parameters: 0.6 1.3 0.5 200 50 # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading dunbrack-2191.atoms # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 53157 examples # computed average trans backbone unit before proline from 2010 examples # computed average cis backbone unit from 97 examples # trans (non-proline) backbone unit: # CA= -2.2087 1.0126 -0.0030 # O= -0.1499 2.2440 0.0016 # C= -0.6889 1.1368 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4581 -0.0000 0.0000 # cis backbone unit: # CA= -0.1436 2.4534 -0.0002 # O= -2.0284 0.9742 0.0015 # C= -0.8018 1.0771 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4668 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2100 1.0631 -0.0014 # O= -0.1236 2.2458 0.0075 # C= -0.6872 1.1517 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading dunbrack-2191.atoms have 2191 chains in training database # Count of chains,residues,atoms: 2191,500310,3902258 # 493341 residues have no bad marker # 3226 residues lack atoms needed to compute omega # 1453 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 4 # HAS_OXT 1167 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 3052 # HAS_UNKNOWN_ATOMS 9 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 979 # NON_PLANAR_PEPTIDE 888 # BAD_PEPTIDE 2680 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-2191.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0331/ # command:# Making conformation for sequence T0331 numbered 1 through 149 Created new target T0331 from T0331.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0331/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0331//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0331/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0331//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0331/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0331/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0331/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g79A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1g79A expands to /projects/compbio/data/pdb/1g79.pdb.gz 1g79A:Skipped atom 805, because occupancy 0.5 <= existing 0.500 in 1g79A Skipped atom 807, because occupancy 0.500 <= existing 0.500 in 1g79A Skipped atom 809, because occupancy 0.500 <= existing 0.500 in 1g79A Skipped atom 811, because occupancy 0.500 <= existing 0.500 in 1g79A Skipped atom 1326, because occupancy 0.500 <= existing 0.500 in 1g79A Skipped atom 1328, because occupancy 0.500 <= existing 0.500 in 1g79A Skipped atom 1330, because occupancy 0.500 <= existing 0.500 in 1g79A Skipped atom 1332, because occupancy 0.500 <= existing 0.500 in 1g79A Skipped atom 1334, because occupancy 0.500 <= existing 0.500 in 1g79A # T0331 read from 1g79A/merged-good-all-a2m # 1g79A read from 1g79A/merged-good-all-a2m # adding 1g79A to template set # found chain 1g79A in template set T0331 4 :KDIMHILEDM 1g79A 29 :ADPLTLFERW # choosing archetypes in rotamer library T0331 15 :VGVFATLDEYGNPHARHAHITAANEEGIFFMTSPETHFYDQLMGDQRVAMTAISEEGYL 1g79A 52 :AMVVATVDEHGQPYQRIVLLKHYDEKGMVFYTNLGSRKAHQIENNPRVSLLFPWHTLER T0331 76 :VVRVEGTARPVENDYLKTVFADNP 1g79A 111 :QVMVIGKAERLSTLEVMKYFHSRP T0331 101 :YQHIYKDES 1g79A 163 :LKQKFQQGE T0331 111 :DTMQVFQIYAGHGFYH 1g79A 176 :SFWGGFRVSLEQIEFW T0331 127 :SLTQGHKYIFSIG 1g79A 193 :GGEHRLHDRFLYQ Number of specific fragments extracted= 6 number of extra gaps= 0 total=6 Number of alignments=1 # 1g79A read from 1g79A/merged-good-all-a2m # found chain 1g79A in template set T0331 4 :KDIMHIL 1g79A 36 :ERWLSQA T0331 11 :EDMK 1g79A 45 :AKLA T0331 15 :VGVFATLDEYGNPHARHAHITAANEEGIFFMTSPETHFYDQLMGDQRVAMTAISEE 1g79A 52 :AMVVATVDEHGQPYQRIVLLKHYDEKGMVFYTNLGSRKAHQIENNPRVSLLFPWHT T0331 73 :LIQVVRVEGTARPVENDYLKTVFADNP 1g79A 108 :LERQVMVIGKAERLSTLEVMKYFHSRP T0331 100 :YYQHIYKDESSD 1g79A 162 :ELKQKFQQGEVP T0331 112 :TMQVFQIYAGHGFYHSLTQG 1g79A 177 :FWGGFRVSLEQIEFWQGGEH T0331 132 :HKYIFSIGQGE 1g79A 200 :DRFLYQRENDA Number of specific fragments extracted= 7 number of extra gaps= 0 total=13 Number of alignments=2 # 1g79A read from 1g79A/merged-good-all-a2m # found chain 1g79A in template set T0331 1 :MELKDIMHILEDMKVGVFATLDEYGNPHARHAHITAANEEGIFFMTSPETHFYDQLMGDQRVAMTAISEE 1g79A 38 :WLSQACEAKLADPTAMVVATVDEHGQPYQRIVLLKHYDEKGMVFYTNLGSRKAHQIENNPRVSLLFPWHT T0331 73 :LIQVVRVEGTARPVENDYLKTVFADNPYYQHIYKDESSDTMQVFQIYAGHGFYHSLTQGHKYIFSIGQGEHSEVRA 1g79A 108 :LERQVMVIGKAERLSTLEVMKYFHSRPRDSQIGAWVSKQSSRISARGILESKFLELKQKFQQGEVPLPSFWGGFRV Number of specific fragments extracted= 2 number of extra gaps= 0 total=15 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1flmA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0331 read from 1flmA/merged-good-all-a2m # 1flmA read from 1flmA/merged-good-all-a2m # found chain 1flmA in training set T0331 4 :KDIMHILEDMKVGVFATLDE 1flmA 4 :GTFFEVLKNEGVVAIATQGE T0331 25 :GNPHA 1flmA 24 :DGPHL T0331 30 :RHAHITAANEEGIFFMTSPETHFYDQLMGDQRVAMTAISEE 1flmA 32 :WNSYLKVLDGNRIVVPVGGMHKTEANVARDERVLMTLGSRK T0331 71 :GYLIQVVRVEGTARPVE 1flmA 77 :NGPGTGFLIRGSAAFRT T0331 97 :DNPYYQHIYKDESSDTMQVFQIYA 1flmA 94 :DGPEFEAIARFKWARAALVITVVS Number of specific fragments extracted= 5 number of extra gaps= 0 total=20 Number of alignments=4 # 1flmA read from 1flmA/merged-good-all-a2m # found chain 1flmA in training set T0331 4 :KDIMHILEDMKVGVFATLDE 1flmA 4 :GTFFEVLKNEGVVAIATQGE T0331 25 :GNPHARHAH 1flmA 24 :DGPHLVNTW T0331 34 :ITAANEEGIFFMTSPETHFYDQLMGDQRVAMTAISE 1flmA 36 :LKVLDGNRIVVPVGGMHKTEANVARDERVLMTLGSR T0331 70 :EG 1flmA 77 :NG T0331 73 :LIQVVRVEGTARPVENDYLKTVFADN 1flmA 79 :PGTGFLIRGSAAFRTDGPEFEAIARF T0331 108 :ESSDTMQVFQIYAGH 1flmA 105 :KWARAALVITVVSAE Number of specific fragments extracted= 6 number of extra gaps= 0 total=26 Number of alignments=5 # 1flmA read from 1flmA/merged-good-all-a2m # found chain 1flmA in training set T0331 4 :KDIMHILEDMKVGVFATLDE 1flmA 4 :GTFFEVLKNEGVVAIATQGE T0331 25 :GNPHARHAH 1flmA 24 :DGPHLVNTW T0331 34 :ITAANEEGIFFMTSPETHFYDQLMGDQRVAMTA 1flmA 36 :LKVLDGNRIVVPVGGMHKTEANVARDERVLMTL T0331 67 :ISEEGYLIQVVRVEGTARPVENDYLKTVFADNPYY 1flmA 73 :VAGRNGPGTGFLIRGSAAFRTDGPEFEAIARFKWA Number of specific fragments extracted= 4 number of extra gaps= 0 total=30 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w3oA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0331 read from 1w3oA/merged-good-all-a2m # 1w3oA read from 1w3oA/merged-good-all-a2m # found chain 1w3oA in training set Warning: unaligning (T0331)S127 because of BadResidue code BAD_PEPTIDE in next template residue (1w3oA)N175 Warning: unaligning (T0331)L128 because of BadResidue code BAD_PEPTIDE at template residue (1w3oA)N175 T0331 2 :ELKDIMHILEDMKVGVFATL 1w3oA 23 :SDEWIRELLLRGTIARVATL T0331 22 :DEYGN 1w3oA 45 :GEDGA T0331 27 :PHARHAHITAANEEGIFFMTSPETH 1w3oA 52 :PFITPLAYAYRPEQGDLVYHTNVVG T0331 58 :GDQ 1w3oA 82 :AGQ T0331 61 :RVAMTAISEEGYL 1w3oA 87 :PATLEVSEIGQFL T0331 74 :IQVVRVEGTARPVENDYLKTVFADN 1w3oA 111 :YRSVMVFGTARVLAGEDARAALTTL T0331 101 :YQHIYKD 1w3oA 136 :SERVFPG T0331 108 :ESSDT 1w3oA 148 :TTRPI T0331 113 :MQVFQIYAGHGFYH 1w3oA 160 :TSVYSLSIDRWSGK T0331 129 :TQGH 1w3oA 176 :WAEQ Number of specific fragments extracted= 10 number of extra gaps= 1 total=40 Number of alignments=7 # 1w3oA read from 1w3oA/merged-good-all-a2m # found chain 1w3oA in training set Warning: unaligning (T0331)S127 because of BadResidue code BAD_PEPTIDE in next template residue (1w3oA)N175 Warning: unaligning (T0331)L128 because of BadResidue code BAD_PEPTIDE at template residue (1w3oA)N175 T0331 2 :ELKDIMHILEDMKVGVFATL 1w3oA 23 :SDEWIRELLLRGTIARVATL T0331 22 :DEYGN 1w3oA 45 :GEDGA T0331 27 :PHARHAHITAANE 1w3oA 52 :PFITPLAYAYRPE T0331 40 :EGIFFMTS 1w3oA 66 :GDLVYHTN T0331 48 :PETH 1w3oA 81 :NAGQ T0331 61 :RVAMTAISE 1w3oA 87 :PATLEVSEI T0331 70 :EGYLIQV 1w3oA 105 :LELSVQY T0331 77 :VRVEGTARPVENDYLKTVFA 1w3oA 114 :VMVFGTARVLAGEDARAALT T0331 100 :YYQHIYKDE 1w3oA 134 :TLSERVFPG T0331 114 :QVFQIYAGHGFYH 1w3oA 161 :SVYSLSIDRWSGK T0331 129 :TQGH 1w3oA 176 :WAEQ Number of specific fragments extracted= 11 number of extra gaps= 1 total=51 Number of alignments=8 # 1w3oA read from 1w3oA/merged-good-all-a2m # found chain 1w3oA in training set T0331 3 :LKDIMHILEDMKVGVFATL 1w3oA 24 :DEWIRELLLRGTIARVATL T0331 22 :DEYGNPHARHAHIT 1w3oA 45 :GEDGAAFPFITPLA T0331 36 :AANEEGIFFMTSPETHFY 1w3oA 62 :RPEQGDLVYHTNVVGRLR T0331 58 :GDQ 1w3oA 80 :ANA T0331 61 :RVAMTA 1w3oA 87 :PATLEV T0331 68 :SEEG 1w3oA 102 :NSPL T0331 72 :YLIQVVRVEGTARPVENDYLKTVFADNPYYQHIYKDESSDTMQVFQIYA 1w3oA 109 :VQYRSVMVFGTARVLAGEDARAALTTLSERVFPGLKVGETTRPISEDDL Number of specific fragments extracted= 7 number of extra gaps= 0 total=58 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vl7A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0331 read from 1vl7A/merged-good-all-a2m # 1vl7A read from 1vl7A/merged-good-all-a2m # found chain 1vl7A in training set T0331 7 :MHILEDMKVGVFATLDEYGNPHARHAHITAANEEGIFFMTSPETHFYDQLMGDQRVAMTAISEEG 1vl7A 12 :AGFIQEFQSAIISTISEQGIPNGSYAPFVIDDAKNIYIYVSGLAVHTKNIEANPLVNVLFVDDEA T0331 74 :IQVVRVEGTARPVENDYLKTVFAD 1vl7A 86 :RLSFDCTATLIERESQKWNQVVDQ T0331 101 :YQHIYKDE 1vl7A 110 :FQERFGQI T0331 110 :SDTMQVFQIYAGHGFYH 1vl7A 124 :LADFRIFQLTPKEGRFV Number of specific fragments extracted= 4 number of extra gaps= 0 total=62 Number of alignments=10 # 1vl7A read from 1vl7A/merged-good-all-a2m # found chain 1vl7A in training set T0331 7 :MHILEDMKVGVFATLDEYGNPHARHAHITAANEEGIFFMTSPETHFYDQLMGDQRVAMTAISEEG 1vl7A 12 :AGFIQEFQSAIISTISEQGIPNGSYAPFVIDDAKNIYIYVSGLAVHTKNIEANPLVNVLFVDDEA T0331 72 :YLIQVVRVEGTARPVEND 1vl7A 82 :FARRRLSFDCTATLIERE T0331 90 :YLKTVFADNP 1vl7A 102 :KWNQVVDQFQ T0331 100 :YYQHIYKDES 1vl7A 117 :IIEVLRGLAD T0331 113 :MQVFQIYAGHGFYH 1vl7A 127 :FRIFQLTPKEGRFV Number of specific fragments extracted= 5 number of extra gaps= 0 total=67 Number of alignments=11 # 1vl7A read from 1vl7A/merged-good-all-a2m # found chain 1vl7A in training set T0331 7 :MHILEDMKVGVFATLDEYGNPHARHAHITAANEEGIFFMTSPETHFYDQLMGDQRVAMTAISEEG 1vl7A 12 :AGFIQEFQSAIISTISEQGIPNGSYAPFVIDDAKNIYIYVSGLAVHTKNIEANPLVNVLFVDDEA T0331 72 :YLIQVVRVEGTARPVEN 1vl7A 82 :FARRRLSFDCTATLIER T0331 111 :DTM 1vl7A 99 :ESQ T0331 117 :QIYAGHGFYHSLTQG 1vl7A 102 :KWNQVVDQFQERFGQ Number of specific fragments extracted= 4 number of extra gaps= 0 total=71 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ty9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0331 read from 1ty9A/merged-good-all-a2m # 1ty9A read from 1ty9A/merged-good-all-a2m # found chain 1ty9A in training set Warning: unaligning (T0331)A36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ty9A)I80 Warning: unaligning (T0331)A37 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ty9A)I80 Warning: unaligning (T0331)Y119 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ty9A)L189 Warning: unaligning (T0331)A120 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ty9A)L189 T0331 5 :DIMHILEDM 1ty9A 36 :DPMSVLHNW T0331 14 :K 1ty9A 54 :R T0331 15 :VGVFATLDEYGNPHARHAHIT 1ty9A 58 :ALALATADSQGRPSTRIVVIS T0331 38 :NEEGIFFMTSPETHFYDQLMGDQRVAMTAISEEGYLI 1ty9A 81 :SDAGVVFSTHAGSQKGRELLHNPWASGVLYWRETSQQ T0331 77 :VRVEGTARPVENDYLKTVFADNPYYQHI 1ty9A 118 :IILNGQAVRLPNAKADDAWLKRPYATHP T0331 107 :DESS 1ty9A 154 :EELQ T0331 111 :DTMQVFQI 1ty9A 180 :EGYCVFEL T0331 121 :GHGFYH 1ty9A 190 :ESLEFW T0331 127 :SLTQGHKYIFSIGQGE 1ty9A 197 :NGQERLHERLRYDRSD Number of specific fragments extracted= 9 number of extra gaps= 2 total=80 Number of alignments=13 # 1ty9A read from 1ty9A/merged-good-all-a2m # found chain 1ty9A in training set Warning: unaligning (T0331)A36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ty9A)I80 Warning: unaligning (T0331)A37 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ty9A)I80 Warning: unaligning (T0331)E108 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ty9A)G174 Warning: unaligning (T0331)S109 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ty9A)G174 Warning: unaligning (T0331)Y119 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ty9A)L189 Warning: unaligning (T0331)A120 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ty9A)L189 T0331 5 :DIMHILED 1ty9A 43 :NWLERARR T0331 13 :MKVGVFATLDEYGNPHARHAHIT 1ty9A 56 :PRALALATADSQGRPSTRIVVIS T0331 38 :NEEGIFFMTSPETHFYDQLMGDQRVAMTAISEEGY 1ty9A 81 :SDAGVVFSTHAGSQKGRELLHNPWASGVLYWRETS T0331 75 :QVVRVEGTARPVENDYLKTVFADNPYYQ 1ty9A 116 :QQIILNGQAVRLPNAKADDAWLKRPYAT T0331 103 :HIYKD 1ty9A 168 :QLAEL T0331 111 :DTMQVFQI 1ty9A 180 :EGYCVFEL T0331 121 :GHGFYHS 1ty9A 190 :ESLEFWG T0331 128 :LTQGHKYIFSIGQGEH 1ty9A 198 :GQERLHERLRYDRSDT Number of specific fragments extracted= 8 number of extra gaps= 3 total=88 Number of alignments=14 # 1ty9A read from 1ty9A/merged-good-all-a2m # found chain 1ty9A in training set Warning: unaligning (T0331)A36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ty9A)I80 Warning: unaligning (T0331)A37 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ty9A)I80 Warning: unaligning (T0331)Y134 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ty9A)G174 Warning: unaligning (T0331)I135 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ty9A)G174 T0331 3 :LKDIMHI 1ty9A 45 :LERARRV T0331 10 :LEDMKVGVFATLDEYGNPHARHAHIT 1ty9A 53 :IREPRALALATADSQGRPSTRIVVIS T0331 38 :NEEGIFFMTSPETHFYDQLMGDQRVAMTAISEE 1ty9A 81 :SDAGVVFSTHAGSQKGRELLHNPWASGVLYWRE T0331 73 :LIQVVRVEGTARPVENDYLKTVFADNPYYQHIYKDESSDTMQVFQIYAGHGFYHSLTQG 1ty9A 114 :TSQQIILNGQAVRLPNAKADDAWLKRPYATHPMSSVSRQSEELQDVQAMRNAARQLAEL T0331 136 :FSIGQGEHSEVRA 1ty9A 175 :PLPRPEGYCVFEL Number of specific fragments extracted= 5 number of extra gaps= 2 total=93 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xhnA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xhnA expands to /projects/compbio/data/pdb/1xhn.pdb.gz 1xhnA:Skipped atom 49, because occupancy 0.500 <= existing 0.500 in 1xhnA Skipped atom 51, because occupancy 0.500 <= existing 0.500 in 1xhnA Skipped atom 53, because occupancy 0.500 <= existing 0.500 in 1xhnA Skipped atom 55, because occupancy 0.500 <= existing 0.500 in 1xhnA Skipped atom 57, because occupancy 0.500 <= existing 0.500 in 1xhnA Skipped atom 514, because occupancy 0.500 <= existing 0.500 in 1xhnA Skipped atom 601, because occupancy 0.500 <= existing 0.500 in 1xhnA Skipped atom 603, because occupancy 0.500 <= existing 0.500 in 1xhnA Skipped atom 605, because occupancy 0.500 <= existing 0.500 in 1xhnA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 689, because occupancy 0.500 <= existing 0.500 in 1xhnA Skipped atom 691, because occupancy 0.500 <= existing 0.500 in 1xhnA Skipped atom 693, because occupancy 0.500 <= existing 0.500 in 1xhnA Skipped atom 695, because occupancy 0.500 <= existing 0.500 in 1xhnA Skipped atom 697, because occupancy 0.500 <= existing 0.500 in 1xhnA Skipped atom 786, because occupancy 0.500 <= existing 0.500 in 1xhnA Skipped atom 788, because occupancy 0.500 <= existing 0.500 in 1xhnA Skipped atom 790, because occupancy 0.500 <= existing 0.500 in 1xhnA Skipped atom 792, because occupancy 0.500 <= existing 0.500 in 1xhnA Skipped atom 794, because occupancy 0.500 <= existing 0.500 in 1xhnA Skipped atom 796, because occupancy 0.500 <= existing 0.500 in 1xhnA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 906, because occupancy 0.500 <= existing 0.500 in 1xhnA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 908, because occupancy 0.500 <= existing 0.500 in 1xhnA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 910, because occupancy 0.500 <= existing 0.500 in 1xhnA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 912, because occupancy 0.500 <= existing 0.500 in 1xhnA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0331 read from 1xhnA/merged-good-all-a2m # 1xhnA read from 1xhnA/merged-good-all-a2m # adding 1xhnA to template set # found chain 1xhnA in template set T0331 2 :ELKDIMHILEDMK 1xhnA 15 :PREDAARVARFVT T0331 15 :VGVFATLD 1xhnA 32 :WGALATIS T0331 23 :E 1xhnA 43 :A T0331 24 :YGNPHARHAHITAANEEG 1xhnA 45 :RGRPFADVLSLSDGPPGA T0331 42 :IFFMTSPETHFYDQLMGDQRVAMTAI 1xhnA 67 :PYFYLSPLQLSVSNLQENPYATLTMT T0331 68 :SEEGYLIQVVRVEGTARPV 1xhnA 105 :DPQSPLCVHIMLSGTVTKV T0331 87 :ENDYLKTVFAD 1xhnA 127 :EMDIAKHSLFI T0331 98 :NPYYQHI 1xhnA 139 :HPEMKTW T0331 108 :ESSDTMQVFQIYAGHGFYHSLTQGHKY 1xhnA 146 :PSSHNWFFAKLNITNIWVLDYFGGPKI Number of specific fragments extracted= 9 number of extra gaps= 0 total=102 Number of alignments=16 # 1xhnA read from 1xhnA/merged-good-all-a2m # found chain 1xhnA in template set T0331 2 :ELKDIMHIL 1xhnA 18 :DAARVARFV T0331 11 :EDMKVGVFATLDE 1xhnA 28 :HVSDWGALATIST T0331 24 :YGNPHARHAHITAANEEG 1xhnA 45 :RGRPFADVLSLSDGPPGA T0331 42 :IFFMTSPETHFYDQLMGDQRVAMTAI 1xhnA 67 :PYFYLSPLQLSVSNLQENPYATLTMT T0331 68 :SEEGYLIQVVRVEGTARPVENDYL 1xhnA 105 :DPQSPLCVHIMLSGTVTKVNETEM T0331 92 :KTVF 1xhnA 132 :KHSL T0331 96 :ADNPYYQHI 1xhnA 137 :IRHPEMKTW T0331 107 :DESSDTM 1xhnA 146 :PSSHNWF T0331 115 :VFQIYAGHGFYHSLTQGHKYI 1xhnA 153 :FAKLNITNIWVLDYFGGPKIV T0331 142 :EHSEVR 1xhnA 174 :TPEEYY Number of specific fragments extracted= 10 number of extra gaps= 0 total=112 Number of alignments=17 # 1xhnA read from 1xhnA/merged-good-all-a2m # found chain 1xhnA in template set T0331 13 :MKVGVFATLD 1xhnA 30 :SDWGALATIS T0331 24 :YGNPHARHAHITAANEE 1xhnA 45 :RGRPFADVLSLSDGPPG T0331 41 :GIFFMTSPETHFYDQLMGDQRVAMTA 1xhnA 66 :VPYFYLSPLQLSVSNLQENPYATLTM T0331 67 :ISEEGYLIQVVRVEGTARPVENDY 1xhnA 104 :FDPQSPLCVHIMLSGTVTKVNETE T0331 118 :IYAGHGFYHSLTQGHKY 1xhnA 128 :MDIAKHSLFIRHPEMKT T0331 137 :SIGQGEHS 1xhnA 145 :WPSSHNWF Number of specific fragments extracted= 6 number of extra gaps= 0 total=118 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t9mA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1t9mA expands to /projects/compbio/data/pdb/1t9m.pdb.gz 1t9mA:Skipped atom 572, because occupancy 0.500 <= existing 0.500 in 1t9mA Skipped atom 574, because occupancy 0.500 <= existing 0.500 in 1t9mA Skipped atom 576, because occupancy 0.500 <= existing 0.500 in 1t9mA Skipped atom 578, because occupancy 0.500 <= existing 0.500 in 1t9mA # T0331 read from 1t9mA/merged-good-all-a2m # 1t9mA read from 1t9mA/merged-good-all-a2m # adding 1t9mA to template set # found chain 1t9mA in template set Warning: unaligning (T0331)S109 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t9mA)E146 Warning: unaligning (T0331)S110 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t9mA)E146 Warning: unaligning (T0331)G139 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t9mA)G206 Warning: unaligning (T0331)Q140 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t9mA)G206 T0331 4 :KDIMHILEDM 1t9mA 27 :ANPMEVLRNW T0331 15 :VGVFATLDEYGNPHARHAHITAANEEGIFFMTSPETHFYDQLMGDQRVAMTAISEEGYLI 1t9mA 50 :ALALATVDGQGRPSTRIVVIAELGERGVVFATHADSQKGRELAQNPWASGVLYWRESSQQ T0331 77 :VRVEGTARPVENDYLKTVFADNPYYQH 1t9mA 110 :IILNGRAERLPDERADAQWLSRPYQTH T0331 104 :IYKDE 1t9mA 140 :IASRQ T0331 111 :DT 1t9mA 147 :TL T0331 113 :MQVFQIYAGHGFYH 1t9mA 174 :YCLFELCLESVEFW T0331 127 :SLTQGHKYIFSI 1t9mA 189 :NGTERLHERLRY T0331 141 :GEH 1t9mA 207 :WKH Number of specific fragments extracted= 8 number of extra gaps= 2 total=126 Number of alignments=19 # 1t9mA read from 1t9mA/merged-good-all-a2m # found chain 1t9mA in template set Warning: unaligning (T0331)Q140 because of BadResidue code BAD_PEPTIDE in next template residue (1t9mA)D203 Warning: unaligning (T0331)G141 because of BadResidue code BAD_PEPTIDE at template residue (1t9mA)D203 Warning: unaligning (T0331)H143 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t9mA)G206 Warning: unaligning (T0331)S144 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t9mA)G206 T0331 5 :DIMHILEDMKV 1t9mA 35 :NWLERARRYGV T0331 16 :GVFATLDEYGNPHARHAHITAANEEGIFFMTSPETHFYDQLMGDQRVAMTAISEEGY 1t9mA 51 :LALATVDGQGRPSTRIVVIAELGERGVVFATHADSQKGRELAQNPWASGVLYWRESS T0331 75 :QVVRVEGTARPVENDYLKTVFADNPYYQ 1t9mA 108 :QQIILNGRAERLPDERADAQWLSRPYQT T0331 103 :HIYKDE 1t9mA 160 :RLAETD T0331 109 :SSDTMQVFQIYAGHGFYHS 1t9mA 170 :RPPGYCLFELCLESVEFWG T0331 128 :LTQGHKYIFSIG 1t9mA 190 :GTERLHERLRYD T0331 142 :E 1t9mA 204 :E Number of specific fragments extracted= 7 number of extra gaps= 2 total=133 Number of alignments=20 # 1t9mA read from 1t9mA/merged-good-all-a2m # found chain 1t9mA in template set Warning: unaligning (T0331)T112 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t9mA)E146 Warning: unaligning (T0331)M113 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t9mA)E146 T0331 3 :LKDIMHI 1t9mA 37 :LERARRY T0331 10 :LEDMKVGVFATLDEYGNPHARHAHITAANEEGIFFMTSPETHFYDQLMGDQRVAMTAISEE 1t9mA 45 :VREPRALALATVDGQGRPSTRIVVIAELGERGVVFATHADSQKGRELAQNPWASGVLYWRE T0331 73 :LIQVVRVEGTARPVENDYLKTVFADNPYYQHIYKDESSD 1t9mA 106 :SSQQIILNGRAERLPDERADAQWLSRPYQTHPMSIASRQ T0331 114 :QVFQIYAGHGFYHSLTQG 1t9mA 147 :TLADIHALRAEARRLAET T0331 134 :YIFSIGQGEHSEVRA 1t9mA 165 :DGPLPRPPGYCLFEL Number of specific fragments extracted= 5 number of extra gaps= 1 total=138 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ejeA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ejeA expands to /projects/compbio/data/pdb/1eje.pdb.gz 1ejeA:# T0331 read from 1ejeA/merged-good-all-a2m # 1ejeA read from 1ejeA/merged-good-all-a2m # adding 1ejeA to template set # found chain 1ejeA in template set Warning: unaligning (T0331)A32 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1ejeA)F48 Warning: unaligning (T0331)H33 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1ejeA)F48 T0331 2 :ELKDIMHILEDMKVGVFATLDEYGNPHAR 1ejeA 16 :PVESAHRILTPRPTVMVTTVDEEGNINAA T0331 31 :H 1ejeA 46 :F T0331 34 :ITAANEEG 1ejeA 49 :TMPVSIDP T0331 42 :IFFMTSPETHFYDQLMGDQRVAMTAISEE 1ejeA 59 :VAFASAPDHHTARNIESTHEFVINITPAD Number of specific fragments extracted= 4 number of extra gaps= 1 total=142 Number of alignments=22 # 1ejeA read from 1ejeA/merged-good-all-a2m # found chain 1ejeA in template set Warning: unaligning (T0331)H33 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1ejeA)F48 Warning: unaligning (T0331)I34 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1ejeA)F48 T0331 15 :VGVFATLDEYGNPHARHA 1ejeA 29 :TVMVTTVDEEGNINAAPF T0331 35 :TAA 1ejeA 49 :TMP T0331 38 :NEEGIFFMTSPETHFYDQLMGDQRVAMTAISE 1ejeA 55 :DPPVVAFASAPDHHTARNIESTHEFVINITPA T0331 71 :G 1ejeA 126 :E T0331 73 :LIQVVRVE 1ejeA 127 :APGHLECE T0331 101 :YQHIYKDESSDTMQ 1ejeA 135 :LLRMFEVGDHNLIT T0331 123 :GFYHSLT 1ejeA 149 :GSVVSAS T0331 130 :QGH 1ejeA 163 :EGL Number of specific fragments extracted= 8 number of extra gaps= 1 total=150 Number of alignments=23 # 1ejeA read from 1ejeA/merged-good-all-a2m # found chain 1ejeA in template set Warning: unaligning (T0331)H33 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1ejeA)F48 Warning: unaligning (T0331)I34 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1ejeA)F48 T0331 15 :VGVFATLDEYGNPHARHA 1ejeA 29 :TVMVTTVDEEGNINAAPF T0331 35 :T 1ejeA 49 :T T0331 36 :AANEEGIFFMTSPETHFYDQLMGDQRVAMTAISEE 1ejeA 53 :SIDPPVVAFASAPDHHTARNIESTHEFVINITPAD T0331 73 :L 1ejeA 88 :I T0331 122 :HGFYHSLTQGHKYIF 1ejeA 89 :IERMWVTARDIPAGE Number of specific fragments extracted= 5 number of extra gaps= 1 total=155 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fg9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fg9A expands to /projects/compbio/data/pdb/2fg9.pdb.gz 2fg9A:Skipped atom 38, because occupancy 0.500 <= existing 0.500 in 2fg9A Skipped atom 40, because occupancy 0.500 <= existing 0.500 in 2fg9A Skipped atom 42, because occupancy 0.500 <= existing 0.500 in 2fg9A Skipped atom 44, because occupancy 0.500 <= existing 0.500 in 2fg9A Skipped atom 46, because occupancy 0.500 <= existing 0.500 in 2fg9A Skipped atom 48, because occupancy 0.500 <= existing 0.500 in 2fg9A Skipped atom 50, because occupancy 0.500 <= existing 0.500 in 2fg9A Skipped atom 52, because occupancy 0.500 <= existing 0.500 in 2fg9A Skipped atom 54, because occupancy 0.500 <= existing 0.500 in 2fg9A Skipped atom 56, because occupancy 0.500 <= existing 0.500 in 2fg9A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 594, because occupancy 0.500 <= existing 0.500 in 2fg9A Skipped atom 596, because occupancy 0.500 <= existing 0.500 in 2fg9A Skipped atom 598, because occupancy 0.500 <= existing 0.500 in 2fg9A Skipped atom 600, because occupancy 0.500 <= existing 0.500 in 2fg9A Skipped atom 602, because occupancy 0.500 <= existing 0.500 in 2fg9A Skipped atom 604, because occupancy 0.500 <= existing 0.500 in 2fg9A Skipped atom 606, because occupancy 0.500 <= existing 0.500 in 2fg9A Skipped atom 608, because occupancy 0.500 <= existing 0.500 in 2fg9A Skipped atom 610, because occupancy 0.500 <= existing 0.500 in 2fg9A Skipped atom 612, because occupancy 0.500 <= existing 0.500 in 2fg9A Skipped atom 614, because occupancy 0.500 <= existing 0.500 in 2fg9A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 872, because occupancy 0.500 <= existing 0.500 in 2fg9A Skipped atom 874, because occupancy 0.500 <= existing 0.500 in 2fg9A Skipped atom 876, because occupancy 0.500 <= existing 0.500 in 2fg9A Skipped atom 878, because occupancy 0.500 <= existing 0.500 in 2fg9A Skipped atom 880, because occupancy 0.500 <= existing 0.500 in 2fg9A Skipped atom 882, because occupancy 0.500 <= existing 0.500 in 2fg9A Skipped atom 884, because occupancy 0.500 <= existing 0.500 in 2fg9A Skipped atom 886, because occupancy 0.500 <= existing 0.500 in 2fg9A Skipped atom 888, because occupancy 0.500 <= existing 0.500 in 2fg9A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1151, because occupancy 0.500 <= existing 0.500 in 2fg9A Skipped atom 1153, because occupancy 0.500 <= existing 0.500 in 2fg9A Skipped atom 1155, because occupancy 0.500 <= existing 0.500 in 2fg9A Skipped atom 1157, because occupancy 0.500 <= existing 0.500 in 2fg9A Skipped atom 1159, because occupancy 0.500 <= existing 0.500 in 2fg9A Skipped atom 1161, because occupancy 0.500 <= existing 0.500 in 2fg9A Skipped atom 1163, because occupancy 0.500 <= existing 0.500 in 2fg9A Skipped atom 1165, because occupancy 0.500 <= existing 0.500 in 2fg9A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0331 read from 2fg9A/merged-good-all-a2m # 2fg9A read from 2fg9A/merged-good-all-a2m # adding 2fg9A to template set # found chain 2fg9A in template set Warning: unaligning (T0331)E49 because of BadResidue code BAD_PEPTIDE in next template residue (2fg9A)G55 Warning: unaligning (T0331)T50 because of BadResidue code BAD_PEPTIDE at template residue (2fg9A)G55 T0331 1 :MELKDIMHILEDMK 2fg9A 7 :EDKQRIESIILQAD T0331 15 :VGVFAT 2fg9A 22 :CFVGIT T0331 22 :DEYGNPHARHAHITA 2fg9A 28 :DLEGNPYVVPMNFGY T0331 38 :NEEGIFFMTSP 2fg9A 43 :ENDTLYLHSGP T0331 51 :HFYDQLMGDQRVAMTAISEEG 2fg9A 56 :GKIEMLQRNNNVCITFSLGHK T0331 72 :YLIQ 2fg9A 88 :YSMR T0331 76 :VVRVEGTARPVEN 2fg9A 94 :SAMCRGKVEFIED T0331 89 :DYLKTVFAD 2fg9A 108 :EEKRHALDI T0331 101 :YQHIYKDESSDT 2fg9A 117 :IMRHYTKDQFSY T0331 113 :MQVFQIYAGHGF 2fg9A 136 :VKVWKVPVDQMT Number of specific fragments extracted= 10 number of extra gaps= 1 total=165 Number of alignments=25 # 2fg9A read from 2fg9A/merged-good-all-a2m # found chain 2fg9A in template set Warning: unaligning (T0331)E49 because of BadResidue code BAD_PEPTIDE in next template residue (2fg9A)G55 Warning: unaligning (T0331)T50 because of BadResidue code BAD_PEPTIDE at template residue (2fg9A)G55 T0331 1 :MELKDIMHILEDMKVGVFATLDEYGNPHARHAHITA 2fg9A 7 :EDKQRIESIILQADACFVGITDLEGNPYVVPMNFGY T0331 38 :NEEGIFFMTSP 2fg9A 43 :ENDTLYLHSGP T0331 51 :HFYDQLMGDQRVAMTAISEEGYLIQ 2fg9A 56 :GKIEMLQRNNNVCITFSLGHKLVYQ T0331 76 :VVRVEGTARPVEND 2fg9A 94 :SAMCRGKVEFIEDM T0331 90 :YLKTVFA 2fg9A 109 :EKRHALD T0331 100 :YYQHIYKDESSD 2fg9A 116 :IIMRHYTKDQFS T0331 113 :MQVFQ 2fg9A 136 :VKVWK T0331 118 :IYAGHGFYHSLT 2fg9A 143 :VDQMTGKVFGLR Number of specific fragments extracted= 8 number of extra gaps= 1 total=173 Number of alignments=26 # 2fg9A read from 2fg9A/merged-good-all-a2m # found chain 2fg9A in template set Warning: unaligning (T0331)E49 because of BadResidue code BAD_PEPTIDE in next template residue (2fg9A)G55 Warning: unaligning (T0331)T50 because of BadResidue code BAD_PEPTIDE at template residue (2fg9A)G55 T0331 3 :LKDIMHILEDMKVGVFATLDEYGNPHARHAHIT 2fg9A 9 :KQRIESIILQADACFVGITDLEGNPYVVPMNFG T0331 37 :ANEEGIFFMTSP 2fg9A 42 :YENDTLYLHSGP T0331 51 :HFYDQLMGDQRVAMTAISEEG 2fg9A 56 :GKIEMLQRNNNVCITFSLGHK T0331 73 :LIQVVRVEGTARPVEN 2fg9A 91 :RSESAMCRGKVEFIED T0331 89 :DYLKTVF 2fg9A 108 :EEKRHAL T0331 126 :HSLTQGHKYIFSIG 2fg9A 115 :DIIMRHYTKDQFSY Number of specific fragments extracted= 6 number of extra gaps= 1 total=179 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2asfA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2asfA expands to /projects/compbio/data/pdb/2asf.pdb.gz 2asfA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 546, because occupancy 0.500 <= existing 0.500 in 2asfA Skipped atom 548, because occupancy 0.250 <= existing 0.750 in 2asfA # T0331 read from 2asfA/merged-good-all-a2m # 2asfA read from 2asfA/merged-good-all-a2m # adding 2asfA to template set # found chain 2asfA in template set Warning: unaligning (T0331)A32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2asfA)G41 Warning: unaligning (T0331)H33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2asfA)G41 T0331 4 :KDIMHILEDMKVGVFATLDEYGNPHARH 2asfA 12 :DDALAFLSERHLAMLTTLRADNSPHVVA T0331 34 :ITAANEEG 2asfA 42 :FTFDPKTH T0331 42 :IFFMTSPETHFYDQLMGDQRVAMTAISEEGY 2asfA 51 :ARVITTGGSQKAVNADRSGLAVLSQVDGARW T0331 77 :VRVEGTARP 2asfA 82 :LSLEGRAAV T0331 86 :VENDYLKTVFA 2asfA 92 :SDIDAVRDAEL T0331 100 :YYQHIYKD 2asfA 103 :RYAQRYRT T0331 108 :ESSDTMQVFQIYAGHGFY 2asfA 112 :RPNPRRVVIEVQIERVLG Number of specific fragments extracted= 7 number of extra gaps= 1 total=186 Number of alignments=28 # 2asfA read from 2asfA/merged-good-all-a2m # found chain 2asfA in template set Warning: unaligning (T0331)A32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2asfA)G41 Warning: unaligning (T0331)H33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2asfA)G41 T0331 4 :KDIMHILEDMKVGVFATLDEYGNPHARH 2asfA 12 :DDALAFLSERHLAMLTTLRADNSPHVVA T0331 34 :ITAANEEG 2asfA 42 :FTFDPKTH T0331 42 :IFFMTSPETHFYDQLMGDQRVAMTAISEE 2asfA 51 :ARVITTGGSQKAVNADRSGLAVLSQVDGA T0331 75 :QVVRVEGTARPVENDYLKTVFAD 2asfA 80 :RWLSLEGRAAVNSDIDAVRDAEL T0331 100 :YYQHIYKDE 2asfA 103 :RYAQRYRTP T0331 109 :SSDTMQVFQIYAGHGFY 2asfA 113 :PNPRRVVIEVQIERVLG Number of specific fragments extracted= 6 number of extra gaps= 1 total=192 Number of alignments=29 # 2asfA read from 2asfA/merged-good-all-a2m # found chain 2asfA in template set Warning: unaligning (T0331)A32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2asfA)G41 Warning: unaligning (T0331)H33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2asfA)G41 T0331 4 :KDIMHILEDMKVGVFATLDEYGNPHARH 2asfA 12 :DDALAFLSERHLAMLTTLRADNSPHVVA T0331 34 :ITAANEE 2asfA 42 :FTFDPKT T0331 41 :GIFFMTSPETHFYDQLMGDQRVAMTAISEE 2asfA 50 :IARVITTGGSQKAVNADRSGLAVLSQVDGA T0331 75 :QVVRVEGTARPV 2asfA 80 :RWLSLEGRAAVN T0331 87 :ENDYLKT 2asfA 93 :DIDAVRD T0331 121 :GHGFYHSL 2asfA 100 :AELRYAQR T0331 135 :IFSIGQGEHSEV 2asfA 108 :YRTPRPNPRRVV Number of specific fragments extracted= 7 number of extra gaps= 1 total=199 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xxoA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xxoA expands to /projects/compbio/data/pdb/1xxo.pdb.gz 1xxoA:# T0331 read from 1xxoA/merged-good-all-a2m # 1xxoA read from 1xxoA/merged-good-all-a2m # adding 1xxoA to template set # found chain 1xxoA in template set T0331 4 :KDIMHILEDMKVGVFATLDEYGNPHARHAHITAANEE 1xxoA 8 :DKLLAVISGNSIGVLATIKHDGRPQLSNVQYHFDPRK T0331 41 :GIFFMTSPETHFYDQLMGDQRVAMTAISEEGYLIQVVRVEGTARPV 1xxoA 46 :LIQVSIAEPRAKTRNLRRDPRASILVDADDGWSYAVAEGTAQLTPP T0331 87 :ENDYLKTVFA 1xxoA 96 :DDDTVEALIA T0331 101 :YQHIYKDESS 1xxoA 106 :LYRNIAGEHS T0331 111 :DTMQVFQIYAGHGFYHSL 1xxoA 127 :DRRVLLTLPISHVYGLPP Number of specific fragments extracted= 5 number of extra gaps= 0 total=204 Number of alignments=31 # 1xxoA read from 1xxoA/merged-good-all-a2m # found chain 1xxoA in template set T0331 4 :KDIMHILEDMKVGVFATLDEYGNPHARHAHITAANEEG 1xxoA 8 :DKLLAVISGNSIGVLATIKHDGRPQLSNVQYHFDPRKL T0331 42 :IFFMTSPETHFYDQLMGDQRVAMTAISEEGY 1xxoA 47 :IQVSIAEPRAKTRNLRRDPRASILVDADDGW T0331 75 :QVVRVEGTARPV 1xxoA 78 :SYAVAEGTAQLT T0331 87 :ENDYLKTVFA 1xxoA 96 :DDDTVEALIA T0331 101 :YQHIYKDE 1xxoA 106 :LYRNIAGE T0331 111 :DTMQVFQIYAGHGFYH 1xxoA 127 :DRRVLLTLPISHVYGL Number of specific fragments extracted= 6 number of extra gaps= 0 total=210 Number of alignments=32 # 1xxoA read from 1xxoA/merged-good-all-a2m # found chain 1xxoA in template set T0331 4 :KDIMHILEDMKVGVFATLDEYGNPHARHAHITAANEE 1xxoA 8 :DKLLAVISGNSIGVLATIKHDGRPQLSNVQYHFDPRK T0331 41 :GIFFMTSPETHFYDQLMGDQRVAMTAISEE 1xxoA 46 :LIQVSIAEPRAKTRNLRRDPRASILVDADD T0331 73 :LIQVVRVEGTARPVE 1xxoA 76 :GWSYAVAEGTAQLTP T0331 88 :NDYLKTVFA 1xxoA 97 :DDTVEALIA T0331 124 :FYHSLTQGHKY 1xxoA 106 :LYRNIAGEHSD Number of specific fragments extracted= 5 number of extra gaps= 0 total=215 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w9aA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0331 read from 1w9aA/merged-good-all-a2m # 1w9aA read from 1w9aA/merged-good-all-a2m # found chain 1w9aA in training set T0331 4 :KDIMHILEDMKVGVFATLDEYGNPHARHAHITAANEEG 1w9aA 8 :DKLLAVISGNSIGVLATIKHDGRPQLSNVQYHFDPRKL T0331 42 :IFFMTSPETHFYDQLMGDQRVAMTAISEEGYLIQVVRVEGTARPV 1w9aA 47 :IQVSIAEPRAKTRNLRRDPRASILVDADDGWSYAVAEGTAQLTPP T0331 87 :ENDYLKTVFA 1w9aA 96 :DDDTVEALIA T0331 101 :YQHIYKDESSDT 1w9aA 106 :LYRNIAGEHSDW T0331 115 :VFQIYAGHGFYHSLTQGH 1w9aA 129 :RVLLTLPISHVYGLPPGM Number of specific fragments extracted= 5 number of extra gaps= 0 total=220 Number of alignments=34 # 1w9aA read from 1w9aA/merged-good-all-a2m # found chain 1w9aA in training set T0331 4 :KDIMHILEDMKVGVFATLDEYGNPHARHAHITAANEEG 1w9aA 8 :DKLLAVISGNSIGVLATIKHDGRPQLSNVQYHFDPRKL T0331 42 :IFFMTSPETHFYDQLMGDQRVAMTAISEEGY 1w9aA 47 :IQVSIAEPRAKTRNLRRDPRASILVDADDGW T0331 75 :QVVRVEGTARPV 1w9aA 78 :SYAVAEGTAQLT T0331 87 :ENDYLKTVFA 1w9aA 96 :DDDTVEALIA Number of specific fragments extracted= 4 number of extra gaps= 0 total=224 Number of alignments=35 # 1w9aA read from 1w9aA/merged-good-all-a2m # found chain 1w9aA in training set T0331 4 :KDIMHILEDMKVGVFATLDEYGNPHARHAHITAANEE 1w9aA 8 :DKLLAVISGNSIGVLATIKHDGRPQLSNVQYHFDPRK T0331 41 :GIFFMTSPETHFYDQLMGDQRVAMTAISEE 1w9aA 46 :LIQVSIAEPRAKTRNLRRDPRASILVDADD T0331 73 :LIQVVRVEGTARPVE 1w9aA 76 :GWSYAVAEGTAQLTP T0331 88 :NDYLKTVFA 1w9aA 97 :DDTVEALIA T0331 124 :FYHSLTQGHKY 1w9aA 106 :LYRNIAGEHSD Number of specific fragments extracted= 5 number of extra gaps= 0 total=229 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2aq6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2aq6A expands to /projects/compbio/data/pdb/2aq6.pdb.gz 2aq6A:# T0331 read from 2aq6A/merged-good-all-a2m # 2aq6A read from 2aq6A/merged-good-all-a2m # adding 2aq6A to template set # found chain 2aq6A in template set Warning: unaligning (T0331)K133 because last residue in template chain is (2aq6A)R147 T0331 3 :LKDIMHILEDMKVGVFATLDEYGNPHARHAHITAANEEG 2aq6A 7 :DDKLLAVISGNSIGVLATIKHDGRPQLSNVQYHFDPRKL T0331 42 :IFFMTSPETHFYDQLMGDQRVAMTAISEEGYLIQVVRVEGTARPV 2aq6A 47 :IQVSIAEPRAKTRNLRRDPRASILVDADDGWSYAVAEGTAQLTPP T0331 87 :ENDYLKTVFA 2aq6A 96 :DDDTVEALIA T0331 101 :YQHIYKDESSDT 2aq6A 106 :LYRNIAGEHSDW T0331 115 :VFQIYAGHGFYHSLTQGH 2aq6A 129 :RVLLTLPISHVYGLPPGM Number of specific fragments extracted= 5 number of extra gaps= 0 total=234 Number of alignments=37 # 2aq6A read from 2aq6A/merged-good-all-a2m # found chain 2aq6A in template set T0331 3 :LKDIMHILEDMKVGVFATLDEYGNPHARHAHITAANEEG 2aq6A 7 :DDKLLAVISGNSIGVLATIKHDGRPQLSNVQYHFDPRKL T0331 42 :IFFMTSPETHFYDQLMGDQRVAMTAISEEGY 2aq6A 47 :IQVSIAEPRAKTRNLRRDPRASILVDADDGW T0331 75 :QVVRVEGTARPV 2aq6A 78 :SYAVAEGTAQLT T0331 87 :ENDYLKTVFA 2aq6A 96 :DDDTVEALIA Number of specific fragments extracted= 4 number of extra gaps= 0 total=238 Number of alignments=38 # 2aq6A read from 2aq6A/merged-good-all-a2m # found chain 2aq6A in template set T0331 2 :ELKDIMHILEDMKVGVFATLDEYGNPHARHAHITAANEE 2aq6A 6 :FDDKLLAVISGNSIGVLATIKHDGRPQLSNVQYHFDPRK T0331 41 :GIFFMTSPETHFYDQLMGDQRVAMTAISEE 2aq6A 46 :LIQVSIAEPRAKTRNLRRDPRASILVDADD T0331 73 :LIQVVRVEGTARPVE 2aq6A 76 :GWSYAVAEGTAQLTP T0331 88 :NDYLKTVFA 2aq6A 97 :DDTVEALIA T0331 103 :HIYKDESSDT 2aq6A 106 :LYRNIAGEHS T0331 117 :QIYAGHGFYHS 2aq6A 116 :DWDDYRQAMVT Number of specific fragments extracted= 6 number of extra gaps= 0 total=244 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nrgA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1nrgA expands to /projects/compbio/data/pdb/1nrg.pdb.gz 1nrgA:Skipped atom 861, because occupancy 0.500 <= existing 0.500 in 1nrgA Skipped atom 863, because occupancy 0.500 <= existing 0.500 in 1nrgA Skipped atom 1438, because occupancy 0.500 <= existing 0.500 in 1nrgA Skipped atom 1440, because occupancy 0.500 <= existing 0.500 in 1nrgA Skipped atom 1442, because occupancy 0.500 <= existing 0.500 in 1nrgA Skipped atom 1444, because occupancy 0.500 <= existing 0.500 in 1nrgA Skipped atom 1446, because occupancy 0.500 <= existing 0.500 in 1nrgA Skipped atom 1448, because occupancy 0.500 <= existing 0.500 in 1nrgA Skipped atom 1450, because occupancy 0.500 <= existing 0.500 in 1nrgA # T0331 read from 1nrgA/merged-good-all-a2m # 1nrgA read from 1nrgA/merged-good-all-a2m # adding 1nrgA to template set # found chain 1nrgA in template set T0331 12 :DMK 1nrgA 74 :DIG T0331 15 :VGVFATLDEYGNPHARHAHITAANEEGIFFMTSPETHFYDQLMGDQRVAMTAISEEGYLI 1nrgA 80 :AMCLATCTRDGKPSARMLLLKGFGKDGFRFFTNFESRKGKELDSNPFASLVFYWEPLNRQ T0331 77 :VRVEGTARPVENDYLKTVFADNP 1nrgA 140 :VRVEGPVKKLPEEEAECYFHSRP T0331 101 :YQHIYKDES 1nrgA 191 :LEQLYQDQE T0331 110 :SDTMQVFQIYAGHGFYHSLT 1nrgA 203 :PKSWGGYVLYPQVMEFWQGQ T0331 130 :QGHKYIFSIGQGEHSEVRAL 1nrgA 224 :NRLHDRIVFRRGLPTGDSPL Number of specific fragments extracted= 6 number of extra gaps= 0 total=250 Number of alignments=40 # 1nrgA read from 1nrgA/merged-good-all-a2m # found chain 1nrgA in template set T0331 3 :LKDIMH 1nrgA 66 :FEEAVQ T0331 11 :EDMK 1nrgA 73 :PDIG T0331 15 :VGVFATLDEYGNPHARHAHITAANEEGIFFMTSPETHFYDQLMGDQRVAMTAISEE 1nrgA 80 :AMCLATCTRDGKPSARMLLLKGFGKDGFRFFTNFESRKGKELDSNPFASLVFYWEP T0331 73 :LIQVVRVEGTARPVENDYLKTVFADNP 1nrgA 136 :LNRQVRVEGPVKKLPEEEAECYFHSRP T0331 100 :YYQHIYKDESSD 1nrgA 190 :ELEQLYQDQEVP T0331 112 :TMQVFQIYAGHGFYHSLTQG 1nrgA 205 :SWGGYVLYPQVMEFWQGQTN T0331 132 :HKYIFSIGQGEHSE 1nrgA 228 :DRIVFRRGLPTGDS Number of specific fragments extracted= 7 number of extra gaps= 0 total=257 Number of alignments=41 # 1nrgA read from 1nrgA/merged-good-all-a2m # found chain 1nrgA in template set T0331 3 :LKDIMHI 1nrgA 66 :FEEAVQC T0331 10 :LEDMKVGVFATLDEYGNPHARHAHITAANEEGIFFMTSPETHFYDQLMGDQRVAMTAISEE 1nrgA 75 :IGEANAMCLATCTRDGKPSARMLLLKGFGKDGFRFFTNFESRKGKELDSNPFASLVFYWEP T0331 73 :LIQVVRVEGTARPVENDYLKTVFADNPYYQHIYKDESSDTMQVFQIYAGHGFYHSLTQGHKYIFSIGQGEHSEVRA 1nrgA 136 :LNRQVRVEGPVKKLPEEEAECYFHSRPKSSQIGAVVSHQSSVIPDREYLRKKNEELEQLYQDQEVPKPKSWGGYVL Number of specific fragments extracted= 3 number of extra gaps= 0 total=260 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1axj/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1axj expands to /projects/compbio/data/pdb/1axj.pdb.gz 1axj:Warning: there is no chain 1axj will retry with 1axjA # T0331 read from 1axj/merged-good-all-a2m # 1axj read from 1axj/merged-good-all-a2m # adding 1axj to template set # found chain 1axj in template set Warning: unaligning (T0331)E49 because of BadResidue code BAD_PEPTIDE in next template residue (1axj)H52 Warning: unaligning (T0331)T50 because of BadResidue code BAD_PEPTIDE at template residue (1axj)H52 Warning: unaligning (T0331)H122 because of BadResidue code BAD_PEPTIDE in next template residue (1axj)A118 Warning: unaligning (T0331)G123 because of BadResidue code BAD_PEPTIDE at template residue (1axj)A118 T0331 4 :KDIMHILEDMK 1axj 4 :GTFFEVLKNEG T0331 15 :VGVFATLD 1axj 16 :VAIATQGE T0331 25 :GNPHA 1axj 24 :DGPHL T0331 30 :RHAHITAANEEGIFFMTSP 1axj 32 :WNSYLKVLDGNRIVVPVGG T0331 51 :HFYDQLMGDQRVAMTAISEE 1axj 53 :KTEANVARDERVLMTLGSRK T0331 71 :GY 1axj 79 :PG T0331 75 :QVVRVEGTARPVENDYLKTVFADNPYY 1axj 81 :TGFLIRGSAAFRTDGPEFEAIARFKWA T0331 113 :MQVFQIYAG 1axj 108 :RAALVITVV Number of specific fragments extracted= 8 number of extra gaps= 2 total=268 Number of alignments=43 # 1axj read from 1axj/merged-good-all-a2m # found chain 1axj in template set Warning: unaligning (T0331)E49 because of BadResidue code BAD_PEPTIDE in next template residue (1axj)H52 Warning: unaligning (T0331)T50 because of BadResidue code BAD_PEPTIDE at template residue (1axj)H52 Warning: unaligning (T0331)H122 because of BadResidue code BAD_PEPTIDE in next template residue (1axj)A118 Warning: unaligning (T0331)G123 because of BadResidue code BAD_PEPTIDE at template residue (1axj)A118 T0331 4 :KDIMHILEDMKVGVFATLDE 1axj 4 :GTFFEVLKNEGVVAIATQGE T0331 25 :GNPHARHAH 1axj 24 :DGPHLVNTW T0331 34 :ITAANEEGIFFMTSP 1axj 36 :LKVLDGNRIVVPVGG T0331 51 :HFYDQLMGDQRVAMTAISE 1axj 53 :KTEANVARDERVLMTLGSR T0331 70 :EGY 1axj 77 :NGP T0331 74 :IQVVRVEGTARPVENDYLKTVFADNPYYQ 1axj 80 :GTGFLIRGSAAFRTDGPEFEAIARFKWAR T0331 114 :QVFQIYAG 1axj 109 :AALVITVV Number of specific fragments extracted= 7 number of extra gaps= 2 total=275 Number of alignments=44 # 1axj read from 1axj/merged-good-all-a2m # found chain 1axj in template set Warning: unaligning (T0331)E49 because of BadResidue code BAD_PEPTIDE in next template residue (1axj)H52 Warning: unaligning (T0331)T50 because of BadResidue code BAD_PEPTIDE at template residue (1axj)H52 T0331 4 :KDIMHILEDMKVGVFATLDE 1axj 4 :GTFFEVLKNEGVVAIATQGE T0331 25 :GNPHARHAH 1axj 24 :DGPHLVNTW T0331 34 :ITAANEEGIFFMTSP 1axj 36 :LKVLDGNRIVVPVGG T0331 51 :HFYDQLMGDQRVAMTAISEEG 1axj 53 :KTEANVARDERVLMTLGSRKV T0331 72 :YLIQVVRVEGTARPVENDYLKTVFADNPY 1axj 78 :GPGTGFLIRGSAAFRTDGPEFEAIARFKW Number of specific fragments extracted= 5 number of extra gaps= 1 total=280 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a2jA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2a2jA expands to /projects/compbio/data/pdb/2a2j.pdb.gz 2a2jA:# T0331 read from 2a2jA/merged-good-all-a2m # 2a2jA read from 2a2jA/merged-good-all-a2m # adding 2a2jA to template set # found chain 2a2jA in template set Warning: unaligning (T0331)H103 because of BadResidue code BAD_PEPTIDE in next template residue (2a2jA)R175 Warning: unaligning (T0331)I104 because of BadResidue code BAD_PEPTIDE at template residue (2a2jA)R175 Warning: unaligning (T0331)T129 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2a2jA)N206 Warning: unaligning (T0331)Q130 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2a2jA)N206 T0331 8 :HILEDM 2a2jA 47 :RWLNDA T0331 15 :VGVFATLDE 2a2jA 62 :AMVLATVAD T0331 25 :GNPHARHAHITAANEEGIFFMTSPETHFYDQLMGDQRVAMTAISEEGYLI 2a2jA 71 :GKPVTRSVLCKILDESGVAFFTSYTSAKGEQLAVTPYASATFPWYQLGRQ T0331 77 :VRVEGTARPVENDYLKTVFADNPY 2a2jA 121 :AHVQGPVSKVSTEEIFTYWSMRPR T0331 101 :YQ 2a2jA 172 :VT T0331 105 :YKDESS 2a2jA 176 :FADQDQ T0331 111 :DTMQVFQIYAGHGFYH 2a2jA 186 :PGWGGYRIAPEIVEFW T0331 127 :SL 2a2jA 203 :GR T0331 131 :GHKYIFSIGQGEHSEVR 2a2jA 207 :RMHNRIRVANGRLERLQ Number of specific fragments extracted= 9 number of extra gaps= 2 total=289 Number of alignments=46 # 2a2jA read from 2a2jA/merged-good-all-a2m # found chain 2a2jA in template set Warning: unaligning (T0331)S110 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2a2jA)P183 Warning: unaligning (T0331)T129 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2a2jA)N206 Warning: unaligning (T0331)Q130 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2a2jA)N206 T0331 6 :IMHILED 2a2jA 48 :WLNDAQR T0331 13 :MKVGVFATLDE 2a2jA 60 :PNAMVLATVAD T0331 25 :GNPHARHAHITAANEEGIFFMTSPETHFYDQLMGDQRVAMTAISEE 2a2jA 71 :GKPVTRSVLCKILDESGVAFFTSYTSAKGEQLAVTPYASATFPWYQ T0331 73 :LIQVVRVEGTARPVENDYLKTVFADNP 2a2jA 117 :LGRQAHVQGPVSKVSTEEIFTYWSMRP T0331 101 :YQHI 2a2jA 169 :LAEV T0331 107 :DES 2a2jA 179 :QDQ T0331 111 :DTMQVFQIYAGHGFYHS 2a2jA 186 :PGWGGYRIAPEIVEFWQ T0331 128 :L 2a2jA 204 :R T0331 131 :GHKYIFSIGQGEH 2a2jA 207 :RMHNRIRVANGRL Number of specific fragments extracted= 9 number of extra gaps= 2 total=298 Number of alignments=47 # 2a2jA read from 2a2jA/merged-good-all-a2m # found chain 2a2jA in template set Warning: unaligning (T0331)Q130 because of BadResidue code BAD_PEPTIDE in next template residue (2a2jA)R175 Warning: unaligning (T0331)G131 because of BadResidue code BAD_PEPTIDE at template residue (2a2jA)R175 Warning: unaligning (T0331)S137 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2a2jA)P183 Warning: unaligning (T0331)I138 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2a2jA)P183 T0331 3 :LKDIMHI 2a2jA 49 :LNDAQRA T0331 10 :LEDMKVGVFATLDE 2a2jA 57 :VSEPNAMVLATVAD T0331 25 :GNPHARHAHITAANEEGIFFMTSPETHFYDQLMGDQRVAMTAISEE 2a2jA 71 :GKPVTRSVLCKILDESGVAFFTSYTSAKGEQLAVTPYASATFPWYQ T0331 73 :LIQVVRVEGTARPVENDYLKTVFADNPYYQHIYKDESSDTMQVFQIYAGHGFYHSLT 2a2jA 117 :LGRQAHVQGPVSKVSTEEIFTYWSMRPRGAQLGAWASQQSRPVGSRAQLDNQLAEVT T0331 132 :HKYI 2a2jA 176 :FADQ T0331 136 :F 2a2jA 181 :Q T0331 139 :GQGEHSEVRA 2a2jA 184 :VPPGWGGYRI Number of specific fragments extracted= 7 number of extra gaps= 2 total=305 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fhqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fhqA expands to /projects/compbio/data/pdb/2fhq.pdb.gz 2fhqA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 121, because occupancy 0.500 <= existing 0.500 in 2fhqA Skipped atom 123, because occupancy 0.500 <= existing 0.500 in 2fhqA Skipped atom 125, because occupancy 0.500 <= existing 0.500 in 2fhqA Skipped atom 127, because occupancy 0.500 <= existing 0.500 in 2fhqA Skipped atom 129, because occupancy 0.500 <= existing 0.500 in 2fhqA Skipped atom 131, because occupancy 0.500 <= existing 0.500 in 2fhqA Skipped atom 133, because occupancy 0.500 <= existing 0.500 in 2fhqA Skipped atom 135, because occupancy 0.500 <= existing 0.500 in 2fhqA Skipped atom 137, because occupancy 0.500 <= existing 0.500 in 2fhqA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 596, because occupancy 0.500 <= existing 0.500 in 2fhqA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 598, because occupancy 0.500 <= existing 0.500 in 2fhqA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 600, because occupancy 0.500 <= existing 0.500 in 2fhqA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 602, because occupancy 0.500 <= existing 0.500 in 2fhqA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 604, because occupancy 0.500 <= existing 0.500 in 2fhqA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 606, because occupancy 0.500 <= existing 0.500 in 2fhqA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 610, because occupancy 0.500 <= existing 0.500 in 2fhqA Skipped atom 705, because occupancy 0.500 <= existing 0.500 in 2fhqA Skipped atom 707, because occupancy 0.500 <= existing 0.500 in 2fhqA Skipped atom 709, because occupancy 0.500 <= existing 0.500 in 2fhqA Skipped atom 711, because occupancy 0.500 <= existing 0.500 in 2fhqA Skipped atom 713, because occupancy 0.500 <= existing 0.500 in 2fhqA Skipped atom 715, because occupancy 0.500 <= existing 0.500 in 2fhqA Skipped atom 717, because occupancy 0.500 <= existing 0.500 in 2fhqA Skipped atom 719, because occupancy 0.500 <= existing 0.500 in 2fhqA Skipped atom 721, because occupancy 0.500 <= existing 0.500 in 2fhqA Skipped atom 949, because occupancy 0.500 <= existing 0.500 in 2fhqA Skipped atom 951, because occupancy 0.500 <= existing 0.500 in 2fhqA Skipped atom 953, because occupancy 0.500 <= existing 0.500 in 2fhqA Skipped atom 955, because occupancy 0.500 <= existing 0.500 in 2fhqA Skipped atom 957, because occupancy 0.500 <= existing 0.500 in 2fhqA Skipped atom 959, because occupancy 0.500 <= existing 0.500 in 2fhqA Skipped atom 961, because occupancy 0.500 <= existing 0.500 in 2fhqA Skipped atom 963, because occupancy 0.500 <= existing 0.500 in 2fhqA # T0331 read from 2fhqA/merged-good-all-a2m # 2fhqA read from 2fhqA/merged-good-all-a2m # adding 2fhqA to template set # found chain 2fhqA in template set T0331 4 :KDIMHILEDMKVGVFATLDEYGNPHARHAHITAANE 2fhqA 8 :EKAVELLQKCEVVTLASVNKEGYPRPVPMSKIAAEG T0331 40 :EGIFFMTSPETHFYDQLMGDQRVAMTAI 2fhqA 45 :STIWMSTGADSLKTIDFLSNPKAGLCFQ T0331 69 :EEGYL 2fhqA 73 :EKGDS T0331 77 :VRVEGTARPV 2fhqA 78 :VALMGEVEVV T0331 87 :ENDYLKTVF 2fhqA 89 :DEKLKQELW T0331 98 :NPYYQHIYKDESSD 2fhqA 98 :QDWFIEHFPGGPTD T0331 112 :TMQVFQIYAGHGFYH 2fhqA 113 :GYVLLKFTANHATYW T0331 129 :TQGHKY 2fhqA 128 :IEGTFI Number of specific fragments extracted= 8 number of extra gaps= 0 total=313 Number of alignments=49 # 2fhqA read from 2fhqA/merged-good-all-a2m # found chain 2fhqA in template set T0331 3 :LKDIMHILEDMKVGVFATLDEYGNPHARHAHITAANE 2fhqA 7 :KEKAVELLQKCEVVTLASVNKEGYPRPVPMSKIAAEG T0331 40 :EGIFFMTSPETHFYDQLMGDQRVAMTAISEE 2fhqA 45 :STIWMSTGADSLKTIDFLSNPKAGLCFQEKG T0331 75 :QVVRVEGTARPVENDYLKTVF 2fhqA 76 :DSVALMGEVEVVTDEKLKQEL T0331 98 :NPYYQHIYK 2fhqA 98 :QDWFIEHFP T0331 107 :DESSDTMQVFQIYAGHGFYHSLTQGHKYI 2fhqA 108 :GPTDPGYVLLKFTANHATYWIEGTFIHKK Number of specific fragments extracted= 5 number of extra gaps= 0 total=318 Number of alignments=50 # 2fhqA read from 2fhqA/merged-good-all-a2m # found chain 2fhqA in template set T0331 2 :ELKDIMHILEDMKVGVFATLDEYGNPHARHAHITAANE 2fhqA 6 :MKEKAVELLQKCEVVTLASVNKEGYPRPVPMSKIAAEG T0331 40 :EGIFFMTSPETHFYDQLMGDQRVAMTAISEE 2fhqA 45 :STIWMSTGADSLKTIDFLSNPKAGLCFQEKG T0331 75 :QVVRVEGTARPV 2fhqA 76 :DSVALMGEVEVV T0331 87 :ENDYLKT 2fhqA 89 :DEKLKQE T0331 100 :YYQHIYKD 2fhqA 97 :WQDWFIEH T0331 132 :HKY 2fhqA 105 :FPG T0331 140 :QGEHSEVRA 2fhqA 108 :GPTDPGYVL Number of specific fragments extracted= 7 number of extra gaps= 0 total=325 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rfeA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1rfeA expands to /projects/compbio/data/pdb/1rfe.pdb.gz 1rfeA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 250, because occupancy 0.350 <= existing 0.650 in 1rfeA Skipped atom 252, because occupancy 0.350 <= existing 0.650 in 1rfeA Skipped atom 254, because occupancy 0.350 <= existing 0.650 in 1rfeA Skipped atom 256, because occupancy 0.350 <= existing 0.650 in 1rfeA Skipped atom 258, because occupancy 0.350 <= existing 0.650 in 1rfeA Skipped atom 260, because occupancy 0.350 <= existing 0.650 in 1rfeA Skipped atom 262, because occupancy 0.350 <= existing 0.650 in 1rfeA Skipped atom 264, because occupancy 0.350 <= existing 0.650 in 1rfeA Skipped atom 266, because occupancy 0.350 <= existing 0.650 in 1rfeA Skipped atom 268, because occupancy 0.350 <= existing 0.650 in 1rfeA Skipped atom 282, because occupancy 0.350 <= existing 0.650 in 1rfeA Skipped atom 284, because occupancy 0.350 <= existing 0.650 in 1rfeA Skipped atom 286, because occupancy 0.350 <= existing 0.650 in 1rfeA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: OD for alphabet: pdb_atoms Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1077, because occupancy 0.350 <= existing 0.650 in 1rfeA Skipped atom 1079, because occupancy 0.350 <= existing 0.650 in 1rfeA Skipped atom 1081, because occupancy 0.350 <= existing 0.650 in 1rfeA Skipped atom 1083, because occupancy 0.350 <= existing 0.650 in 1rfeA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0331 read from 1rfeA/merged-good-all-a2m # 1rfeA read from 1rfeA/merged-good-all-a2m # adding 1rfeA to template set # found chain 1rfeA in template set Warning: unaligning (T0331)A32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rfeA)W43 Warning: unaligning (T0331)H33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rfeA)W43 Warning: unaligning (T0331)A83 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rfeA)E94 Warning: unaligning (T0331)R84 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rfeA)E94 Warning: unaligning (T0331)E108 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rfeA)K122 Warning: unaligning (T0331)S110 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rfeA)K122 T0331 1 :MELKDIMHILEDMKVGVFATLDEYGNPHARH 1rfeA 11 :MSEAEIADFVNSSRTGTLATIGPDGQPHLTA T0331 34 :ITAANE 1rfeA 44 :YAVIDG T0331 41 :GIFFMTSPETHFYDQLMGDQRVAMTAIS 1rfeA 50 :EIWLETKAKSQKAVNLRRDPRVSFLLED T0331 69 :EEGYLIQVVRVEGT 1rfeA 79 :DTYDTLRGVSFEGV T0331 85 :PVE 1rfeA 95 :IVE T0331 88 :NDYLKTVFADN 1rfeA 99 :PEALHRVGVSV T0331 99 :PYYQHIYKD 1rfeA 111 :ERYTGPYTD T0331 111 :DTMQVFQIYAGHGFYHSLT 1rfeA 130 :NKRVGVRIVARRTRSWDHR T0331 130 :QGHK 1rfeA 152 :LPHM Number of specific fragments extracted= 9 number of extra gaps= 2 total=334 Number of alignments=52 # 1rfeA read from 1rfeA/merged-good-all-a2m # found chain 1rfeA in template set Warning: unaligning (T0331)A32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rfeA)W43 Warning: unaligning (T0331)H33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rfeA)W43 Warning: unaligning (T0331)A83 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rfeA)E94 Warning: unaligning (T0331)R84 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rfeA)E94 Warning: unaligning (T0331)A96 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rfeA)K122 Warning: unaligning (T0331)N98 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rfeA)K122 T0331 1 :MELKDIMHILEDMKVGVFATLDEYGNPHARH 1rfeA 11 :MSEAEIADFVNSSRTGTLATIGPDGQPHLTA T0331 34 :ITAA 1rfeA 44 :YAVI T0331 39 :EEGIFFMTSPETHFYDQLMGDQRVAMTAISEEGYLIQV 1rfeA 48 :DGEIWLETKAKSQKAVNLRRDPRVSFLLEDGDTYDTLR T0331 77 :VRVEGT 1rfeA 87 :VSFEGV T0331 85 :PVEND 1rfeA 95 :IVEEP T0331 90 :YLKTVF 1rfeA 101 :ALHRVG T0331 99 :PYYQHIYKD 1rfeA 123 :PMVDQMMNK T0331 113 :MQVFQIYAGHGFYHSLT 1rfeA 132 :RVGVRIVARRTRSWDHR T0331 130 :QG 1rfeA 153 :PH Number of specific fragments extracted= 9 number of extra gaps= 2 total=343 Number of alignments=53 # 1rfeA read from 1rfeA/merged-good-all-a2m # found chain 1rfeA in template set Warning: unaligning (T0331)A32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rfeA)W43 Warning: unaligning (T0331)H33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rfeA)W43 Warning: unaligning (T0331)A83 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rfeA)E94 Warning: unaligning (T0331)R84 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rfeA)E94 Warning: unaligning (T0331)D111 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rfeA)K122 Warning: unaligning (T0331)M113 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rfeA)K122 T0331 2 :ELKDIMHILEDMKVGVFATLDEYGNPHARH 1rfeA 12 :SEAEIADFVNSSRTGTLATIGPDGQPHLTA T0331 34 :ITAA 1rfeA 44 :YAVI T0331 39 :EEGIFFMTSPETHFYDQLMGDQRVAMTAISEEG 1rfeA 48 :DGEIWLETKAKSQKAVNLRRDPRVSFLLEDGDT T0331 72 :YLIQVVRVEGT 1rfeA 82 :DTLRGVSFEGV T0331 85 :PV 1rfeA 95 :IV T0331 87 :ENDYLKTVFADN 1rfeA 98 :EPEALHRVGVSV T0331 101 :YQHIYKDESS 1rfeA 110 :WERYTGPYTD T0331 123 :GFYHSLT 1rfeA 123 :PMVDQMM T0331 141 :GEHSEVRA 1rfeA 130 :NKRVGVRI Number of specific fragments extracted= 9 number of extra gaps= 2 total=352 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ci0A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ci0A expands to /projects/compbio/data/pdb/1ci0.pdb.gz 1ci0A:# T0331 read from 1ci0A/merged-good-all-a2m # 1ci0A read from 1ci0A/merged-good-all-a2m # adding 1ci0A to template set # found chain 1ci0A in template set T0331 4 :KDIMHILEDM 1ci0A 33 :DDPIDLFTKW T0331 15 :VGVFATLDEYGNPHARHAHITAANEEGIFFMT 1ci0A 58 :ITFSSAELPSGRVSSRILLFKELDHRGFTIYS T0331 47 :SPETHFYDQLMGDQRVAMTAISEEGYLI 1ci0A 91 :WGTSRKAHDIATNPNAAIVFFWKDLQRQ T0331 77 :VRVEGTARPVENDYLKTVFADNPY 1ci0A 119 :VRVEGITEHVNRETSERYFKTRPR T0331 101 :YQHIYKDESS 1ci0A 170 :NTERFKDAED T0331 111 :DTMQVFQIYAGHGFYHSLT 1ci0A 184 :DYWGGLRIVPLEIEFWQGR T0331 130 :QGHKYIFSIGQGEHSE 1ci0A 204 :SRLHDRFVYRRKTEND Number of specific fragments extracted= 7 number of extra gaps= 0 total=359 Number of alignments=55 # 1ci0A read from 1ci0A/merged-good-all-a2m # found chain 1ci0A in template set T0331 5 :DIMHILEDMK 1ci0A 41 :KWFNEAKEDP T0331 15 :VGVFATLD 1ci0A 57 :AITFSSAE T0331 23 :EYGNPHARHAHITAANEEGIFFMTS 1ci0A 66 :PSGRVSSRILLFKELDHRGFTIYSN T0331 48 :PETHFYDQLMGDQRVAMTAISEE 1ci0A 92 :GTSRKAHDIATNPNAAIVFFWKD T0331 73 :LIQVVRVEGTARPVENDYLKTVFADNP 1ci0A 115 :LQRQVRVEGITEHVNRETSERYFKTRP T0331 100 :YYQHIYK 1ci0A 162 :ELDELTQ T0331 107 :DES 1ci0A 177 :AED T0331 110 :SDTMQVFQIYAGHGFYHSLT 1ci0A 183 :PDYWGGLRIVPLEIEFWQGR T0331 130 :QGHKYIFSIGQGEHSE 1ci0A 204 :SRLHDRFVYRRKTEND Number of specific fragments extracted= 9 number of extra gaps= 0 total=368 Number of alignments=56 # 1ci0A read from 1ci0A/merged-good-all-a2m # found chain 1ci0A in template set T0331 3 :LKDIMHI 1ci0A 43 :FNEAKED T0331 10 :LEDMKVGVFATLD 1ci0A 52 :ETLPEAITFSSAE T0331 23 :EYGNPHARHAHITAANEEGIFFMTS 1ci0A 66 :PSGRVSSRILLFKELDHRGFTIYSN T0331 48 :PETHFYDQLMGDQRVAMTAISEE 1ci0A 92 :GTSRKAHDIATNPNAAIVFFWKD T0331 73 :LIQVVRVEGTARPVENDYLKTVFADNPYYQHIYKDESSDTMQVFQIYAGHGFYHSLTQGHKYI 1ci0A 115 :LQRQVRVEGITEHVNRETSERYFKTRPRGSKIGAWASRQSDVIKNREELDELTQKNTERFKDA T0331 136 :FSIGQGEHSEVRAL 1ci0A 179 :DIPCPDYWGGLRIV Number of specific fragments extracted= 6 number of extra gaps= 0 total=374 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2furA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2furA expands to /projects/compbio/data/pdb/2fur.pdb.gz 2furA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 253, because occupancy 0.500 <= existing 0.500 in 2furA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 255, because occupancy 0.500 <= existing 0.500 in 2furA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 259, because occupancy 0.500 <= existing 0.500 in 2furA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 265, because occupancy 0.500 <= existing 0.500 in 2furA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 267, because occupancy 0.500 <= existing 0.500 in 2furA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 271, because occupancy 0.500 <= existing 0.500 in 2furA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 709, because occupancy 0.500 <= existing 0.500 in 2furA Skipped atom 711, because occupancy 0.500 <= existing 0.500 in 2furA Skipped atom 713, because occupancy 0.500 <= existing 0.500 in 2furA Skipped atom 715, because occupancy 0.500 <= existing 0.500 in 2furA Skipped atom 717, because occupancy 0.500 <= existing 0.500 in 2furA Skipped atom 719, because occupancy 0.500 <= existing 0.500 in 2furA Skipped atom 721, because occupancy 0.500 <= existing 0.500 in 2furA Skipped atom 953, because occupancy 0.500 <= existing 0.500 in 2furA Skipped atom 955, because occupancy 0.500 <= existing 0.500 in 2furA Skipped atom 957, because occupancy 0.500 <= existing 0.500 in 2furA Skipped atom 959, because occupancy 0.500 <= existing 0.500 in 2furA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1323, because occupancy 0.500 <= existing 0.500 in 2furA Skipped atom 1325, because occupancy 0.500 <= existing 0.500 in 2furA Skipped atom 1327, because occupancy 0.500 <= existing 0.500 in 2furA Skipped atom 1329, because occupancy 0.500 <= existing 0.500 in 2furA Skipped atom 1331, because occupancy 0.500 <= existing 0.500 in 2furA Skipped atom 1347, because occupancy 0.500 <= existing 0.500 in 2furA Skipped atom 1349, because occupancy 0.500 <= existing 0.500 in 2furA Skipped atom 1351, because occupancy 0.500 <= existing 0.500 in 2furA # T0331 read from 2furA/merged-good-all-a2m # 2furA read from 2furA/merged-good-all-a2m # adding 2furA to template set # found chain 2furA in template set Warning: unaligning (T0331)S127 because of BadResidue code BAD_PEPTIDE in next template residue (2furA)R164 Warning: unaligning (T0331)L128 because of BadResidue code BAD_PEPTIDE at template residue (2furA)R164 T0331 2 :ELKDIMHILEDMKVGVFATLDE 2furA 20 :SDEDLVAMLDRNFTCTVSFIDG T0331 25 :GNPHARHAHI 2furA 42 :GIPYAIPMML T0331 36 :AANEEGIFFMTSPETHFYDQLMGDQRVAMTAIS 2furA 52 :ASEGKTIYLHGSMKSRIYGILKTGQLIAISLLE T0331 69 :EEGYLIQVVRVEGTARPVE 2furA 96 :NNSINYVSALIFGRPYEID T0331 88 :NDYLKTVFADN 2furA 116 :TEKKIEVFRLL T0331 99 :PYYQHIYKDESSDT 2furA 133 :GRWDNSIKPSYEDL T0331 113 :MQVFQIYAGHGFYH 2furA 149 :VFVFAVKPETFSMK T0331 129 :TQGHKY 2furA 165 :TGPPHD Number of specific fragments extracted= 8 number of extra gaps= 1 total=382 Number of alignments=58 # 2furA read from 2furA/merged-good-all-a2m # found chain 2furA in template set Warning: unaligning (T0331)S127 because of BadResidue code BAD_PEPTIDE in next template residue (2furA)R164 Warning: unaligning (T0331)L128 because of BadResidue code BAD_PEPTIDE at template residue (2furA)R164 T0331 1 :MELKDIMHILEDMKVGVFATLDE 2furA 19 :YSDEDLVAMLDRNFTCTVSFIDG T0331 25 :GNPHARHAHI 2furA 42 :GIPYAIPMML T0331 36 :AANEEGIFFMTSPETHFYDQLMGDQRVAMTAISE 2furA 52 :ASEGKTIYLHGSMKSRIYGILKTGQLIAISLLEI T0331 70 :EGYLIQVVRVEGTARPVEN 2furA 97 :NSINYVSALIFGRPYEIDD T0331 89 :DYLKTVFADNP 2furA 117 :EKKIEVFRLLT T0331 100 :YYQHIYKDESSD 2furA 130 :LVKGRWDNSIKP T0331 112 :TM 2furA 149 :VF T0331 115 :VFQIYAGHGFYH 2furA 151 :VFAVKPETFSMK T0331 129 :TQGHK 2furA 165 :TGPPH Number of specific fragments extracted= 9 number of extra gaps= 1 total=391 Number of alignments=59 # 2furA read from 2furA/merged-good-all-a2m # found chain 2furA in template set T0331 3 :LKDIMHILEDMKVGVFATLDE 2furA 21 :DEDLVAMLDRNFTCTVSFIDG T0331 25 :GNPHARHAHIT 2furA 42 :GIPYAIPMMLA T0331 37 :ANEEGIFFMTSPETHFYDQLMGDQRVAMTA 2furA 53 :SEGKTIYLHGSMKSRIYGILKTGQLIAISL T0331 67 :ISEEGYLIQ 2furA 92 :KEIKNNSIN T0331 77 :VRVEGTARPVEN 2furA 104 :ALIFGRPYEIDD T0331 89 :DYLKTVFAD 2furA 117 :EKKIEVFRL T0331 100 :YYQHIYKDESSDTMQVFQIYAG 2furA 126 :LTEKLVKGRWDNSIKPSYEDLN T0331 130 :Q 2furA 148 :G T0331 133 :KYIFSIGQGEHSEVR 2furA 167 :PPHDTSTDDIWSGVL Number of specific fragments extracted= 9 number of extra gaps= 0 total=400 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2arzA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2arzA expands to /projects/compbio/data/pdb/2arz.pdb.gz 2arzA:Skipped atom 565, because occupancy 0.500 <= existing 0.500 in 2arzA Skipped atom 567, because occupancy 0.500 <= existing 0.500 in 2arzA Skipped atom 569, because occupancy 0.500 <= existing 0.500 in 2arzA Skipped atom 571, because occupancy 0.500 <= existing 0.500 in 2arzA Skipped atom 573, because occupancy 0.500 <= existing 0.500 in 2arzA Skipped atom 575, because occupancy 0.500 <= existing 0.500 in 2arzA Skipped atom 577, because occupancy 0.500 <= existing 0.500 in 2arzA Skipped atom 579, because occupancy 0.500 <= existing 0.500 in 2arzA Skipped atom 581, because occupancy 0.500 <= existing 0.500 in 2arzA Skipped atom 583, because occupancy 0.500 <= existing 0.500 in 2arzA Skipped atom 585, because occupancy 0.500 <= existing 0.500 in 2arzA # T0331 read from 2arzA/merged-good-all-a2m # 2arzA read from 2arzA/merged-good-all-a2m # adding 2arzA to template set # found chain 2arzA in template set Warning: unaligning (T0331)S109 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2arzA)V119 Warning: unaligning (T0331)S110 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2arzA)V119 Warning: unaligning (T0331)T112 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2arzA)F122 Warning: unaligning (T0331)M113 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2arzA)F122 T0331 4 :KDIMHIL 2arzA 7 :KNARELL T0331 11 :EDMKVGVFATLDEY 2arzA 15 :KEYRAVLSTHSKKW T0331 25 :GNPHARHAHITAANEEGIFFMTSPETHFYDQLMGDQRVAMTAISEE 2arzA 30 :GFPFGSVVPYCLDAEGRPLILISRIAQHTHNLQADPRCSMLVGERG T0331 75 :QVVRVEGTARPVENDYLKTVFA 2arzA 83 :GRLTLLAEARQLAEEEVAAAAE T0331 99 :PYYQHIYKDE 2arzA 108 :RYFPESADYH T0331 111 :D 2arzA 120 :H T0331 114 :QVFQIYA 2arzA 123 :DFWVLQP T0331 121 :GHGFYHSLTQGH 2arzA 137 :GFGAIHWLAAER Number of specific fragments extracted= 8 number of extra gaps= 2 total=408 Number of alignments=61 # 2arzA read from 2arzA/merged-good-all-a2m # found chain 2arzA in template set Warning: unaligning (T0331)S109 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2arzA)V119 Warning: unaligning (T0331)S110 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2arzA)V119 Warning: unaligning (T0331)T112 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2arzA)F122 Warning: unaligning (T0331)M113 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2arzA)F122 T0331 3 :LKDIMHILEDMKVGVFATLDE 2arzA 6 :AKNARELLLKEYRAVLSTHSK T0331 24 :YGNPHARHAHITAANEEGIFFMTSPETHFYDQLMGDQRVAMTAISEEG 2arzA 29 :PGFPFGSVVPYCLDAEGRPLILISRIAQHTHNLQADPRCSMLVGERGA T0331 73 :LIQVVRVEGTARPVENDYLKTVFADNP 2arzA 81 :AVGRLTLLAEARQLAEEEVAAAAERYY T0331 100 :YYQHIYKDE 2arzA 109 :YFPESADYH T0331 111 :D 2arzA 120 :H T0331 114 :QVFQIYAGHGFYHSLTQGHKY 2arzA 123 :DFWVLQPVQWRFIGGFGAIHW T0331 136 :F 2arzA 144 :L Number of specific fragments extracted= 7 number of extra gaps= 2 total=415 Number of alignments=62 # 2arzA read from 2arzA/merged-good-all-a2m # found chain 2arzA in template set Warning: unaligning (T0331)G139 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2arzA)V119 Warning: unaligning (T0331)Q140 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2arzA)V119 Warning: unaligning (T0331)E142 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2arzA)F122 Warning: unaligning (T0331)H143 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2arzA)F122 T0331 16 :GVFATLDE 2arzA 19 :AVLSTHSK T0331 24 :YGNPHARHAHITAANEEGIFFMTSPETHFYDQLMGDQRVAMTAISEEG 2arzA 29 :PGFPFGSVVPYCLDAEGRPLILISRIAQHTHNLQADPRCSMLVGERGA T0331 72 :YLIQVVRVEGTARPVENDYLKT 2arzA 80 :QAVGRLTLLAEARQLAEEEVAA T0331 121 :GHGFYHSLTQGHKY 2arzA 102 :AAERYYRYFPESAD T0331 137 :SI 2arzA 116 :YH T0331 141 :G 2arzA 120 :H T0331 144 :SEVRA 2arzA 123 :DFWVL Number of specific fragments extracted= 7 number of extra gaps= 2 total=422 Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dnlA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0331 read from 1dnlA/merged-good-all-a2m # 1dnlA read from 1dnlA/merged-good-all-a2m # found chain 1dnlA in training set T0331 4 :KDIMHILEDM 1dnlA 29 :ADPLTLFERW T0331 14 :K 1dnlA 46 :K T0331 15 :VGVFATLDEYGNPHARHAHITAANEEGIFFMTSPETHFYDQLMGDQRVAMTAISEEGYLI 1dnlA 52 :AMVVATVDEHGQPYQRIVLLKHYDEKGMVFYTNLGSRKAHQIENNPRVSLLFPWHTLERQ T0331 77 :VRVEGTARPVENDYLKTVFADNPYYQHI 1dnlA 112 :VMVIGKAERLSTLEVMKYFHSRPRDSQI T0331 111 :DTMQVFQIYAGHGFYH 1dnlA 176 :SFWGGFRVSLEQIEFW T0331 127 :SLTQGHKYIFSIGQGEH 1dnlA 193 :GGEHRLHDRFLYQREND Number of specific fragments extracted= 6 number of extra gaps= 0 total=428 Number of alignments=64 # 1dnlA read from 1dnlA/merged-good-all-a2m # found chain 1dnlA in training set T0331 3 :LKDIMHIL 1dnlA 35 :FERWLSQA T0331 11 :EDMK 1dnlA 45 :AKLA T0331 15 :VGVFATLDEYGNPHARHAHITAANEEGIFFMTSPETHFYDQLMGDQRVAMTAISEE 1dnlA 52 :AMVVATVDEHGQPYQRIVLLKHYDEKGMVFYTNLGSRKAHQIENNPRVSLLFPWHT T0331 73 :LIQVVRVEGTARPVENDYLKTVFADNP 1dnlA 108 :LERQVMVIGKAERLSTLEVMKYFHSRP T0331 100 :YYQHIYKDESSD 1dnlA 162 :ELKQKFQQGEVP T0331 112 :TMQVFQIYAGHGFYHSLT 1dnlA 177 :FWGGFRVSLEQIEFWQGG T0331 130 :QGHKYIFSIGQGEH 1dnlA 198 :LHDRFLYQRENDAW Number of specific fragments extracted= 7 number of extra gaps= 0 total=435 Number of alignments=65 # 1dnlA read from 1dnlA/merged-good-all-a2m # found chain 1dnlA in training set T0331 1 :MELKDIMHILEDMKVGVFATLDEYGNPHARHAHITAANEEGIFFMTSPETHFYDQLMGDQRVAMTAISEE 1dnlA 38 :WLSQACEAKLADPTAMVVATVDEHGQPYQRIVLLKHYDEKGMVFYTNLGSRKAHQIENNPRVSLLFPWHT T0331 73 :LIQVVRVEGTARPVENDYLKTVFADNPYYQHIYKDESSDTMQVFQIYAGHGFYHSLTQGHKYIFSIGQGEHSEVRA 1dnlA 108 :LERQVMVIGKAERLSTLEVMKYFHSRPRDSQIGAWVSKQSSRISARGILESKFLELKQKFQQGEVPLPSFWGGFRV Number of specific fragments extracted= 2 number of extra gaps= 0 total=437 Number of alignments=66 # command:# PrintAlignmentsContacts allconstraints.under Using radius: 8.0000 NUMB_ALIGNS: 66 Done printing distance constraints # command: