parameters: 0.6 1.3 0.5 200 50 # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading dunbrack-2191.atoms # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 53157 examples # computed average trans backbone unit before proline from 2010 examples # computed average cis backbone unit from 97 examples # trans (non-proline) backbone unit: # CA= -2.2087 1.0126 -0.0030 # O= -0.1499 2.2440 0.0016 # C= -0.6889 1.1368 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4581 -0.0000 0.0000 # cis backbone unit: # CA= -0.1436 2.4534 -0.0002 # O= -2.0284 0.9742 0.0015 # C= -0.8018 1.0771 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4668 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2100 1.0631 -0.0014 # O= -0.1236 2.2458 0.0075 # C= -0.6872 1.1517 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading dunbrack-2191.atoms have 2191 chains in training database # Count of chains,residues,atoms: 2191,500310,3902258 # 493341 residues have no bad marker # 3226 residues lack atoms needed to compute omega # 1453 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 4 # HAS_OXT 1167 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 3052 # HAS_UNKNOWN_ATOMS 9 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 979 # NON_PLANAR_PEPTIDE 888 # BAD_PEPTIDE 2680 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-2191.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0385/ # command:# Making conformation for sequence T0385 numbered 1 through 162 Created new target T0385 from T0385.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0385/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0385//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0385/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0385//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0385/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0385/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0385/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1za0A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1za0A expands to /projects/compbio/data/pdb/1za0.pdb.gz 1za0A:Skipped atom 1214, because occupancy 0.5 <= existing 0.500 in 1za0A Skipped atom 1216, because occupancy 0.500 <= existing 0.500 in 1za0A Skipped atom 1218, because occupancy 0.500 <= existing 0.500 in 1za0A Skipped atom 1220, because occupancy 0.500 <= existing 0.500 in 1za0A Skipped atom 1222, because occupancy 0.500 <= existing 0.500 in 1za0A Skipped atom 1224, because occupancy 0.500 <= existing 0.500 in 1za0A Skipped atom 1226, because occupancy 0.500 <= existing 0.500 in 1za0A # T0385 read from 1za0A/merged-good-all-a2m # 1za0A read from 1za0A/merged-good-all-a2m # adding 1za0A to template set # found chain 1za0A in template set Warning: unaligning (T0385)A10 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1za0A)D55 Warning: unaligning (T0385)T11 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1za0A)D55 Warning: unaligning (T0385)G50 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1za0A)D94 Warning: unaligning (T0385)Y87 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1za0A)K145 Warning: unaligning (T0385)Q92 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1za0A)K145 T0385 3 :SSEPAHG 1za0A 47 :AFLGGRD # choosing archetypes in rotamer library T0385 12 :PKRSPS 1za0A 56 :PSQSTL T0385 19 :GSADNAALCDALAVEH 1za0A 62 :PRTITDACEILLILKD T0385 51 :VNFLVADALKQHRH 1za0A 95 :WWGRWLGRWTAEEH T0385 65 :RRDDVIVMLS 1za0A 110 :HAIALREYLV T0385 76 :RGVTAPIAA 1za0A 122 :REVDPVANE T0385 85 :AG 1za0A 132 :VR T0385 93 :VSSAADAARLAVR 1za0A 146 :YTQVETLVYMAFY T0385 107 :ENDGATAWRAVVEHAETADDRVFASTALTESAVMATRWNRVL 1za0A 159 :ERCGAVFCRNLAAQIEEPILAGLIDRIARDEVRHEEFFANLV Number of specific fragments extracted= 9 number of extra gaps= 1 total=9 Number of alignments=1 # 1za0A read from 1za0A/merged-good-all-a2m # found chain 1za0A in template set Warning: unaligning (T0385)T11 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1za0A)D55 Warning: unaligning (T0385)P12 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1za0A)D55 Warning: unaligning (T0385)G50 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1za0A)D94 Warning: unaligning (T0385)Y87 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1za0A)K145 Warning: unaligning (T0385)Q92 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1za0A)K145 T0385 5 :EPAHGA 1za0A 48 :FLGGRD T0385 13 :KRSPSEGSADNAALCDALAVEH 1za0A 56 :PSQSTLPRTITDACEILLILKD T0385 51 :VNFLVADALKQHR 1za0A 95 :WWGRWLGRWTAEE T0385 64 :HRRDDVIVMLS 1za0A 109 :LHAIALREYLV T0385 76 :RGV 1za0A 121 :TRE T0385 79 :TAP 1za0A 125 :DPV T0385 82 :IAAAG 1za0A 129 :NEDVR T0385 93 :VSSAADAARLAVR 1za0A 146 :YTQVETLVYMAFY T0385 107 :ENDGATAWRAVVEHAETADDRVFASTALTESAVMATRWNRVL 1za0A 159 :ERCGAVFCRNLAAQIEEPILAGLIDRIARDEVRHEEFFANLV Number of specific fragments extracted= 9 number of extra gaps= 1 total=18 Number of alignments=2 # 1za0A read from 1za0A/merged-good-all-a2m # found chain 1za0A in template set Warning: unaligning (T0385)P12 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1za0A)D55 Warning: unaligning (T0385)K13 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1za0A)D55 Warning: unaligning (T0385)A80 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1za0A)K145 Warning: unaligning (T0385)Q92 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1za0A)K145 T0385 3 :SSEPAHGAT 1za0A 45 :NFAFLGGRD T0385 14 :RSPSEGSADNAALCDALAVEHA 1za0A 56 :PSQSTLPRTITDACEILLILKD T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGV 1za0A 97 :GRWLGRWTAEEHLHAIALREYLVVTREVDP T0385 79 :T 1za0A 133 :R T0385 93 :VSSAADAARLAVR 1za0A 146 :YTQVETLVYMAFY T0385 107 :ENDGATAWRAVVEHAE 1za0A 159 :ERCGAVFCRNLAAQIE T0385 124 :ADDRVFASTALTESAVMATRWNRV 1za0A 175 :EPILAGLIDRIARDEVRHEEFFAN Number of specific fragments extracted= 7 number of extra gaps= 1 total=25 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1h96A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1h96A expands to /projects/compbio/data/pdb/1h96.pdb.gz 1h96A:Skipped atom 77, because occupancy 0.500 <= existing 0.500 in 1h96A Skipped atom 79, because occupancy 0.500 <= existing 0.500 in 1h96A Skipped atom 81, because occupancy 0.500 <= existing 0.500 in 1h96A Skipped atom 311, because occupancy 0.500 <= existing 0.500 in 1h96A Skipped atom 313, because occupancy 0.500 <= existing 0.500 in 1h96A Skipped atom 315, because occupancy 0.500 <= existing 0.500 in 1h96A Skipped atom 317, because occupancy 0.500 <= existing 0.500 in 1h96A Skipped atom 319, because occupancy 0.500 <= existing 0.500 in 1h96A Skipped atom 321, because occupancy 0.500 <= existing 0.500 in 1h96A Skipped atom 323, because occupancy 0.500 <= existing 0.500 in 1h96A Skipped atom 481, because occupancy 0.500 <= existing 0.500 in 1h96A Skipped atom 483, because occupancy 0.500 <= existing 0.500 in 1h96A Skipped atom 485, because occupancy 0.500 <= existing 0.500 in 1h96A Skipped atom 487, because occupancy 0.500 <= existing 0.500 in 1h96A Skipped atom 489, because occupancy 0.500 <= existing 0.500 in 1h96A Skipped atom 491, because occupancy 0.500 <= existing 0.500 in 1h96A Skipped atom 493, because occupancy 0.500 <= existing 0.500 in 1h96A Skipped atom 919, because occupancy 0.330 <= existing 0.660 in 1h96A Skipped atom 921, because occupancy 0.330 <= existing 0.660 in 1h96A Skipped atom 923, because occupancy 0.330 <= existing 0.660 in 1h96A Skipped atom 925, because occupancy 0.330 <= existing 0.660 in 1h96A Skipped atom 927, because occupancy 0.330 <= existing 0.660 in 1h96A Skipped atom 929, because occupancy 0.330 <= existing 0.660 in 1h96A Skipped atom 931, because occupancy 0.330 <= existing 0.660 in 1h96A Skipped atom 933, because occupancy 0.330 <= existing 0.660 in 1h96A Skipped atom 935, because occupancy 0.330 <= existing 0.660 in 1h96A Skipped atom 937, because occupancy 0.330 <= existing 0.660 in 1h96A Skipped atom 960, because occupancy 0.330 <= existing 0.660 in 1h96A Skipped atom 962, because occupancy 0.330 <= existing 0.660 in 1h96A Skipped atom 1051, because occupancy 0.330 <= existing 0.660 in 1h96A Skipped atom 1053, because occupancy 0.330 <= existing 0.660 in 1h96A Skipped atom 1055, because occupancy 0.330 <= existing 0.660 in 1h96A Skipped atom 1057, because occupancy 0.330 <= existing 0.660 in 1h96A Skipped atom 1059, because occupancy 0.330 <= existing 0.660 in 1h96A Skipped atom 1061, because occupancy 0.330 <= existing 0.660 in 1h96A Skipped atom 1063, because occupancy 0.330 <= existing 0.660 in 1h96A Skipped atom 1065, because occupancy 0.330 <= existing 0.660 in 1h96A Skipped atom 1067, because occupancy 0.330 <= existing 0.660 in 1h96A # T0385 read from 1h96A/merged-good-all-a2m # 1h96A read from 1h96A/merged-good-all-a2m # adding 1h96A to template set # found chain 1h96A in template set Warning: unaligning (T0385)P12 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1h96A)S2 Warning: unaligning (T0385)L148 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1h96A)G156 Warning: unaligning (T0385)G149 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1h96A)G156 T0385 13 :KRSPSEGSADNAALCDALAVEHATIYGY 1h96A 3 :QIRQNYSTEVEAAVNRLVNLHLRASYTY T0385 41 :GIVS 1h96A 34 :GFFF T0385 45 :ALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGY 1h96A 41 :DVALEGVGHFFRELAEEKREGAERLLEFQNDRGGRALFQDVQK T0385 90 :PM 1h96A 84 :PS T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAE 1h96A 88 :EWGKTQEAMEAALAMEKNLNQALLDLHALGS T0385 123 :TADDRVFAST 1h96A 122 :DPHLCDFLES T0385 133 :ALTESAVMATRWNRV 1h96A 140 :LIKKMGNHLTNLRRV Number of specific fragments extracted= 7 number of extra gaps= 2 total=32 Number of alignments=4 # 1h96A read from 1h96A/merged-good-all-a2m # found chain 1h96A in template set Warning: unaligning (T0385)P12 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1h96A)S2 Warning: unaligning (T0385)L148 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1h96A)G156 Warning: unaligning (T0385)G149 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1h96A)G156 T0385 13 :KRSPSEGSADNAALCDALAVEHATIYGY 1h96A 3 :QIRQNYSTEVEAAVNRLVNLHLRASYTY T0385 41 :GI 1h96A 34 :GF T0385 43 :VSALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAG 1h96A 39 :RDDVALEGVGHFFRELAEEKREGAERLLEFQNDRGGRALFQDVQ T0385 88 :QLPM 1h96A 83 :KPSQ T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAE 1h96A 88 :EWGKTQEAMEAALAMEKNLNQALLDLHALGS T0385 123 :TADDRVFAS 1h96A 122 :DPHLCDFLE T0385 132 :TALTESAVMATRWNRV 1h96A 139 :KLIKKMGNHLTNLRRV Number of specific fragments extracted= 7 number of extra gaps= 2 total=39 Number of alignments=5 # 1h96A read from 1h96A/merged-good-all-a2m # found chain 1h96A in template set Warning: unaligning (T0385)L148 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1h96A)G156 Warning: unaligning (T0385)G149 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1h96A)G156 Warning: unaligning (T0385)D161 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1h96A)S168 T0385 13 :KRSPSEGSADNAALCDALAVEHATIYGYGIVSALSP 1h96A 3 :QIRQNYSTEVEAAVNRLVNLHLRASYTYLSLGFFFD T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAG 1h96A 45 :EGVGHFFRELAEEKREGAERLLEFQNDRGGRALFQDVQ T0385 90 :PM 1h96A 83 :KP T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHA 1h96A 88 :EWGKTQEAMEAALAMEKNLNQALLDLHALG T0385 122 :ETADDRVFA 1h96A 121 :ADPHLCDFL T0385 131 :STALTESAVMATRWNRV 1h96A 138 :VKLIKKMGNHLTNLRRV Number of specific fragments extracted= 6 number of extra gaps= 1 total=45 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tjoA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0385 read from 1tjoA/merged-good-all-a2m # 1tjoA read from 1tjoA/merged-good-all-a2m # found chain 1tjoA in training set Warning: unaligning (T0385)S3 because first residue in template chain is (1tjoA)S2 Warning: unaligning (T0385)G50 because of BadResidue code BAD_PEPTIDE in next template residue (1tjoA)F60 T0385 4 :SEPAHGATPKRSPSEGS 1tjoA 3 :TQKNARATAGEVEGSDA T0385 21 :ADNAALCDALAVEHATIYGY 1tjoA 25 :DRAEQCVDALNADLANVYVL T0385 41 :GIVSALSPP 1tjoA 50 :KHHWNVEGA T0385 51 :VNFLVADALKQHRHRRDDVIVMLSARGVTAPIAA 1tjoA 63 :LHLFLGEAAETAEEVADELAERVQALGGVPHASP T0385 85 :AGYQLPM 1tjoA 103 :ASVDVED T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAE 1tjoA 111 :DVYDIRTSLANDMAIYGDIIEATREHTELAE T0385 123 :TADDRVFASTALTESAVMATRWNRVLGAWPI 1tjoA 145 :DHATAHMLREGLIELEDDAHHIEHYLEDDTL Number of specific fragments extracted= 7 number of extra gaps= 1 total=52 Number of alignments=7 # 1tjoA read from 1tjoA/merged-good-all-a2m # found chain 1tjoA in training set Warning: unaligning (T0385)S3 because first residue in template chain is (1tjoA)S2 T0385 4 :SEPAHGATPKRSPSEGS 1tjoA 3 :TQKNARATAGEVEGSDA T0385 21 :ADNAALCDALAVEHATIYGY 1tjoA 25 :DRAEQCVDALNADLANVYVL T0385 41 :GIVSALSP 1tjoA 50 :KHHWNVEG T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGVTAP 1tjoA 61 :RDLHLFLGEAAETAEEVADELAERVQALGGVPH T0385 82 :IAAAGYQLPMQ 1tjoA 100 :QAEASVDVEDE T0385 93 :VSSAADAARLAVRMENDGATAWRAVVEHAE 1tjoA 112 :VYDIRTSLANDMAIYGDIIEATREHTELAE T0385 123 :TADDRVFASTALTESAVMATRWNRVLGAWPIT 1tjoA 145 :DHATAHMLREGLIELEDDAHHIEHYLEDDTLV Number of specific fragments extracted= 7 number of extra gaps= 0 total=59 Number of alignments=8 # 1tjoA read from 1tjoA/merged-good-all-a2m # found chain 1tjoA in training set T0385 7 :AHGATPKRSPSEGSADNAALCDALAVEHATIYGYGIVSALSP 1tjoA 11 :AGEVEGSDALRMDADRAEQCVDALNADLANVYVLYHQLKKHH T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGVTAP 1tjoA 61 :RDLHLFLGEAAETAEEVADELAERVQALGGVPH T0385 84 :AAGYQLPM 1tjoA 100 :QAEASVDV T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAET 1tjoA 111 :DVYDIRTSLANDMAIYGDIIEATREHTELAEN T0385 124 :ADDRVFASTALTESAVMATRWNRVLGAWPI 1tjoA 146 :HATAHMLREGLIELEDDAHHIEHYLEDDTL Number of specific fragments extracted= 5 number of extra gaps= 0 total=64 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fha/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1fha expands to /projects/compbio/data/pdb/1fha.pdb.gz 1fha:Warning: there is no chain 1fha will retry with 1fhaA # T0385 read from 1fha/merged-good-all-a2m # 1fha read from 1fha/merged-good-all-a2m # adding 1fha to template set # found chain 1fha in template set Warning: unaligning (T0385)T11 because first residue in template chain is (1fha)T5 Warning: unaligning (T0385)P12 because of BadResidue code BAD_PEPTIDE at template residue (1fha)S6 Warning: unaligning (T0385)Q88 because of BadResidue code BAD_PEPTIDE in next template residue (1fha)K87 Warning: unaligning (T0385)L89 because of BadResidue code BAD_PEPTIDE at template residue (1fha)K87 T0385 13 :KRSPSEGSADNAALCDALAVEHATIYGY 1fha 7 :QVRQNYHQDSEAAINRQINLELYASYVY T0385 41 :GI 1fha 40 :YF T0385 43 :VSALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAA 1fha 43 :RDDVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGRIFLQDI T0385 90 :PM 1fha 88 :PD T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAE 1fha 92 :DWESGLNAMECALHLEKNVNQSLLELHKLAT T0385 123 :TADDRVFAST 1fha 126 :DPHLCDFIET T0385 133 :ALTESAVMATRWNRV 1fha 144 :AIKELGDHVTNLRKM Number of specific fragments extracted= 7 number of extra gaps= 1 total=71 Number of alignments=10 # 1fha read from 1fha/merged-good-all-a2m # found chain 1fha in template set Warning: unaligning (T0385)T11 because first residue in template chain is (1fha)T5 Warning: unaligning (T0385)P12 because of BadResidue code BAD_PEPTIDE at template residue (1fha)S6 Warning: unaligning (T0385)G86 because of BadResidue code BAD_PEPTIDE in next template residue (1fha)K87 Warning: unaligning (T0385)L89 because of BadResidue code BAD_PEPTIDE at template residue (1fha)K87 T0385 13 :KRSPSEGSADNAALCDALAVEHATIYGY 1fha 7 :QVRQNYHQDSEAAINRQINLELYASYVY T0385 44 :S 1fha 38 :S T0385 45 :ALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAA 1fha 45 :DVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGRIFLQDI T0385 90 :P 1fha 88 :P T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAE 1fha 92 :DWESGLNAMECALHLEKNVNQSLLELHKLAT T0385 123 :TADDRVFAS 1fha 126 :DPHLCDFIE T0385 132 :TALTESAVMATRWNRV 1fha 143 :KAIKELGDHVTNLRKM Number of specific fragments extracted= 7 number of extra gaps= 1 total=78 Number of alignments=11 # 1fha read from 1fha/merged-good-all-a2m # found chain 1fha in template set Warning: unaligning (T0385)T11 because first residue in template chain is (1fha)T5 Warning: unaligning (T0385)P12 because of BadResidue code BAD_PEPTIDE at template residue (1fha)S6 Warning: unaligning (T0385)Q88 because of BadResidue code BAD_PEPTIDE in next template residue (1fha)K87 Warning: unaligning (T0385)P90 because of BadResidue code BAD_PEPTIDE at template residue (1fha)K87 T0385 13 :KRSPSEGSADNAALCDALAVEHATIYGYGIVSALSP 1fha 7 :QVRQNYHQDSEAAINRQINLELYASYVYLSMSYYFD T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAA 1fha 49 :KNFAKYFLHQSHEEREHAEKLMKLQNQRGGRIFLQDI T0385 91 :M 1fha 88 :P T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAE 1fha 92 :DWESGLNAMECALHLEKNVNQSLLELHKLAT T0385 123 :TAD 1fha 126 :DPH T0385 126 :DRVFASTALTESAVMATR 1fha 140 :EQVKAIKELGDHVTNLRK T0385 147 :V 1fha 158 :M Number of specific fragments extracted= 7 number of extra gaps= 1 total=85 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fha/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fha expands to /projects/compbio/data/pdb/2fha.pdb.gz 2fha:Warning: there is no chain 2fha will retry with 2fhaA # T0385 read from 2fha/merged-good-all-a2m # 2fha read from 2fha/merged-good-all-a2m # adding 2fha to template set # found chain 2fha in template set Warning: unaligning (T0385)T11 because first residue in template chain is (2fha)T5 T0385 12 :PKRSPSEGSADNAALCDALAVEHATIYGY 2fha 6 :SQVRQNYHQDSEAAINRQINLELYASYVY T0385 41 :GI 2fha 40 :YF T0385 43 :VSALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAA 2fha 43 :RDDVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGRIFLQDI T0385 88 :QLPM 2fha 86 :QKPD T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAE 2fha 92 :DWESGLNAMECALHLEKNVNQSLLELHKLAT T0385 123 :TADDRVFAST 2fha 126 :DPHLCDFIET T0385 133 :ALTESAVMATRWNRV 2fha 144 :AIKELGDHVTNLRKM Number of specific fragments extracted= 7 number of extra gaps= 0 total=92 Number of alignments=13 # 2fha read from 2fha/merged-good-all-a2m # found chain 2fha in template set Warning: unaligning (T0385)T11 because first residue in template chain is (2fha)T5 T0385 12 :PKRSPSEGSADNAALCDALAVEHATIYGY 2fha 6 :SQVRQNYHQDSEAAINRQINLELYASYVY T0385 42 :IVS 2fha 36 :SMS T0385 45 :ALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAG 2fha 45 :DVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGRIFLQDIQ T0385 88 :QLPM 2fha 87 :KPDC T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAE 2fha 92 :DWESGLNAMECALHLEKNVNQSLLELHKLAT T0385 123 :TADDRVFAS 2fha 126 :DPHLCDFIE T0385 132 :TALTESAVMATRWNRV 2fha 143 :KAIKELGDHVTNLRKM Number of specific fragments extracted= 7 number of extra gaps= 0 total=99 Number of alignments=14 # 2fha read from 2fha/merged-good-all-a2m # found chain 2fha in template set Warning: unaligning (T0385)T11 because first residue in template chain is (2fha)T5 T0385 12 :PKRSPSEGSADNAALCDALAVEHATIYGYGIVSALSP 2fha 6 :SQVRQNYHQDSEAAINRQINLELYASYVYLSMSYYFD T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAA 2fha 49 :KNFAKYFLHQSHEEREHAEKLMKLQNQRGGRIFLQDI T0385 88 :Q 2fha 86 :Q T0385 90 :PM 2fha 87 :KP T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAETAD 2fha 92 :DWESGLNAMECALHLEKNVNQSLLELHKLATDKN T0385 126 :DRVFASTALTESAVMATR 2fha 140 :EQVKAIKELGDHVTNLRK Number of specific fragments extracted= 6 number of extra gaps= 0 total=105 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gyqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2gyqA expands to /projects/compbio/data/pdb/2gyq.pdb.gz 2gyqA:Skipped atom 26, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 30, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 32, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 34, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 36, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 38, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 40, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 42, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 45, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 49, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 51, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 81, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 85, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 87, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 89, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 91, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 93, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 111, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 115, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 117, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 119, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 121, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 123, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 245, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 249, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 251, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 253, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 255, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 257, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 313, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 317, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 319, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 321, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 323, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 325, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 328, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 332, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 334, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 336, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 338, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 349, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 353, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 355, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 357, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 359, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 361, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 420, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 424, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 426, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 457, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 461, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 463, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 466, because occupancy 0.300 <= existing 0.700 in 2gyqA Skipped atom 470, because occupancy 0.300 <= existing 0.700 in 2gyqA Skipped atom 472, because occupancy 0.300 <= existing 0.700 in 2gyqA Skipped atom 474, because occupancy 0.300 <= existing 0.700 in 2gyqA Skipped atom 476, because occupancy 0.300 <= existing 0.700 in 2gyqA Skipped atom 478, because occupancy 0.300 <= existing 0.700 in 2gyqA Skipped atom 480, because occupancy 0.300 <= existing 0.700 in 2gyqA Skipped atom 500, because occupancy 0.300 <= existing 0.700 in 2gyqA Skipped atom 504, because occupancy 0.300 <= existing 0.700 in 2gyqA Skipped atom 506, because occupancy 0.300 <= existing 0.700 in 2gyqA Skipped atom 508, because occupancy 0.300 <= existing 0.700 in 2gyqA Skipped atom 510, because occupancy 0.300 <= existing 0.700 in 2gyqA Skipped atom 512, because occupancy 0.300 <= existing 0.700 in 2gyqA Skipped atom 522, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 526, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 528, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 530, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 532, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 534, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 546, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 550, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 552, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 554, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 556, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 558, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 632, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 636, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 638, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 640, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 642, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 644, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 677, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 681, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 683, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 685, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 687, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 689, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 787, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 791, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 793, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 795, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 797, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 799, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 807, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 811, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 813, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 815, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 817, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 820, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 824, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 826, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 828, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 830, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 832, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 881, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 885, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 887, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 889, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 891, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 893, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 990, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 994, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 996, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 998, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 1000, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 1002, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 1132, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1136, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1138, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1140, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1142, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1144, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1268, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1272, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1274, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1276, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1278, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1280, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1326, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1330, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1332, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1334, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1336, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1338, because occupancy 0.400 <= existing 0.600 in 2gyqA # T0385 read from 2gyqA/merged-good-all-a2m # 2gyqA read from 2gyqA/merged-good-all-a2m # adding 2gyqA to template set # found chain 2gyqA in template set Warning: unaligning (T0385)T154 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gyqA)A168 T0385 11 :TPKRSPSEGSADNAALCDALAVEHATIYGY 2gyqA 4 :FSRDIQTMEDLLLHGLRDIYYAEQQITKAL T0385 41 :GIVSALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAP 2gyqA 35 :KMIEQATNRDLSQGLTSHLEETQKQIERLDQVFKKLGQKPS T0385 88 :QLPM 2gyqA 76 :GVNC T0385 92 :QVSS 2gyqA 95 :EIAD T0385 96 :AADAARLAVRMENDGATAWRAVVEHAE 2gyqA 103 :DAAIVANAQAVEHYEIARYGTLIAWAE T0385 123 :TADDRVFASTALTESAVM 2gyqA 133 :HDDIVRFLTTNLNEEKAA T0385 145 :NRVLGAWPI 2gyqA 151 :NTKLNTVAL Number of specific fragments extracted= 7 number of extra gaps= 0 total=112 Number of alignments=16 # 2gyqA read from 2gyqA/merged-good-all-a2m # found chain 2gyqA in template set Warning: unaligning (T0385)H8 because first residue in template chain is (2gyqA)M1 T0385 9 :GATPKRSPSEGSADNAALCDALAVEHATIYGY 2gyqA 2 :GFFSRDIQTMEDLLLHGLRDIYYAEQQITKAL T0385 41 :GIVSALSPPGVNFLVADALK 2gyqA 35 :KMIEQATNRDLSQGLTSHLE T0385 61 :QHRHRRDDVIVML 2gyqA 58 :KQIERLDQVFKKL T0385 77 :GVTAP 2gyqA 71 :GQKPS T0385 86 :G 2gyqA 76 :G T0385 89 :LPM 2gyqA 77 :VNC T0385 92 :QVSS 2gyqA 95 :EIAD T0385 96 :AADAARLAVRMENDGATAWRAVVEHAE 2gyqA 103 :DAAIVANAQAVEHYEIARYGTLIAWAE T0385 123 :TADDRVFASTALTESAVMATRWNR 2gyqA 133 :HDDIVRFLTTNLNEEKAANTKLNT Number of specific fragments extracted= 9 number of extra gaps= 0 total=121 Number of alignments=17 # 2gyqA read from 2gyqA/merged-good-all-a2m # found chain 2gyqA in template set T0385 13 :KRSPSEGSADNAALCDALAVEHATIYGYGIVSALSP 2gyqA 6 :RDIQTMEDLLLHGLRDIYYAEQQITKALPKMIEQAT T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAA 2gyqA 43 :RDLSQGLTSHLEETQKQIERLDQVFKKLGQKPSGVNC T0385 92 :QVSS 2gyqA 95 :EIAD T0385 96 :AADAARLAVRMENDGATAWRAVVEHAE 2gyqA 103 :DAAIVANAQAVEHYEIARYGTLIAWAE T0385 123 :TADDRVFASTALTESAVMATRWNRVL 2gyqA 133 :HDDIVRFLTTNLNEEKAANTKLNTVA Number of specific fragments extracted= 5 number of extra gaps= 0 total=126 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lb3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0385 read from 1lb3A/merged-good-all-a2m # 1lb3A read from 1lb3A/merged-good-all-a2m # found chain 1lb3A in training set Warning: unaligning (T0385)P12 because first residue in template chain is (1lb3A)S6 Warning: unaligning (T0385)L148 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1lb3A)S172 T0385 13 :KRSPSEGSADNAALCDALAVEHATIYGY 1lb3A 7 :QIRQNYSTEVEAAVNRLVNLHLRASYTY T0385 41 :GIVS 1lb3A 38 :GFFF T0385 45 :ALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGYQL 1lb3A 45 :DVALEGVGHFFRELAEEKREGAERLLEFQNDRGGRALFQDVQKPS T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAE 1lb3A 92 :EWGKTQEAMEAALAMEKNLNQALLDLHALGS T0385 123 :TADDRVFAST 1lb3A 126 :DPHLCDFLES T0385 133 :ALTESAVMATRWNRV 1lb3A 144 :LIKKMGNHLTNLRRV Number of specific fragments extracted= 6 number of extra gaps= 0 total=132 Number of alignments=19 # 1lb3A read from 1lb3A/merged-good-all-a2m # found chain 1lb3A in training set Warning: unaligning (T0385)P12 because first residue in template chain is (1lb3A)S6 Warning: unaligning (T0385)L148 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1lb3A)S172 Warning: unaligning (T0385)D161 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lb3A)S172 T0385 13 :KRSPSEGSADNAALCDALAVEHATIYGY 1lb3A 7 :QIRQNYSTEVEAAVNRLVNLHLRASYTY T0385 41 :GI 1lb3A 38 :GF T0385 43 :VSALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAG 1lb3A 43 :RDDVALEGVGHFFRELAEEKREGAERLLEFQNDRGGRALFQDVQ T0385 88 :QLPM 1lb3A 87 :KPSQ T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAE 1lb3A 92 :EWGKTQEAMEAALAMEKNLNQALLDLHALGS T0385 123 :TADDRVFAS 1lb3A 126 :DPHLCDFLE T0385 132 :TALTESAVMATRWNRV 1lb3A 143 :KLIKKMGNHLTNLRRV Number of specific fragments extracted= 7 number of extra gaps= 0 total=139 Number of alignments=20 # 1lb3A read from 1lb3A/merged-good-all-a2m # found chain 1lb3A in training set Warning: unaligning (T0385)L148 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1lb3A)S172 Warning: unaligning (T0385)D161 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lb3A)S172 T0385 13 :KRSPSEGSADNAALCDALAVEHATIYGYGIVSALSP 1lb3A 7 :QIRQNYSTEVEAAVNRLVNLHLRASYTYLSLGFFFD T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAG 1lb3A 49 :EGVGHFFRELAEEKREGAERLLEFQNDRGGRALFQDVQ T0385 90 :PM 1lb3A 87 :KP T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHA 1lb3A 92 :EWGKTQEAMEAALAMEKNLNQALLDLHALG T0385 122 :ETADDRVFA 1lb3A 125 :ADPHLCDFL T0385 131 :STALTESAVMATRWNRV 1lb3A 142 :VKLIKKMGNHLTNLRRV Number of specific fragments extracted= 6 number of extra gaps= 0 total=145 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bjwA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1bjwA expands to /projects/compbio/data/pdb/1bjw.pdb.gz 1bjwA:Bad short name: N1 for alphabet: pdb_atoms Bad short name: C2 for alphabet: pdb_atoms Bad short name: C2' for alphabet: pdb_atoms Bad short name: C3 for alphabet: pdb_atoms Bad short name: O3 for alphabet: pdb_atoms Bad short name: C4 for alphabet: pdb_atoms Bad short name: C4' for alphabet: pdb_atoms Bad short name: C5 for alphabet: pdb_atoms Bad short name: C6 for alphabet: pdb_atoms Bad short name: C5' for alphabet: pdb_atoms Bad short name: OP4 for alphabet: pdb_atoms Bad short name: P for alphabet: pdb_atoms Bad short name: OP1 for alphabet: pdb_atoms Bad short name: OP2 for alphabet: pdb_atoms Bad short name: OP3 for alphabet: pdb_atoms # T0385 read from 1bjwA/merged-good-all-a2m # 1bjwA read from 1bjwA/merged-good-all-a2m # adding 1bjwA to template set # found chain 1bjwA in template set T0385 16 :PSEGSADNAALCDALA 1bjwA 265 :TSPDTIAQWATLEALT T0385 47 :SPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGYQLPM 1bjwA 281 :NQEASRAFVEMAREAYRRRRDLLLEGLTALGLKAVRPSGAFYVLM T0385 92 :QVSSAADAARLAVR 1bjwA 331 :APDEVRAAERLLEA Number of specific fragments extracted= 3 number of extra gaps= 0 total=148 Number of alignments=22 # 1bjwA read from 1bjwA/merged-good-all-a2m # found chain 1bjwA in template set T0385 17 :SEGSADNAALCDALA 1bjwA 266 :SPDTIAQWATLEALT T0385 47 :SPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGYQL 1bjwA 281 :NQEASRAFVEMAREAYRRRRDLLLEGLTALGLKAVRPSGAFYV T0385 90 :PMQVSSAADAARLAVR 1bjwA 329 :PIAPDEVRAAERLLEA Number of specific fragments extracted= 3 number of extra gaps= 0 total=151 Number of alignments=23 # 1bjwA read from 1bjwA/merged-good-all-a2m # found chain 1bjwA in template set T0385 24 :AALCDALAVE 1bjwA 251 :EVIKAMASVS T0385 36 :TIYGYGIVSALSP 1bjwA 269 :TIAQWATLEALTN T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGYQLPMQVSS 1bjwA 283 :EASRAFVEMAREAYRRRRDLLLEGLTALGLKAVRPSGAFYVLMDTSP T0385 96 :AADAARLAVRMEND 1bjwA 331 :APDEVRAAERLLEA T0385 120 :HAETADDRVFASTAL 1bjwA 364 :YATSEENLRKALERF Number of specific fragments extracted= 5 number of extra gaps= 0 total=156 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z6oM/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1z6oM expands to /projects/compbio/data/pdb/1z6o.pdb.gz 1z6oM:# T0385 read from 1z6oM/merged-good-all-a2m # 1z6oM read from 1z6oM/merged-good-all-a2m # adding 1z6oM to template set # found chain 1z6oM in template set T0385 4 :SEPAHGATPKRSP 1z6oM 4 :NVNPVQIPKDWIT T0385 18 :EGSADNAALCDALAVEHATIYGY 1z6oM 17 :MHRSCRNSMRQQIQMEVGASLQY T0385 41 :GIVSA 1z6oM 45 :HFSKD T0385 46 :LSPPGVNFLVADALKQHRHRRDDVIVMLSARG 1z6oM 51 :VNRPGFAQLFFDAASEEREHAMKLIEYLLMRG T0385 81 :PIAAA 1z6oM 87 :DVSSL T0385 87 :YQLPM 1z6oM 92 :LQVRP T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAE 1z6oM 101 :SWKGGVEALEHALSMESDVTKSIRNVIKACE T0385 123 :TADDRVFASTALTESAVMATRWNRVLGA 1z6oM 146 :TGDFLEEQYKGQRDLAGKASTLKKLMDR Number of specific fragments extracted= 8 number of extra gaps= 0 total=164 Number of alignments=25 # 1z6oM read from 1z6oM/merged-good-all-a2m # found chain 1z6oM in template set T0385 2 :TSSEPAHGATPKRSPSE 1z6oM 2 :QCNVNPVQIPKDWITMH T0385 20 :SADNAALCDALAVEHATIYGY 1z6oM 19 :RSCRNSMRQQIQMEVGASLQY T0385 41 :GI 1z6oM 43 :GA T0385 43 :VS 1z6oM 46 :FS T0385 45 :ALSPPGVNFLVADALKQHRHRRDDVIVMLSARGV 1z6oM 50 :VVNRPGFAQLFFDAASEEREHAMKLIEYLLMRGE T0385 79 :TAPIAAA 1z6oM 85 :TNDVSSL T0385 86 :GYQLP 1z6oM 93 :QVRPP T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAE 1z6oM 101 :SWKGGVEALEHALSMESDVTKSIRNVIKACE T0385 123 :TADDRVFASTALTESAVMATRWNRVLGA 1z6oM 146 :TGDFLEEQYKGQRDLAGKASTLKKLMDR Number of specific fragments extracted= 9 number of extra gaps= 0 total=173 Number of alignments=26 # 1z6oM read from 1z6oM/merged-good-all-a2m # found chain 1z6oM in template set T0385 2 :TSSEPAHGATPKRSPS 1z6oM 3 :CNVNPVQIPKDWITMH T0385 20 :SADNAALCDALAVEHATIYGYGIVSALSP 1z6oM 19 :RSCRNSMRQQIQMEVGASLQYLAMGAHFS T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGYQLPM 1z6oM 54 :PGFAQLFFDAASEEREHAMKLIEYLLMRGELTNDVSSLLQVRP T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAET 1z6oM 101 :SWKGGVEALEHALSMESDVTKSIRNVIKACED T0385 124 :ADDRVFASTALTESAVMATRWNRVLGA 1z6oM 147 :GDFLEEQYKGQRDLAGKASTLKKLMDR Number of specific fragments extracted= 5 number of extra gaps= 0 total=178 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mfrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1mfrA expands to /projects/compbio/data/pdb/1mfr.pdb.gz 1mfrA:# T0385 read from 1mfrA/merged-good-all-a2m # 1mfrA read from 1mfrA/merged-good-all-a2m # adding 1mfrA to template set # found chain 1mfrA in template set Warning: unaligning (T0385)T11 because first residue in template chain is (1mfrA)V1 T0385 12 :PKRSPSEGSADNAALCDALAVEHATIYGY 1mfrA 2 :SQVRQNYHSDCEAAVNRMLNLELYASYTY T0385 41 :GIVSALSPPG 1mfrA 32 :SMYAFFDRDD T0385 51 :VNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGYQLPMQVSSAADAARLAVRMENDGATAWRAVVEHAE 1mfrA 47 :VAEFFKEHSHEEREHAEKFMKYQNKRGGRVVLQDIKKPERDEWGNTLEAMQAALQLEKTVNQALLDLHKLAT T0385 123 :TADDRVFAST 1mfrA 122 :DPHLCDFLES T0385 133 :ALTESAVMATRWNRVLG 1mfrA 133 :YLEEQVKDIKRIGDFIT Number of specific fragments extracted= 5 number of extra gaps= 0 total=183 Number of alignments=28 # 1mfrA read from 1mfrA/merged-good-all-a2m # found chain 1mfrA in template set Warning: unaligning (T0385)T11 because first residue in template chain is (1mfrA)V1 T0385 12 :PKRSPSEGSADNAALCDALAVEHATIYGYGIV 1mfrA 2 :SQVRQNYHSDCEAAVNRMLNLELYASYTYSSM T0385 44 :SALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGYQLPMQVSSAADAARLAVRMENDGATAWRAVVEHAE 1mfrA 40 :DDVALHNVAEFFKEHSHEEREHAEKFMKYQNKRGGRVVLQDIKKPERDEWGNTLEAMQAALQLEKTVNQALLDLHKLAT T0385 123 :TADDRVFAS 1mfrA 122 :DPHLCDFLE T0385 132 :TALTESAVMATRWNRVL 1mfrA 132 :EYLEEQVKDIKRIGDFI Number of specific fragments extracted= 4 number of extra gaps= 0 total=187 Number of alignments=29 # 1mfrA read from 1mfrA/merged-good-all-a2m # found chain 1mfrA in template set T0385 12 :PKRSPSEGSADNAALCDALAVEHATIYGYGIVSALSP 1mfrA 2 :SQVRQNYHSDCEAAVNRMLNLELYASYTYSSMYAFFD T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAG 1mfrA 45 :HNVAEFFKEHSHEEREHAEKFMKYQNKRGGRVVLQDIK T0385 90 :PM 1mfrA 83 :KP T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHA 1mfrA 88 :EWGNTLEAMQAALQLEKTVNQALLDLHKLA T0385 122 :ETADDRVFAST 1mfrA 121 :VDPHLCDFLES T0385 133 :ALTESAVMATRWNRV 1mfrA 133 :YLEEQVKDIKRIGDF Number of specific fragments extracted= 6 number of extra gaps= 0 total=193 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bg7/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1bg7 expands to /projects/compbio/data/pdb/1bg7.pdb.gz 1bg7:Warning: there is no chain 1bg7 will retry with 1bg7A # T0385 read from 1bg7/merged-good-all-a2m # 1bg7 read from 1bg7/merged-good-all-a2m # adding 1bg7 to template set # found chain 1bg7 in template set Warning: unaligning (T0385)T11 because first residue in template chain is (1bg7)D1 Warning: unaligning (T0385)P49 because of BadResidue code BAD_PEPTIDE in next template residue (1bg7)D41 Warning: unaligning (T0385)G50 because of BadResidue code BAD_PEPTIDE at template residue (1bg7)D41 Warning: unaligning (T0385)V117 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1bg7)P134 T0385 12 :PKRSPSEGSADNAALCDALAVEHATIYGY 1bg7 2 :SQVRQNFHRDCEAAINRMVNMELYASYTY T0385 41 :GIVSALSP 1bg7 32 :SMAFYFDR T0385 51 :VNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGYQLPMQVSSAADAARLAVRMENDGATAWRA 1bg7 47 :VAKFFKEQSHEEREHAEKLMKDQNKRGGRIVLQDVQKPERDEWGNTLEAMQAALQLEKTVNQALLD Number of specific fragments extracted= 3 number of extra gaps= 1 total=196 Number of alignments=31 # 1bg7 read from 1bg7/merged-good-all-a2m # found chain 1bg7 in template set Warning: unaligning (T0385)T11 because first residue in template chain is (1bg7)D1 Warning: unaligning (T0385)S44 because of BadResidue code BAD_PEPTIDE in next template residue (1bg7)D41 Warning: unaligning (T0385)A45 because of BadResidue code BAD_PEPTIDE at template residue (1bg7)D41 Warning: unaligning (T0385)V117 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1bg7)P134 T0385 12 :PKRSPSEGSADNAALCDALAVEHATIYGY 1bg7 2 :SQVRQNFHRDCEAAINRMVNMELYASYTY T0385 46 :LSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGYQLPMQVSSAADAARLAVRMENDGATAWRA 1bg7 42 :IALHNVAKFFKEQSHEEREHAEKLMKDQNKRGGRIVLQDVQKPERDEWGNTLEAMQAALQLEKTVNQALLD T0385 132 :TALTESAVMATRWNRV 1bg7 139 :KSIKQLGDYITNLKRL Number of specific fragments extracted= 3 number of extra gaps= 1 total=199 Number of alignments=32 # 1bg7 read from 1bg7/merged-good-all-a2m # found chain 1bg7 in template set Warning: unaligning (T0385)T11 because first residue in template chain is (1bg7)D1 Warning: unaligning (T0385)V117 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1bg7)P134 T0385 12 :PKRSPSEGSADNAALCDALAVEHATIYGYGIVSALSP 1bg7 2 :SQVRQNFHRDCEAAINRMVNMELYASYTYLSMAFYFD T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAA 1bg7 45 :HNVAKFFKEQSHEEREHAEKLMKDQNKRGGRIVLQDV T0385 88 :Q 1bg7 82 :Q T0385 90 :PM 1bg7 83 :KP T0385 92 :QVSSAADAARLAVRMENDGATAWRA 1bg7 88 :EWGNTLEAMQAALQLEKTVNQALLD T0385 125 :DDRVFASTALTESAVMATRW 1bg7 135 :EEQVKSIKQLGDYITNLKRL Number of specific fragments extracted= 6 number of extra gaps= 0 total=205 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bcfA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1bcfA expands to /projects/compbio/data/pdb/1bcf.pdb.gz 1bcfA:# T0385 read from 1bcfA/merged-good-all-a2m # 1bcfA read from 1bcfA/merged-good-all-a2m # adding 1bcfA to template set # found chain 1bcfA in template set Warning: unaligning (T0385)P16 because first residue in template chain is (1bcfA)M1 T0385 17 :SEGSADNAALCDALAVEHATIYGY 1bcfA 2 :KGDTKVINYLNKLLGNELVAINQY T0385 44 :S 1bcfA 29 :A T0385 45 :AL 1bcfA 36 :GL T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAA 1bcfA 38 :KRLNDVEYHESIDEMKHADRYIERILFLEGLPNLQD T0385 85 :AGYQ 1bcfA 75 :GKLN T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAE 1bcfA 79 :IGEDVEEMLRSDLALELDGAKNLREAIGYAD T0385 123 :TADDRVFASTALTESAVMATRWNRVLG 1bcfA 113 :DYVSRDMMIEILRDEEGHIDWLETELD Number of specific fragments extracted= 7 number of extra gaps= 0 total=212 Number of alignments=34 # 1bcfA read from 1bcfA/merged-good-all-a2m # found chain 1bcfA in template set Warning: unaligning (T0385)P16 because first residue in template chain is (1bcfA)M1 T0385 17 :SEGSADNAALCDALAVEHATIYGY 1bcfA 2 :KGDTKVINYLNKLLGNELVAINQY T0385 41 :GIVSALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAA 1bcfA 30 :RMFKNWGLKRLNDVEYHESIDEMKHADRYIERILFLEGLPNLQDL T0385 86 :G 1bcfA 76 :K T0385 91 :MQ 1bcfA 77 :LN T0385 93 :VSSAADAARLAVRMENDGATAWRAVVEHAE 1bcfA 80 :GEDVEEMLRSDLALELDGAKNLREAIGYAD T0385 123 :TADDRVFASTALTESAVMATRWNRVL 1bcfA 113 :DYVSRDMMIEILRDEEGHIDWLETEL Number of specific fragments extracted= 6 number of extra gaps= 0 total=218 Number of alignments=35 # 1bcfA read from 1bcfA/merged-good-all-a2m # found chain 1bcfA in template set Warning: unaligning (T0385)P16 because first residue in template chain is (1bcfA)M1 T0385 17 :SEGSADNAALCDALAVEHATIYGYGIVSALSP 1bcfA 2 :KGDTKVINYLNKLLGNELVAINQYFLHARMFK T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAA 1bcfA 38 :KRLNDVEYHESIDEMKHADRYIERILFLEGLPNLQDL T0385 89 :LPM 1bcfA 75 :GKL T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHA 1bcfA 79 :IGEDVEEMLRSDLALELDGAKNLREAIGYA T0385 122 :ETADDRVFASTALTESAVMATRWNRV 1bcfA 112 :HDYVSRDMMIEILRDEEGHIDWLETE Number of specific fragments extracted= 5 number of extra gaps= 0 total=223 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mojA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1mojA expands to /projects/compbio/data/pdb/1moj.pdb.gz 1mojA:# T0385 read from 1mojA/merged-good-all-a2m # 1mojA read from 1mojA/merged-good-all-a2m # adding 1mojA to template set # found chain 1mojA in template set Warning: unaligning (T0385)S3 because first residue in template chain is (1mojA)S2 T0385 4 :SEPAHGATPKRSPSEG 1mojA 3 :TQKNARATAGEVEGSD T0385 21 :ADNAALCDALAVEHATIYGY 1mojA 25 :DRAEQCVDALNADLANVYVL T0385 41 :GIVSALSPPG 1mojA 50 :KHHWNVEGAE T0385 51 :VNFLVADALKQHRHRRDDVIVMLSARGVTAPIAA 1mojA 63 :LHLFLGEAAETAEEVADELAERVQALGGVPHASP T0385 85 :AGYQLPM 1mojA 103 :ASVDVED T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAE 1mojA 111 :DVYDIRTSLANDMAIYGDIIEATREHTELAE T0385 123 :TADDRVFASTALTESAVMATRWNRVLGAWPI 1mojA 145 :DHATAHMLREGLIELEDDAHHIEHYLEDDTL Number of specific fragments extracted= 7 number of extra gaps= 0 total=230 Number of alignments=37 # 1mojA read from 1mojA/merged-good-all-a2m # found chain 1mojA in template set Warning: unaligning (T0385)S3 because first residue in template chain is (1mojA)S2 T0385 4 :SEPAHGATPKRSPSEGS 1mojA 3 :TQKNARATAGEVEGSDA T0385 21 :ADNAALCDALAVEHATIYGY 1mojA 25 :DRAEQCVDALNADLANVYVL T0385 41 :GIVSALSP 1mojA 50 :KHHWNVEG T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAA 1mojA 61 :RDLHLFLGEAAETAEEVADELAERVQALGGVPHASP T0385 85 :AGYQLPMQ 1mojA 103 :ASVDVEDE T0385 93 :VSSAADAARLAVRMENDGATAWRAVVEHAE 1mojA 112 :VYDIRTSLANDMAIYGDIIEATREHTELAE T0385 123 :TADDRVFASTALTESAVMATRWNRVLGAWPI 1mojA 145 :DHATAHMLREGLIELEDDAHHIEHYLEDDTL Number of specific fragments extracted= 7 number of extra gaps= 0 total=237 Number of alignments=38 # 1mojA read from 1mojA/merged-good-all-a2m # found chain 1mojA in template set T0385 7 :AHGATPKRSPSEGSADNAALCDALAVEHATIYGYGIVS 1mojA 11 :AGEVEGSDALRMDADRAEQCVDALNADLANVYVLYHQL T0385 45 :ALSP 1mojA 53 :WNVE T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIA 1mojA 61 :RDLHLFLGEAAETAEEVADELAERVQALGGVPHAS T0385 84 :AAGYQLPM 1mojA 100 :QAEASVDV T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAET 1mojA 111 :DVYDIRTSLANDMAIYGDIIEATREHTELAEN T0385 124 :ADDRVFASTALTESAVMATRWNRVLGAWPI 1mojA 146 :HATAHMLREGLIELEDDAHHIEHYLEDDTL Number of specific fragments extracted= 6 number of extra gaps= 0 total=243 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sofA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0385/1sofA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0385/1sofA/merged-good-all-a2m.gz for input Trying 1sofA/merged-good-all-a2m Error: Couldn't open file 1sofA/merged-good-all-a2m or 1sofA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b5pA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0385 read from 1b5pA/merged-good-all-a2m # 1b5pA read from 1b5pA/merged-good-all-a2m # found chain 1b5pA in training set T0385 16 :PSEGSADNAALCDALA 1b5pA 265 :TSPDTIAQWATLEALT T0385 47 :SPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGYQLPM 1b5pA 281 :NQEASRAFVEMAREAYRRRRDLLLEGLTALGLKAVRPSGAFYVLM T0385 92 :QVSSAADAARLAVR 1b5pA 331 :APDEVRAAERLLEA Number of specific fragments extracted= 3 number of extra gaps= 0 total=246 Number of alignments=40 # 1b5pA read from 1b5pA/merged-good-all-a2m # found chain 1b5pA in training set T0385 17 :SEGSADNAALCDALA 1b5pA 266 :SPDTIAQWATLEALT T0385 47 :SPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGYQL 1b5pA 281 :NQEASRAFVEMAREAYRRRRDLLLEGLTALGLKAVRPSGAFYV T0385 90 :PMQVSSAADAARLAVR 1b5pA 329 :PIAPDEVRAAERLLEA Number of specific fragments extracted= 3 number of extra gaps= 0 total=249 Number of alignments=41 # 1b5pA read from 1b5pA/merged-good-all-a2m # found chain 1b5pA in training set T0385 24 :AALCDALAVEHA 1b5pA 251 :EVIKAMASVSRQ T0385 36 :TIYGYGIVSALSP 1b5pA 269 :TIAQWATLEALTN T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGYQLPMQVSS 1b5pA 283 :EASRAFVEMAREAYRRRRDLLLEGLTALGLKAVRPSGAFYVLMDTSP T0385 96 :AADAARLAVRMEND 1b5pA 331 :APDEVRAAERLLEA Number of specific fragments extracted= 4 number of extra gaps= 0 total=253 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fkzA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fkzA expands to /projects/compbio/data/pdb/2fkz.pdb.gz 2fkzA:Skipped atom 23, because occupancy 0.500 <= existing 0.500 in 2fkzA Skipped atom 25, because occupancy 0.500 <= existing 0.500 in 2fkzA Skipped atom 27, because occupancy 0.500 <= existing 0.500 in 2fkzA Skipped atom 29, because occupancy 0.500 <= existing 0.500 in 2fkzA Skipped atom 31, because occupancy 0.500 <= existing 0.500 in 2fkzA Skipped atom 33, because occupancy 0.500 <= existing 0.500 in 2fkzA Skipped atom 35, because occupancy 0.500 <= existing 0.500 in 2fkzA Skipped atom 37, because occupancy 0.500 <= existing 0.500 in 2fkzA Skipped atom 71, because occupancy 0.500 <= existing 0.500 in 2fkzA Skipped atom 73, because occupancy 0.500 <= existing 0.500 in 2fkzA Skipped atom 75, because occupancy 0.500 <= existing 0.500 in 2fkzA Skipped atom 77, because occupancy 0.500 <= existing 0.500 in 2fkzA Skipped atom 79, because occupancy 0.500 <= existing 0.500 in 2fkzA Skipped atom 81, because occupancy 0.500 <= existing 0.500 in 2fkzA Skipped atom 83, because occupancy 0.500 <= existing 0.500 in 2fkzA Skipped atom 85, because occupancy 0.500 <= existing 0.500 in 2fkzA Skipped atom 87, because occupancy 0.500 <= existing 0.500 in 2fkzA Skipped atom 1029, because occupancy 0.500 <= existing 0.500 in 2fkzA Skipped atom 1031, because occupancy 0.500 <= existing 0.500 in 2fkzA Skipped atom 1033, because occupancy 0.500 <= existing 0.500 in 2fkzA Skipped atom 1035, because occupancy 0.500 <= existing 0.500 in 2fkzA Skipped atom 1037, because occupancy 0.500 <= existing 0.500 in 2fkzA Skipped atom 1039, because occupancy 0.500 <= existing 0.500 in 2fkzA # T0385 read from 2fkzA/merged-good-all-a2m # 2fkzA read from 2fkzA/merged-good-all-a2m # adding 2fkzA to template set # found chain 2fkzA in template set Warning: unaligning (T0385)P16 because first residue in template chain is (2fkzA)M1 T0385 17 :SEGSADNAALCDALAVEHATIYGY 2fkzA 2 :KGDKIVIQHLNKILGNELIAINQY T0385 41 :GIVSALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGYQL 2fkzA 30 :RMYEDWGLEKLGKHEYHESIDEMKHADKLIKRILFLEGLPNLQELGKLL T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAE 2fkzA 79 :IGEHTKEMLECDLKLEQAGLPDLKAAIAYCE T0385 123 :TADDRVFASTALTESAVMATRWNRVLG 2fkzA 113 :DYASRELLEDILESEEDHIDWLETQLD Number of specific fragments extracted= 4 number of extra gaps= 0 total=257 Number of alignments=43 # 2fkzA read from 2fkzA/merged-good-all-a2m # found chain 2fkzA in template set Warning: unaligning (T0385)P16 because first residue in template chain is (2fkzA)M1 T0385 17 :SEGSADNAALCDALAVEHATIYGY 2fkzA 2 :KGDKIVIQHLNKILGNELIAINQY T0385 41 :GIVSALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAG 2fkzA 30 :RMYEDWGLEKLGKHEYHESIDEMKHADKLIKRILFLEGLPNLQELG T0385 89 :LPMQVSSAADAARLAVRMENDGATAWRAVVEHAE 2fkzA 76 :KLLIGEHTKEMLECDLKLEQAGLPDLKAAIAYCE T0385 123 :TADDRVFASTALTESAVMATRWNRVL 2fkzA 113 :DYASRELLEDILESEEDHIDWLETQL Number of specific fragments extracted= 4 number of extra gaps= 0 total=261 Number of alignments=44 # 2fkzA read from 2fkzA/merged-good-all-a2m # found chain 2fkzA in template set T0385 19 :GSADNAALCDALAVEHATIYGYGIVSALSP 2fkzA 4 :DKIVIQHLNKILGNELIAINQYFLHARMYE T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAA 2fkzA 38 :EKLGKHEYHESIDEMKHADKLIKRILFLEGLPNLQEL T0385 88 :QLPMQVSSAADAARLAVRMENDGATAWRAVVEHAE 2fkzA 75 :GKLLIGEHTKEMLECDLKLEQAGLPDLKAAIAYCE T0385 123 :TADDRVFASTALTESAVMATRWNRV 2fkzA 113 :DYASRELLEDILESEEDHIDWLETQ Number of specific fragments extracted= 4 number of extra gaps= 0 total=265 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vlgA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vlgA expands to /projects/compbio/data/pdb/1vlg.pdb.gz 1vlgA:Skipped atom 1084, because occupancy 0.350 <= existing 0.650 in 1vlgA Skipped atom 1086, because occupancy 0.350 <= existing 0.650 in 1vlgA Skipped atom 1088, because occupancy 0.350 <= existing 0.650 in 1vlgA Skipped atom 1090, because occupancy 0.350 <= existing 0.650 in 1vlgA Skipped atom 1092, because occupancy 0.350 <= existing 0.650 in 1vlgA Skipped atom 1094, because occupancy 0.350 <= existing 0.650 in 1vlgA Skipped atom 1096, because occupancy 0.350 <= existing 0.650 in 1vlgA Skipped atom 1098, because occupancy 0.350 <= existing 0.650 in 1vlgA Skipped atom 1100, because occupancy 0.350 <= existing 0.650 in 1vlgA # T0385 read from 1vlgA/merged-good-all-a2m # 1vlgA read from 1vlgA/merged-good-all-a2m # adding 1vlgA to template set # found chain 1vlgA in template set Warning: unaligning (T0385)S15 because first residue in template chain is (1vlgA)M1 Warning: unaligning (T0385)S17 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vlgA)I4 Warning: unaligning (T0385)E18 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vlgA)I4 T0385 16 :P 1vlgA 2 :M T0385 19 :GSADNAALCDALAVEHATIYGY 1vlgA 5 :SEKVRKALNDQLNREIYSSYLY T0385 41 :GIVS 1vlgA 32 :YFDA T0385 45 :AL 1vlgA 37 :GF T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAG 1vlgA 39 :KGFAHWMKKQAQEELTHAMKFYEYIYERGGRVELEAIE T0385 88 :QLPMQVSSAADAARLAVRMENDGATAWRAVVEHAE 1vlgA 77 :KPPSNWNGIKDAFEAALKHEEFVTQSIYNILELAS T0385 123 :TADDRVFASTALTESAVMATRWNRVLG 1vlgA 115 :DHATVSFLKWFVDEQVEEEDQVREILD Number of specific fragments extracted= 7 number of extra gaps= 1 total=272 Number of alignments=46 # 1vlgA read from 1vlgA/merged-good-all-a2m # found chain 1vlgA in template set Warning: unaligning (T0385)S15 because first residue in template chain is (1vlgA)M1 Warning: unaligning (T0385)S17 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vlgA)I4 Warning: unaligning (T0385)E18 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vlgA)I4 T0385 16 :P 1vlgA 2 :M T0385 19 :GSADNAALCDALAVEHATIYGY 1vlgA 5 :SEKVRKALNDQLNREIYSSYLY T0385 41 :GIVSALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAG 1vlgA 31 :TYFDAEGFKGFAHWMKKQAQEELTHAMKFYEYIYERGGRVELEAIE T0385 88 :QLPMQVSSAADAARLAVRMENDGATAWRAVVEHAE 1vlgA 77 :KPPSNWNGIKDAFEAALKHEEFVTQSIYNILELAS T0385 123 :TADDRVFASTALTESAVMATRWNRVL 1vlgA 115 :DHATVSFLKWFVDEQVEEEDQVREIL Number of specific fragments extracted= 5 number of extra gaps= 1 total=277 Number of alignments=47 # 1vlgA read from 1vlgA/merged-good-all-a2m # found chain 1vlgA in template set T0385 19 :GSADNAALCDALAVEHATIYGYGIVSALSP 1vlgA 5 :SEKVRKALNDQLNREIYSSYLYLSMATYFD T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAG 1vlgA 39 :KGFAHWMKKQAQEELTHAMKFYEYIYERGGRVELEAIE T0385 88 :QLPMQVSSAADAARLAVRMENDGATAWRAVVEHAETADD 1vlgA 77 :KPPSNWNGIKDAFEAALKHEEFVTQSIYNILELASEEKD T0385 128 :VFASTALTESAVMATRWNRV 1vlgA 116 :HATVSFLKWFVDEQVEEEDQ Number of specific fragments extracted= 4 number of extra gaps= 0 total=281 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rcd/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1rcd expands to /projects/compbio/data/pdb/1rcd.pdb.gz 1rcd:Warning: there is no chain 1rcd will retry with 1rcdA # T0385 read from 1rcd/merged-good-all-a2m # 1rcd read from 1rcd/merged-good-all-a2m # adding 1rcd to template set # found chain 1rcd in template set Warning: unaligning (T0385)P12 because first residue in template chain is (1rcd)S2 T0385 13 :KRSPSEGSADNAALCDALAVEHATIYGY 1rcd 3 :QVRQNFHQDCEAGLNRTVNLKFHSSYVY T0385 41 :GIVSALSPPG 1rcd 32 :SMASYFNRDD T0385 51 :VNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGYQLPMQVSSAADAARLAVRMENDGATAWRAVVEHAE 1rcd 47 :FAKFFRERSEEEKEHAEKLIEYQNQRGGRVFLQSVEKPERDDWANGLEALQTALKLQKSVNQALLDLHAVAA T0385 123 :TAD 1rcd 122 :DPH T0385 126 :DRVFASTALTESAVMATRWNRVLGAW 1rcd 133 :YLSESVETIKKLGDHITSLKKLWSSH Number of specific fragments extracted= 5 number of extra gaps= 0 total=286 Number of alignments=49 # 1rcd read from 1rcd/merged-good-all-a2m # found chain 1rcd in template set Warning: unaligning (T0385)P12 because first residue in template chain is (1rcd)S2 T0385 13 :KRSPSEGSADNAALCDALAVEHATIYGY 1rcd 3 :QVRQNFHQDCEAGLNRTVNLKFHSSYVY T0385 44 :S 1rcd 35 :S T0385 45 :ALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGYQLPMQVSSAADAARLAVRMENDGATAWRAVVEHAE 1rcd 41 :DVALSNFAKFFRERSEEEKEHAEKLIEYQNQRGGRVFLQSVEKPERDDWANGLEALQTALKLQKSVNQALLDLHAVAA T0385 123 :TADDRVFAS 1rcd 122 :DPHMTDFLE T0385 132 :TALTESAVMATRWNRVLGAW 1rcd 139 :ETIKKLGDHITSLKKLWSSH Number of specific fragments extracted= 5 number of extra gaps= 0 total=291 Number of alignments=50 # 1rcd read from 1rcd/merged-good-all-a2m # found chain 1rcd in template set Warning: unaligning (T0385)P12 because first residue in template chain is (1rcd)S2 T0385 13 :KRSPSEGSADNAALCDALAVEHATIYGYGIVSALSP 1rcd 3 :QVRQNFHQDCEAGLNRTVNLKFHSSYVYLSMASYFN T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAG 1rcd 45 :SNFAKFFRERSEEEKEHAEKLIEYQNQRGGRVFLQSVE T0385 90 :PM 1rcd 83 :KP T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAE 1rcd 88 :DWANGLEALQTALKLQKSVNQALLDLHAVAA T0385 123 :TADDRVFA 1rcd 122 :DPHMTDFL T0385 132 :TALTESAVMATRWNRVLG 1rcd 139 :ETIKKLGDHITSLKKLWS Number of specific fragments extracted= 6 number of extra gaps= 0 total=297 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r03A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1r03A expands to /projects/compbio/data/pdb/1r03.pdb.gz 1r03A:Skipped atom 497, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 499, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 501, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 503, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 505, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 507, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 509, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 511, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 513, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 539, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 541, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 543, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 545, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 547, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 549, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 551, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 553, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 555, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 584, because occupancy 0.300 <= existing 0.700 in 1r03A Skipped atom 586, because occupancy 0.300 <= existing 0.700 in 1r03A Skipped atom 588, because occupancy 0.300 <= existing 0.700 in 1r03A Skipped atom 590, because occupancy 0.300 <= existing 0.700 in 1r03A Skipped atom 592, because occupancy 0.300 <= existing 0.700 in 1r03A Skipped atom 594, because occupancy 0.300 <= existing 0.700 in 1r03A Skipped atom 596, because occupancy 0.300 <= existing 0.700 in 1r03A Skipped atom 598, because occupancy 0.300 <= existing 0.700 in 1r03A Skipped atom 617, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 619, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 621, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 623, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 625, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 627, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 629, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 631, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 633, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 890, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 892, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 894, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 896, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 898, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 900, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 902, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 904, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 906, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 1100, because occupancy 0.330 <= existing 0.670 in 1r03A Skipped atom 1102, because occupancy 0.330 <= existing 0.670 in 1r03A Skipped atom 1104, because occupancy 0.330 <= existing 0.670 in 1r03A Skipped atom 1106, because occupancy 0.330 <= existing 0.670 in 1r03A Skipped atom 1108, because occupancy 0.330 <= existing 0.670 in 1r03A Skipped atom 1110, because occupancy 0.330 <= existing 0.670 in 1r03A Skipped atom 1112, because occupancy 0.330 <= existing 0.670 in 1r03A Skipped atom 1114, because occupancy 0.330 <= existing 0.670 in 1r03A Skipped atom 1116, because occupancy 0.330 <= existing 0.670 in 1r03A Skipped atom 1165, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 1167, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 1169, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 1171, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 1173, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 1175, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 1177, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 1179, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 1181, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 1208, because occupancy 0.330 <= existing 0.670 in 1r03A Skipped atom 1210, because occupancy 0.330 <= existing 0.670 in 1r03A Skipped atom 1212, because occupancy 0.330 <= existing 0.670 in 1r03A Skipped atom 1214, because occupancy 0.330 <= existing 0.670 in 1r03A Skipped atom 1216, because occupancy 0.330 <= existing 0.670 in 1r03A Skipped atom 1218, because occupancy 0.330 <= existing 0.670 in 1r03A Skipped atom 1427, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 1429, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 1431, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 1433, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 1435, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 1437, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 1439, because occupancy 0.500 <= existing 0.500 in 1r03A # T0385 read from 1r03A/merged-good-all-a2m # 1r03A read from 1r03A/merged-good-all-a2m # adding 1r03A to template set # found chain 1r03A in template set Warning: unaligning (T0385)P12 because first residue in template chain is (1r03A)S6 T0385 13 :KRSPSEGSADNAALCDALAVEHATIYGY 1r03A 7 :RVRQNFHPDSEAAINRQINLELYASYVY T0385 41 :GIVSALSPPG 1r03A 36 :SMAYYFSRDD T0385 51 :VNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGY 1r03A 51 :FSRYFLHQSREETEHAEKLMRLQNQRGGRIRLQDIKK T0385 90 :PM 1r03A 88 :PE T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAE 1r03A 92 :DWESGLHAMECALLLEKNVNQSLLELHALAS T0385 123 :TADDRVFAST 1r03A 126 :DPHLCDFLET T0385 133 :ALTESAVMATRWNRVLG 1r03A 137 :YLNEQVKSIKELGDHVH Number of specific fragments extracted= 7 number of extra gaps= 0 total=304 Number of alignments=52 # 1r03A read from 1r03A/merged-good-all-a2m # found chain 1r03A in template set Warning: unaligning (T0385)P12 because first residue in template chain is (1r03A)S6 T0385 13 :KRSPSEGSADNAALCDALAVEHATIYGY 1r03A 7 :RVRQNFHPDSEAAINRQINLELYASYVY T0385 43 :V 1r03A 41 :F T0385 45 :ALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGYQLPMQVSSAADAARLAVRMENDGATAWRAVVEHAE 1r03A 45 :DVALNNFSRYFLHQSREETEHAEKLMRLQNQRGGRIRLQDIKKPEQDDWESGLHAMECALLLEKNVNQSLLELHALAS T0385 123 :TADDRVFAS 1r03A 126 :DPHLCDFLE T0385 132 :TALTESAVMATRWNRV 1r03A 143 :KSIKELGDHVHNLVKM Number of specific fragments extracted= 5 number of extra gaps= 0 total=309 Number of alignments=53 # 1r03A read from 1r03A/merged-good-all-a2m # found chain 1r03A in template set Warning: unaligning (T0385)P12 because first residue in template chain is (1r03A)S6 T0385 13 :KRSPSEGSADNAALCDALAVEHATIYGYGIVSALSP 1r03A 7 :RVRQNFHPDSEAAINRQINLELYASYVYLSMAYYFS T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAG 1r03A 49 :NNFSRYFLHQSREETEHAEKLMRLQNQRGGRIRLQDIK T0385 90 :PM 1r03A 87 :KP T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAETAD 1r03A 92 :DWESGLHAMECALLLEKNVNQSLLELHALASDKG T0385 126 :DRVFASTALTESAVMATRWNR 1r03A 140 :EQVKSIKELGDHVHNLVKMGA Number of specific fragments extracted= 5 number of extra gaps= 0 total=314 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nfvA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1nfvA expands to /projects/compbio/data/pdb/1nfv.pdb.gz 1nfvA:Skipped atom 443, because occupancy 0.400 <= existing 0.600 in 1nfvA Skipped atom 445, because occupancy 0.400 <= existing 0.600 in 1nfvA Skipped atom 447, because occupancy 0.400 <= existing 0.600 in 1nfvA Skipped atom 449, because occupancy 0.400 <= existing 0.600 in 1nfvA Skipped atom 451, because occupancy 0.400 <= existing 0.600 in 1nfvA Skipped atom 453, because occupancy 0.400 <= existing 0.600 in 1nfvA Skipped atom 455, because occupancy 0.400 <= existing 0.600 in 1nfvA Skipped atom 457, because occupancy 0.400 <= existing 0.600 in 1nfvA Skipped atom 459, because occupancy 0.400 <= existing 0.600 in 1nfvA Skipped atom 461, because occupancy 0.400 <= existing 0.600 in 1nfvA Skipped atom 463, because occupancy 0.400 <= existing 0.600 in 1nfvA Skipped atom 990, because occupancy 0.420 <= existing 0.580 in 1nfvA Skipped atom 992, because occupancy 0.420 <= existing 0.580 in 1nfvA Skipped atom 994, because occupancy 0.420 <= existing 0.580 in 1nfvA Skipped atom 996, because occupancy 0.420 <= existing 0.580 in 1nfvA Skipped atom 998, because occupancy 0.420 <= existing 0.580 in 1nfvA Skipped atom 1000, because occupancy 0.420 <= existing 0.580 in 1nfvA Skipped atom 1002, because occupancy 0.420 <= existing 0.580 in 1nfvA Skipped atom 1004, because occupancy 0.420 <= existing 0.580 in 1nfvA Skipped atom 1006, because occupancy 0.420 <= existing 0.580 in 1nfvA Skipped atom 1008, because occupancy 0.420 <= existing 0.580 in 1nfvA Skipped atom 1010, because occupancy 0.420 <= existing 0.580 in 1nfvA Skipped atom 1315, because occupancy 0.470 <= existing 0.520 in 1nfvA Skipped atom 1317, because occupancy 0.470 <= existing 0.520 in 1nfvA Skipped atom 1319, because occupancy 0.470 <= existing 0.520 in 1nfvA Skipped atom 1321, because occupancy 0.470 <= existing 0.520 in 1nfvA Skipped atom 1323, because occupancy 0.470 <= existing 0.520 in 1nfvA Skipped atom 1325, because occupancy 0.470 <= existing 0.520 in 1nfvA Skipped atom 1327, because occupancy 0.300 <= existing 0.700 in 1nfvA Skipped atom 1329, because occupancy 0.300 <= existing 0.700 in 1nfvA Skipped atom 1331, because occupancy 0.300 <= existing 0.700 in 1nfvA Skipped atom 1333, because occupancy 0.300 <= existing 0.700 in 1nfvA Skipped atom 1335, because occupancy 0.300 <= existing 0.700 in 1nfvA Skipped atom 1337, because occupancy 0.300 <= existing 0.700 in 1nfvA Skipped atom 1339, because occupancy 0.300 <= existing 0.700 in 1nfvA Skipped atom 1341, because occupancy 0.300 <= existing 0.700 in 1nfvA Skipped atom 1343, because occupancy 0.300 <= existing 0.700 in 1nfvA # T0385 read from 1nfvA/merged-good-all-a2m # 1nfvA read from 1nfvA/merged-good-all-a2m # adding 1nfvA to template set # found chain 1nfvA in template set T0385 21 :ADNAALCDALAVEHATIYGY 1nfvA 11 :KVIEVLNKARAMELHAIHQY T0385 41 :GIVS 1nfvA 36 :SLDD T0385 46 :LSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGYQL 1nfvA 40 :MDYGELAANMKLIAIDEMRHAENFAERIKELGGEPTTQKEGKVV T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAETAD 1nfvA 84 :TGQAVPVIYESDADQEDATIEAYSQFLKVCKEQG T0385 126 :DRVFASTALTESAVMATRWNRVLG 1nfvA 121 :TARLFERIIEEEQAHLTYYENIGS Number of specific fragments extracted= 5 number of extra gaps= 0 total=319 Number of alignments=55 # 1nfvA read from 1nfvA/merged-good-all-a2m # found chain 1nfvA in template set T0385 21 :ADNAALCDALAVEHATIYGY 1nfvA 11 :KVIEVLNKARAMELHAIHQY T0385 41 :GIVSALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAG 1nfvA 35 :YSLDDMDYGELAANMKLIAIDEMRHAENFAERIKELGGEPTTQKEG T0385 90 :PMQVSSAADAARLAVRMENDGATAWRAVVEHAE 1nfvA 82 :VVTGQAVPVIYESDADQEDATIEAYSQFLKVCK T0385 123 :TADDRVFASTALTESAVMATRWNRVLG 1nfvA 118 :DIVTARLFERIIEEEQAHLTYYENIGS T0385 150 :AWPITAAFPGGDE 1nfvA 159 :GTPSSTGTASKGF Number of specific fragments extracted= 5 number of extra gaps= 0 total=324 Number of alignments=56 # 1nfvA read from 1nfvA/merged-good-all-a2m # found chain 1nfvA in template set Warning: unaligning (T0385)R14 because first residue in template chain is (1nfvA)N4 Warning: unaligning (T0385)P16 because of BadResidue code BAD_PEPTIDE in next template residue (1nfvA)D7 Warning: unaligning (T0385)S17 because of BadResidue code BAD_PEPTIDE at template residue (1nfvA)D7 T0385 15 :S 1nfvA 5 :R T0385 18 :EGSADNAALCDALAVEHATIYGYGIVSALSP 1nfvA 8 :RKAKVIEVLNKARAMELHAIHQYMNQHYSLD T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAG 1nfvA 43 :GELAANMKLIAIDEMRHAENFAERIKELGGEPTTQKEG T0385 90 :PM 1nfvA 81 :KV T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAETAD 1nfvA 84 :TGQAVPVIYESDADQEDATIEAYSQFLKVCKEQG T0385 126 :DRVFASTALTESAVMATRWNRV 1nfvA 121 :TARLFERIIEEEQAHLTYYENI Number of specific fragments extracted= 6 number of extra gaps= 1 total=330 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dat/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1dat expands to /projects/compbio/data/pdb/1dat.pdb.gz 1dat:Warning: there is no chain 1dat will retry with 1datA # T0385 read from 1dat/merged-good-all-a2m # 1dat read from 1dat/merged-good-all-a2m # adding 1dat to template set # found chain 1dat in template set Warning: unaligning (T0385)P12 because of BadResidue code BAD_PEPTIDE at template residue (1dat)S2 Warning: unaligning (T0385)K13 because of BadResidue code BAD_PEPTIDE at template residue (1dat)Q3 T0385 14 :RSPSEGSADNAALCDALAVEHATIYGY 1dat 4 :IRQNYSTEVEAAVNRLVNLYLRASYTY T0385 42 :IVSALSPPG 1dat 33 :LGFYFDRDD T0385 51 :VNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAG 1dat 47 :VCHFFRELAEEKREGAERLLKMQNQRGGRALFQDLQ T0385 89 :LPM 1dat 83 :KPS T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAE 1dat 88 :EWGTTPDAMKAAIVLEKSLNQALLDLHALGS T0385 123 :TADDRVFAST 1dat 122 :DPHLCDFLES T0385 133 :ALTESAVMATRWNRVLG 1dat 140 :LIKKMGDHLTNIQRLVG Number of specific fragments extracted= 7 number of extra gaps= 1 total=337 Number of alignments=58 # 1dat read from 1dat/merged-good-all-a2m # found chain 1dat in template set Warning: unaligning (T0385)P12 because of BadResidue code BAD_PEPTIDE at template residue (1dat)S2 Warning: unaligning (T0385)K13 because of BadResidue code BAD_PEPTIDE at template residue (1dat)Q3 T0385 14 :RSPSEGSADNAALCDALAVEHATIYGY 1dat 4 :IRQNYSTEVEAAVNRLVNLYLRASYTY T0385 41 :GI 1dat 34 :GF T0385 43 :VSALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAG 1dat 39 :RDDVALEGVCHFFRELAEEKREGAERLLKMQNQRGGRALFQDLQ T0385 88 :QLPM 1dat 83 :KPSQ T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAE 1dat 88 :EWGTTPDAMKAAIVLEKSLNQALLDLHALGS T0385 123 :TADDRVFAS 1dat 122 :DPHLCDFLE T0385 132 :TALTESAVMATRWNRVLG 1dat 139 :KLIKKMGDHLTNIQRLVG Number of specific fragments extracted= 7 number of extra gaps= 1 total=344 Number of alignments=59 # 1dat read from 1dat/merged-good-all-a2m # found chain 1dat in template set Warning: unaligning (T0385)T11 because first residue in template chain is (1dat)S1 Warning: unaligning (T0385)P12 because of BadResidue code BAD_PEPTIDE at template residue (1dat)S2 Warning: unaligning (T0385)K13 because of BadResidue code BAD_PEPTIDE at template residue (1dat)Q3 T0385 14 :RSPSEGSADNAALCDALAVEHATIYGYGIVSALSP 1dat 4 :IRQNYSTEVEAAVNRLVNLYLRASYTYLSLGFYFD T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAG 1dat 45 :EGVCHFFRELAEEKREGAERLLKMQNQRGGRALFQDLQ T0385 90 :PM 1dat 83 :KP T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHA 1dat 88 :EWGTTPDAMKAAIVLEKSLNQALLDLHALG T0385 122 :ETADDRVFASTALTESAVMATRWNRV 1dat 121 :ADPHLCDFLESHFLDEEVKLIKKMGD Number of specific fragments extracted= 5 number of extra gaps= 0 total=349 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vjxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vjxA expands to /projects/compbio/data/pdb/1vjx.pdb.gz 1vjxA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 209, because occupancy 0.500 <= existing 0.500 in 1vjxA Skipped atom 211, because occupancy 0.500 <= existing 0.500 in 1vjxA Skipped atom 213, because occupancy 0.500 <= existing 0.500 in 1vjxA Skipped atom 215, because occupancy 0.500 <= existing 0.500 in 1vjxA Skipped atom 217, because occupancy 0.500 <= existing 0.500 in 1vjxA Skipped atom 219, because occupancy 0.500 <= existing 0.500 in 1vjxA Skipped atom 221, because occupancy 0.500 <= existing 0.500 in 1vjxA Skipped atom 223, because occupancy 0.500 <= existing 0.500 in 1vjxA Skipped atom 225, because occupancy 0.500 <= existing 0.500 in 1vjxA Skipped atom 227, because occupancy 0.500 <= existing 0.500 in 1vjxA Skipped atom 229, because occupancy 0.500 <= existing 0.500 in 1vjxA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0385 read from 1vjxA/merged-good-all-a2m # 1vjxA read from 1vjxA/merged-good-all-a2m # adding 1vjxA to template set # found chain 1vjxA in template set Warning: unaligning (T0385)P16 because first residue in template chain is (1vjxA)H-3 Warning: unaligning (T0385)S17 because of BadResidue code BAD_PEPTIDE at template residue (1vjxA)H-2 Warning: unaligning (T0385)S47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vjxA)N29 Warning: unaligning (T0385)P48 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vjxA)N29 T0385 18 :EGSADNAALCDALAVEHATIYGYGIVSAL 1vjxA -1 :HHMKVSDILTVAIRLEEEGERFYRELSEH T0385 49 :PGVNFLVADALKQHRHRRDDVIVM 1vjxA 30 :GEIKKTFLELADQERIHAEIFRKM T0385 76 :RGVTAP 1vjxA 62 :VDSYLA T0385 83 :AAAGYQLPM 1vjxA 68 :GYAFYEVFP T0385 95 :SAADAARLAVRMENDGATAWRAVVEHAETADDRVFASTALTESAVMATRWNRVLG 1vjxA 88 :TLKEVLDIAISVEKDSIILYYELKDGLVNSDAQKTVKKIIDQEKEHLRKLLEMKR Number of specific fragments extracted= 5 number of extra gaps= 1 total=354 Number of alignments=61 # 1vjxA read from 1vjxA/merged-good-all-a2m # found chain 1vjxA in template set Warning: unaligning (T0385)P16 because first residue in template chain is (1vjxA)H-3 Warning: unaligning (T0385)S17 because of BadResidue code BAD_PEPTIDE at template residue (1vjxA)H-2 Warning: unaligning (T0385)S47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vjxA)N29 Warning: unaligning (T0385)P48 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vjxA)N29 T0385 18 :EGSADNAALCDALAVEHATIYGYGIVSAL 1vjxA -1 :HHMKVSDILTVAIRLEEEGERFYRELSEH T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLS 1vjxA 30 :GEIKKTFLELADQERIHAEIFRKMSD T0385 75 :ARGVTAP 1vjxA 61 :EVDSYLA T0385 83 :AAAGYQLPM 1vjxA 68 :GYAFYEVFP T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAETADDRVFASTALTESAVMATRWNRVL 1vjxA 85 :KDLTLKEVLDIAISVEKDSIILYYELKDGLVNSDAQKTVKKIIDQEKEHLRKLLEMK Number of specific fragments extracted= 5 number of extra gaps= 1 total=359 Number of alignments=62 # 1vjxA read from 1vjxA/merged-good-all-a2m # found chain 1vjxA in template set Warning: unaligning (T0385)S47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vjxA)N29 Warning: unaligning (T0385)P48 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vjxA)N29 T0385 22 :DNAALCDALAVEHATIYGYGIVSAL 1vjxA 3 :VSDILTVAIRLEEEGERFYRELSEH T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSAR 1vjxA 30 :GEIKKTFLELADQERIHAEIFRKMSDQE T0385 77 :GVTAPIAAAGYQLPMQV 1vjxA 71 :FYEVFPDTSEILRRKDL T0385 95 :SAADAARLAVRMENDGATAWRAVVEHAETADDRVFASTALTESAVMATRWNRV 1vjxA 88 :TLKEVLDIAISVEKDSIILYYELKDGLVNSDAQKTVKKIIDQEKEHLRKLLEM Number of specific fragments extracted= 4 number of extra gaps= 1 total=363 Number of alignments=63 # command:# PrintAlignmentsContacts allconstraints.under Using radius: 8.0000 NUMB_ALIGNS: 63 Done printing distance constraints # command: