parameters: 0.6 1.3 0.5 200 50 # 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:# PrintAlignmentsContacts allconstraints.under Using radius: 8.0000 NUMB_ALIGNS: 22 Done printing distance constraints # command: