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/T0370/ # command:# Making conformation for sequence T0370 numbered 1 through 154 Created new target T0370 from T0370.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0370/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0370//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0370/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0370//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0370/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0370/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0370/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 # T0370 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 T0370 10 :KQRIQDTLNR 1g79A 36 :ERWLSQACEA # choosing archetypes in rotamer library T0370 20 :LELDVDAWVSTAGAD 1g79A 47 :LADPTAMVVATVDEH T0370 36 :GAPYLVPLSY 1g79A 62 :GQPYQRIVLL T0370 46 :LWDGETFLVATPAASPTGRNLSETGRVRLGIGP 1g79A 73 :HYDEKGMVFYTNLGSRKAHQIENNPRVSLLFPW T0370 79 :TRDLVLVEGTALPLE 1g79A 108 :LERQVMVIGKAERLS T0370 99 :DGVGD 1g79A 124 :LEVMK T0370 104 :TFAEKTGFDPRRLTTSYLYFRISPRRVQAWREAN 1g79A 162 :ELKQKFQQGEVPLPSFWGGFRVSLEQIEFWQGGE T0370 138 :ELSGRELM 1g79A 197 :RLHDRFLY T0370 146 :RDGEWLVT 1g79A 207 :ENDAWKID Number of specific fragments extracted= 9 number of extra gaps= 0 total=9 Number of alignments=1 # 1g79A read from 1g79A/merged-good-all-a2m # found chain 1g79A in template set T0370 1 :MTTPPARTAKQRIQDTLNR 1g79A 27 :LPADPLTLFERWLSQACEA T0370 20 :LE 1g79A 47 :LA T0370 23 :DVD 1g79A 49 :DPT T0370 26 :AWVSTAGAD 1g79A 53 :MVVATVDEH T0370 36 :GAPYLVPLSY 1g79A 62 :GQPYQRIVLL T0370 46 :LWDGETFLVATPAASPTGRNLSETGRVRLGIG 1g79A 73 :HYDEKGMVFYTNLGSRKAHQIENNPRVSLLFP T0370 78 :PTRDLVLVEGTALPLEPAG 1g79A 107 :TLERQVMVIGKAERLSTLE T0370 97 :LPDGVGDTFAEKTGFDPRRLTTSYLYFRISPRRVQAWREA 1g79A 155 :ILESKFLELKQKFQQGEVPLPSFWGGFRVSLEQIEFWQGG T0370 137 :NELSGRELMR 1g79A 196 :HRLHDRFLYQ T0370 147 :DGEW 1g79A 208 :NDAW T0370 151 :L 1g79A 213 :I T0370 152 :VTD 1g79A 216 :LAP Number of specific fragments extracted= 12 number of extra gaps= 0 total=21 Number of alignments=2 # 1g79A read from 1g79A/merged-good-all-a2m # found chain 1g79A in template set T0370 14 :QDTLNRLELD 1g79A 36 :ERWLSQACEA T0370 24 :VDAWVSTAGADGGAPYLVPLSY 1g79A 50 :PTAMVVATVDEHGQPYQRIVLL T0370 46 :LWDGETFLVATPAASPTGRNLSETGRVRLGIGPTRD 1g79A 73 :HYDEKGMVFYTNLGSRKAHQIENNPRVSLLFPWHTL T0370 82 :LVLVEGTALP 1g79A 111 :QVMVIGKAER T0370 92 :LEPAGLPDGVGDTFAEKTGFDPRRLTTSYLYFRISPRRVQAWREA 1g79A 150 :ISARGILESKFLELKQKFQQGEVPLPSFWGGFRVSLEQIEFWQGG Number of specific fragments extracted= 5 number of extra gaps= 0 total=26 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 # T0370 read from 1flmA/merged-good-all-a2m # 1flmA read from 1flmA/merged-good-all-a2m # found chain 1flmA in training set Warning: unaligning (T0370)Q11 because first residue in template chain is (1flmA)M1 T0370 12 :RIQDTLNRLELDVDAWVSTAGAD 1flmA 2 :LPGTFFEVLKNEGVVAIATQGED T0370 36 :G 1flmA 25 :G T0370 38 :PYLVPLS 1flmA 26 :PHLVNTW T0370 46 :LWDGETFLVATPAASPTGRNLSETGRVRLGIG 1flmA 38 :VLDGNRIVVPVGGMHKTEANVARDERVLMTLG T0370 79 :TRD 1flmA 77 :NGP T0370 82 :LVLVEGTALPLEPAGLPDGVG 1flmA 82 :GFLIRGSAAFRTDGPEFEAIA T0370 115 :RLTTSYLYFRISPRRVQA 1flmA 103 :RFKWARAALVITVVSAEQ Number of specific fragments extracted= 7 number of extra gaps= 0 total=33 Number of alignments=4 # 1flmA read from 1flmA/merged-good-all-a2m # found chain 1flmA in training set T0370 14 :QDTLNRLELDVDAWVSTAGAD 1flmA 4 :GTFFEVLKNEGVVAIATQGED T0370 36 :G 1flmA 25 :G T0370 38 :PYLVPLSY 1flmA 26 :PHLVNTWN T0370 46 :LWDGETFLVATPAASPTGRNLSETGRVRLGIG 1flmA 38 :VLDGNRIVVPVGGMHKTEANVARDERVLMTLG T0370 78 :PTRDLVLVEGTALPLEPAGLPDGV 1flmA 78 :GPGTGFLIRGSAAFRTDGPEFEAI T0370 106 :AEKTGF 1flmA 102 :ARFKWA T0370 120 :YLYFRISPRRVQA 1flmA 108 :RAALVITVVSAEQ Number of specific fragments extracted= 7 number of extra gaps= 0 total=40 Number of alignments=5 # 1flmA read from 1flmA/merged-good-all-a2m # found chain 1flmA in training set Warning: unaligning (T0370)R12 because first residue in template chain is (1flmA)M1 T0370 13 :IQDTLNRLELDVDAWVSTAGADGG 1flmA 2 :LPGTFFEVLKNEGVVAIATQGEDG T0370 38 :PYLVPLS 1flmA 26 :PHLVNTW T0370 46 :LWDGETFLVATPAASPTGRNLSETGRVRLGIGP 1flmA 38 :VLDGNRIVVPVGGMHKTEANVARDERVLMTLGS T0370 79 :T 1flmA 77 :N T0370 82 :LVLVEGTALPLEPAGL 1flmA 82 :GFLIRGSAAFRTDGPE T0370 106 :AEKT 1flmA 98 :FEAI T0370 114 :RRLTTSYLYFRISPRRVQ 1flmA 102 :ARFKWARAALVITVVSAE Number of specific fragments extracted= 7 number of extra gaps= 0 total=47 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 # T0370 read from 1w3oA/merged-good-all-a2m # 1w3oA read from 1w3oA/merged-good-all-a2m # found chain 1w3oA in training set Warning: unaligning (T0370)R134 because of BadResidue code BAD_PEPTIDE in next template residue (1w3oA)N175 Warning: unaligning (T0370)E135 because of BadResidue code BAD_PEPTIDE at template residue (1w3oA)N175 T0370 7 :RTAKQRIQDTLNRLELDVDAWVSTA 1w3oA 18 :PQNRQSDEWIRELLLRGTIARVATL T0370 32 :GAD 1w3oA 45 :GED T0370 36 :GA 1w3oA 48 :GA T0370 38 :PYLVPLSYLW 1w3oA 52 :PFITPLAYAY T0370 48 :DG 1w3oA 63 :PE T0370 50 :ETFLVATPAASPTGRNLSETGRVRLGIGP 1w3oA 66 :GDLVYHTNVVGRLRANAGQGHPATLEVSE T0370 79 :TRDL 1w3oA 96 :GQFL T0370 83 :VLVEGTALPLEPAGL 1w3oA 114 :VMVFGTARVLAGEDA T0370 99 :DGVGDTFAEKT 1w3oA 129 :RAALTTLSERV T0370 111 :FDPRRLTTS 1w3oA 140 :FPGLKVGET T0370 120 :YLYFRISPRRVQAW 1w3oA 160 :TSVYSLSIDRWSGK T0370 136 :ANELS 1w3oA 176 :WAEQA Number of specific fragments extracted= 12 number of extra gaps= 1 total=59 Number of alignments=7 # 1w3oA read from 1w3oA/merged-good-all-a2m # found chain 1w3oA in training set Warning: unaligning (T0370)R134 because of BadResidue code BAD_PEPTIDE in next template residue (1w3oA)N175 Warning: unaligning (T0370)E135 because of BadResidue code BAD_PEPTIDE at template residue (1w3oA)N175 T0370 10 :KQR 1w3oA 24 :DEW T0370 16 :TLNRLE 1w3oA 27 :IRELLL T0370 23 :DVD 1w3oA 33 :RGT T0370 26 :AWVSTA 1w3oA 37 :ARVATL T0370 32 :GAD 1w3oA 45 :GED T0370 36 :G 1w3oA 48 :G T0370 37 :APYLVPLSYLWD 1w3oA 51 :FPFITPLAYAYR T0370 49 :G 1w3oA 64 :E T0370 50 :ETFLVATPAASPTGRN 1w3oA 66 :GDLVYHTNVVGRLRAN T0370 70 :G 1w3oA 82 :A T0370 71 :RVRLGIGPTRDL 1w3oA 87 :PATLEVSEIGQF T0370 83 :VLVEGTALPLEPAGL 1w3oA 114 :VMVFGTARVLAGEDA T0370 99 :DGVGDTFAEKTG 1w3oA 129 :RAALTTLSERVF T0370 112 :DPRRLTTSY 1w3oA 141 :PGLKVGETT T0370 121 :LYFRISPRRVQAW 1w3oA 161 :SVYSLSIDRWSGK T0370 136 :A 1w3oA 176 :W T0370 137 :NELS 1w3oA 178 :EQAI Number of specific fragments extracted= 17 number of extra gaps= 1 total=76 Number of alignments=8 # 1w3oA read from 1w3oA/merged-good-all-a2m # found chain 1w3oA in training set Warning: unaligning (T0370)R134 because of BadResidue code BAD_PEPTIDE in next template residue (1w3oA)N175 Warning: unaligning (T0370)E135 because of BadResidue code BAD_PEPTIDE at template residue (1w3oA)N175 T0370 3 :TPPARTAK 1w3oA 11 :DPSVSRRP T0370 11 :QRIQDTLNRLELDVDAWVSTAG 1w3oA 21 :RQSDEWIRELLLRGTIARVATL T0370 33 :ADGG 1w3oA 45 :GEDG T0370 37 :APYLVPLSYLWDGE 1w3oA 51 :FPFITPLAYAYRPE T0370 51 :TFLVATPAASPT 1w3oA 67 :DLVYHTNVVGRL T0370 67 :SETG 1w3oA 79 :RANA T0370 71 :RVRLGIGPTRD 1w3oA 87 :PATLEVSEIGQ T0370 83 :VLVEGTALPLEPAGLPDGVGDTFAEKT 1w3oA 114 :VMVFGTARVLAGEDARAALTTLSERVF T0370 110 :GFDPRRLTTS 1w3oA 142 :GLKVGETTRP T0370 120 :YLYFRISPRRVQAW 1w3oA 160 :TSVYSLSIDRWSGK Number of specific fragments extracted= 10 number of extra gaps= 1 total=86 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 # T0370 read from 1vl7A/merged-good-all-a2m # 1vl7A read from 1vl7A/merged-good-all-a2m # found chain 1vl7A in training set T0370 17 :LNRLELDVDAWVSTAGAD 1vl7A 12 :AGFIQEFQSAIISTISEQ T0370 36 :GAPYLVPLSYLWDGE 1vl7A 30 :GIPNGSYAPFVIDDA T0370 51 :TFLVATPAASPTGRNLSETGRVRLGIGP 1vl7A 46 :NIYIYVSGLAVHTKNIEANPLVNVLFVD T0370 79 :TRDLVLVEGTALPLE 1vl7A 83 :ARRRLSFDCTATLIE T0370 94 :PAGLPDGVGDTFAEKTG 1vl7A 99 :ESQKWNQVVDQFQERFG T0370 117 :TTSYLYFRISPRRVQAWRE 1vl7A 124 :LADFRIFQLTPKEGRFVIG Number of specific fragments extracted= 6 number of extra gaps= 0 total=92 Number of alignments=10 # 1vl7A read from 1vl7A/merged-good-all-a2m # found chain 1vl7A in training set T0370 17 :LNRLE 1vl7A 12 :AGFIQ T0370 23 :DVD 1vl7A 17 :EFQ T0370 26 :AWVSTAGAD 1vl7A 21 :AIISTISEQ T0370 36 :GAPYLVPLSYLWDG 1vl7A 30 :GIPNGSYAPFVIDD T0370 50 :ETFLVATPAASPTGRNLSETGRVRLGIGPTRDL 1vl7A 45 :KNIYIYVSGLAVHTKNIEANPLVNVLFVDDEAK T0370 83 :VLVEGTALPLEPAG 1vl7A 87 :LSFDCTATLIERES T0370 97 :LPDGVGDTFAEKTG 1vl7A 102 :KWNQVVDQFQERFG T0370 111 :F 1vl7A 125 :A T0370 119 :SYLYFRISPRRVQAWREAN 1vl7A 126 :DFRIFQLTPKEGRFVIGFG Number of specific fragments extracted= 9 number of extra gaps= 0 total=101 Number of alignments=11 # 1vl7A read from 1vl7A/merged-good-all-a2m # found chain 1vl7A in training set Warning: unaligning (T0370)L17 because first residue in template chain is (1vl7A)Y11 T0370 18 :NRLELDVDAWVSTAGADGGAPYLVPLSYLWDGET 1vl7A 12 :AGFIQEFQSAIISTISEQGIPNGSYAPFVIDDAK T0370 52 :FLVATPAASPTGRNLSETGRVRLGIGPTRD 1vl7A 47 :IYIYVSGLAVHTKNIEANPLVNVLFVDDEA T0370 83 :VLVEGTALPLEPAG 1vl7A 87 :LSFDCTATLIERES T0370 97 :LPDGVGDTFAEKTGF 1vl7A 102 :KWNQVVDQFQERFGQ T0370 118 :TSYLYFRISPRRV 1vl7A 125 :ADFRIFQLTPKEG Number of specific fragments extracted= 5 number of extra gaps= 0 total=106 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 # T0370 read from 1ty9A/merged-good-all-a2m # 1ty9A read from 1ty9A/merged-good-all-a2m # found chain 1ty9A in training set Warning: unaligning (T0370)L46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ty9A)I80 Warning: unaligning (T0370)W47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ty9A)I80 Warning: unaligning (T0370)D112 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ty9A)G174 Warning: unaligning (T0370)S126 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ty9A)L189 Warning: unaligning (T0370)P127 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ty9A)L189 T0370 3 :TPPARTAKQRIQDTLNR 1ty9A 35 :ADPMSVLHNWLERARRV T0370 20 :LELDVDAWVSTAGAD 1ty9A 53 :IREPRALALATADSQ T0370 36 :GAPYLVPLSY 1ty9A 68 :GRPSTRIVVI T0370 48 :DGETFLVATPAASPTGRNLSETGRVRLGIGPTRD 1ty9A 81 :SDAGVVFSTHAGSQKGRELLHNPWASGVLYWRET T0370 82 :LVLVEGTALPLEPA 1ty9A 117 :QIILNGQAVRLPNA T0370 100 :GVGD 1ty9A 131 :KADD T0370 104 :TFAEKTGF 1ty9A 165 :AARQLAEL T0370 113 :PRRLTTSYLYFRI 1ty9A 175 :PLPRPEGYCVFEL T0370 128 :RRVQAWREAN 1ty9A 190 :ESLEFWGNGQ T0370 138 :ELSGRELM 1ty9A 201 :RLHERLRY T0370 146 :RDGEWLVT 1ty9A 211 :SDTGWNVR Number of specific fragments extracted= 11 number of extra gaps= 3 total=117 Number of alignments=13 # 1ty9A read from 1ty9A/merged-good-all-a2m # found chain 1ty9A in training set Warning: unaligning (T0370)L46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ty9A)I80 Warning: unaligning (T0370)W47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ty9A)I80 Warning: unaligning (T0370)F111 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ty9A)G174 Warning: unaligning (T0370)D112 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ty9A)G174 Warning: unaligning (T0370)S126 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ty9A)L189 Warning: unaligning (T0370)P127 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ty9A)L189 T0370 1 :MTTPPARTAKQRIQDTLNR 1ty9A 33 :LPADPMSVLHNWLERARRV T0370 20 :LE 1ty9A 53 :IR T0370 23 :DVD 1ty9A 55 :EPR T0370 26 :AWVSTAGAD 1ty9A 59 :LALATADSQ T0370 36 :GAPYLVPLSY 1ty9A 68 :GRPSTRIVVI T0370 48 :DGETFLVATPAASPTGRNLSETGRVRLGIG 1ty9A 81 :SDAGVVFSTHAGSQKGRELLHNPWASGVLY T0370 78 :PTRDLVLVEGTALPLEPAG 1ty9A 113 :ETSQQIILNGQAVRLPNAK T0370 97 :LPDGVGDTFAEK 1ty9A 161 :AMRNAARQLAEL T0370 113 :PRRLTTSYLYFRI 1ty9A 175 :PLPRPEGYCVFEL T0370 128 :RRVQAWREA 1ty9A 190 :ESLEFWGNG T0370 137 :NELSGRELMR 1ty9A 200 :ERLHERLRYD T0370 147 :DGEW 1ty9A 212 :DTGW T0370 151 :L 1ty9A 217 :V T0370 152 :VTD 1ty9A 220 :LQP Number of specific fragments extracted= 14 number of extra gaps= 3 total=131 Number of alignments=14 # 1ty9A read from 1ty9A/merged-good-all-a2m # found chain 1ty9A in training set Warning: unaligning (T0370)W47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ty9A)I80 Warning: unaligning (T0370)D112 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ty9A)G174 Warning: unaligning (T0370)S126 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ty9A)L189 Warning: unaligning (T0370)P127 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ty9A)L189 T0370 6 :ARTAKQRIQDTLNRLEL 1ty9A 34 :PADPMSVLHNWLERARR T0370 23 :DVDAWVSTAGADGGAPYLVPLS 1ty9A 55 :EPRALALATADSQGRPSTRIVV T0370 48 :DGETFLVATPAASPTGRNLSETGRVRLGIGPTRD 1ty9A 81 :SDAGVVFSTHAGSQKGRELLHNPWASGVLYWRET T0370 82 :LVLVEGTALPLEPAG 1ty9A 117 :QIILNGQAVRLPNAK T0370 97 :LPDGVGDTFAEKTGF 1ty9A 158 :DVQAMRNAARQLAEL T0370 113 :PRRLTTSYLYFRI 1ty9A 175 :PLPRPEGYCVFEL T0370 128 :RRVQAWR 1ty9A 190 :ESLEFWG Number of specific fragments extracted= 7 number of extra gaps= 3 total=138 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 # T0370 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 T0370 24 :VDAWVSTAGA 1xhnA 31 :DWGALATIST T0370 35 :GGAPYLVPLSYLW 1xhnA 45 :RGRPFADVLSLSD T0370 48 :DGE 1xhnA 59 :PPG T0370 51 :TFLVATPAASPTGRNLSETGRVRLGI 1xhnA 66 :VPYFYLSPLQLSVSNLQENPYATLTM T0370 77 :GPTRD 1xhnA 104 :FDPQS T0370 82 :LVLVEGTALPLEPAG 1xhnA 113 :HIMLSGTVTKVNETE T0370 98 :PDGVGDTFAEKTGF 1xhnA 128 :MDIAKHSLFIRHPE T0370 112 :DPRRLTTSYLYFRISPRRVQAWREANELS 1xhnA 143 :KTWPSSHNWFFAKLNITNIWVLDYFGGPK Number of specific fragments extracted= 8 number of extra gaps= 0 total=146 Number of alignments=16 # 1xhnA read from 1xhnA/merged-good-all-a2m # found chain 1xhnA in template set T0370 24 :VD 1xhnA 30 :SD T0370 26 :AWVSTAG 1xhnA 33 :GALATIS T0370 35 :GGAPYLVPLSYLWD 1xhnA 45 :RGRPFADVLSLSDG T0370 49 :G 1xhnA 60 :P T0370 50 :ETFLVATPAASPTGRNLSETGRVRLGIG 1xhnA 65 :GVPYFYLSPLQLSVSNLQENPYATLTMT T0370 78 :PTRDL 1xhnA 105 :DPQSP T0370 83 :VLVEGTALPLEPAG 1xhnA 114 :IMLSGTVTKVNETE T0370 98 :PDGVGDTFAEKTG 1xhnA 128 :MDIAKHSLFIRHP T0370 111 :FDPRRLTTSYLYFRISPRRVQAWREANELSG 1xhnA 142 :MKTWPSSHNWFFAKLNITNIWVLDYFGGPKI Number of specific fragments extracted= 9 number of extra gaps= 0 total=155 Number of alignments=17 # 1xhnA read from 1xhnA/merged-good-all-a2m # found chain 1xhnA in template set T0370 33 :ADGGAPYLVP 1xhnA 58 :GPPGAGSGVP T0370 53 :LVATPAASPTGRNLSETGRVRLGIG 1xhnA 68 :YFYLSPLQLSVSNLQENPYATLTMT T0370 78 :PTRD 1xhnA 106 :PQSP T0370 82 :LVLVEGTALPLEPA 1xhnA 113 :HIMLSGTVTKVNET T0370 97 :LPDGVGDTFAEKT 1xhnA 127 :EMDIAKHSLFIRH T0370 110 :GFDPRRLTTSYLYFRISPRRVQAWR 1xhnA 141 :EMKTWPSSHNWFFAKLNITNIWVLD Number of specific fragments extracted= 6 number of extra gaps= 0 total=161 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 # T0370 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 (T0370)R146 because of BadResidue code BAD_PEPTIDE at template residue (1t9mA)D203 Warning: unaligning (T0370)G148 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t9mA)G206 Warning: unaligning (T0370)E149 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t9mA)G206 T0370 10 :KQRIQDTLNR 1t9mA 34 :RNWLERARRY T0370 20 :LELDVDAWVSTAGAD 1t9mA 45 :VREPRALALATVDGQ T0370 36 :GAPYLVPLSY 1t9mA 60 :GRPSTRIVVI T0370 46 :LWDGETFLVATPAASPTGRNLSETGRVRLGIGPTRD 1t9mA 71 :ELGERGVVFATHADSQKGRELAQNPWASGVLYWRES T0370 82 :LVLVEGTALPLEPAGLPDGVGD 1t9mA 109 :QIILNGRAERLPDERADAQWLS T0370 104 :TFAEKTGF 1t9mA 157 :EARRLAET T0370 112 :DPRRLTTSYLYFRISPRRVQAWREAN 1t9mA 166 :GPLPRPPGYCLFELCLESVEFWGNGT T0370 138 :ELSGRELM 1t9mA 193 :RLHERLRY T0370 147 :D 1t9mA 204 :E T0370 150 :WLVT 1t9mA 207 :WKHR Number of specific fragments extracted= 10 number of extra gaps= 2 total=171 Number of alignments=19 # 1t9mA read from 1t9mA/merged-good-all-a2m # found chain 1t9mA in template set Warning: unaligning (T0370)G148 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t9mA)G206 Warning: unaligning (T0370)E149 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t9mA)G206 T0370 2 :TTPPARTAKQRIQDTLNR 1t9mA 26 :PANPMEVLRNWLERARRY T0370 20 :LE 1t9mA 45 :VR T0370 23 :DVD 1t9mA 47 :EPR T0370 26 :AWVSTAGAD 1t9mA 51 :LALATVDGQ T0370 36 :GAPYLVPLSY 1t9mA 60 :GRPSTRIVVI T0370 46 :LWDGETFLVATPAASPTGRNLSETGRVRLGIGPTRD 1t9mA 71 :ELGERGVVFATHADSQKGRELAQNPWASGVLYWRES T0370 82 :LVLVEGTALPLEPAG 1t9mA 109 :QIILNGRAERLPDER T0370 97 :LPDGVGDTFAEKTG 1t9mA 150 :DIHALRAEARRLAE T0370 111 :FDPRRLTTSYLYFRISPRRVQAWREA 1t9mA 165 :DGPLPRPPGYCLFELCLESVEFWGNG T0370 137 :NELSGRELMR 1t9mA 192 :ERLHERLRYD T0370 147 :D 1t9mA 204 :E T0370 150 :W 1t9mA 207 :W T0370 152 :VTD 1t9mA 212 :LQP Number of specific fragments extracted= 13 number of extra gaps= 1 total=184 Number of alignments=20 # 1t9mA read from 1t9mA/merged-good-all-a2m # found chain 1t9mA in template set T0370 15 :DTLNRLEL 1t9mA 35 :NWLERARR T0370 23 :DVDAWVSTAGADGGAPYLVPLS 1t9mA 47 :EPRALALATVDGQGRPSTRIVV T0370 45 :YLWDGETFLVATPAASPTGRNLSETGRVRLGIGPTRD 1t9mA 70 :AELGERGVVFATHADSQKGRELAQNPWASGVLYWRES T0370 82 :LVLVEGTALPLEPAG 1t9mA 109 :QIILNGRAERLPDER T0370 97 :LPDGVGDTFAEKT 1t9mA 149 :ADIHALRAEARRL T0370 110 :GFDPRRLTTSYLYFRISPRRVQAWR 1t9mA 164 :TDGPLPRPPGYCLFELCLESVEFWG Number of specific fragments extracted= 6 number of extra gaps= 0 total=190 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:# T0370 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 (T0370)S44 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1ejeA)F48 Warning: unaligning (T0370)Y45 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1ejeA)F48 T0370 2 :TTPPARTAKQRI 1ejeA 14 :DFPVESAHRILT T0370 24 :VDAWVSTAGAD 1ejeA 28 :PTVMVTTVDEE T0370 36 :GAPYLVPL 1ejeA 39 :GNINAAPF T0370 46 :LW 1ejeA 49 :TM T0370 48 :DGETFLVATPAASPTGRNLSETGRVRLGIGP 1ejeA 55 :DPPVVAFASAPDHHTARNIESTHEFVINITP T0370 99 :DGVGDTFAEKT 1ejeA 86 :ADIIERMWVTA T0370 117 :TTSYLYFRISPRRVQAWRE 1ejeA 141 :VGDHNLITGSVVSASVRSG T0370 136 :ANELSGRELMR 1ejeA 162 :KEGLLDVESVK T0370 147 :DGEWLVTD 1ejeA 179 :GNKFVVGD Number of specific fragments extracted= 9 number of extra gaps= 1 total=199 Number of alignments=22 # 1ejeA read from 1ejeA/merged-good-all-a2m # found chain 1ejeA in template set Warning: unaligning (T0370)S44 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1ejeA)F48 Warning: unaligning (T0370)Y45 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1ejeA)F48 T0370 24 :VD 1ejeA 27 :RP T0370 26 :AWVSTAGAD 1ejeA 30 :VMVTTVDEE T0370 36 :GAPYLVPL 1ejeA 39 :GNINAAPF T0370 46 :LWD 1ejeA 51 :PVS T0370 49 :GETFLVATPAASPTGRNLSETGRVRLGIG 1ejeA 56 :PPVVAFASAPDHHTARNIESTHEFVINIT T0370 98 :PDGVGDTFAEKTG 1ejeA 85 :PADIIERMWVTAR T0370 115 :RLTTSYLYFRISPRRVQAWREA 1ejeA 139 :FEVGDHNLITGSVVSASVRSGA T0370 137 :NELSG 1ejeA 163 :EGLLD T0370 142 :RELMRDGEWLVTD 1ejeA 174 :VLHVGGNKFVVGD Number of specific fragments extracted= 9 number of extra gaps= 1 total=208 Number of alignments=23 # 1ejeA read from 1ejeA/merged-good-all-a2m # found chain 1ejeA in template set Warning: unaligning (T0370)S44 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1ejeA)F48 Warning: unaligning (T0370)Y45 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1ejeA)F48 T0370 1 :MTTPPARTAKQRI 1ejeA 13 :EDFPVESAHRILT T0370 23 :DVDAWVSTAGADGGAPYLVPL 1ejeA 26 :PRPTVMVTTVDEEGNINAAPF T0370 46 :L 1ejeA 49 :T T0370 48 :DGETFLVATPAASPTGRNLSETGRVRLGIGP 1ejeA 55 :DPPVVAFASAPDHHTARNIESTHEFVINITP T0370 83 :VLVEGTALPLEPA 1ejeA 129 :GHLECELLRMFEV T0370 118 :TSYLYFRISPRRVQ 1ejeA 142 :GDHNLITGSVVSAS Number of specific fragments extracted= 6 number of extra gaps= 1 total=214 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 # T0370 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 (T0370)A59 because of BadResidue code BAD_PEPTIDE in next template residue (2fg9A)G55 Warning: unaligning (T0370)S60 because of BadResidue code BAD_PEPTIDE at template residue (2fg9A)G55 T0370 12 :RIQDTLNRLELDVDAWVSTAGAD 2fg9A 8 :DKQRIESIILQADACFVGITDLE T0370 36 :GAPYLVPLSYLWDGETFLVATPA 2fg9A 31 :GNPYVVPMNFGYENDTLYLHSGP T0370 61 :PTGRNLSETGRVRLGIGPTRDL 2fg9A 56 :GKIEMLQRNNNVCITFSLGHKL T0370 83 :VLVEGTALPLEPAGLPDGVGDTFAEKTGFDPRRLTT 2fg9A 95 :AMCRGKVEFIEDMEEKRHALDIIMRHYTKDQFSYSD T0370 119 :SYLYFRISPRRVQAWR 2fg9A 135 :NVKVWKVPVDQMTGKV Number of specific fragments extracted= 5 number of extra gaps= 1 total=219 Number of alignments=25 # 2fg9A read from 2fg9A/merged-good-all-a2m # found chain 2fg9A in template set Warning: unaligning (T0370)A59 because of BadResidue code BAD_PEPTIDE in next template residue (2fg9A)G55 Warning: unaligning (T0370)S60 because of BadResidue code BAD_PEPTIDE at template residue (2fg9A)G55 T0370 13 :IQDTLNRLE 2fg9A 9 :KQRIESIIL T0370 23 :DVD 2fg9A 18 :QAD T0370 26 :AWVSTAGAD 2fg9A 22 :CFVGITDLE T0370 36 :GAPYLVPLSYLWDGETFLVATPA 2fg9A 31 :GNPYVVPMNFGYENDTLYLHSGP T0370 61 :PTGRNLSETGRVRLGIGPTRDL 2fg9A 56 :GKIEMLQRNNNVCITFSLGHKL T0370 83 :VLVEGTALPLEPAGLPDGVGDTFAEKTGFDPRRLTT 2fg9A 95 :AMCRGKVEFIEDMEEKRHALDIIMRHYTKDQFSYSD T0370 119 :SYLYFRISPRRVQAWREA 2fg9A 135 :NVKVWKVPVDQMTGKVFG Number of specific fragments extracted= 7 number of extra gaps= 1 total=226 Number of alignments=26 # 2fg9A read from 2fg9A/merged-good-all-a2m # found chain 2fg9A in template set Warning: unaligning (T0370)A59 because of BadResidue code BAD_PEPTIDE in next template residue (2fg9A)G55 Warning: unaligning (T0370)S60 because of BadResidue code BAD_PEPTIDE at template residue (2fg9A)G55 T0370 9 :AKQRIQDTLNRLELDVDAWVSTAGADGGAPYLVPLSYLWDGETFLVATPA 2fg9A 4 :IVIEDKQRIESIILQADACFVGITDLEGNPYVVPMNFGYENDTLYLHSGP T0370 61 :PTGRNLSETGRVRLGIGPTRD 2fg9A 56 :GKIEMLQRNNNVCITFSLGHK T0370 83 :VLVEGTALPLEPAGLPDGVGDTFAEKTGFDPRRLT 2fg9A 95 :AMCRGKVEFIEDMEEKRHALDIIMRHYTKDQFSYS T0370 118 :TSYLYFRISPRRVQA 2fg9A 134 :RNVKVWKVPVDQMTG Number of specific fragments extracted= 4 number of extra gaps= 1 total=230 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 # T0370 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 (T0370)I13 because first residue in template chain is (2asfA)S11 Warning: unaligning (T0370)L43 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2asfA)G41 Warning: unaligning (T0370)S44 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2asfA)G41 Warning: unaligning (T0370)G141 because last residue in template chain is (2asfA)D135 T0370 14 :QDTLNRLELDVDAWVSTAGAD 2asfA 12 :DDALAFLSERHLAMLTTLRAD T0370 36 :GAPYLVP 2asfA 33 :NSPHVVA T0370 45 :YLWDGE 2asfA 42 :FTFDPK T0370 51 :TFLVATPAASPTGRNLSETGRVRLGIGPTRDLVLVEGTALPLEPAGLPDGVGDTFAEKTG 2asfA 50 :IARVITTGGSQKAVNADRSGLAVLSQVDGARWLSLEGRAAVNSDIDAVRDAELRYAQRYR T0370 113 :PRRLTTSYLYFRISPRRVQAW 2asfA 110 :TPRPNPRRVVIEVQIERVLGS T0370 137 :NELS 2asfA 131 :ADLL Number of specific fragments extracted= 6 number of extra gaps= 1 total=236 Number of alignments=28 # 2asfA read from 2asfA/merged-good-all-a2m # found chain 2asfA in template set Warning: unaligning (T0370)I13 because first residue in template chain is (2asfA)S11 Warning: unaligning (T0370)L43 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2asfA)G41 Warning: unaligning (T0370)S44 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2asfA)G41 Warning: unaligning (T0370)G141 because last residue in template chain is (2asfA)D135 T0370 14 :QDTLNRLE 2asfA 12 :DDALAFLS T0370 23 :DVD 2asfA 20 :ERH T0370 26 :AWVSTAGAD 2asfA 24 :AMLTTLRAD T0370 36 :GAPYLVP 2asfA 33 :NSPHVVA T0370 45 :YLWD 2asfA 42 :FTFD T0370 49 :GETFLVATPAASPTGRNLSETGRVRLGIGPTRDLVLVEGTALPLEPAGLPDGVGDTFAEKTGFD 2asfA 48 :THIARVITTGGSQKAVNADRSGLAVLSQVDGARWLSLEGRAAVNSDIDAVRDAELRYAQRYRTP T0370 115 :RLTTSYLYFRISPRRVQAW 2asfA 112 :RPNPRRVVIEVQIERVLGS T0370 137 :NELS 2asfA 131 :ADLL Number of specific fragments extracted= 8 number of extra gaps= 1 total=244 Number of alignments=29 # 2asfA read from 2asfA/merged-good-all-a2m # found chain 2asfA in template set Warning: unaligning (T0370)I13 because first residue in template chain is (2asfA)S11 Warning: unaligning (T0370)L43 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2asfA)G41 Warning: unaligning (T0370)S44 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2asfA)G41 T0370 15 :DTLNRLELDVDAWVSTAGADGGAPYLVP 2asfA 12 :DDALAFLSERHLAMLTTLRADNSPHVVA T0370 45 :YLWDGE 2asfA 42 :FTFDPK T0370 51 :TFLVATPAASPTGRNLSETGRVRLGIGPTRDLVLVEGTALPLEPAGLPDGVGDTFAEKT 2asfA 50 :IARVITTGGSQKAVNADRSGLAVLSQVDGARWLSLEGRAAVNSDIDAVRDAELRYAQRY T0370 112 :DPRRLTTSYLYFRISPRRVQA 2asfA 109 :RTPRPNPRRVVIEVQIERVLG Number of specific fragments extracted= 4 number of extra gaps= 1 total=248 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:# T0370 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 Warning: unaligning (T0370)Q11 because first residue in template chain is (1xxoA)V5 T0370 12 :RIQDTLNRLELDVDAWVSTAGAD 1xxoA 6 :FDDKLLAVISGNSIGVLATIKHD T0370 36 :GAPYLVPLSYLWDGE 1xxoA 29 :GRPQLSNVQYHFDPR T0370 51 :TFLVATPAASPTGRNLSETGRVRLGIG 1xxoA 46 :LIQVSIAEPRAKTRNLRRDPRASILVD T0370 78 :PTRDLVLVEGTALPLE 1xxoA 75 :DGWSYAVAEGTAQLTP T0370 94 :PAGLPDGVGDTFAEKTGFDPRRL 1xxoA 96 :DDDTVEALIALYRNIAGEHSDWD T0370 117 :TTSYLYFRISPRRVQAWREAN 1xxoA 126 :TDRRVLLTLPISHVYGLPPGM Number of specific fragments extracted= 6 number of extra gaps= 0 total=254 Number of alignments=31 # 1xxoA read from 1xxoA/merged-good-all-a2m # found chain 1xxoA in template set T0370 14 :QDTLNRLE 1xxoA 8 :DKLLAVIS T0370 23 :DVD 1xxoA 16 :GNS T0370 26 :AWVSTAGAD 1xxoA 20 :GVLATIKHD T0370 36 :GAPYLVPLSYLWD 1xxoA 29 :GRPQLSNVQYHFD T0370 49 :GETFLVATPAASPTGRNLSETGRVRLGIG 1xxoA 44 :KLLIQVSIAEPRAKTRNLRRDPRASILVD T0370 78 :PTRDLVLVEGTALPLE 1xxoA 75 :DGWSYAVAEGTAQLTP T0370 95 :AG 1xxoA 95 :PD T0370 97 :LPDGVGDTFAE 1xxoA 116 :DWDDYRQAMVT T0370 118 :TSYLYFRISPRRVQAWREAN 1xxoA 127 :DRRVLLTLPISHVYGLPPGM Number of specific fragments extracted= 9 number of extra gaps= 0 total=263 Number of alignments=32 # 1xxoA read from 1xxoA/merged-good-all-a2m # found chain 1xxoA in template set Warning: unaligning (T0370)Q11 because first residue in template chain is (1xxoA)V5 T0370 12 :RIQDTLNRLEL 1xxoA 6 :FDDKLLAVISG T0370 24 :VDAWVSTAGADGGAPYLVPLSYLWDGE 1xxoA 17 :NSIGVLATIKHDGRPQLSNVQYHFDPR T0370 51 :TFLVATPAASPTGRNLSETGRVRLGIGPTRD 1xxoA 46 :LIQVSIAEPRAKTRNLRRDPRASILVDADDG T0370 82 :LVLVEGTALPLEPAG 1xxoA 79 :YAVAEGTAQLTPPAA T0370 97 :LPDGVGDTFAEKTGFDPRRLT 1xxoA 95 :PDDDTVEALIALYRNIAGEHS T0370 118 :TSYLYFRISPRRVQA 1xxoA 127 :DRRVLLTLPISHVYG Number of specific fragments extracted= 6 number of extra gaps= 0 total=269 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 # T0370 read from 1w9aA/merged-good-all-a2m # 1w9aA read from 1w9aA/merged-good-all-a2m # found chain 1w9aA in training set Warning: unaligning (T0370)R12 because first residue in template chain is (1w9aA)F6 T0370 13 :IQDTLNRLELDVDAWVSTAGAD 1w9aA 7 :DDKLLAVISGNSIGVLATIKHD T0370 36 :GAPYLVPLSYLWDGE 1w9aA 29 :GRPQLSNVQYHFDPR T0370 51 :TFLVATPAASPTGRNLSETGRVRLGIG 1w9aA 46 :LIQVSIAEPRAKTRNLRRDPRASILVD T0370 78 :PTRDLVLVEGTALPLE 1w9aA 75 :DGWSYAVAEGTAQLTP T0370 94 :PA 1w9aA 96 :DD T0370 100 :GVGDTFAEKT 1w9aA 98 :DTVEALIALY T0370 110 :GFDPRRL 1w9aA 112 :GEHSDWD T0370 117 :TTSYLYFRISPRRVQAWREAN 1w9aA 126 :TDRRVLLTLPISHVYGLPPGM Number of specific fragments extracted= 8 number of extra gaps= 0 total=277 Number of alignments=34 # 1w9aA read from 1w9aA/merged-good-all-a2m # found chain 1w9aA in training set T0370 14 :QDTLNRLE 1w9aA 8 :DKLLAVIS T0370 23 :DVD 1w9aA 16 :GNS T0370 26 :AWVSTAGAD 1w9aA 20 :GVLATIKHD T0370 36 :GAPYLVPLSYLWD 1w9aA 29 :GRPQLSNVQYHFD T0370 49 :GETFLVATPAASPTGRNLSETGRVRLGIG 1w9aA 44 :KLLIQVSIAEPRAKTRNLRRDPRASILVD T0370 78 :PTRDLVLVEGTALPLE 1w9aA 75 :DGWSYAVAEGTAQLTP T0370 95 :AG 1w9aA 95 :PD T0370 97 :LPDGVGDTFAE 1w9aA 116 :DWDDYRQAMVT T0370 118 :TSYLYFRISPRRVQAWREAN 1w9aA 127 :DRRVLLTLPISHVYGLPPGM Number of specific fragments extracted= 9 number of extra gaps= 0 total=286 Number of alignments=35 # 1w9aA read from 1w9aA/merged-good-all-a2m # found chain 1w9aA in training set Warning: unaligning (T0370)R12 because first residue in template chain is (1w9aA)F6 T0370 13 :IQDTLNRLE 1w9aA 7 :DDKLLAVIS T0370 23 :DVDAWVSTAGADGGAPYLVPLSYLWDGE 1w9aA 16 :GNSIGVLATIKHDGRPQLSNVQYHFDPR T0370 51 :TFLVATPAASPTGRNLSETGRVRLGIGPTRD 1w9aA 46 :LIQVSIAEPRAKTRNLRRDPRASILVDADDG T0370 82 :LVLVEGTALPLEPAG 1w9aA 79 :YAVAEGTAQLTPPAA T0370 97 :LPDGVGDTFAEKTGFDPRRLT 1w9aA 95 :PDDDTVEALIALYRNIAGEHS T0370 118 :TSYLYFRISPRRVQAW 1w9aA 127 :DRRVLLTLPISHVYGL Number of specific fragments extracted= 6 number of extra gaps= 0 total=292 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:# T0370 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 (T0370)Q11 because first residue in template chain is (2aq6A)V5 T0370 12 :RIQDTLNRLELDVDAWVSTAGAD 2aq6A 6 :FDDKLLAVISGNSIGVLATIKHD T0370 36 :GAPYLVPLSYLWDGE 2aq6A 29 :GRPQLSNVQYHFDPR T0370 51 :TFLVATPAASPTGRNLSETGRVRLGIG 2aq6A 46 :LIQVSIAEPRAKTRNLRRDPRASILVD T0370 78 :PTRDLVLVEGTALPLE 2aq6A 75 :DGWSYAVAEGTAQLTP T0370 94 :PAGLPDGVGDTFAEKTGFDPRRL 2aq6A 96 :DDDTVEALIALYRNIAGEHSDWD T0370 117 :TTSYLYFRISPRRVQAWREA 2aq6A 126 :TDRRVLLTLPISHVYGLPPG Number of specific fragments extracted= 6 number of extra gaps= 0 total=298 Number of alignments=37 # 2aq6A read from 2aq6A/merged-good-all-a2m # found chain 2aq6A in template set Warning: unaligning (T0370)P5 because first residue in template chain is (2aq6A)V5 T0370 6 :AR 2aq6A 6 :FD T0370 14 :QDTLNRLE 2aq6A 8 :DKLLAVIS T0370 23 :DVD 2aq6A 16 :GNS T0370 26 :AWVSTAGAD 2aq6A 20 :GVLATIKHD T0370 36 :GAPYLVPLSYLWD 2aq6A 29 :GRPQLSNVQYHFD T0370 49 :GETFLVATPAASPTGRNLSETGRVRLGIG 2aq6A 44 :KLLIQVSIAEPRAKTRNLRRDPRASILVD T0370 78 :PTRDLVLVEGTALPLE 2aq6A 75 :DGWSYAVAEGTAQLTP T0370 95 :AG 2aq6A 95 :PD T0370 97 :LPDGVGDTFAE 2aq6A 116 :DWDDYRQAMVT T0370 118 :TSYLYFRISPRRVQAWREA 2aq6A 127 :DRRVLLTLPISHVYGLPPG Number of specific fragments extracted= 10 number of extra gaps= 0 total=308 Number of alignments=38 # 2aq6A read from 2aq6A/merged-good-all-a2m # found chain 2aq6A in template set Warning: unaligning (T0370)R12 because first residue in template chain is (2aq6A)V5 T0370 13 :IQDTLNRLELDVDAWVSTAGADGGAPYLVPLSYLWDGE 2aq6A 6 :FDDKLLAVISGNSIGVLATIKHDGRPQLSNVQYHFDPR T0370 51 :TFLVATPAASPTGRNLSETGRVRLGIGPTRD 2aq6A 46 :LIQVSIAEPRAKTRNLRRDPRASILVDADDG T0370 82 :LVLVEGTALPLEPAG 2aq6A 79 :YAVAEGTAQLTPPAA T0370 97 :LPDGVGDTFAEKTGFDPRRLT 2aq6A 95 :PDDDTVEALIALYRNIAGEHS T0370 118 :TSYLYFRISPRRVQA 2aq6A 127 :DRRVLLTLPISHVYG Number of specific fragments extracted= 5 number of extra gaps= 0 total=313 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 # T0370 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 T0370 11 :QRIQDTLNR 1nrgA 64 :AWFEEAVQC T0370 20 :LELDVDAWVSTAGAD 1nrgA 75 :IGEANAMCLATCTRD T0370 36 :GAPYLVPLSY 1nrgA 90 :GKPSARMLLL T0370 46 :LWDGETFLVATPAASPTGRNLSETGRVRLGIGP 1nrgA 101 :GFGKDGFRFFTNFESRKGKELDSNPFASLVFYW T0370 79 :TRDLVLVEGTALPLEPAGLPDGVGD 1nrgA 136 :LNRQVRVEGPVKKLPEEEAECYFHS T0370 104 :TFAEKTGFDPRRLTTSYLYFRISPRRVQAWREAN 1nrgA 190 :ELEQLYQDQEVPKPKSWGGYVLYPQVMEFWQGQT T0370 138 :ELSGRELMR 1nrgA 225 :RLHDRIVFR T0370 147 :DGEWLVT 1nrgA 238 :TGDSPLG Number of specific fragments extracted= 8 number of extra gaps= 0 total=321 Number of alignments=40 # 1nrgA read from 1nrgA/merged-good-all-a2m # found chain 1nrgA in template set T0370 2 :TTPPARTAKQRIQDTLNR 1nrgA 55 :SLDPVKQFAAWFEEAVQC T0370 20 :LE 1nrgA 75 :IG T0370 23 :DVD 1nrgA 77 :EAN T0370 26 :AWVSTAGAD 1nrgA 81 :MCLATCTRD T0370 36 :GAPYLVPLSY 1nrgA 90 :GKPSARMLLL T0370 46 :LWDGETFLVATPAASPTGRNLSETGRVRLGIG 1nrgA 101 :GFGKDGFRFFTNFESRKGKELDSNPFASLVFY T0370 78 :PTRDLVLVEGTALPLEPAG 1nrgA 135 :PLNRQVRVEGPVKKLPEEE T0370 97 :LPDGVGDTFAEKTGFDPRRLTTSYLYFRISPRRVQAWREA 1nrgA 183 :YLRKKNEELEQLYQDQEVPKPKSWGGYVLYPQVMEFWQGQ T0370 137 :NELSGRELMR 1nrgA 224 :NRLHDRIVFR Number of specific fragments extracted= 9 number of extra gaps= 0 total=330 Number of alignments=41 # 1nrgA read from 1nrgA/merged-good-all-a2m # found chain 1nrgA in template set T0370 15 :DTLNRLEL 1nrgA 64 :AWFEEAVQ T0370 23 :DVDAWVSTAGADGGAPYLVPLS 1nrgA 77 :EANAMCLATCTRDGKPSARMLL T0370 47 :WDGETFLVATPAASPTGRNLSETGRVRLGIGPTRD 1nrgA 102 :FGKDGFRFFTNFESRKGKELDSNPFASLVFYWEPL T0370 83 :VLVEGTALP 1nrgA 140 :VRVEGPVKK T0370 92 :LEPAGLPDGVGDTFAEKTGFDPRRLTTSYLYFRISPRRVQAWREA 1nrgA 178 :IPDREYLRKKNEELEQLYQDQEVPKPKSWGGYVLYPQVMEFWQGQ Number of specific fragments extracted= 5 number of extra gaps= 0 total=335 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 # T0370 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 (T0370)A59 because of BadResidue code BAD_PEPTIDE in next template residue (1axj)H52 Warning: unaligning (T0370)S60 because of BadResidue code BAD_PEPTIDE at template residue (1axj)H52 Warning: unaligning (T0370)R129 because of BadResidue code BAD_PEPTIDE in next template residue (1axj)A118 Warning: unaligning (T0370)V130 because of BadResidue code BAD_PEPTIDE at template residue (1axj)A118 T0370 12 :RIQDTLNRLELDVDAWVSTAGAD 1axj 2 :LPGTFFEVLKNEGVVAIATQGED T0370 36 :G 1axj 25 :G T0370 38 :PYLVPLSY 1axj 26 :PHLVNTWN T0370 46 :LWDGETFLVATPA 1axj 38 :VLDGNRIVVPVGG T0370 61 :PTGRNLSETGRVRLGIGP 1axj 53 :KTEANVARDERVLMTLGS T0370 79 :TRD 1axj 78 :GPG T0370 82 :LVLVEGTALPLEP 1axj 82 :GFLIRGSAAFRTD T0370 99 :DGVGDTFA 1axj 95 :GPEFEAIA T0370 115 :RLTTSYLYFRISPR 1axj 103 :RFKWARAALVITVV T0370 131 :QA 1axj 119 :EQ Number of specific fragments extracted= 10 number of extra gaps= 2 total=345 Number of alignments=43 # 1axj read from 1axj/merged-good-all-a2m # found chain 1axj in template set Warning: unaligning (T0370)A59 because of BadResidue code BAD_PEPTIDE in next template residue (1axj)H52 Warning: unaligning (T0370)S60 because of BadResidue code BAD_PEPTIDE at template residue (1axj)H52 Warning: unaligning (T0370)R129 because of BadResidue code BAD_PEPTIDE in next template residue (1axj)A118 Warning: unaligning (T0370)V130 because of BadResidue code BAD_PEPTIDE at template residue (1axj)A118 T0370 14 :QDTLNRLELDVDAWVSTAGAD 1axj 4 :GTFFEVLKNEGVVAIATQGED T0370 36 :G 1axj 25 :G T0370 38 :PYLVPLSY 1axj 26 :PHLVNTWN T0370 46 :LWDGETFLVATPA 1axj 38 :VLDGNRIVVPVGG T0370 61 :PTGRNLSETGRVRLGIG 1axj 53 :KTEANVARDERVLMTLG T0370 78 :PTRDLVLVEGTALPLEP 1axj 78 :GPGTGFLIRGSAAFRTD T0370 99 :DGVGDTFAEKTGF 1axj 95 :GPEFEAIARFKWA T0370 120 :YLYFRISPR 1axj 108 :RAALVITVV T0370 131 :QA 1axj 119 :EQ Number of specific fragments extracted= 9 number of extra gaps= 2 total=354 Number of alignments=44 # 1axj read from 1axj/merged-good-all-a2m # found chain 1axj in template set Warning: unaligning (T0370)A59 because of BadResidue code BAD_PEPTIDE in next template residue (1axj)H52 Warning: unaligning (T0370)S60 because of BadResidue code BAD_PEPTIDE at template residue (1axj)H52 Warning: unaligning (T0370)R129 because of BadResidue code BAD_PEPTIDE in next template residue (1axj)A118 Warning: unaligning (T0370)V130 because of BadResidue code BAD_PEPTIDE at template residue (1axj)A118 T0370 13 :IQ 1axj 3 :PG T0370 16 :TLNRLELDVDAWVSTAGADGG 1axj 5 :TFFEVLKNEGVVAIATQGEDG T0370 38 :PYLVPLS 1axj 26 :PHLVNTW T0370 46 :LWDGETFLVATPA 1axj 38 :VLDGNRIVVPVGG T0370 61 :PTGRNLSETGRVRLGIGPTRD 1axj 53 :KTEANVARDERVLMTLGSRKV T0370 82 :LVLVEGTALPLEPAGL 1axj 82 :GFLIRGSAAFRTDGPE T0370 102 :GDTF 1axj 98 :FEAI T0370 114 :RRLTTSYLYFRISPR 1axj 102 :ARFKWARAALVITVV Number of specific fragments extracted= 8 number of extra gaps= 2 total=362 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 Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0370/2a2jA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0370/2a2jA/merged-good-all-a2m.gz for input Trying 2a2jA/merged-good-all-a2m Error: Couldn't open file 2a2jA/merged-good-all-a2m or 2a2jA/merged-good-all-a2m.gz for input # 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 # T0370 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 Warning: unaligning (T0370)A9 because first residue in template chain is (2fhqA)T3 T0370 10 :KQRIQDTLNRLELDVDAWVSTAGAD 2fhqA 4 :KTMKEKAVELLQKCEVVTLASVNKE T0370 36 :GAPYLVPLSY 2fhqA 29 :GYPRPVPMSK T0370 46 :LWDG 2fhqA 40 :AAEG T0370 50 :ETFLVATPAASPTGRNLSETGRVRLGIGPTRDLVLVEGTALPLEPAGLPDGVG 2fhqA 45 :STIWMSTGADSLKTIDFLSNPKAGLCFQEKGDSVALMGEVEVVTDEKLKQELW T0370 110 :GFDPRRLTTSYLYFRISPRRVQAW 2fhqA 104 :HFPGGPTDPGYVLLKFTANHATYW T0370 146 :RDGEWLVTD 2fhqA 128 :IEGTFIHKK Number of specific fragments extracted= 6 number of extra gaps= 0 total=368 Number of alignments=46 # 2fhqA read from 2fhqA/merged-good-all-a2m # found chain 2fhqA in template set Warning: unaligning (T0370)T3 because first residue in template chain is (2fhqA)T3 T0370 4 :PPA 2fhqA 4 :KTM T0370 13 :IQDTLNRLE 2fhqA 7 :KEKAVELLQ T0370 23 :DVD 2fhqA 16 :KCE T0370 26 :AWVSTAGAD 2fhqA 20 :VTLASVNKE T0370 36 :GAPYLVPLSY 2fhqA 29 :GYPRPVPMSK T0370 46 :LWDG 2fhqA 40 :AAEG T0370 50 :ETFLVATPAASPTGRNLSETGRVRLGIGPTRDLVLVEGTALPLEPAGLPDGVG 2fhqA 45 :STIWMSTGADSLKTIDFLSNPKAGLCFQEKGDSVALMGEVEVVTDEKLKQELW T0370 103 :DTFAEKTGFD 2fhqA 99 :DWFIEHFPGG T0370 115 :RLTTSYLYFRISPRRVQAWREANELSG 2fhqA 109 :PTDPGYVLLKFTANHATYWIEGTFIHK Number of specific fragments extracted= 9 number of extra gaps= 0 total=377 Number of alignments=47 # 2fhqA read from 2fhqA/merged-good-all-a2m # found chain 2fhqA in template set Warning: unaligning (T0370)K10 because first residue in template chain is (2fhqA)T3 T0370 11 :QRIQDTLNRLELDVDAWVSTAGADGGAPYLVPLS 2fhqA 4 :KTMKEKAVELLQKCEVVTLASVNKEGYPRPVPMS T0370 45 :YLWDG 2fhqA 39 :IAAEG T0370 50 :ETFLVATPAASPTGRNLSETGRVRLGIGPTRDLVLVEGTALPLEPAGLPDG 2fhqA 45 :STIWMSTGADSLKTIDFLSNPKAGLCFQEKGDSVALMGEVEVVTDEKLKQE T0370 108 :KT 2fhqA 96 :LW T0370 110 :GFDPRRLTTSYLYFRISPRRVQAWR 2fhqA 104 :HFPGGPTDPGYVLLKFTANHATYWI Number of specific fragments extracted= 5 number of extra gaps= 0 total=382 Number of alignments=48 # 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 # T0370 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 (T0370)T3 because first residue in template chain is (1rfeA)T3 Warning: unaligning (T0370)L43 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rfeA)W43 Warning: unaligning (T0370)S44 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rfeA)W43 Warning: unaligning (T0370)A89 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rfeA)E94 Warning: unaligning (T0370)L90 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rfeA)E94 Warning: unaligning (T0370)L116 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rfeA)K122 T0370 4 :PPARTAKQRIQDTLNRLELDVDAWVSTAGAD 1rfeA 4 :KQRADIVMSEAEIADFVNSSRTGTLATIGPD T0370 36 :GAPYLVP 1rfeA 35 :GQPHLTA T0370 45 :YLWDGETFLVATPAASPTGRNLSETGRVRLGIGP 1rfeA 44 :YAVIDGEIWLETKAKSQKAVNLRRDPRVSFLLED T0370 79 :TRD 1rfeA 80 :TYD T0370 82 :LVLVEGT 1rfeA 86 :GVSFEGV T0370 91 :PLEPAGLPDGVGDTFAEKTGFDPRR 1rfeA 95 :IVEEPEALHRVGVSVWERYTGPYTD T0370 117 :TTSYLYFRISPRRVQAWREAN 1rfeA 129 :MNKRVGVRIVARRTRSWDHRK T0370 138 :ELSGRELMRDG 1rfeA 151 :GLPHMSVGGST Number of specific fragments extracted= 8 number of extra gaps= 2 total=390 Number of alignments=49 # 1rfeA read from 1rfeA/merged-good-all-a2m # found chain 1rfeA in template set Warning: unaligning (T0370)L43 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rfeA)W43 Warning: unaligning (T0370)S44 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rfeA)W43 Warning: unaligning (T0370)A89 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rfeA)E94 Warning: unaligning (T0370)L90 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rfeA)E94 T0370 14 :QDTLNRLE 1rfeA 14 :AEIADFVN T0370 23 :DVD 1rfeA 22 :SSR T0370 26 :AWVSTAGAD 1rfeA 26 :GTLATIGPD T0370 36 :GAPYLVP 1rfeA 35 :GQPHLTA T0370 45 :YLWDGETFLVATPAASPTGRNLSETGRVRLGIG 1rfeA 44 :YAVIDGEIWLETKAKSQKAVNLRRDPRVSFLLE T0370 78 :PTRD 1rfeA 79 :DTYD T0370 83 :VLVEGT 1rfeA 87 :VSFEGV T0370 91 :PLEPAGLPDGVGDTFAEKTGFDPR 1rfeA 95 :IVEEPEALHRVGVSVWERYTGPYT T0370 115 :RLTTSYLYFRISPRRVQAWREA 1rfeA 127 :QMMNKRVGVRIVARRTRSWDHR T0370 137 :NEL 1rfeA 151 :GLP Number of specific fragments extracted= 10 number of extra gaps= 2 total=400 Number of alignments=50 # 1rfeA read from 1rfeA/merged-good-all-a2m # found chain 1rfeA in template set Warning: unaligning (T0370)P4 because first residue in template chain is (1rfeA)T3 Warning: unaligning (T0370)L43 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rfeA)W43 Warning: unaligning (T0370)S44 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rfeA)W43 Warning: unaligning (T0370)A89 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rfeA)E94 Warning: unaligning (T0370)L90 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rfeA)E94 Warning: unaligning (T0370)L116 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rfeA)K122 T0370 5 :PARTAKQRIQDTLNRLELDVDAWVSTAGADGGAPYLVP 1rfeA 4 :KQRADIVMSEAEIADFVNSSRTGTLATIGPDGQPHLTA T0370 45 :YLWDGETFLVATPAASPTGRNLSETGRVRLGIGPTRD 1rfeA 44 :YAVIDGEIWLETKAKSQKAVNLRRDPRVSFLLEDGDT T0370 83 :VLVEGT 1rfeA 87 :VSFEGV T0370 91 :PLEPAGLPDGVGDTFAEKTGFDPRR 1rfeA 95 :IVEEPEALHRVGVSVWERYTGPYTD T0370 118 :TSYLYFRISPRRVQAWREA 1rfeA 130 :NKRVGVRIVARRTRSWDHR Number of specific fragments extracted= 5 number of extra gaps= 2 total=405 Number of alignments=51 # 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:# T0370 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 T0370 2 :TTPPARTAKQRIQ 1ci0A 25 :TLNEKQLTDDPID T0370 15 :DTLNRLELDV 1ci0A 41 :KWFNEAKEDP T0370 25 :DAWVSTAGADGGAPYLVPLSYL 1ci0A 57 :AITFSSAELPSGRVSSRILLFK T0370 47 :WDGETFLVATPAA 1ci0A 80 :LDHRGFTIYSNWG T0370 60 :SPTGRNLSETGRVRLGIG 1ci0A 94 :SRKAHDIATNPNAAIVFF T0370 78 :PTRDLVLVEGTALPLEPAGLPDGVGD 1ci0A 114 :DLQRQVRVEGITEHVNRETSERYFKT T0370 104 :TFAEKT 1ci0A 169 :KNTERF T0370 110 :GFDPRRLTTSYLYFRISPRRVQAWREAN 1ci0A 176 :DAEDIPCPDYWGGLRIVPLEIEFWQGRP T0370 138 :ELSGRELMR 1ci0A 205 :RLHDRFVYR T0370 147 :DGEWLVT 1ci0A 218 :NDPWKVV Number of specific fragments extracted= 10 number of extra gaps= 0 total=415 Number of alignments=52 # 1ci0A read from 1ci0A/merged-good-all-a2m # found chain 1ci0A in template set T0370 1 :MTTPPARTAKQRIQDTLNR 1ci0A 31 :LTDDPIDLFTKWFNEAKED T0370 20 :LE 1ci0A 52 :ET T0370 23 :DVD 1ci0A 54 :LPE T0370 26 :AWVSTAGADGGAPYLVPLSY 1ci0A 58 :ITFSSAELPSGRVSSRILLF T0370 46 :LWDGETFLVATPAA 1ci0A 79 :ELDHRGFTIYSNWG T0370 60 :SPTGRNLSETGRVRLGIG 1ci0A 94 :SRKAHDIATNPNAAIVFF T0370 78 :PTRDLVLVEGTALPLEPAG 1ci0A 114 :DLQRQVRVEGITEHVNRET T0370 97 :LPDGVGDTFAEKTG 1ci0A 162 :ELDELTQKNTERFK T0370 111 :FDPRRLTTSYLYFRISPRRVQAWREA 1ci0A 177 :AEDIPCPDYWGGLRIVPLEIEFWQGR T0370 137 :NELSGRELMR 1ci0A 204 :SRLHDRFVYR T0370 147 :DGEW 1ci0A 218 :NDPW T0370 151 :L 1ci0A 223 :V T0370 152 :VTD 1ci0A 226 :LAP Number of specific fragments extracted= 13 number of extra gaps= 0 total=428 Number of alignments=53 # 1ci0A read from 1ci0A/merged-good-all-a2m # found chain 1ci0A in template set T0370 7 :RTAKQRIQDTLNRLELDVD 1ci0A 33 :DDPIDLFTKWFNEAKEDPR T0370 26 :AWVSTAGA 1ci0A 57 :AITFSSAE T0370 34 :DGGAPYLVPLSYL 1ci0A 66 :PSGRVSSRILLFK T0370 47 :WDGETFLVA 1ci0A 80 :LDHRGFTIY T0370 56 :TPAASPTGRNLSETGRVRLGIGPTRD 1ci0A 90 :NWGTSRKAHDIATNPNAAIVFFWKDL T0370 82 :LVLVEGTALP 1ci0A 118 :QVRVEGITEH T0370 92 :LEPAGLPDGVGDTFAEKT 1ci0A 157 :IKNREELDELTQKNTERF T0370 110 :GFDPRRLTTSYLYFRISPRRVQAWREA 1ci0A 176 :DAEDIPCPDYWGGLRIVPLEIEFWQGR Number of specific fragments extracted= 8 number of extra gaps= 0 total=436 Number of alignments=54 # 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 # T0370 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 (T0370)R134 because of BadResidue code BAD_PEPTIDE in next template residue (2furA)R164 Warning: unaligning (T0370)E135 because of BadResidue code BAD_PEPTIDE at template residue (2furA)R164 T0370 12 :RIQDTLNRLELDVDAWVSTAGAD 2furA 20 :SDEDLVAMLDRNFTCTVSFIDGG T0370 37 :APYLVPLSYLWDGETFLVATPAASPTGRNLSETGRVRLGIGP 2furA 43 :IPYAIPMMLASEGKTIYLHGSMKSRIYGILKTGQLIAISLLE T0370 83 :VLVEGTALPLEPAGLPDGVGDTFAEKT 2furA 104 :ALIFGRPYEIDDTEKKIEVFRLLTEKL T0370 110 :GFDPRRLTTS 2furA 133 :GRWDNSIKPS T0370 120 :YLYFRISPRRVQAW 2furA 149 :VFVFAVKPETFSMK T0370 136 :ANELSGR 2furA 165 :TGPPHDT Number of specific fragments extracted= 6 number of extra gaps= 1 total=442 Number of alignments=55 # 2furA read from 2furA/merged-good-all-a2m # found chain 2furA in template set Warning: unaligning (T0370)R134 because of BadResidue code BAD_PEPTIDE in next template residue (2furA)R164 Warning: unaligning (T0370)E135 because of BadResidue code BAD_PEPTIDE at template residue (2furA)R164 T0370 14 :QDTLNRLE 2furA 22 :EDLVAMLD T0370 23 :DVD 2furA 30 :RNF T0370 26 :AWVSTAGAD 2furA 34 :CTVSFIDGG T0370 37 :APYLVPLSYLWDGETFLVATPAASPTGRNLSETGRVRLGIG 2furA 43 :IPYAIPMMLASEGKTIYLHGSMKSRIYGILKTGQLIAISLL T0370 78 :PTRDL 2furA 93 :EIKNN T0370 83 :VLVEGTALPLEPAGLPDGVGDTFAEKTG 2furA 104 :ALIFGRPYEIDDTEKKIEVFRLLTEKLV T0370 111 :FDPRRLTT 2furA 135 :WDNSIKPS T0370 119 :SYLYFRISPRRVQAW 2furA 148 :GVFVFAVKPETFSMK T0370 136 :ANELSG 2furA 165 :TGPPHD Number of specific fragments extracted= 9 number of extra gaps= 1 total=451 Number of alignments=56 # 2furA read from 2furA/merged-good-all-a2m # found chain 2furA in template set Warning: unaligning (T0370)A9 because first residue in template chain is (2furA)R16 T0370 10 :KQRIQDTLNRLELDVDAWVSTAGA 2furA 17 :ASYSDEDLVAMLDRNFTCTVSFID T0370 35 :GGAPYLVPLSYLWDGETFLVATPAASPTGRNLSETGRVRLGIGPTRD 2furA 41 :GGIPYAIPMMLASEGKTIYLHGSMKSRIYGILKTGQLIAISLLEING T0370 83 :VLVEGTALPLEPAGLPDGVGDTFAEKTGFDPRRLT 2furA 104 :ALIFGRPYEIDDTEKKIEVFRLLTEKLVKGRWDNS T0370 118 :TSYLYFRISPRRVQA 2furA 147 :NGVFVFAVKPETFSM Number of specific fragments extracted= 4 number of extra gaps= 0 total=455 Number of alignments=57 # 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 # T0370 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 (T0370)L116 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2arzA)V119 Warning: unaligning (T0370)T117 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2arzA)V119 Warning: unaligning (T0370)S119 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2arzA)F122 Warning: unaligning (T0370)Y120 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2arzA)F122 T0370 10 :KQRIQDTLNRLELDVDAWVSTAGAD 2arzA 3 :VEAAKNARELLLKEYRAVLSTHSKK T0370 35 :GGAPYLVPLSYLW 2arzA 29 :PGFPFGSVVPYCL T0370 48 :DGETFLVATPAASPTGRNLSETGRVRLGIGP 2arzA 43 :AEGRPLILISRIAQHTHNLQADPRCSMLVGE T0370 82 :LVLVEGTALPLE 2arzA 84 :RLTLLAEARQLA T0370 95 :AGLPDGVGDTFAEKTGF 2arzA 96 :EEEVAAAAERYYRYFPE T0370 112 :DPRR 2arzA 114 :ADYH T0370 118 :T 2arzA 120 :H T0370 121 :LYFRISPRRVQAWREANELSG 2arzA 123 :DFWVLQPVQWRFIGGFGAIHW Number of specific fragments extracted= 8 number of extra gaps= 2 total=463 Number of alignments=58 # 2arzA read from 2arzA/merged-good-all-a2m # found chain 2arzA in template set Warning: unaligning (T0370)L116 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2arzA)V119 Warning: unaligning (T0370)T117 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2arzA)V119 Warning: unaligning (T0370)S119 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2arzA)F122 Warning: unaligning (T0370)Y120 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2arzA)F122 T0370 10 :KQRIQDTLNR 2arzA 3 :VEAAKNAREL T0370 20 :LE 2arzA 14 :LK T0370 23 :DVDAWVSTAGAD 2arzA 16 :EYRAVLSTHSKK T0370 35 :GGAPYLVPLSYLWD 2arzA 29 :PGFPFGSVVPYCLD T0370 49 :GETFLVATPAASPTGRNLSETGRVRLGIG 2arzA 44 :EGRPLILISRIAQHTHNLQADPRCSMLVG T0370 78 :PTRD 2arzA 78 :DIQA T0370 82 :LVLVEGTALPLEPAG 2arzA 84 :RLTLLAEARQLAEEE T0370 98 :PDGVGDTFAEKTG 2arzA 99 :VAAAAERYYRYFP T0370 111 :FDPRR 2arzA 113 :SADYH T0370 118 :T 2arzA 120 :H T0370 121 :LYFRISPRRVQAWREANELSGRE 2arzA 123 :DFWVLQPVQWRFIGGFGAIHWLA Number of specific fragments extracted= 11 number of extra gaps= 2 total=474 Number of alignments=59 # 2arzA read from 2arzA/merged-good-all-a2m # found chain 2arzA in template set Warning: unaligning (T0370)S119 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2arzA)F122 Warning: unaligning (T0370)Y120 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2arzA)F122 T0370 14 :QDTLNRLEL 2arzA 3 :VEAAKNARE T0370 23 :DVDAWVSTAGAD 2arzA 15 :KEYRAVLSTHSK T0370 35 :GGAPYLVPLSYLWDGE 2arzA 29 :PGFPFGSVVPYCLDAE T0370 51 :TFLVATPAASPTGRNLSETGRVRLGIGPTRD 2arzA 46 :RPLILISRIAQHTHNLQADPRCSMLVGERGA T0370 82 :LVLVEGTALPLEPA 2arzA 84 :RLTLLAEARQLAEE T0370 97 :LPDGVGDTFAEKT 2arzA 98 :EVAAAAERYYRYF T0370 111 :FDPRRLT 2arzA 111 :PESADYH T0370 118 :T 2arzA 120 :H T0370 121 :LYFRISPRRVQAWR 2arzA 123 :DFWVLQPVQWRFIG Number of specific fragments extracted= 9 number of extra gaps= 1 total=483 Number of alignments=60 # 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 # T0370 read from 1dnlA/merged-good-all-a2m # 1dnlA read from 1dnlA/merged-good-all-a2m # found chain 1dnlA in training set T0370 7 :RTAKQRIQDTLNR 1dnlA 33 :TLFERWLSQACEA T0370 20 :LELDVDAWVSTAGAD 1dnlA 47 :LADPTAMVVATVDEH T0370 36 :GAPYLVPLSY 1dnlA 62 :GQPYQRIVLL T0370 46 :LWDGETFLVATPAASPTGRNLSETGRVRLGIGP 1dnlA 73 :HYDEKGMVFYTNLGSRKAHQIENNPRVSLLFPW T0370 79 :TRDLVLVEGTALPLEPAGLPDGVGD 1dnlA 108 :LERQVMVIGKAERLSTLEVMKYFHS T0370 104 :TFAEKTGFDPRRLTTSYLYFRISPRRVQAWREAN 1dnlA 162 :ELKQKFQQGEVPLPSFWGGFRVSLEQIEFWQGGE T0370 138 :ELSGRELM 1dnlA 197 :RLHDRFLY T0370 147 :DGEWLVT 1dnlA 208 :NDAWKID Number of specific fragments extracted= 8 number of extra gaps= 0 total=491 Number of alignments=61 # 1dnlA read from 1dnlA/merged-good-all-a2m # found chain 1dnlA in training set T0370 1 :MTTPPARTAKQRIQDTLNR 1dnlA 27 :LPADPLTLFERWLSQACEA T0370 20 :LE 1dnlA 47 :LA T0370 23 :DVD 1dnlA 49 :DPT T0370 26 :AWVSTAGAD 1dnlA 53 :MVVATVDEH T0370 36 :GAPYLVPLSY 1dnlA 62 :GQPYQRIVLL T0370 46 :LWDGETFLVATPAASPTGRNLSETGRVRLGIG 1dnlA 73 :HYDEKGMVFYTNLGSRKAHQIENNPRVSLLFP T0370 78 :PTRDLVLVEGTALPLEPAG 1dnlA 107 :TLERQVMVIGKAERLSTLE T0370 97 :LPDGVGDTFAEKTGFDPRRLTTSYLYFRISPRRVQAWREA 1dnlA 155 :ILESKFLELKQKFQQGEVPLPSFWGGFRVSLEQIEFWQGG T0370 137 :NELSGRELMR 1dnlA 196 :HRLHDRFLYQ T0370 147 :DGEW 1dnlA 208 :NDAW T0370 151 :L 1dnlA 213 :I T0370 152 :VTD 1dnlA 216 :LAP Number of specific fragments extracted= 12 number of extra gaps= 0 total=503 Number of alignments=62 # 1dnlA read from 1dnlA/merged-good-all-a2m # found chain 1dnlA in training set T0370 11 :QRIQDTLNRLELD 1dnlA 33 :TLFERWLSQACEA T0370 24 :VDAWVSTAGADGGAPYLVPLSY 1dnlA 50 :PTAMVVATVDEHGQPYQRIVLL T0370 46 :LWDGETFLVATPAASPTGRNLSETGRVRLGIG 1dnlA 73 :HYDEKGMVFYTNLGSRKAHQIENNPRVSLLFP T0370 78 :PTRDLVLVEGTALP 1dnlA 107 :TLERQVMVIGKAER T0370 92 :LEPAGLPDGVGDTFAEKTGFDPRRLTTSYLYFRISPRRVQAWRE 1dnlA 150 :ISARGILESKFLELKQKFQQGEVPLPSFWGGFRVSLEQIEFWQG Number of specific fragments extracted= 5 number of extra gaps= 0 total=508 Number of alignments=63 # command:# PrintAlignmentsContacts allconstraints.under Using radius: 8.0000 NUMB_ALIGNS: 63 Done printing distance constraints # command: