# 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/T0380/ # command:# Making conformation for sequence T0380 numbered 1 through 145 Created new target T0380 from T0380.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0380/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0380//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0380/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0380//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0380/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0380/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0380/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 # T0380 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 T0380 6 :FLIESNEL 1g79A 38 :WLSQACEA # choosing archetypes in rotamer library T0380 14 :VESSKIVMVGTNGENGYPNIKAMMRLKHDGLKKF 1g79A 47 :LADPTAMVVATVDEHGQPYQRIVLLKHYDEKGMV T0380 49 :LSTNTSTRMVERLKKNNKICLYFVDDNKFAGLMLVGTIEILHDRASKEMLWTDGCEIYYP 1g79A 81 :FYTNLGSRKAHQIENNPRVSLLFPWHTLERQVMVIGKAERLSTLEVMKYFHSRPRDSQIG T0380 109 :LGIDDPDYTALCFTAEWGNYY 1g79A 171 :EVPLPSFWGGFRVSLEQIEFW T0380 130 :RHLKNITFKIDE 1g79A 197 :RLHDRFLYQREN Number of specific fragments extracted= 5 number of extra gaps= 0 total=5 Number of alignments=1 # 1g79A read from 1g79A/merged-good-all-a2m # found chain 1g79A in template set T0380 5 :KFLIESNEL 1g79A 37 :RWLSQACEA T0380 14 :VESSKIVMVGTNGENGYPNIKAMMRLKHDGLK 1g79A 47 :LADPTAMVVATVDEHGQPYQRIVLLKHYDEKG T0380 47 :FWLSTNTSTRMVERLKKNNKICLYFVDDNKFAGLMLVGTIEILH 1g79A 79 :MVFYTNLGSRKAHQIENNPRVSLLFPWHTLERQVMVIGKAERLS T0380 92 :RASKEMLWTDGCEIYYP 1g79A 123 :TLEVMKYFHSRPRDSQI T0380 109 :LGIDDPDYTALCFTAEWGNYYRHLKNITFKIDEI 1g79A 171 :EVPLPSFWGGFRVSLEQIEFWQGGEHRLHDRFLY Number of specific fragments extracted= 5 number of extra gaps= 0 total=10 Number of alignments=2 # 1g79A read from 1g79A/merged-good-all-a2m # found chain 1g79A in template set T0380 5 :KFLIESNEL 1g79A 37 :RWLSQACEA T0380 14 :VESSKIVMVGTNGENGYPNIKAM 1g79A 47 :LADPTAMVVATVDEHGQPYQRIV T0380 38 :RLKHDGLKKFWLSTNTSTRMVERLKKNNKICLYFVDDNKFAGLMLVGTIEILH 1g79A 70 :LLKHYDEKGMVFYTNLGSRKAHQIENNPRVSLLFPWHTLERQVMVIGKAERLS T0380 91 :DRASKEMLWTDGCEIYYPLGIDDPD 1g79A 152 :ARGILESKFLELKQKFQQGEVPLPS T0380 116 :YTALCFTAEWGNYYRHLK 1g79A 178 :WGGFRVSLEQIEFWQGGE Number of specific fragments extracted= 5 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 # T0380 read from 1flmA/merged-good-all-a2m # 1flmA read from 1flmA/merged-good-all-a2m # found chain 1flmA in training set T0380 1 :MIDEKFL 1flmA 1 :MLPGTFF T0380 12 :ELVESSKIVMVGTNGENG 1flmA 8 :EVLKNEGVVAIATQGEDG T0380 31 :PNIKAMM 1flmA 26 :PHLVNTW T0380 38 :RLKHDGLKKFWLSTNTSTRMVERLKKNNKICLYFV 1flmA 35 :YLKVLDGNRIVVPVGGMHKTEANVARDERVLMTLG T0380 73 :DDNKFA 1flmA 75 :GRNGPG T0380 79 :GLMLVGTIEILHDRASKEMLW 1flmA 82 :GFLIRGSAAFRTDGPEFEAIA T0380 112 :DDPDY 1flmA 103 :RFKWA T0380 117 :TALCFTAEWGNY 1flmA 109 :AALVITVVSAEQ Number of specific fragments extracted= 8 number of extra gaps= 0 total=23 Number of alignments=4 # 1flmA read from 1flmA/merged-good-all-a2m # found chain 1flmA in training set Warning: unaligning (T0380)K5 because first residue in template chain is (1flmA)M1 T0380 6 :FLIESNELVESSKIVMVGTNGENG 1flmA 2 :LPGTFFEVLKNEGVVAIATQGEDG T0380 31 :PNIKAMM 1flmA 26 :PHLVNTW T0380 38 :RLKHDGLKKFWLSTNTSTRMVERLKKNNKICLYFV 1flmA 35 :YLKVLDGNRIVVPVGGMHKTEANVARDERVLMTLG T0380 73 :DDNKFAGLMLVGTIEILHDRASKEMLW 1flmA 76 :RNGPGTGFLIRGSAAFRTDGPEFEAIA T0380 101 :DG 1flmA 103 :RF T0380 109 :LGID 1flmA 105 :KWAR T0380 117 :TALCFTAEWGNY 1flmA 109 :AALVITVVSAEQ Number of specific fragments extracted= 7 number of extra gaps= 0 total=30 Number of alignments=5 # 1flmA read from 1flmA/merged-good-all-a2m # found chain 1flmA in training set T0380 9 :ESNELVESSKIVMVGTNGENG 1flmA 5 :TFFEVLKNEGVVAIATQGEDG T0380 31 :PNIKAMM 1flmA 26 :PHLVNTW T0380 38 :RLKHDGLKKFWLSTNTSTRMVERLKKNNKICLYFV 1flmA 35 :YLKVLDGNRIVVPVGGMHKTEANVARDERVLMTLG T0380 73 :DDNKFAGLMLVGTIEILHDRASKEMLWTD 1flmA 76 :RNGPGTGFLIRGSAAFRTDGPEFEAIARF T0380 109 :LGID 1flmA 105 :KWAR T0380 117 :TALCFTAEWGNY 1flmA 109 :AALVITVVSAEQ Number of specific fragments extracted= 6 number of extra gaps= 0 total=36 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 # T0380 read from 1w3oA/merged-good-all-a2m # 1w3oA read from 1w3oA/merged-good-all-a2m # found chain 1w3oA in training set Warning: unaligning (T0380)R130 because of BadResidue code BAD_PEPTIDE at template residue (1w3oA)N175 T0380 1 :MIDEKFL 1w3oA 21 :RQSDEWI T0380 11 :NELVESSKIVMVGTN 1w3oA 28 :RELLLRGTIARVATL T0380 26 :GENGY 1w3oA 45 :GEDGA T0380 31 :PNIKAMMRLKHDGLKKFWLSTNTST 1w3oA 52 :PFITPLAYAYRPEQGDLVYHTNVVG T0380 64 :NN 1w3oA 81 :NA T0380 66 :KICLYFVDDNKFA 1w3oA 87 :PATLEVSEIGQFL T0380 79 :GLMLVGTIEILHDRASKEMLWT 1w3oA 113 :SVMVFGTARVLAGEDARAALTT T0380 102 :GCEIYYPLGIDDP 1w3oA 135 :LSERVFPGLKVGE T0380 115 :DYTALCFTAEWGNYY 1w3oA 159 :RTSVYSLSIDRWSGK T0380 131 :HLK 1w3oA 176 :WAE Number of specific fragments extracted= 10 number of extra gaps= 1 total=46 Number of alignments=7 # 1w3oA read from 1w3oA/merged-good-all-a2m # found chain 1w3oA in training set Warning: unaligning (T0380)R130 because of BadResidue code BAD_PEPTIDE in next template residue (1w3oA)N175 Warning: unaligning (T0380)H131 because of BadResidue code BAD_PEPTIDE at template residue (1w3oA)N175 T0380 7 :LIESNELVESSKIVMVGT 1w3oA 24 :DEWIRELLLRGTIARVAT T0380 25 :NGENGY 1w3oA 44 :QGEDGA T0380 31 :PNIKAMMRLKHDGLKKFWLSTNTSTR 1w3oA 52 :PFITPLAYAYRPEQGDLVYHTNVVGR T0380 64 :NN 1w3oA 81 :NA T0380 66 :KICLYFVDDN 1w3oA 87 :PATLEVSEIG T0380 76 :KFAGLMLVGTIEILH 1w3oA 110 :QYRSVMVFGTARVLA T0380 92 :RASKEMLWTDGCEIYYPLGIDDP 1w3oA 125 :GEDARAALTTLSERVFPGLKVGE T0380 115 :DYTALCFTAEWGNYY 1w3oA 159 :RTSVYSLSIDRWSGK T0380 132 :LKNI 1w3oA 176 :WAEQ Number of specific fragments extracted= 9 number of extra gaps= 1 total=55 Number of alignments=8 # 1w3oA read from 1w3oA/merged-good-all-a2m # found chain 1w3oA in training set Warning: unaligning (T0380)R130 because of BadResidue code BAD_PEPTIDE in next template residue (1w3oA)N175 Warning: unaligning (T0380)H131 because of BadResidue code BAD_PEPTIDE at template residue (1w3oA)N175 T0380 6 :F 1w3oA 26 :W T0380 10 :SNELVESSKIVMVGT 1w3oA 27 :IRELLLRGTIARVAT T0380 25 :NGENGY 1w3oA 44 :QGEDGA T0380 31 :PNIKAMMRLKHDGLKKFWLSTNTSTR 1w3oA 52 :PFITPLAYAYRPEQGDLVYHTNVVGR T0380 64 :NNK 1w3oA 81 :NAG T0380 67 :ICLYFVDDNKFA 1w3oA 88 :ATLEVSEIGQFL T0380 79 :GLMLVGTIEILHDRASKEML 1w3oA 113 :SVMVFGTARVLAGEDARAAL T0380 100 :TDGCEIYYPL 1w3oA 133 :TTLSERVFPG T0380 110 :GIDDP 1w3oA 146 :GETTR T0380 115 :DYTALCFTAEWGNYY 1w3oA 159 :RTSVYSLSIDRWSGK T0380 132 :L 1w3oA 176 :W Number of specific fragments extracted= 11 number of extra gaps= 1 total=66 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 # T0380 read from 1vl7A/merged-good-all-a2m # 1vl7A read from 1vl7A/merged-good-all-a2m # found chain 1vl7A in training set T0380 11 :NELVESSKIVMVGTNGENGYPNIKAMMRLKH 1vl7A 12 :AGFIQEFQSAIISTISEQGIPNGSYAPFVID T0380 43 :GLKKFWLSTNTSTRMVERLKKNNKICLYFVDDNKFA 1vl7A 43 :DAKNIYIYVSGLAVHTKNIEANPLVNVLFVDDEAKT T0380 79 :GLMLVGTIEILH 1vl7A 86 :RLSFDCTATLIE T0380 91 :DRASKEMLWTDGCEIYYP 1vl7A 99 :ESQKWNQVVDQFQERFGQ T0380 115 :DYTALCFTAEWGNYY 1vl7A 126 :DFRIFQLTPKEGRFV T0380 130 :RHL 1vl7A 142 :GFG Number of specific fragments extracted= 6 number of extra gaps= 0 total=72 Number of alignments=10 # 1vl7A read from 1vl7A/merged-good-all-a2m # found chain 1vl7A in training set T0380 11 :NELVESSKIVMVGTNGENGYPNIKAMMRLKHDGLK 1vl7A 12 :AGFIQEFQSAIISTISEQGIPNGSYAPFVIDDAKN T0380 47 :FWLSTNTSTRMVERLKKNNKICLYFVDDN 1vl7A 47 :IYIYVSGLAVHTKNIEANPLVNVLFVDDE T0380 76 :KFAGLMLVGTIEILH 1vl7A 83 :ARRRLSFDCTATLIE T0380 91 :DRASKEMLWTDGCEIY 1vl7A 99 :ESQKWNQVVDQFQERF T0380 114 :P 1vl7A 115 :G T0380 115 :DYTALCFTAEWGNYYRHLK 1vl7A 126 :DFRIFQLTPKEGRFVIGFG Number of specific fragments extracted= 6 number of extra gaps= 0 total=78 Number of alignments=11 # 1vl7A read from 1vl7A/merged-good-all-a2m # found chain 1vl7A in training set T0380 11 :NELVESSKIVMVGTNGENGYPNIKAM 1vl7A 12 :AGFIQEFQSAIISTISEQGIPNGSYA T0380 38 :RLKHDGLKKFWLSTNTSTRMVERLKKNNKICLYFVDDNKFA 1vl7A 38 :PFVIDDAKNIYIYVSGLAVHTKNIEANPLVNVLFVDDEAKT T0380 79 :GLMLVGTIEILHDR 1vl7A 86 :RLSFDCTATLIERE T0380 93 :ASKEMLWTDGCEIYYPL 1vl7A 108 :DQFQERFGQIIEVLRGL T0380 114 :PDYTALCFTAEWGNYYRHLK 1vl7A 125 :ADFRIFQLTPKEGRFVIGFG Number of specific fragments extracted= 5 number of extra gaps= 0 total=83 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 # T0380 read from 1ty9A/merged-good-all-a2m # 1ty9A read from 1ty9A/merged-good-all-a2m # found chain 1ty9A in training set Warning: unaligning (T0380)K40 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ty9A)I80 Warning: unaligning (T0380)H41 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ty9A)I80 Warning: unaligning (T0380)T122 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ty9A)L189 Warning: unaligning (T0380)A123 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ty9A)L189 T0380 6 :FLIESNEL 1ty9A 44 :WLERARRV T0380 14 :VESSKIVMVGTNGENGYPNIKAMMRL 1ty9A 53 :IREPRALALATADSQGRPSTRIVVIS T0380 42 :DGLK 1ty9A 81 :SDAG T0380 47 :FWLSTNTSTRMVERLKKNNKICLYFVDDNKFAGLMLVGTIEILHDRASKEMLWTDGCEIYYP 1ty9A 85 :VVFSTHAGSQKGRELLHNPWASGVLYWRETSQQIILNGQAVRLPNAKADDAWLKRPYATHPM T0380 109 :LGIDDPDYTALCF 1ty9A 175 :PLPRPEGYCVFEL T0380 124 :EWGNYY 1ty9A 190 :ESLEFW T0380 130 :RHLKNITFKIDE 1ty9A 201 :RLHERLRYDRSD T0380 142 :I 1ty9A 214 :G Number of specific fragments extracted= 8 number of extra gaps= 2 total=91 Number of alignments=13 # 1ty9A read from 1ty9A/merged-good-all-a2m # found chain 1ty9A in training set Warning: unaligning (T0380)K40 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ty9A)I80 Warning: unaligning (T0380)H41 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ty9A)I80 Warning: unaligning (T0380)T122 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ty9A)L189 Warning: unaligning (T0380)A123 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ty9A)L189 T0380 6 :FLIESNEL 1ty9A 44 :WLERARRV T0380 14 :VESSKIVMVGTNGENGYPNIKAMMRL 1ty9A 53 :IREPRALALATADSQGRPSTRIVVIS T0380 42 :DGLK 1ty9A 81 :SDAG T0380 47 :FWLSTNTSTRMVERLKKNNKICLYFVDDNKFAGLMLVGTIEILH 1ty9A 85 :VVFSTHAGSQKGRELLHNPWASGVLYWRETSQQIILNGQAVRLP T0380 92 :RASKEMLWTDGCEIYYP 1ty9A 129 :NAKADDAWLKRPYATHP T0380 109 :LGIDDPDYTALCF 1ty9A 175 :PLPRPEGYCVFEL T0380 124 :EWGNYYRHLKNITFKIDEI 1ty9A 190 :ESLEFWGNGQERLHERLRY Number of specific fragments extracted= 7 number of extra gaps= 2 total=98 Number of alignments=14 # 1ty9A read from 1ty9A/merged-good-all-a2m # found chain 1ty9A in training set Warning: unaligning (T0380)H41 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ty9A)I80 Warning: unaligning (T0380)D42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ty9A)I80 Warning: unaligning (T0380)P108 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ty9A)G174 Warning: unaligning (T0380)L109 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ty9A)G174 Warning: unaligning (T0380)T122 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ty9A)L189 Warning: unaligning (T0380)A123 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ty9A)L189 T0380 6 :FLIESNEL 1ty9A 44 :WLERARRV T0380 14 :VESSKIVMVGTNGENGYPNIKAM 1ty9A 53 :IREPRALALATADSQGRPSTRIV T0380 38 :RLK 1ty9A 76 :VIS T0380 43 :GLKKFWLSTNTSTRMVERLKKNNKICLYFVDDNKFAGLMLVGTIEILHDRASKEMLWTDGCEIY 1ty9A 81 :SDAGVVFSTHAGSQKGRELLHNPWASGVLYWRETSQQIILNGQAVRLPNAKADDAWLKRPYATH T0380 107 :Y 1ty9A 172 :L T0380 110 :GIDDP 1ty9A 175 :PLPRP T0380 115 :DYTALCF 1ty9A 181 :GYCVFEL T0380 124 :EWGNYYRHLK 1ty9A 190 :ESLEFWGNGQ Number of specific fragments extracted= 8 number of extra gaps= 3 total=106 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 # T0380 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 T0380 17 :SKIVMVGTNG 1xhnA 30 :SDWGALATIS T0380 27 :ENGYPNIKAMMRLKHDGL 1xhnA 44 :VRGRPFADVLSLSDGPPG T0380 45 :KKFWLSTNTSTRMVERLKKNNKICLYFV 1xhnA 65 :GVPYFYLSPLQLSVSNLQENPYATLTMT T0380 73 :DDNKFA 1xhnA 105 :DPQSPL T0380 79 :GLMLVGTIEILH 1xhnA 113 :HIMLSGTVTKVN T0380 92 :RASKEMLWTDGCEIYYP 1xhnA 125 :ETEMDIAKHSLFIRHPE T0380 109 :LGIDDPDYTALCFTAEWGNYY 1xhnA 144 :TWPSSHNWFFAKLNITNIWVL T0380 130 :RHLKNITF 1xhnA 166 :YFGGPKIV Number of specific fragments extracted= 8 number of extra gaps= 0 total=114 Number of alignments=16 # 1xhnA read from 1xhnA/merged-good-all-a2m # found chain 1xhnA in template set T0380 2 :IDEKFLIESNELVESSKIVMVGTNG 1xhnA 15 :PREDAARVARFVTHVSDWGALATIS T0380 27 :ENGYPNIKAMMRLKHDGL 1xhnA 44 :VRGRPFADVLSLSDGPPG T0380 45 :KKFWLSTNTSTRMVERLKKNNKICLYFV 1xhnA 65 :GVPYFYLSPLQLSVSNLQENPYATLTMT T0380 73 :DDN 1xhnA 105 :DPQ T0380 76 :KFAGLMLVGTIEILH 1xhnA 110 :LCVHIMLSGTVTKVN T0380 91 :DRASKEMLWTDGCEIYY 1xhnA 127 :EMDIAKHSLFIRHPEMK T0380 109 :LGIDDPDYTALCFTAEWGNYYRHLKNITF 1xhnA 144 :TWPSSHNWFFAKLNITNIWVLDYFGGPKI T0380 138 :KIDEIYNY 1xhnA 174 :TPEEYYNV Number of specific fragments extracted= 8 number of extra gaps= 0 total=122 Number of alignments=17 # 1xhnA read from 1xhnA/merged-good-all-a2m # found chain 1xhnA in template set T0380 17 :SKIVMVGTNG 1xhnA 30 :SDWGALATIS T0380 27 :ENGYPNIKAMM 1xhnA 44 :VRGRPFADVLS T0380 39 :LKH 1xhnA 55 :LSD T0380 42 :DGLKKFWLSTNTSTRMVERLKKNNKICLYFV 1xhnA 62 :AGSGVPYFYLSPLQLSVSNLQENPYATLTMT T0380 73 :DDNKFA 1xhnA 105 :DPQSPL T0380 79 :GLMLVGTIEILHDRASK 1xhnA 113 :HIMLSGTVTKVNETEMD T0380 97 :M 1xhnA 130 :I T0380 99 :WTDGCEIYYPLGIDDP 1xhnA 131 :AKHSLFIRHPEMKTWP T0380 115 :DYTALCFTAEWGNYYRHLKNI 1xhnA 150 :NWFFAKLNITNIWVLDYFGGP Number of specific fragments extracted= 9 number of extra gaps= 0 total=131 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 # T0380 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 (T0380)I139 because of BadResidue code BAD_PEPTIDE in next template residue (1t9mA)D203 Warning: unaligning (T0380)D140 because of BadResidue code BAD_PEPTIDE at template residue (1t9mA)D203 Warning: unaligning (T0380)I142 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t9mA)G206 Warning: unaligning (T0380)Y143 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t9mA)G206 T0380 7 :LIESNEL 1t9mA 37 :LERARRY T0380 14 :VESSKIVMVGTNGENGYPNIKAMMRLKHDGLK 1t9mA 45 :VREPRALALATVDGQGRPSTRIVVIAELGERG T0380 47 :FWLSTNTSTRMVERLKKNNKICLYFVDDNKFAGLMLVGTIEILHDRASKEMLWTDGCEIYYP 1t9mA 77 :VVFATHADSQKGRELAQNPWASGVLYWRESSQQIILNGRAERLPDERADAQWLSRPYQTHPM T0380 109 :LGIDDPDYTALCFTAEWGNYY 1t9mA 167 :PLPRPPGYCLFELCLESVEFW T0380 130 :RHLKNITFK 1t9mA 193 :RLHERLRYD T0380 141 :E 1t9mA 204 :E Number of specific fragments extracted= 6 number of extra gaps= 2 total=137 Number of alignments=19 # 1t9mA read from 1t9mA/merged-good-all-a2m # found chain 1t9mA in template set T0380 6 :FLIESNEL 1t9mA 36 :WLERARRY T0380 14 :VESSKIVMVGTNGENGYPNIKAMMRLKHDGLK 1t9mA 45 :VREPRALALATVDGQGRPSTRIVVIAELGERG T0380 47 :FWLSTNTSTRMVERLKKNNKICLYFVDDNKFAGLMLVGTIEILH 1t9mA 77 :VVFATHADSQKGRELAQNPWASGVLYWRESSQQIILNGRAERLP T0380 92 :RASKEMLWTDGCEIYYP 1t9mA 121 :DERADAQWLSRPYQTHP T0380 109 :LGIDDPDYTALCFTAEWGNYYRHLKNITFKIDEI 1t9mA 167 :PLPRPPGYCLFELCLESVEFWGNGTERLHERLRY Number of specific fragments extracted= 5 number of extra gaps= 0 total=142 Number of alignments=20 # 1t9mA read from 1t9mA/merged-good-all-a2m # found chain 1t9mA in template set T0380 6 :FLIESNEL 1t9mA 36 :WLERARRY T0380 14 :VESSKIVMVGTNGENGYPNIKAM 1t9mA 45 :VREPRALALATVDGQGRPSTRIV T0380 38 :RLKHDGLKKFWLSTNTSTRMVERLKKNNKICLYFVDDNKFAGLMLVGTIEILHDRASKEML 1t9mA 68 :VIAELGERGVVFATHADSQKGRELAQNPWASGVLYWRESSQQIILNGRAERLPDERADAQW T0380 99 :WTDGCEIYYPLGID 1t9mA 154 :LRAEARRLAETDGP T0380 113 :DPDYTALCFTAEWGNYYRHL 1t9mA 171 :PPGYCLFELCLESVEFWGNG Number of specific fragments extracted= 5 number of extra gaps= 0 total=147 Number of alignments=21 # 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 # T0380 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 (T0380)S54 because of BadResidue code BAD_PEPTIDE in next template residue (2fg9A)G55 Warning: unaligning (T0380)T55 because of BadResidue code BAD_PEPTIDE at template residue (2fg9A)G55 T0380 2 :IDEKFL 2fg9A 8 :DKQRIE T0380 12 :ELVESSKIVMVGTNGENGYPNIKAMMRLK 2fg9A 14 :SIILQADACFVGITDLEGNPYVVPMNFGY T0380 43 :GLKKFWLSTNT 2fg9A 43 :ENDTLYLHSGP T0380 56 :RMVERLKKNNKICLYFVDDNKFA 2fg9A 56 :GKIEMLQRNNNVCITFSLGHKLV T0380 79 :GLMLVGTIEILHDRASKEMLWTDGCEIYYPLGIDDP 2fg9A 94 :SAMCRGKVEFIEDMEEKRHALDIIMRHYTKDQFSYS T0380 115 :DYTALCFTAEWGNYYRHLKNIT 2fg9A 135 :NVKVWKVPVDQMTGKVFGLRAD Number of specific fragments extracted= 6 number of extra gaps= 1 total=153 Number of alignments=22 # 2fg9A read from 2fg9A/merged-good-all-a2m # found chain 2fg9A in template set Warning: unaligning (T0380)S54 because of BadResidue code BAD_PEPTIDE in next template residue (2fg9A)G55 Warning: unaligning (T0380)T55 because of BadResidue code BAD_PEPTIDE at template residue (2fg9A)G55 T0380 7 :LIESNELVESSKIVMVGTNGENGYPNIKAMMRLK 2fg9A 9 :KQRIESIILQADACFVGITDLEGNPYVVPMNFGY T0380 43 :GLKKFWLSTNT 2fg9A 43 :ENDTLYLHSGP T0380 56 :RMVERLKKNNKICLYFVDDNKFAG 2fg9A 56 :GKIEMLQRNNNVCITFSLGHKLVY T0380 80 :LMLVGTIEILHDRASKEMLWTDGCEIYYPLGIDDP 2fg9A 95 :AMCRGKVEFIEDMEEKRHALDIIMRHYTKDQFSYS T0380 115 :DYTALCFTAEWGNYYRHL 2fg9A 135 :NVKVWKVPVDQMTGKVFG Number of specific fragments extracted= 5 number of extra gaps= 1 total=158 Number of alignments=23 # 2fg9A read from 2fg9A/merged-good-all-a2m # found chain 2fg9A in template set Warning: unaligning (T0380)S54 because of BadResidue code BAD_PEPTIDE in next template residue (2fg9A)G55 Warning: unaligning (T0380)T55 because of BadResidue code BAD_PEPTIDE at template residue (2fg9A)G55 T0380 7 :LIESNELVESSKIVMVGTNGENGYPNIKAM 2fg9A 9 :KQRIESIILQADACFVGITDLEGNPYVVPM T0380 39 :LKHDGLKKFWLSTNT 2fg9A 39 :NFGYENDTLYLHSGP T0380 56 :RMVERLKKNNKICLYFVDDNKFA 2fg9A 56 :GKIEMLQRNNNVCITFSLGHKLV T0380 79 :GLMLVGTIEILHDRASKEMLWTDGCEIYYPLGIDDP 2fg9A 94 :SAMCRGKVEFIEDMEEKRHALDIIMRHYTKDQFSYS T0380 115 :DYTALCFTAEWGNYYR 2fg9A 135 :NVKVWKVPVDQMTGKV Number of specific fragments extracted= 5 number of extra gaps= 1 total=163 Number of alignments=24 # 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 # T0380 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 (T0380)D3 because first residue in template chain is (2asfA)S11 Warning: unaligning (T0380)M36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2asfA)G41 Warning: unaligning (T0380)M37 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2asfA)G41 Warning: unaligning (T0380)K133 because last residue in template chain is (2asfA)D135 T0380 4 :EKFL 2asfA 12 :DDAL T0380 12 :ELVESSKIVMVGTNGENGYPNIKA 2asfA 16 :AFLSERHLAMLTTLRADNSPHVVA T0380 38 :RLKHDGLKKFWLSTNTSTRMVERLKKNNKICLYFVDDN 2asfA 42 :FTFDPKTHIARVITTGGSQKAVNADRSGLAVLSQVDGA T0380 78 :AGLMLVGTIEILHDRASKEMLWTDGCEIYY 2asfA 80 :RWLSLEGRAAVNSDIDAVRDAELRYAQRYR T0380 109 :LGIDDPDYTALCFTAEWGNYY 2asfA 110 :TPRPNPRRVVIEVQIERVLGS T0380 130 :RHL 2asfA 132 :DLL Number of specific fragments extracted= 6 number of extra gaps= 1 total=169 Number of alignments=25 # 2asfA read from 2asfA/merged-good-all-a2m # found chain 2asfA in template set Warning: unaligning (T0380)L7 because first residue in template chain is (2asfA)S11 Warning: unaligning (T0380)M36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2asfA)G41 Warning: unaligning (T0380)M37 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2asfA)G41 T0380 8 :IESNELVESSKIVMVGTNGENGYPNIKA 2asfA 12 :DDALAFLSERHLAMLTTLRADNSPHVVA T0380 38 :RLKHDGLKKFWLSTNTSTRMVERLKKNNKICLYFVDDN 2asfA 42 :FTFDPKTHIARVITTGGSQKAVNADRSGLAVLSQVDGA T0380 78 :AGLMLVGTIEILHDRASKEMLWTDGCEIY 2asfA 80 :RWLSLEGRAAVNSDIDAVRDAELRYAQRY T0380 108 :PLGIDDPDYTALCFTAEWGNYYR 2asfA 109 :RTPRPNPRRVVIEVQIERVLGSA T0380 134 :NIT 2asfA 132 :DLL Number of specific fragments extracted= 5 number of extra gaps= 1 total=174 Number of alignments=26 # 2asfA read from 2asfA/merged-good-all-a2m # found chain 2asfA in template set Warning: unaligning (T0380)M36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2asfA)G41 Warning: unaligning (T0380)M37 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2asfA)G41 T0380 9 :ESNELVESSKIVMVGTNGENGYPNIKA 2asfA 13 :DALAFLSERHLAMLTTLRADNSPHVVA T0380 38 :RLKHDGLKKFWLSTNTSTRMVERLKKNNKICLYFVDDNK 2asfA 42 :FTFDPKTHIARVITTGGSQKAVNADRSGLAVLSQVDGAR T0380 79 :GLMLVGTIEILHDRASKEMLWT 2asfA 81 :WLSLEGRAAVNSDIDAVRDAEL T0380 102 :GCEIYYPLGIDDPDYTALCFTAEWGNYYRH 2asfA 103 :RYAQRYRTPRPNPRRVVIEVQIERVLGSAD Number of specific fragments extracted= 4 number of extra gaps= 1 total=178 Number of alignments=27 # 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:# T0380 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 T0380 2 :IDEKFL 1xxoA 6 :FDDKLL T0380 12 :ELVESSKIVMVGTNGENGYPNIKAMMRLKHDGLKKFWLSTNTSTRMVERLKKNNKICLYFVDDNKFAGLMLVGTIEILH 1xxoA 12 :AVISGNSIGVLATIKHDGRPQLSNVQYHFDPRKLLIQVSIAEPRAKTRNLRRDPRASILVDADDGWSYAVAEGTAQLTP T0380 91 :DRASKEMLWTDGCE 1xxoA 96 :DDDTVEALIALYRN T0380 107 :YPLGIDD 1xxoA 110 :IAGEHSD T0380 114 :PDYTALCFTAEWGNYYRHL 1xxoA 127 :DRRVLLTLPISHVYGLPPG Number of specific fragments extracted= 5 number of extra gaps= 0 total=183 Number of alignments=28 # 1xxoA read from 1xxoA/merged-good-all-a2m # found chain 1xxoA in template set Warning: unaligning (T0380)K5 because first residue in template chain is (1xxoA)V5 T0380 6 :FLIESNELVESSKIVMVGTNGENGYPNIKAMMRLKHDGLKKFWLSTNTSTRMVERLKKNNKICLYFVDDNKFAGLMLVGTIEILH 1xxoA 6 :FDDKLLAVISGNSIGVLATIKHDGRPQLSNVQYHFDPRKLLIQVSIAEPRAKTRNLRRDPRASILVDADDGWSYAVAEGTAQLTP T0380 91 :DRASKEMLWT 1xxoA 96 :DDDTVEALIA T0380 102 :GCEIYYPLGIDD 1xxoA 106 :LYRNIAGEHSDW T0380 115 :DYTALCFTAEWGNYYRHL 1xxoA 128 :RRVLLTLPISHVYGLPPG Number of specific fragments extracted= 4 number of extra gaps= 0 total=187 Number of alignments=29 # 1xxoA read from 1xxoA/merged-good-all-a2m # found chain 1xxoA in template set T0380 2 :IDE 1xxoA 6 :FDD T0380 9 :ESNELVESSKIVMVGTNGENGYPNIKAMMRLKHDGLKKFWLSTNTSTRMVERLKKNNKICLYFVDDNKFAGLMLVGTIEILHD 1xxoA 9 :KLLAVISGNSIGVLATIKHDGRPQLSNVQYHFDPRKLLIQVSIAEPRAKTRNLRRDPRASILVDADDGWSYAVAEGTAQLTPP T0380 92 :RASKEMLWT 1xxoA 97 :DDTVEALIA T0380 103 :CEIYYPLGIDD 1xxoA 106 :LYRNIAGEHSD T0380 114 :PDYTALCFTAEWGNYYRHL 1xxoA 127 :DRRVLLTLPISHVYGLPPG Number of specific fragments extracted= 5 number of extra gaps= 0 total=192 Number of alignments=30 # 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 # T0380 read from 1w9aA/merged-good-all-a2m # 1w9aA read from 1w9aA/merged-good-all-a2m # found chain 1w9aA in training set Warning: unaligning (T0380)I2 because first residue in template chain is (1w9aA)F6 T0380 3 :DEKFL 1w9aA 7 :DDKLL T0380 12 :ELVESSKIVMVGTNGENGYPNIKAMMRLKHDGLKKFWLSTNTSTRMVERLKKNNKICLYFVDDNKFAGLMLVGTIEILH 1w9aA 12 :AVISGNSIGVLATIKHDGRPQLSNVQYHFDPRKLLIQVSIAEPRAKTRNLRRDPRASILVDADDGWSYAVAEGTAQLTP T0380 91 :DRASKEMLWTDGCEIY 1w9aA 96 :DDDTVEALIALYRNIA T0380 109 :LGIDD 1w9aA 112 :GEHSD T0380 114 :PDYTALCFTAEWGNYYRH 1w9aA 127 :DRRVLLTLPISHVYGLPP Number of specific fragments extracted= 5 number of extra gaps= 0 total=197 Number of alignments=31 # 1w9aA read from 1w9aA/merged-good-all-a2m # found chain 1w9aA in training set Warning: unaligning (T0380)F6 because first residue in template chain is (1w9aA)F6 T0380 7 :LIESNELVESSKIVMVGTNGENGYPNIKAMMRLKHDGLKKFWLSTNTSTRMVERLKKNNKICLYFVDDNKFAGLMLVGTIEILH 1w9aA 7 :DDKLLAVISGNSIGVLATIKHDGRPQLSNVQYHFDPRKLLIQVSIAEPRAKTRNLRRDPRASILVDADDGWSYAVAEGTAQLTP T0380 91 :DRASKEMLWT 1w9aA 96 :DDDTVEALIA T0380 102 :GCEIYYPLGIDD 1w9aA 106 :LYRNIAGEHSDW T0380 115 :DYTALCFTAEWGNYYRHL 1w9aA 128 :RRVLLTLPISHVYGLPPG Number of specific fragments extracted= 4 number of extra gaps= 0 total=201 Number of alignments=32 # 1w9aA read from 1w9aA/merged-good-all-a2m # found chain 1w9aA in training set T0380 9 :ESNELVESSKIVMVGTNGENGYPNIKAMMRLKHDGLKKFWLSTNTSTRMVERLKKNNKICLYFVDDNKFAGLMLVGTIEILHD 1w9aA 9 :KLLAVISGNSIGVLATIKHDGRPQLSNVQYHFDPRKLLIQVSIAEPRAKTRNLRRDPRASILVDADDGWSYAVAEGTAQLTPP T0380 92 :RASKEMLWT 1w9aA 97 :DDTVEALIA T0380 103 :CEIYYPLGIDD 1w9aA 106 :LYRNIAGEHSD T0380 114 :PDYTALCFTAEWGNYYRHL 1w9aA 127 :DRRVLLTLPISHVYGLPPG Number of specific fragments extracted= 4 number of extra gaps= 0 total=205 Number of alignments=33 # 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:# T0380 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 T0380 8 :IESNELVESSKIVMVGTNGENGYPNIKAMMRLKHDGLKKFWLSTNTSTRMVERLKKNNKICLYFVDDNKFAGLMLVGTIEILH 2aq6A 8 :DKLLAVISGNSIGVLATIKHDGRPQLSNVQYHFDPRKLLIQVSIAEPRAKTRNLRRDPRASILVDADDGWSYAVAEGTAQLTP T0380 91 :DRASKEMLWTDGCE 2aq6A 96 :DDDTVEALIALYRN T0380 107 :YPLGIDD 2aq6A 110 :IAGEHSD T0380 114 :PDYTALCFTAEWGNYY 2aq6A 127 :DRRVLLTLPISHVYGL T0380 131 :H 2aq6A 144 :P Number of specific fragments extracted= 5 number of extra gaps= 0 total=210 Number of alignments=34 # 2aq6A read from 2aq6A/merged-good-all-a2m # found chain 2aq6A in template set Warning: unaligning (T0380)K5 because first residue in template chain is (2aq6A)V5 T0380 6 :FLIESNELVESSKIVMVGTNGENGYPNIKAMMRLKHDGLKKFWLSTNTSTRMVERLKKNNKICLYFVDDNKFAGLMLVGTIEILH 2aq6A 6 :FDDKLLAVISGNSIGVLATIKHDGRPQLSNVQYHFDPRKLLIQVSIAEPRAKTRNLRRDPRASILVDADDGWSYAVAEGTAQLTP T0380 91 :DRASKEMLWT 2aq6A 96 :DDDTVEALIA T0380 102 :GCEIYYPLGID 2aq6A 106 :LYRNIAGEHSD T0380 115 :DYTALCFTAEWGNYY 2aq6A 128 :RRVLLTLPISHVYGL Number of specific fragments extracted= 4 number of extra gaps= 0 total=214 Number of alignments=35 # 2aq6A read from 2aq6A/merged-good-all-a2m # found chain 2aq6A in template set T0380 7 :LIESNELVESSKIVMVGTNGENGYPNIKAMMRLKHDGLKKFWLSTNTSTRMVERLKKNNKICLYFVDDNKFAGLMLVGTIEILHD 2aq6A 7 :DDKLLAVISGNSIGVLATIKHDGRPQLSNVQYHFDPRKLLIQVSIAEPRAKTRNLRRDPRASILVDADDGWSYAVAEGTAQLTPP T0380 92 :RASKEMLWT 2aq6A 97 :DDTVEALIA T0380 103 :CEIYYPLGIDD 2aq6A 106 :LYRNIAGEHSD T0380 114 :PDYTALCFTAEWGNYYRHL 2aq6A 127 :DRRVLLTLPISHVYGLPPG Number of specific fragments extracted= 4 number of extra gaps= 0 total=218 Number of alignments=36 # 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 # T0380 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 T0380 6 :FLIESNEL 1nrgA 65 :WFEEAVQC T0380 14 :VESSKIVMVGTNGENGYPNIKAMMRLKHDGLK 1nrgA 75 :IGEANAMCLATCTRDGKPSARMLLLKGFGKDG T0380 47 :FWLSTNTSTRMVERLKKNNKICLYFVDDNKFAGLMLVGTIEILHDRASKEMLWTDGCEIYYP 1nrgA 107 :FRFFTNFESRKGKELDSNPFASLVFYWEPLNRQVRVEGPVKKLPEEEAECYFHSRPKSSQIG T0380 109 :LGIDDPDYTALCFTAEWGNYY 1nrgA 199 :EVPKPKSWGGYVLYPQVMEFW T0380 130 :RHLKNITFKIDE 1nrgA 225 :RLHDRIVFRRGL T0380 142 :IYNY 1nrgA 239 :GDSP Number of specific fragments extracted= 6 number of extra gaps= 0 total=224 Number of alignments=37 # 1nrgA read from 1nrgA/merged-good-all-a2m # found chain 1nrgA in template set T0380 6 :FLIESNEL 1nrgA 65 :WFEEAVQC T0380 14 :VESSKIVMVGTNGENGYPNIKAMMRLKHDGLK 1nrgA 75 :IGEANAMCLATCTRDGKPSARMLLLKGFGKDG T0380 47 :FWLSTNTSTRMVERLKKNNKICLYFVDDNKFAGLMLVGTIEILH 1nrgA 107 :FRFFTNFESRKGKELDSNPFASLVFYWEPLNRQVRVEGPVKKLP T0380 92 :RASKEMLWTDGCEIYYP 1nrgA 151 :EEEAECYFHSRPKSSQI T0380 109 :LGIDDPDYTALCFTAEWGNYYRHLKNITFKIDEIYNY 1nrgA 199 :EVPKPKSWGGYVLYPQVMEFWQGQTNRLHDRIVFRRG Number of specific fragments extracted= 5 number of extra gaps= 0 total=229 Number of alignments=38 # 1nrgA read from 1nrgA/merged-good-all-a2m # found chain 1nrgA in template set T0380 6 :FLIESNE 1nrgA 65 :WFEEAVQ T0380 14 :VESSKIVMVGTNGENGYPNIKAM 1nrgA 75 :IGEANAMCLATCTRDGKPSARML T0380 38 :RLKHDGLKKFWLSTNTSTRMVERLKKNNKICLYFVDDNKFAGLMLVGTIEILH 1nrgA 98 :LLKGFGKDGFRFFTNFESRKGKELDSNPFASLVFYWEPLNRQVRVEGPVKKLP T0380 91 :DRASKEMLWTDGCEIYYPLGIDDP 1nrgA 180 :DREYLRKKNEELEQLYQDQEVPKP T0380 115 :DYTALCFTAEWGNYYRHLKN 1nrgA 205 :SWGGYVLYPQVMEFWQGQTN Number of specific fragments extracted= 5 number of extra gaps= 0 total=234 Number of alignments=39 # 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 # T0380 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 (T0380)S54 because of BadResidue code BAD_PEPTIDE in next template residue (1axj)H52 Warning: unaligning (T0380)T55 because of BadResidue code BAD_PEPTIDE at template residue (1axj)H52 Warning: unaligning (T0380)W125 because of BadResidue code BAD_PEPTIDE in next template residue (1axj)A118 Warning: unaligning (T0380)G126 because of BadResidue code BAD_PEPTIDE at template residue (1axj)A118 T0380 1 :MIDEKFL 1axj 1 :MLPGTFF T0380 12 :ELVESSKIVMVGTNGENG 1axj 8 :EVLKNEGVVAIATQGEDG T0380 31 :PNIKAMM 1axj 26 :PHLVNTW T0380 38 :RLKHDGLKKFWLSTNT 1axj 35 :YLKVLDGNRIVVPVGG T0380 56 :RMVERLKKNNKICLYFVDD 1axj 53 :KTEANVARDERVLMTLGSR T0380 75 :NKFAGLMLVGTIEILHDRASKEMLWTD 1axj 78 :GPGTGFLIRGSAAFRTDGPEFEAIARF T0380 109 :LGID 1axj 105 :KWAR T0380 117 :TALCFTAE 1axj 109 :AALVITVV T0380 127 :NY 1axj 119 :EQ Number of specific fragments extracted= 9 number of extra gaps= 2 total=243 Number of alignments=40 # 1axj read from 1axj/merged-good-all-a2m # found chain 1axj in template set Warning: unaligning (T0380)S54 because of BadResidue code BAD_PEPTIDE in next template residue (1axj)H52 Warning: unaligning (T0380)T55 because of BadResidue code BAD_PEPTIDE at template residue (1axj)H52 Warning: unaligning (T0380)W125 because of BadResidue code BAD_PEPTIDE in next template residue (1axj)A118 Warning: unaligning (T0380)G126 because of BadResidue code BAD_PEPTIDE at template residue (1axj)A118 T0380 1 :M 1axj 1 :M T0380 6 :FLIESNELVESSKIVMVGTNGENG 1axj 2 :LPGTFFEVLKNEGVVAIATQGEDG T0380 31 :PNIKAMM 1axj 26 :PHLVNTW T0380 38 :RLKHDGLKKFWLSTNT 1axj 35 :YLKVLDGNRIVVPVGG T0380 56 :RMVERLKKNNKICLYFVDDN 1axj 53 :KTEANVARDERVLMTLGSRK T0380 76 :KFAGLMLVGTIEILHDRASKEMLWTD 1axj 79 :PGTGFLIRGSAAFRTDGPEFEAIARF T0380 109 :LGID 1axj 105 :KWAR T0380 117 :TALCFTAE 1axj 109 :AALVITVV T0380 127 :NY 1axj 119 :EQ Number of specific fragments extracted= 9 number of extra gaps= 2 total=252 Number of alignments=41 # 1axj read from 1axj/merged-good-all-a2m # found chain 1axj in template set Warning: unaligning (T0380)S54 because of BadResidue code BAD_PEPTIDE in next template residue (1axj)H52 Warning: unaligning (T0380)T55 because of BadResidue code BAD_PEPTIDE at template residue (1axj)H52 Warning: unaligning (T0380)W125 because of BadResidue code BAD_PEPTIDE in next template residue (1axj)A118 Warning: unaligning (T0380)G126 because of BadResidue code BAD_PEPTIDE at template residue (1axj)A118 T0380 9 :ESNELVESSKIVMVGTNGENG 1axj 5 :TFFEVLKNEGVVAIATQGEDG T0380 31 :PNIKAMM 1axj 26 :PHLVNTW T0380 38 :RLKHDGLKKFWLSTNT 1axj 35 :YLKVLDGNRIVVPVGG T0380 56 :RMVERLKKNNKICLYFV 1axj 53 :KTEANVARDERVLMTLG T0380 73 :DDNKFAGLMLVGTIEILHDRASKEML 1axj 76 :RNGPGTGFLIRGSAAFRTDGPEFEAI T0380 109 :LGIDDPD 1axj 102 :ARFKWAR T0380 117 :TALCFTAE 1axj 109 :AALVITVV T0380 127 :NY 1axj 119 :EQ Number of specific fragments extracted= 8 number of extra gaps= 2 total=260 Number of alignments=42 # 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/T0380/2a2jA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0380/2a2jA/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 # T0380 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 T0380 6 :FLIESNELVESSKIVMVGTNGENGYPNIKAMMRLKHDGLKKFWLSTNTSTRMVERLKKNNKICLYFVDDN 2fhqA 6 :MKEKAVELLQKCEVVTLASVNKEGYPRPVPMSKIAAEGISTIWMSTGADSLKTIDFLSNPKAGLCFQEKG T0380 78 :AGLMLVGTIEILHDRASKEMLWTDGCEIYYPLGIDDPDYTALCFTAEWGNYY 2fhqA 76 :DSVALMGEVEVVTDEKLKQELWQDWFIEHFPGGPTDPGYVLLKFTANHATYW T0380 132 :LKNIT 2fhqA 130 :GTFIH Number of specific fragments extracted= 3 number of extra gaps= 0 total=263 Number of alignments=43 # 2fhqA read from 2fhqA/merged-good-all-a2m # found chain 2fhqA in template set Warning: unaligning (T0380)D3 because first residue in template chain is (2fhqA)T3 T0380 4 :EKFLIESNELVESSKIVMVGTNGENGYPNIKAMMRLKHDGLKKFWLSTNTSTRMVERLKKNNKICLYFVDDN 2fhqA 4 :KTMKEKAVELLQKCEVVTLASVNKEGYPRPVPMSKIAAEGISTIWMSTGADSLKTIDFLSNPKAGLCFQEKG T0380 78 :AGLMLVGTIEILHDRASKEMLWTDGCEIYYPLGIDDPDYTALCFTAEWGNYYRHLKNITFK 2fhqA 76 :DSVALMGEVEVVTDEKLKQELWQDWFIEHFPGGPTDPGYVLLKFTANHATYWIEGTFIHKK Number of specific fragments extracted= 2 number of extra gaps= 0 total=265 Number of alignments=44 # 2fhqA read from 2fhqA/merged-good-all-a2m # found chain 2fhqA in template set T0380 6 :FLIESNELVESSKIVMVGTNGENGYPNIKAMMRLKHDGLKKFWLSTNTSTRMVERLKKNNKICLYFVDDNK 2fhqA 6 :MKEKAVELLQKCEVVTLASVNKEGYPRPVPMSKIAAEGISTIWMSTGADSLKTIDFLSNPKAGLCFQEKGD T0380 79 :GLMLVGTIEILHDRASKEMLWTDGCEIYYPLGIDDPDYTALCFTAEWGNYYRHLKNI 2fhqA 77 :SVALMGEVEVVTDEKLKQELWQDWFIEHFPGGPTDPGYVLLKFTANHATYWIEGTFI Number of specific fragments extracted= 2 number of extra gaps= 0 total=267 Number of alignments=45 # 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 # T0380 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 (T0380)M36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rfeA)W43 Warning: unaligning (T0380)M37 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rfeA)W43 Warning: unaligning (T0380)I86 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rfeA)E94 Warning: unaligning (T0380)E87 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rfeA)E94 Warning: unaligning (T0380)D113 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rfeA)K122 T0380 2 :IDEKFL 1rfeA 11 :MSEAEI T0380 11 :NELVESSKIVMVGTNGENGYPNIKA 1rfeA 17 :ADFVNSSRTGTLATIGPDGQPHLTA T0380 38 :RLKHD 1rfeA 44 :YAVID T0380 45 :KKFWLSTNTSTRMVERLKKNNKICLYFV 1rfeA 49 :GEIWLETKAKSQKAVNLRRDPRVSFLLE T0380 73 :DDNKFAGLMLVGT 1rfeA 80 :TYDTLRGVSFEGV T0380 88 :ILHDRASKEMLWTDGCEIYYPLGID 1rfeA 95 :IVEEPEALHRVGVSVWERYTGPYTD T0380 115 :DYTALCFTAEWGNYY 1rfeA 131 :KRVGVRIVARRTRSW T0380 130 :RHLK 1rfeA 148 :RKLG Number of specific fragments extracted= 8 number of extra gaps= 2 total=275 Number of alignments=46 # 1rfeA read from 1rfeA/merged-good-all-a2m # found chain 1rfeA in template set Warning: unaligning (T0380)M36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rfeA)W43 Warning: unaligning (T0380)M37 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rfeA)W43 Warning: unaligning (T0380)I86 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rfeA)E94 Warning: unaligning (T0380)E87 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rfeA)E94 Warning: unaligning (T0380)P114 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rfeA)K122 T0380 8 :IESNELVESSKIVMVGTNGENGYPNIKA 1rfeA 14 :AEIADFVNSSRTGTLATIGPDGQPHLTA T0380 38 :RLKHD 1rfeA 44 :YAVID T0380 44 :LK 1rfeA 49 :GE T0380 47 :FWLSTNTSTRMVERLKKNNKICLYFV 1rfeA 51 :IWLETKAKSQKAVNLRRDPRVSFLLE T0380 73 :DDNKFAGLMLVGT 1rfeA 80 :TYDTLRGVSFEGV T0380 88 :ILHDRASKEMLWTDGCEIYYPLGID 1rfeA 95 :IVEEPEALHRVGVSVWERYTGPYTD T0380 115 :DYTALCFTAEWGNYYRHL 1rfeA 131 :KRVGVRIVARRTRSWDHR Number of specific fragments extracted= 7 number of extra gaps= 2 total=282 Number of alignments=47 # 1rfeA read from 1rfeA/merged-good-all-a2m # found chain 1rfeA in template set Warning: unaligning (T0380)M36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rfeA)W43 Warning: unaligning (T0380)M37 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rfeA)W43 Warning: unaligning (T0380)I86 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rfeA)E94 Warning: unaligning (T0380)E87 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rfeA)E94 Warning: unaligning (T0380)D113 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rfeA)K122 T0380 9 :ESNELVESSKIVMVGTNGENGYPNIKA 1rfeA 15 :EIADFVNSSRTGTLATIGPDGQPHLTA T0380 38 :RLKH 1rfeA 44 :YAVI T0380 44 :LKKFWLSTNTSTRMVERLKKNNKICLYFV 1rfeA 48 :DGEIWLETKAKSQKAVNLRRDPRVSFLLE T0380 73 :DDNKFAGLMLVGT 1rfeA 80 :TYDTLRGVSFEGV T0380 88 :ILHDRASKEMLWTDGCEIYYPLGID 1rfeA 95 :IVEEPEALHRVGVSVWERYTGPYTD T0380 114 :PDYTALCFTAEWGNYYRH 1rfeA 130 :NKRVGVRIVARRTRSWDH Number of specific fragments extracted= 6 number of extra gaps= 2 total=288 Number of alignments=48 # 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:# T0380 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 T0380 9 :ESNELVES 1ci0A 41 :KWFNEAKE T0380 17 :SKIVMVGTNG 1ci0A 55 :PEAITFSSAE T0380 27 :ENGYPNIKAMMRLKHDGLKKFWLSTNTSTRMVERLKKNNKICLYFVDDNKFAGLMLVGTIEILHDRASKEMLWTDGCEIYYP 1ci0A 66 :PSGRVSSRILLFKELDHRGFTIYSNWGTSRKAHDIATNPNAAIVFFWKDLQRQVRVEGITEHVNRETSERYFKTRPRGSKIG T0380 109 :LGIDDPDYTALCFTAEWGNYY 1ci0A 179 :DIPCPDYWGGLRIVPLEIEFW T0380 130 :RHLKNITFKIDE 1ci0A 205 :RLHDRFVYRRKT T0380 142 :IYN 1ci0A 218 :NDP Number of specific fragments extracted= 6 number of extra gaps= 0 total=294 Number of alignments=49 # 1ci0A read from 1ci0A/merged-good-all-a2m # found chain 1ci0A in template set T0380 2 :IDEKFLIESNELVES 1ci0A 31 :LTDDPIDLFTKWFNE T0380 17 :SKIVMVGTNG 1ci0A 55 :PEAITFSSAE T0380 27 :ENGYPNIKAMMRLKHDGLK 1ci0A 66 :PSGRVSSRILLFKELDHRG T0380 47 :FWLSTNTS 1ci0A 85 :FTIYSNWG T0380 55 :TRMVERLKKNNKICLYFVDDNKFAGLMLVGTIEILH 1ci0A 94 :SRKAHDIATNPNAAIVFFWKDLQRQVRVEGITEHVN T0380 92 :RASKEMLWTDGCEIYYP 1ci0A 130 :RETSERYFKTRPRGSKI T0380 109 :LGIDDPDYTALCFTAEWGNYYRHLKNITFKIDEIYN 1ci0A 179 :DIPCPDYWGGLRIVPLEIEFWQGRPSRLHDRFVYRR Number of specific fragments extracted= 7 number of extra gaps= 0 total=301 Number of alignments=50 # 1ci0A read from 1ci0A/merged-good-all-a2m # found chain 1ci0A in template set T0380 6 :FLIESNE 1ci0A 42 :WFNEAKE T0380 15 :ESSKIVMVGTNG 1ci0A 53 :TLPEAITFSSAE T0380 27 :ENGYPNIKAMMRLKHDGLKKFWLSTNTSTRMVERLKKNNKICLYFVDDNKFAGLMLVGTIEILH 1ci0A 66 :PSGRVSSRILLFKELDHRGFTIYSNWGTSRKAHDIATNPNAAIVFFWKDLQRQVRVEGITEHVN T0380 91 :DRASKEMLWTDGCEIY 1ci0A 159 :NREELDELTQKNTERF T0380 109 :LGIDD 1ci0A 175 :KDAED T0380 114 :PDYTALCFTAEWGNYYRHLKN 1ci0A 184 :DYWGGLRIVPLEIEFWQGRPS Number of specific fragments extracted= 6 number of extra gaps= 0 total=307 Number of alignments=51 # 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 # T0380 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 T0380 2 :IDEKFL 2furA 20 :SDEDLV T0380 12 :ELVESSKIVMVGTNGEN 2furA 26 :AMLDRNFTCTVSFIDGG T0380 30 :YPNIKAMMRLK 2furA 43 :IPYAIPMMLAS T0380 43 :GLKKFWLSTNTSTRMVERLKKNNKICLYFVDDNKFA 2furA 54 :EGKTIYLHGSMKSRIYGILKTGQLIAISLLEINGIV T0380 79 :GLMLVGTIEILHDRASKEMLWTDGCEIYYP 2furA 103 :SALIFGRPYEIDDTEKKIEVFRLLTEKLVK T0380 109 :LGIDDP 2furA 137 :NSIKPS T0380 115 :DYTALCFTAEWGNYY 2furA 148 :GVFVFAVKPETFSMK T0380 130 :RHLKNITFKIDE 2furA 178 :SGVLPIQHTISE Number of specific fragments extracted= 8 number of extra gaps= 0 total=315 Number of alignments=52 # 2furA read from 2furA/merged-good-all-a2m # found chain 2furA in template set Warning: unaligning (T0380)R130 because of BadResidue code BAD_PEPTIDE in next template residue (2furA)R164 Warning: unaligning (T0380)H131 because of BadResidue code BAD_PEPTIDE at template residue (2furA)R164 T0380 7 :LIESNELVESSKIVMVGTNGEN 2furA 21 :DEDLVAMLDRNFTCTVSFIDGG T0380 30 :YPNIKAMMRLK 2furA 43 :IPYAIPMMLAS T0380 43 :GLKKFWLSTNTSTRMVERLKKNNKICLYFVDDN 2furA 54 :EGKTIYLHGSMKSRIYGILKTGQLIAISLLEIN T0380 76 :KFAGLMLVGTIEILHDRASKEMLWTDGCEIYYP 2furA 100 :NYVSALIFGRPYEIDDTEKKIEVFRLLTEKLVK T0380 109 :LGIDDP 2furA 137 :NSIKPS T0380 115 :DYTALCFTAEWGNYY 2furA 148 :GVFVFAVKPETFSMK T0380 132 :LKNITFK 2furA 165 :TGPPHDT Number of specific fragments extracted= 7 number of extra gaps= 1 total=322 Number of alignments=53 # 2furA read from 2furA/merged-good-all-a2m # found chain 2furA in template set Warning: unaligning (T0380)R130 because of BadResidue code BAD_PEPTIDE in next template residue (2furA)R164 Warning: unaligning (T0380)H131 because of BadResidue code BAD_PEPTIDE at template residue (2furA)R164 T0380 4 :E 2furA 22 :E T0380 9 :ESNELVESSKIVMVGTNGENG 2furA 23 :DLVAMLDRNFTCTVSFIDGGI T0380 31 :PNIKAMMR 2furA 44 :PYAIPMML T0380 41 :HDGLKKFWLSTNTSTRMVERLKKNNKICLYFV 2furA 52 :ASEGKTIYLHGSMKSRIYGILKTGQLIAISLL T0380 73 :DDNKFAGLMLVGTIEILHDRASKEMLWTDGCEIYYPLGIDDP 2furA 97 :NSINYVSALIFGRPYEIDDTEKKIEVFRLLTEKLVKGRWDNS T0380 115 :DYTALCFTAEWGNYY 2furA 148 :GVFVFAVKPETFSMK T0380 132 :LKN 2furA 165 :TGP Number of specific fragments extracted= 7 number of extra gaps= 1 total=329 Number of alignments=54 # 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 # T0380 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 (T0380)D3 because first residue in template chain is (2arzA)S2 Warning: unaligning (T0380)D112 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2arzA)V119 Warning: unaligning (T0380)D113 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2arzA)V119 Warning: unaligning (T0380)D115 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2arzA)F122 Warning: unaligning (T0380)Y116 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2arzA)F122 T0380 4 :EKFLIESNELVESSKIVMVGTNG 2arzA 3 :VEAAKNARELLLKEYRAVLSTHS T0380 27 :ENGYPNIKAMMRLKHDGLKKF 2arzA 28 :WPGFPFGSVVPYCLDAEGRPL T0380 49 :LSTNTSTRMVERLKKNNKICLYFVDDNKFA 2arzA 49 :ILISRIAQHTHNLQADPRCSMLVGERGAED T0380 79 :GLMLVGTIEILH 2arzA 84 :RLTLLAEARQLA T0380 92 :RASKEMLWTDGCEIYYP 2arzA 96 :EEEVAAAAERYYRYFPE T0380 109 :LGI 2arzA 115 :DYH T0380 114 :P 2arzA 120 :H T0380 117 :TALCFTAEWGNYY 2arzA 123 :DFWVLQPVQWRFI T0380 130 :RHLKNITFK 2arzA 137 :GFGAIHWLA Number of specific fragments extracted= 9 number of extra gaps= 2 total=338 Number of alignments=55 # 2arzA read from 2arzA/merged-good-all-a2m # found chain 2arzA in template set Warning: unaligning (T0380)D3 because first residue in template chain is (2arzA)S2 Warning: unaligning (T0380)D112 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2arzA)V119 Warning: unaligning (T0380)D113 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2arzA)V119 Warning: unaligning (T0380)D115 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2arzA)F122 Warning: unaligning (T0380)Y116 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2arzA)F122 T0380 4 :EKFLIESNELVESSKIVMVGTNG 2arzA 3 :VEAAKNARELLLKEYRAVLSTHS T0380 27 :ENGYPNIKAMMRLKHDGLK 2arzA 28 :WPGFPFGSVVPYCLDAEGR T0380 47 :FWLSTNTSTRMVERLKKNNKICLYFVDDN 2arzA 47 :PLILISRIAQHTHNLQADPRCSMLVGERG T0380 76 :KFAGLMLVGTIEILH 2arzA 81 :AVGRLTLLAEARQLA T0380 92 :RASKEMLWTDG 2arzA 96 :EEEVAAAAERY T0380 104 :EIYYP 2arzA 107 :YRYFP T0380 109 :LGI 2arzA 115 :DYH T0380 114 :P 2arzA 120 :H T0380 117 :TALCFTAEWGNYYRHLKNITF 2arzA 123 :DFWVLQPVQWRFIGGFGAIHW Number of specific fragments extracted= 9 number of extra gaps= 2 total=347 Number of alignments=56 # 2arzA read from 2arzA/merged-good-all-a2m # found chain 2arzA in template set Warning: unaligning (T0380)D3 because first residue in template chain is (2arzA)S2 Warning: unaligning (T0380)D115 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2arzA)F122 Warning: unaligning (T0380)Y116 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2arzA)F122 T0380 4 :EKFLIESNELVESSKIVMVGTNGE 2arzA 3 :VEAAKNARELLLKEYRAVLSTHSK T0380 28 :NGYPNIKAM 2arzA 29 :PGFPFGSVV T0380 38 :RLKHDGLKKFWLSTNTSTRMVERLKKNNKICLYFV 2arzA 38 :PYCLDAEGRPLILISRIAQHTHNLQADPRCSMLVG T0380 73 :DDNKFAGLMLVGTIEILHDRASK 2arzA 78 :DIQAVGRLTLLAEARQLAEEEVA T0380 97 :MLW 2arzA 101 :AAA T0380 101 :DGCEIYYPLGIDD 2arzA 104 :ERYYRYFPESADY T0380 114 :P 2arzA 120 :H T0380 117 :TALCFTAEWGNYYRHLKN 2arzA 123 :DFWVLQPVQWRFIGGFGA Number of specific fragments extracted= 8 number of extra gaps= 1 total=355 Number of alignments=57 # 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 # T0380 read from 1dnlA/merged-good-all-a2m # 1dnlA read from 1dnlA/merged-good-all-a2m # found chain 1dnlA in training set T0380 5 :KFLIESNEL 1dnlA 37 :RWLSQACEA T0380 14 :VESSKIVMVGTNGENGYPNIKAMMRLKHDGLKKF 1dnlA 47 :LADPTAMVVATVDEHGQPYQRIVLLKHYDEKGMV T0380 49 :LSTNTSTRMVERLKKNNKICLYFVDDNKFAGLMLVGTIEILHDRASKEMLWTDGCEIYYP 1dnlA 81 :FYTNLGSRKAHQIENNPRVSLLFPWHTLERQVMVIGKAERLSTLEVMKYFHSRPRDSQIG T0380 109 :LGIDDPDYTALCFTAEWGNYY 1dnlA 171 :EVPLPSFWGGFRVSLEQIEFW T0380 130 :RHLKNITFKIDE 1dnlA 197 :RLHDRFLYQREN Number of specific fragments extracted= 5 number of extra gaps= 0 total=360 Number of alignments=58 # 1dnlA read from 1dnlA/merged-good-all-a2m # found chain 1dnlA in training set T0380 5 :KFLIESNEL 1dnlA 37 :RWLSQACEA T0380 14 :VESSKIVMVGTNGENGYPNIKAMMRLKHDGLK 1dnlA 47 :LADPTAMVVATVDEHGQPYQRIVLLKHYDEKG T0380 47 :FWLSTNTSTRMVERLKKNNKICLYFVDDNKFAGLMLVGTIEILH 1dnlA 79 :MVFYTNLGSRKAHQIENNPRVSLLFPWHTLERQVMVIGKAERLS T0380 92 :RASKEMLWTDGCEIYYP 1dnlA 123 :TLEVMKYFHSRPRDSQI T0380 109 :LGIDDPDYTALCFTAEWGNYYRHLKNITFKIDEIY 1dnlA 171 :EVPLPSFWGGFRVSLEQIEFWQGGEHRLHDRFLYQ Number of specific fragments extracted= 5 number of extra gaps= 0 total=365 Number of alignments=59 # 1dnlA read from 1dnlA/merged-good-all-a2m # found chain 1dnlA in training set T0380 4 :EKFLIESNEL 1dnlA 36 :ERWLSQACEA T0380 14 :VESSKIVMVGTNGENGYPNIKAM 1dnlA 47 :LADPTAMVVATVDEHGQPYQRIV T0380 38 :RLKHDGLKKFWLSTNTSTRMVERLKKNNKICLYFVDDNKFAGLMLVGTIEILHDRASKEMLWTDGCEIYY 1dnlA 70 :LLKHYDEKGMVFYTNLGSRKAHQIENNPRVSLLFPWHTLERQVMVIGKAERLSTLEVMKYFHSRPRDSQI T0380 108 :PLGIDDPD 1dnlA 169 :QGEVPLPS T0380 116 :YTALCFTAEWGNYYRHLK 1dnlA 178 :WGGFRVSLEQIEFWQGGE Number of specific fragments extracted= 5 number of extra gaps= 0 total=370 Number of alignments=60 # command:Using radius: 8.0000 Alignment mode NUMB_ALIGNS: 60 Adding 836 constraints to all.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all.constraints maxweight: 1.0000 Optimizing... Probability sum: -260.3323, CN propb: -260.3323 weights: 0.4912 constraints: 364 # command:Found ConstraintSet # PrintContacts align.constraints_v3 Number of constraints in align.constraints 364 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_v3 Number of constraints in align.constraints.bonus 364 # command:Found ConstraintSet # PrintContacts rejected.constraints_v3 Number of constraints in rejected.constraints 472 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_v3 Number of constraints in rejected.constraints.bonus 472 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_v3 Number of constraints in noncontact.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_v3 Number of constraints in noncontact.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_v3 Number of constraints in all.constraints 836 # command: