# 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/T0350/ # command:# Making conformation for sequence T0350 numbered 1 through 117 Created new target T0350 from T0350.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0350/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0350//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0350/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0350//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0350/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0350/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0350/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wmvA/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/T0350/1wmvA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0350/1wmvA/merged-good-all-a2m.gz for input Trying 1wmvA/merged-good-all-a2m Error: Couldn't open file 1wmvA/merged-good-all-a2m or 1wmvA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 3proC/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0350 read from 3proC/merged-good-all-a2m # 3proC read from 3proC/merged-good-all-a2m # found chain 3proC in training set Warning: unaligning (T0350)P53 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3proC)L113 T0350 34 :QVSYTNLAEMVGEMNKLLE 3proC 85 :RYSLKQLQSAMEQLDAGAN # choosing archetypes in rotamer library T0350 60 :FELHDKLNEYYVKVI 3proC 119 :WYVDPRSNAVVVKVD T0350 76 :DS 3proC 134 :DG T0350 86 :PPKRWLDFYA 3proC 136 :ATDAGVDFVA Number of specific fragments extracted= 4 number of extra gaps= 0 total=4 Number of alignments=1 # 3proC read from 3proC/merged-good-all-a2m # found chain 3proC in training set Warning: unaligning (T0350)P53 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3proC)L113 T0350 34 :QVSYTNLAEMVGEMNKLLE 3proC 85 :RYSLKQLQSAMEQLDAGAN Number of specific fragments extracted= 1 number of extra gaps= 0 total=5 # 3proC read from 3proC/merged-good-all-a2m # found chain 3proC in training set Warning: unaligning (T0350)P53 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3proC)L113 T0350 34 :QVSYTNLAEMVGEMNKLLE 3proC 85 :RYSLKQLQSAMEQLDAGAN Number of specific fragments extracted= 1 number of extra gaps= 0 total=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jnyA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1jnyA expands to /projects/compbio/data/pdb/1jny.pdb.gz 1jnyA:# T0350 read from 1jnyA/merged-good-all-a2m # 1jnyA read from 1jnyA/merged-good-all-a2m # adding 1jnyA to template set # found chain 1jnyA in template set T0350 32 :VHQVSYTNLAEMVGEMNKLLEPSQ 1jnyA 158 :EPPYDEKRYKEIVDQVSKFMRSYG Number of specific fragments extracted= 1 number of extra gaps= 0 total=7 Number of alignments=2 # 1jnyA read from 1jnyA/merged-good-all-a2m # found chain 1jnyA in template set T0350 32 :VHQVSYTNLAEMVGEMNKLLEPSQV 1jnyA 158 :EPPYDEKRYKEIVDQVSKFMRSYGF Number of specific fragments extracted= 1 number of extra gaps= 0 total=8 Number of alignments=3 # 1jnyA read from 1jnyA/merged-good-all-a2m # found chain 1jnyA in template set T0350 32 :VHQVSYTNLAEMVGEMNKLLEPSQVH 1jnyA 158 :EPPYDEKRYKEIVDQVSKFMRSYGFN Number of specific fragments extracted= 1 number of extra gaps= 0 total=9 Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v5xA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1v5xA expands to /projects/compbio/data/pdb/1v5x.pdb.gz 1v5xA:# T0350 read from 1v5xA/merged-good-all-a2m # 1v5xA read from 1v5xA/merged-good-all-a2m # adding 1v5xA to template set # found chain 1v5xA in template set T0350 34 :QVSYTNLAEMVG 1v5xA 36 :RIAPEAARAIGE T0350 50 :LLEPS 1v5xA 48 :ALGPF T0350 81 :VIREIPPKRWLDFYAA 1v5xA 58 :VFRDQPPEEVLRLMEE Number of specific fragments extracted= 3 number of extra gaps= 0 total=12 Number of alignments=5 # 1v5xA read from 1v5xA/merged-good-all-a2m # found chain 1v5xA in template set T0350 34 :QVSYTNLAEMVG 1v5xA 36 :RIAPEAARAIGE T0350 50 :LLEPS 1v5xA 48 :ALGPF T0350 81 :VIREIPPKRWLDFYAA 1v5xA 58 :VFRDQPPEEVLRLMEE Number of specific fragments extracted= 3 number of extra gaps= 0 total=15 Number of alignments=6 # 1v5xA read from 1v5xA/merged-good-all-a2m # found chain 1v5xA in template set T0350 34 :QVSYTNLAEMVGE 1v5xA 36 :RIAPEAARAIGEA T0350 51 :LEPSQVHL 1v5xA 49 :LGPFVVRV T0350 81 :VIREIPPKRWLDFYA 1v5xA 58 :VFRDQPPEEVLRLME Number of specific fragments extracted= 3 number of extra gaps= 0 total=18 Number of alignments=7 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ohtA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ohtA expands to /projects/compbio/data/pdb/1oht.pdb.gz 1ohtA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0350 read from 1ohtA/merged-good-all-a2m # 1ohtA read from 1ohtA/merged-good-all-a2m # adding 1ohtA to template set # found chain 1ohtA in template set T0350 84 :EIPPKRWLDFYAAMTEF 1ohtA 120 :ELPPKQMLDAAKNLIAF Number of specific fragments extracted= 1 number of extra gaps= 0 total=19 # 1ohtA read from 1ohtA/merged-good-all-a2m # found chain 1ohtA in template set T0350 26 :NDNEVPVH 1ohtA 27 :KSVEHFQG T0350 34 :QVSYTNLAEMVGEMNKLL 1ohtA 50 :CYSTPDCMKSMRDMQDFH T0350 55 :QVH 1ohtA 72 :GWN T0350 66 :LNEYYVK 1ohtA 84 :GDGMIYT T0350 76 :DST 1ohtA 102 :PKY T0350 85 :IPPKRWLDFYAAMTEF 1ohtA 121 :LPPKQMLDAAKNLIAF Number of specific fragments extracted= 6 number of extra gaps= 0 total=25 Number of alignments=8 # 1ohtA read from 1ohtA/merged-good-all-a2m # found chain 1ohtA in template set T0350 32 :VHQVSYTNLAEMVGEMNKLLEPSQV 1ohtA 48 :AVCYSTPDCMKSMRDMQDFHQLERG T0350 57 :H 1ohtA 74 :N T0350 60 :FELH 1ohtA 80 :FGIG T0350 64 :DKLN 1ohtA 102 :PKYN T0350 84 :EIPPKRWLDFYAAMTEF 1ohtA 120 :ELPPKQMLDAAKNLIAF Number of specific fragments extracted= 5 number of extra gaps= 0 total=30 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gnqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2gnqA expands to /projects/compbio/data/pdb/2gnq.pdb.gz 2gnqA:Skipped atom 501, because occupancy 0.5 <= existing 0.500 in 2gnqA Skipped atom 503, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 505, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 507, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 509, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 511, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 602, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 604, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 606, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 608, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 610, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 612, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1355, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1357, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1359, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1361, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1363, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1365, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1430, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1432, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1434, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1436, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1438, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1440, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1442, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1444, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1446, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1811, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1813, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1815, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1817, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1819, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1821, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1823, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1979, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1981, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1983, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1985, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1987, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1989, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1991, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1993, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1995, because occupancy 0.500 <= existing 0.500 in 2gnqA # T0350 read from 2gnqA/merged-good-all-a2m # 2gnqA read from 2gnqA/merged-good-all-a2m # adding 2gnqA to template set # found chain 2gnqA in template set Number of specific fragments extracted= 0 number of extra gaps= 0 total=30 # 2gnqA read from 2gnqA/merged-good-all-a2m # found chain 2gnqA in template set Number of specific fragments extracted= 0 number of extra gaps= 0 total=30 # 2gnqA read from 2gnqA/merged-good-all-a2m # found chain 2gnqA in template set T0350 61 :ELHDKLNEYY 2gnqA 178 :HFNRDGSLIV T0350 71 :VKVIEDSTNEVIREIPPK 2gnqA 195 :CRIWDTASGQCLKTLIDD Number of specific fragments extracted= 2 number of extra gaps= 0 total=32 Number of alignments=10 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a3qA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1a3qA expands to /projects/compbio/data/pdb/1a3q.pdb.gz 1a3qA:# T0350 read from 1a3qA/merged-good-all-a2m # 1a3qA read from 1a3qA/merged-good-all-a2m # adding 1a3qA to template set # found chain 1a3qA in template set T0350 13 :WDRYDTQIHNQKDNDNEV 1a3qA 147 :MGTMIQKLQRQRLRSRPQ T0350 34 :QVSYT 1a3qA 165 :GLTEA T0350 39 :NLAEMVGEMNKLLEPSQVHLKFELH 1a3qA 173 :ELEQEAKELKKVMDLSIVRLRFSAF Number of specific fragments extracted= 3 number of extra gaps= 0 total=35 Number of alignments=11 # 1a3qA read from 1a3qA/merged-good-all-a2m # found chain 1a3qA in template set T0350 13 :WDRYDTQIHNQKDNDNEVPVHQVSYTNLAEMVGEMNKLLEPSQVHLKFELH 1a3qA 147 :MGTMIQKLQRQRLRSRPQGLTEAEQRELEQEAKELKKVMDLSIVRLRFSAF Number of specific fragments extracted= 1 number of extra gaps= 0 total=36 Number of alignments=12 # 1a3qA read from 1a3qA/merged-good-all-a2m # found chain 1a3qA in template set T0350 20 :IHNQKDNDNEVPVHQVSYTNLAEMVGEMNKLLEPSQV 1a3qA 151 :IQKLQRQRLRSRPQGLTEAEQRELEQEAKELKKVMDL T0350 57 :HLKFEL 1a3qA 191 :RLRFSA Number of specific fragments extracted= 2 number of extra gaps= 0 total=38 Number of alignments=13 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qcsA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qcsA expands to /projects/compbio/data/pdb/1qcs.pdb.gz 1qcsA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0350 read from 1qcsA/merged-good-all-a2m # 1qcsA read from 1qcsA/merged-good-all-a2m # adding 1qcsA to template set # found chain 1qcsA in template set T0350 30 :VPVHQVSYT 1qcsA 102 :LQKKNIDSN T0350 39 :NLAEMVGEMNKLLEPS 1qcsA 113 :DTDKMAAEFIQQFNNQ T0350 55 :QVHLKFELHD 1qcsA 133 :GQQLVFSFND T0350 69 :YYVKVI 1qcsA 143 :KLFGLL Number of specific fragments extracted= 4 number of extra gaps= 0 total=42 Number of alignments=14 # 1qcsA read from 1qcsA/merged-good-all-a2m # found chain 1qcsA in template set T0350 26 :NDNEVPVHQVSYTNL 1qcsA 103 :QKKNIDSNPYDTDKM T0350 41 :AEMVGEMNKLLEPSQVHLKFELHD 1qcsA 119 :AEFIQQFNNQAFSVGQQLVFSFND T0350 69 :YYVKVI 1qcsA 143 :KLFGLL Number of specific fragments extracted= 3 number of extra gaps= 0 total=45 Number of alignments=15 # 1qcsA read from 1qcsA/merged-good-all-a2m # found chain 1qcsA in template set T0350 26 :NDNEVPVHQVS 1qcsA 103 :QKKNIDSNPYD T0350 40 :LAEMVGEMNKLLEP 1qcsA 114 :TDKMAAEFIQQFNN T0350 54 :SQVHLKFELHD 1qcsA 132 :VGQQLVFSFND T0350 69 :YYVKVI 1qcsA 143 :KLFGLL Number of specific fragments extracted= 4 number of extra gaps= 0 total=49 Number of alignments=16 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cnqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2cnqA expands to /projects/compbio/data/pdb/2cnq.pdb.gz 2cnqA:Skipped atom 7, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 21, because occupancy 0.390 <= existing 0.610 in 2cnqA Skipped atom 23, because occupancy 0.390 <= existing 0.610 in 2cnqA Skipped atom 25, because occupancy 0.390 <= existing 0.610 in 2cnqA Skipped atom 134, because occupancy 0.410 <= existing 0.590 in 2cnqA Skipped atom 136, because occupancy 0.410 <= existing 0.590 in 2cnqA Skipped atom 138, because occupancy 0.410 <= existing 0.590 in 2cnqA Skipped atom 140, because occupancy 0.410 <= existing 0.590 in 2cnqA Skipped atom 142, because occupancy 0.210 <= existing 0.590 in 2cnqA Skipped atom 174, because occupancy 0.260 <= existing 0.740 in 2cnqA Skipped atom 176, because occupancy 0.260 <= existing 0.740 in 2cnqA Skipped atom 178, because occupancy 0.260 <= existing 0.740 in 2cnqA Skipped atom 180, because occupancy 0.260 <= existing 0.740 in 2cnqA Skipped atom 198, because occupancy 0.440 <= existing 0.560 in 2cnqA Skipped atom 200, because occupancy 0.440 <= existing 0.560 in 2cnqA Skipped atom 202, because occupancy 0.440 <= existing 0.560 in 2cnqA Skipped atom 204, because occupancy 0.440 <= existing 0.560 in 2cnqA Skipped atom 206, because occupancy 0.440 <= existing 0.560 in 2cnqA Skipped atom 236, because occupancy 0.370 <= existing 0.630 in 2cnqA Skipped atom 238, because occupancy 0.370 <= existing 0.630 in 2cnqA Skipped atom 240, because occupancy 0.370 <= existing 0.630 in 2cnqA Skipped atom 350, because occupancy 0.390 <= existing 0.610 in 2cnqA Skipped atom 352, because occupancy 0.390 <= existing 0.610 in 2cnqA Skipped atom 354, because occupancy 0.390 <= existing 0.610 in 2cnqA Skipped atom 377, because occupancy 0.310 <= existing 0.690 in 2cnqA Skipped atom 379, because occupancy 0.310 <= existing 0.690 in 2cnqA Skipped atom 381, because occupancy 0.310 <= existing 0.690 in 2cnqA Skipped atom 383, because occupancy 0.310 <= existing 0.690 in 2cnqA Skipped atom 398, because occupancy 0.370 <= existing 0.630 in 2cnqA Skipped atom 419, because occupancy 0.170 <= existing 0.830 in 2cnqA Skipped atom 421, because occupancy 0.170 <= existing 0.830 in 2cnqA Skipped atom 423, because occupancy 0.170 <= existing 0.830 in 2cnqA Skipped atom 425, because occupancy 0.170 <= existing 0.830 in 2cnqA Skipped atom 427, because occupancy 0.170 <= existing 0.830 in 2cnqA Skipped atom 474, because occupancy 0.500 <= existing 0.500 in 2cnqA Skipped atom 478, because occupancy 0.250 <= existing 0.470 in 2cnqA Skipped atom 479, because occupancy 0.250 <= existing 0.470 in 2cnqA Skipped atom 481, because occupancy 0.250 <= existing 0.470 in 2cnqA Skipped atom 482, because occupancy 0.250 <= existing 0.470 in 2cnqA Skipped atom 484, because occupancy 0.250 <= existing 0.470 in 2cnqA Skipped atom 485, because occupancy 0.250 <= existing 0.470 in 2cnqA Skipped atom 487, because occupancy 0.250 <= existing 0.470 in 2cnqA Skipped atom 488, because occupancy 0.250 <= existing 0.470 in 2cnqA Skipped atom 490, because occupancy 0.250 <= existing 0.470 in 2cnqA Skipped atom 491, because occupancy 0.250 <= existing 0.470 in 2cnqA Skipped atom 552, because occupancy 0.500 <= existing 0.500 in 2cnqA Skipped atom 554, because occupancy 0.500 <= existing 0.500 in 2cnqA Skipped atom 556, because occupancy 0.500 <= existing 0.500 in 2cnqA Skipped atom 558, because occupancy 0.500 <= existing 0.500 in 2cnqA Skipped atom 560, because occupancy 0.500 <= existing 0.500 in 2cnqA Skipped atom 562, because occupancy 0.500 <= existing 0.500 in 2cnqA Skipped atom 564, because occupancy 0.500 <= existing 0.500 in 2cnqA Skipped atom 566, because occupancy 0.500 <= existing 0.500 in 2cnqA Skipped atom 568, because occupancy 0.500 <= existing 0.500 in 2cnqA Skipped atom 622, because occupancy 0.450 <= existing 0.550 in 2cnqA Skipped atom 624, because occupancy 0.450 <= existing 0.550 in 2cnqA Skipped atom 626, because occupancy 0.450 <= existing 0.550 in 2cnqA Skipped atom 628, because occupancy 0.450 <= existing 0.550 in 2cnqA Skipped atom 630, because occupancy 0.450 <= existing 0.550 in 2cnqA Skipped atom 632, because occupancy 0.450 <= existing 0.550 in 2cnqA Skipped atom 634, because occupancy 0.450 <= existing 0.550 in 2cnqA Skipped atom 669, because occupancy 0.200 <= existing 0.800 in 2cnqA Skipped atom 671, because occupancy 0.200 <= existing 0.800 in 2cnqA Skipped atom 673, because occupancy 0.200 <= existing 0.800 in 2cnqA Skipped atom 675, because occupancy 0.200 <= existing 0.800 in 2cnqA Skipped atom 677, because occupancy 0.200 <= existing 0.500 in 2cnqA Skipped atom 679, because occupancy 0.100 <= existing 0.500 in 2cnqA Skipped atom 681, because occupancy 0.100 <= existing 0.500 in 2cnqA Skipped atom 683, because occupancy 0.100 <= existing 0.500 in 2cnqA Skipped atom 685, because occupancy 0.200 <= existing 0.800 in 2cnqA Skipped atom 687, because occupancy 0.200 <= existing 0.800 in 2cnqA Skipped atom 689, because occupancy 0.200 <= existing 0.800 in 2cnqA Skipped atom 691, because occupancy 0.200 <= existing 0.800 in 2cnqA Skipped atom 693, because occupancy 0.200 <= existing 0.800 in 2cnqA Skipped atom 695, because occupancy 0.200 <= existing 0.800 in 2cnqA Skipped atom 697, because occupancy 0.200 <= existing 0.800 in 2cnqA Skipped atom 699, because occupancy 0.200 <= existing 0.800 in 2cnqA Skipped atom 718, because occupancy 0.500 <= existing 0.500 in 2cnqA Skipped atom 722, because occupancy 0.500 <= existing 0.500 in 2cnqA Skipped atom 724, because occupancy 0.500 <= existing 0.500 in 2cnqA Skipped atom 726, because occupancy 0.500 <= existing 0.500 in 2cnqA Skipped atom 728, because occupancy 0.500 <= existing 0.500 in 2cnqA Skipped atom 730, because occupancy 0.500 <= existing 0.500 in 2cnqA Skipped atom 743, because occupancy 0.440 <= existing 0.560 in 2cnqA Skipped atom 745, because occupancy 0.440 <= existing 0.560 in 2cnqA Skipped atom 747, because occupancy 0.440 <= existing 0.560 in 2cnqA Skipped atom 749, because occupancy 0.440 <= existing 0.560 in 2cnqA Skipped atom 806, because occupancy 0.490 <= existing 0.510 in 2cnqA Skipped atom 808, because occupancy 0.490 <= existing 0.510 in 2cnqA Skipped atom 810, because occupancy 0.490 <= existing 0.510 in 2cnqA Skipped atom 812, because occupancy 0.490 <= existing 0.510 in 2cnqA Skipped atom 814, because occupancy 0.490 <= existing 0.510 in 2cnqA Skipped atom 881, because occupancy 0.200 <= existing 0.800 in 2cnqA Skipped atom 883, because occupancy 0.200 <= existing 0.800 in 2cnqA Skipped atom 906, because occupancy 0.430 <= existing 0.570 in 2cnqA Skipped atom 908, because occupancy 0.430 <= existing 0.570 in 2cnqA Skipped atom 910, because occupancy 0.430 <= existing 0.570 in 2cnqA Skipped atom 912, because occupancy 0.430 <= existing 0.570 in 2cnqA Skipped atom 914, because occupancy 0.430 <= existing 0.570 in 2cnqA Skipped atom 968, because occupancy 0.390 <= existing 0.610 in 2cnqA Skipped atom 970, because occupancy 0.390 <= existing 0.610 in 2cnqA Skipped atom 972, because occupancy 0.390 <= existing 0.610 in 2cnqA Skipped atom 974, because occupancy 0.390 <= existing 0.610 in 2cnqA Skipped atom 976, because occupancy 0.390 <= existing 0.610 in 2cnqA Skipped atom 978, because occupancy 0.390 <= existing 0.610 in 2cnqA Skipped atom 984, because occupancy 0.400 <= existing 0.600 in 2cnqA Skipped atom 986, because occupancy 0.400 <= existing 0.600 in 2cnqA Skipped atom 988, because occupancy 0.400 <= existing 0.600 in 2cnqA Skipped atom 990, because occupancy 0.400 <= existing 0.600 in 2cnqA Skipped atom 992, because occupancy 0.400 <= existing 0.600 in 2cnqA Skipped atom 1008, because occupancy 0.350 <= existing 0.650 in 2cnqA Skipped atom 1010, because occupancy 0.350 <= existing 0.650 in 2cnqA Skipped atom 1012, because occupancy 0.250 <= existing 0.650 in 2cnqA Skipped atom 1014, because occupancy 0.250 <= existing 0.650 in 2cnqA Skipped atom 1016, because occupancy 0.250 <= existing 0.450 in 2cnqA Skipped atom 1152, because occupancy 0.500 <= existing 0.500 in 2cnqA Skipped atom 1156, because occupancy 0.500 <= existing 0.500 in 2cnqA Skipped atom 1158, because occupancy 0.200 <= existing 0.500 in 2cnqA Skipped atom 1160, because occupancy 0.200 <= existing 0.500 in 2cnqA Skipped atom 1162, because occupancy 0.200 <= existing 0.500 in 2cnqA Skipped atom 1164, because occupancy 0.200 <= existing 0.500 in 2cnqA Skipped atom 1175, because occupancy 0.200 <= existing 0.800 in 2cnqA Skipped atom 1177, because occupancy 0.200 <= existing 0.800 in 2cnqA Skipped atom 1179, because occupancy 0.200 <= existing 0.800 in 2cnqA Skipped atom 1181, because occupancy 0.200 <= existing 0.800 in 2cnqA Skipped atom 1183, because occupancy 0.200 <= existing 0.800 in 2cnqA Skipped atom 1185, because occupancy 0.200 <= existing 0.800 in 2cnqA Skipped atom 1187, because occupancy 0.200 <= existing 0.800 in 2cnqA Skipped atom 1189, because occupancy 0.200 <= existing 0.800 in 2cnqA Skipped atom 1191, because occupancy 0.200 <= existing 0.800 in 2cnqA Skipped atom 1193, because occupancy 0.200 <= existing 0.800 in 2cnqA Skipped atom 1195, because occupancy 0.200 <= existing 0.800 in 2cnqA Skipped atom 1197, because occupancy 0.200 <= existing 0.800 in 2cnqA Skipped atom 1199, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1201, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1203, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1205, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1207, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1209, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1211, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1213, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1215, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1217, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1219, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1221, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1223, because occupancy 0.500 <= existing 0.500 in 2cnqA Skipped atom 1225, because occupancy 0.500 <= existing 0.500 in 2cnqA Skipped atom 1227, because occupancy 0.500 <= existing 0.500 in 2cnqA Skipped atom 1229, because occupancy 0.500 <= existing 0.500 in 2cnqA Skipped atom 1231, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1233, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1235, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1237, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1239, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1241, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1243, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1245, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1247, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1249, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1251, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1253, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1255, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1257, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1259, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1261, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1263, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1265, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1267, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1269, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1271, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1273, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1275, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1277, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1279, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1303, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1305, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1307, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1309, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1311, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1313, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1315, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1317, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1319, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1321, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1323, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1325, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1327, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1329, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1331, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1333, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1335, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1337, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1339, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1341, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1343, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1345, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1347, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1349, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1351, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1370, because occupancy 0.480 <= existing 0.520 in 2cnqA Skipped atom 1372, because occupancy 0.480 <= existing 0.520 in 2cnqA Skipped atom 1374, because occupancy 0.480 <= existing 0.520 in 2cnqA Skipped atom 1376, because occupancy 0.480 <= existing 0.520 in 2cnqA Skipped atom 1382, because occupancy 0.360 <= existing 0.640 in 2cnqA Skipped atom 1384, because occupancy 0.360 <= existing 0.640 in 2cnqA Skipped atom 1386, because occupancy 0.360 <= existing 0.640 in 2cnqA Skipped atom 1388, because occupancy 0.360 <= existing 0.640 in 2cnqA Skipped atom 1390, because occupancy 0.360 <= existing 0.640 in 2cnqA Skipped atom 1420, because occupancy 0.360 <= existing 0.640 in 2cnqA Skipped atom 1422, because occupancy 0.360 <= existing 0.640 in 2cnqA Skipped atom 1424, because occupancy 0.360 <= existing 0.640 in 2cnqA Skipped atom 1426, because occupancy 0.360 <= existing 0.640 in 2cnqA Skipped atom 1428, because occupancy 0.360 <= existing 0.640 in 2cnqA Skipped atom 1502, because occupancy 0.380 <= existing 0.620 in 2cnqA Skipped atom 1599, because occupancy 0.420 <= existing 0.580 in 2cnqA Skipped atom 1601, because occupancy 0.420 <= existing 0.580 in 2cnqA Skipped atom 1603, because occupancy 0.420 <= existing 0.580 in 2cnqA Skipped atom 1605, because occupancy 0.420 <= existing 0.580 in 2cnqA Skipped atom 1607, because occupancy 0.420 <= existing 0.580 in 2cnqA Skipped atom 1651, because occupancy 0.240 <= existing 0.760 in 2cnqA Skipped atom 1653, because occupancy 0.240 <= existing 0.760 in 2cnqA Skipped atom 1655, because occupancy 0.240 <= existing 0.760 in 2cnqA Skipped atom 1657, because occupancy 0.240 <= existing 0.760 in 2cnqA Skipped atom 1659, because occupancy 0.240 <= existing 0.760 in 2cnqA Skipped atom 1665, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1667, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1669, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1671, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 1685, because occupancy 0.260 <= existing 0.740 in 2cnqA Skipped atom 1687, because occupancy 0.260 <= existing 0.740 in 2cnqA Skipped atom 1724, because occupancy 0.250 <= existing 0.750 in 2cnqA Skipped atom 1728, because occupancy 0.250 <= existing 0.750 in 2cnqA Skipped atom 1730, because occupancy 0.250 <= existing 0.750 in 2cnqA Skipped atom 1732, because occupancy 0.250 <= existing 0.750 in 2cnqA Skipped atom 1734, because occupancy 0.250 <= existing 0.750 in 2cnqA Skipped atom 1736, because occupancy 0.250 <= existing 0.750 in 2cnqA Skipped atom 1762, because occupancy 0.490 <= existing 0.510 in 2cnqA Skipped atom 1764, because occupancy 0.490 <= existing 0.510 in 2cnqA Skipped atom 1766, because occupancy 0.490 <= existing 0.510 in 2cnqA Skipped atom 1768, because occupancy 0.490 <= existing 0.510 in 2cnqA Skipped atom 1770, because occupancy 0.490 <= existing 0.510 in 2cnqA Skipped atom 1817, because occupancy 0.360 <= existing 0.640 in 2cnqA Skipped atom 1819, because occupancy 0.360 <= existing 0.640 in 2cnqA Skipped atom 1821, because occupancy 0.360 <= existing 0.640 in 2cnqA Skipped atom 1823, because occupancy 0.360 <= existing 0.640 in 2cnqA Skipped atom 1825, because occupancy 0.360 <= existing 0.640 in 2cnqA Skipped atom 1856, because occupancy 0.270 <= existing 0.730 in 2cnqA Skipped atom 1858, because occupancy 0.270 <= existing 0.730 in 2cnqA Skipped atom 1860, because occupancy 0.270 <= existing 0.730 in 2cnqA Skipped atom 1862, because occupancy 0.270 <= existing 0.730 in 2cnqA Skipped atom 1864, because occupancy 0.270 <= existing 0.730 in 2cnqA Skipped atom 1892, because occupancy 0.440 <= existing 0.560 in 2cnqA Skipped atom 1894, because occupancy 0.440 <= existing 0.560 in 2cnqA Skipped atom 1896, because occupancy 0.440 <= existing 0.560 in 2cnqA Skipped atom 1898, because occupancy 0.440 <= existing 0.560 in 2cnqA Skipped atom 1969, because occupancy 0.250 <= existing 0.750 in 2cnqA Skipped atom 1971, because occupancy 0.250 <= existing 0.750 in 2cnqA Skipped atom 1973, because occupancy 0.250 <= existing 0.750 in 2cnqA Skipped atom 1975, because occupancy 0.250 <= existing 0.750 in 2cnqA Skipped atom 1977, because occupancy 0.250 <= existing 0.750 in 2cnqA Skipped atom 1979, because occupancy 0.250 <= existing 0.750 in 2cnqA Skipped atom 1981, because occupancy 0.250 <= existing 0.750 in 2cnqA Skipped atom 2012, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 2014, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 2016, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 2018, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 2020, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 2022, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 2024, because occupancy 0.200 <= existing 0.300 in 2cnqA Skipped atom 2026, because occupancy 0.200 <= existing 0.300 in 2cnqA Skipped atom 2028, because occupancy 0.100 <= existing 0.200 in 2cnqA Skipped atom 2030, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 2032, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 2034, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 2036, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 2038, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 2040, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 2042, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 2044, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 2046, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 2048, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 2050, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 2052, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 2054, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 2056, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 2058, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 2060, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 2062, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 2064, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 2066, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 2068, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 2070, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 2072, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 2074, because occupancy 0.300 <= existing 0.300 in 2cnqA Skipped atom 2076, because occupancy 0.300 <= existing 0.300 in 2cnqA Skipped atom 2232, because occupancy 0.350 <= existing 0.650 in 2cnqA Skipped atom 2234, because occupancy 0.350 <= existing 0.650 in 2cnqA Skipped atom 2261, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 2263, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 2265, because occupancy 0.300 <= existing 0.700 in 2cnqA Skipped atom 2307, because occupancy 0.390 <= existing 0.610 in 2cnqA Skipped atom 2309, because occupancy 0.390 <= existing 0.610 in 2cnqA Skipped atom 2335, because occupancy 0.480 <= existing 0.520 in 2cnqA Skipped atom 2337, because occupancy 0.480 <= existing 0.520 in 2cnqA Skipped atom 2339, because occupancy 0.480 <= existing 0.520 in 2cnqA Skipped atom 2341, because occupancy 0.480 <= existing 0.520 in 2cnqA Skipped atom 2343, because occupancy 0.480 <= existing 0.520 in 2cnqA Skipped atom 2455, because occupancy 0.470 <= existing 0.530 in 2cnqA Skipped atom 2457, because occupancy 0.470 <= existing 0.530 in 2cnqA Skipped atom 2459, because occupancy 0.470 <= existing 0.530 in 2cnqA Skipped atom 2461, because occupancy 0.470 <= existing 0.530 in 2cnqA Skipped atom 2521, because occupancy 0.450 <= existing 0.550 in 2cnqA Skipped atom 2523, because occupancy 0.450 <= existing 0.550 in 2cnqA Skipped atom 2525, because occupancy 0.450 <= existing 0.550 in 2cnqA Skipped atom 2527, because occupancy 0.450 <= existing 0.550 in 2cnqA Skipped atom 2529, because occupancy 0.450 <= existing 0.550 in 2cnqA Skipped atom 2563, because occupancy 0.500 <= existing 0.500 in 2cnqA Skipped atom 2567, because occupancy 0.500 <= existing 0.500 in 2cnqA Skipped atom 2569, because occupancy 0.500 <= existing 0.500 in 2cnqA Skipped atom 2571, because occupancy 0.500 <= existing 0.500 in 2cnqA Skipped atom 2573, because occupancy 0.500 <= existing 0.500 in 2cnqA Skipped atom 2575, because occupancy 0.500 <= existing 0.500 in 2cnqA Skipped atom 2577, because occupancy 0.500 <= existing 0.500 in 2cnqA Skipped atom 2579, because occupancy 0.500 <= existing 0.500 in 2cnqA Skipped atom 2698, because occupancy 0.490 <= existing 0.510 in 2cnqA Skipped atom 2700, because occupancy 0.490 <= existing 0.510 in 2cnqA Skipped atom 2726, because occupancy 0.250 <= existing 0.250 in 2cnqA Skipped atom 2730, because occupancy 0.250 <= existing 0.250 in 2cnqA Skipped atom 2732, because occupancy 0.250 <= existing 0.250 in 2cnqA # T0350 read from 2cnqA/merged-good-all-a2m # 2cnqA read from 2cnqA/merged-good-all-a2m # adding 2cnqA to template set # found chain 2cnqA in template set Warning: unaligning (T0350)N26 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cnqA)E169 Warning: unaligning (T0350)D27 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2cnqA)E169 T0350 31 :PVHQVSYTNLAE 2cnqA 170 :HDENISPAQAAE T0350 43 :MVGEMNKLL 2cnqA 187 :LSRRVAELA T0350 55 :QVHLKFELHDKLNEYYV 2cnqA 215 :DTKFEFGIDEKTNEIIL T0350 73 :VIEDST 2cnqA 243 :FWNGAS T0350 85 :IPPKRWLDFYAAMTEFLGLFVDE 2cnqA 280 :MPQDIVDRTRAKYIEAYETLTGS Number of specific fragments extracted= 5 number of extra gaps= 1 total=54 Number of alignments=17 # 2cnqA read from 2cnqA/merged-good-all-a2m # found chain 2cnqA in template set Warning: unaligning (T0350)N26 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cnqA)E169 Warning: unaligning (T0350)D27 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2cnqA)E169 T0350 25 :D 2cnqA 164 :K T0350 31 :PVHQVSYTNLAEMV 2cnqA 170 :HDENISPAQAAELV T0350 45 :GEMNKLL 2cnqA 189 :RRVAELA T0350 56 :VHLKFELHDKLNEYYV 2cnqA 216 :TKFEFGIDEKTNEIIL T0350 73 :VIEDST 2cnqA 243 :FWNGAS T0350 85 :IPPKRWLDFYAAMTEFLGLFVDEKK 2cnqA 280 :MPQDIVDRTRAKYIEAYETLTGSKW Number of specific fragments extracted= 6 number of extra gaps= 1 total=60 Number of alignments=18 # 2cnqA read from 2cnqA/merged-good-all-a2m # found chain 2cnqA in template set Warning: unaligning (T0350)D27 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2cnqA)E169 T0350 31 :PVHQVSYTNLAEM 2cnqA 170 :HDENISPAQAAEL T0350 44 :VGEMNKLL 2cnqA 188 :SRRVAELA T0350 52 :EPSQV 2cnqA 207 :KEKGI T0350 58 :LKFELHDKLNEYYV 2cnqA 218 :FEFGIDEKTNEIIL Number of specific fragments extracted= 4 number of extra gaps= 0 total=64 Number of alignments=19 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t6sA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1t6sA expands to /projects/compbio/data/pdb/1t6s.pdb.gz 1t6sA:# T0350 read from 1t6sA/merged-good-all-a2m # 1t6sA read from 1t6sA/merged-good-all-a2m # adding 1t6sA to template set # found chain 1t6sA in template set T0350 32 :VHQVSYTNLAEMVGEMNKLLEPSQVHLKFELHDK 1t6sA 33 :AHKFTPSELQEAVDELNRDYEATGRTFRIHAIAG T0350 70 :YVKVIEDS 1t6sA 67 :GYRFLTEP T0350 87 :PKRWLDFYAAMTEF 1t6sA 93 :SRSMLEVLAVVAWH T0350 101 :LGLF 1t6sA 111 :KGEI Number of specific fragments extracted= 4 number of extra gaps= 0 total=68 Number of alignments=20 # 1t6sA read from 1t6sA/merged-good-all-a2m # found chain 1t6sA in template set T0350 32 :VHQVSYTNLAEMVGEMNKLLEPSQVHLKFELHDK 1t6sA 33 :AHKFTPSELQEAVDELNRDYEATGRTFRIHAIAG T0350 70 :YVKVIEDS 1t6sA 67 :GYRFLTEP T0350 87 :PKRWLDFYAAMTEF 1t6sA 93 :SRSMLEVLAVVAWH T0350 101 :LGLF 1t6sA 111 :KGEI Number of specific fragments extracted= 4 number of extra gaps= 0 total=72 Number of alignments=21 # 1t6sA read from 1t6sA/merged-good-all-a2m # found chain 1t6sA in template set T0350 30 :VPVHQVSYTNLAEMVGEMNKLLEPSQVHLKFELHDK 1t6sA 31 :ITAHKFTPSELQEAVDELNRDYEATGRTFRIHAIAG T0350 68 :EYYVK 1t6sA 67 :GYRFL T0350 87 :PKRWLDFYAAMTEF 1t6sA 93 :SRSMLEVLAVVAWH Number of specific fragments extracted= 3 number of extra gaps= 0 total=75 Number of alignments=22 # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0350//projects/compbio/experiments/protein-predict/casp7/T0350/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0350//projects/compbio/experiments/protein-predict/casp7/T0350/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0350/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0350/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((T0350)F60.CB, (T0350)V71.CB) [> 3.2734 = 5.4557 < 7.0925] w=1.0000 to align # Constraint # added constraint: constraint((T0350)E61.CB, (T0350)V71.CB) [> 4.5893 = 7.6488 < 9.9435] w=0.9403 to align # Constraint # added constraint: constraint((T0350)E61.CB, (T0350)Y70.CB) [> 3.1978 = 5.3296 < 6.9285] w=0.8784 to align # Constraint # added constraint: constraint((T0350)M47.CB, (T0350)F60.CB) [> 3.7033 = 6.1721 < 8.0238] w=0.8718 to align # Constraint # added constraint: constraint((T0350)F60.CB, (T0350)Y70.CB) [> 4.2157 = 7.0262 < 9.1341] w=0.7895 to align # Constraint # added constraint: constraint((T0350)F60.CB, (T0350)K72.CB) [> 4.4889 = 7.4815 < 9.7260] w=0.7602 to align # Constraint # added constraint: constraint((T0350)K59.CB, (T0350)V71.CB) [> 4.3473 = 7.2455 < 9.4191] w=0.7298 to align # Constraint # added constraint: constraint((T0350)L62.CB, (T0350)V71.CB) [> 3.6090 = 6.0150 < 7.8195] w=0.5952 to align # Constraint # added constraint: constraint((T0350)F60.CB, (T0350)V73.CB) [> 3.2588 = 5.4313 < 7.0607] w=0.5952 to align # Constraint # added constraint: constraint((T0350)K59.CB, (T0350)V73.CB) [> 4.2314 = 7.0523 < 9.1680] w=0.5952 to align # Constraint # added constraint: constraint((T0350)L58.CB, (T0350)V73.CB) [> 2.9894 = 4.9824 < 6.4771] w=0.5952 to align # Constraint # added constraint: constraint((T0350)L51.CB, (T0350)F60.CB) [> 4.6413 = 7.7356 < 10.0562] w=0.5556 to align # Constraint # added constraint: constraint((T0350)L50.CB, (T0350)F60.CB) [> 4.5436 = 7.5727 < 9.8445] w=0.4963 to align # Constraint # added constraint: constraint((T0350)L58.CB, (T0350)K72.CB) [> 4.5752 = 7.6253 < 9.9129] w=0.4900 to align # Constraint # added constraint: constraint((T0350)K59.CB, (T0350)K72.CB) [> 3.7470 = 6.2449 < 8.1184] w=0.4900 to align # Constraint # added constraint: constraint((T0350)I82.CB, (T0350)F93.CB) [> 4.5556 = 7.5927 < 9.8705] w=0.4117 to align # Constraint # added constraint: constraint((T0350)F60.CB, (T0350)Y69.CB) [> 3.2009 = 5.3348 < 6.9352] w=0.4048 to align # Constraint # added constraint: constraint((T0350)K59.CB, (T0350)Y70.CB) [> 3.6693 = 6.1155 < 7.9502] w=0.3847 to align # Constraint # added constraint: constraint((T0350)H57.CB, (T0350)I74.CB) [> 3.4719 = 5.7865 < 7.5225] w=0.3847 to align # Constraint # added constraint: constraint((T0350)H57.CB, (T0350)K72.CB) [> 4.4070 = 7.3450 < 9.5485] w=0.3847 to align # Constraint # added constraint: constraint((T0350)V56.CB, (T0350)I74.CB) [> 4.3413 = 7.2354 < 9.4061] w=0.3847 to align # Constraint # added constraint: constraint((T0350)V56.CB, (T0350)V73.CB) [> 4.7696 = 7.9493 < 10.3341] w=0.3847 to align # Constraint # added constraint: constraint((T0350)Q55.CB, (T0350)I74.CB) [> 4.3752 = 7.2920 < 9.4796] w=0.3847 to align # Constraint # added constraint: constraint((T0350)A41.CB, (T0350)L62.CB) [> 4.0314 = 6.7189 < 8.7346] w=0.3755 to align # Constraint # added constraint: constraint((T0350)V44.CB, (T0350)F60.CB) [> 3.3096 = 5.5159 < 7.1707] w=0.3755 to align # Constraint # added constraint: constraint((T0350)L58.CB, (T0350)V71.CB) [> 3.6723 = 6.1205 < 7.9567] w=0.3451 to align # Constraint # added constraint: constraint((T0350)M43.CB, (T0350)L62.CB) [> 3.5329 = 5.8881 < 7.6546] w=0.3364 to align # Constraint # added constraint: constraint((T0350)E61.CB, (T0350)K72.CB) [> 3.6243 = 6.0405 < 7.8526] w=0.3158 to align # Constraint # added constraint: constraint((T0350)V44.CB, (T0350)V71.CB) [> 3.5602 = 5.9337 < 7.7138] w=0.3078 to align # Constraint # added constraint: constraint((T0350)M47.CB, (T0350)Y69.CB) [> 3.9487 = 6.5812 < 8.5555] w=0.2995 to align # Constraint # added constraint: constraint((T0350)Y37.CB, (T0350)A96.CB) [> 2.4959 = 4.1598 < 5.4077] w=0.2744 to align # Constraint # added constraint: constraint((T0350)V35.CB, (T0350)L62.CB) [> 4.2972 = 7.1620 < 9.3107] w=0.2565 to align # Constraint # added constraint: constraint((T0350)V35.CB, (T0350)Y69.CB) [> 4.7792 = 7.9654 < 10.3550] w=0.2565 to align # Constraint # added constraint: constraint((T0350)E46.CB, (T0350)H63.CB) [> 4.7249 = 7.8748 < 10.2373] w=0.2565 to align # Constraint # added constraint: constraint((T0350)L50.CB, (T0350)Y69.CB) [> 3.4252 = 5.7087 < 7.4213] w=0.2398 to align # Constraint # added constraint: constraint((T0350)H57.CB, (T0350)E75.CB) [> 3.5164 = 5.8607 < 7.6189] w=0.2105 to align # Constraint # added constraint: constraint((T0350)L58.CB, (T0350)I74.CB) [> 3.7703 = 6.2838 < 8.1690] w=0.2105 to align # Constraint # added constraint: constraint((T0350)L58.CB, (T0350)E75.CB) [> 3.1250 = 5.2083 < 6.7708] w=0.2105 to align # Constraint # added constraint: constraint((T0350)L58.CB, (T0350)D76.CB) [> 3.9863 = 6.6438 < 8.6369] w=0.2105 to align # Constraint # added constraint: constraint((T0350)K59.CB, (T0350)I74.CB) [> 3.3830 = 5.6383 < 7.3298] w=0.2105 to align # Constraint # added constraint: constraint((T0350)F93.CB, (T0350)F104.CB) [> 3.6272 = 6.0454 < 7.8590] w=0.2105 to align # Constraint # added constraint: constraint((T0350)Q34.CB, (T0350)M43.CB) [> 2.8738 = 4.7896 < 6.2265] w=0.1945 to align # Constraint # added constraint: constraint((T0350)L40.CB, (T0350)L62.CB) [> 3.1732 = 5.2887 < 6.8752] w=0.1879 to align # Constraint # added constraint: constraint((T0350)E75.CB, (T0350)L103.CB) [> 4.7267 = 7.8779 < 10.2413] w=0.1599 to align # Constraint # added constraint: constraint((T0350)V73.CB, (T0350)F104.CB) [> 4.3695 = 7.2825 < 9.4672] w=0.1599 to align # Constraint # added constraint: constraint((T0350)V73.CB, (T0350)L103.CB) [> 4.7852 = 7.9753 < 10.3680] w=0.1599 to align # Constraint # added constraint: constraint((T0350)V73.CB, (T0350)F100.CB) [> 2.6895 = 4.4826 < 5.8274] w=0.1599 to align # Constraint # added constraint: constraint((T0350)L40.CB, (T0350)N67.CB) [> 3.6148 = 6.0247 < 7.8321] w=0.1569 to align # Constraint # added constraint: constraint((T0350)L40.CB, (T0350)Y69.CB) [> 3.6619 = 6.1031 < 7.9341] w=0.1569 to align # Constraint # added constraint: constraint((T0350)M43.CB, (T0350)Y69.CB) [> 3.9758 = 6.6264 < 8.6143] w=0.1396 to align # Constraint # added constraint: constraint((T0350)L58.CB, (T0350)V81.CB) [> 3.9267 = 6.5444 < 8.5078] w=0.1372 to align # Constraint # added constraint: constraint((T0350)L40.CB, (T0350)H57.CB) [> 4.6206 = 7.7009 < 10.0112] w=0.1372 to align # Constraint # added constraint: constraint((T0350)V30.CB, (T0350)K59.CB) [> 3.5902 = 5.9837 < 7.7788] w=0.1282 to align # Constraint # added constraint: constraint((T0350)V30.CB, (T0350)Y70.CB) [> 2.4940 = 4.1566 < 5.4036] w=0.1282 to align # Constraint # added constraint: constraint((T0350)V30.CB, (T0350)V71.CB) [> 3.4626 = 5.7710 < 7.5023] w=0.1282 to align # Constraint # added constraint: constraint((T0350)Q34.CB, (T0350)Y70.CB) [> 4.0191 = 6.6985 < 8.7080] w=0.1282 to align # Constraint # added constraint: constraint((T0350)N39.CB, (T0350)L62.CB) [> 4.7968 = 7.9946 < 10.3930] w=0.1282 to align # Constraint # added constraint: constraint((T0350)Y37.CB, (T0350)Y69.CB) [> 3.6447 = 6.0745 < 7.8968] w=0.0972 to align # Constraint # added constraint: constraint((T0350)L40.CB, (T0350)E61.CB) [> 4.6092 = 7.6820 < 9.9866] w=0.0972 to align # Constraint # added constraint: constraint((T0350)L40.CB, (T0350)H63.CB) [> 1.9583 = 3.2638 < 4.2430] w=0.0972 to align # Constraint # added constraint: constraint((T0350)L40.CB, (T0350)L66.CB) [> 4.0480 = 6.7466 < 8.7706] w=0.0972 to align # Constraint # added constraint: constraint((T0350)L40.CB, (T0350)V71.CB) [> 4.1061 = 6.8435 < 8.8966] w=0.0972 to align # Constraint # added constraint: constraint((T0350)V35.CB, (T0350)H63.CB) [> 4.7363 = 7.8939 < 10.2620] w=0.0972 to align # Constraint # added constraint: constraint((T0350)Y70.CB, (T0350)M97.CB) [> 3.1286 = 5.2143 < 6.7786] w=0.0972 to align # Constraint # added constraint: constraint((T0350)Y70.CB, (T0350)A96.CB) [> 4.5027 = 7.5044 < 9.7558] w=0.0972 to align # Constraint # added constraint: constraint((T0350)Y70.CB, (T0350)F93.CB) [> 3.2893 = 5.4822 < 7.1268] w=0.0972 to align # Constraint # added constraint: constraint((T0350)E68.CB, (T0350)D92.CB) [> 4.3928 = 7.3213 < 9.5177] w=0.0972 to align # Constraint # added constraint: constraint((T0350)E68.CB, (T0350)R89.CB) [> 1.8459 = 3.0766 < 3.9995] w=0.0972 to align # Constraint # added constraint: constraint((T0350)L66.CB, (T0350)W90.CB) [> 3.7580 = 6.2633 < 8.1423] w=0.0972 to align # Constraint # added constraint: constraint((T0350)F60.CB, (T0350)M97.CB) [> 3.5735 = 5.9559 < 7.7426] w=0.0972 to align # Constraint # added constraint: constraint((T0350)L62.CB, (T0350)W90.CB) [> 3.0630 = 5.1050 < 6.6365] w=0.0972 to align # Constraint # added constraint: constraint((T0350)L62.CB, (T0350)Y94.CB) [> 3.2580 = 5.4301 < 7.0591] w=0.0972 to align # Constraint # added constraint: constraint((T0350)L62.CB, (T0350)M97.CB) [> 4.5205 = 7.5342 < 9.7944] w=0.0972 to align # Constraint # added constraint: constraint((T0350)H63.CB, (T0350)W90.CB) [> 4.3620 = 7.2700 < 9.4510] w=0.0972 to align # Constraint # added constraint: constraint((T0350)L66.CB, (T0350)P87.CB) [> 3.6775 = 6.1292 < 7.9679] w=0.0972 to align # Constraint # added constraint: constraint((T0350)E68.CB, (T0350)I82.CB) [> 4.4645 = 7.4408 < 9.6730] w=0.0889 to align # Constraint # added constraint: constraint((T0350)V71.CB, (T0350)I85.CB) [> 2.4534 = 4.0890 < 5.3156] w=0.0889 to align # Constraint # added constraint: constraint((T0350)V71.CB, (T0350)P86.CB) [> 4.7192 = 7.8654 < 10.2250] w=0.0889 to align # Constraint # added constraint: constraint((T0350)K72.CB, (T0350)V81.CB) [> 3.3204 = 5.5340 < 7.1942] w=0.0889 to align # Constraint # added constraint: constraint((T0350)K72.CB, (T0350)I85.CB) [> 4.4445 = 7.4075 < 9.6297] w=0.0889 to align # Constraint # added constraint: constraint((T0350)V73.CB, (T0350)I82.CB) [> 3.1588 = 5.2646 < 6.8440] w=0.0889 to align # Constraint # added constraint: constraint((T0350)V73.CB, (T0350)R83.CB) [> 2.8577 = 4.7628 < 6.1916] w=0.0889 to align # Constraint # added constraint: constraint((T0350)T98.CB, (T0350)K109.CB) [> 2.8116 = 4.6860 < 6.0917] w=0.0799 to align # Constraint # added constraint: constraint((T0350)L51.CB, (T0350)F93.CB) [> 4.4480 = 7.4134 < 9.6374] w=0.0597 to align # Constraint # added constraint: constraint((T0350)L50.CB, (T0350)F93.CB) [> 3.9153 = 6.5255 < 8.4832] w=0.0597 to align # Constraint # added constraint: constraint((T0350)M47.CB, (T0350)Y94.CB) [> 4.3542 = 7.2571 < 9.4342] w=0.0597 to align # Constraint # added constraint: constraint((T0350)L40.CB, (T0350)E68.CB) [> 4.1819 = 6.9698 < 9.0607] w=0.0597 to align # Constraint # added constraint: constraint((T0350)L40.CB, (T0350)D64.CB) [> 4.5455 = 7.5759 < 9.8486] w=0.0597 to align # Constraint # added constraint: constraint((T0350)V71.CB, (T0350)Y94.CB) [> 3.7940 = 6.3234 < 8.2204] w=0.0597 to align # Constraint # added constraint: constraint((T0350)V73.CB, (T0350)P87.CB) [> 3.5090 = 5.8484 < 7.6029] w=0.0597 to align # Constraint # added constraint: constraint((T0350)V73.CB, (T0350)W90.CB) [> 2.4564 = 4.0939 < 5.3221] w=0.0597 to align # Constraint # added constraint: constraint((T0350)I74.CB, (T0350)P86.CB) [> 2.2828 = 3.8047 < 4.9461] w=0.0597 to align # Constraint # added constraint: constraint((T0350)S77.CB, (T0350)P87.CB) [> 4.2574 = 7.0956 < 9.2243] w=0.0597 to align # Constraint # added constraint: constraint((T0350)I20.CB, (T0350)V44.CB) [> 3.6251 = 6.0419 < 7.8545] w=0.0412 to align # Constraint # added constraint: constraint((T0350)I20.CB, (T0350)M47.CB) [> 4.1663 = 6.9438 < 9.0270] w=0.0412 to align # Constraint # added constraint: constraint((T0350)W13.CB, (T0350)V44.CB) [> 2.9856 = 4.9759 < 6.4687] w=0.0274 to align # Constraint # added constraint: constraint((T0350)W13.CB, (T0350)N48.CB) [> 3.8798 = 6.4663 < 8.4062] w=0.0274 to align # Constraint # added constraint: constraint((T0350)Y16.CB, (T0350)M43.CB) [> 4.5225 = 7.5375 < 9.7987] w=0.0274 to align # Constraint # added constraint: constraint((T0350)Y16.CB, (T0350)M47.CB) [> 3.5367 = 5.8945 < 7.6628] w=0.0274 to align # Constraint # added constraint: constraint((T0350)D17.CB, (T0350)L40.CB) [> 3.5357 = 5.8929 < 7.6607] w=0.0274 to align # Constraint # added constraint: constraint((T0350)I20.CB, (T0350)L40.CB) [> 3.2089 = 5.3482 < 6.9526] w=0.0274 to align # Constraint # added constraint: constraint((T0350)H21.CB, (T0350)L40.CB) [> 3.7524 = 6.2540 < 8.1302] w=0.0274 to align # SetCost created cost = # ( 1.0000 * align ) # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0350/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0350/decoys/ # ReadConformPDB reading from PDB file T0350.edit13.pdb.gz looking for model 1 # Found a chain break before 106 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0350.edit4.pdb.gz looking for model 1 # Found a chain break before 105 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0350 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 T0350 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 T0350 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 T0350 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 T0350 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 T0350 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 T0350 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 T0350 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 T0350 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 T0350 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 T0350 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 T0350 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 T0350 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 T0350 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0350 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS5 # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # Found a chain break before 83 # 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 53 # 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 99 # 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 77 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS4 # ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1 # Found a chain break before 30 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS5 # ReadConformPDB reading from PDB file servers/ABIpro_TS1.pdb.gz looking for model 1 # Found a chain break before 83 # 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 99 # 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 80 # 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 111 # 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 112 # 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 20 # 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 # naming current conformation Bilab-ENABLE_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS2.pdb.gz looking for model 1 # naming current conformation Bilab-ENABLE_TS2 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS3.pdb.gz looking for model 1 # Found a chain break before 116 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS3 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS4.pdb.gz looking for model 1 # Found a chain break before 116 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS4 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS5.pdb.gz looking for model 1 # Found a chain break before 116 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS5 # ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1 # Found a chain break before 112 # 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 T0350 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 # Found a chain break before 110 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS3 # ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1 # Found a chain break before 108 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS4 # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # Found a chain break before 109 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS5 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0350 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 T0350 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 T0350 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: incomplete conformation T0350 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 # Found a chain break before 107 # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS5 # ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0350 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 T0350 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 T0350 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 T0350 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 T0350 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 89 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS1 # ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1 # Found a chain break before 110 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS2 # ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1 # Found a chain break before 109 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS3 # ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0350 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 T0350 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 106 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0350 can't currently be optimized by undertaker # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0350 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 # Found a chain break before 110 # copying to AlignedFragments data structure # naming current conformation FAMS_TS4 # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0350 can't currently be optimized by undertaker # naming current conformation FAMS_TS5 # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # Found a chain break before 106 # 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 83 # 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 110 # 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 79 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS5 # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0350 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 T0350 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 T0350 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 T0350 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL4 # ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0350 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 # WARNING: incomplete conformation T0350 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 T0350 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 T0350 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL3 # ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0350 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 T0350 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 97 # 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 97 # 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 # 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 23 # 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 92 # 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 # naming current conformation FUGMOD_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # Found a chain break before 61 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS2 # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # naming current conformation FUGMOD_TS3 # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0350 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS4 # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # Found a chain break before 72 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS5 # ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0350 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL1 # ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0350 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL2 # ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0350 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL3 # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0350 can't currently be optimized by undertaker # naming current conformation FUGUE_AL4 # ReadConformPDB reading from PDB file servers/FUGUE_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0350 can't currently be optimized by undertaker # naming current conformation FUGUE_AL5 # ReadConformPDB reading from PDB file servers/FUNCTION_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0350 can't currently be optimized by undertaker # naming current conformation FUNCTION_TS1 # ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0350 can't currently be optimized by undertaker # naming current conformation FUNCTION_TS2 # ReadConformPDB reading from PDB file servers/FUNCTION_TS3.pdb.gz looking for model 1 # Found a chain break before 102 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS3 # ReadConformPDB reading from PDB file servers/FUNCTION_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0350 can't currently be optimized by undertaker # naming current conformation FUNCTION_TS4 # ReadConformPDB reading from PDB file servers/FUNCTION_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0350 can't currently be optimized by undertaker # naming current conformation FUNCTION_TS5 # ReadConformPDB reading from PDB file servers/Frankenstein_TS1.pdb.gz looking for model 1 # naming current conformation Frankenstein_TS1 # ReadConformPDB reading from PDB file servers/Frankenstein_TS2.pdb.gz looking for model 1 # Found a chain break before 107 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0350 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 # Found a chain break before 37 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # naming current conformation GeneSilicoMetaServer_TS3 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1 # naming current conformation GeneSilicoMetaServer_TS4 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1 # Found a chain break before 9 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS5 # ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1 # 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 # Found a chain break before 20 # copying to AlignedFragments data structure # naming current conformation HHpred3_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0350 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 T0350 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 T0350 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 T0350 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 T0350 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 # Found a chain break before 84 # copying to AlignedFragments data structure # naming current conformation LOOPP_TS1 # ReadConformPDB reading from PDB file servers/LOOPP_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0350 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 T0350 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 T0350 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 T0350 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 Error: Reading chain '' from PDB file servers/MIG_FROST_AL1.pdb.gz failed---no such chain. # 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 99 # 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 84 # 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 # naming current conformation Ma-OPUS-server2_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS4.pdb.gz looking for model 1 # 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 112 # 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 60 # 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 112 # 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 87 # 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 44 # 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 89 # 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 116 # 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 116 # 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 116 # 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 116 # 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 114 # 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 T0350 can't currently be optimized by undertaker # copying to AlignedFragments data structure # 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 114 # 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 112 # 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 81 # 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 116 # 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 92 # 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 # WARNING: incomplete conformation T0350 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0350 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # Found a chain break before 85 # copying to AlignedFragments data structure # 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 78 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS5 # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # Found a chain break before 96 # copying to AlignedFragments data structure # naming current conformation Pcons6_TS1 # ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0350 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 T0350 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pcons6_TS3 # ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0350 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 T0350 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 T0350 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 110 # 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 108 # 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 111 # 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 111 # 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 108 # 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 # Found a chain break before 112 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS1 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # naming current conformation Pmodeller6_TS2 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # naming current conformation Pmodeller6_TS3 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # naming current conformation Pmodeller6_TS4 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1 # Found a chain break before 96 # copying to AlignedFragments data structure # 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 # naming current conformation RAPTOR-ACE_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1 # Found a chain break before 59 # copying to AlignedFragments data structure # 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 30 # 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 107 # 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 115 # 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 108 # 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 116 # 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 111 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR_TS1.pdb.gz looking for model 1 # 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 # Found a chain break before 109 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR_TS4.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR_TS5.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS5 # ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1 # Found a chain break before 103 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS1 # ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS2 # ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1 # Found a chain break before 108 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS3 # ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS4 # ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1 # Found a chain break before 102 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS5 # ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0350 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS1 # ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0350 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS2 # ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0350 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS3 # ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0350 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS4 # ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0350 can't currently be optimized by undertaker # 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 T0350 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 T0350 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 T0350 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 T0350 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 # WARNING: incomplete conformation T0350 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL5 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1 # Found a chain break before 106 # 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 T0350 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 T0350 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 T0350 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 T0350 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 # naming current conformation SP3_TS1 # ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1 # naming current conformation SP3_TS2 # ReadConformPDB reading from PDB file servers/SP3_TS3.pdb.gz looking for model 1 # Found a chain break before 92 # copying to AlignedFragments data structure # naming current conformation SP3_TS3 # ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1 # Found a chain break before 96 # copying to AlignedFragments data structure # naming current conformation SP3_TS4 # ReadConformPDB reading from PDB file servers/SP3_TS5.pdb.gz looking for model 1 # naming current conformation SP3_TS5 # ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1 # naming current conformation SP4_TS1 # ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1 # Found a chain break before 96 # copying to AlignedFragments data structure # naming current conformation SP4_TS2 # ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1 # Found a chain break before 87 # copying to AlignedFragments data structure # naming current conformation SP4_TS3 # ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1 # naming current conformation SP4_TS4 # ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1 # Found a chain break before 31 # copying to AlignedFragments data structure # naming current conformation SP4_TS5 # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS1 # ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS2 # ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS3 # ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1 # Found a chain break before 92 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS4 # ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0350 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 T0350 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 T0350 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 T0350 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 T0350 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 T0350 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 T0350 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 T0350 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 Skipped atom 22, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 24, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 26, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 28, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 166, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 168, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 170, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 172, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 226, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 228, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 230, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 232, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz # WARNING: incomplete conformation T0350 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 # WARNING: incomplete conformation T0350 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL4 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1 # Found a chain break before 89 # 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 97 # 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 112 # 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 108 # 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 92 # 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 T0350 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation beautshot_TS1 # ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0350 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 T0350 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 T0350 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 T0350 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation forecast-s_AL3 # ReadConformPDB reading from PDB file servers/forecast-s_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0350 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation forecast-s_AL4 # ReadConformPDB reading from PDB file servers/forecast-s_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0350 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 73 # 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 94 # 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 114 # 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 # naming current conformation karypis.srv.2_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS5.pdb.gz looking for model 1 # 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 114 # 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 114 # 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 WARNING: atoms too close: (T0350)D106.O and (T0350)E107.N only 0.000 apart, marking (T0350)E107.N as missing # WARNING: incomplete conformation T0350 can't currently be optimized by undertaker # 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 WARNING: atoms too close: (T0350)Y70.O and (T0350)V71.N only 0.000 apart, marking (T0350)V71.N as missing # WARNING: incomplete conformation T0350 can't currently be optimized by undertaker # 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 # Found a chain break before 114 # 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 T0350 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 T0350 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 T0350 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 T0350 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 T0350 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 # WARNING: incomplete conformation T0350 can't currently be optimized by undertaker # naming current conformation keasar-server_TS1 # ReadConformPDB reading from PDB file servers/keasar-server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0350 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 T0350 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 T0350 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 T0350 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 T0350 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 T0350 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 T0350 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 T0350 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation nFOLD_TS3 # ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0350 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation nFOLD_TS4 # ReadConformPDB reading from PDB file servers/nFOLD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0350 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: (T0350)M97.N and (T0350)T98.N only 0.000 apart, marking (T0350)T98.N as missing WARNING: atoms too close: (T0350)M97.CA and (T0350)T98.CA only 0.000 apart, marking (T0350)T98.CA as missing WARNING: atoms too close: (T0350)M97.CB and (T0350)T98.CB only 0.000 apart, marking (T0350)T98.CB as missing WARNING: atoms too close: (T0350)M97.CG and (T0350)T98.CG2 only 0.000 apart, marking (T0350)T98.CG2 as missing WARNING: atoms too close: (T0350)M97.O and (T0350)T98.O only 0.000 apart, marking (T0350)T98.O as missing WARNING: atoms too close: (T0350)M97.C and (T0350)T98.C only 0.000 apart, marking (T0350)T98.C as missing WARNING: atoms too close: (T0350)T98.N and (T0350)E99.N only 0.000 apart, marking (T0350)T98.N as missing WARNING: atoms too close: (T0350)M97.N and (T0350)E99.N only 0.000 apart, marking (T0350)E99.N as missing WARNING: atoms too close: (T0350)T98.CA and (T0350)E99.CA only 0.000 apart, marking (T0350)E99.CA as missing WARNING: atoms too close: (T0350)M97.CA and (T0350)E99.CA only 0.000 apart, marking (T0350)E99.CA as missing WARNING: atoms too close: (T0350)T98.CB and (T0350)E99.CB only 0.000 apart, marking (T0350)E99.CB as missing WARNING: atoms too close: (T0350)M97.CB and (T0350)E99.CB only 0.000 apart, marking (T0350)E99.CB as missing WARNING: atoms too close: (T0350)T98.CG2 and (T0350)E99.CG only 0.000 apart, marking (T0350)E99.CG as missing WARNING: atoms too close: (T0350)M97.CG and (T0350)E99.CG only 0.000 apart, marking (T0350)E99.CG as missing WARNING: atoms too close: (T0350)T98.O and (T0350)E99.O only 0.000 apart, marking (T0350)E99.O as missing WARNING: atoms too close: (T0350)M97.O and (T0350)E99.O only 0.000 apart, marking (T0350)E99.O as missing WARNING: atoms too close: (T0350)T98.C and (T0350)E99.C only 0.000 apart, marking (T0350)E99.C as missing WARNING: atoms too close: (T0350)M97.C and (T0350)E99.C only 0.000 apart, marking (T0350)E99.C as missing WARNING: atoms too close: (T0350)E99.N and (T0350)F100.N only 0.000 apart, marking (T0350)E99.N as missing WARNING: atoms too close: (T0350)T98.N and (T0350)F100.N only 0.000 apart, marking (T0350)T98.N as missing WARNING: atoms too close: (T0350)M97.N and (T0350)F100.N only 0.000 apart, marking (T0350)F100.N as missing WARNING: atoms too close: (T0350)E99.CA and (T0350)F100.CA only 0.000 apart, marking (T0350)F100.CA as missing WARNING: atoms too close: (T0350)T98.CA and (T0350)F100.CA only 0.000 apart, marking (T0350)F100.CA as missing WARNING: atoms too close: (T0350)M97.CA and (T0350)F100.CA only 0.000 apart, marking (T0350)F100.CA as missing WARNING: atoms too close: (T0350)E99.CB and (T0350)F100.CB only 0.000 apart, marking (T0350)F100.CB as missing WARNING: atoms too close: (T0350)T98.CB and (T0350)F100.CB only 0.000 apart, marking (T0350)F100.CB as missing WARNING: atoms too close: (T0350)M97.CB and (T0350)F100.CB only 0.000 apart, marking (T0350)F100.CB as missing WARNING: atoms too close: (T0350)E99.CG and (T0350)F100.CG only 0.000 apart, marking (T0350)F100.CG as missing WARNING: atoms too close: (T0350)T98.CG2 and (T0350)F100.CG only 0.000 apart, marking (T0350)F100.CG as missing WARNING: atoms too close: (T0350)M97.CG and (T0350)F100.CG only 0.000 apart, marking (T0350)F100.CG as missing WARNING: atoms too close: (T0350)E99.O and (T0350)F100.O only 0.000 apart, marking (T0350)F100.O as missing WARNING: atoms too close: (T0350)T98.O and (T0350)F100.O only 0.000 apart, marking (T0350)F100.O as missing WARNING: atoms too close: (T0350)M97.O and (T0350)F100.O only 0.000 apart, marking (T0350)F100.O as missing WARNING: atoms too close: (T0350)E99.C and (T0350)F100.C only 0.000 apart, marking (T0350)F100.C as missing WARNING: atoms too close: (T0350)T98.C and (T0350)F100.C only 0.000 apart, marking (T0350)F100.C as missing WARNING: atoms too close: (T0350)M97.C and (T0350)F100.C only 0.000 apart, marking (T0350)F100.C as missing # WARNING: incomplete conformation T0350 can't currently be optimized by undertaker # naming current conformation panther2_TS1 # ReadConformPDB reading from PDB file servers/panther3_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0350 can't currently be optimized by undertaker # naming current conformation panther3_TS1 # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0350 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 0.3318 model score 0.6550 model score 1.9480 model score 1.6693 model score 1.9533 model score 1.9447 model score 1.9466 model score 1.2856 model score 1.2747 model score 2.2404 model score 1.2587 model score 1.3015 model score 1.9398 model score 1.2900 model score 2.2615 model score 2.3306 model score 2.3813 model score 0.6203 model score 1.7660 model score 0.3677 model score 1.7204 model score 2.1843 model score 0.6203 model score 0.3677 model score 0.4407 model score 0.6430 model score 0.5669 model score 2.1953 model score 1.2295 model score 1.9798 model score 1.2674 model score 1.2629 model score 1.2591 model score 0.9081 model score 0.6497 model score 1.6162 model score 1.4696 model score 0.7700 model score 1.3862 model score 1.2807 model score 1.2824 model score 1.5800 model score 1.4838 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.5500 model score 1.7154 model score 0.8230 model score 1.8483 model score 1.6859 model score 1.6502 model score 0.6575 model score 0.6497 model score 1.6162 model score 1.6694 model score 1.5737 model score 2.0650 model score 2.1782 model score 1.5463 model score 0.3920 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 2.4149 model score 1.6283 model score 2.4146 model score 1.6098 model score 1.4675 model score 2.0074 model score 2.1945 model score 1.2501 model score 1.7481 model score 1.6984 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.5820 model score 0.7973 model score 1.9038 model score 2.1567 model score 1.6694 model score 1.5841 model score 1.7405 model score 1.2824 model score 2.0098 model score 1.2824 model score 1.6188 model score 2.2405 model score 1.7775 model score 1.7775 model score 2.1953 model score 1.2771 model score 0.7669 model score 2.1302 model score 1.8663 model score 1.2378 model score 0.5563 model score 1.3400 model score 0.6883 model score 1.2815 model score 0.8964 model score 1.0325 model score 0.9278 model score 0.4349 model score 0.6274 model score 0.8989 model score 0.9440 model score 0.8989 model score 0.3211 model score 0.4479 model score 0.5917 model score 0.4506 model score 1.4364 model score 0.3863 model score 0.3911 model score 0.3787 model score 1.2771 model score 1.4611 model score 1.4727 model score 1.6358 model score 2.1291 model score 1.8138 model score 0.3496 model score 0.3609 model score 0.3677 model score 0.3564 model score 0.3533 model score 0.6861 model score 0.7332 model score 0.1613 model score 0.3710 model score 0.3869 model score 0.6791 model score 1.1959 model score 1.5427 model score 1.4545 model score 1.3248 model score 1.3188 model score 1.2677 model score 1.2206 model score 1.9788 model score 1.7042 model score 1.7124 model score 0.1445 model score 0.2615 model score 0.2099 model score 0.2972 model score 0.6791 model score 1.2488 model score 1.9893 model score 2.1102 model score 1.1226 model score 2.4642 model score 0.9816 model score 0.5408 model score 0.5239 model score 0.6162 model score 0.5949 model score 0.9412 model score 0.5173 model score 0.5028 model score 0.5908 model score 0.5550 model score 0.5924 model score 0.2615 model score 0.6598 model score 0.2034 model score 0.6295 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 0.5652 model score 0.8299 model score 0.4873 model score 1.0762 model score 0.3908 model score 1.5313 model score 0.6289 model score 0.7517 model score 1.2674 model score 1.6377 model score 1.5684 model score 1.4582 model score 1.1054 model score 0.2493 model score 0.7093 model score 1.5799 model score 1.5313 model score 1.6041 model score 0.7517 model score 1.3144 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 0.7417 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 0.1497 model score 0.2009 model score 0.2728 model score 0.1412 model score 0.2168 model score 1.1497 model score 1.6971 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 0.5117 model score 1.2701 model score 0.9875 model score 1.2932 model score 2.3093 model score 1.1703 model score 1.4364 model score 1.6033 model score 1.3882 model score 1.4682 model score 0.6964 model score 0.6830 model score 0.8271 model score 0.4488 model score 0.5294 model score 0.7853 model score 0.6328 model score 1.3507 model score 1.2792 model score 0.7163 model score 1.4051 model score 1.1361 model score 2.3062 model score 1.9396 model score 2.4401 model score 1.9868 model score 1.2431 model score 1.2865 model score 2.1082 USE_META, weight: 0.9262 cost: 0.3318 min: 0.1412 max: 2.4642 USE_META, weight: 0.8009 cost: 0.6550 min: 0.1412 max: 2.4642 USE_META, weight: 0.3000 cost: 1.9480 min: 0.1412 max: 2.4642 USE_META, weight: 0.4080 cost: 1.6693 min: 0.1412 max: 2.4642 USE_META, weight: 0.2980 cost: 1.9533 min: 0.1412 max: 2.4642 USE_META, weight: 0.3013 cost: 1.9447 min: 0.1412 max: 2.4642 USE_META, weight: 0.3005 cost: 1.9466 min: 0.1412 max: 2.4642 USE_META, weight: 0.5566 cost: 1.2856 min: 0.1412 max: 2.4642 USE_META, weight: 0.5609 cost: 1.2747 min: 0.1412 max: 2.4642 USE_META, weight: 0.1867 cost: 2.2404 min: 0.1412 max: 2.4642 USE_META, weight: 0.5671 cost: 1.2587 min: 0.1412 max: 2.4642 USE_META, weight: 0.5505 cost: 1.3015 min: 0.1412 max: 2.4642 USE_META, weight: 0.3032 cost: 1.9398 min: 0.1412 max: 2.4642 USE_META, weight: 0.5549 cost: 1.2900 min: 0.1412 max: 2.4642 USE_META, weight: 0.1785 cost: 2.2615 min: 0.1412 max: 2.4642 USE_META, weight: 0.1518 cost: 2.3306 min: 0.1412 max: 2.4642 USE_META, weight: 0.1321 cost: 2.3813 min: 0.1412 max: 2.4642 USE_META, weight: 0.8144 cost: 0.6203 min: 0.1412 max: 2.4642 USE_META, weight: 0.3705 cost: 1.7660 min: 0.1412 max: 2.4642 USE_META, weight: 0.9123 cost: 0.3677 min: 0.1412 max: 2.4642 USE_META, weight: 0.3882 cost: 1.7204 min: 0.1412 max: 2.4642 USE_META, weight: 0.2084 cost: 2.1843 min: 0.1412 max: 2.4642 USE_META, weight: 0.8144 cost: 0.6203 min: 0.1412 max: 2.4642 USE_META, weight: 0.9123 cost: 0.3677 min: 0.1412 max: 2.4642 USE_META, weight: 0.8840 cost: 0.4407 min: 0.1412 max: 2.4642 USE_META, weight: 0.8056 cost: 0.6430 min: 0.1412 max: 2.4642 USE_META, weight: 0.8351 cost: 0.5669 min: 0.1412 max: 2.4642 USE_META, weight: 0.2042 cost: 2.1953 min: 0.1412 max: 2.4642 USE_META, weight: 0.5784 cost: 1.2295 min: 0.1412 max: 2.4642 USE_META, weight: 0.2877 cost: 1.9798 min: 0.1412 max: 2.4642 USE_META, weight: 0.5637 cost: 1.2674 min: 0.1412 max: 2.4642 USE_META, weight: 0.5654 cost: 1.2629 min: 0.1412 max: 2.4642 USE_META, weight: 0.5669 cost: 1.2591 min: 0.1412 max: 2.4642 USE_META, weight: 0.7029 cost: 0.9081 min: 0.1412 max: 2.4642 USE_META, weight: 0.8030 cost: 0.6497 min: 0.1412 max: 2.4642 USE_META, weight: 0.4286 cost: 1.6162 min: 0.1412 max: 2.4642 USE_META, weight: 0.4854 cost: 1.4696 min: 0.1412 max: 2.4642 USE_META, weight: 0.7564 cost: 0.7700 min: 0.1412 max: 2.4642 USE_META, weight: 0.5177 cost: 1.3862 min: 0.1412 max: 2.4642 USE_META, weight: 0.5586 cost: 1.2807 min: 0.1412 max: 2.4642 USE_META, weight: 0.5579 cost: 1.2824 min: 0.1412 max: 2.4642 USE_META, weight: 0.4426 cost: 1.5800 min: 0.1412 max: 2.4642 USE_META, weight: 0.4798 cost: 1.4838 min: 0.1412 max: 2.4642 USE_META, weight: 0.5599 cost: 1.2771 min: 0.1412 max: 2.4642 USE_META, weight: 0.5599 cost: 1.2771 min: 0.1412 max: 2.4642 USE_META, weight: 0.5599 cost: 1.2771 min: 0.1412 max: 2.4642 USE_META, weight: 0.5599 cost: 1.2771 min: 0.1412 max: 2.4642 USE_META, weight: 0.5599 cost: 1.2771 min: 0.1412 max: 2.4642 USE_META, weight: 0.4542 cost: 1.5500 min: 0.1412 max: 2.4642 USE_META, weight: 0.3901 cost: 1.7154 min: 0.1412 max: 2.4642 USE_META, weight: 0.7359 cost: 0.8230 min: 0.1412 max: 2.4642 USE_META, weight: 0.3386 cost: 1.8483 min: 0.1412 max: 2.4642 USE_META, weight: 0.4015 cost: 1.6859 min: 0.1412 max: 2.4642 USE_META, weight: 0.4154 cost: 1.6502 min: 0.1412 max: 2.4642 USE_META, weight: 0.8000 cost: 0.6575 min: 0.1412 max: 2.4642 USE_META, weight: 0.8030 cost: 0.6497 min: 0.1412 max: 2.4642 USE_META, weight: 0.4286 cost: 1.6162 min: 0.1412 max: 2.4642 USE_META, weight: 0.4079 cost: 1.6694 min: 0.1412 max: 2.4642 USE_META, weight: 0.4450 cost: 1.5737 min: 0.1412 max: 2.4642 USE_META, weight: 0.2547 cost: 2.0650 min: 0.1412 max: 2.4642 USE_META, weight: 0.2108 cost: 2.1782 min: 0.1412 max: 2.4642 USE_META, weight: 0.4556 cost: 1.5463 min: 0.1412 max: 2.4642 USE_META, weight: 0.9028 cost: 0.3920 min: 0.1412 max: 2.4642 USE_META, weight: 0.5599 cost: 1.2771 min: 0.1412 max: 2.4642 USE_META, weight: 0.5599 cost: 1.2771 min: 0.1412 max: 2.4642 USE_META, weight: 0.5599 cost: 1.2771 min: 0.1412 max: 2.4642 USE_META, weight: 0.5599 cost: 1.2771 min: 0.1412 max: 2.4642 USE_META, weight: 0.5599 cost: 1.2771 min: 0.1412 max: 2.4642 USE_META, weight: 0.5599 cost: 1.2771 min: 0.1412 max: 2.4642 USE_META, weight: 0.5599 cost: 1.2771 min: 0.1412 max: 2.4642 USE_META, weight: 0.5599 cost: 1.2771 min: 0.1412 max: 2.4642 USE_META, weight: 0.5599 cost: 1.2771 min: 0.1412 max: 2.4642 USE_META, weight: 0.5599 cost: 1.2771 min: 0.1412 max: 2.4642 USE_META, weight: 0.1191 cost: 2.4149 min: 0.1412 max: 2.4642 USE_META, weight: 0.4239 cost: 1.6283 min: 0.1412 max: 2.4642 USE_META, weight: 0.1192 cost: 2.4146 min: 0.1412 max: 2.4642 USE_META, weight: 0.4310 cost: 1.6098 min: 0.1412 max: 2.4642 USE_META, weight: 0.4862 cost: 1.4675 min: 0.1412 max: 2.4642 USE_META, weight: 0.2770 cost: 2.0074 min: 0.1412 max: 2.4642 USE_META, weight: 0.2045 cost: 2.1945 min: 0.1412 max: 2.4642 USE_META, weight: 0.5704 cost: 1.2501 min: 0.1412 max: 2.4642 USE_META, weight: 0.3774 cost: 1.7481 min: 0.1412 max: 2.4642 USE_META, weight: 0.3967 cost: 1.6984 min: 0.1412 max: 2.4642 USE_META, weight: 0.5599 cost: 1.2771 min: 0.1412 max: 2.4642 USE_META, weight: 0.5599 cost: 1.2771 min: 0.1412 max: 2.4642 USE_META, weight: 0.5599 cost: 1.2771 min: 0.1412 max: 2.4642 USE_META, weight: 0.5599 cost: 1.2771 min: 0.1412 max: 2.4642 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USE_META, weight: 0.5599 cost: 1.2771 min: 0.1412 max: 2.4642 USE_META, weight: 0.7576 cost: 0.7669 min: 0.1412 max: 2.4642 USE_META, weight: 0.2294 cost: 2.1302 min: 0.1412 max: 2.4642 USE_META, weight: 0.3317 cost: 1.8663 min: 0.1412 max: 2.4642 USE_META, weight: 0.5752 cost: 1.2378 min: 0.1412 max: 2.4642 USE_META, weight: 0.8392 cost: 0.5563 min: 0.1412 max: 2.4642 USE_META, weight: 0.5356 cost: 1.3400 min: 0.1412 max: 2.4642 USE_META, weight: 0.7880 cost: 0.6883 min: 0.1412 max: 2.4642 USE_META, weight: 0.5582 cost: 1.2815 min: 0.1412 max: 2.4642 USE_META, weight: 0.7074 cost: 0.8964 min: 0.1412 max: 2.4642 USE_META, weight: 0.6547 cost: 1.0325 min: 0.1412 max: 2.4642 USE_META, weight: 0.6953 cost: 0.9278 min: 0.1412 max: 2.4642 USE_META, weight: 0.8862 cost: 0.4349 min: 0.1412 max: 2.4642 USE_META, weight: 0.8116 cost: 0.6274 min: 0.1412 max: 2.4642 USE_META, weight: 0.7065 cost: 0.8989 min: 0.1412 max: 2.4642 USE_META, weight: 0.6890 cost: 0.9440 min: 0.1412 max: 2.4642 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USE_META, weight: 0.9149 cost: 0.3609 min: 0.1412 max: 2.4642 USE_META, weight: 0.9123 cost: 0.3677 min: 0.1412 max: 2.4642 USE_META, weight: 0.9166 cost: 0.3564 min: 0.1412 max: 2.4642 USE_META, weight: 0.9178 cost: 0.3533 min: 0.1412 max: 2.4642 USE_META, weight: 0.7889 cost: 0.6861 min: 0.1412 max: 2.4642 USE_META, weight: 0.7706 cost: 0.7332 min: 0.1412 max: 2.4642 USE_META, weight: 0.9922 cost: 0.1613 min: 0.1412 max: 2.4642 USE_META, weight: 0.9110 cost: 0.3710 min: 0.1412 max: 2.4642 USE_META, weight: 0.9048 cost: 0.3869 min: 0.1412 max: 2.4642 USE_META, weight: 0.7916 cost: 0.6791 min: 0.1412 max: 2.4642 USE_META, weight: 0.5914 cost: 1.1959 min: 0.1412 max: 2.4642 USE_META, weight: 0.4570 cost: 1.5427 min: 0.1412 max: 2.4642 USE_META, weight: 0.4912 cost: 1.4545 min: 0.1412 max: 2.4642 USE_META, weight: 0.5415 cost: 1.3248 min: 0.1412 max: 2.4642 USE_META, weight: 0.5438 cost: 1.3188 min: 0.1412 max: 2.4642 USE_META, weight: 0.5636 cost: 1.2677 min: 0.1412 max: 2.4642 USE_META, weight: 0.5818 cost: 1.2206 min: 0.1412 max: 2.4642 USE_META, weight: 0.2881 cost: 1.9788 min: 0.1412 max: 2.4642 USE_META, weight: 0.3945 cost: 1.7042 min: 0.1412 max: 2.4642 USE_META, weight: 0.3913 cost: 1.7124 min: 0.1412 max: 2.4642 USE_META, weight: 0.9987 cost: 0.1445 min: 0.1412 max: 2.4642 USE_META, weight: 0.9534 cost: 0.2615 min: 0.1412 max: 2.4642 USE_META, weight: 0.9734 cost: 0.2099 min: 0.1412 max: 2.4642 USE_META, weight: 0.9396 cost: 0.2972 min: 0.1412 max: 2.4642 USE_META, weight: 0.7916 cost: 0.6791 min: 0.1412 max: 2.4642 USE_META, weight: 0.5709 cost: 1.2488 min: 0.1412 max: 2.4642 USE_META, weight: 0.2840 cost: 1.9893 min: 0.1412 max: 2.4642 USE_META, weight: 0.2372 cost: 2.1102 min: 0.1412 max: 2.4642 USE_META, weight: 0.6198 cost: 1.1226 min: 0.1412 max: 2.4642 USE_META, weight: 0.1000 cost: 2.4642 min: 0.1412 max: 2.4642 USE_META, weight: 0.6744 cost: 0.9816 min: 0.1412 max: 2.4642 USE_META, weight: 0.8452 cost: 0.5408 min: 0.1412 max: 2.4642 USE_META, weight: 0.8518 cost: 0.5239 min: 0.1412 max: 2.4642 USE_META, weight: 0.8160 cost: 0.6162 min: 0.1412 max: 2.4642 USE_META, weight: 0.8242 cost: 0.5949 min: 0.1412 max: 2.4642 USE_META, weight: 0.6901 cost: 0.9412 min: 0.1412 max: 2.4642 USE_META, weight: 0.8543 cost: 0.5173 min: 0.1412 max: 2.4642 USE_META, weight: 0.8599 cost: 0.5028 min: 0.1412 max: 2.4642 USE_META, weight: 0.8258 cost: 0.5908 min: 0.1412 max: 2.4642 USE_META, weight: 0.8397 cost: 0.5550 min: 0.1412 max: 2.4642 USE_META, weight: 0.8252 cost: 0.5924 min: 0.1412 max: 2.4642 USE_META, weight: 0.9534 cost: 0.2615 min: 0.1412 max: 2.4642 USE_META, weight: 0.7991 cost: 0.6598 min: 0.1412 max: 2.4642 USE_META, weight: 0.9759 cost: 0.2034 min: 0.1412 max: 2.4642 USE_META, weight: 0.8108 cost: 0.6295 min: 0.1412 max: 2.4642 USE_META, weight: 0.5599 cost: 1.2771 min: 0.1412 max: 2.4642 USE_META, weight: 0.5599 cost: 1.2771 min: 0.1412 max: 2.4642 USE_META, weight: 0.5599 cost: 1.2771 min: 0.1412 max: 2.4642 USE_META, weight: 0.5599 cost: 1.2771 min: 0.1412 max: 2.4642 USE_META, weight: 0.5599 cost: 1.2771 min: 0.1412 max: 2.4642 USE_META, weight: 0.5599 cost: 1.2771 min: 0.1412 max: 2.4642 USE_META, weight: 0.5599 cost: 1.2771 min: 0.1412 max: 2.4642 USE_META, weight: 0.5599 cost: 1.2771 min: 0.1412 max: 2.4642 USE_META, weight: 0.5599 cost: 1.2771 min: 0.1412 max: 2.4642 USE_META, weight: 0.5599 cost: 1.2771 min: 0.1412 max: 2.4642 USE_META, weight: 0.8357 cost: 0.5652 min: 0.1412 max: 2.4642 USE_META, weight: 0.7332 cost: 0.8299 min: 0.1412 max: 2.4642 USE_META, weight: 0.8659 cost: 0.4873 min: 0.1412 max: 2.4642 USE_META, weight: 0.6377 cost: 1.0762 min: 0.1412 max: 2.4642 USE_META, weight: 0.9033 cost: 0.3908 min: 0.1412 max: 2.4642 USE_META, weight: 0.4615 cost: 1.5313 min: 0.1412 max: 2.4642 USE_META, weight: 0.8111 cost: 0.6289 min: 0.1412 max: 2.4642 USE_META, weight: 0.7635 cost: 0.7517 min: 0.1412 max: 2.4642 USE_META, weight: 0.5637 cost: 1.2674 min: 0.1412 max: 2.4642 USE_META, weight: 0.4202 cost: 1.6377 min: 0.1412 max: 2.4642 USE_META, weight: 0.4471 cost: 1.5684 min: 0.1412 max: 2.4642 USE_META, weight: 0.4897 cost: 1.4582 min: 0.1412 max: 2.4642 USE_META, weight: 0.6265 cost: 1.1054 min: 0.1412 max: 2.4642 USE_META, weight: 0.9581 cost: 0.2493 min: 0.1412 max: 2.4642 USE_META, weight: 0.7799 cost: 0.7093 min: 0.1412 max: 2.4642 USE_META, weight: 0.4426 cost: 1.5799 min: 0.1412 max: 2.4642 USE_META, weight: 0.4615 cost: 1.5313 min: 0.1412 max: 2.4642 USE_META, weight: 0.4332 cost: 1.6041 min: 0.1412 max: 2.4642 USE_META, weight: 0.7635 cost: 0.7517 min: 0.1412 max: 2.4642 USE_META, weight: 0.5455 cost: 1.3144 min: 0.1412 max: 2.4642 USE_META, weight: 0.5599 cost: 1.2771 min: 0.1412 max: 2.4642 USE_META, weight: 0.5599 cost: 1.2771 min: 0.1412 max: 2.4642 USE_META, weight: 0.5599 cost: 1.2771 min: 0.1412 max: 2.4642 USE_META, weight: 0.5599 cost: 1.2771 min: 0.1412 max: 2.4642 USE_META, weight: 0.5599 cost: 1.2771 min: 0.1412 max: 2.4642 USE_META, weight: 0.7673 cost: 0.7417 min: 0.1412 max: 2.4642 USE_META, weight: 0.5599 cost: 1.2771 min: 0.1412 max: 2.4642 USE_META, weight: 0.5599 cost: 1.2771 min: 0.1412 max: 2.4642 USE_META, weight: 0.5599 cost: 1.2771 min: 0.1412 max: 2.4642 USE_META, weight: 0.5599 cost: 1.2771 min: 0.1412 max: 2.4642 USE_META, weight: 0.9967 cost: 0.1497 min: 0.1412 max: 2.4642 USE_META, weight: 0.9769 cost: 0.2009 min: 0.1412 max: 2.4642 USE_META, weight: 0.9490 cost: 0.2728 min: 0.1412 max: 2.4642 USE_META, weight: 1.0000 cost: 0.1412 min: 0.1412 max: 2.4642 USE_META, weight: 0.9707 cost: 0.2168 min: 0.1412 max: 2.4642 USE_META, weight: 0.6093 cost: 1.1497 min: 0.1412 max: 2.4642 USE_META, weight: 0.3972 cost: 1.6971 min: 0.1412 max: 2.4642 USE_META, weight: 0.5599 cost: 1.2771 min: 0.1412 max: 2.4642 USE_META, weight: 0.5599 cost: 1.2771 min: 0.1412 max: 2.4642 USE_META, weight: 0.5599 cost: 1.2771 min: 0.1412 max: 2.4642 USE_META, weight: 0.5599 cost: 1.2771 min: 0.1412 max: 2.4642 USE_META, weight: 0.5599 cost: 1.2771 min: 0.1412 max: 2.4642 USE_META, weight: 0.8565 cost: 0.5117 min: 0.1412 max: 2.4642 USE_META, weight: 0.5627 cost: 1.2701 min: 0.1412 max: 2.4642 USE_META, weight: 0.6721 cost: 0.9875 min: 0.1412 max: 2.4642 USE_META, weight: 0.5537 cost: 1.2932 min: 0.1412 max: 2.4642 USE_META, weight: 0.1600 cost: 2.3093 min: 0.1412 max: 2.4642 USE_META, weight: 0.6013 cost: 1.1703 min: 0.1412 max: 2.4642 USE_META, weight: 0.4982 cost: 1.4364 min: 0.1412 max: 2.4642 USE_META, weight: 0.4336 cost: 1.6033 min: 0.1412 max: 2.4642 USE_META, weight: 0.5169 cost: 1.3882 min: 0.1412 max: 2.4642 USE_META, weight: 0.4859 cost: 1.4682 min: 0.1412 max: 2.4642 USE_META, weight: 0.7849 cost: 0.6964 min: 0.1412 max: 2.4642 USE_META, weight: 0.7901 cost: 0.6830 min: 0.1412 max: 2.4642 USE_META, weight: 0.7343 cost: 0.8271 min: 0.1412 max: 2.4642 USE_META, weight: 0.8808 cost: 0.4488 min: 0.1412 max: 2.4642 USE_META, weight: 0.8496 cost: 0.5294 min: 0.1412 max: 2.4642 USE_META, weight: 0.7505 cost: 0.7853 min: 0.1412 max: 2.4642 USE_META, weight: 0.8095 cost: 0.6328 min: 0.1412 max: 2.4642 USE_META, weight: 0.5314 cost: 1.3507 min: 0.1412 max: 2.4642 USE_META, weight: 0.5591 cost: 1.2792 min: 0.1412 max: 2.4642 USE_META, weight: 0.7772 cost: 0.7163 min: 0.1412 max: 2.4642 USE_META, weight: 0.5103 cost: 1.4051 min: 0.1412 max: 2.4642 USE_META, weight: 0.6146 cost: 1.1361 min: 0.1412 max: 2.4642 USE_META, weight: 0.1612 cost: 2.3062 min: 0.1412 max: 2.4642 USE_META, weight: 0.3033 cost: 1.9396 min: 0.1412 max: 2.4642 USE_META, weight: 0.1094 cost: 2.4401 min: 0.1412 max: 2.4642 USE_META, weight: 0.2850 cost: 1.9868 min: 0.1412 max: 2.4642 USE_META, weight: 0.5731 cost: 1.2431 min: 0.1412 max: 2.4642 USE_META, weight: 0.5563 cost: 1.2865 min: 0.1412 max: 2.4642 USE_META, weight: 0.2379 cost: 2.1082 min: 0.1412 max: 2.4642 USE_EVALUE, weight: 0.4347 eval: 56.2000 min: 6.8900 max: 85.4000 USE_EVALUE, weight: 0.2800 eval: 69.7000 min: 6.8900 max: 85.4000 USE_EVALUE, weight: 0.2800 eval: 69.7000 min: 6.8900 max: 85.4000 USE_EVALUE, weight: 0.2800 eval: 69.7000 min: 6.8900 max: 85.4000 USE_EVALUE, weight: 1.0000 eval: 6.8900 min: 6.8900 max: 85.4000 USE_EVALUE, weight: 1.0000 eval: 6.8900 min: 6.8900 max: 85.4000 USE_EVALUE, weight: 1.0000 eval: 6.8900 min: 6.8900 max: 85.4000 USE_EVALUE, weight: 0.7087 eval: 32.3000 min: 6.8900 max: 85.4000 USE_EVALUE, weight: 0.7087 eval: 32.3000 min: 6.8900 max: 85.4000 USE_EVALUE, weight: 0.6480 eval: 37.6000 min: 6.8900 max: 85.4000 USE_EVALUE, weight: 0.1000 eval: 85.4000 min: 6.8900 max: 85.4000 USE_EVALUE, weight: 0.1000 eval: 85.4000 min: 6.8900 max: 85.4000 USE_EVALUE, weight: 0.1000 eval: 85.4000 min: 6.8900 max: 85.4000 USE_EVALUE, weight: 0.9345 eval: 12.6000 min: 6.8900 max: 85.4000 USE_EVALUE, weight: 0.9345 eval: 12.6000 min: 6.8900 max: 85.4000 USE_EVALUE, weight: 0.9345 eval: 12.6000 min: 6.8900 max: 85.4000 USE_EVALUE, weight: 0.5826 eval: 43.3000 min: 6.8900 max: 85.4000 USE_EVALUE, weight: 0.5826 eval: 43.3000 min: 6.8900 max: 85.4000 USE_EVALUE, weight: 0.5826 eval: 43.3000 min: 6.8900 max: 85.4000 USE_EVALUE, weight: 0.7672 eval: 27.2000 min: 6.8900 max: 85.4000 USE_EVALUE, weight: 0.7672 eval: 27.2000 min: 6.8900 max: 85.4000 USE_EVALUE, weight: 0.7672 eval: 27.2000 min: 6.8900 max: 85.4000 Number of contacts in models: 261 Number of contacts in alignments: 22 NUMB_ALIGNS: 22 Adding 5124 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: -188.1098, CN propb: -188.1098 weights: 0.2291 constraints: 202 # command:Found ConstraintSet # PrintContacts align.constraints_meta03 Number of constraints in align3.constraints 202 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta03 Number of constraints in align3.constraints.bonus 202 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta03 Number of constraints in rejected3.constraints 4922 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta03 Number of constraints in rejected3.constraints.bonus 4922 # 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 5124 # command: