# 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:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0380//projects/compbio/experiments/protein-predict/casp7/T0380/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0380//projects/compbio/experiments/protein-predict/casp7/T0380/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0380/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0380/align.constraints_v3.costfcn # future Constraint commands -> align # future HelixConstraint commands -> align # future StrandConstraint commands -> align # future SheetConstraint commands -> align # future Hbond commands -> align # future SSbond commands -> align # Constraint # added constraint: constraint((T0380)F47.CB, (T0380)C120.CB) [> 4.2636 = 7.1060 < 9.2378] w=1.0000 to align # Constraint # added constraint: constraint((T0380)T24.CB, (T0380)I67.CB) [> 3.4458 = 5.7430 < 7.4659] w=1.0000 to align # Constraint # added constraint: constraint((T0380)G23.CA, (T0380)L69.CB) [> 4.3254 = 7.2091 < 9.3718] w=1.0000 to align # Constraint # added constraint: constraint((T0380)G23.CA, (T0380)C68.CB) [> 3.0440 = 5.0733 < 6.5953] w=1.0000 to align # Constraint # added constraint: constraint((T0380)G23.CA, (T0380)I67.CB) [> 3.5946 = 5.9910 < 7.7883] w=1.0000 to align # Constraint # added constraint: constraint((T0380)G23.CA, (T0380)K34.CB) [> 4.2778 = 7.1297 < 9.2686] w=1.0000 to align # Constraint # added constraint: constraint((T0380)G23.CA, (T0380)I33.CB) [> 3.0043 = 5.0071 < 6.5092] w=1.0000 to align # Constraint # added constraint: constraint((T0380)G23.CA, (T0380)N32.CB) [> 3.6697 = 6.1162 < 7.9511] w=1.0000 to align # Constraint # added constraint: constraint((T0380)V22.CB, (T0380)L69.CB) [> 3.2070 = 5.3450 < 6.9484] w=1.0000 to align # Constraint # added constraint: constraint((T0380)V22.CB, (T0380)C68.CB) [> 4.4234 = 7.3724 < 9.5841] w=1.0000 to align # Constraint # added constraint: constraint((T0380)V22.CB, (T0380)I67.CB) [> 3.7099 = 6.1832 < 8.0381] w=1.0000 to align # Constraint # added constraint: constraint((T0380)V22.CB, (T0380)K34.CB) [> 3.3725 = 5.6208 < 7.3070] w=1.0000 to align # Constraint # added constraint: constraint((T0380)V22.CB, (T0380)I33.CB) [> 4.2534 = 7.0891 < 9.2158] w=1.0000 to align # Constraint # added constraint: constraint((T0380)M21.CB, (T0380)Y70.CB) [> 2.7677 = 4.6128 < 5.9966] w=1.0000 to align # Constraint # added constraint: constraint((T0380)M21.CB, (T0380)L69.CB) [> 4.1367 = 6.8945 < 8.9628] w=1.0000 to align # Constraint # added constraint: constraint((T0380)M21.CB, (T0380)A35.CB) [> 3.4554 = 5.7590 < 7.4867] w=1.0000 to align # Constraint # added constraint: constraint((T0380)M21.CB, (T0380)K34.CB) [> 4.2435 = 7.0725 < 9.1943] w=1.0000 to align # Constraint # added constraint: constraint((T0380)M21.CB, (T0380)I33.CB) [> 3.3388 = 5.5646 < 7.2340] w=1.0000 to align # Constraint # added constraint: constraint((T0380)V20.CB, (T0380)F71.CB) [> 3.0232 = 5.0387 < 6.5503] w=1.0000 to align # Constraint # added constraint: constraint((T0380)V20.CB, (T0380)Y70.CB) [> 3.7722 = 6.2869 < 8.1730] w=1.0000 to align # Constraint # added constraint: constraint((T0380)V20.CB, (T0380)L69.CB) [> 2.9311 = 4.8852 < 6.3508] w=1.0000 to align # Constraint # added constraint: constraint((T0380)V20.CB, (T0380)A35.CB) [> 4.2592 = 7.0987 < 9.2283] w=1.0000 to align # Constraint # added constraint: constraint((T0380)I19.CB, (T0380)A35.CB) [> 3.3592 = 5.5986 < 7.2782] w=1.0000 to align # Constraint # added constraint: constraint((T0380)L89.CB, (T0380)A118.CB) [> 2.5264 = 4.2106 < 5.4738] w=1.0000 to align # Constraint # added constraint: constraint((T0380)I88.CB, (T0380)L119.CB) [> 3.5454 = 5.9090 < 7.6817] w=1.0000 to align # Constraint # added constraint: constraint((T0380)I88.CB, (T0380)A118.CB) [> 4.3330 = 7.2216 < 9.3881] w=1.0000 to align # Constraint # added constraint: constraint((T0380)I88.CB, (T0380)T117.CB) [> 3.4162 = 5.6936 < 7.4017] w=1.0000 to align # Constraint # added constraint: constraint((T0380)T85.CB, (T0380)F121.CB) [> 4.3672 = 7.2787 < 9.4623] w=1.0000 to align # Constraint # added constraint: constraint((T0380)G84.CA, (T0380)E124.CB) [> 2.7089 = 4.5149 < 5.8694] w=1.0000 to align # Constraint # added constraint: constraint((T0380)G84.CA, (T0380)F121.CB) [> 3.4045 = 5.6741 < 7.3764] w=1.0000 to align # Constraint # added constraint: constraint((T0380)V83.CB, (T0380)E124.CB) [> 3.2888 = 5.4813 < 7.1257] w=1.0000 to align # Constraint # added constraint: constraint((T0380)M81.CB, (T0380)N127.CB) [> 2.7793 = 4.6321 < 6.0218] w=1.0000 to align # Constraint # added constraint: constraint((T0380)L80.CB, (T0380)Y128.CB) [> 3.1050 = 5.1751 < 6.7276] w=1.0000 to align # Constraint # added constraint: constraint((T0380)L80.CB, (T0380)N127.CB) [> 4.2872 = 7.1453 < 9.2889] w=1.0000 to align # Constraint # added constraint: constraint((T0380)F71.CB, (T0380)L80.CB) [> 2.8466 = 4.7443 < 6.1676] w=1.0000 to align # Constraint # added constraint: constraint((T0380)Y70.CB, (T0380)M81.CB) [> 3.0538 = 5.0896 < 6.6165] w=1.0000 to align # Constraint # added constraint: constraint((T0380)Y70.CB, (T0380)L80.CB) [> 4.2317 = 7.0528 < 9.1687] w=1.0000 to align # Constraint # added constraint: constraint((T0380)L69.CB, (T0380)F121.CB) [> 3.8168 = 6.3613 < 8.2697] w=1.0000 to align # Constraint # added constraint: constraint((T0380)L69.CB, (T0380)L82.CB) [> 2.7061 = 4.5101 < 5.8632] w=1.0000 to align # Constraint # added constraint: constraint((T0380)L69.CB, (T0380)M81.CB) [> 4.3022 = 7.1704 < 9.3215] w=1.0000 to align # Constraint # added constraint: constraint((T0380)C68.CB, (T0380)V83.CB) [> 3.2199 = 5.3665 < 6.9764] w=1.0000 to align # Constraint # added constraint: constraint((T0380)C68.CB, (T0380)L82.CB) [> 4.0882 = 6.8137 < 8.8578] w=1.0000 to align # Constraint # added constraint: constraint((T0380)C68.CB, (T0380)M81.CB) [> 3.8077 = 6.3462 < 8.2500] w=1.0000 to align # Constraint # added constraint: constraint((T0380)I67.CB, (T0380)F121.CB) [> 3.3751 = 5.6252 < 7.3128] w=1.0000 to align # Constraint # added constraint: constraint((T0380)I67.CB, (T0380)G84.CA) [> 3.4585 = 5.7642 < 7.4935] w=1.0000 to align # Constraint # added constraint: constraint((T0380)L49.CB, (T0380)L119.CB) [> 3.0751 = 5.1252 < 6.6627] w=1.0000 to align # Constraint # added constraint: constraint((T0380)L49.CB, (T0380)A118.CB) [> 4.3014 = 7.1691 < 9.3198] w=1.0000 to align # Constraint # added constraint: constraint((T0380)L80.CB, (T0380)G126.CA) [> 4.1994 = 6.9990 < 9.0987] w=0.9948 to align # Constraint # added constraint: constraint((T0380)M81.CB, (T0380)G126.CA) [> 3.6496 = 6.0827 < 7.9075] w=0.9948 to align # Constraint # added constraint: constraint((T0380)L82.CB, (T0380)F121.CB) [> 4.0613 = 6.7687 < 8.7994] w=0.9948 to align # Constraint # added constraint: constraint((T0380)L82.CB, (T0380)G126.CA) [> 3.2339 = 5.3899 < 7.0068] w=0.9948 to align # Constraint # added constraint: constraint((T0380)V83.CB, (T0380)W125.CB) [> 2.3744 = 3.9573 < 5.1445] w=0.9948 to align # Constraint # added constraint: constraint((T0380)V83.CB, (T0380)G126.CA) [> 3.7418 = 6.2363 < 8.1071] w=0.9948 to align # Constraint # added constraint: constraint((T0380)G84.CA, (T0380)W125.CB) [> 4.1256 = 6.8761 < 8.9389] w=0.9948 to align # Constraint # added constraint: constraint((T0380)K66.CB, (T0380)T85.CB) [> 3.7097 = 6.1829 < 8.0378] w=0.9825 to align # Constraint # added constraint: constraint((T0380)K66.CB, (T0380)G84.CA) [> 4.0100 = 6.6832 < 8.6882] w=0.9825 to align # Constraint # added constraint: constraint((T0380)G79.CA, (T0380)Y128.CB) [> 3.7599 = 6.2665 < 8.1464] w=0.9825 to align # Constraint # added constraint: constraint((T0380)Y70.CB, (T0380)G79.CA) [> 4.2457 = 7.0762 < 9.1990] w=0.9825 to align # Constraint # added constraint: constraint((T0380)S50.CB, (T0380)A118.CB) [> 3.2476 = 5.4127 < 7.0366] w=0.9651 to align # Constraint # added constraint: constraint((T0380)L49.CB, (T0380)F121.CB) [> 4.3986 = 7.3310 < 9.5303] w=0.9651 to align # Constraint # added constraint: constraint((T0380)T85.CB, (T0380)E124.CB) [> 4.1799 = 6.9665 < 9.0564] w=0.9482 to align # Constraint # added constraint: constraint((T0380)V22.CB, (T0380)A35.CB) [> 4.5296 = 7.5493 < 9.8141] w=0.9476 to align # Constraint # added constraint: constraint((T0380)T24.CB, (T0380)R60.CB) [> 2.6257 = 4.3761 < 5.6889] w=0.9476 to align # Constraint # added constraint: constraint((T0380)N65.CB, (T0380)T85.CB) [> 3.0013 = 5.0022 < 6.5028] w=0.9476 to align # Constraint # added constraint: constraint((T0380)F47.CB, (T0380)F121.CB) [> 2.8356 = 4.7259 < 6.1437] w=0.9476 to align # Constraint # added constraint: constraint((T0380)T51.CB, (T0380)T117.CB) [> 3.5740 = 5.9567 < 7.7437] w=0.9476 to align # Constraint # added constraint: constraint((T0380)C68.CB, (T0380)G84.CA) [> 4.3796 = 7.2994 < 9.4892] w=0.9476 to align # Constraint # added constraint: constraint((T0380)W48.CB, (T0380)C120.CB) [> 3.3392 = 5.5653 < 7.2349] w=0.9476 to align # Constraint # added constraint: constraint((T0380)W48.CB, (T0380)L119.CB) [> 4.1223 = 6.8706 < 8.9317] w=0.9476 to align # Constraint # added constraint: constraint((T0380)W48.CB, (T0380)A118.CB) [> 3.6696 = 6.1160 < 7.9508] w=0.9476 to align # Constraint # added constraint: constraint((T0380)I67.CB, (T0380)V83.CB) [> 4.5459 = 7.5765 < 9.8494] w=0.9476 to align # Constraint # added constraint: constraint((T0380)I67.CB, (T0380)T85.CB) [> 4.2204 = 7.0340 < 9.1442] w=0.9476 to align # Constraint # added constraint: constraint((T0380)I67.CB, (T0380)I86.CB) [> 2.8744 = 4.7906 < 6.2278] w=0.9476 to align # Constraint # added constraint: constraint((T0380)I86.CB, (T0380)L119.CB) [> 2.9763 = 4.9605 < 6.4487] w=0.9476 to align # Constraint # added constraint: constraint((T0380)I86.CB, (T0380)C120.CB) [> 4.1503 = 6.9172 < 8.9924] w=0.9476 to align # Constraint # added constraint: constraint((T0380)I86.CB, (T0380)F121.CB) [> 3.0547 = 5.0911 < 6.6184] w=0.9476 to align # Constraint # added constraint: constraint((T0380)E87.CB, (T0380)L119.CB) [> 4.1438 = 6.9064 < 8.9783] w=0.9476 to align # Constraint # added constraint: constraint((T0380)E87.CB, (T0380)C120.CB) [> 3.1354 = 5.2256 < 6.7933] w=0.9476 to align # Constraint # added constraint: constraint((T0380)L82.CB, (T0380)A123.CB) [> 3.1470 = 5.2449 < 6.8184] w=0.9476 to align # Constraint # added constraint: constraint((T0380)G84.CA, (T0380)T122.CB) [> 3.5355 = 5.8925 < 7.6603] w=0.9476 to align # Constraint # added constraint: constraint((T0380)G84.CA, (T0380)A123.CB) [> 3.5165 = 5.8608 < 7.6191] w=0.9476 to align # Constraint # added constraint: constraint((T0380)T85.CB, (T0380)T122.CB) [> 3.4207 = 5.7011 < 7.4114] w=0.9476 to align # Constraint # added constraint: constraint((T0380)L89.CB, (T0380)L119.CB) [> 4.2245 = 7.0409 < 9.1532] w=0.9426 to align # Constraint # added constraint: constraint((T0380)G79.CA, (T0380)Y129.CB) [> 2.9521 = 4.9201 < 6.3962] w=0.9252 to align # Constraint # added constraint: constraint((T0380)V20.CB, (T0380)R38.CB) [> 3.3594 = 5.5990 < 7.2787] w=0.9251 to align # Constraint # added constraint: constraint((T0380)V22.CB, (T0380)L49.CB) [> 4.1172 = 6.8621 < 8.9207] w=0.9132 to align # Constraint # added constraint: constraint((T0380)S50.CB, (T0380)T117.CB) [> 4.1758 = 6.9597 < 9.0477] w=0.9129 to align # Constraint # added constraint: constraint((T0380)N25.CB, (T0380)K66.CB) [> 3.9312 = 6.5520 < 8.5176] w=0.9127 to align # Constraint # added constraint: constraint((T0380)N25.CB, (T0380)N64.CB) [> 3.2545 = 5.4242 < 7.0514] w=0.9127 to align # Constraint # added constraint: constraint((T0380)T51.CB, (T0380)L119.CB) [> 3.8215 = 6.3692 < 8.2800] w=0.9127 to align # Constraint # added constraint: constraint((T0380)F47.CB, (T0380)L69.CB) [> 3.8175 = 6.3624 < 8.2711] w=0.9127 to align # Constraint # added constraint: constraint((T0380)S50.CB, (T0380)Y116.CB) [> 3.6530 = 6.0884 < 7.9149] w=0.9076 to align # Constraint # added constraint: constraint((T0380)F47.CB, (T0380)L82.CB) [> 3.9471 = 6.5786 < 8.5522] w=0.9074 to align # Constraint # added constraint: constraint((T0380)N32.CB, (T0380)M57.CB) [> 4.1173 = 6.8622 < 8.9209] w=0.8952 to align # Constraint # added constraint: constraint((T0380)T24.CB, (T0380)L61.CB) [> 3.3998 = 5.6663 < 7.3661] w=0.8952 to align # Constraint # added constraint: constraint((T0380)N65.CB, (T0380)I86.CB) [> 3.1411 = 5.2352 < 6.8058] w=0.8952 to align # Constraint # added constraint: constraint((T0380)L61.CB, (T0380)I86.CB) [> 3.1151 = 5.1919 < 6.7495] w=0.8952 to align # Constraint # added constraint: constraint((T0380)L89.CB, (T0380)C120.CB) [> 3.5602 = 5.9337 < 7.7139] w=0.8952 to align # Constraint # added constraint: constraint((T0380)V22.CB, (T0380)M36.CB) [> 3.0436 = 5.0726 < 6.5944] w=0.8952 to align # Constraint # added constraint: constraint((T0380)V20.CB, (T0380)M36.CB) [> 3.3284 = 5.5473 < 7.2115] w=0.8952 to align # Constraint # added constraint: constraint((T0380)I19.CB, (T0380)M36.CB) [> 4.2298 = 7.0497 < 9.1646] w=0.8952 to align # Constraint # added constraint: constraint((T0380)L82.CB, (T0380)W125.CB) [> 4.3394 = 7.2323 < 9.4020] w=0.8900 to align # Constraint # added constraint: constraint((T0380)S50.CB, (T0380)L98.CB) [> 3.9188 = 6.5313 < 8.4907] w=0.8606 to align # Constraint # added constraint: constraint((T0380)S94.CB, (T0380)A118.CB) [> 3.5945 = 5.9908 < 7.7881] w=0.8605 to align # Constraint # added constraint: constraint((T0380)M36.CB, (T0380)L49.CB) [> 2.9093 = 4.8489 < 6.3036] w=0.8603 to align # Constraint # added constraint: constraint((T0380)T53.CB, (T0380)T117.CB) [> 3.2259 = 5.3765 < 6.9895] w=0.8553 to align # Constraint # added constraint: constraint((T0380)N52.CB, (T0380)Y116.CB) [> 3.6879 = 6.1465 < 7.9904] w=0.8552 to align # Constraint # added constraint: constraint((T0380)W48.CB, (T0380)F121.CB) [> 4.4941 = 7.4902 < 9.7372] w=0.8434 to align # Constraint # added constraint: constraint((T0380)K34.CB, (T0380)M57.CB) [> 3.5523 = 5.9205 < 7.6966] w=0.8428 to align # Constraint # added constraint: constraint((T0380)T24.CB, (T0380)M57.CB) [> 3.2331 = 5.3885 < 7.0051] w=0.8428 to align # Constraint # added constraint: constraint((T0380)L89.CB, (T0380)T117.CB) [> 3.9237 = 6.5394 < 8.5013] w=0.8428 to align # Constraint # added constraint: constraint((T0380)T24.CB, (T0380)N64.CB) [> 4.3522 = 7.2537 < 9.4298] w=0.8428 to align # Constraint # added constraint: constraint((T0380)S50.CB, (T0380)L119.CB) [> 4.4169 = 7.3615 < 9.5699] w=0.8428 to align # Constraint # added constraint: constraint((T0380)V83.CB, (T0380)A123.CB) [> 4.2613 = 7.1022 < 9.2328] w=0.8428 to align # Constraint # added constraint: constraint((T0380)T53.CB, (T0380)D115.CB) [> 3.0205 = 5.0341 < 6.5443] w=0.8396 to align # Constraint # added constraint: constraint((T0380)K45.CB, (T0380)T122.CB) [> 3.7100 = 6.1833 < 8.0383] w=0.8032 to align # Constraint # added constraint: constraint((T0380)I19.CB, (T0380)R38.CB) [> 4.1156 = 6.8593 < 8.9171] w=0.8031 to align # Constraint # added constraint: constraint((T0380)M36.CB, (T0380)T51.CB) [> 4.1379 = 6.8965 < 8.9654] w=0.8029 to align # Constraint # added constraint: constraint((T0380)Y70.CB, (T0380)L82.CB) [> 4.5222 = 7.5370 < 9.7980] w=0.7904 to align # Constraint # added constraint: constraint((T0380)K46.CB, (T0380)C120.CB) [> 3.4382 = 5.7303 < 7.4494] w=0.7904 to align # Constraint # added constraint: constraint((T0380)T53.CB, (T0380)Y116.CB) [> 4.2940 = 7.1566 < 9.3036] w=0.7860 to align # Constraint # added constraint: constraint((T0380)R38.CB, (T0380)F47.CB) [> 3.4321 = 5.7202 < 7.4363] w=0.7856 to align # Constraint # added constraint: constraint((T0380)L80.CB, (T0380)Y129.CB) [> 4.4457 = 7.4095 < 9.6324] w=0.7854 to align # Constraint # added constraint: constraint((T0380)N52.CB, (T0380)T117.CB) [> 4.2184 = 7.0307 < 9.1399] w=0.7732 to align # Constraint # added constraint: constraint((T0380)N52.CB, (T0380)D115.CB) [> 3.4838 = 5.8064 < 7.5483] w=0.7696 to align # Constraint # added constraint: constraint((T0380)K18.CB, (T0380)R38.CB) [> 3.3171 = 5.5284 < 7.1870] w=0.7681 to align # Constraint # added constraint: constraint((T0380)K46.CB, (T0380)F121.CB) [> 3.7497 = 6.2495 < 8.1244] w=0.7555 to align # Constraint # added constraint: constraint((T0380)I19.CB, (T0380)M37.CB) [> 3.6050 = 6.0084 < 7.8109] w=0.7555 to align # Constraint # added constraint: constraint((T0380)K18.CB, (T0380)M37.CB) [> 3.6062 = 6.0103 < 7.8134] w=0.7555 to align # Constraint # added constraint: constraint((T0380)L61.CB, (T0380)L119.CB) [> 3.9065 = 6.5108 < 8.4641] w=0.7386 to align # Constraint # added constraint: constraint((T0380)L98.CB, (T0380)A118.CB) [> 3.1827 = 5.3044 < 6.8957] w=0.7384 to align # Constraint # added constraint: constraint((T0380)E87.CB, (T0380)T122.CB) [> 4.1532 = 6.9220 < 8.9986] w=0.7380 to align # Constraint # added constraint: constraint((T0380)S17.CB, (T0380)F71.CB) [> 3.1079 = 5.1798 < 6.7337] w=0.7330 to align # Constraint # added constraint: constraint((T0380)I19.CB, (T0380)F71.CB) [> 4.5868 = 7.6447 < 9.9381] w=0.7328 to align # Constraint # added constraint: constraint((T0380)F47.CB, (T0380)A123.CB) [> 4.1659 = 6.9432 < 9.0261] w=0.7211 to align # Constraint # added constraint: constraint((T0380)T24.CB, (T0380)K66.CB) [> 4.5351 = 7.5585 < 9.8261] w=0.7205 to align # Constraint # added constraint: constraint((T0380)A78.CB, (T0380)Y129.CB) [> 3.6685 = 6.1142 < 7.9484] w=0.7159 to align # Constraint # added constraint: constraint((T0380)T51.CB, (T0380)Y116.CB) [> 4.2458 = 7.0763 < 9.1992] w=0.7155 to align # Constraint # added constraint: constraint((T0380)E27.CB, (T0380)K63.CB) [> 3.6597 = 6.0995 < 7.9294] w=0.7037 to align # Constraint # added constraint: constraint((T0380)A78.CB, (T0380)Y128.CB) [> 4.4128 = 7.3546 < 9.5610] w=0.7035 to align # Constraint # added constraint: constraint((T0380)M37.CB, (T0380)L49.CB) [> 4.0837 = 6.8061 < 8.8480] w=0.6981 to align # Constraint # added constraint: constraint((T0380)V58.CB, (T0380)T117.CB) [> 3.8633 = 6.4387 < 8.3704] w=0.6862 to align # Constraint # added constraint: constraint((T0380)V14.CB, (T0380)F71.CB) [> 3.7339 = 6.2232 < 8.0901] w=0.6860 to align # Constraint # added constraint: constraint((T0380)L13.CB, (T0380)L80.CB) [> 3.2057 = 5.3428 < 6.9457] w=0.6685 to align # Constraint # added constraint: constraint((T0380)M21.CB, (T0380)M36.CB) [> 4.4982 = 7.4970 < 9.7462] w=0.6684 to align # Constraint # added constraint: constraint((T0380)L13.CB, (T0380)F71.CB) [> 3.6654 = 6.1090 < 7.9416] w=0.6510 to align # Constraint # added constraint: constraint((T0380)K46.CB, (T0380)T122.CB) [> 3.3269 = 5.5448 < 7.2082] w=0.6338 to align # Constraint # added constraint: constraint((T0380)F71.CB, (T0380)L82.CB) [> 4.5781 = 7.6302 < 9.9193] w=0.6338 to align # Constraint # added constraint: constraint((T0380)L13.CB, (T0380)G79.CA) [> 3.8446 = 6.4077 < 8.3301] w=0.6336 to align # Constraint # added constraint: constraint((T0380)G23.CA, (T0380)M57.CB) [> 4.6069 = 7.6782 < 9.9817] w=0.6332 to align # Constraint # added constraint: constraint((T0380)K46.CB, (T0380)A123.CB) [> 4.0683 = 6.7805 < 8.8147] w=0.6332 to align # Constraint # added constraint: constraint((T0380)F71.CB, (T0380)M81.CB) [> 4.5946 = 7.6577 < 9.9550] w=0.6288 to align # Constraint # added constraint: constraint((T0380)V20.CB, (T0380)F47.CB) [> 4.4007 = 7.3345 < 9.5348] w=0.6282 to align # Constraint # added constraint: constraint((T0380)M81.CB, (T0380)W125.CB) [> 4.6265 = 7.7109 < 10.0242] w=0.5756 to align # Constraint # added constraint: constraint((T0380)M21.CB, (T0380)F71.CB) [> 4.5594 = 7.5990 < 9.8787] w=0.5756 to align # Constraint # added constraint: constraint((T0380)K66.CB, (T0380)I86.CB) [> 4.3443 = 7.2406 < 9.4128] w=0.5639 to align # Constraint # added constraint: constraint((T0380)F6.CB, (T0380)Y128.CB) [> 3.7614 = 6.2690 < 8.1497] w=0.5586 to align # Constraint # added constraint: constraint((T0380)V20.CB, (T0380)L49.CB) [> 4.4392 = 7.3987 < 9.6183] w=0.5464 to align # Constraint # added constraint: constraint((T0380)S17.CB, (T0380)D73.CB) [> 4.1282 = 6.8804 < 8.9445] w=0.5449 to align # Constraint # added constraint: constraint((T0380)V14.CB, (T0380)L80.CB) [> 3.6868 = 6.1447 < 7.9881] w=0.5413 to align # Constraint # added constraint: constraint((T0380)G23.CA, (T0380)Y70.CB) [> 4.6193 = 7.6988 < 10.0085] w=0.5292 to align # Constraint # added constraint: constraint((T0380)I88.CB, (T0380)C120.CB) [> 4.6409 = 7.7348 < 10.0552] w=0.5290 to align # Constraint # added constraint: constraint((T0380)T24.CB, (T0380)I86.CB) [> 4.5887 = 7.6479 < 9.9422] w=0.5290 to align # Constraint # added constraint: constraint((T0380)I86.CB, (T0380)T122.CB) [> 4.5795 = 7.6325 < 9.9223] w=0.5284 to align # Constraint # added constraint: constraint((T0380)L13.CB, (T0380)D73.CB) [> 3.7775 = 6.2958 < 8.1846] w=0.5275 to align # Constraint # added constraint: constraint((T0380)I67.CB, (T0380)L119.CB) [> 4.5823 = 7.6372 < 9.9284] w=0.5240 to align # Constraint # added constraint: constraint((T0380)V83.CB, (T0380)N127.CB) [> 4.5206 = 7.5343 < 9.7946] w=0.5234 to align # Constraint # added constraint: constraint((T0380)S10.CB, (T0380)L80.CB) [> 3.1249 = 5.2081 < 6.7705] w=0.4922 to align # Constraint # added constraint: constraint((T0380)K95.CB, (T0380)Y116.CB) [> 4.0978 = 6.8296 < 8.8785] w=0.4891 to align # Constraint # added constraint: constraint((T0380)S10.CB, (T0380)Y128.CB) [> 3.3435 = 5.5726 < 7.2444] w=0.4887 to align # Constraint # added constraint: constraint((T0380)R38.CB, (T0380)F71.CB) [> 4.5926 = 7.6543 < 9.9506] w=0.4716 to align # Constraint # added constraint: constraint((T0380)A78.CB, (T0380)H131.CB) [> 3.6438 = 6.0731 < 7.8950] w=0.4714 to align # Constraint # added constraint: constraint((T0380)M36.CB, (T0380)L69.CB) [> 4.5000 = 7.5001 < 9.7501] w=0.4710 to align # Constraint # added constraint: constraint((T0380)M37.CB, (T0380)S50.CB) [> 4.2949 = 7.1582 < 9.3057] w=0.4710 to align # Constraint # added constraint: constraint((T0380)W48.CB, (T0380)L89.CB) [> 4.3993 = 7.3322 < 9.5319] w=0.4536 to align # Constraint # added constraint: constraint((T0380)S54.CB, (T0380)D115.CB) [> 3.4141 = 5.6902 < 7.3972] w=0.4361 to align # Constraint # added constraint: constraint((T0380)M81.CB, (T0380)Y128.CB) [> 3.9731 = 6.6218 < 8.6083] w=0.4244 to align # Constraint # added constraint: constraint((T0380)K62.CB, (T0380)I88.CB) [> 4.0262 = 6.7104 < 8.7235] w=0.4244 to align # Constraint # added constraint: constraint((T0380)V20.CB, (T0380)M37.CB) [> 4.3882 = 7.3136 < 9.5077] w=0.4242 to align # Constraint # added constraint: constraint((T0380)M81.CB, (T0380)Y129.CB) [> 4.3612 = 7.2687 < 9.4493] w=0.4192 to align # Constraint # added constraint: constraint((T0380)M21.CB, (T0380)V72.CB) [> 4.2807 = 7.1345 < 9.2749] w=0.4192 to align # Constraint # added constraint: constraint((T0380)V14.CB, (T0380)F47.CB) [> 4.2433 = 7.0722 < 9.1938] w=0.4190 to align # Constraint # added constraint: constraint((T0380)L44.CB, (T0380)T122.CB) [> 4.1539 = 6.9232 < 9.0001] w=0.4067 to align # Constraint # added constraint: constraint((T0380)S50.CB, (T0380)W99.CB) [> 4.2494 = 7.0822 < 9.2069] w=0.4014 to align # Constraint # added constraint: constraint((T0380)K45.CB, (T0380)C120.CB) [> 2.9335 = 4.8891 < 6.3559] w=0.3843 to align # Constraint # added constraint: constraint((T0380)E15.CB, (T0380)K40.CB) [> 3.5861 = 5.9768 < 7.7698] w=0.3841 to align # Constraint # added constraint: constraint((T0380)S10.CB, (T0380)G126.CA) [> 4.0375 = 6.7292 < 8.7479] w=0.3839 to align # Constraint # added constraint: constraint((T0380)H90.CB, (T0380)T117.CB) [> 3.6389 = 6.0648 < 7.8842] w=0.3718 to align # Constraint # added constraint: constraint((T0380)L69.CB, (T0380)G84.CA) [> 4.4632 = 7.4387 < 9.6704] w=0.3718 to align # Constraint # added constraint: constraint((T0380)T24.CB, (T0380)K34.CB) [> 4.4017 = 7.3361 < 9.5370] w=0.3712 to align # Constraint # added constraint: constraint((T0380)F6.CB, (T0380)L80.CB) [> 3.7018 = 6.1698 < 8.0207] w=0.3685 to align # Constraint # added constraint: constraint((T0380)V58.CB, (T0380)L119.CB) [> 4.5319 = 7.5532 < 9.8191] w=0.3668 to align # Constraint # added constraint: constraint((T0380)K18.CB, (T0380)Y106.CB) [> 3.8211 = 6.3684 < 8.2790] w=0.3664 to align # Constraint # added constraint: constraint((T0380)K66.CB, (T0380)V83.CB) [> 4.5262 = 7.5436 < 9.8067] w=0.3491 to align # Constraint # added constraint: constraint((T0380)M36.CB, (T0380)S50.CB) [> 4.5300 = 7.5500 < 9.8150] w=0.3490 to align # Constraint # added constraint: constraint((T0380)V22.CB, (T0380)Y70.CB) [> 4.6990 = 7.8317 < 10.1812] w=0.3196 to align # Constraint # added constraint: constraint((T0380)V58.CB, (T0380)I88.CB) [> 3.8020 = 6.3367 < 8.2377] w=0.3194 to align # Constraint # added constraint: constraint((T0380)T24.CB, (T0380)I33.CB) [> 4.5718 = 7.6197 < 9.9056] w=0.3194 to align # Constraint # added constraint: constraint((T0380)L69.CB, (T0380)V83.CB) [> 4.7138 = 7.8563 < 10.2132] w=0.3191 to align # Constraint # added constraint: constraint((T0380)S94.CB, (T0380)T117.CB) [> 3.6874 = 6.1456 < 7.9893] w=0.3144 to align # Constraint # added constraint: constraint((T0380)S17.CB, (T0380)V72.CB) [> 4.2837 = 7.1395 < 9.2813] w=0.3144 to align # Constraint # added constraint: constraint((T0380)F77.CB, (T0380)H131.CB) [> 2.4709 = 4.1181 < 5.3535] w=0.3140 to align # Constraint # added constraint: constraint((T0380)W48.CB, (T0380)G102.CA) [> 3.9080 = 6.5133 < 8.4673] w=0.3140 to align # Constraint # added constraint: constraint((T0380)K34.CB, (T0380)R56.CB) [> 4.4096 = 7.3493 < 9.5541] w=0.3138 to align # Constraint # added constraint: constraint((T0380)W99.CB, (T0380)I111.CB) [> 4.0347 = 6.7245 < 8.7419] w=0.3003 to align # Constraint # added constraint: constraint((T0380)E9.CB, (T0380)Y128.CB) [> 3.9839 = 6.6399 < 8.6318] w=0.3001 to align # Constraint # added constraint: constraint((T0380)L39.CB, (T0380)A118.CB) [> 4.4780 = 7.4633 < 9.7022] w=0.2969 to align # Constraint # added constraint: constraint((T0380)K95.CB, (T0380)T117.CB) [> 3.8530 = 6.4217 < 8.3482] w=0.2844 to align # Constraint # added constraint: constraint((T0380)V14.CB, (T0380)D73.CB) [> 3.5052 = 5.8419 < 7.5945] w=0.2795 to align # Constraint # added constraint: constraint((T0380)S10.CB, (T0380)K76.CB) [> 3.9267 = 6.5445 < 8.5078] w=0.2795 to align # Constraint # added constraint: constraint((T0380)L7.CB, (T0380)S17.CB) [> 3.8266 = 6.3776 < 8.2909] w=0.2795 to align # Constraint # added constraint: constraint((T0380)K45.CB, (T0380)F121.CB) [> 3.1265 = 5.2108 < 6.7741] w=0.2795 to align # Constraint # added constraint: constraint((T0380)L44.CB, (T0380)C120.CB) [> 3.9549 = 6.5915 < 8.5689] w=0.2794 to align # Constraint # added constraint: constraint((T0380)F77.CB, (T0380)R130.CB) [> 3.9583 = 6.5971 < 8.5762] w=0.2791 to align # Constraint # added constraint: constraint((T0380)T51.CB, (T0380)A118.CB) [> 4.3648 = 7.2746 < 9.4570] w=0.2670 to align # Constraint # added constraint: constraint((T0380)H90.CB, (T0380)A118.CB) [> 4.4960 = 7.4934 < 9.7414] w=0.2670 to align # Constraint # added constraint: constraint((T0380)L7.CB, (T0380)K18.CB) [> 4.4950 = 7.4917 < 9.7393] w=0.2620 to align # Constraint # added constraint: constraint((T0380)F6.CB, (T0380)A78.CB) [> 3.8871 = 6.4785 < 8.4221] w=0.2620 to align # Constraint # added constraint: constraint((T0380)F77.CB, (T0380)Y129.CB) [> 3.9264 = 6.5440 < 8.5072] w=0.2616 to align # Constraint # added constraint: constraint((T0380)W99.CB, (T0380)Y116.CB) [> 4.0884 = 6.8140 < 8.8582] w=0.2444 to align # Constraint # added constraint: constraint((T0380)H41.CB, (T0380)D101.CB) [> 3.7530 = 6.2550 < 8.1315] w=0.2443 to align # Constraint # added constraint: constraint((T0380)K18.CB, (T0380)I105.CB) [> 4.0176 = 6.6960 < 8.7048] w=0.2443 to align # Constraint # added constraint: constraint((T0380)L39.CB, (T0380)Y106.CB) [> 3.4694 = 5.7824 < 7.5171] w=0.2443 to align # Constraint # added constraint: constraint((T0380)T53.CB, (T0380)P114.CB) [> 4.4292 = 7.3821 < 9.5967] w=0.2442 to align # Constraint # added constraint: constraint((T0380)M37.CB, (T0380)Y106.CB) [> 3.6989 = 6.1648 < 8.0143] w=0.2441 to align # Constraint # added constraint: constraint((T0380)N75.CB, (T0380)L132.CB) [> 4.1696 = 6.9494 < 9.0342] w=0.2271 to align # Constraint # added constraint: constraint((T0380)N11.CB, (T0380)D42.CB) [> 4.0644 = 6.7739 < 8.8061] w=0.2270 to align # Constraint # added constraint: constraint((T0380)S50.CB, (T0380)C103.CB) [> 3.9504 = 6.5841 < 8.5593] w=0.2267 to align # Constraint # added constraint: constraint((T0380)V20.CB, (T0380)V72.CB) [> 4.6502 = 7.7504 < 10.0755] w=0.2148 to align # Constraint # added constraint: constraint((T0380)V22.CB, (T0380)F121.CB) [> 4.5467 = 7.5779 < 9.8512] w=0.2148 to align # Constraint # added constraint: constraint((T0380)P31.CB, (T0380)C68.CB) [> 4.5974 = 7.6623 < 9.9610] w=0.2148 to align # Constraint # added constraint: constraint((T0380)K18.CB, (T0380)F71.CB) [> 4.0037 = 6.6728 < 8.6747] w=0.2146 to align # Constraint # added constraint: constraint((T0380)N52.CB, (T0380)D113.CB) [> 4.2942 = 7.1570 < 9.3041] w=0.2113 to align # Constraint # added constraint: constraint((T0380)L82.CB, (T0380)N127.CB) [> 4.6403 = 7.7338 < 10.0540] w=0.2096 to align # Constraint # added constraint: constraint((T0380)V58.CB, (T0380)D115.CB) [> 4.4742 = 7.4570 < 9.6941] w=0.2096 to align # Constraint # added constraint: constraint((T0380)W99.CB, (T0380)L109.CB) [> 4.2869 = 7.1448 < 9.2882] w=0.2096 to align # Constraint # added constraint: constraint((T0380)D74.CB, (T0380)H131.CB) [> 4.3381 = 7.2301 < 9.3991] w=0.2096 to align # Constraint # added constraint: constraint((T0380)N127.CB, (T0380)T136.CB) [> 3.1492 = 5.2487 < 6.8233] w=0.2092 to align # Constraint # added constraint: constraint((T0380)L49.CB, (T0380)I86.CB) [> 4.4067 = 7.3445 < 9.5479] w=0.2090 to align # Constraint # added constraint: constraint((T0380)S10.CB, (T0380)N127.CB) [> 4.4320 = 7.3867 < 9.6027] w=0.1921 to align # Constraint # added constraint: constraint((T0380)M37.CB, (T0380)G102.CA) [> 4.3317 = 7.2196 < 9.3855] w=0.1919 to align # Constraint # added constraint: constraint((T0380)S16.CB, (T0380)M37.CB) [> 4.3110 = 7.1850 < 9.3405] w=0.1747 to align # Constraint # added constraint: constraint((T0380)W99.CB, (T0380)G110.CA) [> 4.2400 = 7.0667 < 9.1867] w=0.1747 to align # Constraint # added constraint: constraint((T0380)G79.CA, (T0380)H131.CB) [> 4.4874 = 7.4790 < 9.7227] w=0.1747 to align # Constraint # added constraint: constraint((T0380)L49.CB, (T0380)L69.CB) [> 4.5178 = 7.5297 < 9.7886] w=0.1747 to align # Constraint # added constraint: constraint((T0380)A78.CB, (T0380)L132.CB) [> 4.2971 = 7.1618 < 9.3103] w=0.1747 to align # Constraint # added constraint: constraint((T0380)G126.CA, (T0380)T136.CB) [> 3.8248 = 6.3747 < 8.2871] w=0.1745 to align # Constraint # added constraint: constraint((T0380)H41.CB, (T0380)L98.CB) [> 4.0258 = 6.7098 < 8.7227] w=0.1745 to align # Constraint # added constraint: constraint((T0380)N127.CB, (T0380)F137.CB) [> 4.2742 = 7.1236 < 9.2607] w=0.1743 to align # Constraint # added constraint: constraint((T0380)G26.CA, (T0380)E59.CB) [> 4.5545 = 7.5908 < 9.8681] w=0.1624 to align # Constraint # added constraint: constraint((T0380)I33.CB, (T0380)Y70.CB) [> 4.7633 = 7.9388 < 10.3204] w=0.1624 to align # Constraint # added constraint: constraint((T0380)S50.CB, (T0380)G110.CA) [> 4.5807 = 7.6344 < 9.9248] w=0.1603 to align # Constraint # added constraint: constraint((T0380)F6.CB, (T0380)K76.CB) [> 4.7486 = 7.9143 < 10.2886] w=0.1572 to align # Constraint # added constraint: constraint((T0380)F6.CB, (T0380)D73.CB) [> 4.3697 = 7.2828 < 9.4677] w=0.1572 to align # Constraint # added constraint: constraint((T0380)W125.CB, (T0380)T136.CB) [> 4.1262 = 6.8770 < 8.9401] w=0.1572 to align # Constraint # added constraint: constraint((T0380)G79.CA, (T0380)N127.CB) [> 4.7398 = 7.8997 < 10.2696] w=0.1572 to align # Constraint # added constraint: constraint((T0380)W125.CB, (T0380)F137.CB) [> 4.0953 = 6.8255 < 8.8731] w=0.1572 to align # Constraint # added constraint: constraint((T0380)T51.CB, (T0380)L61.CB) [> 4.6712 = 7.7854 < 10.1210] w=0.1572 to align # Constraint # added constraint: constraint((T0380)N65.CB, (T0380)I88.CB) [> 4.1106 = 6.8509 < 8.9062] w=0.1572 to align # Constraint # added constraint: constraint((T0380)T24.CB, (T0380)C68.CB) [> 4.6028 = 7.6713 < 9.9727] w=0.1572 to align # Constraint # added constraint: constraint((T0380)V22.CB, (T0380)T51.CB) [> 4.6217 = 7.7028 < 10.0136] w=0.1572 to align # Constraint # added constraint: constraint((T0380)K34.CB, (T0380)T55.CB) [> 4.4244 = 7.3740 < 9.5862] w=0.1566 to align # Constraint # added constraint: constraint((T0380)W125.CB, (T0380)K138.CB) [> 3.3075 = 5.5124 < 7.1662] w=0.1397 to align # Constraint # added constraint: constraint((T0380)F6.CB, (T0380)G126.CA) [> 3.8433 = 6.4056 < 8.3272] w=0.1396 to align # Constraint # added constraint: constraint((T0380)L98.CB, (T0380)C120.CB) [> 4.1584 = 6.9307 < 9.0099] w=0.1395 to align # Constraint # added constraint: constraint((T0380)L39.CB, (T0380)C103.CB) [> 4.0006 = 6.6676 < 8.6679] w=0.1394 to align # Constraint # added constraint: constraint((T0380)F77.CB, (T0380)L132.CB) [> 4.3928 = 7.3213 < 9.5177] w=0.1394 to align # Constraint # added constraint: constraint((T0380)K45.CB, (T0380)G84.CA) [> 4.7499 = 7.9165 < 10.2915] w=0.1223 to align # Constraint # added constraint: constraint((T0380)H41.CB, (T0380)C120.CB) [> 4.3639 = 7.2731 < 9.4551] w=0.1222 to align # Constraint # added constraint: constraint((T0380)R38.CB, (T0380)Y106.CB) [> 4.6511 = 7.7518 < 10.0774] w=0.1222 to align # Constraint # added constraint: constraint((T0380)G126.CA, (T0380)I142.CB) [> 3.0824 = 5.1374 < 6.6786] w=0.1221 to align # Constraint # added constraint: constraint((T0380)I19.CB, (T0380)L39.CB) [> 4.3434 = 7.2390 < 9.4108] w=0.1221 to align # Constraint # added constraint: constraint((T0380)M37.CB, (T0380)I105.CB) [> 4.3579 = 7.2632 < 9.4422] w=0.1221 to align # Constraint # added constraint: constraint((T0380)F6.CB, (T0380)R130.CB) [> 3.6936 = 6.1560 < 8.0028] w=0.1221 to align # Constraint # added constraint: constraint((T0380)M37.CB, (T0380)Y107.CB) [> 3.5865 = 5.9775 < 7.7708] w=0.1221 to align # Constraint # added constraint: constraint((T0380)L49.CB, (T0380)C120.CB) [> 4.3628 = 7.2713 < 9.4527] w=0.1217 to align # Constraint # added constraint: constraint((T0380)I19.CB, (T0380)V72.CB) [> 4.6395 = 7.7326 < 10.0523] w=0.1100 to align # Constraint # added constraint: constraint((T0380)G26.CA, (T0380)L61.CB) [> 4.4147 = 7.3578 < 9.5651] w=0.1100 to align # Constraint # added constraint: constraint((T0380)S16.CB, (T0380)A35.CB) [> 4.6704 = 7.7839 < 10.1191] w=0.1048 to align # Constraint # added constraint: constraint((T0380)M21.CB, (T0380)C68.CB) [> 4.7293 = 7.8822 < 10.2469] w=0.1048 to align # Constraint # added constraint: constraint((T0380)W125.CB, (T0380)E141.CB) [> 4.0003 = 6.6671 < 8.6672] w=0.1048 to align # Constraint # added constraint: constraint((T0380)W125.CB, (T0380)I142.CB) [> 3.9662 = 6.6104 < 8.5935] w=0.1048 to align # Constraint # added constraint: constraint((T0380)N127.CB, (T0380)I139.CB) [> 3.7923 = 6.3204 < 8.2165] w=0.1048 to align # Constraint # added constraint: constraint((T0380)N127.CB, (T0380)D140.CB) [> 4.1124 = 6.8540 < 8.9102] w=0.1048 to align # Constraint # added constraint: constraint((T0380)N127.CB, (T0380)E141.CB) [> 2.6858 = 4.4763 < 5.8192] w=0.1048 to align # Constraint # added constraint: constraint((T0380)N127.CB, (T0380)I142.CB) [> 4.3998 = 7.3331 < 9.5330] w=0.1048 to align # Constraint # added constraint: constraint((T0380)L39.CB, (T0380)Y107.CB) [> 3.3153 = 5.5255 < 7.1832] w=0.1048 to align # Constraint # added constraint: constraint((T0380)R38.CB, (T0380)Y107.CB) [> 4.3502 = 7.2503 < 9.4254] w=0.1048 to align # Constraint # added constraint: constraint((T0380)T24.CB, (T0380)S54.CB) [> 4.5892 = 7.6487 < 9.9433] w=0.1048 to align # Constraint # added constraint: constraint((T0380)T24.CB, (T0380)V58.CB) [> 4.1353 = 6.8922 < 8.9598] w=0.1048 to align # Constraint # added constraint: constraint((T0380)G26.CA, (T0380)V58.CB) [> 3.7701 = 6.2835 < 8.1686] w=0.1048 to align # Constraint # added constraint: constraint((T0380)N32.CB, (T0380)V58.CB) [> 3.3175 = 5.5291 < 7.1878] w=0.1048 to align # Constraint # added constraint: constraint((T0380)E124.CB, (T0380)I139.CB) [> 3.3484 = 5.5808 < 7.2550] w=0.1046 to align # Constraint # added constraint: constraint((T0380)S50.CB, (T0380)Y107.CB) [> 4.6626 = 7.7710 < 10.1023] w=0.1046 to align # Constraint # added constraint: constraint((T0380)W48.CB, (T0380)C103.CB) [> 3.4997 = 5.8329 < 7.5828] w=0.1046 to align # Constraint # added constraint: constraint((T0380)C68.CB, (T0380)W125.CB) [> 4.7374 = 7.8957 < 10.2644] w=0.1042 to align # Constraint # added constraint: constraint((T0380)K95.CB, (T0380)I111.CB) [> 3.7942 = 6.3237 < 8.2208] w=0.0908 to align # Constraint # added constraint: constraint((T0380)F47.CB, (T0380)A118.CB) [> 3.4142 = 5.6903 < 7.3974] w=0.0873 to align # Constraint # added constraint: constraint((T0380)C103.CB, (T0380)A118.CB) [> 3.8862 = 6.4770 < 8.4201] w=0.0871 to align # Constraint # added constraint: constraint((T0380)F6.CB, (T0380)A123.CB) [> 4.1863 = 6.9772 < 9.0704] w=0.0715 to align # Constraint # added constraint: constraint((T0380)G43.CA, (T0380)A123.CB) [> 3.6440 = 6.0733 < 7.8953] w=0.0699 to align # Constraint # added constraint: constraint((T0380)Y107.CB, (T0380)Y116.CB) [> 2.9511 = 4.9186 < 6.3941] w=0.0699 to align # Constraint # added constraint: constraint((T0380)F6.CB, (T0380)I135.CB) [> 2.8869 = 4.8115 < 6.2549] w=0.0699 to align # Constraint # added constraint: constraint((T0380)I2.CB, (T0380)Y128.CB) [> 3.4564 = 5.7607 < 7.4889] w=0.0699 to align # Constraint # added constraint: constraint((T0380)I33.CB, (T0380)C68.CB) [> 4.6296 = 7.7160 < 10.0308] w=0.0576 to align # Constraint # added constraint: constraint((T0380)F47.CB, (T0380)T122.CB) [> 4.7376 = 7.8959 < 10.2647] w=0.0576 to align # Constraint # added constraint: constraint((T0380)I2.CB, (T0380)A123.CB) [> 4.1652 = 6.9419 < 9.0245] w=0.0541 to align # Constraint # added constraint: constraint((T0380)N65.CB, (T0380)G84.CA) [> 4.7475 = 7.9126 < 10.2863] w=0.0524 to align # Constraint # added constraint: constraint((T0380)W125.CB, (T0380)I139.CB) [> 4.1494 = 6.9156 < 8.9903] w=0.0524 to align # Constraint # added constraint: constraint((T0380)N52.CB, (T0380)Y106.CB) [> 4.4510 = 7.4184 < 9.6439] w=0.0524 to align # Constraint # added constraint: constraint((T0380)C103.CB, (T0380)Y116.CB) [> 4.2627 = 7.1045 < 9.2359] w=0.0524 to align # Constraint # added constraint: constraint((T0380)S17.CB, (T0380)Y106.CB) [> 3.5569 = 5.9282 < 7.7067] w=0.0524 to align # Constraint # added constraint: constraint((T0380)F47.CB, (T0380)I67.CB) [> 4.4937 = 7.4895 < 9.7363] w=0.0524 to align # Constraint # added constraint: constraint((T0380)F47.CB, (T0380)G84.CA) [> 4.7859 = 7.9765 < 10.3694] w=0.0524 to align # Constraint # added constraint: constraint((T0380)L49.CB, (T0380)I67.CB) [> 4.7555 = 7.9259 < 10.3037] w=0.0524 to align # Constraint # added constraint: constraint((T0380)L82.CB, (T0380)E124.CB) [> 4.4852 = 7.4754 < 9.7180] w=0.0524 to align # Constraint # added constraint: constraint((T0380)V72.CB, (T0380)M81.CB) [> 4.7491 = 7.9152 < 10.2898] w=0.0524 to align # Constraint # added constraint: constraint((T0380)E124.CB, (T0380)Y143.CB) [> 4.0734 = 6.7890 < 8.8257] w=0.0524 to align # Constraint # added constraint: constraint((T0380)W125.CB, (T0380)Y143.CB) [> 3.0729 = 5.1214 < 6.6579] w=0.0524 to align # Constraint # added constraint: constraint((T0380)V20.CB, (T0380)K46.CB) [> 4.5170 = 7.5283 < 9.7868] w=0.0524 to align # Constraint # added constraint: constraint((T0380)K66.CB, (T0380)E124.CB) [> 4.3526 = 7.2544 < 9.4307] w=0.0524 to align # Constraint # added constraint: constraint((T0380)N64.CB, (T0380)T85.CB) [> 2.9791 = 4.9652 < 6.4547] w=0.0524 to align # Constraint # added constraint: constraint((T0380)N25.CB, (T0380)N65.CB) [> 4.0847 = 6.8079 < 8.8503] w=0.0524 to align # Constraint # added constraint: constraint((T0380)T24.CB, (T0380)N65.CB) [> 4.2847 = 7.1412 < 9.2835] w=0.0524 to align # Constraint # added constraint: constraint((T0380)F6.CB, (T0380)G79.CA) [> 4.5395 = 7.5658 < 9.8355] w=0.0524 to align # Constraint # added constraint: constraint((T0380)F6.CB, (T0380)N127.CB) [> 4.3661 = 7.2769 < 9.4599] w=0.0524 to align # Constraint # added constraint: constraint((T0380)W48.CB, (T0380)Y106.CB) [> 4.4464 = 7.4107 < 9.6339] w=0.0524 to align # Constraint # added constraint: constraint((T0380)W48.CB, (T0380)I105.CB) [> 4.3772 = 7.2954 < 9.4840] w=0.0524 to align # Constraint # added constraint: constraint((T0380)Y30.CB, (T0380)R60.CB) [> 4.6080 = 7.6801 < 9.9841] w=0.0524 to align # Constraint # added constraint: constraint((T0380)C68.CB, (T0380)F121.CB) [> 4.7466 = 7.9110 < 10.2843] w=0.0524 to align # Constraint # added constraint: constraint((T0380)N25.CB, (T0380)K63.CB) [> 4.3213 = 7.2022 < 9.3629] w=0.0524 to align # Constraint # added constraint: constraint((T0380)K34.CB, (T0380)T53.CB) [> 3.1489 = 5.2482 < 6.8227] w=0.0524 to align # Constraint # added constraint: constraint((T0380)K34.CB, (T0380)T51.CB) [> 3.5294 = 5.8824 < 7.6471] w=0.0524 to align # Constraint # added constraint: constraint((T0380)N32.CB, (T0380)T55.CB) [> 4.1965 = 6.9942 < 9.0925] w=0.0524 to align # Constraint # added constraint: constraint((T0380)N32.CB, (T0380)T53.CB) [> 4.0876 = 6.8127 < 8.8565] w=0.0524 to align # Constraint # added constraint: constraint((T0380)V22.CB, (T0380)N32.CB) [> 4.7597 = 7.9328 < 10.3127] w=0.0524 to align # Constraint # added constraint: constraint((T0380)I2.CB, (T0380)G126.CA) [> 3.7542 = 6.2571 < 8.1342] w=0.0523 to align # Constraint # added constraint: constraint((T0380)A123.CB, (T0380)I139.CB) [> 3.5009 = 5.8348 < 7.5853] w=0.0522 to align # Constraint # added constraint: constraint((T0380)A123.CB, (T0380)I142.CB) [> 4.4075 = 7.3458 < 9.5496] w=0.0522 to align # Constraint # added constraint: constraint((T0380)N52.CB, (T0380)I111.CB) [> 3.4050 = 5.6750 < 7.3774] w=0.0400 to align # Constraint # added constraint: constraint((T0380)T51.CB, (T0380)D112.CB) [> 3.6348 = 6.0580 < 7.8754] w=0.0382 to align # Constraint # added constraint: constraint((T0380)L98.CB, (T0380)L109.CB) [> 4.5465 = 7.5774 < 9.8507] w=0.0367 to align # Constraint # added constraint: constraint((T0380)T51.CB, (T0380)D115.CB) [> 3.0000 = 4.9999 < 6.4999] w=0.0367 to align # Constraint # added constraint: constraint((T0380)D42.CB, (T0380)T122.CB) [> 4.5189 = 7.5316 < 9.7910] w=0.0349 to align # Constraint # added constraint: constraint((T0380)K46.CB, (T0380)G84.CA) [> 4.7406 = 7.9010 < 10.2713] w=0.0349 to align # Constraint # added constraint: constraint((T0380)M81.CB, (T0380)T136.CB) [> 4.5473 = 7.5788 < 9.8524] w=0.0349 to align # Constraint # added constraint: constraint((T0380)V20.CB, (T0380)W48.CB) [> 4.5142 = 7.5237 < 9.7809] w=0.0349 to align # Constraint # added constraint: constraint((T0380)V22.CB, (T0380)W48.CB) [> 3.8132 = 6.3553 < 8.2619] w=0.0349 to align # Constraint # added constraint: constraint((T0380)M36.CB, (T0380)W48.CB) [> 3.1860 = 5.3100 < 6.9030] w=0.0349 to align # Constraint # added constraint: constraint((T0380)M37.CB, (T0380)W48.CB) [> 4.2954 = 7.1589 < 9.3066] w=0.0349 to align # Constraint # added constraint: constraint((T0380)M97.CB, (T0380)C120.CB) [> 3.7101 = 6.1834 < 8.0385] w=0.0349 to align # Constraint # added constraint: constraint((T0380)F6.CB, (T0380)L82.CB) [> 4.4866 = 7.4776 < 9.7209] w=0.0210 to align # Constraint # added constraint: constraint((T0380)M1.CB, (T0380)K45.CB) [> 3.5576 = 5.9293 < 7.7081] w=0.0209 to align # Constraint # added constraint: constraint((T0380)I19.CB, (T0380)K40.CB) [> 4.6971 = 7.8285 < 10.1770] w=0.0175 to align # Constraint # added constraint: constraint((T0380)A78.CB, (T0380)I135.CB) [> 3.5793 = 5.9655 < 7.7552] w=0.0175 to align # Constraint # added constraint: constraint((T0380)L80.CB, (T0380)I135.CB) [> 3.5887 = 5.9813 < 7.7756] w=0.0175 to align # Constraint # added constraint: constraint((T0380)E104.CB, (T0380)P114.CB) [> 4.7324 = 7.8873 < 10.2535] w=0.0175 to align # Constraint # added constraint: constraint((T0380)F6.CB, (T0380)I142.CB) [> 2.3976 = 3.9960 < 5.1948] w=0.0175 to align # Constraint # added constraint: constraint((T0380)M1.CB, (T0380)W125.CB) [> 4.6238 = 7.7064 < 10.0183] w=0.0174 to align # Constraint # added constraint: constraint((T0380)D3.CB, (T0380)A78.CB) [> 4.7591 = 7.9319 < 10.3115] w=0.0173 to align # Constraint # added constraint: constraint((T0380)K46.CB, (T0380)Y143.CB) [> 4.7481 = 7.9134 < 10.2875] w=0.0173 to align # Constraint # added constraint: constraint((T0380)N25.CB, (T0380)I67.CB) [> 3.9464 = 6.5773 < 8.5505] w=0.0052 to align # Constraint # added constraint: constraint((T0380)N25.CB, (T0380)C68.CB) [> 4.5891 = 7.6485 < 9.9431] w=0.0052 to align # Constraint # added constraint: constraint((T0380)P31.CB, (T0380)K66.CB) [> 4.7063 = 7.8438 < 10.1969] w=0.0052 to align # SetCost created cost = # ( 1.0000 * align ) # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0380/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0380/decoys/ # ReadConformPDB reading from PDB file chimera-4-6.pdb.gz looking for model 1 # Found a chain break before 132 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file chimera-4-8.pdb.gz looking for model 1 # Found a chain break before 132 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file tr380.gromacs0.pdb.gz looking for model 1 # ReadConformPDB reading from PDB file tr380.gromacs0.repack-nonPC.pdb.gz looking for model 1 # ReadConformPDB reading from PDB file tr380.pdb.gz looking for model 1 # ReadConformPDB reading from PDB file tr380.repack-nonPC.pdb.gz looking for model 1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # Found a chain break before 139 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS2.pdb.gz looking for model 1 # Found a chain break before 139 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS3.pdb.gz looking for model 1 # Found a chain break before 139 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS4.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS5.pdb.gz looking for model 1 # Found a chain break before 139 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS5 # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # Found a chain break before 106 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS1 # ReadConformPDB reading from PDB file servers/3Dpro_TS2.pdb.gz looking for model 1 # Found a chain break before 110 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS2 # ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1 # Found a chain break before 108 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS3 # ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1 # Found a chain break before 130 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS4 # ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1 # Found a chain break before 128 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS5 # ReadConformPDB reading from PDB file servers/ABIpro_TS1.pdb.gz looking for model 1 # Found a chain break before 141 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS1 # ReadConformPDB reading from PDB file servers/ABIpro_TS2.pdb.gz looking for model 1 # Found a chain break before 134 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS2 # ReadConformPDB reading from PDB file servers/ABIpro_TS3.pdb.gz looking for model 1 # Found a chain break before 128 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS3 # ReadConformPDB reading from PDB file servers/ABIpro_TS4.pdb.gz looking for model 1 # Found a chain break before 130 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS4 # ReadConformPDB reading from PDB file servers/ABIpro_TS5.pdb.gz looking for model 1 # Found a chain break before 138 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS5 # ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1 # naming current conformation BayesHH_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS1.pdb.gz looking for model 1 # Found a chain break before 136 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS2.pdb.gz looking for model 1 # naming current conformation Bilab-ENABLE_TS2 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS3.pdb.gz looking for model 1 # Found a chain break before 143 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS3 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS4.pdb.gz looking for model 1 # naming current conformation Bilab-ENABLE_TS4 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS5.pdb.gz looking for model 1 # Found a chain break before 83 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS5 # ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1 # Found a chain break before 126 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS1 # ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1 # Found a chain break before 142 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS3 # ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS4 # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS5 # ReadConformPDB reading from PDB file servers/CPHmodels_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation CPHmodels_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS2 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS3 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS4.pdb.gz looking for model 1 # Found a chain break before 113 # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS4 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS5.pdb.gz looking for model 1 # Found a chain break before 109 # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS5 # ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation Distill_TS1 # ReadConformPDB reading from PDB file servers/Distill_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation Distill_TS2 # ReadConformPDB reading from PDB file servers/Distill_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation Distill_TS3 # ReadConformPDB reading from PDB file servers/Distill_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation Distill_TS4 # ReadConformPDB reading from PDB file servers/Distill_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation Distill_TS5 # ReadConformPDB reading from PDB file servers/FAMSD_TS1.pdb.gz looking for model 1 # Found a chain break before 143 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS1 # ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation FAMSD_TS2 # ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation FAMSD_TS3 # ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1 # Found a chain break before 114 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS4 # ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1 # Found a chain break before 113 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS5 # ReadConformPDB reading from PDB file servers/FAMS_TS1.pdb.gz looking for model 1 # Found a chain break before 142 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation FAMS_TS3 # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation FAMS_TS4 # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # Found a chain break before 142 # copying to AlignedFragments data structure # naming current conformation FAMS_TS5 # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # Found a chain break before 102 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS1 # ReadConformPDB reading from PDB file servers/FOLDpro_TS2.pdb.gz looking for model 1 # Found a chain break before 122 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS2 # ReadConformPDB reading from PDB file servers/FOLDpro_TS3.pdb.gz looking for model 1 # Found a chain break before 77 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS3 # ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1 # naming current conformation FOLDpro_TS4 # ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1 # naming current conformation FOLDpro_TS5 # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 Skipped atom 62, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 64, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 66, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 68, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 318, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 320, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 322, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 324, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 374, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 376, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 378, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 380, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 490, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 492, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 494, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 496, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation FORTE1_AL1 # ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1 Skipped atom 177, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 514, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation FORTE1_AL2 # ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation FORTE1_AL3 # ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation FORTE1_AL4 # ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1 Skipped atom 126, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz Skipped atom 128, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz Skipped atom 130, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz Skipped atom 132, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation FORTE1_AL5 # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 Skipped atom 62, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 64, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 66, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 68, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 318, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 320, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 322, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 324, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 374, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 376, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 378, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 380, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 490, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 492, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 494, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 496, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation FORTE2_AL1 # ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1 Skipped atom 177, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 514, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation FORTE2_AL2 # ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation FORTE2_AL3 # ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation FORTE2_AL4 # ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1 Skipped atom 126, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 128, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 130, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 132, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation FORTE2_AL5 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS1.pdb.gz looking for model 1 # Found a chain break before 117 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS1 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS2.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS2 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS3.pdb.gz looking for model 1 # Found a chain break before 46 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS3 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS4.pdb.gz looking for model 1 # Found a chain break before 133 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS4 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS5.pdb.gz looking for model 1 # Found a chain break before 144 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS5 # ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1 # Found a chain break before 44 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # Found a chain break before 107 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS2 # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS3 # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # Found a chain break before 35 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS4 # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS5 # ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation FUGUE_AL1 # ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation FUGUE_AL2 # ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1 Skipped atom 58, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz Skipped atom 60, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz Skipped atom 62, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz Skipped atom 64, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz Skipped atom 354, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz Skipped atom 356, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz Skipped atom 358, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz Skipped atom 360, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz Skipped atom 470, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz Skipped atom 472, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz Skipped atom 474, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz Skipped atom 476, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation FUGUE_AL3 # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 Skipped atom 126, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL4.pdb.gz Skipped atom 128, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL4.pdb.gz Skipped atom 130, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL4.pdb.gz Skipped atom 132, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL4.pdb.gz # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation FUGUE_AL4 # ReadConformPDB reading from PDB file servers/FUGUE_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation FUGUE_AL5 # ReadConformPDB reading from PDB file servers/FUNCTION_TS1.pdb.gz looking for model 1 # Found a chain break before 119 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS1 # ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1 # Found a chain break before 108 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS2 # ReadConformPDB reading from PDB file servers/FUNCTION_TS3.pdb.gz looking for model 1 # Found a chain break before 142 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS3 # ReadConformPDB reading from PDB file servers/FUNCTION_TS4.pdb.gz looking for model 1 # Found a chain break before 136 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS4 # ReadConformPDB reading from PDB file servers/FUNCTION_TS5.pdb.gz looking for model 1 # Found a chain break before 144 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # ReadConformPDB reading from PDB file servers/Frankenstein_TS1.pdb.gz looking for model 1 # naming current conformation Frankenstein_TS1 # ReadConformPDB reading from PDB file servers/Frankenstein_TS2.pdb.gz looking for model 1 # Found a chain break before 120 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS2 # ReadConformPDB reading from PDB file servers/Frankenstein_TS3.pdb.gz looking for model 1 # Found a chain break before 130 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS3 # ReadConformPDB reading from PDB file servers/Frankenstein_TS4.pdb.gz looking for model 1 # Found a chain break before 12 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS4 # ReadConformPDB reading from PDB file servers/Frankenstein_TS5.pdb.gz looking for model 1 # Found a chain break before 84 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS5 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS1 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # Found a chain break before 138 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS3 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS4 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS5 # ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1 # naming current conformation HHpred1_TS1 # ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1 # Found a chain break before 89 # copying to AlignedFragments data structure # naming current conformation HHpred2_TS1 # ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1 # Found a chain break before 89 # copying to AlignedFragments data structure # naming current conformation HHpred3_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS2 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS3 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS4 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS5 # ReadConformPDB reading from PDB file servers/LOOPP_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation LOOPP_TS1 # ReadConformPDB reading from PDB file servers/LOOPP_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation LOOPP_TS2 # ReadConformPDB reading from PDB file servers/LOOPP_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation LOOPP_TS3 # ReadConformPDB reading from PDB file servers/LOOPP_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation LOOPP_TS4 # ReadConformPDB reading from PDB file servers/LOOPP_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation LOOPP_TS5 # ReadConformPDB reading from PDB file servers/MIG_FROST_AL1.pdb.gz looking for model 1 Skipped atom 142, because occupancy 1.000 <= existing 1.000 in servers/MIG_FROST_AL1.pdb.gz Skipped atom 144, because occupancy 1.000 <= existing 1.000 in servers/MIG_FROST_AL1.pdb.gz Skipped atom 146, because occupancy 1.000 <= existing 1.000 in servers/MIG_FROST_AL1.pdb.gz Skipped atom 148, because occupancy 1.000 <= existing 1.000 in servers/MIG_FROST_AL1.pdb.gz Skipped atom 291, because occupancy 1.000 <= existing 1.000 in servers/MIG_FROST_AL1.pdb.gz Skipped atom 308, because occupancy 1.000 <= existing 1.000 in servers/MIG_FROST_AL1.pdb.gz Skipped atom 317, because occupancy 1.000 <= existing 1.000 in servers/MIG_FROST_AL1.pdb.gz # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation MIG_FROST_AL1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS1.pdb.gz looking for model 1 # naming current conformation Ma-OPUS-server2_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS2.pdb.gz looking for model 1 # Found a chain break before 73 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS3.pdb.gz looking for model 1 # Found a chain break before 144 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS4.pdb.gz looking for model 1 # Found a chain break before 131 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS5.pdb.gz looking for model 1 # naming current conformation Ma-OPUS-server2_TS5 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # naming current conformation Ma-OPUS-server_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS2.pdb.gz looking for model 1 # Found a chain break before 73 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS3.pdb.gz looking for model 1 # naming current conformation Ma-OPUS-server_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS4.pdb.gz looking for model 1 # Found a chain break before 40 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS5.pdb.gz looking for model 1 # Found a chain break before 114 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS5 # ReadConformPDB reading from PDB file servers/MetaTasser_TS1.pdb.gz looking for model 1 # Found a chain break before 144 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS1 # ReadConformPDB reading from PDB file servers/MetaTasser_TS2.pdb.gz looking for model 1 # Found a chain break before 144 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS2 # ReadConformPDB reading from PDB file servers/MetaTasser_TS3.pdb.gz looking for model 1 # Found a chain break before 144 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS3 # ReadConformPDB reading from PDB file servers/MetaTasser_TS4.pdb.gz looking for model 1 # Found a chain break before 144 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS4 # ReadConformPDB reading from PDB file servers/MetaTasser_TS5.pdb.gz looking for model 1 # Found a chain break before 144 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS5 # ReadConformPDB reading from PDB file servers/NN_PUT_lab_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation NN_PUT_lab_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1 # Found a chain break before 86 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # Found a chain break before 109 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # Found a chain break before 96 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS5 # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation Pcons6_TS1 # ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation Pcons6_TS2 # ReadConformPDB reading from PDB file servers/Pcons6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation Pcons6_TS3 # ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pcons6_TS4 # ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pcons6_TS5 # ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation Phyre-1_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS2.pdb.gz looking for model 1 # Found a chain break before 131 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS2 # ReadConformPDB reading from PDB file servers/Phyre-2_TS3.pdb.gz looking for model 1 # Found a chain break before 131 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS3 # ReadConformPDB reading from PDB file servers/Phyre-2_TS4.pdb.gz looking for model 1 # Found a chain break before 131 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS4 # ReadConformPDB reading from PDB file servers/Phyre-2_TS5.pdb.gz looking for model 1 # Found a chain break before 137 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS5 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1 # Found a chain break before 79 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS1 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # Found a chain break before 75 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS2 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # naming current conformation Pmodeller6_TS3 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # Found a chain break before 73 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS4 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1 # naming current conformation Pmodeller6_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1 # Found a chain break before 36 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS4.pdb.gz looking for model 1 # Found a chain break before 11 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1 # Found a chain break before 83 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS5 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS1.pdb.gz looking for model 1 # naming current conformation RAPTORESS_TS1 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS2.pdb.gz looking for model 1 # Found a chain break before 140 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS2 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS3.pdb.gz looking for model 1 # Found a chain break before 135 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS3 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS4.pdb.gz looking for model 1 # Found a chain break before 77 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS4 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS5.pdb.gz looking for model 1 # Found a chain break before 144 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR_TS1.pdb.gz looking for model 1 # Found a chain break before 89 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR_TS3.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR_TS4.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR_TS5.pdb.gz looking for model 1 # Found a chain break before 105 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS5 # ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1 # Found a chain break before 73 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS1 # ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1 # Found a chain break before 79 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS2 # ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1 # Found a chain break before 75 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS3 # ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS4 # ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS5 # ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1 # Found a chain break before 131 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS1 # ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1 # Found a chain break before 112 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS2 # ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1 # Found a chain break before 129 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS3 # ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1 # Found a chain break before 136 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS4 # ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1 # naming current conformation ROKKY_TS5 # ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1 Skipped atom 62, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 64, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 66, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 68, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 318, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 320, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 322, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 324, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 374, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 376, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 378, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 380, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 490, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 492, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 494, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 496, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL1 # ReadConformPDB reading from PDB file servers/SAM-T02_AL2.pdb.gz looking for model 1 Skipped atom 98, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 100, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 102, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 104, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL2 # ReadConformPDB reading from PDB file servers/SAM-T02_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL3 # ReadConformPDB reading from PDB file servers/SAM-T02_AL4.pdb.gz looking for model 1 Skipped atom 222, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 224, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 226, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 228, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 298, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 300, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 302, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 304, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL4 # ReadConformPDB reading from PDB file servers/SAM-T02_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL5 # ReadConformPDB reading from PDB file servers/SAM-T99_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL1 # ReadConformPDB reading from PDB file servers/SAM-T99_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL2 # ReadConformPDB reading from PDB file servers/SAM-T99_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL3 # ReadConformPDB reading from PDB file servers/SAM-T99_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL4 # ReadConformPDB reading from PDB file servers/SAM-T99_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL5 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1 # Found a chain break before 143 # copying to AlignedFragments data structure # naming current conformation SAM_T06_server_TS1 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS2 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS3 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS4 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS5 # ReadConformPDB reading from PDB file servers/SP3_TS1.pdb.gz looking for model 1 # Found a chain break before 83 # copying to AlignedFragments data structure # naming current conformation SP3_TS1 # ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1 # Found a chain break before 134 # copying to AlignedFragments data structure # naming current conformation SP3_TS2 # ReadConformPDB reading from PDB file servers/SP3_TS3.pdb.gz looking for model 1 # Found a chain break before 122 # copying to AlignedFragments data structure # naming current conformation SP3_TS3 # ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1 # naming current conformation SP3_TS4 # ReadConformPDB reading from PDB file servers/SP3_TS5.pdb.gz looking for model 1 # Found a chain break before 110 # copying to AlignedFragments data structure # naming current conformation SP3_TS5 # ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1 # Found a chain break before 83 # copying to AlignedFragments data structure # naming current conformation SP4_TS1 # ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1 # Found a chain break before 134 # copying to AlignedFragments data structure # naming current conformation SP4_TS2 # ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1 # Found a chain break before 122 # copying to AlignedFragments data structure # naming current conformation SP4_TS3 # ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1 # Found a chain break before 35 # copying to AlignedFragments data structure # naming current conformation SP4_TS4 # ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1 # Found a chain break before 110 # copying to AlignedFragments data structure # naming current conformation SP4_TS5 # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # Found a chain break before 134 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS1 # ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1 # Found a chain break before 122 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS2 # ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1 # Found a chain break before 83 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS3 # ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1 # Found a chain break before 88 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS4 # ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1 # Found a chain break before 35 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS2 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS3 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS4 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_expm_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation UNI-EID_expm_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL1.pdb.gz looking for model 1 Skipped atom 62, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 64, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 66, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 68, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 318, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 320, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 322, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 324, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 374, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 376, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 378, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 380, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 490, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 492, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 494, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 496, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL2.pdb.gz looking for model 1 Skipped atom 98, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 100, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 102, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 104, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL2 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL3 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL4 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL5 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1 # Found a chain break before 83 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS1 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS2.pdb.gz looking for model 1 # Found a chain break before 83 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS2 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS3.pdb.gz looking for model 1 # naming current conformation Zhang-Server_TS3 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS4.pdb.gz looking for model 1 # Found a chain break before 141 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS4 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS5.pdb.gz looking for model 1 # Found a chain break before 137 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS5 # ReadConformPDB reading from PDB file servers/beautshot_TS1.pdb.gz looking for model 1 # Found a chain break before 143 # copying to AlignedFragments data structure # naming current conformation beautshot_TS1 # ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation beautshotbase_TS1 # ReadConformPDB reading from PDB file servers/forecast-s_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation forecast-s_AL1 # ReadConformPDB reading from PDB file servers/forecast-s_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation forecast-s_AL2 # ReadConformPDB reading from PDB file servers/forecast-s_AL3.pdb.gz looking for model 1 Skipped atom 137, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 138, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 139, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 140, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 525, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 526, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 527, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 528, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 533, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 534, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 535, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 536, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 541, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 542, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 543, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 544, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 549, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 550, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 551, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 552, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 557, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 558, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 559, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 560, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 565, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 566, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 567, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 568, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 573, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 574, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 575, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 576, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 581, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 582, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 583, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 584, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 589, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 590, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 591, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 592, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 597, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 598, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 599, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 600, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 605, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 606, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 607, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 608, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 613, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 614, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 615, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 616, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 621, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 622, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 623, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 624, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation forecast-s_AL3 # ReadConformPDB reading from PDB file servers/forecast-s_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation forecast-s_AL4 # ReadConformPDB reading from PDB file servers/forecast-s_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation forecast-s_AL5 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # naming current conformation karypis.srv.2_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS2.pdb.gz looking for model 1 # Found a chain break before 46 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS3.pdb.gz looking for model 1 # naming current conformation karypis.srv.2_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS4.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS5.pdb.gz looking for model 1 # naming current conformation karypis.srv.2_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS1.pdb.gz looking for model 1 # Found a chain break before 142 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS2.pdb.gz looking for model 1 # Found a chain break before 142 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS3.pdb.gz looking for model 1 WARNING: atoms too close: (T0380)F121.O and (T0380)T122.N only 0.000 apart, marking (T0380)T122.N as missing # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS4.pdb.gz looking for model 1 # Found a chain break before 142 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS5.pdb.gz looking for model 1 # Found a chain break before 142 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS5 # ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1 # naming current conformation keasar-server_TS1 # ReadConformPDB reading from PDB file servers/keasar-server_TS2.pdb.gz looking for model 1 # Found a chain break before 128 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS2 # ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1 # Found a chain break before 144 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS3 # ReadConformPDB reading from PDB file servers/keasar-server_TS4.pdb.gz looking for model 1 # naming current conformation keasar-server_TS4 # ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1 # Found a chain break before 84 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS5 # ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation mGen-3D_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation nFOLD_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation nFOLD_TS2 # ReadConformPDB reading from PDB file servers/nFOLD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation nFOLD_TS3 # ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation nFOLD_TS4 # ReadConformPDB reading from PDB file servers/nFOLD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation nFOLD_TS5 # ReadConformPDB reading from PDB file servers/panther2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation panther2_TS1 # ReadConformPDB reading from PDB file servers/panther3_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # naming current conformation panther3_TS1 # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0380 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation shub_TS1 # command:Using radius: 8.0000 Using models AND alignments for constraints model score -0.4542 model score -0.5742 model score -0.5496 model score -0.5504 model score -0.5501 model score -0.5501 model score -0.4084 model score -0.3446 model score 0.2884 model score -0.3414 model score -0.3181 model score 0.3202 model score 0.3193 model score 0.3202 model score 0.3226 model score 0.3322 model score 0.3582 model score -0.3866 model score 0.3324 model score 0.3799 model score 0.3464 model score -0.4677 model score -0.2269 model score -0.5410 model score -0.4740 model score -0.5219 model score 1.2536 model score 1.3936 model score 1.5540 model score 1.3756 model score 1.3562 model score -0.6330 model score -0.5841 model score -0.6106 model score -0.6097 model score -0.5543 model score -0.2944 model score -0.5600 model score -0.5594 model score -0.5059 model score -0.5289 model score -0.5339 model score -0.0944 model score -0.5523 model score -0.4572 model score -0.4596 model score -0.4141 model score -0.5151 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.5593 model score -0.5303 model score -0.5289 model score -0.4818 model score -0.4863 model score -0.5825 model score -0.5059 model score -0.5289 model score -0.5289 model score -0.5594 model score -0.4880 model score -0.1215 model score -0.4781 model score -0.4349 model score -0.5095 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 2.0213 model score 2.2301 model score 2.0646 model score 1.8460 model score 2.3115 model score -0.4742 model score -0.5090 model score -0.2633 model score -0.4566 model score -0.4654 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.4346 model score -0.4764 model score -0.4266 model score -0.4537 model score -0.4710 model score -0.5907 model score -0.3783 model score 0.4809 model score 0.9865 model score 0.9409 model score -0.4767 model score -0.4829 model score -0.5317 model score -0.4894 model score -0.2835 model score -0.5952 model score -0.6369 model score -0.6369 model score -0.5182 model score 0.7840 model score 1.0785 model score 2.0155 model score 1.6484 model score -0.3146 model score -0.4527 model score -0.2691 model score -0.4228 model score -0.3431 model score 1.2771 model score -0.6116 model score -0.6017 model score 0.9022 model score -0.5589 model score -0.5183 model score -0.6116 model score -0.6017 model score -0.5501 model score -0.5284 model score -0.5091 model score -0.5385 model score -0.5850 model score -0.5658 model score -0.5477 model score -0.5878 model score -0.3146 model score -0.4493 model score -0.4527 model score -0.4190 model score -0.4471 model score -0.4494 model score -0.4272 model score -0.4034 model score -0.2958 model score -0.4455 model score -0.4532 model score -0.3390 model score -0.5724 model score -0.4679 model score -0.4903 model score -0.4761 model score -0.4487 model score -0.4844 model score -0.4821 model score -0.4821 model score -0.4910 model score -0.5057 model score -0.6035 model score -0.5967 model score -0.5979 model score -0.4796 model score -0.6127 model score -0.3570 model score -0.3936 model score -0.4764 model score -0.4741 model score -0.2757 model score -0.5411 model score -0.5086 model score -0.4685 model score -0.4948 model score -0.4267 model score -0.5975 model score -0.5346 model score -0.4976 model score -0.4801 model score -0.4930 model score -0.4796 model score -0.6035 model score -0.5967 model score -0.5979 model score -0.6127 model score -0.4541 model score -0.4465 model score -0.4734 model score -0.4206 model score -0.5935 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.5542 model score -0.3010 model score -0.4408 model score -0.1597 model score -0.3714 model score -0.2917 model score -0.5583 model score -0.4176 model score -0.4597 model score -0.5426 model score -0.2917 model score -0.5536 model score -0.4115 model score -0.4682 model score -0.5699 model score -0.5583 model score -0.4176 model score -0.2917 model score -0.4751 model score -0.4942 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.6202 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.5654 model score -0.5815 model score -0.5325 model score -0.5429 model score -0.5851 model score -0.5694 model score -0.4813 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.4952 model score -0.5204 model score -0.5147 model score -0.3109 model score -0.5097 model score 2.1480 model score 2.0226 model score 1.9693 model score 1.9666 model score 1.5020 model score -0.4800 model score -0.3742 model score -0.3335 model score -0.3221 model score 1.3318 model score -0.4140 model score -0.4282 model score -0.4414 model score -0.4116 model score -0.3912 model score -0.4859 model score -0.4520 model score 0.7949 model score -0.4950 model score 0.7848 model score 0.0357 model score 0.5605 model score 1.1851 model score -0.5778 USE_META, weight: 0.9442 cost: -0.4542 min: -0.6369 max: 2.3115 USE_META, weight: 0.9808 cost: -0.5742 min: -0.6369 max: 2.3115 USE_META, weight: 0.9733 cost: -0.5496 min: -0.6369 max: 2.3115 USE_META, weight: 0.9736 cost: -0.5504 min: -0.6369 max: 2.3115 USE_META, weight: 0.9735 cost: -0.5501 min: -0.6369 max: 2.3115 USE_META, weight: 0.9735 cost: -0.5501 min: -0.6369 max: 2.3115 USE_META, weight: 0.9302 cost: -0.4084 min: -0.6369 max: 2.3115 USE_META, weight: 0.9108 cost: -0.3446 min: -0.6369 max: 2.3115 USE_META, weight: 0.7175 cost: 0.2884 min: -0.6369 max: 2.3115 USE_META, weight: 0.9098 cost: -0.3414 min: -0.6369 max: 2.3115 USE_META, weight: 0.9027 cost: -0.3181 min: -0.6369 max: 2.3115 USE_META, weight: 0.7078 cost: 0.3202 min: -0.6369 max: 2.3115 USE_META, weight: 0.7081 cost: 0.3193 min: -0.6369 max: 2.3115 USE_META, weight: 0.7078 cost: 0.3202 min: -0.6369 max: 2.3115 USE_META, weight: 0.7071 cost: 0.3226 min: -0.6369 max: 2.3115 USE_META, weight: 0.7042 cost: 0.3322 min: -0.6369 max: 2.3115 USE_META, weight: 0.6962 cost: 0.3582 min: -0.6369 max: 2.3115 USE_META, weight: 0.9236 cost: -0.3866 min: -0.6369 max: 2.3115 USE_META, weight: 0.7041 cost: 0.3324 min: -0.6369 max: 2.3115 USE_META, weight: 0.6896 cost: 0.3799 min: -0.6369 max: 2.3115 USE_META, weight: 0.6998 cost: 0.3464 min: -0.6369 max: 2.3115 USE_META, weight: 0.9483 cost: -0.4677 min: -0.6369 max: 2.3115 USE_META, weight: 0.8748 cost: -0.2269 min: -0.6369 max: 2.3115 USE_META, weight: 0.9707 cost: -0.5410 min: -0.6369 max: 2.3115 USE_META, weight: 0.9503 cost: -0.4740 min: -0.6369 max: 2.3115 USE_META, weight: 0.9649 cost: -0.5219 min: -0.6369 max: 2.3115 USE_META, weight: 0.4229 cost: 1.2536 min: -0.6369 max: 2.3115 USE_META, weight: 0.3802 cost: 1.3936 min: -0.6369 max: 2.3115 USE_META, weight: 0.3312 cost: 1.5540 min: -0.6369 max: 2.3115 USE_META, weight: 0.3857 cost: 1.3756 min: -0.6369 max: 2.3115 USE_META, weight: 0.3916 cost: 1.3562 min: -0.6369 max: 2.3115 USE_META, weight: 0.9988 cost: -0.6330 min: -0.6369 max: 2.3115 USE_META, weight: 0.9839 cost: -0.5841 min: -0.6369 max: 2.3115 USE_META, weight: 0.9920 cost: -0.6106 min: -0.6369 max: 2.3115 USE_META, weight: 0.9917 cost: -0.6097 min: -0.6369 max: 2.3115 USE_META, weight: 0.9748 cost: -0.5543 min: -0.6369 max: 2.3115 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USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0110 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0110 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0110 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0110 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0110 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0110 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0110 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0110 USE_EVALUE, weight: 0.1000 eval: 0.0110 min: 0.0000 max: 0.0110 USE_EVALUE, weight: 0.1000 eval: 0.0110 min: 0.0000 max: 0.0110 USE_EVALUE, weight: 0.1000 eval: 0.0110 min: 0.0000 max: 0.0110 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0110 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0110 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0110 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0110 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0110 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0110 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0110 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0110 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0110 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0110 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0110 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0110 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0110 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0110 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0110 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0110 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0110 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0110 Number of contacts in models: 271 Number of contacts in alignments: 60 NUMB_ALIGNS: 60 Adding 4347 constraints to all3.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all3.constraints maxweight: 1.0000 Optimizing... Probability sum: -246.6716, CN propb: -246.6716 weights: 0.3568 constraints: 525 # command:Found ConstraintSet # PrintContacts align.constraints_meta03 Number of constraints in align3.constraints 525 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta03 Number of constraints in align3.constraints.bonus 525 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta03 Number of constraints in rejected3.constraints 3822 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta03 Number of constraints in rejected3.constraints.bonus 3822 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_meta03 Number of constraints in noncontact3.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_meta03 Number of constraints in noncontact3.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_meta03 Number of constraints in all3.constraints 4347 # command: