# 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/T0385/ # command:# Making conformation for sequence T0385 numbered 1 through 162 Created new target T0385 from T0385.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0385/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0385//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0385/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0385//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0385/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0385/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0385/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1za0A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1za0A expands to /projects/compbio/data/pdb/1za0.pdb.gz 1za0A:Skipped atom 1214, because occupancy 0.5 <= existing 0.500 in 1za0A Skipped atom 1216, because occupancy 0.500 <= existing 0.500 in 1za0A Skipped atom 1218, because occupancy 0.500 <= existing 0.500 in 1za0A Skipped atom 1220, because occupancy 0.500 <= existing 0.500 in 1za0A Skipped atom 1222, because occupancy 0.500 <= existing 0.500 in 1za0A Skipped atom 1224, because occupancy 0.500 <= existing 0.500 in 1za0A Skipped atom 1226, because occupancy 0.500 <= existing 0.500 in 1za0A # T0385 read from 1za0A/merged-good-all-a2m # 1za0A read from 1za0A/merged-good-all-a2m # adding 1za0A to template set # found chain 1za0A in template set Warning: unaligning (T0385)A10 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1za0A)D55 Warning: unaligning (T0385)T11 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1za0A)D55 Warning: unaligning (T0385)G50 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1za0A)D94 Warning: unaligning (T0385)Y87 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1za0A)K145 Warning: unaligning (T0385)Q92 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1za0A)K145 T0385 3 :SSEPAHG 1za0A 47 :AFLGGRD # choosing archetypes in rotamer library T0385 12 :PKRSPS 1za0A 56 :PSQSTL T0385 19 :GSADNAALCDALAVEH 1za0A 62 :PRTITDACEILLILKD T0385 51 :VNFLVADALKQHRH 1za0A 95 :WWGRWLGRWTAEEH T0385 65 :RRDDVIVMLS 1za0A 110 :HAIALREYLV T0385 76 :RGVTAPIAA 1za0A 122 :REVDPVANE T0385 85 :AG 1za0A 132 :VR T0385 93 :VSSAADAARLAVR 1za0A 146 :YTQVETLVYMAFY T0385 107 :ENDGATAWRAVVEHAETADDRVFASTALTESAVMATRWNRVL 1za0A 159 :ERCGAVFCRNLAAQIEEPILAGLIDRIARDEVRHEEFFANLV Number of specific fragments extracted= 9 number of extra gaps= 1 total=9 Number of alignments=1 # 1za0A read from 1za0A/merged-good-all-a2m # found chain 1za0A in template set Warning: unaligning (T0385)T11 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1za0A)D55 Warning: unaligning (T0385)P12 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1za0A)D55 Warning: unaligning (T0385)G50 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1za0A)D94 Warning: unaligning (T0385)Y87 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1za0A)K145 Warning: unaligning (T0385)Q92 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1za0A)K145 T0385 5 :EPAHGA 1za0A 48 :FLGGRD T0385 13 :KRSPSEGSADNAALCDALAVEH 1za0A 56 :PSQSTLPRTITDACEILLILKD T0385 51 :VNFLVADALKQHR 1za0A 95 :WWGRWLGRWTAEE T0385 64 :HRRDDVIVMLS 1za0A 109 :LHAIALREYLV T0385 76 :RGV 1za0A 121 :TRE T0385 79 :TAP 1za0A 125 :DPV T0385 82 :IAAAG 1za0A 129 :NEDVR T0385 93 :VSSAADAARLAVR 1za0A 146 :YTQVETLVYMAFY T0385 107 :ENDGATAWRAVVEHAETADDRVFASTALTESAVMATRWNRVL 1za0A 159 :ERCGAVFCRNLAAQIEEPILAGLIDRIARDEVRHEEFFANLV Number of specific fragments extracted= 9 number of extra gaps= 1 total=18 Number of alignments=2 # 1za0A read from 1za0A/merged-good-all-a2m # found chain 1za0A in template set Warning: unaligning (T0385)P12 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1za0A)D55 Warning: unaligning (T0385)K13 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1za0A)D55 Warning: unaligning (T0385)A80 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1za0A)K145 Warning: unaligning (T0385)Q92 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1za0A)K145 T0385 3 :SSEPAHGAT 1za0A 45 :NFAFLGGRD T0385 14 :RSPSEGSADNAALCDALAVEHA 1za0A 56 :PSQSTLPRTITDACEILLILKD T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGV 1za0A 97 :GRWLGRWTAEEHLHAIALREYLVVTREVDP T0385 79 :T 1za0A 133 :R T0385 93 :VSSAADAARLAVR 1za0A 146 :YTQVETLVYMAFY T0385 107 :ENDGATAWRAVVEHAE 1za0A 159 :ERCGAVFCRNLAAQIE T0385 124 :ADDRVFASTALTESAVMATRWNRV 1za0A 175 :EPILAGLIDRIARDEVRHEEFFAN Number of specific fragments extracted= 7 number of extra gaps= 1 total=25 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1h96A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1h96A expands to /projects/compbio/data/pdb/1h96.pdb.gz 1h96A:Skipped atom 77, because occupancy 0.500 <= existing 0.500 in 1h96A Skipped atom 79, because occupancy 0.500 <= existing 0.500 in 1h96A Skipped atom 81, because occupancy 0.500 <= existing 0.500 in 1h96A Skipped atom 311, because occupancy 0.500 <= existing 0.500 in 1h96A Skipped atom 313, because occupancy 0.500 <= existing 0.500 in 1h96A Skipped atom 315, because occupancy 0.500 <= existing 0.500 in 1h96A Skipped atom 317, because occupancy 0.500 <= existing 0.500 in 1h96A Skipped atom 319, because occupancy 0.500 <= existing 0.500 in 1h96A Skipped atom 321, because occupancy 0.500 <= existing 0.500 in 1h96A Skipped atom 323, because occupancy 0.500 <= existing 0.500 in 1h96A Skipped atom 481, because occupancy 0.500 <= existing 0.500 in 1h96A Skipped atom 483, because occupancy 0.500 <= existing 0.500 in 1h96A Skipped atom 485, because occupancy 0.500 <= existing 0.500 in 1h96A Skipped atom 487, because occupancy 0.500 <= existing 0.500 in 1h96A Skipped atom 489, because occupancy 0.500 <= existing 0.500 in 1h96A Skipped atom 491, because occupancy 0.500 <= existing 0.500 in 1h96A Skipped atom 493, because occupancy 0.500 <= existing 0.500 in 1h96A Skipped atom 919, because occupancy 0.330 <= existing 0.660 in 1h96A Skipped atom 921, because occupancy 0.330 <= existing 0.660 in 1h96A Skipped atom 923, because occupancy 0.330 <= existing 0.660 in 1h96A Skipped atom 925, because occupancy 0.330 <= existing 0.660 in 1h96A Skipped atom 927, because occupancy 0.330 <= existing 0.660 in 1h96A Skipped atom 929, because occupancy 0.330 <= existing 0.660 in 1h96A Skipped atom 931, because occupancy 0.330 <= existing 0.660 in 1h96A Skipped atom 933, because occupancy 0.330 <= existing 0.660 in 1h96A Skipped atom 935, because occupancy 0.330 <= existing 0.660 in 1h96A Skipped atom 937, because occupancy 0.330 <= existing 0.660 in 1h96A Skipped atom 960, because occupancy 0.330 <= existing 0.660 in 1h96A Skipped atom 962, because occupancy 0.330 <= existing 0.660 in 1h96A Skipped atom 1051, because occupancy 0.330 <= existing 0.660 in 1h96A Skipped atom 1053, because occupancy 0.330 <= existing 0.660 in 1h96A Skipped atom 1055, because occupancy 0.330 <= existing 0.660 in 1h96A Skipped atom 1057, because occupancy 0.330 <= existing 0.660 in 1h96A Skipped atom 1059, because occupancy 0.330 <= existing 0.660 in 1h96A Skipped atom 1061, because occupancy 0.330 <= existing 0.660 in 1h96A Skipped atom 1063, because occupancy 0.330 <= existing 0.660 in 1h96A Skipped atom 1065, because occupancy 0.330 <= existing 0.660 in 1h96A Skipped atom 1067, because occupancy 0.330 <= existing 0.660 in 1h96A # T0385 read from 1h96A/merged-good-all-a2m # 1h96A read from 1h96A/merged-good-all-a2m # adding 1h96A to template set # found chain 1h96A in template set Warning: unaligning (T0385)P12 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1h96A)S2 Warning: unaligning (T0385)L148 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1h96A)G156 Warning: unaligning (T0385)G149 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1h96A)G156 T0385 13 :KRSPSEGSADNAALCDALAVEHATIYGY 1h96A 3 :QIRQNYSTEVEAAVNRLVNLHLRASYTY T0385 41 :GIVS 1h96A 34 :GFFF T0385 45 :ALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGY 1h96A 41 :DVALEGVGHFFRELAEEKREGAERLLEFQNDRGGRALFQDVQK T0385 90 :PM 1h96A 84 :PS T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAE 1h96A 88 :EWGKTQEAMEAALAMEKNLNQALLDLHALGS T0385 123 :TADDRVFAST 1h96A 122 :DPHLCDFLES T0385 133 :ALTESAVMATRWNRV 1h96A 140 :LIKKMGNHLTNLRRV Number of specific fragments extracted= 7 number of extra gaps= 2 total=32 Number of alignments=4 # 1h96A read from 1h96A/merged-good-all-a2m # found chain 1h96A in template set Warning: unaligning (T0385)P12 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1h96A)S2 Warning: unaligning (T0385)L148 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1h96A)G156 Warning: unaligning (T0385)G149 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1h96A)G156 T0385 13 :KRSPSEGSADNAALCDALAVEHATIYGY 1h96A 3 :QIRQNYSTEVEAAVNRLVNLHLRASYTY T0385 41 :GI 1h96A 34 :GF T0385 43 :VSALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAG 1h96A 39 :RDDVALEGVGHFFRELAEEKREGAERLLEFQNDRGGRALFQDVQ T0385 88 :QLPM 1h96A 83 :KPSQ T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAE 1h96A 88 :EWGKTQEAMEAALAMEKNLNQALLDLHALGS T0385 123 :TADDRVFAS 1h96A 122 :DPHLCDFLE T0385 132 :TALTESAVMATRWNRV 1h96A 139 :KLIKKMGNHLTNLRRV Number of specific fragments extracted= 7 number of extra gaps= 2 total=39 Number of alignments=5 # 1h96A read from 1h96A/merged-good-all-a2m # found chain 1h96A in template set Warning: unaligning (T0385)L148 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1h96A)G156 Warning: unaligning (T0385)G149 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1h96A)G156 Warning: unaligning (T0385)D161 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1h96A)S168 T0385 13 :KRSPSEGSADNAALCDALAVEHATIYGYGIVSALSP 1h96A 3 :QIRQNYSTEVEAAVNRLVNLHLRASYTYLSLGFFFD T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAG 1h96A 45 :EGVGHFFRELAEEKREGAERLLEFQNDRGGRALFQDVQ T0385 90 :PM 1h96A 83 :KP T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHA 1h96A 88 :EWGKTQEAMEAALAMEKNLNQALLDLHALG T0385 122 :ETADDRVFA 1h96A 121 :ADPHLCDFL T0385 131 :STALTESAVMATRWNRV 1h96A 138 :VKLIKKMGNHLTNLRRV Number of specific fragments extracted= 6 number of extra gaps= 1 total=45 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tjoA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0385 read from 1tjoA/merged-good-all-a2m # 1tjoA read from 1tjoA/merged-good-all-a2m # found chain 1tjoA in training set Warning: unaligning (T0385)S3 because first residue in template chain is (1tjoA)S2 Warning: unaligning (T0385)G50 because of BadResidue code BAD_PEPTIDE in next template residue (1tjoA)F60 T0385 4 :SEPAHGATPKRSPSEGS 1tjoA 3 :TQKNARATAGEVEGSDA T0385 21 :ADNAALCDALAVEHATIYGY 1tjoA 25 :DRAEQCVDALNADLANVYVL T0385 41 :GIVSALSPP 1tjoA 50 :KHHWNVEGA T0385 51 :VNFLVADALKQHRHRRDDVIVMLSARGVTAPIAA 1tjoA 63 :LHLFLGEAAETAEEVADELAERVQALGGVPHASP T0385 85 :AGYQLPM 1tjoA 103 :ASVDVED T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAE 1tjoA 111 :DVYDIRTSLANDMAIYGDIIEATREHTELAE T0385 123 :TADDRVFASTALTESAVMATRWNRVLGAWPI 1tjoA 145 :DHATAHMLREGLIELEDDAHHIEHYLEDDTL Number of specific fragments extracted= 7 number of extra gaps= 1 total=52 Number of alignments=7 # 1tjoA read from 1tjoA/merged-good-all-a2m # found chain 1tjoA in training set Warning: unaligning (T0385)S3 because first residue in template chain is (1tjoA)S2 T0385 4 :SEPAHGATPKRSPSEGS 1tjoA 3 :TQKNARATAGEVEGSDA T0385 21 :ADNAALCDALAVEHATIYGY 1tjoA 25 :DRAEQCVDALNADLANVYVL T0385 41 :GIVSALSP 1tjoA 50 :KHHWNVEG T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGVTAP 1tjoA 61 :RDLHLFLGEAAETAEEVADELAERVQALGGVPH T0385 82 :IAAAGYQLPMQ 1tjoA 100 :QAEASVDVEDE T0385 93 :VSSAADAARLAVRMENDGATAWRAVVEHAE 1tjoA 112 :VYDIRTSLANDMAIYGDIIEATREHTELAE T0385 123 :TADDRVFASTALTESAVMATRWNRVLGAWPIT 1tjoA 145 :DHATAHMLREGLIELEDDAHHIEHYLEDDTLV Number of specific fragments extracted= 7 number of extra gaps= 0 total=59 Number of alignments=8 # 1tjoA read from 1tjoA/merged-good-all-a2m # found chain 1tjoA in training set T0385 7 :AHGATPKRSPSEGSADNAALCDALAVEHATIYGYGIVSALSP 1tjoA 11 :AGEVEGSDALRMDADRAEQCVDALNADLANVYVLYHQLKKHH T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGVTAP 1tjoA 61 :RDLHLFLGEAAETAEEVADELAERVQALGGVPH T0385 84 :AAGYQLPM 1tjoA 100 :QAEASVDV T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAET 1tjoA 111 :DVYDIRTSLANDMAIYGDIIEATREHTELAEN T0385 124 :ADDRVFASTALTESAVMATRWNRVLGAWPI 1tjoA 146 :HATAHMLREGLIELEDDAHHIEHYLEDDTL Number of specific fragments extracted= 5 number of extra gaps= 0 total=64 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fha/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1fha expands to /projects/compbio/data/pdb/1fha.pdb.gz 1fha:Warning: there is no chain 1fha will retry with 1fhaA # T0385 read from 1fha/merged-good-all-a2m # 1fha read from 1fha/merged-good-all-a2m # adding 1fha to template set # found chain 1fha in template set Warning: unaligning (T0385)T11 because first residue in template chain is (1fha)T5 Warning: unaligning (T0385)P12 because of BadResidue code BAD_PEPTIDE at template residue (1fha)S6 Warning: unaligning (T0385)Q88 because of BadResidue code BAD_PEPTIDE in next template residue (1fha)K87 Warning: unaligning (T0385)L89 because of BadResidue code BAD_PEPTIDE at template residue (1fha)K87 T0385 13 :KRSPSEGSADNAALCDALAVEHATIYGY 1fha 7 :QVRQNYHQDSEAAINRQINLELYASYVY T0385 41 :GI 1fha 40 :YF T0385 43 :VSALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAA 1fha 43 :RDDVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGRIFLQDI T0385 90 :PM 1fha 88 :PD T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAE 1fha 92 :DWESGLNAMECALHLEKNVNQSLLELHKLAT T0385 123 :TADDRVFAST 1fha 126 :DPHLCDFIET T0385 133 :ALTESAVMATRWNRV 1fha 144 :AIKELGDHVTNLRKM Number of specific fragments extracted= 7 number of extra gaps= 1 total=71 Number of alignments=10 # 1fha read from 1fha/merged-good-all-a2m # found chain 1fha in template set Warning: unaligning (T0385)T11 because first residue in template chain is (1fha)T5 Warning: unaligning (T0385)P12 because of BadResidue code BAD_PEPTIDE at template residue (1fha)S6 Warning: unaligning (T0385)G86 because of BadResidue code BAD_PEPTIDE in next template residue (1fha)K87 Warning: unaligning (T0385)L89 because of BadResidue code BAD_PEPTIDE at template residue (1fha)K87 T0385 13 :KRSPSEGSADNAALCDALAVEHATIYGY 1fha 7 :QVRQNYHQDSEAAINRQINLELYASYVY T0385 44 :S 1fha 38 :S T0385 45 :ALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAA 1fha 45 :DVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGRIFLQDI T0385 90 :P 1fha 88 :P T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAE 1fha 92 :DWESGLNAMECALHLEKNVNQSLLELHKLAT T0385 123 :TADDRVFAS 1fha 126 :DPHLCDFIE T0385 132 :TALTESAVMATRWNRV 1fha 143 :KAIKELGDHVTNLRKM Number of specific fragments extracted= 7 number of extra gaps= 1 total=78 Number of alignments=11 # 1fha read from 1fha/merged-good-all-a2m # found chain 1fha in template set Warning: unaligning (T0385)T11 because first residue in template chain is (1fha)T5 Warning: unaligning (T0385)P12 because of BadResidue code BAD_PEPTIDE at template residue (1fha)S6 Warning: unaligning (T0385)Q88 because of BadResidue code BAD_PEPTIDE in next template residue (1fha)K87 Warning: unaligning (T0385)P90 because of BadResidue code BAD_PEPTIDE at template residue (1fha)K87 T0385 13 :KRSPSEGSADNAALCDALAVEHATIYGYGIVSALSP 1fha 7 :QVRQNYHQDSEAAINRQINLELYASYVYLSMSYYFD T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAA 1fha 49 :KNFAKYFLHQSHEEREHAEKLMKLQNQRGGRIFLQDI T0385 91 :M 1fha 88 :P T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAE 1fha 92 :DWESGLNAMECALHLEKNVNQSLLELHKLAT T0385 123 :TAD 1fha 126 :DPH T0385 126 :DRVFASTALTESAVMATR 1fha 140 :EQVKAIKELGDHVTNLRK T0385 147 :V 1fha 158 :M Number of specific fragments extracted= 7 number of extra gaps= 1 total=85 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fha/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fha expands to /projects/compbio/data/pdb/2fha.pdb.gz 2fha:Warning: there is no chain 2fha will retry with 2fhaA # T0385 read from 2fha/merged-good-all-a2m # 2fha read from 2fha/merged-good-all-a2m # adding 2fha to template set # found chain 2fha in template set Warning: unaligning (T0385)T11 because first residue in template chain is (2fha)T5 T0385 12 :PKRSPSEGSADNAALCDALAVEHATIYGY 2fha 6 :SQVRQNYHQDSEAAINRQINLELYASYVY T0385 41 :GI 2fha 40 :YF T0385 43 :VSALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAA 2fha 43 :RDDVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGRIFLQDI T0385 88 :QLPM 2fha 86 :QKPD T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAE 2fha 92 :DWESGLNAMECALHLEKNVNQSLLELHKLAT T0385 123 :TADDRVFAST 2fha 126 :DPHLCDFIET T0385 133 :ALTESAVMATRWNRV 2fha 144 :AIKELGDHVTNLRKM Number of specific fragments extracted= 7 number of extra gaps= 0 total=92 Number of alignments=13 # 2fha read from 2fha/merged-good-all-a2m # found chain 2fha in template set Warning: unaligning (T0385)T11 because first residue in template chain is (2fha)T5 T0385 12 :PKRSPSEGSADNAALCDALAVEHATIYGY 2fha 6 :SQVRQNYHQDSEAAINRQINLELYASYVY T0385 42 :IVS 2fha 36 :SMS T0385 45 :ALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAG 2fha 45 :DVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGRIFLQDIQ T0385 88 :QLPM 2fha 87 :KPDC T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAE 2fha 92 :DWESGLNAMECALHLEKNVNQSLLELHKLAT T0385 123 :TADDRVFAS 2fha 126 :DPHLCDFIE T0385 132 :TALTESAVMATRWNRV 2fha 143 :KAIKELGDHVTNLRKM Number of specific fragments extracted= 7 number of extra gaps= 0 total=99 Number of alignments=14 # 2fha read from 2fha/merged-good-all-a2m # found chain 2fha in template set Warning: unaligning (T0385)T11 because first residue in template chain is (2fha)T5 T0385 12 :PKRSPSEGSADNAALCDALAVEHATIYGYGIVSALSP 2fha 6 :SQVRQNYHQDSEAAINRQINLELYASYVYLSMSYYFD T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAA 2fha 49 :KNFAKYFLHQSHEEREHAEKLMKLQNQRGGRIFLQDI T0385 88 :Q 2fha 86 :Q T0385 90 :PM 2fha 87 :KP T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAETAD 2fha 92 :DWESGLNAMECALHLEKNVNQSLLELHKLATDKN T0385 126 :DRVFASTALTESAVMATR 2fha 140 :EQVKAIKELGDHVTNLRK Number of specific fragments extracted= 6 number of extra gaps= 0 total=105 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gyqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2gyqA expands to /projects/compbio/data/pdb/2gyq.pdb.gz 2gyqA:Skipped atom 26, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 30, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 32, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 34, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 36, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 38, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 40, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 42, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 45, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 49, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 51, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 81, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 85, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 87, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 89, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 91, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 93, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 111, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 115, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 117, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 119, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 121, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 123, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 245, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 249, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 251, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 253, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 255, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 257, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 313, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 317, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 319, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 321, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 323, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 325, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 328, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 332, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 334, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 336, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 338, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 349, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 353, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 355, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 357, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 359, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 361, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 420, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 424, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 426, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 457, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 461, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 463, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 466, because occupancy 0.300 <= existing 0.700 in 2gyqA Skipped atom 470, because occupancy 0.300 <= existing 0.700 in 2gyqA Skipped atom 472, because occupancy 0.300 <= existing 0.700 in 2gyqA Skipped atom 474, because occupancy 0.300 <= existing 0.700 in 2gyqA Skipped atom 476, because occupancy 0.300 <= existing 0.700 in 2gyqA Skipped atom 478, because occupancy 0.300 <= existing 0.700 in 2gyqA Skipped atom 480, because occupancy 0.300 <= existing 0.700 in 2gyqA Skipped atom 500, because occupancy 0.300 <= existing 0.700 in 2gyqA Skipped atom 504, because occupancy 0.300 <= existing 0.700 in 2gyqA Skipped atom 506, because occupancy 0.300 <= existing 0.700 in 2gyqA Skipped atom 508, because occupancy 0.300 <= existing 0.700 in 2gyqA Skipped atom 510, because occupancy 0.300 <= existing 0.700 in 2gyqA Skipped atom 512, because occupancy 0.300 <= existing 0.700 in 2gyqA Skipped atom 522, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 526, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 528, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 530, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 532, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 534, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 546, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 550, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 552, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 554, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 556, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 558, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 632, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 636, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 638, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 640, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 642, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 644, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 677, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 681, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 683, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 685, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 687, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 689, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 787, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 791, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 793, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 795, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 797, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 799, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 807, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 811, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 813, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 815, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 817, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 820, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 824, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 826, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 828, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 830, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 832, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 881, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 885, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 887, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 889, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 891, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 893, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 990, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 994, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 996, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 998, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 1000, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 1002, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 1132, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1136, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1138, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1140, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1142, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1144, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1268, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1272, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1274, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1276, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1278, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1280, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1326, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1330, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1332, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1334, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1336, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1338, because occupancy 0.400 <= existing 0.600 in 2gyqA # T0385 read from 2gyqA/merged-good-all-a2m # 2gyqA read from 2gyqA/merged-good-all-a2m # adding 2gyqA to template set # found chain 2gyqA in template set Warning: unaligning (T0385)T154 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gyqA)A168 T0385 11 :TPKRSPSEGSADNAALCDALAVEHATIYGY 2gyqA 4 :FSRDIQTMEDLLLHGLRDIYYAEQQITKAL T0385 41 :GIVSALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAP 2gyqA 35 :KMIEQATNRDLSQGLTSHLEETQKQIERLDQVFKKLGQKPS T0385 88 :QLPM 2gyqA 76 :GVNC T0385 92 :QVSS 2gyqA 95 :EIAD T0385 96 :AADAARLAVRMENDGATAWRAVVEHAE 2gyqA 103 :DAAIVANAQAVEHYEIARYGTLIAWAE T0385 123 :TADDRVFASTALTESAVM 2gyqA 133 :HDDIVRFLTTNLNEEKAA T0385 145 :NRVLGAWPI 2gyqA 151 :NTKLNTVAL Number of specific fragments extracted= 7 number of extra gaps= 0 total=112 Number of alignments=16 # 2gyqA read from 2gyqA/merged-good-all-a2m # found chain 2gyqA in template set Warning: unaligning (T0385)H8 because first residue in template chain is (2gyqA)M1 T0385 9 :GATPKRSPSEGSADNAALCDALAVEHATIYGY 2gyqA 2 :GFFSRDIQTMEDLLLHGLRDIYYAEQQITKAL T0385 41 :GIVSALSPPGVNFLVADALK 2gyqA 35 :KMIEQATNRDLSQGLTSHLE T0385 61 :QHRHRRDDVIVML 2gyqA 58 :KQIERLDQVFKKL T0385 77 :GVTAP 2gyqA 71 :GQKPS T0385 86 :G 2gyqA 76 :G T0385 89 :LPM 2gyqA 77 :VNC T0385 92 :QVSS 2gyqA 95 :EIAD T0385 96 :AADAARLAVRMENDGATAWRAVVEHAE 2gyqA 103 :DAAIVANAQAVEHYEIARYGTLIAWAE T0385 123 :TADDRVFASTALTESAVMATRWNR 2gyqA 133 :HDDIVRFLTTNLNEEKAANTKLNT Number of specific fragments extracted= 9 number of extra gaps= 0 total=121 Number of alignments=17 # 2gyqA read from 2gyqA/merged-good-all-a2m # found chain 2gyqA in template set T0385 13 :KRSPSEGSADNAALCDALAVEHATIYGYGIVSALSP 2gyqA 6 :RDIQTMEDLLLHGLRDIYYAEQQITKALPKMIEQAT T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAA 2gyqA 43 :RDLSQGLTSHLEETQKQIERLDQVFKKLGQKPSGVNC T0385 92 :QVSS 2gyqA 95 :EIAD T0385 96 :AADAARLAVRMENDGATAWRAVVEHAE 2gyqA 103 :DAAIVANAQAVEHYEIARYGTLIAWAE T0385 123 :TADDRVFASTALTESAVMATRWNRVL 2gyqA 133 :HDDIVRFLTTNLNEEKAANTKLNTVA Number of specific fragments extracted= 5 number of extra gaps= 0 total=126 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lb3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0385 read from 1lb3A/merged-good-all-a2m # 1lb3A read from 1lb3A/merged-good-all-a2m # found chain 1lb3A in training set Warning: unaligning (T0385)P12 because first residue in template chain is (1lb3A)S6 Warning: unaligning (T0385)L148 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1lb3A)S172 T0385 13 :KRSPSEGSADNAALCDALAVEHATIYGY 1lb3A 7 :QIRQNYSTEVEAAVNRLVNLHLRASYTY T0385 41 :GIVS 1lb3A 38 :GFFF T0385 45 :ALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGYQL 1lb3A 45 :DVALEGVGHFFRELAEEKREGAERLLEFQNDRGGRALFQDVQKPS T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAE 1lb3A 92 :EWGKTQEAMEAALAMEKNLNQALLDLHALGS T0385 123 :TADDRVFAST 1lb3A 126 :DPHLCDFLES T0385 133 :ALTESAVMATRWNRV 1lb3A 144 :LIKKMGNHLTNLRRV Number of specific fragments extracted= 6 number of extra gaps= 0 total=132 Number of alignments=19 # 1lb3A read from 1lb3A/merged-good-all-a2m # found chain 1lb3A in training set Warning: unaligning (T0385)P12 because first residue in template chain is (1lb3A)S6 Warning: unaligning (T0385)L148 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1lb3A)S172 Warning: unaligning (T0385)D161 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lb3A)S172 T0385 13 :KRSPSEGSADNAALCDALAVEHATIYGY 1lb3A 7 :QIRQNYSTEVEAAVNRLVNLHLRASYTY T0385 41 :GI 1lb3A 38 :GF T0385 43 :VSALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAG 1lb3A 43 :RDDVALEGVGHFFRELAEEKREGAERLLEFQNDRGGRALFQDVQ T0385 88 :QLPM 1lb3A 87 :KPSQ T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAE 1lb3A 92 :EWGKTQEAMEAALAMEKNLNQALLDLHALGS T0385 123 :TADDRVFAS 1lb3A 126 :DPHLCDFLE T0385 132 :TALTESAVMATRWNRV 1lb3A 143 :KLIKKMGNHLTNLRRV Number of specific fragments extracted= 7 number of extra gaps= 0 total=139 Number of alignments=20 # 1lb3A read from 1lb3A/merged-good-all-a2m # found chain 1lb3A in training set Warning: unaligning (T0385)L148 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1lb3A)S172 Warning: unaligning (T0385)D161 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lb3A)S172 T0385 13 :KRSPSEGSADNAALCDALAVEHATIYGYGIVSALSP 1lb3A 7 :QIRQNYSTEVEAAVNRLVNLHLRASYTYLSLGFFFD T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAG 1lb3A 49 :EGVGHFFRELAEEKREGAERLLEFQNDRGGRALFQDVQ T0385 90 :PM 1lb3A 87 :KP T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHA 1lb3A 92 :EWGKTQEAMEAALAMEKNLNQALLDLHALG T0385 122 :ETADDRVFA 1lb3A 125 :ADPHLCDFL T0385 131 :STALTESAVMATRWNRV 1lb3A 142 :VKLIKKMGNHLTNLRRV Number of specific fragments extracted= 6 number of extra gaps= 0 total=145 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bjwA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1bjwA expands to /projects/compbio/data/pdb/1bjw.pdb.gz 1bjwA:Bad short name: N1 for alphabet: pdb_atoms Bad short name: C2 for alphabet: pdb_atoms Bad short name: C2' for alphabet: pdb_atoms Bad short name: C3 for alphabet: pdb_atoms Bad short name: O3 for alphabet: pdb_atoms Bad short name: C4 for alphabet: pdb_atoms Bad short name: C4' for alphabet: pdb_atoms Bad short name: C5 for alphabet: pdb_atoms Bad short name: C6 for alphabet: pdb_atoms Bad short name: C5' for alphabet: pdb_atoms Bad short name: OP4 for alphabet: pdb_atoms Bad short name: P for alphabet: pdb_atoms Bad short name: OP1 for alphabet: pdb_atoms Bad short name: OP2 for alphabet: pdb_atoms Bad short name: OP3 for alphabet: pdb_atoms # T0385 read from 1bjwA/merged-good-all-a2m # 1bjwA read from 1bjwA/merged-good-all-a2m # adding 1bjwA to template set # found chain 1bjwA in template set T0385 16 :PSEGSADNAALCDALA 1bjwA 265 :TSPDTIAQWATLEALT T0385 47 :SPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGYQLPM 1bjwA 281 :NQEASRAFVEMAREAYRRRRDLLLEGLTALGLKAVRPSGAFYVLM T0385 92 :QVSSAADAARLAVR 1bjwA 331 :APDEVRAAERLLEA Number of specific fragments extracted= 3 number of extra gaps= 0 total=148 Number of alignments=22 # 1bjwA read from 1bjwA/merged-good-all-a2m # found chain 1bjwA in template set T0385 17 :SEGSADNAALCDALA 1bjwA 266 :SPDTIAQWATLEALT T0385 47 :SPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGYQL 1bjwA 281 :NQEASRAFVEMAREAYRRRRDLLLEGLTALGLKAVRPSGAFYV T0385 90 :PMQVSSAADAARLAVR 1bjwA 329 :PIAPDEVRAAERLLEA Number of specific fragments extracted= 3 number of extra gaps= 0 total=151 Number of alignments=23 # 1bjwA read from 1bjwA/merged-good-all-a2m # found chain 1bjwA in template set T0385 24 :AALCDALAVE 1bjwA 251 :EVIKAMASVS T0385 36 :TIYGYGIVSALSP 1bjwA 269 :TIAQWATLEALTN T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGYQLPMQVSS 1bjwA 283 :EASRAFVEMAREAYRRRRDLLLEGLTALGLKAVRPSGAFYVLMDTSP T0385 96 :AADAARLAVRMEND 1bjwA 331 :APDEVRAAERLLEA T0385 120 :HAETADDRVFASTAL 1bjwA 364 :YATSEENLRKALERF Number of specific fragments extracted= 5 number of extra gaps= 0 total=156 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z6oM/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1z6oM expands to /projects/compbio/data/pdb/1z6o.pdb.gz 1z6oM:# T0385 read from 1z6oM/merged-good-all-a2m # 1z6oM read from 1z6oM/merged-good-all-a2m # adding 1z6oM to template set # found chain 1z6oM in template set T0385 4 :SEPAHGATPKRSP 1z6oM 4 :NVNPVQIPKDWIT T0385 18 :EGSADNAALCDALAVEHATIYGY 1z6oM 17 :MHRSCRNSMRQQIQMEVGASLQY T0385 41 :GIVSA 1z6oM 45 :HFSKD T0385 46 :LSPPGVNFLVADALKQHRHRRDDVIVMLSARG 1z6oM 51 :VNRPGFAQLFFDAASEEREHAMKLIEYLLMRG T0385 81 :PIAAA 1z6oM 87 :DVSSL T0385 87 :YQLPM 1z6oM 92 :LQVRP T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAE 1z6oM 101 :SWKGGVEALEHALSMESDVTKSIRNVIKACE T0385 123 :TADDRVFASTALTESAVMATRWNRVLGA 1z6oM 146 :TGDFLEEQYKGQRDLAGKASTLKKLMDR Number of specific fragments extracted= 8 number of extra gaps= 0 total=164 Number of alignments=25 # 1z6oM read from 1z6oM/merged-good-all-a2m # found chain 1z6oM in template set T0385 2 :TSSEPAHGATPKRSPSE 1z6oM 2 :QCNVNPVQIPKDWITMH T0385 20 :SADNAALCDALAVEHATIYGY 1z6oM 19 :RSCRNSMRQQIQMEVGASLQY T0385 41 :GI 1z6oM 43 :GA T0385 43 :VS 1z6oM 46 :FS T0385 45 :ALSPPGVNFLVADALKQHRHRRDDVIVMLSARGV 1z6oM 50 :VVNRPGFAQLFFDAASEEREHAMKLIEYLLMRGE T0385 79 :TAPIAAA 1z6oM 85 :TNDVSSL T0385 86 :GYQLP 1z6oM 93 :QVRPP T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAE 1z6oM 101 :SWKGGVEALEHALSMESDVTKSIRNVIKACE T0385 123 :TADDRVFASTALTESAVMATRWNRVLGA 1z6oM 146 :TGDFLEEQYKGQRDLAGKASTLKKLMDR Number of specific fragments extracted= 9 number of extra gaps= 0 total=173 Number of alignments=26 # 1z6oM read from 1z6oM/merged-good-all-a2m # found chain 1z6oM in template set T0385 2 :TSSEPAHGATPKRSPS 1z6oM 3 :CNVNPVQIPKDWITMH T0385 20 :SADNAALCDALAVEHATIYGYGIVSALSP 1z6oM 19 :RSCRNSMRQQIQMEVGASLQYLAMGAHFS T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGYQLPM 1z6oM 54 :PGFAQLFFDAASEEREHAMKLIEYLLMRGELTNDVSSLLQVRP T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAET 1z6oM 101 :SWKGGVEALEHALSMESDVTKSIRNVIKACED T0385 124 :ADDRVFASTALTESAVMATRWNRVLGA 1z6oM 147 :GDFLEEQYKGQRDLAGKASTLKKLMDR Number of specific fragments extracted= 5 number of extra gaps= 0 total=178 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mfrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1mfrA expands to /projects/compbio/data/pdb/1mfr.pdb.gz 1mfrA:# T0385 read from 1mfrA/merged-good-all-a2m # 1mfrA read from 1mfrA/merged-good-all-a2m # adding 1mfrA to template set # found chain 1mfrA in template set Warning: unaligning (T0385)T11 because first residue in template chain is (1mfrA)V1 T0385 12 :PKRSPSEGSADNAALCDALAVEHATIYGY 1mfrA 2 :SQVRQNYHSDCEAAVNRMLNLELYASYTY T0385 41 :GIVSALSPPG 1mfrA 32 :SMYAFFDRDD T0385 51 :VNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGYQLPMQVSSAADAARLAVRMENDGATAWRAVVEHAE 1mfrA 47 :VAEFFKEHSHEEREHAEKFMKYQNKRGGRVVLQDIKKPERDEWGNTLEAMQAALQLEKTVNQALLDLHKLAT T0385 123 :TADDRVFAST 1mfrA 122 :DPHLCDFLES T0385 133 :ALTESAVMATRWNRVLG 1mfrA 133 :YLEEQVKDIKRIGDFIT Number of specific fragments extracted= 5 number of extra gaps= 0 total=183 Number of alignments=28 # 1mfrA read from 1mfrA/merged-good-all-a2m # found chain 1mfrA in template set Warning: unaligning (T0385)T11 because first residue in template chain is (1mfrA)V1 T0385 12 :PKRSPSEGSADNAALCDALAVEHATIYGYGIV 1mfrA 2 :SQVRQNYHSDCEAAVNRMLNLELYASYTYSSM T0385 44 :SALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGYQLPMQVSSAADAARLAVRMENDGATAWRAVVEHAE 1mfrA 40 :DDVALHNVAEFFKEHSHEEREHAEKFMKYQNKRGGRVVLQDIKKPERDEWGNTLEAMQAALQLEKTVNQALLDLHKLAT T0385 123 :TADDRVFAS 1mfrA 122 :DPHLCDFLE T0385 132 :TALTESAVMATRWNRVL 1mfrA 132 :EYLEEQVKDIKRIGDFI Number of specific fragments extracted= 4 number of extra gaps= 0 total=187 Number of alignments=29 # 1mfrA read from 1mfrA/merged-good-all-a2m # found chain 1mfrA in template set T0385 12 :PKRSPSEGSADNAALCDALAVEHATIYGYGIVSALSP 1mfrA 2 :SQVRQNYHSDCEAAVNRMLNLELYASYTYSSMYAFFD T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAG 1mfrA 45 :HNVAEFFKEHSHEEREHAEKFMKYQNKRGGRVVLQDIK T0385 90 :PM 1mfrA 83 :KP T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHA 1mfrA 88 :EWGNTLEAMQAALQLEKTVNQALLDLHKLA T0385 122 :ETADDRVFAST 1mfrA 121 :VDPHLCDFLES T0385 133 :ALTESAVMATRWNRV 1mfrA 133 :YLEEQVKDIKRIGDF Number of specific fragments extracted= 6 number of extra gaps= 0 total=193 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bg7/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1bg7 expands to /projects/compbio/data/pdb/1bg7.pdb.gz 1bg7:Warning: there is no chain 1bg7 will retry with 1bg7A # T0385 read from 1bg7/merged-good-all-a2m # 1bg7 read from 1bg7/merged-good-all-a2m # adding 1bg7 to template set # found chain 1bg7 in template set Warning: unaligning (T0385)T11 because first residue in template chain is (1bg7)D1 Warning: unaligning (T0385)P49 because of BadResidue code BAD_PEPTIDE in next template residue (1bg7)D41 Warning: unaligning (T0385)G50 because of BadResidue code BAD_PEPTIDE at template residue (1bg7)D41 Warning: unaligning (T0385)V117 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1bg7)P134 T0385 12 :PKRSPSEGSADNAALCDALAVEHATIYGY 1bg7 2 :SQVRQNFHRDCEAAINRMVNMELYASYTY T0385 41 :GIVSALSP 1bg7 32 :SMAFYFDR T0385 51 :VNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGYQLPMQVSSAADAARLAVRMENDGATAWRA 1bg7 47 :VAKFFKEQSHEEREHAEKLMKDQNKRGGRIVLQDVQKPERDEWGNTLEAMQAALQLEKTVNQALLD Number of specific fragments extracted= 3 number of extra gaps= 1 total=196 Number of alignments=31 # 1bg7 read from 1bg7/merged-good-all-a2m # found chain 1bg7 in template set Warning: unaligning (T0385)T11 because first residue in template chain is (1bg7)D1 Warning: unaligning (T0385)S44 because of BadResidue code BAD_PEPTIDE in next template residue (1bg7)D41 Warning: unaligning (T0385)A45 because of BadResidue code BAD_PEPTIDE at template residue (1bg7)D41 Warning: unaligning (T0385)V117 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1bg7)P134 T0385 12 :PKRSPSEGSADNAALCDALAVEHATIYGY 1bg7 2 :SQVRQNFHRDCEAAINRMVNMELYASYTY T0385 46 :LSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGYQLPMQVSSAADAARLAVRMENDGATAWRA 1bg7 42 :IALHNVAKFFKEQSHEEREHAEKLMKDQNKRGGRIVLQDVQKPERDEWGNTLEAMQAALQLEKTVNQALLD T0385 132 :TALTESAVMATRWNRV 1bg7 139 :KSIKQLGDYITNLKRL Number of specific fragments extracted= 3 number of extra gaps= 1 total=199 Number of alignments=32 # 1bg7 read from 1bg7/merged-good-all-a2m # found chain 1bg7 in template set Warning: unaligning (T0385)T11 because first residue in template chain is (1bg7)D1 Warning: unaligning (T0385)V117 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1bg7)P134 T0385 12 :PKRSPSEGSADNAALCDALAVEHATIYGYGIVSALSP 1bg7 2 :SQVRQNFHRDCEAAINRMVNMELYASYTYLSMAFYFD T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAA 1bg7 45 :HNVAKFFKEQSHEEREHAEKLMKDQNKRGGRIVLQDV T0385 88 :Q 1bg7 82 :Q T0385 90 :PM 1bg7 83 :KP T0385 92 :QVSSAADAARLAVRMENDGATAWRA 1bg7 88 :EWGNTLEAMQAALQLEKTVNQALLD T0385 125 :DDRVFASTALTESAVMATRW 1bg7 135 :EEQVKSIKQLGDYITNLKRL Number of specific fragments extracted= 6 number of extra gaps= 0 total=205 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bcfA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1bcfA expands to /projects/compbio/data/pdb/1bcf.pdb.gz 1bcfA:# T0385 read from 1bcfA/merged-good-all-a2m # 1bcfA read from 1bcfA/merged-good-all-a2m # adding 1bcfA to template set # found chain 1bcfA in template set Warning: unaligning (T0385)P16 because first residue in template chain is (1bcfA)M1 T0385 17 :SEGSADNAALCDALAVEHATIYGY 1bcfA 2 :KGDTKVINYLNKLLGNELVAINQY T0385 44 :S 1bcfA 29 :A T0385 45 :AL 1bcfA 36 :GL T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAA 1bcfA 38 :KRLNDVEYHESIDEMKHADRYIERILFLEGLPNLQD T0385 85 :AGYQ 1bcfA 75 :GKLN T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAE 1bcfA 79 :IGEDVEEMLRSDLALELDGAKNLREAIGYAD T0385 123 :TADDRVFASTALTESAVMATRWNRVLG 1bcfA 113 :DYVSRDMMIEILRDEEGHIDWLETELD Number of specific fragments extracted= 7 number of extra gaps= 0 total=212 Number of alignments=34 # 1bcfA read from 1bcfA/merged-good-all-a2m # found chain 1bcfA in template set Warning: unaligning (T0385)P16 because first residue in template chain is (1bcfA)M1 T0385 17 :SEGSADNAALCDALAVEHATIYGY 1bcfA 2 :KGDTKVINYLNKLLGNELVAINQY T0385 41 :GIVSALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAA 1bcfA 30 :RMFKNWGLKRLNDVEYHESIDEMKHADRYIERILFLEGLPNLQDL T0385 86 :G 1bcfA 76 :K T0385 91 :MQ 1bcfA 77 :LN T0385 93 :VSSAADAARLAVRMENDGATAWRAVVEHAE 1bcfA 80 :GEDVEEMLRSDLALELDGAKNLREAIGYAD T0385 123 :TADDRVFASTALTESAVMATRWNRVL 1bcfA 113 :DYVSRDMMIEILRDEEGHIDWLETEL Number of specific fragments extracted= 6 number of extra gaps= 0 total=218 Number of alignments=35 # 1bcfA read from 1bcfA/merged-good-all-a2m # found chain 1bcfA in template set Warning: unaligning (T0385)P16 because first residue in template chain is (1bcfA)M1 T0385 17 :SEGSADNAALCDALAVEHATIYGYGIVSALSP 1bcfA 2 :KGDTKVINYLNKLLGNELVAINQYFLHARMFK T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAA 1bcfA 38 :KRLNDVEYHESIDEMKHADRYIERILFLEGLPNLQDL T0385 89 :LPM 1bcfA 75 :GKL T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHA 1bcfA 79 :IGEDVEEMLRSDLALELDGAKNLREAIGYA T0385 122 :ETADDRVFASTALTESAVMATRWNRV 1bcfA 112 :HDYVSRDMMIEILRDEEGHIDWLETE Number of specific fragments extracted= 5 number of extra gaps= 0 total=223 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mojA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1mojA expands to /projects/compbio/data/pdb/1moj.pdb.gz 1mojA:# T0385 read from 1mojA/merged-good-all-a2m # 1mojA read from 1mojA/merged-good-all-a2m # adding 1mojA to template set # found chain 1mojA in template set Warning: unaligning (T0385)S3 because first residue in template chain is (1mojA)S2 T0385 4 :SEPAHGATPKRSPSEG 1mojA 3 :TQKNARATAGEVEGSD T0385 21 :ADNAALCDALAVEHATIYGY 1mojA 25 :DRAEQCVDALNADLANVYVL T0385 41 :GIVSALSPPG 1mojA 50 :KHHWNVEGAE T0385 51 :VNFLVADALKQHRHRRDDVIVMLSARGVTAPIAA 1mojA 63 :LHLFLGEAAETAEEVADELAERVQALGGVPHASP T0385 85 :AGYQLPM 1mojA 103 :ASVDVED T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAE 1mojA 111 :DVYDIRTSLANDMAIYGDIIEATREHTELAE T0385 123 :TADDRVFASTALTESAVMATRWNRVLGAWPI 1mojA 145 :DHATAHMLREGLIELEDDAHHIEHYLEDDTL Number of specific fragments extracted= 7 number of extra gaps= 0 total=230 Number of alignments=37 # 1mojA read from 1mojA/merged-good-all-a2m # found chain 1mojA in template set Warning: unaligning (T0385)S3 because first residue in template chain is (1mojA)S2 T0385 4 :SEPAHGATPKRSPSEGS 1mojA 3 :TQKNARATAGEVEGSDA T0385 21 :ADNAALCDALAVEHATIYGY 1mojA 25 :DRAEQCVDALNADLANVYVL T0385 41 :GIVSALSP 1mojA 50 :KHHWNVEG T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAA 1mojA 61 :RDLHLFLGEAAETAEEVADELAERVQALGGVPHASP T0385 85 :AGYQLPMQ 1mojA 103 :ASVDVEDE T0385 93 :VSSAADAARLAVRMENDGATAWRAVVEHAE 1mojA 112 :VYDIRTSLANDMAIYGDIIEATREHTELAE T0385 123 :TADDRVFASTALTESAVMATRWNRVLGAWPI 1mojA 145 :DHATAHMLREGLIELEDDAHHIEHYLEDDTL Number of specific fragments extracted= 7 number of extra gaps= 0 total=237 Number of alignments=38 # 1mojA read from 1mojA/merged-good-all-a2m # found chain 1mojA in template set T0385 7 :AHGATPKRSPSEGSADNAALCDALAVEHATIYGYGIVS 1mojA 11 :AGEVEGSDALRMDADRAEQCVDALNADLANVYVLYHQL T0385 45 :ALSP 1mojA 53 :WNVE T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIA 1mojA 61 :RDLHLFLGEAAETAEEVADELAERVQALGGVPHAS T0385 84 :AAGYQLPM 1mojA 100 :QAEASVDV T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAET 1mojA 111 :DVYDIRTSLANDMAIYGDIIEATREHTELAEN T0385 124 :ADDRVFASTALTESAVMATRWNRVLGAWPI 1mojA 146 :HATAHMLREGLIELEDDAHHIEHYLEDDTL Number of specific fragments extracted= 6 number of extra gaps= 0 total=243 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sofA/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/T0385/1sofA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0385/1sofA/merged-good-all-a2m.gz for input Trying 1sofA/merged-good-all-a2m Error: Couldn't open file 1sofA/merged-good-all-a2m or 1sofA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b5pA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0385 read from 1b5pA/merged-good-all-a2m # 1b5pA read from 1b5pA/merged-good-all-a2m # found chain 1b5pA in training set T0385 16 :PSEGSADNAALCDALA 1b5pA 265 :TSPDTIAQWATLEALT T0385 47 :SPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGYQLPM 1b5pA 281 :NQEASRAFVEMAREAYRRRRDLLLEGLTALGLKAVRPSGAFYVLM T0385 92 :QVSSAADAARLAVR 1b5pA 331 :APDEVRAAERLLEA Number of specific fragments extracted= 3 number of extra gaps= 0 total=246 Number of alignments=40 # 1b5pA read from 1b5pA/merged-good-all-a2m # found chain 1b5pA in training set T0385 17 :SEGSADNAALCDALA 1b5pA 266 :SPDTIAQWATLEALT T0385 47 :SPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGYQL 1b5pA 281 :NQEASRAFVEMAREAYRRRRDLLLEGLTALGLKAVRPSGAFYV T0385 90 :PMQVSSAADAARLAVR 1b5pA 329 :PIAPDEVRAAERLLEA Number of specific fragments extracted= 3 number of extra gaps= 0 total=249 Number of alignments=41 # 1b5pA read from 1b5pA/merged-good-all-a2m # found chain 1b5pA in training set T0385 24 :AALCDALAVEHA 1b5pA 251 :EVIKAMASVSRQ T0385 36 :TIYGYGIVSALSP 1b5pA 269 :TIAQWATLEALTN T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGYQLPMQVSS 1b5pA 283 :EASRAFVEMAREAYRRRRDLLLEGLTALGLKAVRPSGAFYVLMDTSP T0385 96 :AADAARLAVRMEND 1b5pA 331 :APDEVRAAERLLEA Number of specific fragments extracted= 4 number of extra gaps= 0 total=253 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fkzA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fkzA expands to /projects/compbio/data/pdb/2fkz.pdb.gz 2fkzA:Skipped atom 23, because occupancy 0.500 <= existing 0.500 in 2fkzA Skipped atom 25, because occupancy 0.500 <= existing 0.500 in 2fkzA Skipped atom 27, because occupancy 0.500 <= existing 0.500 in 2fkzA Skipped atom 29, because occupancy 0.500 <= existing 0.500 in 2fkzA Skipped atom 31, because occupancy 0.500 <= existing 0.500 in 2fkzA Skipped atom 33, because occupancy 0.500 <= existing 0.500 in 2fkzA Skipped atom 35, because occupancy 0.500 <= existing 0.500 in 2fkzA Skipped atom 37, because occupancy 0.500 <= existing 0.500 in 2fkzA Skipped atom 71, because occupancy 0.500 <= existing 0.500 in 2fkzA Skipped atom 73, because occupancy 0.500 <= existing 0.500 in 2fkzA Skipped atom 75, because occupancy 0.500 <= existing 0.500 in 2fkzA Skipped atom 77, because occupancy 0.500 <= existing 0.500 in 2fkzA Skipped atom 79, because occupancy 0.500 <= existing 0.500 in 2fkzA Skipped atom 81, because occupancy 0.500 <= existing 0.500 in 2fkzA Skipped atom 83, because occupancy 0.500 <= existing 0.500 in 2fkzA Skipped atom 85, because occupancy 0.500 <= existing 0.500 in 2fkzA Skipped atom 87, because occupancy 0.500 <= existing 0.500 in 2fkzA Skipped atom 1029, because occupancy 0.500 <= existing 0.500 in 2fkzA Skipped atom 1031, because occupancy 0.500 <= existing 0.500 in 2fkzA Skipped atom 1033, because occupancy 0.500 <= existing 0.500 in 2fkzA Skipped atom 1035, because occupancy 0.500 <= existing 0.500 in 2fkzA Skipped atom 1037, because occupancy 0.500 <= existing 0.500 in 2fkzA Skipped atom 1039, because occupancy 0.500 <= existing 0.500 in 2fkzA # T0385 read from 2fkzA/merged-good-all-a2m # 2fkzA read from 2fkzA/merged-good-all-a2m # adding 2fkzA to template set # found chain 2fkzA in template set Warning: unaligning (T0385)P16 because first residue in template chain is (2fkzA)M1 T0385 17 :SEGSADNAALCDALAVEHATIYGY 2fkzA 2 :KGDKIVIQHLNKILGNELIAINQY T0385 41 :GIVSALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGYQL 2fkzA 30 :RMYEDWGLEKLGKHEYHESIDEMKHADKLIKRILFLEGLPNLQELGKLL T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAE 2fkzA 79 :IGEHTKEMLECDLKLEQAGLPDLKAAIAYCE T0385 123 :TADDRVFASTALTESAVMATRWNRVLG 2fkzA 113 :DYASRELLEDILESEEDHIDWLETQLD Number of specific fragments extracted= 4 number of extra gaps= 0 total=257 Number of alignments=43 # 2fkzA read from 2fkzA/merged-good-all-a2m # found chain 2fkzA in template set Warning: unaligning (T0385)P16 because first residue in template chain is (2fkzA)M1 T0385 17 :SEGSADNAALCDALAVEHATIYGY 2fkzA 2 :KGDKIVIQHLNKILGNELIAINQY T0385 41 :GIVSALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAG 2fkzA 30 :RMYEDWGLEKLGKHEYHESIDEMKHADKLIKRILFLEGLPNLQELG T0385 89 :LPMQVSSAADAARLAVRMENDGATAWRAVVEHAE 2fkzA 76 :KLLIGEHTKEMLECDLKLEQAGLPDLKAAIAYCE T0385 123 :TADDRVFASTALTESAVMATRWNRVL 2fkzA 113 :DYASRELLEDILESEEDHIDWLETQL Number of specific fragments extracted= 4 number of extra gaps= 0 total=261 Number of alignments=44 # 2fkzA read from 2fkzA/merged-good-all-a2m # found chain 2fkzA in template set T0385 19 :GSADNAALCDALAVEHATIYGYGIVSALSP 2fkzA 4 :DKIVIQHLNKILGNELIAINQYFLHARMYE T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAA 2fkzA 38 :EKLGKHEYHESIDEMKHADKLIKRILFLEGLPNLQEL T0385 88 :QLPMQVSSAADAARLAVRMENDGATAWRAVVEHAE 2fkzA 75 :GKLLIGEHTKEMLECDLKLEQAGLPDLKAAIAYCE T0385 123 :TADDRVFASTALTESAVMATRWNRV 2fkzA 113 :DYASRELLEDILESEEDHIDWLETQ Number of specific fragments extracted= 4 number of extra gaps= 0 total=265 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vlgA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vlgA expands to /projects/compbio/data/pdb/1vlg.pdb.gz 1vlgA:Skipped atom 1084, because occupancy 0.350 <= existing 0.650 in 1vlgA Skipped atom 1086, because occupancy 0.350 <= existing 0.650 in 1vlgA Skipped atom 1088, because occupancy 0.350 <= existing 0.650 in 1vlgA Skipped atom 1090, because occupancy 0.350 <= existing 0.650 in 1vlgA Skipped atom 1092, because occupancy 0.350 <= existing 0.650 in 1vlgA Skipped atom 1094, because occupancy 0.350 <= existing 0.650 in 1vlgA Skipped atom 1096, because occupancy 0.350 <= existing 0.650 in 1vlgA Skipped atom 1098, because occupancy 0.350 <= existing 0.650 in 1vlgA Skipped atom 1100, because occupancy 0.350 <= existing 0.650 in 1vlgA # T0385 read from 1vlgA/merged-good-all-a2m # 1vlgA read from 1vlgA/merged-good-all-a2m # adding 1vlgA to template set # found chain 1vlgA in template set Warning: unaligning (T0385)S15 because first residue in template chain is (1vlgA)M1 Warning: unaligning (T0385)S17 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vlgA)I4 Warning: unaligning (T0385)E18 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vlgA)I4 T0385 16 :P 1vlgA 2 :M T0385 19 :GSADNAALCDALAVEHATIYGY 1vlgA 5 :SEKVRKALNDQLNREIYSSYLY T0385 41 :GIVS 1vlgA 32 :YFDA T0385 45 :AL 1vlgA 37 :GF T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAG 1vlgA 39 :KGFAHWMKKQAQEELTHAMKFYEYIYERGGRVELEAIE T0385 88 :QLPMQVSSAADAARLAVRMENDGATAWRAVVEHAE 1vlgA 77 :KPPSNWNGIKDAFEAALKHEEFVTQSIYNILELAS T0385 123 :TADDRVFASTALTESAVMATRWNRVLG 1vlgA 115 :DHATVSFLKWFVDEQVEEEDQVREILD Number of specific fragments extracted= 7 number of extra gaps= 1 total=272 Number of alignments=46 # 1vlgA read from 1vlgA/merged-good-all-a2m # found chain 1vlgA in template set Warning: unaligning (T0385)S15 because first residue in template chain is (1vlgA)M1 Warning: unaligning (T0385)S17 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vlgA)I4 Warning: unaligning (T0385)E18 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vlgA)I4 T0385 16 :P 1vlgA 2 :M T0385 19 :GSADNAALCDALAVEHATIYGY 1vlgA 5 :SEKVRKALNDQLNREIYSSYLY T0385 41 :GIVSALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAG 1vlgA 31 :TYFDAEGFKGFAHWMKKQAQEELTHAMKFYEYIYERGGRVELEAIE T0385 88 :QLPMQVSSAADAARLAVRMENDGATAWRAVVEHAE 1vlgA 77 :KPPSNWNGIKDAFEAALKHEEFVTQSIYNILELAS T0385 123 :TADDRVFASTALTESAVMATRWNRVL 1vlgA 115 :DHATVSFLKWFVDEQVEEEDQVREIL Number of specific fragments extracted= 5 number of extra gaps= 1 total=277 Number of alignments=47 # 1vlgA read from 1vlgA/merged-good-all-a2m # found chain 1vlgA in template set T0385 19 :GSADNAALCDALAVEHATIYGYGIVSALSP 1vlgA 5 :SEKVRKALNDQLNREIYSSYLYLSMATYFD T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAG 1vlgA 39 :KGFAHWMKKQAQEELTHAMKFYEYIYERGGRVELEAIE T0385 88 :QLPMQVSSAADAARLAVRMENDGATAWRAVVEHAETADD 1vlgA 77 :KPPSNWNGIKDAFEAALKHEEFVTQSIYNILELASEEKD T0385 128 :VFASTALTESAVMATRWNRV 1vlgA 116 :HATVSFLKWFVDEQVEEEDQ Number of specific fragments extracted= 4 number of extra gaps= 0 total=281 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rcd/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1rcd expands to /projects/compbio/data/pdb/1rcd.pdb.gz 1rcd:Warning: there is no chain 1rcd will retry with 1rcdA # T0385 read from 1rcd/merged-good-all-a2m # 1rcd read from 1rcd/merged-good-all-a2m # adding 1rcd to template set # found chain 1rcd in template set Warning: unaligning (T0385)P12 because first residue in template chain is (1rcd)S2 T0385 13 :KRSPSEGSADNAALCDALAVEHATIYGY 1rcd 3 :QVRQNFHQDCEAGLNRTVNLKFHSSYVY T0385 41 :GIVSALSPPG 1rcd 32 :SMASYFNRDD T0385 51 :VNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGYQLPMQVSSAADAARLAVRMENDGATAWRAVVEHAE 1rcd 47 :FAKFFRERSEEEKEHAEKLIEYQNQRGGRVFLQSVEKPERDDWANGLEALQTALKLQKSVNQALLDLHAVAA T0385 123 :TAD 1rcd 122 :DPH T0385 126 :DRVFASTALTESAVMATRWNRVLGAW 1rcd 133 :YLSESVETIKKLGDHITSLKKLWSSH Number of specific fragments extracted= 5 number of extra gaps= 0 total=286 Number of alignments=49 # 1rcd read from 1rcd/merged-good-all-a2m # found chain 1rcd in template set Warning: unaligning (T0385)P12 because first residue in template chain is (1rcd)S2 T0385 13 :KRSPSEGSADNAALCDALAVEHATIYGY 1rcd 3 :QVRQNFHQDCEAGLNRTVNLKFHSSYVY T0385 44 :S 1rcd 35 :S T0385 45 :ALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGYQLPMQVSSAADAARLAVRMENDGATAWRAVVEHAE 1rcd 41 :DVALSNFAKFFRERSEEEKEHAEKLIEYQNQRGGRVFLQSVEKPERDDWANGLEALQTALKLQKSVNQALLDLHAVAA T0385 123 :TADDRVFAS 1rcd 122 :DPHMTDFLE T0385 132 :TALTESAVMATRWNRVLGAW 1rcd 139 :ETIKKLGDHITSLKKLWSSH Number of specific fragments extracted= 5 number of extra gaps= 0 total=291 Number of alignments=50 # 1rcd read from 1rcd/merged-good-all-a2m # found chain 1rcd in template set Warning: unaligning (T0385)P12 because first residue in template chain is (1rcd)S2 T0385 13 :KRSPSEGSADNAALCDALAVEHATIYGYGIVSALSP 1rcd 3 :QVRQNFHQDCEAGLNRTVNLKFHSSYVYLSMASYFN T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAG 1rcd 45 :SNFAKFFRERSEEEKEHAEKLIEYQNQRGGRVFLQSVE T0385 90 :PM 1rcd 83 :KP T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAE 1rcd 88 :DWANGLEALQTALKLQKSVNQALLDLHAVAA T0385 123 :TADDRVFA 1rcd 122 :DPHMTDFL T0385 132 :TALTESAVMATRWNRVLG 1rcd 139 :ETIKKLGDHITSLKKLWS Number of specific fragments extracted= 6 number of extra gaps= 0 total=297 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r03A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1r03A expands to /projects/compbio/data/pdb/1r03.pdb.gz 1r03A:Skipped atom 497, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 499, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 501, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 503, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 505, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 507, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 509, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 511, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 513, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 539, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 541, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 543, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 545, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 547, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 549, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 551, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 553, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 555, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 584, because occupancy 0.300 <= existing 0.700 in 1r03A Skipped atom 586, because occupancy 0.300 <= existing 0.700 in 1r03A Skipped atom 588, because occupancy 0.300 <= existing 0.700 in 1r03A Skipped atom 590, because occupancy 0.300 <= existing 0.700 in 1r03A Skipped atom 592, because occupancy 0.300 <= existing 0.700 in 1r03A Skipped atom 594, because occupancy 0.300 <= existing 0.700 in 1r03A Skipped atom 596, because occupancy 0.300 <= existing 0.700 in 1r03A Skipped atom 598, because occupancy 0.300 <= existing 0.700 in 1r03A Skipped atom 617, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 619, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 621, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 623, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 625, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 627, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 629, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 631, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 633, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 890, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 892, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 894, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 896, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 898, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 900, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 902, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 904, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 906, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 1100, because occupancy 0.330 <= existing 0.670 in 1r03A Skipped atom 1102, because occupancy 0.330 <= existing 0.670 in 1r03A Skipped atom 1104, because occupancy 0.330 <= existing 0.670 in 1r03A Skipped atom 1106, because occupancy 0.330 <= existing 0.670 in 1r03A Skipped atom 1108, because occupancy 0.330 <= existing 0.670 in 1r03A Skipped atom 1110, because occupancy 0.330 <= existing 0.670 in 1r03A Skipped atom 1112, because occupancy 0.330 <= existing 0.670 in 1r03A Skipped atom 1114, because occupancy 0.330 <= existing 0.670 in 1r03A Skipped atom 1116, because occupancy 0.330 <= existing 0.670 in 1r03A Skipped atom 1165, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 1167, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 1169, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 1171, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 1173, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 1175, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 1177, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 1179, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 1181, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 1208, because occupancy 0.330 <= existing 0.670 in 1r03A Skipped atom 1210, because occupancy 0.330 <= existing 0.670 in 1r03A Skipped atom 1212, because occupancy 0.330 <= existing 0.670 in 1r03A Skipped atom 1214, because occupancy 0.330 <= existing 0.670 in 1r03A Skipped atom 1216, because occupancy 0.330 <= existing 0.670 in 1r03A Skipped atom 1218, because occupancy 0.330 <= existing 0.670 in 1r03A Skipped atom 1427, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 1429, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 1431, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 1433, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 1435, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 1437, because occupancy 0.500 <= existing 0.500 in 1r03A Skipped atom 1439, because occupancy 0.500 <= existing 0.500 in 1r03A # T0385 read from 1r03A/merged-good-all-a2m # 1r03A read from 1r03A/merged-good-all-a2m # adding 1r03A to template set # found chain 1r03A in template set Warning: unaligning (T0385)P12 because first residue in template chain is (1r03A)S6 T0385 13 :KRSPSEGSADNAALCDALAVEHATIYGY 1r03A 7 :RVRQNFHPDSEAAINRQINLELYASYVY T0385 41 :GIVSALSPPG 1r03A 36 :SMAYYFSRDD T0385 51 :VNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGY 1r03A 51 :FSRYFLHQSREETEHAEKLMRLQNQRGGRIRLQDIKK T0385 90 :PM 1r03A 88 :PE T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAE 1r03A 92 :DWESGLHAMECALLLEKNVNQSLLELHALAS T0385 123 :TADDRVFAST 1r03A 126 :DPHLCDFLET T0385 133 :ALTESAVMATRWNRVLG 1r03A 137 :YLNEQVKSIKELGDHVH Number of specific fragments extracted= 7 number of extra gaps= 0 total=304 Number of alignments=52 # 1r03A read from 1r03A/merged-good-all-a2m # found chain 1r03A in template set Warning: unaligning (T0385)P12 because first residue in template chain is (1r03A)S6 T0385 13 :KRSPSEGSADNAALCDALAVEHATIYGY 1r03A 7 :RVRQNFHPDSEAAINRQINLELYASYVY T0385 43 :V 1r03A 41 :F T0385 45 :ALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGYQLPMQVSSAADAARLAVRMENDGATAWRAVVEHAE 1r03A 45 :DVALNNFSRYFLHQSREETEHAEKLMRLQNQRGGRIRLQDIKKPEQDDWESGLHAMECALLLEKNVNQSLLELHALAS T0385 123 :TADDRVFAS 1r03A 126 :DPHLCDFLE T0385 132 :TALTESAVMATRWNRV 1r03A 143 :KSIKELGDHVHNLVKM Number of specific fragments extracted= 5 number of extra gaps= 0 total=309 Number of alignments=53 # 1r03A read from 1r03A/merged-good-all-a2m # found chain 1r03A in template set Warning: unaligning (T0385)P12 because first residue in template chain is (1r03A)S6 T0385 13 :KRSPSEGSADNAALCDALAVEHATIYGYGIVSALSP 1r03A 7 :RVRQNFHPDSEAAINRQINLELYASYVYLSMAYYFS T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAG 1r03A 49 :NNFSRYFLHQSREETEHAEKLMRLQNQRGGRIRLQDIK T0385 90 :PM 1r03A 87 :KP T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAETAD 1r03A 92 :DWESGLHAMECALLLEKNVNQSLLELHALASDKG T0385 126 :DRVFASTALTESAVMATRWNR 1r03A 140 :EQVKSIKELGDHVHNLVKMGA Number of specific fragments extracted= 5 number of extra gaps= 0 total=314 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nfvA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1nfvA expands to /projects/compbio/data/pdb/1nfv.pdb.gz 1nfvA:Skipped atom 443, because occupancy 0.400 <= existing 0.600 in 1nfvA Skipped atom 445, because occupancy 0.400 <= existing 0.600 in 1nfvA Skipped atom 447, because occupancy 0.400 <= existing 0.600 in 1nfvA Skipped atom 449, because occupancy 0.400 <= existing 0.600 in 1nfvA Skipped atom 451, because occupancy 0.400 <= existing 0.600 in 1nfvA Skipped atom 453, because occupancy 0.400 <= existing 0.600 in 1nfvA Skipped atom 455, because occupancy 0.400 <= existing 0.600 in 1nfvA Skipped atom 457, because occupancy 0.400 <= existing 0.600 in 1nfvA Skipped atom 459, because occupancy 0.400 <= existing 0.600 in 1nfvA Skipped atom 461, because occupancy 0.400 <= existing 0.600 in 1nfvA Skipped atom 463, because occupancy 0.400 <= existing 0.600 in 1nfvA Skipped atom 990, because occupancy 0.420 <= existing 0.580 in 1nfvA Skipped atom 992, because occupancy 0.420 <= existing 0.580 in 1nfvA Skipped atom 994, because occupancy 0.420 <= existing 0.580 in 1nfvA Skipped atom 996, because occupancy 0.420 <= existing 0.580 in 1nfvA Skipped atom 998, because occupancy 0.420 <= existing 0.580 in 1nfvA Skipped atom 1000, because occupancy 0.420 <= existing 0.580 in 1nfvA Skipped atom 1002, because occupancy 0.420 <= existing 0.580 in 1nfvA Skipped atom 1004, because occupancy 0.420 <= existing 0.580 in 1nfvA Skipped atom 1006, because occupancy 0.420 <= existing 0.580 in 1nfvA Skipped atom 1008, because occupancy 0.420 <= existing 0.580 in 1nfvA Skipped atom 1010, because occupancy 0.420 <= existing 0.580 in 1nfvA Skipped atom 1315, because occupancy 0.470 <= existing 0.520 in 1nfvA Skipped atom 1317, because occupancy 0.470 <= existing 0.520 in 1nfvA Skipped atom 1319, because occupancy 0.470 <= existing 0.520 in 1nfvA Skipped atom 1321, because occupancy 0.470 <= existing 0.520 in 1nfvA Skipped atom 1323, because occupancy 0.470 <= existing 0.520 in 1nfvA Skipped atom 1325, because occupancy 0.470 <= existing 0.520 in 1nfvA Skipped atom 1327, because occupancy 0.300 <= existing 0.700 in 1nfvA Skipped atom 1329, because occupancy 0.300 <= existing 0.700 in 1nfvA Skipped atom 1331, because occupancy 0.300 <= existing 0.700 in 1nfvA Skipped atom 1333, because occupancy 0.300 <= existing 0.700 in 1nfvA Skipped atom 1335, because occupancy 0.300 <= existing 0.700 in 1nfvA Skipped atom 1337, because occupancy 0.300 <= existing 0.700 in 1nfvA Skipped atom 1339, because occupancy 0.300 <= existing 0.700 in 1nfvA Skipped atom 1341, because occupancy 0.300 <= existing 0.700 in 1nfvA Skipped atom 1343, because occupancy 0.300 <= existing 0.700 in 1nfvA # T0385 read from 1nfvA/merged-good-all-a2m # 1nfvA read from 1nfvA/merged-good-all-a2m # adding 1nfvA to template set # found chain 1nfvA in template set T0385 21 :ADNAALCDALAVEHATIYGY 1nfvA 11 :KVIEVLNKARAMELHAIHQY T0385 41 :GIVS 1nfvA 36 :SLDD T0385 46 :LSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGYQL 1nfvA 40 :MDYGELAANMKLIAIDEMRHAENFAERIKELGGEPTTQKEGKVV T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAETAD 1nfvA 84 :TGQAVPVIYESDADQEDATIEAYSQFLKVCKEQG T0385 126 :DRVFASTALTESAVMATRWNRVLG 1nfvA 121 :TARLFERIIEEEQAHLTYYENIGS Number of specific fragments extracted= 5 number of extra gaps= 0 total=319 Number of alignments=55 # 1nfvA read from 1nfvA/merged-good-all-a2m # found chain 1nfvA in template set T0385 21 :ADNAALCDALAVEHATIYGY 1nfvA 11 :KVIEVLNKARAMELHAIHQY T0385 41 :GIVSALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAG 1nfvA 35 :YSLDDMDYGELAANMKLIAIDEMRHAENFAERIKELGGEPTTQKEG T0385 90 :PMQVSSAADAARLAVRMENDGATAWRAVVEHAE 1nfvA 82 :VVTGQAVPVIYESDADQEDATIEAYSQFLKVCK T0385 123 :TADDRVFASTALTESAVMATRWNRVLG 1nfvA 118 :DIVTARLFERIIEEEQAHLTYYENIGS T0385 150 :AWPITAAFPGGDE 1nfvA 159 :GTPSSTGTASKGF Number of specific fragments extracted= 5 number of extra gaps= 0 total=324 Number of alignments=56 # 1nfvA read from 1nfvA/merged-good-all-a2m # found chain 1nfvA in template set Warning: unaligning (T0385)R14 because first residue in template chain is (1nfvA)N4 Warning: unaligning (T0385)P16 because of BadResidue code BAD_PEPTIDE in next template residue (1nfvA)D7 Warning: unaligning (T0385)S17 because of BadResidue code BAD_PEPTIDE at template residue (1nfvA)D7 T0385 15 :S 1nfvA 5 :R T0385 18 :EGSADNAALCDALAVEHATIYGYGIVSALSP 1nfvA 8 :RKAKVIEVLNKARAMELHAIHQYMNQHYSLD T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAG 1nfvA 43 :GELAANMKLIAIDEMRHAENFAERIKELGGEPTTQKEG T0385 90 :PM 1nfvA 81 :KV T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAETAD 1nfvA 84 :TGQAVPVIYESDADQEDATIEAYSQFLKVCKEQG T0385 126 :DRVFASTALTESAVMATRWNRV 1nfvA 121 :TARLFERIIEEEQAHLTYYENI Number of specific fragments extracted= 6 number of extra gaps= 1 total=330 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dat/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1dat expands to /projects/compbio/data/pdb/1dat.pdb.gz 1dat:Warning: there is no chain 1dat will retry with 1datA # T0385 read from 1dat/merged-good-all-a2m # 1dat read from 1dat/merged-good-all-a2m # adding 1dat to template set # found chain 1dat in template set Warning: unaligning (T0385)P12 because of BadResidue code BAD_PEPTIDE at template residue (1dat)S2 Warning: unaligning (T0385)K13 because of BadResidue code BAD_PEPTIDE at template residue (1dat)Q3 T0385 14 :RSPSEGSADNAALCDALAVEHATIYGY 1dat 4 :IRQNYSTEVEAAVNRLVNLYLRASYTY T0385 42 :IVSALSPPG 1dat 33 :LGFYFDRDD T0385 51 :VNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAG 1dat 47 :VCHFFRELAEEKREGAERLLKMQNQRGGRALFQDLQ T0385 89 :LPM 1dat 83 :KPS T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAE 1dat 88 :EWGTTPDAMKAAIVLEKSLNQALLDLHALGS T0385 123 :TADDRVFAST 1dat 122 :DPHLCDFLES T0385 133 :ALTESAVMATRWNRVLG 1dat 140 :LIKKMGDHLTNIQRLVG Number of specific fragments extracted= 7 number of extra gaps= 1 total=337 Number of alignments=58 # 1dat read from 1dat/merged-good-all-a2m # found chain 1dat in template set Warning: unaligning (T0385)P12 because of BadResidue code BAD_PEPTIDE at template residue (1dat)S2 Warning: unaligning (T0385)K13 because of BadResidue code BAD_PEPTIDE at template residue (1dat)Q3 T0385 14 :RSPSEGSADNAALCDALAVEHATIYGY 1dat 4 :IRQNYSTEVEAAVNRLVNLYLRASYTY T0385 41 :GI 1dat 34 :GF T0385 43 :VSALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAG 1dat 39 :RDDVALEGVCHFFRELAEEKREGAERLLKMQNQRGGRALFQDLQ T0385 88 :QLPM 1dat 83 :KPSQ T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAE 1dat 88 :EWGTTPDAMKAAIVLEKSLNQALLDLHALGS T0385 123 :TADDRVFAS 1dat 122 :DPHLCDFLE T0385 132 :TALTESAVMATRWNRVLG 1dat 139 :KLIKKMGDHLTNIQRLVG Number of specific fragments extracted= 7 number of extra gaps= 1 total=344 Number of alignments=59 # 1dat read from 1dat/merged-good-all-a2m # found chain 1dat in template set Warning: unaligning (T0385)T11 because first residue in template chain is (1dat)S1 Warning: unaligning (T0385)P12 because of BadResidue code BAD_PEPTIDE at template residue (1dat)S2 Warning: unaligning (T0385)K13 because of BadResidue code BAD_PEPTIDE at template residue (1dat)Q3 T0385 14 :RSPSEGSADNAALCDALAVEHATIYGYGIVSALSP 1dat 4 :IRQNYSTEVEAAVNRLVNLYLRASYTYLSLGFYFD T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAG 1dat 45 :EGVCHFFRELAEEKREGAERLLKMQNQRGGRALFQDLQ T0385 90 :PM 1dat 83 :KP T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHA 1dat 88 :EWGTTPDAMKAAIVLEKSLNQALLDLHALG T0385 122 :ETADDRVFASTALTESAVMATRWNRV 1dat 121 :ADPHLCDFLESHFLDEEVKLIKKMGD Number of specific fragments extracted= 5 number of extra gaps= 0 total=349 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vjxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vjxA expands to /projects/compbio/data/pdb/1vjx.pdb.gz 1vjxA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 209, because occupancy 0.500 <= existing 0.500 in 1vjxA Skipped atom 211, because occupancy 0.500 <= existing 0.500 in 1vjxA Skipped atom 213, because occupancy 0.500 <= existing 0.500 in 1vjxA Skipped atom 215, because occupancy 0.500 <= existing 0.500 in 1vjxA Skipped atom 217, because occupancy 0.500 <= existing 0.500 in 1vjxA Skipped atom 219, because occupancy 0.500 <= existing 0.500 in 1vjxA Skipped atom 221, because occupancy 0.500 <= existing 0.500 in 1vjxA Skipped atom 223, because occupancy 0.500 <= existing 0.500 in 1vjxA Skipped atom 225, because occupancy 0.500 <= existing 0.500 in 1vjxA Skipped atom 227, because occupancy 0.500 <= existing 0.500 in 1vjxA Skipped atom 229, because occupancy 0.500 <= existing 0.500 in 1vjxA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0385 read from 1vjxA/merged-good-all-a2m # 1vjxA read from 1vjxA/merged-good-all-a2m # adding 1vjxA to template set # found chain 1vjxA in template set Warning: unaligning (T0385)P16 because first residue in template chain is (1vjxA)H-3 Warning: unaligning (T0385)S17 because of BadResidue code BAD_PEPTIDE at template residue (1vjxA)H-2 Warning: unaligning (T0385)S47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vjxA)N29 Warning: unaligning (T0385)P48 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vjxA)N29 T0385 18 :EGSADNAALCDALAVEHATIYGYGIVSAL 1vjxA -1 :HHMKVSDILTVAIRLEEEGERFYRELSEH T0385 49 :PGVNFLVADALKQHRHRRDDVIVM 1vjxA 30 :GEIKKTFLELADQERIHAEIFRKM T0385 76 :RGVTAP 1vjxA 62 :VDSYLA T0385 83 :AAAGYQLPM 1vjxA 68 :GYAFYEVFP T0385 95 :SAADAARLAVRMENDGATAWRAVVEHAETADDRVFASTALTESAVMATRWNRVLG 1vjxA 88 :TLKEVLDIAISVEKDSIILYYELKDGLVNSDAQKTVKKIIDQEKEHLRKLLEMKR Number of specific fragments extracted= 5 number of extra gaps= 1 total=354 Number of alignments=61 # 1vjxA read from 1vjxA/merged-good-all-a2m # found chain 1vjxA in template set Warning: unaligning (T0385)P16 because first residue in template chain is (1vjxA)H-3 Warning: unaligning (T0385)S17 because of BadResidue code BAD_PEPTIDE at template residue (1vjxA)H-2 Warning: unaligning (T0385)S47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vjxA)N29 Warning: unaligning (T0385)P48 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vjxA)N29 T0385 18 :EGSADNAALCDALAVEHATIYGYGIVSAL 1vjxA -1 :HHMKVSDILTVAIRLEEEGERFYRELSEH T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLS 1vjxA 30 :GEIKKTFLELADQERIHAEIFRKMSD T0385 75 :ARGVTAP 1vjxA 61 :EVDSYLA T0385 83 :AAAGYQLPM 1vjxA 68 :GYAFYEVFP T0385 92 :QVSSAADAARLAVRMENDGATAWRAVVEHAETADDRVFASTALTESAVMATRWNRVL 1vjxA 85 :KDLTLKEVLDIAISVEKDSIILYYELKDGLVNSDAQKTVKKIIDQEKEHLRKLLEMK Number of specific fragments extracted= 5 number of extra gaps= 1 total=359 Number of alignments=62 # 1vjxA read from 1vjxA/merged-good-all-a2m # found chain 1vjxA in template set Warning: unaligning (T0385)S47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vjxA)N29 Warning: unaligning (T0385)P48 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vjxA)N29 T0385 22 :DNAALCDALAVEHATIYGYGIVSAL 1vjxA 3 :VSDILTVAIRLEEEGERFYRELSEH T0385 49 :PGVNFLVADALKQHRHRRDDVIVMLSAR 1vjxA 30 :GEIKKTFLELADQERIHAEIFRKMSDQE T0385 77 :GVTAPIAAAGYQLPMQV 1vjxA 71 :FYEVFPDTSEILRRKDL T0385 95 :SAADAARLAVRMENDGATAWRAVVEHAETADDRVFASTALTESAVMATRWNRV 1vjxA 88 :TLKEVLDIAISVEKDSIILYYELKDGLVNSDAQKTVKKIIDQEKEHLRKLLEM Number of specific fragments extracted= 4 number of extra gaps= 1 total=363 Number of alignments=63 # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0385//projects/compbio/experiments/protein-predict/casp7/T0385/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0385//projects/compbio/experiments/protein-predict/casp7/T0385/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0385/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0385/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((T0385)H34.CB, (T0385)R66.CB) [> 3.2000 = 5.3333 < 6.9333] w=1.0000 to align # Constraint # added constraint: constraint((T0385)A29.CB, (T0385)A113.CB) [> 3.7712 = 6.2853 < 8.1708] w=0.9994 to align # Constraint # added constraint: constraint((T0385)A29.CB, (T0385)V117.CB) [> 3.4490 = 5.7483 < 7.4728] w=0.9932 to align # Constraint # added constraint: constraint((T0385)E33.CB, (T0385)V69.CB) [> 3.9194 = 6.5323 < 8.4920] w=0.9827 to align # Constraint # added constraint: constraint((T0385)L30.CB, (T0385)V69.CB) [> 2.8121 = 4.6868 < 6.0928] w=0.9827 to align # Constraint # added constraint: constraint((T0385)V51.CB, (T0385)A96.CB) [> 3.6178 = 6.0297 < 7.8386] w=0.9647 to align # Constraint # added constraint: constraint((T0385)T36.CB, (T0385)M106.CB) [> 3.7408 = 6.2346 < 8.1049] w=0.9647 to align # Constraint # added constraint: constraint((T0385)V32.CB, (T0385)A113.CB) [> 3.6494 = 6.0823 < 7.9071] w=0.9647 to align # Constraint # added constraint: constraint((T0385)A25.CB, (T0385)H120.CB) [> 3.4886 = 5.8144 < 7.5587] w=0.9585 to align # Constraint # added constraint: constraint((T0385)L26.CB, (T0385)M72.CB) [> 4.0355 = 6.7258 < 8.7435] w=0.9480 to align # Constraint # added constraint: constraint((T0385)I37.CB, (T0385)H62.CB) [> 2.4912 = 4.1519 < 5.3975] w=0.9480 to align # Constraint # added constraint: constraint((T0385)I37.CB, (T0385)R66.CB) [> 3.8895 = 6.4825 < 8.4273] w=0.9480 to align # Constraint # added constraint: constraint((T0385)Y40.CB, (T0385)H62.CB) [> 3.6724 = 6.1207 < 7.9569] w=0.9480 to align # Constraint # added constraint: constraint((T0385)I70.CB, (T0385)A80.CB) [> 3.1735 = 5.2891 < 6.8759] w=0.9305 to align # Constraint # added constraint: constraint((T0385)C27.CB, (T0385)L73.CB) [> 4.0862 = 6.8103 < 8.8533] w=0.9284 to align # Constraint # added constraint: constraint((T0385)N23.CB, (T0385)V78.CB) [> 2.8280 = 4.7133 < 6.1273] w=0.9183 to align # Constraint # added constraint: constraint((T0385)V118.CB, (T0385)R127.CB) [> 3.4490 = 5.7483 < 7.4728] w=0.9146 to align # Constraint # added constraint: constraint((T0385)W114.CB, (T0385)A130.CB) [> 3.5240 = 5.8733 < 7.6353] w=0.9146 to align # Constraint # added constraint: constraint((T0385)Y40.CB, (T0385)A103.CB) [> 4.3842 = 7.3070 < 9.4990] w=0.9144 to align # Constraint # added constraint: constraint((T0385)L30.CB, (T0385)R66.CB) [> 3.2283 = 5.3805 < 6.9947] w=0.9077 to align # Constraint # added constraint: constraint((T0385)L30.CB, (T0385)L73.CB) [> 4.2895 = 7.1491 < 9.2938] w=0.9050 to align # Constraint # added constraint: constraint((T0385)L26.CB, (T0385)V117.CB) [> 4.2580 = 7.0966 < 9.2256] w=0.9015 to align # Constraint # added constraint: constraint((T0385)D22.CB, (T0385)H120.CB) [> 3.6539 = 6.0898 < 7.9167] w=0.9015 to align # Constraint # added constraint: constraint((T0385)L26.CB, (T0385)V69.CB) [> 3.4061 = 5.6769 < 7.3799] w=0.8904 to align # Constraint # added constraint: constraint((T0385)E33.CB, (T0385)R66.CB) [> 2.3699 = 3.9499 < 5.1349] w=0.8904 to align # Constraint # added constraint: constraint((T0385)A25.CB, (T0385)V117.CB) [> 2.8540 = 4.7566 < 6.1836] w=0.8842 to align # Constraint # added constraint: constraint((T0385)D22.CB, (T0385)A121.CB) [> 3.4791 = 5.7985 < 7.5381] w=0.8842 to align # Constraint # added constraint: constraint((T0385)E33.CB, (T0385)R65.CB) [> 2.8289 = 4.7148 < 6.1292] w=0.8736 to align # Constraint # added constraint: constraint((T0385)A29.CB, (T0385)V69.CB) [> 3.4797 = 5.7996 < 7.5394] w=0.8736 to align # Constraint # added constraint: constraint((T0385)N23.CB, (T0385)R76.CB) [> 3.9028 = 6.5047 < 8.4562] w=0.8703 to align # Constraint # added constraint: constraint((T0385)L26.CB, (T0385)L73.CB) [> 3.2613 = 5.4355 < 7.0662] w=0.8697 to align # Constraint # added constraint: constraint((T0385)V117.CB, (T0385)A130.CB) [> 3.5824 = 5.9707 < 7.7620] w=0.8568 to align # Constraint # added constraint: constraint((T0385)V118.CB, (T0385)A130.CB) [> 2.8700 = 4.7834 < 6.2184] w=0.8568 to align # Constraint # added constraint: constraint((T0385)A121.CB, (T0385)A130.CB) [> 3.9563 = 6.5938 < 8.5720] w=0.8568 to align # Constraint # added constraint: constraint((T0385)A25.CB, (T0385)A116.CB) [> 4.4518 = 7.4198 < 9.6457] w=0.8557 to align # Constraint # added constraint: constraint((T0385)D28.CB, (T0385)A113.CB) [> 4.4303 = 7.3838 < 9.5989] w=0.8557 to align # Constraint # added constraint: constraint((T0385)V32.CB, (T0385)G110.CA) [> 3.6122 = 6.0204 < 7.8265] w=0.8557 to align # Constraint # added constraint: constraint((T0385)E33.CB, (T0385)H62.CB) [> 3.1592 = 5.2653 < 6.8450] w=0.8557 to align # Constraint # added constraint: constraint((T0385)I37.CB, (T0385)L59.CB) [> 3.0780 = 5.1300 < 6.6690] w=0.8557 to align # Constraint # added constraint: constraint((T0385)Y40.CB, (T0385)V55.CB) [> 3.0449 = 5.0748 < 6.5972] w=0.8557 to align # Constraint # added constraint: constraint((T0385)Y40.CB, (T0385)A56.CB) [> 4.4187 = 7.3645 < 9.5738] w=0.8557 to align # Constraint # added constraint: constraint((T0385)Y40.CB, (T0385)A58.CB) [> 2.8322 = 4.7203 < 6.1364] w=0.8557 to align # Constraint # added constraint: constraint((T0385)V104.CB, (T0385)A141.CB) [> 3.8744 = 6.4574 < 8.3946] w=0.8472 to align # Constraint # added constraint: constraint((T0385)A100.CB, (T0385)W144.CB) [> 3.5277 = 5.8795 < 7.6433] w=0.8472 to align # Constraint # added constraint: constraint((T0385)A111.CB, (T0385)L134.CB) [> 4.0427 = 6.7378 < 8.7592] w=0.8413 to align # Constraint # added constraint: constraint((T0385)T36.CB, (T0385)H62.CB) [> 2.6533 = 4.4221 < 5.7488] w=0.8389 to align # Constraint # added constraint: constraint((T0385)N23.CB, (T0385)L73.CB) [> 3.9868 = 6.6446 < 8.6380] w=0.8361 to align # Constraint # added constraint: constraint((T0385)A21.CB, (T0385)H120.CB) [> 3.7641 = 6.2735 < 8.1556] w=0.8220 to align # Constraint # added constraint: constraint((T0385)M72.CB, (T0385)F129.CB) [> 3.6233 = 6.0388 < 7.8505] w=0.8220 to align # Constraint # added constraint: constraint((T0385)C27.CB, (T0385)V78.CB) [> 4.1996 = 6.9993 < 9.0991] w=0.8127 to align # Constraint # added constraint: constraint((T0385)A35.CB, (T0385)A85.CB) [> 3.3894 = 5.6490 < 7.3437] w=0.8121 to align # Constraint # added constraint: constraint((T0385)G39.CA, (T0385)L59.CB) [> 4.4041 = 7.3402 < 9.5423] w=0.8054 to align # Constraint # added constraint: constraint((T0385)V118.CB, (T0385)S131.CB) [> 3.8998 = 6.4998 < 8.4497] w=0.7885 to align # Constraint # added constraint: constraint((T0385)L30.CB, (T0385)A80.CB) [> 4.1088 = 6.8480 < 8.9024] w=0.7879 to align # Constraint # added constraint: constraint((T0385)D22.CB, (T0385)V117.CB) [> 4.5138 = 7.5230 < 9.7799] w=0.7620 to align # Constraint # added constraint: constraint((T0385)R76.CB, (T0385)D126.CB) [> 4.5779 = 7.6298 < 9.9187] w=0.7458 to align # Constraint # added constraint: constraint((T0385)A31.CB, (T0385)A85.CB) [> 4.0600 = 6.7667 < 8.7967] w=0.7410 to align # Constraint # added constraint: constraint((T0385)C27.CB, (T0385)A80.CB) [> 3.9664 = 6.6107 < 8.5939] w=0.7366 to align # Constraint # added constraint: constraint((T0385)C27.CB, (T0385)P81.CB) [> 3.0914 = 5.1524 < 6.6981] w=0.7366 to align # Constraint # added constraint: constraint((T0385)G39.CA, (T0385)M106.CB) [> 4.5260 = 7.5433 < 9.8063] w=0.7298 to align # Constraint # added constraint: constraint((T0385)L26.CB, (T0385)V78.CB) [> 3.9890 = 6.6484 < 8.6429] w=0.7210 to align # Constraint # added constraint: constraint((T0385)V93.CB, (T0385)L102.CB) [> 3.6647 = 6.1078 < 7.9401] w=0.7109 to align # Constraint # added constraint: constraint((T0385)V43.CB, (T0385)V55.CB) [> 2.7974 = 4.6623 < 6.0610] w=0.6904 to align # Constraint # added constraint: constraint((T0385)H34.CB, (T0385)A85.CB) [> 3.3165 = 5.5274 < 7.1857] w=0.6863 to align # Constraint # added constraint: constraint((T0385)E18.CB, (T0385)R76.CB) [> 2.8564 = 4.7607 < 6.1889] w=0.6787 to align # Constraint # added constraint: constraint((T0385)Y38.CB, (T0385)A85.CB) [> 3.6149 = 6.0248 < 7.8323] w=0.6777 to align # Constraint # added constraint: constraint((T0385)T36.CB, (T0385)G110.CA) [> 4.0760 = 6.7934 < 8.8314] w=0.6678 to align # Constraint # added constraint: constraint((T0385)M72.CB, (T0385)D126.CB) [> 3.9781 = 6.6302 < 8.6193] w=0.6664 to align # Constraint # added constraint: constraint((T0385)A58.CB, (T0385)A103.CB) [> 4.4513 = 7.4188 < 9.6445] w=0.6604 to align # Constraint # added constraint: constraint((T0385)G41.CA, (T0385)V55.CB) [> 3.8132 = 6.3553 < 8.2619] w=0.6570 to align # Constraint # added constraint: constraint((T0385)A35.CB, (T0385)G86.CA) [> 3.5819 = 5.9698 < 7.7608] w=0.6519 to align # Constraint # added constraint: constraint((T0385)E18.CB, (T0385)G77.CA) [> 3.9677 = 6.6129 < 8.5968] w=0.6423 to align # Constraint # added constraint: constraint((T0385)D22.CB, (T0385)D126.CB) [> 3.5166 = 5.8609 < 7.6192] w=0.6353 to align # Constraint # added constraint: constraint((T0385)Y38.CB, (T0385)L59.CB) [> 4.5715 = 7.6192 < 9.9049] w=0.6210 to align # Constraint # added constraint: constraint((T0385)V55.CB, (T0385)A103.CB) [> 4.4907 = 7.4844 < 9.7298] w=0.6166 to align # Constraint # added constraint: constraint((T0385)V51.CB, (T0385)A99.CB) [> 4.2304 = 7.0507 < 9.1659] w=0.6091 to align # Constraint # added constraint: constraint((T0385)W114.CB, (T0385)L134.CB) [> 3.0012 = 5.0020 < 6.5026] w=0.6080 to align # Constraint # added constraint: constraint((T0385)A31.CB, (T0385)A83.CB) [> 3.1212 = 5.2019 < 6.7625] w=0.5966 to align # Constraint # added constraint: constraint((T0385)S15.CB, (T0385)R76.CB) [> 3.8739 = 6.4565 < 8.3934] w=0.5945 to align # Constraint # added constraint: constraint((T0385)S15.CB, (T0385)G77.CA) [> 2.6774 = 4.4623 < 5.8011] w=0.5928 to align # Constraint # added constraint: constraint((T0385)E107.CB, (T0385)A141.CB) [> 2.7222 = 4.5371 < 5.8982] w=0.5912 to align # Constraint # added constraint: constraint((T0385)R65.CB, (T0385)A133.CB) [> 3.2862 = 5.4770 < 7.1201] w=0.5899 to align # Constraint # added constraint: constraint((T0385)A111.CB, (T0385)A141.CB) [> 3.9323 = 6.5538 < 8.5199] w=0.5732 to align # Constraint # added constraint: constraint((T0385)V118.CB, (T0385)L134.CB) [> 4.0610 = 6.7683 < 8.7988] w=0.5726 to align # Constraint # added constraint: constraint((T0385)A111.CB, (T0385)A138.CB) [> 3.8726 = 6.4543 < 8.3906] w=0.5717 to align # Constraint # added constraint: constraint((T0385)V104.CB, (T0385)N145.CB) [> 3.7900 = 6.3166 < 8.2116] w=0.5559 to align # Constraint # added constraint: constraint((T0385)E107.CB, (T0385)W144.CB) [> 3.8785 = 6.4641 < 8.4034] w=0.5558 to align # Constraint # added constraint: constraint((T0385)V55.CB, (T0385)A99.CB) [> 4.3930 = 7.3216 < 9.5181] w=0.5547 to align # Constraint # added constraint: constraint((T0385)E107.CB, (T0385)M140.CB) [> 3.3464 = 5.5774 < 7.2506] w=0.5545 to align # Constraint # added constraint: constraint((T0385)A111.CB, (T0385)S137.CB) [> 3.1373 = 5.2288 < 6.7974] w=0.5545 to align # Constraint # added constraint: constraint((T0385)W114.CB, (T0385)A133.CB) [> 3.6532 = 6.0887 < 7.9153] w=0.5545 to align # Constraint # added constraint: constraint((T0385)R115.CB, (T0385)L134.CB) [> 4.1256 = 6.8760 < 8.9388] w=0.5545 to align # Constraint # added constraint: constraint((T0385)L46.CB, (T0385)A99.CB) [> 4.2395 = 7.0659 < 9.1856] w=0.5477 to align # Constraint # added constraint: constraint((T0385)G41.CA, (T0385)L59.CB) [> 3.2087 = 5.3479 < 6.9523] w=0.5406 to align # Constraint # added constraint: constraint((T0385)N108.CB, (T0385)A141.CB) [> 3.8699 = 6.4498 < 8.3847] w=0.5377 to align # Constraint # added constraint: constraint((T0385)A103.CB, (T0385)W144.CB) [> 3.1881 = 5.3136 < 6.9077] w=0.5377 to align # Constraint # added constraint: constraint((T0385)V43.CB, (T0385)A99.CB) [> 3.6498 = 6.0830 < 7.9078] w=0.5363 to align # Constraint # added constraint: constraint((T0385)L30.CB, (T0385)I82.CB) [> 4.6167 = 7.6946 < 10.0029] w=0.5313 to align # Constraint # added constraint: constraint((T0385)R14.CB, (T0385)G77.CA) [> 3.1676 = 5.2793 < 6.8630] w=0.5218 to align # Constraint # added constraint: constraint((T0385)V43.CB, (T0385)N52.CB) [> 3.2950 = 5.4917 < 7.1392] w=0.5199 to align # Constraint # added constraint: constraint((T0385)A97.CB, (T0385)L148.CB) [> 3.9586 = 6.5977 < 8.5771] w=0.5180 to align # Constraint # added constraint: constraint((T0385)V104.CB, (T0385)W144.CB) [> 2.7406 = 4.5677 < 5.9380] w=0.5030 to align # Constraint # added constraint: constraint((T0385)A31.CB, (T0385)I82.CB) [> 4.4850 = 7.4750 < 9.7176] w=0.5019 to align # Constraint # added constraint: constraint((T0385)N23.CB, (T0385)T79.CB) [> 4.3241 = 7.2069 < 9.3689] w=0.5019 to align # Constraint # added constraint: constraint((T0385)G41.CA, (T0385)A56.CB) [> 3.7870 = 6.3116 < 8.2051] w=0.4890 to align # Constraint # added constraint: constraint((T0385)A100.CB, (T0385)V147.CB) [> 3.3194 = 5.5323 < 7.1920] w=0.4863 to align # Constraint # added constraint: constraint((T0385)R14.CB, (T0385)R76.CB) [> 4.3935 = 7.3225 < 9.5193] w=0.4838 to align # Constraint # added constraint: constraint((T0385)R65.CB, (T0385)E136.CB) [> 4.2302 = 7.0504 < 9.1655] w=0.4804 to align # Constraint # added constraint: constraint((T0385)D68.CB, (T0385)A133.CB) [> 4.0463 = 6.7439 < 8.7671] w=0.4781 to align # Constraint # added constraint: constraint((T0385)L26.CB, (T0385)D126.CB) [> 4.1084 = 6.8474 < 8.9016] w=0.4623 to align # Constraint # added constraint: constraint((T0385)S44.CB, (T0385)V55.CB) [> 2.5459 = 4.2431 < 5.5160] w=0.4544 to align # Constraint # added constraint: constraint((T0385)D68.CB, (T0385)F129.CB) [> 3.5513 = 5.9189 < 7.6945] w=0.4406 to align # Constraint # added constraint: constraint((T0385)R76.CB, (T0385)D125.CB) [> 4.4915 = 7.4858 < 9.7315] w=0.4367 to align # Constraint # added constraint: constraint((T0385)A58.CB, (T0385)M140.CB) [> 3.2225 = 5.3708 < 6.9820] w=0.4262 to align # Constraint # added constraint: constraint((T0385)C27.CB, (T0385)A83.CB) [> 4.5030 = 7.5049 < 9.7564] w=0.4201 to align # Constraint # added constraint: constraint((T0385)A100.CB, (T0385)L148.CB) [> 3.2004 = 5.3340 < 6.9342] w=0.4196 to align # Constraint # added constraint: constraint((T0385)A97.CB, (T0385)A141.CB) [> 3.8489 = 6.4147 < 8.3392] w=0.4067 to align # Constraint # added constraint: constraint((T0385)A100.CB, (T0385)A141.CB) [> 3.1560 = 5.2600 < 6.8380] w=0.4067 to align # Constraint # added constraint: constraint((T0385)V104.CB, (T0385)L134.CB) [> 3.7119 = 6.1865 < 8.0424] w=0.4067 to align # Constraint # added constraint: constraint((T0385)V104.CB, (T0385)A138.CB) [> 3.8640 = 6.4401 < 8.3721] w=0.4067 to align # Constraint # added constraint: constraint((T0385)V43.CB, (T0385)A103.CB) [> 4.2030 = 7.0049 < 9.1064] w=0.4026 to align # Constraint # added constraint: constraint((T0385)Y38.CB, (T0385)G86.CA) [> 4.2506 = 7.0843 < 9.2096] w=0.3997 to align # Constraint # added constraint: constraint((T0385)L54.CB, (T0385)R143.CB) [> 4.0419 = 6.7365 < 8.7575] w=0.3892 to align # Constraint # added constraint: constraint((T0385)L26.CB, (T0385)R76.CB) [> 4.1719 = 6.9532 < 9.0391] w=0.3892 to align # Constraint # added constraint: constraint((T0385)S47.CB, (T0385)A96.CB) [> 4.2708 = 7.1180 < 9.2534] w=0.3891 to align # Constraint # added constraint: constraint((T0385)V104.CB, (T0385)L148.CB) [> 3.9870 = 6.6450 < 8.6384] w=0.3849 to align # Constraint # added constraint: constraint((T0385)I42.CB, (T0385)A99.CB) [> 3.6964 = 6.1607 < 8.0089] w=0.3824 to align # Constraint # added constraint: constraint((T0385)V32.CB, (T0385)D109.CB) [> 4.5525 = 7.5874 < 9.8636] w=0.3783 to align # Constraint # added constraint: constraint((T0385)R101.CB, (T0385)L148.CB) [> 3.9028 = 6.5046 < 8.4560] w=0.3682 to align # Constraint # added constraint: constraint((T0385)Y38.CB, (T0385)P90.CB) [> 3.8440 = 6.4066 < 8.3286] w=0.3614 to align # Constraint # added constraint: constraint((T0385)A25.CB, (T0385)A121.CB) [> 4.4667 = 7.4445 < 9.6779] w=0.3525 to align # Constraint # added constraint: constraint((T0385)N23.CB, (T0385)G77.CA) [> 3.9920 = 6.6533 < 8.6493] w=0.3523 to align # Constraint # added constraint: constraint((T0385)E107.CB, (T0385)A133.CB) [> 3.3217 = 5.5361 < 7.1969] w=0.3442 to align # Constraint # added constraint: constraint((T0385)V104.CB, (T0385)S137.CB) [> 2.6317 = 4.3862 < 5.7020] w=0.3442 to align # Constraint # added constraint: constraint((T0385)A103.CB, (T0385)S137.CB) [> 3.4534 = 5.7556 < 7.4823] w=0.3442 to align # Constraint # added constraint: constraint((T0385)A100.CB, (T0385)M140.CB) [> 3.2584 = 5.4307 < 7.0599] w=0.3442 to align # Constraint # added constraint: constraint((T0385)A97.CB, (T0385)N145.CB) [> 3.8777 = 6.4629 < 8.4018] w=0.3442 to align # Constraint # added constraint: constraint((T0385)A97.CB, (T0385)W144.CB) [> 2.8342 = 4.7238 < 6.1409] w=0.3442 to align # Constraint # added constraint: constraint((T0385)A96.CB, (T0385)W144.CB) [> 3.6175 = 6.0292 < 7.8379] w=0.3442 to align # Constraint # added constraint: constraint((T0385)G39.CA, (T0385)L89.CB) [> 3.5959 = 5.9931 < 7.7911] w=0.3309 to align # Constraint # added constraint: constraint((T0385)V69.CB, (T0385)A80.CB) [> 4.4027 = 7.3378 < 9.5391] w=0.3270 to align # Constraint # added constraint: constraint((T0385)I42.CB, (T0385)V93.CB) [> 4.1578 = 6.9297 < 9.0086] w=0.3262 to align # Constraint # added constraint: constraint((T0385)G39.CA, (T0385)M91.CB) [> 3.2634 = 5.4390 < 7.0706] w=0.3238 to align # Constraint # added constraint: constraint((T0385)A31.CB, (T0385)P81.CB) [> 3.6565 = 6.0942 < 7.9225] w=0.3142 to align # Constraint # added constraint: constraint((T0385)S47.CB, (T0385)A99.CB) [> 4.2866 = 7.1443 < 9.2875] w=0.3009 to align # Constraint # added constraint: constraint((T0385)V43.CB, (T0385)L102.CB) [> 4.5488 = 7.5814 < 9.8558] w=0.2997 to align # Constraint # added constraint: constraint((T0385)G41.CA, (T0385)N52.CB) [> 3.5519 = 5.9198 < 7.6957] w=0.2959 to align # Constraint # added constraint: constraint((T0385)A58.CB, (T0385)R143.CB) [> 4.4959 = 7.4932 < 9.7412] w=0.2937 to align # Constraint # added constraint: constraint((T0385)I42.CB, (T0385)M91.CB) [> 3.3093 = 5.5155 < 7.1702] w=0.2830 to align # Constraint # added constraint: constraint((T0385)L46.CB, (T0385)V93.CB) [> 3.4057 = 5.6761 < 7.3790] w=0.2814 to align # Constraint # added constraint: constraint((T0385)G39.CA, (T0385)P90.CB) [> 3.2556 = 5.4260 < 7.0537] w=0.2789 to align # Constraint # added constraint: constraint((T0385)I70.CB, (T0385)I82.CB) [> 4.3084 = 7.1807 < 9.3350] w=0.2773 to align # Constraint # added constraint: constraint((T0385)P90.CB, (T0385)L102.CB) [> 4.1320 = 6.8866 < 8.9526] w=0.2566 to align # Constraint # added constraint: constraint((T0385)A35.CB, (T0385)P90.CB) [> 4.0463 = 6.7438 < 8.7670] w=0.2533 to align # Constraint # added constraint: constraint((T0385)V51.CB, (T0385)V147.CB) [> 4.1993 = 6.9988 < 9.0984] w=0.2486 to align # Constraint # added constraint: constraint((T0385)Y38.CB, (T0385)M91.CB) [> 3.7347 = 6.2245 < 8.0919] w=0.2486 to align # Constraint # added constraint: constraint((T0385)C27.CB, (T0385)I82.CB) [> 4.5498 = 7.5831 < 9.8580] w=0.2433 to align # Constraint # added constraint: constraint((T0385)D28.CB, (T0385)V117.CB) [> 4.4743 = 7.4572 < 9.6944] w=0.2414 to align # Constraint # added constraint: constraint((T0385)V69.CB, (T0385)A133.CB) [> 4.5526 = 7.5876 < 9.8639] w=0.2394 to align # Constraint # added constraint: constraint((T0385)H34.CB, (T0385)I82.CB) [> 4.3879 = 7.3131 < 9.5071] w=0.2388 to align # Constraint # added constraint: constraint((T0385)D68.CB, (T0385)T132.CB) [> 4.4439 = 7.4066 < 9.6285] w=0.2369 to align # Constraint # added constraint: constraint((T0385)M91.CB, (T0385)L102.CB) [> 3.9558 = 6.5931 < 8.5710] w=0.2359 to align # Constraint # added constraint: constraint((T0385)I42.CB, (T0385)N52.CB) [> 3.5839 = 5.9731 < 7.7651] w=0.2357 to align # Constraint # added constraint: constraint((T0385)L30.CB, (T0385)P81.CB) [> 4.0284 = 6.7140 < 8.7282] w=0.2347 to align # Constraint # added constraint: constraint((T0385)S17.CB, (T0385)G77.CA) [> 3.7123 = 6.1872 < 8.0433] w=0.2295 to align # Constraint # added constraint: constraint((T0385)A31.CB, (T0385)A84.CB) [> 3.4566 = 5.7610 < 7.4893] w=0.2204 to align # Constraint # added constraint: constraint((T0385)Y38.CB, (T0385)L89.CB) [> 3.8942 = 6.4904 < 8.4375] w=0.2189 to align # Constraint # added constraint: constraint((T0385)I42.CB, (T0385)V51.CB) [> 3.7016 = 6.1694 < 8.0202] w=0.2094 to align # Constraint # added constraint: constraint((T0385)A25.CB, (T0385)A113.CB) [> 4.3166 = 7.1943 < 9.3526] w=0.2090 to align # Constraint # added constraint: constraint((T0385)V69.CB, (T0385)F129.CB) [> 4.3269 = 7.2116 < 9.3750] w=0.2076 to align # Constraint # added constraint: constraint((T0385)L54.CB, (T0385)V147.CB) [> 4.4116 = 7.3526 < 9.5584] w=0.2047 to align # Constraint # added constraint: constraint((T0385)V32.CB, (T0385)M106.CB) [> 4.6912 = 7.8186 < 10.1642] w=0.1860 to align # Constraint # added constraint: constraint((T0385)A45.CB, (T0385)A99.CB) [> 4.3101 = 7.1836 < 9.3386] w=0.1846 to align # Constraint # added constraint: constraint((T0385)A29.CB, (T0385)A130.CB) [> 4.4159 = 7.3598 < 9.5677] w=0.1844 to align # Constraint # added constraint: constraint((T0385)G39.CA, (T0385)Q88.CB) [> 2.8036 = 4.6726 < 6.0744] w=0.1773 to align # Constraint # added constraint: constraint((T0385)H34.CB, (T0385)P81.CB) [> 3.8593 = 6.4321 < 8.3617] w=0.1697 to align # Constraint # added constraint: constraint((T0385)A111.CB, (T0385)S131.CB) [> 4.2668 = 7.1114 < 9.2448] w=0.1690 to align # Constraint # added constraint: constraint((T0385)P16.CB, (T0385)G77.CA) [> 3.2361 = 5.3934 < 7.0114] w=0.1626 to align # Constraint # added constraint: constraint((T0385)P12.CB, (T0385)G77.CA) [> 2.4857 = 4.1427 < 5.3856] w=0.1614 to align # Constraint # added constraint: constraint((T0385)A35.CB, (T0385)L89.CB) [> 4.2614 = 7.1023 < 9.2330] w=0.1577 to align # Constraint # added constraint: constraint((T0385)I42.CB, (T0385)P90.CB) [> 4.5541 = 7.5901 < 9.8672] w=0.1507 to align # Constraint # added constraint: constraint((T0385)G19.CA, (T0385)R76.CB) [> 4.0700 = 6.7833 < 8.8182] w=0.1440 to align # Constraint # added constraint: constraint((T0385)W114.CB, (T0385)R127.CB) [> 3.6584 = 6.0974 < 7.9266] w=0.1384 to align # Constraint # added constraint: constraint((T0385)A111.CB, (T0385)R127.CB) [> 3.5014 = 5.8356 < 7.5863] w=0.1384 to align # Constraint # added constraint: constraint((T0385)G41.CA, (T0385)V93.CB) [> 4.3476 = 7.2460 < 9.4197] w=0.1377 to align # Constraint # added constraint: constraint((T0385)Q88.CB, (T0385)M106.CB) [> 4.2922 = 7.1537 < 9.2998] w=0.1348 to align # Constraint # added constraint: constraint((T0385)A35.CB, (T0385)M91.CB) [> 4.2127 = 7.0211 < 9.1275] w=0.1338 to align # Constraint # added constraint: constraint((T0385)G39.CA, (T0385)Y87.CB) [> 3.7209 = 6.2014 < 8.0619] w=0.1297 to align # Constraint # added constraint: constraint((T0385)C27.CB, (T0385)R76.CB) [> 3.3147 = 5.5245 < 7.1818] w=0.1264 to align # Constraint # added constraint: constraint((T0385)L30.CB, (T0385)V117.CB) [> 4.3962 = 7.3269 < 9.5250] w=0.1264 to align # Constraint # added constraint: constraint((T0385)Q92.CB, (T0385)L102.CB) [> 3.9079 = 6.5132 < 8.4672] w=0.1238 to align # Constraint # added constraint: constraint((T0385)S15.CB, (T0385)A24.CB) [> 2.8814 = 4.8023 < 6.2429] w=0.1230 to align # Constraint # added constraint: constraint((T0385)L89.CB, (T0385)L102.CB) [> 4.0964 = 6.8273 < 8.8755] w=0.1187 to align # Constraint # added constraint: constraint((T0385)A35.CB, (T0385)A84.CB) [> 3.0672 = 5.1120 < 6.6456] w=0.1162 to align # Constraint # added constraint: constraint((T0385)Y87.CB, (T0385)G110.CA) [> 4.3733 = 7.2889 < 9.4756] w=0.1141 to align # Constraint # added constraint: constraint((T0385)Y87.CB, (T0385)D109.CB) [> 3.5203 = 5.8672 < 7.6273] w=0.1141 to align # Constraint # added constraint: constraint((T0385)M72.CB, (T0385)A130.CB) [> 4.6046 = 7.6743 < 9.9766] w=0.1138 to align # Constraint # added constraint: constraint((T0385)A96.CB, (T0385)L148.CB) [> 4.7188 = 7.8646 < 10.2240] w=0.1122 to align # Constraint # added constraint: constraint((T0385)E33.CB, (T0385)A113.CB) [> 3.6560 = 6.0933 < 7.9213] w=0.1090 to align # Constraint # added constraint: constraint((T0385)A29.CB, (T0385)A121.CB) [> 4.4979 = 7.4966 < 9.7456] w=0.1090 to align # Constraint # added constraint: constraint((T0385)V71.CB, (T0385)A80.CB) [> 4.6418 = 7.7364 < 10.0573] w=0.1090 to align # Constraint # added constraint: constraint((T0385)I70.CB, (T0385)P81.CB) [> 4.7120 = 7.8533 < 10.2093] w=0.1090 to align # Constraint # added constraint: constraint((T0385)I37.CB, (T0385)S137.CB) [> 4.7725 = 7.9541 < 10.3403] w=0.1090 to align # Constraint # added constraint: constraint((T0385)I37.CB, (T0385)G110.CA) [> 4.4914 = 7.4857 < 9.7314] w=0.1090 to align # Constraint # added constraint: constraint((T0385)T36.CB, (T0385)A113.CB) [> 4.2457 = 7.0762 < 9.1990] w=0.1090 to align # Constraint # added constraint: constraint((T0385)H34.CB, (T0385)L73.CB) [> 4.0904 = 6.8173 < 8.8625] w=0.1090 to align # Constraint # added constraint: constraint((T0385)V43.CB, (T0385)M91.CB) [> 4.4595 = 7.4325 < 9.6622] w=0.1052 to align # Constraint # added constraint: constraint((T0385)E107.CB, (T0385)N145.CB) [> 3.6822 = 6.1370 < 7.9781] w=0.1049 to align # Constraint # added constraint: constraint((T0385)G39.CA, (T0385)Q92.CB) [> 3.9815 = 6.6359 < 8.6266] w=0.1032 to align # Constraint # added constraint: constraint((T0385)A21.CB, (T0385)A124.CB) [> 3.6788 = 6.1314 < 7.9708] w=0.0993 to align # Constraint # added constraint: constraint((T0385)V32.CB, (T0385)A85.CB) [> 3.1887 = 5.3144 < 6.9088] w=0.0980 to align # Constraint # added constraint: constraint((T0385)A29.CB, (T0385)A133.CB) [> 4.5236 = 7.5394 < 9.8012] w=0.0966 to align # Constraint # added constraint: constraint((T0385)Q88.CB, (T0385)R105.CB) [> 4.0455 = 6.7425 < 8.7652] w=0.0933 to align # Constraint # added constraint: constraint((T0385)S95.CB, (T0385)L148.CB) [> 4.4889 = 7.4815 < 9.7259] w=0.0930 to align # Constraint # added constraint: constraint((T0385)L89.CB, (T0385)M106.CB) [> 3.6699 = 6.1165 < 7.9514] w=0.0912 to align # Constraint # added constraint: constraint((T0385)I70.CB, (T0385)L89.CB) [> 4.3485 = 7.2475 < 9.4217] w=0.0848 to align # Constraint # added constraint: constraint((T0385)M91.CB, (T0385)M106.CB) [> 3.6903 = 6.1505 < 7.9956] w=0.0827 to align # Constraint # added constraint: constraint((T0385)A100.CB, (T0385)N145.CB) [> 4.5006 = 7.5010 < 9.7513] w=0.0786 to align # Constraint # added constraint: constraint((T0385)D28.CB, (T0385)A85.CB) [> 3.9563 = 6.5939 < 8.5721] w=0.0774 to align # Constraint # added constraint: constraint((T0385)A111.CB, (T0385)A130.CB) [> 2.5500 = 4.2500 < 5.5249] w=0.0759 to align # Constraint # added constraint: constraint((T0385)G110.CA, (T0385)A130.CB) [> 4.1185 = 6.8642 < 8.9234] w=0.0759 to align # Constraint # added constraint: constraint((T0385)D28.CB, (T0385)L89.CB) [> 3.8117 = 6.3528 < 8.2587] w=0.0750 to align # Constraint # added constraint: constraint((T0385)A10.CB, (T0385)G77.CA) [> 4.0606 = 6.7676 < 8.7979] w=0.0748 to align # Constraint # added constraint: constraint((T0385)R65.CB, (T0385)F129.CB) [> 4.2336 = 7.0560 < 9.1728] w=0.0737 to align # Constraint # added constraint: constraint((T0385)T11.CB, (T0385)T79.CB) [> 4.3241 = 7.2069 < 9.3689] w=0.0727 to align # Constraint # added constraint: constraint((T0385)P12.CB, (T0385)P81.CB) [> 4.7652 = 7.9420 < 10.3246] w=0.0727 to align # Constraint # added constraint: constraint((T0385)Y87.CB, (T0385)R105.CB) [> 4.5127 = 7.5212 < 9.7775] w=0.0727 to align # Constraint # added constraint: constraint((T0385)A97.CB, (T0385)T142.CB) [> 4.0181 = 6.6969 < 8.7060] w=0.0626 to align # Constraint # added constraint: constraint((T0385)V104.CB, (T0385)S131.CB) [> 4.0149 = 6.6915 < 8.6989] w=0.0626 to align # Constraint # added constraint: constraint((T0385)V104.CB, (T0385)T135.CB) [> 3.8683 = 6.4472 < 8.3814] w=0.0626 to align # Constraint # added constraint: constraint((T0385)A111.CB, (T0385)V128.CB) [> 4.6006 = 7.6676 < 9.9679] w=0.0626 to align # Constraint # added constraint: constraint((T0385)A96.CB, (T0385)V147.CB) [> 4.1105 = 6.8508 < 8.9061] w=0.0622 to align # Constraint # added constraint: constraint((T0385)H34.CB, (T0385)A83.CB) [> 4.2988 = 7.1647 < 9.3141] w=0.0606 to align # Constraint # added constraint: constraint((T0385)H34.CB, (T0385)Y87.CB) [> 3.5544 = 5.9240 < 7.7012] w=0.0569 to align # Constraint # added constraint: constraint((T0385)A24.CB, (T0385)H120.CB) [> 4.7556 = 7.9261 < 10.3039] w=0.0569 to align # Constraint # added constraint: constraint((T0385)A21.CB, (T0385)A121.CB) [> 4.6624 = 7.7706 < 10.1018] w=0.0569 to align # Constraint # added constraint: constraint((T0385)L73.CB, (T0385)M91.CB) [> 3.9688 = 6.6147 < 8.5991] w=0.0566 to align # Constraint # added constraint: constraint((T0385)P81.CB, (T0385)P90.CB) [> 3.6445 = 6.0742 < 7.8964] w=0.0566 to align # Constraint # added constraint: constraint((T0385)K13.CB, (T0385)G77.CA) [> 3.8619 = 6.4366 < 8.3675] w=0.0553 to align # Constraint # added constraint: constraint((T0385)W114.CB, (T0385)A138.CB) [> 3.7021 = 6.1702 < 8.0213] w=0.0535 to align # Constraint # added constraint: constraint((T0385)A25.CB, (T0385)A85.CB) [> 3.8340 = 6.3900 < 8.3070] w=0.0414 to align # Constraint # added constraint: constraint((T0385)A24.CB, (T0385)A85.CB) [> 4.7846 = 7.9743 < 10.3666] w=0.0414 to align # Constraint # added constraint: constraint((T0385)A21.CB, (T0385)A80.CB) [> 4.2955 = 7.1592 < 9.3069] w=0.0414 to align # Constraint # added constraint: constraint((T0385)A21.CB, (T0385)R76.CB) [> 4.1694 = 6.9490 < 9.0338] w=0.0414 to align # Constraint # added constraint: constraint((T0385)Y87.CB, (T0385)A116.CB) [> 4.5446 = 7.5744 < 9.8467] w=0.0414 to align # Constraint # added constraint: constraint((T0385)Y87.CB, (T0385)T112.CB) [> 4.5952 = 7.6587 < 9.9563] w=0.0414 to align # Constraint # added constraint: constraint((T0385)A85.CB, (T0385)A116.CB) [> 3.1717 = 5.2862 < 6.8721] w=0.0414 to align # Constraint # added constraint: constraint((T0385)A25.CB, (T0385)Y87.CB) [> 4.5931 = 7.6551 < 9.9517] w=0.0414 to align # Constraint # added constraint: constraint((T0385)V32.CB, (T0385)P90.CB) [> 3.4151 = 5.6919 < 7.3995] w=0.0414 to align # Constraint # added constraint: constraint((T0385)V78.CB, (T0385)H120.CB) [> 3.8519 = 6.4198 < 8.3458] w=0.0414 to align # Constraint # added constraint: constraint((T0385)V78.CB, (T0385)E122.CB) [> 4.5605 = 7.6007 < 9.8810] w=0.0414 to align # Constraint # added constraint: constraint((T0385)A80.CB, (T0385)E119.CB) [> 4.3220 = 7.2033 < 9.3643] w=0.0414 to align # Constraint # added constraint: constraint((T0385)A80.CB, (T0385)H120.CB) [> 2.7401 = 4.5669 < 5.9370] w=0.0414 to align # Constraint # added constraint: constraint((T0385)M91.CB, (T0385)R105.CB) [> 3.7584 = 6.2641 < 8.1433] w=0.0413 to align # Constraint # added constraint: constraint((T0385)L46.CB, (T0385)S94.CB) [> 3.7266 = 6.2110 < 8.0743] w=0.0409 to align # Constraint # added constraint: constraint((T0385)A10.CB, (T0385)R76.CB) [> 4.0779 = 6.7965 < 8.8354] w=0.0363 to align # Constraint # added constraint: constraint((T0385)A10.CB, (T0385)V78.CB) [> 2.7994 = 4.6656 < 6.0653] w=0.0363 to align # Constraint # added constraint: constraint((T0385)T11.CB, (T0385)N23.CB) [> 4.5328 = 7.5547 < 9.8211] w=0.0363 to align # Constraint # added constraint: constraint((T0385)T11.CB, (T0385)G77.CA) [> 2.6847 = 4.4746 < 5.8169] w=0.0363 to align # Constraint # added constraint: constraint((T0385)A10.CB, (T0385)A24.CB) [> 2.4253 = 4.0422 < 5.2549] w=0.0363 to align # Constraint # added constraint: constraint((T0385)A10.CB, (T0385)S20.CB) [> 3.3829 = 5.6381 < 7.3296] w=0.0363 to align # Constraint # added constraint: constraint((T0385)G9.CA, (T0385)G77.CA) [> 4.7537 = 7.9228 < 10.2997] w=0.0363 to align # Constraint # added constraint: constraint((T0385)G9.CA, (T0385)A24.CB) [> 4.6012 = 7.6686 < 9.9692] w=0.0363 to align # Constraint # added constraint: constraint((T0385)A7.CB, (T0385)T79.CB) [> 2.9503 = 4.9171 < 6.3923] w=0.0363 to align # Constraint # added constraint: constraint((T0385)A121.CB, (T0385)S131.CB) [> 3.2171 = 5.3618 < 6.9704] w=0.0355 to align # Constraint # added constraint: constraint((T0385)E107.CB, (T0385)T142.CB) [> 2.7095 = 4.5158 < 5.8706] w=0.0354 to align # Constraint # added constraint: constraint((T0385)N108.CB, (T0385)T142.CB) [> 3.4561 = 5.7602 < 7.4882] w=0.0354 to align # Constraint # added constraint: constraint((T0385)G110.CA, (T0385)A138.CB) [> 3.5681 = 5.9468 < 7.7309] w=0.0354 to align # Constraint # added constraint: constraint((T0385)A111.CB, (T0385)V139.CB) [> 3.7966 = 6.3277 < 8.2261] w=0.0354 to align # Constraint # added constraint: constraint((T0385)A111.CB, (T0385)T142.CB) [> 3.5778 = 5.9630 < 7.7518] w=0.0354 to align # Constraint # added constraint: constraint((T0385)V118.CB, (T0385)T135.CB) [> 3.8437 = 6.4061 < 8.3280] w=0.0354 to align # Constraint # added constraint: constraint((T0385)V55.CB, (T0385)R143.CB) [> 4.1744 = 6.9573 < 9.0445] w=0.0347 to align # Constraint # added constraint: constraint((T0385)G110.CA, (T0385)L134.CB) [> 4.7883 = 7.9805 < 10.3747] w=0.0347 to align # Constraint # added constraint: constraint((T0385)A111.CB, (T0385)M140.CB) [> 4.5349 = 7.5582 < 9.8257] w=0.0347 to align # Constraint # added constraint: constraint((T0385)D28.CB, (T0385)P90.CB) [> 4.6623 = 7.7706 < 10.1017] w=0.0335 to align # Constraint # added constraint: constraint((T0385)S44.CB, (T0385)V93.CB) [> 4.7226 = 7.8709 < 10.2322] w=0.0305 to align # Constraint # added constraint: constraint((T0385)G77.CA, (T0385)S95.CB) [> 4.4333 = 7.3889 < 9.6055] w=0.0283 to align # Constraint # added constraint: constraint((T0385)D28.CB, (T0385)A80.CB) [> 4.4600 = 7.4333 < 9.6633] w=0.0207 to align # Constraint # added constraint: constraint((T0385)Y87.CB, (T0385)D98.CB) [> 4.6206 = 7.7010 < 10.0114] w=0.0207 to align # Constraint # added constraint: constraint((T0385)V78.CB, (T0385)T112.CB) [> 4.6704 = 7.7840 < 10.1192] w=0.0207 to align # Constraint # added constraint: constraint((T0385)G77.CA, (T0385)T112.CB) [> 3.8626 = 6.4377 < 8.3690] w=0.0207 to align # Constraint # added constraint: constraint((T0385)S44.CB, (T0385)I153.CB) [> 3.3340 = 5.5566 < 7.2236] w=0.0202 to align # Constraint # added constraint: constraint((T0385)N52.CB, (T0385)I153.CB) [> 2.8969 = 4.8282 < 6.2767] w=0.0202 to align # Constraint # added constraint: constraint((T0385)F53.CB, (T0385)A155.CB) [> 3.0882 = 5.1470 < 6.6911] w=0.0202 to align # Constraint # added constraint: constraint((T0385)A56.CB, (T0385)A155.CB) [> 3.1177 = 5.1961 < 6.7549] w=0.0202 to align # Constraint # added constraint: constraint((T0385)A35.CB, (T0385)I82.CB) [> 4.4324 = 7.3873 < 9.6035] w=0.0192 to align # Constraint # added constraint: constraint((T0385)R76.CB, (T0385)F129.CB) [> 4.1272 = 6.8787 < 8.9424] w=0.0181 to align # Constraint # added constraint: constraint((T0385)R115.CB, (T0385)A138.CB) [> 4.5894 = 7.6491 < 9.9438] w=0.0181 to align # Constraint # added constraint: constraint((T0385)V118.CB, (T0385)A138.CB) [> 4.2596 = 7.0994 < 9.2292] w=0.0181 to align # Constraint # added constraint: constraint((T0385)E122.CB, (T0385)S131.CB) [> 3.1837 = 5.3062 < 6.8980] w=0.0181 to align # Constraint # added constraint: constraint((T0385)V104.CB, (T0385)T142.CB) [> 3.8633 = 6.4388 < 8.3704] w=0.0180 to align # Constraint # added constraint: constraint((T0385)V104.CB, (T0385)R146.CB) [> 4.0244 = 6.7073 < 8.7195] w=0.0180 to align # Constraint # added constraint: constraint((T0385)P16.CB, (T0385)S74.CB) [> 2.3750 = 3.9583 < 5.1458] w=0.0173 to align # Constraint # added constraint: constraint((T0385)W114.CB, (T0385)T132.CB) [> 4.7456 = 7.9093 < 10.2820] w=0.0173 to align # Constraint # added constraint: constraint((T0385)A111.CB, (T0385)T135.CB) [> 3.6719 = 6.1198 < 7.9557] w=0.0173 to align # Constraint # added constraint: constraint((T0385)G110.CA, (T0385)T142.CB) [> 4.6989 = 7.8315 < 10.1809] w=0.0173 to align # Constraint # added constraint: constraint((T0385)G50.CA, (T0385)V147.CB) [> 3.7922 = 6.3204 < 8.2165] w=0.0168 to align # Constraint # added constraint: constraint((T0385)V51.CB, (T0385)W151.CB) [> 3.5224 = 5.8707 < 7.6319] w=0.0168 to align # Constraint # added constraint: constraint((T0385)V51.CB, (T0385)I153.CB) [> 4.2104 = 7.0174 < 9.1226] w=0.0168 to align # Constraint # added constraint: constraint((T0385)L54.CB, (T0385)W151.CB) [> 3.7439 = 6.2399 < 8.1118] w=0.0168 to align # Constraint # added constraint: constraint((T0385)A96.CB, (T0385)I153.CB) [> 3.3972 = 5.6620 < 7.3605] w=0.0168 to align # Constraint # added constraint: constraint((T0385)V104.CB, (T0385)G149.CA) [> 4.1465 = 6.9108 < 8.9841] w=0.0168 to align # Constraint # added constraint: constraint((T0385)R76.CB, (T0385)S131.CB) [> 4.5197 = 7.5328 < 9.7927] w=0.0141 to align # SetCost created cost = # ( 1.0000 * align ) # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0385/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0385/decoys/ # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0385 can't currently be optimized by undertaker # 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 83 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0385 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0385 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0385 can't currently be optimized by undertaker # 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 T0385 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 T0385 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 T0385 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 T0385 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 T0385 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 T0385 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 T0385 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0385 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 T0385 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 T0385 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 132 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS1 # ReadConformPDB reading from PDB file servers/3Dpro_TS2.pdb.gz looking for model 1 # naming current conformation 3Dpro_TS2 # ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1 # Found a chain break before 132 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS3 # ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1 # naming current conformation 3Dpro_TS4 # ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1 # Found a chain break before 132 # 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 154 # 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 151 # 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 131 # 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 155 # 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 141 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS5 # ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1 # Found a chain break before 23 # copying to AlignedFragments data structure # naming current conformation BayesHH_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS1.pdb.gz looking for model 1 # naming current conformation Bilab-ENABLE_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS2.pdb.gz looking for model 1 # Found a chain break before 159 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1 # Found a chain break before 151 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS1 # ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0385 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # Found a chain break before 161 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS3 # ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1 # Found a chain break before 161 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS4 # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # Found a chain break before 157 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS5 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0385 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 T0385 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 T0385 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 # WARNING: incomplete conformation T0385 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS4 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0385 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS5 # ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0385 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 T0385 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 T0385 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 T0385 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 T0385 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 157 # 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 T0385 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 T0385 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 # WARNING: incomplete conformation T0385 can't currently be optimized by undertaker # naming current conformation FAMSD_TS4 # ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0385 can't currently be optimized by undertaker # naming current conformation FAMSD_TS5 # ReadConformPDB reading from PDB file servers/FAMS_TS1.pdb.gz looking for model 1 # Found a chain break before 157 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # Found a chain break before 161 # copying to AlignedFragments data structure # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # Found a chain break before 161 # copying to AlignedFragments data structure # naming current conformation FAMS_TS3 # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0385 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 157 # 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 132 # 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 132 # 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 80 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS3 # ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1 # Found a chain break before 47 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS4 # ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1 # Found a chain break before 119 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS5 # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0385 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 101, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 103, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 105, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 107, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz # WARNING: incomplete conformation T0385 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 T0385 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 T0385 can't currently be optimized by undertaker # naming current conformation FORTE1_AL4 # ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0385 can't currently be optimized by undertaker # naming current conformation FORTE1_AL5 # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0385 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 101, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 103, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 105, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 107, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz # WARNING: incomplete conformation T0385 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 T0385 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 T0385 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 38, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 40, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 42, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 44, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 74, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 76, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 78, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 80, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 90, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 92, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 94, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 96, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 178, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 180, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 182, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 184, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 198, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 200, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 202, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 204, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 214, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 216, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 218, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 220, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 294, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 296, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 298, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 300, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 310, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 312, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 314, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 316, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 458, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 460, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 462, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 464, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 502, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 504, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 506, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 508, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 518, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 520, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 522, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 524, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 542, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 544, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 546, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 548, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 550, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 552, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 554, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 556, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 578, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 580, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 582, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 584, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz # WARNING: incomplete conformation T0385 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 161 # 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 92 # 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 70 # 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 134 # 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 85 # 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 160 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0385 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS2 # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0385 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 # WARNING: incomplete conformation T0385 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS4 # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0385 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 T0385 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 T0385 can't currently be optimized by undertaker # naming current conformation FUGUE_AL2 # ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0385 can't currently be optimized by undertaker # naming current conformation FUGUE_AL3 # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0385 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 Skipped atom 94, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL5.pdb.gz Skipped atom 96, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL5.pdb.gz Skipped atom 98, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL5.pdb.gz Skipped atom 100, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL5.pdb.gz # WARNING: incomplete conformation T0385 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 # WARNING: incomplete conformation T0385 can't currently be optimized by undertaker # naming current conformation FUNCTION_TS1 # ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0385 can't currently be optimized by undertaker # naming current conformation FUNCTION_TS2 # ReadConformPDB reading from PDB file servers/FUNCTION_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0385 can't currently be optimized by undertaker # naming current conformation FUNCTION_TS3 # ReadConformPDB reading from PDB file servers/FUNCTION_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0385 can't currently be optimized by undertaker # naming current conformation FUNCTION_TS4 # ReadConformPDB reading from PDB file servers/FUNCTION_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0385 can't currently be optimized by undertaker # naming current conformation FUNCTION_TS5 # ReadConformPDB reading from PDB file servers/Frankenstein_TS1.pdb.gz looking for model 1 # Found a chain break before 128 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS1 # ReadConformPDB reading from PDB file servers/Frankenstein_TS2.pdb.gz looking for model 1 # Found a chain break before 153 # 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 47 # 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 134 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS4 # ReadConformPDB reading from PDB file servers/Frankenstein_TS5.pdb.gz looking for model 1 # naming current conformation Frankenstein_TS5 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0385 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 # WARNING: incomplete conformation T0385 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0385 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 T0385 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 T0385 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 # Found a chain break before 84 # copying to AlignedFragments data structure # naming current conformation HHpred1_TS1 # ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1 # naming current conformation HHpred2_TS1 # ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1 # naming current conformation HHpred3_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0385 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 T0385 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 T0385 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 T0385 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 T0385 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 T0385 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 T0385 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 T0385 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 # naming current conformation LOOPP_TS4 # ReadConformPDB reading from PDB file servers/LOOPP_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0385 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 # WARNING: incomplete conformation T0385 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 40 # 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 # naming current conformation Ma-OPUS-server2_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS4.pdb.gz looking for model 1 # 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 # Found a chain break before 88 # copying to AlignedFragments data structure # 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 47 # 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 # Found a chain break before 77 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS4.pdb.gz looking for model 1 # Found a chain break before 152 # 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 # 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 159 # 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 161 # 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 159 # 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 156 # 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 160 # 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 T0385 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation NN_PUT_lab_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS1.pdb.gz looking for model 1 # Found a chain break before 106 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS2.pdb.gz looking for model 1 # Found a chain break before 142 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS2 # ReadConformPDB reading from PDB file servers/POMYSL_TS3.pdb.gz looking for model 1 # Found a chain break before 149 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS3 # ReadConformPDB reading from PDB file servers/POMYSL_TS4.pdb.gz looking for model 1 WARNING: atom 1 has residue number 25 < previous residue 162 in servers/POMYSL_TS4.pdb.gz # WARNING: incomplete conformation T0385 can't currently be optimized by undertaker # naming current conformation POMYSL_TS4 # ReadConformPDB reading from PDB file servers/POMYSL_TS5.pdb.gz looking for model 1 # Found a chain break before 145 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1 # 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 152 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0385 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0385 can't currently be optimized by undertaker # 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 # Found a chain break before 152 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS5 # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0385 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 T0385 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 T0385 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 T0385 can't currently be optimized by undertaker # naming current conformation Pcons6_TS4 # ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0385 can't currently be optimized by undertaker # naming current conformation Pcons6_TS5 # ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0385 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 # Found a chain break before 127 # 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 # WARNING: incomplete conformation T0385 can't currently be optimized by undertaker # 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 # WARNING: incomplete conformation T0385 can't currently be optimized by undertaker # 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 # WARNING: incomplete conformation T0385 can't currently be optimized by undertaker # 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 # WARNING: incomplete conformation T0385 can't currently be optimized by undertaker # 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 93 # 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 150 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS2 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS3 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # Found a chain break before 145 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS4 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0385 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1 # Found a chain break before 109 # 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 38 # 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 38 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS5 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS1.pdb.gz looking for model 1 # Found a chain break before 157 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS1 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS2.pdb.gz looking for model 1 # Found a chain break before 158 # 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 123 # 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 156 # 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 157 # 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 38 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1 # Found a chain break before 38 # copying to AlignedFragments data structure # 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 # naming current conformation RAPTOR_TS5 # ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1 # Found a chain break before 147 # 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 145 # 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 124 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS3 # ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1 # Found a chain break before 93 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS4 # ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1 # Found a chain break before 150 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS5 # ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1 # Found a chain break before 62 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS1 # ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1 # naming current conformation ROKKY_TS2 # ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1 # Found a chain break before 157 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS3 # ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0385 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL1 # ReadConformPDB reading from PDB file servers/SAM-T02_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0385 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 Skipped atom 218, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 220, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 222, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 224, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 238, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 240, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 242, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 244, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 254, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 256, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 258, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 260, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 390, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 392, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 394, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 396, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz # WARNING: incomplete conformation T0385 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 74, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 76, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 78, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 80, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz # WARNING: incomplete conformation T0385 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 Skipped atom 22, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 24, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 26, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 28, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 58, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 60, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 62, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 64, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 74, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 76, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 78, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 80, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 162, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 164, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 166, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 168, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 182, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 184, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 186, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 188, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 198, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 200, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 202, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 204, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 278, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 280, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 282, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 284, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 294, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 296, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 298, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 300, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 482, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 484, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 486, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 488, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 518, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 520, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 522, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 524, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz # WARNING: incomplete conformation T0385 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL5 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1 # Found a chain break before 148 # 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 T0385 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 T0385 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 T0385 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 T0385 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 5 # 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 84 # 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 87 # 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 # naming current conformation SP3_TS5 # ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1 # Found a chain break before 5 # 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 87 # 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 12 # copying to AlignedFragments data structure # naming current conformation SP4_TS3 # ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1 # naming current conformation SP4_TS4 # ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1 # Found a chain break before 20 # 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 84 # 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 87 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS2 # ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS3 # ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1 # Found a chain break before 5 # 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 152 # 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 T0385 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 T0385 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 T0385 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 T0385 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 T0385 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 T0385 can't currently be optimized by undertaker # 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 178, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 180, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 182, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 184, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 218, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 220, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 222, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 224, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 294, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 296, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 298, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 300, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz # WARNING: incomplete conformation T0385 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0385 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 T0385 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 Skipped atom 2, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 4, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 6, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 8, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 26, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 28, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 30, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 32, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 470, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 472, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 474, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 476, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz # WARNING: incomplete conformation T0385 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 T0385 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 87 # 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 157 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS2 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS3.pdb.gz looking for model 1 # Found a chain break before 155 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS3 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS4.pdb.gz looking for model 1 # Found a chain break before 155 # 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 # WARNING: incomplete conformation T0385 can't currently be optimized by undertaker # 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 161 # 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 T0385 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 Skipped atom 194, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 196, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 198, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 200, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz # WARNING: incomplete conformation T0385 can't currently be optimized by undertaker # naming current conformation forecast-s_AL1 # ReadConformPDB reading from PDB file servers/forecast-s_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0385 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 # WARNING: incomplete conformation T0385 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 T0385 can't currently be optimized by undertaker # naming current conformation forecast-s_AL4 # ReadConformPDB reading from PDB file servers/forecast-s_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0385 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 # Found a chain break before 24 # copying to AlignedFragments data structure # 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 120 # 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 # Found a chain break before 140 # copying to AlignedFragments data structure # 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 89 # 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 # Found a chain break before 130 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS1.pdb.gz looking for model 1 WARNING: atoms too close: (T0385)A10.O and (T0385)T11.N only 0.000 apart, marking (T0385)T11.N as missing # WARNING: incomplete conformation T0385 can't currently be optimized by undertaker # 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 WARNING: atoms too close: (T0385)W151.O and (T0385)P152.N only 0.000 apart, marking (T0385)P152.N as missing # WARNING: incomplete conformation T0385 can't currently be optimized by undertaker # 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: (T0385)R105.O and (T0385)M106.N only 0.000 apart, marking (T0385)M106.N as missing WARNING: atoms too close: (T0385)A150.O and (T0385)W151.N only 0.000 apart, marking (T0385)W151.N as missing # WARNING: incomplete conformation T0385 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 WARNING: atoms too close: (T0385)A35.O and (T0385)T36.N only 0.000 apart, marking (T0385)T36.N as missing WARNING: atoms too close: (T0385)V93.O and (T0385)S94.N only 0.000 apart, marking (T0385)S94.N as missing # WARNING: incomplete conformation T0385 can't currently be optimized by undertaker # 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 WARNING: atoms too close: (T0385)P158.O and (T0385)G159.N only 0.000 apart, marking (T0385)G159.N as missing # WARNING: incomplete conformation T0385 can't currently be optimized by undertaker # 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 T0385 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 T0385 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 T0385 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 T0385 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 T0385 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 # naming current conformation keasar-server_TS2 # ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1 # naming current conformation keasar-server_TS3 # ReadConformPDB reading from PDB file servers/keasar-server_TS4.pdb.gz looking for model 1 # Found a chain break before 48 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS4 # ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1 # naming current conformation keasar-server_TS5 # ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0385 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 T0385 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation nFOLD_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0385 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 T0385 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 T0385 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 T0385 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 T0385 can't currently be optimized by undertaker # naming current conformation panther2_TS1 # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0385 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 0.2652 model score 0.4069 model score 0.3955 model score 0.7326 model score -0.2247 model score -0.2014 model score -0.2020 model score -0.1731 model score -0.0626 model score -0.0181 model score -0.0302 model score -0.2377 model score 0.3830 model score 0.6036 model score -0.0669 model score -0.1483 model score 0.5357 model score -0.2443 model score 0.4114 model score -0.1973 model score 1.5114 model score 1.3080 model score 1.6560 model score 1.4605 model score 1.6870 model score -0.1165 model score -0.1655 model score 1.5702 model score -0.2494 model score -0.2494 model score -0.1872 model score -0.1814 model score -0.2670 model score 0.2418 model score -0.2074 model score 0.7146 model score -0.3000 model score -0.3088 model score 1.2774 model score 1.2775 model score 1.2775 model score 1.2775 model score 1.2775 model score -0.2155 model score -0.1871 model score -0.1288 model score -0.1311 model score -0.2454 model score -0.3346 model score -0.1872 model score -0.1814 model score -0.1871 model score -0.2670 model score -0.1915 model score -0.2597 model score 0.3593 model score 0.5045 model score 0.6268 model score 1.2771 model score 1.2771 model score 1.2766 model score 1.2768 model score 1.2768 model score 1.2771 model score 1.2771 model score 1.2768 model score 1.2768 model score 1.2771 model score 1.9624 model score 2.3924 model score 2.1803 model score 2.0846 model score 2.3368 model score 1.8655 model score 0.1331 model score -0.4069 model score -0.4031 model score 0.1808 model score 1.2774 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.2102 model score -0.1645 model score -0.2216 model score -0.3050 model score -0.3262 model score 0.9299 model score 1.6540 model score 1.1632 model score 0.8848 model score 1.9683 model score -0.3664 model score -0.3007 model score -0.3576 model score -0.2112 model score -0.2766 model score -0.0850 model score -0.1241 model score -0.1241 model score 1.2664 model score 0.0831 model score 0.3100 model score 1.6478 model score 1.6540 model score 0.2094 model score 0.2162 model score 0.2574 model score 0.5736 model score 0.2415 model score 1.2771 model score -0.2480 model score -0.0313 model score -0.0116 model score 0.0052 model score -0.1003 model score -0.1410 model score -0.2280 model score -0.0213 model score 0.0039 model score -0.0442 model score -0.3166 model score -0.2994 model score -0.3297 model score -0.3188 model score -0.3169 model score -0.2465 model score 2.0711 model score 2.0927 model score 2.1694 model score 1.7029 model score 2.2045 model score -0.2333 model score -0.2669 model score -0.2144 model score -0.2502 model score -0.2508 model score -0.3305 model score -0.2636 model score -0.2090 model score -0.2307 model score -0.2136 model score -0.3560 model score -0.3095 model score -0.4608 model score -0.3692 model score -0.2462 model score 1.2618 model score 0.3209 model score 2.1615 model score 2.1428 model score 2.1782 model score 1.2905 model score -0.3226 model score -0.3530 model score -0.4285 model score -0.3507 model score -0.2411 model score -0.4201 model score -0.4338 model score -0.4203 model score -0.3027 model score -0.2434 model score -0.2367 model score -0.1922 model score -0.1586 model score -0.1979 model score -0.1699 model score -0.2573 model score -0.2952 model score -0.2318 model score -0.2572 model score -0.1741 model score -0.3614 model score -0.3507 model score -0.4285 model score -0.3226 model score -0.3530 model score 0.2336 model score -0.0289 model score 0.1085 model score 1.2771 model score 1.2770 model score 1.2771 model score 1.2771 model score 1.2771 model score 0.0657 model score -0.2847 model score -0.3692 model score 0.0940 model score 0.1643 model score -0.2142 model score -0.1070 model score -0.2825 model score 0.1417 model score -0.3033 model score -0.2269 model score -0.2802 model score -0.0528 model score -0.3213 model score 0.1204 model score -0.0846 model score -0.2750 model score -0.1820 model score -0.2142 model score -0.1675 model score 1.2774 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.3328 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.3014 model score -0.3241 model score -0.2997 model score -0.2545 model score -0.3126 model score -0.3068 model score -0.2962 model score 1.2771 model score 1.2771 model score 1.2765 model score 1.2771 model score 1.2771 model score -0.2326 model score 0.3159 model score -0.1646 model score -0.0437 model score -0.0744 model score 1.8283 model score 1.9092 model score 2.1019 model score 1.6409 model score 1.6484 model score -0.2497 model score -0.1624 model score -0.2628 model score -0.2772 model score -0.1624 model score -0.2598 model score -0.2700 model score -0.2700 model score -0.2863 model score -0.2097 model score -0.2852 model score -0.2465 model score -0.2966 model score -0.2847 model score -0.4334 model score -0.0739 model score 1.3891 model score -0.3866 USE_META, weight: 0.7710 cost: 0.2652 min: -0.4608 max: 2.3924 USE_META, weight: 0.7263 cost: 0.4069 min: -0.4608 max: 2.3924 USE_META, weight: 0.7299 cost: 0.3955 min: -0.4608 max: 2.3924 USE_META, weight: 0.6236 cost: 0.7326 min: -0.4608 max: 2.3924 USE_META, weight: 0.9255 cost: -0.2247 min: -0.4608 max: 2.3924 USE_META, weight: 0.9182 cost: -0.2014 min: -0.4608 max: 2.3924 USE_META, weight: 0.9183 cost: -0.2020 min: -0.4608 max: 2.3924 USE_META, weight: 0.9092 cost: -0.1731 min: -0.4608 max: 2.3924 USE_META, weight: 0.8744 cost: -0.0626 min: -0.4608 max: 2.3924 USE_META, weight: 0.8604 cost: -0.0181 min: -0.4608 max: 2.3924 USE_META, weight: 0.8642 cost: -0.0302 min: -0.4608 max: 2.3924 USE_META, weight: 0.9296 cost: -0.2377 min: -0.4608 max: 2.3924 USE_META, weight: 0.7338 cost: 0.3830 min: -0.4608 max: 2.3924 USE_META, weight: 0.6642 cost: 0.6036 min: -0.4608 max: 2.3924 USE_META, weight: 0.8757 cost: -0.0669 min: -0.4608 max: 2.3924 USE_META, weight: 0.9014 cost: -0.1483 min: -0.4608 max: 2.3924 USE_META, weight: 0.6857 cost: 0.5357 min: -0.4608 max: 2.3924 USE_META, weight: 0.9317 cost: -0.2443 min: -0.4608 max: 2.3924 USE_META, weight: 0.7249 cost: 0.4114 min: -0.4608 max: 2.3924 USE_META, weight: 0.9169 cost: -0.1973 min: -0.4608 max: 2.3924 USE_META, weight: 0.3779 cost: 1.5114 min: -0.4608 max: 2.3924 USE_META, weight: 0.4421 cost: 1.3080 min: -0.4608 max: 2.3924 USE_META, weight: 0.3323 cost: 1.6560 min: -0.4608 max: 2.3924 USE_META, weight: 0.3940 cost: 1.4605 min: -0.4608 max: 2.3924 USE_META, weight: 0.3225 cost: 1.6870 min: -0.4608 max: 2.3924 USE_META, weight: 0.8914 cost: -0.1165 min: -0.4608 max: 2.3924 USE_META, weight: 0.9068 cost: -0.1655 min: -0.4608 max: 2.3924 USE_META, weight: 0.3594 cost: 1.5702 min: -0.4608 max: 2.3924 USE_META, weight: 0.9333 cost: -0.2494 min: -0.4608 max: 2.3924 USE_META, weight: 0.9333 cost: -0.2494 min: -0.4608 max: 2.3924 USE_META, weight: 0.9137 cost: -0.1872 min: -0.4608 max: 2.3924 USE_META, weight: 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1.2774 min: -0.4608 max: 2.3924 USE_META, weight: 0.4518 cost: 1.2771 min: -0.4608 max: 2.3924 USE_META, weight: 0.4518 cost: 1.2771 min: -0.4608 max: 2.3924 USE_META, weight: 0.4518 cost: 1.2771 min: -0.4608 max: 2.3924 USE_META, weight: 0.4518 cost: 1.2771 min: -0.4608 max: 2.3924 USE_META, weight: 0.9210 cost: -0.2102 min: -0.4608 max: 2.3924 USE_META, weight: 0.9065 cost: -0.1645 min: -0.4608 max: 2.3924 USE_META, weight: 0.9245 cost: -0.2216 min: -0.4608 max: 2.3924 USE_META, weight: 0.9508 cost: -0.3050 min: -0.4608 max: 2.3924 USE_META, weight: 0.9575 cost: -0.3262 min: -0.4608 max: 2.3924 USE_META, weight: 0.5613 cost: 0.9299 min: -0.4608 max: 2.3924 USE_META, weight: 0.3329 cost: 1.6540 min: -0.4608 max: 2.3924 USE_META, weight: 0.4877 cost: 1.1632 min: -0.4608 max: 2.3924 USE_META, weight: 0.5755 cost: 0.8848 min: -0.4608 max: 2.3924 USE_META, weight: 0.2338 cost: 1.9683 min: -0.4608 max: 2.3924 USE_META, weight: 0.9702 cost: -0.3664 min: -0.4608 max: 2.3924 USE_META, weight: 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USE_META, weight: 0.7785 cost: 0.2415 min: -0.4608 max: 2.3924 USE_META, weight: 0.4518 cost: 1.2771 min: -0.4608 max: 2.3924 USE_META, weight: 0.9329 cost: -0.2480 min: -0.4608 max: 2.3924 USE_META, weight: 0.8645 cost: -0.0313 min: -0.4608 max: 2.3924 USE_META, weight: 0.8583 cost: -0.0116 min: -0.4608 max: 2.3924 USE_META, weight: 0.8530 cost: 0.0052 min: -0.4608 max: 2.3924 USE_META, weight: 0.8863 cost: -0.1003 min: -0.4608 max: 2.3924 USE_META, weight: 0.8991 cost: -0.1410 min: -0.4608 max: 2.3924 USE_META, weight: 0.9265 cost: -0.2280 min: -0.4608 max: 2.3924 USE_META, weight: 0.8613 cost: -0.0213 min: -0.4608 max: 2.3924 USE_META, weight: 0.8534 cost: 0.0039 min: -0.4608 max: 2.3924 USE_META, weight: 0.8686 cost: -0.0442 min: -0.4608 max: 2.3924 USE_META, weight: 0.9545 cost: -0.3166 min: -0.4608 max: 2.3924 USE_META, weight: 0.9491 cost: -0.2994 min: -0.4608 max: 2.3924 USE_META, weight: 0.9586 cost: -0.3297 min: -0.4608 max: 2.3924 USE_META, weight: 0.9552 cost: -0.3188 min: 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USE_META, weight: 0.9324 cost: -0.2465 min: -0.4608 max: 2.3924 USE_META, weight: 0.9482 cost: -0.2966 min: -0.4608 max: 2.3924 USE_META, weight: 0.9444 cost: -0.2847 min: -0.4608 max: 2.3924 USE_META, weight: 0.9914 cost: -0.4334 min: -0.4608 max: 2.3924 USE_META, weight: 0.8779 cost: -0.0739 min: -0.4608 max: 2.3924 USE_META, weight: 0.4165 cost: 1.3891 min: -0.4608 max: 2.3924 USE_META, weight: 0.9766 cost: -0.3866 min: -0.4608 max: 2.3924 USE_EVALUE, weight: 0.8371 eval: 0.5991 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.8371 eval: 0.5991 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.8371 eval: 0.5991 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.7394 eval: 0.9570 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.7394 eval: 0.9570 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.7394 eval: 0.9570 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.9287 eval: 0.2634 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.9287 eval: 0.2634 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.9287 eval: 0.2634 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.9509 eval: 0.1820 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.9509 eval: 0.1820 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.9509 eval: 0.1820 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.9899 eval: 0.0390 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.9899 eval: 0.0390 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.9899 eval: 0.0390 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.8092 eval: 0.7013 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.8092 eval: 0.7013 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.8092 eval: 0.7013 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.7342 eval: 0.9759 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.7342 eval: 0.9759 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.7342 eval: 0.9759 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.6794 eval: 1.1769 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.6794 eval: 1.1769 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.6794 eval: 1.1769 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.9160 eval: 0.3098 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.9160 eval: 0.3098 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.9160 eval: 0.3098 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.9224 eval: 0.2862 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.9224 eval: 0.2862 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.9224 eval: 0.2862 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.1000 eval: 3.3000 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.1000 eval: 3.3000 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.1000 eval: 3.3000 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.9951 eval: 0.0200 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.9951 eval: 0.0200 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.9951 eval: 0.0200 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.8255 eval: 0.6414 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.8255 eval: 0.6414 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.8255 eval: 0.6414 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.6854 eval: 1.1550 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.6854 eval: 1.1550 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.6854 eval: 1.1550 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.9967 eval: 0.0141 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.9967 eval: 0.0141 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.9967 eval: 0.0141 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.8746 eval: 0.4614 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.8746 eval: 0.4614 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.8746 eval: 0.4614 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.9136 eval: 0.3185 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.9136 eval: 0.3185 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.9136 eval: 0.3185 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.9783 eval: 0.0816 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.9783 eval: 0.0816 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.9783 eval: 0.0816 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.9752 eval: 0.0929 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.9752 eval: 0.0929 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.9752 eval: 0.0929 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.8700 eval: 0.4785 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.8700 eval: 0.4785 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 0.8700 eval: 0.4785 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 1.0000 eval: 0.0020 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 1.0000 eval: 0.0020 min: 0.0020 max: 3.3000 USE_EVALUE, weight: 1.0000 eval: 0.0020 min: 0.0020 max: 3.3000 Number of contacts in models: 258 Number of contacts in alignments: 63 NUMB_ALIGNS: 63 Adding 6242 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: -317.8339, CN propb: -317.8339 weights: 0.2968 constraints: 427 # command:Found ConstraintSet # PrintContacts align.constraints_meta03 Number of constraints in align3.constraints 427 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta03 Number of constraints in align3.constraints.bonus 427 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta03 Number of constraints in rejected3.constraints 5815 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta03 Number of constraints in rejected3.constraints.bonus 5815 # 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 6242 # command: