# 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/T0283/ # command:# Making conformation for sequence T0283 numbered 1 through 112 Created new target T0283 from T0283.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0283/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0283//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0283/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0283//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0283/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0283/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0283/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2hpaA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2hpaA expands to /projects/compbio/data/pdb/2hpa.pdb.gz 2hpaA:# T0283 read from 2hpaA/merged-good-all-a2m # 2hpaA read from 2hpaA/merged-good-all-a2m # adding 2hpaA to template set # found chain 2hpaA in template set T0283 4 :IEKMIGSLNDKREWKAMEARAK 2hpaA 1129 :CPRFQELESETLKSEEFQKRLH # choosing archetypes in rotamer library T0283 30 :EYHHAYKAIQK 2hpaA 1151 :PYKDFIATLGK T0283 45 :SGGPTD 2hpaA 1162 :LSGLHG T0283 52 :QDTKRIFGGILDLFEEGAAEGKKVTDLTGEDVAAFCDELMK 2hpaA 1168 :QDLFGIWSKVYDPLYCESVHNFTLPSWATEDTMTKLRELSE Number of specific fragments extracted= 4 number of extra gaps= 0 total=4 Number of alignments=1 # 2hpaA read from 2hpaA/merged-good-all-a2m # found chain 2hpaA in template set T0283 4 :IEKMIGSLNDKREWKAMEARAK 2hpaA 1129 :CPRFQELESETLKSEEFQKRLH T0283 30 :EYHHAYKAIQK 2hpaA 1151 :PYKDFIATLGK T0283 45 :SGGPTD 2hpaA 1162 :LSGLHG T0283 52 :QDTKRIFGGILDLFEEGAAEGKKVTDLTGEDVAAFCDELMK 2hpaA 1168 :QDLFGIWSKVYDPLYCESVHNFTLPSWATEDTMTKLRELSE Number of specific fragments extracted= 4 number of extra gaps= 0 total=8 Number of alignments=2 # 2hpaA read from 2hpaA/merged-good-all-a2m # found chain 2hpaA in template set T0283 2 :SFIEKMIGSLNDKREWKAMEARAK 2hpaA 1127 :RNCPRFQELESETLKSEEFQKRLH T0283 30 :EYHHAYKAIQKY 2hpaA 1151 :PYKDFIATLGKL T0283 45 :SGGPT 2hpaA 1163 :SGLHG T0283 52 :QDTKRIFGGILDLFEEGAAEGKKVTDLTGEDVAAFCDELMKD 2hpaA 1168 :QDLFGIWSKVYDPLYCESVHNFTLPSWATEDTMTKLRELSEL Number of specific fragments extracted= 4 number of extra gaps= 0 total=12 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nox/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0283 read from 1nox/merged-good-all-a2m # 1nox read from 1nox/merged-good-all-a2m # found chain 1nox in training set T0283 11 :LNDKREWKAMEARAKALPKEYH 1nox 107 :ERREAQKQAIQRAFAAMGQEAR T0283 39 :QKYMWT 1nox 129 :KAWASG T0283 53 :DTKRIFGGILDLFEE 1nox 135 :QSYILLGYLLLLLEA T0283 71 :EGKKVTDLTG 1nox 150 :YGLGSVPMLG T0283 81 :EDVAAFC 1nox 163 :ERVRAIL Number of specific fragments extracted= 5 number of extra gaps= 0 total=17 Number of alignments=4 # 1nox read from 1nox/merged-good-all-a2m # found chain 1nox in training set T0283 12 :NDKREWKAMEARAKALPKEYH 1nox 108 :RREAQKQAIQRAFAAMGQEAR T0283 39 :QKYMWT 1nox 129 :KAWASG T0283 53 :DTKRIFGGILDLFEE 1nox 135 :QSYILLGYLLLLLEA T0283 71 :EGKKVTDLTG 1nox 150 :YGLGSVPMLG T0283 81 :EDVAAFC 1nox 163 :ERVRAIL Number of specific fragments extracted= 5 number of extra gaps= 0 total=22 Number of alignments=5 # 1nox read from 1nox/merged-good-all-a2m # found chain 1nox in training set T0283 10 :SLNDKREWKAMEARAKALPKEYHHAYKA 1nox 106 :GERREAQKQAIQRAFAAMGQEARKAWAS T0283 52 :QDTKRIFGGILDLFEE 1nox 134 :GQSYILLGYLLLLLEA T0283 71 :EGKKVTDLTG 1nox 150 :YGLGSVPMLG T0283 81 :EDVAAF 1nox 163 :ERVRAI Number of specific fragments extracted= 4 number of extra gaps= 0 total=26 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kw4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0283 read from 1kw4A/merged-good-all-a2m # 1kw4A read from 1kw4A/merged-good-all-a2m # found chain 1kw4A in training set T0283 18 :KAMEARAKALP 1kw4A 20 :DDVSNFIRELP T0283 29 :KEYHHAYKA 1kw4A 33 :QDYVDDFIQ T0283 47 :GPTDWQDTKRI 1kw4A 42 :QEIDGQALLRL T0283 66 :E 1kw4A 54 :E T0283 88 :DELMKD 1kw4A 55 :KHLVNA T0283 94 :TKTWMDKYRTKLND 1kw4A 64 :KLGPALKIVAKVES Number of specific fragments extracted= 6 number of extra gaps= 0 total=32 Number of alignments=7 # 1kw4A read from 1kw4A/merged-good-all-a2m # found chain 1kw4A in training set T0283 18 :KAMEARAKALP 1kw4A 20 :DDVSNFIRELP T0283 29 :KEYHHAYKA 1kw4A 33 :QDYVDDFIQ T0283 47 :GPTDWQDTKRI 1kw4A 42 :QEIDGQALLRL T0283 88 :DELMKD 1kw4A 55 :KHLVNA T0283 94 :TKTWMDKYRTKLND 1kw4A 64 :KLGPALKIVAKVES Number of specific fragments extracted= 5 number of extra gaps= 0 total=37 Number of alignments=8 # 1kw4A read from 1kw4A/merged-good-all-a2m # found chain 1kw4A in training set T0283 18 :KAMEARAKALP 1kw4A 20 :DDVSNFIRELP T0283 30 :EYHHAY 1kw4A 34 :DYVDDF T0283 36 :KAIQK 1kw4A 47 :QALLR T0283 41 :YMWTSGGPT 1kw4A 56 :HLVNAMGMK T0283 51 :WQDTKRIFGGI 1kw4A 65 :LGPALKIVAKV Number of specific fragments extracted= 5 number of extra gaps= 0 total=42 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1colA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1colA expands to /projects/compbio/data/pdb/1col.pdb.gz 1colA:# T0283 read from 1colA/merged-good-all-a2m # 1colA read from 1colA/merged-good-all-a2m # adding 1colA to template set # found chain 1colA in template set T0283 2 :SFIEKMIGS 1colA 10 :ELLEKTSEL T0283 17 :WKAMEARA 1colA 19 :IAGMGDKI T0283 25 :KALPKEYHHAYKAIQKYMWTSGGPT 1colA 28 :EHLGDKYKAIAKDIADNIKNFQGKT T0283 50 :DWQDTKRIFGGIL 1colA 55 :SFDDAMASLNKIT T0283 77 :DLTGEDVAAFC 1colA 73 :KINKADRDALV T0283 89 :ELMKD 1colA 84 :NAWKH T0283 94 :TKTWMDKYRT 1colA 91 :AQDMANKLGN Number of specific fragments extracted= 7 number of extra gaps= 0 total=49 Number of alignments=10 # 1colA read from 1colA/merged-good-all-a2m # found chain 1colA in template set T0283 2 :SFIEKMIGS 1colA 10 :ELLEKTSEL T0283 17 :WKAMEARA 1colA 19 :IAGMGDKI T0283 25 :KALPKEYHHAYKAIQKYMWTSGGPT 1colA 28 :EHLGDKYKAIAKDIADNIKNFQGKT T0283 50 :DWQDTKRIFGGIL 1colA 55 :SFDDAMASLNKIT T0283 77 :DLTGEDVAAFCD 1colA 73 :KINKADRDALVN T0283 90 :LMKD 1colA 85 :AWKH T0283 94 :TKTWMDKYR 1colA 91 :AQDMANKLG Number of specific fragments extracted= 7 number of extra gaps= 0 total=56 Number of alignments=11 # 1colA read from 1colA/merged-good-all-a2m # found chain 1colA in template set T0283 2 :SFIEKMIGS 1colA 10 :ELLEKTSEL T0283 17 :WKAMEARA 1colA 19 :IAGMGDKI T0283 25 :KALPKEYHHAYKAIQKYMWTSGGPT 1colA 28 :EHLGDKYKAIAKDIADNIKNFQGKT T0283 50 :DWQDTKRIFGGIL 1colA 55 :SFDDAMASLNKIT T0283 63 :DLFEEGAAE 1colA 80 :DALVNAWKH T0283 78 :LTG 1colA 89 :VDA T0283 96 :TWMDKYRTKLNDSI 1colA 92 :QDMANKLGNLSKAF Number of specific fragments extracted= 7 number of extra gaps= 0 total=63 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nd6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1nd6A expands to /projects/compbio/data/pdb/1nd6.pdb.gz 1nd6A:# T0283 read from 1nd6A/merged-good-all-a2m # 1nd6A read from 1nd6A/merged-good-all-a2m # adding 1nd6A to template set # found chain 1nd6A in template set T0283 2 :SFIEKMIGSLNDKREWKAMEARAK 1nd6A 127 :RNCPRFQELESETLKSEEFQKRLH T0283 30 :EYHHAYKAIQK 1nd6A 151 :PYKDFIATLGK T0283 45 :SGGPTD 1nd6A 162 :LSGLHG T0283 52 :QDTKRIFGGILDLFEEGAAEGKKVTDLTGEDVAAFCDELMK 1nd6A 168 :QDLFGIWSKVYDPLYCESVHNFTLPSWATEDTMTKLRELSE Number of specific fragments extracted= 4 number of extra gaps= 0 total=67 Number of alignments=13 # 1nd6A read from 1nd6A/merged-good-all-a2m # found chain 1nd6A in template set T0283 3 :FIEKMIGSLNDKREWKAMEARAK 1nd6A 128 :NCPRFQELESETLKSEEFQKRLH T0283 30 :EYHHAYKAIQK 1nd6A 151 :PYKDFIATLGK T0283 45 :SGGPTD 1nd6A 162 :LSGLHG T0283 52 :QDTKRIFGGILDLFEEGAAEGKKVTDLTGEDVAAFCDELMK 1nd6A 168 :QDLFGIWSKVYDPLYCESVHNFTLPSWATEDTMTKLRELSE Number of specific fragments extracted= 4 number of extra gaps= 0 total=71 Number of alignments=14 # 1nd6A read from 1nd6A/merged-good-all-a2m # found chain 1nd6A in template set T0283 2 :SFIEKMIGSLNDKREWKAMEARAK 1nd6A 127 :RNCPRFQELESETLKSEEFQKRLH T0283 30 :EYHHAYKAIQK 1nd6A 151 :PYKDFIATLGK T0283 44 :TSGGPT 1nd6A 162 :LSGLHG T0283 52 :QDTKRIFGGILDLFEEGAAEGKKVTDLTGEDVAAFCDELMKD 1nd6A 168 :QDLFGIWSKVYDPLYCESVHNFTLPSWATEDTMTKLRELSEL Number of specific fragments extracted= 4 number of extra gaps= 0 total=75 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a0p/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1a0p expands to /projects/compbio/data/pdb/1a0p.pdb.gz 1a0p:Warning: there is no chain 1a0p will retry with 1a0pA # T0283 read from 1a0p/merged-good-all-a2m # 1a0p read from 1a0p/merged-good-all-a2m # adding 1a0p to template set # found chain 1a0p in template set Warning: unaligning (T0283)G46 because of BadResidue code BAD_PEPTIDE in next template residue (1a0p)K19 Warning: unaligning (T0283)G47 because of BadResidue code BAD_PEPTIDE at template residue (1a0p)K19 Warning: unaligning (T0283)P48 because of BadResidue code BAD_PEPTIDE at template residue (1a0p)N20 Warning: unaligning (T0283)W51 because of BadResidue code BAD_PEPTIDE in next template residue (1a0p)N24 Warning: unaligning (T0283)Q52 because of BadResidue code BAD_PEPTIDE at template residue (1a0p)N24 Warning: unaligning (T0283)F58 because of BadResidue code BAD_PEPTIDE in next template residue (1a0p)R31 Warning: unaligning (T0283)G59 because of BadResidue code BAD_PEPTIDE at template residue (1a0p)R31 Warning: unaligning (T0283)G72 because of BadResidue code BAD_PEPTIDE in next template residue (1a0p)L45 Warning: unaligning (T0283)K73 because of BadResidue code BAD_PEPTIDE at template residue (1a0p)L45 Warning: unaligning (T0283)D93 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1a0p)R62 Warning: unaligning (T0283)W97 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1a0p)S71 T0283 32 :HHAYKAIQKYMWT 1a0p 5 :LARIEQFLDALWL T0283 49 :TD 1a0p 21 :LA T0283 53 :DTKRI 1a0p 25 :TLNAY T0283 60 :GILDLFEEGAAE 1a0p 32 :DLSMMVEWLHHR T0283 74 :KVTDLTGEDVA 1a0p 46 :TLATAQSDDLQ T0283 89 :ELMK 1a0p 57 :ALLA T0283 98 :MDKYRTKLN 1a0p 72 :SARLLSAVR Number of specific fragments extracted= 7 number of extra gaps= 5 total=82 Number of alignments=16 # 1a0p read from 1a0p/merged-good-all-a2m # found chain 1a0p in template set Warning: unaligning (T0283)G46 because of BadResidue code BAD_PEPTIDE in next template residue (1a0p)K19 Warning: unaligning (T0283)G47 because of BadResidue code BAD_PEPTIDE at template residue (1a0p)K19 Warning: unaligning (T0283)P48 because of BadResidue code BAD_PEPTIDE at template residue (1a0p)N20 Warning: unaligning (T0283)W51 because of BadResidue code BAD_PEPTIDE in next template residue (1a0p)N24 Warning: unaligning (T0283)Q52 because of BadResidue code BAD_PEPTIDE at template residue (1a0p)N24 Warning: unaligning (T0283)F58 because of BadResidue code BAD_PEPTIDE in next template residue (1a0p)R31 Warning: unaligning (T0283)G59 because of BadResidue code BAD_PEPTIDE at template residue (1a0p)R31 Warning: unaligning (T0283)G72 because of BadResidue code BAD_PEPTIDE in next template residue (1a0p)L45 Warning: unaligning (T0283)K73 because of BadResidue code BAD_PEPTIDE at template residue (1a0p)L45 Warning: unaligning (T0283)D93 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1a0p)R62 Warning: unaligning (T0283)W97 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1a0p)S71 T0283 32 :HHAYKAIQKYMWT 1a0p 5 :LARIEQFLDALWL T0283 49 :TD 1a0p 21 :LA T0283 53 :DTKRI 1a0p 25 :TLNAY T0283 60 :GILDLFEEGAAE 1a0p 32 :DLSMMVEWLHHR T0283 74 :KVTDLTGEDVA 1a0p 46 :TLATAQSDDLQ T0283 89 :ELMK 1a0p 57 :ALLA T0283 98 :MDKYRTKLN 1a0p 72 :SARLLSAVR Number of specific fragments extracted= 7 number of extra gaps= 5 total=89 Number of alignments=17 # 1a0p read from 1a0p/merged-good-all-a2m # found chain 1a0p in template set Warning: unaligning (T0283)S45 because of BadResidue code BAD_PEPTIDE in next template residue (1a0p)K19 Warning: unaligning (T0283)G46 because of BadResidue code BAD_PEPTIDE at template residue (1a0p)K19 Warning: unaligning (T0283)G47 because of BadResidue code BAD_PEPTIDE at template residue (1a0p)N20 Warning: unaligning (T0283)D50 because of BadResidue code BAD_PEPTIDE in next template residue (1a0p)N24 Warning: unaligning (T0283)Q52 because of BadResidue code BAD_PEPTIDE at template residue (1a0p)N24 Warning: unaligning (T0283)F58 because of BadResidue code BAD_PEPTIDE in next template residue (1a0p)R31 Warning: unaligning (T0283)G59 because of BadResidue code BAD_PEPTIDE at template residue (1a0p)R31 Warning: unaligning (T0283)G72 because of BadResidue code BAD_PEPTIDE in next template residue (1a0p)L45 Warning: unaligning (T0283)K73 because of BadResidue code BAD_PEPTIDE at template residue (1a0p)L45 Warning: unaligning (T0283)D93 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1a0p)R62 Warning: unaligning (T0283)T94 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1a0p)R62 T0283 32 :HHAYKAIQKYMWT 1a0p 5 :LARIEQFLDALWL T0283 48 :PT 1a0p 21 :LA T0283 53 :DTKRI 1a0p 25 :TLNAY T0283 60 :GILDLFEEGAAE 1a0p 32 :DLSMMVEWLHHR T0283 74 :KVTDLTGEDVAAF 1a0p 46 :TLATAQSDDLQAL T0283 91 :MK 1a0p 59 :LA Number of specific fragments extracted= 6 number of extra gaps= 5 total=95 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1csn/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1csn expands to /projects/compbio/data/pdb/1csn.pdb.gz 1csn:Warning: there is no chain 1csn will retry with 1csnA # T0283 read from 1csn/merged-good-all-a2m # 1csn read from 1csn/merged-good-all-a2m # adding 1csn to template set # found chain 1csn in template set T0283 13 :DKREWKAMEARAKA 1csn 226 :NKQKYERIGEKKQS T0283 27 :LPKEYHHAYKAIQK 1csn 249 :FPEEFYKYMHYARN T0283 45 :SGGPTDWQDTKRIFGGILD 1csn 265 :FDATPDYDYLQGLFSKVLE Number of specific fragments extracted= 3 number of extra gaps= 0 total=98 Number of alignments=18 # 1csn read from 1csn/merged-good-all-a2m # found chain 1csn in template set T0283 13 :DKREWKAMEARAKA 1csn 226 :NKQKYERIGEKKQS T0283 27 :LPKEYHHAYKAIQK 1csn 249 :FPEEFYKYMHYARN T0283 45 :SGGPTDWQDTKRIFGGILD 1csn 265 :FDATPDYDYLQGLFSKVLE Number of specific fragments extracted= 3 number of extra gaps= 0 total=101 Number of alignments=19 # 1csn read from 1csn/merged-good-all-a2m # found chain 1csn in template set T0283 12 :NDKREWKAMEARAKA 1csn 225 :TNKQKYERIGEKKQS T0283 27 :LPKEYHHAYKAIQK 1csn 249 :FPEEFYKYMHYARN T0283 45 :SGGPTDWQDTKRIFGGILD 1csn 265 :FDATPDYDYLQGLFSKVLE Number of specific fragments extracted= 3 number of extra gaps= 0 total=104 Number of alignments=20 # 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:# T0283 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 T0283 3 :FIEKMIGSLND 1mojA 47 :QLKKHHWNVEG T0283 15 :REWKAMEARAKALPKEYHHAYKAIQKYMWTSGGPTD 1mojA 58 :AEFRDLHLFLGEAAETAEEVADELAERVQALGGVPH T0283 51 :WQDTKRIFGGILDLF 1mojA 119 :LANDMAIYGDIIEAT T0283 66 :EEGAAEG 1mojA 138 :ELAENLG T0283 80 :GEDVAAFCDELMKD 1mojA 145 :DHATAHMLREGLIE T0283 98 :MDKYRTKLNDSIGRD 1mojA 159 :LEDDAHHIEHYLEDD Number of specific fragments extracted= 6 number of extra gaps= 0 total=110 Number of alignments=21 # 1mojA read from 1mojA/merged-good-all-a2m # found chain 1mojA in template set T0283 3 :FIEKMIGSLND 1mojA 47 :QLKKHHWNVEG T0283 15 :REWKAMEARAKALPKEYHHAYKAIQKYMWTSGGPTD 1mojA 58 :AEFRDLHLFLGEAAETAEEVADELAERVQALGGVPH T0283 51 :WQDTKRIFGGILDLF 1mojA 119 :LANDMAIYGDIIEAT T0283 66 :EEGAAEG 1mojA 138 :ELAENLG T0283 80 :GEDVAAFCDELMKD 1mojA 145 :DHATAHMLREGLIE T0283 98 :MDKYRTKLNDSIGRD 1mojA 159 :LEDDAHHIEHYLEDD Number of specific fragments extracted= 6 number of extra gaps= 0 total=116 Number of alignments=22 # 1mojA read from 1mojA/merged-good-all-a2m # found chain 1mojA in template set T0283 3 :FIEKMIGSLNDK 1mojA 47 :QLKKHHWNVEGA T0283 16 :EWKAMEARAKALPKEYHHAYKAIQKYMWTSG 1mojA 59 :EFRDLHLFLGEAAETAEEVADELAERVQALG T0283 47 :GPTD 1mojA 108 :EDED T0283 51 :WQDTKRIFGGILDLF 1mojA 119 :LANDMAIYGDIIEAT T0283 66 :EEGAAEGK 1mojA 138 :ELAENLGD T0283 81 :EDVAAFCDELMKDTKTWMDKYRTKLNDSIGRD 1mojA 146 :HATAHMLREGLIELEDDAHHIEHYLEDDTLVT Number of specific fragments extracted= 6 number of extra gaps= 0 total=122 Number of alignments=23 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ay7B/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0283 read from 1ay7B/merged-good-all-a2m # 1ay7B read from 1ay7B/merged-good-all-a2m # found chain 1ay7B in training set Warning: unaligning (T0283)Q39 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1ay7B)D39 Warning: unaligning (T0283)K40 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1ay7B)D39 Warning: unaligning (T0283)S45 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1ay7B)V45 Warning: unaligning (T0283)G46 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1ay7B)V45 Warning: unaligning (T0283)P48 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ay7B)P48 Warning: unaligning (T0283)T49 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ay7B)P48 Warning: unaligning (T0283)I61 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1ay7B)L71 Warning: unaligning (T0283)L62 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1ay7B)L71 T0283 14 :KREWKA 1ay7B 13 :ISDLHQ T0283 20 :MEARA 1ay7B 20 :LKKEL T0283 26 :ALPKEY 1ay7B 25 :ALPEYY T0283 35 :YKAI 1ay7B 34 :LDAL T0283 41 :YMWT 1ay7B 40 :CLTG T0283 47 :G 1ay7B 46 :E T0283 50 :DWQDTKRI 1ay7B 55 :QFEQSKQL T0283 58 :FGG 1ay7B 67 :AES T0283 63 :DLFEEGAAEGKKVTD 1ay7B 72 :QVFREAKAEGCDITI Number of specific fragments extracted= 9 number of extra gaps= 4 total=131 Number of alignments=24 # 1ay7B read from 1ay7B/merged-good-all-a2m # found chain 1ay7B in training set Warning: unaligning (T0283)Q39 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1ay7B)D39 Warning: unaligning (T0283)K40 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1ay7B)D39 Warning: unaligning (T0283)S45 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1ay7B)V45 Warning: unaligning (T0283)G46 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1ay7B)V45 Warning: unaligning (T0283)P48 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ay7B)P48 Warning: unaligning (T0283)T49 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ay7B)P48 Warning: unaligning (T0283)I61 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1ay7B)L71 Warning: unaligning (T0283)L62 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1ay7B)L71 T0283 14 :KREWKA 1ay7B 13 :ISDLHQ T0283 20 :MEARA 1ay7B 20 :LKKEL T0283 26 :ALPKEY 1ay7B 25 :ALPEYY T0283 35 :YKAI 1ay7B 34 :LDAL T0283 41 :YMWT 1ay7B 40 :CLTG T0283 47 :G 1ay7B 46 :E T0283 50 :DWQDTKRI 1ay7B 55 :QFEQSKQL T0283 58 :FGG 1ay7B 67 :AES T0283 63 :DLFEEGAAEGKKVTD 1ay7B 72 :QVFREAKAEGCDITI Number of specific fragments extracted= 9 number of extra gaps= 4 total=140 Number of alignments=25 # 1ay7B read from 1ay7B/merged-good-all-a2m # found chain 1ay7B in training set Warning: unaligning (T0283)Q39 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1ay7B)D39 Warning: unaligning (T0283)K40 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1ay7B)D39 Warning: unaligning (T0283)S45 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1ay7B)V45 Warning: unaligning (T0283)G46 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1ay7B)V45 Warning: unaligning (T0283)P48 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ay7B)P48 Warning: unaligning (T0283)T49 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ay7B)P48 Warning: unaligning (T0283)I61 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1ay7B)L71 Warning: unaligning (T0283)L62 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1ay7B)L71 T0283 13 :DKREWKA 1ay7B 12 :SISDLHQ T0283 20 :MEARA 1ay7B 20 :LKKEL T0283 26 :ALPKEY 1ay7B 25 :ALPEYY T0283 35 :YKAI 1ay7B 34 :LDAL T0283 41 :YMWT 1ay7B 40 :CLTG T0283 47 :G 1ay7B 46 :E T0283 50 :DWQDTKRI 1ay7B 55 :QFEQSKQL T0283 58 :FGG 1ay7B 67 :AES T0283 63 :DLFEEGAAEGKKVTDL 1ay7B 72 :QVFREAKAEGCDITII Number of specific fragments extracted= 9 number of extra gaps= 4 total=149 Number of alignments=26 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b8zA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0283 read from 1b8zA/merged-good-all-a2m # 1b8zA read from 1b8zA/merged-good-all-a2m # found chain 1b8zA in training set T0283 14 :KREWKAMEAR 1b8zA 4 :KELIDRVAKK T0283 45 :S 1b8zA 14 :A T0283 48 :PTDWQDTKRIFGGILDLFEEGAAEGKKV 1b8zA 15 :GAKKKDVKLILDTILETITEALAKGEKV Number of specific fragments extracted= 3 number of extra gaps= 0 total=152 Number of alignments=27 # 1b8zA read from 1b8zA/merged-good-all-a2m # found chain 1b8zA in training set T0283 14 :KREWKAMEAR 1b8zA 4 :KELIDRVAKK T0283 45 :S 1b8zA 14 :A T0283 48 :PTDWQDTKRIFGGILDLFEEGAAEGKKV 1b8zA 15 :GAKKKDVKLILDTILETITEALAKGEKV Number of specific fragments extracted= 3 number of extra gaps= 0 total=155 Number of alignments=28 # 1b8zA read from 1b8zA/merged-good-all-a2m # found chain 1b8zA in training set T0283 12 :NDKREWKAMEAR 1b8zA 2 :NKKELIDRVAKK T0283 45 :S 1b8zA 14 :A T0283 48 :PTDWQDTKRIFGGILDLFEEGAAEGKKV 1b8zA 15 :GAKKKDVKLILDTILETITEALAKGEKV Number of specific fragments extracted= 3 number of extra gaps= 0 total=158 Number of alignments=29 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fvhA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fvhA expands to /projects/compbio/data/pdb/2fvh.pdb.gz 2fvhA:# T0283 read from 2fvhA/merged-good-all-a2m # 2fvhA read from 2fvhA/merged-good-all-a2m # adding 2fvhA to template set # found chain 2fvhA in template set T0283 8 :IGSLNDKREWKAMEARAKA 2fvhA 8 :QERLLLSYAAELARRRRAR T0283 46 :GGPTDWQDTKRIFGG 2fvhA 27 :GLRLNHPEAIAVIAD T0283 64 :LFEEGAAEGKKV 2fvhA 42 :HILEGARDGRTV T0283 88 :DELMKD 2fvhA 54 :AELMAS T0283 105 :LN 2fvhA 60 :GR Number of specific fragments extracted= 5 number of extra gaps= 0 total=163 Number of alignments=30 # 2fvhA read from 2fvhA/merged-good-all-a2m # found chain 2fvhA in template set T0283 8 :IGSLNDKREWKAMEARAKA 2fvhA 8 :QERLLLSYAAELARRRRAR T0283 46 :GGPTDWQDTKRIFGG 2fvhA 27 :GLRLNHPEAIAVIAD T0283 64 :LFEEGAAEGKKV 2fvhA 42 :HILEGARDGRTV T0283 88 :DELMKD 2fvhA 54 :AELMAS Number of specific fragments extracted= 4 number of extra gaps= 0 total=167 Number of alignments=31 # 2fvhA read from 2fvhA/merged-good-all-a2m # found chain 2fvhA in template set T0283 5 :EKMIGSLNDKREWKAMEARAKA 2fvhA 5 :PHEQERLLLSYAAELARRRRAR T0283 46 :GGPTDWQDTKRIFG 2fvhA 27 :GLRLNHPEAIAVIA T0283 63 :DLFEEGAAEGKK 2fvhA 41 :DHILEGARDGRT T0283 87 :CDELMKDTKTWMD 2fvhA 53 :VAELMASGREVLG Number of specific fragments extracted= 4 number of extra gaps= 0 total=171 Number of alignments=32 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tx4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0283 read from 1tx4A/merged-good-all-a2m # 1tx4A read from 1tx4A/merged-good-all-a2m # found chain 1tx4A in training set T0283 3 :FIEKMIG 1tx4A 137 :LYPHVVG T0283 10 :SLNDKREWKAMEARAKALPKEYHHAYKAIQKYMWTSG 1tx4A 146 :NIDESQRVPATLQVLQTLPEENYQVLRFLTAFLVQIS T0283 48 :PTDWQDTKRIFGGIL 1tx4A 189 :KMTNTNLAVVFGPNL T0283 81 :EDVAAFCDELMKDTKTW 1tx4A 217 :NPINTFTKFLLDHQGEL Number of specific fragments extracted= 4 number of extra gaps= 0 total=175 Number of alignments=33 # 1tx4A read from 1tx4A/merged-good-all-a2m # found chain 1tx4A in training set T0283 3 :FIEKMIGS 1tx4A 137 :LYPHVVGF T0283 11 :LNDKREWKAMEARAKALPKEYHHAYKAIQKYMWTSG 1tx4A 147 :IDESQRVPATLQVLQTLPEENYQVLRFLTAFLVQIS T0283 48 :PTDWQDTKRIFGGIL 1tx4A 189 :KMTNTNLAVVFGPNL T0283 81 :EDVAAFCDELMKDTKTW 1tx4A 217 :NPINTFTKFLLDHQGEL Number of specific fragments extracted= 4 number of extra gaps= 0 total=179 Number of alignments=34 # 1tx4A read from 1tx4A/merged-good-all-a2m # found chain 1tx4A in training set T0283 11 :LNDKREWKAMEARAKALPKEYHHAYKAIQKYMWTSG 1tx4A 147 :IDESQRVPATLQVLQTLPEENYQVLRFLTAFLVQIS T0283 47 :GP 1tx4A 189 :KM T0283 50 :DWQDTKRIFGGIL 1tx4A 191 :TNTNLAVVFGPNL T0283 65 :FEEGA 1tx4A 212 :TLKAI T0283 81 :EDVAAFCDELMKDTKT 1tx4A 217 :NPINTFTKFLLDHQGE Number of specific fragments extracted= 5 number of extra gaps= 0 total=184 Number of alignments=35 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qs1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0283 read from 1qs1A/merged-good-all-a2m # 1qs1A read from 1qs1A/merged-good-all-a2m # found chain 1qs1A in training set T0283 5 :EKMI 1qs1A 278 :SWGM T0283 18 :KAMEARAKALPKEYHHA 1qs1A 282 :KNYEEWAKDLTDSQREA T0283 35 :YKAIQKYMWTSGGPTD 1qs1A 307 :YKEINNYLRNQGGSGN T0283 52 :QDTKRIFGGILDLF 1qs1A 323 :EKLDAQIKNISDAL T0283 71 :EGKKVTDLT 1qs1A 337 :GKKPIPENI Number of specific fragments extracted= 5 number of extra gaps= 0 total=189 Number of alignments=36 # 1qs1A read from 1qs1A/merged-good-all-a2m # found chain 1qs1A in training set T0283 4 :IEKMIG 1qs1A 277 :HSWGMK T0283 19 :AMEARAKALPKEYHHA 1qs1A 283 :NYEEWAKDLTDSQREA T0283 35 :YKAIQKYMWTSGGPTD 1qs1A 307 :YKEINNYLRNQGGSGN T0283 52 :QDTKRIFGGILDLF 1qs1A 323 :EKLDAQIKNISDAL T0283 71 :EGKKVTDLT 1qs1A 337 :GKKPIPENI Number of specific fragments extracted= 5 number of extra gaps= 0 total=194 Number of alignments=37 # 1qs1A read from 1qs1A/merged-good-all-a2m # found chain 1qs1A in training set T0283 4 :IEKMI 1qs1A 277 :HSWGM T0283 18 :KAMEARAKALPKEYHHA 1qs1A 282 :KNYEEWAKDLTDSQREA T0283 35 :YKAIQKYMWTSGGPTD 1qs1A 307 :YKEINNYLRNQGGSGN T0283 52 :QDTKRIFGGILDLF 1qs1A 323 :EKLDAQIKNISDAL T0283 71 :EGKKVTD 1qs1A 337 :GKKPIPE Number of specific fragments extracted= 5 number of extra gaps= 0 total=199 Number of alignments=38 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sheA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1sheA expands to Error: no filename for 1sheA 1sheA expands to Error: no filename for 1sheA 1sheA expands to Error: no filename for 1sheA # T0283 read from 1sheA/merged-good-all-a2m # 1sheA read from 1sheA/merged-good-all-a2m # adding 1sheA to template set Error: can't find template for 1sheA or 1sheA, so skipping it. # 1sheA read from 1sheA/merged-good-all-a2m # adding 1sheA to template set Error: can't find template for 1sheA or 1sheA, so skipping it. # 1sheA read from 1sheA/merged-good-all-a2m # adding 1sheA to template set Error: can't find template for 1sheA or 1sheA, so skipping it. # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tffA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1tffA expands to /projects/compbio/data/pdb/1tff.pdb.gz 1tffA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0283 read from 1tffA/merged-good-all-a2m # 1tffA read from 1tffA/merged-good-all-a2m # adding 1tffA to template set # found chain 1tffA in template set T0283 6 :KMIGSLNDKREWKAMEARAKALP 1tffA 60 :YLESLLGKSREIFKFKERVLQTP T0283 29 :KEYHHAYKAIQKYMWTSG 1tffA 96 :RNFFNAFYSVVELVEKDG T0283 50 :DWQDTKRIF 1tffA 114 :SVSSLLKVF T0283 59 :GGILDLFEEGAA 1tffA 129 :DHIVQFLRLLTS T0283 82 :DVAAFCDELMKDTKTWMDKYRTKL 1tffA 145 :NRADFFRHFIDEEMDIKDFCTHEV Number of specific fragments extracted= 5 number of extra gaps= 0 total=204 Number of alignments=39 # 1tffA read from 1tffA/merged-good-all-a2m # found chain 1tffA in template set T0283 6 :KMIGSLNDKREWKAMEARAKALP 1tffA 60 :YLESLLGKSREIFKFKERVLQTP T0283 29 :KEYHHAYKAIQKYMWTSG 1tffA 96 :RNFFNAFYSVVELVEKDG T0283 50 :DWQDTKRIF 1tffA 114 :SVSSLLKVF T0283 59 :GGILDLFEEGAA 1tffA 129 :DHIVQFLRLLTS T0283 82 :DVAAFCDELMKDTKTWMDKYRTKL 1tffA 145 :NRADFFRHFIDEEMDIKDFCTHEV Number of specific fragments extracted= 5 number of extra gaps= 0 total=209 Number of alignments=40 # 1tffA read from 1tffA/merged-good-all-a2m # found chain 1tffA in template set T0283 8 :IGSLNDKREWKAMEARAKALP 1tffA 62 :ESLLGKSREIFKFKERVLQTP T0283 29 :KEYHHAYKAIQKYMWTSG 1tffA 96 :RNFFNAFYSVVELVEKDG T0283 50 :DWQDTKRIF 1tffA 114 :SVSSLLKVF T0283 59 :GGILDLFE 1tffA 129 :DHIVQFLR Number of specific fragments extracted= 4 number of extra gaps= 0 total=213 Number of alignments=41 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1am4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1am4A expands to /projects/compbio/data/pdb/1am4.pdb.gz 1am4A:# T0283 read from 1am4A/merged-good-all-a2m # 1am4A read from 1am4A/merged-good-all-a2m # adding 1am4A to template set # found chain 1am4A in template set Warning: unaligning (T0283)K29 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)E166 Warning: unaligning (T0283)E30 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)E166 Warning: unaligning (T0283)W43 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)Q180 Warning: unaligning (T0283)T44 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)Q180 Warning: unaligning (T0283)G46 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)A183 Warning: unaligning (T0283)G47 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)A183 Warning: unaligning (T0283)I57 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)F199 Warning: unaligning (T0283)F58 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)F199 Warning: unaligning (T0283)G60 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)N202 Warning: unaligning (T0283)I61 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)N202 Warning: unaligning (T0283)K74 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)I211 Warning: unaligning (T0283)V75 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)I211 Warning: unaligning (T0283)T76 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)L213 Warning: unaligning (T0283)D77 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)L213 Warning: unaligning (T0283)T79 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)I216 Warning: unaligning (T0283)G80 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)I216 Warning: unaligning (T0283)E81 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)N217 Warning: unaligning (T0283)A85 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)F222 Warning: unaligning (T0283)F86 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)F222 T0283 3 :FIEKMIG 1am4A 137 :LYPHVVG T0283 10 :SLNDKREWKAMEARAKALP 1am4A 146 :NIDESQRVPATLQVLQTLP T0283 31 :YHHAYKAIQKYM 1am4A 167 :NYQVLRFLTAFL T0283 45 :S 1am4A 181 :I T0283 48 :PTDWQDTKR 1am4A 189 :KMTNTNLAV T0283 59 :G 1am4A 200 :G T0283 62 :L 1am4A 203 :L T0283 71 :EGK 1am4A 207 :KDA T0283 78 :L 1am4A 214 :K T0283 82 :DVA 1am4A 218 :PIN T0283 87 :CDELMKDTKTW 1am4A 223 :TKFLLDHQGEL Number of specific fragments extracted= 11 number of extra gaps= 8 total=224 Number of alignments=42 # 1am4A read from 1am4A/merged-good-all-a2m # found chain 1am4A in template set Warning: unaligning (T0283)K29 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)E166 Warning: unaligning (T0283)E30 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)E166 Warning: unaligning (T0283)W43 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)Q180 Warning: unaligning (T0283)T44 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)Q180 Warning: unaligning (T0283)G46 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)A183 Warning: unaligning (T0283)G47 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)A183 Warning: unaligning (T0283)I57 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)F199 Warning: unaligning (T0283)F58 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)F199 Warning: unaligning (T0283)G60 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)N202 Warning: unaligning (T0283)I61 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)N202 Warning: unaligning (T0283)K74 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)I211 Warning: unaligning (T0283)V75 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)I211 Warning: unaligning (T0283)T76 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)L213 Warning: unaligning (T0283)D77 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)L213 Warning: unaligning (T0283)T79 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)I216 Warning: unaligning (T0283)G80 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)I216 Warning: unaligning (T0283)E81 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)N217 Warning: unaligning (T0283)A85 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)F222 Warning: unaligning (T0283)F86 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)F222 T0283 3 :FIEKMIGS 1am4A 137 :LYPHVVGF T0283 11 :LNDKREWKAMEARAKALP 1am4A 147 :IDESQRVPATLQVLQTLP T0283 31 :YHHAYKAIQKYM 1am4A 167 :NYQVLRFLTAFL T0283 45 :S 1am4A 181 :I T0283 48 :PTDWQDTKR 1am4A 189 :KMTNTNLAV T0283 59 :G 1am4A 200 :G T0283 62 :L 1am4A 203 :L T0283 71 :EGK 1am4A 207 :KDA T0283 78 :L 1am4A 214 :K T0283 82 :DVA 1am4A 218 :PIN T0283 87 :CDELMKDTKTW 1am4A 223 :TKFLLDHQGEL Number of specific fragments extracted= 11 number of extra gaps= 8 total=235 Number of alignments=43 # 1am4A read from 1am4A/merged-good-all-a2m # found chain 1am4A in template set Warning: unaligning (T0283)K29 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)E166 Warning: unaligning (T0283)E30 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)E166 Warning: unaligning (T0283)W43 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)Q180 Warning: unaligning (T0283)T44 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)Q180 Warning: unaligning (T0283)G46 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)A183 Warning: unaligning (T0283)G47 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)A183 Warning: unaligning (T0283)I57 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)F199 Warning: unaligning (T0283)F58 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)F199 Warning: unaligning (T0283)G60 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)N202 Warning: unaligning (T0283)I61 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)N202 Warning: unaligning (T0283)K74 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)I211 Warning: unaligning (T0283)V75 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)I211 Warning: unaligning (T0283)T76 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)L213 Warning: unaligning (T0283)D77 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)L213 Warning: unaligning (T0283)T79 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)I216 Warning: unaligning (T0283)G80 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)I216 Warning: unaligning (T0283)E81 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)N217 Warning: unaligning (T0283)A85 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)F222 Warning: unaligning (T0283)F86 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)F222 T0283 11 :LNDKREWKAMEARAKALP 1am4A 147 :IDESQRVPATLQVLQTLP T0283 31 :YHHAYKAIQKYM 1am4A 167 :NYQVLRFLTAFL T0283 45 :S 1am4A 181 :I T0283 48 :P 1am4A 184 :H T0283 50 :DWQDTKR 1am4A 191 :TNTNLAV T0283 59 :G 1am4A 200 :G T0283 62 :L 1am4A 203 :L T0283 70 :AEGK 1am4A 206 :AKDA T0283 78 :L 1am4A 214 :K T0283 82 :DVA 1am4A 218 :PIN T0283 87 :CDELMKDTKT 1am4A 223 :TKFLLDHQGE Number of specific fragments extracted= 11 number of extra gaps= 8 total=246 Number of alignments=44 # 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 # T0283 read from 1tjoA/merged-good-all-a2m # 1tjoA read from 1tjoA/merged-good-all-a2m # found chain 1tjoA in training set Warning: unaligning (T0283)E16 because of BadResidue code BAD_PEPTIDE in next template residue (1tjoA)F60 Warning: unaligning (T0283)W17 because of BadResidue code BAD_PEPTIDE at template residue (1tjoA)F60 T0283 3 :FIEKMIGSLND 1tjoA 47 :QLKKHHWNVEG T0283 15 :R 1tjoA 58 :A T0283 18 :KAMEARAKALPKEYHHAYKAIQKYMWTSGGPTD 1tjoA 61 :RDLHLFLGEAAETAEEVADELAERVQALGGVPH T0283 51 :WQDTKRIFGGILDLF 1tjoA 119 :LANDMAIYGDIIEAT T0283 66 :EEGAAEG 1tjoA 138 :ELAENLG T0283 80 :GEDVAAFCDELMKD 1tjoA 145 :DHATAHMLREGLIE T0283 98 :MDKYRTKLNDSIGRD 1tjoA 159 :LEDDAHHIEHYLEDD Number of specific fragments extracted= 7 number of extra gaps= 1 total=253 Number of alignments=45 # 1tjoA read from 1tjoA/merged-good-all-a2m # found chain 1tjoA in training set Warning: unaligning (T0283)E16 because of BadResidue code BAD_PEPTIDE in next template residue (1tjoA)F60 Warning: unaligning (T0283)W17 because of BadResidue code BAD_PEPTIDE at template residue (1tjoA)F60 T0283 3 :FIEKMIGSLND 1tjoA 47 :QLKKHHWNVEG T0283 15 :R 1tjoA 58 :A T0283 18 :KAMEARAKALPKEYHHAYKAIQKYMWTSGGPTD 1tjoA 61 :RDLHLFLGEAAETAEEVADELAERVQALGGVPH T0283 51 :WQDTKRIFGGILDLF 1tjoA 119 :LANDMAIYGDIIEAT T0283 66 :EEGAAEG 1tjoA 138 :ELAENLG T0283 80 :GEDVAAFCDELMKD 1tjoA 145 :DHATAHMLREGLIE T0283 98 :MDKYRTKLNDSIGRD 1tjoA 159 :LEDDAHHIEHYLEDD Number of specific fragments extracted= 7 number of extra gaps= 1 total=260 Number of alignments=46 # 1tjoA read from 1tjoA/merged-good-all-a2m # found chain 1tjoA in training set Warning: unaligning (T0283)E16 because of BadResidue code BAD_PEPTIDE in next template residue (1tjoA)F60 Warning: unaligning (T0283)W17 because of BadResidue code BAD_PEPTIDE at template residue (1tjoA)F60 T0283 3 :FIEKMIGSLNDK 1tjoA 47 :QLKKHHWNVEGA T0283 18 :KAMEARAKALPKEYHHAYKAIQKYMWTSG 1tjoA 61 :RDLHLFLGEAAETAEEVADELAERVQALG T0283 47 :GPTD 1tjoA 108 :EDED T0283 51 :WQDTKRIFGGILDLF 1tjoA 119 :LANDMAIYGDIIEAT T0283 66 :EEGAAEGK 1tjoA 138 :ELAENLGD T0283 81 :EDVAAFCDELMKDTKTWMDKYRTKLNDSIGRD 1tjoA 146 :HATAHMLREGLIELEDDAHHIEHYLEDDTLVT Number of specific fragments extracted= 6 number of extra gaps= 1 total=266 Number of alignments=47 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gk9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0283 read from 1gk9A/merged-good-all-a2m # 1gk9A read from 1gk9A/merged-good-all-a2m # found chain 1gk9A in training set T0283 11 :LNDKREWKA 1gk9A 63 :VKFDKDIRR T0283 20 :MEARAKALPKE 1gk9A 78 :IRAQIAALSPE T0283 31 :YHHAYKAIQK 1gk9A 100 :MNAWIDKVNT T0283 41 :YMWTSGGPTDWQDTKRI 1gk9A 118 :QFNTFGFTPKRWEPFDV T0283 60 :GILDLFEEGAAEGKK 1gk9A 135 :AMIFVGTMANRFSDS T0283 79 :TGEDVAAFCDELMKD 1gk9A 151 :SEIDNLALLTALKDK T0283 94 :TKTWMDKYRT 1gk9A 168 :VSQGMAVFNQ Number of specific fragments extracted= 7 number of extra gaps= 0 total=273 Number of alignments=48 # 1gk9A read from 1gk9A/merged-good-all-a2m # found chain 1gk9A in training set T0283 10 :SLNDKREWKA 1gk9A 62 :FVKFDKDIRR T0283 20 :MEARAKALPKE 1gk9A 78 :IRAQIAALSPE T0283 31 :YHHAYKAIQK 1gk9A 100 :MNAWIDKVNT T0283 41 :YMWTSGGPTDWQDTKRI 1gk9A 118 :QFNTFGFTPKRWEPFDV T0283 60 :GILDLFEEGAAEGKK 1gk9A 135 :AMIFVGTMANRFSDS T0283 78 :LTGEDVAAFCDELMKD 1gk9A 150 :TSEIDNLALLTALKDK T0283 94 :TKTWMDKYRT 1gk9A 168 :VSQGMAVFNQ Number of specific fragments extracted= 7 number of extra gaps= 0 total=280 Number of alignments=49 # 1gk9A read from 1gk9A/merged-good-all-a2m # found chain 1gk9A in training set T0283 9 :GSLNDKREWKA 1gk9A 61 :DFVKFDKDIRR T0283 20 :MEARAKALPKE 1gk9A 78 :IRAQIAALSPE T0283 53 :D 1gk9A 89 :D T0283 55 :KRIFGGIL 1gk9A 90 :MSILQGYA T0283 81 :EDVAAFCDELMKDTKTWMDKYRTKLNDSIGR 1gk9A 98 :DGMNAWIDKVNTNPETLLPKQFNTFGFTPKR Number of specific fragments extracted= 5 number of extra gaps= 0 total=285 Number of alignments=50 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dbhA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1dbhA expands to /projects/compbio/data/pdb/1dbh.pdb.gz 1dbhA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0283 read from 1dbhA/merged-good-all-a2m # 1dbhA read from 1dbhA/merged-good-all-a2m # adding 1dbhA to template set # found chain 1dbhA in template set T0283 4 :IEKM 1dbhA 202 :YDLV T0283 18 :KAMEARAKA 1dbhA 206 :KAFMAEIRQ T0283 31 :YHHAYKAIQ 1dbhA 215 :YIRELNLII T0283 40 :KYMWTSGGPTDWQDTKRIFGGILDLFEEGAA 1dbhA 228 :EPFVSNSKLFSANDVENIFSRIVDIHELSVK T0283 71 :EGKK 1dbhA 272 :EGSP T0283 76 :TDLTGEDVAAFCD 1dbhA 276 :HPLVGSCFEDLAE T0283 89 :ELMKD 1dbhA 297 :SYARD T0283 94 :TKTWMDKYRTKLND 1dbhA 304 :RPGFHDRFLSQLSK Number of specific fragments extracted= 8 number of extra gaps= 0 total=293 Number of alignments=51 # 1dbhA read from 1dbhA/merged-good-all-a2m # found chain 1dbhA in template set T0283 2 :SFIEKMIGSLN 1dbhA 200 :TYYDLVKAFMA T0283 16 :EWKAMEARAKALPKEYHHAYKA 1dbhA 211 :EIRQYIRELNLIIKVFREPFVS T0283 39 :QKYMWTS 1dbhA 242 :VENIFSR T0283 51 :WQDTKRIFGGILDLFEEGAA 1dbhA 249 :IVDIHELSVKLLGHIEDTVE T0283 71 :EGKK 1dbhA 272 :EGSP T0283 76 :TDLTGEDVAAFCD 1dbhA 276 :HPLVGSCFEDLAE T0283 89 :ELMKD 1dbhA 297 :SYARD T0283 94 :TKTWMDKYRTKLND 1dbhA 304 :RPGFHDRFLSQLSK Number of specific fragments extracted= 8 number of extra gaps= 0 total=301 Number of alignments=52 # 1dbhA read from 1dbhA/merged-good-all-a2m # found chain 1dbhA in template set T0283 2 :SFIEKMIGSLNDKREWKAMEARA 1dbhA 200 :TYYDLVKAFMAEIRQYIRELNLI T0283 25 :KALPKEYHH 1dbhA 224 :KVFREPFVS T0283 34 :AYKAI 1dbhA 241 :DVENI T0283 43 :WTS 1dbhA 246 :FSR T0283 51 :WQDTKRIFGGILDLFEEGAA 1dbhA 249 :IVDIHELSVKLLGHIEDTVE T0283 71 :EGKK 1dbhA 272 :EGSP T0283 76 :TDLTGEDVAAFCD 1dbhA 276 :HPLVGSCFEDLAE Number of specific fragments extracted= 7 number of extra gaps= 0 total=308 Number of alignments=53 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ex3B/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2ex3B expands to /projects/compbio/data/pdb/2ex3.pdb.gz 2ex3B:Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X # T0283 read from 2ex3B/merged-good-all-a2m # 2ex3B read from 2ex3B/merged-good-all-a2m # adding 2ex3B to template set # found chain 2ex3B in template set Warning: unaligning (T0283)P48 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ex3B)G234 Warning: unaligning (T0283)K73 because last residue in template chain is (2ex3B)F259 T0283 2 :SFIEKMIGSLNDKREWKAMEARAKALP 2ex3B 185 :NFIKSVEGSFNSFDAADELIEELKKIP T0283 29 :KEYHHAYKAIQK 2ex3B 213 :DDFYELFLRISE T0283 49 :TDWQDTKRIFGGILDLFEEGAAEG 2ex3B 235 :NTVENVEGNVYKILSYLEQYRRGD Number of specific fragments extracted= 3 number of extra gaps= 0 total=311 Number of alignments=54 # 2ex3B read from 2ex3B/merged-good-all-a2m # found chain 2ex3B in template set Warning: unaligning (T0283)P48 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ex3B)G234 Warning: unaligning (T0283)K73 because last residue in template chain is (2ex3B)F259 T0283 2 :SFIEKMIGSLNDKREWKAMEARAKALP 2ex3B 185 :NFIKSVEGSFNSFDAADELIEELKKIP T0283 29 :KEYHHAYKAIQK 2ex3B 213 :DDFYELFLRISE T0283 49 :TDWQDTKRIFGGILDLFEEGAAEG 2ex3B 235 :NTVENVEGNVYKILSYLEQYRRGD Number of specific fragments extracted= 3 number of extra gaps= 0 total=314 Number of alignments=55 # 2ex3B read from 2ex3B/merged-good-all-a2m # found chain 2ex3B in template set Warning: unaligning (T0283)P48 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ex3B)G234 Warning: unaligning (T0283)K73 because last residue in template chain is (2ex3B)F259 T0283 2 :SFIEKMIGSLNDKREWKAMEARAKALP 2ex3B 185 :NFIKSVEGSFNSFDAADELIEELKKIP T0283 29 :KEYHHAYKAI 2ex3B 213 :DDFYELFLRI T0283 49 :TDWQDTKRIFGGILDLFEEGAAEG 2ex3B 235 :NTVENVEGNVYKILSYLEQYRRGD Number of specific fragments extracted= 3 number of extra gaps= 0 total=317 Number of alignments=56 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qs2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qs2A expands to /projects/compbio/data/pdb/1qs2.pdb.gz 1qs2A:# T0283 read from 1qs2A/merged-good-all-a2m # 1qs2A read from 1qs2A/merged-good-all-a2m # adding 1qs2A to template set # found chain 1qs2A in template set T0283 5 :EKMI 1qs2A 278 :SWGM T0283 18 :KAMEARAKALPKEYHHA 1qs2A 282 :KNYEEWAKDLTDSQREA T0283 35 :YKAIQKYMWTSGGPTD 1qs2A 307 :YKEINNYLRNQGGSGN T0283 52 :QDTKRIFGGILDLFE 1qs2A 323 :EKLDAQIKNISDALG T0283 71 :EGKKVTD 1qs2A 360 :ISDPLPS T0283 83 :VAAFCDELMK 1qs2A 367 :LKDFEEQFLN Number of specific fragments extracted= 6 number of extra gaps= 0 total=323 Number of alignments=57 # 1qs2A read from 1qs2A/merged-good-all-a2m # found chain 1qs2A in template set T0283 5 :EKMI 1qs2A 278 :SWGM T0283 18 :KAMEARAKALPKEYHHA 1qs2A 282 :KNYEEWAKDLTDSQREA T0283 35 :YKAIQKYMWTSGGPTD 1qs2A 307 :YKEINNYLRNQGGSGN T0283 52 :QDTKRIFGGILDLFE 1qs2A 323 :EKLDAQIKNISDALG T0283 71 :EGKKVTD 1qs2A 360 :ISDPLPS T0283 83 :VAAFCDELMK 1qs2A 367 :LKDFEEQFLN Number of specific fragments extracted= 6 number of extra gaps= 0 total=329 Number of alignments=58 # 1qs2A read from 1qs2A/merged-good-all-a2m # found chain 1qs2A in template set T0283 4 :IEKMI 1qs2A 277 :HSWGM T0283 18 :KAMEARAKALPKEYHHA 1qs2A 282 :KNYEEWAKDLTDSQREA T0283 35 :YKAIQKYMWTSGGPTD 1qs2A 307 :YKEINNYLRNQGGSGN T0283 52 :QDTKRIFGGILDLFE 1qs2A 323 :EKLDAQIKNISDALG Number of specific fragments extracted= 4 number of extra gaps= 0 total=333 Number of alignments=59 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tn6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0283 read from 1tn6A/merged-good-all-a2m # 1tn6A read from 1tn6A/merged-good-all-a2m # found chain 1tn6A in training set Warning: unaligning (T0283)R111 because last residue in template chain is (1tn6A)T369 T0283 13 :DKREWKAMEARAKALPKE 1tn6A 256 :LEREVQYTLEMIKLVPHN T0283 33 :HAYKAIQKYMWTSGGPTDWQDTKRIFGG 1tn6A 274 :ESAWNYLKGILQDRGLSKYPNLLNQLLD T0283 62 :LDLFEEGAAEGKK 1tn6A 316 :VDIYEDMLENQCD T0283 78 :LTGEDVAAFCDELMKD 1tn6A 332 :DILNKALELCEILAKE T0283 94 :TKTWMDKYRTKLNDSIG 1tn6A 352 :RKEYWRYIGRSLQSKHS Number of specific fragments extracted= 5 number of extra gaps= 0 total=338 Number of alignments=60 # 1tn6A read from 1tn6A/merged-good-all-a2m # found chain 1tn6A in training set Warning: unaligning (T0283)R111 because last residue in template chain is (1tn6A)T369 T0283 13 :DKREWKAMEARAKALPKE 1tn6A 256 :LEREVQYTLEMIKLVPHN T0283 33 :HAYKAIQKYMWTSGGPTDWQDTKRIFGG 1tn6A 274 :ESAWNYLKGILQDRGLSKYPNLLNQLLD T0283 62 :LDLFEEGAAEGKK 1tn6A 316 :VDIYEDMLENQCD T0283 77 :DLTGEDVAAFCDELMKD 1tn6A 331 :EDILNKALELCEILAKE T0283 94 :TKTWMDKYRTKLNDSIG 1tn6A 352 :RKEYWRYIGRSLQSKHS Number of specific fragments extracted= 5 number of extra gaps= 0 total=343 Number of alignments=61 # 1tn6A read from 1tn6A/merged-good-all-a2m # found chain 1tn6A in training set T0283 4 :IEKMIGSL 1tn6A 134 :WHFRRVLL T0283 12 :NDKREWKAMEARAKALPKEYH 1tn6A 147 :DLHEEMNYITAIIEEQPKNYQ T0283 34 :AYKAIQKYMWTSGGPTD 1tn6A 168 :VWHHRRVLVEWLRDPSQ T0283 51 :WQDTKRIFGG 1tn6A 186 :LEFIADILNQ T0283 61 :ILDLFEEGAAEGK 1tn6A 202 :AWQHRQWVIQEFK T0283 79 :TGEDVAAFCDELMKDTK 1tn6A 215 :LWDNELQYVDQLLKEDV Number of specific fragments extracted= 6 number of extra gaps= 0 total=349 Number of alignments=62 # command:Using radius: 8.0000 Alignment mode NUMB_ALIGNS: 62 Adding 833 constraints to all.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all.constraints maxweight: 1.0000 Optimizing... Probability sum: -174.3206, CN propb: -174.3206 weights: 0.2571 constraints: 169 # command:Found ConstraintSet # PrintContacts align.constraints_v3 Number of constraints in align.constraints 169 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_v3 Number of constraints in align.constraints.bonus 169 # command:Found ConstraintSet # PrintContacts rejected.constraints_v3 Number of constraints in rejected.constraints 664 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_v3 Number of constraints in rejected.constraints.bonus 664 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_v3 Number of constraints in noncontact.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_v3 Number of constraints in noncontact.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_v3 Number of constraints in all.constraints 833 # command: