# 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 T0307 numbered 1 through 133 Created new target T0307 from T0307.a2m # command:CPU_time= 6.200 sec, elapsed time= 6.240 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 256bA/T0307-256bA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 256bA expands to /projects/compbio/data/pdb/256b.pdb.gz 256bA:# T0307 read from 256bA/T0307-256bA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 256bA read from 256bA/T0307-256bA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 256bA to template set # found chain 256bA in template set T0307 16 :QELTAIIKMAKSMVMADGKIKPAEI 256bA 24 :AQVKDALTKMRAAALDAQKATPPKL # choosing archetypes in rotamer library T0307 41 :AVMTREFMRFGILQDQVDLLLKASDSIEASQAVALIARMDEERKKYVASY 256bA 56 :PEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYHQKY Number of specific fragments extracted= 2 number of extra gaps= 0 total=2 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 256bA/T0307-256bA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0307 read from 256bA/T0307-256bA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 256bA read from 256bA/T0307-256bA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 256bA in template set T0307 17 :ELTAIIKMAKSMVMADGKIKPAEI 256bA 25 :QVKDALTKMRAAALDAQKATPPKL T0307 41 :AVMTREFMRFGILQDQVDLLLKASDSIEASQAVALIARMDEERKKYVASY 256bA 56 :PEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYHQKY Number of specific fragments extracted= 2 number of extra gaps= 0 total=4 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 256bA/T0307-256bA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0307 read from 256bA/T0307-256bA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 256bA read from 256bA/T0307-256bA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 256bA in template set T0307 15 :GQELTAIIKMAKSMVMADGKIKP 256bA 24 :AQVKDALTKMRAAALDAQKATPP T0307 38 :AEIAVMTREFMRF 256bA 56 :PEMKDFRHGFDIL T0307 54 :QDQVDLLLKASDSIEASQAVALIARMDEERKKY 256bA 69 :VGQIDDALKLANEGKVKEAQAAAEQLKTTRNAY Number of specific fragments extracted= 3 number of extra gaps= 0 total=7 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 1auiB/T0307-1auiB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1auiB expands to /projects/compbio/data/pdb/1aui.pdb.gz 1auiB:# T0307 read from 1auiB/T0307-1auiB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1auiB read from 1auiB/T0307-1auiB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1auiB to template set # found chain 1auiB in template set T0307 12 :TFSGQELTAIIKMAKSMVMADGKIKPAEIAVMTREFMRFGILQDQVDLLL 1auiB 13 :HFDADEIKRLGKRFKKLDLDNSGSLSVEEFMSLPELQQNPLVQRVIDIFD T0307 62 :KASDSIEASQAVALIA 1auiB 64 :DGNGEVDFKEFIEGVS T0307 78 :RMDEERK 1auiB 84 :KGDKEQK T0307 85 :KYVASYL 1auiB 92 :RFAFRIY T0307 94 :IMASDGDIDDNELALWTLISTLCGLPTMTVMEAINN 1auiB 99 :DMDKDGYISNGELFQVLKMMVGNNLKDTQLQQIVDK Number of specific fragments extracted= 5 number of extra gaps= 0 total=12 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 1auiB/T0307-1auiB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0307 read from 1auiB/T0307-1auiB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1auiB read from 1auiB/T0307-1auiB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1auiB in template set T0307 12 :TFSGQELTAIIKMAKSMVMADGKIKPAEIAVMTREFMRFGILQDQVDLLL 1auiB 13 :HFDADEIKRLGKRFKKLDLDNSGSLSVEEFMSLPELQQNPLVQRVIDIFD T0307 62 :KASDSIEASQAVALIA 1auiB 64 :DGNGEVDFKEFIEGVS T0307 78 :RM 1auiB 84 :KG T0307 80 :DEERKKYVASYL 1auiB 87 :KEQKLRFAFRIY T0307 94 :IMASDGDIDDNELALWTLISTLCGLPTMTVMEAINN 1auiB 99 :DMDKDGYISNGELFQVLKMMVGNNLKDTQLQQIVDK Number of specific fragments extracted= 5 number of extra gaps= 0 total=17 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 1auiB/T0307-1auiB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0307 read from 1auiB/T0307-1auiB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1auiB read from 1auiB/T0307-1auiB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1auiB in template set T0307 34 :KIKPAEIAVMTREFMRFGI 1auiB 13 :HFDADEIKRLGKRFKKLDL T0307 53 :LQDQ 1auiB 38 :SVEE T0307 57 :VDLLLK 1auiB 71 :FKEFIE T0307 63 :ASDSIEASQAVALI 1auiB 81 :FSVKGDKEQKLRFA T0307 77 :ARM 1auiB 96 :RIY T0307 84 :KKYVASYLG 1auiB 108 :NGELFQVLK T0307 95 :MASDGDIDDNELA 1auiB 117 :MMVGNNLKDTQLQ Number of specific fragments extracted= 7 number of extra gaps= 0 total=24 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 1ugpA/T0307-1ugpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ugpA expands to /projects/compbio/data/pdb/1ugp.pdb.gz 1ugpA:Bad short name: OD for alphabet: pdb_atoms # T0307 read from 1ugpA/T0307-1ugpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ugpA read from 1ugpA/T0307-1ugpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ugpA to template set # found chain 1ugpA in template set T0307 16 :QELTAIIKMAKSMVMADGKIKPAEIAVMTREF 1ugpA 15 :KEITARVKALESMLIEQGILTTSMIDRMAEIY T0307 62 :KASDSIEASQAVALIARMDEERKKYVAS 1ugpA 47 :ENEVGPHLGAKVVVKAWTDPEFKKRLLA Number of specific fragments extracted= 2 number of extra gaps= 0 total=26 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 1ugpA/T0307-1ugpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0307 read from 1ugpA/T0307-1ugpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ugpA read from 1ugpA/T0307-1ugpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ugpA in template set T0307 16 :QELTAIIKMAKSMVMADGKIKPAEIAVMTREFM 1ugpA 15 :KEITARVKALESMLIEQGILTTSMIDRMAEIYE T0307 65 :DSIEASQAVALIAR 1ugpA 48 :NEVGPHLGAKVVVK T0307 79 :MDEERKKYVAS 1ugpA 64 :TDPEFKKRLLA Number of specific fragments extracted= 3 number of extra gaps= 0 total=29 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 1ugpA/T0307-1ugpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0307 read from 1ugpA/T0307-1ugpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ugpA read from 1ugpA/T0307-1ugpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ugpA in template set T0307 16 :QELTAIIKMAKSMVMADGKIKPAEIAVMTREFM 1ugpA 15 :KEITARVKALESMLIEQGILTTSMIDRMAEIYE T0307 65 :DSIEASQAVALIARM 1ugpA 48 :NEVGPHLGAKVVVKA T0307 80 :DEERKKYVASYL 1ugpA 65 :DPEFKKRLLADG T0307 110 :TLISTLCGLPTMTV 1ugpA 77 :TEACKELGIGGLQG Number of specific fragments extracted= 4 number of extra gaps= 0 total=33 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 1uhnA/T0307-1uhnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1uhnA expands to /projects/compbio/data/pdb/1uhn.pdb.gz 1uhnA:# T0307 read from 1uhnA/T0307-1uhnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1uhnA read from 1uhnA/T0307-1uhnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1uhnA to template set # found chain 1uhnA in template set T0307 17 :ELTAIIKMAKSMVMADGKIKPAEIAVM 1uhnA 49 :ALYELFKKISSAVIDDGLINKEEFQLA T0307 49 :RFGILQDQVDLLLKASDSI 1uhnA 83 :ESLFADRVFDLFDTKHNGI T0307 68 :EASQAVALIARM 1uhnA 103 :GFEEFARALSVF T0307 80 :DEERKKYVASYLG 1uhnA 120 :IDDKIHFSFQLYD T0307 95 :MASDGDIDDNELA 1uhnA 133 :LKQQGFIERQEVK T0307 108 :LWTLISTLCGLPTMTVMEAINNM 1uhnA 149 :VATLAESGMNLKDTVIEDIIDKT Number of specific fragments extracted= 6 number of extra gaps= 0 total=39 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 1uhnA/T0307-1uhnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0307 read from 1uhnA/T0307-1uhnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1uhnA read from 1uhnA/T0307-1uhnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1uhnA in template set T0307 13 :FSGQELTAIIKMAKSMVMA 1uhnA 42 :FSVSEIEALYELFKKISSA T0307 32 :DGKIKPAEIAVM 1uhnA 64 :DGLINKEEFQLA T0307 49 :RFGILQDQVDLLLKASDSI 1uhnA 83 :ESLFADRVFDLFDTKHNGI T0307 68 :EASQAVALIARM 1uhnA 103 :GFEEFARALSVF T0307 80 :DEERKKYVASYLG 1uhnA 120 :IDDKIHFSFQLYD T0307 95 :MASDGDIDDNELA 1uhnA 133 :LKQQGFIERQEVK T0307 108 :LWTLISTLCGLPTMTVMEAINNM 1uhnA 149 :VATLAESGMNLKDTVIEDIIDKT Number of specific fragments extracted= 7 number of extra gaps= 0 total=46 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 1uhnA/T0307-1uhnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0307 read from 1uhnA/T0307-1uhnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1uhnA read from 1uhnA/T0307-1uhnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1uhnA in template set T0307 12 :TFSGQELTAIIKMAKSMVMA 1uhnA 41 :VFSVSEIEALYELFKKISSA T0307 32 :DGKIKPAEIAVM 1uhnA 64 :DGLINKEEFQLA T0307 50 :FGILQDQ 1uhnA 76 :LFKTNKK T0307 57 :VDLLLKASDS 1uhnA 87 :ADRVFDLFDT T0307 67 :IEASQAVALIARM 1uhnA 102 :LGFEEFARALSVF T0307 80 :DEERKKYVASYL 1uhnA 120 :IDDKIHFSFQLY T0307 96 :ASDGDIDDNE 1uhnA 134 :KQQGFIERQE T0307 106 :LALWTLISTLCGLPTMT 1uhnA 145 :KQMVVATLAESGMNLKD Number of specific fragments extracted= 8 number of extra gaps= 0 total=54 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 1tn4/T0307-1tn4-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1tn4 expands to /projects/compbio/data/pdb/1tn4.pdb.gz 1tn4:Warning: there is no chain 1tn4 will retry with 1tn4A # T0307 read from 1tn4/T0307-1tn4-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tn4 read from 1tn4/T0307-1tn4-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1tn4 to template set # found chain 1tn4 in template set T0307 15 :GQELTAIIKMAKSMVMADGK 1tn4 12 :SEEMIAEFKAAFDMFDADGG T0307 35 :IKPAEIAVMTREF 1tn4 34 :ISVKELGTVMRML T0307 51 :G 1tn4 47 :G T0307 52 :ILQDQVDLLLKA 1tn4 50 :PTKEELDAIIEE T0307 64 :SDSIEASQAVALIAR 1tn4 67 :SGTIDFEEFLVMMVR T0307 79 :MDEERKKYVASYLG 1tn4 83 :MKEDAKGKSEEELA T0307 93 :VI 1tn4 101 :IF T0307 95 :MASDGDIDDNELALWT 1tn4 104 :RNADGYIDAEELAEIF T0307 112 :ISTLCGLPTMTVMEAINNM 1tn4 120 :RASGEHVTDEEIESLMKDG Number of specific fragments extracted= 9 number of extra gaps= 0 total=63 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 1tn4/T0307-1tn4-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0307 read from 1tn4/T0307-1tn4-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tn4 read from 1tn4/T0307-1tn4-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tn4 in template set T0307 15 :GQELTAIIKMAKSMVMADGK 1tn4 12 :SEEMIAEFKAAFDMFDADGG T0307 35 :IKPAEIAVMTRE 1tn4 34 :ISVKELGTVMRM T0307 50 :FG 1tn4 46 :LG T0307 52 :ILQDQVDLLLKA 1tn4 50 :PTKEELDAIIEE T0307 64 :SDSIEASQAVAL 1tn4 67 :SGTIDFEEFLVM T0307 76 :IARMDEERK 1tn4 80 :VRQMKEDAK T0307 85 :KYVASYLGVIM 1tn4 93 :EELAELFRIFD T0307 96 :ASDGDIDDNELALW 1tn4 105 :NADGYIDAEELAEI T0307 112 :ISTLCG 1tn4 119 :FRASGE T0307 118 :LPTMTVMEAINNM 1tn4 126 :VTDEEIESLMKDG Number of specific fragments extracted= 10 number of extra gaps= 0 total=73 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 1tn4/T0307-1tn4-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0307 read from 1tn4/T0307-1tn4-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tn4 read from 1tn4/T0307-1tn4-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tn4 in template set T0307 16 :QELTAIIKMAKSMVMADGK 1tn4 13 :EEMIAEFKAAFDMFDADGG T0307 35 :IKPAE 1tn4 34 :ISVKE T0307 43 :MTREFMRFGI 1tn4 39 :LGTVMRMLGQ T0307 53 :LQDQVDLLLKASDS 1tn4 51 :TKEELDAIIEEVDE T0307 67 :IEASQAVA 1tn4 70 :IDFEEFLV T0307 75 :LIARMDEERKKY 1tn4 79 :MVRQMKEDAKGK T0307 87 :VAS 1tn4 95 :LAE T0307 90 :YLGVIMASDGD 1tn4 114 :ELAEIFRASGE T0307 101 :IDDNELALWT 1tn4 126 :VTDEEIESLM Number of specific fragments extracted= 9 number of extra gaps= 0 total=82 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 1svmA/T0307-1svmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1svmA expands to /projects/compbio/data/pdb/1svm.pdb.gz 1svmA:# T0307 read from 1svmA/T0307-1svmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1svmA read from 1svmA/T0307-1svmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1svmA to template set # found chain 1svmA in template set T0307 16 :QELTAIIKMAKSMVMA 1svmA 331 :KNQKTICQQAVDTVLA T0307 37 :PAEIAVMTREFM 1svmA 349 :RVDSLQLTREQM T0307 49 :RFGILQDQVDLLLKASDSIEASQAVALIARMD 1svmA 364 :RFNDLLDRMDIMFGSTGSADIEEWMAGVAWLH T0307 81 :EERKKYVASYLGVIM 1svmA 399 :PKMDSVVYDFLKCMV T0307 96 :ASD 1svmA 415 :NIP T0307 99 :GDIDDNELALWTLISTLCG 1svmA 426 :GPIDSGKTTLAAALLELCG T0307 118 :LPTMTVMEAIN 1svmA 452 :LPLDRLNFELG Number of specific fragments extracted= 7 number of extra gaps= 0 total=89 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 1svmA/T0307-1svmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0307 read from 1svmA/T0307-1svmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1svmA read from 1svmA/T0307-1svmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1svmA in template set T0307 16 :QELTAIIKMAKSMVMA 1svmA 331 :KNQKTICQQAVDTVLA T0307 37 :PAEIAVMTREFM 1svmA 349 :RVDSLQLTREQM T0307 49 :RFGILQDQVDLLLKASDSIEASQAVALIA 1svmA 364 :RFNDLLDRMDIMFGSTGSADIEEWMAGVA T0307 78 :RMDEERKKYVASYLG 1svmA 400 :KMDSVVYDFLKCMVY T0307 99 :GDIDDNELALWTLISTLCG 1svmA 426 :GPIDSGKTTLAAALLELCG Number of specific fragments extracted= 5 number of extra gaps= 0 total=94 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 1svmA/T0307-1svmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0307 read from 1svmA/T0307-1svmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1svmA read from 1svmA/T0307-1svmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1svmA in template set T0307 24 :MA 1svmA 326 :IF T0307 31 :ADGKIKPAEIAVMTREFMR 1svmA 328 :ADSKNQKTICQQAVDTVLA T0307 50 :FGILQDQ 1svmA 353 :LQLTREQ T0307 57 :VDLLLKASD 1svmA 365 :FNDLLDRMD T0307 66 :SIEASQAVA 1svmA 381 :SADIEEWMA T0307 75 :LIARMDEERKKYVASYLGVIMAS 1svmA 393 :WLHCLLPKMDSVVYDFLKCMVYN Number of specific fragments extracted= 6 number of extra gaps= 0 total=100 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 1ff9A/T0307-1ff9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ff9A expands to /projects/compbio/data/pdb/1ff9.pdb.gz 1ff9A:# T0307 read from 1ff9A/T0307-1ff9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ff9A read from 1ff9A/T0307-1ff9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ff9A to template set # found chain 1ff9A in template set T0307 54 :QDQVDLLLKAS 1ff9A 279 :KEATQKIVKAS T0307 66 :SIEASQAVALIARM 1ff9A 290 :SASEQDIVSTIVSN T0307 80 :DEERKKYVASYLGVI 1ff9A 308 :STEEQKRIVAGLKWL T0307 95 :MASDGDIDDNELALWTLISTL 1ff9A 324 :IFSDKKITPRGNALDTLCATL Number of specific fragments extracted= 4 number of extra gaps= 0 total=104 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 1ff9A/T0307-1ff9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0307 read from 1ff9A/T0307-1ff9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ff9A read from 1ff9A/T0307-1ff9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ff9A in template set T0307 16 :QELTAIIKMAKSMVMADGKIKPA 1ff9A 249 :QGFPQFIKVLVDIGFLSDEEQPF T0307 51 :GILQDQVDLLLKAS 1ff9A 276 :IPWKEATQKIVKAS T0307 66 :SIEASQAVALIAR 1ff9A 290 :SASEQDIVSTIVS T0307 80 :DEERKKYVASYLGVIMASDGDIDDNELALWTLISTL 1ff9A 309 :TEEQKRIVAGLKWLGIFSDKKITPRGNALDTLCATL Number of specific fragments extracted= 4 number of extra gaps= 0 total=108 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 1ff9A/T0307-1ff9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0307 read from 1ff9A/T0307-1ff9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ff9A read from 1ff9A/T0307-1ff9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ff9A in template set T0307 18 :LTAIIKMAKSMVMADGKIKP 1ff9A 251 :FPQFIKVLVDIGFLSDEEQP T0307 43 :MTR 1ff9A 278 :WKE T0307 46 :EFMRFG 1ff9A 282 :TQKIVK T0307 64 :SDSIEASQAVALI 1ff9A 288 :ASSASEQDIVSTI T0307 77 :ARM 1ff9A 302 :SNA T0307 80 :DEERKKYVASYLGVI 1ff9A 308 :STEEQKRIVAGLKWL T0307 95 :MASDGDID 1ff9A 324 :IFSDKKIT T0307 104 :NELALWTLISTL 1ff9A 335 :NALDTLCATLEE Number of specific fragments extracted= 8 number of extra gaps= 0 total=116 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 2ap1A/T0307-2ap1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2ap1A expands to /projects/compbio/data/pdb/2ap1.pdb.gz 2ap1A:Skipped atom 67, because occupancy 0.5 <= existing 0.500 in 2ap1A Skipped atom 69, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 71, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 319, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 655, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 728, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 730, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 732, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 734, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 736, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 738, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 740, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 742, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 744, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 746, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 748, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 759, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 763, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 765, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 767, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 769, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 833, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 837, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 839, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 841, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 843, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1053, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1055, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1376, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1380, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1382, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1384, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1386, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1388, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1390, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1392, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1718, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1722, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1724, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1726, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1728, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1730, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1869, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1873, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1875, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1877, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1983, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1987, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1989, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1991, because occupancy 0.500 <= existing 0.500 in 2ap1A # T0307 read from 2ap1A/T0307-2ap1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ap1A read from 2ap1A/T0307-2ap1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2ap1A to template set # found chain 2ap1A in template set T0307 57 :VDLLLK 2ap1A 194 :FAWLYQ T0307 63 :ASDSIEASQAVALIARMDEERKKYVASYLGVI 2ap1A 202 :YDQSLQAPEIIALWEQGDEQAHAHVERYLDLL T0307 105 :ELALWTLIST 2ap1A 234 :AVCLGNILTI Number of specific fragments extracted= 3 number of extra gaps= 0 total=119 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 2ap1A/T0307-2ap1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0307 read from 2ap1A/T0307-2ap1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ap1A read from 2ap1A/T0307-2ap1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ap1A in template set T0307 54 :QDQVDLLLK 2ap1A 191 :GRGFAWLYQ T0307 63 :ASDSIEASQAVALIARMDEERKKYVASYLGVI 2ap1A 202 :YDQSLQAPEIIALWEQGDEQAHAHVERYLDLL T0307 105 :ELALWTLIST 2ap1A 234 :AVCLGNILTI Number of specific fragments extracted= 3 number of extra gaps= 0 total=122 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 2ap1A/T0307-2ap1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0307 read from 2ap1A/T0307-2ap1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ap1A read from 2ap1A/T0307-2ap1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ap1A in template set T0307 34 :KIKPAEIAVM 2ap1A 159 :RLPVDALTLM T0307 50 :FGILQDQ 2ap1A 170 :FDFPLRR T0307 57 :VDLLLKASD 2ap1A 194 :FAWLYQHYY T0307 66 :SIEASQAVALIARMDEERKKYVASYLGVIMA 2ap1A 205 :SLQAPEIIALWEQGDEQAHAHVERYLDLLAV T0307 108 :LWTLISTLCGL 2ap1A 236 :CLGNILTIVDP T0307 122 :TVMEAINNMKN 2ap1A 247 :DLLVIGGGLSN Number of specific fragments extracted= 6 number of extra gaps= 0 total=128 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 1a2xA/T0307-1a2xA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1a2xA expands to /projects/compbio/data/pdb/1a2x.pdb.gz 1a2xA:# T0307 read from 1a2xA/T0307-1a2xA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1a2xA read from 1a2xA/T0307-1a2xA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1a2xA to template set # found chain 1a2xA in template set T0307 16 :QELTAIIKMAKSMVMAD 1a2xA 13 :EEMIAEFKAAFDMFDAD T0307 33 :GKIKPAEIAVMTRE 1a2xA 32 :GDISVKELGTVMRM T0307 48 :MRFGILQDQVDLLLKA 1a2xA 46 :LGQTPTKEELDAIIEE T0307 64 :SDSIEASQAVALIARM 1a2xA 67 :SGTIDFEEFLVMMVRQ T0307 80 :DEERKKYVASYLG 1a2xA 92 :EEELAECFRIFDR T0307 96 :ASDGDIDDNELALW 1a2xA 105 :NADGYIDAEELAEI T0307 114 :TLCGLPTMTVMEAINNM 1a2xA 119 :FRASGEHVTDEEIESLM Number of specific fragments extracted= 7 number of extra gaps= 0 total=135 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 1a2xA/T0307-1a2xA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0307 read from 1a2xA/T0307-1a2xA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1a2xA read from 1a2xA/T0307-1a2xA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1a2xA in template set T0307 16 :QELTAIIKM 1a2xA 37 :KELGTVMRM T0307 31 :ADGKIKPAEIAVMTREFMR 1a2xA 46 :LGQTPTKEELDAIIEEVDE T0307 63 :ASDSIEASQAVALIARM 1a2xA 66 :GSGTIDFEEFLVMMVRQ T0307 80 :DEERKKYVASYLG 1a2xA 92 :EEELAECFRIFDR T0307 96 :ASDGDIDDNELALW 1a2xA 105 :NADGYIDAEELAEI T0307 115 :LCG 1a2xA 119 :FRA T0307 118 :LPTMTVMEA 1a2xA 126 :VTDEEIESL Number of specific fragments extracted= 7 number of extra gaps= 0 total=142 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 1a2xA/T0307-1a2xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0307 read from 1a2xA/T0307-1a2xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1a2xA read from 1a2xA/T0307-1a2xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1a2xA in template set T0307 12 :TFSGQELTAIIKM 1a2xA 33 :DISVKELGTVMRM T0307 31 :ADGKIKPAEIAVMTREFMRFGIL 1a2xA 46 :LGQTPTKEELDAIIEEVDEDGSG T0307 54 :QDQ 1a2xA 72 :FEE T0307 57 :VDLLLKASDSIEASQAVALIARMD 1a2xA 80 :VRQMKEDAKGKSEEELAECFRIFD T0307 88 :ASYLGVIMASDGD 1a2xA 112 :AEELAEIFRASGE T0307 101 :IDDNELALWTL 1a2xA 126 :VTDEEIESLMK Number of specific fragments extracted= 6 number of extra gaps= 0 total=148 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 2fkiA/T0307-2fkiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2fkiA expands to /projects/compbio/data/pdb/2fki.pdb.gz 2fkiA:# T0307 read from 2fkiA/T0307-2fkiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fkiA read from 2fkiA/T0307-2fkiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2fkiA to template set # found chain 2fkiA in template set Warning: unaligning (T0307)Y90 because last residue in template chain is (2fkiA)L118 T0307 4 :GRQSLNIMT 2fkiA 44 :NRPAVSLKT T0307 15 :GQELTAIIKMAKSMVMADGKIKPAEIAVMT 2fkiA 53 :SPELAELLRQQHSDVRPSRHLNKAHWSTVY T0307 48 :MRFGILQDQVDLLLKAS 2fkiA 83 :LDGSLPDSQIYYLVDAS T0307 72 :AVALIARMDEERKKYVAS 2fkiA 100 :YQQAVNLLPEEKRKLLVQ Number of specific fragments extracted= 4 number of extra gaps= 0 total=152 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 2fkiA/T0307-2fkiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0307 read from 2fkiA/T0307-2fkiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fkiA read from 2fkiA/T0307-2fkiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fkiA in template set Warning: unaligning (T0307)Y90 because last residue in template chain is (2fkiA)L118 T0307 5 :RQSLNI 2fkiA 45 :RPAVSL T0307 13 :FSGQELTAIIKMAKSMVMADGKIKPAEIAVMT 2fkiA 51 :KTSPELAELLRQQHSDVRPSRHLNKAHWSTVY T0307 48 :MRFGILQDQVDLLLKAS 2fkiA 83 :LDGSLPDSQIYYLVDAS T0307 72 :AVALIARMDEERKKYVAS 2fkiA 100 :YQQAVNLLPEEKRKLLVQ Number of specific fragments extracted= 4 number of extra gaps= 0 total=156 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 2fkiA/T0307-2fkiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0307 read from 2fkiA/T0307-2fkiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fkiA read from 2fkiA/T0307-2fkiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fkiA in template set Warning: unaligning (T0307)Y90 because last residue in template chain is (2fkiA)L118 T0307 51 :GILQDQVDLLLKASDS 2fkiA 86 :SLPDSQIYYLVDASYQ T0307 74 :ALIARMDEERKKYVAS 2fkiA 102 :QAVNLLPEEKRKLLVQ Number of specific fragments extracted= 2 number of extra gaps= 0 total=158 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 1s6cA/T0307-1s6cA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1s6cA expands to /projects/compbio/data/pdb/1s6c.pdb.gz 1s6cA:Bad short name: AS for alphabet: pdb_atoms Bad short name: AS for alphabet: pdb_atoms # T0307 read from 1s6cA/T0307-1s6cA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1s6cA read from 1s6cA/T0307-1s6cA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1s6cA to template set # found chain 1s6cA in template set Warning: unaligning (T0307)M28 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1s6cA)P65 Warning: unaligning (T0307)A31 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1s6cA)P65 Warning: unaligning (T0307)G117 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1s6cA)P171 Warning: unaligning (T0307)P119 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1s6cA)P171 T0307 13 :FSGQELTAIIKMAKS 1s6cA 48 :FTKRELQVLYRGFKN T0307 32 :DGKIKPAEIAVMTREFMRFGILQDQVDLLLKA 1s6cA 66 :SGVVNEETFKQIYAQFFPHGDASTYAHYLFNA T0307 64 :SDSIEAS 1s6cA 103 :TGSVKFE T0307 71 :QAVALIARMD 1s6cA 113 :TALSILLRGT T0307 81 :EERKKYVASYLG 1s6cA 124 :HEKLRWTFNLYD T0307 95 :MASDGDIDDNEL 1s6cA 136 :INKDGYINKEEM T0307 107 :ALWTLISTLC 1s6cA 149 :DIVKAIYDMM T0307 120 :TMTVMEAINNM 1s6cA 172 :RQHVDVFFQKM Number of specific fragments extracted= 8 number of extra gaps= 0 total=166 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 1s6cA/T0307-1s6cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0307 read from 1s6cA/T0307-1s6cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1s6cA read from 1s6cA/T0307-1s6cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1s6cA in template set Warning: unaligning (T0307)M28 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1s6cA)P65 Warning: unaligning (T0307)A31 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1s6cA)P65 Warning: unaligning (T0307)G117 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1s6cA)P171 T0307 13 :FSGQELTAIIKMAKS 1s6cA 48 :FTKRELQVLYRGFKN T0307 32 :DGKIKPAEIAVMTREFMRFGILQDQVDLLLKA 1s6cA 66 :SGVVNEETFKQIYAQFFPHGDASTYAHYLFNA T0307 64 :SDSIEASQAVA 1s6cA 103 :TGSVKFEDFVT T0307 75 :LIARM 1s6cA 117 :ILLRG T0307 80 :DEERKKYVASYLGV 1s6cA 123 :VHEKLRWTFNLYDI T0307 96 :ASDGDIDDNELA 1s6cA 137 :NKDGYINKEEMM T0307 108 :LWTLISTLC 1s6cA 150 :IVKAIYDMM Number of specific fragments extracted= 7 number of extra gaps= 0 total=173 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 1s6cA/T0307-1s6cA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0307 read from 1s6cA/T0307-1s6cA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1s6cA read from 1s6cA/T0307-1s6cA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1s6cA in template set Warning: unaligning (T0307)I52 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1s6cA)P171 Warning: unaligning (T0307)E68 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1s6cA)P171 T0307 14 :SGQELTAIIKMAKS 1s6cA 122 :TVHEKLRWTFNLYD T0307 29 :VMADGKIKPAEIAVMTREFMRFG 1s6cA 136 :INKDGYINKEEMMDIVKAIYDMM T0307 69 :AS 1s6cA 172 :RQ Number of specific fragments extracted= 3 number of extra gaps= 0 total=176 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 2mysB/T0307-2mysB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2mysB expands to /projects/compbio/data/pdb-ca-mod/2mys.brk_ca_mod.gz 2mysB:# T0307 read from 2mysB/T0307-2mysB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2mysB read from 2mysB/T0307-2mysB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2mysB to template set # found chain 2mysB in template set Warning: unaligning (T0307)S14 because first residue in template chain is (2mysB)F19 Warning: unaligning (T0307)M24 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)A30 Warning: unaligning (T0307)A25 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)A30 Warning: unaligning (T0307)K36 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)K44 Warning: unaligning (T0307)P37 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)K44 Warning: unaligning (T0307)R45 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)A53 Warning: unaligning (T0307)E46 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)A53 Warning: unaligning (T0307)F47 because of BadResidue code BAD_PEPTIDE in next template residue (2mysB)G55 Warning: unaligning (T0307)M48 because of BadResidue code BAD_PEPTIDE at template residue (2mysB)G55 Warning: unaligning (T0307)R49 because of BadResidue code BAD_PEPTIDE in next template residue (2mysB)L57 Warning: unaligning (T0307)F50 because of BadResidue code BAD_PEPTIDE at template residue (2mysB)L57 Warning: unaligning (T0307)D58 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)A66 Warning: unaligning (T0307)L59 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)A66 Warning: unaligning (T0307)V73 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2mysB)T82 Warning: unaligning (T0307)A74 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2mysB)T82 Warning: unaligning (T0307)A77 because of BadResidue code BAD_PEPTIDE in next template residue (2mysB)E86 Warning: unaligning (T0307)R78 because of BadResidue code BAD_PEPTIDE at template residue (2mysB)E86 Warning: unaligning (T0307)D80 because of BadResidue code BAD_PEPTIDE in next template residue (2mysB)E94 Warning: unaligning (T0307)E81 because of BadResidue code BAD_PEPTIDE at template residue (2mysB)E94 Warning: unaligning (T0307)K85 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)G99 Warning: unaligning (T0307)Y86 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)G99 Warning: unaligning (T0307)A88 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)K102 Warning: unaligning (T0307)S89 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)K102 Warning: unaligning (T0307)G99 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)K109 Warning: unaligning (T0307)D100 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)K109 Warning: unaligning (T0307)I101 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)G110 Warning: unaligning (T0307)D102 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)I112 Warning: unaligning (T0307)D103 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)I112 Warning: unaligning (T0307)N104 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)K113 Warning: unaligning (T0307)S113 because of BadResidue code BAD_PEPTIDE in next template residue (2mysB)T123 Warning: unaligning (T0307)T114 because of BadResidue code BAD_PEPTIDE at template residue (2mysB)T123 Warning: unaligning (T0307)T120 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)P130 Warning: unaligning (T0307)M121 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)P130 T0307 15 :GQELTAIIK 2mysB 20 :DETEIEDFK T0307 26 :KSMVM 2mysB 31 :FTVID T0307 31 :ADGKI 2mysB 38 :ADGII T0307 38 :AEIAVMT 2mysB 45 :DDLRETF T0307 51 :GILQDQV 2mysB 58 :NVKNEEL T0307 60 :LLK 2mysB 67 :MIK T0307 63 :ASDSIEASQA 2mysB 71 :ASGPINFTVF T0307 75 :LI 2mysB 83 :MF T0307 79 :M 2mysB 87 :K T0307 82 :ERK 2mysB 95 :DVI T0307 87 :V 2mysB 100 :A T0307 94 :IMASD 2mysB 103 :VLDPD T0307 105 :ELALWTLI 2mysB 114 :KSFLEELL T0307 115 :LCG 2mysB 124 :GGG T0307 119 :P 2mysB 128 :F T0307 122 :TVMEAIN 2mysB 131 :EEIKNMW Number of specific fragments extracted= 16 number of extra gaps= 12 total=192 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 2mysB/T0307-2mysB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0307 read from 2mysB/T0307-2mysB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2mysB read from 2mysB/T0307-2mysB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2mysB in template set Warning: unaligning (T0307)S14 because first residue in template chain is (2mysB)F19 Warning: unaligning (T0307)M24 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)A30 Warning: unaligning (T0307)A25 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)A30 Warning: unaligning (T0307)K36 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)K44 Warning: unaligning (T0307)P37 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)K44 Warning: unaligning (T0307)R45 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)A53 Warning: unaligning (T0307)E46 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)A53 Warning: unaligning (T0307)F47 because of BadResidue code BAD_PEPTIDE in next template residue (2mysB)G55 Warning: unaligning (T0307)M48 because of BadResidue code BAD_PEPTIDE at template residue (2mysB)G55 Warning: unaligning (T0307)R49 because of BadResidue code BAD_PEPTIDE in next template residue (2mysB)L57 Warning: unaligning (T0307)F50 because of BadResidue code BAD_PEPTIDE at template residue (2mysB)L57 Warning: unaligning (T0307)D58 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)A66 Warning: unaligning (T0307)L59 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)A66 Warning: unaligning (T0307)V73 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2mysB)T82 Warning: unaligning (T0307)A74 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2mysB)T82 Warning: unaligning (T0307)A77 because of BadResidue code BAD_PEPTIDE in next template residue (2mysB)E86 Warning: unaligning (T0307)R78 because of BadResidue code BAD_PEPTIDE at template residue (2mysB)E86 Warning: unaligning (T0307)D80 because of BadResidue code BAD_PEPTIDE in next template residue (2mysB)E94 Warning: unaligning (T0307)E81 because of BadResidue code BAD_PEPTIDE at template residue (2mysB)E94 Warning: unaligning (T0307)K85 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)G99 Warning: unaligning (T0307)Y86 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)G99 Warning: unaligning (T0307)A88 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)K102 Warning: unaligning (T0307)S89 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)K102 Warning: unaligning (T0307)G99 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)K109 Warning: unaligning (T0307)D100 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)K109 Warning: unaligning (T0307)I101 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)G110 Warning: unaligning (T0307)D102 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)I112 Warning: unaligning (T0307)D103 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)I112 Warning: unaligning (T0307)N104 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)K113 Warning: unaligning (T0307)S113 because of BadResidue code BAD_PEPTIDE in next template residue (2mysB)T123 Warning: unaligning (T0307)T114 because of BadResidue code BAD_PEPTIDE at template residue (2mysB)T123 Warning: unaligning (T0307)T120 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)P130 Warning: unaligning (T0307)M121 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)P130 T0307 15 :GQELTAIIK 2mysB 20 :DETEIEDFK T0307 26 :KSMVM 2mysB 31 :FTVID T0307 31 :ADGKI 2mysB 38 :ADGII T0307 38 :AEIAVMT 2mysB 45 :DDLRETF T0307 51 :GILQDQV 2mysB 58 :NVKNEEL T0307 60 :LLK 2mysB 67 :MIK T0307 63 :ASDSIEASQA 2mysB 71 :ASGPINFTVF T0307 75 :LI 2mysB 83 :MF T0307 79 :M 2mysB 87 :K T0307 82 :ERK 2mysB 95 :DVI T0307 87 :V 2mysB 100 :A T0307 94 :IMASD 2mysB 103 :VLDPD T0307 105 :ELALWTLI 2mysB 114 :KSFLEELL T0307 115 :LCG 2mysB 124 :GGG T0307 119 :P 2mysB 128 :F T0307 122 :TVMEAIN 2mysB 131 :EEIKNMW Number of specific fragments extracted= 16 number of extra gaps= 12 total=208 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 2mysB/T0307-2mysB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0307 read from 2mysB/T0307-2mysB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2mysB read from 2mysB/T0307-2mysB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2mysB in template set Warning: unaligning (T0307)S14 because first residue in template chain is (2mysB)F19 Warning: unaligning (T0307)M24 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)A30 Warning: unaligning (T0307)A25 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)A30 Warning: unaligning (T0307)K36 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)K44 Warning: unaligning (T0307)P37 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)K44 Warning: unaligning (T0307)R45 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)A53 Warning: unaligning (T0307)E46 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)A53 Warning: unaligning (T0307)F47 because of BadResidue code BAD_PEPTIDE in next template residue (2mysB)G55 Warning: unaligning (T0307)M48 because of BadResidue code BAD_PEPTIDE at template residue (2mysB)G55 Warning: unaligning (T0307)R49 because of BadResidue code BAD_PEPTIDE in next template residue (2mysB)L57 Warning: unaligning (T0307)F50 because of BadResidue code BAD_PEPTIDE at template residue (2mysB)L57 Warning: unaligning (T0307)D58 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)A66 Warning: unaligning (T0307)L59 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)A66 Warning: unaligning (T0307)V73 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2mysB)T82 Warning: unaligning (T0307)A74 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2mysB)T82 Warning: unaligning (T0307)A77 because of BadResidue code BAD_PEPTIDE in next template residue (2mysB)E86 Warning: unaligning (T0307)E82 because of BadResidue code BAD_PEPTIDE at template residue (2mysB)E86 Warning: unaligning (T0307)K84 because of BadResidue code BAD_PEPTIDE at template residue (2mysB)E94 Warning: unaligning (T0307)A88 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)G99 Warning: unaligning (T0307)S89 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)G99 Warning: unaligning (T0307)L91 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)K102 Warning: unaligning (T0307)G92 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)K102 Warning: unaligning (T0307)S97 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)K109 Warning: unaligning (T0307)D98 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)K109 Warning: unaligning (T0307)G99 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)G110 Warning: unaligning (T0307)D100 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)I112 Warning: unaligning (T0307)I101 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)I112 Warning: unaligning (T0307)D102 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)K113 Warning: unaligning (T0307)T114 because of BadResidue code BAD_PEPTIDE in next template residue (2mysB)T123 Warning: unaligning (T0307)L115 because of BadResidue code BAD_PEPTIDE at template residue (2mysB)T123 T0307 15 :GQELTAIIK 2mysB 20 :DETEIEDFK T0307 26 :KSMV 2mysB 31 :FTVI T0307 30 :MADGKI 2mysB 37 :NADGII T0307 38 :AEIAVMT 2mysB 45 :DDLRETF T0307 51 :GILQDQV 2mysB 58 :NVKNEEL T0307 60 :LLKASDS 2mysB 67 :MIKEASG T0307 67 :IEASQA 2mysB 75 :INFTVF T0307 75 :LI 2mysB 83 :MF T0307 83 :R 2mysB 87 :K T0307 85 :KYV 2mysB 95 :DVI T0307 90 :Y 2mysB 100 :A T0307 93 :VI 2mysB 103 :VL T0307 95 :MA 2mysB 106 :PD T0307 103 :DN 2mysB 114 :KS T0307 108 :LWTLIS 2mysB 116 :FLEELL T0307 116 :CGL 2mysB 124 :GGG Number of specific fragments extracted= 16 number of extra gaps= 11 total=224 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 1top/T0307-1top-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1top expands to /projects/compbio/data/pdb/1top.pdb.gz 1top:Warning: there is no chain 1top will retry with 1topA Skipped atom 474, because occupancy 0.500 <= existing 0.500 in 1top Skipped atom 476, because occupancy 0.500 <= existing 0.500 in 1top Skipped atom 478, because occupancy 0.500 <= existing 0.500 in 1top Skipped atom 480, because occupancy 0.500 <= existing 0.500 in 1top Skipped atom 482, because occupancy 0.500 <= existing 0.500 in 1top Skipped atom 779, because occupancy 0.500 <= existing 0.500 in 1top Skipped atom 781, because occupancy 0.500 <= existing 0.500 in 1top Skipped atom 960, because occupancy 0.500 <= existing 0.500 in 1top Skipped atom 962, because occupancy 0.500 <= existing 0.500 in 1top Skipped atom 964, because occupancy 0.500 <= existing 0.500 in 1top Skipped atom 966, because occupancy 0.500 <= existing 0.500 in 1top Skipped atom 968, because occupancy 0.500 <= existing 0.500 in 1top Skipped atom 970, because occupancy 0.500 <= existing 0.500 in 1top Skipped atom 972, because occupancy 0.500 <= existing 0.500 in 1top Skipped atom 1103, because occupancy 0.500 <= existing 0.500 in 1top Skipped atom 1105, because occupancy 0.500 <= existing 0.500 in 1top Skipped atom 1107, because occupancy 0.500 <= existing 0.500 in 1top Skipped atom 1109, because occupancy 0.500 <= existing 0.500 in 1top Skipped atom 1204, because occupancy 0.500 <= existing 0.500 in 1top Skipped atom 1206, because occupancy 0.500 <= existing 0.500 in 1top Skipped atom 1208, because occupancy 0.500 <= existing 0.500 in 1top Skipped atom 1210, because occupancy 0.500 <= existing 0.500 in 1top # T0307 read from 1top/T0307-1top-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1top read from 1top/T0307-1top-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1top to template set # found chain 1top in template set T0307 15 :GQELTAIIKMAKSMVMADGK 1top 15 :SEEMIAEFKAAFDMFDADGG T0307 35 :IKPAEIAVMTREF 1top 37 :ISTKELGTVMRML T0307 49 :RFGILQDQVDLLLKA 1top 50 :GQNPTKEELDAIIEE T0307 64 :SDSIEASQAVALIARMDEERKK 1top 70 :SGTIDFEEFLVMMVRQMKEDAK T0307 86 :YVASYLGVI 1top 97 :ELANCFRIF T0307 95 :MASDGDIDDNELALW 1top 107 :KNADGFIDIEELGEI T0307 111 :LISTLCGLPTMTVMEAINNM 1top 122 :LRATGEHVTEEDIEDLMKDS Number of specific fragments extracted= 7 number of extra gaps= 0 total=231 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 1top/T0307-1top-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0307 read from 1top/T0307-1top-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1top read from 1top/T0307-1top-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1top in template set T0307 17 :ELTAIIKMAKSMVMADGK 1top 17 :EMIAEFKAAFDMFDADGG T0307 35 :IKPAEIAVMTREF 1top 37 :ISTKELGTVMRML T0307 51 :GILQDQVDLLLKA 1top 52 :NPTKEELDAIIEE T0307 64 :SDSIEASQAVALIARMDEERKK 1top 70 :SGTIDFEEFLVMMVRQMKEDAK T0307 86 :YVASYLGVIM 1top 97 :ELANCFRIFD T0307 96 :ASDGDIDDNELALW 1top 108 :NADGFIDIEELGEI T0307 111 :LISTLCGLPTMTVMEAINNM 1top 122 :LRATGEHVTEEDIEDLMKDS Number of specific fragments extracted= 7 number of extra gaps= 0 total=238 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 1top/T0307-1top-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0307 read from 1top/T0307-1top-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1top read from 1top/T0307-1top-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1top in template set T0307 14 :SGQELTAIIKMA 1top 2 :SMTDQQAEARAF T0307 35 :IKPAEIAVMTREFMRF 1top 14 :LSEEMIAEFKAAFDMF T0307 51 :GILQDQVDLLLKASDS 1top 52 :NPTKEELDAIIEEVDE T0307 67 :IEASQAVALI 1top 73 :IDFEEFLVMM T0307 77 :ARMDEERKKYVASYLGVI 1top 88 :EDAKGKSEEELANCFRIF T0307 95 :MASDGDIDDNE 1top 107 :KNADGFIDIEE T0307 109 :WTLISTLCG 1top 118 :LGEILRATG Number of specific fragments extracted= 7 number of extra gaps= 0 total=245 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 1u61A/T0307-1u61A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1u61A expands to /projects/compbio/data/pdb/1u61.pdb.gz 1u61A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0307 read from 1u61A/T0307-1u61A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u61A read from 1u61A/T0307-1u61A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1u61A to template set # found chain 1u61A in template set Warning: unaligning (T0307)L91 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1u61A)N78 Warning: unaligning (T0307)G92 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1u61A)N78 Warning: unaligning (T0307)A96 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1u61A)N80 Warning: unaligning (T0307)S97 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1u61A)N80 Warning: unaligning (T0307)D98 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1u61A)S81 T0307 14 :SGQELTAIIKMA 1u61A 5 :KQLNSLALAYMG T0307 26 :KSMVMADGKIKPAEIAVMTREFMRFGILQDQVDLLLKAS 1u61A 25 :RYHLLQKGKVRPNQLHRLGTSFVSAKAQAKVVYHLLETA T0307 78 :RMDEERKKYVASY 1u61A 64 :FLTEEEEAVLRRG T0307 99 :GDIDDN 1u61A 82 :GTVPKN T0307 105 :ELALWTLISTLCGL 1u61A 96 :STAFEALIGYHHLL T0307 119 :PTMTVMEAIN 1u61A 111 :NRERLDEIVY Number of specific fragments extracted= 6 number of extra gaps= 1 total=251 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 1u61A/T0307-1u61A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0307 read from 1u61A/T0307-1u61A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u61A read from 1u61A/T0307-1u61A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1u61A in template set Warning: unaligning (T0307)L91 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1u61A)N78 Warning: unaligning (T0307)G92 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1u61A)N78 Warning: unaligning (T0307)A96 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1u61A)N80 Warning: unaligning (T0307)S97 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1u61A)N80 Warning: unaligning (T0307)D98 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1u61A)S81 T0307 20 :AIIKMAKSMVMADGKIKPAEIAVMTREFMRFGILQDQVDLLLKAS 1u61A 19 :VYEQYIRYHLLQKGKVRPNQLHRLGTSFVSAKAQAKVVYHLLETA T0307 78 :RMDEERKKYVASY 1u61A 64 :FLTEEEEAVLRRG T0307 99 :GDIDDN 1u61A 82 :GTVPKN T0307 105 :ELALWTLISTLC 1u61A 96 :STAFEALIGYHH T0307 117 :GLPTMTVMEAINN 1u61A 109 :LNNRERLDEIVYK Number of specific fragments extracted= 5 number of extra gaps= 1 total=256 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 1u61A/T0307-1u61A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0307 read from 1u61A/T0307-1u61A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u61A read from 1u61A/T0307-1u61A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1u61A in template set T0307 19 :TAIIKMAKSMVM 1u61A 50 :KAQAKVVYHLLE T0307 32 :DGKIKPAEIAVM 1u61A 62 :TAFLTEEEEAVL T0307 110 :TLI 1u61A 74 :RRG Number of specific fragments extracted= 3 number of extra gaps= 0 total=259 Will force an alignment to be made, even if fragment is small Number of alignments=42 # command:CPU_time= 12.656 sec, elapsed time= 14.338 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 42 Adding 8778 constraints to all_contacts Done adding distance constraints # command:CPU_time= 12.684 sec, elapsed time= 14.371 sec. # command:Reading probabilities from T0307.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 7.491 Optimizing... Probability sum: -254.673, CN propb: -254.673 weights: 0.218 constraints: 209 # command:CPU_time= 20.083 sec, elapsed time= 21.799 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 209 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 209 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 705 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 705 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 6836 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 6836 # command:CPU_time= 20.218 sec, elapsed time= 22.071 sec. # command: