# 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 /projects/compbio/data/pdb/1she.pdb.gz 1sheA:Skipped atom 145, because occupancy 0.4 <= existing 0.600 in 1sheA Skipped atom 147, because occupancy 0.400 <= existing 0.600 in 1sheA Skipped atom 149, because occupancy 0.400 <= existing 0.600 in 1sheA Skipped atom 151, because occupancy 0.400 <= existing 0.600 in 1sheA Skipped atom 153, because occupancy 0.400 <= existing 0.600 in 1sheA Skipped atom 176, because occupancy 0.500 <= existing 0.500 in 1sheA Skipped atom 178, because occupancy 0.300 <= existing 0.500 in 1sheA Skipped atom 180, because occupancy 0.300 <= existing 0.500 in 1sheA Skipped atom 182, because occupancy 0.300 <= existing 0.500 in 1sheA Skipped atom 284, because occupancy 0.350 <= existing 0.650 in 1sheA Skipped atom 286, because occupancy 0.350 <= existing 0.650 in 1sheA Skipped atom 288, because occupancy 0.350 <= existing 0.650 in 1sheA Skipped atom 290, because occupancy 0.350 <= existing 0.650 in 1sheA Skipped atom 292, because occupancy 0.350 <= existing 0.650 in 1sheA Skipped atom 538, because occupancy 0.350 <= existing 0.650 in 1sheA Skipped atom 540, because occupancy 0.350 <= existing 0.650 in 1sheA Skipped atom 542, because occupancy 0.350 <= existing 0.650 in 1sheA Skipped atom 544, because occupancy 0.350 <= existing 0.650 in 1sheA Skipped atom 546, because occupancy 0.350 <= existing 0.650 in 1sheA # T0283 read from 1sheA/merged-good-all-a2m # 1sheA read from 1sheA/merged-good-all-a2m # adding 1sheA to template set # found chain 1sheA in template set Warning: unaligning (T0283)T49 because first residue in template chain is (1sheA)S2 T0283 50 :DWQDTKRIFGGILDLFEEGAAEGKKVTDLT 1sheA 3 :TRGDLIRILGEIEEKMNELKMDGFNPDIIL T0283 80 :GEDVAAFCDELMKD 1sheA 34 :GREAYNFLSNLLKK Number of specific fragments extracted= 2 number of extra gaps= 0 total=201 Number of alignments=39 # 1sheA read from 1sheA/merged-good-all-a2m # found chain 1sheA in template set Warning: unaligning (T0283)T49 because first residue in template chain is (1sheA)S2 T0283 50 :DWQDTKRIFGGILDLFEEGAAEGKKVTDLT 1sheA 3 :TRGDLIRILGEIEEKMNELKMDGFNPDIIL T0283 80 :GEDVAAFCDELMKD 1sheA 34 :GREAYNFLSNLLKK Number of specific fragments extracted= 2 number of extra gaps= 0 total=203 Number of alignments=40 # 1sheA read from 1sheA/merged-good-all-a2m # found chain 1sheA in template set Warning: unaligning (T0283)P48 because first residue in template chain is (1sheA)S2 T0283 49 :T 1sheA 3 :T T0283 51 :WQDTKRIFGGILDLFEEGAAEGKKVTDL 1sheA 4 :RGDLIRILGEIEEKMNELKMDGFNPDII T0283 79 :TGEDVAAFCDELMKDTKT 1sheA 33 :FGREAYNFLSNLLKKEME Number of specific fragments extracted= 3 number of extra gaps= 0 total=206 Number of alignments=41 # 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=211 Number of alignments=42 # 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=216 Number of alignments=43 # 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=220 Number of alignments=44 # 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=231 Number of alignments=45 # 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=242 Number of alignments=46 # 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=253 Number of alignments=47 # 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=260 Number of alignments=48 # 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=267 Number of alignments=49 # 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=273 Number of alignments=50 # 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=280 Number of alignments=51 # 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=287 Number of alignments=52 # 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=292 Number of alignments=53 # 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=300 Number of alignments=54 # 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=308 Number of alignments=55 # 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=315 Number of alignments=56 # 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=318 Number of alignments=57 # 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=321 Number of alignments=58 # 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=324 Number of alignments=59 # 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=330 Number of alignments=60 # 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=336 Number of alignments=61 # 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=340 Number of alignments=62 # 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=345 Number of alignments=63 # 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=350 Number of alignments=64 # 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=356 Number of alignments=65 # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0283//projects/compbio/experiments/protein-predict/casp7/T0283/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0283//projects/compbio/experiments/protein-predict/casp7/T0283/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0283/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0283/align.constraints_v3.costfcn # future Constraint commands -> align # future HelixConstraint commands -> align # future StrandConstraint commands -> align # future SheetConstraint commands -> align # future Hbond commands -> align # future SSbond commands -> align # Constraint # added constraint: constraint((T0283)I38.CB, (T0283)I61.CB) [> 4.0885 = 6.8141 < 8.8583] w=1.0000 to align # Constraint # added constraint: constraint((T0283)A24.CB, (T0283)Y35.CB) [> 4.0370 = 6.7284 < 8.7469] w=0.9348 to align # Constraint # added constraint: constraint((T0283)F65.CB, (T0283)V75.CB) [> 3.3312 = 5.5521 < 7.2177] w=0.8376 to align # Constraint # added constraint: constraint((T0283)I38.CB, (T0283)I57.CB) [> 4.1054 = 6.8424 < 8.8951] w=0.8311 to align # Constraint # added constraint: constraint((T0283)L62.CB, (T0283)C87.CB) [> 2.9577 = 4.9296 < 6.4084] w=0.7016 to align # Constraint # added constraint: constraint((T0283)M42.CB, (T0283)T54.CB) [> 3.4635 = 5.7725 < 7.5043] w=0.6896 to align # Constraint # added constraint: constraint((T0283)Y35.CB, (T0283)L90.CB) [> 4.4806 = 7.4677 < 9.7080] w=0.6145 to align # Constraint # added constraint: constraint((T0283)M7.CB, (T0283)M20.CB) [> 3.9458 = 6.5763 < 8.5492] w=0.6012 to align # Constraint # added constraint: constraint((T0283)Q39.CB, (T0283)T49.CB) [> 3.0796 = 5.1327 < 6.6725] w=0.5741 to align # Constraint # added constraint: constraint((T0283)E30.CB, (T0283)G60.CA) [> 4.0279 = 6.7133 < 8.7272] w=0.5734 to align # Constraint # added constraint: constraint((T0283)Y31.CB, (T0283)I61.CB) [> 4.6296 = 7.7160 < 10.0309] w=0.5734 to align # Constraint # added constraint: constraint((T0283)A34.CB, (T0283)L64.CB) [> 4.2646 = 7.1077 < 9.2401] w=0.5512 to align # Constraint # added constraint: constraint((T0283)F65.CB, (T0283)C87.CB) [> 3.7710 = 6.2850 < 8.1705] w=0.5489 to align # Constraint # added constraint: constraint((T0283)L62.CB, (T0283)M91.CB) [> 3.1988 = 5.3314 < 6.9309] w=0.5489 to align # Constraint # added constraint: constraint((T0283)S45.CB, (T0283)T54.CB) [> 4.0527 = 6.7545 < 8.7809] w=0.4677 to align # Constraint # added constraint: constraint((T0283)M42.CB, (T0283)F58.CB) [> 4.2044 = 7.0074 < 9.1096] w=0.4501 to align # Constraint # added constraint: constraint((T0283)K6.CB, (T0283)A19.CB) [> 3.9944 = 6.6574 < 8.6546] w=0.4479 to align # Constraint # added constraint: constraint((T0283)I38.CB, (T0283)F58.CB) [> 4.1538 = 6.9230 < 8.9999] w=0.4354 to align # Constraint # added constraint: constraint((T0283)W17.CB, (T0283)F58.CB) [> 3.7750 = 6.2916 < 8.1791] w=0.4336 to align # Constraint # added constraint: constraint((T0283)E66.CB, (T0283)A84.CB) [> 4.5633 = 7.6055 < 9.8872] w=0.4335 to align # Constraint # added constraint: constraint((T0283)E21.CB, (T0283)Q39.CB) [> 3.7502 = 6.2503 < 8.1255] w=0.4314 to align # Constraint # added constraint: constraint((T0283)A24.CB, (T0283)T54.CB) [> 4.2159 = 7.0265 < 9.1345] w=0.4297 to align # Constraint # added constraint: constraint((T0283)Y31.CB, (T0283)G60.CA) [> 3.1657 = 5.2761 < 6.8590] w=0.4294 to align # Constraint # added constraint: constraint((T0283)Y31.CB, (T0283)D63.CB) [> 3.4298 = 5.7163 < 7.4312] w=0.4294 to align # Constraint # added constraint: constraint((T0283)Y31.CB, (T0283)L64.CB) [> 2.4013 = 4.0022 < 5.2029] w=0.4294 to align # Constraint # added constraint: constraint((T0283)A34.CB, (T0283)I61.CB) [> 3.2013 = 5.3356 < 6.9363] w=0.4294 to align # Constraint # added constraint: constraint((T0283)I38.CB, (T0283)T54.CB) [> 3.8756 = 6.4594 < 8.3972] w=0.4294 to align # Constraint # added constraint: constraint((T0283)Y41.CB, (T0283)D50.CB) [> 4.3111 = 7.1852 < 9.3407] w=0.4294 to align # Constraint # added constraint: constraint((T0283)L62.CB, (T0283)V83.CB) [> 3.8342 = 6.3904 < 8.3075] w=0.4287 to align # Constraint # added constraint: constraint((T0283)F65.CB, (T0283)T79.CB) [> 3.0944 = 5.1573 < 6.7045] w=0.4223 to align # Constraint # added constraint: constraint((T0283)L62.CB, (T0283)L90.CB) [> 4.1851 = 6.9752 < 9.0678] w=0.4102 to align # Constraint # added constraint: constraint((T0283)A34.CB, (T0283)I57.CB) [> 2.9951 = 4.9919 < 6.4894] w=0.3916 to align # Constraint # added constraint: constraint((T0283)L62.CB, (T0283)A84.CB) [> 4.4364 = 7.3940 < 9.6122] w=0.3734 to align # Constraint # added constraint: constraint((T0283)M20.CB, (T0283)T54.CB) [> 3.5566 = 5.9277 < 7.7060] w=0.3707 to align # Constraint # added constraint: constraint((T0283)M20.CB, (T0283)T49.CB) [> 3.9828 = 6.6380 < 8.6293] w=0.3707 to align # Constraint # added constraint: constraint((T0283)Y35.CB, (T0283)L64.CB) [> 3.0036 = 5.0060 < 6.5078] w=0.3669 to align # Constraint # added constraint: constraint((T0283)F58.CB, (T0283)L90.CB) [> 4.0948 = 6.8247 < 8.8721] w=0.3667 to align # Constraint # added constraint: constraint((T0283)E66.CB, (T0283)D88.CB) [> 4.5365 = 7.5608 < 9.8291] w=0.3641 to align # Constraint # added constraint: constraint((T0283)F65.CB, (T0283)L90.CB) [> 3.7338 = 6.2230 < 8.0899] w=0.3502 to align # Constraint # added constraint: constraint((T0283)L11.CB, (T0283)M20.CB) [> 3.4872 = 5.8120 < 7.5557] w=0.3476 to align # Constraint # added constraint: constraint((T0283)M7.CB, (T0283)A24.CB) [> 3.4343 = 5.7238 < 7.4409] w=0.3476 to align # Constraint # added constraint: constraint((T0283)I4.CB, (T0283)A24.CB) [> 3.2752 = 5.4587 < 7.0963] w=0.3476 to align # Constraint # added constraint: constraint((T0283)M7.CB, (T0283)T54.CB) [> 3.7674 = 6.2789 < 8.1626] w=0.3469 to align # Constraint # added constraint: constraint((T0283)T54.CB, (T0283)L90.CB) [> 3.2109 = 5.3515 < 6.9570] w=0.3292 to align # Constraint # added constraint: constraint((T0283)Y31.CB, (T0283)E89.CB) [> 4.5313 = 7.5521 < 9.8177] w=0.3231 to align # Constraint # added constraint: constraint((T0283)A34.CB, (T0283)F86.CB) [> 3.2857 = 5.4762 < 7.1190] w=0.3231 to align # Constraint # added constraint: constraint((T0283)Y35.CB, (T0283)I57.CB) [> 4.1564 = 6.9273 < 9.0055] w=0.3231 to align # Constraint # added constraint: constraint((T0283)I38.CB, (T0283)V83.CB) [> 4.5261 = 7.5435 < 9.8065] w=0.3231 to align # Constraint # added constraint: constraint((T0283)I38.CB, (T0283)C87.CB) [> 4.6056 = 7.6760 < 9.9788] w=0.3231 to align # Constraint # added constraint: constraint((T0283)I57.CB, (T0283)C87.CB) [> 4.0944 = 6.8241 < 8.8713] w=0.3231 to align # Constraint # added constraint: constraint((T0283)F58.CB, (T0283)M91.CB) [> 2.2397 = 3.7328 < 4.8526] w=0.3231 to align # Constraint # added constraint: constraint((T0283)G59.CA, (T0283)M91.CB) [> 4.5116 = 7.5193 < 9.7752] w=0.3231 to align # Constraint # added constraint: constraint((T0283)I61.CB, (T0283)C87.CB) [> 3.7953 = 6.3256 < 8.2232] w=0.3231 to align # Constraint # added constraint: constraint((T0283)F58.CB, (T0283)C87.CB) [> 3.9882 = 6.6470 < 8.6411] w=0.3165 to align # Constraint # added constraint: constraint((T0283)K55.CB, (T0283)L105.CB) [> 3.5506 = 5.9176 < 7.6929] w=0.3078 to align # Constraint # added constraint: constraint((T0283)W43.CB, (T0283)T54.CB) [> 3.6580 = 6.0967 < 7.9257] w=0.3036 to align # Constraint # added constraint: constraint((T0283)M20.CB, (T0283)F58.CB) [> 3.9622 = 6.6037 < 8.5848] w=0.2921 to align # Constraint # added constraint: constraint((T0283)M42.CB, (T0283)W51.CB) [> 4.4886 = 7.4810 < 9.7253] w=0.2914 to align # Constraint # added constraint: constraint((T0283)W51.CB, (T0283)M91.CB) [> 2.2056 = 3.6760 < 4.7788] w=0.2914 to align # Constraint # added constraint: constraint((T0283)T54.CB, (T0283)C87.CB) [> 4.5507 = 7.5846 < 9.8599] w=0.2914 to align # Constraint # added constraint: constraint((T0283)K55.CB, (T0283)C87.CB) [> 2.3967 = 3.9946 < 5.1929] w=0.2914 to align # Constraint # added constraint: constraint((T0283)E21.CB, (T0283)H32.CB) [> 3.0893 = 5.1488 < 6.6935] w=0.2856 to align # Constraint # added constraint: constraint((T0283)M7.CB, (T0283)M42.CB) [> 3.2521 = 5.4202 < 7.0463] w=0.2837 to align # Constraint # added constraint: constraint((T0283)A69.CB, (T0283)G80.CA) [> 3.8462 = 6.4103 < 8.3334] w=0.2812 to align # Constraint # added constraint: constraint((T0283)A69.CB, (T0283)E81.CB) [> 3.8339 = 6.3898 < 8.3068] w=0.2776 to align # Constraint # added constraint: constraint((T0283)G68.CA, (T0283)V83.CB) [> 3.3384 = 5.5641 < 7.2333] w=0.2776 to align # Constraint # added constraint: constraint((T0283)Y41.CB, (T0283)D53.CB) [> 3.6874 = 6.1457 < 7.9894] w=0.2725 to align # Constraint # added constraint: constraint((T0283)W17.CB, (T0283)W43.CB) [> 3.5916 = 5.9860 < 7.7818] w=0.2689 to align # Constraint # added constraint: constraint((T0283)A24.CB, (T0283)K36.CB) [> 3.8449 = 6.4082 < 8.3307] w=0.2689 to align # Constraint # added constraint: constraint((T0283)F58.CB, (T0283)M98.CB) [> 3.3333 = 5.5555 < 7.2221] w=0.2673 to align # Constraint # added constraint: constraint((T0283)Y41.CB, (T0283)F58.CB) [> 4.7010 = 7.8350 < 10.1855] w=0.2476 to align # Constraint # added constraint: constraint((T0283)P28.CB, (T0283)L64.CB) [> 4.5895 = 7.6491 < 9.9439] w=0.2476 to align # Constraint # added constraint: constraint((T0283)L27.CB, (T0283)L64.CB) [> 3.4713 = 5.7856 < 7.5212] w=0.2476 to align # Constraint # added constraint: constraint((T0283)L27.CB, (T0283)K104.CB) [> 4.2815 = 7.1358 < 9.2765] w=0.2325 to align # Constraint # added constraint: constraint((T0283)T54.CB, (T0283)L105.CB) [> 3.6134 = 6.0224 < 7.8291] w=0.2325 to align # Constraint # added constraint: constraint((T0283)L27.CB, (T0283)Y41.CB) [> 3.6456 = 6.0760 < 7.8988] w=0.2263 to align # Constraint # added constraint: constraint((T0283)L11.CB, (T0283)A24.CB) [> 3.9017 = 6.5029 < 8.4537] w=0.2258 to align # Constraint # added constraint: constraint((T0283)M7.CB, (T0283)W51.CB) [> 4.3033 = 7.1722 < 9.3239] w=0.2258 to align # Constraint # added constraint: constraint((T0283)I4.CB, (T0283)P28.CB) [> 2.3406 = 3.9011 < 5.0714] w=0.2258 to align # Constraint # added constraint: constraint((T0283)F3.CB, (T0283)I57.CB) [> 3.9866 = 6.6444 < 8.6377] w=0.2258 to align # Constraint # added constraint: constraint((T0283)F3.CB, (T0283)T54.CB) [> 3.6404 = 6.0673 < 7.8875] w=0.2258 to align # Constraint # added constraint: constraint((T0283)G68.CA, (T0283)C87.CB) [> 4.6168 = 7.6947 < 10.0032] w=0.2258 to align # Constraint # added constraint: constraint((T0283)F65.CB, (T0283)M91.CB) [> 2.8451 = 4.7419 < 6.1644] w=0.2258 to align # Constraint # added constraint: constraint((T0283)L62.CB, (T0283)M98.CB) [> 3.6272 = 6.0453 < 7.8589] w=0.2258 to align # Constraint # added constraint: constraint((T0283)F58.CB, (T0283)Y101.CB) [> 4.0873 = 6.8122 < 8.8559] w=0.2258 to align # Constraint # added constraint: constraint((T0283)S45.CB, (T0283)V83.CB) [> 4.5841 = 7.6402 < 9.9323] w=0.2258 to align # Constraint # added constraint: constraint((T0283)Y41.CB, (T0283)F86.CB) [> 3.6670 = 6.1118 < 7.9453] w=0.2258 to align # Constraint # added constraint: constraint((T0283)A37.CB, (T0283)F86.CB) [> 3.5106 = 5.8509 < 7.6062] w=0.2258 to align # Constraint # added constraint: constraint((T0283)C87.CB, (T0283)W97.CB) [> 3.6689 = 6.1148 < 7.9492] w=0.2217 to align # Constraint # added constraint: constraint((T0283)S45.CB, (T0283)T76.CB) [> 4.3732 = 7.2886 < 9.4752] w=0.2154 to align # Constraint # added constraint: constraint((T0283)S45.CB, (T0283)L78.CB) [> 2.8101 = 4.6835 < 6.0886] w=0.2154 to align # Constraint # added constraint: constraint((T0283)S45.CB, (T0283)T79.CB) [> 4.6832 = 7.8053 < 10.1469] w=0.2154 to align # Constraint # added constraint: constraint((T0283)G46.CA, (T0283)I61.CB) [> 3.6532 = 6.0886 < 7.9152] w=0.2154 to align # Constraint # added constraint: constraint((T0283)E66.CB, (T0283)L105.CB) [> 3.7273 = 6.2121 < 8.0758] w=0.2083 to align # Constraint # added constraint: constraint((T0283)W17.CB, (T0283)W97.CB) [> 4.1783 = 6.9638 < 9.0529] w=0.1943 to align # Constraint # added constraint: constraint((T0283)E21.CB, (T0283)W97.CB) [> 3.7610 = 6.2682 < 8.1487] w=0.1943 to align # Constraint # added constraint: constraint((T0283)F58.CB, (T0283)L105.CB) [> 3.9758 = 6.6263 < 8.6142] w=0.1920 to align # Constraint # added constraint: constraint((T0283)C87.CB, (T0283)Y101.CB) [> 3.0921 = 5.1536 < 6.6996] w=0.1876 to align # Constraint # added constraint: constraint((T0283)I8.CB, (T0283)W51.CB) [> 3.6895 = 6.1491 < 7.9939] w=0.1818 to align # Constraint # added constraint: constraint((T0283)S10.CB, (T0283)M42.CB) [> 3.3020 = 5.5033 < 7.1543] w=0.1818 to align # Constraint # added constraint: constraint((T0283)L11.CB, (T0283)G46.CA) [> 3.0497 = 5.0829 < 6.6077] w=0.1818 to align # Constraint # added constraint: constraint((T0283)E21.CB, (T0283)K40.CB) [> 4.7950 = 7.9917 < 10.3892] w=0.1818 to align # Constraint # added constraint: constraint((T0283)E21.CB, (T0283)W43.CB) [> 3.8459 = 6.4099 < 8.3329] w=0.1818 to align # Constraint # added constraint: constraint((T0283)E21.CB, (T0283)T54.CB) [> 2.9116 = 4.8527 < 6.3086] w=0.1703 to align # Constraint # added constraint: constraint((T0283)E21.CB, (T0283)S45.CB) [> 3.8798 = 6.4664 < 8.4063] w=0.1642 to align # Constraint # added constraint: constraint((T0283)E21.CB, (T0283)P48.CB) [> 4.5843 = 7.6405 < 9.9327] w=0.1642 to align # Constraint # added constraint: constraint((T0283)E21.CB, (T0283)T49.CB) [> 3.3838 = 5.6397 < 7.3316] w=0.1642 to align # Constraint # added constraint: constraint((T0283)I4.CB, (T0283)W43.CB) [> 3.6011 = 6.0018 < 7.8024] w=0.1626 to align # Constraint # added constraint: constraint((T0283)I4.CB, (T0283)T44.CB) [> 4.6414 = 7.7356 < 10.0563] w=0.1626 to align # Constraint # added constraint: constraint((T0283)I4.CB, (T0283)G46.CA) [> 3.8033 = 6.3388 < 8.2405] w=0.1626 to align # Constraint # added constraint: constraint((T0283)E5.CB, (T0283)W43.CB) [> 3.5249 = 5.8748 < 7.6372] w=0.1626 to align # Constraint # added constraint: constraint((T0283)I8.CB, (T0283)W43.CB) [> 2.4931 = 4.1551 < 5.4016] w=0.1626 to align # Constraint # added constraint: constraint((T0283)E21.CB, (T0283)A34.CB) [> 4.5958 = 7.6596 < 9.9575] w=0.1626 to align # Constraint # added constraint: constraint((T0283)L27.CB, (T0283)W97.CB) [> 3.7088 = 6.1814 < 8.0358] w=0.1573 to align # Constraint # added constraint: constraint((T0283)W43.CB, (T0283)M91.CB) [> 3.3878 = 5.6463 < 7.3402] w=0.1554 to align # Constraint # added constraint: constraint((T0283)W51.CB, (T0283)I109.CB) [> 3.4580 = 5.7633 < 7.4923] w=0.1505 to align # Constraint # added constraint: constraint((T0283)R23.CB, (T0283)S108.CB) [> 4.7157 = 7.8595 < 10.2174] w=0.1505 to align # Constraint # added constraint: constraint((T0283)E71.CB, (T0283)G80.CA) [> 3.1916 = 5.3194 < 6.9152] w=0.1505 to align # Constraint # added constraint: constraint((T0283)L62.CB, (T0283)R102.CB) [> 3.8150 = 6.3584 < 8.2659] w=0.1505 to align # Constraint # added constraint: constraint((T0283)G68.CA, (T0283)L78.CB) [> 3.9398 = 6.5663 < 8.5362] w=0.1449 to align # Constraint # added constraint: constraint((T0283)A69.CB, (T0283)T79.CB) [> 3.4962 = 5.8271 < 7.5752] w=0.1428 to align # Constraint # added constraint: constraint((T0283)G68.CA, (T0283)T79.CB) [> 4.0269 = 6.7116 < 8.7250] w=0.1428 to align # Constraint # added constraint: constraint((T0283)F65.CB, (T0283)V83.CB) [> 3.0976 = 5.1627 < 6.7115] w=0.1389 to align # Constraint # added constraint: constraint((T0283)L62.CB, (T0283)V75.CB) [> 3.6706 = 6.1176 < 7.9529] w=0.1361 to align # Constraint # added constraint: constraint((T0283)E66.CB, (T0283)V75.CB) [> 4.6166 = 7.6943 < 10.0025] w=0.1361 to align # Constraint # added constraint: constraint((T0283)M42.CB, (T0283)F65.CB) [> 4.2475 = 7.0791 < 9.2028] w=0.1355 to align # Constraint # added constraint: constraint((T0283)M42.CB, (T0283)V75.CB) [> 4.6473 = 7.7455 < 10.0692] w=0.1355 to align # Constraint # added constraint: constraint((T0283)M7.CB, (T0283)E21.CB) [> 3.8225 = 6.3708 < 8.2820] w=0.1278 to align # Constraint # added constraint: constraint((T0283)R23.CB, (T0283)G47.CA) [> 3.2680 = 5.4468 < 7.0808] w=0.1244 to align # Constraint # added constraint: constraint((T0283)K14.CB, (T0283)E66.CB) [> 3.8330 = 6.3884 < 8.3049] w=0.1244 to align # Constraint # added constraint: constraint((T0283)S10.CB, (T0283)E66.CB) [> 4.3308 = 7.2180 < 9.3834] w=0.1244 to align # Constraint # added constraint: constraint((T0283)K25.CB, (T0283)G46.CA) [> 4.1449 = 6.9082 < 8.9807] w=0.1244 to align # Constraint # added constraint: constraint((T0283)S10.CB, (T0283)T54.CB) [> 4.7837 = 7.9728 < 10.3646] w=0.1218 to align # Constraint # added constraint: constraint((T0283)R23.CB, (T0283)F65.CB) [> 3.3280 = 5.5466 < 7.2106] w=0.1218 to align # Constraint # added constraint: constraint((T0283)A70.CB, (T0283)Y101.CB) [> 2.5632 = 4.2721 < 5.5537] w=0.1212 to align # Constraint # added constraint: constraint((T0283)A70.CB, (T0283)L105.CB) [> 2.6630 = 4.4383 < 5.7698] w=0.1212 to align # Constraint # added constraint: constraint((T0283)G47.CA, (T0283)I61.CB) [> 4.5492 = 7.5820 < 9.8566] w=0.1077 to align # Constraint # added constraint: constraint((T0283)G46.CA, (T0283)L78.CB) [> 4.7776 = 7.9627 < 10.3515] w=0.1074 to align # Constraint # added constraint: constraint((T0283)K6.CB, (T0283)F86.CB) [> 4.7926 = 7.9876 < 10.3839] w=0.1036 to align # Constraint # added constraint: constraint((T0283)T44.CB, (T0283)T54.CB) [> 4.2675 = 7.1125 < 9.2463] w=0.0908 to align # Constraint # added constraint: constraint((T0283)T49.CB, (T0283)A70.CB) [> 4.2442 = 7.0737 < 9.1958] w=0.0871 to align # Constraint # added constraint: constraint((T0283)T49.CB, (T0283)G68.CA) [> 2.1307 = 3.5512 < 4.6166] w=0.0871 to align # Constraint # added constraint: constraint((T0283)P48.CB, (T0283)E66.CB) [> 4.5447 = 7.5745 < 9.8468] w=0.0871 to align # Constraint # added constraint: constraint((T0283)G47.CA, (T0283)E67.CB) [> 3.0333 = 5.0555 < 6.5722] w=0.0871 to align # Constraint # added constraint: constraint((T0283)T44.CB, (T0283)D63.CB) [> 4.7603 = 7.9338 < 10.3139] w=0.0871 to align # Constraint # added constraint: constraint((T0283)A84.CB, (T0283)N106.CB) [> 4.4176 = 7.3627 < 9.5716] w=0.0871 to align # Constraint # added constraint: constraint((T0283)G80.CA, (T0283)I109.CB) [> 3.8588 = 6.4313 < 8.3607] w=0.0871 to align # Constraint # added constraint: constraint((T0283)A69.CB, (T0283)I109.CB) [> 2.6899 = 4.4833 < 5.8282] w=0.0871 to align # Constraint # added constraint: constraint((T0283)L62.CB, (T0283)Y101.CB) [> 3.9868 = 6.6447 < 8.6381] w=0.0871 to align # Constraint # added constraint: constraint((T0283)L62.CB, (T0283)F86.CB) [> 3.0450 = 5.0751 < 6.5976] w=0.0871 to align # Constraint # added constraint: constraint((T0283)R56.CB, (T0283)K100.CB) [> 3.4424 = 5.7373 < 7.4585] w=0.0847 to align # Constraint # added constraint: constraint((T0283)T76.CB, (T0283)A85.CB) [> 2.4191 = 4.0319 < 5.2414] w=0.0836 to align # Constraint # added constraint: constraint((T0283)V75.CB, (T0283)F86.CB) [> 4.2893 = 7.1488 < 9.2935] w=0.0836 to align # Constraint # added constraint: constraint((T0283)T54.CB, (T0283)Y101.CB) [> 3.5570 = 5.9284 < 7.7069] w=0.0753 to align # Constraint # added constraint: constraint((T0283)I61.CB, (T0283)V83.CB) [> 4.1488 = 6.9147 < 8.9891] w=0.0624 to align # Constraint # added constraint: constraint((T0283)F3.CB, (T0283)S108.CB) [> 2.3591 = 3.9319 < 5.1115] w=0.0542 to align # Constraint # added constraint: constraint((T0283)F3.CB, (T0283)I109.CB) [> 3.9333 = 6.5556 < 8.5223] w=0.0542 to align # Constraint # added constraint: constraint((T0283)L78.CB, (T0283)M98.CB) [> 3.3564 = 5.5939 < 7.2721] w=0.0542 to align # Constraint # added constraint: constraint((T0283)T44.CB, (T0283)T79.CB) [> 4.6868 = 7.8113 < 10.1547] w=0.0540 to align # Constraint # added constraint: constraint((T0283)T44.CB, (T0283)L78.CB) [> 2.8328 = 4.7214 < 6.1378] w=0.0540 to align # Constraint # added constraint: constraint((T0283)L62.CB, (T0283)D82.CB) [> 4.4427 = 7.4045 < 9.6258] w=0.0502 to align # Constraint # added constraint: constraint((T0283)C87.CB, (T0283)I109.CB) [> 3.0426 = 5.0709 < 6.5922] w=0.0502 to align # Constraint # added constraint: constraint((T0283)K14.CB, (T0283)S45.CB) [> 4.4927 = 7.4878 < 9.7341] w=0.0435 to align # Constraint # added constraint: constraint((T0283)K74.CB, (T0283)C87.CB) [> 3.2147 = 5.3578 < 6.9652] w=0.0415 to align # Constraint # added constraint: constraint((T0283)E21.CB, (T0283)F58.CB) [> 3.4504 = 5.7506 < 7.4758] w=0.0121 to align # Constraint # added constraint: constraint((T0283)E21.CB, (T0283)L62.CB) [> 3.9382 = 6.5637 < 8.5328] w=0.0061 to align # Constraint # added constraint: constraint((T0283)K14.CB, (T0283)L62.CB) [> 3.1116 = 5.1860 < 6.7419] w=0.0061 to align # Constraint # added constraint: constraint((T0283)K14.CB, (T0283)F58.CB) [> 3.7903 = 6.3172 < 8.2124] w=0.0061 to align # Constraint # added constraint: constraint((T0283)S45.CB, (T0283)D93.CB) [> 4.2715 = 7.1192 < 9.2549] w=0.0061 to align # SetCost created cost = # ( 1.0000 * align ) # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0283/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0283/decoys/ # ReadConformPDB reading from PDB file crazyCapHelix75-77tighter.renum.pdb.gz looking for model 1 # Found a chain break before 110 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file crazyCapHelixTake3.renum.pdb.gz looking for model 1 # Found a chain break before 110 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file g80.randomPerturbOfG80coil.renum.gromacs0.pdb.gz looking for model 1 # Found a chain break before 94 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file g80.randomPerturbOfG80coil.renum.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file helix80-93rotateFromTry6.renum.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file helix81-92rotateFromTry6.renum.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file liftTyr31.fromTry9.renum.pdb.gz looking for model 1 # Found a chain break before 110 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file robetta-model1.pdb.gz looking for model 1 # ReadConformPDB reading from PDB file robetta-model10.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file robetta-model2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file robetta-model3.pdb.gz looking for model 1 # ReadConformPDB reading from PDB file robetta-model4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file robetta-model5.pdb.gz looking for model 1 # ReadConformPDB reading from PDB file robetta-model6.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file robetta-model7.pdb.gz looking for model 1 # ReadConformPDB reading from PDB file robetta-model8.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file robetta-model9.pdb.gz looking for model 1 # ReadConformPDB reading from PDB file rotNtermFromTry26.renum.pdb.gz looking for model 1 # Found a chain break before 110 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file rotNtermLessFromTry26.renum.pdb.gz looking for model 1 # Found a chain break before 110 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_RECOM_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_RECOM_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS4.pdb.gz looking for model 1 # Found a chain break before 94 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_TS4 # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # Found a chain break before 47 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS1 # ReadConformPDB reading from PDB file servers/3Dpro_TS2.pdb.gz looking for model 1 # Found a chain break before 39 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS2 # ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1 # Found a chain break before 28 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS3 # ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1 # naming current conformation 3Dpro_TS4 # ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1 # naming current conformation 3Dpro_TS5 # ReadConformPDB reading from PDB file servers/ABIpro_TS1.pdb.gz looking for model 1 # Found a chain break before 106 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS1 # ReadConformPDB reading from PDB file servers/ABIpro_TS2.pdb.gz looking for model 1 # Found a chain break before 106 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS2 # ReadConformPDB reading from PDB file servers/ABIpro_TS3.pdb.gz looking for model 1 # Found a chain break before 77 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS3 # ReadConformPDB reading from PDB file servers/ABIpro_TS4.pdb.gz looking for model 1 # Found a chain break before 102 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS4 # ReadConformPDB reading from PDB file servers/ABIpro_TS5.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS5 # ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # naming current conformation BayesHH_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS1.pdb.gz looking for model 1 # Found a chain break before 58 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS2.pdb.gz looking for model 1 # Found a chain break before 58 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS2 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS3.pdb.gz looking for model 1 # Found a chain break before 111 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS3 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS4.pdb.gz looking for model 1 # Found a chain break before 58 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS4 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS5.pdb.gz looking for model 1 # Found a chain break before 69 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS5 # ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1 # Found a chain break before 104 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS1 # ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1 # Found a chain break before 109 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # Found a chain break before 102 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS3 # ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1 # Found a chain break before 102 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS4 # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # Found a chain break before 105 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS5 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS2 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS3.pdb.gz looking for model 1 # Found a chain break before 81 # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS3 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS4.pdb.gz looking for model 1 # Found a chain break before 105 # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS4 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS5 # ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation Distill_TS1 # ReadConformPDB reading from PDB file servers/Distill_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation Distill_TS2 # ReadConformPDB reading from PDB file servers/Distill_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation Distill_TS3 # ReadConformPDB reading from PDB file servers/Distill_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation Distill_TS4 # ReadConformPDB reading from PDB file servers/Distill_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation Distill_TS5 # ReadConformPDB reading from PDB file servers/FAMSD_TS1.pdb.gz looking for model 1 # Found a chain break before 111 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS1 # ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1 # Found a chain break before 106 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS2 # ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1 # Found a chain break before 104 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS3 # ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1 # Found a chain break before 110 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS4 # ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation FAMSD_TS5 # ReadConformPDB reading from PDB file servers/FAMS_TS1.pdb.gz looking for model 1 # Found a chain break before 109 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # Found a chain break before 104 # copying to AlignedFragments data structure # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # Found a chain break before 102 # copying to AlignedFragments data structure # naming current conformation FAMS_TS3 # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # Found a chain break before 105 # copying to AlignedFragments data structure # naming current conformation FAMS_TS4 # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # Found a chain break before 102 # copying to AlignedFragments data structure # naming current conformation FAMS_TS5 # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # Found a chain break before 47 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS1 # ReadConformPDB reading from PDB file servers/FOLDpro_TS2.pdb.gz looking for model 1 # Found a chain break before 87 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS2 # ReadConformPDB reading from PDB file servers/FOLDpro_TS3.pdb.gz looking for model 1 # Found a chain break before 39 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS3 # ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1 # naming current conformation FOLDpro_TS4 # ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1 # naming current conformation FOLDpro_TS5 # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation FORTE1_AL1 # ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL2 # ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL3 # ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation FORTE1_AL4 # ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation FORTE1_AL5 # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL1 # ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL2 # ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation FORTE2_AL3 # ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation FORTE2_AL4 # ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation FORTE2_AL5 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1 # Found a chain break before 89 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS2 # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS3 # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # naming current conformation FUGMOD_TS4 # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # Found a chain break before 59 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS5 # ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL1 # ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation FUGUE_AL2 # ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation FUGUE_AL3 # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL4 # ReadConformPDB reading from PDB file servers/FUGUE_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL5 # ReadConformPDB reading from PDB file servers/FUNCTION_TS1.pdb.gz looking for model 1 # Found a chain break before 106 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS1 # ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS2 # ReadConformPDB reading from PDB file servers/FUNCTION_TS3.pdb.gz looking for model 1 # Found a chain break before 101 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS3 # ReadConformPDB reading from PDB file servers/FUNCTION_TS4.pdb.gz looking for model 1 # Found a chain break before 111 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS4 # ReadConformPDB reading from PDB file servers/FUNCTION_TS5.pdb.gz looking for model 1 # Found a chain break before 106 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1 # naming current conformation HHpred1_TS1 # ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1 # Found a chain break before 93 # copying to AlignedFragments data structure # naming current conformation HHpred2_TS1 # ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1 # naming current conformation HHpred3_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS2 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS3 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS4 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS5 # ReadConformPDB reading from PDB file servers/LOOPP_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation LOOPP_TS1 # ReadConformPDB reading from PDB file servers/LOOPP_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation LOOPP_TS2 # ReadConformPDB reading from PDB file servers/LOOPP_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation LOOPP_TS3 # ReadConformPDB reading from PDB file servers/LOOPP_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation LOOPP_TS4 # ReadConformPDB reading from PDB file servers/LOOPP_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation LOOPP_TS5 # ReadConformPDB reading from PDB file servers/MIG_FROST_AL1.pdb.gz looking for model 1 Error: Reading chain '' from PDB file servers/MIG_FROST_AL1.pdb.gz failed---no such chain. # naming current conformation MIG_FROST_AL1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # naming current conformation Ma-OPUS-server_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS2.pdb.gz looking for model 1 # naming current conformation Ma-OPUS-server_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS3.pdb.gz looking for model 1 # Found a chain break before 105 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS4.pdb.gz looking for model 1 # naming current conformation Ma-OPUS-server_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS5.pdb.gz looking for model 1 # Found a chain break before 42 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS5 # ReadConformPDB reading from PDB file servers/MetaTasser_TS1.pdb.gz looking for model 1 # Found a chain break before 81 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS1 # ReadConformPDB reading from PDB file servers/MetaTasser_TS2.pdb.gz looking for model 1 # Found a chain break before 81 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS2 # ReadConformPDB reading from PDB file servers/MetaTasser_TS3.pdb.gz looking for model 1 # Found a chain break before 91 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS3 # ReadConformPDB reading from PDB file servers/MetaTasser_TS4.pdb.gz looking for model 1 # Found a chain break before 82 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS4 # ReadConformPDB reading from PDB file servers/MetaTasser_TS5.pdb.gz looking for model 1 # Found a chain break before 68 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS5 # ReadConformPDB reading from PDB file servers/POMYSL_TS1.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS2.pdb.gz looking for model 1 # Found a chain break before 103 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS2 # ReadConformPDB reading from PDB file servers/POMYSL_TS3.pdb.gz looking for model 1 # Found a chain break before 87 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS3 # ReadConformPDB reading from PDB file servers/POMYSL_TS4.pdb.gz looking for model 1 # Found a chain break before 101 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS4 # ReadConformPDB reading from PDB file servers/POMYSL_TS5.pdb.gz looking for model 1 # Found a chain break before 66 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation PROTINFO-AB_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # Found a chain break before 27 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS5 # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pcons6_TS1 # ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pcons6_TS2 # ReadConformPDB reading from PDB file servers/Pcons6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation Pcons6_TS3 # ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation Pcons6_TS4 # ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation Pcons6_TS5 # ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation Phyre-1_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation Phyre-2_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation Phyre-2_TS2 # ReadConformPDB reading from PDB file servers/Phyre-2_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation Phyre-2_TS3 # ReadConformPDB reading from PDB file servers/Phyre-2_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation Phyre-2_TS4 # ReadConformPDB reading from PDB file servers/Phyre-2_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation Phyre-2_TS5 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS1 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS2 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS3 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS4 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS4.pdb.gz looking for model 1 # Found a chain break before 27 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1 # Found a chain break before 27 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS5 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS1.pdb.gz looking for model 1 # Found a chain break before 14 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS1 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS2.pdb.gz looking for model 1 # Found a chain break before 58 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS2 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS3.pdb.gz looking for model 1 # naming current conformation RAPTORESS_TS3 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS4.pdb.gz looking for model 1 # Found a chain break before 26 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS4 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS5.pdb.gz looking for model 1 # Found a chain break before 102 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR_TS1.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR_TS3.pdb.gz looking for model 1 # Found a chain break before 99 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR_TS4.pdb.gz looking for model 1 # Found a chain break before 34 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR_TS5.pdb.gz looking for model 1 # Found a chain break before 7 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS5 # ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS1 # ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS2 # ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS3 # ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS4 # ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS5 # ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS1 # ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS2 # ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS3 # ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS4 # ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS5 # ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL1 # ReadConformPDB reading from PDB file servers/SAM-T02_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL2 # ReadConformPDB reading from PDB file servers/SAM-T02_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL3 # ReadConformPDB reading from PDB file servers/SAM-T02_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL4 # ReadConformPDB reading from PDB file servers/SAM-T02_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL5 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # naming current conformation SAM_T06_server_TS1 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS2 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS3 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS4 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS5 # ReadConformPDB reading from PDB file servers/SP3_TS1.pdb.gz looking for model 1 # Found a chain break before 8 # copying to AlignedFragments data structure # naming current conformation SP3_TS1 # ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1 # naming current conformation SP3_TS2 # ReadConformPDB reading from PDB file servers/SP3_TS3.pdb.gz looking for model 1 # Found a chain break before 71 # copying to AlignedFragments data structure # naming current conformation SP3_TS3 # ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1 # naming current conformation SP3_TS4 # ReadConformPDB reading from PDB file servers/SP3_TS5.pdb.gz looking for model 1 # Found a chain break before 27 # copying to AlignedFragments data structure # naming current conformation SP3_TS5 # ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1 # Found a chain break before 8 # copying to AlignedFragments data structure # naming current conformation SP4_TS1 # ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1 # naming current conformation SP4_TS2 # ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1 # naming current conformation SP4_TS3 # ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1 # naming current conformation SP4_TS4 # ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1 # Found a chain break before 81 # copying to AlignedFragments data structure # naming current conformation SP4_TS5 # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # Found a chain break before 8 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS1 # ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS2 # ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS3 # ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS4 # ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS2 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS3 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS4 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_expm_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation UNI-EID_expm_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL2 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL3 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL4 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL5 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1 # Found a chain break before 94 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS1 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS2.pdb.gz looking for model 1 # Found a chain break before 28 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS2 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS3.pdb.gz looking for model 1 # Found a chain break before 108 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS3 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS4.pdb.gz looking for model 1 # Found a chain break before 82 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS4 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS5.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS5 # ReadConformPDB reading from PDB file servers/beautshot_TS1.pdb.gz looking for model 1 # Found a chain break before 106 # copying to AlignedFragments data structure # naming current conformation beautshot_TS1 # ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation beautshotbase_TS1 # ReadConformPDB reading from PDB file servers/gtg_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation gtg_AL1 # ReadConformPDB reading from PDB file servers/gtg_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation gtg_AL2 # ReadConformPDB reading from PDB file servers/gtg_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation gtg_AL3 # ReadConformPDB reading from PDB file servers/gtg_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation gtg_AL4 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # naming current conformation karypis.srv.2_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS2.pdb.gz looking for model 1 # Found a chain break before 81 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS3.pdb.gz looking for model 1 # naming current conformation karypis.srv.2_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS4.pdb.gz looking for model 1 # Found a chain break before 75 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS5.pdb.gz looking for model 1 # naming current conformation karypis.srv.2_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS1.pdb.gz looking for model 1 # Found a chain break before 109 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS5 # ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1 # Found a chain break before 82 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS1 # ReadConformPDB reading from PDB file servers/keasar-server_TS2.pdb.gz looking for model 1 # Found a chain break before 83 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS2 # ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1 # Found a chain break before 82 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS3 # ReadConformPDB reading from PDB file servers/keasar-server_TS4.pdb.gz looking for model 1 # naming current conformation keasar-server_TS4 # ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1 # Found a chain break before 47 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS5 # ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation mGen-3D_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation nFOLD_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation nFOLD_TS2 # ReadConformPDB reading from PDB file servers/nFOLD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation nFOLD_TS3 # ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1 WARNING: atom 1 has residue number 1 < previous residue 112 in servers/nFOLD_TS4.pdb.gz # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation nFOLD_TS4 # ReadConformPDB reading from PDB file servers/nFOLD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation nFOLD_TS5 # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0283 can't currently be optimized by undertaker # naming current conformation shub_TS1 # command:Using radius: 8.0000 Using models AND alignments for constraints model score 1.2695 model score 1.2993 model score 1.2096 model score 1.1912 model score 1.2637 model score 1.3669 model score 1.2506 model score 1.1878 model score 1.7189 model score 1.7269 model score 1.1716 model score 1.8346 model score 1.2252 model score 1.7077 model score 1.1637 model score 1.7798 model score 1.2224 model score 1.2824 model score 1.2304 model score 2.2836 model score 1.7914 model score 1.6669 model score 2.2223 model score 2.3782 model score 1.8642 model score 1.7802 model score 1.8197 model score 1.8211 model score 1.8550 model score 1.9311 model score 1.8182 model score 1.8354 model score 1.5723 model score 1.3367 model score 1.7975 model score 1.8517 model score 1.7388 model score 1.9754 model score 1.0008 model score 1.2351 model score 1.3416 model score 1.3069 model score 0.9839 model score 1.5874 model score 1.3483 model score 1.1401 model score 1.2598 model score 1.2497 model score 1.9457 model score 1.1951 model score 1.4659 model score 1.6389 model score 1.8279 model score 2.2836 model score 1.6162 model score 1.6352 model score 2.4018 model score 1.6227 model score 1.5306 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.6406 model score 1.6058 model score 1.9124 model score 2.1540 model score 1.5713 model score 1.4659 model score 1.1951 model score 1.6389 model score 2.2836 model score 1.8279 model score 1.3367 model score 1.4978 model score 1.7975 model score 1.8585 model score 1.8490 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.8658 model score 1.5599 model score 1.5462 model score 1.2646 model score 1.3045 model score 2.2915 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.6058 model score 2.0629 model score 1.9939 model score 1.9807 model score 2.1028 model score 2.0941 model score 2.1699 model score 1.7502 model score 1.7287 model score 1.5270 model score 1.3388 model score 1.4164 model score 1.7043 model score 1.5512 model score 2.0169 model score 1.3277 model score 1.3476 model score 1.3790 model score 2.0613 model score 1.9208 model score 2.0542 model score 1.7248 model score 1.9992 model score 1.1920 model score 1.2161 model score 1.2030 model score 1.5250 model score 1.2675 model score 1.3961 model score 1.3841 model score 1.6861 model score 1.4787 model score 1.2802 model score 1.5436 model score 1.5354 model score 1.5106 model score 1.5230 model score 1.3828 model score 2.1080 model score 2.1221 model score 2.1998 model score 2.1126 model score 2.0174 model score 1.8346 model score 1.7269 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USE_META, weight: 0.7841 cost: 1.1954 min: 0.7854 max: 2.4948 USE_META, weight: 1.0000 cost: 0.7854 min: 0.7854 max: 2.4948 USE_META, weight: 0.4902 cost: 1.7536 min: 0.7854 max: 2.4948 USE_META, weight: 0.5122 cost: 1.7118 min: 0.7854 max: 2.4948 USE_META, weight: 0.7411 cost: 1.2771 min: 0.7854 max: 2.4948 USE_META, weight: 0.7411 cost: 1.2771 min: 0.7854 max: 2.4948 USE_META, weight: 0.7411 cost: 1.2771 min: 0.7854 max: 2.4948 USE_META, weight: 0.7411 cost: 1.2771 min: 0.7854 max: 2.4948 USE_META, weight: 0.3312 cost: 2.0556 min: 0.7854 max: 2.4948 USE_META, weight: 0.6496 cost: 1.4510 min: 0.7854 max: 2.4948 USE_META, weight: 0.1584 cost: 2.3839 min: 0.7854 max: 2.4948 USE_META, weight: 0.5971 cost: 1.5506 min: 0.7854 max: 2.4948 USE_META, weight: 0.4463 cost: 1.8370 min: 0.7854 max: 2.4948 USE_META, weight: 0.2975 cost: 2.1197 min: 0.7854 max: 2.4948 USE_META, weight: 0.6167 cost: 1.5135 min: 0.7854 max: 2.4948 USE_META, weight: 0.7132 cost: 1.3301 min: 0.7854 max: 2.4948 USE_META, weight: 0.7689 cost: 1.2244 min: 0.7854 max: 2.4948 USE_META, weight: 0.3726 cost: 1.9769 min: 0.7854 max: 2.4948 USE_META, weight: 0.4496 cost: 1.8309 min: 0.7854 max: 2.4948 USE_META, weight: 0.2668 cost: 2.1780 min: 0.7854 max: 2.4948 USE_META, weight: 0.2663 cost: 2.1789 min: 0.7854 max: 2.4948 USE_META, weight: 0.2860 cost: 2.1416 min: 0.7854 max: 2.4948 USE_META, weight: 0.2184 cost: 2.2698 min: 0.7854 max: 2.4948 USE_META, weight: 0.3424 cost: 2.0344 min: 0.7854 max: 2.4948 USE_META, weight: 0.4325 cost: 1.8633 min: 0.7854 max: 2.4948 USE_META, weight: 0.3853 cost: 1.9530 min: 0.7854 max: 2.4948 USE_META, weight: 0.5421 cost: 1.6550 min: 0.7854 max: 2.4948 USE_META, weight: 0.4844 cost: 1.7647 min: 0.7854 max: 2.4948 USE_META, weight: 0.3184 cost: 2.0800 min: 0.7854 max: 2.4948 USE_META, weight: 0.3355 cost: 2.0475 min: 0.7854 max: 2.4948 USE_META, weight: 0.5271 cost: 1.6836 min: 0.7854 max: 2.4948 USE_EVALUE, weight: 0.8862 eval: 13.3640 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.8862 eval: 13.3640 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.8862 eval: 13.3640 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.7490 eval: 24.3260 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.7490 eval: 24.3260 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.7490 eval: 24.3260 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.6769 eval: 30.0900 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.6769 eval: 30.0900 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.6769 eval: 30.0900 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.8945 eval: 12.7000 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.8945 eval: 12.7000 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.8945 eval: 12.7000 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.8916 eval: 12.9260 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.8916 eval: 12.9260 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.8916 eval: 12.9260 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.6490 eval: 32.3210 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.6490 eval: 32.3210 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.7922 eval: 20.8700 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.7922 eval: 20.8700 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.7922 eval: 20.8700 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.6070 eval: 35.6790 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.6070 eval: 35.6790 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.6070 eval: 35.6790 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.7455 eval: 24.6100 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.7455 eval: 24.6100 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.7455 eval: 24.6100 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.9036 eval: 11.9710 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.9036 eval: 11.9710 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.9036 eval: 11.9710 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.6846 eval: 29.4760 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.6846 eval: 29.4760 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.6846 eval: 29.4760 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.8551 eval: 15.8430 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.8551 eval: 15.8430 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.8551 eval: 15.8430 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.6722 eval: 30.4630 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.6722 eval: 30.4630 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.6722 eval: 30.4630 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.8940 eval: 12.7400 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.8940 eval: 12.7400 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.8940 eval: 12.7400 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 1.0000 eval: 4.2643 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 1.0000 eval: 4.2643 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 1.0000 eval: 4.2643 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.7480 eval: 24.4090 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.7480 eval: 24.4090 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.7480 eval: 24.4090 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.6352 eval: 33.4230 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.6352 eval: 33.4230 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.6352 eval: 33.4230 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.8293 eval: 17.9120 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.8293 eval: 17.9120 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.8293 eval: 17.9120 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.1000 eval: 76.2000 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.1000 eval: 76.2000 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.1000 eval: 76.2000 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.6700 eval: 30.6400 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.6700 eval: 30.6400 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.6700 eval: 30.6400 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.6901 eval: 29.0320 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.6901 eval: 29.0320 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.6901 eval: 29.0320 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.7188 eval: 26.7420 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.7188 eval: 26.7420 min: 4.2643 max: 76.2000 USE_EVALUE, weight: 0.7188 eval: 26.7420 min: 4.2643 max: 76.2000 Number of contacts in models: 254 Number of contacts in alignments: 65 NUMB_ALIGNS: 65 Adding 4203 constraints to all3.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all3.constraints maxweight: 1.0000 Optimizing... Probability sum: -181.1444, CN propb: -181.1444 weights: 0.3022 constraints: 187 # command:Found ConstraintSet # PrintContacts align.constraints_meta03 Number of constraints in align3.constraints 187 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta03 Number of constraints in align3.constraints.bonus 187 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta03 Number of constraints in rejected3.constraints 4016 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta03 Number of constraints in rejected3.constraints.bonus 4016 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_meta03 Number of constraints in noncontact3.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_meta03 Number of constraints in noncontact3.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_meta03 Number of constraints in all3.constraints 4203 # command: