# 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/T0347/ # command:# Making conformation for sequence T0347 numbered 1 through 205 Created new target T0347 from T0347.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0347/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0347//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0347/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0347//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0347/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0347/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0347/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yzsA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yzsA expands to /projects/compbio/data/pdb/1yzs.pdb.gz 1yzsA:# T0347 read from 1yzsA/merged-good-all-a2m # 1yzsA read from 1yzsA/merged-good-all-a2m # adding 1yzsA to template set # found chain 1yzsA in template set T0347 1 :MTHIYEPRLSRIAIDKL 1yzsA 33 :IHSGRIAAVHNVPLSVL # choosing archetypes in rotamer library T0347 18 :RPTQIAVGFREVELKRKEWRETRKK 1yzsA 51 :RPLPSVLDPAKVQSLVDTIREDPDS T0347 44 :G 1yzsA 77 :P T0347 50 :NHIVPVVAGPKDRAYLID 1yzsA 78 :PIDVLWIKGAQGGDYFYS T0347 68 :HHHLVLALSKEGVEHVLTSEVA 1yzsA 98 :GCHRYAAYQQLQRETIPAKLVQ T0347 94 :LGKDEFWSVMDHR 1yzsA 120 :STLSDLRVYLGAS Number of specific fragments extracted= 6 number of extra gaps= 0 total=6 Number of alignments=1 # 1yzsA read from 1yzsA/merged-good-all-a2m # found chain 1yzsA in template set T0347 1 :MTHIYEPRLSRIAIDKL 1yzsA 33 :IHSGRIAAVHNVPLSVL T0347 18 :RPTQIAVGFREVELKRKEWRETR 1yzsA 51 :RPLPSVLDPAKVQSLVDTIREDP T0347 46 :DFLGNHIVPVVAGPKDRAYLID 1yzsA 74 :DSVPPIDVLWIKGAQGGDYFYS T0347 68 :HHHLVLALSKEGVEHVLTSEVA 1yzsA 98 :GCHRYAAYQQLQRETIPAKLVQ T0347 94 :LGKDEFWSVMDHR 1yzsA 120 :STLSDLRVYLGAS Number of specific fragments extracted= 5 number of extra gaps= 0 total=11 Number of alignments=2 # 1yzsA read from 1yzsA/merged-good-all-a2m # found chain 1yzsA in template set T0347 1 :MTHIYEPRLSRIAIDKL 1yzsA 33 :IHSGRIAAVHNVPLSVL T0347 23 :AVGFREVELKRKEWRETRKK 1yzsA 56 :VLDPAKVQSLVDTIREDPDS T0347 53 :VPVVAGPKDRAYLID 1yzsA 81 :VLWIKGAQGGDYFYS T0347 68 :HHHLVLALSKEGVEHVLTSEVA 1yzsA 98 :GCHRYAAYQQLQRETIPAKLVQ T0347 94 :LGKDEFWSVMDHR 1yzsA 120 :STLSDLRVYLGAS Number of specific fragments extracted= 5 number of extra gaps= 0 total=16 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c4jA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2c4jA expands to /projects/compbio/data/pdb/2c4j.pdb.gz 2c4jA:Skipped atom 120, because occupancy 0.5 <= existing 0.500 in 2c4jA Skipped atom 122, because occupancy 0.500 <= existing 0.500 in 2c4jA Skipped atom 1604, because occupancy 0.500 <= existing 0.500 in 2c4jA Skipped atom 1606, because occupancy 0.500 <= existing 0.500 in 2c4jA # T0347 read from 2c4jA/merged-good-all-a2m # 2c4jA read from 2c4jA/merged-good-all-a2m # adding 2c4jA to template set # found chain 2c4jA in template set T0347 70 :HLVLALSKE 2c4jA 15 :HSIRLLLEY T0347 79 :GVE 2c4jA 25 :DSS T0347 82 :HVLTSEVAKFSHLGKDEFW 2c4jA 29 :EEKKYTMGDAPDYDRSQWL T0347 104 :DHRNLI 2c4jA 48 :NEKFKL T0347 118 :RRQSGDIP 2c4jA 54 :GLDFPNLP T0347 134 :DPFRSLAGALRMAGGYAKV 2c4jA 72 :QSNAILRYIARKHNLCGES T0347 158 :EFGWADFLRRR 2c4jA 93 :EQIREDILENQ T0347 178 :FDDALAEAMKLAKSREA 2c4jA 104 :FMDSRMQLAKLCYDPDF Number of specific fragments extracted= 8 number of extra gaps= 0 total=24 Number of alignments=4 # 2c4jA read from 2c4jA/merged-good-all-a2m # found chain 2c4jA in template set T0347 70 :HLVLALSK 2c4jA 15 :HSIRLLLE T0347 78 :EGVE 2c4jA 24 :TDSS T0347 82 :HVLTSEVAKFSHLGKDEFW 2c4jA 29 :EEKKYTMGDAPDYDRSQWL T0347 104 :DHRN 2c4jA 48 :NEKF T0347 108 :LIYPFDAQG 2c4jA 60 :LPYLIDGTH T0347 118 :RRQ 2c4jA 69 :KIT T0347 134 :DPFRSLAGALRMAGGYAKV 2c4jA 72 :QSNAILRYIARKHNLCGES T0347 157 :SEFGWADFLRRR 2c4jA 92 :KEQIREDILENQ T0347 178 :FDDALAEAMKLAKSRE 2c4jA 104 :FMDSRMQLAKLCYDPD Number of specific fragments extracted= 9 number of extra gaps= 0 total=33 Number of alignments=5 # 2c4jA read from 2c4jA/merged-good-all-a2m # found chain 2c4jA in template set T0347 69 :HHLVLALSKEGVE 2c4jA 15 :HSIRLLLEYTDSS T0347 82 :HVLTSEVAKFSHLGKDEFW 2c4jA 29 :EEKKYTMGDAPDYDRSQWL T0347 104 :DHRN 2c4jA 48 :NEKF T0347 108 :LIYPFDAQ 2c4jA 60 :LPYLIDGT T0347 117 :LRRQ 2c4jA 68 :HKIT T0347 134 :DPFRSLAGALRMAGGYAKV 2c4jA 72 :QSNAILRYIARKHNLCGES T0347 158 :EFGWADFLRRR 2c4jA 93 :EQIREDILENQ T0347 178 :FDDALAEAMKLAKSREARHL 2c4jA 104 :FMDSRMQLAKLCYDPDFEKL Number of specific fragments extracted= 8 number of extra gaps= 0 total=41 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bbrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bbrA expands to /projects/compbio/data/pdb/2bbr.pdb.gz 2bbrA:# T0347 read from 2bbrA/merged-good-all-a2m # 2bbrA read from 2bbrA/merged-good-all-a2m # adding 2bbrA to template set # found chain 2bbrA in template set T0347 30 :ELKRKEWRETRKKDGDDFLGNHIVP 2bbrA 70 :MDLLKSRFGLSKEGAEQLLGTSFLT T0347 69 :HHLVLALSKEGV 2bbrA 96 :YRKLMVCVGEEL T0347 95 :G 2bbrA 108 :D T0347 97 :DEFWSVMDH 2bbrA 109 :SSELRALRL T0347 123 :DIPKNIHDL 2bbrA 121 :NLNPSLSTA T0347 132 :EDDPFRSLAGALRMAGGYAKVII 2bbrA 132 :ESSRFVELVLALENVGLVSPSSV T0347 159 :FGWADFLRRRIDRDLL 2bbrA 155 :SVLADMLRTLRRLDLC T0347 176 :DSFDDALAEAMKL 2bbrA 171 :QQLVEYEQQEQAR Number of specific fragments extracted= 8 number of extra gaps= 0 total=49 Number of alignments=7 # 2bbrA read from 2bbrA/merged-good-all-a2m # found chain 2bbrA in template set T0347 26 :FRE 2bbrA 70 :MDL T0347 33 :RKEWRETRKKDGDDFLGNHIVP 2bbrA 73 :LKSRFGLSKEGAEQLLGTSFLT T0347 68 :HHHLVLALSKE 2bbrA 96 :YRKLMVCVGEE T0347 94 :LG 2bbrA 107 :LD T0347 97 :DEFWSVMDH 2bbrA 109 :SSELRALRL T0347 121 :SGDIPKNIH 2bbrA 123 :NPSLSTALS T0347 132 :EDDPFRSLAGALRMAGGYAKVII 2bbrA 132 :ESSRFVELVLALENVGLVSPSSV T0347 159 :FGWADFLRRRIDRDL 2bbrA 155 :SVLADMLRTLRRLDL T0347 182 :LAEAMKLAKS 2bbrA 170 :CQQLVEYEQQ Number of specific fragments extracted= 9 number of extra gaps= 0 total=58 Number of alignments=8 # 2bbrA read from 2bbrA/merged-good-all-a2m # found chain 2bbrA in template set T0347 23 :AVGFREVELKRKEWRE 2bbrA 60 :LVEMLYVLQRMDLLKS T0347 39 :TRKKDGDDFLGNHIVP 2bbrA 79 :LSKEGAEQLLGTSFLT T0347 69 :HHLVLALSKEGVE 2bbrA 96 :YRKLMVCVGEELD T0347 96 :KDEFWSVMDHRN 2bbrA 112 :LRALRLFACNLN T0347 122 :GDIPKNIH 2bbrA 124 :PSLSTALS T0347 132 :EDDPFRSLAGALRMAGGYAKVII 2bbrA 132 :ESSRFVELVLALENVGLVSPSSV T0347 159 :FGWADFLRRR 2bbrA 155 :SVLADMLRTL T0347 177 :SFDDALAEAMKLAKSREARH 2bbrA 165 :RRLDLCQQLVEYEQQEQARY Number of specific fragments extracted= 8 number of extra gaps= 0 total=66 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1exqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1exqA expands to /projects/compbio/data/pdb/1exq.pdb.gz 1exqA:# T0347 read from 1exqA/merged-good-all-a2m # 1exqA read from 1exqA/merged-good-all-a2m # adding 1exqA to template set # found chain 1exqA in template set Warning: unaligning (T0347)F156 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1exqA)V151 T0347 60 :KDRAYLIDHH 1exqA 69 :EGKVILVAVH T0347 76 :SKEG 1exqA 79 :VASG T0347 85 :TSEVAKFSHLGKDEFWSVMDH 1exqA 83 :YIEAEVIPAETGQETAYFLLK T0347 106 :RNLI 1exqA 107 :RWPV T0347 110 :YPFDAQG 1exqA 114 :HTDNGSN T0347 128 :IHD 1exqA 121 :FTG T0347 137 :RSLAGALRMAGGYAKVIIP 1exqA 124 :ATVRAACDWAGIKQEDGIP T0347 162 :ADFLRRRID 1exqA 155 :NKELKKIIG T0347 172 :DLLSDSFDDALAEAMKLAKSR 1exqA 166 :RDQAEHLKTAVQMAVFIHNKK Number of specific fragments extracted= 9 number of extra gaps= 0 total=75 Number of alignments=10 # 1exqA read from 1exqA/merged-good-all-a2m # found chain 1exqA in template set Warning: unaligning (T0347)F156 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1exqA)V151 T0347 60 :KDRAYLIDHH 1exqA 69 :EGKVILVAVH T0347 78 :EGVEHVLTSEV 1exqA 79 :VASGYIEAEVI T0347 92 :SHLGKDEFWSVMDH 1exqA 90 :PAETGQETAYFLLK T0347 109 :IYPFD 1exqA 113 :IHTDN T0347 125 :PKNIHD 1exqA 118 :GSNFTG T0347 137 :RSLAGALRMAGGYAKVIIP 1exqA 124 :ATVRAACDWAGIKQEDGIP T0347 162 :ADFLRRRID 1exqA 155 :NKELKKIIG T0347 171 :RDLLSDSFDDALAEAMKLAKS 1exqA 165 :VRDQAEHLKTAVQMAVFIHNK Number of specific fragments extracted= 8 number of extra gaps= 0 total=83 Number of alignments=11 # 1exqA read from 1exqA/merged-good-all-a2m # found chain 1exqA in template set Warning: unaligning (T0347)F156 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1exqA)V151 T0347 60 :KDRAYLIDHH 1exqA 69 :EGKVILVAVH T0347 78 :EGVE 1exqA 79 :VASG T0347 85 :TSEVAKFSHLGKDEFWSVMDH 1exqA 83 :YIEAEVIPAETGQETAYFLLK T0347 107 :NLIYPFDA 1exqA 111 :KTIHTDNG T0347 126 :KNIH 1exqA 119 :SNFT T0347 137 :RSLAGALRMAGGYAKVIIP 1exqA 124 :ATVRAACDWAGIKQEDGIP T0347 162 :ADFLRRRIDR 1exqA 155 :NKELKKIIGQ T0347 172 :DLLSDSFDDALAEAMKLAKS 1exqA 166 :RDQAEHLKTAVQMAVFIHNK Number of specific fragments extracted= 8 number of extra gaps= 0 total=91 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xb4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xb4A expands to /projects/compbio/data/pdb/1xb4.pdb.gz 1xb4A:# T0347 read from 1xb4A/merged-good-all-a2m # 1xb4A read from 1xb4A/merged-good-all-a2m # adding 1xb4A to template set # found chain 1xb4A in template set Warning: unaligning (T0347)H68 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xb4A)K73 Warning: unaligning (T0347)S86 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xb4A)K73 Warning: unaligning (T0347)R119 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xb4A)T116 Warning: unaligning (T0347)G122 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xb4A)T116 T0347 32 :KRKEWRETRKKDGDDFLGNHIVPVV 1xb4A 22 :TRRQQISTWIDIISQYCKTKKIWYM T0347 58 :GPKDRA 1xb4A 47 :SVDGTV T0347 87 :EVAKFSHLGK 1xb4A 74 :NLFNNEDIQR T0347 97 :DEFWSVMDHRNLIYPFDAQGLR 1xb4A 91 :DEIWSQMTKEGKCLPIDQSGRR T0347 123 :D 1xb4A 117 :T T0347 174 :LSDSFDDALAEAMKLAKSR 1xb4A 124 :LWKSLDSWASLILQWFEDS T0347 199 :GWCG 1xb4A 143 :GKLN Number of specific fragments extracted= 7 number of extra gaps= 0 total=98 Number of alignments=13 # 1xb4A read from 1xb4A/merged-good-all-a2m # found chain 1xb4A in template set Warning: unaligning (T0347)H68 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xb4A)K73 Warning: unaligning (T0347)S86 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xb4A)K73 Warning: unaligning (T0347)R119 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xb4A)T116 Warning: unaligning (T0347)G122 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xb4A)T116 T0347 31 :LKRKEWRETRKKDGDDFLGNHIVPV 1xb4A 21 :LTRRQQISTWIDIISQYCKTKKIWY T0347 57 :AGPKDRA 1xb4A 46 :MSVDGTV T0347 87 :EVAKFSHLG 1xb4A 74 :NLFNNEDIQ T0347 96 :KDEFWSVMDHRNLIYPFDAQGLR 1xb4A 90 :IDEIWSQMTKEGKCLPIDQSGRR T0347 123 :DIP 1xb4A 117 :TTT T0347 174 :LSDSFDDALAEAMKLAKSREAR 1xb4A 124 :LWKSLDSWASLILQWFEDSGKL Number of specific fragments extracted= 6 number of extra gaps= 0 total=104 Number of alignments=14 # 1xb4A read from 1xb4A/merged-good-all-a2m # found chain 1xb4A in template set Warning: unaligning (T0347)H68 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xb4A)K73 Warning: unaligning (T0347)S86 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xb4A)K73 Warning: unaligning (T0347)R119 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xb4A)T116 Warning: unaligning (T0347)G122 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xb4A)T116 T0347 32 :KRKEWRETRKKDGDDFLGNHIVPVV 1xb4A 22 :TRRQQISTWIDIISQYCKTKKIWYM T0347 58 :GPKDRA 1xb4A 47 :SVDGTV T0347 87 :EVAKFSHL 1xb4A 74 :NLFNNEDI T0347 95 :GK 1xb4A 86 :SQ T0347 97 :DEFWSVMDHRNLIYPFDAQGLR 1xb4A 91 :DEIWSQMTKEGKCLPIDQSGRR T0347 152 :VII 1xb4A 117 :TTT T0347 174 :LSDSFDDALAEAMKLAKS 1xb4A 124 :LWKSLDSWASLILQWFED Number of specific fragments extracted= 7 number of extra gaps= 0 total=111 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t6t1/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0347 read from 1t6t1/merged-good-all-a2m # 1t6t1 read from 1t6t1/merged-good-all-a2m # found chain 1t6t1 in training set T0347 31 :LKRKEWRE 1t6t1 10 :EWIKELKK T0347 47 :FLGNH 1t6t1 18 :ASREA T0347 54 :PVVAGP 1t6t1 23 :VILVEG T0347 69 :HHLVLALSKEGVEHVLT 1t6t1 29 :KNDKKALSKFSIKNVID T0347 91 :FSHLGKDEFWSVMDHRN 1t6t1 46 :LSGKRYADVVDMLEGKW T0347 108 :LIYPFDAQGLR 1t6t1 67 :LLFDLDTHGER T0347 135 :PFRSLAGALRMAGG 1t6t1 78 :INQKMKELLSSQGF T0347 156 :FSEFGWADFLRRRIDRDL 1t6t1 92 :LVDENFRNFLKKWNIIHI Number of specific fragments extracted= 8 number of extra gaps= 0 total=119 Number of alignments=16 # 1t6t1 read from 1t6t1/merged-good-all-a2m # found chain 1t6t1 in training set T0347 31 :LKRKEWR 1t6t1 10 :EWIKELK T0347 46 :DFLGNHI 1t6t1 17 :KASREAV T0347 55 :VVA 1t6t1 24 :ILV T0347 67 :DHHHLVLALSKEGVEHVL 1t6t1 27 :EGKNDKKALSKFSIKNVI T0347 90 :KFSHLGKDEFWSVMDHRN 1t6t1 45 :DLSGKRYADVVDMLEGKW T0347 109 :IYPFDAQ 1t6t1 66 :ILLFDLD T0347 136 :FRSLAGALRMAGGY 1t6t1 79 :NQKMKELLSSQGFL T0347 157 :SEFGWADFLRRRIDRDLLS 1t6t1 93 :VDENFRNFLKKWNIIHIEE Number of specific fragments extracted= 8 number of extra gaps= 0 total=127 Number of alignments=17 # 1t6t1 read from 1t6t1/merged-good-all-a2m # found chain 1t6t1 in training set T0347 43 :DGDDFLGNH 1t6t1 10 :EWIKELKKA T0347 59 :PKDRAYLIDHHHLVLALSKEGVEHVL 1t6t1 19 :SREAVILVEGKNDKKALSKFSIKNVI T0347 90 :KFSHLGKDEFWSVMDHRN 1t6t1 45 :DLSGKRYADVVDMLEGKW T0347 109 :IYPFDAQ 1t6t1 66 :ILLFDLD T0347 135 :PFRSLAGALRMAGGY 1t6t1 78 :INQKMKELLSSQGFL T0347 157 :SEFGWADFLRRRIDRDL 1t6t1 93 :VDENFRNFLKKWNIIHI Number of specific fragments extracted= 6 number of extra gaps= 0 total=133 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q7fA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1q7fA expands to /projects/compbio/data/pdb/1q7f.pdb.gz 1q7fA:# T0347 read from 1q7fA/merged-good-all-a2m # 1q7fA read from 1q7fA/merged-good-all-a2m # adding 1q7fA to template set # found chain 1q7fA in template set T0347 52 :IVPVVAGPKDRAYLIDHH 1q7fA 960 :PIGVGINSNGEILIADNH Number of specific fragments extracted= 1 number of extra gaps= 0 total=134 # 1q7fA read from 1q7fA/merged-good-all-a2m # found chain 1q7fA in template set T0347 55 :VVAGPKDRAYLIDH 1q7fA 877 :VTVDNKGRIIVVEC T0347 105 :HRNLIYPFDAQGLRRQSGDIPKNIH 1q7fA 891 :KVMRVIIFDQNGNVLHKFGCSKHLE Number of specific fragments extracted= 2 number of extra gaps= 0 total=136 Number of alignments=19 # 1q7fA read from 1q7fA/merged-good-all-a2m # found chain 1q7fA in template set T0347 53 :VPVVAGPKDRAYLIDHH 1q7fA 961 :IGVGINSNGEILIADNH T0347 81 :EHVLTSEV 1q7fA 978 :NNFNLTIF T0347 113 :DAQGLR 1q7fA 986 :TQDGQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=139 Number of alignments=20 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a0fA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2a0fA expands to /projects/compbio/data/pdb/2a0f.pdb.gz 2a0fA:# T0347 read from 2a0fA/merged-good-all-a2m # 2a0fA read from 2a0fA/merged-good-all-a2m # adding 2a0fA to template set # found chain 2a0fA in template set T0347 68 :HHHLVLALSKEGVEHVLTSE 2a0fA 169 :VHSLTQALAKFDGNRFYFIA T0347 91 :FSHLG 2a0fA 189 :PDALA T0347 96 :KDEFWSVMDHRNLIYPFDA 2a0fA 195 :PQYILDMLDEKGIAWSLHS Number of specific fragments extracted= 3 number of extra gaps= 0 total=142 Number of alignments=21 # 2a0fA read from 2a0fA/merged-good-all-a2m # found chain 2a0fA in template set T0347 68 :HHHLVLALSKEGVEHVLTSEVAKFS 2a0fA 169 :VHSLTQALAKFDGNRFYFIAPDALA T0347 96 :KDEFWSVMDHRNLIYPFDA 2a0fA 195 :PQYILDMLDEKGIAWSLHS T0347 120 :QSGDIPKNI 2a0fA 214 :SIEEVMAEV Number of specific fragments extracted= 3 number of extra gaps= 0 total=145 Number of alignments=22 # 2a0fA read from 2a0fA/merged-good-all-a2m # found chain 2a0fA in template set T0347 19 :PTQIAVGFREVELK 2a0fA 135 :PTQTLLDLFTIQET T0347 59 :PKD 2a0fA 152 :LDN T0347 62 :RAYLIDH 2a0fA 156 :HVAMVGD T0347 69 :HHLVLALSKEGVEHVLTSEVAKFSH 2a0fA 170 :HSLTQALAKFDGNRFYFIAPDALAM T0347 96 :KDEFWSVMDHRNLIYPFD 2a0fA 195 :PQYILDMLDEKGIAWSLH Number of specific fragments extracted= 5 number of extra gaps= 0 total=150 Number of alignments=23 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z5zA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1z5zA expands to /projects/compbio/data/pdb/1z5z.pdb.gz 1z5zA:# T0347 read from 1z5zA/merged-good-all-a2m # 1z5zA read from 1z5zA/merged-good-all-a2m # adding 1z5zA to template set # found chain 1z5zA in template set T0347 10 :SRIA 1z5zA 668 :VYCN T0347 17 :LRPTQIAVGFREVELKRKEWRETRKKDGDDFL 1z5zA 672 :LTPEQAAMYKAEVENLFNNIDSVTGIKRKGMI T0347 49 :GNHIVPVVAGP 1z5zA 746 :EGDKIAIFTQF T0347 68 :HHHLVLALSKEGVEHVLTSEVAKFSHLGKDEFWSVMDHRNLIYP 1z5zA 759 :MGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKF T0347 112 :FDAQGLRRQSGDI 1z5zA 807 :VKAGGFGINLTSA Number of specific fragments extracted= 5 number of extra gaps= 0 total=155 Number of alignments=24 # 1z5zA read from 1z5zA/merged-good-all-a2m # found chain 1z5zA in template set T0347 17 :LRPTQIAVGFREVELKRKEWRETRKKDGDDFL 1z5zA 672 :LTPEQAAMYKAEVENLFNNIDSVTGIKRKGMI T0347 49 :GNHIVPVVAGP 1z5zA 746 :EGDKIAIFTQF T0347 68 :HHHLVLALSKEGVE 1z5zA 759 :MGKIIRNIIEKELN T0347 82 :HVLT 1z5zA 774 :EVPF T0347 87 :E 1z5zA 778 :L T0347 91 :FSHLGKDE 1z5zA 779 :YGELSKKE T0347 99 :FWSVMDHRNLIYP 1z5zA 790 :IISKFQNNPSVKF T0347 112 :FDAQGLRRQSGD 1z5zA 807 :VKAGGFGINLTS Number of specific fragments extracted= 8 number of extra gaps= 0 total=163 Number of alignments=25 # 1z5zA read from 1z5zA/merged-good-all-a2m # found chain 1z5zA in template set T0347 9 :LSRIA 1z5zA 667 :NVYCN T0347 17 :LRPTQIAVGFREVELKRKEWRETRKKDGDDFLGN 1z5zA 672 :LTPEQAAMYKAEVENLFNNIDSVTGIKRKGMILS T0347 59 :PKDRAYLIDHH 1z5zA 746 :EGDKIAIFTQF T0347 71 :LVLALS 1z5zA 762 :IIRNII T0347 77 :KEGVEHVLTS 1z5zA 770 :ELNTEVPFLY T0347 92 :SHLGKDE 1z5zA 780 :GELSKKE T0347 99 :FWSVMDHRN 1z5zA 790 :IISKFQNNP T0347 108 :LIYPFDAQGLRRQSG 1z5zA 803 :IVLSVKAGGFGINLT Number of specific fragments extracted= 8 number of extra gaps= 0 total=171 Number of alignments=26 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wkaA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wkaA expands to /projects/compbio/data/pdb/1wka.pdb.gz 1wkaA:# T0347 read from 1wkaA/merged-good-all-a2m # 1wkaA read from 1wkaA/merged-good-all-a2m # adding 1wkaA to template set # found chain 1wkaA in template set T0347 5 :YEPRLSRIA 1wkaA 205 :EGGGFIEIA T0347 14 :IDKLRPTQIAV 1wkaA 217 :PETVFADQAIA T0347 39 :TRKKDGDDFL 1wkaA 230 :PEDERYRHLL T0347 50 :NHIVPVVAGPK 1wkaA 249 :EVWIPILADPA T0347 77 :KEGVEHVL 1wkaA 261 :EKDFGTGA T0347 89 :AKFSHLGKDEFWSVMDHRN 1wkaA 269 :LKVTPAHDPLDYEIGERHG T0347 108 :LIYPFDAQGLRR 1wkaA 290 :PVSVINLEGRME T0347 121 :SGDIPKNIHDLED 1wkaA 302 :GERVPEALRGLDR T0347 135 :PFRSLAGALRMAGG 1wkaA 317 :ARRKAVELFREAGH Number of specific fragments extracted= 9 number of extra gaps= 0 total=180 Number of alignments=27 # 1wkaA read from 1wkaA/merged-good-all-a2m # found chain 1wkaA in template set T0347 4 :IYEPRLSRIA 1wkaA 204 :VEGGGFIEIA T0347 14 :IDKLRPTQIAV 1wkaA 217 :PETVFADQAIA T0347 38 :ETRKKDGDDFL 1wkaA 229 :HPEDERYRHLL T0347 49 :GNHIVPVVAGP 1wkaA 248 :TEVWIPILADP T0347 62 :RAYLIDH 1wkaA 267 :GALKVTP T0347 94 :LGKDEFWSVMDHRN 1wkaA 274 :AHDPLDYEIGERHG T0347 108 :LIYPFDAQGL 1wkaA 290 :PVSVINLEGR T0347 119 :RQSGDIPKNIHDLED 1wkaA 300 :MEGERVPEALRGLDR T0347 136 :FRSLAGALRMAGGYAK 1wkaA 318 :RRKAVELFREAGHLVK Number of specific fragments extracted= 9 number of extra gaps= 0 total=189 Number of alignments=28 # 1wkaA read from 1wkaA/merged-good-all-a2m # found chain 1wkaA in template set T0347 51 :HIVPVVAGPK 1wkaA 250 :VWIPILADPA T0347 77 :KEGVEHVLTSE 1wkaA 261 :EKDFGTGALKV T0347 92 :SHLGKDEFWSVMDHRN 1wkaA 272 :TPAHDPLDYEIGERHG T0347 108 :LIYPFDAQGL 1wkaA 290 :PVSVINLEGR T0347 119 :RQSGDIPKNIHDLE 1wkaA 300 :MEGERVPEALRGLD T0347 178 :FDDALAEAMKLAKSR 1wkaA 314 :RFEARRKAVELFREA Number of specific fragments extracted= 6 number of extra gaps= 0 total=195 Number of alignments=29 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gs5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0347 read from 1gs5A/merged-good-all-a2m # 1gs5A read from 1gs5A/merged-good-all-a2m # found chain 1gs5A in training set T0347 8 :RLSRIA 1gs5A 111 :KVTQLD T0347 15 :DKLRPTQIA 1gs5A 117 :EELGHVGLA T0347 39 :TRKKDGDDFLGNHIVPVV 1gs5A 128 :GSPKLINSLLENGYLPVV T0347 57 :AGPKDRAYLIDHHHLVLALSKE 1gs5A 150 :VTDEGQLMNVNADQAATALAAT T0347 79 :GVEHVLTSE 1gs5A 173 :GADLILLSD T0347 108 :LIYPFDAQGLRR 1gs5A 182 :VSGILDGKGQRI T0347 137 :RSLAGALRMAGGYAKV 1gs5A 198 :AAKAEQLIEQGIITDG T0347 156 :FSEFGWADFLRRRID 1gs5A 215 :IVKVNAALDAARTLG Number of specific fragments extracted= 8 number of extra gaps= 0 total=203 Number of alignments=30 # 1gs5A read from 1gs5A/merged-good-all-a2m # found chain 1gs5A in training set T0347 8 :RLSRIA 1gs5A 111 :KVTQLD T0347 15 :DKLRPTQIAVG 1gs5A 117 :EELGHVGLAQP T0347 39 :TRKKDGDDFLGNHIVPVV 1gs5A 128 :GSPKLINSLLENGYLPVV T0347 57 :AGPKDRAYLIDHHHLVLALSKE 1gs5A 150 :VTDEGQLMNVNADQAATALAAT T0347 79 :G 1gs5A 173 :G T0347 83 :VLTSEVAKFSH 1gs5A 174 :ADLILLSDVSG T0347 111 :PFDAQGLRRQ 1gs5A 185 :ILDGKGQRIA T0347 137 :RSLAGALRMAGGYAKV 1gs5A 198 :AAKAEQLIEQGIITDG T0347 156 :FSEFGWADFLRRRIDR 1gs5A 215 :IVKVNAALDAARTLGR Number of specific fragments extracted= 9 number of extra gaps= 0 total=212 Number of alignments=31 # 1gs5A read from 1gs5A/merged-good-all-a2m # found chain 1gs5A in training set T0347 40 :RKKDGDDFLGNHIVPVV 1gs5A 129 :SPKLINSLLENGYLPVV T0347 57 :AGPKDRAYLIDHHHLVLALSKE 1gs5A 150 :VTDEGQLMNVNADQAATALAAT T0347 79 :GV 1gs5A 173 :GA T0347 84 :LTSEVAKFS 1gs5A 175 :DLILLSDVS T0347 110 :YPFDAQGLRRQ 1gs5A 184 :GILDGKGQRIA T0347 137 :RSLAGALRMAGGYAK 1gs5A 198 :AAKAEQLIEQGIITD T0347 157 :SEFGWADFLRRR 1gs5A 216 :VKVNAALDAART Number of specific fragments extracted= 7 number of extra gaps= 0 total=219 Number of alignments=32 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f9sA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2f9sA expands to /projects/compbio/data/pdb/2f9s.pdb.gz 2f9sA:Skipped atom 182, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 184, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 186, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 188, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 190, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 201, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 203, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 205, because occupancy 0.000 <= existing 0.000 in 2f9sA Skipped atom 207, because occupancy 0.000 <= existing 0.000 in 2f9sA Skipped atom 284, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 288, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 290, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 292, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 294, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 296, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 298, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 300, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 302, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 304, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 306, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 312, because occupancy 0.300 <= existing 0.700 in 2f9sA Skipped atom 314, because occupancy 0.300 <= existing 0.700 in 2f9sA Skipped atom 320, because occupancy 0.000 <= existing 1.000 in 2f9sA Skipped atom 322, because occupancy 0.000 <= existing 1.000 in 2f9sA Skipped atom 324, because occupancy 0.000 <= existing 1.000 in 2f9sA Skipped atom 326, because occupancy 0.000 <= existing 1.000 in 2f9sA Skipped atom 328, because occupancy 0.000 <= existing 1.000 in 2f9sA Skipped atom 357, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 359, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 361, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 363, because occupancy 0.500 <= existing 0.500 in 2f9sA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 424, because occupancy 0.200 <= existing 0.800 in 2f9sA Skipped atom 426, because occupancy 0.200 <= existing 0.800 in 2f9sA Skipped atom 428, because occupancy 0.200 <= existing 0.800 in 2f9sA Skipped atom 430, because occupancy 0.200 <= existing 0.800 in 2f9sA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 749, because occupancy 0.400 <= existing 0.600 in 2f9sA Skipped atom 751, because occupancy 0.400 <= existing 0.600 in 2f9sA Skipped atom 753, because occupancy 0.400 <= existing 0.600 in 2f9sA Skipped atom 755, because occupancy 0.400 <= existing 0.600 in 2f9sA Skipped atom 770, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 772, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 778, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 780, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 782, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 784, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 865, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 867, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 951, because occupancy 0.000 <= existing 1.000 in 2f9sA Skipped atom 953, because occupancy 0.000 <= existing 1.000 in 2f9sA Skipped atom 955, because occupancy 0.000 <= existing 1.000 in 2f9sA Skipped atom 957, because occupancy 0.000 <= existing 1.000 in 2f9sA Skipped atom 959, because occupancy 0.000 <= existing 1.000 in 2f9sA Skipped atom 970, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 972, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 974, because occupancy 0.000 <= existing 0.000 in 2f9sA Skipped atom 976, because occupancy 0.000 <= existing 0.000 in 2f9sA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1038, because occupancy 0.000 <= existing 1.000 in 2f9sA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1040, because occupancy 0.000 <= existing 1.000 in 2f9sA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1042, because occupancy 0.000 <= existing 1.000 in 2f9sA Skipped atom 1064, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 1066, because occupancy 0.500 <= existing 0.500 in 2f9sA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1119, because occupancy 0.000 <= existing 1.000 in 2f9sA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1121, because occupancy 0.000 <= existing 1.000 in 2f9sA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1123, because occupancy 0.000 <= existing 1.000 in 2f9sA # T0347 read from 2f9sA/merged-good-all-a2m # 2f9sA read from 2f9sA/merged-good-all-a2m # adding 2f9sA to template set # found chain 2f9sA in template set T0347 8 :RLSRIAIDKLRPTQIAV 2f9sA 51 :NGKRIELSDLKGKGVFL T0347 26 :FREVELKRKEWRE 2f9sA 78 :KKEFPYMANQYKH T0347 39 :TRKKDGDDFLG 2f9sA 105 :ESKIAVHNFMK T0347 50 :NHIVPVVAGPKD 2f9sA 118 :GVNFPVVLDTDR T0347 74 :ALSKEGVEHVLTSEV 2f9sA 131 :VLDAYDVSPLPTTFL T0347 89 :AK 2f9sA 153 :VK T0347 91 :FSHLGKDEFWSVMD 2f9sA 157 :TGTMTESMIHDYMN Number of specific fragments extracted= 7 number of extra gaps= 0 total=226 Number of alignments=33 # 2f9sA read from 2f9sA/merged-good-all-a2m # found chain 2f9sA in template set T0347 8 :RLSRIAIDKLRPTQIAV 2f9sA 51 :NGKRIELSDLKGKGVFL T0347 26 :FREVELKRKEWRE 2f9sA 78 :KKEFPYMANQYKH T0347 40 :RKKDGDDFLG 2f9sA 106 :SKIAVHNFMK T0347 50 :NHIVPVVAGPKD 2f9sA 118 :GVNFPVVLDTDR T0347 75 :LSKE 2f9sA 131 :VLDA T0347 79 :GVE 2f9sA 136 :DVS T0347 82 :HVLTSEV 2f9sA 140 :LPTTFLI T0347 89 :AKFSHLGKDEFWSVMD 2f9sA 155 :VVTGTMTESMIHDYMN Number of specific fragments extracted= 8 number of extra gaps= 0 total=234 Number of alignments=34 # 2f9sA read from 2f9sA/merged-good-all-a2m # found chain 2f9sA in template set T0347 7 :PRLSRIAIDKLRP 2f9sA 50 :TNGKRIELSDLKG T0347 21 :QIAVGFREVELKRKEWR 2f9sA 76 :PCKKEFPYMANQYKHFK T0347 38 :ETRKKDGDDFLG 2f9sA 104 :GESKIAVHNFMK T0347 50 :NHIVPVVAGPKD 2f9sA 118 :GVNFPVVLDTDR T0347 73 :LALSKEGVEHVLTSEV 2f9sA 130 :QVLDAYDVSPLPTTFL T0347 89 :AKF 2f9sA 153 :VKV T0347 92 :SHLGKDEFWSVMD 2f9sA 158 :GTMTESMIHDYMN Number of specific fragments extracted= 7 number of extra gaps= 0 total=241 Number of alignments=35 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wd5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wd5A expands to /projects/compbio/data/pdb/1wd5.pdb.gz 1wd5A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0347 read from 1wd5A/merged-good-all-a2m # 1wd5A read from 1wd5A/merged-good-all-a2m # adding 1wd5A to template set # found chain 1wd5A in template set T0347 28 :EVELKRKEWRETRKKDGDDFLGNHIVP 1wd5A 90 :YLEREAARQRDVLRKRAERYRRVRPKA T0347 58 :GPKDRAYLIDH 1wd5A 118 :RKGRDVVLVDD T0347 69 :HHLVLALSKEGVEHVLTSEV 1wd5A 137 :EAALSVVFQEGPRRVVVAVP T0347 96 :KDEFWSVMDHRNLIYPFDAQGLRRQSGDIPKNIHDLEDDPFRSLA 1wd5A 159 :SPEAVERLKARAEVVALSVPQDFAAVGAYYLDFGEVTDEDVEAIL Number of specific fragments extracted= 4 number of extra gaps= 0 total=245 Number of alignments=36 # 1wd5A read from 1wd5A/merged-good-all-a2m # found chain 1wd5A in template set T0347 28 :EVELKRKEWRETRKKDGDDFLGNHIVP 1wd5A 90 :YLEREAARQRDVLRKRAERYRRVRPKA T0347 57 :AGPKDRAYLIDH 1wd5A 117 :ARKGRDVVLVDD T0347 70 :HLVLALSKEGVEHVLTSEV 1wd5A 138 :AALSVVFQEGPRRVVVAVP T0347 96 :KDEFWSVMDHRNLIYPFD 1wd5A 159 :SPEAVERLKARAEVVALS T0347 124 :IPKNIHDLE 1wd5A 177 :VPQDFAAVG Number of specific fragments extracted= 5 number of extra gaps= 0 total=250 Number of alignments=37 # 1wd5A read from 1wd5A/merged-good-all-a2m # found chain 1wd5A in template set T0347 27 :REVELKRKEWRETRKKDGDDFLGNHIVP 1wd5A 89 :SYLEREAARQRDVLRKRAERYRRVRPKA T0347 57 :AGPKDRAYLIDHH 1wd5A 117 :ARKGRDVVLVDDG T0347 70 :HLVLALSKEGVEHVLTSEV 1wd5A 138 :AALSVVFQEGPRRVVVAVP T0347 96 :KDEFWSVMDHRNLIYPF 1wd5A 159 :SPEAVERLKARAEVVAL T0347 113 :DAQ 1wd5A 178 :PQD T0347 118 :RRQSGDIPKNIHDLED 1wd5A 181 :FAAVGAYYLDFGEVTD Number of specific fragments extracted= 6 number of extra gaps= 0 total=256 Number of alignments=38 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vk1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0347 read from 1vk1A/merged-good-all-a2m # 1vk1A read from 1vk1A/merged-good-all-a2m # found chain 1vk1A in training set Warning: unaligning (T0347)L17 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vk1A)P28 Warning: unaligning (T0347)P19 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vk1A)P28 Warning: unaligning (T0347)D97 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vk1A)V113 Warning: unaligning (T0347)F99 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vk1A)V113 Warning: unaligning (T0347)A142 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vk1A)A134 Warning: unaligning (T0347)R144 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vk1A)A134 Warning: unaligning (T0347)M145 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vk1A)G137 Warning: unaligning (T0347)G147 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vk1A)G137 Warning: unaligning (T0347)E158 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vk1A)K160 Warning: unaligning (T0347)F159 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vk1A)K160 Warning: unaligning (T0347)R171 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vk1A)E173 T0347 5 :YEPRLSRIAIDK 1vk1A 14 :KKVEYVFIELDK T0347 20 :TQIAV 1vk1A 29 :HEQLV T0347 26 :FREVELKRKEWRETR 1vk1A 34 :QRELEDFIESVTGSG T0347 50 :NHIVPVVAGPK 1vk1A 51 :WKPMLLAKIPG T0347 61 :DRAYLIDHHHLVLALSKEGVEHVLTSEV 1vk1A 63 :DEYLIVDGHHRWAGLQKLGAKRAPSVIL T0347 95 :GK 1vk1A 109 :DV T0347 100 :WSVMDHRNLIYPFDAQ 1vk1A 114 :IERLKAEGLEVIEDEK T0347 140 :AG 1vk1A 130 :AE T0347 148 :GY 1vk1A 138 :EI T0347 150 :AKV 1vk1A 146 :EKS T0347 157 :S 1vk1A 157 :E T0347 161 :WADFLRRRID 1vk1A 161 :VSKVLDEMDQ Number of specific fragments extracted= 12 number of extra gaps= 1 total=268 Number of alignments=39 # 1vk1A read from 1vk1A/merged-good-all-a2m # found chain 1vk1A in training set Warning: unaligning (T0347)L17 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vk1A)P28 Warning: unaligning (T0347)P19 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vk1A)P28 Warning: unaligning (T0347)D97 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vk1A)V113 Warning: unaligning (T0347)F99 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vk1A)V113 Warning: unaligning (T0347)A142 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vk1A)A134 Warning: unaligning (T0347)R144 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vk1A)A134 Warning: unaligning (T0347)M145 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vk1A)G137 Warning: unaligning (T0347)G147 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vk1A)G137 T0347 3 :HIYEPRLSRIAIDK 1vk1A 12 :PVKKVEYVFIELDK T0347 20 :TQIAV 1vk1A 29 :HEQLV T0347 26 :FREVELKRKEWRETR 1vk1A 34 :QRELEDFIESVTGSG T0347 50 :NHIVPVVAGPK 1vk1A 51 :WKPMLLAKIPG T0347 61 :DRAYLIDHHHLVLALSKEGVEHVLTSEV 1vk1A 63 :DEYLIVDGHHRWAGLQKLGAKRAPSVIL T0347 90 :KFS 1vk1A 98 :KVY T0347 95 :GK 1vk1A 109 :DV T0347 100 :WSVMDHRNLIYPFDAQ 1vk1A 114 :IERLKAEGLEVIEDEK T0347 140 :AG 1vk1A 130 :AE T0347 148 :GY 1vk1A 138 :EI Number of specific fragments extracted= 10 number of extra gaps= 0 total=278 Number of alignments=40 # 1vk1A read from 1vk1A/merged-good-all-a2m # found chain 1vk1A in training set Warning: unaligning (T0347)L17 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vk1A)P28 Warning: unaligning (T0347)P19 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vk1A)P28 Warning: unaligning (T0347)D97 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vk1A)V113 Warning: unaligning (T0347)F99 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vk1A)V113 Warning: unaligning (T0347)A142 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vk1A)A134 Warning: unaligning (T0347)R144 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vk1A)A134 Warning: unaligning (T0347)M145 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vk1A)G137 Warning: unaligning (T0347)G147 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vk1A)G137 Warning: unaligning (T0347)E158 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vk1A)K160 Warning: unaligning (T0347)F159 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vk1A)K160 Warning: unaligning (T0347)R171 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vk1A)E173 T0347 5 :YEPRLSRIAIDK 1vk1A 14 :KKVEYVFIELDK T0347 20 :TQI 1vk1A 29 :HEQ T0347 24 :VGFREVELKRKEWRETR 1vk1A 32 :LVQRELEDFIESVTGSG T0347 50 :NHIVPVVAGPK 1vk1A 51 :WKPMLLAKIPG T0347 61 :DRAYLIDHHHLVLALSKEGVEHVLTSEV 1vk1A 63 :DEYLIVDGHHRWAGLQKLGAKRAPSVIL T0347 89 :AKFSHL 1vk1A 97 :VKVYTW T0347 95 :GK 1vk1A 109 :DV T0347 100 :WSVMDHRNLIYPFDAQ 1vk1A 114 :IERLKAEGLEVIEDEK T0347 140 :AG 1vk1A 130 :AE T0347 148 :GYA 1vk1A 138 :EIA T0347 151 :K 1vk1A 147 :K T0347 152 :VIIPFS 1vk1A 152 :PGGLEE T0347 161 :WADFLRRRID 1vk1A 161 :VSKVLDEMDQ Number of specific fragments extracted= 13 number of extra gaps= 1 total=291 Number of alignments=41 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3csuA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 3csuA expands to /projects/compbio/data/pdb/3csu.pdb.gz 3csuA:# T0347 read from 3csuA/merged-good-all-a2m # 3csuA read from 3csuA/merged-good-all-a2m # adding 3csuA to template set # found chain 3csuA in template set T0347 49 :GNHIVPVVAGPKDR 3csuA 153 :DNLHVAMVGDLKYG T0347 68 :HHHLVLALSK 3csuA 169 :VHSLTQALAK T0347 80 :VEHVLTSEVAKFSHLGKDEFWSVMDHRNLIY 3csuA 179 :FDGNRFYFIAPDALAMPQYILDMLDEKGIAW T0347 123 :DIPKNIHDL 3csuA 210 :SLHSSIEEV Number of specific fragments extracted= 4 number of extra gaps= 0 total=295 Number of alignments=42 # 3csuA read from 3csuA/merged-good-all-a2m # found chain 3csuA in template set T0347 12 :IAIDKLR 3csuA 10 :ISINDLS T0347 26 :FREVELKRKEWRETRKKDGDDFL 3csuA 17 :RDDLNLVLATAAKLKANPQPELL T0347 49 :GNHIVPVVAGPKDR 3csuA 153 :DNLHVAMVGDLKYG T0347 68 :HHHLVLALS 3csuA 169 :VHSLTQALA T0347 79 :GVEHVLTSEVAKFSHLGKDEFWSV 3csuA 178 :KFDGNRFYFIAPDALAMPQYILDM T0347 143 :LRMAGGYAKVIIPFSE 3csuA 202 :LDEKGIAWSLHSSIEE Number of specific fragments extracted= 6 number of extra gaps= 0 total=301 Number of alignments=43 # 3csuA read from 3csuA/merged-good-all-a2m # found chain 3csuA in template set T0347 41 :KKDGDDFLGNHIVPVVAGPKDR 3csuA 112 :ARLATEFSGNVPVLNAGDGSNQ T0347 63 :AYLIDH 3csuA 157 :VAMVGD T0347 69 :HHLVLALSK 3csuA 170 :HSLTQALAK T0347 80 :VEHVLTSEVAKFSHLGKDEFWSVMDHRNLIYPFDA 3csuA 179 :FDGNRFYFIAPDALAMPQYILDMLDEKGIAWSLHS T0347 120 :QSGDIPKNI 3csuA 214 :SIEEVMAEV Number of specific fragments extracted= 5 number of extra gaps= 0 total=306 Number of alignments=44 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xw4X/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xw4X expands to /projects/compbio/data/pdb/1xw4.pdb.gz 1xw4X:# T0347 read from 1xw4X/merged-good-all-a2m # 1xw4X read from 1xw4X/merged-good-all-a2m # adding 1xw4X to template set # found chain 1xw4X in template set Warning: unaligning (T0347)H68 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xw4X)H100 Warning: unaligning (T0347)H70 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xw4X)H100 T0347 1 :MTHIYEPRLSRIAIDKL 1xw4X 33 :IHSGRIAAVHNVPLSVL T0347 18 :RPTQIAVGFREVELKRKEWRETRKK 1xw4X 51 :RPLPSVLDPAKVQSLVDTIREDPDS T0347 51 :HIVP 1xw4X 77 :PPID T0347 55 :VVAGPKDRAYLID 1xw4X 83 :WIKGAQGGDYFYS T0347 71 :LVLALSKEGVEHVLTSEVAK 1xw4X 101 :RYAAYQQLQRETIPAKLVQS Number of specific fragments extracted= 5 number of extra gaps= 0 total=311 Number of alignments=45 # 1xw4X read from 1xw4X/merged-good-all-a2m # found chain 1xw4X in template set Warning: unaligning (T0347)H68 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xw4X)H100 Warning: unaligning (T0347)H70 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xw4X)H100 T0347 1 :MTHIYEPRLSRIAIDKL 1xw4X 33 :IHSGRIAAVHNVPLSVL T0347 18 :RPTQIAVGFREVELKRKEWRETR 1xw4X 51 :RPLPSVLDPAKVQSLVDTIREDP T0347 46 :DFLGNHIVPVVAGPKDRAYLID 1xw4X 74 :DSVPPIDVLWIKGAQGGDYFYS T0347 71 :LVLALSKEGVEHVLTSEVAKF 1xw4X 101 :RYAAYQQLQRETIPAKLVQST Number of specific fragments extracted= 4 number of extra gaps= 0 total=315 Number of alignments=46 # 1xw4X read from 1xw4X/merged-good-all-a2m # found chain 1xw4X in template set Warning: unaligning (T0347)H68 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xw4X)H100 Warning: unaligning (T0347)H70 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xw4X)H100 T0347 1 :MTHIYEPRLSRIAIDKL 1xw4X 33 :IHSGRIAAVHNVPLSVL T0347 22 :IAVGFREVELKRKEWRETRKK 1xw4X 55 :SVLDPAKVQSLVDTIREDPDS T0347 53 :V 1xw4X 76 :V T0347 54 :PVVAGPKDRAYLID 1xw4X 82 :LWIKGAQGGDYFYS T0347 71 :LVLALSKEGVEHVLTSEVAK 1xw4X 101 :RYAAYQQLQRETIPAKLVQS T0347 95 :GKDEFWSVM 1xw4X 121 :TLSDLRVYL Number of specific fragments extracted= 6 number of extra gaps= 0 total=321 Number of alignments=47 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u5tC/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1u5tC expands to /projects/compbio/data/pdb/1u5t.pdb.gz 1u5tC:# T0347 read from 1u5tC/merged-good-all-a2m # 1u5tC read from 1u5tC/merged-good-all-a2m # adding 1u5tC to template set # found chain 1u5tC in template set Warning: unaligning (T0347)R62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u5tC)S72 Warning: unaligning (T0347)K90 because of BadResidue code BAD_PEPTIDE in next template residue (1u5tC)Q82 Warning: unaligning (T0347)F91 because of BadResidue code BAD_PEPTIDE at template residue (1u5tC)Q82 T0347 32 :KRKEWRETRKKDGDDFLGNHIVPVV 1u5tC 22 :TRRQQISTWIDIISQYCKTKKIWYM T0347 58 :GPKD 1u5tC 47 :SVDG T0347 84 :LTSEVA 1u5tC 75 :LFNNED T0347 92 :SHLGK 1u5tC 83 :RSVSQ T0347 97 :DEFWSVMDHRNLIYPFDAQGLRRQSGD 1u5tC 91 :DEIWSQMTKEGKCLPIDQSGRRSSNTT T0347 133 :DDPFRSLAGALR 1u5tC 125 :WKSLDSWASLIL T0347 145 :MAGGYAKVI 1u5tC 141 :DSGKLNQVI Number of specific fragments extracted= 7 number of extra gaps= 1 total=328 Number of alignments=48 # 1u5tC read from 1u5tC/merged-good-all-a2m # found chain 1u5tC in template set Warning: unaligning (T0347)R62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u5tC)S72 Warning: unaligning (T0347)H93 because of BadResidue code BAD_PEPTIDE in next template residue (1u5tC)Q82 Warning: unaligning (T0347)L94 because of BadResidue code BAD_PEPTIDE at template residue (1u5tC)Q82 T0347 31 :LKRKEWRETRKKDGDDFLGNHIVPVV 1u5tC 21 :LTRRQQISTWIDIISQYCKTKKIWYM T0347 58 :GPKD 1u5tC 47 :SVDG T0347 89 :AKFS 1u5tC 77 :NNED T0347 95 :G 1u5tC 83 :R T0347 97 :DEFWSVMDHRNLIYPFDAQGLRRQSGDI 1u5tC 91 :DEIWSQMTKEGKCLPIDQSGRRSSNTTT T0347 131 :LEDDPFRSLAGALR 1u5tC 123 :ILWKSLDSWASLIL T0347 145 :MAGGYAKVII 1u5tC 141 :DSGKLNQVIT Number of specific fragments extracted= 7 number of extra gaps= 1 total=335 Number of alignments=49 # 1u5tC read from 1u5tC/merged-good-all-a2m # found chain 1u5tC in template set Warning: unaligning (T0347)R62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u5tC)S72 T0347 32 :KRKEWRETRKKDGDDFLGNHIVPVVAG 1u5tC 22 :TRRQQISTWIDIISQYCKTKKIWYMSV T0347 60 :KD 1u5tC 49 :DG T0347 92 :SHLGK 1u5tC 83 :RSVSQ T0347 97 :DEFWSVMDHRNLIYPFDAQGLRRQSGDI 1u5tC 91 :DEIWSQMTKEGKCLPIDQSGRRSSNTTT T0347 175 :SD 1u5tC 119 :TR T0347 177 :SFDDALAEAMKLAK 1u5tC 127 :SLDSWASLILQWFE Number of specific fragments extracted= 6 number of extra gaps= 0 total=341 Number of alignments=50 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1st9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0347 read from 1st9A/merged-good-all-a2m # 1st9A read from 1st9A/merged-good-all-a2m # found chain 1st9A in training set T0347 8 :RLSRIAIDKLRPTQIAV 1st9A 50 :NGKRIELSDLKGKGVFL T0347 26 :FREVELKRKEWRE 1st9A 77 :KKEFPYMANQYKH T0347 39 :TRKKDGDDFLG 1st9A 104 :ESKIAVHNFMK T0347 50 :NHIVPVVAGPKD 1st9A 117 :GVNFPVVLDTDR T0347 74 :ALSKEGVEHVLTSEV 1st9A 130 :VLDAYDVSPLPTTFL T0347 89 :AK 1st9A 152 :VK T0347 91 :FSHLGKDEFWSVMD 1st9A 156 :TGTMTESMIHDYMN Number of specific fragments extracted= 7 number of extra gaps= 0 total=348 Number of alignments=51 # 1st9A read from 1st9A/merged-good-all-a2m # found chain 1st9A in training set Warning: unaligning (T0347)Y5 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1st9A)D48 Warning: unaligning (T0347)E6 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1st9A)D48 T0347 7 :PRLSRIAIDKLRPTQIAV 1st9A 49 :TNGKRIELSDLKGKGVFL T0347 26 :FREVELKRKEWRE 1st9A 77 :KKEFPYMANQYKH T0347 40 :RKKDGDDFL 1st9A 105 :SKIAVHNFM T0347 50 :NHIVPVVAGPKD 1st9A 117 :GVNFPVVLDTDR T0347 75 :LSKE 1st9A 130 :VLDA T0347 79 :GVE 1st9A 135 :DVS T0347 82 :HVLTSEV 1st9A 139 :LPTTFLI T0347 89 :AKFSHLGKDEFWSVMD 1st9A 154 :VVTGTMTESMIHDYMN Number of specific fragments extracted= 8 number of extra gaps= 1 total=356 Number of alignments=52 # 1st9A read from 1st9A/merged-good-all-a2m # found chain 1st9A in training set T0347 8 :RLSRIAIDKLRP 1st9A 50 :NGKRIELSDLKG T0347 21 :QIAVGFREVELKRKEWR 1st9A 75 :PCKKEFPYMANQYKHFK T0347 38 :ETRKKDGDDFLGNH 1st9A 103 :GESKIAVHNFMKSY T0347 52 :IVPVVAGPKD 1st9A 119 :NFPVVLDTDR T0347 73 :LALSKEGVEHVLTSEV 1st9A 129 :QVLDAYDVSPLPTTFL T0347 89 :AKF 1st9A 152 :VKV T0347 92 :SHLGKDEFWSVMD 1st9A 157 :GTMTESMIHDYMN Number of specific fragments extracted= 7 number of extra gaps= 0 total=363 Number of alignments=53 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b4pA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0347 read from 1b4pA/merged-good-all-a2m # 1b4pA read from 1b4pA/merged-good-all-a2m # found chain 1b4pA in training set Warning: unaligning (T0347)D134 because of BadResidue code BAD_PEPTIDE at template residue (1b4pA)Q71 Warning: unaligning (T0347)L139 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1b4pA)R77 Warning: unaligning (T0347)A140 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1b4pA)R77 Warning: unaligning (T0347)I169 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1b4pA)M104 Warning: unaligning (T0347)D179 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1b4pA)M104 T0347 70 :HLVLALSKE 1b4pA 14 :HPIRLLLEY T0347 79 :GVE 1b4pA 24 :DSS T0347 82 :HVLTSEVAKFSHLGKDEFWSVMDHRNL 1b4pA 28 :EEKRYAMGDAPDYDRSQWLNEKFKLGL T0347 109 :IYPFDAQ 1b4pA 60 :PYLIDGS T0347 135 :PFRS 1b4pA 72 :SNAI T0347 141 :GALRMAGGYAKV 1b4pA 78 :YLARKHHLCGET T0347 158 :EFGWADFLRRR 1b4pA 92 :ERIRVDVLENQ T0347 180 :DALAEAMKLAKSREA 1b4pA 105 :DTRLQLAMVCYSPDF Number of specific fragments extracted= 8 number of extra gaps= 3 total=371 Number of alignments=54 # 1b4pA read from 1b4pA/merged-good-all-a2m # found chain 1b4pA in training set Warning: unaligning (T0347)Q120 because of BadResidue code BAD_PEPTIDE in next template residue (1b4pA)Q71 Warning: unaligning (T0347)P135 because of BadResidue code BAD_PEPTIDE at template residue (1b4pA)Q71 Warning: unaligning (T0347)A140 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1b4pA)R77 Warning: unaligning (T0347)G141 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1b4pA)R77 Warning: unaligning (T0347)I169 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1b4pA)M104 Warning: unaligning (T0347)D179 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1b4pA)M104 T0347 69 :HHLVLALSKE 1b4pA 13 :THPIRLLLEY T0347 79 :GVE 1b4pA 24 :DSS T0347 82 :HVLTSEVAKFSHLGKDEFWSVMDHRNL 1b4pA 28 :EEKRYAMGDAPDYDRSQWLNEKFKLGL T0347 109 :IYPFDAQ 1b4pA 60 :PYLIDGS T0347 117 :LRR 1b4pA 67 :RKI T0347 136 :FRSL 1b4pA 72 :SNAI T0347 142 :ALRMAGGY 1b4pA 78 :YLARKHHL T0347 150 :AKV 1b4pA 87 :GET T0347 157 :SEFGWADFLRRR 1b4pA 91 :EERIRVDVLENQ T0347 180 :DALAEAMKLAKSRE 1b4pA 105 :DTRLQLAMVCYSPD Number of specific fragments extracted= 10 number of extra gaps= 3 total=381 Number of alignments=55 # 1b4pA read from 1b4pA/merged-good-all-a2m # found chain 1b4pA in training set Warning: unaligning (T0347)Q120 because of BadResidue code BAD_PEPTIDE in next template residue (1b4pA)Q71 Warning: unaligning (T0347)D134 because of BadResidue code BAD_PEPTIDE at template residue (1b4pA)Q71 Warning: unaligning (T0347)L139 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1b4pA)R77 Warning: unaligning (T0347)A140 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1b4pA)R77 Warning: unaligning (T0347)I169 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1b4pA)M104 Warning: unaligning (T0347)D179 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1b4pA)M104 T0347 69 :HHLVLALSKEGVE 1b4pA 14 :HPIRLLLEYTDSS T0347 82 :HVLTSEVAKFSHLGKDEFWSVMDH 1b4pA 28 :EEKRYAMGDAPDYDRSQWLNEKFK T0347 106 :RNLIYPFDAQ 1b4pA 57 :PNLPYLIDGS T0347 117 :LRR 1b4pA 67 :RKI T0347 135 :PFRS 1b4pA 72 :SNAI T0347 141 :GALRMAGGYAKV 1b4pA 78 :YLARKHHLCGET T0347 158 :EFGWADFLRRR 1b4pA 92 :ERIRVDVLENQ T0347 180 :DALAEAMKLAKSREARH 1b4pA 105 :DTRLQLAMVCYSPDFER Number of specific fragments extracted= 8 number of extra gaps= 3 total=389 Number of alignments=56 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1p3dA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0347 read from 1p3dA/merged-good-all-a2m # 1p3dA read from 1p3dA/merged-good-all-a2m # found chain 1p3dA in training set T0347 5 :YEPRLSRIAID 1p3dA 276 :PNNERINVLLN T0347 24 :VGFREVELK 1p3dA 288 :PGKHNALNA T0347 38 :ETRKKDGDDFL 1p3dA 307 :GIANEAILEAL T0347 56 :VAGPKDRAYLID 1p3dA 333 :FIRPNGKVRLVD T0347 68 :HHH 1p3dA 347 :GHH T0347 72 :VLALSKEGVEHVLTSEV 1p3dA 357 :IKAAREGWGDKRIVMIF T0347 97 :DEFWSVMDHRNLI 1p3dA 386 :DDFVQVLSQVDAL T0347 110 :YPFDAQGLRR 1p3dA 402 :DVYAAGEAPI T0347 132 :EDDPFRSLAGALRMAGGY 1p3dA 412 :VGADSKSLCRSIRNLGKV T0347 151 :KVIIPFSEFGWADFLRRRIDRD 1p3dA 430 :DPILVSDTSQLGDVLDQIIQDG Number of specific fragments extracted= 10 number of extra gaps= 0 total=399 Number of alignments=57 # 1p3dA read from 1p3dA/merged-good-all-a2m # found chain 1p3dA in training set T0347 5 :YEPRLSRIAID 1p3dA 276 :PNNERINVLLN T0347 23 :AVGFREVELK 1p3dA 287 :VPGKHNALNA T0347 38 :ETRKKDGDDFL 1p3dA 307 :GIANEAILEAL T0347 58 :GPKDRAYLID 1p3dA 335 :RPNGKVRLVD T0347 68 :HHH 1p3dA 347 :GHH T0347 71 :LVLALSKEGVEHVLTSEV 1p3dA 356 :TIKAAREGWGDKRIVMIF T0347 96 :KDEFWSVMDHRNL 1p3dA 385 :FDDFVQVLSQVDA T0347 109 :IYPFDAQGLRR 1p3dA 401 :LDVYAAGEAPI T0347 132 :EDDPFRSLAGALRMAGGYAKVII 1p3dA 412 :VGADSKSLCRSIRNLGKVDPILV T0347 156 :FSEFGWADFLRRRIDRD 1p3dA 435 :SDTSQLGDVLDQIIQDG Number of specific fragments extracted= 10 number of extra gaps= 0 total=409 Number of alignments=58 # 1p3dA read from 1p3dA/merged-good-all-a2m # found chain 1p3dA in training set T0347 40 :RKKDGDDFLGNHIV 1p3dA 309 :ANEAILEALADFQG T0347 60 :KDRAYLIDHHHLVLALSKE 1p3dA 366 :DKRIVMIFQPHRYSRTRDL T0347 96 :KDEFWSVMDHRNLIY 1p3dA 385 :FDDFVQVLSQVDALI T0347 111 :PFDAQGLR 1p3dA 403 :VYAAGEAP T0347 131 :LEDDPFRSLAGALRMAGGYAK 1p3dA 411 :IVGADSKSLCRSIRNLGKVDP T0347 152 :V 1p3dA 436 :D T0347 158 :EFGWADFLRRRIDRD 1p3dA 437 :TSQLGDVLDQIIQDG Number of specific fragments extracted= 7 number of extra gaps= 0 total=416 Number of alignments=59 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ekxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ekxA expands to /projects/compbio/data/pdb/1ekx.pdb.gz 1ekxA:# T0347 read from 1ekxA/merged-good-all-a2m # 1ekxA read from 1ekxA/merged-good-all-a2m # adding 1ekxA to template set # found chain 1ekxA in template set T0347 12 :IAIDKLR 1ekxA 10 :ISINDLS T0347 26 :FREVELKRKEWRETRKKDGDDFL 1ekxA 17 :RDDLNLVLATAAKLKANPQPELL T0347 49 :GNHIVPVVAGPKDR 1ekxA 153 :DNLHVAMVGDLKYG T0347 68 :HHHLVLALSKEGVEHVLTS 1ekxA 169 :VHSLTQALAKFDGNRFYFI T0347 88 :VAK 1ekxA 188 :APD T0347 92 :SHLGKDEFWSVMDHRNLIYPF 1ekxA 191 :ALAMPQYILDMLDEKGIAWSL T0347 121 :SGDIPKNIHDL 1ekxA 212 :HSSIEEVMAEV Number of specific fragments extracted= 7 number of extra gaps= 0 total=423 Number of alignments=60 # 1ekxA read from 1ekxA/merged-good-all-a2m # found chain 1ekxA in template set T0347 12 :IAIDKLR 1ekxA 10 :ISINDLS T0347 26 :FREVELKRKEWRETRKKDGDDFL 1ekxA 17 :RDDLNLVLATAAKLKANPQPELL T0347 49 :GNHIVPVVAGPKDR 1ekxA 153 :DNLHVAMVGDLKYG T0347 69 :HHLVLAL 1ekxA 170 :HSLTQAL T0347 78 :EGVEHVLTSEVAKFSHLGKDEFWSVMDHRNLIYPF 1ekxA 177 :AKFDGNRFYFIAPDALAMPQYILDMLDEKGIAWSL T0347 121 :SGDIPKNIHDLE 1ekxA 212 :HSSIEEVMAEVD T0347 154 :IP 1ekxA 228 :TR T0347 166 :RRRIDRDLLSD 1ekxA 232 :KERLDPSEYAN T0347 177 :SF 1ekxA 246 :QF T0347 189 :AKSREARHLPG 1ekxA 249 :LRASDLHNAKA Number of specific fragments extracted= 10 number of extra gaps= 0 total=433 Number of alignments=61 # 1ekxA read from 1ekxA/merged-good-all-a2m # found chain 1ekxA in template set T0347 12 :IAIDKLRPTQIAVGFREVELKRKEWRE 1ekxA 10 :ISINDLSRDDLNLVLATAAKLKANPQP T0347 46 :DFLGNHIV 1ekxA 37 :ELLKHKVI T0347 59 :PKDRAYLIDH 1ekxA 153 :DNLHVAMVGD T0347 69 :HHLVLALSK 1ekxA 170 :HSLTQALAK T0347 80 :VEHVLTSEVAKFSHLGKDEFWSVMDHRNLIYPFDAQG 1ekxA 179 :FDGNRFYFIAPDALAMPQYILDMLDEKGIAWSLHSSI T0347 117 :LRRQSGDIPKNIHD 1ekxA 228 :TRVQKERLDPSEYA Number of specific fragments extracted= 6 number of extra gaps= 0 total=439 Number of alignments=62 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xw3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xw3A expands to /projects/compbio/data/pdb/1xw3.pdb.gz 1xw3A:Skipped atom 133, because occupancy 0.500 <= existing 0.500 in 1xw3A Skipped atom 135, because occupancy 0.500 <= existing 0.500 in 1xw3A Skipped atom 137, because occupancy 0.500 <= existing 0.500 in 1xw3A Skipped atom 139, because occupancy 0.500 <= existing 0.500 in 1xw3A Skipped atom 141, because occupancy 0.500 <= existing 0.500 in 1xw3A Skipped atom 143, because occupancy 0.500 <= existing 0.500 in 1xw3A Skipped atom 145, because occupancy 0.500 <= existing 0.500 in 1xw3A Skipped atom 147, because occupancy 0.500 <= existing 0.500 in 1xw3A Skipped atom 766, because occupancy 0.500 <= existing 0.500 in 1xw3A Skipped atom 768, because occupancy 0.500 <= existing 0.500 in 1xw3A Skipped atom 770, because occupancy 0.500 <= existing 0.500 in 1xw3A Skipped atom 772, because occupancy 0.500 <= existing 0.500 in 1xw3A Skipped atom 774, because occupancy 0.500 <= existing 0.500 in 1xw3A Skipped atom 776, because occupancy 0.500 <= existing 0.500 in 1xw3A Skipped atom 778, because occupancy 0.500 <= existing 0.500 in 1xw3A Skipped atom 780, because occupancy 0.500 <= existing 0.500 in 1xw3A Skipped atom 782, because occupancy 0.500 <= existing 0.500 in 1xw3A Skipped atom 784, because occupancy 0.500 <= existing 0.500 in 1xw3A Skipped atom 786, because occupancy 0.500 <= existing 0.500 in 1xw3A # T0347 read from 1xw3A/merged-good-all-a2m # 1xw3A read from 1xw3A/merged-good-all-a2m # adding 1xw3A to template set # found chain 1xw3A in template set T0347 1 :MTHIYEPRLSRIAIDKL 1xw3A 33 :IHSGRIAAVHNVPLSVL T0347 18 :RPTQIAVGFREVELKRKEWRETRKK 1xw3A 51 :RPLPSVLDPAKVQSLVDTIREDPDS T0347 48 :LGNHIVPVVAGPKDRAYLID 1xw3A 76 :VPPIDVLWIKGAQGGDYFYS T0347 68 :HHHLVLALSKEGVEHVLTSEVA 1xw3A 98 :GCHRYAAYQQLQRETIPAKLVQ T0347 94 :LGKDEFWSVM 1xw3A 120 :STLSDLRVYL Number of specific fragments extracted= 5 number of extra gaps= 0 total=444 Number of alignments=63 # 1xw3A read from 1xw3A/merged-good-all-a2m # found chain 1xw3A in template set T0347 1 :MTHIYEPRLSRIAIDKL 1xw3A 33 :IHSGRIAAVHNVPLSVL T0347 18 :RPTQIAVGFREVELKRKEWRET 1xw3A 51 :RPLPSVLDPAKVQSLVDTIRED T0347 45 :DDFLGNHIVPVVAGPKDRAYLID 1xw3A 73 :PDSVPPIDVLWIKGAQGGDYFYS T0347 68 :HHHLVLALSKEGVEHVLTSEVAK 1xw3A 98 :GCHRYAAYQQLQRETIPAKLVQS T0347 95 :GKDEFWSVM 1xw3A 121 :TLSDLRVYL Number of specific fragments extracted= 5 number of extra gaps= 0 total=449 Number of alignments=64 # 1xw3A read from 1xw3A/merged-good-all-a2m # found chain 1xw3A in template set T0347 1 :MTHIYEPRLSRIAIDKL 1xw3A 33 :IHSGRIAAVHNVPLSVL T0347 23 :AVGFREVELKRKEWRETRKK 1xw3A 56 :VLDPAKVQSLVDTIREDPDS T0347 53 :VPVVAGPKDRAYLID 1xw3A 81 :VLWIKGAQGGDYFYS T0347 68 :HHHLVLALSKEGVEHVLTSEVAK 1xw3A 98 :GCHRYAAYQQLQRETIPAKLVQS T0347 95 :GKDEFWSVM 1xw3A 121 :TLSDLRVYL T0347 121 :SGDIP 1xw3A 130 :GASTP Number of specific fragments extracted= 6 number of extra gaps= 0 total=455 Number of alignments=65 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1acmA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1acmA expands to /projects/compbio/data/pdb/1acm.pdb.gz 1acmA:# T0347 read from 1acmA/merged-good-all-a2m # 1acmA read from 1acmA/merged-good-all-a2m # adding 1acmA to template set # found chain 1acmA in template set Warning: unaligning (T0347)G44 because of BadResidue code BAD_PEPTIDE in next template residue (1acmA)P36 Warning: unaligning (T0347)D45 because of BadResidue code BAD_PEPTIDE at template residue (1acmA)P36 Warning: unaligning (T0347)V88 because of BadResidue code BAD_PEPTIDE in next template residue (1acmA)P189 Warning: unaligning (T0347)A89 because of BadResidue code BAD_PEPTIDE at template residue (1acmA)P189 T0347 13 :AIDKLR 1acmA 11 :SINDLS T0347 26 :FREVELKRKEWRETRKKD 1acmA 17 :RDDLNLVLATAAKLKANP T0347 46 :DFL 1acmA 37 :ELL T0347 49 :GNHIVPVVAGPK 1acmA 153 :DNLHVAMVGDLK T0347 69 :HHLVLALSKEGVEHVL 1acmA 170 :HSLTQALAKFDGNRFY T0347 86 :SE 1acmA 186 :FI T0347 90 :KF 1acmA 190 :DA T0347 93 :HLGKDEFWSVMDHRNLIY 1acmA 192 :LAMPEYILDMLDEKGIAW Number of specific fragments extracted= 8 number of extra gaps= 2 total=463 Number of alignments=66 # 1acmA read from 1acmA/merged-good-all-a2m # found chain 1acmA in template set Warning: unaligning (T0347)G44 because of BadResidue code BAD_PEPTIDE in next template residue (1acmA)P36 Warning: unaligning (T0347)D45 because of BadResidue code BAD_PEPTIDE at template residue (1acmA)P36 Warning: unaligning (T0347)A89 because of BadResidue code BAD_PEPTIDE in next template residue (1acmA)P189 Warning: unaligning (T0347)K90 because of BadResidue code BAD_PEPTIDE at template residue (1acmA)P189 T0347 12 :IAIDKLR 1acmA 10 :ISINDLS T0347 26 :FREVELKRKEWRETRKKD 1acmA 17 :RDDLNLVLATAAKLKANP T0347 46 :DFL 1acmA 37 :ELL T0347 49 :GNHIVPVVAGPKDR 1acmA 153 :DNLHVAMVGDLKYG T0347 69 :HHLVLAL 1acmA 170 :HSLTQAL T0347 78 :EGVEHVLTSEV 1acmA 177 :AKFDGNRFYFI T0347 91 :FSHLGKDEFWSVMDHRNLIYPFD 1acmA 190 :DALAMPEYILDMLDEKGIAWSLH T0347 114 :AQG 1acmA 220 :AEV T0347 118 :RRQSGDIPKNIHDLEDDPF 1acmA 229 :RVQKERLDPSEYANVKAQF T0347 168 :RIDRDLLSDS 1acmA 248 :VLRASDLHNA Number of specific fragments extracted= 10 number of extra gaps= 2 total=473 Number of alignments=67 # 1acmA read from 1acmA/merged-good-all-a2m # found chain 1acmA in template set Warning: unaligning (T0347)R37 because of BadResidue code BAD_PEPTIDE in next template residue (1acmA)P36 Warning: unaligning (T0347)E38 because of BadResidue code BAD_PEPTIDE at template residue (1acmA)P36 Warning: unaligning (T0347)A89 because of BadResidue code BAD_PEPTIDE in next template residue (1acmA)P189 Warning: unaligning (T0347)K90 because of BadResidue code BAD_PEPTIDE at template residue (1acmA)P189 T0347 13 :AIDKLRPTQIAVGFREVELKRKEW 1acmA 11 :SINDLSRDDLNLVLATAAKLKANP T0347 46 :DFLGNHIV 1acmA 37 :ELLKHKVI T0347 59 :PKDRAYLIDH 1acmA 153 :DNLHVAMVGD T0347 69 :HHLVLALSK 1acmA 170 :HSLTQALAK T0347 80 :VEHVLTSEV 1acmA 179 :FDGNRFYFI T0347 91 :FSHLGKDEFWSVMDHRNLIYPFDA 1acmA 190 :DALAMPEYILDMLDEKGIAWSLHS T0347 118 :RRQSGDIPKNIHDLEDDPF 1acmA 229 :RVQKERLDPSEYANVKAQF T0347 168 :RIDRDLLSD 1acmA 248 :VLRASDLHN Number of specific fragments extracted= 8 number of extra gaps= 2 total=481 Number of alignments=68 # command:Using radius: 8.0000 Alignment mode NUMB_ALIGNS: 68 Adding 2231 constraints to all.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all.constraints maxweight: 1.0000 Optimizing... Probability sum: -379.4635, CN propb: -379.4635 weights: 0.2027 constraints: 544 # command:Found ConstraintSet # PrintContacts align.constraints_v3 Number of constraints in align.constraints 544 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_v3 Number of constraints in align.constraints.bonus 544 # command:Found ConstraintSet # PrintContacts rejected.constraints_v3 Number of constraints in rejected.constraints 1687 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_v3 Number of constraints in rejected.constraints.bonus 1687 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_v3 Number of constraints in noncontact.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_v3 Number of constraints in noncontact.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_v3 Number of constraints in all.constraints 2231 # command: