoys//var/tmp/from_scwrl_291614384_b.pdb.gz for input
Trying /var/tmp/from_scwrl_291614384_b.pdb
Error: Couldn't open file /var/tmp/from_scwrl_291614384_b.pdb or /var/tmp/from_scwrl_291614384_b.pdb.gz for input
Warning: Couldn't open file decoys//var/tmp/from_scwrl_291614384_a.pdb or decoys//var/tmp/from_scwrl_291614384_a.pdb.gz for input
Trying /var/tmp/from_scwrl_291614384_a.pdb
Error: Couldn't open file /var/tmp/from_scwrl_291614384_a.pdb or /var/tmp/from_scwrl_291614384_a.pdb.gz for input
Error: can't open any of /var/tmp/from_scwrl_291614384.pdb or /var/tmp/from_scwrl_291614384_b.pdb or /var/tmp/from_scwrl_291614384_a.pdb
Error: no new SCWRL conformation added
# naming current conformation UNI-EID_expm_TS1-scwrl
# ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation UNI-EID_sfst_AL1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_2095043455.pdb -s /var/tmp/to_scwrl_2095043455.seq -o /var/tmp/from_scwrl_2095043455.pdb > /var/tmp/scwrl_2095043455.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2095043455.pdb
# conformation set from SCWRL output
# naming current conformation UNI-EID_sfst_AL1-scwrl
# ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation UNI-EID_sfst_AL2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1059968597.pdb -s /var/tmp/to_scwrl_1059968597.seq -o /var/tmp/from_scwrl_1059968597.pdb > /var/tmp/scwrl_1059968597.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1059968597.pdb
# conformation set from SCWRL output
# naming current conformation UNI-EID_sfst_AL2-scwrl
# ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation UNI-EID_sfst_AL3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1231372761.pdb -s /var/tmp/to_scwrl_1231372761.seq -o /var/tmp/from_scwrl_1231372761.pdb > /var/tmp/scwrl_1231372761.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1231372761.pdb
# conformation set from SCWRL output
# naming current conformation UNI-EID_sfst_AL3-scwrl
# ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL4.pdb.gz looking for model 1
Skipped atom 58, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz
Skipped atom 60, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz
Skipped atom 62, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz
Skipped atom 64, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz
Skipped atom 170, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz
Skipped atom 172, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz
Skipped atom 174, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz
Skipped atom 176, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz
Skipped atom 222, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz
Skipped atom 224, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz
Skipped atom 226, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz
Skipped atom 228, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation UNI-EID_sfst_AL4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_11395339.pdb -s /var/tmp/to_scwrl_11395339.seq -o /var/tmp/from_scwrl_11395339.pdb > /var/tmp/scwrl_11395339.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_11395339.pdb
# conformation set from SCWRL output
# naming current conformation UNI-EID_sfst_AL4-scwrl
# ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation UNI-EID_sfst_AL5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_617482041.pdb -s /var/tmp/to_scwrl_617482041.seq -o /var/tmp/from_scwrl_617482041.pdb > /var/tmp/scwrl_617482041.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_617482041.pdb
# conformation set from SCWRL output
# naming current conformation UNI-EID_sfst_AL5-scwrl
# ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1
# Found a chain break before 97
# copying to AlignedFragments data structure
# naming current conformation Zhang-Server_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_298308743.pdb -s /var/tmp/to_scwrl_298308743.seq -o /var/tmp/from_scwrl_298308743.pdb > /var/tmp/scwrl_298308743.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_298308743.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 65
# copying to AlignedFragments data structure
# naming current conformation Zhang-Server_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1100294666.pdb -s /var/tmp/to_scwrl_1100294666.seq -o /var/tmp/from_scwrl_1100294666.pdb > /var/tmp/scwrl_1100294666.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1100294666.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 79
# copying to AlignedFragments data structure
# naming current conformation Zhang-Server_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_2016747945.pdb -s /var/tmp/to_scwrl_2016747945.seq -o /var/tmp/from_scwrl_2016747945.pdb > /var/tmp/scwrl_2016747945.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2016747945.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 100
# copying to AlignedFragments data structure
# naming current conformation Zhang-Server_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1771628035.pdb -s /var/tmp/to_scwrl_1771628035.seq -o /var/tmp/from_scwrl_1771628035.pdb > /var/tmp/scwrl_1771628035.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1771628035.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 98
# copying to AlignedFragments data structure
# naming current conformation Zhang-Server_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_2113288997.pdb -s /var/tmp/to_scwrl_2113288997.seq -o /var/tmp/from_scwrl_2113288997.pdb > /var/tmp/scwrl_2113288997.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2113288997.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 101
# copying to AlignedFragments data structure
# naming current conformation beautshot_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_645605759.pdb -s /var/tmp/to_scwrl_645605759.seq -o /var/tmp/from_scwrl_645605759.pdb > /var/tmp/scwrl_645605759.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_645605759.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 T0327 can't currently be optimized by undertaker
# naming current conformation beautshotbase_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1995067366.pdb -s /var/tmp/to_scwrl_1995067366.seq -o /var/tmp/from_scwrl_1995067366.pdb > /var/tmp/scwrl_1995067366.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1995067366.pdb
# conformation set from SCWRL output
# naming current conformation beautshotbase_TS1-scwrl
# ReadConformPDB reading from PDB file servers/forecast-s_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation forecast-s_AL1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1607942851.pdb -s /var/tmp/to_scwrl_1607942851.seq -o /var/tmp/from_scwrl_1607942851.pdb > /var/tmp/scwrl_1607942851.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1607942851.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 T0327 can't currently be optimized by undertaker
# naming current conformation forecast-s_AL2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1053699560.pdb -s /var/tmp/to_scwrl_1053699560.seq -o /var/tmp/from_scwrl_1053699560.pdb > /var/tmp/scwrl_1053699560.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1053699560.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 T0327 can't currently be optimized by undertaker
# naming current conformation forecast-s_AL3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1424381039.pdb -s /var/tmp/to_scwrl_1424381039.seq -o /var/tmp/from_scwrl_1424381039.pdb > /var/tmp/scwrl_1424381039.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1424381039.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 T0327 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation forecast-s_AL4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_626920604.pdb -s /var/tmp/to_scwrl_626920604.seq -o /var/tmp/from_scwrl_626920604.pdb > /var/tmp/scwrl_626920604.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_626920604.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
Skipped atom 138, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL5.pdb.gz
Skipped atom 140, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL5.pdb.gz
Skipped atom 142, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL5.pdb.gz
Skipped atom 144, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL5.pdb.gz
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation forecast-s_AL5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1284438793.pdb -s /var/tmp/to_scwrl_1284438793.seq -o /var/tmp/from_scwrl_1284438793.pdb > /var/tmp/scwrl_1284438793.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1284438793.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 T0327 can't currently be optimized by undertaker
# naming current conformation gtg_AL1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_932806456.pdb -s /var/tmp/to_scwrl_932806456.seq -o /var/tmp/from_scwrl_932806456.pdb > /var/tmp/scwrl_932806456.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_932806456.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 T0327 can't currently be optimized by undertaker
# naming current conformation gtg_AL2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_282247759.pdb -s /var/tmp/to_scwrl_282247759.seq -o /var/tmp/from_scwrl_282247759.pdb > /var/tmp/scwrl_282247759.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_282247759.pdb
# conformation set from SCWRL output
# naming current conformation gtg_AL2-scwrl
# ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1
# Found a chain break before 85
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.2_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_796073778.pdb -s /var/tmp/to_scwrl_796073778.seq -o /var/tmp/from_scwrl_796073778.pdb > /var/tmp/scwrl_796073778.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_796073778.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 92
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.2_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_756482971.pdb -s /var/tmp/to_scwrl_756482971.seq -o /var/tmp/from_scwrl_756482971.pdb > /var/tmp/scwrl_756482971.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_756482971.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 92
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.2_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_512980268.pdb -s /var/tmp/to_scwrl_512980268.seq -o /var/tmp/from_scwrl_512980268.pdb > /var/tmp/scwrl_512980268.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_512980268.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 91
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.2_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_922448714.pdb -s /var/tmp/to_scwrl_922448714.seq -o /var/tmp/from_scwrl_922448714.pdb > /var/tmp/scwrl_922448714.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_922448714.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 91
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.2_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_866974754.pdb -s /var/tmp/to_scwrl_866974754.seq -o /var/tmp/from_scwrl_866974754.pdb > /var/tmp/scwrl_866974754.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_866974754.pdb
# conformation set from SCWRL output
# naming current conformation karypis.srv.2_TS5-scwrl
# ReadConformPDB reading from PDB file servers/karypis.srv.4_TS1.pdb.gz looking for model 1
# Found a chain break before 93
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.4_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_304461051.pdb -s /var/tmp/to_scwrl_304461051.seq -o /var/tmp/from_scwrl_304461051.pdb > /var/tmp/scwrl_304461051.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_304461051.pdb
# conformation set from SCWRL output
# naming current conformation karypis.srv.4_TS1-scwrl
# ReadConformPDB reading from PDB file servers/karypis.srv.4_TS2.pdb.gz looking for model 1
# Found a chain break before 99
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.4_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1751989548.pdb -s /var/tmp/to_scwrl_1751989548.seq -o /var/tmp/from_scwrl_1751989548.pdb > /var/tmp/scwrl_1751989548.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1751989548.pdb
# conformation set from SCWRL output
# naming current conformation karypis.srv.4_TS2-scwrl
# ReadConformPDB reading from PDB file servers/karypis.srv.4_TS3.pdb.gz looking for model 1
# Found a chain break before 99
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.4_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1752860443.pdb -s /var/tmp/to_scwrl_1752860443.seq -o /var/tmp/from_scwrl_1752860443.pdb > /var/tmp/scwrl_1752860443.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1752860443.pdb
# conformation set from SCWRL output
# naming current conformation karypis.srv.4_TS3-scwrl
# ReadConformPDB reading from PDB file servers/karypis.srv.4_TS4.pdb.gz looking for model 1
# Found a chain break before 99
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.4_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1149304995.pdb -s /var/tmp/to_scwrl_1149304995.seq -o /var/tmp/from_scwrl_1149304995.pdb > /var/tmp/scwrl_1149304995.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1149304995.pdb
# conformation set from SCWRL output
# naming current conformation karypis.srv.4_TS4-scwrl
# ReadConformPDB reading from PDB file servers/karypis.srv.4_TS5.pdb.gz looking for model 1
# Found a chain break before 99
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.4_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_424949532.pdb -s /var/tmp/to_scwrl_424949532.seq -o /var/tmp/from_scwrl_424949532.pdb > /var/tmp/scwrl_424949532.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_424949532.pdb
# conformation set from SCWRL output
# naming current conformation karypis.srv.4_TS5-scwrl
# ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation karypis.srv_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_223146900.pdb -s /var/tmp/to_scwrl_223146900.seq -o /var/tmp/from_scwrl_223146900.pdb > /var/tmp/scwrl_223146900.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_223146900.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 T0327 can't currently be optimized by undertaker
# naming current conformation karypis.srv_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1440919379.pdb -s /var/tmp/to_scwrl_1440919379.seq -o /var/tmp/from_scwrl_1440919379.pdb > /var/tmp/scwrl_1440919379.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1440919379.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 T0327 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation karypis.srv_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_372509340.pdb -s /var/tmp/to_scwrl_372509340.seq -o /var/tmp/from_scwrl_372509340.pdb > /var/tmp/scwrl_372509340.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_372509340.pdb
# conformation set from SCWRL output
# naming current conformation karypis.srv_TS3-scwrl
# ReadConformPDB reading from PDB file servers/karypis.srv_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation karypis.srv_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1283115496.pdb -s /var/tmp/to_scwrl_1283115496.seq -o /var/tmp/from_scwrl_1283115496.pdb > /var/tmp/scwrl_1283115496.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1283115496.pdb
# conformation set from SCWRL output
# naming current conformation karypis.srv_TS4-scwrl
# ReadConformPDB reading from PDB file servers/karypis.srv_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation karypis.srv_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_524808494.pdb -s /var/tmp/to_scwrl_524808494.seq -o /var/tmp/from_scwrl_524808494.pdb > /var/tmp/scwrl_524808494.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_524808494.pdb
# conformation set from SCWRL output
# naming current conformation karypis.srv_TS5-scwrl
# ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1
# Found a chain break before 84
# copying to AlignedFragments data structure
# naming current conformation keasar-server_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_383904679.pdb -s /var/tmp/to_scwrl_383904679.seq -o /var/tmp/from_scwrl_383904679.pdb > /var/tmp/scwrl_383904679.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_383904679.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 86
# copying to AlignedFragments data structure
# naming current conformation keasar-server_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1900597537.pdb -s /var/tmp/to_scwrl_1900597537.seq -o /var/tmp/from_scwrl_1900597537.pdb > /var/tmp/scwrl_1900597537.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1900597537.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 73
# copying to AlignedFragments data structure
# naming current conformation keasar-server_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_823117237.pdb -s /var/tmp/to_scwrl_823117237.seq -o /var/tmp/from_scwrl_823117237.pdb > /var/tmp/scwrl_823117237.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_823117237.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
# naming current conformation keasar-server_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1484199345.pdb -s /var/tmp/to_scwrl_1484199345.seq -o /var/tmp/from_scwrl_1484199345.pdb > /var/tmp/scwrl_1484199345.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1484199345.pdb
# conformation set from SCWRL output
# naming current conformation keasar-server_TS4-scwrl
# ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1
# Found a chain break before 19
# copying to AlignedFragments data structure
# naming current conformation keasar-server_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1769861836.pdb -s /var/tmp/to_scwrl_1769861836.seq -o /var/tmp/from_scwrl_1769861836.pdb > /var/tmp/scwrl_1769861836.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1769861836.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 T0327 can't currently be optimized by undertaker
# naming current conformation mGen-3D_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_447261625.pdb -s /var/tmp/to_scwrl_447261625.seq -o /var/tmp/from_scwrl_447261625.pdb > /var/tmp/scwrl_447261625.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_447261625.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 T0327 can't currently be optimized by undertaker
# naming current conformation nFOLD_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1450004695.pdb -s /var/tmp/to_scwrl_1450004695.seq -o /var/tmp/from_scwrl_1450004695.pdb > /var/tmp/scwrl_1450004695.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1450004695.pdb
# conformation set from SCWRL output
# naming current conformation nFOLD_TS1-scwrl
# ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation nFOLD_TS2
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_267983948.pdb -s /var/tmp/to_scwrl_267983948.seq -o /var/tmp/from_scwrl_267983948.pdb > /var/tmp/scwrl_267983948.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_267983948.pdb
# conformation set from SCWRL output
# naming current conformation nFOLD_TS2-scwrl
# ReadConformPDB reading from PDB file servers/nFOLD_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation nFOLD_TS3
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_294845345.pdb -s /var/tmp/to_scwrl_294845345.seq -o /var/tmp/from_scwrl_294845345.pdb > /var/tmp/scwrl_294845345.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_294845345.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 T0327 can't currently be optimized by undertaker
# naming current conformation nFOLD_TS4
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_910463901.pdb -s /var/tmp/to_scwrl_910463901.seq -o /var/tmp/from_scwrl_910463901.pdb > /var/tmp/scwrl_910463901.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_910463901.pdb
# conformation set from SCWRL output
# naming current conformation nFOLD_TS4-scwrl
# ReadConformPDB reading from PDB file servers/nFOLD_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation nFOLD_TS5
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1321683507.pdb -s /var/tmp/to_scwrl_1321683507.seq -o /var/tmp/from_scwrl_1321683507.pdb > /var/tmp/scwrl_1321683507.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1321683507.pdb
# conformation set from SCWRL output
# naming current conformation nFOLD_TS5-scwrl
# ReadConformPDB reading from PDB file servers/panther2_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation panther2_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1719226384.pdb -s /var/tmp/to_scwrl_1719226384.seq -o /var/tmp/from_scwrl_1719226384.pdb > /var/tmp/scwrl_1719226384.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1719226384.pdb
# conformation set from SCWRL output
# naming current conformation panther2_TS1-scwrl
# ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0327 can't currently be optimized by undertaker
# naming current conformation shub_TS1
# request to SCWRL produces command: ulimit -t 92 ; scwrl3 -i /var/tmp/to_scwrl_1537384504.pdb -s /var/tmp/to_scwrl_1537384504.seq -o /var/tmp/from_scwrl_1537384504.pdb > /var/tmp/scwrl_1537384504.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1537384504.pdb
# conformation set from SCWRL output
# naming current conformation shub_TS1-scwrl
# command:CPU_time= 33.035 sec, elapsed time= 222.473 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 = -36.0408
shub_TS1	costs 0	real_cost = -36.1525
panther2_TS1-scwrl	costs 0	real_cost = 282.132
panther2_TS1	costs 0	real_cost = 299.708
nFOLD_TS5-scwrl	costs 0	real_cost = 86.4879
nFOLD_TS5	costs 0	real_cost = 130.438
nFOLD_TS4-scwrl	costs 0	real_cost = 5.38262
nFOLD_TS4	costs 0	real_cost = 51.5111
nFOLD_TS3-scwrl	costs 0	real_cost = 34.16
nFOLD_TS3	costs 0	real_cost = 75.2302
nFOLD_TS2-scwrl	costs 0	real_cost = -20.9777
nFOLD_TS2	costs 0	real_cost = 48.3101
nFOLD_TS1-scwrl	costs 0	real_cost = 21.8452
nFOLD_TS1	costs 0	real_cost = 84.8859
mGen-3D_TS1-scwrl	costs 0	real_cost = 24.2612
mGen-3D_TS1	costs 0	real_cost = 85.7178
keasar-server_TS5-scwrl	costs 0	real_cost = 2.38604
keasar-server_TS5	costs 0	real_cost = 13.0111
keasar-server_TS4-scwrl	costs 0	real_cost = -2.21137
keasar-server_TS4	costs 0	real_cost = 3.95518
keasar-server_TS3-scwrl	costs 0	real_cost = 2.07844
keasar-server_TS3	costs 0	real_cost = 13.5558
keasar-server_TS2-scwrl	costs 0	real_cost = 25.1719
keasar-server_TS2	costs 0	real_cost = 42.3032
keasar-server_TS1-scwrl	costs 0	real_cost = -23.8519
keasar-server_TS1	costs 0	real_cost = 20.2524
karypis.srv_TS5-scwrl	costs 0	real_cost = -19.3517
karypis.srv_TS5	costs 0	real_cost = -21.3517
karypis.srv_TS4-scwrl	costs 0	real_cost = -1.95905
karypis.srv_TS4	costs 0	real_cost = -3.95905
karypis.srv_TS3-scwrl	costs 0	real_cost = -10.5396
karypis.srv_TS3	costs 0	real_cost = -10.5396
karypis.srv_TS2-scwrl	costs 0	real_cost = -64.1257
karypis.srv_TS2	costs 0	real_cost = -66.1257
karypis.srv_TS1-scwrl	costs 0	real_cost = -59.9807
karypis.srv_TS1	costs 0	real_cost = -61.9807
karypis.srv.4_TS5-scwrl	costs 0	real_cost = 272.264
karypis.srv.4_TS5	costs 0	real_cost = 272.266
karypis.srv.4_TS4-scwrl	costs 0	real_cost = 272.024
karypis.srv.4_TS4	costs 0	real_cost = 272.086
karypis.srv.4_TS3-scwrl	costs 0	real_cost = 268.514
karypis.srv.4_TS3	costs 0	real_cost = 268.514
karypis.srv.4_TS2-scwrl	costs 0	real_cost = 220.771
karypis.srv.4_TS2	costs 0	real_cost = 220.771
karypis.srv.4_TS1-scwrl	costs 0	real_cost = 203.989
karypis.srv.4_TS1	costs 0	real_cost = 203.989
karypis.srv.2_TS5-scwrl	costs 0	real_cost = 47.9586
karypis.srv.2_TS5	costs 0	real_cost = 47.9586
karypis.srv.2_TS4-scwrl	costs 0	real_cost = -35.2707
karypis.srv.2_TS4	costs 0	real_cost = -35.2707
karypis.srv.2_TS3-scwrl	costs 0	real_cost = -38.15
karypis.srv.2_TS3	costs 0	real_cost = -38.15
karypis.srv.2_TS2-scwrl	costs 0	real_cost = -23.0243
karypis.srv.2_TS2	costs 0	real_cost = -23.0243
karypis.srv.2_TS1-scwrl	costs 0	real_cost = -63.5485
karypis.srv.2_TS1	costs 0	real_cost = -63.5485
gtg_AL2-scwrl	costs 0	real_cost = 433.265
gtg_AL2	costs 0	real_cost = 454.928
gtg_AL1-scwrl	costs 0	real_cost = 440.672
gtg_AL1	costs 0	real_cost = 453.218
forecast-s_AL5-scwrl	costs 0	real_cost = 31.2527
forecast-s_AL5	costs 0	real_cost = 71.6696
forecast-s_AL4-scwrl	costs 0	real_cost = 130.453
forecast-s_AL4	costs 0	real_cost = 209.829
forecast-s_AL3-scwrl	costs 0	real_cost = 165.971
forecast-s_AL3	costs 0	real_cost = 228.346
forecast-s_AL2-scwrl	costs 0	real_cost = 136.491
forecast-s_AL2	costs 0	real_cost = 157.427
forecast-s_AL1-scwrl	costs 0	real_cost = 70.0525
forecast-s_AL1	costs 0	real_cost = 126.351
beautshotbase_TS1-scwrl	costs 0	real_cost = -26.9421
beautshotbase_TS1	costs 0	real_cost = -29.0827
beautshot_TS1-scwrl	costs 0	real_cost = -66.3191
beautshot_TS1	costs 0	real_cost = -54.6037
Zhang-Server_TS5-scwrl	costs 0	real_cost = -116.631
Zhang-Server_TS5	costs 0	real_cost = -100.035
Zhang-Server_TS4-scwrl	costs 0	real_cost = -72.1938
Zhang-Server_TS4	costs 0	real_cost = -63.8204
Zhang-Server_TS3-scwrl	costs 0	real_cost = -83.0443
Zhang-Server_TS3	costs 0	real_cost = -80.1515
Zhang-Server_TS2-scwrl	costs 0	real_cost = -108.26
Zhang-Server_TS2	costs 0	real_cost = -99.1393
Zhang-Server_TS1-scwrl	costs 0	real_cost = -65.2658
Zhang-Server_TS1	costs 0	real_cost = -53.6324
UNI-EID_sfst_AL5-scwrl	costs 0	real_cost = 99.6277
UNI-EID_sfst_AL5	costs 0	real_cost = 174.98
UNI-EID_sfst_AL4-scwrl	costs 0	real_cost = 142.284
UNI-EID_sfst_AL4	costs 0	real_cost = 181.898
UNI-EID_sfst_AL3-scwrl	costs 0	real_cost = 122.811
UNI-EID_sfst_AL3	costs 0	real_cost = 146.39
UNI-EID_sfst_AL2-scwrl	costs 0	real_cost = 65.8664
UNI-EID_sfst_AL2	costs 0	real_cost = 147.544
UNI-EID_sfst_AL1-scwrl	costs 0	real_cost = 157.933
UNI-EID_sfst_AL1	costs 0	real_cost = 177.219
UNI-EID_expm_TS1-scwrl	costs 0	real_cost = 155.917
UNI-EID_bnmx_TS5-scwrl	costs 0	real_cost = 74.1533
UNI-EID_bnmx_TS5	costs 0	real_cost = 133.428
UNI-EID_bnmx_TS4-scwrl	costs 0	real_cost = 149.573
UNI-EID_bnmx_TS4	costs 0	real_cost = 194.131
UNI-EID_bnmx_TS3-scwrl	costs 0	real_cost = 111.308
UNI-EID_bnmx_TS3	costs 0	real_cost = 165.316
UNI-EID_bnmx_TS2-scwrl	costs 0	real_cost = 97.1882
UNI-EID_bnmx_TS2	costs 0	real_cost = 160.513
UNI-EID_bnmx_TS1-scwrl	costs 0	real_cost = 145.108
UNI-EID_bnmx_TS1	costs 0	real_cost = 174.484
SPARKS2_TS5-scwrl	costs 0	real_cost = 218.241
SPARKS2_TS5	costs 0	real_cost = 215.746
SPARKS2_TS4-scwrl	costs 0	real_cost = 41.9608
SPARKS2_TS4	costs 0	real_cost = 37.8741
SPARKS2_TS3-scwrl	costs 0	real_cost = -44.4027
SPARKS2_TS3	costs 0	real_cost = -44.1766
SPARKS2_TS2-scwrl	costs 0	real_cost = -56.1893
SPARKS2_TS2	costs 0	real_cost = -61.0038
SPARKS2_TS1-scwrl	costs 0	real_cost = -64.6099
SPARKS2_TS1	costs 0	real_cost = -65.641
SP4_TS5-scwrl	costs 0	real_cost = 74.4099
SP4_TS5	costs 0	real_cost = 80.8993
SP4_TS4-scwrl	costs 0	real_cost = 278.405
SP4_TS4	costs 0	real_cost = 274.389
SP4_TS3-scwrl	costs 0	real_cost = -14.2076
SP4_TS3	costs 0	real_cost = -18.3088
SP4_TS2-scwrl	costs 0	real_cost = -51.5661
SP4_TS2	costs 0	real_cost = -41.505
SP4_TS1-scwrl	costs 0	real_cost = -74.1502
SP4_TS1	costs 0	real_cost = -75.8372
SP3_TS5-scwrl	costs 0	real_cost = -44.8202
SP3_TS5	costs 0	real_cost = -43.4079
SP3_TS4-scwrl	costs 0	real_cost = 28.5081
SP3_TS4	costs 0	real_cost = 32.8711
SP3_TS3-scwrl	costs 0	real_cost = -27.5158
SP3_TS3	costs 0	real_cost = -25.189
SP3_TS2-scwrl	costs 0	real_cost = -15.1684
SP3_TS2	costs 0	real_cost = -2.5756
SP3_TS1-scwrl	costs 0	real_cost = -64.6099
SP3_TS1	costs 0	real_cost = -65.641
SAM_T06_server_TS5-scwrl	costs 0	real_cost = 194.214
SAM_T06_server_TS5	costs 0	real_cost = 158.581
SAM_T06_server_TS4-scwrl	costs 0	real_cost = -17.8819
SAM_T06_server_TS4	costs 0	real_cost = -23.4907
SAM_T06_server_TS3-scwrl	costs 0	real_cost = 121.11
SAM_T06_server_TS3	costs 0	real_cost = 78.8561
SAM_T06_server_TS2-scwrl	costs 0	real_cost = 108.237
SAM_T06_server_TS2	costs 0	real_cost = 107.394
SAM_T06_server_TS1-scwrl	costs 0	real_cost = 53.83
SAM_T06_server_TS1	costs 0	real_cost = 61.745
SAM-T99_AL5-scwrl	costs 0	real_cost = 35.7144
SAM-T99_AL5	costs 0	real_cost = 86.4285
SAM-T99_AL4-scwrl	costs 0	real_cost = -37.173
SAM-T99_AL4	costs 0	real_cost = 32.6645
SAM-T99_AL3-scwrl	costs 0	real_cost = 18.2808
SAM-T99_AL3	costs 0	real_cost = 65.2043
SAM-T99_AL2-scwrl	costs 0	real_cost = 102.068
SAM-T99_AL2	costs 0	real_cost = 155.817
SAM-T99_AL1-scwrl	costs 0	real_cost = 8.84855
SAM-T99_AL1	costs 0	real_cost = 64.941
SAM-T02_AL5-scwrl	costs 0	real_cost = 120.976
SAM-T02_AL5	costs 0	real_cost = 157.415
SAM-T02_AL4-scwrl	costs 0	real_cost = 74.8942
SAM-T02_AL4	costs 0	real_cost = 115.844
SAM-T02_AL3-scwrl	costs 0	real_cost = 156.807
SAM-T02_AL3	costs 0	real_cost = 188.495
SAM-T02_AL2-scwrl	costs 0	real_cost = 77.4112
SAM-T02_AL2	costs 0	real_cost = 123.267
SAM-T02_AL1-scwrl	costs 0	real_cost = 147.664
SAM-T02_AL1	costs 0	real_cost = 164.933
ROKKY_TS5-scwrl	costs 0	real_cost = 51.2804
ROKKY_TS5	costs 0	real_cost = 132.437
ROKKY_TS4-scwrl	costs 0	real_cost = 38.2655
ROKKY_TS4	costs 0	real_cost = 123.769
ROKKY_TS3-scwrl	costs 0	real_cost = 22.018
ROKKY_TS3	costs 0	real_cost = 107.859
ROKKY_TS2-scwrl	costs 0	real_cost = 10.7646
ROKKY_TS2	costs 0	real_cost = 90.2822
ROKKY_TS1-scwrl	costs 0	real_cost = 62.5002
ROKKY_TS1	costs 0	real_cost = 148.473
ROBETTA_TS5-scwrl	costs 0	real_cost = -12.3668
ROBETTA_TS5	costs 0	real_cost = -2.16931
ROBETTA_TS4-scwrl	costs 0	real_cost = -45.6558
ROBETTA_TS4	costs 0	real_cost = -44.1793
ROBETTA_TS3-scwrl	costs 0	real_cost = -17.1963
ROBETTA_TS3	costs 0	real_cost = -17.87
ROBETTA_TS2-scwrl	costs 0	real_cost = -13.2743
ROBETTA_TS2	costs 0	real_cost = -6.08103
ROBETTA_TS1-scwrl	costs 0	real_cost = -28.2805
ROBETTA_TS1	costs 0	real_cost = -28.3006
RAPTOR_TS5-scwrl	costs 0	real_cost = 7.88813
RAPTOR_TS5	costs 0	real_cost = 5.50632
RAPTOR_TS4-scwrl	costs 0	real_cost = -47.5467
RAPTOR_TS4	costs 0	real_cost = -32.2473
RAPTOR_TS3-scwrl	costs 0	real_cost = -2.98277
RAPTOR_TS3	costs 0	real_cost = -10.0146
RAPTOR_TS2-scwrl	costs 0	real_cost = -52.9233
RAPTOR_TS2	costs 0	real_cost = -44.4565
RAPTOR_TS1-scwrl	costs 0	real_cost = -23.4945
RAPTOR_TS1	costs 0	real_cost = -24.853
RAPTORESS_TS5-scwrl	costs 0	real_cost = 17.8456
RAPTORESS_TS5	costs 0	real_cost = 13.3012
RAPTORESS_TS4-scwrl	costs 0	real_cost = -4.24879
RAPTORESS_TS4	costs 0	real_cost = 4.46875
RAPTORESS_TS3-scwrl	costs 0	real_cost = 18.554
RAPTORESS_TS3	costs 0	real_cost = 12.5123
RAPTORESS_TS2-scwrl	costs 0	real_cost = -12.8527
RAPTORESS_TS2	costs 0	real_cost = -7.73153
RAPTORESS_TS1-scwrl	costs 0	real_cost = -23.3907
RAPTORESS_TS1	costs 0	real_cost = -7.65894
RAPTOR-ACE_TS5-scwrl	costs 0	real_cost = -46.8347
RAPTOR-ACE_TS5	costs 0	real_cost = -34.9665
RAPTOR-ACE_TS4-scwrl	costs 0	real_cost = -76.342
RAPTOR-ACE_TS4	costs 0	real_cost = -73.2943
RAPTOR-ACE_TS3-scwrl	costs 0	real_cost = -64.6099
RAPTOR-ACE_TS3	costs 0	real_cost = -65.641
RAPTOR-ACE_TS2-scwrl	costs 0	real_cost = -71.6169
RAPTOR-ACE_TS2	costs 0	real_cost = -65.2791
RAPTOR-ACE_TS1-scwrl	costs 0	real_cost = -44.8202
RAPTOR-ACE_TS1	costs 0	real_cost = -43.4079
Pmodeller6_TS5-scwrl	costs 0	real_cost = -45.6558
Pmodeller6_TS5	costs 0	real_cost = -44.1793
Pmodeller6_TS4-scwrl	costs 0	real_cost = -53.1588
Pmodeller6_TS4	costs 0	real_cost = -55.1964
Pmodeller6_TS3-scwrl	costs 0	real_cost = -28.2805
Pmodeller6_TS3	costs 0	real_cost = -28.3006
Pmodeller6_TS2-scwrl	costs 0	real_cost = -12.3668
Pmodeller6_TS2	costs 0	real_cost = -2.16931
Pmodeller6_TS1-scwrl	costs 0	real_cost = -81.2737
Pmodeller6_TS1	costs 0	real_cost = -83.0737
Phyre-2_TS5-scwrl	costs 0	real_cost = -8.47298
Phyre-2_TS5	costs 0	real_cost = -14.5996
Phyre-2_TS4-scwrl	costs 0	real_cost = 4.02098
Phyre-2_TS4	costs 0	real_cost = 7.77155
Phyre-2_TS3-scwrl	costs 0	real_cost = -13.9849
Phyre-2_TS3	costs 0	real_cost = -23.2127
Phyre-2_TS2-scwrl	costs 0	real_cost = -44.3929
Phyre-2_TS2	costs 0	real_cost = -45.1477
Phyre-2_TS1-scwrl	costs 0	real_cost = 4.02098
Phyre-2_TS1	costs 0	real_cost = 7.77155
Phyre-1_TS1-scwrl	costs 0	real_cost = 105.469
Phyre-1_TS1	costs 0	real_cost = 101.639
Pcons6_TS5-scwrl	costs 0	real_cost = -18.039
Pcons6_TS5	costs 0	real_cost = -22.439
Pcons6_TS4-scwrl	costs 0	real_cost = 92.4862
Pcons6_TS4	costs 0	real_cost = 88.8862
Pcons6_TS3-scwrl	costs 0	real_cost = -91.274
Pcons6_TS3	costs 0	real_cost = -92.874
Pcons6_TS2-scwrl	costs 0	real_cost = -66.3313
Pcons6_TS2	costs 0	real_cost = -69.5313
Pcons6_TS1-scwrl	costs 0	real_cost = -70.1305
Pcons6_TS1	costs 0	real_cost = -72.1305
PROTINFO_TS5-scwrl	costs 0	real_cost = -42.7749
PROTINFO_TS5	costs 0	real_cost = -45.8733
PROTINFO_TS4-scwrl	costs 0	real_cost = -38.2457
PROTINFO_TS4	costs 0	real_cost = -37.5868
PROTINFO_TS3-scwrl	costs 0	real_cost = -66.2658
PROTINFO_TS3	costs 0	real_cost = -56.5393
PROTINFO_TS2-scwrl	costs 0	real_cost = -61.2217
PROTINFO_TS2	costs 0	real_cost = -56.6084
PROTINFO_TS1-scwrl	costs 0	real_cost = -43.2051
PROTINFO_TS1	costs 0	real_cost = -42.7091
PROTINFO-AB_TS5-scwrl	costs 0	real_cost = -55.0439
PROTINFO-AB_TS5	costs 0	real_cost = -66.9033
PROTINFO-AB_TS4-scwrl	costs 0	real_cost = -62.6867
PROTINFO-AB_TS4	costs 0	real_cost = -64.2167
PROTINFO-AB_TS3-scwrl	costs 0	real_cost = -58.8946
PROTINFO-AB_TS3	costs 0	real_cost = -66.605
PROTINFO-AB_TS2-scwrl	costs 0	real_cost = -59.9273
PROTINFO-AB_TS2	costs 0	real_cost = -65.4483
PROTINFO-AB_TS1-scwrl	costs 0	real_cost = -62.6518
PROTINFO-AB_TS1	costs 0	real_cost = -76.304
POMYSL_TS5-scwrl	costs 0	real_cost = 238.639
POMYSL_TS5	costs 0	real_cost = 248.555
POMYSL_TS4-scwrl	costs 0	real_cost = 181.406
POMYSL_TS4	costs 0	real_cost = 214.038
POMYSL_TS3-scwrl	costs 0	real_cost = 264.989
POMYSL_TS3	costs 0	real_cost = 261.005
POMYSL_TS2-scwrl	costs 0	real_cost = 164.527
POMYSL_TS2	costs 0	real_cost = 187.156
POMYSL_TS1-scwrl	costs 0	real_cost = 211.561
POMYSL_TS1	costs 0	real_cost = 227.417
NN_PUT_lab_TS1-scwrl	costs 0	real_cost = -64.6099
NN_PUT_lab_TS1	costs 0	real_cost = -65.641
MetaTasser_TS5-scwrl	costs 0	real_cost = -58.4414
MetaTasser_TS5	costs 0	real_cost = -53.6184
MetaTasser_TS4-scwrl	costs 0	real_cost = -32.8853
MetaTasser_TS4	costs 0	real_cost = -31.2985
MetaTasser_TS3-scwrl	costs 0	real_cost = -67.6727
MetaTasser_TS3	costs 0	real_cost = -59.3213
MetaTasser_TS2-scwrl	costs 0	real_cost = -39.8155
MetaTasser_TS2	costs 0	real_cost = -41.218
MetaTasser_TS1-scwrl	costs 0	real_cost = -61.3269
MetaTasser_TS1	costs 0	real_cost = -58.2495
Ma-OPUS-server_TS5-scwrl	costs 0	real_cost = 262.378
Ma-OPUS-server_TS5	costs 0	real_cost = 266.852
Ma-OPUS-server_TS4-scwrl	costs 0	real_cost = 77.7324
Ma-OPUS-server_TS4	costs 0	real_cost = 78.1345
Ma-OPUS-server_TS3-scwrl	costs 0	real_cost = 196.459
Ma-OPUS-server_TS3	costs 0	real_cost = 197.837
Ma-OPUS-server_TS2-scwrl	costs 0	real_cost = 25.8766
Ma-OPUS-server_TS2	costs 0	real_cost = 45.1144
Ma-OPUS-server_TS1-scwrl	costs 0	real_cost = -92.7117
Ma-OPUS-server_TS1	costs 0	real_cost = -89.2563
Ma-OPUS-server2_TS5-scwrl	costs 0	real_cost = 262.378
Ma-OPUS-server2_TS5	costs 0	real_cost = 266.852
Ma-OPUS-server2_TS4-scwrl	costs 0	real_cost = 84.5465
Ma-OPUS-server2_TS4	costs 0	real_cost = 91.488
Ma-OPUS-server2_TS3-scwrl	costs 0	real_cost = 196.459
Ma-OPUS-server2_TS3	costs 0	real_cost = 197.837
Ma-OPUS-server2_TS2-scwrl	costs 0	real_cost = -58.9627
Ma-OPUS-server2_TS2	costs 0	real_cost = -49.3465
Ma-OPUS-server2_TS1-scwrl	costs 0	real_cost = -70.0989
Ma-OPUS-server2_TS1	costs 0	real_cost = -61.6113
MIG_FROST_AL1-scwrl	costs 0	real_cost = 215.928
MIG_FROST_AL1	costs 0	real_cost = 215.928
LOOPP_TS5	costs 0	real_cost = 206.805
LOOPP_TS4-scwrl	costs 0	real_cost = 210.023
LOOPP_TS4	costs 0	real_cost = 201.712
LOOPP_TS3-scwrl	costs 0	real_cost = -1.20854
LOOPP_TS3	costs 0	real_cost = -0.0717539
LOOPP_TS2-scwrl	costs 0	real_cost = 10.0414
LOOPP_TS2	costs 0	real_cost = 22.3602
LOOPP_TS1-scwrl	costs 0	real_cost = -20.0618
LOOPP_TS1	costs 0	real_cost = -23.8052
Huber-Torda-Server_TS5-scwrl	costs 0	real_cost = 189.819
Huber-Torda-Server_TS5	costs 0	real_cost = 233.126
Huber-Torda-Server_TS4-scwrl	costs 0	real_cost = 239.071
Huber-Torda-Server_TS4	costs 0	real_cost = 252.469
Huber-Torda-Server_TS3-scwrl	costs 0	real_cost = 206.467
Huber-Torda-Server_TS3	costs 0	real_cost = 256.504
Huber-Torda-Server_TS2-scwrl	costs 0	real_cost = 119.504
Huber-Torda-Server_TS2	costs 0	real_cost = 138.55
Huber-Torda-Server_TS1-scwrl	costs 0	real_cost = 43.4829
Huber-Torda-Server_TS1	costs 0	real_cost = 79.3506
HHpred3_TS1-scwrl	costs 0	real_cost = -47.5134
HHpred3_TS1	costs 0	real_cost = -45.5941
HHpred2_TS1-scwrl	costs 0	real_cost = -47.5134
HHpred2_TS1	costs 0	real_cost = -45.5941
HHpred1_TS1-scwrl	costs 0	real_cost = -68.0386
HHpred1_TS1	costs 0	real_cost = -60.8523
GeneSilicoMetaServer_TS5-scwrl	costs 0	real_cost = -67.5317
GeneSilicoMetaServer_TS5	costs 0	real_cost = -63.0477
GeneSilicoMetaServer_TS4-scwrl	costs 0	real_cost = 83.1483
GeneSilicoMetaServer_TS4	costs 0	real_cost = 90.7615
GeneSilicoMetaServer_TS3-scwrl	costs 0	real_cost = -33.9738
GeneSilicoMetaServer_TS3	costs 0	real_cost = -42.9599
GeneSilicoMetaServer_TS2-scwrl	costs 0	real_cost = -6.20598
GeneSilicoMetaServer_TS2	costs 0	real_cost = -3.02089
GeneSilicoMetaServer_TS1-scwrl	costs 0	real_cost = -93.6605
GeneSilicoMetaServer_TS1	costs 0	real_cost = -88.6797
FUNCTION_TS5-scwrl	costs 0	real_cost = -9.52922
FUNCTION_TS5	costs 0	real_cost = 1.67569
FUNCTION_TS4-scwrl	costs 0	real_cost = 19.7092
FUNCTION_TS4	costs 0	real_cost = 20.9179
FUNCTION_TS3-scwrl	costs 0	real_cost = -4.23251
FUNCTION_TS3	costs 0	real_cost = 5.52568
FUNCTION_TS2-scwrl	costs 0	real_cost = 79.6181
FUNCTION_TS2	costs 0	real_cost = 82.769
FUNCTION_TS1-scwrl	costs 0	real_cost = -31.9764
FUNCTION_TS1	costs 0	real_cost = -29.4253
FUGUE_AL5-scwrl	costs 0	real_cost = 266.835
FUGUE_AL5	costs 0	real_cost = 266.835
FUGUE_AL4-scwrl	costs 0	real_cost = 229.098
FUGUE_AL4	costs 0	real_cost = 291.807
FUGUE_AL3-scwrl	costs 0	real_cost = -89.372
FUGUE_AL3	costs 0	real_cost = -14.3563
FUGUE_AL2-scwrl	costs 0	real_cost = 175.208
FUGUE_AL2	costs 0	real_cost = 246.222
FUGUE_AL1-scwrl	costs 0	real_cost = 216.031
FUGUE_AL1	costs 0	real_cost = 293.18
FUGMOD_TS5-scwrl	costs 0	real_cost = 166.282
FUGMOD_TS5	costs 0	real_cost = 169.594
FUGMOD_TS4-scwrl	costs 0	real_cost = 192.109
FUGMOD_TS4	costs 0	real_cost = 195.675
FUGMOD_TS3-scwrl	costs 0	real_cost = -58.0344
FUGMOD_TS3	costs 0	real_cost = -45.2929
FUGMOD_TS2-scwrl	costs 0	real_cost = 142.209
FUGMOD_TS2	costs 0	real_cost = 156.881
FUGMOD_TS1-scwrl	costs 0	real_cost = 205.777
FUGMOD_TS1	costs 0	real_cost = 205.332
FPSOLVER-SERVER_TS5-scwrl	costs 0	real_cost = 218.573
FPSOLVER-SERVER_TS5	costs 0	real_cost = 224.395
FPSOLVER-SERVER_TS4-scwrl	costs 0	real_cost = 185.249
FPSOLVER-SERVER_TS4	costs 0	real_cost = 189.838
FPSOLVER-SERVER_TS3-scwrl	costs 0	real_cost = 165.882
FPSOLVER-SERVER_TS3	costs 0	real_cost = 163.874
FPSOLVER-SERVER_TS2-scwrl	costs 0	real_cost = 193.162
FPSOLVER-SERVER_TS2	costs 0	real_cost = 200.908
FPSOLVER-SERVER_TS1-scwrl	costs 0	real_cost = 233.859
FPSOLVER-SERVER_TS1	costs 0	real_cost = 235.476
FORTE2_AL5-scwrl	costs 0	real_cost = 268.345
FORTE2_AL5	costs 0	real_cost = 334.483
FORTE2_AL4-scwrl	costs 0	real_cost = 44.1228
FORTE2_AL4	costs 0	real_cost = 135.689
FORTE2_AL3-scwrl	costs 0	real_cost = 3.08912
FORTE2_AL3	costs 0	real_cost = 57.3308
FORTE2_AL2-scwrl	costs 0	real_cost = 105.381
FORTE2_AL2	costs 0	real_cost = 151.257
FORTE2_AL1-scwrl	costs 0	real_cost = 326.668
FORTE2_AL1	costs 0	real_cost = 404.729
FORTE1_AL5-scwrl	costs 0	real_cost = 268.345
FORTE1_AL5	costs 0	real_cost = 334.483
FORTE1_AL4-scwrl	costs 0	real_cost = 44.1228
FORTE1_AL4	costs 0	real_cost = 135.689
FORTE1_AL3-scwrl	costs 0	real_cost = 105.381
FORTE1_AL3	costs 0	real_cost = 151.257
FORTE1_AL2-scwrl	costs 0	real_cost = 326.668
FORTE1_AL2	costs 0	real_cost = 404.729
FORTE1_AL1-scwrl	costs 0	real_cost = 67.8547
FORTE1_AL1	costs 0	real_cost = 120.753
FOLDpro_TS5-scwrl	costs 0	real_cost = -4.36852
FOLDpro_TS5	costs 0	real_cost = 1.01191
FOLDpro_TS4-scwrl	costs 0	real_cost = 157.261
FOLDpro_TS4	costs 0	real_cost = 162.257
FOLDpro_TS3-scwrl	costs 0	real_cost = 126.83
FOLDpro_TS3	costs 0	real_cost = 130.762
FOLDpro_TS2-scwrl	costs 0	real_cost = -112.572
FOLDpro_TS2	costs 0	real_cost = -98.1116
FOLDpro_TS1-scwrl	costs 0	real_cost = -21.0905
FOLDpro_TS1	costs 0	real_cost = -15.8487
FAMS_TS5-scwrl	costs 0	real_cost = -22.8985
FAMS_TS5	costs 0	real_cost = -17.2128
FAMS_TS4-scwrl	costs 0	real_cost = -63.227
FAMS_TS4	costs 0	real_cost = -58.5521
FAMS_TS3-scwrl	costs 0	real_cost = -73.8168
FAMS_TS3	costs 0	real_cost = -65.8994
FAMS_TS2-scwrl	costs 0	real_cost = -62.9621
FAMS_TS2	costs 0	real_cost = -67.8925
FAMS_TS1-scwrl	costs 0	real_cost = -3.47071
FAMS_TS1	costs 0	real_cost = 13.3604
FAMSD_TS5-scwrl	costs 0	real_cost = -24.6179
FAMSD_TS5	costs 0	real_cost = -29.258
FAMSD_TS4-scwrl	costs 0	real_cost = 26.2793
FAMSD_TS4	costs 0	real_cost = 26.3041
FAMSD_TS3-scwrl	costs 0	real_cost = -22.8985
FAMSD_TS3	costs 0	real_cost = -17.2128
FAMSD_TS2-scwrl	costs 0	real_cost = 33.9182
FAMSD_TS2	costs 0	real_cost = 38.6862
FAMSD_TS1-scwrl	costs 0	real_cost = -17.6561
FAMSD_TS1	costs 0	real_cost = -1.2628
Distill_TS5-scwrl	costs 0	real_cost = 293.626
Distill_TS4-scwrl	costs 0	real_cost = 299.414
Distill_TS3-scwrl	costs 0	real_cost = 301.725
Distill_TS2-scwrl	costs 0	real_cost = 302.686
Distill_TS1-scwrl	costs 0	real_cost = 302.357
CaspIta-FOX_TS5-scwrl	costs 0	real_cost = 85.9521
CaspIta-FOX_TS5	costs 0	real_cost = 83.1996
CaspIta-FOX_TS4-scwrl	costs 0	real_cost = -41.4303
CaspIta-FOX_TS4	costs 0	real_cost = -46.017
CaspIta-FOX_TS3-scwrl	costs 0	real_cost = -65.4944
CaspIta-FOX_TS3	costs 0	real_cost = -68.2431
CaspIta-FOX_TS2-scwrl	costs 0	real_cost = 1.35226
CaspIta-FOX_TS2	costs 0	real_cost = -5.16282
CaspIta-FOX_TS1-scwrl	costs 0	real_cost = 41.7854
CaspIta-FOX_TS1	costs 0	real_cost = 31.0689
CIRCLE_TS5-scwrl	costs 0	real_cost = 33.9182
CIRCLE_TS5	costs 0	real_cost = 38.6862
CIRCLE_TS4-scwrl	costs 0	real_cost = -52.3336
CIRCLE_TS4	costs 0	real_cost = -45.7053
CIRCLE_TS3-scwrl	costs 0	real_cost = -63.227
CIRCLE_TS3	costs 0	real_cost = -58.5521
CIRCLE_TS2-scwrl	costs 0	real_cost = -73.8168
CIRCLE_TS2	costs 0	real_cost = -65.8994
CIRCLE_TS1-scwrl	costs 0	real_cost = -62.9621
CIRCLE_TS1	costs 0	real_cost = -67.8925
Bilab-ENABLE_TS5-scwrl	costs 0	real_cost = -78.1538
Bilab-ENABLE_TS5	costs 0	real_cost = -78.1538
Bilab-ENABLE_TS4-scwrl	costs 0	real_cost = -78.1538
Bilab-ENABLE_TS4	costs 0	real_cost = -78.1538
Bilab-ENABLE_TS3-scwrl	costs 0	real_cost = -78.1538
Bilab-ENABLE_TS3	costs 0	real_cost = -78.1538
Bilab-ENABLE_TS2-scwrl	costs 0	real_cost = 149.953
Bilab-ENABLE_TS2	costs 0	real_cost = 152.185
Bilab-ENABLE_TS1-scwrl	costs 0	real_cost = 176.019
Bilab-ENABLE_TS1	costs 0	real_cost = 176.019
BayesHH_TS1-scwrl	costs 0	real_cost = -47.5134
BayesHH_TS1	costs 0	real_cost = -45.5941
ABIpro_TS5-scwrl	costs 0	real_cost = 107.888
ABIpro_TS5	costs 0	real_cost = 107.888
ABIpro_TS4-scwrl	costs 0	real_cost = 163.66
ABIpro_TS4	costs 0	real_cost = 166.471
ABIpro_TS3-scwrl	costs 0	real_cost = 104.773
ABIpro_TS3	costs 0	real_cost = 104.773
ABIpro_TS2-scwrl	costs 0	real_cost = 103.809
ABIpro_TS2	costs 0	real_cost = 103.929
ABIpro_TS1-scwrl	costs 0	real_cost = 126.606
ABIpro_TS1	costs 0	real_cost = 125.015
3Dpro_TS5-scwrl	costs 0	real_cost = 126.606
3Dpro_TS5	costs 0	real_cost = 125.015
3Dpro_TS4-scwrl	costs 0	real_cost = 127.86
3Dpro_TS4	costs 0	real_cost = 125.143
3Dpro_TS3-scwrl	costs 0	real_cost = 51.978
3Dpro_TS3	costs 0	real_cost = 68.3487
3Dpro_TS2-scwrl	costs 0	real_cost = 135.564
3Dpro_TS2	costs 0	real_cost = 142.58
3Dpro_TS1-scwrl	costs 0	real_cost = -20.7324
3Dpro_TS1	costs 0	real_cost = -19.8766
3D-JIGSAW_TS5-scwrl	costs 0	real_cost = 36.3613
3D-JIGSAW_TS5	costs 0	real_cost = 43.699
3D-JIGSAW_TS4-scwrl	costs 0	real_cost = 236.409
3D-JIGSAW_TS4	costs 0	real_cost = 233.523
3D-JIGSAW_TS3-scwrl	costs 0	real_cost = 49.6341
3D-JIGSAW_TS3	costs 0	real_cost = 58.7134
3D-JIGSAW_TS2-scwrl	costs 0	real_cost = 77.1398
3D-JIGSAW_TS2	costs 0	real_cost = 85.8682
3D-JIGSAW_TS1-scwrl	costs 0	real_cost = 93.6079
3D-JIGSAW_TS1	costs 0	real_cost = 97.1645
3D-JIGSAW_RECOM_TS5-scwrl	costs 0	real_cost = 7.44059
3D-JIGSAW_RECOM_TS5	costs 0	real_cost = 8.98705
3D-JIGSAW_RECOM_TS4-scwrl	costs 0	real_cost = 50.3781
3D-JIGSAW_RECOM_TS4	costs 0	real_cost = 52.8703
3D-JIGSAW_RECOM_TS3-scwrl	costs 0	real_cost = -17.1022
3D-JIGSAW_RECOM_TS3	costs 0	real_cost = -14.2697
3D-JIGSAW_RECOM_TS2-scwrl	costs 0	real_cost = -15.4176
3D-JIGSAW_RECOM_TS2	costs 0	real_cost = -14.7668
3D-JIGSAW_RECOM_TS1-scwrl	costs 0	real_cost = 44.1321
3D-JIGSAW_RECOM_TS1	costs 0	real_cost = 51.3299
3D-JIGSAW_POPULUS_TS5-scwrl	costs 0	real_cost = 97.3842
3D-JIGSAW_POPULUS_TS5	costs 0	real_cost = 95.3842
3D-JIGSAW_POPULUS_TS4-scwrl	costs 0	real_cost = 1.63836
3D-JIGSAW_POPULUS_TS4	costs 0	real_cost = -0.361644
3D-JIGSAW_POPULUS_TS3-scwrl	costs 0	real_cost = 2.58338
3D-JIGSAW_POPULUS_TS3	costs 0	real_cost = 0.583382
3D-JIGSAW_POPULUS_TS2-scwrl	costs 0	real_cost = 51.5841
3D-JIGSAW_POPULUS_TS2	costs 0	real_cost = 49.5841
3D-JIGSAW_POPULUS_TS1-scwrl	costs 0	real_cost = 2.90131
3D-JIGSAW_POPULUS_TS1	costs 0	real_cost = 0.901308
dimer//dimer3-1tbxA-dimer6	costs 0	real_cost = 20.0771
dimer//dimer2-1tbxA-dimer6	costs 0	real_cost = 20.0549
dimer//dimer1-1tbxA-dimer6	costs 0	real_cost = 20.0783
dimer//dimer-1ub9A-dimer11	costs 0	real_cost = 29.8499
dimer//dimer-1tbxA-try1-opt2	costs 0	real_cost = -5.05487
dimer//dimer-1tbxA-try1-opt2-proteinshop	costs 0	real_cost = 15.3653
dimer//try9-opt2.unpack	costs 0	real_cost = 30.8313
dimer//try9-opt2.unpack.gromacs0.repack-nonPC	costs 0	real_cost = 23.4435
dimer//try9-opt2.unpack.gromacs0	costs 0	real_cost = 32.944
dimer//try9-opt2.repack-nonPC	costs 0	real_cost = 25.9752
dimer//try9-opt2	costs 0	real_cost = 30.8313
dimer//try9-opt2.gromacs0	costs 0	real_cost = 32.0198
dimer//try9-opt1	costs 0	real_cost = 31.2699
dimer//try9-opt1-scwrl	costs 0	real_cost = 28.429
dimer//try8-opt2.unpack	costs 0	real_cost = 28.839
dimer//try8-opt2.unpack.gromacs0.repack-nonPC	costs 0	real_cost = 24.7867
dimer//try8-opt2.unpack.gromacs0	costs 0	real_cost = 27.6689
dimer//try8-opt2.repack-nonPC	costs 0	real_cost = 27.3943
dimer//try8-opt2	costs 0	real_cost = 28.839
dimer//try8-opt2.gromacs0	costs 0	real_cost = 28.6772
dimer//try8-opt1	costs 0	real_cost = 27.3711
dimer//try8-opt1-scwrl	costs 0	real_cost = 25.7635
dimer//try7-opt2.unpack	costs 0	real_cost = 25.0551
dimer//try7-opt2.unpack.gromacs0.repack-nonPC	costs 0	real_cost = 19.7455
dimer//try7-opt2.unpack.gromacs0	costs 0	real_cost = 22.5127
dimer//try7-opt2.repack-nonPC	costs 0	real_cost = 23.0468
dimer//try7-opt2	costs 0	real_cost = 25.0551
dimer//try7-opt2.gromacs0	costs 0	real_cost = 32.1507
dimer//try7-opt1	costs 0	real_cost = 24.201
dimer//try7-opt1-scwrl	costs 0	real_cost = 20.9509
dimer//try6-opt2.unpack	costs 0	real_cost = 20.0665
dimer//try6-opt2.unpack.gromacs0.repack-nonPC	costs 0	real_cost = 15.1446
dimer//try6-opt2.unpack.gromacs0	costs 0	real_cost = 17.2923
dimer//try6-opt2.repack-nonPC	costs 0	real_cost = 18.8147
dimer//try6-opt2	costs 0	real_cost = 20.0665
dimer//try6-opt2.gromacs0	costs 0	real_cost = 18.3391
dimer//try6-opt1	costs 0	real_cost = 21.795
dimer//try6-opt1-scwrl	costs 0	real_cost = 20.8928
dimer//try5-opt2.unpack	costs 0	real_cost = 17.1231
dimer//try5-opt2.unpack.gromacs0.repack-nonPC	costs 0	real_cost = 9.79794
dimer//try5-opt2.unpack.gromacs0	costs 0	real_cost = 21.9823
dimer//try5-opt2.repack-nonPC	costs 0	real_cost = 18.8947
dimer//try5-opt2	costs 0	real_cost = 17.1231
dimer//try5-opt2.gromacs0	costs 0	real_cost = 21.8101
dimer//try5-opt1	costs 0	real_cost = 16.4515
dimer//try5-opt1-scwrl	costs 0	real_cost = 16.5505
dimer//try4-opt2.unpack	costs 0	real_cost = 18.7302
dimer//try4-opt2.unpack.gromacs0.repack-nonPC	costs 0	real_cost = 15.1923
dimer//try4-opt2.unpack.gromacs0	costs 0	real_cost = 14.0688
dimer//try4-opt2.repack-nonPC	costs 0	real_cost = 19.293
dimer//try4-opt2	costs 0	real_cost = 18.7302
dimer//try4-opt2.gromacs0	costs 0	real_cost = 16.1364
dimer//try4-opt1	costs 0	real_cost = 22.0614
dimer//try4-opt1-scwrl	costs 0	real_cost = 22.5038
dimer//try3-opt2.unpack	costs 0	real_cost = -3.80122
dimer//try3-opt2.unpack.gromacs0.repack-nonPC	costs 0	real_cost = -6.4698
dimer//try3-opt2.unpack.gromacs0	costs 0	real_cost = -8.32947
dimer//try3-opt2.repack-nonPC	costs 0	real_cost = -3.48974
dimer//try3-opt2	costs 0	real_cost = -3.80122
dimer//try3-opt2.gromacs0	costs 0	real_cost = -9.36313
dimer//try3-opt1	costs 0	real_cost = -3.69933
dimer//try3-opt1-scwrl	costs 0	real_cost = -1.50916
dimer//try2-opt2.unpack	costs 0	real_cost = 95.5864
dimer//try2-opt2.unpack.gromacs0.repack-nonPC	costs 0	real_cost = 97.4014
dimer//try2-opt2.unpack.gromacs0	costs 0	real_cost = 92.7752
dimer//try2-opt2.repack-nonPC	costs 0	real_cost = 96.0937
dimer//try2-opt2	costs 0	real_cost = 95.5864
dimer//try2-opt2.gromacs0	costs 0	real_cost = 94.3468
dimer//try2-opt1	costs 0	real_cost = 96.8335
dimer//try2-opt1-scwrl	costs 0	real_cost = 98.9457
dimer//try15-opt2.unpack	costs 0	real_cost = 28.1131
dimer//try15-opt2.unpack.gromacs0.repack-nonPC	costs 0	real_cost = 23.4107
dimer//try15-opt2.unpack.gromacs0	costs 0	real_cost = 26.1869
dimer//try15-opt2.repack-nonPC	costs 0	real_cost = 26.3595
dimer//try15-opt2	costs 0	real_cost = 28.1131
dimer//try15-opt1	costs 0	real_cost = 26.0797
dimer//try15-opt1-scwrl	costs 0	real_cost = 26.5685
dimer//try14-opt2.unpack	costs 0	real_cost = 30.8918
dimer//try14-opt2.unpack.gromacs0.repack-nonPC	costs 0	real_cost = 30.0537
dimer//try14-opt2.unpack.gromacs0	costs 0	real_cost = 31.5825
dimer//try14-opt2.repack-nonPC	costs 0	real_cost = 26.8851
dimer//try14-opt2	costs 0	real_cost = 30.8918
dimer//try14-opt2.gromacs0	costs 0	real_cost = 33.644
dimer//try14-opt1	costs 0	real_cost = 30.0577
dimer//try14-opt1-scwrl	costs 0	real_cost = 28.3901
dimer//try13-opt2.unpack	costs 0	real_cost = 13.903
dimer//try13-opt2.unpack.gromacs0.repack-nonPC	costs 0	real_cost = 6.68823
dimer//try13-opt2.unpack.gromacs0	costs 0	real_cost = 9.68464
dimer//try13-opt2.repack-nonPC	costs 0	real_cost = 9.68246
dimer//try13-opt2	costs 0	real_cost = 13.903
dimer//try13-opt2.gromacs0	costs 0	real_cost = 12.2828
dimer//try13-opt1	costs 0	real_cost = 14.2894
dimer//try13-opt1-scwrl	costs 0	real_cost = 10.3299
dimer//try12-opt2.unpack	costs 0	real_cost = 11.2169
dimer//try12-opt2.unpack.gromacs0.repack-nonPC	costs 0	real_cost = 9.56525
dimer//try12-opt2.unpack.gromacs0	costs 0	real_cost = 10.8933
dimer//try12-opt2.repack-nonPC	costs 0	real_cost = 7.62613
dimer//try12-opt2	costs 0	real_cost = 11.2169
dimer//try12-opt2.gromacs0	costs 0	real_cost = 13.6191
dimer//try12-opt1	costs 0	real_cost = 13.6113
dimer//try12-opt1-scwrl	costs 0	real_cost = 10.8169
dimer//try11-opt2.unpack	costs 0	real_cost = 30.1699
dimer//try11-opt2.unpack.gromacs0.repack-nonPC	costs 0	real_cost = 24.7418
dimer//try11-opt2.unpack.gromacs0	costs 0	real_cost = 29.2956
dimer//try11-opt2.repack-nonPC	costs 0	real_cost = 24.9204
dimer//try11-opt2	costs 0	real_cost = 30.1699
dimer//try11-opt2.gromacs0	costs 0	real_cost = 30.5699
dimer//try11-opt1	costs 0	real_cost = 30.1577
dimer//try11-opt1-scwrl	costs 0	real_cost = 24.999
dimer//try10-opt2.unpack	costs 0	real_cost = 31.6591
dimer//try10-opt2.unpack.gromacs0.repack-nonPC	costs 0	real_cost = 25.7272
dimer//try10-opt2.unpack.gromacs0	costs 0	real_cost = 35.5329
dimer//try10-opt2.repack-nonPC	costs 0	real_cost = 24.2862
dimer//try10-opt2	costs 0	real_cost = 31.6591
dimer//try10-opt2.gromacs0	costs 0	real_cost = 36.7327
dimer//try10-opt1	costs 0	real_cost = 30.0786
dimer//try10-opt1-scwrl	costs 0	real_cost = 24.7975
dimer//try1-opt2.unpack	costs 0	real_cost = 77.3819
dimer//try1-opt2.unpack.gromacs0.repack-nonPC	costs 0	real_cost = 80.1456
dimer//try1-opt2.unpack.gromacs0	costs 0	real_cost = 79.4136
dimer//try1-opt2.repack-nonPC	costs 0	real_cost = 80.325
dimer//try1-opt2	costs 0	real_cost = 77.3819
dimer//try1-opt2.gromacs0	costs 0	real_cost = 80.1349
dimer//try1-opt1	costs 0	real_cost = 86.3638
dimer//try1-opt1-scwrl	costs 0	real_cost = 80.6595
T0327.try4-opt2.repack-nonPC.pdb.gz	costs 0	real_cost = 41.9176
T0327.try4-opt2.pdb.gz	costs 0	real_cost = 45.8474
T0327.try4-opt2.gromacs0.pdb.gz	costs 0	real_cost = 46.2651
T0327.try4-opt1.pdb.gz	costs 0	real_cost = 38.5757
T0327.try4-opt1-scwrl.pdb.gz	costs 0	real_cost = 39.4056
T0327.try3-opt2.repack-nonPC.pdb.gz	costs 0	real_cost = 83.5423
T0327.try3-opt2.pdb.gz	costs 0	real_cost = 81.2981
T0327.try3-opt2.gromacs0.pdb.gz	costs 0	real_cost = 79.6439
T0327.try3-opt1.pdb.gz	costs 0	real_cost = 80.0803
T0327.try3-opt1-scwrl.pdb.gz	costs 0	real_cost = 77.6176
T0327.try2-opt2.repack-nonPC.pdb.gz	costs 0	real_cost = -11.185
T0327.try2-opt2.pdb.gz	costs 0	real_cost = -7.40696
T0327.try2-opt2.gromacs0.pdb.gz	costs 0	real_cost = -6.83098
T0327.try2-opt1.pdb.gz	costs 0	real_cost = -7.37116
T0327.try2-opt1-scwrl.pdb.gz	costs 0	real_cost = -7.38925
T0327.try1-opt2.repack-nonPC.pdb.gz	costs 0	real_cost = -2.01367
T0327.try1-opt2.pdb.gz	costs 0	real_cost = -5.0458
T0327.try1-opt2.gromacs0.pdb.gz	costs 0	real_cost = -5.96059
T0327.try1-opt2-proteinshop.pdb.gz	costs 0	real_cost = 15.375
T0327.try1-opt2-proteinshop-2.pdb.gz	costs 0	real_cost = 15.375
T0327.try1-opt1.pdb.gz	costs 0	real_cost = -3.61773
T0327.try1-opt1-scwrl.pdb.gz	costs 0	real_cost = -3.32304
../model5.ts-submitted	costs 0	real_cost = -29.086
../model4.ts-submitted	costs 0	real_cost = -7.18743
../model3.ts-submitted	costs 0	real_cost = 46.577
../model2.ts-submitted	costs 0	real_cost = 13.8761
../model1.ts-submitted	costs 0	real_cost = 30.9044
align5	costs 0	real_cost = 61.2526
align4	costs 0	real_cost = -14.5865
align3	costs 0	real_cost = -8.18731
align2	costs 0	real_cost = -19.5595
align1	costs 0	real_cost = -0.812491
T0327.try1-opt2.pdb	costs 0	real_cost = -5.0458
model5-scwrl	costs 0	real_cost = -25.2415
model5.ts-submitted	costs 0	real_cost = -29.086
model4-scwrl	costs 0	real_cost = 7.00895
model4.ts-submitted	costs 0	real_cost = -7.18743
model3-scwrl	costs 0	real_cost = 44.2536
model3.ts-submitted	costs 0	real_cost = 46.577
model2-scwrl	costs 0	real_cost = 11.5072
model2.ts-submitted	costs 0	real_cost = 13.8761
model1-scwrl	costs 0	real_cost = 28.5254
model1.ts-submitted	costs 0	real_cost = 30.9044
T0327_1.real.pdb	costs 0	real_cost = -842.8
# command:CPU_time= 138.977 sec, elapsed time= 328.5 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