# 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:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0352//projects/compbio/experiments/protein-predict/casp7/T0352/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0352//projects/compbio/experiments/protein-predict/casp7/T0352/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0352/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0352/align.constraints_v3.costfcn # future Constraint commands -> align # future HelixConstraint commands -> align # future StrandConstraint commands -> align # future SheetConstraint commands -> align # future Hbond commands -> align # future SSbond commands -> align # Constraint # added constraint: constraint((T0352)A82.CB, (T0352)I93.CB) [> 4.1106 = 6.8510 < 8.9063] w=1.0000 to align # Constraint # added constraint: constraint((T0352)M59.CB, (T0352)I93.CB) [> 3.7539 = 6.2565 < 8.1335] w=0.9420 to align # Constraint # added constraint: constraint((T0352)Y78.CB, (T0352)I93.CB) [> 3.4542 = 5.7571 < 7.4842] w=0.8177 to align # Constraint # added constraint: constraint((T0352)L14.CB, (T0352)L62.CB) [> 4.1947 = 6.9912 < 9.0885] w=0.7987 to align # Constraint # added constraint: constraint((T0352)I56.CB, (T0352)V75.CB) [> 3.2322 = 5.3870 < 7.0030] w=0.6664 to align # Constraint # added constraint: constraint((T0352)A82.CB, (T0352)E96.CB) [> 3.5719 = 5.9532 < 7.7392] w=0.6464 to align # Constraint # added constraint: constraint((T0352)Y78.CB, (T0352)R90.CB) [> 3.0345 = 5.0576 < 6.5749] w=0.5956 to align # Constraint # added constraint: constraint((T0352)Y78.CB, (T0352)L94.CB) [> 4.1081 = 6.8469 < 8.9010] w=0.5956 to align # Constraint # added constraint: constraint((T0352)M81.CB, (T0352)R90.CB) [> 2.7911 = 4.6519 < 6.0474] w=0.5956 to align # Constraint # added constraint: constraint((T0352)P47.CB, (T0352)I56.CB) [> 4.2252 = 7.0420 < 9.1546] w=0.5726 to align # Constraint # added constraint: constraint((T0352)L14.CB, (T0352)R58.CB) [> 3.8585 = 6.4309 < 8.3601] w=0.5571 to align # Constraint # added constraint: constraint((T0352)A82.CB, (T0352)L97.CB) [> 4.5064 = 7.5107 < 9.7639] w=0.5501 to align # Constraint # added constraint: constraint((T0352)A82.CB, (T0352)L100.CB) [> 4.0780 = 6.7966 < 8.8356] w=0.5406 to align # Constraint # added constraint: constraint((T0352)L55.CB, (T0352)Y78.CB) [> 3.6158 = 6.0264 < 7.8343] w=0.5378 to align # Constraint # added constraint: constraint((T0352)R8.CB, (T0352)F34.CB) [> 3.4164 = 5.6940 < 7.4022] w=0.5273 to align # Constraint # added constraint: constraint((T0352)L11.CB, (T0352)V54.CB) [> 3.3590 = 5.5984 < 7.2779] w=0.5205 to align # Constraint # added constraint: constraint((T0352)I56.CB, (T0352)Y79.CB) [> 4.0805 = 6.8007 < 8.8410] w=0.5092 to align # Constraint # added constraint: constraint((T0352)M59.CB, (T0352)F73.CB) [> 3.9666 = 6.6111 < 8.5944] w=0.4966 to align # Constraint # added constraint: constraint((T0352)Y79.CB, (T0352)L103.CB) [> 4.5055 = 7.5091 < 9.7618] w=0.4803 to align # Constraint # added constraint: constraint((T0352)V7.CB, (T0352)F34.CB) [> 3.2761 = 5.4602 < 7.0983] w=0.4468 to align # Constraint # added constraint: constraint((T0352)H4.CB, (T0352)F34.CB) [> 2.9256 = 4.8760 < 6.3387] w=0.4468 to align # Constraint # added constraint: constraint((T0352)L55.CB, (T0352)L97.CB) [> 3.7735 = 6.2892 < 8.1760] w=0.4466 to align # Constraint # added constraint: constraint((T0352)F73.CB, (T0352)R90.CB) [> 3.8654 = 6.4424 < 8.3751] w=0.4428 to align # Constraint # added constraint: constraint((T0352)P77.CB, (T0352)I93.CB) [> 4.5348 = 7.5581 < 9.8255] w=0.4250 to align # Constraint # added constraint: constraint((T0352)F40.CB, (T0352)Q52.CB) [> 3.9548 = 6.5913 < 8.5687] w=0.4244 to align # Constraint # added constraint: constraint((T0352)L63.CB, (T0352)I93.CB) [> 4.3889 = 7.3148 < 9.5093] w=0.4180 to align # Constraint # added constraint: constraint((T0352)M59.CB, (T0352)V75.CB) [> 3.3145 = 5.5242 < 7.1814] w=0.4082 to align # Constraint # added constraint: constraint((T0352)E15.CB, (T0352)P29.CB) [> 3.2774 = 5.4623 < 7.1010] w=0.4039 to align # Constraint # added constraint: constraint((T0352)I56.CB, (T0352)F73.CB) [> 3.5606 = 5.9344 < 7.7147] w=0.4028 to align # Constraint # added constraint: constraint((T0352)H60.CB, (T0352)P70.CB) [> 3.0278 = 5.0463 < 6.5602] w=0.4028 to align # Constraint # added constraint: constraint((T0352)H60.CB, (T0352)G71.CA) [> 4.4907 = 7.4845 < 9.7298] w=0.4028 to align # Constraint # added constraint: constraint((T0352)H60.CB, (T0352)F73.CB) [> 4.1759 = 6.9598 < 9.0478] w=0.4028 to align # Constraint # added constraint: constraint((T0352)L18.CB, (T0352)F34.CB) [> 3.6589 = 6.0981 < 7.9275] w=0.3955 to align # Constraint # added constraint: constraint((T0352)L63.CB, (T0352)F73.CB) [> 4.3354 = 7.2257 < 9.3934] w=0.3950 to align # Constraint # added constraint: constraint((T0352)I56.CB, (T0352)A76.CB) [> 3.5252 = 5.8753 < 7.6380] w=0.3950 to align # Constraint # added constraint: constraint((T0352)A76.CB, (T0352)L103.CB) [> 4.4679 = 7.4465 < 9.6804] w=0.3929 to align # Constraint # added constraint: constraint((T0352)M45.CB, (T0352)R58.CB) [> 4.4460 = 7.4100 < 9.6330] w=0.3847 to align # Constraint # added constraint: constraint((T0352)L18.CB, (T0352)P29.CB) [> 2.9204 = 4.8673 < 6.3275] w=0.3823 to align # Constraint # added constraint: constraint((T0352)Y79.CB, (T0352)L100.CB) [> 3.2595 = 5.4325 < 7.0623] w=0.3764 to align # Constraint # added constraint: constraint((T0352)L69.CB, (T0352)L83.CB) [> 4.2907 = 7.1511 < 9.2965] w=0.3713 to align # Constraint # added constraint: constraint((T0352)P70.CB, (T0352)E80.CB) [> 4.7728 = 7.9547 < 10.3411] w=0.3713 to align # Constraint # added constraint: constraint((T0352)G71.CA, (T0352)E80.CB) [> 2.6049 = 4.3416 < 5.6441] w=0.3713 to align # Constraint # added constraint: constraint((T0352)G71.CA, (T0352)L83.CB) [> 4.4413 = 7.4021 < 9.6227] w=0.3713 to align # Constraint # added constraint: constraint((T0352)A76.CB, (T0352)L110.CB) [> 2.4874 = 4.1457 < 5.3894] w=0.3713 to align # Constraint # added constraint: constraint((T0352)Y78.CB, (T0352)L103.CB) [> 3.6328 = 6.0547 < 7.8711] w=0.3713 to align # Constraint # added constraint: constraint((T0352)Y78.CB, (T0352)L110.CB) [> 3.7729 = 6.2881 < 8.1746] w=0.3713 to align # Constraint # added constraint: constraint((T0352)Y79.CB, (T0352)L110.CB) [> 4.3132 = 7.1886 < 9.3452] w=0.3713 to align # Constraint # added constraint: constraint((T0352)Q10.CB, (T0352)R58.CB) [> 4.5018 = 7.5030 < 9.7539] w=0.3607 to align # Constraint # added constraint: constraint((T0352)L83.CB, (T0352)F104.CB) [> 4.1393 = 6.8988 < 8.9685] w=0.3548 to align # Constraint # added constraint: constraint((T0352)H4.CB, (T0352)N35.CB) [> 4.5000 = 7.4999 < 9.7499] w=0.3536 to align # Constraint # added constraint: constraint((T0352)M45.CB, (T0352)V54.CB) [> 3.3608 = 5.6013 < 7.2817] w=0.3519 to align # Constraint # added constraint: constraint((T0352)L55.CB, (T0352)V75.CB) [> 3.1262 = 5.2104 < 6.7735] w=0.3519 to align # Constraint # added constraint: constraint((T0352)L14.CB, (T0352)V54.CB) [> 4.4418 = 7.4030 < 9.6239] w=0.3446 to align # Constraint # added constraint: constraint((T0352)L11.CB, (T0352)L62.CB) [> 4.6129 = 7.6882 < 9.9946] w=0.3398 to align # Constraint # added constraint: constraint((T0352)Q52.CB, (T0352)I93.CB) [> 4.1516 = 6.9193 < 8.9951] w=0.3394 to align # Constraint # added constraint: constraint((T0352)E49.CB, (T0352)L97.CB) [> 4.3865 = 7.3108 < 9.5040] w=0.3394 to align # Constraint # added constraint: constraint((T0352)Y79.CB, (T0352)L94.CB) [> 3.8641 = 6.4401 < 8.3721] w=0.3392 to align # Constraint # added constraint: constraint((T0352)Y79.CB, (T0352)R90.CB) [> 4.3893 = 7.3155 < 9.5102] w=0.3392 to align # Constraint # added constraint: constraint((T0352)A13.CB, (T0352)N65.CB) [> 3.2138 = 5.3564 < 6.9633] w=0.3389 to align # Constraint # added constraint: constraint((T0352)L17.CB, (T0352)D61.CB) [> 2.8419 = 4.7366 < 6.1575] w=0.3389 to align # Constraint # added constraint: constraint((T0352)L17.CB, (T0352)N65.CB) [> 3.7884 = 6.3140 < 8.2081] w=0.3389 to align # Constraint # added constraint: constraint((T0352)L62.CB, (T0352)L92.CB) [> 3.4590 = 5.7649 < 7.4944] w=0.3381 to align # Constraint # added constraint: constraint((T0352)R58.CB, (T0352)E96.CB) [> 3.2729 = 5.4548 < 7.0912] w=0.3381 to align # Constraint # added constraint: constraint((T0352)R58.CB, (T0352)I93.CB) [> 2.4992 = 4.1653 < 5.4149] w=0.3381 to align # Constraint # added constraint: constraint((T0352)M59.CB, (T0352)P77.CB) [> 4.0778 = 6.7963 < 8.8351] w=0.3375 to align # Constraint # added constraint: constraint((T0352)L11.CB, (T0352)M59.CB) [> 3.2152 = 5.3586 < 6.9662] w=0.3272 to align # Constraint # added constraint: constraint((T0352)M45.CB, (T0352)L97.CB) [> 3.9920 = 6.6533 < 8.6492] w=0.3230 to align # Constraint # added constraint: constraint((T0352)A82.CB, (T0352)K99.CB) [> 3.6472 = 6.0787 < 7.9023] w=0.3185 to align # Constraint # added constraint: constraint((T0352)P70.CB, (T0352)Y79.CB) [> 4.1350 = 6.8917 < 8.9591] w=0.3158 to align # Constraint # added constraint: constraint((T0352)L63.CB, (T0352)V75.CB) [> 4.2068 = 7.0114 < 9.1148] w=0.3145 to align # Constraint # added constraint: constraint((T0352)H60.CB, (T0352)V75.CB) [> 3.1250 = 5.2083 < 6.7708] w=0.3145 to align # Constraint # added constraint: constraint((T0352)W50.CB, (T0352)M59.CB) [> 3.5954 = 5.9924 < 7.7901] w=0.3145 to align # Constraint # added constraint: constraint((T0352)L51.CB, (T0352)L97.CB) [> 3.3150 = 5.5249 < 7.1824] w=0.3032 to align # Constraint # added constraint: constraint((T0352)E15.CB, (T0352)D61.CB) [> 3.8394 = 6.3990 < 8.3187] w=0.2989 to align # Constraint # added constraint: constraint((T0352)L55.CB, (T0352)L94.CB) [> 4.2613 = 7.1022 < 9.2329] w=0.2985 to align # Constraint # added constraint: constraint((T0352)L18.CB, (T0352)T44.CB) [> 4.5551 = 7.5918 < 9.8693] w=0.2859 to align # Constraint # added constraint: constraint((T0352)L17.CB, (T0352)H60.CB) [> 4.6523 = 7.7538 < 10.0800] w=0.2829 to align # Constraint # added constraint: constraint((T0352)M59.CB, (T0352)Y78.CB) [> 3.3784 = 5.6307 < 7.3199] w=0.2797 to align # Constraint # added constraint: constraint((T0352)W24.CB, (T0352)F40.CB) [> 4.0142 = 6.6903 < 8.6973] w=0.2797 to align # Constraint # added constraint: constraint((T0352)W24.CB, (T0352)P39.CB) [> 4.4483 = 7.4138 < 9.6379] w=0.2797 to align # Constraint # added constraint: constraint((T0352)Q12.CB, (T0352)V54.CB) [> 4.7099 = 7.8499 < 10.2049] w=0.2797 to align # Constraint # added constraint: constraint((T0352)L11.CB, (T0352)R58.CB) [> 3.3935 = 5.6558 < 7.3525] w=0.2797 to align # Constraint # added constraint: constraint((T0352)L55.CB, (T0352)P77.CB) [> 2.7136 = 4.5226 < 5.8794] w=0.2797 to align # Constraint # added constraint: constraint((T0352)Q52.CB, (T0352)E80.CB) [> 3.1081 = 5.1801 < 6.7342] w=0.2797 to align # Constraint # added constraint: constraint((T0352)F40.CB, (T0352)V54.CB) [> 3.7263 = 6.2105 < 8.0736] w=0.2797 to align # Constraint # added constraint: constraint((T0352)F40.CB, (T0352)W53.CB) [> 4.3394 = 7.2323 < 9.4020] w=0.2797 to align # Constraint # added constraint: constraint((T0352)Q38.CB, (T0352)F73.CB) [> 4.4710 = 7.4516 < 9.6871] w=0.2797 to align # Constraint # added constraint: constraint((T0352)T37.CB, (T0352)F73.CB) [> 4.3459 = 7.2432 < 9.4161] w=0.2797 to align # Constraint # added constraint: constraint((T0352)L69.CB, (T0352)Y79.CB) [> 3.6369 = 6.0615 < 7.8800] w=0.2752 to align # Constraint # added constraint: constraint((T0352)P47.CB, (T0352)V75.CB) [> 2.2181 = 3.6969 < 4.8059] w=0.2739 to align # Constraint # added constraint: constraint((T0352)T44.CB, (T0352)L100.CB) [> 3.4254 = 5.7090 < 7.4217] w=0.2581 to align # Constraint # added constraint: constraint((T0352)T44.CB, (T0352)L97.CB) [> 4.2728 = 7.1213 < 9.2576] w=0.2581 to align # Constraint # added constraint: constraint((T0352)T44.CB, (T0352)R58.CB) [> 3.4157 = 5.6928 < 7.4007] w=0.2581 to align # Constraint # added constraint: constraint((T0352)T44.CB, (T0352)P57.CB) [> 3.5887 = 5.9812 < 7.7755] w=0.2581 to align # Constraint # added constraint: constraint((T0352)T44.CB, (T0352)V54.CB) [> 2.5729 = 4.2882 < 5.5746] w=0.2581 to align # Constraint # added constraint: constraint((T0352)D43.CB, (T0352)P57.CB) [> 3.4807 = 5.8011 < 7.5415] w=0.2581 to align # Constraint # added constraint: constraint((T0352)D43.CB, (T0352)V54.CB) [> 3.5260 = 5.8766 < 7.6396] w=0.2581 to align # Constraint # added constraint: constraint((T0352)L14.CB, (T0352)E96.CB) [> 4.7208 = 7.8680 < 10.2284] w=0.2581 to align # Constraint # added constraint: constraint((T0352)L14.CB, (T0352)T44.CB) [> 4.5205 = 7.5341 < 9.7944] w=0.2581 to align # Constraint # added constraint: constraint((T0352)A82.CB, (T0352)L94.CB) [> 2.4665 = 4.1108 < 5.3440] w=0.2581 to align # Constraint # added constraint: constraint((T0352)M59.CB, (T0352)P70.CB) [> 3.9799 = 6.6331 < 8.6231] w=0.2581 to align # Constraint # added constraint: constraint((T0352)L48.CB, (T0352)V75.CB) [> 3.7509 = 6.2515 < 8.1269] w=0.2581 to align # Constraint # added constraint: constraint((T0352)M45.CB, (T0352)L100.CB) [> 3.6415 = 6.0692 < 7.8900] w=0.2581 to align # Constraint # added constraint: constraint((T0352)E15.CB, (T0352)M59.CB) [> 3.4909 = 5.8182 < 7.5636] w=0.2574 to align # Constraint # added constraint: constraint((T0352)P47.CB, (T0352)H60.CB) [> 3.5323 = 5.8872 < 7.6533] w=0.2469 to align # Constraint # added constraint: constraint((T0352)H23.CB, (T0352)Q33.CB) [> 3.2859 = 5.4764 < 7.1194] w=0.2433 to align # Constraint # added constraint: constraint((T0352)M59.CB, (T0352)L69.CB) [> 3.8280 = 6.3800 < 8.2940] w=0.2385 to align # Constraint # added constraint: constraint((T0352)L48.CB, (T0352)H60.CB) [> 4.3310 = 7.2184 < 9.3839] w=0.2345 to align # Constraint # added constraint: constraint((T0352)N35.CB, (T0352)M45.CB) [> 4.1246 = 6.8743 < 8.9366] w=0.2221 to align # Constraint # added constraint: constraint((T0352)M45.CB, (T0352)H60.CB) [> 3.1623 = 5.2705 < 6.8517] w=0.2221 to align # Constraint # added constraint: constraint((T0352)E46.CB, (T0352)H60.CB) [> 4.2773 = 7.1288 < 9.2675] w=0.2221 to align # Constraint # added constraint: constraint((T0352)V7.CB, (T0352)F40.CB) [> 4.7445 = 7.9075 < 10.2798] w=0.2142 to align # Constraint # added constraint: constraint((T0352)E15.CB, (T0352)F40.CB) [> 3.7865 = 6.3108 < 8.2040] w=0.2142 to align # Constraint # added constraint: constraint((T0352)W53.CB, (T0352)L83.CB) [> 4.6752 = 7.7921 < 10.1297] w=0.2071 to align # Constraint # added constraint: constraint((T0352)L51.CB, (T0352)L100.CB) [> 4.7460 = 7.9100 < 10.2830] w=0.2071 to align # Constraint # added constraint: constraint((T0352)M42.CB, (T0352)L51.CB) [> 3.8797 = 6.4662 < 8.4061] w=0.1947 to align # Constraint # added constraint: constraint((T0352)F41.CB, (T0352)W50.CB) [> 2.7165 = 4.5274 < 5.8857] w=0.1947 to align # Constraint # added constraint: constraint((T0352)S36.CB, (T0352)V54.CB) [> 3.2971 = 5.4952 < 7.1438] w=0.1947 to align # Constraint # added constraint: constraint((T0352)E15.CB, (T0352)M42.CB) [> 3.9384 = 6.5640 < 8.5332] w=0.1947 to align # Constraint # added constraint: constraint((T0352)L11.CB, (T0352)M42.CB) [> 3.5878 = 5.9796 < 7.7735] w=0.1947 to align # Constraint # added constraint: constraint((T0352)Q10.CB, (T0352)F104.CB) [> 4.0304 = 6.7172 < 8.7324] w=0.1947 to align # Constraint # added constraint: constraint((T0352)V7.CB, (T0352)L97.CB) [> 3.4364 = 5.7273 < 7.4455] w=0.1947 to align # Constraint # added constraint: constraint((T0352)R6.CB, (T0352)D101.CB) [> 4.1973 = 6.9955 < 9.0942] w=0.1947 to align # Constraint # added constraint: constraint((T0352)V7.CB, (T0352)H60.CB) [> 4.7086 = 7.8476 < 10.2019] w=0.1887 to align # Constraint # added constraint: constraint((T0352)H21.CB, (T0352)F34.CB) [> 3.4157 = 5.6929 < 7.4008] w=0.1884 to align # Constraint # added constraint: constraint((T0352)Q38.CB, (T0352)W53.CB) [> 4.5025 = 7.5042 < 9.7554] w=0.1864 to align # Constraint # added constraint: constraint((T0352)P39.CB, (T0352)P70.CB) [> 4.5629 = 7.6048 < 9.8862] w=0.1864 to align # Constraint # added constraint: constraint((T0352)P39.CB, (T0352)P77.CB) [> 4.6574 = 7.7622 < 10.0909] w=0.1864 to align # Constraint # added constraint: constraint((T0352)F40.CB, (T0352)L51.CB) [> 3.4129 = 5.6882 < 7.3946] w=0.1864 to align # Constraint # added constraint: constraint((T0352)L51.CB, (T0352)P77.CB) [> 2.5581 = 4.2635 < 5.5426] w=0.1864 to align # Constraint # added constraint: constraint((T0352)M59.CB, (T0352)L83.CB) [> 3.6053 = 6.0088 < 7.8114] w=0.1857 to align # Constraint # added constraint: constraint((T0352)F73.CB, (T0352)H87.CB) [> 3.2164 = 5.3606 < 6.9688] w=0.1847 to align # Constraint # added constraint: constraint((T0352)L18.CB, (T0352)S36.CB) [> 3.8712 = 6.4519 < 8.3875] w=0.1704 to align # Constraint # added constraint: constraint((T0352)L11.CB, (T0352)H60.CB) [> 3.2199 = 5.3666 < 6.9765] w=0.1609 to align # Constraint # added constraint: constraint((T0352)L14.CB, (T0352)L97.CB) [> 4.7772 = 7.9620 < 10.3506] w=0.1609 to align # Constraint # added constraint: constraint((T0352)Q33.CB, (T0352)R58.CB) [> 2.9045 = 4.8409 < 6.2932] w=0.1609 to align # Constraint # added constraint: constraint((T0352)V7.CB, (T0352)P39.CB) [> 4.0901 = 6.8168 < 8.8618] w=0.1489 to align # Constraint # added constraint: constraint((T0352)H23.CB, (T0352)P47.CB) [> 3.6056 = 6.0094 < 7.8122] w=0.1482 to align # Constraint # added constraint: constraint((T0352)F73.CB, (T0352)L94.CB) [> 3.9610 = 6.6017 < 8.5822] w=0.1447 to align # Constraint # added constraint: constraint((T0352)H60.CB, (T0352)A72.CB) [> 3.6908 = 6.1513 < 7.9967] w=0.1447 to align # Constraint # added constraint: constraint((T0352)M59.CB, (T0352)A72.CB) [> 3.1732 = 5.2887 < 6.8753] w=0.1447 to align # Constraint # added constraint: constraint((T0352)R6.CB, (T0352)F104.CB) [> 4.1969 = 6.9949 < 9.0934] w=0.1298 to align # Constraint # added constraint: constraint((T0352)R8.CB, (T0352)M42.CB) [> 2.9859 = 4.9764 < 6.4693] w=0.1298 to align # Constraint # added constraint: constraint((T0352)R8.CB, (T0352)D43.CB) [> 4.2099 = 7.0166 < 9.1215] w=0.1298 to align # Constraint # added constraint: constraint((T0352)L63.CB, (T0352)L83.CB) [> 3.1229 = 5.2048 < 6.7662] w=0.1211 to align # Constraint # added constraint: constraint((T0352)E15.CB, (T0352)P47.CB) [> 3.9799 = 6.6332 < 8.6232] w=0.1111 to align # Constraint # added constraint: constraint((T0352)E15.CB, (T0352)W50.CB) [> 3.8647 = 6.4412 < 8.3735] w=0.1111 to align # Constraint # added constraint: constraint((T0352)H23.CB, (T0352)W50.CB) [> 3.2951 = 5.4918 < 7.1394] w=0.1111 to align # Constraint # added constraint: constraint((T0352)P39.CB, (T0352)W53.CB) [> 3.9614 = 6.6024 < 8.5831] w=0.1090 to align # Constraint # added constraint: constraint((T0352)H21.CB, (T0352)S36.CB) [> 3.0058 = 5.0096 < 6.5125] w=0.1055 to align # Constraint # added constraint: constraint((T0352)R19.CB, (T0352)Q38.CB) [> 4.5125 = 7.5208 < 9.7771] w=0.1055 to align # Constraint # added constraint: constraint((T0352)E15.CB, (T0352)A72.CB) [> 3.6304 = 6.0506 < 7.8658] w=0.0965 to align # Constraint # added constraint: constraint((T0352)H21.CB, (T0352)F40.CB) [> 4.3792 = 7.2987 < 9.4883] w=0.0965 to align # Constraint # added constraint: constraint((T0352)L51.CB, (T0352)V75.CB) [> 3.0487 = 5.0811 < 6.6055] w=0.0937 to align # Constraint # added constraint: constraint((T0352)Q38.CB, (T0352)P70.CB) [> 4.5379 = 7.5631 < 9.8321] w=0.0932 to align # Constraint # added constraint: constraint((T0352)Q38.CB, (T0352)P77.CB) [> 4.5784 = 7.6307 < 9.9199] w=0.0932 to align # Constraint # added constraint: constraint((T0352)F40.CB, (T0352)P77.CB) [> 2.6385 = 4.3975 < 5.7168] w=0.0932 to align # Constraint # added constraint: constraint((T0352)E15.CB, (T0352)P39.CB) [> 3.4397 = 5.7328 < 7.4526] w=0.0860 to align # Constraint # added constraint: constraint((T0352)F41.CB, (T0352)L100.CB) [> 4.6107 = 7.6844 < 9.9898] w=0.0860 to align # Constraint # added constraint: constraint((T0352)M45.CB, (T0352)D101.CB) [> 3.8985 = 6.4975 < 8.4467] w=0.0860 to align # Constraint # added constraint: constraint((T0352)P47.CB, (T0352)M59.CB) [> 4.4431 = 7.4051 < 9.6266] w=0.0826 to align # Constraint # added constraint: constraint((T0352)W24.CB, (T0352)R58.CB) [> 3.9023 = 6.5038 < 8.4550] w=0.0807 to align # Constraint # added constraint: constraint((T0352)L48.CB, (T0352)E98.CB) [> 4.3041 = 7.1735 < 9.3255] w=0.0807 to align # Constraint # added constraint: constraint((T0352)M59.CB, (T0352)A76.CB) [> 3.4145 = 5.6908 < 7.3981] w=0.0805 to align # Constraint # added constraint: constraint((T0352)H60.CB, (T0352)A76.CB) [> 4.2787 = 7.1312 < 9.2706] w=0.0805 to align # Constraint # added constraint: constraint((T0352)R58.CB, (T0352)A95.CB) [> 4.5790 = 7.6317 < 9.9212] w=0.0800 to align # Constraint # added constraint: constraint((T0352)G71.CA, (T0352)H87.CB) [> 4.1944 = 6.9907 < 9.0879] w=0.0800 to align # Constraint # added constraint: constraint((T0352)E46.CB, (T0352)R58.CB) [> 4.1719 = 6.9532 < 9.0392] w=0.0702 to align # Constraint # added constraint: constraint((T0352)Q10.CB, (T0352)Q52.CB) [> 4.5453 = 7.5755 < 9.8482] w=0.0649 to align # Constraint # added constraint: constraint((T0352)V7.CB, (T0352)R58.CB) [> 3.3670 = 5.6117 < 7.2952] w=0.0602 to align # Constraint # added constraint: constraint((T0352)E15.CB, (T0352)W24.CB) [> 3.7172 = 6.1953 < 8.0538] w=0.0595 to align # Constraint # added constraint: constraint((T0352)M42.CB, (T0352)L69.CB) [> 3.6571 = 6.0952 < 7.9237] w=0.0578 to align # Constraint # added constraint: constraint((T0352)M42.CB, (T0352)Q67.CB) [> 2.8660 = 4.7767 < 6.2097] w=0.0578 to align # Constraint # added constraint: constraint((T0352)M42.CB, (T0352)M59.CB) [> 4.2229 = 7.0383 < 9.1497] w=0.0578 to align # Constraint # added constraint: constraint((T0352)F41.CB, (T0352)Q67.CB) [> 4.3410 = 7.2351 < 9.4056] w=0.0578 to align # Constraint # added constraint: constraint((T0352)F41.CB, (T0352)R58.CB) [> 4.6781 = 7.7969 < 10.1359] w=0.0578 to align # Constraint # added constraint: constraint((T0352)M45.CB, (T0352)M59.CB) [> 3.8454 = 6.4089 < 8.3316] w=0.0578 to align # Constraint # added constraint: constraint((T0352)D43.CB, (T0352)P77.CB) [> 3.7470 = 6.2449 < 8.1184] w=0.0578 to align # Constraint # added constraint: constraint((T0352)D43.CB, (T0352)A76.CB) [> 4.7633 = 7.9389 < 10.3205] w=0.0578 to align # Constraint # added constraint: constraint((T0352)D43.CB, (T0352)G71.CA) [> 4.4622 = 7.4371 < 9.6682] w=0.0578 to align # Constraint # added constraint: constraint((T0352)M42.CB, (T0352)P77.CB) [> 3.1941 = 5.3235 < 6.9206] w=0.0578 to align # Constraint # added constraint: constraint((T0352)A74.CB, (T0352)A91.CB) [> 4.0545 = 6.7574 < 8.7847] w=0.0482 to align # Constraint # added constraint: constraint((T0352)E15.CB, (T0352)T44.CB) [> 4.7586 = 7.9310 < 10.3103] w=0.0437 to align # Constraint # added constraint: constraint((T0352)E15.CB, (T0352)F41.CB) [> 3.8226 = 6.3710 < 8.2823] w=0.0390 to align # Constraint # added constraint: constraint((T0352)V7.CB, (T0352)F41.CB) [> 4.4562 = 7.4269 < 9.6550] w=0.0386 to align # Constraint # added constraint: constraint((T0352)H23.CB, (T0352)L103.CB) [> 3.4022 = 5.6703 < 7.3714] w=0.0371 to align # Constraint # added constraint: constraint((T0352)L63.CB, (T0352)A74.CB) [> 4.3118 = 7.1863 < 9.3422] w=0.0371 to align # Constraint # added constraint: constraint((T0352)L62.CB, (T0352)A74.CB) [> 4.7565 = 7.9275 < 10.3057] w=0.0248 to align # Constraint # added constraint: constraint((T0352)Q38.CB, (T0352)L92.CB) [> 4.3533 = 7.2554 < 9.4321] w=0.0216 to align # Constraint # added constraint: constraint((T0352)A72.CB, (T0352)E98.CB) [> 4.7835 = 7.9725 < 10.3643] w=0.0216 to align # Constraint # added constraint: constraint((T0352)F40.CB, (T0352)A74.CB) [> 3.1622 = 5.2704 < 6.8515] w=0.0216 to align # Constraint # added constraint: constraint((T0352)F41.CB, (T0352)L55.CB) [> 3.1716 = 5.2859 < 6.8717] w=0.0216 to align # Constraint # added constraint: constraint((T0352)F41.CB, (T0352)L92.CB) [> 4.6584 = 7.7640 < 10.0931] w=0.0216 to align # Constraint # added constraint: constraint((T0352)E15.CB, (T0352)Q38.CB) [> 3.1382 = 5.2304 < 6.7995] w=0.0195 to align # Constraint # added constraint: constraint((T0352)W50.CB, (T0352)F104.CB) [> 4.3400 = 7.2333 < 9.4033] w=0.0158 to align # Constraint # added constraint: constraint((T0352)L48.CB, (T0352)M59.CB) [> 4.4474 = 7.4123 < 9.6360] w=0.0124 to align # Constraint # added constraint: constraint((T0352)E46.CB, (T0352)M59.CB) [> 3.7455 = 6.2424 < 8.1152] w=0.0124 to align # Constraint # added constraint: constraint((T0352)W53.CB, (T0352)A74.CB) [> 4.7797 = 7.9661 < 10.3560] w=0.0124 to align # SetCost created cost = # ( 1.0000 * align ) # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0352/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0352/decoys/ # ReadConformPDB reading from PDB file chimera-5-3.pdb.gz looking for model 1 # Found a chain break before 113 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file chimera-M1-S106-10+HIS.pdb.gz looking for model 1 # Found a chain break before 109 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS3.pdb.gz looking for model 1 # Found a chain break before 115 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS4 # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # Found a chain break before 91 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS1 # ReadConformPDB reading from PDB file servers/3Dpro_TS2.pdb.gz looking for model 1 # Found a chain break before 67 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS2 # ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1 # Found a chain break before 53 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS3 # ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1 # Found a chain break before 101 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS4 # ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1 # Found a chain break before 94 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS5 # ReadConformPDB reading from PDB file servers/ABIpro_TS1.pdb.gz looking for model 1 # Found a chain break before 91 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS1 # ReadConformPDB reading from PDB file servers/ABIpro_TS2.pdb.gz looking for model 1 # Found a chain break before 53 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS2 # ReadConformPDB reading from PDB file servers/ABIpro_TS3.pdb.gz looking for model 1 # Found a chain break before 104 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS3 # ReadConformPDB reading from PDB file servers/ABIpro_TS4.pdb.gz looking for model 1 # Found a chain break before 75 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS4 # ReadConformPDB reading from PDB file servers/ABIpro_TS5.pdb.gz looking for model 1 # Found a chain break before 34 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS5 # ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1 # Found a chain break before 87 # copying to AlignedFragments data structure # naming current conformation BayesHH_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS1.pdb.gz looking for model 1 # Found a chain break before 85 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS2.pdb.gz looking for model 1 # Found a chain break before 85 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS2 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS3.pdb.gz looking for model 1 # Found a chain break before 85 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS3 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS4.pdb.gz looking for model 1 # Found a chain break before 85 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS4 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS5.pdb.gz looking for model 1 # Found a chain break before 85 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS5 # ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1 # Found a chain break before 108 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS1 # ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS3 # ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS4 # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS5 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS2 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS3 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS4 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS5.pdb.gz looking for model 1 # Found a chain break before 112 # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS5 # ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation Distill_TS1 # ReadConformPDB reading from PDB file servers/Distill_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation Distill_TS2 # ReadConformPDB reading from PDB file servers/Distill_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation Distill_TS3 # ReadConformPDB reading from PDB file servers/Distill_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation Distill_TS4 # ReadConformPDB reading from PDB file servers/Distill_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation Distill_TS5 # ReadConformPDB reading from PDB file servers/FAMSD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FAMSD_TS1 # ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation FAMSD_TS2 # ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1 # Found a chain break before 104 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS3 # ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1 # Found a chain break before 116 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS4 # ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation FAMSD_TS5 # ReadConformPDB reading from PDB file servers/FAMS_TS1.pdb.gz looking for model 1 # Found a chain break before 116 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # Found a chain break before 110 # copying to AlignedFragments data structure # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # Found a chain break before 111 # copying to AlignedFragments data structure # naming current conformation FAMS_TS3 # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # Found a chain break before 106 # copying to AlignedFragments data structure # naming current conformation FAMS_TS4 # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # Found a chain break before 115 # copying to AlignedFragments data structure # naming current conformation FAMS_TS5 # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # Found a chain break before 43 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS1 # ReadConformPDB reading from PDB file servers/FOLDpro_TS2.pdb.gz looking for model 1 # naming current conformation FOLDpro_TS2 # ReadConformPDB reading from PDB file servers/FOLDpro_TS3.pdb.gz looking for model 1 # Found a chain break before 54 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS3 # ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1 # naming current conformation FOLDpro_TS4 # ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1 # Found a chain break before 85 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS5 # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation FORTE1_AL1 # ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation FORTE1_AL2 # ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1 Skipped atom 391, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation FORTE1_AL3 # ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation FORTE1_AL4 # ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1 Skipped atom 286, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz Skipped atom 288, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz Skipped atom 290, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz Skipped atom 292, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz Skipped atom 362, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz Skipped atom 364, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz Skipped atom 366, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz Skipped atom 368, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation FORTE1_AL5 # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation FORTE2_AL1 # ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation FORTE2_AL2 # ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1 Skipped atom 391, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation FORTE2_AL3 # ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation FORTE2_AL4 # ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1 Skipped atom 286, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 288, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 290, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 292, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 362, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 364, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 366, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 368, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation FORTE2_AL5 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS1.pdb.gz looking for model 1 # Found a chain break before 2 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS1 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS2.pdb.gz looking for model 1 # naming current conformation FPSOLVER-SERVER_TS2 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS3.pdb.gz looking for model 1 # naming current conformation FPSOLVER-SERVER_TS3 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS4.pdb.gz looking for model 1 # Found a chain break before 116 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS4 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS5.pdb.gz looking for model 1 # Found a chain break before 106 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS5 # ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1 # Found a chain break before 104 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # Found a chain break before 85 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS2 # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # naming current conformation FUGMOD_TS3 # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS4 # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # Found a chain break before 95 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS5 # ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation FUGUE_AL1 # ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL2 # ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation FUGUE_AL3 # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation FUGUE_AL4 # ReadConformPDB reading from PDB file servers/FUGUE_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL5 # ReadConformPDB reading from PDB file servers/FUNCTION_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation FUNCTION_TS1 # ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation FUNCTION_TS2 # ReadConformPDB reading from PDB file servers/FUNCTION_TS3.pdb.gz looking for model 1 # Found a chain break before 115 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS3 # ReadConformPDB reading from PDB file servers/FUNCTION_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation FUNCTION_TS4 # ReadConformPDB reading from PDB file servers/FUNCTION_TS5.pdb.gz looking for model 1 # Found a chain break before 113 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # ReadConformPDB reading from PDB file servers/Frankenstein_TS1.pdb.gz looking for model 1 # Found a chain break before 69 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS1 # ReadConformPDB reading from PDB file servers/Frankenstein_TS2.pdb.gz looking for model 1 # Found a chain break before 56 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # naming current conformation GeneSilicoMetaServer_TS1 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # Found a chain break before 30 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS3 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS4 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS5 # ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1 # Found a chain break before 82 # copying to AlignedFragments data structure # naming current conformation HHpred1_TS1 # ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1 # Found a chain break before 82 # copying to AlignedFragments data structure # naming current conformation HHpred2_TS1 # ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1 # Found a chain break before 27 # copying to AlignedFragments data structure # naming current conformation HHpred3_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS2 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS3 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS4 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS5 # ReadConformPDB reading from PDB file servers/LOOPP_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation LOOPP_TS1 # ReadConformPDB reading from PDB file servers/LOOPP_TS2.pdb.gz looking for model 1 # naming current conformation LOOPP_TS2 # ReadConformPDB reading from PDB file servers/LOOPP_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation LOOPP_TS3 # ReadConformPDB reading from PDB file servers/LOOPP_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation LOOPP_TS4 # ReadConformPDB reading from PDB file servers/LOOPP_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation LOOPP_TS5 # ReadConformPDB reading from PDB file servers/MIG_FROST_AL1.pdb.gz looking for model 1 Error: Reading chain '' from PDB file servers/MIG_FROST_AL1.pdb.gz failed---no such chain. # naming current conformation MIG_FROST_AL1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS1.pdb.gz looking for model 1 # Found a chain break before 44 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS2.pdb.gz looking for model 1 # Found a chain break before 111 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS3.pdb.gz looking for model 1 # Found a chain break before 68 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS4.pdb.gz looking for model 1 # Found a chain break before 70 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS5.pdb.gz looking for model 1 # naming current conformation Ma-OPUS-server2_TS5 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # Found a chain break before 74 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS2.pdb.gz looking for model 1 # naming current conformation Ma-OPUS-server_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS3.pdb.gz looking for model 1 # naming current conformation Ma-OPUS-server_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS4.pdb.gz looking for model 1 # Found a chain break before 35 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS5.pdb.gz looking for model 1 # Found a chain break before 104 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS5 # ReadConformPDB reading from PDB file servers/MetaTasser_TS1.pdb.gz looking for model 1 # Found a chain break before 116 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS1 # ReadConformPDB reading from PDB file servers/MetaTasser_TS2.pdb.gz looking for model 1 # Found a chain break before 116 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS2 # ReadConformPDB reading from PDB file servers/MetaTasser_TS3.pdb.gz looking for model 1 # Found a chain break before 116 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS3 # ReadConformPDB reading from PDB file servers/MetaTasser_TS4.pdb.gz looking for model 1 # Found a chain break before 116 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS4 # ReadConformPDB reading from PDB file servers/MetaTasser_TS5.pdb.gz looking for model 1 # Found a chain break before 110 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS5 # ReadConformPDB reading from PDB file servers/NN_PUT_lab_TS1.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # naming current conformation NN_PUT_lab_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS1.pdb.gz looking for model 1 # Found a chain break before 115 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS2.pdb.gz looking for model 1 # Found a chain break before 88 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS2 # ReadConformPDB reading from PDB file servers/POMYSL_TS3.pdb.gz looking for model 1 # Found a chain break before 96 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS3 # ReadConformPDB reading from PDB file servers/POMYSL_TS4.pdb.gz looking for model 1 # Found a chain break before 111 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS4 # ReadConformPDB reading from PDB file servers/POMYSL_TS5.pdb.gz looking for model 1 # Found a chain break before 86 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # Found a chain break before 73 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # Found a chain break before 8 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS5 # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # Found a chain break before 95 # copying to AlignedFragments data structure # naming current conformation Pcons6_TS1 # ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation Pcons6_TS2 # ReadConformPDB reading from PDB file servers/Pcons6_TS3.pdb.gz looking for model 1 # Found a chain break before 5 # copying to AlignedFragments data structure # naming current conformation Pcons6_TS3 # ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation Pcons6_TS4 # ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation Pcons6_TS5 # ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation Phyre-1_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS2 # ReadConformPDB reading from PDB file servers/Phyre-2_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS3 # ReadConformPDB reading from PDB file servers/Phyre-2_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS4 # ReadConformPDB reading from PDB file servers/Phyre-2_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS5 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1 # naming current conformation Pmodeller6_TS1 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # naming current conformation Pmodeller6_TS2 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS3 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS4 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1 # Found a chain break before 45 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS4.pdb.gz looking for model 1 # Found a chain break before 88 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS5 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS1.pdb.gz looking for model 1 # Found a chain break before 112 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS1 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS2.pdb.gz looking for model 1 # Found a chain break before 28 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS2 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS3.pdb.gz looking for model 1 # Found a chain break before 111 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS3 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS4.pdb.gz looking for model 1 # Found a chain break before 115 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS4 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS5.pdb.gz looking for model 1 # Found a chain break before 113 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR_TS1.pdb.gz looking for model 1 # Found a chain break before 78 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1 # Found a chain break before 52 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR_TS3.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR_TS4.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR_TS5.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS5 # ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1 # Found a chain break before 77 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS1 # ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS2 # ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1 # Found a chain break before 5 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS3 # ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS4 # ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1 # Found a chain break before 77 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS5 # ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL1 # ReadConformPDB reading from PDB file servers/SAM-T02_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL2 # ReadConformPDB reading from PDB file servers/SAM-T02_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL3 # ReadConformPDB reading from PDB file servers/SAM-T02_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL4 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1 # Found a chain break before 87 # copying to AlignedFragments data structure # naming current conformation SAM_T06_server_TS1 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS2 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS3 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS4 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS5 # ReadConformPDB reading from PDB file servers/SP3_TS1.pdb.gz looking for model 1 # Found a chain break before 82 # copying to AlignedFragments data structure # naming current conformation SP3_TS1 # ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1 # Found a chain break before 55 # copying to AlignedFragments data structure # naming current conformation SP3_TS2 # ReadConformPDB reading from PDB file servers/SP3_TS3.pdb.gz looking for model 1 # Found a chain break before 74 # copying to AlignedFragments data structure # naming current conformation SP3_TS3 # ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1 # Found a chain break before 44 # copying to AlignedFragments data structure # naming current conformation SP3_TS4 # ReadConformPDB reading from PDB file servers/SP3_TS5.pdb.gz looking for model 1 # Found a chain break before 45 # copying to AlignedFragments data structure # naming current conformation SP3_TS5 # ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1 # Found a chain break before 25 # copying to AlignedFragments data structure # naming current conformation SP4_TS1 # ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1 # Found a chain break before 29 # copying to AlignedFragments data structure # naming current conformation SP4_TS2 # ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1 # naming current conformation SP4_TS3 # ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1 # Found a chain break before 85 # copying to AlignedFragments data structure # naming current conformation SP4_TS4 # ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1 # Found a chain break before 86 # copying to AlignedFragments data structure # naming current conformation SP4_TS5 # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS1 # ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1 # Found a chain break before 45 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS2 # ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1 # Found a chain break before 43 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS3 # ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS4 # ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS2 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS3 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS4 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_expm_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation UNI-EID_expm_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL2 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL3 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL4 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL5 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1 # Found a chain break before 114 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS1 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS2.pdb.gz looking for model 1 # Found a chain break before 89 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS2 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS3.pdb.gz looking for model 1 # Found a chain break before 112 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS3 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS4.pdb.gz looking for model 1 # Found a chain break before 115 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS4 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS5.pdb.gz looking for model 1 # Found a chain break before 93 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS5 # ReadConformPDB reading from PDB file servers/beautshot_TS1.pdb.gz looking for model 1 # Found a chain break before 116 # copying to AlignedFragments data structure # naming current conformation beautshot_TS1 # ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation beautshotbase_TS1 # ReadConformPDB reading from PDB file servers/forecast-s_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation forecast-s_AL1 # ReadConformPDB reading from PDB file servers/forecast-s_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation forecast-s_AL2 # ReadConformPDB reading from PDB file servers/forecast-s_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation forecast-s_AL3 # ReadConformPDB reading from PDB file servers/forecast-s_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation forecast-s_AL4 # ReadConformPDB reading from PDB file servers/forecast-s_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation forecast-s_AL5 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # Found a chain break before 113 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS2.pdb.gz looking for model 1 # naming current conformation karypis.srv.2_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS3.pdb.gz looking for model 1 # Found a chain break before 92 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS4.pdb.gz looking for model 1 # Found a chain break before 50 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS5.pdb.gz looking for model 1 # naming current conformation karypis.srv.2_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS1.pdb.gz looking for model 1 # Found a chain break before 114 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS2.pdb.gz looking for model 1 # Found a chain break before 116 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS3.pdb.gz looking for model 1 WARNING: atoms too close: (T0352)A108.O and (T0352)S109.N only 0.000 apart, marking (T0352)S109.N as missing # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS4.pdb.gz looking for model 1 WARNING: atoms too close: (T0352)T44.O and (T0352)M45.N only 0.000 apart, marking (T0352)M45.N as missing WARNING: atoms too close: (T0352)W53.O and (T0352)V54.N only 0.000 apart, marking (T0352)V54.N as missing # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS5.pdb.gz looking for model 1 # Found a chain break before 114 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1 # Found a chain break before 17 # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv_TS2.pdb.gz looking for model 1 # Found a chain break before 91 # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv_TS4.pdb.gz looking for model 1 # Found a chain break before 56 # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv_TS5.pdb.gz looking for model 1 # Found a chain break before 86 # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS5 # ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1 # naming current conformation keasar-server_TS1 # ReadConformPDB reading from PDB file servers/keasar-server_TS2.pdb.gz looking for model 1 # naming current conformation keasar-server_TS2 # ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1 # naming current conformation keasar-server_TS3 # ReadConformPDB reading from PDB file servers/keasar-server_TS4.pdb.gz looking for model 1 # naming current conformation keasar-server_TS4 # ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1 # naming current conformation keasar-server_TS5 # ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation mGen-3D_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation nFOLD_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation nFOLD_TS2 # ReadConformPDB reading from PDB file servers/nFOLD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation nFOLD_TS3 # ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation nFOLD_TS4 # ReadConformPDB reading from PDB file servers/nFOLD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation nFOLD_TS5 # ReadConformPDB reading from PDB file servers/panther2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation panther2_TS1 # ReadConformPDB reading from PDB file servers/panther3_TS1.pdb.gz looking for model 1 WARNING: atoms too close: (T0352)Q89.N and (T0352)R90.N only 0.000 apart, marking (T0352)R90.N as missing WARNING: atoms too close: (T0352)Q89.CA and (T0352)R90.CA only 0.000 apart, marking (T0352)R90.CA as missing WARNING: atoms too close: (T0352)Q89.O and (T0352)R90.O only 0.000 apart, marking (T0352)R90.O as missing WARNING: atoms too close: (T0352)Q89.C and (T0352)R90.C only 0.000 apart, marking (T0352)R90.C as missing # WARNING: incomplete conformation T0352 can't currently be optimized by undertaker # naming current conformation panther3_TS1 # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # Found a chain break before 116 # copying to AlignedFragments data structure # naming current conformation shub_TS1 # command:Using radius: 8.0000 Using models AND alignments for constraints model score 1.6423 model score 1.6053 model score 2.1673 model score 2.1204 model score 1.8922 model score 2.0819 model score 1.9545 model score 1.5596 model score 1.6099 model score 2.1724 model score 2.2431 model score 2.2483 model score 2.0446 model score 1.5660 model score 2.0883 model score 2.2431 model score 1.2438 model score 2.2501 model score 1.2667 model score 2.0637 model score 2.0534 model score 1.2438 model score 1.2667 model score 1.2913 model score 1.1884 model score 1.2938 model score 2.1673 model score 1.9813 model score 2.2126 model score 2.1461 model score 2.1355 model score 2.0995 model score 1.9334 model score 1.3915 model score 1.4297 model score 1.4804 model score 1.3363 model score 1.2604 model score 1.5506 model score 1.2529 model score 1.5631 model score 1.9601 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.6820 model score 1.9887 model score 1.9201 model score 1.9141 model score 1.6814 model score 1.6440 model score 1.2860 model score 1.2860 model score 1.5036 model score 1.6911 model score 1.9381 model score 1.9386 model score 2.2649 model score 2.5212 model score 1.9616 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 2.0172 model score 1.8399 model score 1.9176 model score 1.8030 model score 2.0037 model score 1.6089 model score 1.9747 model score 1.7791 model score 1.7901 model score 1.9662 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 2.4529 model score 1.6921 model score 1.6250 model score 1.9493 model score 1.9252 model score 2.0912 model score 1.6763 model score 2.0589 model score 1.7431 model score 1.6552 model score 2.0292 model score 1.9771 model score 2.2391 model score 2.2391 model score 2.0987 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.8065 model score 1.8708 model score 1.6549 model score 1.5999 model score 1.5112 model score 2.2853 model score 1.4957 model score 1.2190 model score 2.4048 model score 1.4839 model score 1.8652 model score 1.2238 model score 1.5718 model score 2.1301 model score 1.9046 model score 1.9935 model score 1.1324 model score 1.2292 model score 1.1822 model score 1.4120 model score 1.1663 model score 1.8641 model score 1.6938 model score 1.5984 model score 1.8428 model score 1.7275 model score 1.5918 model score 1.2622 model score 1.4220 model score 1.6203 model score 1.5031 model score 1.7285 model score 2.1065 model score 2.1174 model score 1.3260 model score 1.8640 model score 1.3889 model score 2.1454 model score 1.9390 model score 2.1484 model score 2.0485 model score 1.9083 model score 1.5268 model score 2.2315 model score 2.0218 model score 1.7162 model score 1.8950 model score 1.6714 model score 1.3378 model score 1.6369 model score 1.5230 model score 1.9083 model score 1.9083 model score 1.5127 model score 1.4776 model score 2.1058 model score 1.3519 model score 2.0087 model score 1.9816 model score 1.5359 model score 2.5383 model score 2.1645 model score 2.0216 model score 1.9663 model score 1.3881 model score 2.5446 model score 2.1340 model score 2.0067 model score 1.7007 model score 1.6369 model score 2.1484 model score 1.4681 model score 1.5397 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.6860 model score 1.2308 model score 1.9081 model score 1.4376 model score 1.3949 model score 1.9335 model score 1.5591 model score 2.1609 model score 1.9422 model score 1.5127 model score 1.5773 model score 2.1369 model score 1.5364 model score 1.6724 model score 1.6412 model score 1.8641 model score 1.2768 model score 1.9701 model score 2.0517 model score 2.0921 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.7694 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.0418 model score 1.1143 model score 1.0246 model score 1.1626 model score 1.2459 model score 1.7681 model score 1.8701 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.7172 model score 1.8674 model score 2.1932 model score 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USE_META, weight: 0.9183 cost: 1.1626 min: 1.0246 max: 2.5446 USE_META, weight: 0.8689 cost: 1.2459 min: 1.0246 max: 2.5446 USE_META, weight: 0.5597 cost: 1.7681 min: 1.0246 max: 2.5446 USE_META, weight: 0.4994 cost: 1.8701 min: 1.0246 max: 2.5446 USE_META, weight: 0.8505 cost: 1.2771 min: 1.0246 max: 2.5446 USE_META, weight: 0.8505 cost: 1.2771 min: 1.0246 max: 2.5446 USE_META, weight: 0.8505 cost: 1.2771 min: 1.0246 max: 2.5446 USE_META, weight: 0.8505 cost: 1.2771 min: 1.0246 max: 2.5446 USE_META, weight: 0.8505 cost: 1.2771 min: 1.0246 max: 2.5446 USE_META, weight: 0.5899 cost: 1.7172 min: 1.0246 max: 2.5446 USE_META, weight: 0.5010 cost: 1.8674 min: 1.0246 max: 2.5446 USE_META, weight: 0.3080 cost: 2.1932 min: 1.0246 max: 2.5446 USE_META, weight: 0.4126 cost: 2.0167 min: 1.0246 max: 2.5446 USE_META, weight: 0.4432 cost: 1.9649 min: 1.0246 max: 2.5446 USE_META, weight: 0.3248 cost: 2.1649 min: 1.0246 max: 2.5446 USE_META, weight: 0.3916 cost: 2.0520 min: 1.0246 max: 2.5446 USE_META, weight: 0.5232 cost: 1.8298 min: 1.0246 max: 2.5446 USE_META, weight: 0.4154 cost: 2.0119 min: 1.0246 max: 2.5446 USE_META, weight: 0.4497 cost: 1.9541 min: 1.0246 max: 2.5446 USE_META, weight: 0.7201 cost: 1.4973 min: 1.0246 max: 2.5446 USE_META, weight: 0.6697 cost: 1.5825 min: 1.0246 max: 2.5446 USE_META, weight: 0.7109 cost: 1.5128 min: 1.0246 max: 2.5446 USE_META, weight: 0.4173 cost: 2.0086 min: 1.0246 max: 2.5446 USE_META, weight: 0.6140 cost: 1.6765 min: 1.0246 max: 2.5446 USE_META, weight: 0.3152 cost: 2.1812 min: 1.0246 max: 2.5446 USE_META, weight: 0.3201 cost: 2.1728 min: 1.0246 max: 2.5446 USE_META, weight: 0.3078 cost: 2.1936 min: 1.0246 max: 2.5446 USE_META, weight: 0.3778 cost: 2.0754 min: 1.0246 max: 2.5446 USE_META, weight: 0.3324 cost: 2.1522 min: 1.0246 max: 2.5446 USE_META, weight: 0.5307 cost: 1.8172 min: 1.0246 max: 2.5446 USE_META, weight: 0.6580 cost: 1.6022 min: 1.0246 max: 2.5446 USE_META, weight: 0.3600 cost: 2.1055 min: 1.0246 max: 2.5446 USE_META, weight: 0.7530 cost: 1.4418 min: 1.0246 max: 2.5446 USE_META, weight: 0.5358 cost: 1.8086 min: 1.0246 max: 2.5446 USE_META, weight: 0.7345 cost: 1.4730 min: 1.0246 max: 2.5446 USE_META, weight: 0.8505 cost: 1.2771 min: 1.0246 max: 2.5446 USE_META, weight: 0.8017 cost: 1.3594 min: 1.0246 max: 2.5446 USE_META, weight: 0.2881 cost: 2.2269 min: 1.0246 max: 2.5446 USE_EVALUE, weight: 0.7533 eval: 9.8500 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.7533 eval: 9.8500 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.7533 eval: 9.8500 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.3898 eval: 20.9820 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.3898 eval: 20.9820 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.3898 eval: 20.9820 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.1745 eval: 27.5770 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.1745 eval: 27.5770 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.1745 eval: 27.5770 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.1558 eval: 28.1490 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.1558 eval: 28.1490 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.1558 eval: 28.1490 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.2068 eval: 26.5880 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.2068 eval: 26.5880 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.2068 eval: 26.5880 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.7575 eval: 9.7207 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.7575 eval: 9.7207 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.7575 eval: 9.7207 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.2241 eval: 26.0560 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.2241 eval: 26.0560 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.3262 eval: 22.9300 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.3262 eval: 22.9300 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.3262 eval: 22.9300 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.3231 eval: 23.0250 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.3231 eval: 23.0250 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.3231 eval: 23.0250 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.6952 eval: 11.6280 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.6952 eval: 11.6280 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.6952 eval: 11.6280 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.5441 eval: 16.2570 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.5441 eval: 16.2570 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.5441 eval: 16.2570 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.2184 eval: 26.2330 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.2184 eval: 26.2330 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.2184 eval: 26.2330 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.6501 eval: 13.0090 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.6501 eval: 13.0090 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.6501 eval: 13.0090 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 1.0000 eval: 2.2934 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 1.0000 eval: 2.2934 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 1.0000 eval: 2.2934 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.1574 eval: 28.1000 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.1574 eval: 28.1000 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.1574 eval: 28.1000 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.3421 eval: 22.4430 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.3421 eval: 22.4430 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.3421 eval: 22.4430 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.1651 eval: 27.8630 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.1651 eval: 27.8630 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.1651 eval: 27.8630 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.1000 eval: 29.8580 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.1000 eval: 29.8580 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.1000 eval: 29.8580 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.4502 eval: 19.1320 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.4502 eval: 19.1320 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.4502 eval: 19.1320 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.5244 eval: 16.8590 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.5244 eval: 16.8590 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.5244 eval: 16.8590 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.1274 eval: 29.0180 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.1274 eval: 29.0180 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.3533 eval: 22.1000 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.3533 eval: 22.1000 min: 2.2934 max: 29.8580 USE_EVALUE, weight: 0.3533 eval: 22.1000 min: 2.2934 max: 29.8580 Number of contacts in models: 255 Number of contacts in alignments: 64 NUMB_ALIGNS: 64 Adding 5042 constraints to all3.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all3.constraints maxweight: 1.0000 Optimizing... Probability sum: -206.1569, CN propb: -206.1569 weights: 0.2464 constraints: 229 # command:Found ConstraintSet # PrintContacts align.constraints_meta03 Number of constraints in align3.constraints 229 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta03 Number of constraints in align3.constraints.bonus 229 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta03 Number of constraints in rejected3.constraints 4813 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta03 Number of constraints in rejected3.constraints.bonus 4813 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_meta03 Number of constraints in noncontact3.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_meta03 Number of constraints in noncontact3.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_meta03 Number of constraints in all3.constraints 5042 # command: