# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading dunbrack-2191.atoms # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 53157 examples # computed average trans backbone unit before proline from 2010 examples # computed average cis backbone unit from 97 examples # trans (non-proline) backbone unit: # CA= -2.2087 1.0126 -0.0030 # O= -0.1499 2.2440 0.0016 # 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= -0.1436 2.4534 -0.0002 # O= -2.0284 0.9742 0.0015 # C= -0.8018 1.0771 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4668 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2100 1.0631 -0.0014 # O= -0.1236 2.2458 0.0075 # C= -0.6872 1.1517 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading dunbrack-2191.atoms have 2191 chains in training database # Count of chains,residues,atoms: 2191,500310,3902258 # 493341 residues have no bad marker # 3226 residues lack atoms needed to compute omega # 1453 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 4 # HAS_OXT 1167 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 3052 # HAS_UNKNOWN_ATOMS 9 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 979 # NON_PLANAR_PEPTIDE 888 # BAD_PEPTIDE 2680 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-2191.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:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0364/ # command:# Making conformation for sequence T0364 numbered 1 through 156 Created new target T0364 from T0364.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0364/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0364//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0364/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0364//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0364/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0364/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0364/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cyeA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2cyeA expands to /projects/compbio/data/pdb/2cye.pdb.gz 2cyeA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0364 read from 2cyeA/merged-good-all-a2m # 2cyeA read from 2cyeA/merged-good-all-a2m # adding 2cyeA to template set # found chain 2cyeA in template set Warning: unaligning (T0364)I42 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cyeA)D46 Warning: unaligning (T0364)D45 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2cyeA)D46 T0364 4 :LITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDR 2cyeA 5 :PVRVRVDVRFRDLDPLGHVNNAVFLSYMELARIRYFQR # choosing archetypes in rotamer library T0364 46 :ADSRGQ 2cyeA 47 :WLEEGH T0364 56 :LFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRA 2cyeA 53 :FVVARMEVDYLRPILLGDEVFVGVRTVGLGRSSLRMEHLVTAN T0364 101 :DEVLAASEQMLLHV 2cyeA 96 :GESAAKGLGVLVWL T0364 117 :AGPQSAPFGHTTVCRLNHLVEQ 2cyeA 110 :EGGRPAPLPEAIRERIRALEGR Number of specific fragments extracted= 5 number of extra gaps= 0 total=5 Number of alignments=1 # 2cyeA read from 2cyeA/merged-good-all-a2m # found chain 2cyeA in template set Warning: unaligning (T0364)I42 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cyeA)D46 Warning: unaligning (T0364)D45 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2cyeA)D46 Warning: unaligning (T0364)Q139 because last residue in template chain is (2cyeA)P132 T0364 3 :A 2cyeA 3 :G T0364 4 :LITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDR 2cyeA 5 :PVRVRVDVRFRDLDPLGHVNNAVFLSYMELARIRYFQR T0364 46 :ADSRGQ 2cyeA 47 :WLEEGH T0364 56 :LFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRA 2cyeA 53 :FVVARMEVDYLRPILLGDEVFVGVRTVGLGRSSLRMEHLVTAN T0364 101 :DEVLAASEQMLLHV 2cyeA 96 :GESAAKGLGVLVWL T0364 117 :AGPQSAPFGHTTVCRLNHLVEQ 2cyeA 110 :EGGRPAPLPEAIRERIRALEGR Number of specific fragments extracted= 6 number of extra gaps= 0 total=11 Number of alignments=2 # 2cyeA read from 2cyeA/merged-good-all-a2m # found chain 2cyeA in template set Warning: unaligning (T0364)I42 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cyeA)D46 Warning: unaligning (T0364)D45 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2cyeA)D46 T0364 4 :LITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDR 2cyeA 5 :PVRVRVDVRFRDLDPLGHVNNAVFLSYMELARIRYFQR T0364 46 :ADSR 2cyeA 47 :WLEE T0364 54 :NSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHR 2cyeA 51 :GHFVVARMEVDYLRPILLGDEVFVGVRTVGLGRSSLRMEHLVTA T0364 100 :FDEVLAASEQMLLHVD 2cyeA 95 :NGESAAKGLGVLVWLE T0364 118 :GPQSAPFGHTTVCRLNHLV 2cyeA 111 :GGRPAPLPEAIRERIRALE Number of specific fragments extracted= 5 number of extra gaps= 0 total=16 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y7uA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0364/1y7uA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0364/1y7uA/merged-good-all-a2m.gz for input Trying 1y7uA/merged-good-all-a2m Error: Couldn't open file 1y7uA/merged-good-all-a2m or 1y7uA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ixlA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ixlA expands to /projects/compbio/data/pdb/1ixl.pdb.gz 1ixlA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0364 read from 1ixlA/merged-good-all-a2m # 1ixlA read from 1ixlA/merged-good-all-a2m # adding 1ixlA to template set # found chain 1ixlA in template set T0364 3 :ALITYRTTVQEDWV 1ixlA 26 :GYAEVELETIDEMK T0364 17 :DYNGHLRDAFYLLIFSYATDALM 1ixlA 41 :DEKGLVHGGFTFGLADYAAMLAV T0364 50 :GQSGN 1ixlA 64 :NEPTV T0364 57 :FTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRA 1ixlA 69 :VLGKAEVRFTKPVKVGDKLVAKAKIIEDLGKKKIVEVKVYRE T0364 101 :DEVLAASEQMLLHV 1ixlA 111 :EEVVLEGKFYCYVL T0364 117 :AG 1ixlA 125 :EK Number of specific fragments extracted= 6 number of extra gaps= 0 total=22 Number of alignments=4 # 1ixlA read from 1ixlA/merged-good-all-a2m # found chain 1ixlA in template set T0364 5 :ITYRTTVQEDWV 1ixlA 28 :AEVELETIDEMK T0364 17 :DYNGHLRDAFYLLIFSYATD 1ixlA 41 :DEKGLVHGGFTFGLADYAAM T0364 46 :ADS 1ixlA 61 :LAV T0364 50 :GQS 1ixlA 64 :NEP T0364 55 :SLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRA 1ixlA 67 :TVVLGKAEVRFTKPVKVGDKLVAKAKIIEDLGKKKIVEVKVYRE T0364 101 :DEVLAASEQMLLHV 1ixlA 111 :EEVVLEGKFYCYVL T0364 117 :AG 1ixlA 125 :EK Number of specific fragments extracted= 7 number of extra gaps= 0 total=29 Number of alignments=5 # 1ixlA read from 1ixlA/merged-good-all-a2m # found chain 1ixlA in template set T0364 7 :YRTTVQEDW 1ixlA 30 :VELETIDEM T0364 17 :DYNGHLRDAFYLLIFSYATDALM 1ixlA 41 :DEKGLVHGGFTFGLADYAAMLAV T0364 54 :NSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHR 1ixlA 66 :PTVVLGKAEVRFTKPVKVGDKLVAKAKIIEDLGKKKIVEVKVYR T0364 100 :FDEVLAASEQMLL 1ixlA 110 :EEEVVLEGKFYCY Number of specific fragments extracted= 4 number of extra gaps= 0 total=33 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2aliA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2aliA expands to /projects/compbio/data/pdb/2ali.pdb.gz 2aliA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 157, because occupancy 0.5 <= existing 0.500 in 2aliA Skipped atom 161, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 163, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 165, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 167, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 169, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 171, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 197, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 201, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 203, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 205, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 718, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 722, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 724, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 726, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 728, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 730, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 732, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 734, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 745, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 749, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 751, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 753, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 755, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 757, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 759, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 860, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 864, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 866, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 886, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 890, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 892, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 894, because occupancy 0.400 <= existing 0.600 in 2aliA # T0364 read from 2aliA/merged-good-all-a2m # 2aliA read from 2aliA/merged-good-all-a2m # adding 2aliA to template set # found chain 2aliA in template set Warning: unaligning (T0364)P2 because first residue in template chain is (2aliA)Q5 Warning: unaligning (T0364)A46 because of BadResidue code BAD_PEPTIDE in next template residue (2aliA)E50 Warning: unaligning (T0364)D47 because of BadResidue code BAD_PEPTIDE at template residue (2aliA)E50 T0364 3 :ALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIGLD 2aliA 6 :LLHTAHIPVRWGDMDSYGHVNNTLYFQYLEEARVAWFETLGID T0364 51 :QSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRAG 2aliA 51 :GAAEGPVVLQSLHTYLKPVVHPATVVVELYAGRLGTSSLVLEHRLHTLE T0364 100 :FDEVLAASEQMLLHVDLAGPQSAPFGHTTVCRL 2aliA 101 :PQGTYGEGHCKLVWVRHAENRSTPVPDSIRAAI Number of specific fragments extracted= 3 number of extra gaps= 1 total=36 Number of alignments=7 # 2aliA read from 2aliA/merged-good-all-a2m # found chain 2aliA in template set Warning: unaligning (T0364)A46 because of BadResidue code BAD_PEPTIDE in next template residue (2aliA)E50 Warning: unaligning (T0364)D47 because of BadResidue code BAD_PEPTIDE at template residue (2aliA)E50 T0364 4 :LITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIGLD 2aliA 7 :LHTAHIPVRWGDMDSYGHVNNTLYFQYLEEARVAWFETLGID T0364 51 :QSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRAG 2aliA 51 :GAAEGPVVLQSLHTYLKPVVHPATVVVELYAGRLGTSSLVLEHRLHTLE T0364 100 :FDEVLAASEQMLLHVDLAGPQSAPFGHTTVCRL 2aliA 101 :PQGTYGEGHCKLVWVRHAENRSTPVPDSIRAAI Number of specific fragments extracted= 3 number of extra gaps= 1 total=39 Number of alignments=8 # 2aliA read from 2aliA/merged-good-all-a2m # found chain 2aliA in template set T0364 3 :ALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIGLD 2aliA 6 :LLHTAHIPVRWGDMDSYGHVNNTLYFQYLEEARVAWFETLGID T0364 52 :SGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRAGFD 2aliA 52 :AAEGPVVLQSLHTYLKPVVHPATVVVELYAGRLGTSSLVLEHRLHTLEDP T0364 102 :EVLAASEQMLLHVDLAGPQSAPFGHTTVCRL 2aliA 103 :GTYGEGHCKLVWVRHAENRSTPVPDSIRAAI Number of specific fragments extracted= 3 number of extra gaps= 0 total=42 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zkiA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zkiA expands to /projects/compbio/data/pdb/1zki.pdb.gz 1zkiA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 33, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 35, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 37, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 39, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 41, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 43, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 45, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 47, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 49, because occupancy 0.500 <= existing 0.500 in 1zkiA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 141, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 143, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 145, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 147, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 149, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 151, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 153, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 155, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 201, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 203, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 205, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 207, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 209, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 211, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 213, because occupancy 0.500 <= existing 0.500 in 1zkiA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 299, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 303, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 305, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 307, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 309, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 311, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 313, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 315, because occupancy 0.500 <= existing 0.500 in 1zkiA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 528, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 532, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 534, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 536, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 538, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 540, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 542, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 544, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 754, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 756, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 758, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 760, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 762, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 764, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 766, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 768, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 770, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 772, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 887, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 889, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 891, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 893, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 895, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 897, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 899, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 901, because occupancy 0.500 <= existing 0.500 in 1zkiA # T0364 read from 1zkiA/merged-good-all-a2m # 1zkiA read from 1zkiA/merged-good-all-a2m # adding 1zkiA to template set # found chain 1zkiA in template set T0364 2 :PALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDAL 1zkiA 27 :DGVAEVRLPMAAHLRNRGGVMHGGALFSLMDVTMGLA T0364 46 :ADSRGQSGNSLFTLEAHINYLHEVK 1zkiA 64 :CSSSHGFDRQSVTLECKINYIRAVA T0364 72 :GTEVWVQTQILGFDRKRLHVYHSLHRA 1zkiA 89 :DGEVRCVARVLHAGRRSLVVEAEVRQG T0364 101 :DEVLAASEQMLL 1zkiA 116 :DKLVAKGQGTFA Number of specific fragments extracted= 4 number of extra gaps= 0 total=46 Number of alignments=10 # 1zkiA read from 1zkiA/merged-good-all-a2m # found chain 1zkiA in template set T0364 2 :PALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDR 1zkiA 27 :DGVAEVRLPMAAHLRNRGGVMHGGALFSLMDVTMGLACSS T0364 49 :RGQSGNSLFTLEAHINYLHEVK 1zkiA 67 :SHGFDRQSVTLECKINYIRAVA T0364 72 :GTEVWVQTQILGFDRKRLHVYHSLHRA 1zkiA 89 :DGEVRCVARVLHAGRRSLVVEAEVRQG T0364 101 :DEVLAASEQMLL 1zkiA 116 :DKLVAKGQGTFA Number of specific fragments extracted= 4 number of extra gaps= 0 total=50 Number of alignments=11 # 1zkiA read from 1zkiA/merged-good-all-a2m # found chain 1zkiA in template set T0364 2 :PALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRI 1zkiA 27 :DGVAEVRLPMAAHLRNRGGVMHGGALFSLMDVTMGLACSSS T0364 50 :GQSGNSLFTLEAHINYLHEVK 1zkiA 68 :HGFDRQSVTLECKINYIRAVA T0364 72 :GTEVWVQTQILGFDRKRLHVYHSLHR 1zkiA 89 :DGEVRCVARVLHAGRRSLVVEAEVRQ T0364 100 :FDEVLAASEQMLL 1zkiA 115 :GDKLVAKGQGTFA Number of specific fragments extracted= 4 number of extra gaps= 0 total=54 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yliA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yliA expands to /projects/compbio/data/pdb/1yli.pdb.gz 1yliA:Skipped atom 122, because occupancy 0.500 <= existing 0.500 in 1yliA Skipped atom 124, because occupancy 0.500 <= existing 0.500 in 1yliA Skipped atom 588, because occupancy 0.500 <= existing 0.500 in 1yliA Skipped atom 590, because occupancy 0.500 <= existing 0.500 in 1yliA Skipped atom 592, because occupancy 0.500 <= existing 0.500 in 1yliA Skipped atom 594, because occupancy 0.500 <= existing 0.500 in 1yliA Skipped atom 596, because occupancy 0.500 <= existing 0.500 in 1yliA Skipped atom 598, because occupancy 0.500 <= existing 0.500 in 1yliA Skipped atom 600, because occupancy 0.500 <= existing 0.500 in 1yliA # T0364 read from 1yliA/merged-good-all-a2m # 1yliA read from 1yliA/merged-good-all-a2m # adding 1yliA to template set # found chain 1yliA in template set Warning: unaligning (T0364)R8 because of BadResidue code BAD_PEPTIDE in next template residue (1yliA)T21 Warning: unaligning (T0364)T9 because of BadResidue code BAD_PEPTIDE at template residue (1yliA)T21 Warning: unaligning (T0364)A142 because last residue in template chain is (1yliA)Q152 T0364 7 :Y 1yliA 19 :L T0364 10 :TVQEDWVDYNGHLRDAFYLLIFSYATDAL 1yliA 22 :LAMPSDTNANGDIFGGWIMSQMDMGGAIL T0364 46 :ADSRGQSGNSLFTLE 1yliA 51 :AKEIAHGRVVTVAVE T0364 62 :HINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHR 1yliA 66 :SMNFIKPISVGDVVCCYGQCLKVGRSSIKIKVEVWV T0364 100 :FDEVLAASEQMLLHVD 1yliA 111 :ERYCVTDAVFTFVAVD T0364 117 :AGPQSAPFGHTTVCRLNHLVEQQEG 1yliA 127 :NNGRSRTIPRENNQELEKALALISE Number of specific fragments extracted= 6 number of extra gaps= 1 total=60 Number of alignments=13 # 1yliA read from 1yliA/merged-good-all-a2m # found chain 1yliA in template set Warning: unaligning (T0364)R8 because of BadResidue code BAD_PEPTIDE in next template residue (1yliA)T21 Warning: unaligning (T0364)T9 because of BadResidue code BAD_PEPTIDE at template residue (1yliA)T21 Warning: unaligning (T0364)A142 because last residue in template chain is (1yliA)Q152 T0364 4 :LITY 1yliA 16 :VLLL T0364 10 :TVQEDWVDYNGHLRDAFYLLIFSYATDALMDRI 1yliA 22 :LAMPSDTNANGDIFGGWIMSQMDMGGAILAKEI T0364 46 :A 1yliA 55 :A T0364 53 :GNSLFTLEAH 1yliA 56 :HGRVVTVAVE T0364 63 :INYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHR 1yliA 67 :MNFIKPISVGDVVCCYGQCLKVGRSSIKIKVEVWV T0364 98 :AGFDEVLAASEQMLLHVD 1yliA 109 :IGERYCVTDAVFTFVAVD T0364 117 :AGPQSAPFGHTTVCRLNHLVEQQEG 1yliA 127 :NNGRSRTIPRENNQELEKALALISE Number of specific fragments extracted= 7 number of extra gaps= 1 total=67 Number of alignments=14 # 1yliA read from 1yliA/merged-good-all-a2m # found chain 1yliA in template set Warning: unaligning (T0364)R8 because of BadResidue code BAD_PEPTIDE in next template residue (1yliA)T21 Warning: unaligning (T0364)T9 because of BadResidue code BAD_PEPTIDE at template residue (1yliA)T21 Warning: unaligning (T0364)A142 because last residue in template chain is (1yliA)Q152 T0364 7 :Y 1yliA 19 :L T0364 10 :TVQEDWVDYNGHLRDAFYLLIFSYATDALMDRI 1yliA 22 :LAMPSDTNANGDIFGGWIMSQMDMGGAILAKEI T0364 51 :QSG 1yliA 55 :AHG T0364 55 :SLFTLEAH 1yliA 58 :RVVTVAVE T0364 63 :INYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLH 1yliA 67 :MNFIKPISVGDVVCCYGQCLKVGRSSIKIKVEVW T0364 98 :AGFDEVLAASEQMLLHVD 1yliA 109 :IGERYCVTDAVFTFVAVD T0364 117 :AGPQSAPFGHTTVCRLNHLVEQQEG 1yliA 127 :NNGRSRTIPRENNQELEKALALISE Number of specific fragments extracted= 7 number of extra gaps= 1 total=74 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q4uA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0364 read from 1q4uA/merged-good-all-a2m # 1q4uA read from 1q4uA/merged-good-all-a2m # found chain 1q4uA in training set Warning: unaligning (T0364)P123 because last residue in template chain is (1q4uA)R150 T0364 5 :ITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALM 1q4uA 46 :ATASVEVTDTLRQRWGLVHGGAYCALAEMLATEAT T0364 46 :ADSRGQSGNSLFTLEAHINYLHEVKLG 1q4uA 81 :VAVVHEKGMMAVGQSNHTSFFRPVKEG T0364 74 :EVWVQTQILGFDRKRLHVYHSLHRAG 1q4uA 108 :HVRAEAVRIHAGSTTWFWDVSLRDDA T0364 101 :DEVLAASEQMLLH 1q4uA 134 :GRLCAVSSMSIAV T0364 120 :QSA 1q4uA 147 :RPR Number of specific fragments extracted= 5 number of extra gaps= 0 total=79 Number of alignments=16 # 1q4uA read from 1q4uA/merged-good-all-a2m # found chain 1q4uA in training set Warning: unaligning (T0364)P123 because last residue in template chain is (1q4uA)R150 T0364 5 :ITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALM 1q4uA 46 :ATASVEVTDTLRQRWGLVHGGAYCALAEMLATEAT T0364 46 :ADSRGQSGNSLFTLEAHINYLHEVKLG 1q4uA 81 :VAVVHEKGMMAVGQSNHTSFFRPVKEG T0364 74 :EVWVQTQILGFDRKRLHVYHSLHR 1q4uA 108 :HVRAEAVRIHAGSTTWFWDVSLRD T0364 99 :GFDEVLAASEQMLLH 1q4uA 132 :DAGRLCAVSSMSIAV T0364 120 :QSA 1q4uA 147 :RPR Number of specific fragments extracted= 5 number of extra gaps= 0 total=84 Number of alignments=17 # 1q4uA read from 1q4uA/merged-good-all-a2m # found chain 1q4uA in training set Warning: unaligning (T0364)P123 because last residue in template chain is (1q4uA)R150 T0364 6 :TYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALM 1q4uA 47 :TASVEVTDTLRQRWGLVHGGAYCALAEMLATEAT T0364 46 :ADSRGQSGNSLFTLEAHINYLHEVKLG 1q4uA 81 :VAVVHEKGMMAVGQSNHTSFFRPVKEG T0364 74 :EVWVQTQILGFDRKRLHVYHSLHR 1q4uA 108 :HVRAEAVRIHAGSTTWFWDVSLRD T0364 99 :GFDEVLAASEQMLLH 1q4uA 132 :DAGRLCAVSSMSIAV T0364 120 :QSA 1q4uA 147 :RPR Number of specific fragments extracted= 5 number of extra gaps= 0 total=89 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gf6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2gf6A expands to /projects/compbio/data/pdb/2gf6.pdb.gz 2gf6A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0364 read from 2gf6A/merged-good-all-a2m # 2gf6A read from 2gf6A/merged-good-all-a2m # adding 2gf6A to template set # found chain 2gf6A in template set Warning: unaligning (T0364)V114 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gf6A)N114 Warning: unaligning (T0364)D115 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gf6A)N114 T0364 3 :ALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALM 2gf6A 4 :IEYVFEDVVRIYDTDAQGIAHYAAYYRFFTNTIEKFI T0364 40 :DRIGLDA 2gf6A 42 :EKVGIPY T0364 51 :QSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRA 2gf6A 52 :NENLWFVIAESHAIYHRPVKLGDKLTVLLNPKILSNKTIKFEFKVLKD T0364 101 :DEVLAASEQMLLH 2gf6A 100 :GELTTEGYVIQIA T0364 116 :LAGPQSAPFGHTTVCRL 2gf6A 115 :PKIWKSTEMPKEIMDKL Number of specific fragments extracted= 5 number of extra gaps= 1 total=94 Number of alignments=19 # 2gf6A read from 2gf6A/merged-good-all-a2m # found chain 2gf6A in template set Warning: unaligning (T0364)V114 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gf6A)N114 Warning: unaligning (T0364)D115 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gf6A)N114 T0364 1 :MPAL 2gf6A 1 :MENI T0364 5 :ITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDR 2gf6A 6 :YVFEDVVRIYDTDAQGIAHYAAYYRFFTNTIEKFIKE T0364 42 :IGLDAD 2gf6A 44 :VGIPYP T0364 51 :QSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRA 2gf6A 52 :NENLWFVIAESHAIYHRPVKLGDKLTVLLNPKILSNKTIKFEFKVLKD T0364 101 :DEVLAASEQMLLH 2gf6A 100 :GELTTEGYVIQIA T0364 116 :LAGPQSAPFGHTTVCRL 2gf6A 115 :PKIWKSTEMPKEIMDKL Number of specific fragments extracted= 6 number of extra gaps= 1 total=100 Number of alignments=20 # 2gf6A read from 2gf6A/merged-good-all-a2m # found chain 2gf6A in template set Warning: unaligning (T0364)V114 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gf6A)N114 Warning: unaligning (T0364)D115 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gf6A)N114 T0364 6 :TYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALM 2gf6A 7 :VFEDVVRIYDTDAQGIAHYAAYYRFFTNTIEKFI T0364 40 :DRIGLDA 2gf6A 42 :EKVGIPY T0364 52 :SGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHR 2gf6A 53 :ENLWFVIAESHAIYHRPVKLGDKLTVLLNPKILSNKTIKFEFKVLK T0364 100 :FDEVLAASEQMLLH 2gf6A 99 :DGELTTEGYVIQIA T0364 116 :LAGPQSAPFGHTTVCRL 2gf6A 115 :PKIWKSTEMPKEIMDKL Number of specific fragments extracted= 5 number of extra gaps= 1 total=105 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b3nA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2b3nA expands to /projects/compbio/data/pdb/2b3n.pdb.gz 2b3nA:Skipped atom 125, because occupancy 0.330 <= existing 0.330 in 2b3nA Skipped atom 126, because occupancy 0.330 <= existing 0.330 in 2b3nA Skipped atom 130, because occupancy 0.330 <= existing 0.330 in 2b3nA Skipped atom 131, because occupancy 0.330 <= existing 0.330 in 2b3nA Skipped atom 133, because occupancy 0.330 <= existing 0.330 in 2b3nA Skipped atom 134, because occupancy 0.330 <= existing 0.330 in 2b3nA Skipped atom 146, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 150, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 152, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 154, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 156, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 158, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 254, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 258, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 260, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 262, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 264, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 266, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 269, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 273, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 275, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 277, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 279, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 338, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 342, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 344, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 346, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 348, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 350, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 365, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 369, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 371, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 373, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 375, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 377, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 448, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 450, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 452, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 454, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 456, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 458, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 460, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 462, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 676, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 680, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 682, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 684, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 731, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 735, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 737, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 827, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 831, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 833, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 835, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 853, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 855, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 857, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 859, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 861, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 863, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 865, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 867, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 869, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 880, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 882, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 884, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 886, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 888, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 890, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1017, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1021, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1023, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1025, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1027, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1029, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1036, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1040, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1042, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1044, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1054, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1058, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1060, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1092, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1096, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1098, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1100, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1102, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1245, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1249, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1251, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1253, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1262, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1264, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1266, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1268, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1270, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1272, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1274, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1276, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1278, because occupancy 0.500 <= existing 0.500 in 2b3nA # T0364 read from 2b3nA/merged-good-all-a2m # 2b3nA read from 2b3nA/merged-good-all-a2m # adding 2b3nA to template set # found chain 2b3nA in template set Warning: unaligning (T0364)H96 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2b3nA)T144 Warning: unaligning (T0364)R97 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2b3nA)T144 T0364 2 :PALITYRTTVQE 2b3nA 39 :GYRFEYEKKLCE T0364 33 :YATDALMDRIGL 2b3nA 51 :IDVAMFGLISGD T0364 45 :DADSRGQS 2b3nA 69 :DEDFASKT T0364 53 :GNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSL 2b3nA 100 :PGTVVLLEQSFRYTSPVRIGDVVRVEGVVSGVEKNRYTIDVKC T0364 98 :A 2b3nA 145 :G T0364 101 :DEVLAASEQMLLH 2b3nA 146 :DKVVAEGVVKVLI Number of specific fragments extracted= 6 number of extra gaps= 1 total=111 Number of alignments=22 # 2b3nA read from 2b3nA/merged-good-all-a2m # found chain 2b3nA in template set Warning: unaligning (T0364)H96 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2b3nA)T144 Warning: unaligning (T0364)R97 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2b3nA)T144 T0364 2 :PALITYRTTVQE 2b3nA 39 :GYRFEYEKKLCE T0364 33 :YATDALMDRIGLDAD 2b3nA 51 :IDVAMFGLISGDLNP T0364 48 :SRGQSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSL 2b3nA 95 :AVARLPGTVVLLEQSFRYTSPVRIGDVVRVEGVVSGVEKNRYTIDVKC T0364 98 :A 2b3nA 145 :G T0364 101 :DEVLAASEQMLLH 2b3nA 146 :DKVVAEGVVKVLI Number of specific fragments extracted= 5 number of extra gaps= 1 total=116 Number of alignments=23 # 2b3nA read from 2b3nA/merged-good-all-a2m # found chain 2b3nA in template set Warning: unaligning (T0364)H96 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2b3nA)T144 Warning: unaligning (T0364)R97 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2b3nA)T144 T0364 3 :ALITYRTTVQEDWVDYNG 2b3nA 40 :YRFEYEKKLCEIDVAMFG T0364 21 :HLRDAFYLLIFSYA 2b3nA 82 :VVHGMLTTSLVSAA T0364 49 :RGQSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSL 2b3nA 96 :VARLPGTVVLLEQSFRYTSPVRIGDVVRVEGVVSGVEKNRYTIDVKC T0364 100 :FDEVLAASEQMLLH 2b3nA 145 :GDKVVAEGVVKVLI Number of specific fragments extracted= 4 number of extra gaps= 1 total=120 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2av9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2av9A expands to /projects/compbio/data/pdb/2av9.pdb.gz 2av9A:Skipped atom 226, because occupancy 0.500 <= existing 0.500 in 2av9A Skipped atom 230, because occupancy 0.500 <= existing 0.500 in 2av9A Skipped atom 232, because occupancy 0.500 <= existing 0.500 in 2av9A Skipped atom 234, because occupancy 0.500 <= existing 0.500 in 2av9A Skipped atom 236, because occupancy 0.500 <= existing 0.500 in 2av9A Skipped atom 238, because occupancy 0.500 <= existing 0.500 in 2av9A Skipped atom 240, because occupancy 0.500 <= existing 0.500 in 2av9A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0364 read from 2av9A/merged-good-all-a2m # 2av9A read from 2av9A/merged-good-all-a2m # adding 2av9A to template set # found chain 2av9A in template set Warning: unaligning (T0364)K70 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2av9A)F78 Warning: unaligning (T0364)L71 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2av9A)F78 T0364 4 :LITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALM 2av9A 13 :LHFQPISTRWHDNDIYGHVNNVTYYAFFDTAVNTYL T0364 40 :DRIGLDAD 2av9A 50 :ERGGLDIQ T0364 51 :QSGNSLFTLEAHINYLHEV 2av9A 58 :GGEVIGLVVSSSCDYFAPV T0364 72 :GTEVWVQTQILGFDRKRLHVYHSLHRAGFDEVLAASEQMLLHVDLAGPQSAPFGHTTVCRLNH 2av9A 79 :PQRIEMGLRVARLGNSSVQYELALFLEGQREACAAGRFVHVFVERRSSRPVAIPQELRDALAA Number of specific fragments extracted= 4 number of extra gaps= 1 total=124 Number of alignments=25 # 2av9A read from 2av9A/merged-good-all-a2m # found chain 2av9A in template set Warning: unaligning (T0364)K70 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2av9A)F78 Warning: unaligning (T0364)L71 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2av9A)F78 T0364 4 :LITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDR 2av9A 13 :LHFQPISTRWHDNDIYGHVNNVTYYAFFDTAVNTYLIE T0364 42 :IGLDAD 2av9A 52 :GGLDIQ T0364 51 :QSGNSLFTLEAHINYLHEV 2av9A 58 :GGEVIGLVVSSSCDYFAPV T0364 72 :GTEVWVQTQILGFDRKRLHVYHSLHRAGFDEVLAASEQMLLHVDLAGPQSAPFGHTTVCRLNH 2av9A 79 :PQRIEMGLRVARLGNSSVQYELALFLEGQREACAAGRFVHVFVERRSSRPVAIPQELRDALAA Number of specific fragments extracted= 4 number of extra gaps= 1 total=128 Number of alignments=26 # 2av9A read from 2av9A/merged-good-all-a2m # found chain 2av9A in template set Warning: unaligning (T0364)K70 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2av9A)F78 Warning: unaligning (T0364)L71 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2av9A)F78 T0364 4 :LITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALM 2av9A 13 :LHFQPISTRWHDNDIYGHVNNVTYYAFFDTAVNTYL T0364 40 :DRIGLD 2av9A 50 :ERGGLD T0364 51 :QSGN 2av9A 56 :IQGG T0364 55 :SLFTLEAHINYLHEV 2av9A 62 :IGLVVSSSCDYFAPV T0364 72 :GTEVWVQTQILGFDRKRLHVYHSLHRAGFDEVLAASEQMLLHVDLAGPQSAPFGHTTVCRLNH 2av9A 79 :PQRIEMGLRVARLGNSSVQYELALFLEGQREACAAGRFVHVFVERRSSRPVAIPQELRDALAA Number of specific fragments extracted= 5 number of extra gaps= 1 total=133 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2h4uA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2h4uA expands to /projects/compbio/data/pdb/2h4u.pdb.gz 2h4uA:# T0364 read from 2h4uA/merged-good-all-a2m # 2h4uA read from 2h4uA/merged-good-all-a2m # adding 2h4uA to template set # found chain 2h4uA in template set T0364 3 :ALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRI 2h4uA 36 :GKVICEMKVEEEHTNAIGTLHGGLTATLVDNISTMALLCT T0364 51 :QSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRAGFDEVLAASEQMLL 2h4uA 76 :ERGAPGVSVDMNITYMSPAKLGEDIVITAHVLKQGKTLAFTSVDLTNKATGKLIAQGRHTKH Number of specific fragments extracted= 2 number of extra gaps= 0 total=135 Number of alignments=28 # 2h4uA read from 2h4uA/merged-good-all-a2m # found chain 2h4uA in template set T0364 4 :LITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRI 2h4uA 37 :KVICEMKVEEEHTNAIGTLHGGLTATLVDNISTMALLCT T0364 51 :QSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRAGFDEVLAASEQMLL 2h4uA 76 :ERGAPGVSVDMNITYMSPAKLGEDIVITAHVLKQGKTLAFTSVDLTNKATGKLIAQGRHTKH Number of specific fragments extracted= 2 number of extra gaps= 0 total=137 Number of alignments=29 # 2h4uA read from 2h4uA/merged-good-all-a2m # found chain 2h4uA in template set T0364 6 :TYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRI 2h4uA 39 :ICEMKVEEEHTNAIGTLHGGLTATLVDNISTMALLCT T0364 51 :QSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRAGFDEVLAASEQML 2h4uA 76 :ERGAPGVSVDMNITYMSPAKLGEDIVITAHVLKQGKTLAFTSVDLTNKATGKLIAQGRHTK Number of specific fragments extracted= 2 number of extra gaps= 0 total=139 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gvhA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2gvhA expands to /projects/compbio/data/pdb/2gvh.pdb.gz 2gvhA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0364 read from 2gvhA/merged-good-all-a2m # 2gvhA read from 2gvhA/merged-good-all-a2m # adding 2gvhA to template set # found chain 2gvhA in template set Warning: unaligning (T0364)L4 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gvhA)A147 Warning: unaligning (T0364)D115 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gvhA)R258 Warning: unaligning (T0364)Q120 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gvhA)R258 Warning: unaligning (T0364)F124 because last residue in template chain is (2gvhA)I262 T0364 5 :ITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALM 2gvhA 148 :VTMVEIVFPDQANSAGRMFGGEAIAYMTKAAFVAA T0364 47 :DSRG 2gvhA 183 :SRYC T0364 53 :GNSLFTLEAH 2gvhA 187 :GKLVVLASSE T0364 63 :INYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRAG 2gvhA 198 :IDFARAIEIGEIVEAQAHVERVGRSSMSIQTKLWSEN T0364 100 :FDEVLAASEQMLLHV 2gvhA 239 :ERHITATGHFTMVAV T0364 121 :SAP 2gvhA 259 :PAT Number of specific fragments extracted= 6 number of extra gaps= 0 total=145 Number of alignments=31 # 2gvhA read from 2gvhA/merged-good-all-a2m # found chain 2gvhA in template set Warning: unaligning (T0364)L4 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gvhA)A147 Warning: unaligning (T0364)D115 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gvhA)R258 Warning: unaligning (T0364)Q120 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gvhA)R258 Warning: unaligning (T0364)F124 because last residue in template chain is (2gvhA)I262 T0364 5 :ITYRTTVQEDWVDYNGHLRDAFYLLIFSYATD 2gvhA 148 :VTMVEIVFPDQANSAGRMFGGEAIAYMTKAAF T0364 46 :ADSRGQSGNSLFTLEAH 2gvhA 180 :VAASRYCGKLVVLASSE T0364 63 :INYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRAG 2gvhA 198 :IDFARAIEIGEIVEAQAHVERVGRSSMSIQTKLWSEN T0364 100 :FDEVLAASEQMLLHV 2gvhA 239 :ERHITATGHFTMVAV T0364 121 :SAP 2gvhA 259 :PAT Number of specific fragments extracted= 5 number of extra gaps= 0 total=150 Number of alignments=32 # 2gvhA read from 2gvhA/merged-good-all-a2m # found chain 2gvhA in template set Warning: unaligning (T0364)L4 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gvhA)A147 Warning: unaligning (T0364)D115 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gvhA)R258 Warning: unaligning (T0364)Q120 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gvhA)R258 Warning: unaligning (T0364)F124 because last residue in template chain is (2gvhA)I262 T0364 5 :ITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALM 2gvhA 148 :VTMVEIVFPDQANSAGRMFGGEAIAYMTKAAFVAA T0364 49 :RGQSGNSLFTLEAH 2gvhA 183 :SRYCGKLVVLASSE T0364 63 :INYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLH 2gvhA 198 :IDFARAIEIGEIVEAQAHVERVGRSSMSIQTKLW T0364 97 :RAGFD 2gvhA 234 :NLLTG T0364 102 :EVLAASEQMLLHV 2gvhA 241 :HITATGHFTMVAV T0364 121 :SAP 2gvhA 259 :PAT Number of specific fragments extracted= 6 number of extra gaps= 0 total=156 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1njkA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1njkA expands to /projects/compbio/data/pdb/1njk.pdb.gz 1njkA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0364 read from 1njkA/merged-good-all-a2m # 1njkA read from 1njkA/merged-good-all-a2m # adding 1njkA to template set # found chain 1njkA in template set Warning: unaligning (T0364)L4 because first residue in template chain is (1njkA)H0 Warning: unaligning (T0364)E137 because last residue in template chain is (1njkA)K132 T0364 5 :ITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMD 1njkA 1 :MQTQIKVRGYHLDVYQHVNNARYLEFLEEARWDGLE T0364 46 :ADSRGQSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRAGFDEVLAASEQMLLHVDLAGPQSAPFGHTTVCRLNHLV 1njkA 41 :FQWMTAHNIAFVVVNININYRRPAVLSDLLTITSQLQQLNGKSGILSQVITLEPEGQVVADALITFVCIDLKTQKALALEGELREKLEQMV Number of specific fragments extracted= 2 number of extra gaps= 0 total=158 Number of alignments=34 # 1njkA read from 1njkA/merged-good-all-a2m # found chain 1njkA in template set Warning: unaligning (T0364)L4 because first residue in template chain is (1njkA)H0 Warning: unaligning (T0364)E137 because last residue in template chain is (1njkA)K132 T0364 5 :ITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMD 1njkA 1 :MQTQIKVRGYHLDVYQHVNNARYLEFLEEARWDGLE T0364 46 :ADSRGQSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRAGFDEVLAASEQMLLHVDLAGPQSAPFGHTTVCRLNHLV 1njkA 41 :FQWMTAHNIAFVVVNININYRRPAVLSDLLTITSQLQQLNGKSGILSQVITLEPEGQVVADALITFVCIDLKTQKALALEGELREKLEQMV Number of specific fragments extracted= 2 number of extra gaps= 0 total=160 Number of alignments=35 # 1njkA read from 1njkA/merged-good-all-a2m # found chain 1njkA in template set Warning: unaligning (T0364)L4 because first residue in template chain is (1njkA)H0 Warning: unaligning (T0364)E137 because last residue in template chain is (1njkA)K132 T0364 5 :ITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMD 1njkA 1 :MQTQIKVRGYHLDVYQHVNNARYLEFLEEARWDGLE T0364 46 :ADSRGQSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRAGFDEVLAASEQMLLHVDLAGPQSAPFGHTTVCRLNHLV 1njkA 41 :FQWMTAHNIAFVVVNININYRRPAVLSDLLTITSQLQQLNGKSGILSQVITLEPEGQVVADALITFVCIDLKTQKALALEGELREKLEQMV Number of specific fragments extracted= 2 number of extra gaps= 0 total=162 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s5uA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0364 read from 1s5uA/merged-good-all-a2m # 1s5uA read from 1s5uA/merged-good-all-a2m # found chain 1s5uA in training set Warning: unaligning (T0364)A3 because first residue in template chain is (1s5uA)T4 Warning: unaligning (T0364)L132 because last residue in template chain is (1s5uA)F132 T0364 4 :LITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIGLDADSRGQSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRAG 1s5uA 5 :LFRWPVRVYYEDTDAGGVVYHASYVAFYERARTEMLRHHHFSQQALMAERVAFVVRKMTVEYYAPARLDDMLEIQTEITSMRGTSLVFTQRIVNAE T0364 101 :DEVLAASEQMLLHVDLAGPQSAPFGHTTVCR 1s5uA 101 :NTLLNEAEVLVVCVDPLKMKPRALPKSIVAE Number of specific fragments extracted= 2 number of extra gaps= 0 total=164 Number of alignments=37 # 1s5uA read from 1s5uA/merged-good-all-a2m # found chain 1s5uA in training set Warning: unaligning (T0364)A3 because first residue in template chain is (1s5uA)T4 Warning: unaligning (T0364)L132 because last residue in template chain is (1s5uA)F132 T0364 4 :LITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIGLDADSRGQSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHR 1s5uA 5 :LFRWPVRVYYEDTDAGGVVYHASYVAFYERARTEMLRHHHFSQQALMAERVAFVVRKMTVEYYAPARLDDMLEIQTEITSMRGTSLVFTQRIVN T0364 99 :GFDEVLAASEQMLLHVDLAGPQSAPFGHTTVCR 1s5uA 99 :AENTLLNEAEVLVVCVDPLKMKPRALPKSIVAE Number of specific fragments extracted= 2 number of extra gaps= 0 total=166 Number of alignments=38 # 1s5uA read from 1s5uA/merged-good-all-a2m # found chain 1s5uA in training set Warning: unaligning (T0364)A3 because first residue in template chain is (1s5uA)T4 Warning: unaligning (T0364)L132 because last residue in template chain is (1s5uA)F132 T0364 4 :LITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIGLDADSRGQSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHR 1s5uA 5 :LFRWPVRVYYEDTDAGGVVYHASYVAFYERARTEMLRHHHFSQQALMAERVAFVVRKMTVEYYAPARLDDMLEIQTEITSMRGTSLVFTQRIVN T0364 99 :GFDEVLAASEQMLLHVDLAGPQSAPFGHTTVCR 1s5uA 99 :AENTLLNEAEVLVVCVDPLKMKPRALPKSIVAE Number of specific fragments extracted= 2 number of extra gaps= 0 total=168 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cwzA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2cwzA expands to /projects/compbio/data/pdb/2cwz.pdb.gz 2cwzA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0364 read from 2cwzA/merged-good-all-a2m # 2cwzA read from 2cwzA/merged-good-all-a2m # adding 2cwzA to template set # found chain 2cwzA in template set Warning: unaligning (T0364)Q143 because last residue in template chain is (2cwzA)R138 T0364 2 :PALITYRTTVQEDWV 2cwzA 7 :GYEAVFETVVTPEMT T0364 22 :LRDAFYLLIFSYATDAL 2cwzA 34 :YATYWMVKHMELAGRKI T0364 46 :ADSRGQSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRAG 2cwzA 51 :ILPFLEEGEEGIGSYVEARHLASALPGMRVRVVARHEKTEGNRVYARVEAYNEL T0364 101 :DEVLAASEQMLLHVD 2cwzA 105 :GDLIGVGRTEQVILP T0364 125 :GHTTVCRLNHLVEQQEGA 2cwzA 120 :KAKVEALFRRLKERWEAE Number of specific fragments extracted= 5 number of extra gaps= 0 total=173 Number of alignments=40 # 2cwzA read from 2cwzA/merged-good-all-a2m # found chain 2cwzA in template set Warning: unaligning (T0364)Q143 because last residue in template chain is (2cwzA)R138 T0364 1 :M 2cwzA 5 :P T0364 2 :PALITYRTTVQEDWV 2cwzA 7 :GYEAVFETVVTPEMT T0364 24 :DAFYLLIFSYATDAL 2cwzA 36 :TYWMVKHMELAGRKI T0364 46 :ADSRGQSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHR 2cwzA 51 :ILPFLEEGEEGIGSYVEARHLASALPGMRVRVVARHEKTEGNRVYARVEAYN T0364 99 :GFDEVLAASEQMLLHVD 2cwzA 103 :ELGDLIGVGRTEQVILP T0364 125 :GHTTVCRLNHLVEQQEGA 2cwzA 120 :KAKVEALFRRLKERWEAE Number of specific fragments extracted= 6 number of extra gaps= 0 total=179 Number of alignments=41 # 2cwzA read from 2cwzA/merged-good-all-a2m # found chain 2cwzA in template set Warning: unaligning (T0364)Q143 because last residue in template chain is (2cwzA)R138 T0364 3 :ALITYRTTVQEDWV 2cwzA 8 :YEAVFETVVTPEMT T0364 22 :LRDAFYLLIFSYATDALMDRI 2cwzA 34 :YATYWMVKHMELAGRKIILPF T0364 44 :L 2cwzA 55 :L T0364 51 :QSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHR 2cwzA 56 :EEGEEGIGSYVEARHLASALPGMRVRVVARHEKTEGNRVYARVEAYN T0364 99 :GFDEVLAASEQMLLHVD 2cwzA 103 :ELGDLIGVGRTEQVILP T0364 125 :GHTTVCRLNHLVEQQEGA 2cwzA 120 :KAKVEALFRRLKERWEAE Number of specific fragments extracted= 6 number of extra gaps= 0 total=185 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vpmA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0364 read from 1vpmA/merged-good-all-a2m # 1vpmA read from 1vpmA/merged-good-all-a2m # found chain 1vpmA in training set Warning: unaligning (T0364)N54 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1vpmA)A53 Warning: unaligning (T0364)S55 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1vpmA)A53 T0364 4 :LITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRI 1vpmA 11 :RTIQTRLVLPPDTNHLGTIFGGKVLAYIDEIAALTAMKH T0364 52 :SG 1vpmA 50 :AN T0364 56 :LFTLEAH 1vpmA 54 :VVTASID T0364 63 :INYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRAG 1vpmA 62 :VDFKSSATVGDALELEGFVTHTGRTSMEVYVRVHSNN T0364 100 :FDEVLAASEQMLLHVD 1vpmA 103 :ERTLTTESFLTMVAVD T0364 117 :AGPQSAPFG 1vpmA 119 :ESGKPKPVP T0364 126 :HTTVCRLNHLVEQQEG 1vpmA 134 :EEEKRLYETAPARKEN Number of specific fragments extracted= 7 number of extra gaps= 1 total=192 Number of alignments=43 # 1vpmA read from 1vpmA/merged-good-all-a2m # found chain 1vpmA in training set Warning: unaligning (T0364)N54 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1vpmA)A53 Warning: unaligning (T0364)S55 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1vpmA)A53 T0364 4 :LITYRTTVQEDWVDYNGHLRDAFYLLIFSYATD 1vpmA 11 :RTIQTRLVLPPDTNHLGTIFGGKVLAYIDEIAA T0364 46 :ADSRGQSG 1vpmA 44 :LTAMKHAN T0364 56 :LFTLEAH 1vpmA 54 :VVTASID T0364 63 :INYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRAG 1vpmA 62 :VDFKSSATVGDALELEGFVTHTGRTSMEVYVRVHSNN T0364 100 :FDEVLAASEQMLLHVD 1vpmA 103 :ERTLTTESFLTMVAVD T0364 117 :AGPQSAPFG 1vpmA 119 :ESGKPKPVP T0364 126 :HTTVCRLNHLVEQQE 1vpmA 134 :EEEKRLYETAPARKE Number of specific fragments extracted= 7 number of extra gaps= 1 total=199 Number of alignments=44 # 1vpmA read from 1vpmA/merged-good-all-a2m # found chain 1vpmA in training set Warning: unaligning (T0364)N54 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1vpmA)A53 Warning: unaligning (T0364)S55 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1vpmA)A53 T0364 4 :LITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRI 1vpmA 11 :RTIQTRLVLPPDTNHLGTIFGGKVLAYIDEIAALTAMKH T0364 52 :SG 1vpmA 50 :AN T0364 56 :LFTLEAH 1vpmA 54 :VVTASID T0364 63 :INYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLH 1vpmA 62 :VDFKSSATVGDALELEGFVTHTGRTSMEVYVRVH T0364 97 :RAGFD 1vpmA 98 :NLLTG T0364 102 :EVLAASEQMLLHVD 1vpmA 105 :TLTTESFLTMVAVD T0364 117 :AGPQSAPFG 1vpmA 119 :ESGKPKPVP T0364 126 :HTTVCRLNHLVEQQEG 1vpmA 134 :EEEKRLYETAPARKEN Number of specific fragments extracted= 8 number of extra gaps= 1 total=207 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t82A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0364 read from 1t82A/merged-good-all-a2m # 1t82A read from 1t82A/merged-good-all-a2m # found chain 1t82A in training set Warning: unaligning (T0364)D115 because last residue in template chain is (1t82A)P143 T0364 13 :EDWVDYNGHLRDAFYLLIFSYATDALMDR 1t82A 41 :APNINLHHTMFAGSIYTIMTLTGWGMVWL T0364 46 :ADSRGQSGNSLFTLEAHINYLHEVKLGTEVWVQ 1t82A 70 :QQQLLNVDGDIVLADAHIRYLAPVTSAPEVKVR T0364 83 :GFDRKRLHVYHSLHRA 1t82A 113 :RGRKAKVKLEVQLFCD T0364 101 :DEVLAASEQMLLHV 1t82A 129 :GKLCAQFDGLYVSV Number of specific fragments extracted= 4 number of extra gaps= 0 total=211 Number of alignments=46 # 1t82A read from 1t82A/merged-good-all-a2m # found chain 1t82A in training set Warning: unaligning (T0364)D115 because last residue in template chain is (1t82A)P143 T0364 13 :EDWVDYNGHLRDAFYLLIFSYATDALMDR 1t82A 41 :APNINLHHTMFAGSIYTIMTLTGWGMVWL T0364 46 :ADSRGQSGNSLFTLEAHINYLHEVKLGTEVWVQ 1t82A 70 :QQQLLNVDGDIVLADAHIRYLAPVTSAPEVKVR T0364 82 :LGFDRKRLHVYHSLHRA 1t82A 112 :QRGRKAKVKLEVQLFCD T0364 101 :DEVLAASEQMLLHV 1t82A 129 :GKLCAQFDGLYVSV Number of specific fragments extracted= 4 number of extra gaps= 0 total=215 Number of alignments=47 # 1t82A read from 1t82A/merged-good-all-a2m # found chain 1t82A in training set Warning: unaligning (T0364)D115 because last residue in template chain is (1t82A)P143 T0364 22 :LRDAFYLLIFSYATDALMDR 1t82A 50 :MFAGSIYTIMTLTGWGMVWL T0364 46 :ADSRGQSGNSLFTLEAHINYLHEVKLGTEVWVQ 1t82A 70 :QQQLLNVDGDIVLADAHIRYLAPVTSAPEVKVR T0364 82 :LGFDRKRLHVYHSLHR 1t82A 112 :QRGRKAKVKLEVQLFC T0364 100 :FDEVLAASEQMLLHV 1t82A 128 :DGKLCAQFDGLYVSV Number of specific fragments extracted= 4 number of extra gaps= 0 total=219 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lo7A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0364 read from 1lo7A/merged-good-all-a2m # 1lo7A read from 1lo7A/merged-good-all-a2m # found chain 1lo7A in training set Warning: unaligning (T0364)P2 because first residue in template chain is (1lo7A)A2 T0364 3 :ALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIGLD 1lo7A 3 :RSITMQQRIEFGDCDPAGIVWYPNYHRWLDAASRNYFIKCGLP T0364 46 :ADSRG 1lo7A 47 :WRQTV T0364 51 :QSGN 1lo7A 53 :ERGI T0364 55 :SLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHR 1lo7A 58 :GTPIVSCNASFVCTASYDDVLTIETCIKEWRRKSFVQRHSVSR T0364 99 :GFD 1lo7A 103 :PGG T0364 102 :EVLAASEQMLLHV 1lo7A 108 :QLVMRADEIRVFA T0364 115 :DLAGPQSAPFGHTTVCRL 1lo7A 123 :DGERLRAIEVPADYIELC Number of specific fragments extracted= 7 number of extra gaps= 0 total=226 Number of alignments=49 # 1lo7A read from 1lo7A/merged-good-all-a2m # found chain 1lo7A in training set Warning: unaligning (T0364)P2 because first residue in template chain is (1lo7A)A2 T0364 3 :ALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIGL 1lo7A 3 :RSITMQQRIEFGDCDPAGIVWYPNYHRWLDAASRNYFIKCGL T0364 45 :DADSRG 1lo7A 46 :PWRQTV T0364 51 :QSGN 1lo7A 53 :ERGI T0364 55 :SLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHR 1lo7A 58 :GTPIVSCNASFVCTASYDDVLTIETCIKEWRRKSFVQRHSVSR T0364 99 :GFD 1lo7A 103 :PGG T0364 102 :EVLAASEQMLLHVDLAGPQSA 1lo7A 108 :QLVMRADEIRVFAMNDGERLR T0364 123 :PFGHTTVCRL 1lo7A 131 :EVPADYIELC Number of specific fragments extracted= 7 number of extra gaps= 0 total=233 Number of alignments=50 # 1lo7A read from 1lo7A/merged-good-all-a2m # found chain 1lo7A in training set Warning: unaligning (T0364)P2 because first residue in template chain is (1lo7A)A2 T0364 3 :ALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIGL 1lo7A 3 :RSITMQQRIEFGDCDPAGIVWYPNYHRWLDAASRNYFIKCGL T0364 45 :DADSRGQSGNS 1lo7A 46 :PWRQTVVERGI T0364 56 :LFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRAGFD 1lo7A 59 :TPIVSCNASFVCTASYDDVLTIETCIKEWRRKSFVQRHSVSRTTPG T0364 102 :EVLAASEQML 1lo7A 108 :QLVMRADEIR T0364 112 :LHVDLAGPQSAPFGHTTVCRL 1lo7A 120 :AMNDGERLRAIEVPADYIELC Number of specific fragments extracted= 5 number of extra gaps= 0 total=238 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vh5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0364 read from 1vh5A/merged-good-all-a2m # 1vh5A read from 1vh5A/merged-good-all-a2m # found chain 1vh5A in training set Warning: unaligning (T0364)D115 because last residue in template chain is (1vh5A)E137 T0364 2 :PALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIG 1vh5A 33 :DDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCT T0364 51 :QSGNSLFTLEAHINYLHEVKL 1vh5A 75 :EGEQKVVGLEINANHVRSARE T0364 73 :TEVWVQTQILGFDRKRLHVYHSLHRAG 1vh5A 96 :GRVRGVCKPLHLGSRHQVWQIEIFDEK T0364 101 :DEVLAASEQMLLHV 1vh5A 123 :GRLCCSSRLTTAIL Number of specific fragments extracted= 4 number of extra gaps= 0 total=242 Number of alignments=52 # 1vh5A read from 1vh5A/merged-good-all-a2m # found chain 1vh5A in training set T0364 2 :PALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIG 1vh5A 33 :DDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCT T0364 51 :QSGNSLFTLEAHINYLHEVK 1vh5A 75 :EGEQKVVGLEINANHVRSAR T0364 72 :GTEVWVQTQILGFDRKRLHVYHSLHR 1vh5A 95 :EGRVRGVCKPLHLGSRHQVWQIEIFD T0364 99 :GFDEVLAASEQMLLHV 1vh5A 121 :EKGRLCCSSRLTTAIL Number of specific fragments extracted= 4 number of extra gaps= 0 total=246 Number of alignments=53 # 1vh5A read from 1vh5A/merged-good-all-a2m # found chain 1vh5A in training set T0364 4 :LITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIG 1vh5A 35 :TLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCT T0364 51 :QSGNSLFTLEAHINYLHEVK 1vh5A 75 :EGEQKVVGLEINANHVRSAR T0364 72 :GTEVWVQTQILGFDRKRLHVYHSLHR 1vh5A 95 :EGRVRGVCKPLHLGSRHQVWQIEIFD T0364 99 :GFDEVLAASEQMLLHV 1vh5A 121 :EKGRLCCSSRLTTAIL Number of specific fragments extracted= 4 number of extra gaps= 0 total=250 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u1zA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1u1zA expands to /projects/compbio/data/pdb/1u1z.pdb.gz 1u1zA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0364 read from 1u1zA/merged-good-all-a2m # 1u1zA read from 1u1zA/merged-good-all-a2m # adding 1u1zA to template set # found chain 1u1zA in template set Warning: unaligning (T0364)H21 because of BadResidue code BAD_PEPTIDE in next template residue (1u1zA)F50 Warning: unaligning (T0364)A46 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u1zA)T85 Warning: unaligning (T0364)N54 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u1zA)T85 T0364 3 :ALITYRTTVQEDWVDYNG 1u1zA 31 :KRIRAYKNVSINEPFFNG T0364 22 :LRDAFYLLIFSYATDALMDRI 1u1zA 56 :MPGVLIIEAMAQAAGILGFKM T0364 43 :GLD 1u1zA 78 :DVK T0364 55 :SLFTLEAH 1u1zA 86 :LYYFVGSD T0364 63 :INYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRA 1u1zA 95 :LRFRQPVLPGDQLQLHAKFISVKRSIWKFDCHATVD T0364 101 :DEVLAASEQMLL 1u1zA 131 :DKPVCSAEIICA Number of specific fragments extracted= 6 number of extra gaps= 1 total=256 Number of alignments=55 # 1u1zA read from 1u1zA/merged-good-all-a2m # found chain 1u1zA in template set Warning: unaligning (T0364)H21 because of BadResidue code BAD_PEPTIDE in next template residue (1u1zA)F50 Warning: unaligning (T0364)A46 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u1zA)T85 Warning: unaligning (T0364)N54 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u1zA)T85 T0364 6 :TYRTTVQEDWVDYNG 1u1zA 34 :RAYKNVSINEPFFNG T0364 22 :LRDAFYLLIFSYATDALMDR 1u1zA 56 :MPGVLIIEAMAQAAGILGFK T0364 42 :IGLD 1u1zA 77 :LDVK T0364 55 :SLFTLEAH 1u1zA 86 :LYYFVGSD T0364 63 :INYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRA 1u1zA 95 :LRFRQPVLPGDQLQLHAKFISVKRSIWKFDCHATVD T0364 101 :DEVLAASEQMLL 1u1zA 131 :DKPVCSAEIICA Number of specific fragments extracted= 6 number of extra gaps= 1 total=262 Number of alignments=56 # 1u1zA read from 1u1zA/merged-good-all-a2m # found chain 1u1zA in template set Warning: unaligning (T0364)A46 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u1zA)T85 Warning: unaligning (T0364)N54 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u1zA)T85 T0364 24 :DAFYLLIFSYATDALMDRI 1u1zA 58 :GVLIIEAMAQAAGILGFKM T0364 43 :GLD 1u1zA 78 :DVK T0364 55 :SLFTLEA 1u1zA 86 :LYYFVGS T0364 63 :INYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHR 1u1zA 95 :LRFRQPVLPGDQLQLHAKFISVKRSIWKFDCHATV T0364 100 :FDEVLAASEQMLLH 1u1zA 130 :DDKPVCSAEIICAE Number of specific fragments extracted= 5 number of extra gaps= 0 total=267 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sh8A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0364 read from 1sh8A/merged-good-all-a2m # 1sh8A read from 1sh8A/merged-good-all-a2m # found chain 1sh8A in training set T0364 13 :EDWVDYNGHLRDAFYLLIFSYATDALMDRI 1sh8A 41 :AGNENHIGSMYAGALFTLAELPGGALFLTS T0364 44 :LDA 1sh8A 71 :FDS T0364 52 :SGNSLFTLEAHINYLHEVK 1sh8A 74 :ARFYPIVKEMTLRFRRPAK T0364 73 :TEVWVQTQIL 1sh8A 93 :GDIRVEARLD T0364 85 :DRKRLHVYHSLHRAG 1sh8A 117 :GKAEYSLELQLTDEQ T0364 101 :DEVLAASEQMLLHVDLAG 1sh8A 132 :GEVVAESAALYQLRSHAR Number of specific fragments extracted= 6 number of extra gaps= 0 total=273 Number of alignments=58 # 1sh8A read from 1sh8A/merged-good-all-a2m # found chain 1sh8A in training set T0364 13 :EDWVDYNGHLRDAFYLLIFSYATDALMDRI 1sh8A 41 :AGNENHIGSMYAGALFTLAELPGGALFLTS T0364 44 :LDAD 1sh8A 71 :FDSA T0364 53 :GNSLFTLEAHINYLHEVKL 1sh8A 75 :RFYPIVKEMTLRFRRPAKG T0364 74 :EVWVQTQIL 1sh8A 94 :DIRVEARLD T0364 85 :DRKRLHVYHSLHR 1sh8A 117 :GKAEYSLELQLTD T0364 99 :GFDEVLAASEQMLLHVDLAG 1sh8A 130 :EQGEVVAESAALYQLRSHAR Number of specific fragments extracted= 6 number of extra gaps= 0 total=279 Number of alignments=59 # 1sh8A read from 1sh8A/merged-good-all-a2m # found chain 1sh8A in training set T0364 19 :NGHLRDAFYLLIFSYATDALMDRI 1sh8A 47 :IGSMYAGALFTLAELPGGALFLTS T0364 44 :LD 1sh8A 71 :FD T0364 51 :QSGNSLFTLEAHINYLHEVK 1sh8A 73 :SARFYPIVKEMTLRFRRPAK T0364 73 :TEVWVQTQI 1sh8A 93 :GDIRVEARL T0364 85 :DRKRLHVYHSLHR 1sh8A 117 :GKAEYSLELQLTD T0364 99 :GFDEVLAASEQMLLHVD 1sh8A 130 :EQGEVVAESAALYQLRS Number of specific fragments extracted= 6 number of extra gaps= 0 total=285 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lo9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0364/1lo9A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0364/1lo9A/merged-good-all-a2m.gz for input Trying 1lo9A/merged-good-all-a2m Error: Couldn't open file 1lo9A/merged-good-all-a2m or 1lo9A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j1yA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0364 read from 1j1yA/merged-good-all-a2m # 1j1yA read from 1j1yA/merged-good-all-a2m # found chain 1j1yA in training set Warning: unaligning (T0364)V114 because last residue in template chain is (1j1yA)L117 T0364 2 :PALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIGL 1j1yA 18 :PGEAVVAGEVRADHLNLHGTAHGGFLYALADSAFALASNTRGP T0364 56 :LFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRA 1j1yA 61 :AVALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVSE T0364 101 :DEVLAASEQMLLH 1j1yA 104 :GKLVALFTGTVFR Number of specific fragments extracted= 3 number of extra gaps= 0 total=288 Number of alignments=61 # 1j1yA read from 1j1yA/merged-good-all-a2m # found chain 1j1yA in training set Warning: unaligning (T0364)V114 because last residue in template chain is (1j1yA)L117 T0364 5 :ITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIGL 1j1yA 21 :AVVAGEVRADHLNLHGTAHGGFLYALADSAFALASNTRGP T0364 56 :LFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRA 1j1yA 61 :AVALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVSE T0364 101 :DEVLAASEQMLLH 1j1yA 104 :GKLVALFTGTVFR Number of specific fragments extracted= 3 number of extra gaps= 0 total=291 Number of alignments=62 # 1j1yA read from 1j1yA/merged-good-all-a2m # found chain 1j1yA in training set T0364 7 :YRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRI 1j1yA 23 :VAGEVRADHLNLHGTAHGGFLYALADSAFALASNTR T0364 54 :NSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHR 1j1yA 59 :GPAVALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVS T0364 100 :FDEVLAASEQMLLH 1j1yA 103 :EGKLVALFTGTVFR Number of specific fragments extracted= 3 number of extra gaps= 0 total=294 Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2essA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2essA expands to /projects/compbio/data/pdb/2ess.pdb.gz 2essA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 3, because occupancy 0.500 <= existing 0.500 in 2essA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 7, because occupancy 0.500 <= existing 0.500 in 2essA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 9, because occupancy 0.500 <= existing 0.500 in 2essA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 13, because occupancy 0.500 <= existing 0.500 in 2essA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 331, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 335, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 337, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 472, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 476, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 478, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 480, because occupancy 0.500 <= existing 0.500 in 2essA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1165, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1169, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1171, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1173, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1175, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1177, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1179, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1181, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1218, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1222, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1224, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1226, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1228, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1255, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1259, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1261, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1263, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1357, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1361, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1363, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1365, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1367, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1369, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1371, because occupancy 0.500 <= existing 0.500 in 2essA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0364 read from 2essA/merged-good-all-a2m # 2essA read from 2essA/merged-good-all-a2m # adding 2essA to template set # found chain 2essA in template set Warning: unaligning (T0364)G118 because of BadResidue code BAD_PEPTIDE in next template residue (2essA)R121 Warning: unaligning (T0364)P119 because of BadResidue code BAD_PEPTIDE at template residue (2essA)R121 Warning: unaligning (T0364)S121 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2essA)A124 Warning: unaligning (T0364)A122 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2essA)A124 Warning: unaligning (T0364)Q139 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2essA)L129 Warning: unaligning (T0364)E140 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2essA)H130 T0364 3 :ALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIGLDADSRGQSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRAG 2essA 6 :KIGTYQFVAEPFHVDFNGRLTMGVLGNHLLNCAGFHASDRGFGIATLNEDNYTWVLSRLAIELDEMPYQYEKFSVQTWVENVYRLFTDRNFAVIDKD T0364 101 :DEVLAASEQMLLHVDLA 2essA 103 :GKKIGYARSVWAMINLN T0364 120 :Q 2essA 122 :K T0364 141 :GAQAPQ 2essA 131 :GGSIVD Number of specific fragments extracted= 4 number of extra gaps= 2 total=298 Number of alignments=64 # 2essA read from 2essA/merged-good-all-a2m # found chain 2essA in template set Warning: unaligning (T0364)G118 because of BadResidue code BAD_PEPTIDE in next template residue (2essA)R121 Warning: unaligning (T0364)P119 because of BadResidue code BAD_PEPTIDE at template residue (2essA)R121 Warning: unaligning (T0364)S121 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2essA)A124 Warning: unaligning (T0364)A122 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2essA)A124 Warning: unaligning (T0364)Q139 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2essA)L129 Warning: unaligning (T0364)E140 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2essA)H130 T0364 3 :ALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIGLDADSRGQSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHR 2essA 6 :KIGTYQFVAEPFHVDFNGRLTMGVLGNHLLNCAGFHASDRGFGIATLNEDNYTWVLSRLAIELDEMPYQYEKFSVQTWVENVYRLFTDRNFAVID T0364 99 :GFDEVLAASEQMLLHVDLA 2essA 101 :KDGKKIGYARSVWAMINLN T0364 120 :Q 2essA 122 :K T0364 141 :GAQAPQYM 2essA 131 :GGSIVDYI T0364 149 :GRTIKLPA 2essA 140 :DEPCPIEK Number of specific fragments extracted= 5 number of extra gaps= 2 total=303 Number of alignments=65 # 2essA read from 2essA/merged-good-all-a2m # found chain 2essA in template set Warning: unaligning (T0364)G118 because of BadResidue code BAD_PEPTIDE in next template residue (2essA)R121 Warning: unaligning (T0364)P119 because of BadResidue code BAD_PEPTIDE at template residue (2essA)R121 Warning: unaligning (T0364)S121 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2essA)A124 Warning: unaligning (T0364)A122 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2essA)A124 T0364 4 :LITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIGLDADSRGQSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHR 2essA 7 :IGTYQFVAEPFHVDFNGRLTMGVLGNHLLNCAGFHASDRGFGIATLNEDNYTWVLSRLAIELDEMPYQYEKFSVQTWVENVYRLFTDRNFAVID T0364 99 :GFDEVLAASEQMLLHVDLA 2essA 101 :KDGKKIGYARSVWAMINLN T0364 120 :Q 2essA 122 :K Number of specific fragments extracted= 3 number of extra gaps= 2 total=306 Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b6eA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2b6eA expands to /projects/compbio/data/pdb/2b6e.pdb.gz 2b6eA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0364 read from 2b6eA/merged-good-all-a2m # 2b6eA read from 2b6eA/merged-good-all-a2m # adding 2b6eA to template set # found chain 2b6eA in template set Warning: unaligning (T0364)D115 because last residue in template chain is (2b6eA)N137 T0364 2 :PALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRI 2b6eA 33 :EDWIEATMPVDHRTMQPFGVLHGGVSVALAETIGSLAGSLC T0364 44 :L 2b6eA 74 :L T0364 51 :QSGNSLFTLEAHINYLHEVKL 2b6eA 75 :EEGKTVVGLDINANHLRPVRS T0364 73 :TEVWVQTQILGFDRKRLHVYHSLHRAG 2b6eA 96 :GKVTARATPINLGRNIQVWQIDIRTEE T0364 101 :DEVLAASEQMLLHV 2b6eA 123 :NKLCCVSRLTLSVI Number of specific fragments extracted= 5 number of extra gaps= 0 total=311 Number of alignments=67 # 2b6eA read from 2b6eA/merged-good-all-a2m # found chain 2b6eA in template set Warning: unaligning (T0364)D115 because last residue in template chain is (2b6eA)N137 T0364 2 :PALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRI 2b6eA 33 :EDWIEATMPVDHRTMQPFGVLHGGVSVALAETIGSLAGSLC T0364 44 :L 2b6eA 74 :L T0364 51 :QSGNSLFTLEAHINYLHEVK 2b6eA 75 :EEGKTVVGLDINANHLRPVR T0364 72 :GTEVWVQTQILGFDRKRLHVYHSLHR 2b6eA 95 :SGKVTARATPINLGRNIQVWQIDIRT T0364 99 :GFDEVLAASEQMLLHV 2b6eA 121 :EENKLCCVSRLTLSVI Number of specific fragments extracted= 5 number of extra gaps= 0 total=316 Number of alignments=68 # 2b6eA read from 2b6eA/merged-good-all-a2m # found chain 2b6eA in template set Warning: unaligning (T0364)D115 because last residue in template chain is (2b6eA)N137 T0364 2 :PALITYRTTVQEDWVDYNGHLRDAFYLLIFS 2b6eA 33 :EDWIEATMPVDHRTMQPFGVLHGGVSVALAE T0364 34 :ATDALMDRIGL 2b6eA 64 :TIGSLAGSLCL T0364 51 :QSGNSLFTLEAHINYLHEVK 2b6eA 75 :EEGKTVVGLDINANHLRPVR T0364 72 :GTEVWVQTQILGFDRKRLHVYHSLHR 2b6eA 95 :SGKVTARATPINLGRNIQVWQIDIRT T0364 99 :GFDEVLAASEQMLLHV 2b6eA 121 :EENKLCCVSRLTLSVI Number of specific fragments extracted= 5 number of extra gaps= 0 total=321 Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o0iA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1o0iA expands to /projects/compbio/data/pdb/1o0i.pdb.gz 1o0iA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0364 read from 1o0iA/merged-good-all-a2m # 1o0iA read from 1o0iA/merged-good-all-a2m # adding 1o0iA to template set # found chain 1o0iA in template set T0364 2 :PALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRI 1o0iA 33 :EDWIEATMPVDHRTMQPFGVLHGGVSVALAETIGSLAGSLC T0364 44 :L 1o0iA 74 :L T0364 51 :QSGNSLFTLEAHINYLHEVKL 1o0iA 75 :EEGKTVVGLDINANHLRPVRS T0364 73 :TEVWVQTQILGFDRKRLHVYHSLHRAG 1o0iA 96 :GKVTARATPINLGRNIQVWQIDIRTEE T0364 101 :DEVLAASEQMLLHV 1o0iA 123 :NKLCCVSRLTLSVI Number of specific fragments extracted= 5 number of extra gaps= 0 total=326 Number of alignments=70 # 1o0iA read from 1o0iA/merged-good-all-a2m # found chain 1o0iA in template set T0364 2 :PALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRI 1o0iA 33 :EDWIEATMPVDHRTMQPFGVLHGGVSVALAETIGSLAGSLC T0364 44 :L 1o0iA 74 :L T0364 51 :QSGNSLFTLEAHINYLHEVK 1o0iA 75 :EEGKTVVGLDINANHLRPVR T0364 72 :GTEVWVQTQILGFDRKRLHVYHSLHR 1o0iA 95 :SGKVTARATPINLGRNIQVWQIDIRT T0364 99 :GFDEVLAASEQMLLHV 1o0iA 121 :EENKLCCVSRLTLSVI Number of specific fragments extracted= 5 number of extra gaps= 0 total=331 Number of alignments=71 # 1o0iA read from 1o0iA/merged-good-all-a2m # found chain 1o0iA in template set T0364 2 :PALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRI 1o0iA 33 :EDWIEATMPVDHRTMQPFGVLHGGVSVALAETIGSLAGSLC T0364 44 :L 1o0iA 74 :L T0364 51 :QSGNSLFTLEAHINYLHEVK 1o0iA 75 :EEGKTVVGLDINANHLRPVR T0364 72 :GTEVWVQTQILGFDRKRLHVYHSLHR 1o0iA 95 :SGKVTARATPINLGRNIQVWQIDIRT T0364 99 :GFDEVLAASEQMLLH 1o0iA 121 :EENKLCCVSRLTLSV Number of specific fragments extracted= 5 number of extra gaps= 0 total=336 Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bvqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1bvqA expands to /projects/compbio/data/pdb/1bvq.pdb.gz 1bvqA:# T0364 read from 1bvqA/merged-good-all-a2m # 1bvqA read from 1bvqA/merged-good-all-a2m # adding 1bvqA to template set # found chain 1bvqA in template set Warning: unaligning (T0364)P2 because first residue in template chain is (1bvqA)A2 Warning: unaligning (T0364)H126 because of BadResidue code BAD_PEPTIDE in next template residue (1bvqA)D135 Warning: unaligning (T0364)T127 because of BadResidue code BAD_PEPTIDE at template residue (1bvqA)D135 Warning: unaligning (T0364)L132 because last residue in template chain is (1bvqA)C140 T0364 3 :ALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIGLD 1bvqA 3 :RSITMQQRIEFGDCDPAGIVWYPNYHRWLDAASRNYFIKCGLP T0364 46 :ADSRG 1bvqA 47 :WRQTV T0364 51 :QSGN 1bvqA 53 :ERGI T0364 55 :SLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHR 1bvqA 58 :GTPIVSCNASFVCTASYDDVLTIETCIKEWRRKSFVQRHSVSR T0364 98 :A 1bvqA 103 :P T0364 100 :FD 1bvqA 104 :GG T0364 102 :EVLAASEQMLLHV 1bvqA 108 :QLVMRADEIRVFA T0364 115 :DLAGPQSAPFG 1bvqA 123 :DGERLRAIEVP T0364 128 :TVCR 1bvqA 136 :YIEL Number of specific fragments extracted= 9 number of extra gaps= 1 total=345 Number of alignments=73 # 1bvqA read from 1bvqA/merged-good-all-a2m # found chain 1bvqA in template set Warning: unaligning (T0364)P2 because first residue in template chain is (1bvqA)A2 Warning: unaligning (T0364)H126 because of BadResidue code BAD_PEPTIDE in next template residue (1bvqA)D135 Warning: unaligning (T0364)T127 because of BadResidue code BAD_PEPTIDE at template residue (1bvqA)D135 T0364 3 :ALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIGL 1bvqA 3 :RSITMQQRIEFGDCDPAGIVWYPNYHRWLDAASRNYFIKCGL T0364 45 :DADSRGQSGN 1bvqA 46 :PWRQTVVERG T0364 55 :SLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHR 1bvqA 58 :GTPIVSCNASFVCTASYDDVLTIETCIKEWRRKSFVQRHSVSR T0364 99 :GFD 1bvqA 103 :PGG T0364 102 :EVLAASEQMLLHV 1bvqA 108 :QLVMRADEIRVFA T0364 115 :DLAGPQSAPFG 1bvqA 123 :DGERLRAIEVP T0364 128 :TVCR 1bvqA 136 :YIEL Number of specific fragments extracted= 7 number of extra gaps= 1 total=352 Number of alignments=74 # 1bvqA read from 1bvqA/merged-good-all-a2m # found chain 1bvqA in template set Warning: unaligning (T0364)P2 because first residue in template chain is (1bvqA)A2 Warning: unaligning (T0364)H126 because of BadResidue code BAD_PEPTIDE in next template residue (1bvqA)D135 Warning: unaligning (T0364)T127 because of BadResidue code BAD_PEPTIDE at template residue (1bvqA)D135 T0364 3 :ALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIGL 1bvqA 3 :RSITMQQRIEFGDCDPAGIVWYPNYHRWLDAASRNYFIKCGL T0364 45 :DADSRGQSGNS 1bvqA 46 :PWRQTVVERGI T0364 56 :LFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRAGFD 1bvqA 59 :TPIVSCNASFVCTASYDDVLTIETCIKEWRRKSFVQRHSVSRTTPG T0364 102 :EVLAASEQML 1bvqA 108 :QLVMRADEIR T0364 112 :LHVDLAGPQSAPFG 1bvqA 120 :AMNDGERLRAIEVP T0364 128 :TVCR 1bvqA 136 :YIEL Number of specific fragments extracted= 6 number of extra gaps= 1 total=358 Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fs2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fs2A expands to /projects/compbio/data/pdb/2fs2.pdb.gz 2fs2A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0364 read from 2fs2A/merged-good-all-a2m # 2fs2A read from 2fs2A/merged-good-all-a2m # adding 2fs2A to template set # found chain 2fs2A in template set Warning: unaligning (T0364)T9 because of BadResidue code BAD_PEPTIDE in next template residue (2fs2A)T39 Warning: unaligning (T0364)T10 because of BadResidue code BAD_PEPTIDE at template residue (2fs2A)T39 Warning: unaligning (T0364)I63 because of BadResidue code BAD_PEPTIDE in next template residue (2fs2A)D83 Warning: unaligning (T0364)N64 because of BadResidue code BAD_PEPTIDE at template residue (2fs2A)D83 Warning: unaligning (T0364)S107 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fs2A)R126 Warning: unaligning (T0364)E108 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fs2A)R126 Warning: unaligning (T0364)L112 because of BadResidue code BAD_PEPTIDE in next template residue (2fs2A)R131 T0364 3 :ALITYR 2fs2A 32 :GFAVVT T0364 11 :VQEDWVDYNGHLRDAFYLLIFSYATDAL 2fs2A 40 :VTAQMLNGHQSCHGGQLFSLADTAFAYA T0364 49 :RGQSGNSLFTLEAH 2fs2A 68 :CNSQGLAAVASACT T0364 65 :YLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRAG 2fs2A 84 :FLRPGFAGDTLTATAQVRHQGKQTGVYDIEIVNQQ T0364 101 :DEVLAA 2fs2A 119 :QKTVAL T0364 109 :QML 2fs2A 127 :GKS Number of specific fragments extracted= 6 number of extra gaps= 4 total=364 Number of alignments=76 # 2fs2A read from 2fs2A/merged-good-all-a2m # found chain 2fs2A in template set Warning: unaligning (T0364)T9 because of BadResidue code BAD_PEPTIDE in next template residue (2fs2A)T39 Warning: unaligning (T0364)T10 because of BadResidue code BAD_PEPTIDE at template residue (2fs2A)T39 Warning: unaligning (T0364)I63 because of BadResidue code BAD_PEPTIDE in next template residue (2fs2A)D83 Warning: unaligning (T0364)N64 because of BadResidue code BAD_PEPTIDE at template residue (2fs2A)D83 Warning: unaligning (T0364)S107 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fs2A)R126 Warning: unaligning (T0364)E108 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fs2A)R126 Warning: unaligning (T0364)L112 because of BadResidue code BAD_PEPTIDE in next template residue (2fs2A)R131 T0364 5 :ITYR 2fs2A 34 :AVVT T0364 11 :VQEDWVDYNGHLRDAFYLLIFSYATD 2fs2A 40 :VTAQMLNGHQSCHGGQLFSLADTAFA T0364 47 :DSRGQSGNSLFTLEAH 2fs2A 66 :YACNSQGLAAVASACT T0364 65 :YLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHR 2fs2A 84 :FLRPGFAGDTLTATAQVRHQGKQTGVYDIEIVN T0364 99 :GFDEVLAA 2fs2A 117 :QQQKTVAL T0364 109 :QML 2fs2A 127 :GKS Number of specific fragments extracted= 6 number of extra gaps= 4 total=370 Number of alignments=77 # 2fs2A read from 2fs2A/merged-good-all-a2m # found chain 2fs2A in template set Warning: unaligning (T0364)T9 because of BadResidue code BAD_PEPTIDE in next template residue (2fs2A)T39 Warning: unaligning (T0364)T10 because of BadResidue code BAD_PEPTIDE at template residue (2fs2A)T39 Warning: unaligning (T0364)I63 because of BadResidue code BAD_PEPTIDE in next template residue (2fs2A)D83 Warning: unaligning (T0364)N64 because of BadResidue code BAD_PEPTIDE at template residue (2fs2A)D83 Warning: unaligning (T0364)S107 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fs2A)R126 Warning: unaligning (T0364)E108 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fs2A)R126 T0364 11 :VQEDWVDYNGHLRDAFYLLIFSYATDALMD 2fs2A 40 :VTAQMLNGHQSCHGGQLFSLADTAFAYACN T0364 51 :QSGNSLFTLEAH 2fs2A 70 :SQGLAAVASACT T0364 65 :YLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHR 2fs2A 84 :FLRPGFAGDTLTATAQVRHQGKQTGVYDIEIVN T0364 99 :GFDEVLAA 2fs2A 117 :QQQKTVAL T0364 109 :QML 2fs2A 127 :GKS Number of specific fragments extracted= 5 number of extra gaps= 3 total=375 Number of alignments=78 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z54A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1z54A expands to /projects/compbio/data/pdb/1z54.pdb.gz 1z54A:# T0364 read from 1z54A/merged-good-all-a2m # 1z54A read from 1z54A/merged-good-all-a2m # adding 1z54A to template set # found chain 1z54A in template set Warning: unaligning (T0364)A3 because first residue in template chain is (1z54A)M1 T0364 4 :LITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIGLDADSRGQSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRA 1z54A 2 :ESVTRIKVRYAETDQMGVVHHSVYAVYLEAARVDFLERAGLPYHRVEARGVFFPVVELGLTFRAPARFGEVVEVRTRLAELSSRALLFRYRVERE T0364 101 :DEVLAASEQMLLHV 1z54A 97 :GVLLAEGFTRHLCQ T0364 117 :AGPQSAPFGHTTVCRLNHL 1z54A 111 :VGERAARIPEDIYRALSVL Number of specific fragments extracted= 3 number of extra gaps= 0 total=378 Number of alignments=79 # 1z54A read from 1z54A/merged-good-all-a2m # found chain 1z54A in template set T0364 4 :LITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIGLDADSRGQSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRA 1z54A 2 :ESVTRIKVRYAETDQMGVVHHSVYAVYLEAARVDFLERAGLPYHRVEARGVFFPVVELGLTFRAPARFGEVVEVRTRLAELSSRALLFRYRVERE T0364 101 :DEVLAASEQMLLHVD 1z54A 97 :GVLLAEGFTRHLCQV T0364 118 :GPQSAPFGHTTVCRLNHL 1z54A 112 :GERAARIPEDIYRALSVL Number of specific fragments extracted= 3 number of extra gaps= 0 total=381 Number of alignments=80 # 1z54A read from 1z54A/merged-good-all-a2m # found chain 1z54A in template set Warning: unaligning (T0364)A3 because first residue in template chain is (1z54A)M1 T0364 4 :LITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIGLDADSRGQSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHR 1z54A 2 :ESVTRIKVRYAETDQMGVVHHSVYAVYLEAARVDFLERAGLPYHRVEARGVFFPVVELGLTFRAPARFGEVVEVRTRLAELSSRALLFRYRVER T0364 100 :FDEVLAASEQMLLHVD 1z54A 96 :EGVLLAEGFTRHLCQV T0364 118 :GPQSAPFGHTTVCRLNHL 1z54A 112 :GERAARIPEDIYRALSVL Number of specific fragments extracted= 3 number of extra gaps= 0 total=384 Number of alignments=81 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wluA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wluA expands to /projects/compbio/data/pdb/1wlu.pdb.gz 1wluA:# T0364 read from 1wluA/merged-good-all-a2m # 1wluA read from 1wluA/merged-good-all-a2m # adding 1wluA to template set # found chain 1wluA in template set Warning: unaligning (T0364)V114 because last residue in template chain is (1wluA)L117 T0364 2 :PALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIGL 1wluA 18 :PGEAVVAGEVRADHLNLHGTAHGGFLYALADSAFALASNTRGP T0364 56 :LFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRA 1wluA 61 :AVALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVSE T0364 101 :DEVLAASEQMLLH 1wluA 104 :GKLVALFTGTVFR Number of specific fragments extracted= 3 number of extra gaps= 0 total=387 Number of alignments=82 # 1wluA read from 1wluA/merged-good-all-a2m # found chain 1wluA in template set Warning: unaligning (T0364)V114 because last residue in template chain is (1wluA)L117 T0364 3 :ALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIG 1wluA 19 :GEAVVAGEVRADHLNLHGTAHGGFLYALADSAFALASNTRG T0364 55 :SLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRA 1wluA 60 :PAVALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVSE T0364 101 :DEVLAASEQMLLH 1wluA 104 :GKLVALFTGTVFR Number of specific fragments extracted= 3 number of extra gaps= 0 total=390 Number of alignments=83 # 1wluA read from 1wluA/merged-good-all-a2m # found chain 1wluA in template set T0364 9 :TTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRI 1wluA 25 :GEVRADHLNLHGTAHGGFLYALADSAFALASNTR T0364 54 :NSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHR 1wluA 59 :GPAVALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVS T0364 100 :FDEVLAASEQMLLH 1wluA 103 :EGKLVALFTGTVFR Number of specific fragments extracted= 3 number of extra gaps= 0 total=393 Number of alignments=84 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1psuA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1psuA expands to /projects/compbio/data/pdb/1psu.pdb.gz 1psuA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0364 read from 1psuA/merged-good-all-a2m # 1psuA read from 1psuA/merged-good-all-a2m # adding 1psuA to template set # found chain 1psuA in template set T0364 3 :ALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDAL 1psuA 32 :GFAVVTMTVTAQMLNGHQSCHGGQLFSLADTAFAYA T0364 49 :RGQSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRAG 1psuA 68 :CNSQGLAAVASACTIDFLRPGFAGDTLTATAQVRHQGKQTGVYDIEIVNQQ T0364 101 :DEVLAASEQMLL 1psuA 119 :QKTVALFRGKSH Number of specific fragments extracted= 3 number of extra gaps= 0 total=396 Number of alignments=85 # 1psuA read from 1psuA/merged-good-all-a2m # found chain 1psuA in template set T0364 5 :ITYRTTVQEDWVDYNGHLRDAFYLLIFSYATD 1psuA 34 :AVVTMTVTAQMLNGHQSCHGGQLFSLADTAFA T0364 47 :DSRGQSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHR 1psuA 66 :YACNSQGLAAVASACTIDFLRPGFAGDTLTATAQVRHQGKQTGVYDIEIVN T0364 99 :GFDEVLAASEQMLL 1psuA 117 :QQQKTVALFRGKSH Number of specific fragments extracted= 3 number of extra gaps= 0 total=399 Number of alignments=86 # 1psuA read from 1psuA/merged-good-all-a2m # found chain 1psuA in template set T0364 8 :RTTVQEDWVDYNGHLRDAFYLLIFSYATDALM 1psuA 37 :TMTVTAQMLNGHQSCHGGQLFSLADTAFAYAC T0364 50 :GQSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHR 1psuA 69 :NSQGLAAVASACTIDFLRPGFAGDTLTATAQVRHQGKQTGVYDIEIVN T0364 99 :GFDEVLAASEQML 1psuA 117 :QQQKTVALFRGKS Number of specific fragments extracted= 3 number of extra gaps= 0 total=402 Number of alignments=87 # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0364//projects/compbio/experiments/protein-predict/casp7/T0364/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0364//projects/compbio/experiments/protein-predict/casp7/T0364/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0364/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0364/align.constraints_v3.costfcn # future Constraint commands -> align # future HelixConstraint commands -> align # future StrandConstraint commands -> align # future SheetConstraint commands -> align # future Hbond commands -> align # future SSbond commands -> align # Constraint # added constraint: constraint((T0364)F57.CB, (T0364)L111.CB) [> 4.0192 = 6.6986 < 8.7082] w=1.0000 to align # Constraint # added constraint: constraint((T0364)T58.CB, (T0364)Q109.CB) [> 3.5121 = 5.8535 < 7.6096] w=1.0000 to align # Constraint # added constraint: constraint((T0364)T58.CB, (T0364)M110.CB) [> 4.3015 = 7.1691 < 9.3199] w=1.0000 to align # Constraint # added constraint: constraint((T0364)L59.CB, (T0364)M110.CB) [> 2.8034 = 4.6723 < 6.0740] w=1.0000 to align # Constraint # added constraint: constraint((T0364)E60.CB, (T0364)Q109.CB) [> 4.2020 = 7.0033 < 9.1042] w=1.0000 to align # Constraint # added constraint: constraint((T0364)Y65.CB, (T0364)A105.CB) [> 3.0770 = 5.1284 < 6.6669] w=1.0000 to align # Constraint # added constraint: constraint((T0364)L66.CB, (T0364)L104.CB) [> 3.6600 = 6.1000 < 7.9300] w=1.0000 to align # Constraint # added constraint: constraint((T0364)L66.CB, (T0364)A105.CB) [> 3.6725 = 6.1209 < 7.9572] w=1.0000 to align # Constraint # added constraint: constraint((T0364)H67.CB, (T0364)L104.CB) [> 3.1431 = 5.2384 < 6.8100] w=1.0000 to align # Constraint # added constraint: constraint((T0364)V69.CB, (T0364)L104.CB) [> 3.3359 = 5.5598 < 7.2277] w=1.0000 to align # Constraint # added constraint: constraint((T0364)V75.CB, (T0364)L95.CB) [> 3.4458 = 5.7430 < 7.4659] w=1.0000 to align # Constraint # added constraint: constraint((T0364)W76.CB, (T0364)L95.CB) [> 4.2510 = 7.0850 < 9.2105] w=1.0000 to align # Constraint # added constraint: constraint((T0364)V77.CB, (T0364)H93.CB) [> 3.5348 = 5.8913 < 7.6587] w=1.0000 to align # Constraint # added constraint: constraint((T0364)V77.CB, (T0364)S94.CB) [> 4.4035 = 7.3392 < 9.5410] w=1.0000 to align # Constraint # added constraint: constraint((T0364)L95.CB, (T0364)A106.CB) [> 4.3582 = 7.2637 < 9.4428] w=1.0000 to align # Constraint # added constraint: constraint((T0364)L95.CB, (T0364)A105.CB) [> 2.6113 = 4.3522 < 5.6578] w=1.0000 to align # Constraint # added constraint: constraint((T0364)L95.CB, (T0364)L104.CB) [> 2.7825 = 4.6376 < 6.0288] w=1.0000 to align # Constraint # added constraint: constraint((T0364)S94.CB, (T0364)A106.CB) [> 3.1566 = 5.2610 < 6.8392] w=1.0000 to align # Constraint # added constraint: constraint((T0364)S94.CB, (T0364)V103.CB) [> 3.7417 = 6.2362 < 8.1070] w=1.0000 to align # Constraint # added constraint: constraint((T0364)H93.CB, (T0364)Q109.CB) [> 4.0820 = 6.8034 < 8.8444] w=1.0000 to align # Constraint # added constraint: constraint((T0364)H93.CB, (T0364)A106.CB) [> 4.1697 = 6.9495 < 9.0343] w=1.0000 to align # Constraint # added constraint: constraint((T0364)V91.CB, (T0364)Q109.CB) [> 2.9761 = 4.9602 < 6.4482] w=1.0000 to align # Constraint # added constraint: constraint((T0364)H90.CB, (T0364)M110.CB) [> 3.2433 = 5.4056 < 7.0272] w=1.0000 to align # Constraint # added constraint: constraint((T0364)H90.CB, (T0364)Q109.CB) [> 4.3461 = 7.2436 < 9.4167] w=1.0000 to align # Constraint # added constraint: constraint((T0364)L89.CB, (T0364)L111.CB) [> 2.9067 = 4.8444 < 6.2978] w=1.0000 to align # Constraint # added constraint: constraint((T0364)L89.CB, (T0364)M110.CB) [> 4.3845 = 7.3075 < 9.4997] w=1.0000 to align # Constraint # added constraint: constraint((T0364)R88.CB, (T0364)L111.CB) [> 4.0320 = 6.7200 < 8.7360] w=1.0000 to align # Constraint # added constraint: constraint((T0364)R88.CB, (T0364)M110.CB) [> 3.6637 = 6.1062 < 7.9380] w=1.0000 to align # Constraint # added constraint: constraint((T0364)L56.CB, (T0364)L111.CB) [> 2.7338 = 4.5563 < 5.9232] w=0.9878 to align # Constraint # added constraint: constraint((T0364)A61.CB, (T0364)Q109.CB) [> 2.8280 = 4.7134 < 6.1274] w=0.9878 to align # Constraint # added constraint: constraint((T0364)E60.CB, (T0364)M110.CB) [> 2.5900 = 4.3166 < 5.6116] w=0.9878 to align # Constraint # added constraint: constraint((T0364)L59.CB, (T0364)L111.CB) [> 3.8514 = 6.4190 < 8.3447] w=0.9878 to align # Constraint # added constraint: constraint((T0364)T58.CB, (T0364)L111.CB) [> 3.4428 = 5.7380 < 7.4595] w=0.9878 to align # Constraint # added constraint: constraint((T0364)Y27.CB, (T0364)L95.CB) [> 3.7613 = 6.2689 < 8.1496] w=0.9758 to align # Constraint # added constraint: constraint((T0364)A34.CB, (T0364)V77.CB) [> 2.5823 = 4.3039 < 5.5950] w=0.9758 to align # Constraint # added constraint: constraint((T0364)A34.CB, (T0364)H93.CB) [> 3.6436 = 6.0726 < 7.8944] w=0.9668 to align # Constraint # added constraint: constraint((T0364)T79.CB, (T0364)H93.CB) [> 3.0086 = 5.0144 < 6.5187] w=0.9650 to align # Constraint # added constraint: constraint((T0364)T79.CB, (T0364)V91.CB) [> 3.3470 = 5.5782 < 7.2517] w=0.9650 to align # Constraint # added constraint: constraint((T0364)Q78.CB, (T0364)H93.CB) [> 4.1063 = 6.8438 < 8.8969] w=0.9650 to align # Constraint # added constraint: constraint((T0364)V77.CB, (T0364)L95.CB) [> 3.1812 = 5.3020 < 6.8926] w=0.9650 to align # Constraint # added constraint: constraint((T0364)V75.CB, (T0364)L104.CB) [> 4.0192 = 6.6986 < 8.7082] w=0.9650 to align # Constraint # added constraint: constraint((T0364)W76.CB, (T0364)H96.CB) [> 2.8770 = 4.7950 < 6.2334] w=0.9636 to align # Constraint # added constraint: constraint((T0364)V75.CB, (T0364)H96.CB) [> 4.1308 = 6.8847 < 8.9501] w=0.9636 to align # Constraint # added constraint: constraint((T0364)V91.CB, (T0364)L111.CB) [> 3.9586 = 6.5976 < 8.5769] w=0.9635 to align # Constraint # added constraint: constraint((T0364)H93.CB, (T0364)S107.CB) [> 2.8289 = 4.7148 < 6.1293] w=0.9635 to align # Constraint # added constraint: constraint((T0364)Y92.CB, (T0364)E108.CB) [> 3.3445 = 5.5742 < 7.2464] w=0.9635 to align # Constraint # added constraint: constraint((T0364)V91.CB, (T0364)E108.CB) [> 4.2293 = 7.0489 < 9.1635] w=0.9635 to align # Constraint # added constraint: constraint((T0364)H90.CB, (T0364)E108.CB) [> 3.8401 = 6.4002 < 8.3203] w=0.9635 to align # Constraint # added constraint: constraint((T0364)N64.CB, (T0364)A105.CB) [> 3.8788 = 6.4646 < 8.4039] w=0.9635 to align # Constraint # added constraint: constraint((T0364)I63.CB, (T0364)S107.CB) [> 2.5124 = 4.1874 < 5.4436] w=0.9635 to align # Constraint # added constraint: constraint((T0364)I63.CB, (T0364)A106.CB) [> 4.3316 = 7.2193 < 9.3851] w=0.9635 to align # Constraint # added constraint: constraint((T0364)I63.CB, (T0364)A105.CB) [> 3.5276 = 5.8794 < 7.6432] w=0.9635 to align # Constraint # added constraint: constraint((T0364)L66.CB, (T0364)V103.CB) [> 3.3039 = 5.5064 < 7.1584] w=0.9634 to align # Constraint # added constraint: constraint((T0364)Y65.CB, (T0364)L104.CB) [> 4.4454 = 7.4090 < 9.6317] w=0.9634 to align # Constraint # added constraint: constraint((T0364)L22.CB, (T0364)V69.CB) [> 2.4455 = 4.0759 < 5.2986] w=0.9624 to align # Constraint # added constraint: constraint((T0364)L22.CB, (T0364)E68.CB) [> 4.1353 = 6.8922 < 8.9598] w=0.9624 to align # Constraint # added constraint: constraint((T0364)H62.CB, (T0364)S107.CB) [> 3.6146 = 6.0244 < 7.8317] w=0.9598 to align # Constraint # added constraint: constraint((T0364)T35.CB, (T0364)Q109.CB) [> 3.3210 = 5.5350 < 7.1955] w=0.9547 to align # Constraint # added constraint: constraint((T0364)T35.CB, (T0364)V91.CB) [> 3.0371 = 5.0619 < 6.5804] w=0.9547 to align # Constraint # added constraint: constraint((T0364)W15.CB, (T0364)F26.CB) [> 2.8600 = 4.7667 < 6.1968] w=0.9528 to align # Constraint # added constraint: constraint((T0364)A61.CB, (T0364)E108.CB) [> 4.3190 = 7.1983 < 9.3578] w=0.9513 to align # Constraint # added constraint: constraint((T0364)A61.CB, (T0364)S107.CB) [> 3.8242 = 6.3737 < 8.2858] w=0.9513 to align # Constraint # added constraint: constraint((T0364)A61.CB, (T0364)M110.CB) [> 4.4261 = 7.3767 < 9.5898] w=0.9513 to align # Constraint # added constraint: constraint((T0364)H62.CB, (T0364)E108.CB) [> 2.9483 = 4.9138 < 6.3880] w=0.9500 to align # Constraint # added constraint: constraint((T0364)Q78.CB, (T0364)S94.CB) [> 3.0067 = 5.0112 < 6.5146] w=0.9420 to align # Constraint # added constraint: constraint((T0364)T79.CB, (T0364)Y92.CB) [> 4.2162 = 7.0270 < 9.1351] w=0.9420 to align # Constraint # added constraint: constraint((T0364)Q80.CB, (T0364)V91.CB) [> 4.1500 = 6.9167 < 8.9916] w=0.9420 to align # Constraint # added constraint: constraint((T0364)Q80.CB, (T0364)Y92.CB) [> 3.1144 = 5.1907 < 6.7479] w=0.9420 to align # Constraint # added constraint: constraint((T0364)I81.CB, (T0364)V91.CB) [> 3.3355 = 5.5592 < 7.2270] w=0.9420 to align # Constraint # added constraint: constraint((T0364)L82.CB, (T0364)V91.CB) [> 3.8576 = 6.4294 < 8.3582] w=0.9420 to align # Constraint # added constraint: constraint((T0364)L82.CB, (T0364)Y92.CB) [> 3.0127 = 5.0211 < 6.5275] w=0.9420 to align # Constraint # added constraint: constraint((T0364)V11.CB, (T0364)V69.CB) [> 3.4066 = 5.6777 < 7.3810] w=0.9408 to align # Constraint # added constraint: constraint((T0364)I30.CB, (T0364)V77.CB) [> 3.2473 = 5.4123 < 7.0359] w=0.9408 to align # Constraint # added constraint: constraint((T0364)F57.CB, (T0364)L112.CB) [> 3.2414 = 5.4023 < 7.0230] w=0.9393 to align # Constraint # added constraint: constraint((T0364)I30.CB, (T0364)L95.CB) [> 4.0586 = 6.7643 < 8.7936] w=0.9392 to align # Constraint # added constraint: constraint((T0364)Y27.CB, (T0364)A105.CB) [> 3.3113 = 5.5188 < 7.1744] w=0.9392 to align # Constraint # added constraint: constraint((T0364)A34.CB, (T0364)T79.CB) [> 2.7479 = 4.5799 < 5.9538] w=0.9318 to align # Constraint # added constraint: constraint((T0364)T35.CB, (T0364)T79.CB) [> 3.3483 = 5.5806 < 7.2547] w=0.9286 to align # Constraint # added constraint: constraint((T0364)F31.CB, (T0364)S107.CB) [> 3.1227 = 5.2045 < 6.7659] w=0.9271 to align # Constraint # added constraint: constraint((T0364)V69.CB, (T0364)R97.CB) [> 3.6210 = 6.0349 < 7.8454] w=0.9271 to align # Constraint # added constraint: constraint((T0364)H93.CB, (T0364)E108.CB) [> 4.3678 = 7.2797 < 9.4636] w=0.9269 to align # Constraint # added constraint: constraint((T0364)H67.CB, (T0364)E102.CB) [> 3.6011 = 6.0018 < 7.8024] w=0.9269 to align # Constraint # added constraint: constraint((T0364)Y92.CB, (T0364)S107.CB) [> 4.5026 = 7.5044 < 9.7556] w=0.9234 to align # Constraint # added constraint: constraint((T0364)L59.CB, (T0364)R88.CB) [> 4.2387 = 7.0645 < 9.1839] w=0.9157 to align # Constraint # added constraint: constraint((T0364)L56.CB, (T0364)L112.CB) [> 4.0646 = 6.7743 < 8.8066] w=0.9149 to align # Constraint # added constraint: constraint((T0364)R88.CB, (T0364)L112.CB) [> 3.3521 = 5.5868 < 7.2629] w=0.9149 to align # Constraint # added constraint: constraint((T0364)K87.CB, (T0364)L112.CB) [> 3.7652 = 6.2753 < 8.1579] w=0.9149 to align # Constraint # added constraint: constraint((T0364)V11.CB, (T0364)G72.CA) [> 3.0427 = 5.0711 < 6.5924] w=0.9079 to align # Constraint # added constraint: constraint((T0364)I81.CB, (T0364)H90.CB) [> 4.3201 = 7.2002 < 9.3602] w=0.9054 to align # Constraint # added constraint: constraint((T0364)Y7.CB, (T0364)W76.CB) [> 4.3587 = 7.2645 < 9.4438] w=0.9044 to align # Constraint # added constraint: constraint((T0364)Y7.CB, (T0364)V77.CB) [> 2.8568 = 4.7614 < 6.1898] w=0.9044 to align # Constraint # added constraint: constraint((T0364)V11.CB, (T0364)L22.CB) [> 3.2761 = 5.4602 < 7.0982] w=0.9044 to align # Constraint # added constraint: constraint((T0364)V11.CB, (T0364)T73.CB) [> 3.0053 = 5.0088 < 6.5115] w=0.9043 to align # Constraint # added constraint: constraint((T0364)V11.CB, (T0364)V75.CB) [> 3.8426 = 6.4044 < 8.3257] w=0.9042 to align # Constraint # added constraint: constraint((T0364)F31.CB, (T0364)V77.CB) [> 3.6444 = 6.0740 < 7.8962] w=0.9042 to align # Constraint # added constraint: constraint((T0364)L59.CB, (T0364)L112.CB) [> 3.0380 = 5.0634 < 6.5824] w=0.9027 to align # Constraint # added constraint: constraint((T0364)Y27.CB, (T0364)Y65.CB) [> 4.3978 = 7.3297 < 9.5286] w=0.9027 to align # Constraint # added constraint: constraint((T0364)I30.CB, (T0364)V75.CB) [> 3.9001 = 6.5002 < 8.4502] w=0.9027 to align # Constraint # added constraint: constraint((T0364)D24.CB, (T0364)Y65.CB) [> 3.6153 = 6.0254 < 7.8330] w=0.9027 to align # Constraint # added constraint: constraint((T0364)V75.CB, (T0364)R97.CB) [> 3.5459 = 5.9099 < 7.6829] w=0.8921 to align # Constraint # added constraint: constraint((T0364)L28.CB, (T0364)A61.CB) [> 4.1824 = 6.9707 < 9.0618] w=0.8905 to align # Constraint # added constraint: constraint((T0364)S94.CB, (T0364)A105.CB) [> 4.4882 = 7.4803 < 9.7244] w=0.8903 to align # Constraint # added constraint: constraint((T0364)H21.CB, (T0364)E68.CB) [> 2.5470 = 4.2451 < 5.5186] w=0.8874 to align # Constraint # added constraint: constraint((T0364)H21.CB, (T0364)V69.CB) [> 3.7883 = 6.3138 < 8.2079] w=0.8874 to align # Constraint # added constraint: constraint((T0364)Y92.CB, (T0364)A106.CB) [> 4.4934 = 7.4890 < 9.7357] w=0.8869 to align # Constraint # added constraint: constraint((T0364)H67.CB, (T0364)V103.CB) [> 4.2511 = 7.0852 < 9.2107] w=0.8867 to align # Constraint # added constraint: constraint((T0364)Y7.CB, (T0364)A34.CB) [> 2.7738 = 4.6229 < 6.0098] w=0.8801 to align # Constraint # added constraint: constraint((T0364)R8.CB, (T0364)W76.CB) [> 3.1849 = 5.3082 < 6.9007] w=0.8798 to align # Constraint # added constraint: constraint((T0364)R8.CB, (T0364)V75.CB) [> 4.1571 = 6.9285 < 9.0071] w=0.8798 to align # Constraint # added constraint: constraint((T0364)Q78.CB, (T0364)H96.CB) [> 4.3522 = 7.2537 < 9.4298] w=0.8691 to align # Constraint # added constraint: constraint((T0364)L38.CB, (T0364)T79.CB) [> 2.8668 = 4.7781 < 6.2115] w=0.8679 to align # Constraint # added constraint: constraint((T0364)T9.CB, (T0364)V75.CB) [> 3.1088 = 5.1813 < 6.7357] w=0.8677 to align # Constraint # added constraint: constraint((T0364)T10.CB, (T0364)E74.CB) [> 3.3705 = 5.6175 < 7.3027] w=0.8677 to align # Constraint # added constraint: constraint((T0364)T6.CB, (T0364)Q78.CB) [> 3.0843 = 5.1405 < 6.6826] w=0.8557 to align # Constraint # added constraint: constraint((T0364)T6.CB, (T0364)V77.CB) [> 4.0381 = 6.7302 < 8.7493] w=0.8557 to align # Constraint # added constraint: constraint((T0364)H90.CB, (T0364)L111.CB) [> 4.5626 = 7.6044 < 9.8856] w=0.8541 to align # Constraint # added constraint: constraint((T0364)L66.CB, (T0364)A106.CB) [> 4.2039 = 7.0065 < 9.1084] w=0.8538 to align # Constraint # added constraint: constraint((T0364)T35.CB, (T0364)L111.CB) [> 4.2168 = 7.0280 < 9.1365] w=0.8451 to align # Constraint # added constraint: constraint((T0364)T6.CB, (T0364)W76.CB) [> 3.6806 = 6.1342 < 7.9745] w=0.8435 to align # Constraint # added constraint: constraint((T0364)T9.CB, (T0364)I30.CB) [> 3.2952 = 5.4920 < 7.1396] w=0.8434 to align # Constraint # added constraint: constraint((T0364)R8.CB, (T0364)V77.CB) [> 4.5205 = 7.5341 < 9.7944] w=0.8433 to align # Constraint # added constraint: constraint((T0364)R8.CB, (T0364)E74.CB) [> 3.5721 = 5.9535 < 7.7395] w=0.8433 to align # Constraint # added constraint: constraint((T0364)V11.CB, (T0364)K70.CB) [> 4.0405 = 6.7342 < 8.7545] w=0.8313 to align # Constraint # added constraint: constraint((T0364)L28.CB, (T0364)I63.CB) [> 3.6601 = 6.1002 < 7.9302] w=0.8296 to align # Constraint # added constraint: constraint((T0364)F31.CB, (T0364)L95.CB) [> 3.9977 = 6.6628 < 8.6616] w=0.8296 to align # Constraint # added constraint: constraint((T0364)I5.CB, (T0364)T79.CB) [> 2.9524 = 4.9206 < 6.3968] w=0.8179 to align # Constraint # added constraint: constraint((T0364)I5.CB, (T0364)Q78.CB) [> 4.3439 = 7.2398 < 9.4118] w=0.8179 to align # Constraint # added constraint: constraint((T0364)N64.CB, (T0364)S107.CB) [> 4.2890 = 7.1483 < 9.2928] w=0.8178 to align # Constraint # added constraint: constraint((T0364)G20.CA, (T0364)K70.CB) [> 3.9331 = 6.5552 < 8.5217] w=0.8154 to align # Constraint # added constraint: constraint((T0364)V11.CB, (T0364)L71.CB) [> 2.9993 = 4.9988 < 6.4985] w=0.8019 to align # Constraint # added constraint: constraint((T0364)L82.CB, (T0364)E108.CB) [> 4.3559 = 7.2598 < 9.4377] w=0.7959 to align # Constraint # added constraint: constraint((T0364)T9.CB, (T0364)E74.CB) [> 4.2417 = 7.0694 < 9.1903] w=0.7946 to align # Constraint # added constraint: constraint((T0364)T35.CB, (T0364)H93.CB) [> 3.6424 = 6.0707 < 7.8919] w=0.7944 to align # Constraint # added constraint: constraint((T0364)L56.CB, (T0364)H113.CB) [> 3.4444 = 5.7407 < 7.4628] w=0.7910 to align # Constraint # added constraint: constraint((T0364)F31.CB, (T0364)I63.CB) [> 4.2028 = 7.0047 < 9.1060] w=0.7893 to align # Constraint # added constraint: constraint((T0364)E74.CB, (T0364)R97.CB) [> 4.2162 = 7.0271 < 9.1352] w=0.7797 to align # Constraint # added constraint: constraint((T0364)K87.CB, (T0364)H113.CB) [> 3.2726 = 5.4543 < 7.0906] w=0.7788 to align # Constraint # added constraint: constraint((T0364)Y27.CB, (T0364)I63.CB) [> 3.9834 = 6.6390 < 8.6307] w=0.7772 to align # Constraint # added constraint: constraint((T0364)Y7.CB, (T0364)Y33.CB) [> 3.7989 = 6.3316 < 8.2311] w=0.7591 to align # Constraint # added constraint: constraint((T0364)I5.CB, (T0364)A34.CB) [> 3.6989 = 6.1648 < 8.0143] w=0.7482 to align # Constraint # added constraint: constraint((T0364)S32.CB, (T0364)T58.CB) [> 3.8833 = 6.4723 < 8.4139] w=0.7443 to align # Constraint # added constraint: constraint((T0364)T6.CB, (T0364)T79.CB) [> 4.5102 = 7.5169 < 9.7720] w=0.7436 to align # Constraint # added constraint: constraint((T0364)E13.CB, (T0364)L71.CB) [> 3.4585 = 5.7641 < 7.4933] w=0.7403 to align # Constraint # added constraint: constraint((T0364)F31.CB, (T0364)T79.CB) [> 4.5403 = 7.5672 < 9.8374] w=0.7350 to align # Constraint # added constraint: constraint((T0364)Y7.CB, (T0364)A37.CB) [> 3.7143 = 6.1906 < 8.0478] w=0.7264 to align # Constraint # added constraint: constraint((T0364)L56.CB, (T0364)L89.CB) [> 4.1797 = 6.9662 < 9.0561] w=0.7229 to align # Constraint # added constraint: constraint((T0364)T9.CB, (T0364)V77.CB) [> 4.1746 = 6.9577 < 9.0449] w=0.7219 to align # Constraint # added constraint: constraint((T0364)V11.CB, (T0364)E74.CB) [> 4.3521 = 7.2534 < 9.4295] w=0.7215 to align # Constraint # added constraint: constraint((T0364)L38.CB, (T0364)V91.CB) [> 3.7752 = 6.2920 < 8.1796] w=0.7112 to align # Constraint # added constraint: constraint((T0364)I5.CB, (T0364)L38.CB) [> 2.7233 = 4.5389 < 5.9006] w=0.7086 to align # Constraint # added constraint: constraint((T0364)Q12.CB, (T0364)L71.CB) [> 3.9729 = 6.6216 < 8.6081] w=0.6960 to align # Constraint # added constraint: constraint((T0364)V16.CB, (T0364)L71.CB) [> 3.4852 = 5.8088 < 7.5514] w=0.6938 to align # Constraint # added constraint: constraint((T0364)L89.CB, (T0364)H113.CB) [> 4.2068 = 7.0114 < 9.1148] w=0.6935 to align # Constraint # added constraint: constraint((T0364)Y27.CB, (T0364)L104.CB) [> 4.2522 = 7.0870 < 9.2130] w=0.6833 to align # Constraint # added constraint: constraint((T0364)L38.CB, (T0364)I81.CB) [> 3.9134 = 6.5224 < 8.4791] w=0.6762 to align # Constraint # added constraint: constraint((T0364)S55.CB, (T0364)H113.CB) [> 4.3029 = 7.1715 < 9.3229] w=0.6692 to align # Constraint # added constraint: constraint((T0364)N54.CB, (T0364)H113.CB) [> 3.4292 = 5.7153 < 7.4299] w=0.6679 to align # Constraint # added constraint: constraint((T0364)M39.CB, (T0364)L56.CB) [> 3.2801 = 5.4669 < 7.1070] w=0.6627 to align # Constraint # added constraint: constraint((T0364)L4.CB, (T0364)T79.CB) [> 4.0139 = 6.6898 < 8.6967] w=0.6598 to align # Constraint # added constraint: constraint((T0364)L4.CB, (T0364)Q80.CB) [> 3.0132 = 5.0220 < 6.5286] w=0.6476 to align # Constraint # added constraint: constraint((T0364)I81.CB, (T0364)Y92.CB) [> 4.5689 = 7.6148 < 9.8992] w=0.6467 to align # Constraint # added constraint: constraint((T0364)T10.CB, (T0364)G72.CA) [> 3.6821 = 6.1369 < 7.9780] w=0.6466 to align # Constraint # added constraint: constraint((T0364)D24.CB, (T0364)I63.CB) [> 4.3216 = 7.2026 < 9.3634] w=0.6447 to align # Constraint # added constraint: constraint((T0364)I5.CB, (T0364)A37.CB) [> 3.4326 = 5.7211 < 7.4374] w=0.6388 to align # Constraint # added constraint: constraint((T0364)Y7.CB, (T0364)T79.CB) [> 4.5553 = 7.5921 < 9.8697] w=0.6232 to align # Constraint # added constraint: constraint((T0364)T10.CB, (T0364)V75.CB) [> 4.5433 = 7.5722 < 9.8439] w=0.6230 to align # Constraint # added constraint: constraint((T0364)Q12.CB, (T0364)G72.CA) [> 4.3959 = 7.3264 < 9.5244] w=0.6106 to align # Constraint # added constraint: constraint((T0364)F57.CB, (T0364)V114.CB) [> 3.5001 = 5.8335 < 7.5835] w=0.6074 to align # Constraint # added constraint: constraint((T0364)L28.CB, (T0364)S107.CB) [> 4.3343 = 7.2239 < 9.3910] w=0.5877 to align # Constraint # added constraint: constraint((T0364)Y7.CB, (T0364)I30.CB) [> 3.9554 = 6.5924 < 8.5701] w=0.5853 to align # Constraint # added constraint: constraint((T0364)L4.CB, (T0364)Q78.CB) [> 3.9125 = 6.5208 < 8.4770] w=0.5745 to align # Constraint # added constraint: constraint((T0364)F31.CB, (T0364)A105.CB) [> 4.2602 = 7.1003 < 9.2304] w=0.5617 to align # Constraint # added constraint: constraint((T0364)A34.CB, (T0364)Q78.CB) [> 4.2471 = 7.0785 < 9.2021] w=0.5553 to align # Constraint # added constraint: constraint((T0364)G20.CA, (T0364)L71.CB) [> 3.9460 = 6.5767 < 8.5497] w=0.5477 to align # Constraint # added constraint: constraint((T0364)S55.CB, (T0364)V114.CB) [> 3.3447 = 5.5745 < 7.2468] w=0.5465 to align # Constraint # added constraint: constraint((T0364)Y27.CB, (T0364)V75.CB) [> 4.3016 = 7.1694 < 9.3202] w=0.5388 to align # Constraint # added constraint: constraint((T0364)S94.CB, (T0364)S107.CB) [> 4.6214 = 7.7024 < 10.0131] w=0.5349 to align # Constraint # added constraint: constraint((T0364)N54.CB, (T0364)V114.CB) [> 4.1848 = 6.9746 < 9.0670] w=0.5221 to align # Constraint # added constraint: constraint((T0364)D36.CB, (T0364)L56.CB) [> 3.7429 = 6.2381 < 8.1096] w=0.5166 to align # Constraint # added constraint: constraint((T0364)L22.CB, (T0364)V75.CB) [> 4.3002 = 7.1670 < 9.3170] w=0.5132 to align # Constraint # added constraint: constraint((T0364)Y27.CB, (T0364)V69.CB) [> 4.1138 = 6.8564 < 8.9133] w=0.5118 to align # Constraint # added constraint: constraint((T0364)S32.CB, (T0364)A61.CB) [> 3.8243 = 6.3739 < 8.2860] w=0.5097 to align # Constraint # added constraint: constraint((T0364)E74.CB, (T0364)A98.CB) [> 3.3298 = 5.5497 < 7.2147] w=0.5031 to align # Constraint # added constraint: constraint((T0364)F31.CB, (T0364)A61.CB) [> 4.2668 = 7.1114 < 9.2448] w=0.4985 to align # Constraint # added constraint: constraint((T0364)T35.CB, (T0364)T58.CB) [> 4.2583 = 7.0972 < 9.2264] w=0.4762 to align # Constraint # added constraint: constraint((T0364)L38.CB, (T0364)Q80.CB) [> 4.2472 = 7.0786 < 9.2022] w=0.4733 to align # Constraint # added constraint: constraint((T0364)I5.CB, (T0364)R41.CB) [> 3.9522 = 6.5870 < 8.5632] w=0.4686 to align # Constraint # added constraint: constraint((T0364)Q80.CB, (T0364)H93.CB) [> 4.6260 = 7.7100 < 10.0230] w=0.4683 to align # Constraint # added constraint: constraint((T0364)T58.CB, (T0364)L112.CB) [> 4.6563 = 7.7605 < 10.0886] w=0.4631 to align # Constraint # added constraint: constraint((T0364)M39.CB, (T0364)L111.CB) [> 3.0351 = 5.0585 < 6.5761] w=0.4556 to align # Constraint # added constraint: constraint((T0364)L89.CB, (T0364)L112.CB) [> 4.6574 = 7.7624 < 10.0911] w=0.4537 to align # Constraint # added constraint: constraint((T0364)L56.CB, (T0364)V114.CB) [> 4.3202 = 7.2003 < 9.3603] w=0.4506 to align # Constraint # added constraint: constraint((T0364)D36.CB, (T0364)T58.CB) [> 4.0683 = 6.7805 < 8.8147] w=0.4501 to align # Constraint # added constraint: constraint((T0364)L22.CB, (T0364)L71.CB) [> 4.3361 = 7.2268 < 9.3948] w=0.4403 to align # Constraint # added constraint: constraint((T0364)M39.CB, (T0364)L89.CB) [> 3.2459 = 5.4099 < 7.0329] w=0.4326 to align # Constraint # added constraint: constraint((T0364)D36.CB, (T0364)L111.CB) [> 4.0757 = 6.7929 < 8.8308] w=0.4294 to align # Constraint # added constraint: constraint((T0364)M39.CB, (T0364)V91.CB) [> 3.9070 = 6.5116 < 8.4651] w=0.4294 to align # Constraint # added constraint: constraint((T0364)V16.CB, (T0364)K70.CB) [> 4.3689 = 7.2815 < 9.4659] w=0.4286 to align # Constraint # added constraint: constraint((T0364)I5.CB, (T0364)Q80.CB) [> 4.3446 = 7.2409 < 9.4132] w=0.4275 to align # Constraint # added constraint: constraint((T0364)K87.CB, (T0364)S121.CB) [> 2.7362 = 4.5604 < 5.9285] w=0.4264 to align # Constraint # added constraint: constraint((T0364)L112.CB, (T0364)S121.CB) [> 3.1372 = 5.2288 < 6.7974] w=0.4264 to align # Constraint # added constraint: constraint((T0364)H113.CB, (T0364)A122.CB) [> 3.1806 = 5.3011 < 6.8914] w=0.4264 to align # Constraint # added constraint: constraint((T0364)T73.CB, (T0364)A98.CB) [> 4.0310 = 6.7182 < 8.7337] w=0.4205 to align # Constraint # added constraint: constraint((T0364)A3.CB, (T0364)Q80.CB) [> 3.8708 = 6.4514 < 8.3868] w=0.4164 to align # Constraint # added constraint: constraint((T0364)E60.CB, (T0364)E108.CB) [> 4.5677 = 7.6129 < 9.8967] w=0.4138 to align # Constraint # added constraint: constraint((T0364)H93.CB, (T0364)A105.CB) [> 4.6849 = 7.8082 < 10.1506] w=0.4051 to align # Constraint # added constraint: constraint((T0364)E74.CB, (T0364)G99.CA) [> 3.7852 = 6.3087 < 8.2013] w=0.3974 to align # Constraint # added constraint: constraint((T0364)T9.CB, (T0364)W76.CB) [> 4.5797 = 7.6328 < 9.9226] w=0.3910 to align # Constraint # added constraint: constraint((T0364)T35.CB, (T0364)S107.CB) [> 4.4191 = 7.3652 < 9.5748] w=0.3799 to align # Constraint # added constraint: constraint((T0364)H113.CB, (T0364)F124.CB) [> 3.0940 = 5.1567 < 6.7037] w=0.3777 to align # Constraint # added constraint: constraint((T0364)R86.CB, (T0364)F124.CB) [> 4.2952 = 7.1587 < 9.3063] w=0.3655 to align # Constraint # added constraint: constraint((T0364)L89.CB, (T0364)F124.CB) [> 3.9832 = 6.6387 < 8.6304] w=0.3655 to align # Constraint # added constraint: constraint((T0364)D36.CB, (T0364)A46.CB) [> 3.6699 = 6.1165 < 7.9515] w=0.3653 to align # Constraint # added constraint: constraint((T0364)T9.CB, (T0364)Y33.CB) [> 3.9207 = 6.5346 < 8.4950] w=0.3411 to align # Constraint # added constraint: constraint((T0364)N19.CB, (T0364)E68.CB) [> 4.5354 = 7.5590 < 9.8267] w=0.3152 to align # Constraint # added constraint: constraint((T0364)D24.CB, (T0364)A105.CB) [> 4.4553 = 7.4255 < 9.6532] w=0.2969 to align # Constraint # added constraint: constraint((T0364)D40.CB, (T0364)L56.CB) [> 3.4821 = 5.8035 < 7.5446] w=0.2956 to align # Constraint # added constraint: constraint((T0364)F84.CB, (T0364)F124.CB) [> 3.7365 = 6.2275 < 8.0957] w=0.2924 to align # Constraint # added constraint: constraint((T0364)F84.CB, (T0364)V129.CB) [> 4.0683 = 6.7805 < 8.8147] w=0.2924 to align # Constraint # added constraint: constraint((T0364)M39.CB, (T0364)I81.CB) [> 4.2878 = 7.1463 < 9.2902] w=0.2923 to align # Constraint # added constraint: constraint((T0364)K87.CB, (T0364)V114.CB) [> 4.6274 = 7.7123 < 10.0259] w=0.2910 to align # Constraint # added constraint: constraint((T0364)L59.CB, (T0364)Q109.CB) [> 4.6594 = 7.7657 < 10.0954] w=0.2887 to align # Constraint # added constraint: constraint((T0364)I42.CB, (T0364)I81.CB) [> 4.0700 = 6.7833 < 8.8183] w=0.2857 to align # Constraint # added constraint: constraint((T0364)I63.CB, (T0364)E108.CB) [> 4.7056 = 7.8427 < 10.1955] w=0.2835 to align # Constraint # added constraint: constraint((T0364)T9.CB, (T0364)F26.CB) [> 4.4351 = 7.3918 < 9.6094] w=0.2812 to align # Constraint # added constraint: constraint((T0364)N54.CB, (T0364)A122.CB) [> 3.9923 = 6.6539 < 8.6500] w=0.2801 to align # Constraint # added constraint: constraint((T0364)N54.CB, (T0364)D115.CB) [> 3.6662 = 6.1103 < 7.9434] w=0.2788 to align # Constraint # added constraint: constraint((T0364)Y92.CB, (T0364)Q109.CB) [> 4.6979 = 7.8298 < 10.1787] w=0.2788 to align # Constraint # added constraint: constraint((T0364)G53.CA, (T0364)D115.CB) [> 3.6176 = 6.0293 < 7.8381] w=0.2666 to align # Constraint # added constraint: constraint((T0364)I5.CB, (T0364)T35.CB) [> 4.5938 = 7.6564 < 9.9532] w=0.2654 to align # Constraint # added constraint: constraint((T0364)W76.CB, (T0364)A98.CB) [> 3.8281 = 6.3801 < 8.2942] w=0.2643 to align # Constraint # added constraint: constraint((T0364)I81.CB, (T0364)L132.CB) [> 3.6153 = 6.0256 < 7.8332] w=0.2559 to align # Constraint # added constraint: constraint((T0364)L22.CB, (T0364)L104.CB) [> 4.4441 = 7.4068 < 9.6289] w=0.2555 to align # Constraint # added constraint: constraint((T0364)G53.CA, (T0364)L116.CB) [> 3.4580 = 5.7634 < 7.4924] w=0.2468 to align # Constraint # added constraint: constraint((T0364)S55.CB, (T0364)L116.CB) [> 3.4759 = 5.7932 < 7.5312] w=0.2347 to align # Constraint # added constraint: constraint((T0364)A46.CB, (T0364)L56.CB) [> 3.5782 = 5.9637 < 7.7528] w=0.2313 to align # Constraint # added constraint: constraint((T0364)Y7.CB, (T0364)L38.CB) [> 4.4590 = 7.4316 < 9.6611] w=0.2282 to align # Constraint # added constraint: constraint((T0364)L28.CB, (T0364)A105.CB) [> 4.5427 = 7.5711 < 9.8424] w=0.2240 to align # Constraint # added constraint: constraint((T0364)I42.CB, (T0364)L89.CB) [> 3.8375 = 6.3959 < 8.3147] w=0.2237 to align # Constraint # added constraint: constraint((T0364)W76.CB, (T0364)D101.CB) [> 4.6358 = 7.7263 < 10.0442] w=0.2228 to align # Constraint # added constraint: constraint((T0364)G53.CA, (T0364)A117.CB) [> 4.1095 = 6.8492 < 8.9039] w=0.2193 to align # Constraint # added constraint: constraint((T0364)L89.CB, (T0364)L132.CB) [> 4.3120 = 7.1867 < 9.3428] w=0.2193 to align # Constraint # added constraint: constraint((T0364)F84.CB, (T0364)L132.CB) [> 3.6871 = 6.1452 < 7.9888] w=0.2193 to align # Constraint # added constraint: constraint((T0364)L44.CB, (T0364)T128.CB) [> 3.8333 = 6.3888 < 8.3055] w=0.2193 to align # Constraint # added constraint: constraint((T0364)G43.CA, (T0364)R131.CB) [> 3.9549 = 6.5915 < 8.5689] w=0.2193 to align # Constraint # added constraint: constraint((T0364)T35.CB, (T0364)L56.CB) [> 4.4140 = 7.3567 < 9.5637] w=0.2094 to align # Constraint # added constraint: constraint((T0364)D85.CB, (T0364)H113.CB) [> 4.6069 = 7.6782 < 9.9816] w=0.2081 to align # Constraint # added constraint: constraint((T0364)T35.CB, (T0364)A61.CB) [> 4.4574 = 7.4290 < 9.6577] w=0.1993 to align # Constraint # added constraint: constraint((T0364)N54.CB, (T0364)L116.CB) [> 4.2967 = 7.1612 < 9.3095] w=0.1981 to align # Constraint # added constraint: constraint((T0364)A46.CB, (T0364)S55.CB) [> 3.8059 = 6.3432 < 8.2462] w=0.1981 to align # Constraint # added constraint: constraint((T0364)V16.CB, (T0364)F26.CB) [> 4.6339 = 7.7232 < 10.0402] w=0.1939 to align # Constraint # added constraint: constraint((T0364)L44.CB, (T0364)L56.CB) [> 4.1207 = 6.8679 < 8.9282] w=0.1849 to align # Constraint # added constraint: constraint((T0364)F57.CB, (T0364)H113.CB) [> 4.6215 = 7.7024 < 10.0132] w=0.1838 to align # Constraint # added constraint: constraint((T0364)T10.CB, (T0364)L71.CB) [> 4.4997 = 7.4994 < 9.7493] w=0.1825 to align # Constraint # added constraint: constraint((T0364)V11.CB, (T0364)H21.CB) [> 4.6801 = 7.8002 < 10.1403] w=0.1717 to align # Constraint # added constraint: constraint((T0364)D36.CB, (T0364)Q109.CB) [> 4.3066 = 7.1777 < 9.3311] w=0.1716 to align # Constraint # added constraint: constraint((T0364)S55.CB, (T0364)D115.CB) [> 4.3157 = 7.1929 < 9.3507] w=0.1705 to align # Constraint # added constraint: constraint((T0364)G53.CA, (T0364)H113.CB) [> 4.3272 = 7.2120 < 9.3756] w=0.1688 to align # Constraint # added constraint: constraint((T0364)Y7.CB, (T0364)Q78.CB) [> 4.6410 = 7.7349 < 10.0554] w=0.1605 to align # Constraint # added constraint: constraint((T0364)H113.CB, (T0364)T128.CB) [> 4.2896 = 7.1493 < 9.2941] w=0.1584 to align # Constraint # added constraint: constraint((T0364)T35.CB, (T0364)A46.CB) [> 4.3383 = 7.2304 < 9.3996] w=0.1583 to align # Constraint # added constraint: constraint((T0364)T79.CB, (T0364)Q109.CB) [> 4.4982 = 7.4970 < 9.7460] w=0.1494 to align # Constraint # added constraint: constraint((T0364)L44.CB, (T0364)S55.CB) [> 4.0806 = 6.8010 < 8.8412] w=0.1483 to align # Constraint # added constraint: constraint((T0364)L44.CB, (T0364)R131.CB) [> 3.7724 = 6.2872 < 8.1734] w=0.1462 to align # Constraint # added constraint: constraint((T0364)I63.CB, (T0364)H93.CB) [> 4.6239 = 7.7065 < 10.0185] w=0.1459 to align # Constraint # added constraint: constraint((T0364)I30.CB, (T0364)H93.CB) [> 4.5475 = 7.5792 < 9.8529] w=0.1451 to align # Constraint # added constraint: constraint((T0364)L22.CB, (T0364)G72.CA) [> 4.5806 = 7.6343 < 9.9245] w=0.1373 to align # Constraint # added constraint: constraint((T0364)D36.CB, (T0364)D47.CB) [> 3.9017 = 6.5029 < 8.4537] w=0.1338 to align # Constraint # added constraint: constraint((T0364)G20.CA, (T0364)E68.CB) [> 4.6405 = 7.7342 < 10.0544] w=0.1327 to align # Constraint # added constraint: constraint((T0364)D36.CB, (T0364)R49.CB) [> 3.7476 = 6.2460 < 8.1198] w=0.1215 to align # Constraint # added constraint: constraint((T0364)M39.CB, (T0364)S55.CB) [> 4.1634 = 6.9391 < 9.0208] w=0.1203 to align # Constraint # added constraint: constraint((T0364)L44.CB, (T0364)N54.CB) [> 2.7389 = 4.5648 < 5.9342] w=0.1104 to align # Constraint # added constraint: constraint((T0364)I81.CB, (T0364)L135.CB) [> 3.3890 = 5.6484 < 7.3429] w=0.1097 to align # Constraint # added constraint: constraint((T0364)W15.CB, (T0364)V69.CB) [> 4.6305 = 7.7175 < 10.0328] w=0.1097 to align # Constraint # added constraint: constraint((T0364)L4.CB, (T0364)R41.CB) [> 4.2259 = 7.0433 < 9.1562] w=0.1096 to align # Constraint # added constraint: constraint((T0364)S52.CB, (T0364)H113.CB) [> 3.2252 = 5.3753 < 6.9879] w=0.1095 to align # Constraint # added constraint: constraint((T0364)I42.CB, (T0364)L56.CB) [> 4.2441 = 7.0735 < 9.1956] w=0.1086 to align # Constraint # added constraint: constraint((T0364)T9.CB, (T0364)Y27.CB) [> 4.6961 = 7.8268 < 10.1749] w=0.0996 to align # Constraint # added constraint: constraint((T0364)L112.CB, (T0364)A122.CB) [> 4.4110 = 7.3516 < 9.5571] w=0.0975 to align # Constraint # added constraint: constraint((T0364)T35.CB, (T0364)Y92.CB) [> 4.6575 = 7.7626 < 10.0913] w=0.0907 to align # Constraint # added constraint: constraint((T0364)G43.CA, (T0364)H113.CB) [> 4.1610 = 6.9350 < 9.0155] w=0.0843 to align # Constraint # added constraint: constraint((T0364)I5.CB, (T0364)I42.CB) [> 4.2378 = 7.0629 < 9.1818] w=0.0820 to align # Constraint # added constraint: constraint((T0364)L28.CB, (T0364)Q109.CB) [> 4.7425 = 7.9042 < 10.2754] w=0.0768 to align # Constraint # added constraint: constraint((T0364)G50.CA, (T0364)L116.CB) [> 3.6637 = 6.1061 < 7.9380] w=0.0731 to align # Constraint # added constraint: constraint((T0364)I81.CB, (T0364)V136.CB) [> 3.1405 = 5.2342 < 6.8044] w=0.0731 to align # Constraint # added constraint: constraint((T0364)Q80.CB, (T0364)V136.CB) [> 4.1971 = 6.9952 < 9.0938] w=0.0731 to align # Constraint # added constraint: constraint((T0364)F57.CB, (T0364)S121.CB) [> 4.5703 = 7.6172 < 9.9024] w=0.0731 to align # Constraint # added constraint: constraint((T0364)F84.CB, (T0364)N133.CB) [> 3.9184 = 6.5306 < 8.4898] w=0.0731 to align # Constraint # added constraint: constraint((T0364)F84.CB, (T0364)L135.CB) [> 4.2387 = 7.0645 < 9.1839] w=0.0731 to align # Constraint # added constraint: constraint((T0364)G83.CA, (T0364)L135.CB) [> 3.7542 = 6.2571 < 8.1342] w=0.0731 to align # Constraint # added constraint: constraint((T0364)G83.CA, (T0364)L132.CB) [> 3.9125 = 6.5208 < 8.4771] w=0.0731 to align # Constraint # added constraint: constraint((T0364)D36.CB, (T0364)F57.CB) [> 4.2501 = 7.0836 < 9.2086] w=0.0730 to align # Constraint # added constraint: constraint((T0364)S52.CB, (T0364)I81.CB) [> 4.6351 = 7.7252 < 10.0427] w=0.0726 to align # Constraint # added constraint: constraint((T0364)T9.CB, (T0364)L29.CB) [> 4.6739 = 7.7899 < 10.1268] w=0.0721 to align # Constraint # added constraint: constraint((T0364)Q78.CB, (T0364)Y92.CB) [> 4.4894 = 7.4824 < 9.7271] w=0.0716 to align # Constraint # added constraint: constraint((T0364)V77.CB, (T0364)A105.CB) [> 4.7744 = 7.9573 < 10.3445] w=0.0631 to align # Constraint # added constraint: constraint((T0364)D36.CB, (T0364)S55.CB) [> 3.6547 = 6.0911 < 7.9184] w=0.0609 to align # Constraint # added constraint: constraint((T0364)A46.CB, (T0364)L111.CB) [> 3.3854 = 5.6423 < 7.3350] w=0.0608 to align # Constraint # added constraint: constraint((T0364)D115.CB, (T0364)G125.CA) [> 3.3966 = 5.6610 < 7.3593] w=0.0608 to align # Constraint # added constraint: constraint((T0364)D14.CB, (T0364)F26.CB) [> 4.7660 = 7.9434 < 10.3264] w=0.0599 to align # Constraint # added constraint: constraint((T0364)F26.CB, (T0364)V75.CB) [> 4.4216 = 7.3693 < 9.5801] w=0.0594 to align # Constraint # added constraint: constraint((T0364)R86.CB, (T0364)V114.CB) [> 2.8159 = 4.6931 < 6.1010] w=0.0580 to align # Constraint # added constraint: constraint((T0364)S52.CB, (T0364)A122.CB) [> 4.3455 = 7.2425 < 9.4153] w=0.0487 to align # Constraint # added constraint: constraint((T0364)S55.CB, (T0364)L111.CB) [> 4.3997 = 7.3328 < 9.5327] w=0.0487 to align # Constraint # added constraint: constraint((T0364)E74.CB, (T0364)F100.CB) [> 4.2445 = 7.0741 < 9.1963] w=0.0487 to align # Constraint # added constraint: constraint((T0364)D24.CB, (T0364)V69.CB) [> 4.5225 = 7.5375 < 9.7988] w=0.0487 to align # Constraint # added constraint: constraint((T0364)P2.CB, (T0364)Q80.CB) [> 3.7992 = 6.3320 < 8.2316] w=0.0485 to align # Constraint # added constraint: constraint((T0364)D17.CB, (T0364)F26.CB) [> 4.6418 = 7.7363 < 10.0572] w=0.0390 to align # Constraint # added constraint: constraint((T0364)Y65.CB, (T0364)L95.CB) [> 4.1662 = 6.9436 < 9.0267] w=0.0366 to align # Constraint # added constraint: constraint((T0364)D36.CB, (T0364)D45.CB) [> 4.0701 = 6.7835 < 8.8185] w=0.0366 to align # Constraint # added constraint: constraint((T0364)Q78.CB, (T0364)V103.CB) [> 4.4428 = 7.4046 < 9.6260] w=0.0366 to align # Constraint # added constraint: constraint((T0364)L44.CB, (T0364)L132.CB) [> 4.4024 = 7.3373 < 9.5385] w=0.0366 to align # Constraint # added constraint: constraint((T0364)A3.CB, (T0364)Q78.CB) [> 3.9589 = 6.5981 < 8.5775] w=0.0366 to align # Constraint # added constraint: constraint((T0364)W15.CB, (T0364)L29.CB) [> 4.0379 = 6.7298 < 8.7488] w=0.0366 to align # Constraint # added constraint: constraint((T0364)F57.CB, (T0364)L116.CB) [> 4.7258 = 7.8764 < 10.2393] w=0.0366 to align # Constraint # added constraint: constraint((T0364)L82.CB, (T0364)M110.CB) [> 4.5184 = 7.5307 < 9.7900] w=0.0366 to align # Constraint # added constraint: constraint((T0364)V16.CB, (T0364)V69.CB) [> 4.7678 = 7.9464 < 10.3303] w=0.0366 to align # Constraint # added constraint: constraint((T0364)L82.CB, (T0364)L132.CB) [> 3.7045 = 6.1742 < 8.0265] w=0.0366 to align # Constraint # added constraint: constraint((T0364)G83.CA, (T0364)R131.CB) [> 4.5642 = 7.6071 < 9.8892] w=0.0366 to align # Constraint # added constraint: constraint((T0364)H90.CB, (T0364)L135.CB) [> 3.1557 = 5.2595 < 6.8373] w=0.0366 to align # Constraint # added constraint: constraint((T0364)S55.CB, (T0364)L112.CB) [> 3.9997 = 6.6661 < 8.6659] w=0.0366 to align # Constraint # added constraint: constraint((T0364)T58.CB, (T0364)V91.CB) [> 4.6929 = 7.8215 < 10.1679] w=0.0365 to align # Constraint # added constraint: constraint((T0364)H62.CB, (T0364)A106.CB) [> 4.7968 = 7.9947 < 10.3931] w=0.0365 to align # Constraint # added constraint: constraint((T0364)L44.CB, (T0364)F57.CB) [> 4.6490 = 7.7483 < 10.0728] w=0.0365 to align # Constraint # added constraint: constraint((T0364)F57.CB, (T0364)T128.CB) [> 3.6304 = 6.0507 < 7.8660] w=0.0365 to align # Constraint # added constraint: constraint((T0364)V114.CB, (T0364)G125.CA) [> 3.7318 = 6.2197 < 8.0857] w=0.0365 to align # Constraint # added constraint: constraint((T0364)V114.CB, (T0364)T128.CB) [> 3.2825 = 5.4708 < 7.1120] w=0.0365 to align # Constraint # added constraint: constraint((T0364)D115.CB, (T0364)T127.CB) [> 2.6867 = 4.4778 < 5.8212] w=0.0365 to align # Constraint # added constraint: constraint((T0364)D115.CB, (T0364)T128.CB) [> 4.4777 = 7.4628 < 9.7016] w=0.0365 to align # Constraint # added constraint: constraint((T0364)F57.CB, (T0364)Q120.CB) [> 4.6904 = 7.8173 < 10.1625] w=0.0364 to align # Constraint # added constraint: constraint((T0364)E60.CB, (T0364)H90.CB) [> 4.7850 = 7.9751 < 10.3676] w=0.0364 to align # Constraint # added constraint: constraint((T0364)T73.CB, (T0364)H96.CB) [> 3.5639 = 5.9398 < 7.7217] w=0.0350 to align # Constraint # added constraint: constraint((T0364)W76.CB, (T0364)H93.CB) [> 4.3732 = 7.2887 < 9.4753] w=0.0350 to align # Constraint # added constraint: constraint((T0364)I42.CB, (T0364)V129.CB) [> 4.5015 = 7.5025 < 9.7533] w=0.0244 to align # Constraint # added constraint: constraint((T0364)L59.CB, (T0364)S121.CB) [> 4.6628 = 7.7714 < 10.1028] w=0.0244 to align # Constraint # added constraint: constraint((T0364)L112.CB, (T0364)F124.CB) [> 4.7090 = 7.8484 < 10.2029] w=0.0244 to align # Constraint # added constraint: constraint((T0364)N54.CB, (T0364)L112.CB) [> 4.0423 = 6.7371 < 8.7582] w=0.0244 to align # Constraint # added constraint: constraint((T0364)G53.CA, (T0364)V114.CB) [> 3.3302 = 5.5504 < 7.2155] w=0.0244 to align # Constraint # added constraint: constraint((T0364)Q12.CB, (T0364)T35.CB) [> 4.5679 = 7.6131 < 9.8970] w=0.0242 to align # Constraint # added constraint: constraint((T0364)E13.CB, (T0364)T35.CB) [> 3.5838 = 5.9731 < 7.7650] w=0.0242 to align # Constraint # added constraint: constraint((T0364)E13.CB, (T0364)D36.CB) [> 3.7485 = 6.2474 < 8.1216] w=0.0242 to align # Constraint # added constraint: constraint((T0364)R49.CB, (T0364)T58.CB) [> 4.0314 = 6.7189 < 8.7346] w=0.0242 to align # Constraint # added constraint: constraint((T0364)W15.CB, (T0364)I30.CB) [> 4.7258 = 7.8764 < 10.2393] w=0.0233 to align # Constraint # added constraint: constraint((T0364)T6.CB, (T0364)T35.CB) [> 4.0970 = 6.8282 < 8.8767] w=0.0211 to align # Constraint # added constraint: constraint((T0364)L56.CB, (T0364)Q109.CB) [> 3.5735 = 5.9559 < 7.7426] w=0.0122 to align # Constraint # added constraint: constraint((T0364)F57.CB, (T0364)M110.CB) [> 3.1942 = 5.3237 < 6.9208] w=0.0122 to align # Constraint # added constraint: constraint((T0364)L59.CB, (T0364)S107.CB) [> 3.4773 = 5.7955 < 7.5342] w=0.0122 to align # Constraint # added constraint: constraint((T0364)L59.CB, (T0364)E108.CB) [> 4.3821 = 7.3035 < 9.4945] w=0.0122 to align # Constraint # added constraint: constraint((T0364)E60.CB, (T0364)S107.CB) [> 2.8723 = 4.7871 < 6.2233] w=0.0122 to align # Constraint # added constraint: constraint((T0364)A3.CB, (T0364)M148.CB) [> 4.4620 = 7.4368 < 9.6678] w=0.0122 to align # Constraint # added constraint: constraint((T0364)T6.CB, (T0364)H93.CB) [> 4.5690 = 7.6150 < 9.8995] w=0.0122 to align # Constraint # added constraint: constraint((T0364)L28.CB, (T0364)L59.CB) [> 4.5727 = 7.6211 < 9.9075] w=0.0122 to align # Constraint # added constraint: constraint((T0364)Y92.CB, (T0364)I152.CB) [> 2.4937 = 4.1562 < 5.4031] w=0.0122 to align # Constraint # added constraint: constraint((T0364)H93.CB, (T0364)I152.CB) [> 4.2172 = 7.0286 < 9.1372] w=0.0122 to align # Constraint # added constraint: constraint((T0364)S94.CB, (T0364)I152.CB) [> 4.0403 = 6.7339 < 8.7540] w=0.0122 to align # Constraint # added constraint: constraint((T0364)A106.CB, (T0364)I152.CB) [> 2.8843 = 4.8072 < 6.2494] w=0.0122 to align # Constraint # added constraint: constraint((T0364)A106.CB, (T0364)L154.CB) [> 2.8001 = 4.6668 < 6.0668] w=0.0122 to align # Constraint # added constraint: constraint((T0364)E108.CB, (T0364)I152.CB) [> 3.7940 = 6.3233 < 8.2203] w=0.0122 to align # Constraint # added constraint: constraint((T0364)E108.CB, (T0364)L154.CB) [> 3.8051 = 6.3418 < 8.2443] w=0.0122 to align # Constraint # added constraint: constraint((T0364)E108.CB, (T0364)A156.CB) [> 3.6056 = 6.0093 < 7.8121] w=0.0122 to align # Constraint # added constraint: constraint((T0364)H62.CB, (T0364)L154.CB) [> 3.9103 = 6.5171 < 8.4723] w=0.0122 to align # Constraint # added constraint: constraint((T0364)L82.CB, (T0364)M148.CB) [> 4.2653 = 7.1088 < 9.2415] w=0.0122 to align # Constraint # added constraint: constraint((T0364)G83.CA, (T0364)M148.CB) [> 3.2041 = 5.3401 < 6.9421] w=0.0122 to align # Constraint # added constraint: constraint((T0364)L28.CB, (T0364)Y65.CB) [> 4.7950 = 7.9916 < 10.3891] w=0.0121 to align # Constraint # added constraint: constraint((T0364)D36.CB, (T0364)H93.CB) [> 2.8623 = 4.7705 < 6.2016] w=0.0089 to align # Constraint # added constraint: constraint((T0364)D36.CB, (T0364)Y92.CB) [> 4.7751 = 7.9584 < 10.3460] w=0.0089 to align # Constraint # added constraint: constraint((T0364)D36.CB, (T0364)A61.CB) [> 4.5854 = 7.6424 < 9.9351] w=0.0089 to align # Constraint # added constraint: constraint((T0364)T35.CB, (T0364)Q78.CB) [> 4.5168 = 7.5280 < 9.7864] w=0.0089 to align # Constraint # added constraint: constraint((T0364)F31.CB, (T0364)Q78.CB) [> 4.7909 = 7.9847 < 10.3802] w=0.0037 to align # Constraint # added constraint: constraint((T0364)L29.CB, (T0364)T58.CB) [> 4.6968 = 7.8280 < 10.1764] w=0.0037 to align # SetCost created cost = # ( 1.0000 * align ) # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0364/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0364/decoys/ # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS4 # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # Found a chain break before 137 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS1 # ReadConformPDB reading from PDB file servers/3Dpro_TS2.pdb.gz looking for model 1 # Found a chain break before 153 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS2 # ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS3 # ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS4 # ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1 # naming current conformation 3Dpro_TS5 # ReadConformPDB reading from PDB file servers/ABIpro_TS1.pdb.gz looking for model 1 # Found a chain break before 91 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS1 # ReadConformPDB reading from PDB file servers/ABIpro_TS2.pdb.gz looking for model 1 # Found a chain break before 135 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS2 # ReadConformPDB reading from PDB file servers/ABIpro_TS3.pdb.gz looking for model 1 # Found a chain break before 106 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS3 # ReadConformPDB reading from PDB file servers/ABIpro_TS4.pdb.gz looking for model 1 # Found a chain break before 102 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS4 # ReadConformPDB reading from PDB file servers/ABIpro_TS5.pdb.gz looking for model 1 # Found a chain break before 151 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS5 # ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1 # Found a chain break before 2 # copying to AlignedFragments data structure # naming current conformation BayesHH_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS1.pdb.gz looking for model 1 # Found a chain break before 125 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS1 # ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1 # Found a chain break before 155 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS1 # ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS3 # ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1 # Found a chain break before 147 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS4 # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS5 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS2 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS3 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS4.pdb.gz looking for model 1 WARNING: atoms too close: (T0364)H134.C and (T0364)L135.N only 0.000 apart, marking (T0364)L135.N as missing WARNING: atoms too close: (T0364)L135.N and (T0364)L135.CA only 0.000 apart, marking (T0364)L135.CA as missing WARNING: atoms too close: (T0364)H134.C and (T0364)L135.CA only 0.000 apart, marking (T0364)L135.CA as missing WARNING: atoms too close: (T0364)L135.CA and (T0364)L135.CB only 0.000 apart, marking (T0364)L135.CB as missing WARNING: atoms too close: (T0364)L135.N and (T0364)L135.CB only 0.000 apart, marking (T0364)L135.CB as missing WARNING: atoms too close: (T0364)H134.C and (T0364)L135.CB only 0.000 apart, marking (T0364)L135.CB as missing WARNING: atoms too close: (T0364)L135.CB and (T0364)L135.CG only 0.000 apart, marking (T0364)L135.CG as missing WARNING: atoms too close: (T0364)L135.CA and (T0364)L135.CG only 0.000 apart, marking (T0364)L135.CG as missing WARNING: atoms too close: (T0364)L135.N and (T0364)L135.CG only 0.000 apart, marking (T0364)L135.CG as missing WARNING: atoms too close: (T0364)H134.C and (T0364)L135.CG only 0.000 apart, marking (T0364)L135.CG as missing WARNING: atoms too close: (T0364)L135.CG and (T0364)L135.CD1 only 0.000 apart, marking (T0364)L135.CD1 as missing WARNING: atoms too close: (T0364)L135.CB and (T0364)L135.CD1 only 0.000 apart, marking (T0364)L135.CD1 as missing WARNING: atoms too close: (T0364)L135.CA and (T0364)L135.CD1 only 0.000 apart, marking (T0364)L135.CD1 as missing WARNING: atoms too close: (T0364)L135.N and (T0364)L135.CD1 only 0.000 apart, marking (T0364)L135.CD1 as missing WARNING: atoms too close: (T0364)H134.C and (T0364)L135.CD1 only 0.000 apart, marking (T0364)L135.CD1 as missing WARNING: atoms too close: (T0364)L135.CD1 and (T0364)L135.CD2 only 0.000 apart, marking (T0364)L135.CD2 as missing WARNING: atoms too close: (T0364)L135.CG and (T0364)L135.CD2 only 0.000 apart, marking (T0364)L135.CD2 as missing WARNING: atoms too close: (T0364)L135.CB and (T0364)L135.CD2 only 0.000 apart, marking (T0364)L135.CD2 as missing WARNING: atoms too close: (T0364)L135.CA and (T0364)L135.CD2 only 0.000 apart, marking (T0364)L135.CD2 as missing WARNING: atoms too close: (T0364)L135.N and (T0364)L135.CD2 only 0.000 apart, marking (T0364)L135.CD2 as missing WARNING: atoms too close: (T0364)H134.C and (T0364)L135.CD2 only 0.000 apart, marking (T0364)L135.CD2 as missing WARNING: atoms too close: (T0364)L135.CD2 and (T0364)L135.O only 0.000 apart, marking (T0364)L135.O as missing WARNING: atoms too close: (T0364)L135.CD1 and (T0364)L135.O only 0.000 apart, marking (T0364)L135.O as missing WARNING: atoms too close: (T0364)L135.CG and (T0364)L135.O only 0.000 apart, marking (T0364)L135.O as missing WARNING: atoms too close: (T0364)L135.CB and (T0364)L135.O only 0.000 apart, marking (T0364)L135.O as missing WARNING: atoms too close: (T0364)L135.CA and (T0364)L135.O only 0.000 apart, marking (T0364)L135.O as missing WARNING: atoms too close: (T0364)L135.N and (T0364)L135.O only 0.000 apart, marking (T0364)L135.O as missing WARNING: atoms too close: (T0364)H134.C and (T0364)L135.O only 0.000 apart, marking (T0364)L135.O as missing WARNING: atoms too close: (T0364)L135.O and (T0364)L135.C only 0.000 apart, marking (T0364)L135.C as missing WARNING: atoms too close: (T0364)L135.CD2 and (T0364)L135.C only 0.000 apart, marking (T0364)L135.C as missing WARNING: atoms too close: (T0364)L135.CD1 and (T0364)L135.C only 0.000 apart, marking (T0364)L135.C as missing WARNING: atoms too close: (T0364)L135.CG and (T0364)L135.C only 0.000 apart, marking (T0364)L135.C as missing WARNING: atoms too close: (T0364)L135.CB and (T0364)L135.C only 0.000 apart, marking (T0364)L135.C as missing WARNING: atoms too close: (T0364)L135.CA and (T0364)L135.C only 0.000 apart, marking (T0364)L135.C as missing WARNING: atoms too close: (T0364)L135.N and (T0364)L135.C only 0.000 apart, marking (T0364)L135.C as missing WARNING: atoms too close: (T0364)H134.C and (T0364)L135.C only 0.000 apart, marking (T0364)L135.C as missing # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS4 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS5 # ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation Distill_TS1 # ReadConformPDB reading from PDB file servers/Distill_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation Distill_TS2 # ReadConformPDB reading from PDB file servers/Distill_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation Distill_TS3 # ReadConformPDB reading from PDB file servers/Distill_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation Distill_TS4 # ReadConformPDB reading from PDB file servers/Distill_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation Distill_TS5 # ReadConformPDB reading from PDB file servers/FAMSD_TS1.pdb.gz looking for model 1 # Found a chain break before 155 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS1 # ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation FAMSD_TS2 # ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation FAMSD_TS3 # ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation FAMSD_TS4 # ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation FAMSD_TS5 # ReadConformPDB reading from PDB file servers/FAMS_TS1.pdb.gz looking for model 1 # Found a chain break before 155 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # Found a chain break before 155 # copying to AlignedFragments data structure # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation FAMS_TS3 # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation FAMS_TS4 # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # Found a chain break before 153 # copying to AlignedFragments data structure # naming current conformation FAMS_TS5 # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # Found a chain break before 71 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS1 # ReadConformPDB reading from PDB file servers/FOLDpro_TS2.pdb.gz looking for model 1 # naming current conformation FOLDpro_TS2 # ReadConformPDB reading from PDB file servers/FOLDpro_TS3.pdb.gz looking for model 1 # Found a chain break before 87 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS3 # ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1 # Found a chain break before 133 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS4 # ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS5 # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 Skipped atom 83, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation FORTE1_AL1 # ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation FORTE1_AL2 # ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation FORTE1_AL3 # ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation FORTE1_AL4 # ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1 Skipped atom 159, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz Skipped atom 228, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation FORTE1_AL5 # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 Skipped atom 83, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation FORTE2_AL1 # ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation FORTE2_AL2 # ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation FORTE2_AL3 # ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1 Skipped atom 159, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 228, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation FORTE2_AL4 # ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation FORTE2_AL5 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS1.pdb.gz looking for model 1 # Found a chain break before 125 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS1 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS2.pdb.gz looking for model 1 # Found a chain break before 122 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS2 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS3.pdb.gz looking for model 1 # Found a chain break before 146 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS3 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS4.pdb.gz looking for model 1 # Found a chain break before 132 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS4 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS5.pdb.gz looking for model 1 # Found a chain break before 140 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS5 # ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS2 # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS3 # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS4 # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS5 # ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation FUGUE_AL1 # ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation FUGUE_AL2 # ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation FUGUE_AL3 # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 Skipped atom 155, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL4.pdb.gz Skipped atom 224, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL4.pdb.gz Skipped atom 561, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL4.pdb.gz Skipped atom 586, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL4.pdb.gz Skipped atom 607, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL4.pdb.gz # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL4 # ReadConformPDB reading from PDB file servers/FUNCTION_TS1.pdb.gz looking for model 1 # Found a chain break before 155 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS1 # ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1 # Found a chain break before 150 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS2 # ReadConformPDB reading from PDB file servers/FUNCTION_TS3.pdb.gz looking for model 1 # Found a chain break before 154 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS3 # ReadConformPDB reading from PDB file servers/FUNCTION_TS4.pdb.gz looking for model 1 # Found a chain break before 148 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS4 # ReadConformPDB reading from PDB file servers/FUNCTION_TS5.pdb.gz looking for model 1 # Found a chain break before 153 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # ReadConformPDB reading from PDB file servers/Frankenstein_TS1.pdb.gz looking for model 1 # Found a chain break before 135 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS1 # ReadConformPDB reading from PDB file servers/Frankenstein_TS2.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS2 # ReadConformPDB reading from PDB file servers/Frankenstein_TS3.pdb.gz looking for model 1 # naming current conformation Frankenstein_TS3 # ReadConformPDB reading from PDB file servers/Frankenstein_TS4.pdb.gz looking for model 1 # Found a chain break before 110 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS4 # ReadConformPDB reading from PDB file servers/Frankenstein_TS5.pdb.gz looking for model 1 # Found a chain break before 41 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS5 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS1 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # Found a chain break before 125 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS3 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS4 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS5 # ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation HHpred1_TS1 # ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1 # naming current conformation HHpred2_TS1 # ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1 # naming current conformation HHpred3_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS2 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS3 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS4 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS5 # ReadConformPDB reading from PDB file servers/LOOPP_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation LOOPP_TS1 # ReadConformPDB reading from PDB file servers/LOOPP_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation LOOPP_TS2 # ReadConformPDB reading from PDB file servers/LOOPP_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation LOOPP_TS3 # ReadConformPDB reading from PDB file servers/LOOPP_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation LOOPP_TS4 # ReadConformPDB reading from PDB file servers/LOOPP_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation LOOPP_TS5 # ReadConformPDB reading from PDB file servers/MIG_FROST_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation MIG_FROST_AL1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS1.pdb.gz looking for model 1 # Found a chain break before 147 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS2.pdb.gz looking for model 1 # Found a chain break before 148 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS3.pdb.gz looking for model 1 # Found a chain break before 135 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS4.pdb.gz looking for model 1 # Found a chain break before 43 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS5.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS5 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # Found a chain break before 148 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS2.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS3.pdb.gz looking for model 1 # Found a chain break before 135 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS4.pdb.gz looking for model 1 # Found a chain break before 43 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS5.pdb.gz looking for model 1 # Found a chain break before 149 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS5 # ReadConformPDB reading from PDB file servers/MetaTasser_TS1.pdb.gz looking for model 1 # Found a chain break before 155 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS1 # ReadConformPDB reading from PDB file servers/MetaTasser_TS2.pdb.gz looking for model 1 # Found a chain break before 155 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS2 # ReadConformPDB reading from PDB file servers/MetaTasser_TS3.pdb.gz looking for model 1 # Found a chain break before 153 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS3 # ReadConformPDB reading from PDB file servers/MetaTasser_TS4.pdb.gz looking for model 1 # Found a chain break before 154 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS4 # ReadConformPDB reading from PDB file servers/MetaTasser_TS5.pdb.gz looking for model 1 # Found a chain break before 155 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS5 # ReadConformPDB reading from PDB file servers/NN_PUT_lab_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation NN_PUT_lab_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS1.pdb.gz looking for model 1 # Found a chain break before 103 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS2.pdb.gz looking for model 1 # Found a chain break before 145 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS2 # ReadConformPDB reading from PDB file servers/POMYSL_TS3.pdb.gz looking for model 1 # Found a chain break before 147 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS3 # ReadConformPDB reading from PDB file servers/POMYSL_TS4.pdb.gz looking for model 1 # Found a chain break before 125 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS4 # ReadConformPDB reading from PDB file servers/POMYSL_TS5.pdb.gz looking for model 1 # Found a chain break before 111 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # Found a chain break before 122 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS5 # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation Pcons6_TS1 # ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation Pcons6_TS2 # ReadConformPDB reading from PDB file servers/Pcons6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation Pcons6_TS3 # ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation Pcons6_TS4 # ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation Pcons6_TS5 # ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation Phyre-1_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS1.pdb.gz looking for model 1 # Found a chain break before 154 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS2.pdb.gz looking for model 1 # Found a chain break before 154 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS2 # ReadConformPDB reading from PDB file servers/Phyre-2_TS3.pdb.gz looking for model 1 # Found a chain break before 145 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS3 # ReadConformPDB reading from PDB file servers/Phyre-2_TS4.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS4 # ReadConformPDB reading from PDB file servers/Phyre-2_TS5.pdb.gz looking for model 1 # Found a chain break before 152 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS5 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS1 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS2 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS3 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS4 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1 # Found a chain break before 136 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS4.pdb.gz looking for model 1 # Found a chain break before 116 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS5 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS1.pdb.gz looking for model 1 # Found a chain break before 154 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS1 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS2.pdb.gz looking for model 1 # Found a chain break before 151 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS2 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS3.pdb.gz looking for model 1 # Found a chain break before 151 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS3 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS4.pdb.gz looking for model 1 # Found a chain break before 153 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS4 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS5.pdb.gz looking for model 1 # Found a chain break before 154 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR_TS1.pdb.gz looking for model 1 # Found a chain break before 43 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR_TS3.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR_TS4.pdb.gz looking for model 1 # Found a chain break before 116 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR_TS5.pdb.gz looking for model 1 # Found a chain break before 43 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS5 # ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1 # Found a chain break before 71 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS1 # ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1 # Found a chain break before 71 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS2 # ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1 # Found a chain break before 139 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS3 # ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1 # Found a chain break before 132 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS4 # ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1 # Found a chain break before 98 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS5 # ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1 # Found a chain break before 146 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS1 # ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS2 # ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1 # Found a chain break before 141 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS3 # ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS4 # ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1 # Found a chain break before 112 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS5 # ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL1 # ReadConformPDB reading from PDB file servers/SAM-T02_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL2 # ReadConformPDB reading from PDB file servers/SAM-T02_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL3 # ReadConformPDB reading from PDB file servers/SAM-T02_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL4 # ReadConformPDB reading from PDB file servers/SAM-T02_AL5.pdb.gz looking for model 1 Skipped atom 71, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 88, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 353, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 362, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 415, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 428, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL5 # ReadConformPDB reading from PDB file servers/SAM-T99_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL1 # ReadConformPDB reading from PDB file servers/SAM-T99_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL2 # ReadConformPDB reading from PDB file servers/SAM-T99_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL3 # ReadConformPDB reading from PDB file servers/SAM-T99_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL4 # ReadConformPDB reading from PDB file servers/SAM-T99_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL5 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1 # Found a chain break before 152 # copying to AlignedFragments data structure # naming current conformation SAM_T06_server_TS1 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS2 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS3 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS4 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS5 # ReadConformPDB reading from PDB file servers/SP3_TS1.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation SP3_TS1 # ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1 # Found a chain break before 43 # copying to AlignedFragments data structure # naming current conformation SP3_TS2 # ReadConformPDB reading from PDB file servers/SP3_TS3.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation SP3_TS3 # ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1 # naming current conformation SP3_TS4 # ReadConformPDB reading from PDB file servers/SP3_TS5.pdb.gz looking for model 1 # Found a chain break before 77 # copying to AlignedFragments data structure # naming current conformation SP3_TS5 # ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation SP4_TS1 # ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1 # Found a chain break before 115 # copying to AlignedFragments data structure # naming current conformation SP4_TS2 # ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1 # naming current conformation SP4_TS3 # ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation SP4_TS4 # ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1 # naming current conformation SP4_TS5 # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # Found a chain break before 131 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS1 # ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1 # Found a chain break before 43 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS2 # ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS3 # ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1 # Found a chain break before 47 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS4 # ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS2 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS3 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS4 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_expm_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation UNI-EID_expm_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL2 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL3 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL4.pdb.gz looking for model 1 Skipped atom 79, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL4 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL5.pdb.gz looking for model 1 Skipped atom 71, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz Skipped atom 88, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz Skipped atom 353, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz Skipped atom 362, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz Skipped atom 415, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz Skipped atom 428, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL5 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1 # Found a chain break before 155 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS1 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS2.pdb.gz looking for model 1 # Found a chain break before 154 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS2 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS3.pdb.gz looking for model 1 # Found a chain break before 148 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS3 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS4.pdb.gz looking for model 1 # Found a chain break before 154 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS4 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS5.pdb.gz looking for model 1 # Found a chain break before 154 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS5 # ReadConformPDB reading from PDB file servers/beautshot_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation beautshot_TS1 # ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation beautshotbase_TS1 # ReadConformPDB reading from PDB file servers/forecast-s_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation forecast-s_AL1 # ReadConformPDB reading from PDB file servers/forecast-s_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation forecast-s_AL2 # ReadConformPDB reading from PDB file servers/forecast-s_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation forecast-s_AL3 # ReadConformPDB reading from PDB file servers/forecast-s_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation forecast-s_AL5 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS2.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS3.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS4.pdb.gz looking for model 1 # Found a chain break before 21 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS5.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS1.pdb.gz looking for model 1 # Found a chain break before 153 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS2.pdb.gz looking for model 1 # Found a chain break before 153 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS3.pdb.gz looking for model 1 # Found a chain break before 153 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS4.pdb.gz looking for model 1 # Found a chain break before 154 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS5.pdb.gz looking for model 1 WARNING: atoms too close: (T0364)I81.O and (T0364)L82.N only 0.000 apart, marking (T0364)L82.N as missing # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS5 # ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1 # Found a chain break before 154 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS1 # ReadConformPDB reading from PDB file servers/keasar-server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation keasar-server_TS2 # ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation keasar-server_TS3 # ReadConformPDB reading from PDB file servers/keasar-server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation keasar-server_TS4 # ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation keasar-server_TS5 # ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation mGen-3D_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation nFOLD_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation nFOLD_TS2 # ReadConformPDB reading from PDB file servers/nFOLD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation nFOLD_TS3 # ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation nFOLD_TS4 # ReadConformPDB reading from PDB file servers/nFOLD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation nFOLD_TS5 # ReadConformPDB reading from PDB file servers/panther2_TS1.pdb.gz looking for model 1 WARNING: atoms too close: (T0364)T58.N and (T0364)R88.N only 0.000 apart, marking (T0364)R88.N as missing WARNING: atoms too close: (T0364)T58.CA and (T0364)R88.CA only 0.000 apart, marking (T0364)R88.CA as missing WARNING: atoms too close: (T0364)T58.CB and (T0364)R88.CB only 0.000 apart, marking (T0364)R88.CB as missing WARNING: atoms too close: (T0364)T58.CG2 and (T0364)R88.CG only 0.000 apart, marking (T0364)R88.CG as missing WARNING: atoms too close: (T0364)T58.O and (T0364)R88.O only 0.000 apart, marking (T0364)R88.O as missing WARNING: atoms too close: (T0364)T58.C and (T0364)R88.C only 0.000 apart, marking (T0364)R88.C as missing WARNING: atoms too close: (T0364)R88.N and (T0364)L89.N only 0.000 apart, marking (T0364)R88.N as missing WARNING: atoms too close: (T0364)T58.N and (T0364)L89.N only 0.000 apart, marking (T0364)L89.N as missing WARNING: atoms too close: (T0364)R88.CA and (T0364)L89.CA only 0.000 apart, marking (T0364)L89.CA as missing WARNING: atoms too close: (T0364)T58.CA and (T0364)L89.CA only 0.000 apart, marking (T0364)L89.CA as missing WARNING: atoms too close: (T0364)R88.CB and (T0364)L89.CB only 0.000 apart, marking (T0364)L89.CB as missing WARNING: atoms too close: (T0364)T58.CB and (T0364)L89.CB only 0.000 apart, marking (T0364)L89.CB as missing WARNING: atoms too close: (T0364)R88.CG and (T0364)L89.CG only 0.000 apart, marking (T0364)L89.CG as missing WARNING: atoms too close: (T0364)T58.CG2 and (T0364)L89.CG only 0.000 apart, marking (T0364)L89.CG as missing WARNING: atoms too close: (T0364)R88.O and (T0364)L89.O only 0.000 apart, marking (T0364)L89.O as missing WARNING: atoms too close: (T0364)T58.O and (T0364)L89.O only 0.000 apart, marking (T0364)L89.O as missing WARNING: atoms too close: (T0364)R88.C and (T0364)L89.C only 0.000 apart, marking (T0364)L89.C as missing WARNING: atoms too close: (T0364)T58.C and (T0364)L89.C only 0.000 apart, marking (T0364)L89.C as missing WARNING: atoms too close: (T0364)L89.N and (T0364)H90.N only 0.000 apart, marking (T0364)L89.N as missing WARNING: atoms too close: (T0364)R88.N and (T0364)H90.N only 0.000 apart, marking (T0364)R88.N as missing WARNING: atoms too close: (T0364)T58.N and (T0364)H90.N only 0.000 apart, marking (T0364)H90.N as missing WARNING: atoms too close: (T0364)L89.CA and (T0364)H90.CA only 0.000 apart, marking (T0364)H90.CA as missing WARNING: atoms too close: (T0364)R88.CA and (T0364)H90.CA only 0.000 apart, marking (T0364)H90.CA as missing WARNING: atoms too close: (T0364)T58.CA and (T0364)H90.CA only 0.000 apart, marking (T0364)H90.CA as missing WARNING: atoms too close: (T0364)L89.CB and (T0364)H90.CB only 0.000 apart, marking (T0364)H90.CB as missing WARNING: atoms too close: (T0364)R88.CB and (T0364)H90.CB only 0.000 apart, marking (T0364)H90.CB as missing WARNING: atoms too close: (T0364)T58.CB and (T0364)H90.CB only 0.000 apart, marking (T0364)H90.CB as missing WARNING: atoms too close: (T0364)L89.CG and (T0364)H90.CG only 0.000 apart, marking (T0364)H90.CG as missing WARNING: atoms too close: (T0364)R88.CG and (T0364)H90.CG only 0.000 apart, marking (T0364)H90.CG as missing WARNING: atoms too close: (T0364)T58.CG2 and (T0364)H90.CG only 0.000 apart, marking (T0364)H90.CG as missing WARNING: atoms too close: (T0364)L89.O and (T0364)H90.O only 0.000 apart, marking (T0364)H90.O as missing WARNING: atoms too close: (T0364)R88.O and (T0364)H90.O only 0.000 apart, marking (T0364)H90.O as missing WARNING: atoms too close: (T0364)T58.O and (T0364)H90.O only 0.000 apart, marking (T0364)H90.O as missing WARNING: atoms too close: (T0364)L89.C and (T0364)H90.C only 0.000 apart, marking (T0364)H90.C as missing WARNING: atoms too close: (T0364)R88.C and (T0364)H90.C only 0.000 apart, marking (T0364)H90.C as missing WARNING: atoms too close: (T0364)T58.C and (T0364)H90.C only 0.000 apart, marking (T0364)H90.C as missing WARNING: atoms too close: (T0364)H90.N and (T0364)V91.N only 0.000 apart, marking (T0364)H90.N as missing WARNING: atoms too close: (T0364)L89.N and (T0364)V91.N only 0.000 apart, marking (T0364)L89.N as missing WARNING: atoms too close: (T0364)R88.N and (T0364)V91.N only 0.000 apart, marking (T0364)R88.N as missing WARNING: atoms too close: (T0364)T58.N and (T0364)V91.N only 0.000 apart, marking (T0364)V91.N as missing WARNING: atoms too close: (T0364)H90.CA and (T0364)V91.CA only 0.000 apart, marking (T0364)V91.CA as missing WARNING: atoms too close: (T0364)L89.CA and (T0364)V91.CA only 0.000 apart, marking (T0364)V91.CA as missing WARNING: atoms too close: (T0364)R88.CA and (T0364)V91.CA only 0.000 apart, marking (T0364)V91.CA as missing WARNING: atoms too close: (T0364)T58.CA and (T0364)V91.CA only 0.000 apart, marking (T0364)V91.CA as missing WARNING: atoms too close: (T0364)H90.CB and (T0364)V91.CB only 0.000 apart, marking (T0364)V91.CB as missing WARNING: atoms too close: (T0364)L89.CB and (T0364)V91.CB only 0.000 apart, marking (T0364)V91.CB as missing WARNING: atoms too close: (T0364)R88.CB and (T0364)V91.CB only 0.000 apart, marking (T0364)V91.CB as missing WARNING: atoms too close: (T0364)T58.CB and (T0364)V91.CB only 0.000 apart, marking (T0364)V91.CB as missing WARNING: atoms too close: (T0364)H90.CG and (T0364)V91.CG1 only 0.000 apart, marking (T0364)V91.CG1 as missing WARNING: atoms too close: (T0364)L89.CG and (T0364)V91.CG1 only 0.000 apart, marking (T0364)V91.CG1 as missing WARNING: atoms too close: (T0364)R88.CG and (T0364)V91.CG1 only 0.000 apart, marking (T0364)V91.CG1 as missing WARNING: atoms too close: (T0364)T58.CG2 and (T0364)V91.CG1 only 0.000 apart, marking (T0364)V91.CG1 as missing WARNING: atoms too close: (T0364)H90.O and (T0364)V91.O only 0.000 apart, marking (T0364)V91.O as missing WARNING: atoms too close: (T0364)L89.O and (T0364)V91.O only 0.000 apart, marking (T0364)V91.O as missing WARNING: atoms too close: (T0364)R88.O and (T0364)V91.O only 0.000 apart, marking (T0364)V91.O as missing WARNING: atoms too close: (T0364)T58.O and (T0364)V91.O only 0.000 apart, marking (T0364)V91.O as missing WARNING: atoms too close: (T0364)H90.C and (T0364)V91.C only 0.000 apart, marking (T0364)V91.C as missing WARNING: atoms too close: (T0364)L89.C and (T0364)V91.C only 0.000 apart, marking (T0364)V91.C as missing WARNING: atoms too close: (T0364)R88.C and (T0364)V91.C only 0.000 apart, marking (T0364)V91.C as missing WARNING: atoms too close: (T0364)T58.C and (T0364)V91.C only 0.000 apart, marking (T0364)V91.C as missing WARNING: atoms too close: (T0364)V91.N and (T0364)Y92.N only 0.000 apart, marking (T0364)V91.N as missing WARNING: atoms too close: (T0364)H90.N and (T0364)Y92.N only 0.000 apart, marking (T0364)H90.N as missing WARNING: atoms too close: (T0364)L89.N and (T0364)Y92.N only 0.000 apart, marking (T0364)L89.N as missing WARNING: atoms too close: (T0364)R88.N and (T0364)Y92.N only 0.000 apart, marking (T0364)R88.N as missing WARNING: atoms too close: (T0364)T58.N and (T0364)Y92.N only 0.000 apart, marking (T0364)Y92.N as missing WARNING: atoms too close: (T0364)V91.CA and (T0364)Y92.CA only 0.000 apart, marking (T0364)Y92.CA as missing WARNING: atoms too close: (T0364)H90.CA and (T0364)Y92.CA only 0.000 apart, marking (T0364)Y92.CA as missing WARNING: atoms too close: (T0364)L89.CA and (T0364)Y92.CA only 0.000 apart, marking (T0364)Y92.CA as missing WARNING: atoms too close: (T0364)R88.CA and (T0364)Y92.CA only 0.000 apart, marking (T0364)Y92.CA as missing WARNING: atoms too close: (T0364)T58.CA and (T0364)Y92.CA only 0.000 apart, marking (T0364)Y92.CA as missing WARNING: atoms too close: (T0364)V91.CB and (T0364)Y92.CB only 0.000 apart, marking (T0364)Y92.CB as missing WARNING: atoms too close: (T0364)H90.CB and (T0364)Y92.CB only 0.000 apart, marking (T0364)Y92.CB as missing WARNING: atoms too close: (T0364)L89.CB and (T0364)Y92.CB only 0.000 apart, marking (T0364)Y92.CB as missing WARNING: atoms too close: (T0364)R88.CB and (T0364)Y92.CB only 0.000 apart, marking (T0364)Y92.CB as missing WARNING: atoms too close: (T0364)T58.CB and (T0364)Y92.CB only 0.000 apart, marking (T0364)Y92.CB as missing WARNING: atoms too close: (T0364)V91.CG1 and (T0364)Y92.CG only 0.000 apart, marking (T0364)Y92.CG as missing WARNING: atoms too close: (T0364)H90.CG and (T0364)Y92.CG only 0.000 apart, marking (T0364)Y92.CG as missing WARNING: atoms too close: (T0364)L89.CG and (T0364)Y92.CG only 0.000 apart, marking (T0364)Y92.CG as missing WARNING: atoms too close: (T0364)R88.CG and (T0364)Y92.CG only 0.000 apart, marking (T0364)Y92.CG as missing WARNING: atoms too close: (T0364)T58.CG2 and (T0364)Y92.CG only 0.000 apart, marking (T0364)Y92.CG as missing WARNING: atoms too close: (T0364)V91.O and (T0364)Y92.O only 0.000 apart, marking (T0364)Y92.O as missing WARNING: atoms too close: (T0364)H90.O and (T0364)Y92.O only 0.000 apart, marking (T0364)Y92.O as missing WARNING: atoms too close: (T0364)L89.O and (T0364)Y92.O only 0.000 apart, marking (T0364)Y92.O as missing WARNING: atoms too close: (T0364)R88.O and (T0364)Y92.O only 0.000 apart, marking (T0364)Y92.O as missing WARNING: atoms too close: (T0364)T58.O and (T0364)Y92.O only 0.000 apart, marking (T0364)Y92.O as missing WARNING: atoms too close: (T0364)V91.C and (T0364)Y92.C only 0.000 apart, marking (T0364)Y92.C as missing WARNING: atoms too close: (T0364)H90.C and (T0364)Y92.C only 0.000 apart, marking (T0364)Y92.C as missing WARNING: atoms too close: (T0364)L89.C and (T0364)Y92.C only 0.000 apart, marking (T0364)Y92.C as missing WARNING: atoms too close: (T0364)R88.C and (T0364)Y92.C only 0.000 apart, marking (T0364)Y92.C as missing WARNING: atoms too close: (T0364)T58.C and (T0364)Y92.C only 0.000 apart, marking (T0364)Y92.C as missing WARNING: atoms too close: (T0364)Y92.N and (T0364)Q109.N only 0.000 apart, marking (T0364)Y92.N as missing WARNING: atoms too close: (T0364)V91.N and (T0364)Q109.N only 0.000 apart, marking (T0364)V91.N as missing WARNING: atoms too close: (T0364)H90.N and (T0364)Q109.N only 0.000 apart, marking (T0364)H90.N as missing WARNING: atoms too close: (T0364)L89.N and (T0364)Q109.N only 0.000 apart, marking (T0364)L89.N as missing WARNING: atoms too close: (T0364)R88.N and (T0364)Q109.N only 0.000 apart, marking (T0364)R88.N as missing WARNING: atoms too close: (T0364)T58.N and (T0364)Q109.N only 0.000 apart, marking (T0364)Q109.N as missing WARNING: atoms too close: (T0364)Y92.CA and (T0364)Q109.CA only 0.000 apart, marking (T0364)Q109.CA as missing WARNING: atoms too close: (T0364)V91.CA and (T0364)Q109.CA only 0.000 apart, marking (T0364)Q109.CA as missing WARNING: atoms too close: (T0364)H90.CA and (T0364)Q109.CA only 0.000 apart, marking (T0364)Q109.CA as missing WARNING: atoms too close: (T0364)L89.CA and (T0364)Q109.CA only 0.000 apart, marking (T0364)Q109.CA as missing WARNING: atoms too close: (T0364)R88.CA and (T0364)Q109.CA only 0.000 apart, marking (T0364)Q109.CA as missing WARNING: atoms too close: (T0364)T58.CA and (T0364)Q109.CA only 0.000 apart, marking (T0364)Q109.CA as missing WARNING: atoms too close: (T0364)Y92.CB and (T0364)Q109.CB only 0.000 apart, marking (T0364)Q109.CB as missing WARNING: atoms too close: (T0364)V91.CB and (T0364)Q109.CB only 0.000 apart, marking (T0364)Q109.CB as missing WARNING: atoms too close: (T0364)H90.CB and (T0364)Q109.CB only 0.000 apart, marking (T0364)Q109.CB as missing WARNING: atoms too close: (T0364)L89.CB and (T0364)Q109.CB only 0.000 apart, marking (T0364)Q109.CB as missing WARNING: atoms too close: (T0364)R88.CB and (T0364)Q109.CB only 0.000 apart, marking (T0364)Q109.CB as missing WARNING: atoms too close: (T0364)T58.CB and (T0364)Q109.CB only 0.000 apart, marking (T0364)Q109.CB as missing WARNING: atoms too close: (T0364)Y92.CG and (T0364)Q109.CG only 0.000 apart, marking (T0364)Q109.CG as missing WARNING: atoms too close: (T0364)V91.CG1 and (T0364)Q109.CG only 0.000 apart, marking (T0364)Q109.CG as missing WARNING: atoms too close: (T0364)H90.CG and (T0364)Q109.CG only 0.000 apart, marking (T0364)Q109.CG as missing WARNING: atoms too close: (T0364)L89.CG and (T0364)Q109.CG only 0.000 apart, marking (T0364)Q109.CG as missing WARNING: atoms too close: (T0364)R88.CG and (T0364)Q109.CG only 0.000 apart, marking (T0364)Q109.CG as missing WARNING: atoms too close: (T0364)T58.CG2 and (T0364)Q109.CG only 0.000 apart, marking (T0364)Q109.CG as missing WARNING: atoms too close: (T0364)Y92.O and (T0364)Q109.O only 0.000 apart, marking (T0364)Q109.O as missing WARNING: atoms too close: (T0364)V91.O and (T0364)Q109.O only 0.000 apart, marking (T0364)Q109.O as missing WARNING: atoms too close: (T0364)H90.O and (T0364)Q109.O only 0.000 apart, marking (T0364)Q109.O as missing WARNING: atoms too close: (T0364)L89.O and (T0364)Q109.O only 0.000 apart, marking (T0364)Q109.O as missing WARNING: atoms too close: (T0364)R88.O and (T0364)Q109.O only 0.000 apart, marking (T0364)Q109.O as missing WARNING: atoms too close: (T0364)T58.O and (T0364)Q109.O only 0.000 apart, marking (T0364)Q109.O as missing WARNING: atoms too close: (T0364)Y92.C and (T0364)Q109.C only 0.000 apart, marking (T0364)Q109.C as missing WARNING: atoms too close: (T0364)V91.C and (T0364)Q109.C only 0.000 apart, marking (T0364)Q109.C as missing WARNING: atoms too close: (T0364)H90.C and (T0364)Q109.C only 0.000 apart, marking (T0364)Q109.C as missing WARNING: atoms too close: (T0364)L89.C and (T0364)Q109.C only 0.000 apart, marking (T0364)Q109.C as missing WARNING: atoms too close: (T0364)R88.C and (T0364)Q109.C only 0.000 apart, marking (T0364)Q109.C as missing WARNING: atoms too close: (T0364)T58.C and (T0364)Q109.C only 0.000 apart, marking (T0364)Q109.C as missing WARNING: atoms too close: (T0364)Q109.N and (T0364)L132.N only 0.000 apart, marking (T0364)Q109.N as missing WARNING: atoms too close: (T0364)Y92.N and (T0364)L132.N only 0.000 apart, marking (T0364)Y92.N as missing WARNING: atoms too close: (T0364)V91.N and (T0364)L132.N only 0.000 apart, marking (T0364)V91.N as missing WARNING: atoms too close: (T0364)H90.N and (T0364)L132.N only 0.000 apart, marking (T0364)H90.N as missing WARNING: atoms too close: (T0364)L89.N and (T0364)L132.N only 0.000 apart, marking (T0364)L89.N as missing WARNING: atoms too close: (T0364)R88.N and (T0364)L132.N only 0.000 apart, marking (T0364)R88.N as missing WARNING: atoms too close: (T0364)T58.N and (T0364)L132.N only 0.000 apart, marking (T0364)L132.N as missing WARNING: atoms too close: (T0364)Q109.CA and (T0364)L132.CA only 0.000 apart, marking (T0364)L132.CA as missing WARNING: atoms too close: (T0364)Y92.CA and (T0364)L132.CA only 0.000 apart, marking (T0364)L132.CA as missing WARNING: atoms too close: (T0364)V91.CA and (T0364)L132.CA only 0.000 apart, marking (T0364)L132.CA as missing WARNING: atoms too close: (T0364)H90.CA and (T0364)L132.CA only 0.000 apart, marking (T0364)L132.CA as missing WARNING: atoms too close: (T0364)L89.CA and (T0364)L132.CA only 0.000 apart, marking (T0364)L132.CA as missing WARNING: atoms too close: (T0364)R88.CA and (T0364)L132.CA only 0.000 apart, marking (T0364)L132.CA as missing WARNING: atoms too close: (T0364)T58.CA and (T0364)L132.CA only 0.000 apart, marking (T0364)L132.CA as missing WARNING: atoms too close: (T0364)Q109.CB and (T0364)L132.CB only 0.000 apart, marking (T0364)L132.CB as missing WARNING: atoms too close: (T0364)Y92.CB and (T0364)L132.CB only 0.000 apart, marking (T0364)L132.CB as missing WARNING: atoms too close: (T0364)V91.CB and (T0364)L132.CB only 0.000 apart, marking (T0364)L132.CB as missing WARNING: atoms too close: (T0364)H90.CB and (T0364)L132.CB only 0.000 apart, marking (T0364)L132.CB as missing WARNING: atoms too close: (T0364)L89.CB and (T0364)L132.CB only 0.000 apart, marking (T0364)L132.CB as missing WARNING: atoms too close: (T0364)R88.CB and (T0364)L132.CB only 0.000 apart, marking (T0364)L132.CB as missing WARNING: atoms too close: (T0364)T58.CB and (T0364)L132.CB only 0.000 apart, marking (T0364)L132.CB as missing WARNING: atoms too close: (T0364)Q109.CG and (T0364)L132.CG only 0.000 apart, marking (T0364)L132.CG as missing WARNING: atoms too close: (T0364)Y92.CG and (T0364)L132.CG only 0.000 apart, marking (T0364)L132.CG as missing WARNING: atoms too close: (T0364)V91.CG1 and (T0364)L132.CG only 0.000 apart, marking (T0364)L132.CG as missing WARNING: atoms too close: (T0364)H90.CG and (T0364)L132.CG only 0.000 apart, marking (T0364)L132.CG as missing WARNING: atoms too close: (T0364)L89.CG and (T0364)L132.CG only 0.000 apart, marking (T0364)L132.CG as missing WARNING: atoms too close: (T0364)R88.CG and (T0364)L132.CG only 0.000 apart, marking (T0364)L132.CG as missing WARNING: atoms too close: (T0364)T58.CG2 and (T0364)L132.CG only 0.000 apart, marking (T0364)L132.CG as missing WARNING: atoms too close: (T0364)Q109.O and (T0364)L132.O only 0.000 apart, marking (T0364)L132.O as missing WARNING: atoms too close: (T0364)Y92.O and (T0364)L132.O only 0.000 apart, marking (T0364)L132.O as missing WARNING: atoms too close: (T0364)V91.O and (T0364)L132.O only 0.000 apart, marking (T0364)L132.O as missing WARNING: atoms too close: (T0364)H90.O and (T0364)L132.O only 0.000 apart, marking (T0364)L132.O as missing WARNING: atoms too close: (T0364)L89.O and (T0364)L132.O only 0.000 apart, marking (T0364)L132.O as missing WARNING: atoms too close: (T0364)R88.O and (T0364)L132.O only 0.000 apart, marking (T0364)L132.O as missing WARNING: atoms too close: (T0364)T58.O and (T0364)L132.O only 0.000 apart, marking (T0364)L132.O as missing WARNING: atoms too close: (T0364)Q109.C and (T0364)L132.C only 0.000 apart, marking (T0364)L132.C as missing WARNING: atoms too close: (T0364)Y92.C and (T0364)L132.C only 0.000 apart, marking (T0364)L132.C as missing WARNING: atoms too close: (T0364)V91.C and (T0364)L132.C only 0.000 apart, marking (T0364)L132.C as missing WARNING: atoms too close: (T0364)H90.C and (T0364)L132.C only 0.000 apart, marking (T0364)L132.C as missing WARNING: atoms too close: (T0364)L89.C and (T0364)L132.C only 0.000 apart, marking (T0364)L132.C as missing WARNING: atoms too close: (T0364)R88.C and (T0364)L132.C only 0.000 apart, marking (T0364)L132.C as missing WARNING: atoms too close: (T0364)T58.C and (T0364)L132.C only 0.000 apart, marking (T0364)L132.C as missing # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation panther2_TS1 # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0364 can't currently be optimized by undertaker # naming current conformation shub_TS1 # command:Using radius: 8.0000 Using models AND alignments for constraints model score -0.5419 model score -0.4327 model score -0.5247 model score -0.5379 model score -0.4434 model score -0.4955 model score -0.4861 model score -0.4924 model score -0.4986 model score -0.4931 model score -0.4951 model score -0.2599 model score -0.4439 model score -0.4761 model score -0.6518 model score -0.6278 model score -0.5429 model score -0.0939 model score -0.0999 model score 1.1923 model score 1.4317 model score 1.3409 model score 1.5130 model score 1.2597 model score -0.6611 model score -0.2176 model score -0.5787 model score -0.6206 model score -0.6296 model score -0.5861 model score -0.6052 model score -0.1634 model score -0.1099 model score -0.3424 model score -0.5035 model score -0.6281 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.5487 model score -0.6363 model score -0.3562 model score -0.5190 model score -0.5132 model score -0.5553 model score -0.5787 model score -0.6206 model score -0.3562 model score -0.5082 model score -0.6747 model score -0.6691 model score -0.6340 model score -0.5972 model score -0.6319 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 2.1700 model score 2.4214 model score 2.3776 model score 2.3726 model score 1.9082 model score -0.5168 model score -0.5207 model score -0.5262 model score -0.1770 model score -0.3843 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.5383 model score -0.4887 model score -0.5690 model score -0.5310 model score -0.5082 model score 0.0550 model score -0.3257 model score -0.3109 model score -0.2387 model score 0.7538 model score -0.6499 model score -0.5661 model score -0.5120 model score -0.6201 model score -0.5805 model score -0.5849 model score -0.6468 model score -0.6468 model score 0.0447 model score 0.6125 model score -0.2867 model score 1.4053 model score 0.6066 model score -0.6089 model score -0.2360 model score -0.4442 model score -0.5608 model score -0.0284 model score 1.2771 model score -0.5585 model score -0.3388 model score -0.5725 model score -0.6100 model score -0.5842 model score -0.3388 model score -0.5557 model score -0.5725 model score -0.6100 model score -0.5808 model score -0.6622 model score -0.6223 model score -0.6700 model score -0.6682 model score -0.6726 model score -0.6089 model score 1.9760 model score 2.0746 model score 1.8911 model score 2.0876 model score 1.8916 model score -0.5963 model score -0.5955 model score -0.5928 model score -0.6114 model score -0.6018 model score -0.6128 model score -0.6217 model score -0.6145 model score -0.6180 model score -0.6026 model score -0.6502 model score -0.6281 model score -0.6490 model score -0.6290 model score -0.6255 model score -0.6501 model score -0.6344 model score -0.6305 model score -0.6388 model score -0.6381 model score -0.6392 model score -0.6366 model score -0.5821 model score -0.6490 model score -0.5292 model score -0.5835 model score -0.6401 model score -0.5344 model score -0.6401 model score -0.6317 model score -0.5806 model score -0.5757 model score -0.6339 model score -0.6339 model score -0.5780 model score -0.5757 model score -0.6186 model score -0.6491 model score -0.6491 model score -0.6321 model score -0.6186 model score -0.5605 model score -0.5534 model score -0.4749 model score -0.5454 model score -0.4848 model score -0.6409 model score -0.4969 model score -0.4496 model score -0.5438 model score -0.5866 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.6403 model score -0.6351 model score -0.6054 model score -0.5847 model score 0.0991 model score -0.6380 model score -0.5976 model score -0.5380 model score -0.5694 model score -0.4320 model score -0.6392 model score -0.5974 model score -0.5694 model score -0.5380 model score -0.4953 model score -0.6452 model score -0.6169 model score -0.5380 model score -0.4998 model score -0.3934 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.5729 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.6345 model score -0.6105 model score -0.6394 model score -0.6370 model score -0.6366 model score -0.6212 model score -0.6215 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.5787 model score -0.5747 model score -0.5525 model score -0.6132 model score -0.6339 model score 2.0906 model score 2.2218 model score 2.0865 model score 2.0915 model score 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min: 0.0000 max: 0.0674 USE_EVALUE, weight: 0.9998 eval: 0.0000 min: 0.0000 max: 0.0674 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0674 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0674 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0674 USE_EVALUE, weight: 0.7325 eval: 0.0200 min: 0.0000 max: 0.0674 USE_EVALUE, weight: 0.7325 eval: 0.0200 min: 0.0000 max: 0.0674 USE_EVALUE, weight: 0.7325 eval: 0.0200 min: 0.0000 max: 0.0674 USE_EVALUE, weight: 0.9927 eval: 0.0005 min: 0.0000 max: 0.0674 USE_EVALUE, weight: 0.9927 eval: 0.0005 min: 0.0000 max: 0.0674 USE_EVALUE, weight: 0.9927 eval: 0.0005 min: 0.0000 max: 0.0674 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0674 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0674 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0674 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0674 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0674 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0674 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0674 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0674 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0674 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0674 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0674 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0674 USE_EVALUE, weight: 0.9858 eval: 0.0011 min: 0.0000 max: 0.0674 USE_EVALUE, weight: 0.9858 eval: 0.0011 min: 0.0000 max: 0.0674 USE_EVALUE, weight: 0.9858 eval: 0.0011 min: 0.0000 max: 0.0674 Number of contacts in models: 261 Number of contacts in alignments: 87 NUMB_ALIGNS: 87 Adding 5401 constraints to all3.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all3.constraints maxweight: 1.0000 Optimizing... Probability sum: -282.9821, CN propb: -282.9821 weights: 0.3638 constraints: 542 # command:Found ConstraintSet # PrintContacts align.constraints_meta03 Number of constraints in align3.constraints 542 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta03 Number of constraints in align3.constraints.bonus 542 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta03 Number of constraints in rejected3.constraints 4859 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta03 Number of constraints in rejected3.constraints.bonus 4859 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_meta03 Number of constraints in noncontact3.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_meta03 Number of constraints in noncontact3.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_meta03 Number of constraints in all3.constraints 5401 # command: