# 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/T0352/ # command:# Making conformation for sequence T0352 numbered 1 through 117 Created new target T0352 from T0352.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0352/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0352//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0352/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0352//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0352/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0352/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0352/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1myo/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1myo expands to /projects/compbio/data/pdb/1myo.pdb.gz 1myo:Warning: there is no chain 1myo will retry with 1myoA # T0352 read from 1myo/merged-good-all-a2m # 1myo read from 1myo/merged-good-all-a2m # adding 1myo to template set # found chain 1myo in template set Warning: unaligning (T0352)T2 because first residue in template chain is (1myo)M1 T0352 3 :THDRVRLQLQ 1myo 2 :CDKEFMWALK # choosing archetypes in rotamer library T0352 13 :ALEALLREHQHWRND 1myo 17 :EVKDYVAKGEDVNRT T0352 34 :FNSTQPF 1myo 32 :LEGGRKP T0352 51 :LQWVL 1myo 39 :LHYAA T0352 56 :IPRMHDLLDNKQ 1myo 48 :LEILEFLLLKGA T0352 68 :PLPGAFAVAPYYEMALATDHPQRALIL 1myo 62 :NAPDKHHITPLLSAVYEGHVSCVKLLL Number of specific fragments extracted= 6 number of extra gaps= 0 total=6 Number of alignments=1 # 1myo read from 1myo/merged-good-all-a2m # found chain 1myo in template set Warning: unaligning (T0352)T2 because first residue in template chain is (1myo)M1 T0352 3 :THDRVRLQLQ 1myo 2 :CDKEFMWALK T0352 13 :ALEALLREHQHWRND 1myo 17 :EVKDYVAKGEDVNRT T0352 34 :FNSTQPF 1myo 32 :LEGGRKP T0352 51 :LQWVL 1myo 39 :LHYAA T0352 56 :IPRMHDLLDNKQ 1myo 48 :LEILEFLLLKGA T0352 68 :PLPGAFAVAPYYEMALATDHPQRALIL 1myo 62 :NAPDKHHITPLLSAVYEGHVSCVKLLL Number of specific fragments extracted= 6 number of extra gaps= 0 total=12 Number of alignments=2 # 1myo read from 1myo/merged-good-all-a2m # found chain 1myo in template set T0352 3 :THDRVRLQLQ 1myo 2 :CDKEFMWALK T0352 13 :ALEALLREHQHWRND 1myo 17 :EVKDYVAKGEDVNRT T0352 34 :F 1myo 32 :L T0352 35 :NSTQPF 1myo 34 :GGRKPL T0352 52 :QWVL 1myo 40 :HYAA T0352 56 :IPRMHDLLDNKQ 1myo 48 :LEILEFLLLKGA T0352 68 :PLPGAFAVAPYYEMALATDHPQRALIL 1myo 62 :NAPDKHHITPLLSAVYEGHVSCVKLLL Number of specific fragments extracted= 7 number of extra gaps= 0 total=19 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c4jA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2c4jA expands to /projects/compbio/data/pdb/2c4j.pdb.gz 2c4jA:Skipped atom 120, because occupancy 0.5 <= existing 0.500 in 2c4jA Skipped atom 122, because occupancy 0.500 <= existing 0.500 in 2c4jA Skipped atom 1604, because occupancy 0.500 <= existing 0.500 in 2c4jA Skipped atom 1606, because occupancy 0.500 <= existing 0.500 in 2c4jA # T0352 read from 2c4jA/merged-good-all-a2m # 2c4jA read from 2c4jA/merged-good-all-a2m # adding 2c4jA to template set # found chain 2c4jA in template set T0352 4 :HDRVRLQLQALEALLREH 2c4jA 124 :KPEYLQALPEMLKLYSQF T0352 34 :FNSTQPFFMDTMEPLEWLQWVLIPRMHDL 2c4jA 142 :LGKQPWFLGDKITFVDFIAYDVLERNQVF T0352 69 :LPGAF 2c4jA 171 :EPSCL T0352 85 :TDHPQRALILAELE 2c4jA 176 :DAFPNLKDFISRFE T0352 99 :KLDALFADDA 2c4jA 193 :KISAYMKSSR Number of specific fragments extracted= 5 number of extra gaps= 0 total=24 Number of alignments=4 # 2c4jA read from 2c4jA/merged-good-all-a2m # found chain 2c4jA in template set T0352 4 :HDRVRLQLQALEALL 2c4jA 128 :LQALPEMLKLYSQFL T0352 35 :NSTQPFFMDTMEPLEWLQWVLIPRMHDL 2c4jA 143 :GKQPWFLGDKITFVDFIAYDVLERNQVF T0352 69 :LPGAFA 2c4jA 171 :EPSCLD T0352 86 :DHPQRALILAELE 2c4jA 177 :AFPNLKDFISRFE T0352 99 :KLDALFADD 2c4jA 193 :KISAYMKSS Number of specific fragments extracted= 5 number of extra gaps= 0 total=29 Number of alignments=5 # 2c4jA read from 2c4jA/merged-good-all-a2m # found chain 2c4jA in template set T0352 4 :HDRVRLQLQALEALLREH 2c4jA 124 :KPEYLQALPEMLKLYSQF T0352 34 :FNSTQPFFMDTMEPLEWLQWVLIPRMHDL 2c4jA 142 :LGKQPWFLGDKITFVDFIAYDVLERNQVF T0352 69 :LPGAF 2c4jA 171 :EPSCL T0352 85 :TDHPQRALILAELEK 2c4jA 176 :DAFPNLKDFISRFEG T0352 100 :LDALFADDA 2c4jA 194 :ISAYMKSSR Number of specific fragments extracted= 5 number of extra gaps= 0 total=34 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2wrpR/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2wrpR expands to Error: no filename for 2wrpR 2wrpR expands to Error: no filename for 2wrpR 2wrpR expands to Error: no filename for 2wrpR # T0352 read from 2wrpR/merged-good-all-a2m # 2wrpR read from 2wrpR/merged-good-all-a2m # adding 2wrpR to template set Error: can't find template for 2wrpR or 2wrpR, so skipping it. # 2wrpR read from 2wrpR/merged-good-all-a2m # adding 2wrpR to template set Error: can't find template for 2wrpR or 2wrpR, so skipping it. # 2wrpR read from 2wrpR/merged-good-all-a2m # adding 2wrpR to template set Error: can't find template for 2wrpR or 2wrpR, so skipping it. # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m6jA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1m6jA expands to /projects/compbio/data/pdb/1m6j.pdb.gz 1m6jA:Skipped atom 398, because occupancy 0.500 <= existing 0.500 in 1m6jA Skipped atom 400, because occupancy 0.500 <= existing 0.500 in 1m6jA Skipped atom 402, because occupancy 0.500 <= existing 0.500 in 1m6jA Skipped atom 404, because occupancy 0.500 <= existing 0.500 in 1m6jA Skipped atom 406, because occupancy 0.500 <= existing 0.500 in 1m6jA Skipped atom 546, because occupancy 0.500 <= existing 0.500 in 1m6jA Skipped atom 548, because occupancy 0.500 <= existing 0.500 in 1m6jA Skipped atom 550, because occupancy 0.500 <= existing 0.500 in 1m6jA Skipped atom 786, because occupancy 0.500 <= existing 0.500 in 1m6jA Skipped atom 788, because occupancy 0.500 <= existing 0.500 in 1m6jA Skipped atom 790, because occupancy 0.500 <= existing 0.500 in 1m6jA Skipped atom 792, because occupancy 0.500 <= existing 0.500 in 1m6jA Skipped atom 794, because occupancy 0.500 <= existing 0.500 in 1m6jA Skipped atom 1089, because occupancy 0.500 <= existing 0.500 in 1m6jA Skipped atom 1091, because occupancy 0.500 <= existing 0.500 in 1m6jA Skipped atom 1093, because occupancy 0.500 <= existing 0.500 in 1m6jA Skipped atom 1095, because occupancy 0.500 <= existing 0.500 in 1m6jA Skipped atom 1097, because occupancy 0.500 <= existing 0.500 in 1m6jA Skipped atom 1119, because occupancy 0.500 <= existing 0.500 in 1m6jA Skipped atom 1121, because occupancy 0.500 <= existing 0.500 in 1m6jA Skipped atom 1123, because occupancy 0.500 <= existing 0.500 in 1m6jA Skipped atom 1125, because occupancy 0.500 <= existing 0.500 in 1m6jA Skipped atom 1127, because occupancy 0.500 <= existing 0.500 in 1m6jA Skipped atom 1269, because occupancy 0.500 <= existing 0.500 in 1m6jA Skipped atom 1271, because occupancy 0.500 <= existing 0.500 in 1m6jA Skipped atom 1273, because occupancy 0.500 <= existing 0.500 in 1m6jA Skipped atom 1275, because occupancy 0.500 <= existing 0.500 in 1m6jA Skipped atom 1574, because occupancy 0.500 <= existing 0.500 in 1m6jA Skipped atom 1576, because occupancy 0.500 <= existing 0.500 in 1m6jA Skipped atom 1578, because occupancy 0.500 <= existing 0.500 in 1m6jA Skipped atom 1580, because occupancy 0.500 <= existing 0.500 in 1m6jA Skipped atom 1582, because occupancy 0.500 <= existing 0.500 in 1m6jA Skipped atom 1710, because occupancy 0.500 <= existing 0.500 in 1m6jA Skipped atom 1930, because occupancy 0.500 <= existing 0.500 in 1m6jA Skipped atom 1932, because occupancy 0.500 <= existing 0.500 in 1m6jA Skipped atom 1934, because occupancy 0.500 <= existing 0.500 in 1m6jA Skipped atom 1936, because occupancy 0.500 <= existing 0.500 in 1m6jA # T0352 read from 1m6jA/merged-good-all-a2m # 1m6jA read from 1m6jA/merged-good-all-a2m # adding 1m6jA to template set # found chain 1m6jA in template set T0352 4 :HDRVRLQLQALEAL 1m6jA 147 :EEVVAAQLKAINNA T0352 29 :PQPHQFNS 1m6jA 161 :ISKEAWKN T0352 37 :TQPFFMDT 1m6jA 174 :EPVWAIGT T0352 85 :TDHPQRALILAELEKLDALFAD 1m6jA 182 :GKTATPDQAQEVHQYIRKWMTE Number of specific fragments extracted= 4 number of extra gaps= 0 total=38 Number of alignments=7 # 1m6jA read from 1m6jA/merged-good-all-a2m # found chain 1m6jA in template set T0352 13 :ALEALLREHQH 1m6jA 53 :KVQQILAGEAN T0352 24 :WRNDEPQPHQFN 1m6jA 75 :WTKSGAYTGEVH T0352 59 :MHDLLDNKQP 1m6jA 87 :VGMLVDCQVP T0352 70 :PGAFAVAPYYEMALATD 1m6jA 111 :ESNEQVAEKVKVAIDAG T0352 87 :HPQRALILAELEKLDALFADDA 1m6jA 144 :NQTEEVVAAQLKAINNAISKEA Number of specific fragments extracted= 5 number of extra gaps= 0 total=43 Number of alignments=8 # 1m6jA read from 1m6jA/merged-good-all-a2m # found chain 1m6jA in template set T0352 3 :THDRVRLQLQALEAL 1m6jA 17 :TLASIETLTKGVAAS T0352 29 :PQPHQFNS 1m6jA 32 :VDAELAKK T0352 39 :PFF 1m6jA 47 :PFI T0352 55 :LIPRMHDLLDN 1m6jA 50 :YIPKVQQILAG T0352 66 :KQPLPGAFAVAPYY 1m6jA 77 :KSGAYTGEVHVGML T0352 80 :EMALATDHPQRALILAELEKLDA 1m6jA 103 :SERRQIFHESNEQVAEKVKVAID Number of specific fragments extracted= 6 number of extra gaps= 0 total=49 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tbmA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1tbmA expands to Error: no filename for 1tbmA 1tbmA expands to Error: no filename for 1tbmA 1tbmA expands to Error: no filename for 1tbmA # T0352 read from 1tbmA/merged-good-all-a2m # 1tbmA read from 1tbmA/merged-good-all-a2m # adding 1tbmA to template set Error: can't find template for 1tbmA or 1tbmA, so skipping it. # 1tbmA read from 1tbmA/merged-good-all-a2m # adding 1tbmA to template set Error: can't find template for 1tbmA or 1tbmA, so skipping it. # 1tbmA read from 1tbmA/merged-good-all-a2m # adding 1tbmA to template set Error: can't find template for 1tbmA or 1tbmA, so skipping it. # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bd8/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1bd8 expands to /projects/compbio/data/pdb/1bd8.pdb.gz 1bd8:Warning: there is no chain 1bd8 will retry with 1bd8A # T0352 read from 1bd8/merged-good-all-a2m # 1bd8 read from 1bd8/merged-good-all-a2m # adding 1bd8 to template set # found chain 1bd8 in template set T0352 4 :HDRVRLQLQ 1bd8 21 :VQEVRRLLH T0352 26 :NDEPQPHQFNSTQPFFMDTMEP 1bd8 30 :RELVHPDALNRFGKTALQVMMF T0352 56 :IPRMHDLLDNKQP 1bd8 54 :TAIALELLKQGAS T0352 69 :LPGAFAVAPYYEMALATDHPQRALILA 1bd8 69 :VQDTSGTSPVHDAARTGFLDTLKVLVE Number of specific fragments extracted= 4 number of extra gaps= 0 total=53 Number of alignments=10 # 1bd8 read from 1bd8/merged-good-all-a2m # found chain 1bd8 in template set T0352 4 :HDRVRLQLQ 1bd8 21 :VQEVRRLLH T0352 26 :NDEPQPHQFNSTQPFFMDTMEPL 1bd8 30 :RELVHPDALNRFGKTALQVMMFG T0352 56 :IPRMHDLLDNKQP 1bd8 54 :TAIALELLKQGAS T0352 69 :LPGAFAVAPYYEMALATDHPQRALILA 1bd8 69 :VQDTSGTSPVHDAARTGFLDTLKVLVE Number of specific fragments extracted= 4 number of extra gaps= 0 total=57 Number of alignments=11 # 1bd8 read from 1bd8/merged-good-all-a2m # found chain 1bd8 in template set T0352 4 :HDR 1bd8 21 :VQE T0352 14 :LEALLREHQHWRNDEPQ 1bd8 24 :VRRLLHRELVHPDALNR T0352 37 :TQPFFMDTMEP 1bd8 41 :FGKTALQVMMF T0352 56 :IPRMHDLLDNKQP 1bd8 54 :TAIALELLKQGAS T0352 69 :LPGAFAVAPYYEMALATDHPQRALILA 1bd8 69 :VQDTSGTSPVHDAARTGFLDTLKVLVE Number of specific fragments extracted= 5 number of extra gaps= 0 total=62 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2esnA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2esnA expands to /projects/compbio/data/pdb/2esn.pdb.gz 2esnA:Skipped atom 983, because occupancy 0.500 <= existing 0.500 in 2esnA Skipped atom 985, because occupancy 0.500 <= existing 0.500 in 2esnA Skipped atom 987, because occupancy 0.500 <= existing 0.500 in 2esnA Skipped atom 989, because occupancy 0.500 <= existing 0.500 in 2esnA Skipped atom 991, because occupancy 0.500 <= existing 0.500 in 2esnA Skipped atom 993, because occupancy 0.500 <= existing 0.500 in 2esnA Skipped atom 995, because occupancy 0.500 <= existing 0.500 in 2esnA Skipped atom 997, because occupancy 0.500 <= existing 0.500 in 2esnA Skipped atom 999, because occupancy 0.500 <= existing 0.500 in 2esnA Skipped atom 1001, because occupancy 0.500 <= existing 0.500 in 2esnA Skipped atom 1003, because occupancy 0.500 <= existing 0.500 in 2esnA Skipped atom 1251, because occupancy 0.500 <= existing 0.500 in 2esnA Skipped atom 1253, because occupancy 0.500 <= existing 0.500 in 2esnA Skipped atom 1255, because occupancy 0.500 <= existing 0.500 in 2esnA Skipped atom 1257, because occupancy 0.500 <= existing 0.500 in 2esnA Skipped atom 1259, because occupancy 0.500 <= existing 0.500 in 2esnA Skipped atom 1261, because occupancy 0.500 <= existing 0.500 in 2esnA Skipped atom 1263, because occupancy 0.500 <= existing 0.500 in 2esnA Skipped atom 1265, because occupancy 0.500 <= existing 0.500 in 2esnA Skipped atom 1267, because occupancy 0.500 <= existing 0.500 in 2esnA Skipped atom 1269, because occupancy 0.500 <= existing 0.500 in 2esnA Skipped atom 1271, because occupancy 0.500 <= existing 0.500 in 2esnA # T0352 read from 2esnA/merged-good-all-a2m # 2esnA read from 2esnA/merged-good-all-a2m # adding 2esnA to template set # found chain 2esnA in template set T0352 4 :HDRVRLQLQALEALLREHQ 2esnA 65 :TQRAEHLAAAVAAALRALG T0352 23 :HWRNDEPQPH 2esnA 86 :LEEWRPFVPG T0352 35 :NSTQPFFMDTM 2esnA 96 :QSQRTFVFAAT T0352 49 :EWLQWVLIPRMHDLLDNKQP 2esnA 107 :DYTAFALLPPLMNRLQHSAP Number of specific fragments extracted= 4 number of extra gaps= 0 total=66 Number of alignments=13 # 2esnA read from 2esnA/merged-good-all-a2m # found chain 2esnA in template set T0352 4 :HDRVRLQLQALEALLREHQ 2esnA 65 :TQRAEHLAAAVAAALRALG T0352 23 :HWRNDEPQPH 2esnA 86 :LEEWRPFVPG T0352 35 :NSTQPFFMDTME 2esnA 96 :QSQRTFVFAATD T0352 50 :WLQWVLIPRMHDLLDNK 2esnA 108 :YTAFALLPPLMNRLQHS Number of specific fragments extracted= 4 number of extra gaps= 0 total=70 Number of alignments=14 # 2esnA read from 2esnA/merged-good-all-a2m # found chain 2esnA in template set T0352 5 :DRVRLQL 2esnA 66 :QRAEHLA T0352 12 :QALEALLREHQHWRNDEPQ 2esnA 77 :AALRALGEGLEEWRPFVPG T0352 35 :NSTQPFFMDTM 2esnA 96 :QSQRTFVFAAT T0352 49 :EWLQWVLIPRMHDLLDN 2esnA 107 :DYTAFALLPPLMNRLQH Number of specific fragments extracted= 4 number of extra gaps= 0 total=74 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zd3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zd3A expands to /projects/compbio/data/pdb/1zd3.pdb.gz 1zd3A:# T0352 read from 1zd3A/merged-good-all-a2m # 1zd3A read from 1zd3A/merged-good-all-a2m # adding 1zd3A to template set # found chain 1zd3A in template set T0352 43 :DTMEPLEW 1zd3A 56 :GEITLSQW T0352 56 :IPRMHDLLD 1zd3A 64 :IPLMEENCR T0352 65 :NKQPLPGAFAVAPYYEMALATD 1zd3A 78 :AKVCLPKNFSIKEIFDKAISAR T0352 90 :RALILAELEKLD 1zd3A 102 :NRPMLQAALMLR Number of specific fragments extracted= 4 number of extra gaps= 0 total=78 Number of alignments=16 # 1zd3A read from 1zd3A/merged-good-all-a2m # found chain 1zd3A in template set T0352 43 :DTMEPLEWLQ 1zd3A 56 :GEITLSQWIP T0352 54 :VLIPRMHDLLD 1zd3A 66 :LMEENCRKCSE T0352 65 :NKQPLPGAFAVAPYYEMALATD 1zd3A 78 :AKVCLPKNFSIKEIFDKAISAR T0352 88 :PQRALILAELEKLD 1zd3A 100 :KINRPMLQAALMLR Number of specific fragments extracted= 4 number of extra gaps= 0 total=82 Number of alignments=17 # 1zd3A read from 1zd3A/merged-good-all-a2m # found chain 1zd3A in template set T0352 43 :DTMEPLEW 1zd3A 56 :GEITLSQW T0352 56 :IPRMHDLLD 1zd3A 64 :IPLMEENCR T0352 65 :NKQPLPGAFAVAPYYEMALATD 1zd3A 78 :AKVCLPKNFSIKEIFDKAISAR T0352 90 :RALILAELEKLD 1zd3A 102 :NRPMLQAALMLR Number of specific fragments extracted= 4 number of extra gaps= 0 total=86 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ihp/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ihp expands to /projects/compbio/data/pdb/1ihp.pdb.gz 1ihp:Warning: there is no chain 1ihp will retry with 1ihpA # T0352 read from 1ihp/merged-good-all-a2m # 1ihp read from 1ihp/merged-good-all-a2m # adding 1ihp to template set # found chain 1ihp in template set T0352 4 :HDRVRLQLQALEAL 1ihp 69 :GKKYSALIEEIQQN T0352 26 :NDEPQPHQF 1ihp 83 :ATTFDGKYA T0352 35 :NSTQPFFMDTME 1ihp 95 :TYNYSLGADDLT T0352 47 :PLEWL 1ihp 109 :GEQEL T0352 52 :QWVLIPRMHDLLDNKQP 1ihp 117 :GIKFYQRYESLTRNIVP T0352 86 :DHPQRALILAELEK 1ihp 139 :GSSRVIASGKKFIE T0352 100 :LDALFADDASLEHHHHH 1ihp 154 :FQSTKLKDPRAQPGQSS Number of specific fragments extracted= 7 number of extra gaps= 0 total=93 Number of alignments=19 # 1ihp read from 1ihp/merged-good-all-a2m # found chain 1ihp in template set Number of specific fragments extracted= 0 number of extra gaps= 0 total=93 # 1ihp read from 1ihp/merged-good-all-a2m # found chain 1ihp in template set Warning: unaligning (T0352)S36 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ihp)T253 T0352 2 :TTHDRVRLQ 1ihp 199 :ELADTVEAN T0352 11 :LQALEALLREH 1ihp 213 :VPSIRQRLEND T0352 24 :WRNDEPQPHQF 1ihp 224 :LSGVTLTDTEV T0352 37 :TQPFFMDTMEPLEWLQWVLIPRMHDLLDN 1ihp 254 :KLSPFCDLFTHDEWINYDYLQSLKKYYGH T0352 66 :KQPLPGAFAVAPYYEMAL 1ihp 285 :GNPLGPTQGVGYANELIA Number of specific fragments extracted= 5 number of extra gaps= 0 total=98 Number of alignments=20 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fiyA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fiyA expands to /projects/compbio/data/pdb/2fiy.pdb.gz 2fiyA:# T0352 read from 2fiyA/merged-good-all-a2m # 2fiyA read from 2fiyA/merged-good-all-a2m # adding 2fiyA to template set # found chain 2fiyA in template set T0352 6 :RVRLQLQALEALLR 2fiyA 51 :LVAGLCRLQQALLD T0352 22 :QHWRNDEPQPHQF 2fiyA 65 :NPPALAPLDPERL T0352 36 :STQP 2fiyA 83 :HGMP T0352 44 :TMEPLEWLQW 2fiyA 87 :PLAYDLLVRE T0352 55 :LIPRMHDLLDN 2fiyA 99 :WLPWLDALLAG T0352 67 :QPLPGAFAVAPYYEMALAT 2fiyA 110 :YPAPANAAVGAALEQLREA T0352 89 :QRALILAELEKL 2fiyA 129 :EEGQRKAWAIAL Number of specific fragments extracted= 7 number of extra gaps= 0 total=105 Number of alignments=21 # 2fiyA read from 2fiyA/merged-good-all-a2m # found chain 2fiyA in template set T0352 27 :DEPQPHQF 2fiyA 70 :APLDPERL T0352 35 :NSTQ 2fiyA 83 :HGMP T0352 44 :TMEPLEWLQW 2fiyA 87 :PLAYDLLVRE T0352 54 :VLIPRMHDLLDN 2fiyA 98 :AWLPWLDALLAG T0352 67 :QPLPGAFAVAPYYEMALAT 2fiyA 110 :YPAPANAAVGAALEQLREA T0352 89 :QRALILAELEKL 2fiyA 129 :EEGQRKAWAIAL Number of specific fragments extracted= 6 number of extra gaps= 0 total=111 Number of alignments=22 # 2fiyA read from 2fiyA/merged-good-all-a2m # found chain 2fiyA in template set T0352 4 :HDRVRLQLQALEALLR 2fiyA 49 :LRLVAGLCRLQQALLD T0352 22 :QHWRNDEPQPHQFN 2fiyA 65 :NPPALAPLDPERLR T0352 36 :STQP 2fiyA 83 :HGMP T0352 44 :TMEPLEWLQW 2fiyA 87 :PLAYDLLVRE T0352 55 :LIPRMHDLLDN 2fiyA 99 :WLPWLDALLAG T0352 67 :QPLPGAFAVAPYYEMALATDHPQRALILA 2fiyA 110 :YPAPANAAVGAALEQLREAEEGQRKAWAI T0352 102 :ALFADD 2fiyA 139 :ALLSGQ Number of specific fragments extracted= 7 number of extra gaps= 0 total=118 Number of alignments=23 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2aheA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2aheA expands to /projects/compbio/data/pdb/2ahe.pdb.gz 2aheA:# T0352 read from 2aheA/merged-good-all-a2m # 2aheA read from 2aheA/merged-good-all-a2m # adding 2aheA to template set # found chain 2aheA in template set Warning: unaligning (T0352)A108 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2aheA)S174 T0352 13 :ALEALLREH 2aheA 90 :KIEEFLEEV T0352 22 :QHWRNDEPQPHQFNS 2aheA 102 :PKYLKLSPKHPESNT T0352 55 :LIPRMHDLLDNKQ 2aheA 121 :IFAKFSAYIKNSR T0352 70 :PGAF 2aheA 134 :PEAN T0352 87 :HPQRALILAELEKLDALFADD 2aheA 138 :EALERGLLKTLQKLDEYLNSP Number of specific fragments extracted= 5 number of extra gaps= 0 total=123 Number of alignments=24 # 2aheA read from 2aheA/merged-good-all-a2m # found chain 2aheA in template set Warning: unaligning (T0352)A108 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2aheA)S174 T0352 4 :HDRVRLQLQALEALL 2aheA 141 :ERGLLKTLQKLDEYL T0352 105 :ADD 2aheA 156 :NSP Number of specific fragments extracted= 2 number of extra gaps= 0 total=125 Number of alignments=25 # 2aheA read from 2aheA/merged-good-all-a2m # found chain 2aheA in template set Warning: unaligning (T0352)A108 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2aheA)S174 T0352 13 :ALEALLREH 2aheA 90 :KIEEFLEEV T0352 22 :QHWRNDEPQPHQFNS 2aheA 102 :PKYLKLSPKHPESNT T0352 55 :LIPRMHDLLDNKQ 2aheA 121 :IFAKFSAYIKNSR T0352 70 :PGA 2aheA 134 :PEA T0352 86 :DHPQRALILAELEKLDALFADD 2aheA 137 :NEALERGLLKTLQKLDEYLNSP Number of specific fragments extracted= 5 number of extra gaps= 0 total=130 Number of alignments=26 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sz2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1sz2A expands to /projects/compbio/data/pdb/1sz2.pdb.gz 1sz2A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 533, because occupancy 0.500 <= existing 0.500 in 1sz2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 535, because occupancy 0.500 <= existing 0.500 in 1sz2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 537, because occupancy 0.500 <= existing 0.500 in 1sz2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 539, because occupancy 0.500 <= existing 0.500 in 1sz2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 652, because occupancy 0.500 <= existing 0.500 in 1sz2A Skipped atom 654, because occupancy 0.500 <= existing 0.500 in 1sz2A Skipped atom 656, because occupancy 0.500 <= existing 0.500 in 1sz2A Skipped atom 658, because occupancy 0.500 <= existing 0.500 in 1sz2A Skipped atom 660, because occupancy 0.500 <= existing 0.500 in 1sz2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1311, because occupancy 0.500 <= existing 0.500 in 1sz2A Skipped atom 1313, because occupancy 0.500 <= existing 0.500 in 1sz2A Skipped atom 1315, because occupancy 0.500 <= existing 0.500 in 1sz2A Skipped atom 1317, because occupancy 0.500 <= existing 0.500 in 1sz2A Skipped atom 1319, because occupancy 0.500 <= existing 0.500 in 1sz2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1825, because occupancy 0.500 <= existing 0.500 in 1sz2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1827, because occupancy 0.500 <= existing 0.500 in 1sz2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1829, because occupancy 0.500 <= existing 0.500 in 1sz2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1831, because occupancy 0.500 <= existing 0.500 in 1sz2A Skipped atom 2309, because occupancy 0.500 <= existing 0.500 in 1sz2A Skipped atom 2311, because occupancy 0.500 <= existing 0.500 in 1sz2A Skipped atom 2313, because occupancy 0.500 <= existing 0.500 in 1sz2A Skipped atom 2315, because occupancy 0.500 <= existing 0.500 in 1sz2A # T0352 read from 1sz2A/merged-good-all-a2m # 1sz2A read from 1sz2A/merged-good-all-a2m # adding 1sz2A to template set # found chain 1sz2A in template set T0352 12 :QALEALLREH 1sz2A 171 :AIILEILRAE T0352 26 :NDEPQP 1sz2A 181 :IGHVSA T0352 42 :MDTMEPL 1sz2A 187 :ERVLSGP T0352 54 :VLIPRMHDLLDNKQPLPGAFAVAPYYEMALATDHPQRALILAELEKL 1sz2A 194 :GLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSLFCVI Number of specific fragments extracted= 4 number of extra gaps= 0 total=134 Number of alignments=27 # 1sz2A read from 1sz2A/merged-good-all-a2m # found chain 1sz2A in template set T0352 5 :DRVR 1sz2A 168 :EEEA T0352 13 :ALEALLREH 1sz2A 172 :IILEILRAE T0352 26 :NDEPQPH 1sz2A 181 :IGHVSAE T0352 43 :DTMEPL 1sz2A 188 :RVLSGP T0352 54 :VLIPRMHDLLDNKQPLPGAFAVAPYYEMALATDHPQRALILAELEKL 1sz2A 194 :GLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSLFCVI Number of specific fragments extracted= 5 number of extra gaps= 0 total=139 Number of alignments=28 # 1sz2A read from 1sz2A/merged-good-all-a2m # found chain 1sz2A in template set T0352 12 :QALEALLREH 1sz2A 171 :AIILEILRAE T0352 36 :STQPFFMDTMEPL 1sz2A 181 :IGHVSAERVLSGP T0352 54 :VLIPRMHDLLDNKQPLPGAFAVAPYYEMALATDHPQRALILAELEKLD 1sz2A 194 :GLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSLFCVIM Number of specific fragments extracted= 3 number of extra gaps= 0 total=142 Number of alignments=29 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jhgA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0352 read from 1jhgA/merged-good-all-a2m # 1jhgA read from 1jhgA/merged-good-all-a2m # found chain 1jhgA in training set T0352 5 :DRVRLQLQALEALLR 1jhgA 14 :QRHQEWLRFVDLLKN T0352 20 :EHQH 1jhgA 31 :QNDL T0352 31 :PHQFN 1jhgA 36 :LPLLN T0352 45 :MEPLE 1jhgA 43 :LTPDE T0352 60 :HDLLDNK 1jhgA 48 :REALGTR T0352 76 :APYYEMALATDH 1jhgA 55 :VRIIEELLRGEM T0352 89 :QRALILA 1jhgA 67 :SQRELKN T0352 96 :ELEKLDALFADDASLEH 1jhgA 81 :TITRGSNSLKAAPVELR Number of specific fragments extracted= 8 number of extra gaps= 0 total=150 Number of alignments=30 # 1jhgA read from 1jhgA/merged-good-all-a2m # found chain 1jhgA in training set T0352 4 :HDRVRLQLQALEALLREHQH 1jhgA 15 :RHQEWLRFVDLLKNAYQNDL T0352 47 :PLEWLQWVLIPRMHDLLDNK 1jhgA 35 :HLPLLNLMLTPDEREALGTR T0352 76 :APYYEMALATDHP 1jhgA 55 :VRIIEELLRGEMS T0352 90 :RALILA 1jhgA 68 :QRELKN T0352 96 :ELEKLDALFADDASLEH 1jhgA 81 :TITRGSNSLKAAPVELR Number of specific fragments extracted= 5 number of extra gaps= 0 total=155 Number of alignments=31 # 1jhgA read from 1jhgA/merged-good-all-a2m # found chain 1jhgA in training set T0352 4 :HDRVRLQLQALEALLR 1jhgA 13 :EQRHQEWLRFVDLLKN T0352 20 :EHQH 1jhgA 31 :QNDL T0352 31 :PHQFNS 1jhgA 36 :LPLLNL T0352 44 :TMEPLE 1jhgA 42 :MLTPDE T0352 60 :HDLLDN 1jhgA 48 :REALGT T0352 76 :APYYEMALATDHPQRALILA 1jhgA 54 :RVRIIEELLRGEMSQRELKN T0352 96 :ELEKLDALFADDASLEHH 1jhgA 81 :TITRGSNSLKAAPVELRQ Number of specific fragments extracted= 7 number of extra gaps= 0 total=162 Number of alignments=32 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b4pA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0352 read from 1b4pA/merged-good-all-a2m # 1b4pA read from 1b4pA/merged-good-all-a2m # found chain 1b4pA in training set Warning: unaligning (T0352)V7 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1b4pA)M104 Warning: unaligning (T0352)R8 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1b4pA)M104 Warning: unaligning (T0352)F73 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1b4pA)L158 Warning: unaligning (T0352)A74 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1b4pA)L158 T0352 4 :HDR 1b4pA 100 :ENQ T0352 9 :LQLQALEALLR 1b4pA 105 :DTRLQLAMVCY T0352 33 :QFNS 1b4pA 118 :DFER T0352 46 :EPLEWLQ 1b4pA 122 :KKPEYLE T0352 55 :LIPRMHDLLD 1b4pA 130 :LPEKMKLYSE T0352 65 :NKQPL 1b4pA 142 :GKQPW T0352 70 :PGA 1b4pA 149 :GNK T0352 75 :VAPYYEMALA 1b4pA 159 :VYDVLDQHRI T0352 85 :TDHPQRALILAELE 1b4pA 175 :DAFPNLKDFVARFE T0352 99 :KLDALFADDA 1b4pA 192 :KISDYMKSGR Number of specific fragments extracted= 10 number of extra gaps= 2 total=172 Number of alignments=33 # 1b4pA read from 1b4pA/merged-good-all-a2m # found chain 1b4pA in training set Warning: unaligning (T0352)V7 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1b4pA)M104 Warning: unaligning (T0352)R8 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1b4pA)M104 Warning: unaligning (T0352)F73 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1b4pA)L158 Warning: unaligning (T0352)A74 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1b4pA)L158 T0352 5 :DR 1b4pA 101 :NQ T0352 9 :LQLQALEALLREHQ 1b4pA 105 :DTRLQLAMVCYSPD T0352 34 :F 1b4pA 119 :F T0352 46 :EPLEWLQ 1b4pA 122 :KKPEYLE T0352 54 :VLIPRMHDLLD 1b4pA 129 :GLPEKMKLYSE T0352 65 :NKQPL 1b4pA 142 :GKQPW T0352 71 :G 1b4pA 150 :N T0352 72 :A 1b4pA 156 :D T0352 75 :VAPYYEMALA 1b4pA 159 :VYDVLDQHRI T0352 85 :TDHPQRALILAELE 1b4pA 175 :DAFPNLKDFVARFE T0352 99 :KLDALFADD 1b4pA 192 :KISDYMKSG Number of specific fragments extracted= 11 number of extra gaps= 2 total=183 Number of alignments=34 # 1b4pA read from 1b4pA/merged-good-all-a2m # found chain 1b4pA in training set Warning: unaligning (T0352)V7 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1b4pA)M104 Warning: unaligning (T0352)R8 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1b4pA)M104 T0352 4 :HDR 1b4pA 100 :ENQ T0352 9 :LQLQALEALLR 1b4pA 105 :DTRLQLAMVCY T0352 29 :PQPHQF 1b4pA 117 :PDFERK T0352 47 :PLEWLQ 1b4pA 123 :KPEYLE T0352 55 :LIPRMHDLLD 1b4pA 130 :LPEKMKLYSE T0352 65 :NKQPL 1b4pA 142 :GKQPW T0352 70 :PGAFA 1b4pA 149 :GNKIT T0352 75 :VAPYYEMALA 1b4pA 159 :VYDVLDQHRI T0352 85 :TDHPQRALILAELE 1b4pA 175 :DAFPNLKDFVARFE T0352 99 :KLDALFADD 1b4pA 192 :KISDYMKSG Number of specific fragments extracted= 10 number of extra gaps= 1 total=193 Number of alignments=35 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zv1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zv1A expands to /projects/compbio/data/pdb/1zv1.pdb.gz 1zv1A:Skipped atom 58, because occupancy 0.300 <= existing 0.700 in 1zv1A Skipped atom 60, because occupancy 0.300 <= existing 0.700 in 1zv1A Skipped atom 62, because occupancy 0.300 <= existing 0.700 in 1zv1A Skipped atom 64, because occupancy 0.300 <= existing 0.700 in 1zv1A Skipped atom 66, because occupancy 0.300 <= existing 0.700 in 1zv1A Skipped atom 68, because occupancy 0.300 <= existing 0.700 in 1zv1A Skipped atom 70, because occupancy 0.300 <= existing 0.700 in 1zv1A Skipped atom 93, because occupancy 0.500 <= existing 0.500 in 1zv1A Skipped atom 95, because occupancy 0.500 <= existing 0.500 in 1zv1A Skipped atom 97, because occupancy 0.500 <= existing 0.500 in 1zv1A Skipped atom 194, because occupancy 0.300 <= existing 0.700 in 1zv1A Skipped atom 196, because occupancy 0.300 <= existing 0.700 in 1zv1A Skipped atom 198, because occupancy 0.300 <= existing 0.700 in 1zv1A Skipped atom 271, because occupancy 0.300 <= existing 0.700 in 1zv1A Skipped atom 273, because occupancy 0.300 <= existing 0.700 in 1zv1A Skipped atom 275, because occupancy 0.300 <= existing 0.700 in 1zv1A # T0352 read from 1zv1A/merged-good-all-a2m # 1zv1A read from 1zv1A/merged-good-all-a2m # adding 1zv1A to template set # found chain 1zv1A in template set T0352 5 :DRVRLQLQALEALL 1zv1A 7 :DVFLDYCQKLLEKF T0352 28 :EPQPHQ 1zv1A 21 :RYPWEL T0352 56 :IPRMHDLLDN 1zv1A 27 :MPLMYVILKD T0352 85 :TD 1zv1A 37 :AD T0352 88 :PQRALILAELEKLDALFADDASLEH 1zv1A 39 :ANIEEASRRIEEGQYVVNEYSRQHN Number of specific fragments extracted= 5 number of extra gaps= 0 total=198 Number of alignments=36 # 1zv1A read from 1zv1A/merged-good-all-a2m # found chain 1zv1A in template set Warning: unaligning (T0352)H4 because first residue in template chain is (1zv1A)Q6 T0352 5 :DRVRLQLQALEAL 1zv1A 7 :DVFLDYCQKLLEK T0352 27 :DEPQPHQF 1zv1A 20 :FRYPWELM T0352 57 :PRMHDL 1zv1A 28 :PLMYVI T0352 83 :LATDHPQRALILAELEKLDALFADDASLEH 1zv1A 34 :LKDADANIEEASRRIEEGQYVVNEYSRQHN Number of specific fragments extracted= 4 number of extra gaps= 0 total=202 Number of alignments=37 # 1zv1A read from 1zv1A/merged-good-all-a2m # found chain 1zv1A in template set T0352 55 :LIPRMHDLLD 1zv1A 9 :FLDYCQKLLE T0352 65 :NK 1zv1A 20 :FR T0352 69 :LPGAF 1zv1A 22 :YPWEL T0352 76 :APYYEMALATDHPQRALILAELEKLDALFADDAS 1zv1A 27 :MPLMYVILKDADANIEEASRRIEEGQYVVNEYSR Number of specific fragments extracted= 4 number of extra gaps= 0 total=206 Number of alignments=38 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jpaA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1jpaA expands to /projects/compbio/data/pdb/1jpa.pdb.gz 1jpaA:# T0352 read from 1jpaA/merged-good-all-a2m # 1jpaA read from 1jpaA/merged-good-all-a2m # adding 1jpaA to template set # found chain 1jpaA in template set Warning: unaligning (T0352)H112 because last residue in template chain is (1jpaA)A900 T0352 57 :PRMHDLLDNKQPLPGAFAVAPYYEMALA 1jpaA 841 :QDVINAIEQDYRLPPPMDCPSALHQLML T0352 85 :TDHPQRALILAELEK 1jpaA 876 :NHRPKFGQIVNTLDK T0352 103 :LFADDASLE 1jpaA 891 :MIRNPNSLK Number of specific fragments extracted= 3 number of extra gaps= 0 total=209 Number of alignments=39 # 1jpaA read from 1jpaA/merged-good-all-a2m # found chain 1jpaA in template set Warning: unaligning (T0352)H112 because last residue in template chain is (1jpaA)A900 T0352 57 :PRMHDLLDNKQPLPGAFAVAPYYEMALA 1jpaA 841 :QDVINAIEQDYRLPPPMDCPSALHQLML T0352 85 :TDHPQRALILAELEKLDALFADDASLE 1jpaA 873 :KDRNHRPKFGQIVNTLDKMIRNPNSLK Number of specific fragments extracted= 2 number of extra gaps= 0 total=211 Number of alignments=40 # 1jpaA read from 1jpaA/merged-good-all-a2m # found chain 1jpaA in template set Warning: unaligning (T0352)H112 because last residue in template chain is (1jpaA)A900 T0352 57 :PRMHDLLDNKQPLPGAFAVAPYYEMALAT 1jpaA 841 :QDVINAIEQDYRLPPPMDCPSALHQLMLD T0352 86 :DHPQ 1jpaA 874 :DRNH T0352 90 :RALILAELE 1jpaA 881 :FGQIVNTLD T0352 102 :ALFADDASLE 1jpaA 890 :KMIRNPNSLK Number of specific fragments extracted= 4 number of extra gaps= 0 total=215 Number of alignments=41 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zejA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zejA expands to /projects/compbio/data/pdb/1zej.pdb.gz 1zejA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 93, because occupancy 0.500 <= existing 0.500 in 1zejA Skipped atom 95, because occupancy 0.500 <= existing 0.500 in 1zejA Skipped atom 97, because occupancy 0.500 <= existing 0.500 in 1zejA Skipped atom 99, because occupancy 0.500 <= existing 0.500 in 1zejA Skipped atom 101, because occupancy 0.500 <= existing 0.500 in 1zejA Skipped atom 103, because occupancy 0.500 <= existing 0.500 in 1zejA Skipped atom 105, because occupancy 0.500 <= existing 0.500 in 1zejA Skipped atom 489, because occupancy 0.500 <= existing 0.500 in 1zejA Skipped atom 491, because occupancy 0.500 <= existing 0.500 in 1zejA Skipped atom 493, because occupancy 0.500 <= existing 0.500 in 1zejA Skipped atom 495, because occupancy 0.500 <= existing 0.500 in 1zejA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 613, because occupancy 0.500 <= existing 0.500 in 1zejA Skipped atom 615, because occupancy 0.500 <= existing 0.500 in 1zejA Skipped atom 617, because occupancy 0.500 <= existing 0.500 in 1zejA Skipped atom 651, because occupancy 0.500 <= existing 0.500 in 1zejA Skipped atom 653, because occupancy 0.500 <= existing 0.500 in 1zejA Skipped atom 655, because occupancy 0.500 <= existing 0.500 in 1zejA Skipped atom 670, because occupancy 0.500 <= existing 0.500 in 1zejA Skipped atom 672, because occupancy 0.500 <= existing 0.500 in 1zejA Skipped atom 674, because occupancy 0.500 <= existing 0.500 in 1zejA Skipped atom 676, because occupancy 0.500 <= existing 0.500 in 1zejA Skipped atom 678, because occupancy 0.500 <= existing 0.500 in 1zejA Skipped atom 680, because occupancy 0.500 <= existing 0.500 in 1zejA Skipped atom 682, because occupancy 0.500 <= existing 0.500 in 1zejA Skipped atom 849, because occupancy 0.500 <= existing 0.500 in 1zejA Skipped atom 851, because occupancy 0.500 <= existing 0.500 in 1zejA Skipped atom 853, because occupancy 0.500 <= existing 0.500 in 1zejA Skipped atom 855, because occupancy 0.500 <= existing 0.500 in 1zejA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1097, because occupancy 0.500 <= existing 0.500 in 1zejA Skipped atom 1099, because occupancy 0.500 <= existing 0.500 in 1zejA Skipped atom 1360, because occupancy 0.500 <= existing 0.500 in 1zejA Skipped atom 1362, because occupancy 0.500 <= existing 0.500 in 1zejA Skipped atom 1382, because occupancy 0.500 <= existing 0.500 in 1zejA Skipped atom 1384, because occupancy 0.500 <= existing 0.500 in 1zejA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1746, because occupancy 0.500 <= existing 0.500 in 1zejA Skipped atom 1748, because occupancy 0.500 <= existing 0.500 in 1zejA Skipped atom 2112, because occupancy 0.500 <= existing 0.500 in 1zejA Skipped atom 2114, because occupancy 0.500 <= existing 0.500 in 1zejA Skipped atom 2116, because occupancy 0.500 <= existing 0.500 in 1zejA Skipped atom 2118, because occupancy 0.500 <= existing 0.500 in 1zejA Skipped atom 2120, because occupancy 0.500 <= existing 0.500 in 1zejA Skipped atom 2122, because occupancy 0.500 <= existing 0.500 in 1zejA Skipped atom 2124, because occupancy 0.500 <= existing 0.500 in 1zejA # T0352 read from 1zejA/merged-good-all-a2m # 1zejA read from 1zejA/merged-good-all-a2m # adding 1zejA to template set # found chain 1zejA in template set Warning: unaligning (T0352)H114 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1zejA)G229 Warning: unaligning (T0352)H115 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1zejA)G229 T0352 10 :QLQALEALLREHQ 1zejA 140 :TVAFVEGFLRELG T0352 36 :STQPFFMDTM 1zejA 153 :KEVVVCKGQS T0352 47 :PLEWLQWVLIPRMHDLLDNKQP 1zejA 163 :LVNRFNAAVLSEASRMIEEGVR T0352 77 :PYYEMALATDHPQRALILAELEK 1zejA 186 :EDVDRVWKHHLGLLYTLFGPLGN T0352 100 :LDALFADDASLEHH 1zejA 214 :LDVAYYASLYLYKR T0352 116 :H 1zejA 230 :D Number of specific fragments extracted= 6 number of extra gaps= 1 total=221 Number of alignments=42 # 1zejA read from 1zejA/merged-good-all-a2m # found chain 1zejA in template set Warning: unaligning (T0352)H114 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1zejA)G229 T0352 10 :QLQALEALLREHQ 1zejA 140 :TVAFVEGFLRELG T0352 40 :FFMDTMEPLEWLQWVLIPRMHDLLDNKQP 1zejA 156 :VVCKGQSLVNRFNAAVLSEASRMIEEGVR T0352 76 :APYYEMALATDHPQRALILAELEK 1zejA 185 :AEDVDRVWKHHLGLLYTLFGPLGN T0352 100 :LDALFADDASLEHH 1zejA 214 :LDVAYYASLYLYKR Number of specific fragments extracted= 4 number of extra gaps= 1 total=225 Number of alignments=43 # 1zejA read from 1zejA/merged-good-all-a2m # found chain 1zejA in template set T0352 11 :LQALEALLREHQ 1zejA 141 :VAFVEGFLRELG T0352 40 :FFMDTMEPLEWLQWVLIPRMHDLLDNKQP 1zejA 156 :VVCKGQSLVNRFNAAVLSEASRMIEEGVR T0352 77 :PYYEMALATDHPQRALILAELEKLD 1zejA 186 :EDVDRVWKHHLGLLYTLFGPLGNLD Number of specific fragments extracted= 3 number of extra gaps= 0 total=228 Number of alignments=44 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vj5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vj5A expands to /projects/compbio/data/pdb/1vj5.pdb.gz 1vj5A:# T0352 read from 1vj5A/merged-good-all-a2m # 1vj5A read from 1vj5A/merged-good-all-a2m # adding 1vj5A to template set # found chain 1vj5A in template set T0352 43 :DTMEPLEW 1vj5A 56 :GEITLSQW T0352 56 :IPRMHDLL 1vj5A 64 :IPLMEENC T0352 64 :DNKQPLPGAFAVAPYYEMALATD 1vj5A 77 :TAKVCLPKNFSIKEIFDKAISAR T0352 91 :ALILAELEKLD 1vj5A 103 :RPMLQAALMLR Number of specific fragments extracted= 4 number of extra gaps= 0 total=232 Number of alignments=45 # 1vj5A read from 1vj5A/merged-good-all-a2m # found chain 1vj5A in template set T0352 43 :DTMEPLEW 1vj5A 56 :GEITLSQW T0352 56 :IPRMHDLL 1vj5A 64 :IPLMEENC T0352 64 :DNKQPLPGAFAVAPYYEMALATD 1vj5A 77 :TAKVCLPKNFSIKEIFDKAISAR T0352 88 :PQRALILAELEKLD 1vj5A 100 :KINRPMLQAALMLR Number of specific fragments extracted= 4 number of extra gaps= 0 total=236 Number of alignments=46 # 1vj5A read from 1vj5A/merged-good-all-a2m # found chain 1vj5A in template set T0352 43 :DTMEPLEW 1vj5A 56 :GEITLSQW T0352 56 :IPRMHDLL 1vj5A 64 :IPLMEENC T0352 64 :DNKQPLPGAFAVAPYYEMALATD 1vj5A 77 :TAKVCLPKNFSIKEIFDKAISAR T0352 90 :RALILAELEKL 1vj5A 102 :NRPMLQAALML Number of specific fragments extracted= 4 number of extra gaps= 0 total=240 Number of alignments=47 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ufaA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ufaA expands to /projects/compbio/data/pdb/1ufa.pdb.gz 1ufaA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0352 read from 1ufaA/merged-good-all-a2m # 1ufaA read from 1ufaA/merged-good-all-a2m # adding 1ufaA to template set # found chain 1ufaA in template set T0352 50 :W 1ufaA 36 :Y T0352 53 :WVLIPRMHDLLDNKQPLPGAFAVAPYYEMALATD 1ufaA 37 :LPLIRVLERLRAEGVEAPFTLGITPILAEQLADA T0352 88 :PQRALILAELEKLDALFADDASLEHHH 1ufaA 71 :RIKEGFWAYAKDRLERAQGDYQRYRGT Number of specific fragments extracted= 3 number of extra gaps= 0 total=243 Number of alignments=48 # 1ufaA read from 1ufaA/merged-good-all-a2m # found chain 1ufaA in template set T0352 53 :WVLIPRMHDLLDNKQPLPGAFAVAPYYEMALA 1ufaA 37 :LPLIRVLERLRAEGVEAPFTLGITPILAEQLA T0352 86 :DHPQRALILAELEKLDALFADDASLEHHH 1ufaA 69 :DARIKEGFWAYAKDRLERAQGDYQRYRGT Number of specific fragments extracted= 2 number of extra gaps= 0 total=245 Number of alignments=49 # 1ufaA read from 1ufaA/merged-good-all-a2m # found chain 1ufaA in template set T0352 53 :WVLIPRMHDLLDNKQPLPGAFAVAPYYEMALA 1ufaA 37 :LPLIRVLERLRAEGVEAPFTLGITPILAEQLA T0352 86 :DHPQRALILAELEKLDALFADD 1ufaA 69 :DARIKEGFWAYAKDRLERAQGD Number of specific fragments extracted= 2 number of extra gaps= 0 total=247 Number of alignments=50 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mzbA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0352 read from 1mzbA/merged-good-all-a2m # 1mzbA read from 1mzbA/merged-good-all-a2m # found chain 1mzbA in training set Warning: unaligning (T0352)L69 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1mzbA)Q30 Warning: unaligning (T0352)G71 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1mzbA)Q30 T0352 16 :ALLREHQH 1mzbA 5 :SELRKAGL T0352 28 :EP 1mzbA 13 :KV T0352 44 :TMEPLEWLQW 1mzbA 15 :TLPRVKILQM T0352 63 :LD 1mzbA 25 :LD T0352 68 :P 1mzbA 27 :S T0352 72 :AFAVAPYYEMALATD 1mzbA 31 :RHMSAEDVYKALMEA T0352 87 :HPQRALILAELEKLDAL 1mzbA 48 :DVGLATVYRVLTQFEAA Number of specific fragments extracted= 7 number of extra gaps= 0 total=254 Number of alignments=51 # 1mzbA read from 1mzbA/merged-good-all-a2m # found chain 1mzbA in training set Warning: unaligning (T0352)L69 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1mzbA)Q30 Warning: unaligning (T0352)G71 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1mzbA)Q30 T0352 16 :ALLREHQH 1mzbA 5 :SELRKAGL T0352 28 :EP 1mzbA 13 :KV T0352 44 :TMEPL 1mzbA 15 :TLPRV T0352 58 :RMHDLLD 1mzbA 20 :KILQMLD T0352 68 :P 1mzbA 27 :S T0352 72 :AFAVAPYYEMALATD 1mzbA 31 :RHMSAEDVYKALMEA T0352 87 :HPQRALILAELEKLDAL 1mzbA 48 :DVGLATVYRVLTQFEAA Number of specific fragments extracted= 7 number of extra gaps= 0 total=261 Number of alignments=52 # 1mzbA read from 1mzbA/merged-good-all-a2m # found chain 1mzbA in training set Warning: unaligning (T0352)L69 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1mzbA)Q30 Warning: unaligning (T0352)G71 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1mzbA)Q30 T0352 16 :ALLREHQH 1mzbA 5 :SELRKAGL T0352 28 :EPQPH 1mzbA 13 :KVTLP T0352 47 :P 1mzbA 18 :R T0352 57 :PRMHDLLD 1mzbA 19 :VKILQMLD T0352 68 :P 1mzbA 27 :S T0352 72 :AFAVAPYYEMALATDH 1mzbA 31 :RHMSAEDVYKALMEAG T0352 89 :QRALILAELEKLDAL 1mzbA 50 :GLATVYRVLTQFEAA Number of specific fragments extracted= 7 number of extra gaps= 0 total=268 Number of alignments=53 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2furA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2furA expands to /projects/compbio/data/pdb/2fur.pdb.gz 2furA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 253, because occupancy 0.500 <= existing 0.500 in 2furA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 255, because occupancy 0.500 <= existing 0.500 in 2furA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 259, because occupancy 0.500 <= existing 0.500 in 2furA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 265, because occupancy 0.500 <= existing 0.500 in 2furA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 267, because occupancy 0.500 <= existing 0.500 in 2furA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 271, because occupancy 0.500 <= existing 0.500 in 2furA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 709, because occupancy 0.500 <= existing 0.500 in 2furA Skipped atom 711, because occupancy 0.500 <= existing 0.500 in 2furA Skipped atom 713, because occupancy 0.500 <= existing 0.500 in 2furA Skipped atom 715, because occupancy 0.500 <= existing 0.500 in 2furA Skipped atom 717, because occupancy 0.500 <= existing 0.500 in 2furA Skipped atom 719, because occupancy 0.500 <= existing 0.500 in 2furA Skipped atom 721, because occupancy 0.500 <= existing 0.500 in 2furA Skipped atom 953, because occupancy 0.500 <= existing 0.500 in 2furA Skipped atom 955, because occupancy 0.500 <= existing 0.500 in 2furA Skipped atom 957, because occupancy 0.500 <= existing 0.500 in 2furA Skipped atom 959, because occupancy 0.500 <= existing 0.500 in 2furA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1323, because occupancy 0.500 <= existing 0.500 in 2furA Skipped atom 1325, because occupancy 0.500 <= existing 0.500 in 2furA Skipped atom 1327, because occupancy 0.500 <= existing 0.500 in 2furA Skipped atom 1329, because occupancy 0.500 <= existing 0.500 in 2furA Skipped atom 1331, because occupancy 0.500 <= existing 0.500 in 2furA Skipped atom 1347, because occupancy 0.500 <= existing 0.500 in 2furA Skipped atom 1349, because occupancy 0.500 <= existing 0.500 in 2furA Skipped atom 1351, because occupancy 0.500 <= existing 0.500 in 2furA # T0352 read from 2furA/merged-good-all-a2m # 2furA read from 2furA/merged-good-all-a2m # adding 2furA to template set # found chain 2furA in template set T0352 1 :MTTHDRVRLQLQALEALLREHQHWRNDEPQPHQFNST 2furA 113 :IDDTEKKIEVFRLLTEKLVKGRWDNSIKPSYEDLNGV Number of specific fragments extracted= 1 number of extra gaps= 0 total=269 Number of alignments=54 # 2furA read from 2furA/merged-good-all-a2m # found chain 2furA in template set T0352 1 :MTTHDRVRLQLQALEALLREHQHWRNDEPQPHQFNST 2furA 113 :IDDTEKKIEVFRLLTEKLVKGRWDNSIKPSYEDLNGV Number of specific fragments extracted= 1 number of extra gaps= 0 total=270 Number of alignments=55 # 2furA read from 2furA/merged-good-all-a2m # found chain 2furA in template set T0352 1 :MTTHDRVRLQLQALEALLREHQHWRNDEPQPHQFNSTQPFFM 2furA 113 :IDDTEKKIEVFRLLTEKLVKGRWDNSIKPSYEDLNGVFVFAV Number of specific fragments extracted= 1 number of extra gaps= 0 total=271 Number of alignments=56 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zboA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zboA expands to /projects/compbio/data/pdb/1zbo.pdb.gz 1zboA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0352 read from 1zboA/merged-good-all-a2m # 1zboA read from 1zboA/merged-good-all-a2m # adding 1zboA to template set # found chain 1zboA in template set Warning: unaligning (T0352)D106 because last residue in template chain is (1zboA)A198 T0352 5 :DRVRLQLQALEALLREHQ 1zboA 125 :ARSASALGRLIARLQREG T0352 29 :PQPHQFNSTQPFFMDT 1zboA 143 :VPPHIMPMAAPFRLDD T0352 48 :LEWLQWVLIPR 1zboA 159 :CGWVADRWAEM T0352 67 :QPLP 1zboA 170 :LSLP T0352 76 :APYYEMALATD 1zboA 174 :PADKARLLLLP T0352 93 :ILAELEKLDALFA 1zboA 185 :PLDRLREIDAVLA Number of specific fragments extracted= 6 number of extra gaps= 0 total=277 Number of alignments=57 # 1zboA read from 1zboA/merged-good-all-a2m # found chain 1zboA in template set Warning: unaligning (T0352)D106 because last residue in template chain is (1zboA)A198 T0352 1 :MTTHDRVRLQLQALEALLREHQH 1zboA 118 :LEVPPELARSASALGRLIARLQR T0352 27 :DEPQPHQFNSTQPFFMDTM 1zboA 141 :EGVPPHIMPMAAPFRLDDC T0352 49 :EWLQWVLIPR 1zboA 160 :GWVADRWAEM T0352 67 :QPLP 1zboA 170 :LSLP T0352 76 :APYYEMALATD 1zboA 174 :PADKARLLLLP T0352 93 :ILAELEKLDALFA 1zboA 185 :PLDRLREIDAVLA Number of specific fragments extracted= 6 number of extra gaps= 0 total=283 Number of alignments=58 # 1zboA read from 1zboA/merged-good-all-a2m # found chain 1zboA in template set Warning: unaligning (T0352)D106 because last residue in template chain is (1zboA)A198 T0352 5 :DRVRLQLQALEALLREHQH 1zboA 125 :ARSASALGRLIARLQREGV T0352 30 :QPHQFNSTQPFFMDT 1zboA 144 :PPHIMPMAAPFRLDD T0352 48 :LEWLQWVLIPR 1zboA 159 :CGWVADRWAEM T0352 67 :QPLP 1zboA 170 :LSLP T0352 76 :APYYEMALATD 1zboA 174 :PADKARLLLLP T0352 93 :ILAELEKLDALFA 1zboA 185 :PLDRLREIDAVLA Number of specific fragments extracted= 6 number of extra gaps= 0 total=289 Number of alignments=59 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w1oA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0352 read from 1w1oA/merged-good-all-a2m # 1w1oA read from 1w1oA/merged-good-all-a2m # found chain 1w1oA in training set Warning: unaligning (T0352)P88 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1w1oA)N465 T0352 10 :QLQALEALLREHQHWRNDEPQ 1w1oA 377 :RVHGEEVALNKLGLWRVPHPW T0352 31 :PHQ 1w1oA 404 :RSR T0352 47 :PLEWLQWVL 1w1oA 407 :IADFDRGVF T0352 65 :NKQPLPGAFAVAP 1w1oA 420 :QGTDIVGPLIVYP T0352 82 :ALATD 1w1oA 437 :MWDDG T0352 89 :QRALILAELEKLDALFAD 1w1oA 466 :DLARLQEQNRRILRFCDL Number of specific fragments extracted= 6 number of extra gaps= 0 total=295 Number of alignments=60 # 1w1oA read from 1w1oA/merged-good-all-a2m # found chain 1w1oA in training set Warning: unaligning (T0352)P88 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1w1oA)N465 T0352 89 :QRALILAELEKLDALFAD 1w1oA 466 :DLARLQEQNRRILRFCDL Number of specific fragments extracted= 1 number of extra gaps= 0 total=296 # 1w1oA read from 1w1oA/merged-good-all-a2m # found chain 1w1oA in training set Warning: unaligning (T0352)T2 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1w1oA)N465 T0352 3 :THDRVRLQLQALEALLREHQH 1w1oA 466 :DLARLQEQNRRILRFCDLAGI T0352 39 :PFFMDTMEPLEWLQWV 1w1oA 490 :TYLARHTDRSDWVRHF T0352 86 :DHPQRALILAELEKL 1w1oA 506 :GAAKWNRFVEMKNKY Number of specific fragments extracted= 3 number of extra gaps= 0 total=299 Number of alignments=61 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1trrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1trrA expands to /projects/compbio/data/pdb/1trr.pdb.gz 1trrA:# T0352 read from 1trrA/merged-good-all-a2m # 1trrA read from 1trrA/merged-good-all-a2m # adding 1trrA to template set # found chain 1trrA in template set T0352 3 :THDRVRLQLQALEALLREHQH 1trrA 14 :QRHEEWLRFVDLLKNAYQNDL T0352 34 :FN 1trrA 38 :LL T0352 45 :MEPLE 1trrA 43 :LTPDE T0352 60 :HDLLDNK 1trrA 48 :REALGTR T0352 76 :APYYEMALATD 1trrA 55 :VRIVEELLRGE T0352 88 :PQRALILA 1trrA 66 :MSQRELKN T0352 96 :ELEKLDALFADDASLEH 1trrA 81 :TITRGSNSLKAAPVELR Number of specific fragments extracted= 7 number of extra gaps= 0 total=306 Number of alignments=62 # 1trrA read from 1trrA/merged-good-all-a2m # found chain 1trrA in template set T0352 4 :HDRVRLQLQALEALLREHQH 1trrA 15 :RHEEWLRFVDLLKNAYQNDL T0352 47 :PLEWLQWVLIPRMHDLLDNK 1trrA 35 :HLPLLNLMLTPDEREALGTR T0352 76 :APYYEMALATDHP 1trrA 55 :VRIVEELLRGEMS T0352 90 :RALILA 1trrA 68 :QRELKN T0352 96 :ELEKLDALFADDASLE 1trrA 81 :TITRGSNSLKAAPVEL Number of specific fragments extracted= 5 number of extra gaps= 0 total=311 Number of alignments=63 # 1trrA read from 1trrA/merged-good-all-a2m # found chain 1trrA in template set T0352 3 :THDRVRLQLQALEALLREHQHW 1trrA 14 :QRHEEWLRFVDLLKNAYQNDLH T0352 31 :PHQFN 1trrA 36 :LPLLN T0352 44 :TMEPLE 1trrA 42 :MLTPDE T0352 60 :HDLLDNK 1trrA 48 :REALGTR T0352 77 :PYYEMALATDHPQRALILA 1trrA 55 :VRIVEELLRGEMSQRELKN T0352 96 :ELEKLDALFADDASLEH 1trrA 81 :TITRGSNSLKAAPVELR Number of specific fragments extracted= 6 number of extra gaps= 0 total=317 Number of alignments=64 # command:Using radius: 8.0000 Alignment mode NUMB_ALIGNS: 64 Adding 1104 constraints to all.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all.constraints maxweight: 1.0000 Optimizing... Probability sum: -196.0129, CN propb: -196.0129 weights: 0.2584 constraints: 198 # command:Found ConstraintSet # PrintContacts align.constraints_v3 Number of constraints in align.constraints 198 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_v3 Number of constraints in align.constraints.bonus 198 # command:Found ConstraintSet # PrintContacts rejected.constraints_v3 Number of constraints in rejected.constraints 906 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_v3 Number of constraints in rejected.constraints.bonus 906 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_v3 Number of constraints in noncontact.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_v3 Number of constraints in noncontact.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_v3 Number of constraints in all.constraints 1104 # command: