# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 1600 examples # computed average trans backbone unit before proline from 52 examples # trans (non-proline) backbone unit: # CA= -2.2097 1.0151 -0.0046 # O= -0.1488 2.2425 0.0020 # C= -0.6903 1.1357 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4580 -0.0000 -0.0000 # cis backbone unit: # CA= -0.1462 2.4515 0.0018 # O= -2.0272 0.9713 0.0022 # C= -0.8006 1.0755 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4659 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2063 1.0654 0.0002 # O= -0.1193 2.2442 0.0054 # C= -0.6842 1.1479 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4661 -0.0000 0.0000 # After reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz have 408 chains in training database # Count of chains,residues,atoms: 408,82795,639989 # 81291 residues have no bad marker # 565 residues lack atoms needed to compute omega # 313 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 1 # HAS_OXT 265 # TOO_MANY_ATOMS 0 # TOO_FEW_ATOMS 378 # HAS_UNKNOWN_ATOMS 0 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 139 # NON_PLANAR_PEPTIDE 424 # BAD_PEPTIDE 803 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-40pc-3157.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 # command:# Making conformation for sequence T0313 numbered 1 through 322 Created new target T0313 from T0313.a2m # command:CPU_time= 5.163 sec, elapsed time= 5.199 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bg2/T0313-1bg2-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1bg2 expands to /projects/compbio/data/pdb/1bg2.pdb.gz 1bg2:Warning: there is no chain 1bg2 will retry with 1bg2A # T0313 read from 1bg2/T0313-1bg2-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bg2 read from 1bg2/T0313-1bg2-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1bg2 to template set # found chain 1bg2 in template set T0313 1 :NIRVIARVRPVTKEDGEGPEATNAVTFDADDDSI 1bg2 8 :NIKVMCRFRPLNESEVNRGDKYIAKFQGEDTVVI # choosing archetypes in rotamer library T0313 42 :KPVSFELDKVFSPQASQQDVFQEV 1bg2 42 :ASKPYAFDRVFQSSTSQEQVYNDC T0313 66 :QALVTSCIDGFNVCIFAYGQTGAGKTYTMEG 1bg2 67 :KKIVKDVLEGYNGTIFAYGQTSSGKTHTMEG T0313 97 :TAENPGINQRALQLLFSEVQEKASDWEYTITVSAAEIYNEVLRDLLGKEPQE 1bg2 101 :DPEGMGIIPRIVQDIFNYIYSMDENLEFHIKVSYFEIYLDKIRDLLDVSKTN T0313 152 :IRLCPDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTGLRTTGKLNLVDLAGSERVGKSGAEGSRLREAQHINKSLSALGDVIAALRSRQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1bg2 153 :LSVHEDKNRVPYVKGCTERFVCSPDEVMDTIDEGKSNRHVAVTNMNEHSSRSHSIFLINVKQENTQTEQKLSGKLYLVDLAGSEKVSKTGAEGAVLDEAKNINKSLSALGNVISALAEGSTYVPYRDSKMTRILQDSLGGNCRTTIVICCSPSSYNESETKSTLLFGQRAK Number of specific fragments extracted= 5 number of extra gaps= 0 total=5 Will force an alignment to be made, even if fragment is small Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bg2/T0313-1bg2-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0313 read from 1bg2/T0313-1bg2-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bg2 read from 1bg2/T0313-1bg2-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1bg2 in template set T0313 2 :IRVIARVRPVTKEDGEGPEATNAVTFDADDDSII 1bg2 9 :IKVMCRFRPLNESEVNRGDKYIAKFQGEDTVVIA T0313 43 :PVSFELDKVFSPQASQQDVFQEV 1bg2 43 :SKPYAFDRVFQSSTSQEQVYNDC T0313 66 :QALVTSCIDGFNVCIFAYGQTGAGKTYTMEG 1bg2 67 :KKIVKDVLEGYNGTIFAYGQTSSGKTHTMEG T0313 97 :TAENPGINQRALQLLFSEVQEKASDWEYTITVSAAEIYNEVLRDLLGKEPQ 1bg2 101 :DPEGMGIIPRIVQDIFNYIYSMDENLEFHIKVSYFEIYLDKIRDLLDVSKT T0313 151 :EIRLCPDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTGLRTTGKLNLVDLAGSERVGKSGAEGS 1bg2 152 :NLSVHEDKNRVPYVKGCTERFVCSPDEVMDTIDEGKSNRHVAVTNMNEHSSRSHSIFLINVKQENTQTEQKLSGKLYLVDLAGSEKVSKTGAEGA T0313 246 :R 1bg2 254 :I T0313 254 :NKSLSALGDVIAALRSRQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1bg2 255 :NKSLSALGNVISALAEGSTYVPYRDSKMTRILQDSLGGNCRTTIVICCSPSSYNESETKSTLLFGQRAK Number of specific fragments extracted= 7 number of extra gaps= 0 total=12 Will force an alignment to be made, even if fragment is small Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bg2/T0313-1bg2-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0313 read from 1bg2/T0313-1bg2-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bg2 read from 1bg2/T0313-1bg2-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1bg2 in template set T0313 1 :NIRVIARVRPVTKEDGEGPEATNAVTFDADDDSII 1bg2 8 :NIKVMCRFRPLNESEVNRGDKYIAKFQGEDTVVIA T0313 43 :PVSFELDKVFSPQASQQDVFQ 1bg2 43 :SKPYAFDRVFQSSTSQEQVYN T0313 64 :EVQALVTSCIDGFNVCIFAYGQTGAGKTYTMEG 1bg2 65 :CAKKIVKDVLEGYNGTIFAYGQTSSGKTHTMEG T0313 97 :TAENPGINQRALQLLFSEVQEKASDWEYTITVSAAEIYNEVLRDLLGKEPQE 1bg2 101 :DPEGMGIIPRIVQDIFNYIYSMDENLEFHIKVSYFEIYLDKIRDLLDVSKTN T0313 152 :IRLCPDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTGLRTTGKLNLVDLAGSERVGKSGAEG 1bg2 153 :LSVHEDKNRVPYVKGCTERFVCSPDEVMDTIDEGKSNRHVAVTNMNEHSSRSHSIFLINVKQENTQTEQKLSGKLYLVDLAGSEKVSKTGAEG T0313 254 :NKSLSALGDVIAALRSRQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1bg2 255 :NKSLSALGNVISALAEGSTYVPYRDSKMTRILQDSLGGNCRTTIVICCSPSSYNESETKSTLLFGQRAK Number of specific fragments extracted= 6 number of extra gaps= 0 total=18 Will force an alignment to be made, even if fragment is small Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1x88A/T0313-1x88A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1x88A expands to /projects/compbio/data/pdb/1x88.pdb.gz 1x88A:# T0313 read from 1x88A/T0313-1x88A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1x88A read from 1x88A/T0313-1x88A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1x88A to template set # found chain 1x88A in template set Warning: unaligning (T0313)R236 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1x88A)N287 Warning: unaligning (T0313)H252 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1x88A)N287 T0313 1 :NIRVIARVRPVTKEDGEGPEATNAVTFDADDDSIIHLLHKGKP 1x88A 18 :NIQVVVRCRPFNLAERKASAHSIVECDPVRKEVSVRTGGLADK T0313 44 :VSFELDKVFSPQASQQDVFQE 1x88A 64 :KTYTFDMVFGASTKQIDVYRS T0313 65 :VQALVTSCIDGFNVCIFAYGQTGAGKTYTMEGT 1x88A 86 :VCPILDEVIMGYNCTIFAYGQTGTGKTFTMEGE T0313 98 :AENP 1x88A 128 :EEDP T0313 102 :GINQRALQLLFSEV 1x88A 134 :GIIPRTLHQIFEKL T0313 118 :KASDWEYTITVSAAEIYNEVLRDLLGKEPQEKLEIRLCPDGSG 1x88A 148 :TDNGTEFSVKVSLLEIYNEELFDLLNPSSDVSERLQMFDDPRN T0313 161 :QLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDC 1x88A 193 :GVIIKGLEEITVHNKDEVYQILEKGAAKRTTAATLMNAYSSRSHSVFSVTIHMKET T0313 217 :STG 1x88A 250 :IDG T0313 220 :LRTTGKLNLVDLAGSE 1x88A 255 :LVKIGKLNLVDLAGSE T0313 253 :INKSLSALGDVIAALRSRQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1x88A 288 :INQSLLTLGRVITALVERTPHVPYRESKLTRILQDSLGGRTRTSIIATISPASLNLEETLSTLEYAHRAK Number of specific fragments extracted= 10 number of extra gaps= 0 total=28 Will force an alignment to be made, even if fragment is small Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1x88A/T0313-1x88A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0313 read from 1x88A/T0313-1x88A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1x88A read from 1x88A/T0313-1x88A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1x88A in template set Warning: unaligning (T0313)R236 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1x88A)N287 Warning: unaligning (T0313)H252 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1x88A)N287 T0313 1 :NIRVIARVRPVTKEDGEGPEATNAVTFDADDDSIIH 1x88A 18 :NIQVVVRCRPFNLAERKASAHSIVECDPVRKEVSVR T0313 37 :LLHKGKPVSFELDKVFSPQASQQDVFQEV 1x88A 57 :LADKSSRKTYTFDMVFGASTKQIDVYRSV T0313 66 :QALVTSCIDGFNVCIFAYGQTGAGKTYTMEGTAENP 1x88A 87 :CPILDEVIMGYNCTIFAYGQTGTGKTFTMEGERSPN T0313 102 :GINQRALQLLFSEV 1x88A 134 :GIIPRTLHQIFEKL T0313 118 :KASDWEYTITVSAAEIYNEVLRDLLGKEPQEKLEIRLCPDGS 1x88A 148 :TDNGTEFSVKVSLLEIYNEELFDLLNPSSDVSERLQMFDDPR T0313 160 :GQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDC 1x88A 192 :RGVIIKGLEEITVHNKDEVYQILEKGAAKRTTAATLMNAYSSRSHSVFSVTIHMKET T0313 217 :STG 1x88A 250 :IDG T0313 220 :LRTTGKLNLVDLAGSE 1x88A 255 :LVKIGKLNLVDLAGSE T0313 253 :INKSLSALGDVIAALRSRQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1x88A 288 :INQSLLTLGRVITALVERTPHVPYRESKLTRILQDSLGGRTRTSIIATISPASLNLEETLSTLEYAHRAK Number of specific fragments extracted= 9 number of extra gaps= 0 total=37 Will force an alignment to be made, even if fragment is small Number of alignments=5 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1x88A/T0313-1x88A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0313 read from 1x88A/T0313-1x88A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1x88A read from 1x88A/T0313-1x88A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1x88A in template set Warning: unaligning (T0313)R236 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1x88A)N287 Warning: unaligning (T0313)H252 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1x88A)N287 T0313 1 :NIRVIARVRPVTKEDGEGPEATNAVTFDADDDSIIHLLHKGK 1x88A 18 :NIQVVVRCRPFNLAERKASAHSIVECDPVRKEVSVRTGGLAD T0313 43 :PVSFELDKVFSPQASQQDVFQ 1x88A 63 :RKTYTFDMVFGASTKQIDVYR T0313 64 :EVQALVTSCIDGFNVCIFAYGQTGAGKTYTMEG 1x88A 85 :VVCPILDEVIMGYNCTIFAYGQTGTGKTFTMEG T0313 97 :TAENPGINQRALQLLFSEV 1x88A 129 :EDPLAGIIPRTLHQIFEKL T0313 118 :KASDWEYTITVSAAEIYNEVLRDLLGKEPQEKLEIRLCPDGS 1x88A 148 :TDNGTEFSVKVSLLEIYNEELFDLLNPSSDVSERLQMFDDPR T0313 160 :GQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTGL 1x88A 192 :RGVIIKGLEEITVHNKDEVYQILEKGAAKRTTAATLMNAYSSRSHSVFSVTIHMKETTIDG T0313 221 :RTTGKLNLVDLAGSE 1x88A 256 :VKIGKLNLVDLAGSE T0313 253 :INKSLSALGDVIAALRSRQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1x88A 288 :INQSLLTLGRVITALVERTPHVPYRESKLTRILQDSLGGRTRTSIIATISPASLNLEETLSTLEYAHRAK Number of specific fragments extracted= 8 number of extra gaps= 0 total=45 Will force an alignment to be made, even if fragment is small Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vfvA/T0313-1vfvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vfvA expands to /projects/compbio/data/pdb/1vfv.pdb.gz 1vfvA:# T0313 read from 1vfvA/T0313-1vfvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vfvA read from 1vfvA/T0313-1vfvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vfvA to template set # found chain 1vfvA in template set Warning: unaligning (T0313)T190 because of BadResidue code BAD_PEPTIDE in next template residue (1vfvA)V205 Warning: unaligning (T0313)T191 because of BadResidue code BAD_PEPTIDE at template residue (1vfvA)V205 Warning: unaligning (T0313)H199 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vfvA)T213 Warning: unaligning (T0313)S201 because of BadResidue code BAD_PEPTIDE in next template residue (1vfvA)R216 Warning: unaligning (T0313)R202 because of BadResidue code BAD_PEPTIDE at template residue (1vfvA)R216 Warning: unaligning (T0313)G219 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vfvA)T234 Warning: unaligning (T0313)L220 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vfvA)T234 Warning: unaligning (T0313)E235 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vfvA)A269 Warning: unaligning (T0313)Q251 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vfvA)A269 Warning: unaligning (T0313)H273 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vfvA)F303 T0313 1 :NIRVIARVRPVTKEDGEGPEATNAVT 1vfvA 5 :SVKVAVRVRPFNSREMSRDSKCIIQM T0313 28 :DADDDSIIHLLHKGKP 1vfvA 31 :SGSTTTIVNPKQPKET T0313 44 :VSFELDKVF 1vfvA 48 :KSFSFDYSY T0313 53 :SPQ 1vfvA 61 :SPE T0313 56 :ASQQDVFQEV 1vfvA 68 :ASQKQVYRDI T0313 66 :QALVTSCIDGFNVCIFAYGQTGAGKTYTMEG 1vfvA 79 :EEMLQHAFEGYNVCIFAYGQTGAGKSYTMMG T0313 97 :TAENPGINQRALQLLFSEVQEKA 1vfvA 112 :EKDQQGIIPQLCEDLFSRINDTT T0313 120 :SDWEYTITVSAAEIYNEVLRDLLGKEPQEK 1vfvA 136 :DNMSYSVEVSYMEIYCERVRDLLNPKNKGN T0313 152 :IRLCPDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNR 1vfvA 166 :LRVREHPLLGPYVEDLSKLAVTSYNDIQDLMDSGNKPR T0313 200 :S 1vfvA 214 :S T0313 203 :SHALLIVTVRGVDCST 1vfvA 217 :SHAVFNIIFTQKRHDA T0313 222 :TTGKLNLVDLAGS 1vfvA 240 :KVSKISLVDLAGS T0313 252 :HINKSLSALGDVIAALR 1vfvA 270 :NINKSLTTLGKVISALA T0313 274 :VPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1vfvA 304 :IPYRDSVLTWLLRENLGGNSRTAMVAALSPADINYDETLSTLRYADRAK Number of specific fragments extracted= 14 number of extra gaps= 3 total=59 Will force an alignment to be made, even if fragment is small Number of alignments=7 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vfvA/T0313-1vfvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0313 read from 1vfvA/T0313-1vfvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vfvA read from 1vfvA/T0313-1vfvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vfvA in template set Warning: unaligning (T0313)T190 because of BadResidue code BAD_PEPTIDE in next template residue (1vfvA)V205 Warning: unaligning (T0313)T191 because of BadResidue code BAD_PEPTIDE at template residue (1vfvA)V205 Warning: unaligning (T0313)H199 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vfvA)T213 Warning: unaligning (T0313)S201 because of BadResidue code BAD_PEPTIDE in next template residue (1vfvA)R216 Warning: unaligning (T0313)R202 because of BadResidue code BAD_PEPTIDE at template residue (1vfvA)R216 Warning: unaligning (T0313)G219 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vfvA)T234 Warning: unaligning (T0313)E235 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vfvA)A269 Warning: unaligning (T0313)Q251 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vfvA)A269 Warning: unaligning (T0313)H273 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vfvA)F303 T0313 2 :IRVIARVRPVTKEDGEGPEATNA 1vfvA 6 :VKVAVRVRPFNSREMSRDSKCII T0313 26 :TFDADDDSIIHLLHKGKP 1vfvA 29 :QMSGSTTTIVNPKQPKET T0313 44 :VSFELDKVF 1vfvA 48 :KSFSFDYSY T0313 53 :SPQ 1vfvA 61 :SPE T0313 56 :ASQQDVFQEV 1vfvA 68 :ASQKQVYRDI T0313 66 :QALVTSCIDGFNVCIFAYGQTGAGKTYTMEG 1vfvA 79 :EEMLQHAFEGYNVCIFAYGQTGAGKSYTMMG T0313 97 :TAENPGINQRALQLLFSEVQEKA 1vfvA 112 :EKDQQGIIPQLCEDLFSRINDTT T0313 120 :SDWEYTITVSAAEIYNEVLRDLLGKEPQE 1vfvA 136 :DNMSYSVEVSYMEIYCERVRDLLNPKNKG T0313 151 :EIRLCPDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNR 1vfvA 165 :NLRVREHPLLGPYVEDLSKLAVTSYNDIQDLMDSGNKPR T0313 200 :S 1vfvA 214 :S T0313 203 :SHALLIVTVRGVDCST 1vfvA 217 :SHAVFNIIFTQKRHDA T0313 220 :LRTTGKLNLVDLAGS 1vfvA 238 :TEKVSKISLVDLAGS T0313 252 :HINKSLSALGDVIAAL 1vfvA 270 :NINKSLTTLGKVISAL T0313 274 :VPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1vfvA 304 :IPYRDSVLTWLLRENLGGNSRTAMVAALSPADINYDETLSTLRYADRAK Number of specific fragments extracted= 14 number of extra gaps= 3 total=73 Will force an alignment to be made, even if fragment is small Number of alignments=8 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vfvA/T0313-1vfvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0313 read from 1vfvA/T0313-1vfvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vfvA read from 1vfvA/T0313-1vfvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vfvA in template set Warning: unaligning (T0313)T190 because of BadResidue code BAD_PEPTIDE in next template residue (1vfvA)V205 Warning: unaligning (T0313)T191 because of BadResidue code BAD_PEPTIDE at template residue (1vfvA)V205 Warning: unaligning (T0313)H199 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vfvA)T213 Warning: unaligning (T0313)S201 because of BadResidue code BAD_PEPTIDE in next template residue (1vfvA)R216 Warning: unaligning (T0313)R202 because of BadResidue code BAD_PEPTIDE at template residue (1vfvA)R216 Warning: unaligning (T0313)G219 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vfvA)T234 Warning: unaligning (T0313)L220 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vfvA)T234 Warning: unaligning (T0313)E235 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vfvA)A269 Warning: unaligning (T0313)Q251 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vfvA)A269 Warning: unaligning (T0313)H273 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vfvA)F303 T0313 2 :IRVIARVRPVTKEDGEGPEATNAVTFDADDDSIIHLLHKGKPVSFELDKVF 1vfvA 6 :VKVAVRVRPFNSREMSRDSKCIIQMSGSTTTIVNPKQPKETPKSFSFDYSY T0313 53 :SPQ 1vfvA 61 :SPE T0313 56 :ASQQDVFQ 1vfvA 68 :ASQKQVYR T0313 64 :EVQALVTSCIDGFNVCIFAYGQTGAGKTYTMEG 1vfvA 77 :IGEEMLQHAFEGYNVCIFAYGQTGAGKSYTMMG T0313 97 :TAENPGINQRALQLLFSEVQEKA 1vfvA 112 :EKDQQGIIPQLCEDLFSRINDTT T0313 120 :SDWEYTITVSAAEIYNEVLRDLLGKEPQEK 1vfvA 136 :DNMSYSVEVSYMEIYCERVRDLLNPKNKGN T0313 152 :IRLCPDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNR 1vfvA 166 :LRVREHPLLGPYVEDLSKLAVTSYNDIQDLMDSGNKPR T0313 200 :S 1vfvA 214 :S T0313 203 :SHALLIVTVRGVDCST 1vfvA 217 :SHAVFNIIFTQKRHDA T0313 221 :RTTGKLNLVDLAGS 1vfvA 239 :EKVSKISLVDLAGS T0313 252 :HINKSLSALGDVIAALRS 1vfvA 270 :NINKSLTTLGKVISALAE T0313 274 :VPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1vfvA 304 :IPYRDSVLTWLLRENLGGNSRTAMVAALSPADINYDETLSTLRYADRAK Number of specific fragments extracted= 12 number of extra gaps= 3 total=85 Will force an alignment to be made, even if fragment is small Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f9vA/T0313-1f9vA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1f9vA expands to /projects/compbio/data/pdb/1f9v.pdb.gz 1f9vA:# T0313 read from 1f9vA/T0313-1f9vA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f9vA read from 1f9vA/T0313-1f9vA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1f9vA to template set # found chain 1f9vA in template set Warning: unaligning (T0313)G143 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f9vA)K546 Warning: unaligning (T0313)E151 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f9vA)K546 Warning: unaligning (T0313)H186 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f9vA)E594 Warning: unaligning (T0313)E198 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f9vA)E594 Warning: unaligning (T0313)C216 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f9vA)G615 Warning: unaligning (T0313)G219 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f9vA)G615 Warning: unaligning (T0313)Q271 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f9vA)R671 T0313 1 :NIRVIARVRPVTKEDGEGPEATNAVT 1f9vA 386 :NIRVYCRIRPALKNLENSDTSLINVN T0313 27 :FDADD 1f9vA 414 :DDNSG T0313 32 :DSIIHLLHKGKPVSFELDKVFSPQASQQDVFQEVQALVTSCIDGFNVCIFAYGQTGAGKTYTMEGTA 1f9vA 422 :MEVTKIQNTAQVHEFKFDKIFDQQDTNVDVFKEVGQLVQSSLDGYNVCIFAYGQTGSGKTFTMLNPG T0313 101 :PGINQRALQLLFSEVQEKA 1f9vA 489 :DGIIPSTISHIFNWINKLK T0313 120 :SDWEYTITVSAAEIYNEVLRDLL 1f9vA 509 :KGWDYKVNCEFIEIYNENIVDLL T0313 152 :IRLCPDGS 1f9vA 547 :HEIRHDQE T0313 160 :GQLYVPGLTEFQVQSVDDINKVFEFG 1f9vA 556 :KTTTITNVTSCKLESEEMVEIILKKA T0313 199 :HSSRSHALLIVTVRGVD 1f9vA 595 :HSSASHSIFIIHLSGSN T0313 220 :LRTTGKLNLVDLAGSERVGKSGAEGSRLREAQHINKSLSALGDVIAALRSR 1f9vA 616 :AHSYGTLNLVDLAGSERINVSQVVGDRLRETQNINKSLSCLGDVIHALGQP T0313 273 :HVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1f9vA 672 :HIPFRNSKLTYLLQYSLTGDSKTLMFVNISPSSSHINETLNSLRFASKVN Number of specific fragments extracted= 10 number of extra gaps= 0 total=95 Will force an alignment to be made, even if fragment is small Number of alignments=10 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f9vA/T0313-1f9vA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0313 read from 1f9vA/T0313-1f9vA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f9vA read from 1f9vA/T0313-1f9vA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1f9vA in template set Warning: unaligning (T0313)E151 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f9vA)K546 Warning: unaligning (T0313)H186 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f9vA)E594 Warning: unaligning (T0313)E198 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f9vA)E594 Warning: unaligning (T0313)C216 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f9vA)G615 Warning: unaligning (T0313)G219 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f9vA)G615 Warning: unaligning (T0313)Q271 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f9vA)R671 T0313 2 :IRVIARVRPVTKEDGEGPEATNAVT 1f9vA 387 :IRVYCRIRPALKNLENSDTSLINVN T0313 27 :FDAD 1f9vA 414 :DDNS T0313 31 :DDSIIHLLHKGKPVSFELDKVFSPQASQQDVFQEVQALVTSCIDGFNVCIFAYGQTGAGKTYTME 1f9vA 421 :SMEVTKIQNTAQVHEFKFDKIFDQQDTNVDVFKEVGQLVQSSLDGYNVCIFAYGQTGSGKTFTML T0313 98 :AENPGINQRALQLLFSEVQEKA 1f9vA 486 :NPGDGIIPSTISHIFNWINKLK T0313 120 :SDWEYTITVSAAEIYNEVLRDLL 1f9vA 509 :KGWDYKVNCEFIEIYNENIVDLL T0313 152 :IRLC 1f9vA 547 :HEIR T0313 156 :PDGSGQLYVPGLTEFQVQSVDDINKVFEFG 1f9vA 552 :DQETKTTTITNVTSCKLESEEMVEIILKKA T0313 199 :HSSRSHALLIVTVRGVD 1f9vA 595 :HSSASHSIFIIHLSGSN T0313 220 :LRTTGKLNLVDLAGSERVGKSGAEGSRLREAQHINKSLSALGDVIAALRSR 1f9vA 616 :AHSYGTLNLVDLAGSERINVSQVVGDRLRETQNINKSLSCLGDVIHALGQP T0313 273 :HVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1f9vA 672 :HIPFRNSKLTYLLQYSLTGDSKTLMFVNISPSSSHINETLNSLRFASKVN Number of specific fragments extracted= 10 number of extra gaps= 0 total=105 Will force an alignment to be made, even if fragment is small Number of alignments=11 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f9vA/T0313-1f9vA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0313 read from 1f9vA/T0313-1f9vA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f9vA read from 1f9vA/T0313-1f9vA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1f9vA in template set Warning: unaligning (T0313)K149 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f9vA)K546 Warning: unaligning (T0313)H186 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f9vA)E594 Warning: unaligning (T0313)E198 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f9vA)E594 Warning: unaligning (T0313)C216 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f9vA)G615 Warning: unaligning (T0313)G219 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f9vA)G615 Warning: unaligning (T0313)G272 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f9vA)R671 T0313 1 :NIRVIARVRPVTKEDGEGPEATNAV 1f9vA 386 :NIRVYCRIRPALKNLENSDTSLINV T0313 26 :TFDADDDSI 1f9vA 412 :EFDDNSGVQ T0313 35 :IHLLHKGKPVSFELDKVFSPQASQQDVFQEVQALVTSCIDGFNVCIFAYGQTGAGKTYTME 1f9vA 425 :TKIQNTAQVHEFKFDKIFDQQDTNVDVFKEVGQLVQSSLDGYNVCIFAYGQTGSGKTFTML T0313 98 :AENPGINQRALQLLFSEVQEKAS 1f9vA 486 :NPGDGIIPSTISHIFNWINKLKT T0313 121 :DWEYTITVSAAEIYNEVLRDLL 1f9vA 510 :GWDYKVNCEFIEIYNENIVDLL T0313 150 :LEIRL 1f9vA 547 :HEIRH T0313 156 :PDGSGQLYVPGLTEFQVQSVDDINKVFEFG 1f9vA 552 :DQETKTTTITNVTSCKLESEEMVEIILKKA T0313 199 :HSSRSHALLIVTVRGVD 1f9vA 595 :HSSASHSIFIIHLSGSN T0313 220 :LRTTGKLNLVDLAGSERVGKSGAEGSRLREAQHINKSLSALGDVIAALRS 1f9vA 616 :AHSYGTLNLVDLAGSERINVSQVVGDRLRETQNINKSLSCLGDVIHALGQ T0313 273 :HVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERV 1f9vA 672 :HIPFRNSKLTYLLQYSLTGDSKTLMFVNISPSSSHINETLNSLRFASKV Number of specific fragments extracted= 10 number of extra gaps= 0 total=115 Will force an alignment to be made, even if fragment is small Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ry6A/T0313-1ry6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ry6A expands to /projects/compbio/data/pdb/1ry6.pdb.gz 1ry6A:# T0313 read from 1ry6A/T0313-1ry6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ry6A read from 1ry6A/T0313-1ry6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ry6A to template set # found chain 1ry6A in template set Warning: unaligning (T0313)G143 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ry6A)K168 Warning: unaligning (T0313)K144 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ry6A)K168 Warning: unaligning (T0313)R270 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ry6A)K278 Warning: unaligning (T0313)Q271 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ry6A)K278 T0313 1 :NIRVIARVRPVTKEDGEGPEATNAVTFDADDDSI 1ry6A 1 :MIKVVVRKRPLSELEKKKKDSDIITVKNNCTLYI T0313 35 :IHLLHKGKP 1ry6A 36 :EPRYKVDMT T0313 44 :VSFELDKVFSPQASQQDVFQE 1ry6A 50 :HEFIVDKVFDDTVDNFTVYEN T0313 65 :VQALVTSCI 1ry6A 72 :IKPLIIDLY T0313 74 :DGFNVCIFAYGQTGAGKTYTMEGT 1ry6A 82 :NGCVCSCFAYGQTGSGKTYTMLGS T0313 98 :AENPGINQRALQLLFSEVQEKASDWEYTITVSAAEIYNEVLRDLL 1ry6A 111 :SDTPGIFQYAAGDIFTFLNIYDKDNTKGIFISFYEIYCGKLYDLL T0313 160 :GQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRG 1ry6A 169 :KEVVVKDLKILRVLTKEELILKMIDGVLLRKIGVNSQNDESSRSHAILNIDLKD T0313 217 :STGLRTTGKLNLVDLAGSERVGKSGAEGS 1ry6A 223 :INKNTSLGKIAFIDLAGSERGADTVSQNK T0313 246 :RLREAQHINKSLSALGDVIAALRS 1ry6A 253 :TQTDGANINRSLLALKECIRAMDS T0313 272 :GHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1ry6A 279 :NHIPFRDSELTKVLRDIFVGKSKSIMIANISPTISCCEQTLNTLRYSSRVK Number of specific fragments extracted= 10 number of extra gaps= 2 total=125 Will force an alignment to be made, even if fragment is small Number of alignments=13 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ry6A/T0313-1ry6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0313 read from 1ry6A/T0313-1ry6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ry6A read from 1ry6A/T0313-1ry6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ry6A in template set Warning: unaligning (T0313)G143 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ry6A)K168 Warning: unaligning (T0313)K144 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ry6A)K168 Warning: unaligning (T0313)R270 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ry6A)K278 Warning: unaligning (T0313)Q271 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ry6A)K278 T0313 2 :IRVIARVRPVTKEDGEGPEATNAVTFDADDDSIIH 1ry6A 2 :IKVVVRKRPLSELEKKKKDSDIITVKNNCTLYIDE T0313 37 :LLHKGKPVSFELDKVFSPQASQQDVFQEV 1ry6A 43 :MTKYIERHEFIVDKVFDDTVDNFTVYENT T0313 66 :QALVTSCI 1ry6A 73 :KPLIIDLY T0313 74 :DGFNVCIFAYGQTGAGKTYTMEG 1ry6A 82 :NGCVCSCFAYGQTGSGKTYTMLG T0313 97 :TAE 1ry6A 110 :QSD T0313 102 :GINQRALQLLFSEVQEKASDWEYTITVSAAEIYNEVLRDLL 1ry6A 115 :GIFQYAAGDIFTFLNIYDKDNTKGIFISFYEIYCGKLYDLL T0313 160 :GQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGV 1ry6A 169 :KEVVVKDLKILRVLTKEELILKMIDGVLLRKIGVNSQNDESSRSHAILNIDLKDI T0313 218 :TGLRTTGKLNLVDLAGSERVGKSGAEGSR 1ry6A 224 :NKNTSLGKIAFIDLAGSERGADTVSQNKQ T0313 247 :LREAQHINKSLSALGDVIAALRS 1ry6A 254 :QTDGANINRSLLALKECIRAMDS T0313 272 :GHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1ry6A 279 :NHIPFRDSELTKVLRDIFVGKSKSIMIANISPTISCCEQTLNTLRYSSRVK Number of specific fragments extracted= 10 number of extra gaps= 2 total=135 Will force an alignment to be made, even if fragment is small Number of alignments=14 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ry6A/T0313-1ry6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0313 read from 1ry6A/T0313-1ry6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ry6A read from 1ry6A/T0313-1ry6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ry6A in template set Warning: unaligning (T0313)G143 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ry6A)K168 Warning: unaligning (T0313)K144 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ry6A)K168 Warning: unaligning (T0313)R270 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ry6A)K278 Warning: unaligning (T0313)Q271 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ry6A)K278 T0313 2 :IRVIARVRPVTKEDGEGPEATNAVTFDADDDSI 1ry6A 2 :IKVVVRKRPLSELEKKKKDSDIITVKNNCTLYI T0313 35 :IHLLHKGK 1ry6A 37 :PRYKVDMT T0313 43 :PVSFELDKVFSPQASQQDVFQ 1ry6A 49 :RHEFIVDKVFDDTVDNFTVYE T0313 64 :EVQALVTSCI 1ry6A 71 :TIKPLIIDLY T0313 74 :DGFNVCIFAYGQTGAGKTYTMEG 1ry6A 82 :NGCVCSCFAYGQTGSGKTYTMLG T0313 97 :TAENPGINQRALQLLFSEVQEKASDWEYTITVSAAEIYNEVLRDLL 1ry6A 110 :QSDTPGIFQYAAGDIFTFLNIYDKDNTKGIFISFYEIYCGKLYDLL T0313 160 :GQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGV 1ry6A 169 :KEVVVKDLKILRVLTKEELILKMIDGVLLRKIGVNSQNDESSRSHAILNIDLKDI T0313 218 :TGLRTTGKLNLVDLAGSERVGKSGAEG 1ry6A 224 :NKNTSLGKIAFIDLAGSERGADTVSQN T0313 245 :SRLREAQHINKSLSALGDVIAALRS 1ry6A 252 :QTQTDGANINRSLLALKECIRAMDS T0313 272 :GHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1ry6A 279 :NHIPFRDSELTKVLRDIFVGKSKSIMIANISPTISCCEQTLNTLRYSSRVK Number of specific fragments extracted= 10 number of extra gaps= 2 total=145 Will force an alignment to be made, even if fragment is small Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i6iA/T0313-1i6iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1i6iA expands to /projects/compbio/data/pdb/1i6i.pdb.gz 1i6iA:Skipped atom 113, because occupancy 0.5 <= existing 0.500 in 1i6iA Skipped atom 115, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 117, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 119, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 121, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 123, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 125, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 127, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 129, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 131, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 133, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 158, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 160, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 162, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 164, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 166, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 168, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 170, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 172, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 174, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 176, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 178, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 571, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 573, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 575, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 577, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 579, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 581, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 583, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 585, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 587, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 627, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 629, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 631, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 633, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 635, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 637, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 639, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 641, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 681, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 683, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 685, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 687, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 689, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 691, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 693, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 695, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 697, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 1176, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 1178, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 1180, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 1182, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 1184, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 1186, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 1699, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 1701, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 1703, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 1705, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 1707, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 1709, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 1711, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 1713, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 1966, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 1968, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 1970, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 1972, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 1974, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 1976, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 1995, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 1997, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 1999, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 2001, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 2003, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 2005, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 2504, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 2506, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 2508, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 2510, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 2512, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 2514, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 2516, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 2518, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 2520, because occupancy 0.500 <= existing 0.500 in 1i6iA # T0313 read from 1i6iA/T0313-1i6iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i6iA read from 1i6iA/T0313-1i6iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1i6iA to template set # found chain 1i6iA in template set Warning: unaligning (T0313)T97 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i6iA)K113 Warning: unaligning (T0313)A98 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1i6iA)K113 Warning: unaligning (T0313)E148 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i6iA)N165 Warning: unaligning (T0313)K149 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1i6iA)N165 Warning: unaligning (T0313)E235 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1i6iA)A269 Warning: unaligning (T0313)Q251 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1i6iA)A269 Warning: unaligning (T0313)H273 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1i6iA)F303 T0313 1 :NIRVIARVRPVTKEDGEGPEATNAVT 1i6iA 5 :SVKVAVRVRPFNSREMSRDSKCIIQM T0313 28 :DADDDSIIHLLHKGKP 1i6iA 31 :SGSTTTIVNPKQPKET T0313 44 :VSFELDKVF 1i6iA 48 :KSFSFDYSY T0313 53 :SPQ 1i6iA 61 :SPE T0313 56 :ASQQDVFQEV 1i6iA 68 :ASQKQVYRDI T0313 66 :QALVTSCIDGFNVCIFAYGQTGAGKTYTMEG 1i6iA 79 :EEMLQHAFEGYNVCIFAYGQTGAGKSYTMMG T0313 99 :ENPGINQRALQLLFSEVQEKA 1i6iA 114 :DQQGIIPQLCEDLFSRINDTT T0313 120 :SDWEYTITVSAAEIYNEVLRDLLGKEPQ 1i6iA 136 :DNMSYSVEVSYMEIYCERVRDLLNPKNK T0313 152 :IRLCPDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTG 1i6iA 166 :LRVREHPLLGPYVEDLSKLAVTSYNDIQDLMDSGNKARTVAATNMNETSSRSHAVFNIIFTQKRHDAE T0313 220 :LRTTGKLNLVDLAGS 1i6iA 238 :TEKVSKISLVDLAGS T0313 252 :HINKSLSALGDVIAALR 1i6iA 270 :NINKSLTTLGKVISALA T0313 274 :VPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1i6iA 304 :IPYRDSVLTWLLRENLGGNSRTAMVAALSPADINYDETLSTLRYADRAK Number of specific fragments extracted= 12 number of extra gaps= 2 total=157 Will force an alignment to be made, even if fragment is small Number of alignments=16 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i6iA/T0313-1i6iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0313 read from 1i6iA/T0313-1i6iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i6iA read from 1i6iA/T0313-1i6iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1i6iA in template set Warning: unaligning (T0313)T97 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i6iA)K113 Warning: unaligning (T0313)A98 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1i6iA)K113 Warning: unaligning (T0313)E148 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i6iA)N165 Warning: unaligning (T0313)E151 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1i6iA)N165 Warning: unaligning (T0313)E235 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1i6iA)A269 Warning: unaligning (T0313)Q251 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1i6iA)A269 Warning: unaligning (T0313)H273 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1i6iA)F303 T0313 2 :IRVIARVRPVTKEDGEGPEATNA 1i6iA 6 :VKVAVRVRPFNSREMSRDSKCII T0313 26 :TFDADDDSIIH 1i6iA 29 :QMSGSTTTIVN T0313 37 :LLHKGKPVSFELDKVF 1i6iA 41 :KQPKETPKSFSFDYSY T0313 53 :SPQ 1i6iA 61 :SPE T0313 56 :ASQQDVFQEV 1i6iA 68 :ASQKQVYRDI T0313 66 :QALVTSCIDGFNVCIFAYGQTGAGKTYTMEG 1i6iA 79 :EEMLQHAFEGYNVCIFAYGQTGAGKSYTMMG T0313 99 :ENPGINQRALQLLFSEVQEKA 1i6iA 114 :DQQGIIPQLCEDLFSRINDTT T0313 120 :SDWEYTITVSAAEIYNEVLRDLLGKEPQ 1i6iA 136 :DNMSYSVEVSYMEIYCERVRDLLNPKNK T0313 152 :IRLCPDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTG 1i6iA 166 :LRVREHPLLGPYVEDLSKLAVTSYNDIQDLMDSGNKARTVAATNMNETSSRSHAVFNIIFTQKRHDAE T0313 220 :LRTTGKLNLVDLAGS 1i6iA 238 :TEKVSKISLVDLAGS T0313 252 :HINKSLSALGDVIAAL 1i6iA 270 :NINKSLTTLGKVISAL T0313 274 :VPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1i6iA 304 :IPYRDSVLTWLLRENLGGNSRTAMVAALSPADINYDETLSTLRYADRAK Number of specific fragments extracted= 12 number of extra gaps= 2 total=169 Will force an alignment to be made, even if fragment is small Number of alignments=17 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i6iA/T0313-1i6iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0313 read from 1i6iA/T0313-1i6iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i6iA read from 1i6iA/T0313-1i6iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1i6iA in template set Warning: unaligning (T0313)T97 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i6iA)K113 Warning: unaligning (T0313)A98 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1i6iA)K113 Warning: unaligning (T0313)E148 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i6iA)N165 Warning: unaligning (T0313)K149 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1i6iA)N165 Warning: unaligning (T0313)E235 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1i6iA)A269 Warning: unaligning (T0313)Q251 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1i6iA)A269 Warning: unaligning (T0313)H273 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1i6iA)F303 T0313 2 :IRVIARVRPVTKEDGEGPEATNAVTFDADDDSIIHLLHKGKPVSFELDKVF 1i6iA 6 :VKVAVRVRPFNSREMSRDSKCIIQMSGSTTTIVNPKQPKETPKSFSFDYSY T0313 53 :SPQ 1i6iA 61 :SPE T0313 56 :ASQQDVFQ 1i6iA 68 :ASQKQVYR T0313 64 :EVQALVTSCIDGFNVCIFAYGQTGAGKTYTMEG 1i6iA 77 :IGEEMLQHAFEGYNVCIFAYGQTGAGKSYTMMG T0313 99 :ENPGINQRALQLLFSEVQEKA 1i6iA 114 :DQQGIIPQLCEDLFSRINDTT T0313 120 :SDWEYTITVSAAEIYNEVLRDLLGKEPQ 1i6iA 136 :DNMSYSVEVSYMEIYCERVRDLLNPKNK T0313 152 :IRLCPDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTGL 1i6iA 166 :LRVREHPLLGPYVEDLSKLAVTSYNDIQDLMDSGNKARTVAATNMNETSSRSHAVFNIIFTQKRHDAET T0313 221 :RTTGKLNLVDLAGS 1i6iA 239 :EKVSKISLVDLAGS T0313 252 :HINKSLSALGDVIAALRS 1i6iA 270 :NINKSLTTLGKVISALAE T0313 274 :VPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1i6iA 304 :IPYRDSVLTWLLRENLGGNSRTAMVAALSPADINYDETLSTLRYADRAK Number of specific fragments extracted= 10 number of extra gaps= 2 total=179 Will force an alignment to be made, even if fragment is small Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q0bA/T0313-1q0bA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1q0bA expands to /projects/compbio/data/pdb/1q0b.pdb.gz 1q0bA:# T0313 read from 1q0bA/T0313-1q0bA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q0bA read from 1q0bA/T0313-1q0bA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1q0bA to template set # found chain 1q0bA in template set Warning: unaligning (T0313)R236 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1q0bA)I288 Warning: unaligning (T0313)V237 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1q0bA)I288 T0313 1 :NIRVIARVRPVTKEDGEGPEATNAVTFDADDDSIIHLLHKGKP 1q0bA 18 :NIQVVVRCRPFNLAERKASAHSIVECDPVRKEVSVRTGGLADK T0313 44 :VSFELDKVFSPQASQQDVFQE 1q0bA 64 :KTYTFDMVFGASTKQIDVYRS T0313 65 :VQALVTSCIDGFNVCIFAYGQTGAGKTYTMEGT 1q0bA 86 :VCPILDEVIMGYNCTIFAYGQTGTGKTFTMEGE T0313 98 :AENP 1q0bA 128 :EEDP T0313 102 :GINQRALQLLFSEVQE 1q0bA 134 :GIIPRTLHQIFEKLTD T0313 120 :SDWEYTITVSAAEIYNEVLRDLLGKEPQEKLEIRLCPDG 1q0bA 150 :NGTEFSVKVSLLEIYNEELFDLLNPSSDVSERLQMFDDP T0313 159 :SGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDC 1q0bA 191 :KRGVIIKGLEEITVHNKDEVYQILEKGAAKRTTAATLMNAYSSRSHSVFSVTIHMKET T0313 217 :STG 1q0bA 250 :IDG T0313 220 :LRTTGKLNLVDLAGSE 1q0bA 255 :LVKIGKLNLVDLAGSE T0313 254 :NKSLSALGDVIAALRSRQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1q0bA 289 :NQSLLTLGRVITALVERTPHVPYRESKLTRILQDSLGGRTRTSIIATISPASLNLEETLSTLEYAHRAK Number of specific fragments extracted= 10 number of extra gaps= 1 total=189 Will force an alignment to be made, even if fragment is small Number of alignments=19 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q0bA/T0313-1q0bA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0313 read from 1q0bA/T0313-1q0bA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q0bA read from 1q0bA/T0313-1q0bA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1q0bA in template set Warning: unaligning (T0313)R236 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1q0bA)I288 Warning: unaligning (T0313)V237 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1q0bA)I288 T0313 2 :IRVIARVRPVTKEDGEGPEATNAVTFD 1q0bA 19 :IQVVVRCRPFNLAERKASAHSIVECDP T0313 29 :ADDDSIIHLLHKGKP 1q0bA 47 :RKEVSVRTGGLADKS T0313 44 :VSFELDKVFSPQASQQDVFQEV 1q0bA 64 :KTYTFDMVFGASTKQIDVYRSV T0313 66 :QALVTSCIDGFNVCIFAYGQTGAGKTYTMEG 1q0bA 87 :CPILDEVIMGYNCTIFAYGQTGTGKTFTMEG T0313 102 :GINQRALQLLFSEVQE 1q0bA 134 :GIIPRTLHQIFEKLTD T0313 120 :SDWEYTITVSAAEIYNEVLRDLLGKEPQEKLEIRLCPDG 1q0bA 150 :NGTEFSVKVSLLEIYNEELFDLLNPSSDVSERLQMFDDP T0313 159 :SGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGV 1q0bA 191 :KRGVIIKGLEEITVHNKDEVYQILEKGAAKRTTAATLMNAYSSRSHSVFSVTIHMK T0313 215 :DCSTG 1q0bA 248 :TTIDG T0313 220 :LRTTGKLNLVDLAGSE 1q0bA 255 :LVKIGKLNLVDLAGSE T0313 254 :NKSLSALGDVIAALRSRQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1q0bA 289 :NQSLLTLGRVITALVERTPHVPYRESKLTRILQDSLGGRTRTSIIATISPASLNLEETLSTLEYAHRAK Number of specific fragments extracted= 10 number of extra gaps= 1 total=199 Will force an alignment to be made, even if fragment is small Number of alignments=20 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q0bA/T0313-1q0bA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0313 read from 1q0bA/T0313-1q0bA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q0bA read from 1q0bA/T0313-1q0bA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1q0bA in template set Warning: unaligning (T0313)R236 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1q0bA)I288 Warning: unaligning (T0313)V237 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1q0bA)I288 T0313 2 :IRVIARVRPVTKEDGEGPEATNAVTFDADDDSIIHLLHKGK 1q0bA 19 :IQVVVRCRPFNLAERKASAHSIVECDPVRKEVSVRTGGLAD T0313 43 :PVSFELDKVFSPQASQQDVFQ 1q0bA 63 :RKTYTFDMVFGASTKQIDVYR T0313 64 :EVQALVTSCIDGFNVCIFAYGQTGAGKTYTMEG 1q0bA 85 :VVCPILDEVIMGYNCTIFAYGQTGTGKTFTMEG T0313 97 :TAENPGINQRALQLLFSEVQE 1q0bA 129 :EDPLAGIIPRTLHQIFEKLTD T0313 120 :SDWEYTITVSAAEIYNEVLRDLLGKEPQEKLEIRLCPDG 1q0bA 150 :NGTEFSVKVSLLEIYNEELFDLLNPSSDVSERLQMFDDP T0313 159 :SGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTGL 1q0bA 191 :KRGVIIKGLEEITVHNKDEVYQILEKGAAKRTTAATLMNAYSSRSHSVFSVTIHMKETTIDG T0313 221 :RTTGKLNLVDLAGSE 1q0bA 256 :VKIGKLNLVDLAGSE T0313 254 :NKSLSALGDVIAALRSRQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1q0bA 289 :NQSLLTLGRVITALVERTPHVPYRESKLTRILQDSLGGRTRTSIIATISPASLNLEETLSTLEYAHRAK Number of specific fragments extracted= 8 number of extra gaps= 1 total=207 Will force an alignment to be made, even if fragment is small Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i5sA/T0313-1i5sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1i5sA expands to /projects/compbio/data/pdb/1i5s.pdb.gz 1i5sA:Skipped atom 226, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 228, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 230, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 232, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 234, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 236, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 598, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 600, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 602, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 604, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 606, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 608, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 610, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 612, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 661, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 663, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 665, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 667, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 669, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 671, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 673, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 675, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 677, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 679, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 884, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 886, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 888, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 890, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 892, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 894, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 896, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 898, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 900, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 928, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 930, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 932, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 934, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 936, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 938, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 940, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 942, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 944, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 1166, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 1168, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 1170, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 1172, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 1174, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 1176, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 1923, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 1925, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 1927, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 1929, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 1931, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 1933, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 1935, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 1937, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 1939, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 2425, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 2427, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 2429, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 2431, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 2433, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 2435, because occupancy 0.500 <= existing 0.500 in 1i5sA # T0313 read from 1i5sA/T0313-1i5sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i5sA read from 1i5sA/T0313-1i5sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1i5sA to template set # found chain 1i5sA in template set Warning: unaligning (T0313)K42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i5sA)T46 Warning: unaligning (T0313)P43 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1i5sA)T46 Warning: unaligning (T0313)E99 because of BadResidue code BAD_PEPTIDE in next template residue (1i5sA)Q115 Warning: unaligning (T0313)N100 because of BadResidue code BAD_PEPTIDE at template residue (1i5sA)Q115 Warning: unaligning (T0313)P146 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i5sA)K163 Warning: unaligning (T0313)Q147 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1i5sA)K163 Warning: unaligning (T0313)V237 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1i5sA)K261 Warning: unaligning (T0313)E243 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1i5sA)K261 Warning: unaligning (T0313)Q271 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1i5sA)I304 Warning: unaligning (T0313)V274 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1i5sA)I304 Warning: unaligning (T0313)P303 because of BadResidue code BAD_PEPTIDE in next template residue (1i5sA)A334 Warning: unaligning (T0313)V304 because of BadResidue code BAD_PEPTIDE at template residue (1i5sA)A334 T0313 1 :NIRVIARVRPVTKEDGEGPEATNAVT 1i5sA 5 :SVKVAVRVRPFNSREMSRDSKCIIQM T0313 28 :DADDDSIIHLLHKG 1i5sA 31 :SGSTTTIVNPKQPK T0313 44 :VSFELDKVF 1i5sA 48 :KSFSFDYSY T0313 53 :SPQ 1i5sA 61 :SPE T0313 56 :ASQQDVFQE 1i5sA 68 :ASQKQVYRD T0313 65 :VQALVTSCIDGFNVCIFAYGQTGAGKTYTMEG 1i5sA 78 :GEEMLQHAFEGYNVCIFAYGQTGAGKSYTMMG T0313 97 :TA 1i5sA 112 :EK T0313 101 :PGINQRALQLLFSEVQEKA 1i5sA 116 :QGIIPQLCEDLFSRINDTT T0313 120 :SDWEYTITVSAAEIYNEVLRDLLGKE 1i5sA 136 :DNMSYSVEVSYMEIYCERVRDLLNPK T0313 148 :EK 1i5sA 164 :GN T0313 152 :IRLCPDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTG 1i5sA 166 :LRVREHPLLGPYVEDLSKLAVTSYNDIQDLMDSGNKARTVAATNMNETSSRSHAVFNIIFTQKRHDAE T0313 220 :LRTTGKLNLVDLAGSER 1i5sA 238 :TEKVSKISLVDLAGSER T0313 244 :GSRLREAQHINKSLSALGDVIAALRSR 1i5sA 262 :GTRLKEGANINKSLTTLGKVISALAEM T0313 275 :PFRNSKLTYLLQDSLSGDSKTLMVVQVS 1i5sA 305 :PYRDSVLTWLLRENLGGNSRTAMVAALS T0313 305 :EKNTSETLYSLKFAERVR 1i5sA 335 :DINYDETLSTLRYADRAK Number of specific fragments extracted= 15 number of extra gaps= 4 total=222 Will force an alignment to be made, even if fragment is small Number of alignments=22 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i5sA/T0313-1i5sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0313 read from 1i5sA/T0313-1i5sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i5sA read from 1i5sA/T0313-1i5sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1i5sA in template set Warning: unaligning (T0313)K42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i5sA)T46 Warning: unaligning (T0313)P43 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1i5sA)T46 Warning: unaligning (T0313)E99 because of BadResidue code BAD_PEPTIDE in next template residue (1i5sA)Q115 Warning: unaligning (T0313)N100 because of BadResidue code BAD_PEPTIDE at template residue (1i5sA)Q115 Warning: unaligning (T0313)P146 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i5sA)K163 Warning: unaligning (T0313)Q147 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1i5sA)K163 Warning: unaligning (T0313)V237 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1i5sA)K261 Warning: unaligning (T0313)E243 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1i5sA)K261 Warning: unaligning (T0313)Q271 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1i5sA)I304 Warning: unaligning (T0313)V274 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1i5sA)I304 Warning: unaligning (T0313)P303 because of BadResidue code BAD_PEPTIDE in next template residue (1i5sA)A334 Warning: unaligning (T0313)V304 because of BadResidue code BAD_PEPTIDE at template residue (1i5sA)A334 T0313 1 :NIRVIARVRPVTKEDGEGPEAT 1i5sA 5 :SVKVAVRVRPFNSREMSRDSKC T0313 24 :AVTFDADDDSIIHLLHKG 1i5sA 27 :IIQMSGSTTTIVNPKQPK T0313 44 :VSFELDKVF 1i5sA 48 :KSFSFDYSY T0313 53 :SPQ 1i5sA 61 :SPE T0313 56 :ASQQDVFQEV 1i5sA 68 :ASQKQVYRDI T0313 66 :QALVTSCIDGFNVCIFAYGQTGAGKTYTMEG 1i5sA 79 :EEMLQHAFEGYNVCIFAYGQTGAGKSYTMMG T0313 97 :TA 1i5sA 112 :EK T0313 101 :PGINQRALQLLFSEVQEKA 1i5sA 116 :QGIIPQLCEDLFSRINDTT T0313 120 :SDWEYTITVSAAEIYNEVLRDLLGKE 1i5sA 136 :DNMSYSVEVSYMEIYCERVRDLLNPK T0313 148 :E 1i5sA 164 :G T0313 151 :EIRLCPDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTG 1i5sA 165 :NLRVREHPLLGPYVEDLSKLAVTSYNDIQDLMDSGNKARTVAATNMNETSSRSHAVFNIIFTQKRHDAE T0313 220 :LRTTGKLNLVDLAGSER 1i5sA 238 :TEKVSKISLVDLAGSER T0313 244 :GSRLREAQHINKSLSALGDVIAALRSR 1i5sA 262 :GTRLKEGANINKSLTTLGKVISALAEM T0313 275 :PFRNSKLTYLLQDSLSGDSKTLMVVQVS 1i5sA 305 :PYRDSVLTWLLRENLGGNSRTAMVAALS T0313 305 :EKNTSETLYSLKFAERVR 1i5sA 335 :DINYDETLSTLRYADRAK Number of specific fragments extracted= 15 number of extra gaps= 4 total=237 Will force an alignment to be made, even if fragment is small Number of alignments=23 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i5sA/T0313-1i5sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0313 read from 1i5sA/T0313-1i5sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i5sA read from 1i5sA/T0313-1i5sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1i5sA in template set Warning: unaligning (T0313)K42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i5sA)T46 Warning: unaligning (T0313)E99 because of BadResidue code BAD_PEPTIDE in next template residue (1i5sA)Q115 Warning: unaligning (T0313)N100 because of BadResidue code BAD_PEPTIDE at template residue (1i5sA)Q115 Warning: unaligning (T0313)P146 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i5sA)K163 Warning: unaligning (T0313)Q147 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1i5sA)K163 Warning: unaligning (T0313)L220 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i5sA)N235 Warning: unaligning (T0313)V237 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1i5sA)K261 Warning: unaligning (T0313)E243 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1i5sA)K261 Warning: unaligning (T0313)V274 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1i5sA)I304 Warning: unaligning (T0313)P303 because of BadResidue code BAD_PEPTIDE in next template residue (1i5sA)A334 Warning: unaligning (T0313)V304 because of BadResidue code BAD_PEPTIDE at template residue (1i5sA)A334 T0313 1 :NIRVIARVRPVTKEDGEGPEATNA 1i5sA 5 :SVKVAVRVRPFNSREMSRDSKCII T0313 26 :TFDADDDSIIHLLHKG 1i5sA 29 :QMSGSTTTIVNPKQPK T0313 43 :PVSFELDKVF 1i5sA 47 :PKSFSFDYSY T0313 53 :SPQ 1i5sA 61 :SPE T0313 56 :ASQQDVFQ 1i5sA 68 :ASQKQVYR T0313 64 :EVQALVTSCIDGFNVCIFAYGQTGAGKTYTMEG 1i5sA 77 :IGEEMLQHAFEGYNVCIFAYGQTGAGKSYTMMG T0313 97 :TA 1i5sA 112 :EK T0313 101 :PGINQRALQLLFSEVQE 1i5sA 116 :QGIIPQLCEDLFSRIND T0313 118 :KASDWEYTITVSAAEIYNEVLRDLLGKE 1i5sA 134 :TNDNMSYSVEVSYMEIYCERVRDLLNPK T0313 148 :EK 1i5sA 164 :GN T0313 152 :IRLCPDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTG 1i5sA 166 :LRVREHPLLGPYVEDLSKLAVTSYNDIQDLMDSGNKARTVAATNMNETSSRSHAVFNIIFTQKRHDAE T0313 221 :RTTGKLNLVDLAGSER 1i5sA 239 :EKVSKISLVDLAGSER T0313 244 :GSRLREAQHINKSLSALGDVIAALRS 1i5sA 262 :GTRLKEGANINKSLTTLGKVISALAE T0313 275 :PFRNSKLTYLLQDSLSGDSKTLMVVQVS 1i5sA 305 :PYRDSVLTWLLRENLGGNSRTAMVAALS T0313 305 :EKNTSETLYSLKFAERVR 1i5sA 335 :DINYDETLSTLRYADRAK Number of specific fragments extracted= 15 number of extra gaps= 5 total=252 Will force an alignment to be made, even if fragment is small Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ii6A/T0313-1ii6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ii6A expands to /projects/compbio/data/pdb/1ii6.pdb.gz 1ii6A:# T0313 read from 1ii6A/T0313-1ii6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ii6A read from 1ii6A/T0313-1ii6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ii6A to template set # found chain 1ii6A in template set Warning: unaligning (T0313)E235 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ii6A)R281 Warning: unaligning (T0313)R246 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ii6A)R281 T0313 1 :NIRVIARVRPVTKEDGEGPEATNAVTFDADDDSIIHLLHKGKP 1ii6A 18 :NIQVVVRCRPFNLAERKASAHSIVECDPVRKEVSVRTGGLADK T0313 44 :VSFELDKVFSPQASQQDVFQE 1ii6A 64 :KTYTFDMVFGASTKQIDVYRS T0313 65 :VQALVTSCIDGFNVCIFAYGQTGAGKTYTMEG 1ii6A 86 :VCPILDEVIMGYNCTIFAYGQTGTGKTFTMEG T0313 102 :GINQRALQLLFSEVQE 1ii6A 134 :GIIPRTLHQIFEKLTD T0313 120 :SDWEYTITVSAAEIYNEVLRDLLGKEPQEKLEIRLCPDG 1ii6A 150 :NGTEFSVKVSLLEIYNEELFDLLNPSSDVSERLQMFDDP T0313 159 :SGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTG 1ii6A 191 :KRGVIIKGLEEITVHNKDEVYQILEKGAAKRTTAATLMNAYSSRSHSVFSVTIHMKETTID T0313 220 :LRTTGKLNLVDLAGS 1ii6A 255 :LVKIGKLNLVDLAGS T0313 247 :LREAQHINKSLSALGDVIAALRSRQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1ii6A 282 :AREAGNINQSLLTLGRVITALVERTPHVPYRESKLTRILQDSLGGRTRTSIIATISPASLNLEETLSTLEYAHRAK Number of specific fragments extracted= 8 number of extra gaps= 0 total=260 Will force an alignment to be made, even if fragment is small Number of alignments=25 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ii6A/T0313-1ii6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0313 read from 1ii6A/T0313-1ii6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ii6A read from 1ii6A/T0313-1ii6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ii6A in template set Warning: unaligning (T0313)E235 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ii6A)R281 Warning: unaligning (T0313)R246 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ii6A)R281 T0313 1 :NIRVIARVRPVTKEDGEGPEATNAVTFDADDDSIIHLLHKGKP 1ii6A 18 :NIQVVVRCRPFNLAERKASAHSIVECDPVRKEVSVRTGGLADK T0313 44 :VSFELDKVFSPQASQQDVFQEV 1ii6A 64 :KTYTFDMVFGASTKQIDVYRSV T0313 66 :QALVTSCIDGFNVCIFAYGQTGAGKTYTMEG 1ii6A 87 :CPILDEVIMGYNCTIFAYGQTGTGKTFTMEG T0313 97 :TAENP 1ii6A 120 :SPNEE T0313 102 :GINQRALQLLFSEVQE 1ii6A 134 :GIIPRTLHQIFEKLTD T0313 120 :SDWEYTITVSAAEIYNEVLRDLLGKEPQEKLEIRLCPDG 1ii6A 150 :NGTEFSVKVSLLEIYNEELFDLLNPSSDVSERLQMFDDP T0313 159 :SGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDC 1ii6A 191 :KRGVIIKGLEEITVHNKDEVYQILEKGAAKRTTAATLMNAYSSRSHSVFSVTIHMKET T0313 217 :STG 1ii6A 250 :IDG T0313 220 :LRTTGKLNLVDLAGS 1ii6A 255 :LVKIGKLNLVDLAGS T0313 247 :LREAQHINKSLSALGDVIAALRSRQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1ii6A 282 :AREAGNINQSLLTLGRVITALVERTPHVPYRESKLTRILQDSLGGRTRTSIIATISPASLNLEETLSTLEYAHRAK Number of specific fragments extracted= 10 number of extra gaps= 0 total=270 Will force an alignment to be made, even if fragment is small Number of alignments=26 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ii6A/T0313-1ii6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0313 read from 1ii6A/T0313-1ii6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ii6A read from 1ii6A/T0313-1ii6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ii6A in template set Warning: unaligning (T0313)E235 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ii6A)R281 Warning: unaligning (T0313)R246 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ii6A)R281 T0313 1 :NIRVIARVRPVTKEDGEGPEATNAVTFDADDDSIIHLLHKGK 1ii6A 18 :NIQVVVRCRPFNLAERKASAHSIVECDPVRKEVSVRTGGLAD T0313 43 :PVSFELDKVFSPQASQQDVFQ 1ii6A 63 :RKTYTFDMVFGASTKQIDVYR T0313 64 :EVQALVTSCIDGFNVCIFAYGQTGAGKTYTMEG 1ii6A 85 :VVCPILDEVIMGYNCTIFAYGQTGTGKTFTMEG T0313 97 :TAENPGINQRALQLLFSEVQE 1ii6A 129 :EDPLAGIIPRTLHQIFEKLTD T0313 120 :SDWEYTITVSAAEIYNEVLRDLLGKEPQEKLEIRLCPDG 1ii6A 150 :NGTEFSVKVSLLEIYNEELFDLLNPSSDVSERLQMFDDP T0313 159 :SGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTGL 1ii6A 191 :KRGVIIKGLEEITVHNKDEVYQILEKGAAKRTTAATLMNAYSSRSHSVFSVTIHMKETTIDG T0313 221 :RTTGKLNLVDLAGS 1ii6A 256 :VKIGKLNLVDLAGS T0313 247 :LREAQHINKSLSALGDVIAALRSRQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1ii6A 282 :AREAGNINQSLLTLGRVITALVERTPHVPYRESKLTRILQDSLGGRTRTSIIATISPASLNLEETLSTLEYAHRAK Number of specific fragments extracted= 8 number of extra gaps= 0 total=278 Will force an alignment to be made, even if fragment is small Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cz7A/T0313-1cz7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1cz7A expands to /projects/compbio/data/pdb/1cz7.pdb.gz 1cz7A:# T0313 read from 1cz7A/T0313-1cz7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cz7A read from 1cz7A/T0313-1cz7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1cz7A to template set # found chain 1cz7A in template set Warning: unaligning (T0313)G241 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cz7A)I599 Warning: unaligning (T0313)I253 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cz7A)I599 T0313 2 :IRVIARVRPVTKEDG 1cz7A 349 :IRVFCRIRPPLESEE T0313 19 :PEATNAVTFDADDDSIIHLLHKG 1cz7A 364 :NRMCCTWTYHDESTVELQSIDAQ T0313 42 :KPVSFELDKVFSPQASQQDVFQEVQALVTSCIDGFNVCIFAYGQTGAGKTYTMEGTAENPGINQRALQLLFSEVQEKAS 1cz7A 392 :GQQIFSFDQVFHPLSSQSDIFEMVSPLIQSALDGYNICIFAYGQTGSGKTYTMDGVPESVGVIPRTVDLLFDSIRGYRN T0313 121 :DWEYTITVSAAEIYNEVLRDLLGKEPQE 1cz7A 472 :GWEYEIKATFLEIYNEVLYDLLSNEQKD T0313 152 :IRLCPDGSGQ 1cz7A 500 :MEIRMAKNNK T0313 162 :LYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTGLRTTGKLNLVDLAGSE 1cz7A 512 :IYVSNITEETVLDPNHLRHLMHTAKMNRATASTAGNERSSRSHAVTKLELIGRHAEKQEISVGSINLVDLAGSE T0313 240 :S 1cz7A 586 :S T0313 254 :NKSLSALGDVIAALRSRQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERV 1cz7A 600 :NRSLSELTNVILALLQKQDHIPYRNSKLTHLLMPSLGGNSKTLMFINVSPFQDCFQESVKSLRFAASV Number of specific fragments extracted= 8 number of extra gaps= 0 total=286 Will force an alignment to be made, even if fragment is small Number of alignments=28 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cz7A/T0313-1cz7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0313 read from 1cz7A/T0313-1cz7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cz7A read from 1cz7A/T0313-1cz7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cz7A in template set Warning: unaligning (T0313)G241 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cz7A)I599 Warning: unaligning (T0313)I253 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cz7A)I599 T0313 2 :IRVIARVRPVTKEDGE 1cz7A 349 :IRVFCRIRPPLESEEN T0313 19 :PEATNAVTFDADDDSIIH 1cz7A 365 :RMCCTWTYHDESTVELQS T0313 37 :LLHKGKPVSFELDKVFSPQASQQDVFQEVQALVTSCIDGFNVCIFAYGQTGAGKTYTMEGTAENPGINQRALQLLFSEVQEKAS 1cz7A 387 :AKSKMGQQIFSFDQVFHPLSSQSDIFEMVSPLIQSALDGYNICIFAYGQTGSGKTYTMDGVPESVGVIPRTVDLLFDSIRGYRN T0313 121 :DWEYTITVSAAEIYNEVLRDLLGKEPQ 1cz7A 472 :GWEYEIKATFLEIYNEVLYDLLSNEQK T0313 149 :KLEIRLCPDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTGLRTTGKLNLVDLAGSE 1cz7A 499 :DMEIRMAKNNKNDIYVSNITEETVLDPNHLRHLMHTAKMNRATASTAGNERSSRSHAVTKLELIGRHAEKQEISVGSINLVDLAGSE T0313 240 :S 1cz7A 586 :S T0313 254 :NKSLSALGDVIAALRSRQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1cz7A 600 :NRSLSELTNVILALLQKQDHIPYRNSKLTHLLMPSLGGNSKTLMFINVSPFQDCFQESVKSLRFAASVN Number of specific fragments extracted= 7 number of extra gaps= 0 total=293 Will force an alignment to be made, even if fragment is small Number of alignments=29 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cz7A/T0313-1cz7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0313 read from 1cz7A/T0313-1cz7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cz7A read from 1cz7A/T0313-1cz7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cz7A in template set Warning: unaligning (T0313)G241 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cz7A)I599 Warning: unaligning (T0313)I253 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cz7A)I599 T0313 1 :NIRVIARVRPVTKEDGEGPEA 1cz7A 348 :NIRVFCRIRPPLESEENRMCC T0313 24 :AVTFDADDDSIIHLL 1cz7A 369 :TWTYHDESTVELQSI T0313 39 :HKGKPVSFELDKVFSPQASQQDVFQEVQALVTSCIDGFNVCIFAYGQTGAGKTYTMEGTAENPGINQRALQLLFSEVQEKAS 1cz7A 389 :SKMGQQIFSFDQVFHPLSSQSDIFEMVSPLIQSALDGYNICIFAYGQTGSGKTYTMDGVPESVGVIPRTVDLLFDSIRGYRN T0313 121 :DWEYTITVSAAEIYNEVLRDLLGKEPQE 1cz7A 472 :GWEYEIKATFLEIYNEVLYDLLSNEQKD T0313 150 :LEIRLCPDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTGLRTTGKLNLVDLAGSE 1cz7A 500 :MEIRMAKNNKNDIYVSNITEETVLDPNHLRHLMHTAKMNRATASTAGNERSSRSHAVTKLELIGRHAEKQEISVGSINLVDLAGSE T0313 240 :S 1cz7A 586 :S T0313 254 :NKSLSALGDVIAALRSRQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERV 1cz7A 600 :NRSLSELTNVILALLQKQDHIPYRNSKLTHLLMPSLGGNSKTLMFINVSPFQDCFQESVKSLRFAASV Number of specific fragments extracted= 7 number of extra gaps= 0 total=300 Will force an alignment to be made, even if fragment is small Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2kinA/T0313-2kinA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2kinA expands to /projects/compbio/data/pdb/2kin.pdb.gz 2kinA:Skipped atom 1516, because occupancy 0.500 <= existing 0.500 in 2kinA Skipped atom 1518, because occupancy 0.500 <= existing 0.500 in 2kinA Skipped atom 1520, because occupancy 0.500 <= existing 0.500 in 2kinA Skipped atom 1522, because occupancy 0.500 <= existing 0.500 in 2kinA Skipped atom 1524, because occupancy 0.500 <= existing 0.500 in 2kinA Skipped atom 1526, because occupancy 0.500 <= existing 0.500 in 2kinA Skipped atom 1528, because occupancy 0.500 <= existing 0.500 in 2kinA Skipped atom 1636, because occupancy 0.500 <= existing 0.500 in 2kinA Skipped atom 1638, because occupancy 0.500 <= existing 0.500 in 2kinA # T0313 read from 2kinA/T0313-2kinA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2kinA read from 2kinA/T0313-2kinA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2kinA to template set # found chain 2kinA in template set Warning: unaligning (T0313)T86 because of BadResidue code BAD_PEPTIDE in next template residue (2kinA)S89 Warning: unaligning (T0313)G87 because of BadResidue code BAD_PEPTIDE at template residue (2kinA)S89 T0313 2 :IRVIARVRPVTKEDGEGPEATNAVTFDADDDSI 2kinA 9 :IKVMCRFRPLNEAEILRGDKFIPKFKGEETVVI T0313 41 :GKPVSFELDKVFSPQASQQDVFQEV 2kinA 42 :GQGKPYVFDRVLPPNTTQEQVYNAC T0313 66 :QALVTSCIDGFNVCIFAYGQ 2kinA 68 :KQIVKDVLEGYNGTIFAYGQ T0313 88 :AGKTYTMEGTAENP 2kinA 90 :SGKTHTMEGKLHDP T0313 102 :GINQRALQLLFSEVQEKASDWEYTITVSAAEIYNEVLRDLLGKEPQE 2kinA 107 :GIIPRIAHDIFDHIYSMDENLEFHIKVSYFEIYLDKIRDLLDVSKTN T0313 152 :IRLCPDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTGLRTTGKLNLVDLAGSER 2kinA 154 :LAVHEDKNRVPYVKGCTERFVSSPEEVMDVIDEGKANRHVAVTNMNEHSSRSHSIFLINIKQENVETEKKLSGKLYLVDLAGSEK Number of specific fragments extracted= 6 number of extra gaps= 1 total=306 Will force an alignment to be made, even if fragment is small Number of alignments=31 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2kinA/T0313-2kinA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0313 read from 2kinA/T0313-2kinA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2kinA read from 2kinA/T0313-2kinA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2kinA in template set Warning: unaligning (T0313)T86 because of BadResidue code BAD_PEPTIDE in next template residue (2kinA)S89 Warning: unaligning (T0313)G87 because of BadResidue code BAD_PEPTIDE at template residue (2kinA)S89 T0313 3 :RVIARVRPVTKEDGEGPEATNAVTFDADDDSI 2kinA 10 :KVMCRFRPLNEAEILRGDKFIPKFKGEETVVI T0313 39 :HKGKP 2kinA 42 :GQGKP T0313 46 :FELDKVFSPQASQQDVFQEV 2kinA 47 :YVFDRVLPPNTTQEQVYNAC T0313 66 :QALVTSCIDGFNVCIFAYGQ 2kinA 68 :KQIVKDVLEGYNGTIFAYGQ T0313 88 :AGKTYTMEG 2kinA 90 :SGKTHTMEG T0313 97 :TAENPGINQRALQLLFSEVQEKASDWEYTITVSAAEIYNEVLRDLLGKEPQ 2kinA 102 :DPQLMGIIPRIAHDIFDHIYSMDENLEFHIKVSYFEIYLDKIRDLLDVSKT T0313 151 :EIRLCPDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTGLRTTGKLNLVDLAGSER 2kinA 153 :NLAVHEDKNRVPYVKGCTERFVSSPEEVMDVIDEGKANRHVAVTNMNEHSSRSHSIFLINIKQENVETEKKLSGKLYLVDLAGSEK Number of specific fragments extracted= 7 number of extra gaps= 1 total=313 Will force an alignment to be made, even if fragment is small Number of alignments=32 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2kinA/T0313-2kinA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0313 read from 2kinA/T0313-2kinA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2kinA read from 2kinA/T0313-2kinA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2kinA in template set Warning: unaligning (T0313)T86 because of BadResidue code BAD_PEPTIDE in next template residue (2kinA)S89 Warning: unaligning (T0313)G87 because of BadResidue code BAD_PEPTIDE at template residue (2kinA)S89 T0313 3 :RVIARVRPVTKEDGEGPEATNAVTFDADDDSI 2kinA 10 :KVMCRFRPLNEAEILRGDKFIPKFKGEETVVI T0313 41 :GKPVSFELDKVFSPQASQQDVFQ 2kinA 42 :GQGKPYVFDRVLPPNTTQEQVYN T0313 64 :EVQALVTSCIDGFNVCIFAYGQ 2kinA 66 :CAKQIVKDVLEGYNGTIFAYGQ T0313 88 :AGKTYTMEG 2kinA 90 :SGKTHTMEG T0313 97 :TAENPGINQRALQLLFSEVQEKASDWEYTITVSAAEIYNEVLRDLLGKEPQE 2kinA 102 :DPQLMGIIPRIAHDIFDHIYSMDENLEFHIKVSYFEIYLDKIRDLLDVSKTN T0313 152 :IRLCPDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTGLRTTGKLNLVDLAGSER 2kinA 154 :LAVHEDKNRVPYVKGCTERFVSSPEEVMDVIDEGKANRHVAVTNMNEHSSRSHSIFLINIKQENVETEKKLSGKLYLVDLAGSEK Number of specific fragments extracted= 6 number of extra gaps= 1 total=319 Will force an alignment to be made, even if fragment is small Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3kar/T0313-3kar-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3kar expands to /projects/compbio/data/pdb/3kar.pdb.gz 3kar:Warning: there is no chain 3kar will retry with 3karA # T0313 read from 3kar/T0313-3kar-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3kar read from 3kar/T0313-3kar-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3kar to template set # found chain 3kar in template set Warning: unaligning (T0313)K144 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3kar)L545 Warning: unaligning (T0313)L150 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3kar)L545 Warning: unaligning (T0313)S240 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3kar)D641 Warning: unaligning (T0313)S245 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3kar)D641 T0313 1 :NIRVIARVRPVTKEDGEGPEATNAVT 3kar 386 :NIRVYCRIRPALKNLENSDTSLINVN T0313 27 :FDADDDSIIHLLHKGKP 3kar 414 :DDNSGVQSMEVTKIQNT T0313 44 :VSFELDKVFSPQASQQDVFQEVQALVTSCIDGFNVCIFAYGQTGAGKTYTMEGTA 3kar 434 :HEFKFDKIFDQQDTNVDVFKEVGQLVQSSLDGYNVCIFAYGQTGSGKTFTMLNPG T0313 101 :PGINQRALQLLFSEVQEK 3kar 489 :DGIIPSTISHIFNWINKL T0313 119 :ASDWEYTITVSAAEIYNEVLRDLLG 3kar 508 :TKGWDYKVNCEFIEIYNENIVDLLR T0313 151 :EIRLCPDGSGQ 3kar 546 :KHEIRHDQETK T0313 162 :LYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTGLRTTGKLNLVDLAGSERVGK 3kar 558 :TTITNVTSCKLESEEMVEIILKKANKLRSTASTASNEHSSRSHSIFIIHLSGSNAKTGAHSYGTLNLVDLAGSERINV T0313 246 :RLREAQHINKSLSALGDVIAALRS 3kar 642 :RLRETQNINKSLSCLGDVIHALGQ T0313 270 :RQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERV 3kar 669 :TKRHIPFRNSKLTYLLQYSLTGDSKTLMFVNISPSSSHINETLNSLRFASKV Number of specific fragments extracted= 9 number of extra gaps= 0 total=328 Will force an alignment to be made, even if fragment is small Number of alignments=34 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3kar/T0313-3kar-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0313 read from 3kar/T0313-3kar-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3kar read from 3kar/T0313-3kar-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3kar in template set Warning: unaligning (T0313)K144 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3kar)L545 Warning: unaligning (T0313)L150 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3kar)L545 Warning: unaligning (T0313)S240 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3kar)D641 Warning: unaligning (T0313)S245 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3kar)D641 T0313 1 :NIRVIARVRPVTKEDGEGPEATNAVT 3kar 386 :NIRVYCRIRPALKNLENSDTSLINVN T0313 27 :FDADDDSIIH 3kar 414 :DDNSGVQSME T0313 37 :LLHKGKPVSFELDKVFSPQASQQDVFQEVQALVTSCIDGFNVCIFAYGQTGAGKTYTME 3kar 427 :IQNTAQVHEFKFDKIFDQQDTNVDVFKEVGQLVQSSLDGYNVCIFAYGQTGSGKTFTML T0313 98 :AENPGINQRALQLLFSEVQEK 3kar 486 :NPGDGIIPSTISHIFNWINKL T0313 119 :ASDWEYTITVSAAEIYNEVLRDLLG 3kar 508 :TKGWDYKVNCEFIEIYNENIVDLLR T0313 151 :EIRLCPDGS 3kar 546 :KHEIRHDQE T0313 160 :GQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTGLRTTGKLNLVDLAGSERVGK 3kar 556 :KTTTITNVTSCKLESEEMVEIILKKANKLRSTASTASNEHSSRSHSIFIIHLSGSNAKTGAHSYGTLNLVDLAGSERINV T0313 246 :RLREAQHINKSLSALGDVIAALRS 3kar 642 :RLRETQNINKSLSCLGDVIHALGQ T0313 270 :RQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERV 3kar 669 :TKRHIPFRNSKLTYLLQYSLTGDSKTLMFVNISPSSSHINETLNSLRFASKV Number of specific fragments extracted= 9 number of extra gaps= 0 total=337 Will force an alignment to be made, even if fragment is small Number of alignments=35 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3kar/T0313-3kar-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0313 read from 3kar/T0313-3kar-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3kar read from 3kar/T0313-3kar-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3kar in template set Warning: unaligning (T0313)E148 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3kar)L545 Warning: unaligning (T0313)S240 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3kar)D641 Warning: unaligning (T0313)S245 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3kar)D641 T0313 1 :NIRVIARVRPVTKEDGEGPEATNAV 3kar 386 :NIRVYCRIRPALKNLENSDTSLINV T0313 26 :TFDADDDSI 3kar 412 :EFDDNSGVQ T0313 35 :IHLLHKGKPVSFELDKVFSPQASQQDVFQEVQALVTSCIDGFNVCIFAYGQTGAGKTYTME 3kar 425 :TKIQNTAQVHEFKFDKIFDQQDTNVDVFKEVGQLVQSSLDGYNVCIFAYGQTGSGKTFTML T0313 98 :AENPGINQRALQLLFSEVQE 3kar 486 :NPGDGIIPSTISHIFNWINK T0313 118 :KASDWEYTITVSAAEIYNEVLRDLL 3kar 507 :KTKGWDYKVNCEFIEIYNENIVDLL T0313 149 :KLEIRL 3kar 546 :KHEIRH T0313 156 :PDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTGLRTTGKLNLVDLAGSERVGK 3kar 552 :DQETKTTTITNVTSCKLESEEMVEIILKKANKLRSTASTASNEHSSRSHSIFIIHLSGSNAKTGAHSYGTLNLVDLAGSERINV T0313 246 :RLREAQHINKSLSALGDVIAALRS 3kar 642 :RLRETQNINKSLSCLGDVIHALGQ T0313 270 :RQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERV 3kar 669 :TKRHIPFRNSKLTYLLQYSLTGDSKTLMFVNISPSSSHINETLNSLRFASKV Number of specific fragments extracted= 9 number of extra gaps= 0 total=346 Will force an alignment to be made, even if fragment is small Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2kinB/T0313-2kinB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2kinB expands to /projects/compbio/data/pdb/2kin.pdb.gz 2kinB:# T0313 read from 2kinB/T0313-2kinB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2kinB read from 2kinB/T0313-2kinB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2kinB to template set # found chain 2kinB in template set Warning: unaligning (T0313)G272 because of BadResidue code BAD_PEPTIDE at template residue (2kinB)T275 T0313 255 :KSLSALGDVIAALRSRQ 2kinB 257 :KSLSALGNVISALAEGT T0313 273 :HVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 2kinB 276 :HVPYRDSKMTRILQDSLDGNCRTTIVICCSPSVFNEAETKSTLMFGQRAK Number of specific fragments extracted= 2 number of extra gaps= 1 total=348 Will force an alignment to be made, even if fragment is small Number of alignments=37 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2kinB/T0313-2kinB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0313 read from 2kinB/T0313-2kinB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2kinB read from 2kinB/T0313-2kinB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2kinB in template set Warning: unaligning (T0313)G272 because of BadResidue code BAD_PEPTIDE in next template residue (2kinB)T275 T0313 255 :KSLSALGDVIAALRSRQ 2kinB 257 :KSLSALGNVISALAEGT T0313 273 :HVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 2kinB 276 :HVPYRDSKMTRILQDSLDGNCRTTIVICCSPSVFNEAETKSTLMFGQRAK Number of specific fragments extracted= 2 number of extra gaps= 1 total=350 Will force an alignment to be made, even if fragment is small Number of alignments=38 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2kinB/T0313-2kinB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0313 read from 2kinB/T0313-2kinB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2kinB read from 2kinB/T0313-2kinB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2kinB in template set Warning: unaligning (T0313)Q271 because of BadResidue code BAD_PEPTIDE in next template residue (2kinB)T275 Warning: unaligning (T0313)G272 because of BadResidue code BAD_PEPTIDE at template residue (2kinB)T275 T0313 255 :KSLSALGDVIAALRS 2kinB 257 :KSLSALGNVISALAE T0313 270 :R 2kinB 273 :T T0313 273 :HVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 2kinB 276 :HVPYRDSKMTRILQDSLDGNCRTTIVICCSPSVFNEAETKSTLMFGQRAK Number of specific fragments extracted= 3 number of extra gaps= 1 total=353 Will force an alignment to be made, even if fragment is small Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mkjA/T0313-1mkjA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1mkjA expands to /projects/compbio/data/pdb/1mkj.pdb.gz 1mkjA:# T0313 read from 1mkjA/T0313-1mkjA-t06-local-adpstyle5.a2m # 1mkjA read from 1mkjA/T0313-1mkjA-t06-local-adpstyle5.a2m # adding 1mkjA to template set # found chain 1mkjA in template set Warning: unaligning (T0313)V237 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1mkjA)A251 Warning: unaligning (T0313)A250 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1mkjA)A251 T0313 1 :NIRVIARVRPVTKEDGEGPEATNAVTFDADDDSI 1mkjA 8 :NIKVMCRFRPLNESEVNRGDKYIAKFQGEDTVVI T0313 42 :KPVSFELDKVFSPQASQQDVFQE 1mkjA 42 :ASKPYAFDRVFQSSTSQEQVYND T0313 65 :VQALVTSCIDGFNVCIFAYGQTGAGKTYTMEG 1mkjA 66 :AKKIVKDVLEGYNGTIFAYGQTSSGKTHTMEG T0313 97 :TAENPGINQRALQLLFSEVQEKASDWEYTITVSAAEIYNEVLRDLLGKEPQE 1mkjA 101 :DPEGMGIIPRIVQDIFNYIYSMDENLEFHIKVSYFEIYLDKIRDLLDVSKTN T0313 152 :IRLCPDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTGLRTTGKLNLVDLAGSER 1mkjA 153 :LSVHEDKNRVPYVKGCTERFVCSPDEVMDTIDEGKSNRHVAVTNMNEHSSRSHSIFLINVKQENTQTEQKLSGKLYLVDLAGSEK T0313 251 :QHINKSLSALGDVIAALRSRQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1mkjA 252 :KNINKSLSALGNVISALAEGSTYVPYRDSKMTRILQDSLGGNCRTTIVICCSPSSYNESETKSTLLFGQRAK Number of specific fragments extracted= 6 number of extra gaps= 0 total=359 Will force an alignment to be made, even if fragment is small Number of alignments=40 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gojA/T0313-1gojA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1gojA expands to /projects/compbio/data/pdb/1goj.pdb.gz 1gojA:# T0313 read from 1gojA/T0313-1gojA-t06-local-adpstyle5.a2m # 1gojA read from 1gojA/T0313-1gojA-t06-local-adpstyle5.a2m # adding 1gojA to template set # found chain 1gojA in template set T0313 2 :IRVIARVRPVTKEDGEGPEATNAVTFDADDDSII 1gojA 8 :IKVVARFRPQNRVEIESGGQPIVTFQGPDTCTVD T0313 39 :HKGKPVSFELDKVFSPQASQQDVFQE 1gojA 42 :SKEAQGSFTFDRVFDMSCKQSDIFDF T0313 65 :VQALVTSCIDGFNVCIFAYGQTGAGKTYTMEGT 1gojA 69 :IKPTVDDILNGYNGTVFAYGQTGAGKSYTMMGT T0313 98 :AENPGINQRALQLLFSEVQEKASDWEYTITVSAAEIYNEVLRDLLGKEPQE 1gojA 106 :PDGRGVIPRIVEQIFTSILSSAANIEYTVRVSYMEIYMERIRDLLAPQNDN T0313 152 :IRLCPDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTGLRTTGKLNLVDLAGSERVGKSGAEGSRLREAQHINKSLSALGDVIAALRSRQG 1gojA 157 :LPVHEEKNRGVYVKGLLEIYVSSVQEVYEVMRRGGNARAVAATNMNQESSRSHSIFVITITQKNVETGSAKSGQLFLVDLAGSEKVGKTGASGQTLEEAKKINKSLSALGMVINALTDGKS T0313 273 :HVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1gojA 279 :HVPYRDSKLTRILQESLGGNSRTTLIINCSPSSYNDAETLSTLRFGMRAK Number of specific fragments extracted= 6 number of extra gaps= 0 total=365 Will force an alignment to be made, even if fragment is small Number of alignments=41 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ia0K/T0313-1ia0K-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ia0K expands to /projects/compbio/data/pdb/1ia0.pdb.gz 1ia0K:Skipped atom 6904, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 6906, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 6908, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 6910, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 6912, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 6914, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 6916, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 6918, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 6920, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 6922, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 6924, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 6949, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 6951, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 6953, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 6955, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 6957, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 6959, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 6961, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 6963, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 6965, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 6967, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 6969, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 7362, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 7364, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 7366, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 7368, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 7370, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 7372, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 7374, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 7376, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 7378, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 7418, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 7420, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 7422, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 7424, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 7426, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 7428, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 7430, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 7432, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 7472, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 7474, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 7476, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 7478, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 7480, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 7482, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 7484, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 7486, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 7488, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 7967, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 7969, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 7971, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 7973, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 7975, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 7977, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 8490, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 8492, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 8494, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 8496, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 8498, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 8500, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 8502, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 8504, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 8757, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 8759, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 8761, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 8763, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 8765, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 8767, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 8786, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 8788, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 8790, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 8792, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 8794, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 8796, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 9295, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 9297, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 9299, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 9301, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 9303, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 9305, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 9307, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 9309, because occupancy 0.500 <= existing 0.500 in 1ia0K Skipped atom 9311, because occupancy 0.500 <= existing 0.500 in 1ia0K # T0313 read from 1ia0K/T0313-1ia0K-t06-local-adpstyle5.a2m # 1ia0K read from 1ia0K/T0313-1ia0K-t06-local-adpstyle5.a2m # adding 1ia0K to template set # found chain 1ia0K in template set Warning: unaligning (T0313)T97 because of BadResidue code BAD_PEPTIDE in next template residue (1ia0K)K113 Warning: unaligning (T0313)A98 because of BadResidue code BAD_PEPTIDE at template residue (1ia0K)K113 Warning: unaligning (T0313)E235 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ia0K)A269 Warning: unaligning (T0313)Q251 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ia0K)A269 Warning: unaligning (T0313)H273 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ia0K)F303 T0313 2 :IRVIARVRPVTKEDGEGPEATNAVTFDADDDSIIHLLHKGKPVSFELDKVF 1ia0K 6 :VKVAVRVRPFNSREMSRDSKCIIQMSGSTTTIVNPKQPKETPKSFSFDYSY T0313 56 :ASQQDVFQEV 1ia0K 68 :ASQKQVYRDI T0313 66 :QALVTSCIDGFNVCIFAYGQTGAGKTYTMEG 1ia0K 79 :EEMLQHAFEGYNVCIFAYGQTGAGKSYTMMG T0313 99 :ENPGINQRALQLLFSEVQEKA 1ia0K 114 :DQQGIIPQLCEDLFSRINDTT T0313 120 :SDWEYTITVSAAEIYNEVLRDLLGKEPQEK 1ia0K 136 :DNMSYSVEVSYMEIYCERVRDLLNPKNKGN T0313 152 :IRLCPDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTGLR 1ia0K 166 :LRVREHPLLGPYVEDLSKLAVTSYNDIQDLMDSGNKARTVAATNMNETSSRSHAVFNIIFTQKRHDAETN T0313 222 :TTGKLNLVDLAGS 1ia0K 240 :KVSKISLVDLAGS T0313 252 :HINKSLSALGDVIAALR 1ia0K 270 :NINKSLTTLGKVISALA T0313 274 :VPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1ia0K 304 :IPYRDSVLTWLLRENLGGNSRTAMVAALSPADINYDETLSTLRYADRAK Number of specific fragments extracted= 9 number of extra gaps= 1 total=374 Will force an alignment to be made, even if fragment is small Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sdmA/T0313-1sdmA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1sdmA expands to /projects/compbio/data/pdb/1sdm.pdb.gz 1sdmA:# T0313 read from 1sdmA/T0313-1sdmA-t06-local-adpstyle5.a2m # 1sdmA read from 1sdmA/T0313-1sdmA-t06-local-adpstyle5.a2m # adding 1sdmA to template set # found chain 1sdmA in template set Warning: unaligning (T0313)H36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1sdmA)K925 Warning: unaligning (T0313)L37 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1sdmA)K925 Warning: unaligning (T0313)L38 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1sdmA)D926 Warning: unaligning (T0313)H39 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1sdmA)D927 Warning: unaligning (T0313)K40 because of BadResidue code BAD_PEPTIDE at template residue (1sdmA)K928 Warning: unaligning (T0313)P43 because of BadResidue code BAD_PEPTIDE at template residue (1sdmA)A929 Warning: unaligning (T0313)K239 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1sdmA)E1135 Warning: unaligning (T0313)E249 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1sdmA)E1135 Warning: unaligning (T0313)A250 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1sdmA)A1136 Warning: unaligning (T0313)I253 because of BadResidue code BAD_PEPTIDE in next template residue (1sdmA)N1140 Warning: unaligning (T0313)N254 because of BadResidue code BAD_PEPTIDE at template residue (1sdmA)N1140 T0313 1 :NIRVIARVRPVTKEDGEGPEATNAVTFDADDDSII 1sdmA 889 :KIRVYCRLRPLCEKEIIAKERNAIRSVDEFTVEHL T0313 44 :VSFELDKVFSPQASQQDVFQEVQALVTSCIDGFNVCIFAYGQTGAGKTYTMEGTAENPGINQRALQLLFSEVQEKASDWEYTITVSAAEIYNEVLRDLLGKEPQEKLEIRLCPDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTGLRTTGKLNLVDLAGSERVG 1sdmA 930 :KQHMYDRVFDGNATQDDVFEDTKYLVQSAVDGYNVCIFAYGQTGSGKTFTIYGADSNPGLTPRAMSELFRIMKKDSNKFSFSLKAYMVELYQDTLVDLLLPKQAKRLKLDIKKDSKGMVSVENVTVVSISTYEELKTIIQRGSEQRHTTGTLMNEQSSRSHLIVSVIIESTNLQTQAIARGKLSFVDLAGSERVK T0313 251 :QH 1sdmA 1137 :QS T0313 255 :KSLSALGDVIAALRSRQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1sdmA 1141 :KSLSALGDVISALSSGNQHIPYRNHKLTMLMSDSLGGNAKTLMFVNISPAESNLDETHNSLTYASRVR Number of specific fragments extracted= 4 number of extra gaps= 2 total=378 Will force an alignment to be made, even if fragment is small Number of alignments=43 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t5cA/T0313-1t5cA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1t5cA expands to /projects/compbio/data/pdb/1t5c.pdb.gz 1t5cA:Skipped atom 220, because occupancy 0.300 <= existing 0.700 in 1t5cA Skipped atom 222, because occupancy 0.300 <= existing 0.700 in 1t5cA Skipped atom 224, because occupancy 0.300 <= existing 0.700 in 1t5cA Skipped atom 226, because occupancy 0.300 <= existing 0.700 in 1t5cA Skipped atom 228, because occupancy 0.300 <= existing 0.700 in 1t5cA Skipped atom 230, because occupancy 0.300 <= existing 0.700 in 1t5cA Skipped atom 232, because occupancy 0.300 <= existing 0.700 in 1t5cA Skipped atom 234, because occupancy 0.300 <= existing 0.700 in 1t5cA Skipped atom 236, because occupancy 0.300 <= existing 0.700 in 1t5cA Skipped atom 967, because occupancy 0.500 <= existing 0.500 in 1t5cA Skipped atom 969, because occupancy 0.400 <= existing 0.600 in 1t5cA Skipped atom 971, because occupancy 0.500 <= existing 0.500 in 1t5cA Skipped atom 973, because occupancy 0.500 <= existing 0.500 in 1t5cA Skipped atom 975, because occupancy 0.500 <= existing 0.500 in 1t5cA Skipped atom 977, because occupancy 0.500 <= existing 0.500 in 1t5cA Skipped atom 979, because occupancy 0.500 <= existing 0.500 in 1t5cA Skipped atom 981, because occupancy 0.500 <= existing 0.500 in 1t5cA Skipped atom 983, because occupancy 0.500 <= existing 0.500 in 1t5cA Skipped atom 985, because occupancy 0.500 <= existing 0.500 in 1t5cA Skipped atom 987, because occupancy 0.500 <= existing 0.500 in 1t5cA Skipped atom 1967, because occupancy 0.500 <= existing 0.500 in 1t5cA Skipped atom 1969, because occupancy 0.500 <= existing 0.500 in 1t5cA Skipped atom 1971, because occupancy 0.500 <= existing 0.500 in 1t5cA Skipped atom 1973, because occupancy 0.500 <= existing 0.500 in 1t5cA Skipped atom 1975, because occupancy 0.500 <= existing 0.500 in 1t5cA Skipped atom 1977, because occupancy 0.500 <= existing 0.500 in 1t5cA # T0313 read from 1t5cA/T0313-1t5cA-t06-local-adpstyle5.a2m # 1t5cA read from 1t5cA/T0313-1t5cA-t06-local-adpstyle5.a2m # adding 1t5cA to template set # found chain 1t5cA in template set Warning: unaligning (T0313)K13 because of BadResidue code BAD_PEPTIDE in next template residue (1t5cA)R19 Warning: unaligning (T0313)E14 because of BadResidue code BAD_PEPTIDE at template residue (1t5cA)R19 Warning: unaligning (T0313)E17 because of BadResidue code BAD_PEPTIDE in next template residue (1t5cA)L23 Warning: unaligning (T0313)G18 because of BadResidue code BAD_PEPTIDE at template residue (1t5cA)L23 Warning: unaligning (T0313)P19 because of BadResidue code BAD_PEPTIDE at template residue (1t5cA)G24 Warning: unaligning (T0313)Y124 because of BadResidue code BAD_PEPTIDE in next template residue (1t5cA)L126 Warning: unaligning (T0313)T125 because of BadResidue code BAD_PEPTIDE at template residue (1t5cA)L126 Warning: unaligning (T0313)V137 because of BadResidue code BAD_PEPTIDE in next template residue (1t5cA)I139 Warning: unaligning (T0313)L138 because of BadResidue code BAD_PEPTIDE at template residue (1t5cA)I139 Warning: unaligning (T0313)K144 because of BadResidue code BAD_PEPTIDE in next template residue (1t5cA)T146 Warning: unaligning (T0313)E145 because of BadResidue code BAD_PEPTIDE at template residue (1t5cA)T146 Warning: unaligning (T0313)P146 because of BadResidue code BAD_PEPTIDE in next template residue (1t5cA)K148 Warning: unaligning (T0313)Q147 because of BadResidue code BAD_PEPTIDE at template residue (1t5cA)K148 Warning: unaligning (T0313)P156 because of BadResidue code BAD_PEPTIDE in next template residue (1t5cA)D157 Warning: unaligning (T0313)D157 because of BadResidue code BAD_PEPTIDE at template residue (1t5cA)D157 Warning: unaligning (T0313)G166 because of BadResidue code BAD_PEPTIDE in next template residue (1t5cA)L167 Warning: unaligning (T0313)L167 because of BadResidue code BAD_PEPTIDE at template residue (1t5cA)L167 Warning: unaligning (T0313)T190 because of BadResidue code BAD_PEPTIDE in next template residue (1t5cA)Y191 Warning: unaligning (T0313)T191 because of BadResidue code BAD_PEPTIDE at template residue (1t5cA)Y191 Warning: unaligning (T0313)E192 because of BadResidue code BAD_PEPTIDE at template residue (1t5cA)G192 Warning: unaligning (T0313)T194 because of BadResidue code BAD_PEPTIDE in next template residue (1t5cA)K195 Warning: unaligning (T0313)N195 because of BadResidue code BAD_PEPTIDE at template residue (1t5cA)K195 Warning: unaligning (T0313)L196 because of BadResidue code BAD_PEPTIDE at template residue (1t5cA)M196 Warning: unaligning (T0313)C216 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1t5cA)G224 Warning: unaligning (T0313)S217 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1t5cA)G224 Warning: unaligning (T0313)G238 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1t5cA)R251 Warning: unaligning (T0313)R246 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1t5cA)R251 T0313 2 :IRVIARVRPVT 1t5cA 7 :VAVCVRVRPLN T0313 15 :DG 1t5cA 20 :EE T0313 20 :EATNAVTFDADDDSII 1t5cA 25 :ETAQVYWKTDNNVIYQ T0313 40 :KGKPVSFELDKVFSPQASQQDVFQE 1t5cA 41 :VDGSKSFNFDRVFHGNETTKNVYEE T0313 65 :VQALVTSCIDGFNVCIFAYGQTGAGKTYTMEGTAENPGINQRALQLLFSEVQEKASD 1t5cA 67 :AAPIIDSAIQGYNGTIFAYGQTASGKTYTMMGSEDHLGVIPRAIHDIFQKIKKFPDR T0313 123 :E 1t5cA 124 :E T0313 126 :ITVSAAEIYNE 1t5cA 127 :LRVSYMEIYNE T0313 139 :RDLLG 1t5cA 140 :TDLLC T0313 148 :EKL 1t5cA 149 :MKP T0313 152 :IRLC 1t5cA 152 :LIIR T0313 158 :GSGQLYVP 1t5cA 158 :VNRNVYVA T0313 168 :TEFQVQSVDDINKVFEFGHTNR 1t5cA 168 :TEEVVYTSEMALKWITKGEKSR T0313 193 :F 1t5cA 193 :E T0313 197 :NEHSSRSHALLIVTVRGVD 1t5cA 197 :NQRSSRSHTIFRMILESRE T0313 220 :LRTTGKLNLVDLAGSERV 1t5cA 225 :SVKVSHLNLVDLAGSERA T0313 247 :LREAQHINKSLSALGDVIAALRSRQG 1t5cA 252 :LKEGCNINRSLFILGQVIKKLSDGQV T0313 273 :HVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPV 1t5cA 280 :FINYRDSKLTRILQNSLGGNAKTRIICTITPV T0313 307 :NTSETLYSLKFAERVR 1t5cA 312 :SFDETLTALQFASTAK Number of specific fragments extracted= 18 number of extra gaps= 10 total=396 Will force an alignment to be made, even if fragment is small Number of alignments=44 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ncdA/T0313-2ncdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2ncdA expands to /projects/compbio/data/pdb/2ncd.pdb.gz 2ncdA:# T0313 read from 2ncdA/T0313-2ncdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ncdA read from 2ncdA/T0313-2ncdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2ncdA to template set # found chain 2ncdA in template set Warning: unaligning (T0313)G241 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ncdA)N598 Warning: unaligning (T0313)H252 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ncdA)N598 T0313 1 :NIRVIARVRPVTKEDG 2ncdA 348 :NIRVFCRIRPPLESEE T0313 19 :PEATNAVTFDADDDSIIHLL 2ncdA 364 :NRMCCTWTYHDESTVELQSI T0313 39 :HKGKPVSFELDKVFSPQASQQDVFQEVQALVTSCIDGFNVCIFAYGQTGAGKTYTMEGTAENPGINQRALQLLFSEVQEKAS 2ncdA 389 :SKMGQQIFSFDQVFHPLSSQSDIFEMVSPLIQSALDGYNICIFAYGQTGSGKTYTMDGVPESVGVIPRTVDLLFDSIRGYRN T0313 121 :DWEYTITVSAAEIYNEVLRDLLGKEPQE 2ncdA 472 :GWEYEIKATFLEIYNEVLYDLLSNEQKD T0313 152 :IRLCPDG 2ncdA 500 :MEIRMAK T0313 159 :SGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTGLRTTGKLNLVDLAGSER 2ncdA 509 :KNDIYVSNITEETVLDPNHLRHLMHTAKMNRATASTAGNERSSRSHAVTKLELIGRHAEKQEISVGSINLVDLAGSES T0313 253 :INKSLSALGDVIAALRSRQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERV 2ncdA 599 :INRSLSELTNVILALLQKQDHIPYRNSKLTHLLMPSLGGNSKTLMFINVSPFQDCFQESVKSLRFAASV Number of specific fragments extracted= 7 number of extra gaps= 0 total=403 Will force an alignment to be made, even if fragment is small Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ncdA/T0313-2ncdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0313 read from 2ncdA/T0313-2ncdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ncdA read from 2ncdA/T0313-2ncdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ncdA in template set Warning: unaligning (T0313)G241 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ncdA)N598 Warning: unaligning (T0313)H252 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ncdA)N598 T0313 2 :IRVIARVRPVTKEDGEGP 2ncdA 349 :IRVFCRIRPPLESEENRM T0313 21 :ATNAVTFDADDDSIIHLL 2ncdA 367 :CCTWTYHDESTVELQSID T0313 39 :HKGKPVSFELDKVFSPQASQQDVFQEVQALVTSCIDGFNVCIFAYGQTGAGKTYTMEGTAENPGINQRALQLLFSEVQEKAS 2ncdA 389 :SKMGQQIFSFDQVFHPLSSQSDIFEMVSPLIQSALDGYNICIFAYGQTGSGKTYTMDGVPESVGVIPRTVDLLFDSIRGYRN T0313 121 :DWEYTITVSAAEIYNEVLRDLLGKEPQ 2ncdA 472 :GWEYEIKATFLEIYNEVLYDLLSNEQK T0313 149 :KLEIRLCPDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTGLRTTGKLNLVDLAGSE 2ncdA 499 :DMEIRMAKNNKNDIYVSNITEETVLDPNHLRHLMHTAKMNRATASTAGNERSSRSHAVTKLELIGRHAEKQEISVGSINLVDLAGSE T0313 240 :S 2ncdA 586 :S T0313 253 :INKSLSALGDVIAALRSRQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERV 2ncdA 599 :INRSLSELTNVILALLQKQDHIPYRNSKLTHLLMPSLGGNSKTLMFINVSPFQDCFQESVKSLRFAASV Number of specific fragments extracted= 7 number of extra gaps= 0 total=410 Will force an alignment to be made, even if fragment is small Number of alignments=46 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ncdA/T0313-2ncdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0313 read from 2ncdA/T0313-2ncdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ncdA read from 2ncdA/T0313-2ncdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ncdA in template set Warning: unaligning (T0313)G241 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ncdA)N598 Warning: unaligning (T0313)H252 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ncdA)N598 T0313 1 :NIRVIARVRPVTKEDGEGPEAT 2ncdA 348 :NIRVFCRIRPPLESEENRMCCT T0313 25 :VTFDADDDSIIHLL 2ncdA 370 :WTYHDESTVELQSI T0313 39 :HKGKPVSFELDKVFSPQASQQDVFQEVQALVTSCIDGFNVCIFAYGQTGAGKTYTMEGTAENPGINQRALQLLFSEVQE 2ncdA 389 :SKMGQQIFSFDQVFHPLSSQSDIFEMVSPLIQSALDGYNICIFAYGQTGSGKTYTMDGVPESVGVIPRTVDLLFDSIRG T0313 118 :KASDWEYTITVSAAEIYNEVLRDLLGKEPQE 2ncdA 469 :RNLGWEYEIKATFLEIYNEVLYDLLSNEQKD T0313 150 :LEIRLCPDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTGLRTTGKLNLVDLAGSE 2ncdA 500 :MEIRMAKNNKNDIYVSNITEETVLDPNHLRHLMHTAKMNRATASTAGNERSSRSHAVTKLELIGRHAEKQEISVGSINLVDLAGSE T0313 240 :S 2ncdA 586 :S T0313 253 :INKSLSALGDVIAALRSRQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERV 2ncdA 599 :INRSLSELTNVILALLQKQDHIPYRNSKLTHLLMPSLGGNSKTLMFINVSPFQDCFQESVKSLRFAASV Number of specific fragments extracted= 7 number of extra gaps= 0 total=417 Will force an alignment to be made, even if fragment is small Number of alignments=47 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1n6mA/T0313-1n6mA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1n6mA expands to /projects/compbio/data/pdb/1n6m.pdb.gz 1n6mA:# T0313 read from 1n6mA/T0313-1n6mA-t06-local-adpstyle5.a2m # 1n6mA read from 1n6mA/T0313-1n6mA-t06-local-adpstyle5.a2m # adding 1n6mA to template set # found chain 1n6mA in template set Warning: unaligning (T0313)G41 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1n6mA)M391 Warning: unaligning (T0313)T190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1n6mA)S550 Warning: unaligning (T0313)S200 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1n6mA)S550 Warning: unaligning (T0313)E243 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1n6mA)E595 Warning: unaligning (T0313)E249 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1n6mA)E595 T0313 1 :NIRVIARVRPVTKEDG 1n6mA 348 :NIRVFCRIRPPLESEE T0313 19 :PEATNAVTFDADDDSIIHLLHK 1n6mA 364 :NRMCCTWTYHDESTVELQSIDA T0313 44 :VSFELDKVFSPQASQQDVFQEVQALVTSCIDGFNVCIFAYGQTGAGKTYTMEGTAENPGINQRALQLLFSEVQEKAS 1n6mA 394 :QIFSFDQVFHPLSSQSDIFEMVSPLIQSALDGYNICIFAYGQTGSGKTYTMDGVPESVGVIPRTVDLLFDSIRGYRN T0313 121 :DWEYTITVSAAEIYNEVLRDLLGKEPQE 1n6mA 472 :GWEYEIKATFLEIYNEVLYDLLSNEQKD T0313 150 :LEIRLCPDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNR 1n6mA 500 :MEIRMAKNNKNDIYVSNITEETVLDPNHLRHLMHTAKMNR T0313 201 :SRSHALLIVTVRGVDCSTGLRTTGKLNLVDLAGSERVG 1n6mA 551 :SRSHAVTKLELIGRHAEKQEISVGSINLVDLAGSESPK T0313 250 :AQHINKSLSALGDVIAALRSRQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERV 1n6mA 596 :TKNIKRSLSELTNVILALLQKQDHIPYRNSKLTHLLMPSLGGNSKTLMFINVSPFQDCFQESVKSLRFAASV Number of specific fragments extracted= 7 number of extra gaps= 0 total=424 Will force an alignment to be made, even if fragment is small Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f9tA/T0313-1f9tA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1f9tA expands to /projects/compbio/data/pdb/1f9t.pdb.gz 1f9tA:# T0313 read from 1f9tA/T0313-1f9tA-t06-local-adpstyle5.a2m # 1f9tA read from 1f9tA/T0313-1f9tA-t06-local-adpstyle5.a2m # adding 1f9tA to template set # found chain 1f9tA in template set Warning: unaligning (T0313)L142 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f9tA)K546 Warning: unaligning (T0313)E151 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f9tA)K546 Warning: unaligning (T0313)C216 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f9tA)T614 Warning: unaligning (T0313)T218 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f9tA)T614 Warning: unaligning (T0313)R236 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f9tA)R644 Warning: unaligning (T0313)R248 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f9tA)R644 Warning: unaligning (T0313)S269 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f9tA)H672 Warning: unaligning (T0313)H273 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f9tA)H672 Warning: unaligning (T0313)V321 because last residue in template chain is (1f9tA)V720 T0313 1 :NIRVIARVRPVTKE 1f9tA 386 :NIRVYCRIRPALKN T0313 15 :DGEGPEATNAVTFDADDDSIIHLLHKGKP 1f9tA 401 :ENSDTSLINVNEFDDNSGVQSMEVTKIQN T0313 44 :VSFELDKVFSPQASQQDVFQEVQALVTSCIDGFNVCIFAYGQTGAGKTYTMEGT 1f9tA 434 :HEFKFDKIFDQQDTNVDVFKEVGQLVQSSLDGYNVCIFAYGQTGSGKTFTMLNP T0313 100 :NPGINQRALQLLFSEVQEKA 1f9tA 488 :GDGIIPSTISHIFNWINKLK T0313 120 :SDWEYTITVSAAEIYNEVLRDL 1f9tA 509 :KGWDYKVNCEFIEIYNENIVDL T0313 152 :IRLCPDG 1f9tA 547 :HEIRHDQ T0313 159 :SGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVD 1f9tA 555 :TKTTTITNVTSCKLESEEMVEIILKKANKLRSTASTASNEHSSRSHSIFIIHLSGSN T0313 219 :GLRTTGKLNLVDLAGSE 1f9tA 615 :GAHSYGTLNLVDLAGSE T0313 249 :EAQHINKSLSALGDVIAALR 1f9tA 645 :ETQNINKSLSCLGDVIHALG T0313 274 :VPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAER 1f9tA 673 :IPFRNSKLTYLLQYSLTGDSKTLMFVNISPSSSHINETLNSLRFASK Number of specific fragments extracted= 10 number of extra gaps= 0 total=434 Will force an alignment to be made, even if fragment is small Number of alignments=49 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f9uA/T0313-1f9uA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1f9uA expands to /projects/compbio/data/pdb/1f9u.pdb.gz 1f9uA:# T0313 read from 1f9uA/T0313-1f9uA-t06-local-adpstyle5.a2m # 1f9uA read from 1f9uA/T0313-1f9uA-t06-local-adpstyle5.a2m # adding 1f9uA to template set # found chain 1f9uA in template set Warning: unaligning (T0313)L142 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f9uA)K546 Warning: unaligning (T0313)E151 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f9uA)K546 Warning: unaligning (T0313)R236 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f9uA)R642 Warning: unaligning (T0313)R246 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f9uA)R642 Warning: unaligning (T0313)R270 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f9uA)H672 Warning: unaligning (T0313)H273 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f9uA)H672 T0313 1 :NIRVIARVRPVTKE 1f9uA 386 :NIRVYCRIRPALKN T0313 15 :DGEGPEATNAVTFDADDDSIIHLLHKGKP 1f9uA 401 :ENSDTSLINVNEFDDNSGVQSMEVTKIQN T0313 44 :VSFELDKVFSPQASQQDVFQEVQALVTSCIDGFNVCIFAYGQTGAGKTYTMEGT 1f9uA 434 :HEFKFDKIFDQQDTNVDVFKEVGQLVQSSLDGYNVCIFAYGQTGSGKTFTMLNP T0313 100 :NPGINQRALQLLFSEVQEKA 1f9uA 488 :GDGIIPSTISHIFNWINKLK T0313 120 :SDWEYTITVSAAEIYNEVLRDL 1f9uA 509 :KGWDYKVNCEFIEIYNENIVDL T0313 152 :IRLCPDG 1f9uA 547 :HEIRHDQ T0313 159 :SGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTGLRTTGKLNLVDLAGSE 1f9uA 555 :TKTTTITNVTSCKLESEEMVEIILKKANKLRSTASTASNEHSSRSHSIFIIHLSGSNAKTGAHSYGTLNLVDLAGSE T0313 247 :LREAQHINKSLSALGDVIAALRS 1f9uA 643 :LRETQNIKKSLSCLGDVIHALGQ T0313 274 :VPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERV 1f9uA 673 :IPFRNSKLTYLLQYSLTGDSKTLMFVNISPSSSHINETLNSLRFASKV Number of specific fragments extracted= 9 number of extra gaps= 0 total=443 Will force an alignment to be made, even if fragment is small Number of alignments=50 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f9wA/T0313-1f9wA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1f9wA expands to /projects/compbio/data/pdb/1f9w.pdb.gz 1f9wA:# T0313 read from 1f9wA/T0313-1f9wA-t06-local-adpstyle5.a2m # 1f9wA read from 1f9wA/T0313-1f9wA-t06-local-adpstyle5.a2m # adding 1f9wA to template set # found chain 1f9wA in template set Warning: unaligning (T0313)D15 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f9wA)D404 Warning: unaligning (T0313)G18 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f9wA)D404 Warning: unaligning (T0313)H39 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f9wA)V433 Warning: unaligning (T0313)G143 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f9wA)L545 Warning: unaligning (T0313)L150 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f9wA)L545 Warning: unaligning (T0313)T191 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f9wA)H595 Warning: unaligning (T0313)H199 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f9wA)H595 Warning: unaligning (T0313)R236 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f9wA)L643 Warning: unaligning (T0313)L247 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f9wA)L643 T0313 1 :NIRVIARVRPVTKE 1f9wA 386 :NIRVYCRIRPALKN T0313 19 :PEATNAVTFDADDDSIIHLL 1f9wA 405 :TSLINVNEFDDNSGVQSMEV T0313 44 :VSFELDKVFSPQASQQDVFQEVQALVTSCIDGFNVCIFAYGQTGAGKTYTMEGT 1f9wA 434 :HEFKFDKIFDQQDTNVDVFKEVGQLVQSSLDGYNVCIFAYGQTGSGKTFTMLNP T0313 100 :NPGINQRALQLLFSEVQEKA 1f9wA 488 :GDGIIPSTISHIFNWINKLK T0313 120 :SDWEYTITVSAAEIYNEVLRDLL 1f9wA 509 :KGWDYKVNCEFIEIYNENIVDLL T0313 151 :EIRLCPDG 1f9wA 546 :KHEIRHDQ T0313 159 :SGQLYVPGLTEFQVQSVDDINKVFEFGHTNRT 1f9wA 555 :TKTTTITNVTSCKLESEEMVEIILKKANKLRS T0313 200 :SSRSHALLIVTVRGVDCSTGLRTTGKLNLVDLAGSE 1f9wA 596 :SSRSHSIFIIHLSGSNAKTGAHSYGTLNLVDLAGSA T0313 248 :REAQHINKSLSALGDVIAALRSRQG 1f9wA 644 :RETQNINKSLSCLGDVIHALGQPDS T0313 273 :HVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERV 1f9wA 672 :HIPFRNSKLTYLLQYSLTGDSKTLMFVNISPSSSHINETLNSLRFASKV Number of specific fragments extracted= 10 number of extra gaps= 0 total=453 Will force an alignment to be made, even if fragment is small Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gryA/T0313-2gryA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2gryA expands to /projects/compbio/data/pdb/2gry.pdb.gz 2gryA:Skipped atom 210, because occupancy 0.500 <= existing 0.500 in 2gryA Skipped atom 214, because occupancy 0.500 <= existing 0.500 in 2gryA Skipped atom 216, because occupancy 0.500 <= existing 0.500 in 2gryA # T0313 read from 2gryA/T0313-2gryA-t06-local-adpstyle5.a2m # 2gryA read from 2gryA/T0313-2gryA-t06-local-adpstyle5.a2m # adding 2gryA to template set # found chain 2gryA in template set Warning: unaligning (T0313)F27 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gryA)S223 Warning: unaligning (T0313)D28 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gryA)S223 Warning: unaligning (T0313)A29 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gryA)D225 Warning: unaligning (T0313)D30 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gryA)D225 Warning: unaligning (T0313)G96 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gryA)S308 Warning: unaligning (T0313)N100 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gryA)S308 Warning: unaligning (T0313)T190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gryA)H404 Warning: unaligning (T0313)H199 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gryA)H404 Warning: unaligning (T0313)R236 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gryA)D444 Warning: unaligning (T0313)E243 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gryA)D444 Warning: unaligning (T0313)V321 because last residue in template chain is (2gryA)V523 T0313 2 :IRVIARVRPVTKEDGEGPEATNAVT 2gryA 197 :ICVCVRKRPLNKKETQMKDLDVITI T0313 31 :DDSI 2gryA 226 :VVMV T0313 35 :IHLLHKGKPVSFELDKVFSPQASQQDVFQE 2gryA 236 :VDLTRYLENQTFRFDYAFDDSAPNEMVYRF T0313 65 :VQALVTSCIDGFNVCIFAYGQTGAGKTYTME 2gryA 267 :ARPLVETIFERGMATCFAYGQTGSGKTHTMG T0313 101 :PGINQRALQLLFSEVQEKA 2gryA 309 :KGIYALAARDVFLMLKKPN T0313 120 :SDWEYTITVSAAEIYNEVLRDLLGKEPQ 2gryA 329 :KKLELQVYATFFEIYSGKVFDLLNRKTK T0313 152 :IRLCPDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNR 2gryA 357 :LRVLEDGKQQVQVVGLQEREVKCVEDVLKLIDIGNSCR T0313 200 :SSRSHALLIVTVRGVDC 2gryA 405 :SSRSHAVFQIILRRKGK T0313 222 :TTGKLNLVDLAGSE 2gryA 422 :LHGKFSLIDLAGNE T0313 244 :GSRLREAQHINKSLSALGDVIAALRSRQGHVPFRNSKLTYLLQDSL 2gryA 445 :RQTRLEGAEINKSLLALKECIRALGRNKPHTPFRASKLTQVLRDSF T0313 290 :SGDSKTLMVVQVSPVEKNTSETLYSLKFAER 2gryA 492 :GENSRTCMIATISPGMASCENTLNTLRYANR Number of specific fragments extracted= 11 number of extra gaps= 1 total=464 Will force an alignment to be made, even if fragment is small Number of alignments=52 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v8kA/T0313-1v8kA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1v8kA expands to /projects/compbio/data/pdb/1v8k.pdb.gz 1v8kA:# T0313 read from 1v8kA/T0313-1v8kA-t06-local-adpstyle5.a2m # 1v8kA read from 1v8kA/T0313-1v8kA-t06-local-adpstyle5.a2m # adding 1v8kA to template set # found chain 1v8kA in template set Warning: unaligning (T0313)G160 because of BadResidue code BAD_PEPTIDE in next template residue (1v8kA)Q242 Warning: unaligning (T0313)Q161 because of BadResidue code BAD_PEPTIDE at template residue (1v8kA)Q242 Warning: unaligning (T0313)T190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1v8kA)N280 Warning: unaligning (T0313)H199 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1v8kA)N280 Warning: unaligning (T0313)S201 because of BadResidue code BAD_PEPTIDE in next template residue (1v8kA)R283 Warning: unaligning (T0313)R202 because of BadResidue code BAD_PEPTIDE at template residue (1v8kA)R283 Warning: unaligning (T0313)S203 because of BadResidue code BAD_PEPTIDE in next template residue (1v8kA)H285 Warning: unaligning (T0313)H204 because of BadResidue code BAD_PEPTIDE at template residue (1v8kA)H285 Warning: unaligning (T0313)E235 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1v8kA)R324 Warning: unaligning (T0313)R236 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1v8kA)R324 Warning: unaligning (T0313)S269 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1v8kA)F353 Warning: unaligning (T0313)F276 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1v8kA)F353 Warning: unaligning (T0313)R277 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1v8kA)R354 T0313 2 :IRVIARVRPVTKEDGEGPEATNAVTFDADDDSI 1v8kA 73 :ICVCVRKRPLNKQELAKKEIDVISVPSKCLLLV T0313 35 :IHLLHKGKPVSFELDKVFSPQASQQDVFQE 1v8kA 112 :VDLTKYLENQAFCFDFAFDETASNEVVYRF T0313 65 :VQALVTSCIDGFNVCIFAYGQTGAGKTYTMEGT 1v8kA 143 :ARPLVQTIFEGGKATCFAYGQTGSGKTHTMGGD T0313 98 :AENPGINQRALQLLFSEVQEKA 1v8kA 182 :NASKGIYAMASRDVFLLKNQPR T0313 120 :SDWEYTITVSAAEIYNEVLRDLLGKEPQ 1v8kA 205 :RNLNLEVYVTFFEIYNGKVFDLLNKKAK T0313 152 :IRLCPDGS 1v8kA 233 :LRVLEDSR T0313 162 :LYVPGLTEFQVQSVDDINKVFEFGHTNR 1v8kA 243 :VQVVGLQEYLVTCADDVIKMINMGSACR T0313 200 :S 1v8kA 281 :S T0313 205 :ALLIVTVRGVDC 1v8kA 286 :ACFQILLRTKGR T0313 222 :TTGKLNLVDLAGS 1v8kA 298 :LHGKFSLVDLAGN T0313 248 :REAQHINKSLSALGDVIAALR 1v8kA 325 :MEGAEINKSLLALKECIRALG T0313 278 :NSKLTYLLQDSL 1v8kA 355 :ESKLTQVLRDSF T0313 290 :SGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1v8kA 368 :GENSRTCMIAMISPGISSCEYTLNTLRYADRVK Number of specific fragments extracted= 13 number of extra gaps= 3 total=477 Will force an alignment to be made, even if fragment is small Number of alignments=53 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3kinB/T0313-3kinB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3kinB expands to /projects/compbio/data/pdb/3kin.pdb.gz 3kinB:# T0313 read from 3kinB/T0313-3kinB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3kinB read from 3kinB/T0313-3kinB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3kinB to template set # found chain 3kinB in template set T0313 256 :SLSALGDVIAALRSRQG 3kinB 258 :SLSALGNVISALAEGTK T0313 273 :HVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 3kinB 276 :HVPYRDSKMTRILQDSLGGNCRTTIVICCSPSVFNEAETKSTLMFGQRAK Number of specific fragments extracted= 2 number of extra gaps= 0 total=479 Will force an alignment to be made, even if fragment is small Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3kinB/T0313-3kinB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0313 read from 3kinB/T0313-3kinB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3kinB read from 3kinB/T0313-3kinB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3kinB in template set T0313 256 :SLSALGDVIAALRSRQG 3kinB 258 :SLSALGNVISALAEGTK T0313 273 :HVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 3kinB 276 :HVPYRDSKMTRILQDSLGGNCRTTIVICCSPSVFNEAETKSTLMFGQRAK Number of specific fragments extracted= 2 number of extra gaps= 0 total=481 Will force an alignment to be made, even if fragment is small Number of alignments=55 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3kinB/T0313-3kinB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0313 read from 3kinB/T0313-3kinB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3kinB read from 3kinB/T0313-3kinB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3kinB in template set T0313 256 :SLSALGDVIAALRS 3kinB 258 :SLSALGNVISALAE T0313 270 :RQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 3kinB 273 :TKTHVPYRDSKMTRILQDSLGGNCRTTIVICCSPSVFNEAETKSTLMFGQRAK Number of specific fragments extracted= 2 number of extra gaps= 0 total=483 Will force an alignment to be made, even if fragment is small Number of alignments=56 # command:CPU_time= 19.490 sec, elapsed time= 21.504 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 56 Adding 1394 constraints to all_contacts Done adding distance constraints # command:CPU_time= 19.609 sec, elapsed time= 21.639 sec. # command:Reading probabilities from T0313.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 10.535 Optimizing... Probability sum: -573.850, CN propb: -573.850 weights: 0.660 constraints: 743 # command:CPU_time= 27.254 sec, elapsed time= 29.306 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 743 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 743 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 651 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 651 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 0 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 0 # command:CPU_time= 27.275 sec, elapsed time= 29.391 sec. # command: