# 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 T0325 numbered 1 through 262 Created new target T0325 from T0325.a2m # command:CPU_time= 6.431 sec, elapsed time= 6.463 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v6tA/T0325-1v6tA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1v6tA expands to /projects/compbio/data/pdb/1v6t.pdb.gz 1v6tA:# T0325 read from 1v6tA/T0325-1v6tA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v6tA read from 1v6tA/T0325-1v6tA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1v6tA to template set # found chain 1v6tA in template set Warning: unaligning (T0325)K4 because first residue in template chain is (1v6tA)M1 Warning: unaligning (T0325)D177 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1v6tA)A184 Warning: unaligning (T0325)D185 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1v6tA)A184 T0325 5 :KLIINAD 1v6tA 2 :RVDLNSD # choosing archetypes in rotamer library T0325 13 :FGYTPAV 1v6tA 18 :LGLDEEV T0325 29 :RGVVTSTTALPTS 1v6tA 25 :MKYITSANVACGW T0325 42 :PYFLEAMESARI 1v6tA 43 :LVMRKTVRLAKE T0325 56 :PTLAIGVH 1v6tA 55 :NDVQVGAH T0325 73 :PILP 1v6tA 63 :PGYP T0325 85 :DEAGYFWH 1v6tA 67 :DLMGFGRR T0325 97 :EEKVNLEEVYNEWDAQIISFMKS 1v6tA 75 :YMKLTPEEARNYILYQVGALYAF T0325 120 :GRRPDHIDSHHNVHG 1v6tA 102 :GLELQHVKPHGALYN T0325 135 :KNKKLLGVALAL 1v6tA 124 :LARAVIEGILDF T0325 147 :ARKYQLPLRNASRSI 1v6tA 153 :AEEMGLKVAHEVFAD T0325 167 :LELYQDVRTP 1v6tA 168 :RAYNPDGTLV T0325 186 :KAISTETILQLLDMV 1v6tA 185 :VIEDKEEIAERVISM T0325 202 :CSEGEVF 1v6tA 207 :AINGEWV T0325 209 :EINCHP 1v6tA 219 :TICVHG T0325 218 :DTI 1v6tA 225 :DNP T0325 230 :PR 1v6tA 228 :KA T0325 235 :VEILT 1v6tA 230 :VEITS T0325 242 :EVKEAIEERGILLANYES 1v6tA 235 :YIRKVLEEEGVKIVPMKE Number of specific fragments extracted= 19 number of extra gaps= 0 total=19 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 1v6tA/T0325-1v6tA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1v6tA/T0325-1v6tA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v6tA read from 1v6tA/T0325-1v6tA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1v6tA in template set Warning: unaligning (T0325)K4 because first residue in template chain is (1v6tA)M1 Warning: unaligning (T0325)D177 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1v6tA)A184 Warning: unaligning (T0325)D185 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1v6tA)A184 T0325 5 :KLIINAD 1v6tA 2 :RVDLNSD T0325 13 :FGYTPAV 1v6tA 18 :LGLDEEV T0325 29 :RGVVTSTTALPTS 1v6tA 25 :MKYITSANVACGW T0325 42 :PYFLEAMESARI 1v6tA 43 :LVMRKTVRLAKE T0325 56 :PTLAIGVH 1v6tA 55 :NDVQVGAH T0325 73 :PILPR 1v6tA 63 :PGYPD T0325 86 :EAGYFWHQ 1v6tA 68 :LMGFGRRY T0325 98 :EKVNLEEVYNEWDAQIISFMKS 1v6tA 76 :MKLTPEEARNYILYQVGALYAF T0325 120 :GRRPDHIDSHHNVHG 1v6tA 102 :GLELQHVKPHGALYN T0325 135 :KNKKLLGVAL 1v6tA 124 :LARAVIEGIL T0325 145 :ALARKYQLPLRNASRS 1v6tA 151 :DIAEEMGLKVAHEVFA T0325 166 :YLELYQDVRTP 1v6tA 167 :DRAYNPDGTLV T0325 186 :KAISTETILQLLDMVVCS 1v6tA 185 :VIEDKEEIAERVISMVKD T0325 204 :EGE 1v6tA 208 :ING T0325 207 :VFEINCHP 1v6tA 217 :VDTICVHG T0325 218 :DTI 1v6tA 225 :DNP T0325 230 :PRIREVE 1v6tA 228 :KAVEITS T0325 242 :EVKEAIEERGILLANYES 1v6tA 235 :YIRKVLEEEGVKIVPMKE Number of specific fragments extracted= 18 number of extra gaps= 0 total=37 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 1v6tA/T0325-1v6tA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1v6tA/T0325-1v6tA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v6tA read from 1v6tA/T0325-1v6tA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1v6tA in template set Warning: unaligning (T0325)K4 because first residue in template chain is (1v6tA)M1 Warning: unaligning (T0325)E178 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1v6tA)A184 Warning: unaligning (T0325)Y184 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1v6tA)A184 T0325 5 :KLIINAD 1v6tA 2 :RVDLNSD T0325 13 :FGYTPAV 1v6tA 18 :LGLDEEV T0325 29 :RGVVTSTTALPTS 1v6tA 25 :MKYITSANVACGW T0325 42 :PYFLEAMESARI 1v6tA 43 :LVMRKTVRLAKE T0325 56 :PTLAIGVH 1v6tA 55 :NDVQVGAH T0325 79 :MVPSLVDEAGYFW 1v6tA 63 :PGYPDLMGFGRRY T0325 98 :EKVNLEEVYNEWDAQIISFMK 1v6tA 76 :MKLTPEEARNYILYQVGALYA T0325 119 :SGRRPDHIDSHHNVHGKN 1v6tA 101 :EGLELQHVKPHGALYNAM T0325 137 :KKLLGV 1v6tA 126 :RAVIEG T0325 143 :ALALARKYQLPLRNASR 1v6tA 149 :VADIAEEMGLKVAHEVF T0325 166 :YLELYQDVRTPD 1v6tA 166 :ADRAYNPDGTLV T0325 185 :DKAISTETILQLLDMVV 1v6tA 185 :VIEDKEEIAERVISMVK T0325 202 :CSEGEVF 1v6tA 207 :AINGEWV T0325 209 :EINCHP 1v6tA 219 :TICVHG T0325 218 :DTI 1v6tA 225 :DNP T0325 233 :REVEILT 1v6tA 228 :KAVEITS T0325 242 :EVKEAIEERGILLANYES 1v6tA 235 :YIRKVLEEEGVKIVPMKE Number of specific fragments extracted= 17 number of extra gaps= 0 total=54 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 1ny1A/T0325-1ny1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ny1A expands to /projects/compbio/data/pdb/1ny1.pdb.gz 1ny1A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 # T0325 read from 1ny1A/T0325-1ny1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ny1A read from 1ny1A/T0325-1ny1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ny1A to template set # found chain 1ny1A in template set T0325 3 :NKKLIINADD 1ny1A 65 :EKTIYLTFDN T0325 14 :GYTPAVTQGIIEAHKRGVVTSTT 1ny1A 75 :GYENGYTPKVLDVLKKHRVTGTF T0325 38 :LPTSPYFL 1ny1A 98 :FVTGHFVK T0325 46 :EAMESARI 1ny1A 109 :QLIKRMSD T0325 56 :PTLAIGVH 1ny1A 117 :EGHIIGNH T0325 67 :T 1ny1A 125 :S T0325 70 :QA 1ny1A 126 :FH T0325 80 :VPSLV 1ny1A 128 :HPDLT T0325 99 :KVNLEEVYNEWDAQIISFMKS 1ny1A 133 :TKTADQIQDELDSVNEEVYKI T0325 120 :GRRPDHIDS 1ny1A 155 :GKQDNLYLR T0325 136 :NKK 1ny1A 164 :PPR T0325 139 :LLGVALALARKYQLPLRNASRSIETKD 1ny1A 169 :FSEYVLKETKRLGYQTVFWSVAFVDWK T0325 184 :YDKAISTETILQ 1ny1A 196 :INNQKGKKYAYD T0325 198 :DMVVCSEGEVF 1ny1A 208 :HMIKQAHPGAI T0325 210 :INCHPAFIDTI 1ny1A 219 :YLLHTVSRDNA T0325 236 :EILT 1ny1A 230 :EALD T0325 242 :EVKEAIEERGILLANYES 1ny1A 234 :DAITDLKKQGYTFKSIDD Number of specific fragments extracted= 17 number of extra gaps= 0 total=71 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 1ny1A/T0325-1ny1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1ny1A/T0325-1ny1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ny1A read from 1ny1A/T0325-1ny1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ny1A in template set T0325 3 :NKKLIINADD 1ny1A 65 :EKTIYLTFDN T0325 14 :GYTPAVTQGIIEAHKRGVVTSTTA 1ny1A 75 :GYENGYTPKVLDVLKKHRVTGTFF T0325 39 :PTSPYFL 1ny1A 99 :VTGHFVK T0325 46 :EAMESARI 1ny1A 109 :QLIKRMSD T0325 56 :PTLAIGVH 1ny1A 117 :EGHIIGNH T0325 67 :T 1ny1A 125 :S T0325 70 :QA 1ny1A 126 :FH T0325 80 :VPSLV 1ny1A 128 :HPDLT T0325 99 :KVNLEEVYNEWDAQIISFMKS 1ny1A 133 :TKTADQIQDELDSVNEEVYKI T0325 120 :GRRPDHIDS 1ny1A 155 :GKQDNLYLR T0325 136 :NKK 1ny1A 164 :PPR T0325 139 :LLGVALALARKYQLPLRNASRSIETKD 1ny1A 169 :FSEYVLKETKRLGYQTVFWSVAFVDWK T0325 184 :YDKAISTETI 1ny1A 196 :INNQKGKKYA T0325 197 :LDMVVCSEGEVFEINCHPAFID 1ny1A 206 :YDHMIKQAHPGAIYLLHTVSRD T0325 231 :RI 1ny1A 228 :NA T0325 236 :EILT 1ny1A 230 :EALD T0325 242 :EVKEAIEERGILLANYE 1ny1A 234 :DAITDLKKQGYTFKSID Number of specific fragments extracted= 17 number of extra gaps= 0 total=88 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 1ny1A/T0325-1ny1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1ny1A/T0325-1ny1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ny1A read from 1ny1A/T0325-1ny1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ny1A in template set T0325 2 :SNKKLIINADD 1ny1A 64 :KEKTIYLTFDN T0325 14 :GYTPAVTQGIIEAHKRGVVTSTTA 1ny1A 75 :GYENGYTPKVLDVLKKHRVTGTFF T0325 39 :PTSPYFL 1ny1A 99 :VTGHFVK T0325 46 :EAMESARI 1ny1A 109 :QLIKRMSD T0325 56 :PTLAIGVH 1ny1A 117 :EGHIIGNH T0325 75 :LPREMVP 1ny1A 125 :SFHHPDL T0325 98 :EKVNLEEVYNEWDAQIISFMK 1ny1A 132 :TTKTADQIQDELDSVNEEVYK T0325 119 :SGRRPDHI 1ny1A 154 :TGKQDNLY T0325 132 :VHGKNKKLLGVALALARKYQLPLRNASRS 1ny1A 162 :LRPPRGVFSEYVLKETKRLGYQTVFWSVA T0325 171 :QDVRTPDEML 1ny1A 191 :FVDWKINNQK T0325 192 :TILQLLDMVVCSEGEVFEINCHPAFIDTI 1ny1A 201 :GKKYAYDHMIKQAHPGAIYLLHTVSRDNA T0325 236 :EILT 1ny1A 230 :EALD T0325 242 :EVKEAIEERGILLANYESL 1ny1A 234 :DAITDLKKQGYTFKSIDDL Number of specific fragments extracted= 13 number of extra gaps= 0 total=101 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 2c71A/T0325-2c71A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 2c71A/T0325-2c71A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c71A read from 2c71A/T0325-2c71A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2c71A in training set Warning: unaligning (T0325)K4 because first residue in template chain is (2c71A)K480 Warning: unaligning (T0325)D11 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c71A)D488 Warning: unaligning (T0325)D12 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c71A)D488 Warning: unaligning (T0325)R122 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c71A)P573 Warning: unaligning (T0325)P123 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c71A)P573 T0325 5 :KLIINA 2c71A 481 :LVALTF T0325 14 :GYTPAVTQGIIEAHKRGVVTSTTALPT 2c71A 489 :GPDNVLTARVLDKLDKYNVKATFMVVG T0325 41 :SPYFLEAMESAR 2c71A 519 :NDSTAAIIRRMV T0325 55 :APTLAIGVH 2c71A 531 :NSGHEIGNH T0325 67 :T 2c71A 540 :S T0325 75 :LPRE 2c71A 541 :WSYS T0325 82 :SL 2c71A 545 :GM T0325 98 :EKVNLEEVYNEWDAQIISFMKS 2c71A 547 :ANMSPDQIRKSIADTNAVIQKY T0325 120 :GR 2c71A 570 :GT T0325 124 :DHIDS 2c71A 574 :KFFRP T0325 130 :HNVH 2c71A 579 :PNLE T0325 135 :KNKKLLGV 2c71A 583 :TSPTLFNN T0325 152 :LPLRNASR 2c71A 591 :VDLVFVGG T0325 174 :RTPD 2c71A 599 :LTAN T0325 183 :FYDKAISTETILQ 2c71A 603 :DWIPSTTAEQRAA T0325 196 :LLDMV 2c71A 617 :VINGV T0325 204 :EGEVF 2c71A 622 :RDGTI T0325 210 :INCHPAFIDT 2c71A 627 :ILLHDVQPEP T0325 229 :MPRIREVE 2c71A 637 :HPTPEALD T0325 242 :EVKEAIEERGILLAN 2c71A 645 :IIIPTLKSRGYEFVT Number of specific fragments extracted= 20 number of extra gaps= 2 total=121 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 2c71A/T0325-2c71A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 2c71A/T0325-2c71A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c71A read from 2c71A/T0325-2c71A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2c71A in training set Warning: unaligning (T0325)K4 because first residue in template chain is (2c71A)K480 Warning: unaligning (T0325)D11 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c71A)D488 Warning: unaligning (T0325)D12 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c71A)D488 Warning: unaligning (T0325)R122 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c71A)P573 Warning: unaligning (T0325)P123 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c71A)P573 T0325 5 :KLIINA 2c71A 481 :LVALTF T0325 14 :GYTPAVTQGIIEAHKRGVVTSTTALP 2c71A 489 :GPDNVLTARVLDKLDKYNVKATFMVV T0325 40 :TSPYFLEAMESAR 2c71A 518 :VNDSTAAIIRRMV T0325 55 :APTLAIGVH 2c71A 531 :NSGHEIGNH T0325 74 :ILPREMV 2c71A 540 :SWSYSGM T0325 98 :EKVNLEEVYNEWDAQIISFMKS 2c71A 547 :ANMSPDQIRKSIADTNAVIQKY T0325 120 :GR 2c71A 570 :GT T0325 124 :DHIDS 2c71A 574 :KFFRP T0325 130 :HNVH 2c71A 579 :PNLE T0325 135 :KNKKLLGV 2c71A 583 :TSPTLFNN T0325 152 :LPLRNA 2c71A 591 :VDLVFV T0325 177 :DEMLYQFYDKAISTETILQ 2c71A 597 :GGLTANDWIPSTTAEQRAA T0325 199 :MVVCSEGEVFEINCHPAF 2c71A 616 :AVINGVRDGTIILLHDVQ T0325 226 :GYCMPRIREVEIL 2c71A 634 :PEPHPTPEALDII T0325 244 :KEAIEERGILLA 2c71A 647 :IPTLKSRGYEFV Number of specific fragments extracted= 15 number of extra gaps= 2 total=136 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 2c71A/T0325-2c71A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 2c71A/T0325-2c71A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c71A read from 2c71A/T0325-2c71A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2c71A in training set Warning: unaligning (T0325)K4 because first residue in template chain is (2c71A)K480 Warning: unaligning (T0325)D11 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c71A)D488 Warning: unaligning (T0325)D12 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c71A)D488 Warning: unaligning (T0325)R122 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c71A)P573 Warning: unaligning (T0325)P123 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c71A)P573 T0325 5 :KLIINA 2c71A 481 :LVALTF T0325 14 :GYTPAVTQGIIEAHKRGVVTSTTALPTS 2c71A 489 :GPDNVLTARVLDKLDKYNVKATFMVVGQ T0325 42 :PYFLEAMESARI 2c71A 520 :DSTAAIIRRMVN T0325 56 :PTLAIGVH 2c71A 532 :SGHEIGNH T0325 69 :NQAKPIL 2c71A 540 :SWSYSGM T0325 98 :EKVNLEEVYNEWDAQIISFMK 2c71A 547 :ANMSPDQIRKSIADTNAVIQK T0325 119 :SGR 2c71A 569 :AGT T0325 124 :DHIDS 2c71A 574 :KFFRP T0325 130 :HNVHGK 2c71A 579 :PNLETS T0325 137 :KKLLGV 2c71A 585 :PTLFNN T0325 152 :LPLRNASRSI 2c71A 591 :VDLVFVGGLT T0325 181 :YQFYDKAI 2c71A 601 :ANDWIPST T0325 192 :TILQLLDMVVCSEGEVFEINCHPAFID 2c71A 609 :TAEQRAAAVINGVRDGTIILLHDVQPE T0325 228 :CMPRIREVEILT 2c71A 636 :PHPTPEALDIII T0325 245 :EAIEERGILLANY 2c71A 648 :PTLKSRGYEFVTL Number of specific fragments extracted= 15 number of extra gaps= 2 total=151 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 1mi3A/T0325-1mi3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1mi3A expands to /projects/compbio/data/pdb/1mi3.pdb.gz 1mi3A:# T0325 read from 1mi3A/T0325-1mi3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mi3A read from 1mi3A/T0325-1mi3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1mi3A to template set # found chain 1mi3A in template set T0325 4 :KKLIINADDFGYTPAVTQGIIEAHKRGV 1mi3A 43 :YRLFDGAEDYGNEKEVGDGVKRAIDEGL T0325 32 :VTSTTALPT 1mi3A 76 :IFLTSKLWN T0325 41 :SPYFLEAMESARISAPTLAIGVHLTLTL 1mi3A 89 :PKNVETALNKTLADLKVDYVDLFLIHFP T0325 70 :QAKPILPREM 1mi3A 117 :IAFKFVPIEE T0325 89 :YFWHQSI 1mi3A 127 :KYPPGFY T0325 96 :FEEKVNLEEVYNEWDA 1mi3A 141 :VYEDVPILETWKALEK T0325 116 :FMKSGRRPDHIDS 1mi3A 157 :LVAAGKIKSIGVS T0325 135 :KNK 1mi3A 170 :NFP T0325 140 :LGVALALARKYQLPLRNA 1mi3A 173 :GALLLDLLRGATIKPAVL T0325 173 :VR 1mi3A 192 :VE T0325 183 :FYDKAISTETILQLLD 1mi3A 194 :HHPYLQQPKLIEFAQK T0325 205 :GEVF 1mi3A 210 :AGVT T0325 210 :INCHPAFIDTILQNQS 1mi3A 214 :ITAYSSFGPQSFVEMN T0325 230 :PRIR 1mi3A 231 :GRAL T0325 237 :ILTSQEVKEAIEERGIL 1mi3A 239 :LFAHDTIKAIAAKYNKT Number of specific fragments extracted= 15 number of extra gaps= 0 total=166 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 1mi3A/T0325-1mi3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1mi3A/T0325-1mi3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mi3A read from 1mi3A/T0325-1mi3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mi3A in template set T0325 4 :KKLIINADDFGYTPAVTQGIIEAHKRGV 1mi3A 43 :YRLFDGAEDYGNEKEVGDGVKRAIDEGL T0325 32 :VTSTTALP 1mi3A 76 :IFLTSKLW T0325 40 :TSPYFLEAMESARISAPTLAIGVHLTLTL 1mi3A 88 :DPKNVETALNKTLADLKVDYVDLFLIHFP T0325 70 :QAKPILPREMVPSL 1mi3A 117 :IAFKFVPIEEKYPP T0325 84 :VDEAGYFWH 1mi3A 134 :CGDGNNFVY T0325 98 :EKVNLEEVYNEWDA 1mi3A 143 :EDVPILETWKALEK T0325 116 :FMKSGRRPDHIDS 1mi3A 157 :LVAAGKIKSIGVS T0325 135 :KNK 1mi3A 170 :NFP T0325 140 :LGVALALARKYQLPLRN 1mi3A 173 :GALLLDLLRGATIKPAV T0325 181 :YQFYDKAISTE 1mi3A 192 :VEHHPYLQQPK T0325 196 :LLDMVVCSE 1mi3A 203 :LIEFAQKAG T0325 208 :FEINCHPAFIDTILQNQS 1mi3A 212 :VTITAYSSFGPQSFVEMN T0325 226 :GYCM 1mi3A 235 :NTPT T0325 237 :ILTSQEVKEAIEERGIL 1mi3A 239 :LFAHDTIKAIAAKYNKT Number of specific fragments extracted= 14 number of extra gaps= 0 total=180 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 1mi3A/T0325-1mi3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1mi3A/T0325-1mi3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mi3A read from 1mi3A/T0325-1mi3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mi3A in template set T0325 4 :KKLIINADDFGYTPAVTQGIIEAHKRGV 1mi3A 43 :YRLFDGAEDYGNEKEVGDGVKRAIDEGL T0325 32 :VTSTTALPTS 1mi3A 76 :IFLTSKLWNN T0325 42 :PYFLEAMESARISAPTLAIGVHLT 1mi3A 90 :KNVETALNKTLADLKVDYVDLFLI T0325 66 :LTLNQAKPILPREMVPSLVDEAGYFW 1mi3A 117 :IAFKFVPIEEKYPPGFYCGDGNNFVY T0325 98 :EKVNLEEVYNEWDAQII 1mi3A 143 :EDVPILETWKALEKLVA T0325 115 :SFMK 1mi3A 178 :DLLR T0325 119 :SGRRPDHIDSHHNVHGK 1mi3A 183 :ATIKPAVLQVEHHPYLQ T0325 139 :LLGV 1mi3A 200 :QPKL T0325 144 :LALARKYQLPLRNASRSIE 1mi3A 204 :IEFAQKAGVTITAYSSFGP T0325 163 :TKDYLELYQDVRTPDEMLYQ 1mi3A 226 :VEMNQGRALNTPTLFAHDTI T0325 183 :FYDKAISTETILQLLDMVVCSE 1mi3A 247 :AIAAKYNKTPAEVLLRWAAQRG T0325 209 :EINCHPAFIDTILQNQSGYCMP 1mi3A 269 :IAVIPKSNLPERLVQNRSFNTF T0325 239 :TSQEVKEAIEER 1mi3A 292 :LTKEDFEEIAKL Number of specific fragments extracted= 13 number of extra gaps= 0 total=193 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 1xw8A/T0325-1xw8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xw8A expands to /projects/compbio/data/pdb/1xw8.pdb.gz 1xw8A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0325 read from 1xw8A/T0325-1xw8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xw8A read from 1xw8A/T0325-1xw8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xw8A to template set # found chain 1xw8A in template set Warning: unaligning (T0325)K4 because first residue in template chain is (1xw8A)M1 Warning: unaligning (T0325)P76 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xw8A)S69 Warning: unaligning (T0325)F96 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xw8A)S69 Warning: unaligning (T0325)R174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xw8A)E184 Warning: unaligning (T0325)K186 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xw8A)E184 Warning: unaligning (T0325)F216 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xw8A)H223 Warning: unaligning (T0325)D218 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xw8A)H223 T0325 5 :KLIINADDFGYTPAVTQGII 1xw8A 2 :KIDLNADLGEGCASDAELLT T0325 31 :VVTSTTALPTS 1xw8A 22 :LVSSANIACGF T0325 42 :PYFLEAMESAR 1xw8A 38 :QIMQACVREAI T0325 54 :SA 1xw8A 49 :KN T0325 57 :TLAIGVH 1xw8A 51 :GVAIGAH T0325 73 :PIL 1xw8A 58 :PSF T0325 97 :EEKVNLEEVYNEWDAQIISFMK 1xw8A 70 :AMQLPPETVYAQTLYQIGALAT T0325 119 :SGRRPDHIDSH 1xw8A 96 :QGGVMRHVKPH T0325 130 :HNVH 1xw8A 111 :NQAA T0325 135 :KNKKLLGVALAL 1xw8A 115 :KEAQLADAIARA T0325 147 :ARKYQLPLRNASR 1xw8A 148 :GKQYGLTTREEVF T0325 160 :SIETKDYLELYQDV 1xw8A 164 :GYQADGSLVPRSQS T0325 187 :AISTETILQLLDM 1xw8A 185 :EQALAQTLEMVQH T0325 202 :CSEGEVF 1xw8A 202 :SITGEWA T0325 209 :EINCHPA 1xw8A 214 :TVCLHGD T0325 219 :TI 1xw8A 224 :AL T0325 229 :MPRI 1xw8A 226 :AFAR T0325 242 :EVKEA 1xw8A 230 :RLRSA Number of specific fragments extracted= 18 number of extra gaps= 0 total=211 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 1xw8A/T0325-1xw8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1xw8A/T0325-1xw8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xw8A read from 1xw8A/T0325-1xw8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xw8A in template set Warning: unaligning (T0325)K4 because first residue in template chain is (1xw8A)M1 Warning: unaligning (T0325)P73 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xw8A)S69 Warning: unaligning (T0325)F96 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xw8A)S69 T0325 5 :KLIINADDFGYTPAVTQGIIE 1xw8A 2 :KIDLNADLGEGCASDAELLTL T0325 32 :VTSTTALPTS 1xw8A 23 :VSSANIACGF T0325 42 :PYFLEAMESAR 1xw8A 38 :QIMQACVREAI T0325 54 :SA 1xw8A 49 :KN T0325 57 :TLAIGVH 1xw8A 51 :GVAIGAH T0325 70 :QAK 1xw8A 58 :PSF T0325 97 :EEKVNLEEVYNEWDAQIISFMK 1xw8A 70 :AMQLPPETVYAQTLYQIGALAT T0325 119 :SGRRPDHIDSH 1xw8A 96 :QGGVMRHVKPH T0325 130 :HNVH 1xw8A 111 :NQAA T0325 135 :KNKKLLGVALALARKY 1xw8A 115 :KEAQLADAIARAVYAC T0325 151 :QLPLRNASR 1xw8A 133 :ALILVGLAG T0325 164 :KDYLELY 1xw8A 142 :SELIRAG T0325 204 :EGEVF 1xw8A 204 :TGEWA T0325 209 :EINCHP 1xw8A 214 :TVCLHG Number of specific fragments extracted= 14 number of extra gaps= 0 total=225 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 1xw8A/T0325-1xw8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1xw8A/T0325-1xw8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xw8A read from 1xw8A/T0325-1xw8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xw8A in template set Warning: unaligning (T0325)K4 because first residue in template chain is (1xw8A)M1 Warning: unaligning (T0325)M79 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xw8A)S69 Warning: unaligning (T0325)A87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xw8A)S69 T0325 5 :KLIINADDFGYTPAVTQGII 1xw8A 2 :KIDLNADLGEGCASDAELLT T0325 31 :VVTSTTALPTS 1xw8A 22 :LVSSANIACGF T0325 42 :PYFLEAMESARI 1xw8A 38 :QIMQACVREAIK T0325 56 :PTLAIGVH 1xw8A 50 :NGVAIGAH T0325 71 :AKP 1xw8A 58 :PSF T0325 97 :EEKVNLEEVYNEWDAQIISFMK 1xw8A 70 :AMQLPPETVYAQTLYQIGALAT T0325 119 :SGRRPDHIDSH 1xw8A 96 :QGGVMRHVKPH T0325 137 :KKLLGVA 1xw8A 107 :GMLYNQA T0325 187 :AISTETILQLLDMVVCSEGEVFEINC 1xw8A 114 :AKEAQLADAIARAVYACDPALILVGL T0325 217 :IDT 1xw8A 140 :AGS T0325 242 :EVKEAIEERGILLAN 1xw8A 143 :ELIRAGKQYGLTTRE Number of specific fragments extracted= 11 number of extra gaps= 0 total=236 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 2cc0A/T0325-2cc0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2cc0A expands to /projects/compbio/data/pdb/2cc0.pdb.gz 2cc0A:Skipped atom 13, because occupancy 0.2 <= existing 0.800 in 2cc0A Skipped atom 17, because occupancy 0.200 <= existing 0.800 in 2cc0A Skipped atom 19, because occupancy 0.200 <= existing 0.800 in 2cc0A Skipped atom 120, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 124, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 126, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 346, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 350, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 352, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 523, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 527, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 529, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 531, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 533, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 626, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 630, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 632, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 635, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 639, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 641, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 643, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 645, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 647, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 649, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 651, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 732, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 736, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 738, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 740, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 742, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 744, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 862, because occupancy 0.330 <= existing 0.330 in 2cc0A Skipped atom 863, because occupancy 0.330 <= existing 0.330 in 2cc0A Skipped atom 867, because occupancy 0.330 <= existing 0.330 in 2cc0A Skipped atom 868, because occupancy 0.330 <= existing 0.330 in 2cc0A Skipped atom 870, because occupancy 0.330 <= existing 0.330 in 2cc0A Skipped atom 871, because occupancy 0.330 <= existing 0.330 in 2cc0A Skipped atom 951, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 955, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 957, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 959, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 961, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 1100, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 1104, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 1106, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 1108, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 1110, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 1112, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 1378, because occupancy 0.200 <= existing 0.800 in 2cc0A Skipped atom 1382, because occupancy 0.200 <= existing 0.800 in 2cc0A Skipped atom 1384, because occupancy 0.200 <= existing 0.800 in 2cc0A Skipped atom 1397, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 1401, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 1403, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 1405, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 1407, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 1431, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 1435, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 1437, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 1439, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 1441, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 1443, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 1457, because occupancy 0.330 <= existing 0.330 in 2cc0A Skipped atom 1458, because occupancy 0.330 <= existing 0.330 in 2cc0A Skipped atom 1462, because occupancy 0.330 <= existing 0.330 in 2cc0A Skipped atom 1463, because occupancy 0.330 <= existing 0.330 in 2cc0A Skipped atom 1465, because occupancy 0.330 <= existing 0.330 in 2cc0A Skipped atom 1466, because occupancy 0.330 <= existing 0.330 in 2cc0A Skipped atom 1468, because occupancy 0.330 <= existing 0.330 in 2cc0A Skipped atom 1469, because occupancy 0.330 <= existing 0.330 in 2cc0A Skipped atom 1471, because occupancy 0.330 <= existing 0.330 in 2cc0A Skipped atom 1472, because occupancy 0.330 <= existing 0.330 in 2cc0A Skipped atom 1474, because occupancy 0.330 <= existing 0.330 in 2cc0A Skipped atom 1475, because occupancy 0.330 <= existing 0.330 in 2cc0A Skipped atom 1477, because occupancy 0.330 <= existing 0.330 in 2cc0A Skipped atom 1478, because occupancy 0.330 <= existing 0.330 in 2cc0A Skipped atom 1480, because occupancy 0.330 <= existing 0.330 in 2cc0A Skipped atom 1481, because occupancy 0.330 <= existing 0.330 in 2cc0A # T0325 read from 2cc0A/T0325-2cc0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cc0A read from 2cc0A/T0325-2cc0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2cc0A to template set # found chain 2cc0A in template set Warning: unaligning (T0325)D11 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2cc0A)D13 Warning: unaligning (T0325)D12 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cc0A)D13 Warning: unaligning (T0325)Y15 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2cc0A)S16 Warning: unaligning (T0325)T16 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cc0A)S16 T0325 2 :SNKKLIINA 2cc0A 3 :CNGYVGLTF T0325 14 :G 2cc0A 14 :G T0325 17 :PAVTQGIIEAHKRGV 2cc0A 17 :GSTQSLLNALRQNGL T0325 33 :T 2cc0A 32 :R T0325 35 :TTALPTSPYFL 2cc0A 33 :ATMFNQGQYAA T0325 46 :EAMESARI 2cc0A 47 :SLVRAQVD T0325 56 :PTLAIGVH 2cc0A 55 :AGMWVANH T0325 67 :T 2cc0A 63 :S T0325 70 :QAKP 2cc0A 64 :YTHP T0325 82 :SL 2cc0A 68 :HM T0325 98 :EKVNLEEVYNEWDAQIISFMKS 2cc0A 70 :TQLGQAQMDSEISRTQQAIAGA T0325 120 :GRRPDHID 2cc0A 93 :GGTPKLFR T0325 133 :H 2cc0A 101 :P T0325 135 :KNKKLLGVALALARKYQLPLRNASRS 2cc0A 102 :PYGETNATLRSVEAKYGLTEVIWDVD T0325 175 :TPDE 2cc0A 128 :SQDW T0325 186 :KAISTETILQLLDMV 2cc0A 132 :NNASTDAIVQAVSRL T0325 204 :EGEVF 2cc0A 147 :GNGQV T0325 210 :INCHP 2cc0A 152 :ILMHD T0325 230 :PRIREVEIL 2cc0A 157 :WPANTLAAI T0325 241 :QEVKEAIEERGILLA 2cc0A 166 :PRIAQTLAGKGLCSG Number of specific fragments extracted= 20 number of extra gaps= 2 total=256 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 2cc0A/T0325-2cc0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 2cc0A/T0325-2cc0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cc0A read from 2cc0A/T0325-2cc0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2cc0A in template set Warning: unaligning (T0325)D11 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2cc0A)D13 Warning: unaligning (T0325)D12 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cc0A)D13 Warning: unaligning (T0325)Y15 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2cc0A)S16 Warning: unaligning (T0325)T16 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cc0A)S16 T0325 2 :SNKKLIINA 2cc0A 3 :CNGYVGLTF T0325 14 :G 2cc0A 14 :G T0325 17 :PAVTQGIIEAHKRG 2cc0A 17 :GSTQSLLNALRQNG T0325 32 :VTS 2cc0A 31 :LRA T0325 36 :TALPTSPYFL 2cc0A 34 :TMFNQGQYAA T0325 46 :EAMESAR 2cc0A 47 :SLVRAQV T0325 54 :S 2cc0A 54 :D T0325 56 :PTLAIGVH 2cc0A 55 :AGMWVANH T0325 67 :T 2cc0A 63 :S T0325 70 :QAK 2cc0A 64 :YTH T0325 81 :PSL 2cc0A 67 :PHM T0325 98 :EKVNLEEVYNEWDAQIISFMKS 2cc0A 70 :TQLGQAQMDSEISRTQQAIAGA T0325 120 :GRRPDHID 2cc0A 93 :GGTPKLFR T0325 133 :H 2cc0A 101 :P T0325 135 :KNKKLLGVALALARKYQLPLRNASRSIE 2cc0A 102 :PYGETNATLRSVEAKYGLTEVIWDVDSQ T0325 177 :DE 2cc0A 130 :DW T0325 186 :KAISTETILQLLDMV 2cc0A 132 :NNASTDAIVQAVSRL T0325 204 :EGEVFEINCH 2cc0A 147 :GNGQVILMHD T0325 227 :YC 2cc0A 157 :WP T0325 232 :IREVEIL 2cc0A 159 :ANTLAAI T0325 241 :QEVKEAIEERGILLA 2cc0A 166 :PRIAQTLAGKGLCSG Number of specific fragments extracted= 21 number of extra gaps= 2 total=277 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 2cc0A/T0325-2cc0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 2cc0A/T0325-2cc0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cc0A read from 2cc0A/T0325-2cc0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2cc0A in template set Warning: unaligning (T0325)D11 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2cc0A)D13 Warning: unaligning (T0325)D12 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cc0A)D13 Warning: unaligning (T0325)Y15 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2cc0A)S16 Warning: unaligning (T0325)T16 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cc0A)S16 T0325 2 :SNKKLIINA 2cc0A 3 :CNGYVGLTF T0325 14 :G 2cc0A 14 :G T0325 17 :PAVTQGIIEAHKRG 2cc0A 17 :GSTQSLLNALRQNG T0325 32 :VTS 2cc0A 31 :LRA T0325 36 :TALPTSPYFL 2cc0A 34 :TMFNQGQYAA T0325 46 :EAMESARI 2cc0A 47 :SLVRAQVD T0325 56 :PTLAIGVH 2cc0A 55 :AGMWVANH T0325 71 :AKPILP 2cc0A 63 :SYTHPH T0325 97 :EEKVNLEEVYNEWDAQIISFMK 2cc0A 69 :MTQLGQAQMDSEISRTQQAIAG T0325 119 :SGRRPDHID 2cc0A 92 :GGGTPKLFR T0325 133 :HGK 2cc0A 101 :PPY T0325 137 :KKLLGVALALARKYQLPLRNASRSIETKDYLE 2cc0A 104 :GETNATLRSVEAKYGLTEVIWDVDSQDWNNAS T0325 193 :ILQLLDMVVCSEGEVFEINCH 2cc0A 136 :TDAIVQAVSRLGNGQVILMHD T0325 216 :FI 2cc0A 157 :WP T0325 232 :IREVEIL 2cc0A 159 :ANTLAAI T0325 241 :QEVKEAIEERGILL 2cc0A 166 :PRIAQTLAGKGLCS Number of specific fragments extracted= 16 number of extra gaps= 2 total=293 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 1w5qA/T0325-1w5qA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1w5qA expands to /projects/compbio/data/pdb/1w5q.pdb.gz 1w5qA:Skipped atom 260, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 262, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 264, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 266, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 268, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 270, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 272, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 321, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 323, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 325, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 327, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 329, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 331, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 333, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 479, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 481, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 483, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 485, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 487, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 489, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 491, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 493, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 495, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 497, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 499, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 578, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 580, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 582, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 584, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 586, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 588, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 590, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 592, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 594, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 596, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 598, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 600, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 602, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 604, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 606, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 608, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 610, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 612, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 732, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 734, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 736, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 738, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 740, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 742, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 744, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 881, because occupancy 0.250 <= existing 0.750 in 1w5qA Skipped atom 883, because occupancy 0.250 <= existing 0.750 in 1w5qA Skipped atom 885, because occupancy 0.250 <= existing 0.750 in 1w5qA Skipped atom 887, because occupancy 0.250 <= existing 0.750 in 1w5qA Skipped atom 889, because occupancy 0.250 <= existing 0.750 in 1w5qA Skipped atom 891, because occupancy 0.250 <= existing 0.750 in 1w5qA Skipped atom 893, because occupancy 0.250 <= existing 0.750 in 1w5qA Skipped atom 895, because occupancy 0.250 <= existing 0.750 in 1w5qA Skipped atom 897, because occupancy 0.250 <= existing 0.750 in 1w5qA Skipped atom 899, because occupancy 0.250 <= existing 0.750 in 1w5qA Skipped atom 901, because occupancy 0.250 <= existing 0.750 in 1w5qA Skipped atom 915, because occupancy 0.750 <= existing 0.750 in 1w5qA Skipped atom 917, because occupancy 0.250 <= existing 0.750 in 1w5qA Skipped atom 919, because occupancy 0.250 <= existing 0.750 in 1w5qA Skipped atom 921, because occupancy 0.250 <= existing 0.750 in 1w5qA Skipped atom 923, because occupancy 0.250 <= existing 0.750 in 1w5qA Skipped atom 925, because occupancy 0.250 <= existing 0.750 in 1w5qA Skipped atom 927, because occupancy 0.250 <= existing 0.750 in 1w5qA Skipped atom 929, because occupancy 0.250 <= existing 0.750 in 1w5qA Skipped atom 931, because occupancy 0.250 <= existing 0.750 in 1w5qA Skipped atom 933, because occupancy 0.250 <= existing 0.750 in 1w5qA Skipped atom 935, because occupancy 0.250 <= existing 0.750 in 1w5qA Skipped atom 1078, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1080, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1082, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1084, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1086, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1088, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1090, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1092, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1094, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1121, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1123, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1125, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1127, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1129, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1131, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1133, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1135, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1137, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1139, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1272, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1274, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1276, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1278, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1280, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1282, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1284, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1286, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1310, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1312, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1314, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1316, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1318, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1320, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1322, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1324, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1326, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1328, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1330, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1375, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1377, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1379, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1381, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1383, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1385, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1387, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1389, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1391, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1531, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1533, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1535, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1537, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1539, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1541, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1543, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1545, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1547, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1571, because occupancy 0.200 <= existing 0.800 in 1w5qA Skipped atom 1573, because occupancy 0.200 <= existing 0.800 in 1w5qA Skipped atom 1575, because occupancy 0.200 <= existing 0.800 in 1w5qA Skipped atom 1577, because occupancy 0.200 <= existing 0.800 in 1w5qA Skipped atom 1579, because occupancy 0.200 <= existing 0.800 in 1w5qA Skipped atom 1581, because occupancy 0.200 <= existing 0.800 in 1w5qA Skipped atom 1992, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1994, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1996, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1998, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2000, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2002, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2004, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2006, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2015, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2017, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2019, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2021, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2023, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2025, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2027, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2029, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2058, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2060, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2062, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2064, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2066, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2068, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2070, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2072, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2124, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2126, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2128, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2130, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2132, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2134, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2136, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2138, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2140, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2142, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2144, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2181, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2183, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2185, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2187, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2189, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2191, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2193, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2195, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2197, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2210, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2212, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2214, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2216, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2218, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2220, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2222, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2224, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2226, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2228, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2230, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2333, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2335, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2337, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2339, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2341, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2343, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2345, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2347, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2359, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2361, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2363, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2365, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2367, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2369, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2371, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2373, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2470, because occupancy 0.400 <= existing 0.600 in 1w5qA Skipped atom 2472, because occupancy 0.400 <= existing 0.600 in 1w5qA Skipped atom 2474, because occupancy 0.400 <= existing 0.600 in 1w5qA Skipped atom 2476, because occupancy 0.400 <= existing 0.600 in 1w5qA Skipped atom 2478, because occupancy 0.400 <= existing 0.600 in 1w5qA Skipped atom 2480, because occupancy 0.400 <= existing 0.600 in 1w5qA Skipped atom 2482, because occupancy 0.400 <= existing 0.600 in 1w5qA Skipped atom 2484, because occupancy 0.400 <= existing 0.600 in 1w5qA # T0325 read from 1w5qA/T0325-1w5qA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1w5qA read from 1w5qA/T0325-1w5qA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1w5qA to template set # found chain 1w5qA in template set Warning: unaligning (T0325)S160 because of BadResidue code BAD_PEPTIDE in next template residue (1w5qA)S208 Warning: unaligning (T0325)I161 because of BadResidue code BAD_PEPTIDE at template residue (1w5qA)S208 Warning: unaligning (T0325)Y170 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1w5qA)N228 Warning: unaligning (T0325)E178 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1w5qA)N228 Warning: unaligning (T0325)P214 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w5qA)G262 Warning: unaligning (T0325)A215 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w5qA)G262 T0325 17 :PAVTQGIIEAHKRGVVTSTTALPT 1w5qA 66 :DQLLIEAEEWVALGIPALALFPVT T0325 42 :P 1w5qA 90 :P T0325 43 :YFLEAMESARISAPTLAIGVHLTLT 1w5qA 107 :IAQRATRALRERFPELGIITDVCLC T0325 73 :PILPRE 1w5qA 132 :EFTTHG T0325 80 :VPSLVDEAGYF 1w5qA 138 :QCGILDDDGYV T0325 101 :NLEEVYNEWDAQIISFMKSGRRPDHIDS 1w5qA 149 :LNDVSIDVLVRQALSHAEAGAQVVAPSD T0325 135 :KNKKLLGVALALARKYQLPLRNA 1w5qA 177 :MMDGRIGAIREALESAGHTNVRV T0325 158 :SR 1w5qA 205 :KY T0325 162 :ETKDYLEL 1w5qA 209 :AYYGPFRD T0325 179 :MLYQFYDKA 1w5qA 229 :RATYQMDPA T0325 189 :STETILQLLDMVVC 1w5qA 238 :NSDEALHEVAADLA T0325 205 :GEVFEINCH 1w5qA 252 :EGADMVMVK T0325 216 :FI 1w5qA 263 :MP T0325 227 :YCMPRIREVEIL 1w5qA 265 :YLDIVRRVKDEF Number of specific fragments extracted= 14 number of extra gaps= 2 total=307 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 1w5qA/T0325-1w5qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1w5qA/T0325-1w5qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1w5qA read from 1w5qA/T0325-1w5qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1w5qA in template set Warning: unaligning (T0325)N156 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1w5qA)Y202 Warning: unaligning (T0325)S160 because of BadResidue code BAD_PEPTIDE in next template residue (1w5qA)S208 Warning: unaligning (T0325)I161 because of BadResidue code BAD_PEPTIDE at template residue (1w5qA)S208 Warning: unaligning (T0325)Y170 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1w5qA)N228 Warning: unaligning (T0325)E178 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1w5qA)N228 Warning: unaligning (T0325)P214 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w5qA)G262 Warning: unaligning (T0325)A215 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w5qA)G262 T0325 17 :PAVTQGIIEAHKRG 1w5qA 66 :DQLLIEAEEWVALG T0325 32 :VTSTTALPTSP 1w5qA 80 :IPALALFPVTP T0325 43 :YFLEAMESARISAPTLAIGVHLTLT 1w5qA 107 :IAQRATRALRERFPELGIITDVCLC T0325 73 :PILPR 1w5qA 132 :EFTTH T0325 79 :MVPSLVDEAGYFW 1w5qA 137 :GQCGILDDDGYVL T0325 102 :LEEVYNEWDAQIISFMKSGRRPDHIDS 1w5qA 150 :NDVSIDVLVRQALSHAEAGAQVVAPSD T0325 135 :KNKKLLGVALALARKY 1w5qA 177 :MMDGRIGAIREALESA T0325 151 :QLPLR 1w5qA 196 :NVRVM T0325 157 :ASR 1w5qA 204 :AKY T0325 162 :ETKDYLEL 1w5qA 209 :AYYGPFRD T0325 179 :MLYQFYDKAIS 1w5qA 229 :RATYQMDPANS T0325 191 :ETILQLLDMVVCS 1w5qA 240 :DEALHEVAADLAE T0325 206 :EVFEINCH 1w5qA 253 :GADMVMVK T0325 216 :F 1w5qA 263 :M T0325 226 :GYCMPRIREVEIL 1w5qA 264 :PYLDIVRRVKDEF Number of specific fragments extracted= 15 number of extra gaps= 3 total=322 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 1w5qA/T0325-1w5qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1w5qA/T0325-1w5qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1w5qA read from 1w5qA/T0325-1w5qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1w5qA in template set Warning: unaligning (T0325)S160 because of BadResidue code BAD_PEPTIDE in next template residue (1w5qA)S208 Warning: unaligning (T0325)I161 because of BadResidue code BAD_PEPTIDE at template residue (1w5qA)S208 Warning: unaligning (T0325)M179 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1w5qA)N228 Warning: unaligning (T0325)P214 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w5qA)G262 Warning: unaligning (T0325)A215 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w5qA)G262 T0325 26 :AHKRG 1w5qA 75 :WVALG T0325 32 :VTSTTALPTSP 1w5qA 80 :IPALALFPVTP T0325 43 :YFLEAMESARISAPTLAIGVHLTLTLN 1w5qA 107 :IAQRATRALRERFPELGIITDVCLCEF T0325 74 :ILPREMVPSLVDEAG 1w5qA 134 :TTHGQCGILDDDGYV T0325 101 :NLEEVYNEWDAQIISFMKSGRRP 1w5qA 149 :LNDVSIDVLVRQALSHAEAGAQV T0325 126 :IDSH 1w5qA 172 :VAPS T0325 133 :HGK 1w5qA 176 :DMM T0325 137 :KKLLGVALALARKYQLPLRNA 1w5qA 179 :DGRIGAIREALESAGHTNVRV T0325 158 :SR 1w5qA 205 :KY T0325 162 :ETKDYLEL 1w5qA 209 :AYYGPFRD T0325 180 :LYQFYDKAISTETILQLLDMVVCS 1w5qA 229 :RATYQMDPANSDEALHEVAADLAE T0325 206 :EVFEINCH 1w5qA 253 :GADMVMVK T0325 216 :FID 1w5qA 263 :MPY T0325 219 :TI 1w5qA 267 :DI T0325 231 :RIREVEIL 1w5qA 269 :VRRVKDEF Number of specific fragments extracted= 15 number of extra gaps= 2 total=337 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 2c1iA/T0325-2c1iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2c1iA expands to /projects/compbio/data/pdb/2c1i.pdb.gz 2c1iA:# T0325 read from 2c1iA/T0325-2c1iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c1iA read from 2c1iA/T0325-2c1iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2c1iA to template set # found chain 2c1iA in template set Warning: unaligning (T0325)D11 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c1iA)D276 Warning: unaligning (T0325)D12 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c1iA)D276 T0325 3 :NKKLIINA 2c1iA 267 :QKVVALTF T0325 14 :GYTPAVTQGIIEAHKRGVVTSTTALPT 2c1iA 277 :GPNPATTPQVLETLAKYDIKATFFVLG T0325 41 :SPYFLEAMESARI 2c1iA 306 :VSGNEDLVKRIKS T0325 56 :PTLAIGVH 2c1iA 319 :EGHVVGNH T0325 67 :T 2c1iA 327 :S T0325 70 :QAKPILPR 2c1iA 328 :WSHPILSQ T0325 100 :VNLEEVYNEWDAQIISFMKS 2c1iA 336 :LSLDEAKKQITDTEDVLTKV T0325 120 :GRRPDHIDS 2c1iA 357 :GSSSKLMRP T0325 131 :NVHGKNKKLLG 2c1iA 366 :PYGAITDDIRN T0325 151 :QLPLRNASRS 2c1iA 377 :SLDLSFIMWD T0325 173 :VRTPDEM 2c1iA 387 :VDSLDWK T0325 187 :AISTETILQLLD 2c1iA 394 :SKNEASILTEIQ T0325 201 :VCSEGEVF 2c1iA 406 :HQVANGSI T0325 210 :INCHP 2c1iA 414 :VLMHD T0325 227 :YCMPRIREV 2c1iA 419 :IHSPTVNAL T0325 241 :QEVKEAIEERGILLAN 2c1iA 428 :PRVIEYLKNQGYTFVT Number of specific fragments extracted= 16 number of extra gaps= 1 total=353 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 2c1iA/T0325-2c1iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 2c1iA/T0325-2c1iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c1iA read from 2c1iA/T0325-2c1iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2c1iA in template set Warning: unaligning (T0325)D11 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c1iA)D276 Warning: unaligning (T0325)D12 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c1iA)D276 T0325 2 :SNKKLIINA 2c1iA 266 :HQKVVALTF T0325 14 :GYTPAVTQGIIEAHKRGVVTSTTALP 2c1iA 277 :GPNPATTPQVLETLAKYDIKATFFVL T0325 40 :TSPYFLEAMESAR 2c1iA 305 :NVSGNEDLVKRIK T0325 54 :SA 2c1iA 318 :SE T0325 57 :TLAIGVH 2c1iA 320 :GHVVGNH T0325 67 :T 2c1iA 327 :S T0325 70 :QAKPIL 2c1iA 328 :WSHPIL T0325 98 :EKVNLEEVYNEWDAQIISFMKS 2c1iA 334 :SQLSLDEAKKQITDTEDVLTKV T0325 120 :GRRPDHIDS 2c1iA 357 :GSSSKLMRP T0325 135 :KNKKLLGVALA 2c1iA 366 :PYGAITDDIRN T0325 151 :QLPLRNASR 2c1iA 377 :SLDLSFIMW T0325 172 :DVRTPDEML 2c1iA 386 :DVDSLDWKS T0325 188 :ISTETILQLLDMV 2c1iA 395 :KNEASILTEIQHQ T0325 203 :SEGEVF 2c1iA 408 :VANGSI T0325 210 :INCHP 2c1iA 414 :VLMHD T0325 227 :YCMPRIREV 2c1iA 419 :IHSPTVNAL T0325 241 :QEVKEAIEERGILLAN 2c1iA 428 :PRVIEYLKNQGYTFVT Number of specific fragments extracted= 17 number of extra gaps= 1 total=370 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 2c1iA/T0325-2c1iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 2c1iA/T0325-2c1iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c1iA read from 2c1iA/T0325-2c1iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2c1iA in template set Warning: unaligning (T0325)D11 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c1iA)D276 Warning: unaligning (T0325)D12 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c1iA)D276 T0325 3 :NKKLIINA 2c1iA 267 :QKVVALTF T0325 14 :GYTPAVTQGIIEAHKRGVVTSTTALP 2c1iA 277 :GPNPATTPQVLETLAKYDIKATFFVL T0325 40 :TSPYFLEAMESARI 2c1iA 305 :NVSGNEDLVKRIKS T0325 56 :PTLAIGVH 2c1iA 319 :EGHVVGNH T0325 67 :TLNQAKP 2c1iA 327 :SWSHPIL T0325 98 :EKVNLEEVYNEWDAQIISFMK 2c1iA 334 :SQLSLDEAKKQITDTEDVLTK T0325 119 :SGRRPDHID 2c1iA 356 :LGSSSKLMR T0325 133 :HGK 2c1iA 365 :PPY T0325 137 :KKLLGVALA 2c1iA 368 :GAITDDIRN T0325 151 :QLPLRNASRSIET 2c1iA 377 :SLDLSFIMWDVDS T0325 183 :FYDKAISTETILQLLD 2c1iA 390 :LDWKSKNEASILTEIQ T0325 201 :VCSEGEVFEIN 2c1iA 406 :HQVANGSIVLM T0325 213 :H 2c1iA 417 :H T0325 226 :GYCMPRI 2c1iA 418 :DIHSPTV T0325 236 :EIL 2c1iA 425 :NAL T0325 241 :QEVKEAIEERGILLANY 2c1iA 428 :PRVIEYLKNQGYTFVTI Number of specific fragments extracted= 16 number of extra gaps= 1 total=386 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 1xm8A/T0325-1xm8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xm8A expands to /projects/compbio/data/pdb/1xm8.pdb.gz 1xm8A:Skipped atom 796, because occupancy 0.350 <= existing 0.650 in 1xm8A Skipped atom 798, because occupancy 0.350 <= existing 0.650 in 1xm8A Skipped atom 800, because occupancy 0.350 <= existing 0.650 in 1xm8A Skipped atom 802, because occupancy 0.350 <= existing 0.650 in 1xm8A Skipped atom 804, because occupancy 0.350 <= existing 0.650 in 1xm8A Skipped atom 806, because occupancy 0.350 <= existing 0.650 in 1xm8A Skipped atom 812, because occupancy 0.350 <= existing 0.650 in 1xm8A Skipped atom 814, because occupancy 0.350 <= existing 0.650 in 1xm8A Skipped atom 816, because occupancy 0.350 <= existing 0.650 in 1xm8A Skipped atom 818, because occupancy 0.350 <= existing 0.650 in 1xm8A Skipped atom 820, because occupancy 0.350 <= existing 0.650 in 1xm8A Skipped atom 1080, because occupancy 0.350 <= existing 0.650 in 1xm8A Skipped atom 1082, because occupancy 0.350 <= existing 0.650 in 1xm8A Skipped atom 1239, because occupancy 0.350 <= existing 0.650 in 1xm8A Skipped atom 1241, because occupancy 0.350 <= existing 0.650 in 1xm8A Skipped atom 1367, because occupancy 0.350 <= existing 0.650 in 1xm8A Skipped atom 1369, because occupancy 0.350 <= existing 0.650 in 1xm8A Skipped atom 1501, because occupancy 0.350 <= existing 0.650 in 1xm8A Skipped atom 1503, because occupancy 0.350 <= existing 0.650 in 1xm8A Skipped atom 1581, because occupancy 0.330 <= existing 0.340 in 1xm8A Skipped atom 1582, because occupancy 0.330 <= existing 0.340 in 1xm8A Skipped atom 1584, because occupancy 0.330 <= existing 0.340 in 1xm8A Skipped atom 1585, because occupancy 0.330 <= existing 0.340 in 1xm8A Skipped atom 1889, because occupancy 0.350 <= existing 0.650 in 1xm8A Skipped atom 1891, because occupancy 0.350 <= existing 0.650 in 1xm8A Skipped atom 1893, because occupancy 0.350 <= existing 0.650 in 1xm8A Skipped atom 1895, because occupancy 0.350 <= existing 0.650 in 1xm8A Skipped atom 1897, because occupancy 0.350 <= existing 0.650 in 1xm8A Skipped atom 1908, because occupancy 0.500 <= existing 0.500 in 1xm8A Skipped atom 1910, because occupancy 0.500 <= existing 0.500 in 1xm8A Skipped atom 1912, because occupancy 0.500 <= existing 0.500 in 1xm8A Skipped atom 1914, because occupancy 0.500 <= existing 0.500 in 1xm8A Skipped atom 1916, because occupancy 0.500 <= existing 0.500 in 1xm8A # T0325 read from 1xm8A/T0325-1xm8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xm8A read from 1xm8A/T0325-1xm8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xm8A to template set # found chain 1xm8A in template set T0325 100 :VNLEEVYNEWDA 1xm8A 31 :SEAEPIIDSLKR T0325 119 :SGRRPDHIDSHH 1xm8A 43 :SGRNLTYILNTH T0325 135 :KNKKLLGVALALARKYQLPLRNASRSIETKDY 1xm8A 55 :HHYDHTGGNLELKDRYGAKVIGSAMDKDRIPG T0325 170 :Y 1xm8A 87 :I T0325 184 :YDKAISTETILQLLDMVVCSEGEVF 1xm8A 140 :KLFEGTPKQMLASLQKITSLPDDTS T0325 210 :INCHP 1xm8A 165 :IYCGH T0325 229 :MPRIREVEILTS 1xm8A 170 :EYTLSNSKFALS T0325 241 :QEVKEAIEE 1xm8A 187 :EVLQSYAAH Number of specific fragments extracted= 8 number of extra gaps= 0 total=394 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 1xm8A/T0325-1xm8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1xm8A/T0325-1xm8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xm8A read from 1xm8A/T0325-1xm8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xm8A in template set T0325 100 :VNLEEVYNEWDA 1xm8A 31 :SEAEPIIDSLKR T0325 119 :SGRRPDHIDSHH 1xm8A 43 :SGRNLTYILNTH T0325 135 :KNKKLLGVALALARKYQLPLRNASRSIETKDYLELY 1xm8A 55 :HHYDHTGGNLELKDRYGAKVIGSAMDKDRIPGIDMA T0325 185 :DKAISTETILQLLDMVVCSEGEV 1xm8A 141 :LFEGTPKQMLASLQKITSLPDDT T0325 209 :EINC 1xm8A 164 :SIYC T0325 224 :QSGYCMPRIREVEILT 1xm8A 168 :GHEYTLSNSKFALSLE T0325 240 :SQEVKEAIEE 1xm8A 186 :NEVLQSYAAH Number of specific fragments extracted= 7 number of extra gaps= 0 total=401 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 1xm8A/T0325-1xm8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1xm8A/T0325-1xm8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xm8A read from 1xm8A/T0325-1xm8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xm8A in template set T0325 101 :NLEEVYNEWDA 1xm8A 32 :EAEPIIDSLKR T0325 119 :SGRRPDHIDSH 1xm8A 43 :SGRNLTYILNT T0325 133 :HGK 1xm8A 54 :HHH T0325 137 :KKLLGVALALARKYQLPLRNASRSIETKDYLEL 1xm8A 57 :YDHTGGNLELKDRYGAKVIGSAMDKDRIPGIDM T0325 184 :YDKAISTETILQLLDMVVCSEGEVFEINCHPAFID 1xm8A 140 :KLFEGTPKQMLASLQKITSLPDDTSIYCGHEYTLS T0325 219 :TILQNQSGY 1xm8A 177 :KFALSLEPN T0325 240 :SQEVKEAIEE 1xm8A 186 :NEVLQSYAAH Number of specific fragments extracted= 7 number of extra gaps= 0 total=408 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 1zxxA/T0325-1zxxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zxxA expands to /projects/compbio/data/pdb/1zxx.pdb.gz 1zxxA:# T0325 read from 1zxxA/T0325-1zxxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zxxA read from 1zxxA/T0325-1zxxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zxxA to template set # found chain 1zxxA in template set T0325 4 :KKLIINAD 1zxxA 2 :KRIGILTS T0325 13 :FGYTPAVTQGIIEAHK 1zxxA 10 :GGDAPGMNAAVRAVTR T0325 29 :RGVVTSTTA 1zxxA 29 :ANGLEVFGI T0325 41 :SPYFLEAME 1zxxA 38 :RYGFAGLVA T0325 54 :SA 1zxxA 47 :GD T0325 72 :K 1zxxA 50 :F T0325 74 :ILPREMVPSLVDEAGYFWHQSI 1zxxA 51 :PLESEDVAHLINVSGTFLYSAR T0325 96 :FEE 1zxxA 76 :FAE T0325 103 :EEVYNEWDAQII 1zxxA 79 :EEGQLAGIEQLK T0325 118 :KSGRRPDHIDS 1zxxA 91 :KHGIDAVVVIG T0325 136 :NKKLLGVALALA 1zxxA 102 :GDGSYHGALQLT T0325 149 :KYQLPLRNASRSIET 1zxxA 114 :RHGFNSIGLPGTIDN T0325 166 :YLELY 1zxxA 129 :DIPYT T0325 171 :QDVRT 1zxxA 184 :CGADA T0325 181 :YQFYDKAISTETILQLLDMVVCSEGEVFEINCHPAFIDT 1zxxA 189 :IVIPERPYDVEEIANRLKQAQESGKDHGLVVVAEGVMTA T0325 241 :QEVKEAIEER 1zxxA 228 :DQFMAELKKY T0325 251 :GILLANYESL 1zxxA 241 :DVRANVLGHM Number of specific fragments extracted= 17 number of extra gaps= 0 total=425 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 1zxxA/T0325-1zxxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1zxxA/T0325-1zxxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zxxA read from 1zxxA/T0325-1zxxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zxxA in template set T0325 4 :KKLIINAD 1zxxA 2 :KRIGILTS T0325 13 :FGYTPAVTQGIIEAHK 1zxxA 10 :GGDAPGMNAAVRAVTR T0325 29 :RGVVTSTTA 1zxxA 29 :ANGLEVFGI T0325 41 :SPYFLEAME 1zxxA 38 :RYGFAGLVA T0325 54 :SA 1zxxA 47 :GD T0325 66 :L 1zxxA 49 :I T0325 72 :KP 1zxxA 50 :FP T0325 75 :LPREMVPSLVDEAGYFWH 1zxxA 52 :LESEDVAHLINVSGTFLY T0325 93 :QSIFEE 1zxxA 73 :YPEFAE T0325 103 :EEVYNEWDAQIIS 1zxxA 79 :EEGQLAGIEQLKK T0325 119 :SGRRPDHIDS 1zxxA 92 :HGIDAVVVIG T0325 136 :NKKLLGVALALA 1zxxA 102 :GDGSYHGALQLT T0325 149 :KYQLPLRNASRSI 1zxxA 114 :RHGFNSIGLPGTI T0325 171 :QDVRTP 1zxxA 184 :CGADAI T0325 182 :QFYDKAISTETILQLLDMVVCSEGEVFEINCHPAFIDT 1zxxA 190 :VIPERPYDVEEIANRLKQAQESGKDHGLVVVAEGVMTA T0325 241 :QEVKEAIEER 1zxxA 228 :DQFMAELKKY T0325 251 :GILLANYESL 1zxxA 241 :DVRANVLGHM Number of specific fragments extracted= 17 number of extra gaps= 0 total=442 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 1zxxA/T0325-1zxxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1zxxA/T0325-1zxxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zxxA read from 1zxxA/T0325-1zxxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zxxA in template set T0325 4 :KKLIINA 1zxxA 95 :DAVVVIG T0325 16 :TPAVTQGIIEAHKRGV 1zxxA 102 :GDGSYHGALQLTRHGF T0325 33 :TSTTA 1zxxA 118 :NSIGL T0325 38 :LPTSPYFLEAMESARI 1zxxA 144 :MTAMDAIDKIRDTASS T0325 55 :APT 1zxxA 160 :HHR T0325 60 :IGVH 1zxxA 163 :VFIV T0325 65 :TL 1zxxA 167 :NV T0325 82 :SLVDE 1zxxA 169 :MGRNC T0325 89 :YFWHQSIFE 1zxxA 174 :GDIAMRVGV T0325 98 :EKVNLEEVYNEWDA 1zxxA 194 :RPYDVEEIANRLKQ T0325 116 :FMKSGRRPDHI 1zxxA 208 :AQESGKDHGLV T0325 132 :VHGKNKKLLGVALALARKYQ 1zxxA 219 :VVAEGVMTADQFMAELKKYG T0325 152 :LPLRNASRSIETKDYLEL 1zxxA 240 :FDVRANVLGHMQRGGTPT T0325 177 :DE 1zxxA 258 :VS T0325 185 :DKAISTETILQLLDMVVCSEGEVFEI 1zxxA 260 :DRVLASKLGSEAVHLLLEGKGGLAVG Number of specific fragments extracted= 15 number of extra gaps= 0 total=457 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 1s1pA/T0325-1s1pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1s1pA/T0325-1s1pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1s1pA read from 1s1pA/T0325-1s1pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1s1pA in training set T0325 4 :KKLIINADDFGYTPAVTQGIIEAHKRGV 1s1pA 46 :FRHIDSAHLYNNEEQVGLAIRSKIADGS T0325 32 :VTSTTALPT 1s1pA 79 :IFYTSKLWS T0325 41 :SPYFLEAMESAR 1s1pA 92 :PELVRPALENSL T0325 53 :ISAPTLAIGV 1s1pA 106 :AQLDYVDLYL T0325 66 :LT 1s1pA 116 :IH T0325 70 :QAKPILPREMVPS 1s1pA 118 :SPMSLKPGEELSP T0325 84 :VDEAGYFWHQ 1s1pA 131 :TDENGKVIFD T0325 99 :KVNLEEVYNEW 1s1pA 141 :IVDLCTTWEAM T0325 110 :DAQIISFMKS 1s1pA 170 :RRQLEMILNK T0325 120 :GRRPD 1s1pA 181 :GLKYK T0325 125 :HIDSHHNVH 1s1pA 190 :QVECHPYFN T0325 139 :LLG 1s1pA 199 :RSK T0325 143 :ALALARKYQLPLRNASRSIETKDYLELYQDVRTPDEM 1s1pA 202 :LLDFCKSKDIVLVAYSALGSQRDKRWVDPNSPVLLED T0325 191 :ETILQLLDMVVCS 1s1pA 239 :PVLCALAKKHKRT T0325 204 :EGEVFEINC 1s1pA 262 :QRGVVVLAK T0325 215 :AFIDTILQNQSGYC 1s1pA 271 :SYNEQRIRQNVQVF T0325 240 :SQEVKEAIEER 1s1pA 289 :TAEDMKAIDGL Number of specific fragments extracted= 17 number of extra gaps= 0 total=474 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 1s1pA/T0325-1s1pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1s1pA/T0325-1s1pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1s1pA read from 1s1pA/T0325-1s1pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1s1pA in training set T0325 4 :KKLIINADDFGYTPAVTQGIIEAHKRGV 1s1pA 46 :FRHIDSAHLYNNEEQVGLAIRSKIADGS T0325 32 :VTSTTALP 1s1pA 79 :IFYTSKLW T0325 40 :TSPYFLEAMESARI 1s1pA 91 :RPELVRPALENSLK T0325 54 :SAPT 1s1pA 107 :QLDY T0325 60 :IGVHLT 1s1pA 111 :VDLYLI T0325 67 :T 1s1pA 117 :H T0325 70 :QAKPI 1s1pA 118 :SPMSL T0325 76 :PREMVPSLVDEAGYFWH 1s1pA 123 :KPGEELSPTDENGKVIF T0325 98 :EKVNLEEVYNEW 1s1pA 140 :DIVDLCTTWEAM T0325 110 :DAQIISFMKS 1s1pA 170 :RRQLEMILNK T0325 120 :GRRPD 1s1pA 181 :GLKYK T0325 125 :HIDSHHNVH 1s1pA 190 :QVECHPYFN T0325 139 :LLGV 1s1pA 199 :RSKL T0325 144 :LALARKYQLPLRNASRSIETKDYLELYQDVRTPDEM 1s1pA 203 :LDFCKSKDIVLVAYSALGSQRDKRWVDPNSPVLLED T0325 191 :ETILQLLDMVVCS 1s1pA 239 :PVLCALAKKHKRT T0325 204 :EGEVFEINC 1s1pA 262 :QRGVVVLAK T0325 215 :AFIDTILQNQSGY 1s1pA 271 :SYNEQRIRQNVQV T0325 240 :SQEVKEAIEER 1s1pA 289 :TAEDMKAIDGL Number of specific fragments extracted= 18 number of extra gaps= 0 total=492 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 1s1pA/T0325-1s1pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1s1pA/T0325-1s1pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1s1pA read from 1s1pA/T0325-1s1pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1s1pA in training set T0325 4 :KKLIINADDFGYTPAVTQGIIEAHKRGV 1s1pA 46 :FRHIDSAHLYNNEEQVGLAIRSKIADGS T0325 32 :VTSTTAL 1s1pA 79 :IFYTSKL T0325 39 :PTSPYFLEAMESARIS 1s1pA 90 :HRPELVRPALENSLKK T0325 56 :PTLA 1s1pA 106 :AQLD T0325 62 :VHLTLTLNQAKPILPREMVPSLVDEAG 1s1pA 111 :VDLYLIHSPMSLKPGEELSPTDENGKV T0325 90 :FWHQSIFE 1s1pA 146 :TTWEAMEK T0325 110 :DAQIISFMK 1s1pA 170 :RRQLEMILN T0325 119 :SGRRPD 1s1pA 180 :PGLKYK T0325 125 :HIDSHH 1s1pA 190 :QVECHP T0325 135 :K 1s1pA 196 :Y T0325 138 :KLLGVALALARKYQLPLRNASR 1s1pA 197 :FNRSKLLDFCKSKDIVLVAYSA T0325 166 :YLELYQDVRTPDEM 1s1pA 219 :LGSQRDKRWVDPNS T0325 185 :DKAISTETILQLLDMVVCSE 1s1pA 233 :PVLLEDPVLCALAKKHKRTP T0325 205 :GEVFEIN 1s1pA 263 :RGVVVLA T0325 214 :PAFIDTILQNQSGYCM 1s1pA 270 :KSYNEQRIRQNVQVFE T0325 239 :TSQEVKEAIEER 1s1pA 288 :LTAEDMKAIDGL Number of specific fragments extracted= 16 number of extra gaps= 0 total=508 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 1qwkA/T0325-1qwkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1qwkA expands to /projects/compbio/data/pdb/1qwk.pdb.gz 1qwkA:# T0325 read from 1qwkA/T0325-1qwkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qwkA read from 1qwkA/T0325-1qwkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1qwkA to template set # found chain 1qwkA in template set T0325 4 :KKLIINADDFGYTPAVTQGIIEAHKRGVVT 1qwkA 43 :YRLIDTASVYQNEEAIGTAIKELLEEGVVK T0325 34 :STTALPT 1qwkA 79 :TTKAWTH T0325 42 :PYFLEAMESA 1qwkA 90 :GKLEGGLRES T0325 52 :RISAPTLAIGV 1qwkA 102 :KLQLEYVDLYL T0325 70 :QAKPILPREMVPSLV 1qwkA 113 :AHMPAAFNDDMSEHI T0325 99 :KVNLEEVYNEWDA 1qwkA 128 :ASPVEDVWRQFDA T0325 112 :QIISFMKSGRRPDHIDSHHNVH 1qwkA 159 :QISRALALGLTPVHNSQVELHL T0325 135 :KNK 1qwkA 181 :YFP T0325 139 :LLGV 1qwkA 184 :QHDH T0325 144 :LALARKYQL 1qwkA 188 :VDFCKKHNI T0325 153 :PLRNASRSIETKDYLE 1qwkA 207 :PGRVNFTLPTGQKLDW T0325 174 :RTPDEMLYQ 1qwkA 223 :APAPSDLQD T0325 191 :ETILQLLDMVVCS 1qwkA 232 :QNVLALAEKTHKT T0325 204 :EGEVFEI 1qwkA 255 :DRGCAIL T0325 214 :P 1qwkA 262 :P T0325 225 :SGYCMPRIREV 1qwkA 263 :KSIQENRIKEN T0325 238 :L 1qwkA 274 :F T0325 240 :SQEVKEAIEERG 1qwkA 282 :TEEDIAKLEESK Number of specific fragments extracted= 18 number of extra gaps= 0 total=526 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 1qwkA/T0325-1qwkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1qwkA/T0325-1qwkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qwkA read from 1qwkA/T0325-1qwkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qwkA in template set T0325 4 :KKLIINADDFGYTPAVTQGIIEAHKRGVVT 1qwkA 43 :YRLIDTASVYQNEEAIGTAIKELLEEGVVK T0325 34 :STTAL 1qwkA 78 :ITTKA T0325 39 :PTSPYFLEAMESA 1qwkA 87 :LAPGKLEGGLRES T0325 52 :RISAPTLAIGV 1qwkA 102 :KLQLEYVDLYL T0325 70 :QAKPILPREMVPSLV 1qwkA 113 :AHMPAAFNDDMSEHI T0325 99 :KVNLEEVYNEWDA 1qwkA 128 :ASPVEDVWRQFDA T0325 112 :QIISFMKSGRRPDHIDSHHNVH 1qwkA 159 :QISRALALGLTPVHNSQVELHL T0325 135 :KNK 1qwkA 181 :YFP T0325 139 :LLGVA 1qwkA 184 :QHDHV T0325 145 :ALARKYQL 1qwkA 189 :DFCKKHNI T0325 153 :PLRNASRSIETKDYLELYQD 1qwkA 207 :PGRVNFTLPTGQKLDWAPAP T0325 176 :PDEML 1qwkA 227 :SDLQD T0325 191 :ETILQLLDMVVCS 1qwkA 232 :QNVLALAEKTHKT T0325 204 :EGEVFEI 1qwkA 255 :DRGCAIL T0325 214 :P 1qwkA 262 :P T0325 225 :SGYCMPRIREV 1qwkA 263 :KSIQENRIKEN T0325 238 :L 1qwkA 274 :F T0325 240 :SQEVKEAIEERG 1qwkA 282 :TEEDIAKLEESK Number of specific fragments extracted= 18 number of extra gaps= 0 total=544 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 1qwkA/T0325-1qwkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1qwkA/T0325-1qwkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qwkA read from 1qwkA/T0325-1qwkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qwkA in template set T0325 4 :KKLIINADDFGYTPAVTQGIIEAHKRGVVT 1qwkA 43 :YRLIDTASVYQNEEAIGTAIKELLEEGVVK T0325 34 :STTALPT 1qwkA 79 :TTKAWTH T0325 42 :PYFLEAMESARI 1qwkA 90 :GKLEGGLRESLK T0325 54 :SAPTLAI 1qwkA 104 :QLEYVDL T0325 63 :HLTL 1qwkA 111 :YLAH T0325 78 :EMVPSLVDEAG 1qwkA 115 :MPAAFNDDMSE T0325 99 :KVNLEEVYNEWDA 1qwkA 128 :ASPVEDVWRQFDA T0325 112 :QIISFMKSGRRPDHI 1qwkA 159 :QISRALALGLTPVHN T0325 128 :SHHNVHGK 1qwkA 174 :SQVELHLY T0325 137 :KKLLGVA 1qwkA 182 :FPQHDHV T0325 145 :ALARKYQL 1qwkA 189 :DFCKKHNI T0325 153 :PLRNASRSIETKDYLELYQDVRTPDEMLYQFYDKA 1qwkA 207 :PGRVNFTLPTGQKLDWAPAPSDLQDQNVLALAEKT T0325 189 :STETILQLLDMVVCSE 1qwkA 242 :HKTPAQVLLRYALDRG T0325 207 :V 1qwkA 258 :C T0325 211 :NCHPAFIDTI 1qwkA 259 :AILPKSIQEN T0325 231 :RIREV 1qwkA 269 :RIKEN T0325 238 :L 1qwkA 274 :F T0325 239 :TSQEVKEAIEERG 1qwkA 281 :LTEEDIAKLEESK Number of specific fragments extracted= 18 number of extra gaps= 0 total=562 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 1tv8A/T0325-1tv8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1tv8A expands to /projects/compbio/data/pdb/1tv8.pdb.gz 1tv8A:# T0325 read from 1tv8A/T0325-1tv8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tv8A read from 1tv8A/T0325-1tv8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1tv8A to template set # found chain 1tv8A in template set Warning: unaligning (T0325)A10 because of BadResidue code BAD_PEPTIDE in next template residue (1tv8A)G75 Warning: unaligning (T0325)D11 because of BadResidue code BAD_PEPTIDE at template residue (1tv8A)G75 Warning: unaligning (T0325)K164 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1tv8A)D202 Warning: unaligning (T0325)D165 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tv8A)D202 Warning: unaligning (T0325)Y166 because of BadResidue code BAD_PEPTIDE at template residue (1tv8A)N203 Warning: unaligning (T0325)G251 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1tv8A)Q329 T0325 4 :KKLIIN 1tv8A 68 :KKIRIT T0325 12 :DFGYTPAVTQGIIEAHKRGVVTSTTALPTSPYFLEAMESARIS 1tv8A 76 :EPLMRRDLDVLIAKLNQIDGIEDIGLTTNGLLLKKHGQKLYDA T0325 57 :TLA 1tv8A 119 :GLR T0325 61 :GVHLTLT 1tv8A 122 :RINVSLD T0325 74 :ILPR 1tv8A 129 :AIDD T0325 91 :WHQSIFEEKVNLEEVYN 1tv8A 134 :LFQSINNRNIKATTILE T0325 112 :QIISFMKSGRRPDH 1tv8A 151 :QIDYATSIGLNVKV T0325 127 :DSHHNVHGKNKKLLG 1tv8A 165 :NVVIQKGINDDQIIP T0325 143 :ALALARKYQLPLRNASRSIET 1tv8A 180 :MLEYFKDKHIEIRFIEFMDVG T0325 167 :LELY 1tv8A 204 :GWDF T0325 171 :QDVRTPDEM 1tv8A 283 :VDGFNVKAF T0325 184 :YDKAISTETILQLL 1tv8A 292 :IRSGVTDEELKEQF T0325 198 :DMVVCSEGE 1tv8A 307 :ALWQIRDDR T0325 229 :MP 1tv8A 316 :YS T0325 241 :QEVKEAIEER 1tv8A 318 :DERTAQTVAN Number of specific fragments extracted= 15 number of extra gaps= 3 total=577 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 1tv8A/T0325-1tv8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1tv8A/T0325-1tv8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tv8A read from 1tv8A/T0325-1tv8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tv8A in template set Warning: unaligning (T0325)A10 because of BadResidue code BAD_PEPTIDE in next template residue (1tv8A)G75 Warning: unaligning (T0325)D11 because of BadResidue code BAD_PEPTIDE at template residue (1tv8A)G75 Warning: unaligning (T0325)T163 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1tv8A)D202 Warning: unaligning (T0325)K164 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tv8A)D202 Warning: unaligning (T0325)D165 because of BadResidue code BAD_PEPTIDE at template residue (1tv8A)N203 Warning: unaligning (T0325)G251 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1tv8A)Q329 T0325 4 :KKLIIN 1tv8A 68 :KKIRIT T0325 12 :DFGYTPAVTQGIIEAHKRGVVTSTTALPTSPYFLEAMESARI 1tv8A 76 :EPLMRRDLDVLIAKLNQIDGIEDIGLTTNGLLLKKHGQKLYD T0325 54 :SAP 1tv8A 119 :GLR T0325 61 :GVHLTLT 1tv8A 122 :RINVSLD T0325 74 :ILPRE 1tv8A 129 :AIDDT T0325 91 :WHQSIFEEKVNLEEVY 1tv8A 134 :LFQSINNRNIKATTIL T0325 111 :AQIISFMKSGRRPDH 1tv8A 150 :EQIDYATSIGLNVKV T0325 127 :DSHHNVHGKNKKLLG 1tv8A 165 :NVVIQKGINDDQIIP T0325 143 :ALALARKYQLPLR 1tv8A 180 :MLEYFKDKHIEIR T0325 156 :NASRSIE 1tv8A 194 :IEFMDVG T0325 166 :YLELY 1tv8A 204 :GWDFS T0325 171 :QDVRTPDEML 1tv8A 283 :VDGFNVKAFI T0325 185 :DKAISTETILQLLDMVVCSEGEV 1tv8A 293 :RSGVTDEELKEQFKALWQIRDDR T0325 227 :Y 1tv8A 316 :Y T0325 240 :SQEVKEAIEER 1tv8A 317 :SDERTAQTVAN Number of specific fragments extracted= 15 number of extra gaps= 3 total=592 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 1tv8A/T0325-1tv8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1tv8A/T0325-1tv8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tv8A read from 1tv8A/T0325-1tv8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tv8A in template set Warning: unaligning (T0325)A10 because of BadResidue code BAD_PEPTIDE in next template residue (1tv8A)G75 Warning: unaligning (T0325)D11 because of BadResidue code BAD_PEPTIDE at template residue (1tv8A)G75 Warning: unaligning (T0325)I161 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1tv8A)D202 Warning: unaligning (T0325)E162 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tv8A)D202 Warning: unaligning (T0325)T163 because of BadResidue code BAD_PEPTIDE at template residue (1tv8A)N203 Warning: unaligning (T0325)G251 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1tv8A)Q329 T0325 3 :NKKLIIN 1tv8A 67 :VKKIRIT T0325 12 :DFGYTPAVTQGIIEAHKRGVVTSTTALPTSPYFLEAMESARI 1tv8A 76 :EPLMRRDLDVLIAKLNQIDGIEDIGLTTNGLLLKKHGQKLYD T0325 56 :PTLA 1tv8A 118 :AGLR T0325 60 :I 1tv8A 123 :I T0325 65 :TLT 1tv8A 124 :NVS T0325 79 :MVPSL 1tv8A 127 :LDAID T0325 89 :YFWHQSIFEEKVNLEEVYN 1tv8A 132 :DTLFQSINNRNIKATTILE T0325 112 :QIISFMKSGRRPDH 1tv8A 151 :QIDYATSIGLNVKV T0325 127 :DSHHNVHGK 1tv8A 165 :NVVIQKGIN T0325 137 :KKLLGVALALARKYQLPLR 1tv8A 174 :DDQIIPMLEYFKDKHIEIR T0325 156 :NASRS 1tv8A 196 :FMDVG T0325 164 :KDYL 1tv8A 204 :GWDF T0325 170 :YQDVRTPDEMLYQFYDKAISTETILQLLDMVVCSEGEV 1tv8A 278 :CLFATVDGFNVKAFIRSGVTDEELKEQFKALWQIRDDR T0325 227 :YCM 1tv8A 316 :YSD T0325 242 :EVKEAIEER 1tv8A 319 :ERTAQTVAN Number of specific fragments extracted= 15 number of extra gaps= 3 total=607 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 1gca/T0325-1gca-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1gca expands to /projects/compbio/data/pdb/1gca.pdb.gz 1gca:Warning: there is no chain 1gca will retry with 1gcaA # T0325 read from 1gca/T0325-1gca-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gca read from 1gca/T0325-1gca-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1gca to template set # found chain 1gca in template set Warning: unaligning (T0325)S2 because first residue in template chain is (1gca)A1 T0325 3 :NKKLIINA 1gca 2 :DTRIGVTI T0325 15 :YTPAVTQ 1gca 10 :YKYDDNF T0325 41 :SPYFLEAMESARISAPTLAIGV 1gca 17 :MSVVRKAIEKDGKSAPDVQLLM T0325 66 :LTLNQ 1gca 39 :NDSQN T0325 101 :N 1gca 44 :D T0325 106 :YNEWDAQIISFMKSGRRPDHIDS 1gca 45 :QSKQNDQIDVLLAKGVKALAINL T0325 135 :KNKKLLGVALALARKYQLPLRNASRSIE 1gca 68 :VDPAAAGTVIEKARGQNVPVVFFNKEPS T0325 164 :KDYLELY 1gca 96 :RKALDSY T0325 174 :RTPDEMLYQF 1gca 110 :TDSKESGVIQ T0325 190 :TETILQLLDM 1gca 120 :GDLIAKHWQA T0325 200 :VV 1gca 133 :WD T0325 202 :CSEGEVFEINCHP 1gca 136 :NKDGKIQYVLLKG T0325 225 :SGYCMPRIREVEI 1gca 149 :EPGHPDAEARTTY T0325 243 :VKEAIEERGILLANY 1gca 162 :VVKELNDKGIQTEQL Number of specific fragments extracted= 14 number of extra gaps= 0 total=621 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 1gca/T0325-1gca-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1gca/T0325-1gca-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gca read from 1gca/T0325-1gca-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gca in template set T0325 6 :LIINADDFGYT 1gca 34 :VQLLMNDSQND T0325 17 :PAVTQGIIEAHKRGVVTSTTALPTSPYFLEAMESARIS 1gca 46 :SKQNDQIDVLLAKGVKALAINLVDPAAAGTVIEKARGQ T0325 57 :TLAIGV 1gca 84 :NVPVVF T0325 66 :LT 1gca 90 :FN T0325 71 :AK 1gca 92 :KE T0325 91 :WHQSIFEEK 1gca 94 :PSRKALDSY T0325 100 :VNLEEVYNEWDAQIISFMK 1gca 110 :TDSKESGVIQGDLIAKHWQ T0325 119 :S 1gca 135 :L T0325 120 :GRRPDHID 1gca 138 :DGKIQYVL T0325 130 :HNVHGKNK 1gca 146 :LKGEPGHP T0325 138 :KLLGVALALARKYQLPLRNAS 1gca 157 :ARTTYVVKELNDKGIQTEQLA T0325 183 :FYDKAISTETILQLLDMVVCSEGE 1gca 178 :LDTAMWDTAQAKDKMDAWLSGPNA T0325 207 :VFEINCHPA 1gca 204 :IEVVIANND T0325 229 :MPRIREVEILTS 1gca 213 :AMAMGAVEALKA T0325 241 :QEVKEAIEER 1gca 239 :PEALALVKSG Number of specific fragments extracted= 15 number of extra gaps= 0 total=636 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 1gca/T0325-1gca-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1gca/T0325-1gca-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gca read from 1gca/T0325-1gca-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gca in template set Warning: unaligning (T0325)S2 because first residue in template chain is (1gca)A1 T0325 3 :NKKLIINA 1gca 2 :DTRIGVTI T0325 15 :YTPAVT 1gca 10 :YKYDDN T0325 40 :TSPYFLEAMESARISAPTLAIGVH 1gca 16 :FMSVVRKAIEKDGKSAPDVQLLMN T0325 75 :L 1gca 41 :S T0325 99 :KVNLE 1gca 42 :QNDQS T0325 108 :EWDAQIISFMKSGRRPDHI 1gca 47 :KQNDQIDVLLAKGVKALAI T0325 133 :HGKNKKLLGVALALARKYQLPLRNASRSIETKDYLEL 1gca 66 :NLVDPAAAGTVIEKARGQNVPVVFFNKEPSRKALDSY T0325 186 :KAISTETILQLLDMVV 1gca 112 :SKESGVIQGDLIAKHW T0325 202 :CSEGEVFEINCH 1gca 136 :NKDGKIQYVLLK T0325 215 :A 1gca 148 :G T0325 225 :SGYCMPRIREVEI 1gca 149 :EPGHPDAEARTTY T0325 243 :VKEAIEERGILLAN 1gca 162 :VVKELNDKGIQTEQ Number of specific fragments extracted= 12 number of extra gaps= 0 total=648 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 2c1gA/T0325-2c1gA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2c1gA expands to /projects/compbio/data/pdb/2c1g.pdb.gz 2c1gA:# T0325 read from 2c1gA/T0325-2c1gA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c1gA read from 2c1gA/T0325-2c1gA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2c1gA to template set # found chain 2c1gA in template set T0325 3 :NKKLIINADD 2c1gA 267 :QKVVALTFDD T0325 14 :GYTPAVTQGIIEAHKRGVVTSTTALPT 2c1gA 277 :GPNPATTPQVLETLAKYDIKATFFVLG T0325 41 :SPYFLEAMESARI 2c1gA 306 :VSGNEDLVKRIKS T0325 56 :PTLAIGVH 2c1gA 319 :EGHVVGNH T0325 67 :T 2c1gA 327 :S T0325 70 :QAKPILP 2c1gA 328 :WSHPILS T0325 99 :KVNLEEVYNEWDAQIISFMKS 2c1gA 335 :QLSLDEAKKQITDTEDVLTKV T0325 120 :GRRPDHIDS 2c1gA 357 :GSSSKLMRP T0325 131 :NVHGKNKKLLG 2c1gA 366 :PYGAITDDIRN T0325 149 :KYQLPLRNAS 2c1gA 377 :SLDLSFIMWD T0325 173 :VRTPDEM 2c1gA 387 :VDSLDWK T0325 187 :AISTETILQLLD 2c1gA 394 :SKNEASILTEIQ T0325 201 :VCSEGEVF 2c1gA 406 :HQVANGSI T0325 210 :INCHP 2c1gA 414 :VLMHD T0325 227 :YCMPRIREV 2c1gA 419 :IHSPTVNAL T0325 241 :QEVKEAIEERGILLAN 2c1gA 428 :PRVIEYLKNQGYTFVT Number of specific fragments extracted= 16 number of extra gaps= 0 total=664 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 2c1gA/T0325-2c1gA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 2c1gA/T0325-2c1gA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c1gA read from 2c1gA/T0325-2c1gA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2c1gA in template set T0325 2 :SNKKLIINADD 2c1gA 266 :HQKVVALTFDD T0325 14 :GYTPAVTQGIIEAHKRGVVTSTTALP 2c1gA 277 :GPNPATTPQVLETLAKYDIKATFFVL T0325 40 :TSPYFLEAMESARI 2c1gA 305 :NVSGNEDLVKRIKS T0325 56 :PTLAIGVH 2c1gA 319 :EGHVVGNH T0325 67 :T 2c1gA 327 :S T0325 70 :QAKPIL 2c1gA 328 :WSHPIL T0325 98 :EKVNLEEVYNEWDAQIISFMKS 2c1gA 334 :SQLSLDEAKKQITDTEDVLTKV T0325 120 :GRRPDHIDS 2c1gA 357 :GSSSKLMRP T0325 135 :KNKKLLG 2c1gA 366 :PYGAITD T0325 145 :ALARKYQLPLRNA 2c1gA 373 :DIRNSLDLSFIMW T0325 172 :DVRTPDEML 2c1gA 386 :DVDSLDWKS T0325 188 :ISTETILQLLDM 2c1gA 395 :KNEASILTEIQH T0325 203 :SEGEVFEINCHP 2c1gA 407 :QVANGSIVLMHD T0325 227 :YCMPRIREV 2c1gA 419 :IHSPTVNAL T0325 241 :QEVKEAIEERGILLA 2c1gA 428 :PRVIEYLKNQGYTFV Number of specific fragments extracted= 15 number of extra gaps= 0 total=679 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 2c1gA/T0325-2c1gA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 2c1gA/T0325-2c1gA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c1gA read from 2c1gA/T0325-2c1gA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2c1gA in template set T0325 2 :SNKKLIINADD 2c1gA 266 :HQKVVALTFDD T0325 14 :GYTPAVTQGIIEAHKRGVVTSTTALP 2c1gA 277 :GPNPATTPQVLETLAKYDIKATFFVL T0325 40 :TSPYFLEAMESARI 2c1gA 305 :NVSGNEDLVKRIKS T0325 56 :PTLAIGVH 2c1gA 319 :EGHVVGNH T0325 67 :TLNQAKP 2c1gA 327 :SWSHPIL T0325 98 :EKVNLEEVYNEWDAQIISFMK 2c1gA 334 :SQLSLDEAKKQITDTEDVLTK T0325 119 :SGRRPDHI 2c1gA 356 :LGSSSKLM T0325 132 :VHGK 2c1gA 364 :RPPY T0325 137 :KKLLGVALA 2c1gA 368 :GAITDDIRN T0325 149 :KYQLPLRNASRSI 2c1gA 377 :SLDLSFIMWDVDS T0325 186 :KAISTETILQLLDMVVCSEGEVFEINCHP 2c1gA 390 :LDWKSKNEASILTEIQHQVANGSIVLMHD T0325 227 :YCMP 2c1gA 419 :IHSP T0325 234 :EVEIL 2c1gA 423 :TVNAL T0325 241 :QEVKEAIEERGILLANY 2c1gA 428 :PRVIEYLKNQGYTFVTI Number of specific fragments extracted= 14 number of extra gaps= 0 total=693 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 1us0A/T0325-1us0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1us0A/T0325-1us0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1us0A read from 1us0A/T0325-1us0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1us0A in training set Warning: unaligning (T0325)H92 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1us0A)S133 Warning: unaligning (T0325)Q93 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1us0A)S133 T0325 4 :KKLIINADDFGYTPAVTQGIIEAHKRGVVT 1us0A 39 :YRHIDCAHVYQNENEVGVAIQEKLREQVVK T0325 34 :STTAL 1us0A 74 :IVSKL T0325 39 :PTSPYFLEAMESAR 1us0A 83 :HEKGLVKGACQKTL T0325 53 :ISAPTLAIGV 1us0A 99 :LKLDYLDLYL T0325 66 :LT 1us0A 109 :IH T0325 70 :QAKPILPREMVPSL 1us0A 111 :WPTGFKPGKEFFPL T0325 85 :DEAGYFW 1us0A 125 :DESGNVV T0325 99 :KVNLEEVYNE 1us0A 134 :DTNILDTWAA T0325 113 :IISFMKSGRRPDHIDS 1us0A 144 :MEELVDEGLVKAIGIS T0325 130 :H 1us0A 160 :N T0325 135 :KNKKLLGVAL 1us0A 161 :FNHLQVEMIL T0325 151 :Q 1us0A 171 :N T0325 170 :YQDVRTPDEMLYQ 1us0A 172 :KPGLKYKPAVNQI T0325 183 :FYDKAISTETILQLLDM 1us0A 186 :CHPYLTQEKLIQYCQSK T0325 206 :EVFEINCHP 1us0A 203 :GIVVTAYSP T0325 216 :FIDTILQNQSGYCMP 1us0A 212 :LGSPDRPWAKPEDPS T0325 237 :ILTSQEVKEAIEERGIL 1us0A 227 :LLEDPRIKAIAAKHNKT Number of specific fragments extracted= 17 number of extra gaps= 1 total=710 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 1us0A/T0325-1us0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1us0A/T0325-1us0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1us0A read from 1us0A/T0325-1us0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1us0A in training set Warning: unaligning (T0325)H92 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1us0A)S133 Warning: unaligning (T0325)L253 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1us0A)V297 Warning: unaligning (T0325)L254 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1us0A)V297 T0325 4 :KKLIINADDFGYTPAVTQGIIEAHKRGV 1us0A 39 :YRHIDCAHVYQNENEVGVAIQEKLREQV T0325 32 :VTSTTAL 1us0A 72 :LFIVSKL T0325 39 :PTSPYFLEAMESARI 1us0A 83 :HEKGLVKGACQKTLS T0325 54 :SAPTLAIGV 1us0A 100 :KLDYLDLYL T0325 66 :LT 1us0A 109 :IH T0325 70 :QAKPILPREMVPS 1us0A 111 :WPTGFKPGKEFFP T0325 84 :VDEAGYFW 1us0A 124 :LDESGNVV T0325 93 :QSIFEEK 1us0A 145 :EELVDEG T0325 110 :DAQIISFMKS 1us0A 163 :HLQVEMILNK T0325 120 :GRR 1us0A 174 :GLK T0325 123 :PDHIDSHHNVH 1us0A 181 :VNQIECHPYLT T0325 135 :K 1us0A 192 :Q T0325 140 :LGVA 1us0A 193 :EKLI T0325 145 :ALARKYQLPLRNASR 1us0A 197 :QYCQSKGIVVTAYSP T0325 161 :IETKDYLELYQDVRTPDE 1us0A 212 :LGSPDRPWAKPEDPSLLE T0325 191 :ETILQLLDMVVCS 1us0A 231 :PRIKAIAAKHNKT T0325 206 :E 1us0A 256 :N T0325 210 :INCHPAFIDTILQN 1us0A 257 :LVVIPKSVTPERIA T0325 236 :EILT 1us0A 271 :ENFK T0325 240 :SQEVKEAIEER 1us0A 281 :SSQDMTTLLSY T0325 251 :GI 1us0A 294 :NW T0325 255 :ANYESL 1us0A 298 :CALLSC Number of specific fragments extracted= 22 number of extra gaps= 2 total=732 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 1us0A/T0325-1us0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1us0A/T0325-1us0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1us0A read from 1us0A/T0325-1us0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1us0A in training set T0325 4 :KKLIINADDFGYTPAVTQGIIEAHKRGVVT 1us0A 39 :YRHIDCAHVYQNENEVGVAIQEKLREQVVK T0325 34 :STTAL 1us0A 74 :IVSKL T0325 39 :PTSPYFLEAMESARI 1us0A 83 :HEKGLVKGACQKTLS T0325 54 :SAPTLAI 1us0A 100 :KLDYLDL T0325 65 :TLTLNQAKPILPREMVPSLVDEAG 1us0A 107 :YLIHWPTGFKPGKEFFPLDESGNV T0325 89 :YFWHQSIFE 1us0A 141 :WAAMEELVD T0325 110 :DAQIISFMK 1us0A 163 :HLQVEMILN T0325 119 :SGRR 1us0A 173 :PGLK T0325 123 :PDHIDSHHNVHGK 1us0A 181 :VNQIECHPYLTQE T0325 141 :GV 1us0A 194 :KL T0325 144 :LALARKYQL 1us0A 196 :IQYCQSKGI T0325 209 :EINCHPAFIDTILQNQSGYCMP 1us0A 205 :VVTAYSPLGSPDRPWAKPEDPS T0325 237 :ILTSQEVKEAIEERGIL 1us0A 227 :LLEDPRIKAIAAKHNKT Number of specific fragments extracted= 13 number of extra gaps= 0 total=745 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 1ls1A/T0325-1ls1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1ls1A/T0325-1ls1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ls1A read from 1ls1A/T0325-1ls1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ls1A in training set Warning: unaligning (T0325)S82 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ls1A)L103 Warning: unaligning (T0325)L83 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ls1A)L103 T0325 18 :AVTQGIIEAHKRGV 1ls1A 29 :ATLREIRRALMDAD T0325 39 :PTSPYFLEAMESAR 1ls1A 43 :VNLEVARDFVERVR T0325 54 :SAPTL 1ls1A 63 :QVLES T0325 68 :LNQAKPILPREMVP 1ls1A 88 :GEARLPVLKDRNLW T0325 84 :VDEAGYFWH 1ls1A 104 :VGLQGSGKT T0325 107 :NEWDAQIISFMKSGRRPDHIDSH 1ls1A 113 :TTAAKLALYYKGKGRRPLLVAAD T0325 134 :GKNKKLLGVALALARKYQLPLRNASRSIETKDYLELY 1ls1A 136 :TQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRV T0325 183 :FYDKAISTETILQLLDMVVCSEGEVFEINCHPAFIDTILQ 1ls1A 189 :AGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALS T0325 237 :I 1ls1A 229 :V T0325 243 :VKEAIEERGIL 1ls1A 230 :ARAFDEKVGVT T0325 254 :LANYESLA 1ls1A 244 :LTKLDGDA Number of specific fragments extracted= 11 number of extra gaps= 1 total=756 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 1ls1A/T0325-1ls1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1ls1A/T0325-1ls1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ls1A read from 1ls1A/T0325-1ls1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ls1A in training set Warning: unaligning (T0325)S82 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ls1A)L103 Warning: unaligning (T0325)L83 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ls1A)L103 T0325 18 :AVTQGIIEAHKRGV 1ls1A 29 :ATLREIRRALMDAD T0325 39 :PTSPYFLEAMESARI 1ls1A 43 :VNLEVARDFVERVRE T0325 54 :SAPTL 1ls1A 63 :QVLES T0325 68 :LNQAKPILPREMVP 1ls1A 88 :GEARLPVLKDRNLW T0325 84 :VDEAGYFWH 1ls1A 104 :VGLQGSGKT T0325 107 :NEWDAQIISFMKSGRRPDHIDSH 1ls1A 113 :TTAAKLALYYKGKGRRPLLVAAD T0325 134 :GKNKKLLGVALALARKYQLPLRNASRSIETKDYLELY 1ls1A 136 :TQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRV T0325 182 :QFYDKAISTET 1ls1A 188 :TAGRLQIDEPL T0325 193 :ILQLLDMV 1ls1A 202 :LARLKEVL T0325 204 :EGEVFEINCHPAFIDTILQN 1ls1A 210 :GPDEVLLVLDAMTGQEALSV T0325 243 :VKEAIEERGIL 1ls1A 230 :ARAFDEKVGVT T0325 254 :LANYESLAM 1ls1A 244 :LTKLDGDAR Number of specific fragments extracted= 12 number of extra gaps= 1 total=768 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 1ls1A/T0325-1ls1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1ls1A/T0325-1ls1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ls1A read from 1ls1A/T0325-1ls1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ls1A in training set Warning: unaligning (T0325)P81 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ls1A)L103 T0325 19 :VTQGIIEAHKRGVV 1ls1A 30 :TLREIRRALMDADV T0325 40 :TSPYFLEAMESARI 1ls1A 44 :NLEVARDFVERVRE T0325 68 :LNQAKPILPREMV 1ls1A 87 :GGEARLPVLKDRN T0325 82 :SLVDEAG 1ls1A 104 :VGLQGSG T0325 89 :YFWHQSI 1ls1A 112 :TTTAAKL T0325 113 :IISFMKSGRRPDHIDSH 1ls1A 119 :ALYYKGKGRRPLLVAAD T0325 133 :HGK 1ls1A 136 :TQR T0325 137 :KKLLGVALALARKYQLPLRNASRSIETKDYLEL 1ls1A 139 :PAAREQLRLLGEKVGVPVLEVMDGESPESIRRR T0325 182 :QFYDKAISTETILQLLDMVVCSEGEVFEINCHPAFIDTILQ 1ls1A 188 :TAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALS T0325 242 :EVKEAIEERGIL 1ls1A 229 :VARAFDEKVGVT T0325 254 :LANYESLA 1ls1A 244 :LTKLDGDA Number of specific fragments extracted= 11 number of extra gaps= 1 total=779 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 1zzmA/T0325-1zzmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zzmA expands to /projects/compbio/data/pdb/1zzm.pdb.gz 1zzmA:# T0325 read from 1zzmA/T0325-1zzmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zzmA read from 1zzmA/T0325-1zzmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zzmA to template set # found chain 1zzmA in template set Warning: unaligning (T0325)S2 because first residue in template chain is (1zzmA)M1 T0325 3 :NKKLIINADDFGY 1zzmA 2 :ICRFIDTHCHFDF T0325 16 :TPAVTQGIIEAHKRGVVTSTTALPTSPYFLEAMESAR 1zzmA 18 :SGDEEASLQRAAQAGVGKIIVPATEAENFARVLALAE T0325 54 :SAPTLAIGV 1zzmA 55 :NYQPLYAAL T0325 74 :ILPREMVPSL 1zzmA 64 :GLHPGMLEKH T0325 92 :HQSI 1zzmA 74 :SDVS T0325 96 :FEEKVNLEEVYNEWDAQIISFMKSGR 1zzmA 103 :FGDDPQFERQQWLLDEQLKLAKRYDL T0325 123 :PDHIDS 1zzmA 129 :PVILHS T0325 138 :KLLGVALALARKYQLPLRNA 1zzmA 136 :RTHDKLAMHLKRHDLPRTGV T0325 159 :RSIETKDYLELY 1zzmA 158 :GFSGSLQQAERF T0325 171 :QDVR 1zzmA 172 :LGYK T0325 175 :TPDEM 1zzmA 178 :VGGTI T0325 183 :FYDKAIS 1zzmA 183 :TYPRASK T0325 196 :LLDMVVCSEGEVFEINCHPAFID 1zzmA 190 :TRDVIAKLPLASLLLETDAPDMP T0325 219 :TILQNQSGYCMPRIREVEILTS 1zzmA 214 :NGFQGQPNRPEQAARVFAVLCE T0325 241 :QEVKEAIEER 1zzmA 242 :DEIAQALLNN Number of specific fragments extracted= 15 number of extra gaps= 0 total=794 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 1zzmA/T0325-1zzmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1zzmA/T0325-1zzmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zzmA read from 1zzmA/T0325-1zzmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zzmA in template set Warning: unaligning (T0325)S2 because first residue in template chain is (1zzmA)M1 T0325 3 :NKKLIINADDFGY 1zzmA 2 :ICRFIDTHCHFDF T0325 16 :TPAVTQGIIEAHKRGVVTSTTALPTSPYFLEAMESAR 1zzmA 18 :SGDEEASLQRAAQAGVGKIIVPATEAENFARVLALAE T0325 54 :SAPTLAIGV 1zzmA 55 :NYQPLYAAL T0325 74 :ILPREMVPSL 1zzmA 64 :GLHPGMLEKH T0325 92 :H 1zzmA 74 :S T0325 94 :SIFEEKVNLEEVYNEWDAQIISFMKSGR 1zzmA 101 :DLFGDDPQFERQQWLLDEQLKLAKRYDL T0325 123 :PDHIDS 1zzmA 129 :PVILHS T0325 138 :KLLGVALALARKYQL 1zzmA 136 :RTHDKLAMHLKRHDL T0325 153 :PLRNASRSIETK 1zzmA 153 :TGVVHGFSGSLQ T0325 166 :YLELY 1zzmA 165 :QAERF T0325 171 :QDVR 1zzmA 172 :LGYK T0325 175 :TPDEML 1zzmA 178 :VGGTIT T0325 184 :YDKAIS 1zzmA 184 :YPRASK T0325 196 :LLDMVVCSEGEVFEINCHPAFID 1zzmA 190 :TRDVIAKLPLASLLLETDAPDMP T0325 219 :TILQNQSGYCMPRIREVEILT 1zzmA 214 :NGFQGQPNRPEQAARVFAVLC T0325 240 :SQEVKEAIEER 1zzmA 241 :ADEIAQALLNN Number of specific fragments extracted= 16 number of extra gaps= 0 total=810 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 1zzmA/T0325-1zzmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1zzmA/T0325-1zzmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zzmA read from 1zzmA/T0325-1zzmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zzmA in template set T0325 4 :KKLIINA 1zzmA 34 :GKIIVPA T0325 15 :YTPAVTQGIIEAHKR 1zzmA 41 :TEAENFARVLALAEN T0325 30 :GVVTSTTALPTS 1zzmA 57 :QPLYAALGLHPG T0325 42 :PYFLEAMESARI 1zzmA 76 :VSLEQLQQALER T0325 98 :EKVNLEEVYNEWDAQIISFMKSGR 1zzmA 105 :DDPQFERQQWLLDEQLKLAKRYDL T0325 123 :PDHIDS 1zzmA 129 :PVILHS T0325 137 :KKLLGVALALARKYQLPLRN 1zzmA 135 :RRTHDKLAMHLKRHDLPRTG T0325 159 :RSIETKDYLELYQDVRTPDEMLYQFYDKAIST 1zzmA 158 :GFSGSLQQAERFVQLGYKIGVGGTITYPRASK T0325 196 :LLDMVVCSEGEVFEINCHPAFID 1zzmA 190 :TRDVIAKLPLASLLLETDAPDMP T0325 219 :TILQNQSGYCMPRIREVEILT 1zzmA 214 :NGFQGQPNRPEQAARVFAVLC T0325 241 :QEVKEAIEER 1zzmA 242 :DEIAQALLNN Number of specific fragments extracted= 11 number of extra gaps= 0 total=821 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 1r85A/T0325-1r85A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1r85A expands to /projects/compbio/data/pdb/1r85.pdb.gz 1r85A:Skipped atom 43, because occupancy 0.400 <= existing 0.610 in 1r85A Skipped atom 45, because occupancy 0.400 <= existing 0.610 in 1r85A Skipped atom 47, because occupancy 0.400 <= existing 0.610 in 1r85A Skipped atom 49, because occupancy 0.400 <= existing 0.610 in 1r85A Skipped atom 51, because occupancy 0.400 <= existing 0.610 in 1r85A Skipped atom 53, because occupancy 0.400 <= existing 0.610 in 1r85A Skipped atom 55, because occupancy 0.400 <= existing 0.610 in 1r85A Skipped atom 57, because occupancy 0.400 <= existing 0.610 in 1r85A Skipped atom 59, because occupancy 0.400 <= existing 0.610 in 1r85A Skipped atom 61, because occupancy 0.400 <= existing 0.610 in 1r85A Skipped atom 63, because occupancy 0.400 <= existing 0.610 in 1r85A Skipped atom 65, because occupancy 0.400 <= existing 0.610 in 1r85A Skipped atom 67, because occupancy 0.400 <= existing 0.610 in 1r85A Skipped atom 69, because occupancy 0.400 <= existing 0.610 in 1r85A Skipped atom 71, because occupancy 0.400 <= existing 0.610 in 1r85A Skipped atom 73, because occupancy 0.400 <= existing 0.610 in 1r85A Skipped atom 152, because occupancy 0.380 <= existing 0.620 in 1r85A Skipped atom 474, because occupancy 0.430 <= existing 0.570 in 1r85A Skipped atom 476, because occupancy 0.430 <= existing 0.570 in 1r85A Skipped atom 478, because occupancy 0.430 <= existing 0.570 in 1r85A Skipped atom 480, because occupancy 0.430 <= existing 0.570 in 1r85A Skipped atom 482, because occupancy 0.430 <= existing 0.570 in 1r85A Skipped atom 575, because occupancy 0.500 <= existing 0.500 in 1r85A Skipped atom 577, because occupancy 0.500 <= existing 0.500 in 1r85A Skipped atom 579, because occupancy 0.500 <= existing 0.500 in 1r85A Skipped atom 581, because occupancy 0.500 <= existing 0.500 in 1r85A Skipped atom 817, because occupancy 0.420 <= existing 0.580 in 1r85A Skipped atom 819, because occupancy 0.420 <= existing 0.580 in 1r85A Skipped atom 821, because occupancy 0.420 <= existing 0.580 in 1r85A Skipped atom 823, because occupancy 0.420 <= existing 0.580 in 1r85A Skipped atom 825, because occupancy 0.420 <= existing 0.580 in 1r85A Skipped atom 827, because occupancy 0.420 <= existing 0.580 in 1r85A Skipped atom 829, because occupancy 0.430 <= existing 0.570 in 1r85A Skipped atom 831, because occupancy 0.430 <= existing 0.570 in 1r85A Skipped atom 833, because occupancy 0.430 <= existing 0.570 in 1r85A Skipped atom 835, because occupancy 0.430 <= existing 0.570 in 1r85A Skipped atom 837, because occupancy 0.430 <= existing 0.570 in 1r85A Skipped atom 839, because occupancy 0.430 <= existing 0.570 in 1r85A Skipped atom 841, because occupancy 0.430 <= existing 0.570 in 1r85A Skipped atom 843, because occupancy 0.430 <= existing 0.570 in 1r85A Skipped atom 845, because occupancy 0.430 <= existing 0.570 in 1r85A Skipped atom 847, because occupancy 0.430 <= existing 0.570 in 1r85A Skipped atom 849, because occupancy 0.430 <= existing 0.570 in 1r85A Skipped atom 851, because occupancy 0.430 <= existing 0.570 in 1r85A Skipped atom 853, because occupancy 0.430 <= existing 0.570 in 1r85A Skipped atom 855, because occupancy 0.430 <= existing 0.570 in 1r85A Skipped atom 857, because occupancy 0.430 <= existing 0.570 in 1r85A Skipped atom 859, because occupancy 0.430 <= existing 0.570 in 1r85A Skipped atom 1118, because occupancy 0.440 <= existing 0.560 in 1r85A Skipped atom 1120, because occupancy 0.440 <= existing 0.560 in 1r85A Skipped atom 1122, because occupancy 0.440 <= existing 0.560 in 1r85A Skipped atom 1248, because occupancy 0.430 <= existing 0.570 in 1r85A Skipped atom 1281, because occupancy 0.260 <= existing 0.370 in 1r85A Skipped atom 1284, because occupancy 0.260 <= existing 0.370 in 1r85A Skipped atom 1287, because occupancy 0.260 <= existing 0.370 in 1r85A Skipped atom 1604, because occupancy 0.120 <= existing 0.880 in 1r85A Skipped atom 2107, because occupancy 0.440 <= existing 0.560 in 1r85A Skipped atom 2109, because occupancy 0.440 <= existing 0.560 in 1r85A Skipped atom 2111, because occupancy 0.440 <= existing 0.560 in 1r85A Skipped atom 2508, because occupancy 0.340 <= existing 0.660 in 1r85A Skipped atom 2510, because occupancy 0.340 <= existing 0.660 in 1r85A Skipped atom 2512, because occupancy 0.340 <= existing 0.660 in 1r85A Skipped atom 2529, because occupancy 0.400 <= existing 0.600 in 1r85A Skipped atom 2531, because occupancy 0.400 <= existing 0.600 in 1r85A Skipped atom 2533, because occupancy 0.400 <= existing 0.600 in 1r85A Skipped atom 2535, because occupancy 0.400 <= existing 0.600 in 1r85A Skipped atom 2537, because occupancy 0.400 <= existing 0.600 in 1r85A Skipped atom 2937, because occupancy 0.420 <= existing 0.580 in 1r85A Skipped atom 2939, because occupancy 0.420 <= existing 0.580 in 1r85A Skipped atom 2941, because occupancy 0.420 <= existing 0.580 in 1r85A Skipped atom 2943, because occupancy 0.420 <= existing 0.580 in 1r85A Skipped atom 3156, because occupancy 0.440 <= existing 0.560 in 1r85A Skipped atom 3158, because occupancy 0.440 <= existing 0.560 in 1r85A Skipped atom 3160, because occupancy 0.440 <= existing 0.560 in 1r85A Skipped atom 3162, because occupancy 0.440 <= existing 0.560 in 1r85A Skipped atom 3164, because occupancy 0.440 <= existing 0.560 in 1r85A Skipped atom 3166, because occupancy 0.440 <= existing 0.560 in 1r85A # T0325 read from 1r85A/T0325-1r85A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r85A read from 1r85A/T0325-1r85A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1r85A to template set # found chain 1r85A in template set Warning: unaligning (T0325)H63 because of BadResidue code BAD_PEPTIDE in next template residue (1r85A)T96 Warning: unaligning (T0325)L64 because of BadResidue code BAD_PEPTIDE at template residue (1r85A)T96 Warning: unaligning (T0325)L75 because of BadResidue code BAD_PEPTIDE in next template residue (1r85A)P104 Warning: unaligning (T0325)P76 because of BadResidue code BAD_PEPTIDE at template residue (1r85A)P104 Warning: unaligning (T0325)D198 because of BadResidue code BAD_PEPTIDE in next template residue (1r85A)M253 Warning: unaligning (T0325)M199 because of BadResidue code BAD_PEPTIDE at template residue (1r85A)M253 Warning: unaligning (T0325)E209 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1r85A)T264 Warning: unaligning (T0325)I210 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1r85A)T264 T0325 4 :KKLIINADDFGYTPAVTQG 1r85A 28 :FTIGAAVEPYQLQNEKDVQ T0325 26 :AHKRG 1r85A 47 :MLKRH T0325 32 :VTSTTA 1r85A 52 :FNSIVA T0325 39 :PTSPYFLEAMESARI 1r85A 73 :FNFEQADRIVKFAKA T0325 56 :PTLAIGV 1r85A 88 :NGMDIRF T0325 65 :TLTLNQ 1r85A 97 :LVWHSQ T0325 77 :REM 1r85A 105 :QWF T0325 83 :LVDEAGYFWHQSI 1r85A 108 :FLDKEGKPMVNET T0325 96 :FEEKVNLEEVYNEWDAQIISFMKS 1r85A 123 :VKREQNKQLLLKRLETHIKTIVER T0325 120 :GRRPDHIDSHHNVHG 1r85A 148 :KDDIKYWDVVNEVVG T0325 139 :LLGVALALARKY 1r85A 180 :YIKVAFQAARKY T0325 151 :QLPLRNASRSIETKDYLELY 1r85A 195 :NIKLYMNDYNTEVEPKRTAL T0325 171 :QDVRTP 1r85A 224 :EGVPID T0325 180 :LYQFYDKAISTETILQLL 1r85A 234 :QSHIQIGWPSEAEIEKTI T0325 200 :VVCSEGEVF 1r85A 254 :FAALGLDNQ T0325 211 :NCHPAFID 1r85A 265 :ELDVSMYG T0325 220 :ILQNQSGYCMPRIREVEILTS 1r85A 277 :AYPTYDAIPKQKFLDQAARYD T0325 242 :EVKEAIEER 1r85A 298 :RLFKLYEKL Number of specific fragments extracted= 18 number of extra gaps= 4 total=839 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 1r85A/T0325-1r85A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1r85A/T0325-1r85A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r85A read from 1r85A/T0325-1r85A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1r85A in template set Warning: unaligning (T0325)H63 because of BadResidue code BAD_PEPTIDE in next template residue (1r85A)T96 Warning: unaligning (T0325)L64 because of BadResidue code BAD_PEPTIDE at template residue (1r85A)T96 Warning: unaligning (T0325)L75 because of BadResidue code BAD_PEPTIDE in next template residue (1r85A)P104 Warning: unaligning (T0325)P76 because of BadResidue code BAD_PEPTIDE at template residue (1r85A)P104 Warning: unaligning (T0325)D198 because of BadResidue code BAD_PEPTIDE in next template residue (1r85A)M253 Warning: unaligning (T0325)M199 because of BadResidue code BAD_PEPTIDE at template residue (1r85A)M253 Warning: unaligning (T0325)E209 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1r85A)T264 Warning: unaligning (T0325)I210 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1r85A)T264 T0325 4 :KKLIINADDFGYTPAVTQGIIE 1r85A 28 :FTIGAAVEPYQLQNEKDVQMLK T0325 29 :RG 1r85A 50 :RH T0325 32 :VTSTTA 1r85A 52 :FNSIVA T0325 39 :PTSPYFLEAMESARI 1r85A 73 :FNFEQADRIVKFAKA T0325 55 :A 1r85A 88 :N T0325 57 :TLAIGV 1r85A 89 :GMDIRF T0325 65 :TLTLNQ 1r85A 97 :LVWHSQ T0325 77 :REM 1r85A 105 :QWF T0325 83 :LVDEAGYFWH 1r85A 108 :FLDKEGKPMV T0325 97 :EEKVNLEEVYNEWDAQIISFMKS 1r85A 124 :KREQNKQLLLKRLETHIKTIVER T0325 120 :GRRPDHIDSHHNVHG 1r85A 148 :KDDIKYWDVVNEVVG T0325 139 :LLGVALALARKY 1r85A 180 :YIKVAFQAARKY T0325 151 :QLPLRNASRSIETKDYLELY 1r85A 195 :NIKLYMNDYNTEVEPKRTAL T0325 171 :QDVRT 1r85A 224 :EGVPI T0325 180 :LYQFYDKAISTETILQLL 1r85A 234 :QSHIQIGWPSEAEIEKTI T0325 200 :VVCSEGEVF 1r85A 254 :FAALGLDNQ T0325 211 :NCHPAFID 1r85A 265 :ELDVSMYG T0325 220 :ILQNQSGYCMPR 1r85A 277 :AYPTYDAIPKQK T0325 232 :IREVEILT 1r85A 290 :LDQAARYD T0325 242 :EVKEAIEER 1r85A 298 :RLFKLYEKL Number of specific fragments extracted= 20 number of extra gaps= 4 total=859 Will force an alignment to be made, even if fragment is small Number of alignments=56 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r85A/T0325-1r85A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1r85A/T0325-1r85A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r85A read from 1r85A/T0325-1r85A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1r85A in template set Warning: unaligning (T0325)H63 because of BadResidue code BAD_PEPTIDE in next template residue (1r85A)T96 Warning: unaligning (T0325)L64 because of BadResidue code BAD_PEPTIDE at template residue (1r85A)T96 Warning: unaligning (T0325)A71 because of BadResidue code BAD_PEPTIDE in next template residue (1r85A)P104 Warning: unaligning (T0325)K72 because of BadResidue code BAD_PEPTIDE at template residue (1r85A)P104 Warning: unaligning (T0325)D198 because of BadResidue code BAD_PEPTIDE in next template residue (1r85A)M253 Warning: unaligning (T0325)M199 because of BadResidue code BAD_PEPTIDE at template residue (1r85A)M253 Warning: unaligning (T0325)E209 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1r85A)T264 Warning: unaligning (T0325)I210 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1r85A)T264 T0325 4 :KKLIINADDFGY 1r85A 28 :FTIGAAVEPYQL T0325 16 :TPAVTQGI 1r85A 41 :NEKDVQML T0325 28 :KRGV 1r85A 49 :KRHF T0325 33 :TSTTA 1r85A 53 :NSIVA T0325 39 :PTSPYFLEAMESARI 1r85A 73 :FNFEQADRIVKFAKA T0325 56 :PTLAIGV 1r85A 88 :NGMDIRF T0325 65 :TLTLNQ 1r85A 97 :LVWHSQ T0325 73 :PIL 1r85A 105 :QWF T0325 81 :PSLVDEAG 1r85A 108 :FLDKEGKP T0325 90 :FWHQSI 1r85A 123 :VKREQN T0325 102 :LEEVYNEWDAQIISFMK 1r85A 129 :KQLLLKRLETHIKTIVE T0325 119 :SGRRPDHIDSHHNVHGKNKK 1r85A 147 :YKDDIKYWDVVNEVVGDDGK T0325 139 :LLGVALALARKY 1r85A 180 :YIKVAFQAARKY T0325 151 :QLPLRNASRSIETKDYLEL 1r85A 195 :NIKLYMNDYNTEVEPKRTA T0325 180 :LYQFYDKAISTETILQLL 1r85A 234 :QSHIQIGWPSEAEIEKTI T0325 200 :VVCSEGEVF 1r85A 254 :FAALGLDNQ T0325 211 :NCHPAFIDTILQ 1r85A 265 :ELDVSMYGWPPR T0325 223 :NQSGYCMPRIREVE 1r85A 280 :TYDAIPKQKFLDQA T0325 245 :EAIEE 1r85A 294 :ARYDR Number of specific fragments extracted= 19 number of extra gaps= 4 total=878 Will force an alignment to be made, even if fragment is small Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j96A/T0325-1j96A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1j96A expands to /projects/compbio/data/pdb/1j96.pdb.gz 1j96A:Skipped atom 2590, because occupancy 1.000 <= existing 1.000 in 1j96A # T0325 read from 1j96A/T0325-1j96A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j96A read from 1j96A/T0325-1j96A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1j96A to template set # found chain 1j96A in template set Warning: unaligning (T0325)L221 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1j96A)P226 Warning: unaligning (T0325)Q222 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1j96A)P226 T0325 5 :KLIINADDFGYTPAVTQGIIEAHKRGV 1j96A 47 :HHIDSAHVYNNEEQVGLAIRSKIADGS T0325 32 :VTSTTALPT 1j96A 79 :IFYTSKLWS T0325 41 :SPYFLEAMESARISA 1j96A 92 :PELVRPALERSLKNL T0325 57 :TLA 1j96A 107 :QLD T0325 60 :IGVHL 1j96A 111 :VDLYL T0325 66 :LT 1j96A 116 :IH T0325 70 :QAKPILPREMVPS 1j96A 118 :FPVSVKPGEEVIP T0325 84 :VDEAGYFWH 1j96A 131 :KDENGKILF T0325 98 :EKVNLEEVYNEWD 1j96A 140 :DTVDLCATWEAME T0325 115 :SFMKSGR 1j96A 153 :KCKDAGL T0325 123 :PDHIDSHHNVH 1j96A 160 :AKSIGVSNFNH T0325 138 :KLLGVAL 1j96A 171 :RLLEMIL T0325 151 :QLP 1j96A 178 :NKP T0325 172 :DVRTPDEMLYQFYDKAIS 1j96A 181 :GLKYKPVCNQVECHPYFN T0325 190 :T 1j96A 200 :R T0325 195 :QLLDMVVC 1j96A 201 :KLLDFCKS T0325 205 :GEVFEINCHPAFIDTI 1j96A 209 :KDIVLVAYSALGSHRE T0325 223 :NQSGYCMP 1j96A 227 :WVDPNSPV T0325 237 :ILTSQEVKEAIEERGIL 1j96A 235 :LLEDPVLCALAKKHKRT Number of specific fragments extracted= 19 number of extra gaps= 1 total=897 Will force an alignment to be made, even if fragment is small Number of alignments=58 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j96A/T0325-1j96A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1j96A/T0325-1j96A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j96A read from 1j96A/T0325-1j96A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1j96A in template set Warning: unaligning (T0325)Y166 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1j96A)P226 Warning: unaligning (T0325)L167 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1j96A)P226 T0325 5 :KLIINADDFGYTPAVTQGIIEAHKRGV 1j96A 47 :HHIDSAHVYNNEEQVGLAIRSKIADGS T0325 32 :VTSTTAL 1j96A 79 :IFYTSKL T0325 39 :PTSPYFLEAMESARI 1j96A 90 :HRPELVRPALERSLK T0325 54 :SAPT 1j96A 107 :QLDY T0325 60 :IGVHL 1j96A 111 :VDLYL T0325 66 :LT 1j96A 116 :IH T0325 70 :QAKPILPREMVPS 1j96A 118 :FPVSVKPGEEVIP T0325 84 :VDEAGYFWH 1j96A 131 :KDENGKILF T0325 98 :EKVNLEEVYNEW 1j96A 140 :DTVDLCATWEAM T0325 110 :DAQIISFMKS 1j96A 170 :HRLLEMILNK T0325 120 :GRRPD 1j96A 181 :GLKYK T0325 125 :HIDSHHNVH 1j96A 190 :QVECHPYFN T0325 139 :LLG 1j96A 199 :QRK T0325 143 :ALALARKYQLPLRNASRSIETKD 1j96A 202 :LLDFCKSKDIVLVAYSALGSHRE T0325 168 :ELYQDVRTPDEM 1j96A 227 :WVDPNSPVLLED T0325 191 :ETILQLLDMVVCS 1j96A 239 :PVLCALAKKHKRT T0325 204 :EGEVFEIN 1j96A 262 :QRGVVVLA Number of specific fragments extracted= 17 number of extra gaps= 1 total=914 Will force an alignment to be made, even if fragment is small Number of alignments=59 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j96A/T0325-1j96A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1j96A/T0325-1j96A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j96A read from 1j96A/T0325-1j96A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1j96A in template set T0325 5 :KLIINADDFGYTPAVTQGIIEAHKRGV 1j96A 47 :HHIDSAHVYNNEEQVGLAIRSKIADGS T0325 32 :VTSTTAL 1j96A 79 :IFYTSKL T0325 39 :PTSPYFLEAMESARI 1j96A 90 :HRPELVRPALERSLK T0325 55 :APTLA 1j96A 105 :NLQLD T0325 62 :VHLTLTLNQAKPILPREMVPSLVDEAGYF 1j96A 111 :VDLYLIHFPVSVKPGEEVIPKDENGKILF T0325 98 :EKVNLEEVYNEW 1j96A 140 :DTVDLCATWEAM T0325 114 :ISFMKSGRRPDHIDSH 1j96A 152 :EKCKDAGLAKSIGVSN T0325 135 :K 1j96A 168 :F T0325 140 :L 1j96A 169 :N T0325 194 :LQLLDMVVCSEG 1j96A 170 :HRLLEMILNKPG T0325 206 :EVFEINCHPAFIDTI 1j96A 187 :VCNQVECHPYFNQRK T0325 243 :VKEAIEERGILLANY 1j96A 202 :LLDFCKSKDIVLVAY Number of specific fragments extracted= 12 number of extra gaps= 0 total=926 Will force an alignment to be made, even if fragment is small Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1frb/T0325-1frb-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1frb expands to /projects/compbio/data/pdb/1frb.pdb.gz 1frb:Warning: there is no chain 1frb will retry with 1frbA # T0325 read from 1frb/T0325-1frb-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1frb read from 1frb/T0325-1frb-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1frb to template set # found chain 1frb in template set T0325 4 :KKLIINADDFGYTPAVTQGIIEAHKRGV 1frb 39 :YRHIDCAYAYCNENEVGEAIQEKIKEKA T0325 32 :VTSTTALPT 1frb 72 :LFIVSKLWP T0325 41 :SPYFLEAMESAR 1frb 85 :KKLLKEAFQKTL T0325 53 :ISAPTLAIGV 1frb 99 :LKLDYLDLYL T0325 66 :LT 1frb 109 :IH T0325 70 :QAKPILPREMVPS 1frb 111 :WPQGLQPGKELFP T0325 84 :VDEAGYFWHQSI 1frb 124 :KDDQGRILTSKT T0325 96 :FEEK 1frb 148 :VDQG T0325 110 :DAQIISFMK 1frb 163 :HFQIERLLN T0325 120 :GRR 1frb 174 :GLK T0325 123 :PDHIDSHHNVH 1frb 181 :TNQVECHPYLT T0325 140 :LGVALALARKYQLPLR 1frb 192 :QEKLIQYCHSKGISVT T0325 156 :NASRSIETKDYLELY 1frb 213 :GSPDRPSAKPEDPSL T0325 238 :LTSQEVKEAIEERGIL 1frb 228 :LEDPKIKEIAAKHEKT Number of specific fragments extracted= 14 number of extra gaps= 0 total=940 Will force an alignment to be made, even if fragment is small Number of alignments=61 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1frb/T0325-1frb-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1frb/T0325-1frb-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1frb read from 1frb/T0325-1frb-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1frb in template set T0325 4 :KKLIINADDFGYTPAVTQGIIEAHKRGV 1frb 39 :YRHIDCAYAYCNENEVGEAIQEKIKEKA T0325 32 :VTSTTAL 1frb 72 :LFIVSKL T0325 39 :PTSPYFLEAMESA 1frb 83 :FEKKLLKEAFQKT T0325 52 :RISAPTLAIGV 1frb 98 :DLKLDYLDLYL T0325 66 :LT 1frb 109 :IH T0325 70 :QAKPILPREMVP 1frb 111 :WPQGLQPGKELF T0325 83 :LVDEAGYFWH 1frb 123 :PKDDQGRILT T0325 93 :QSIFEEK 1frb 145 :EELVDQG T0325 110 :DAQIISFMKS 1frb 163 :HFQIERLLNK T0325 120 :GRR 1frb 174 :GLK T0325 123 :PDHIDSHHNVH 1frb 181 :TNQVECHPYLT T0325 135 :K 1frb 192 :Q T0325 141 :GVALALARKYQLPLR 1frb 193 :EKLIQYCHSKGISVT T0325 156 :NASRSIETKDYLELY 1frb 213 :GSPDRPSAKPEDPSL T0325 171 :QDVRTPDEMLYQFY 1frb 240 :HEKTSAQVLIRFHI Number of specific fragments extracted= 15 number of extra gaps= 0 total=955 Will force an alignment to be made, even if fragment is small Number of alignments=62 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1frb/T0325-1frb-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1frb/T0325-1frb-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1frb read from 1frb/T0325-1frb-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1frb in template set T0325 4 :KKLIINADDFGYTPAVTQGIIEAHKRGV 1frb 39 :YRHIDCAYAYCNENEVGEAIQEKIKEKA T0325 32 :VTSTTAL 1frb 72 :LFIVSKL T0325 39 :PTSPYFLEAMESARI 1frb 83 :FEKKLLKEAFQKTLT T0325 54 :SAPTLA 1frb 100 :KLDYLD T0325 64 :LTLTLNQAKPILPREMVPSLVDEAG 1frb 106 :LYLIHWPQGLQPGKELFPKDDQGRI T0325 90 :FWHQSIFE 1frb 135 :TTFLEAWE T0325 110 :DAQIISFMK 1frb 163 :HFQIERLLN T0325 119 :SGRRPDHIDSHHNVHGK 1frb 173 :PGLKHKPVTNQVECHPY T0325 138 :KLLGVALALARKYQL 1frb 190 :LTQEKLIQYCHSKGI T0325 209 :EINCHPAFIDTILQNQSGYCMP 1frb 205 :SVTAYSPLGSPDRPSAKPEDPS T0325 237 :ILTSQEVKEAIEERGIL 1frb 227 :LLEDPKIKEIAAKHEKT Number of specific fragments extracted= 11 number of extra gaps= 0 total=966 Will force an alignment to be made, even if fragment is small Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zhaA/T0325-1zhaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zhaA expands to /projects/compbio/data/pdb/1zha.pdb.gz 1zhaA:# T0325 read from 1zhaA/T0325-1zhaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zhaA read from 1zhaA/T0325-1zhaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zhaA to template set # found chain 1zhaA in template set Warning: unaligning (T0325)N3 because first residue in template chain is (1zhaA)E1002 T0325 4 :KKLIINADDFGYTPAVTQGI 1zhaA 1003 :KFLVIAGPCAIESEELLLKV T0325 44 :FLEAMESAR 1zhaA 1023 :GEEIKRLSE T0325 54 :SAPTLAIGV 1zhaA 1032 :KFKEVEFVF T0325 65 :TLT 1zhaA 1041 :KSS T0325 70 :QAKPILPREM 1zhaA 1044 :FDKANRSSIH T0325 96 :FEEKVNLEEVYNEWD 1zhaA 1054 :SFRGHGLEYGVKALR T0325 115 :SFMK 1zhaA 1069 :KVKE T0325 119 :SGRRP 1zhaA 1074 :FGLKI T0325 125 :HIDSHHNVH 1zhaA 1079 :TTDIHESWQ T0325 136 :NKKLL 1zhaA 1088 :AEPVA T0325 141 :GVA 1zhaA 1109 :DLL T0325 145 :ALARKYQLPL 1zhaA 1112 :LAAAKTGRAV T0325 155 :RNASRSIETKDYLELY 1zhaA 1123 :VKKGQFLAPWDTKNVV T0325 178 :EMLYQ 1zhaA 1185 :HSVQL T0325 189 :STETILQLLDMVVCSEGEVFEINCHPAF 1zhaA 1200 :MREFIFPLIRAAVAVGCDGVFMETHPEP T0325 219 :TILQNQSGYC 1zhaA 1228 :EKALSDASTQ T0325 230 :PRIREVE 1zhaA 1242 :QLEGIIE T0325 242 :EVKEAIEE 1zhaA 1249 :AILEIREV Number of specific fragments extracted= 18 number of extra gaps= 0 total=984 Will force an alignment to be made, even if fragment is small Number of alignments=64 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zhaA/T0325-1zhaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1zhaA/T0325-1zhaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zhaA read from 1zhaA/T0325-1zhaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zhaA in template set Warning: unaligning (T0325)N3 because first residue in template chain is (1zhaA)E1002 T0325 4 :KKLIINADDFGYTPAVTQGI 1zhaA 1003 :KFLVIAGPCAIESEELLLKV T0325 44 :FLEAMESAR 1zhaA 1023 :GEEIKRLSE T0325 54 :SAPTLAIGV 1zhaA 1032 :KFKEVEFVF T0325 65 :TLT 1zhaA 1041 :KSS T0325 70 :QAKPILPREMVPSLV 1zhaA 1044 :FDKANRSSIHSFRGH T0325 101 :NLEEVYNEWD 1zhaA 1059 :GLEYGVKALR T0325 115 :SFMK 1zhaA 1069 :KVKE T0325 119 :SGRRP 1zhaA 1074 :FGLKI T0325 125 :HIDSHHNVH 1zhaA 1079 :TTDIHESWQ T0325 136 :NKKLL 1zhaA 1088 :AEPVA T0325 141 :GVA 1zhaA 1109 :DLL T0325 145 :ALARKYQLPLR 1zhaA 1112 :LAAAKTGRAVN T0325 156 :NASRSIETKDYLELY 1zhaA 1124 :KKGQFLAPWDTKNVV T0325 178 :EMLYQ 1zhaA 1185 :HSVQL T0325 189 :STETILQLLDMVVCSEGEVFEINCHP 1zhaA 1200 :MREFIFPLIRAAVAVGCDGVFMETHP T0325 215 :AFID 1zhaA 1230 :ALSD T0325 226 :GYCM 1zhaA 1241 :SQLE T0325 233 :REVE 1zhaA 1245 :GIIE T0325 242 :EVKEAIEE 1zhaA 1249 :AILEIREV Number of specific fragments extracted= 19 number of extra gaps= 0 total=1003 Will force an alignment to be made, even if fragment is small Number of alignments=65 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zhaA/T0325-1zhaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1zhaA/T0325-1zhaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zhaA read from 1zhaA/T0325-1zhaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zhaA in template set Warning: unaligning (T0325)N3 because first residue in template chain is (1zhaA)E1002 Warning: unaligning (T0325)L180 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1zhaA)G1199 Warning: unaligning (T0325)Y181 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zhaA)G1199 T0325 4 :KKLIINA 1zhaA 1003 :KFLVIAG T0325 35 :TTALPTSPYFLEAMESARI 1zhaA 1010 :PCAIESEELLLKVGEEIKR T0325 54 :SAPTLAI 1zhaA 1032 :KFKEVEF T0325 65 :TLTLNQAKPILPR 1zhaA 1039 :VFKSSFDKANRSS T0325 85 :DEAGYF 1zhaA 1052 :IHSFRG T0325 100 :VNLEEVYNEWD 1zhaA 1058 :HGLEYGVKALR T0325 115 :SFMK 1zhaA 1069 :KVKE T0325 119 :SGRRP 1zhaA 1074 :FGLKI T0325 125 :HIDSH 1zhaA 1079 :TTDIH T0325 130 :HNVHGKNKK 1zhaA 1099 :QIPAFLCGQ T0325 141 :GVALALARKYQLPL 1zhaA 1108 :TDLLLAAAKTGRAV T0325 155 :RNASRSIETKDYLE 1zhaA 1123 :VKKGQFLAPWDTKN T0325 175 :TPDEM 1zhaA 1186 :SVQLP T0325 189 :STETILQLLDMVVCSEGEVFEINCHPAF 1zhaA 1200 :MREFIFPLIRAAVAVGCDGVFMETHPEP T0325 219 :TILQNQSGYC 1zhaA 1228 :EKALSDASTQ T0325 255 :ANYESL 1zhaA 1238 :LPLSQL Number of specific fragments extracted= 16 number of extra gaps= 1 total=1019 Will force an alignment to be made, even if fragment is small Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pe1A/T0325-1pe1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1pe1A expands to /projects/compbio/data/pdb/1pe1.pdb.gz 1pe1A:# T0325 read from 1pe1A/T0325-1pe1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pe1A read from 1pe1A/T0325-1pe1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1pe1A to template set # found chain 1pe1A in template set Warning: unaligning (T0325)S2 because first residue in template chain is (1pe1A)M1001 T0325 3 :NKKLIINADDFGYTPAVTQGI 1pe1A 1002 :EKFLVIAGPCAIESEELLLKV T0325 44 :FLEAMESAR 1pe1A 1023 :GEEIKRLSE T0325 54 :SAPTLAIGV 1pe1A 1032 :KFKEVEFVF T0325 65 :TLT 1pe1A 1041 :KSS T0325 70 :QAKPILPREMV 1pe1A 1044 :FDKANRSSIHS T0325 97 :EEKVNLEEVYNEWD 1pe1A 1055 :FRGHGLEYGVKALR T0325 115 :SFMK 1pe1A 1069 :KVKE T0325 119 :SGRRP 1pe1A 1074 :FGLKI T0325 125 :HIDSHHNVH 1pe1A 1079 :TTDIHESWQ T0325 136 :NKKLL 1pe1A 1088 :AEPVA T0325 141 :GVALALA 1pe1A 1109 :DLLLAAA T0325 149 :KYQLPL 1pe1A 1116 :KTGRAV T0325 155 :RNASRSIETKDYLELY 1pe1A 1123 :VKKGQFLAPWDTKNVV T0325 178 :EMLYQ 1pe1A 1185 :HSVQL T0325 188 :ISTETILQLLDMVVCSEGEVFEINCHPAF 1pe1A 1199 :GMREFIFPLIRAAVAVGCDGVFMETHPEP T0325 219 :TILQNQSGYC 1pe1A 1228 :EKALSDASTQ T0325 230 :PRIREVE 1pe1A 1242 :QLEGIIE T0325 242 :EVKEAIEE 1pe1A 1249 :AILEIREV Number of specific fragments extracted= 18 number of extra gaps= 0 total=1037 Will force an alignment to be made, even if fragment is small Number of alignments=67 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pe1A/T0325-1pe1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1pe1A/T0325-1pe1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pe1A read from 1pe1A/T0325-1pe1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1pe1A in template set Warning: unaligning (T0325)S2 because first residue in template chain is (1pe1A)M1001 Warning: unaligning (T0325)Y184 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1pe1A)G1198 T0325 3 :NKKLIINADDFGYTPAVTQGI 1pe1A 1002 :EKFLVIAGPCAIESEELLLKV T0325 44 :FLEAMESAR 1pe1A 1023 :GEEIKRLSE T0325 54 :SAPTLAIGV 1pe1A 1032 :KFKEVEFVF T0325 65 :TLT 1pe1A 1041 :KSS T0325 70 :QAKPILPREMVPSLV 1pe1A 1044 :FDKANRSSIHSFRGH T0325 101 :NLEEVYNEWD 1pe1A 1059 :GLEYGVKALR T0325 115 :SFMK 1pe1A 1069 :KVKE T0325 119 :SGRRP 1pe1A 1074 :FGLKI T0325 125 :HIDSHHNV 1pe1A 1079 :TTDIHESW T0325 135 :KNKKLL 1pe1A 1087 :QAEPVA T0325 141 :GVALALA 1pe1A 1109 :DLLLAAA T0325 149 :KYQLPLR 1pe1A 1116 :KTGRAVN T0325 156 :NASRSIETKDYLELY 1pe1A 1124 :KKGQFLAPWDTKNVV T0325 171 :QDVRT 1pe1A 1175 :QWAKV T0325 176 :PDEMLYQF 1pe1A 1183 :ATHSVQLP T0325 188 :ISTETILQLLDMVVCSEGEVFEINCHP 1pe1A 1199 :GMREFIFPLIRAAVAVGCDGVFMETHP T0325 215 :AFID 1pe1A 1230 :ALSD T0325 226 :GY 1pe1A 1241 :SQ T0325 231 :RIREVE 1pe1A 1243 :LEGIIE T0325 242 :EVKEAIEE 1pe1A 1249 :AILEIREV Number of specific fragments extracted= 20 number of extra gaps= 1 total=1057 Will force an alignment to be made, even if fragment is small Number of alignments=68 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pe1A/T0325-1pe1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1pe1A/T0325-1pe1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pe1A read from 1pe1A/T0325-1pe1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1pe1A in template set Warning: unaligning (T0325)S2 because first residue in template chain is (1pe1A)M1001 Warning: unaligning (T0325)P176 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1pe1A)G1198 Warning: unaligning (T0325)D177 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1pe1A)G1198 T0325 3 :NKKLIINA 1pe1A 1002 :EKFLVIAG T0325 35 :TTALPTSPYFLEAMESARI 1pe1A 1010 :PCAIESEELLLKVGEEIKR T0325 54 :SAPTLAI 1pe1A 1032 :KFKEVEF T0325 65 :TLTLNQAKPILPR 1pe1A 1039 :VFKSSFDKANRSS T0325 85 :DEAGYF 1pe1A 1052 :IHSFRG T0325 100 :VNLEEVYNEWD 1pe1A 1058 :HGLEYGVKALR T0325 115 :SFMK 1pe1A 1069 :KVKE T0325 119 :SGRRP 1pe1A 1074 :FGLKI T0325 125 :HIDSH 1pe1A 1079 :TTDIH T0325 130 :HNVHGK 1pe1A 1099 :QIPAFL T0325 137 :KKLLGVALA 1pe1A 1105 :CRQTDLLLA T0325 147 :ARKYQLPLR 1pe1A 1114 :AAKTGRAVN T0325 156 :NASRSIETKDYLE 1pe1A 1124 :KKGQFLAPWDTKN T0325 170 :YQDVRT 1pe1A 1185 :HSVQLP T0325 188 :ISTETILQLLDMVVCSEGEVFEINCHPAFI 1pe1A 1199 :GMREFIFPLIRAAVAVGCDGVFMETHPEPE T0325 220 :ILQNQSGYC 1pe1A 1229 :KALSDASTQ T0325 229 :MPRIREVE 1pe1A 1241 :SQLEGIIE T0325 242 :EVKEAIE 1pe1A 1249 :AILEIRE Number of specific fragments extracted= 18 number of extra gaps= 1 total=1075 Will force an alignment to be made, even if fragment is small Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o98A/T0325-1o98A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1o98A expands to /projects/compbio/data/pdb/1o98.pdb.gz 1o98A:Skipped atom 105, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 107, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 109, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 111, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 113, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 115, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 117, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 119, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 211, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 213, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 215, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 217, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 219, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 221, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 223, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 225, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 270, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 272, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 274, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 276, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 278, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 280, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 282, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 284, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 286, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 288, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 290, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 400, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 402, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 404, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 406, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 408, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 410, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 666, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 668, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 670, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 672, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 674, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 676, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 678, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 680, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 747, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 749, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 751, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 753, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 755, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 757, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 759, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 761, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 763, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 765, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 767, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 830, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 832, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 834, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 836, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 838, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 840, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 842, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 844, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 856, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 858, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 860, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 862, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 864, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 866, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 868, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 870, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 872, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 874, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 876, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 878, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 880, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 882, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 884, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 886, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 973, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 975, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 977, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 979, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 981, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 983, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 985, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 987, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1142, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1144, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1146, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1148, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1150, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1152, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1154, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1156, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1158, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1219, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1221, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1223, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1225, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1227, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1229, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1231, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1233, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1345, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1347, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1349, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1351, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1353, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1355, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1357, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1359, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1361, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1427, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1429, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1431, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1433, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1435, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1437, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1439, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1441, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1443, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1487, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1489, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1491, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1493, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1495, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1497, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1499, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1505, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1507, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1509, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1511, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1513, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1515, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1517, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1519, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1521, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1551, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1553, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1555, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1557, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1559, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1561, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1643, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1645, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1647, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1649, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1651, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1653, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1655, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1657, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1659, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1721, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1723, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1725, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1727, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1729, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1731, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1733, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1735, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1737, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1780, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1782, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1784, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1786, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1788, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1790, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1792, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1883, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1885, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1887, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1889, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1891, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1893, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1895, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1897, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1899, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1907, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1909, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1911, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1913, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1915, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1917, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1919, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1921, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1923, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1925, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1927, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1929, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1931, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1933, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1935, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1937, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1939, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1967, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1969, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1971, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1973, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1975, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1977, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1979, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1981, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1983, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 1999, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2001, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2003, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2005, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2007, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2009, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2011, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2013, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2105, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2107, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2109, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2111, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2113, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2115, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2117, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2119, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2121, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2123, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2125, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2258, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2260, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2262, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2264, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2266, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2268, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2270, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2272, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2274, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2276, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2278, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2280, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2407, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2409, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2411, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2413, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2415, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2417, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2419, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2421, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2462, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2464, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2466, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2468, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2470, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2472, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2474, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2476, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2478, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2510, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2512, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2514, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2516, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2518, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2520, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2522, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2524, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2526, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2528, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2530, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2532, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2534, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2536, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2538, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2540, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2542, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2544, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2546, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2548, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2550, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2552, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2554, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2556, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2558, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2560, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2562, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2564, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2566, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2568, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2709, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2711, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2713, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 2715, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 3295, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 3297, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 3299, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 3301, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 3303, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 3305, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 3307, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 3309, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 3311, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 3313, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 3315, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 3317, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 3342, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 3344, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 3346, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 3348, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 3350, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 3352, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 3354, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 3356, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 3405, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 3407, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 3409, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 3411, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 3413, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 3415, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 3417, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 3419, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 3421, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 3629, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 3631, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 3633, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 3635, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 3637, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 3639, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 3641, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 3643, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 3645, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 3789, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 3791, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 3793, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 3795, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 3797, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 3799, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 3801, because occupancy 0.500 <= existing 0.500 in 1o98A Skipped atom 3803, because occupancy 0.500 <= existing 0.500 in 1o98A # T0325 read from 1o98A/T0325-1o98A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o98A read from 1o98A/T0325-1o98A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1o98A to template set # found chain 1o98A in template set T0325 2 :SNKKLIINADDFGYTP 1o98A 3 :KKPVALIILDGFALRD T0325 22 :GIIE 1o98A 24 :AVAQ T0325 39 :PTSPYFLEAME 1o98A 28 :ANKPNFDRYWN T0325 54 :SAP 1o98A 39 :EYP T0325 63 :HLTLT 1o98A 42 :HTTLK T0325 75 :LPREMV 1o98A 47 :ACGEAV T0325 82 :SL 1o98A 53 :GL T0325 86 :EAGYFWHQSI 1o98A 55 :PEGQMGNSEV T0325 97 :EEK 1o98A 87 :REG T0325 107 :NEWDAQIISFMKSGRRPDHIDS 1o98A 95 :ETFLAAMNHVKQHGTSLHLFGL T0325 131 :NVH 1o98A 121 :GVH T0325 135 :KNKKLLGVALALARKYQLPLR 1o98A 124 :SHIHHLYALLRLAAKEGVKRV T0325 156 :NASRSIETKDYLELY 1o98A 153 :RDVGPQTAPQYIKEL T0325 171 :QDVRTPDE 1o98A 363 :PKVPTYDL T0325 185 :DKAISTETILQ 1o98A 371 :KPEMSAYEVTD T0325 196 :LLDMVVCSEGEVFEINC 1o98A 383 :LLKEIEADKYDAIILNY T0325 217 :IDTILQNQSGYCMPRIREVEILTS 1o98A 400 :ANPDMVGHSGKLEPTIKAVEAVDE T0325 241 :QEVKEAIEERGILLA 1o98A 426 :GKVVDAILAKGGIAI Number of specific fragments extracted= 18 number of extra gaps= 0 total=1093 Will force an alignment to be made, even if fragment is small Number of alignments=70 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o98A/T0325-1o98A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1o98A/T0325-1o98A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o98A read from 1o98A/T0325-1o98A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1o98A in template set T0325 3 :NKKLIINADDFGYTP 1o98A 4 :KPVALIILDGFALRD T0325 22 :GIIE 1o98A 24 :AVAQ T0325 39 :PTSPYFLEAME 1o98A 28 :ANKPNFDRYWN T0325 54 :SAP 1o98A 39 :EYP T0325 63 :HLTLT 1o98A 42 :HTTLK T0325 74 :ILPR 1o98A 47 :ACGE T0325 79 :M 1o98A 51 :A T0325 81 :PSL 1o98A 52 :VGL T0325 86 :EAGYFWH 1o98A 55 :PEGQMGN T0325 94 :SIFEEK 1o98A 84 :IAIREG T0325 107 :NEWDAQIISFMKSGRRPDHIDS 1o98A 95 :ETFLAAMNHVKQHGTSLHLFGL T0325 131 :NVH 1o98A 121 :GVH T0325 135 :KNKKLLGVALALARKYQLPLR 1o98A 124 :SHIHHLYALLRLAAKEGVKRV T0325 156 :NASRSIETKDYLELY 1o98A 150 :LDGRDVGPQTAPQYI T0325 171 :QDVRTPDEML 1o98A 363 :PKVPTYDLKP T0325 187 :AISTETILQ 1o98A 373 :EMSAYEVTD T0325 196 :LLDMVVCSEGEVFEINC 1o98A 383 :LLKEIEADKYDAIILNY T0325 217 :IDTILQNQSGYCMPRIREVEILTS 1o98A 400 :ANPDMVGHSGKLEPTIKAVEAVDE T0325 242 :EVKEAIEERGILLA 1o98A 427 :KVVDAILAKGGIAI Number of specific fragments extracted= 19 number of extra gaps= 0 total=1112 Will force an alignment to be made, even if fragment is small Number of alignments=71 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o98A/T0325-1o98A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1o98A/T0325-1o98A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o98A read from 1o98A/T0325-1o98A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1o98A in template set T0325 13 :FGYTPAVTQGIIEAHKRGV 1o98A 91 :FDRNETFLAAMNHVKQHGT T0325 32 :VTSTTALPTS 1o98A 111 :LHLFGLLSDG T0325 42 :PYFLEAMESARI 1o98A 127 :HHLYALLRLAAK T0325 56 :PTL 1o98A 139 :EGV T0325 59 :AIGVHLTLTLNQAKPIL 1o98A 143 :RVYIHGFLDGRDVGPQT T0325 91 :W 1o98A 160 :A T0325 93 :QSI 1o98A 161 :PQY T0325 102 :LEEVYNEWD 1o98A 164 :IKELQEKIK T0325 118 :KSGR 1o98A 173 :EYGV T0325 122 :RPDHIDSHHNVHGK 1o98A 178 :EIATLSGRYYSMDR T0325 137 :KKLLGVALALA 1o98A 192 :DKRWDRVEKAY T0325 170 :YQDVRTPDEMLYQFYDKAISTETILQLLDMVVCSEGEVFEINC 1o98A 357 :RILINSPKVPTYDLKPEMSAYEVTDALLKEIEADKYDAIILNY T0325 217 :IDTILQNQSGYCMPRIREVEILTS 1o98A 400 :ANPDMVGHSGKLEPTIKAVEAVDE T0325 242 :EVKEAIEERGILLA 1o98A 427 :KVVDAILAKGGIAI Number of specific fragments extracted= 14 number of extra gaps= 0 total=1126 Will force an alignment to be made, even if fragment is small Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gjlA/T0325-2gjlA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2gjlA expands to /projects/compbio/data/pdb/2gjl.pdb.gz 2gjlA:# T0325 read from 2gjlA/T0325-2gjlA-t06-local-adpstyle5.a2m # 2gjlA read from 2gjlA/T0325-2gjlA-t06-local-adpstyle5.a2m # adding 2gjlA to template set # found chain 2gjlA in template set T0325 29 :RGVVTSTTALPTSPYFLEAMESAR 2gjlA 38 :AGGLATLSALTQPSPEALAAEIAR T0325 53 :ISAPTLAIGVHLTLTL 2gjlA 63 :RELTDRPFGVNLTLLP T0325 70 :QAKPILPREMVPSLVDE 2gjlA 79 :TQKPVPYAEYRAAIIEA T0325 98 :EKVNLEEVYNEWDAQIISFMKSGRRPDH 2gjlA 96 :GIRVVETAGNDPGEHIAEFRRHGVKVIH Number of specific fragments extracted= 4 number of extra gaps= 0 total=1130 Will force an alignment to be made, even if fragment is small Number of alignments=73 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w5nA/T0325-1w5nA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1w5nA expands to /projects/compbio/data/pdb/1w5n.pdb.gz 1w5nA:Skipped atom 233, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 235, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 237, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 239, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 241, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 243, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 245, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 262, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 264, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 266, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 268, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 270, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 272, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 274, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 323, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 325, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 327, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 329, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 331, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 333, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 335, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 375, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 377, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 379, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 381, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 383, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 385, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 387, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 576, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 578, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 580, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 582, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 584, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 586, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 588, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 590, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 592, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 721, because occupancy 0.250 <= existing 0.750 in 1w5nA Skipped atom 723, because occupancy 0.250 <= existing 0.750 in 1w5nA Skipped atom 725, because occupancy 0.250 <= existing 0.750 in 1w5nA Skipped atom 727, because occupancy 0.250 <= existing 0.750 in 1w5nA Skipped atom 729, because occupancy 0.250 <= existing 0.750 in 1w5nA Skipped atom 731, because occupancy 0.250 <= existing 0.750 in 1w5nA Skipped atom 733, because occupancy 0.250 <= existing 0.750 in 1w5nA Skipped atom 893, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 895, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 897, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 899, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 901, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 903, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 905, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 907, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 909, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 911, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 913, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 1101, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 1103, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 1105, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 1107, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 1109, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 1111, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 1113, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 1115, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 1117, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 1267, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 1269, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 1271, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 1273, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 1275, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 1277, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 1279, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 1281, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 1283, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 1285, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 1287, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 1396, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 1398, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 1400, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 1402, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 1404, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 1406, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 1408, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 1410, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 1487, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 1489, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 1491, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 1493, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 1495, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 1497, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 1499, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 1501, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 1503, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 1552, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 1554, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 1556, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 1558, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 1560, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 1562, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 1564, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 1964, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 1966, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 1968, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 1970, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 1972, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 1974, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 1976, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 1978, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 1987, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 1989, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 1991, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 1993, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 1995, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 1997, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 1999, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 2001, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 2030, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 2032, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 2034, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 2036, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 2038, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 2040, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 2042, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 2044, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 2096, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 2098, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 2100, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 2102, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 2104, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 2106, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 2108, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 2110, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 2112, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 2114, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 2116, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 2136, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 2138, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 2140, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 2142, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 2144, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 2146, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 2148, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 2150, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 2152, because occupancy 0.500 <= existing 0.500 in 1w5nA Skipped atom 2162, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 2164, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 2166, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 2168, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 2170, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 2172, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 2174, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 2176, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 2178, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 2192, because occupancy 0.300 <= existing 0.400 in 1w5nA Skipped atom 2195, because occupancy 0.300 <= existing 0.400 in 1w5nA Skipped atom 2198, because occupancy 0.300 <= existing 0.400 in 1w5nA Skipped atom 2201, because occupancy 0.400 <= existing 0.500 in 1w5nA Skipped atom 2204, because occupancy 0.300 <= existing 0.400 in 1w5nA Skipped atom 2207, because occupancy 0.300 <= existing 0.400 in 1w5nA Skipped atom 2210, because occupancy 0.300 <= existing 0.400 in 1w5nA Skipped atom 2213, because occupancy 0.300 <= existing 0.400 in 1w5nA Skipped atom 2216, because occupancy 0.300 <= existing 0.400 in 1w5nA Skipped atom 2219, because occupancy 0.300 <= existing 0.400 in 1w5nA Skipped atom 2222, because occupancy 0.300 <= existing 0.400 in 1w5nA Skipped atom 2325, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 2327, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 2329, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 2331, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 2333, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 2335, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 2337, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 2339, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 2351, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 2353, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 2355, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 2357, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 2359, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 2361, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 2363, because occupancy 0.300 <= existing 0.700 in 1w5nA Skipped atom 2365, because occupancy 0.300 <= existing 0.700 in 1w5nA # T0325 read from 1w5nA/T0325-1w5nA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1w5nA read from 1w5nA/T0325-1w5nA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1w5nA to template set # found chain 1w5nA in template set Warning: unaligning (T0325)D127 because of BadResidue code BAD_PEPTIDE in next template residue (1w5nA)D176 Warning: unaligning (T0325)S128 because of BadResidue code BAD_PEPTIDE at template residue (1w5nA)D176 Warning: unaligning (T0325)V173 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1w5nA)N228 T0325 17 :PAVTQGIIEAHKRGVVTSTTALPT 1w5nA 66 :DQLLIEAEEWVALGIPALALFPVT T0325 43 :YFLEAMESARISAPTLAIGVHLTL 1w5nA 107 :IAQRATRALRERFPELGIITDVAL T0325 72 :KPILPREMV 1w5nA 131 :CPFTTHGQC T0325 82 :SLVDEAGY 1w5nA 140 :GILDDDGY T0325 100 :VNLEEVYNEWDAQIISFMKSGRRPDHI 1w5nA 148 :VLNDVSIDVLVRQALSHAEAGAQVVAP T0325 135 :KNKKLLGVALALARKYQLPLRNA 1w5nA 177 :MMDGRIGAIREALESAGHTNVRV T0325 158 :SRSIETKDYLELYQD 1w5nA 205 :KYASAYYGPFRDAVG T0325 180 :LYQFYDKA 1w5nA 230 :ATYQMDPA T0325 189 :STETILQLLDMVVC 1w5nA 238 :NSDEALHEVAADLA T0325 205 :GEVFEINCHPAFID 1w5nA 252 :EGADMVMVKPGMPY Number of specific fragments extracted= 10 number of extra gaps= 1 total=1140 Will force an alignment to be made, even if fragment is small Number of alignments=74 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w5nA/T0325-1w5nA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1w5nA/T0325-1w5nA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1w5nA read from 1w5nA/T0325-1w5nA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1w5nA in template set Warning: unaligning (T0325)D127 because of BadResidue code BAD_PEPTIDE in next template residue (1w5nA)D176 Warning: unaligning (T0325)S128 because of BadResidue code BAD_PEPTIDE at template residue (1w5nA)D176 Warning: unaligning (T0325)V173 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1w5nA)N228 T0325 17 :PAVTQGIIEAHKRG 1w5nA 66 :DQLLIEAEEWVALG T0325 32 :VTSTTALPTSP 1w5nA 80 :IPALALFPVTP T0325 43 :YFLEAMESARISAPTLAIGVHL 1w5nA 107 :IAQRATRALRERFPELGIITDV T0325 70 :QAKPILPREMV 1w5nA 129 :ALCPFTTHGQC T0325 82 :SLVDEAGY 1w5nA 140 :GILDDDGY T0325 100 :VNLEEVYNEWDAQIISFMKSGRRPDHI 1w5nA 148 :VLNDVSIDVLVRQALSHAEAGAQVVAP T0325 135 :KNKKLLGVALALARKY 1w5nA 177 :MMDGRIGAIREALESA T0325 151 :QLPLRN 1w5nA 196 :NVRVMA T0325 157 :ASRSIETKDYLELYQD 1w5nA 204 :AKYASAYYGPFRDAVG T0325 179 :MLYQFYDKAIS 1w5nA 229 :KATYQMDPANS T0325 191 :ETILQLLDMVVCS 1w5nA 240 :DEALHEVAADLAE T0325 206 :EVFEINCHPAF 1w5nA 253 :GADMVMVKPGM T0325 226 :GYCMPRIREVEIL 1w5nA 264 :PYLDIVRRVKDEF Number of specific fragments extracted= 13 number of extra gaps= 1 total=1153 Will force an alignment to be made, even if fragment is small Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w5nA/T0325-1w5nA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1w5nA/T0325-1w5nA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1w5nA read from 1w5nA/T0325-1w5nA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1w5nA in template set Warning: unaligning (T0325)H129 because of BadResidue code BAD_PEPTIDE in next template residue (1w5nA)D176 Warning: unaligning (T0325)H133 because of BadResidue code BAD_PEPTIDE at template residue (1w5nA)D176 Warning: unaligning (T0325)Y170 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1w5nA)N228 Warning: unaligning (T0325)M179 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1w5nA)N228 T0325 17 :PAVTQGIIEAHKRGVVTSTTALPT 1w5nA 66 :DQLLIEAEEWVALGIPALALFPVT T0325 42 :P 1w5nA 90 :P T0325 43 :YFLEAMESARISAPTLAIGVHLTLT 1w5nA 107 :IAQRATRALRERFPELGIITDVALC T0325 72 :KPILPREMVPSLVDEAG 1w5nA 132 :PFTTHGQCGILDDDGYV T0325 101 :NLEEVYNEWDAQIISFMKSGRR 1w5nA 149 :LNDVSIDVLVRQALSHAEAGAQ T0325 125 :HIDS 1w5nA 171 :VVAP T0325 134 :GK 1w5nA 177 :MM T0325 137 :KKLLGVALALARKYQLPLRNA 1w5nA 179 :DGRIGAIREALESAGHTNVRV T0325 158 :SRSIETKDYLEL 1w5nA 205 :KYASAYYGPFRD T0325 180 :LYQFYDKAISTETILQLLDMVVCS 1w5nA 229 :KATYQMDPANSDEALHEVAADLAE T0325 206 :EVFEINCHPAFID 1w5nA 253 :GADMVMVKPGMPY T0325 219 :TIL 1w5nA 267 :DIV T0325 232 :IR 1w5nA 270 :RR T0325 243 :VKE 1w5nA 272 :VKD Number of specific fragments extracted= 14 number of extra gaps= 1 total=1167 Will force an alignment to be made, even if fragment is small Number of alignments=76 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z7aA/T0325-1z7aA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1z7aA expands to /projects/compbio/data/pdb/1z7a.pdb.gz 1z7aA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 520, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 524, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 526, because occupancy 0.500 <= existing 0.500 in 1z7aA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 855, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 859, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 861, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 863, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 865, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 867, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 885, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 889, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 891, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 893, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 895, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 897, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 899, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 901, because occupancy 0.500 <= existing 0.500 in 1z7aA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1039, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 1043, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 1045, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 1047, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 1049, because occupancy 0.500 <= existing 0.500 in 1z7aA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1144, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 1148, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 1150, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 1152, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 1154, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 1156, because occupancy 0.500 <= existing 0.500 in 1z7aA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1241, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 1245, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 1247, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 1249, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 1251, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 1253, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 1264, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 1268, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 1270, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 1272, because occupancy 0.500 <= existing 0.500 in 1z7aA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1812, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 1816, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 1818, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 1820, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 1822, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 1824, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 1826, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 1828, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 1830, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 1832, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 1834, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 1836, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 1838, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 1840, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 1842, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 1844, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 1846, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 1848, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 1850, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 1852, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 1854, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 1856, because occupancy 0.500 <= existing 0.500 in 1z7aA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2325, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 2329, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 2331, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 2333, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 2335, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 2384, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 2388, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 2390, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 2392, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 2394, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 2396, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 2398, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 2400, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 2444, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 2448, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 2450, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 2452, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 2454, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 2456, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 2458, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 2460, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 2507, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 2509, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 2511, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 2513, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 2515, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 2517, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 2519, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 2521, because occupancy 0.500 <= existing 0.500 in 1z7aA Skipped atom 2523, because occupancy 0.500 <= existing 0.500 in 1z7aA # T0325 read from 1z7aA/T0325-1z7aA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z7aA read from 1z7aA/T0325-1z7aA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1z7aA to template set # found chain 1z7aA in template set Warning: unaligning (T0325)S34 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1z7aA)T98 Warning: unaligning (T0325)T35 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1z7aA)T98 Warning: unaligning (T0325)R159 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1z7aA)D190 Warning: unaligning (T0325)S160 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1z7aA)D190 Warning: unaligning (T0325)D185 because of BadResidue code BAD_PEPTIDE in next template residue (1z7aA)G225 Warning: unaligning (T0325)K186 because of BadResidue code BAD_PEPTIDE at template residue (1z7aA)G225 T0325 17 :PAVTQGIIEAHKRGVVT 1z7aA 80 :RAGVWRLLKLFKRRNVP T0325 36 :TALPTSPYFL 1z7aA 99 :VFAVAMAAQR T0325 46 :EAMESARI 1z7aA 111 :EVIRAMVA T0325 56 :PTLAIGV 1z7aA 119 :DGHEICS T0325 70 :QAKPILP 1z7aA 126 :HGYRWID T0325 97 :EEKVNLEEVYNEWDAQIISFMKS 1z7aA 133 :YQYMDEAQEREHMLEAIRILTEL T0325 120 :GRRPDHIDS 1z7aA 157 :GQRPVGWYT T0325 133 :HGKNKKLLGVALAL 1z7aA 166 :GRTGPNTRRLVMEE T0325 151 :QLPLRNAS 1z7aA 181 :GFLYDSDT T0325 161 :IET 1z7aA 191 :DDL T0325 171 :QDVRTPDEM 1z7aA 213 :LDTNDMRFT T0325 181 :Y 1z7aA 222 :Q T0325 184 :Y 1z7aA 223 :V T0325 187 :AISTETILQLL 1z7aA 226 :FNNGEQFFQYL T0325 198 :DMV 1z7aA 241 :DVL T0325 201 :VCSEGE 1z7aA 245 :EEGATA T0325 207 :VFEINCHPAFIDTI 1z7aA 253 :MLSIGLHCRLIGRP T0325 230 :PRIREVE 1z7aA 267 :ARMAALE T0325 242 :EVKEAIEERGILLA 1z7aA 274 :RFIQYAQSHDKVWF Number of specific fragments extracted= 19 number of extra gaps= 3 total=1186 Will force an alignment to be made, even if fragment is small Number of alignments=77 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z7aA/T0325-1z7aA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1z7aA/T0325-1z7aA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z7aA read from 1z7aA/T0325-1z7aA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1z7aA in template set Warning: unaligning (T0325)S34 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1z7aA)T98 Warning: unaligning (T0325)T35 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1z7aA)T98 Warning: unaligning (T0325)R159 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1z7aA)D190 Warning: unaligning (T0325)S160 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1z7aA)D190 Warning: unaligning (T0325)Q182 because of BadResidue code BAD_PEPTIDE in next template residue (1z7aA)G225 Warning: unaligning (T0325)F183 because of BadResidue code BAD_PEPTIDE at template residue (1z7aA)G225 T0325 17 :PAVTQGIIEAHKRGVVT 1z7aA 80 :RAGVWRLLKLFKRRNVP T0325 36 :TALPTSPYFL 1z7aA 99 :VFAVAMAAQR T0325 46 :EAMESARI 1z7aA 111 :EVIRAMVA T0325 56 :PTLAIGV 1z7aA 119 :DGHEICS T0325 70 :QAKPILPR 1z7aA 126 :HGYRWIDY T0325 98 :EKVNLEEVYNEWDAQIISFMKS 1z7aA 134 :QYMDEAQEREHMLEAIRILTEL T0325 120 :GRRPDHIDS 1z7aA 157 :GQRPVGWYT T0325 133 :HGKNKKLLGVALAL 1z7aA 166 :GRTGPNTRRLVMEE T0325 151 :QLPLRNAS 1z7aA 181 :GFLYDSDT T0325 161 :IE 1z7aA 191 :DD T0325 171 :QDVRTPDEMLY 1z7aA 213 :LDTNDMRFTQV T0325 184 :Y 1z7aA 226 :F T0325 188 :ISTETILQLLDMVVCS 1z7aA 227 :NNGEQFFQYLKDAFDV T0325 204 :EGE 1z7aA 248 :ATA T0325 207 :VFEINCHPAFIDTI 1z7aA 253 :MLSIGLHCRLIGRP T0325 230 :PRIREVE 1z7aA 267 :ARMAALE T0325 242 :EVKEAIEERGILLA 1z7aA 274 :RFIQYAQSHDKVWF Number of specific fragments extracted= 17 number of extra gaps= 3 total=1203 Will force an alignment to be made, even if fragment is small Number of alignments=78 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z7aA/T0325-1z7aA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1z7aA/T0325-1z7aA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z7aA read from 1z7aA/T0325-1z7aA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1z7aA in template set Warning: unaligning (T0325)S34 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1z7aA)T98 Warning: unaligning (T0325)T35 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1z7aA)T98 Warning: unaligning (T0325)F183 because of BadResidue code BAD_PEPTIDE in next template residue (1z7aA)G225 Warning: unaligning (T0325)Y184 because of BadResidue code BAD_PEPTIDE at template residue (1z7aA)G225 T0325 17 :PAVTQGIIEAHKRGVVT 1z7aA 80 :RAGVWRLLKLFKRRNVP T0325 36 :TALPTSPYFL 1z7aA 99 :VFAVAMAAQR T0325 46 :EAMESARI 1z7aA 111 :EVIRAMVA T0325 56 :PTLAIGVH 1z7aA 119 :DGHEICSH T0325 69 :NQAKPIL 1z7aA 127 :GYRWIDY T0325 98 :EKVNLEEVYNEWDAQIISFMK 1z7aA 134 :QYMDEAQEREHMLEAIRILTE T0325 119 :SGRRPDHIDS 1z7aA 156 :TGQRPVGWYT T0325 132 :VHGK 1z7aA 166 :GRTG T0325 137 :KKLLGVALAL 1z7aA 170 :PNTRRLVMEE T0325 170 :YQDVRTPDEMLYQ 1z7aA 211 :YTLDTNDMRFTQV T0325 185 :D 1z7aA 226 :F T0325 188 :ISTETILQLLDMVV 1z7aA 227 :NNGEQFFQYLKDAF T0325 202 :CSEGEVFEINCHPAFIDTI 1z7aA 248 :ATAPKMLSIGLHCRLIGRP T0325 230 :PRIREVE 1z7aA 267 :ARMAALE T0325 242 :EVKEAIEERGILLA 1z7aA 274 :RFIQYAQSHDKVWF Number of specific fragments extracted= 15 number of extra gaps= 2 total=1218 Will force an alignment to be made, even if fragment is small Number of alignments=79 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b4kA/T0325-1b4kA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1b4kA expands to /projects/compbio/data/pdb/1b4k.pdb.gz 1b4kA:# T0325 read from 1b4kA/T0325-1b4kA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1b4kA read from 1b4kA/T0325-1b4kA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1b4kA to template set # found chain 1b4kA in template set T0325 17 :PAVTQGIIEAHKRGVVTSTTALPT 1b4kA 66 :DQLLIEAEEWVALGIPALALFPVT T0325 43 :YFLEAMESARISAPTLAIGVHLTLT 1b4kA 107 :IAQRATRALRERFPELGIITDVALD T0325 73 :PILPR 1b4kA 132 :PFTTH T0325 79 :MVPSLVDEAGY 1b4kA 137 :GQDGILDDDGY T0325 100 :VNLEEVYNEWDAQIISFMKSGRRPDHIDS 1b4kA 148 :VLNDVSIDVLVRQALSHAEAGAQVVAPSD T0325 135 :KNKKLLGVALALARKYQLPLRNA 1b4kA 177 :MMDGRIGAIREALESAGHTNVRI T0325 158 :SRSIETKDYLELY 1b4kA 205 :KYASAYYGPFRDA T0325 171 :QDVRTPDE 1b4kA 225 :GKGNKATY T0325 183 :FYDKA 1b4kA 233 :QMDPA T0325 189 :STETILQLLDMVVC 1b4kA 238 :NSDEALHEVAADLA T0325 205 :GEVFEINCHPAFID 1b4kA 252 :EGADMVMVKPGMPY T0325 228 :CMPRIREVEIL 1b4kA 266 :LDIVRRVKDEF Number of specific fragments extracted= 12 number of extra gaps= 0 total=1230 Will force an alignment to be made, even if fragment is small Number of alignments=80 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b4kA/T0325-1b4kA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1b4kA/T0325-1b4kA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1b4kA read from 1b4kA/T0325-1b4kA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1b4kA in template set T0325 17 :PAVTQGIIEAHKRG 1b4kA 66 :DQLLIEAEEWVALG T0325 32 :VTSTTALPTSP 1b4kA 80 :IPALALFPVTP T0325 43 :YFLEAMESARISAPTLAIGVHLTLT 1b4kA 107 :IAQRATRALRERFPELGIITDVALD T0325 73 :PILPR 1b4kA 132 :PFTTH T0325 79 :MVPSLVDEAGY 1b4kA 137 :GQDGILDDDGY T0325 100 :VNLEEVYNEWDAQIISFMKSGRRPDHIDS 1b4kA 148 :VLNDVSIDVLVRQALSHAEAGAQVVAPSD T0325 135 :KNKKLLGVALALARKY 1b4kA 177 :MMDGRIGAIREALESA T0325 151 :QLPLRN 1b4kA 196 :NVRIMA T0325 157 :ASRSIETKDYLE 1b4kA 204 :AKYASAYYGPFR T0325 171 :QDVRTPD 1b4kA 225 :GKGNKAT T0325 182 :QFYDKAIS 1b4kA 232 :YQMDPANS T0325 191 :ETILQLLDMVVCS 1b4kA 240 :DEALHEVAADLAE T0325 206 :EVFEINCHPAFI 1b4kA 253 :GADMVMVKPGMP T0325 227 :YCMPRIREVEIL 1b4kA 265 :YLDIVRRVKDEF Number of specific fragments extracted= 14 number of extra gaps= 0 total=1244 Will force an alignment to be made, even if fragment is small Number of alignments=81 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b4kA/T0325-1b4kA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1b4kA/T0325-1b4kA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1b4kA read from 1b4kA/T0325-1b4kA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1b4kA in template set T0325 17 :PAVTQGIIEAHKRG 1b4kA 66 :DQLLIEAEEWVALG T0325 32 :VTSTTALPTSP 1b4kA 80 :IPALALFPVTP T0325 43 :YFLEAMESARISAPTLAIGVHLTL 1b4kA 107 :IAQRATRALRERFPELGIITDVAL T0325 71 :AKPILPREMVPSLVDEAG 1b4kA 131 :DPFTTHGQDGILDDDGYV T0325 101 :NLEEVYNEWDAQIISFMKSGRR 1b4kA 149 :LNDVSIDVLVRQALSHAEAGAQ T0325 125 :HIDSH 1b4kA 171 :VVAPS T0325 133 :HGK 1b4kA 176 :DMM T0325 137 :KKLLGVALALARKYQLPLRNA 1b4kA 179 :DGRIGAIREALESAGHTNVRI T0325 158 :SRSIETKDYLEL 1b4kA 205 :KYASAYYGPFRD T0325 175 :TPDEMLYQFYDKAISTETILQLLDMVVCS 1b4kA 224 :LGKGNKATYQMDPANSDEALHEVAADLAE T0325 206 :EVFEINCHPAFID 1b4kA 253 :GADMVMVKPGMPY T0325 219 :TI 1b4kA 267 :DI T0325 231 :RIREVEI 1b4kA 269 :VRRVKDE Number of specific fragments extracted= 13 number of extra gaps= 0 total=1257 Will force an alignment to be made, even if fragment is small Number of alignments=82 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a53/T0325-1a53-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1a53 expands to /projects/compbio/data/pdb/1a53.pdb.gz 1a53:Warning: there is no chain 1a53 will retry with 1a53A # T0325 read from 1a53/T0325-1a53-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1a53 read from 1a53/T0325-1a53-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1a53 to template set # found chain 1a53 in template set T0325 18 :AVTQGIIEAHKRGVVTSTTALPT 1a53 32 :SLNERILEFNKRNITAIIAEYKR T0325 44 :FLEAMESAR 1a53 66 :PIEYSKFME T0325 57 :TLAIGVHLTLT 1a53 75 :RYAVGLSILTE T0325 81 :PS 1a53 86 :EK T0325 97 :EEKVNLEEVYNEW 1a53 88 :YFNGSYETLRKIA T0325 110 :DAQIISFMKSGRRPDHI 1a53 116 :ESQIDDAYNLGADTVLL T0325 131 :NVHGKNKKLLGVALALARKYQLPLRNASR 1a53 133 :IVKILTERELESLLEYARSYGMEPLIEIN T0325 163 :TKDYLELY 1a53 162 :DENDLDIA T0325 171 :QDVRTPDEMLYQFYDKAISTETILQLLDMV 1a53 172 :IGARFIGINSRDLETLEINKENQRKLISMI T0325 204 :EGEVFEINCHPAFID 1a53 202 :PSNVVKVAESGISER T0325 241 :QEV 1a53 217 :NEI T0325 245 :EAIEERGILLA 1a53 220 :EELRKLGVNAF Number of specific fragments extracted= 12 number of extra gaps= 0 total=1269 Will force an alignment to be made, even if fragment is small Number of alignments=83 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a53/T0325-1a53-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1a53/T0325-1a53-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1a53 read from 1a53/T0325-1a53-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1a53 in template set T0325 18 :AVTQGIIEAHKRGVVTSTTALPT 1a53 32 :SLNERILEFNKRNITAIIAEYKR T0325 41 :SPY 1a53 56 :SPS T0325 44 :FLEAMESAR 1a53 66 :PIEYSKFME T0325 57 :TLAIGVHLTLT 1a53 75 :RYAVGLSILTE T0325 81 :PSLV 1a53 86 :EKYF T0325 99 :KVNLEEVYNEW 1a53 90 :NGSYETLRKIA T0325 110 :DAQIISFMKSGRRPDHI 1a53 116 :ESQIDDAYNLGADTVLL T0325 131 :NVHGKNKKLLGVALALARKYQLPLRNASRSIETKDYLE 1a53 133 :IVKILTERELESLLEYARSYGMEPLIEINDENDLDIAL T0325 171 :QDVRTPDEMLYQFYDKAISTETILQLLDMV 1a53 172 :IGARFIGINSRDLETLEINKENQRKLISMI T0325 204 :EGEVFEINCHP 1a53 202 :PSNVVKVAESG T0325 217 :IDT 1a53 213 :ISE T0325 240 :SQEVKE 1a53 216 :RNEIEE T0325 247 :IEERGILLA 1a53 222 :LRKLGVNAF Number of specific fragments extracted= 13 number of extra gaps= 0 total=1282 Will force an alignment to be made, even if fragment is small Number of alignments=84 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a53/T0325-1a53-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1a53/T0325-1a53-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1a53 read from 1a53/T0325-1a53-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1a53 in template set T0325 19 :VTQGIIEAHKRGVVTSTTALPT 1a53 33 :LNERILEFNKRNITAIIAEYKR T0325 44 :FLEAMESARI 1a53 66 :PIEYSKFMER T0325 58 :LAIGVHLT 1a53 76 :YAVGLSIL T0325 67 :TLN 1a53 84 :TEE T0325 86 :E 1a53 87 :K T0325 97 :EEKVNLEEVYNEW 1a53 88 :YFNGSYETLRKIA T0325 110 :DAQIISFMKSGRRPDHI 1a53 116 :ESQIDDAYNLGADTVLL T0325 131 :NVHGKNKKLLGVALALARKYQLPLRNASRSIETKDYLEL 1a53 133 :IVKILTERELESLLEYARSYGMEPLIEINDENDLDIALR T0325 170 :YQDVRT 1a53 182 :RDLETL T0325 190 :TETILQLLDMVVCSEGEVFEINCHPAFID 1a53 188 :EINKENQRKLISMIPSNVVKVAESGISER T0325 241 :QEVKE 1a53 217 :NEIEE T0325 247 :IEERGILLA 1a53 222 :LRKLGVNAF Number of specific fragments extracted= 12 number of extra gaps= 0 total=1294 Will force an alignment to be made, even if fragment is small Number of alignments=85 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wraA/T0325-1wraA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1wraA expands to /projects/compbio/data/pdb/1wra.pdb.gz 1wraA:Skipped atom 863, because occupancy 0.500 <= existing 0.500 in 1wraA Skipped atom 2168, because occupancy 0.500 <= existing 0.500 in 1wraA Skipped atom 2170, because occupancy 0.500 <= existing 0.500 in 1wraA Skipped atom 2172, because occupancy 0.500 <= existing 0.500 in 1wraA Skipped atom 2174, because occupancy 0.500 <= existing 0.500 in 1wraA Skipped atom 2176, because occupancy 0.500 <= existing 0.500 in 1wraA Skipped atom 2178, because occupancy 0.500 <= existing 0.500 in 1wraA # T0325 read from 1wraA/T0325-1wraA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wraA read from 1wraA/T0325-1wraA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1wraA to template set # found chain 1wraA in template set Warning: unaligning (T0325)V31 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1wraA)K102 Warning: unaligning (T0325)L58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1wraA)P127 Warning: unaligning (T0325)A59 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1wraA)P127 Warning: unaligning (T0325)G61 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1wraA)R130 Warning: unaligning (T0325)V62 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1wraA)R130 Warning: unaligning (T0325)L75 because of BadResidue code BAD_PEPTIDE in next template residue (1wraA)S137 Warning: unaligning (T0325)P76 because of BadResidue code BAD_PEPTIDE at template residue (1wraA)S137 Warning: unaligning (T0325)F90 because of BadResidue code BAD_PEPTIDE in next template residue (1wraA)D149 Warning: unaligning (T0325)K135 because of BadResidue code BAD_PEPTIDE at template residue (1wraA)D149 Warning: unaligning (T0325)L140 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1wraA)D155 Warning: unaligning (T0325)G141 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1wraA)D155 Warning: unaligning (T0325)S160 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1wraA)G175 Warning: unaligning (T0325)I161 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1wraA)G175 Warning: unaligning (T0325)E162 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1wraA)D176 Warning: unaligning (T0325)I188 because of BadResidue code BAD_PEPTIDE in next template residue (1wraA)T262 Warning: unaligning (T0325)S189 because of BadResidue code BAD_PEPTIDE at template residue (1wraA)T262 Warning: unaligning (T0325)L221 because of BadResidue code BAD_PEPTIDE in next template residue (1wraA)W283 Warning: unaligning (T0325)Q222 because of BadResidue code BAD_PEPTIDE at template residue (1wraA)W283 T0325 20 :TQGIIEAHKRG 1wraA 88 :TDRVFRRLKEL T0325 32 :VTSTTALPTSPYFL 1wraA 103 :LDFILVTHTHSDHI T0325 46 :EAMESAR 1wraA 118 :NVDELLS T0325 57 :T 1wraA 125 :T T0325 60 :I 1wraA 128 :V T0325 64 :LTLT 1wraA 131 :VYLK T0325 74 :I 1wraA 135 :K T0325 77 :REMVPS 1wraA 138 :DSRITN T0325 86 :EAGY 1wraA 144 :SERL T0325 136 :NKKL 1wraA 150 :NLYG T0325 142 :VALALARKYQLPLRNASR 1wraA 156 :KVLQTATETGVSVIQNIT T0325 181 :YQFYDKA 1wraA 254 :HHDTNKS T0325 190 :TETI 1wraA 263 :KDFI T0325 198 :DMV 1wraA 267 :KNL T0325 204 :EGEVF 1wraA 270 :SPSLI T0325 210 :IN 1wraA 275 :VQ T0325 216 :FIDTI 1wraA 277 :TSDSL T0325 223 :NQS 1wraA 284 :KNG T0325 239 :TSQEVKEAIEERGILLANY 1wraA 287 :VDSEYVNWLKERGIERINA Number of specific fragments extracted= 19 number of extra gaps= 9 total=1313 Will force an alignment to be made, even if fragment is small Number of alignments=86 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wraA/T0325-1wraA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1wraA/T0325-1wraA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wraA read from 1wraA/T0325-1wraA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wraA in template set Warning: unaligning (T0325)V31 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1wraA)K102 Warning: unaligning (T0325)L58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1wraA)P127 Warning: unaligning (T0325)A59 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1wraA)P127 Warning: unaligning (T0325)G61 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1wraA)R130 Warning: unaligning (T0325)V62 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1wraA)R130 Warning: unaligning (T0325)L75 because of BadResidue code BAD_PEPTIDE in next template residue (1wraA)S137 Warning: unaligning (T0325)P76 because of BadResidue code BAD_PEPTIDE at template residue (1wraA)S137 Warning: unaligning (T0325)G134 because of BadResidue code BAD_PEPTIDE in next template residue (1wraA)D149 Warning: unaligning (T0325)K135 because of BadResidue code BAD_PEPTIDE at template residue (1wraA)D149 Warning: unaligning (T0325)L140 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1wraA)D155 Warning: unaligning (T0325)G141 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1wraA)D155 Warning: unaligning (T0325)S160 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1wraA)G175 Warning: unaligning (T0325)I161 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1wraA)G175 Warning: unaligning (T0325)E162 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1wraA)D176 Warning: unaligning (T0325)I188 because of BadResidue code BAD_PEPTIDE in next template residue (1wraA)T262 Warning: unaligning (T0325)S189 because of BadResidue code BAD_PEPTIDE at template residue (1wraA)T262 Warning: unaligning (T0325)L221 because of BadResidue code BAD_PEPTIDE in next template residue (1wraA)W283 Warning: unaligning (T0325)Q222 because of BadResidue code BAD_PEPTIDE at template residue (1wraA)W283 T0325 20 :TQGIIEAHKRG 1wraA 88 :TDRVFRRLKEL T0325 32 :VTSTTALPTSPYFL 1wraA 103 :LDFILVTHTHSDHI T0325 46 :EAMESAR 1wraA 118 :NVDELLS T0325 57 :T 1wraA 125 :T T0325 60 :I 1wraA 128 :V T0325 64 :LTLT 1wraA 131 :VYLK T0325 74 :I 1wraA 135 :K T0325 77 :REMVPS 1wraA 138 :DSRITN T0325 86 :EAGY 1wraA 144 :SERL T0325 136 :NKKL 1wraA 150 :NLYG T0325 142 :VALALARKYQLPLRNASR 1wraA 156 :KVLQTATETGVSVIQNIT T0325 180 :LYQFYDKA 1wraA 253 :HHHDTNKS T0325 190 :TE 1wraA 263 :KD T0325 196 :LLDMV 1wraA 265 :FIKNL T0325 204 :EGEVFEINC 1wraA 270 :SPSLIVQTS T0325 218 :DTI 1wraA 279 :DSL T0325 223 :N 1wraA 284 :K T0325 225 :SG 1wraA 285 :NG T0325 239 :TSQEVKEAIEERGILLANY 1wraA 287 :VDSEYVNWLKERGIERINA Number of specific fragments extracted= 19 number of extra gaps= 9 total=1332 Will force an alignment to be made, even if fragment is small Number of alignments=87 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wraA/T0325-1wraA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1wraA/T0325-1wraA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wraA read from 1wraA/T0325-1wraA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wraA in template set Warning: unaligning (T0325)Y89 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1wraA)E77 Warning: unaligning (T0325)R121 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1wraA)K102 Warning: unaligning (T0325)R122 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1wraA)K102 Warning: unaligning (T0325)L140 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1wraA)D155 Warning: unaligning (T0325)G141 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1wraA)D155 Warning: unaligning (T0325)S160 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1wraA)G175 Warning: unaligning (T0325)I161 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1wraA)G175 Warning: unaligning (T0325)E162 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1wraA)D176 Warning: unaligning (T0325)T163 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1wraA)H178 Warning: unaligning (T0325)E168 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1wraA)H178 Warning: unaligning (T0325)L169 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1wraA)Q180 Warning: unaligning (T0325)M179 because of BadResidue code BAD_PEPTIDE in next template residue (1wraA)T262 Warning: unaligning (T0325)I193 because of BadResidue code BAD_PEPTIDE at template residue (1wraA)T262 Warning: unaligning (T0325)F216 because of BadResidue code BAD_PEPTIDE in next template residue (1wraA)W283 Warning: unaligning (T0325)I217 because of BadResidue code BAD_PEPTIDE at template residue (1wraA)W283 T0325 78 :EMVPSLVDEAG 1wraA 65 :FPDGSDSRYPW T0325 96 :FEEKVNLEEVYNEWDA 1wraA 82 :SYKHVLTDRVFRRLKE T0325 119 :SG 1wraA 98 :LS T0325 123 :PDHID 1wraA 103 :LDFIL T0325 128 :SHHNVHGKN 1wraA 109 :THTHSDHIG T0325 142 :VALALARKYQLPLRNASR 1wraA 156 :KVLQTATETGVSVIQNIT T0325 176 :PDE 1wraA 258 :NKS T0325 194 :LQLLD 1wraA 263 :KDFIK T0325 202 :CSEGEVFEINCHPA 1wraA 268 :NLSPSLIVQTSDSL T0325 218 :DT 1wraA 284 :KN T0325 225 :S 1wraA 286 :G T0325 239 :TSQEVKEAIEERGILLANY 1wraA 287 :VDSEYVNWLKERGIERINA Number of specific fragments extracted= 12 number of extra gaps= 6 total=1344 Will force an alignment to be made, even if fragment is small Number of alignments=88 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xg5A/T0325-1xg5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xg5A expands to /projects/compbio/data/pdb/1xg5.pdb.gz 1xg5A:Skipped atom 494, because occupancy 0.350 <= existing 0.650 in 1xg5A Skipped atom 496, because occupancy 0.350 <= existing 0.650 in 1xg5A Skipped atom 498, because occupancy 0.350 <= existing 0.650 in 1xg5A Skipped atom 500, because occupancy 0.350 <= existing 0.650 in 1xg5A Skipped atom 584, because occupancy 0.500 <= existing 0.500 in 1xg5A Skipped atom 588, because occupancy 0.500 <= existing 0.500 in 1xg5A Skipped atom 590, because occupancy 0.500 <= existing 0.500 in 1xg5A Skipped atom 728, because occupancy 0.350 <= existing 0.650 in 1xg5A Skipped atom 730, because occupancy 0.350 <= existing 0.650 in 1xg5A Skipped atom 732, because occupancy 0.350 <= existing 0.650 in 1xg5A Skipped atom 734, because occupancy 0.350 <= existing 0.650 in 1xg5A Skipped atom 736, because occupancy 0.350 <= existing 0.650 in 1xg5A Skipped atom 738, because occupancy 0.350 <= existing 0.650 in 1xg5A Skipped atom 1237, because occupancy 0.500 <= existing 0.500 in 1xg5A Skipped atom 1241, because occupancy 0.500 <= existing 0.500 in 1xg5A Skipped atom 1243, because occupancy 0.500 <= existing 0.500 in 1xg5A Skipped atom 1452, because occupancy 0.500 <= existing 0.500 in 1xg5A Skipped atom 1456, because occupancy 0.500 <= existing 0.500 in 1xg5A Skipped atom 1458, because occupancy 0.500 <= existing 0.500 in 1xg5A Skipped atom 1769, because occupancy 0.350 <= existing 0.650 in 1xg5A Skipped atom 1771, because occupancy 0.350 <= existing 0.650 in 1xg5A # T0325 read from 1xg5A/T0325-1xg5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xg5A read from 1xg5A/T0325-1xg5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xg5A to template set # found chain 1xg5A in template set Warning: unaligning (T0325)A47 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1xg5A)A52 Warning: unaligning (T0325)M48 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1xg5A)A52 Warning: unaligning (T0325)G61 because of BadResidue code BAD_PEPTIDE in next template residue (1xg5A)P66 Warning: unaligning (T0325)V62 because of BadResidue code BAD_PEPTIDE at template residue (1xg5A)P66 Warning: unaligning (T0325)I210 because of BadResidue code BAD_PEPTIDE in next template residue (1xg5A)C195 Warning: unaligning (T0325)N211 because of BadResidue code BAD_PEPTIDE at template residue (1xg5A)C195 Warning: unaligning (T0325)P214 because of BadResidue code BAD_PEPTIDE in next template residue (1xg5A)G199 Warning: unaligning (T0325)A215 because of BadResidue code BAD_PEPTIDE at template residue (1xg5A)G199 Warning: unaligning (T0325)I237 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xg5A)C226 T0325 3 :NKKLIIN 1xg5A 11 :DRLALVT T0325 14 :GYTPAVTQGIIEAHKRGVVTSTTALPTSPYFLE 1xg5A 18 :GASGGIGAAVARALVQQGLKVVGCARTVGNIEE T0325 49 :ESARISAPTLAI 1xg5A 53 :AECKSAGYPGTL T0325 66 :LT 1xg5A 67 :YR T0325 81 :PSLVD 1xg5A 69 :CDLSN T0325 106 :YNEWDAQIISFMKSGRRPD 1xg5A 74 :EEDILSMFSAIRSQHSGVD T0325 125 :HIDS 1xg5A 94 :CINN T0325 131 :NVHGKNKKLLGVALALARKYQLP 1xg5A 120 :VNVLALSICTREAYQSMKERNVD T0325 154 :LRNA 1xg5A 148 :NINS T0325 168 :ELYQDVRTPDEMLYQF 1xg5A 152 :MSGHRVLPLSVTHFYS T0325 190 :TETILQLLDMVVCSEGEVFE 1xg5A 174 :TALTEGLRQELREAQTHIRA T0325 212 :CH 1xg5A 196 :IS T0325 216 :FID 1xg5A 200 :VVE T0325 219 :TILQNQSGYCMPRIREV 1xg5A 204 :QFAFKLHDKDPEKAAAT T0325 238 :LTSQEVKEAIEE 1xg5A 227 :LKPEDVAEAVIY Number of specific fragments extracted= 15 number of extra gaps= 4 total=1359 Will force an alignment to be made, even if fragment is small Number of alignments=89 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xg5A/T0325-1xg5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1xg5A/T0325-1xg5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xg5A read from 1xg5A/T0325-1xg5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xg5A in template set Warning: unaligning (T0325)A47 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1xg5A)A52 Warning: unaligning (T0325)M48 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1xg5A)A52 Warning: unaligning (T0325)G61 because of BadResidue code BAD_PEPTIDE in next template residue (1xg5A)P66 Warning: unaligning (T0325)V62 because of BadResidue code BAD_PEPTIDE at template residue (1xg5A)P66 Warning: unaligning (T0325)I210 because of BadResidue code BAD_PEPTIDE in next template residue (1xg5A)C195 Warning: unaligning (T0325)N211 because of BadResidue code BAD_PEPTIDE at template residue (1xg5A)C195 Warning: unaligning (T0325)P214 because of BadResidue code BAD_PEPTIDE in next template residue (1xg5A)G199 Warning: unaligning (T0325)A215 because of BadResidue code BAD_PEPTIDE at template residue (1xg5A)G199 Warning: unaligning (T0325)I237 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xg5A)C226 T0325 3 :NKKLIIN 1xg5A 11 :DRLALVT T0325 14 :GYTPAVTQGIIEAHKRGVVTSTTALPTSPYFLE 1xg5A 18 :GASGGIGAAVARALVQQGLKVVGCARTVGNIEE T0325 49 :ESARISAPTLAI 1xg5A 53 :AECKSAGYPGTL T0325 66 :LT 1xg5A 67 :YR T0325 81 :PSLVD 1xg5A 69 :CDLSN T0325 106 :YNEWDAQIISFMKSGRRPD 1xg5A 74 :EEDILSMFSAIRSQHSGVD T0325 125 :HIDS 1xg5A 94 :CINN T0325 131 :NVHGKNKKLLGVALALARKYQLP 1xg5A 120 :VNVLALSICTREAYQSMKERNVD T0325 154 :LRNASRSIETKDYLELY 1xg5A 148 :NINSMSGHRVLPLSVTH T0325 175 :TPDEMLYQF 1xg5A 165 :FYSATKYAV T0325 190 :TETILQLLDMVVCSEGEVFE 1xg5A 174 :TALTEGLRQELREAQTHIRA T0325 212 :CH 1xg5A 196 :IS T0325 216 :FID 1xg5A 200 :VVE T0325 219 :TILQN 1xg5A 204 :QFAFK T0325 224 :QSGYCMPRIREV 1xg5A 210 :HDKDPEKAAATY T0325 238 :LTSQEVKEAIEE 1xg5A 227 :LKPEDVAEAVIY Number of specific fragments extracted= 16 number of extra gaps= 4 total=1375 Will force an alignment to be made, even if fragment is small Number of alignments=90 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xg5A/T0325-1xg5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1xg5A/T0325-1xg5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xg5A read from 1xg5A/T0325-1xg5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xg5A in template set Warning: unaligning (T0325)A47 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1xg5A)A52 Warning: unaligning (T0325)M48 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1xg5A)A52 Warning: unaligning (T0325)G61 because of BadResidue code BAD_PEPTIDE in next template residue (1xg5A)P66 Warning: unaligning (T0325)V62 because of BadResidue code BAD_PEPTIDE at template residue (1xg5A)P66 Warning: unaligning (T0325)I210 because of BadResidue code BAD_PEPTIDE in next template residue (1xg5A)C195 Warning: unaligning (T0325)N211 because of BadResidue code BAD_PEPTIDE at template residue (1xg5A)C195 Warning: unaligning (T0325)P214 because of BadResidue code BAD_PEPTIDE in next template residue (1xg5A)G199 Warning: unaligning (T0325)A215 because of BadResidue code BAD_PEPTIDE at template residue (1xg5A)G199 Warning: unaligning (T0325)I237 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xg5A)C226 T0325 3 :NKKLIIN 1xg5A 11 :DRLALVT T0325 14 :GYTPAVTQGIIEAHKRGVVTSTTALPTSPYFLE 1xg5A 18 :GASGGIGAAVARALVQQGLKVVGCARTVGNIEE T0325 49 :ESARISAPTLAI 1xg5A 53 :AECKSAGYPGTL T0325 63 :H 1xg5A 67 :Y T0325 78 :EMVPS 1xg5A 68 :RCDLS T0325 101 :NLE 1xg5A 73 :NEE T0325 108 :EWDAQIISFMKSGRRPDH 1xg5A 76 :DILSMFSAIRSQHSGVDI T0325 126 :IDS 1xg5A 95 :INN T0325 139 :LLGVALALARKYQLP 1xg5A 128 :CTREAYQSMKERNVD T0325 170 :YQDVRTPDEMLYQFYDKAISTETILQLLDMVVCSEGEVFE 1xg5A 154 :GHRVLPLSVTHFYSATKYAVTALTEGLRQELREAQTHIRA T0325 212 :CH 1xg5A 196 :IS T0325 216 :FID 1xg5A 200 :VVE T0325 219 :TILQNQSGYCMPRIREV 1xg5A 204 :QFAFKLHDKDPEKAAAT T0325 238 :LTSQEVKEAIEE 1xg5A 227 :LKPEDVAEAVIY Number of specific fragments extracted= 14 number of extra gaps= 4 total=1389 Will force an alignment to be made, even if fragment is small Number of alignments=91 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gzgA/T0325-1gzgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1gzgA expands to /projects/compbio/data/pdb/1gzg.pdb.gz 1gzgA:Skipped atom 233, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 235, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 237, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 239, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 241, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 243, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 245, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 262, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 264, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 266, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 268, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 270, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 272, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 274, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 323, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 325, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 327, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 329, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 331, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 333, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 335, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 419, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 421, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 423, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 425, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 427, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 429, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 575, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 577, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 579, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 581, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 583, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 585, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 587, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 1241, because occupancy 0.200 <= existing 0.800 in 1gzgA Skipped atom 1243, because occupancy 0.200 <= existing 0.800 in 1gzgA Skipped atom 1245, because occupancy 0.200 <= existing 0.800 in 1gzgA Skipped atom 1247, because occupancy 0.200 <= existing 0.800 in 1gzgA Skipped atom 1249, because occupancy 0.200 <= existing 0.800 in 1gzgA Skipped atom 1251, because occupancy 0.200 <= existing 0.800 in 1gzgA Skipped atom 1253, because occupancy 0.200 <= existing 0.800 in 1gzgA Skipped atom 1255, because occupancy 0.200 <= existing 0.800 in 1gzgA Skipped atom 1257, because occupancy 0.200 <= existing 0.800 in 1gzgA Skipped atom 1259, because occupancy 0.200 <= existing 0.800 in 1gzgA Skipped atom 1261, because occupancy 0.200 <= existing 0.800 in 1gzgA Skipped atom 1453, because occupancy 0.200 <= existing 0.800 in 1gzgA Skipped atom 1455, because occupancy 0.200 <= existing 0.800 in 1gzgA Skipped atom 1457, because occupancy 0.200 <= existing 0.800 in 1gzgA Skipped atom 1459, because occupancy 0.200 <= existing 0.800 in 1gzgA Skipped atom 1461, because occupancy 0.200 <= existing 0.800 in 1gzgA Skipped atom 1463, because occupancy 0.200 <= existing 0.800 in 1gzgA Skipped atom 1465, because occupancy 0.200 <= existing 0.800 in 1gzgA Skipped atom 1491, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 1493, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 1495, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 1497, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 1499, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 1501, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 2021, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 2023, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 2025, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 2027, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 2029, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 2031, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 2033, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 2035, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 2116, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 2118, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 2120, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 2122, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 2124, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 2126, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 2128, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 2130, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 2132, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 2162, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 2164, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 2166, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 2168, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 2170, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 2172, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 2174, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 2176, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 2178, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 2180, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 2182, because occupancy 0.500 <= existing 0.500 in 1gzgA # T0325 read from 1gzgA/T0325-1gzgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gzgA read from 1gzgA/T0325-1gzgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1gzgA to template set # found chain 1gzgA in template set Warning: unaligning (T0325)S158 because of BadResidue code BAD_PEPTIDE at template residue (1gzgA)K205 Warning: unaligning (T0325)C212 because of BadResidue code BAD_PEPTIDE in next template residue (1gzgA)K260 Warning: unaligning (T0325)H213 because of BadResidue code BAD_PEPTIDE at template residue (1gzgA)K260 Warning: unaligning (T0325)P214 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gzgA)P261 T0325 17 :PAVTQGIIEAHKRGVVTSTTALPT 1gzgA 66 :DQLLIEAEEWVALGIPALALFPVT T0325 43 :YFLEAMESARISAPTLAIGVHLTLT 1gzgA 107 :IAQRATRALRERFPELGIITDVALD T0325 73 :PILPR 1gzgA 132 :PFTTH T0325 79 :MVPSLVDEAGYF 1gzgA 137 :GQNGILDDDGYV T0325 101 :NLEEVYNEWDAQIISFMKSGRRPDHIDS 1gzgA 149 :LNDVSIDVLVRQALSHAEAGAQVVAPSD T0325 135 :KNKKLLGVALALARKYQLPLRNA 1gzgA 177 :MMDGRIGAIREALESAGHTNVRV T0325 159 :RSIETKDYLELY 1gzgA 206 :YASAYYGPFRDA T0325 171 :QDVRTPDE 1gzgA 225 :GKGNKATY T0325 183 :FYDKA 1gzgA 233 :QMDPA T0325 189 :STETILQLLDMVVC 1gzgA 238 :NSDEALHEVAADLA T0325 205 :GEVFEIN 1gzgA 252 :EGADMVM T0325 215 :AFID 1gzgA 262 :GMPY T0325 229 :MPRIREVEIL 1gzgA 267 :DIVRRVKDEF Number of specific fragments extracted= 13 number of extra gaps= 2 total=1402 Will force an alignment to be made, even if fragment is small Number of alignments=92 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gzgA/T0325-1gzgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1gzgA/T0325-1gzgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gzgA read from 1gzgA/T0325-1gzgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gzgA in template set Warning: unaligning (T0325)A157 because of BadResidue code BAD_PEPTIDE in next template residue (1gzgA)K205 Warning: unaligning (T0325)S158 because of BadResidue code BAD_PEPTIDE at template residue (1gzgA)K205 Warning: unaligning (T0325)C212 because of BadResidue code BAD_PEPTIDE in next template residue (1gzgA)K260 Warning: unaligning (T0325)H213 because of BadResidue code BAD_PEPTIDE at template residue (1gzgA)K260 Warning: unaligning (T0325)P214 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gzgA)P261 T0325 17 :PAVTQGIIEAHKRG 1gzgA 66 :DQLLIEAEEWVALG T0325 32 :VTSTTALPTSP 1gzgA 80 :IPALALFPVTP T0325 43 :YFLEAMESARISAPTLAIGVHLTLT 1gzgA 107 :IAQRATRALRERFPELGIITDVALD T0325 73 :PILPR 1gzgA 132 :PFTTH T0325 79 :MVPSLVDEAGYF 1gzgA 137 :GQNGILDDDGYV T0325 101 :NLEEVYNEWDAQIISFMKSGRRPDHIDS 1gzgA 149 :LNDVSIDVLVRQALSHAEAGAQVVAPSD T0325 135 :KNKKLLGVALALARKY 1gzgA 177 :MMDGRIGAIREALESA T0325 151 :QLPLRN 1gzgA 196 :NVRVMA T0325 159 :RSIETKDYLELY 1gzgA 206 :YASAYYGPFRDA T0325 171 :QDVRTPD 1gzgA 225 :GKGNKAT T0325 182 :QFYDKAIS 1gzgA 232 :YQMDPANS T0325 191 :ETILQLLDMVVCS 1gzgA 240 :DEALHEVAADLAE T0325 206 :EVFEIN 1gzgA 253 :GADMVM T0325 215 :AF 1gzgA 262 :GM T0325 226 :GYCMPRIREVEIL 1gzgA 264 :PYLDIVRRVKDEF Number of specific fragments extracted= 15 number of extra gaps= 2 total=1417 Will force an alignment to be made, even if fragment is small Number of alignments=93 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gzgA/T0325-1gzgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1gzgA/T0325-1gzgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gzgA read from 1gzgA/T0325-1gzgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gzgA in template set Warning: unaligning (T0325)S158 because of BadResidue code BAD_PEPTIDE at template residue (1gzgA)K205 Warning: unaligning (T0325)C212 because of BadResidue code BAD_PEPTIDE in next template residue (1gzgA)K260 Warning: unaligning (T0325)H213 because of BadResidue code BAD_PEPTIDE at template residue (1gzgA)K260 Warning: unaligning (T0325)P214 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gzgA)P261 T0325 17 :PAVTQGIIEAHKRGV 1gzgA 66 :DQLLIEAEEWVALGI T0325 33 :TSTTALPTSP 1gzgA 81 :PALALFPVTP T0325 43 :YFLEAMESARISAPTLAIGVHLTL 1gzgA 107 :IAQRATRALRERFPELGIITDVAL T0325 69 :NQ 1gzgA 131 :DP T0325 73 :PILPREMVPSLVDEAG 1gzgA 133 :FTTHGQNGILDDDGYV T0325 101 :NLEEVYNEWDAQIISFMKSGRRP 1gzgA 149 :LNDVSIDVLVRQALSHAEAGAQV T0325 126 :IDSH 1gzgA 172 :VAPS T0325 133 :HGK 1gzgA 176 :DMM T0325 137 :KKLLGVALALARKYQLPLRNA 1gzgA 179 :DGRIGAIREALESAGHTNVRV T0325 159 :RSIETKDYLEL 1gzgA 206 :YASAYYGPFRD T0325 175 :TPDEMLYQFYDKAISTETILQLLDMVVCS 1gzgA 224 :LGKGNKATYQMDPANSDEALHEVAADLAE T0325 206 :EVFEIN 1gzgA 253 :GADMVM T0325 215 :AFID 1gzgA 262 :GMPY T0325 219 :TI 1gzgA 267 :DI T0325 231 :RIREVEI 1gzgA 269 :VRRVKDE Number of specific fragments extracted= 15 number of extra gaps= 2 total=1432 Will force an alignment to be made, even if fragment is small Number of alignments=94 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1oltA/T0325-1oltA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1oltA expands to /projects/compbio/data/pdb/1olt.pdb.gz 1oltA:Skipped atom 28, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 30, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 32, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 34, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 36, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 38, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 40, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 42, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 116, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 118, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 120, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 122, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 124, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 126, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 128, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 130, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 132, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 134, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 136, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 138, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 140, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 142, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 144, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 146, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 148, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 150, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 152, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 154, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 156, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 158, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 160, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 162, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 164, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 272, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 274, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 276, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 278, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 280, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 282, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 284, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 286, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 288, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 340, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 341, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 343, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 344, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 346, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 347, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 349, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 350, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 352, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 353, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 355, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 356, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 358, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 359, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 361, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 362, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 364, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 365, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 367, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 368, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 370, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 371, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 392, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 394, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 396, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 398, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 400, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 402, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 404, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 406, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 408, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 577, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 579, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 581, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 583, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 585, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 587, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 589, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 591, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 593, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 595, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 597, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 599, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 601, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 603, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 605, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 607, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 609, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 611, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 613, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 615, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 617, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 619, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 621, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 859, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 861, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 863, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 865, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 867, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 869, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 871, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 873, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 875, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 877, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 879, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 904, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 906, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 908, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 910, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 912, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 914, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 916, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 918, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 920, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 1071, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 1073, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 1075, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 1077, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 1079, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 1081, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 1083, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 1085, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 1087, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 1089, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 1091, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 1093, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 1095, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 1097, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 1099, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 1101, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 1103, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 1206, because occupancy 0.700 <= existing 0.700 in 1oltA Skipped atom 1208, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 1210, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 1212, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 1214, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 1216, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 1218, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 1220, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 1222, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 1305, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 1307, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 1309, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 1311, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 1313, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 1315, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 1317, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 1319, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 1321, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 1428, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 1430, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 1432, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 1434, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 1436, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 1438, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 1440, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 1442, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 1444, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 1446, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 1448, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 1450, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 1452, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 1454, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 1456, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 1458, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 1460, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 1462, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 1464, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 1472, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 1474, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 1476, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 1478, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 1480, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 1482, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 1484, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 1486, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 1569, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 1571, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 1573, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 1575, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 1577, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 1579, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 1581, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 1583, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 1585, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 1587, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 1589, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 1720, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 1722, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 1724, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 1726, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 1728, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 1730, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 1732, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 1734, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 1762, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 1764, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 1766, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 1768, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 1770, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 1772, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 1774, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 1776, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 1778, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 1810, because occupancy 0.400 <= existing 0.600 in 1oltA Skipped atom 1812, because occupancy 0.400 <= existing 0.600 in 1oltA Skipped atom 1814, because occupancy 0.400 <= existing 0.600 in 1oltA Skipped atom 1816, because occupancy 0.400 <= existing 0.600 in 1oltA Skipped atom 1818, because occupancy 0.400 <= existing 0.600 in 1oltA Skipped atom 1820, because occupancy 0.400 <= existing 0.600 in 1oltA Skipped atom 1932, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 1934, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 1936, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 1938, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 1940, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 1942, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 1944, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 1946, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 1948, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2007, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 2009, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 2011, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 2012, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 2014, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 2015, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 2017, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 2019, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 2021, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 2022, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 2024, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 2025, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 2027, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 2028, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 2030, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 2031, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 2033, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 2034, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 2048, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2050, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2052, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2054, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2056, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2058, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2060, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2062, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2064, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2097, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 2099, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 2101, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 2103, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 2105, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 2107, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 2109, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 2111, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 2113, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 2115, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 2117, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 2208, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 2210, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 2212, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 2214, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 2216, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 2218, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 2220, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 2222, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 2265, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 2267, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 2269, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 2271, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 2273, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 2275, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 2277, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 2279, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 2281, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 2291, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2293, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2295, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2297, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2299, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2301, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2303, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2305, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2307, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2358, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 2360, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 2362, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 2364, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 2366, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 2368, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 2370, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 2372, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 2374, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 2385, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2387, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2389, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2391, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2393, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2395, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2397, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2399, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2401, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2444, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 2446, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 2448, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 2450, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 2452, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 2454, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 2456, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 2458, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 2460, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 2501, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2503, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2505, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2507, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2509, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2511, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2513, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2578, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2580, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2582, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2584, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2586, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2588, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2590, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2592, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2594, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 2595, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 2597, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 2598, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 2600, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 2601, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 2603, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 2604, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 2606, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 2607, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 2609, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 2610, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 2612, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 2613, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 2615, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 2616, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 2644, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2646, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2648, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2650, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2652, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2654, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2656, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2658, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2660, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2662, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2664, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2673, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 2675, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 2677, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 2679, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 2681, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 2683, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 2685, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 2687, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 2800, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2802, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2804, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2806, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2808, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2810, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2812, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2814, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2922, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2924, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2926, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2928, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2930, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2932, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2934, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 2936, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3008, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 3010, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 3012, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 3014, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 3016, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 3018, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 3020, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 3022, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 3024, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 3026, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 3028, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 3030, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 3063, because occupancy 0.200 <= existing 0.500 in 1oltA Skipped atom 3064, because occupancy 0.300 <= existing 0.500 in 1oltA Skipped atom 3066, because occupancy 0.200 <= existing 0.500 in 1oltA Skipped atom 3067, because occupancy 0.300 <= existing 0.500 in 1oltA Skipped atom 3069, because occupancy 0.200 <= existing 0.500 in 1oltA Skipped atom 3070, because occupancy 0.300 <= existing 0.500 in 1oltA Skipped atom 3072, because occupancy 0.200 <= existing 0.500 in 1oltA Skipped atom 3073, because occupancy 0.300 <= existing 0.500 in 1oltA Skipped atom 3075, because occupancy 0.200 <= existing 0.500 in 1oltA Skipped atom 3076, because occupancy 0.300 <= existing 0.500 in 1oltA Skipped atom 3078, because occupancy 0.200 <= existing 0.500 in 1oltA Skipped atom 3079, because occupancy 0.300 <= existing 0.500 in 1oltA Skipped atom 3081, because occupancy 0.200 <= existing 0.500 in 1oltA Skipped atom 3082, because occupancy 0.300 <= existing 0.500 in 1oltA Skipped atom 3084, because occupancy 0.200 <= existing 0.500 in 1oltA Skipped atom 3085, because occupancy 0.300 <= existing 0.500 in 1oltA Skipped atom 3087, because occupancy 0.200 <= existing 0.500 in 1oltA Skipped atom 3088, because occupancy 0.300 <= existing 0.500 in 1oltA Skipped atom 3090, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 3092, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 3094, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 3096, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 3098, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 3100, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 3102, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 3104, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 3106, because occupancy 0.200 <= existing 0.800 in 1oltA Skipped atom 3125, because occupancy 0.300 <= existing 0.800 in 1oltA Skipped atom 3127, because occupancy 0.300 <= existing 0.800 in 1oltA Skipped atom 3129, because occupancy 0.300 <= existing 0.800 in 1oltA Skipped atom 3131, because occupancy 0.300 <= existing 0.800 in 1oltA Skipped atom 3133, because occupancy 0.300 <= existing 0.800 in 1oltA Skipped atom 3135, because occupancy 0.300 <= existing 0.800 in 1oltA Skipped atom 3137, because occupancy 0.300 <= existing 0.800 in 1oltA Skipped atom 3139, because occupancy 0.300 <= existing 0.800 in 1oltA Skipped atom 3141, because occupancy 0.300 <= existing 0.800 in 1oltA Skipped atom 3272, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3274, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3276, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3278, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3280, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3282, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3284, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3286, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3308, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 3310, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 3312, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 3314, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 3316, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 3318, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 3320, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 3322, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 3324, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 3326, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 3328, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 3352, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3354, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3356, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3358, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3360, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3362, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3364, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3366, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3436, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3438, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3440, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3442, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3444, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3446, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3448, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3450, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3477, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 3478, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 3480, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 3481, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 3483, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 3484, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 3486, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 3487, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 3489, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 3490, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 3492, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 3493, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 3495, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 3496, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 3498, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 3499, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 3501, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 3502, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 3504, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 3505, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 3507, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 3508, because occupancy 0.330 <= existing 0.330 in 1oltA Skipped atom 3568, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3570, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3572, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3574, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3576, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3578, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3580, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3582, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3584, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3649, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 3651, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 3653, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 3655, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 3657, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 3659, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 3661, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 3663, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 3693, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3695, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3697, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3699, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3701, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3703, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3705, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3707, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3709, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3727, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3729, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3731, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3733, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3735, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3737, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3739, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3741, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3743, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3773, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3775, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3777, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3779, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3781, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3783, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3785, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3787, because occupancy 0.500 <= existing 0.500 in 1oltA Skipped atom 3935, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 3937, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 3939, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 3941, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 3943, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 3945, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 3947, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 3949, because occupancy 0.300 <= existing 0.700 in 1oltA Skipped atom 4052, because occupancy 0.400 <= existing 0.400 in 1oltA Skipped atom 4054, because occupancy 0.400 <= existing 0.400 in 1oltA Skipped atom 4056, because occupancy 0.400 <= existing 0.400 in 1oltA Skipped atom 4058, because occupancy 0.400 <= existing 0.400 in 1oltA Skipped atom 4060, because occupancy 0.400 <= existing 0.400 in 1oltA Skipped atom 4062, because occupancy 0.400 <= existing 0.400 in 1oltA Skipped atom 4064, because occupancy 0.400 <= existing 0.400 in 1oltA Skipped atom 4066, because occupancy 0.400 <= existing 0.400 in 1oltA # T0325 read from 1oltA/T0325-1oltA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1oltA read from 1oltA/T0325-1oltA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1oltA to template set # found chain 1oltA in template set Warning: unaligning (T0325)F90 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1oltA)C69 Warning: unaligning (T0325)W91 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1oltA)C69 Warning: unaligning (T0325)S128 because of BadResidue code BAD_PEPTIDE in next template residue (1oltA)G113 Warning: unaligning (T0325)H129 because of BadResidue code BAD_PEPTIDE at template residue (1oltA)G113 Warning: unaligning (T0325)D177 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1oltA)I208 Warning: unaligning (T0325)M179 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1oltA)I208 T0325 45 :LEAMESARISAPTLAIGVHLTLT 1oltA 38 :EQAFLQAVARYPERPLSLYVHIP T0325 70 :Q 1oltA 61 :F T0325 80 :VPSLV 1oltA 62 :CHKLC T0325 89 :Y 1oltA 67 :Y T0325 92 :HQSI 1oltA 70 :GCNK T0325 96 :FEEKVNLEEVYNEWDAQIISFMKS 1oltA 76 :TRQQHKADQYLDALEQEIVHRAPL T0325 120 :GRRPD 1oltA 102 :GRHVS T0325 125 :HID 1oltA 109 :HWG T0325 130 :HNVH 1oltA 114 :TPTY T0325 135 :KNKKLLGVALALARKY 1oltA 118 :LNKAQISRLMKLLREN T0325 152 :LPL 1oltA 134 :FQF T0325 155 :RNASRSIETKDYLELY 1oltA 144 :IEVDPREIELDVLDHL T0325 171 :QDVRTP 1oltA 201 :IGFTST T0325 180 :LYQFYDKAISTETILQLLDMVVCSEGEVFEINCHPAFID 1oltA 209 :DLIYGLPKQTPESFAFTLKRVAELNPDRLSVFNYAHLPT T0325 219 :TILQNQS 1oltA 250 :AAQRKIK T0325 226 :GYCMPRIREVEILT 1oltA 258 :ADLPSPQQKLDILQ T0325 242 :EVKEAIEERGILLA 1oltA 272 :ETIAFLTQSGYQFI Number of specific fragments extracted= 17 number of extra gaps= 3 total=1449 Will force an alignment to be made, even if fragment is small Number of alignments=95 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1oltA/T0325-1oltA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1oltA/T0325-1oltA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1oltA read from 1oltA/T0325-1oltA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1oltA in template set Warning: unaligning (T0325)F90 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1oltA)C69 Warning: unaligning (T0325)W91 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1oltA)C69 Warning: unaligning (T0325)S128 because of BadResidue code BAD_PEPTIDE in next template residue (1oltA)G113 Warning: unaligning (T0325)H129 because of BadResidue code BAD_PEPTIDE at template residue (1oltA)G113 Warning: unaligning (T0325)D177 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1oltA)I208 Warning: unaligning (T0325)M179 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1oltA)I208 T0325 45 :LEAMESARISAPTLAIGVHLTLT 1oltA 38 :EQAFLQAVARYPERPLSLYVHIP T0325 70 :Q 1oltA 61 :F T0325 80 :VPSLV 1oltA 62 :CHKLC T0325 89 :Y 1oltA 67 :Y T0325 92 :H 1oltA 70 :G T0325 95 :IFEEKVNLEEVYNEWDAQIISFMKS 1oltA 75 :VTRQQHKADQYLDALEQEIVHRAPL T0325 120 :GRRPD 1oltA 102 :GRHVS T0325 125 :HID 1oltA 109 :HWG T0325 130 :HNVH 1oltA 114 :TPTY T0325 135 :KNKKLLGVALALARKY 1oltA 118 :LNKAQISRLMKLLREN T0325 154 :LRNASRSIE 1oltA 144 :IEVDPREIE T0325 164 :KDYLELY 1oltA 153 :LDVLDHL T0325 171 :QDVRTP 1oltA 201 :IGFTST T0325 180 :LYQFYDKAISTETILQLLDMVVCSEGEVFEINCHPAFID 1oltA 209 :DLIYGLPKQTPESFAFTLKRVAELNPDRLSVFNYAHLPT T0325 219 :TILQNQS 1oltA 250 :AAQRKIK T0325 226 :GYCMPRIREVEILT 1oltA 258 :ADLPSPQQKLDILQ T0325 242 :EVKEAIEERGILLAN 1oltA 272 :ETIAFLTQSGYQFIG Number of specific fragments extracted= 17 number of extra gaps= 3 total=1466 Will force an alignment to be made, even if fragment is small Number of alignments=96 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1oltA/T0325-1oltA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1oltA/T0325-1oltA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1oltA read from 1oltA/T0325-1oltA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1oltA in template set Warning: unaligning (T0325)A10 because of BadResidue code BAD_PEPTIDE in next template residue (1oltA)G113 Warning: unaligning (T0325)H125 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1oltA)I208 Warning: unaligning (T0325)I126 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1oltA)I208 T0325 5 :KLIIN 1oltA 107 :QLHWG T0325 13 :FGYTPAVTQGIIEAHKRGV 1oltA 116 :TYLNKAQISRLMKLLRENF T0325 32 :VTSTTALPTSPYFLEAMESARI 1oltA 140 :AEISIEVDPREIELDVLDHLRA T0325 56 :PTLA 1oltA 162 :EGFN T0325 89 :YFWHQSIFEEKVNLEEVYNEW 1oltA 175 :NKEVQRLVNREQDEEFIFALL T0325 114 :ISFMKSGRRPD 1oltA 196 :NHAREIGFTST T0325 127 :DSHHNVHGKNKKLLGVALALARKYQLP 1oltA 209 :DLIYGLPKQTPESFAFTLKRVAELNPD T0325 154 :LRNASRSIETKDYLELYQDVRTP 1oltA 239 :VFNYAHLPTIFAAQRKIKDADLP T0325 185 :DKAISTETILQLLDMVVCSEGEVF 1oltA 262 :SPQQKLDILQETIAFLTQSGYQFI Number of specific fragments extracted= 9 number of extra gaps= 2 total=1475 Will force an alignment to be made, even if fragment is small Number of alignments=97 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2amxA/T0325-2amxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2amxA expands to /projects/compbio/data/pdb/2amx.pdb.gz 2amxA:# T0325 read from 2amxA/T0325-2amxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2amxA read from 2amxA/T0325-2amxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2amxA to template set # found chain 2amxA in template set Warning: unaligning (T0325)P73 because first residue in template chain is (2amxA)G13 Warning: unaligning (T0325)D124 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2amxA)K51 Warning: unaligning (T0325)H125 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2amxA)K51 T0325 74 :ILPREMVP 2amxA 14 :LVPRGSEI T0325 89 :YFWHQSI 2amxA 22 :KFLKKED T0325 96 :FEEKVNLEEVYNEWDA 2amxA 33 :DLNGMSKKERYEIWRR T0325 123 :P 2amxA 49 :I T0325 126 :IDSHHNVHGKNK 2amxA 52 :VELHCHLDLTFS T0325 140 :LGVALALARKYQLP 2amxA 64 :AEFFLKWARKYNLQ T0325 159 :RSIETKDYLELY 2amxA 78 :PNMSDDEILDHY T0325 171 :QDVRTPDEM 2amxA 214 :GREIDLKDH T0325 190 :TETILQLLD 2amxA 223 :KDVYHSVRD T0325 205 :GEV 2amxA 232 :HGL T0325 209 :EINCHPAFI 2amxA 235 :HLTVHAGED T0325 223 :NQSGYCMPRIREVEILT 2amxA 244 :ATLPNLNTLYTAINILN T0325 240 :SQEVKEAIEERGILLAN 2amxA 273 :SDELIELVKKKDILLEV Number of specific fragments extracted= 13 number of extra gaps= 1 total=1488 Will force an alignment to be made, even if fragment is small Number of alignments=98 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2amxA/T0325-2amxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 2amxA/T0325-2amxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2amxA read from 2amxA/T0325-2amxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2amxA in template set Warning: unaligning (T0325)P73 because first residue in template chain is (2amxA)G13 Warning: unaligning (T0325)D124 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2amxA)K51 Warning: unaligning (T0325)H125 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2amxA)K51 T0325 74 :ILPREMVPSLVDEA 2amxA 14 :LVPRGSEIKFLKKE T0325 93 :QSIFEEKVNLEEVYNEWDA 2amxA 30 :QNIDLNGMSKKERYEIWRR T0325 123 :P 2amxA 49 :I T0325 126 :IDSHHNVHGKNK 2amxA 52 :VELHCHLDLTFS T0325 140 :LGVALALARKYQLP 2amxA 64 :AEFFLKWARKYNLQ T0325 159 :RSIETKDYLELY 2amxA 78 :PNMSDDEILDHY T0325 183 :FYDKAISTETILQLLDMVVC 2amxA 108 :VSDLYRDYDFIEDLAKWAVI T0325 204 :EGEVFEINC 2amxA 131 :KEGVVLMEF T0325 216 :FIDTILQN 2amxA 140 :RYSPTFVS T0325 225 :SGYCMPRIREVEILTS 2amxA 148 :SSYGLDVELIHKAFIK T0325 242 :EVKEAIEERG 2amxA 164 :GIKNATELLN T0325 252 :ILLAN 2amxA 176 :IHVAL Number of specific fragments extracted= 12 number of extra gaps= 1 total=1500 Will force an alignment to be made, even if fragment is small Number of alignments=99 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2amxA/T0325-2amxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 2amxA/T0325-2amxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2amxA read from 2amxA/T0325-2amxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2amxA in template set Warning: unaligning (T0325)D124 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2amxA)K51 Warning: unaligning (T0325)H125 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2amxA)K51 T0325 97 :EEKVNLEEVYNEWDA 2amxA 34 :LNGMSKKERYEIWRR T0325 123 :P 2amxA 49 :I T0325 126 :IDSHHNVHGKNK 2amxA 52 :VELHCHLDLTFS T0325 140 :LGVALALARKYQLPL 2amxA 64 :AEFFLKWARKYNLQP T0325 158 :SRSIETKDYLELYQDVRTPDEMLYQ 2amxA 79 :NMSDDEILDHYLFTKEGKSLAEFIR T0325 183 :FYDKAISTETILQLLDMVV 2amxA 108 :VSDLYRDYDFIEDLAKWAV T0325 202 :CSEGEVFEINC 2amxA 129 :KYKEGVVLMEF T0325 216 :FIDTILQN 2amxA 140 :RYSPTFVS T0325 225 :SGYCMPRIREVEIL 2amxA 148 :SSYGLDVELIHKAF T0325 244 :KEAIEE 2amxA 162 :IKGIKN T0325 251 :G 2amxA 173 :N T0325 252 :ILL 2amxA 176 :IHV Number of specific fragments extracted= 12 number of extra gaps= 1 total=1512 Will force an alignment to be made, even if fragment is small Number of alignments=100 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hjsA/T0325-1hjsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1hjsA expands to /projects/compbio/data/pdb/1hjs.pdb.gz 1hjsA:Skipped atom 1871, because occupancy 0.500 <= existing 0.500 in 1hjsA Skipped atom 1875, because occupancy 0.500 <= existing 0.500 in 1hjsA Skipped atom 1877, because occupancy 0.500 <= existing 0.500 in 1hjsA Skipped atom 1879, because occupancy 0.500 <= existing 0.500 in 1hjsA Skipped atom 1881, because occupancy 0.500 <= existing 0.500 in 1hjsA # T0325 read from 1hjsA/T0325-1hjsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hjsA read from 1hjsA/T0325-1hjsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1hjsA to template set # found chain 1hjsA in template set T0325 23 :IIEAHKRGVVTSTTALP 1hjsA 32 :LENILAANGVNTVRQRV T0325 40 :TSPYFLEAMESARIS 1hjsA 58 :NLDYNIAIAKRAKAA T0325 57 :TLAIGVHLTLT 1hjsA 73 :GLGVYIDFHYS T0325 70 :QA 1hjsA 84 :DT T0325 74 :ILPREMV 1hjsA 86 :WADPAHQ T0325 82 :SLV 1hjsA 93 :TMP T0325 86 :EA 1hjsA 96 :AG T0325 89 :Y 1hjsA 98 :W T0325 99 :KVNLE 1hjsA 99 :PSDID T0325 104 :EVYNEWDAQIISFMKSGRRPDHIDSHHNVHG 1hjsA 108 :KLYNYTLDAANKLQNAGIQPTIVSIGNEIRA T0325 135 :KNKKLLGVALALARKY 1hjsA 149 :NWANIARLLHSAAWGI T0325 151 :QLP 1hjsA 168 :SLS T0325 154 :LRNASRSIETKDYLELY 1hjsA 176 :MIHLDNGWDWGTQNWWY T0325 171 :QDVRTPDEMLYQ 1hjsA 198 :QGTLELSDFDMM T0325 183 :FYDKAISTETILQLLDMVV 1hjsA 216 :FYSSSATLSALKSSLDNMA T0325 202 :CSEGEVFEINCH 1hjsA 236 :TWNKEIAVVETN T0325 214 :PAF 1hjsA 249 :PIS T0325 219 :TILQNQSGYCMPRIREVEILT 1hjsA 258 :SFPSDVKNIPFSPEGQTTFIT T0325 242 :EVKEAIEER 1hjsA 279 :NVANIVSSV Number of specific fragments extracted= 19 number of extra gaps= 0 total=1531 Will force an alignment to be made, even if fragment is small Number of alignments=101 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hjsA/T0325-1hjsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1hjsA/T0325-1hjsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hjsA read from 1hjsA/T0325-1hjsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1hjsA in template set T0325 23 :IIEAHKRGVVTSTTALP 1hjsA 32 :LENILAANGVNTVRQRV T0325 40 :TSPYFLEAMESARIS 1hjsA 58 :NLDYNIAIAKRAKAA T0325 57 :TLAIGVHLTLT 1hjsA 73 :GLGVYIDFHYS T0325 70 :QA 1hjsA 84 :DT T0325 74 :ILPREMV 1hjsA 86 :WADPAHQ T0325 82 :SLV 1hjsA 93 :TMP T0325 87 :AGYF 1hjsA 96 :AGWP T0325 100 :VNLE 1hjsA 100 :SDID T0325 104 :EVYNEWDAQIISFMKSGRRPDHIDSHHNVHG 1hjsA 108 :KLYNYTLDAANKLQNAGIQPTIVSIGNEIRA T0325 135 :KNKKLLGVALALARKY 1hjsA 149 :NWANIARLLHSAAWGI T0325 151 :QL 1hjsA 168 :SL T0325 154 :LRNASRSIETKDYLELY 1hjsA 176 :MIHLDNGWDWGTQNWWY T0325 171 :QDVRTPDEMLYQ 1hjsA 198 :QGTLELSDFDMM T0325 183 :FYDKAISTETILQLLDMVVCSEGEVFEIN 1hjsA 216 :FYSSSATLSALKSSLDNMAKTWNKEIAVV T0325 212 :CHPAFID 1hjsA 247 :NWPISCP T0325 219 :TILQNQSGYCMPRIREVEILTS 1hjsA 258 :SFPSDVKNIPFSPEGQTTFITN T0325 243 :VKEAIEER 1hjsA 280 :VANIVSSV Number of specific fragments extracted= 17 number of extra gaps= 0 total=1548 Will force an alignment to be made, even if fragment is small Number of alignments=102 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hjsA/T0325-1hjsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1hjsA/T0325-1hjsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hjsA read from 1hjsA/T0325-1hjsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1hjsA in template set T0325 23 :IIEAHKRGVVTSTTALP 1hjsA 32 :LENILAANGVNTVRQRV T0325 40 :TSPYFLEAMESARI 1hjsA 58 :NLDYNIAIAKRAKA T0325 56 :PTL 1hjsA 72 :AGL T0325 61 :GVHLTLTLNQAKPILPREMVP 1hjsA 75 :GVYIDFHYSDTWADPAHQTMP T0325 85 :DEAGYFWHQSI 1hjsA 96 :AGWPSDIDNLS T0325 103 :EEVYNEWDAQIISFMKSGRRPDHIDSHHNVHG 1hjsA 107 :WKLYNYTLDAANKLQNAGIQPTIVSIGNEIRA T0325 137 :K 1hjsA 143 :P T0325 138 :KLLGVALALARKYQLP 1hjsA 155 :RLLHSAAWGIKDSSLS T0325 154 :LRNASRSIETKDYLEL 1hjsA 176 :MIHLDNGWDWGTQNWW T0325 170 :YQDVRTPDEMLYQ 1hjsA 196 :LKQGTLELSDFDM T0325 183 :FYDKAISTETILQLLDMVVCSEGEVFEINCHPAFID 1hjsA 216 :FYSSSATLSALKSSLDNMAKTWNKEIAVVETNWPIS T0325 219 :TILQNQSGYCMPRIREVEILT 1hjsA 258 :SFPSDVKNIPFSPEGQTTFIT T0325 242 :EVKEAIEE 1hjsA 279 :NVANIVSS Number of specific fragments extracted= 13 number of extra gaps= 0 total=1561 Will force an alignment to be made, even if fragment is small Number of alignments=103 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vcoA/T0325-1vcoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vcoA expands to /projects/compbio/data/pdb/1vco.pdb.gz 1vcoA:# T0325 read from 1vcoA/T0325-1vcoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vcoA read from 1vcoA/T0325-1vcoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vcoA to template set # found chain 1vcoA in template set Warning: unaligning (T0325)I217 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vcoA)D314 Warning: unaligning (T0325)S225 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vcoA)D314 Warning: unaligning (T0325)L260 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vcoA)A347 T0325 17 :PAVTQGIIEAHKRGVVTSTTALPTS 1vcoA 130 :DEIKERIRKVAEEQKAEIVVVEVGG T0325 42 :PYFLEAMESAR 1vcoA 162 :LPFLEAIRQFR T0325 53 :ISAPTLAIGVHLTLT 1vcoA 174 :DEGEGNTLYLHLTLV T0325 73 :PILPR 1vcoA 189 :PYLET T0325 87 :AGYFWHQ 1vcoA 194 :SEEFKTK T0325 108 :EWDAQIISFMKSGRRPDHIDSH 1vcoA 201 :PTQHSVATLRGVGIQPDILVLR T0325 132 :VHGKNKK 1vcoA 223 :SARPVPE T0325 141 :GVALALARKYQLP 1vcoA 230 :EVRRKVALFTNVR T0325 154 :LRNASRSIETKDYLELY 1vcoA 246 :VFSSPTVEHLYEVPLLL T0325 171 :QDVRT 1vcoA 275 :LGLEA T0325 186 :KAISTETILQLLDMVVCS 1vcoA 280 :VIPNLSFWQEAVRVLKHP T0325 205 :GEVFEINCHPAF 1vcoA 298 :ERTVKIAIAGKY T0325 226 :G 1vcoA 315 :A T0325 228 :CMPRIREVEILT 1vcoA 316 :YLSLLEALRHAG T0325 249 :ERG 1vcoA 329 :KNR T0325 252 :ILLANYES 1vcoA 336 :VKWVDAES Number of specific fragments extracted= 16 number of extra gaps= 0 total=1577 Will force an alignment to be made, even if fragment is small Number of alignments=104 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vcoA/T0325-1vcoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1vcoA/T0325-1vcoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vcoA read from 1vcoA/T0325-1vcoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vcoA in template set Warning: unaligning (T0325)I217 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vcoA)D314 Warning: unaligning (T0325)G226 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vcoA)D314 Warning: unaligning (T0325)L260 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vcoA)A347 T0325 17 :PAVTQGIIEAHKRGVVTSTTALPTS 1vcoA 130 :DEIKERIRKVAEEQKAEIVVVEVGG T0325 42 :PYFLEAMESARI 1vcoA 162 :LPFLEAIRQFRF T0325 54 :SAPTLAIGVHLTLT 1vcoA 175 :EGEGNTLYLHLTLV T0325 73 :PILPR 1vcoA 189 :PYLET T0325 87 :AGYFW 1vcoA 194 :SEEFK T0325 102 :LEE 1vcoA 199 :TKP T0325 109 :WDAQIISFMKSGRRPDHIDSH 1vcoA 202 :TQHSVATLRGVGIQPDILVLR T0325 132 :VHGKNKK 1vcoA 223 :SARPVPE T0325 141 :GVALALARKYQLP 1vcoA 230 :EVRRKVALFTNVR T0325 154 :LRNASRSIETKDYLELY 1vcoA 246 :VFSSPTVEHLYEVPLLL T0325 181 :YQFYDKAISTETILQLLDMV 1vcoA 275 :LGLEAVIPNLSFWQEAVRVL T0325 202 :CSEGEVFEINCHPAF 1vcoA 295 :KHPERTVKIAIAGKY T0325 227 :YCMPRIREVEILT 1vcoA 315 :AYLSLLEALRHAG T0325 249 :ERG 1vcoA 329 :KNR T0325 252 :ILLANYES 1vcoA 336 :VKWVDAES Number of specific fragments extracted= 15 number of extra gaps= 0 total=1592 Will force an alignment to be made, even if fragment is small Number of alignments=105 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vcoA/T0325-1vcoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1vcoA/T0325-1vcoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vcoA read from 1vcoA/T0325-1vcoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vcoA in template set Warning: unaligning (T0325)I217 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vcoA)D314 Warning: unaligning (T0325)G226 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vcoA)D314 Warning: unaligning (T0325)L260 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vcoA)A347 T0325 17 :PAVTQGIIEAHKRGVVTSTTALPTS 1vcoA 130 :DEIKERIRKVAEEQKAEIVVVEVGG T0325 42 :PYFLEAMESARI 1vcoA 162 :LPFLEAIRQFRF T0325 54 :SAPTLAIGVHLTLT 1vcoA 175 :EGEGNTLYLHLTLV T0325 80 :VPSLVDEAGYF 1vcoA 189 :PYLETSEEFKT T0325 103 :E 1vcoA 200 :K T0325 108 :EWDAQIISFMKSGRRPDHI 1vcoA 201 :PTQHSVATLRGVGIQPDIL T0325 131 :NVHGK 1vcoA 220 :VLRSA T0325 137 :KKL 1vcoA 225 :RPV T0325 140 :LGVALALARKYQLP 1vcoA 229 :EEVRRKVALFTNVR T0325 154 :LRNASRSIETKDYLEL 1vcoA 246 :VFSSPTVEHLYEVPLL T0325 172 :DVRTP 1vcoA 274 :ALGLE T0325 185 :DKAISTETILQLLDMVV 1vcoA 279 :AVIPNLSFWQEAVRVLK T0325 203 :SEGEVFEINCHPAF 1vcoA 296 :HPERTVKIAIAGKY T0325 227 :YCMPRIREVEILT 1vcoA 315 :AYLSLLEALRHAG T0325 249 :ERG 1vcoA 329 :KNR T0325 252 :ILLANYES 1vcoA 336 :VKWVDAES Number of specific fragments extracted= 16 number of extra gaps= 0 total=1608 Will force an alignment to be made, even if fragment is small Number of alignments=106 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fobA/T0325-1fobA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1fobA expands to /projects/compbio/data/pdb/1fob.pdb.gz 1fobA:Skipped atom 397, because occupancy 0.500 <= existing 0.500 in 1fobA Skipped atom 399, because occupancy 0.500 <= existing 0.500 in 1fobA Skipped atom 401, because occupancy 0.500 <= existing 0.500 in 1fobA Skipped atom 712, because occupancy 0.500 <= existing 0.500 in 1fobA Skipped atom 714, because occupancy 0.500 <= existing 0.500 in 1fobA Skipped atom 716, because occupancy 0.500 <= existing 0.500 in 1fobA Skipped atom 884, because occupancy 0.500 <= existing 0.500 in 1fobA Skipped atom 886, because occupancy 0.500 <= existing 0.500 in 1fobA Skipped atom 888, because occupancy 0.500 <= existing 0.500 in 1fobA # T0325 read from 1fobA/T0325-1fobA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fobA read from 1fobA/T0325-1fobA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1fobA to template set # found chain 1fobA in template set T0325 23 :IIEAHKRGVVTSTTALPT 1fobA 32 :LETILADAGINSIRQRVW T0325 41 :SPYFLEAMESARIS 1fobA 59 :LDYNLELAKRVKAA T0325 57 :TLAIGVHLTLT 1fobA 73 :GMSLYLDLHLS T0325 70 :QAK 1fobA 84 :DTW T0325 75 :LPREMV 1fobA 87 :ADPSDQ T0325 84 :VDEAG 1fobA 93 :TTPSG T0325 97 :EEKVNLE 1fobA 98 :WSTTDLG T0325 104 :EVYNEWDAQIISFMKSGRRPDHIDSHHNVHG 1fobA 109 :QLYNYTLEVCNTFAENDIDIEIISIGNEIRA T0325 135 :KNKK 1fobA 142 :LWPL T0325 139 :LLGVALALARKYQLP 1fobA 157 :LLHSGAWGVKDSNLA T0325 154 :LRNASRSIETKDYLELY 1fobA 177 :MIHLDDGWSWDQQNYFY T0325 171 :QDVRTPDEMLYQ 1fobA 199 :TGELLSTDFDYF T0325 183 :FYDKAISTETILQLLDMV 1fobA 217 :FYSASATLASLKTSLANL T0325 201 :VCSEGEVFEINCH 1fobA 236 :STYDKPVVVVETN T0325 214 :PAFID 1fobA 250 :PVSCP T0325 219 :TILQNQSGYCMPRIREVEILT 1fobA 259 :AFPSDLSSIPFSVAGQQEFLE T0325 242 :EVKEAIEERGILLANY 1fobA 280 :KLAAVVEATTDGLGVY Number of specific fragments extracted= 17 number of extra gaps= 0 total=1625 Will force an alignment to be made, even if fragment is small Number of alignments=107 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fobA/T0325-1fobA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1fobA/T0325-1fobA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fobA read from 1fobA/T0325-1fobA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fobA in template set T0325 23 :IIEAHKRGVVTSTTALP 1fobA 32 :LETILADAGINSIRQRV T0325 40 :TSPYFLEAMESARIS 1fobA 58 :DLDYNLELAKRVKAA T0325 57 :TLAIGVHLTLTLNQA 1fobA 73 :GMSLYLDLHLSDTWA T0325 76 :PREMVPSL 1fobA 88 :DPSDQTTP T0325 86 :EA 1fobA 96 :SG T0325 97 :EEKVNLE 1fobA 98 :WSTTDLG T0325 104 :EVYNEWDAQIISFMKSGRRPDHIDSHHNVHG 1fobA 109 :QLYNYTLEVCNTFAENDIDIEIISIGNEIRA T0325 135 :KNKK 1fobA 142 :LWPL T0325 139 :LLGVALALARKYQL 1fobA 157 :LLHSGAWGVKDSNL T0325 153 :PLRNASRSIETKDYLELY 1fobA 175 :KIMIHLDDGWSWDQQNYF T0325 171 :QDVRTPDEMLYQ 1fobA 199 :TGELLSTDFDYF T0325 183 :FYDKAISTETILQLLDMVVCSEGEVFEIN 1fobA 217 :FYSASATLASLKTSLANLQSTYDKPVVVV T0325 212 :CHPAFID 1fobA 248 :NWPVSCP T0325 219 :TILQNQSGYCMPRIREVEILT 1fobA 259 :AFPSDLSSIPFSVAGQQEFLE T0325 242 :EVKEAIEERGILLAN 1fobA 280 :KLAAVVEATTDGLGV Number of specific fragments extracted= 15 number of extra gaps= 0 total=1640 Will force an alignment to be made, even if fragment is small Number of alignments=108 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fobA/T0325-1fobA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1fobA/T0325-1fobA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fobA read from 1fobA/T0325-1fobA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fobA in template set T0325 23 :IIEAHKRGVVTSTTALPTS 1fobA 32 :LETILADAGINSIRQRVWV T0325 42 :PYFLEAMESARI 1fobA 60 :DYNLELAKRVKA T0325 56 :PTLAIGVHLTLTLNQAKPILPREMVPSLVD 1fobA 72 :AGMSLYLDLHLSDTWADPSDQTTPSGWSTT T0325 90 :FWHQS 1fobA 102 :DLGTL T0325 102 :LEEVYNEWDAQIISFMKSGRRPDHIDSHHNVHGKN 1fobA 107 :KWQLYNYTLEVCNTFAENDIDIEIISIGNEIRAGL T0325 138 :KLLGVALALARKYQLP 1fobA 156 :ALLHSGAWGVKDSNLA T0325 154 :LRNASRSIETKDYLEL 1fobA 176 :IMIHLDDGWSWDQQNY T0325 170 :YQDVRTPDEMLYQ 1fobA 197 :LATGELLSTDFDY T0325 183 :FYDKAISTETILQLLDMVVCSEGEVFEINCHPAFID 1fobA 217 :FYSASATLASLKTSLANLQSTYDKPVVVVETNWPVS T0325 219 :TILQNQSGYCMPRIREVEILT 1fobA 259 :AFPSDLSSIPFSVAGQQEFLE T0325 242 :EVKEAIEERGILLA 1fobA 280 :KLAAVVEATTDGLG Number of specific fragments extracted= 11 number of extra gaps= 0 total=1651 Will force an alignment to be made, even if fragment is small Number of alignments=109 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xfkA/T0325-1xfkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xfkA expands to /projects/compbio/data/pdb/1xfk.pdb.gz 1xfkA:# T0325 read from 1xfkA/T0325-1xfkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xfkA read from 1xfkA/T0325-1xfkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xfkA to template set # found chain 1xfkA in template set T0325 17 :PAVTQGIIEAHKRGVVTSTTALPTSPYFL 1xfkA 105 :QECAQVIQQALPHARAIVLGGGHEIAWAT T0325 46 :EAMESAR 1xfkA 136 :GLAQHFL T0325 53 :ISAPTLAIGV 1xfkA 144 :TGVKQPRIGI T0325 64 :LTLTLNQAKPILPREM 1xfkA 154 :INFDAHFDLRTFESEL T0325 81 :PSLVDEAGYFW 1xfkA 170 :APVRPSSGTPF T0325 111 :AQIISFMK 1xfkA 181 :NQIHHFCQ T0325 119 :SGRRPDHIDSHHNVHGKNKK 1xfkA 190 :QGWDFHYACLGVSRASNTPA T0325 143 :ALALARKYQLPLRNASR 1xfkA 210 :LFERADKLGVWYVEDKA T0325 160 :SIETKDYLELY 1xfkA 229 :PLSLKDHLTQL T0325 171 :QDVRTPD 1xfkA 261 :ASAPGVS T0325 182 :QFYDKAISTETILQLLDMVVCSEGEVF 1xfkA 268 :APAARGVSLEALAPYFDRILHYKNKLM T0325 210 :INCHPAFIDTILQ 1xfkA 295 :IADIAEYNPSFDI T0325 227 :YCMPRIREVEIL 1xfkA 308 :DQHTARLAARLC Number of specific fragments extracted= 13 number of extra gaps= 0 total=1664 Will force an alignment to be made, even if fragment is small Number of alignments=110 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xfkA/T0325-1xfkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1xfkA/T0325-1xfkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xfkA read from 1xfkA/T0325-1xfkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xfkA in template set T0325 17 :PAVTQGIIEAHKRGVVTSTTALPTSPYFL 1xfkA 105 :QECAQVIQQALPHARAIVLGGGHEIAWAT T0325 46 :EAMESARI 1xfkA 136 :GLAQHFLA T0325 54 :SAPTLAIGV 1xfkA 145 :GVKQPRIGI T0325 64 :LTLTLNQAKPILPREMVPSLVDE 1xfkA 154 :INFDAHFDLRTFESELAPVRPSS T0325 88 :GYFW 1xfkA 177 :GTPF T0325 111 :AQIISFMK 1xfkA 181 :NQIHHFCQ T0325 119 :SGRRPDHIDSHHNVHGKNKKL 1xfkA 190 :QGWDFHYACLGVSRASNTPAL T0325 144 :LALARKYQLPLRNASR 1xfkA 211 :FERADKLGVWYVEDKA T0325 160 :SIETKDYLELY 1xfkA 229 :PLSLKDHLTQL T0325 171 :QDVRTPD 1xfkA 261 :ASAPGVS T0325 182 :QFYDKAISTETILQLLDMVVCSEGEVFEIN 1xfkA 268 :APAARGVSLEALAPYFDRILHYKNKLMIAD T0325 212 :CHPAFIDT 1xfkA 301 :YNPSFDID T0325 227 :Y 1xfkA 309 :Q T0325 229 :MPRIREVEI 1xfkA 310 :HTARLAARL Number of specific fragments extracted= 14 number of extra gaps= 0 total=1678 Will force an alignment to be made, even if fragment is small Number of alignments=111 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xfkA/T0325-1xfkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1xfkA/T0325-1xfkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xfkA read from 1xfkA/T0325-1xfkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xfkA in template set T0325 17 :PAVTQGIIEAHKRGVVTSTTALPTSPYFL 1xfkA 105 :QECAQVIQQALPHARAIVLGGGHEIAWAT T0325 46 :EAMESARI 1xfkA 136 :GLAQHFLA T0325 54 :SAPTLAIGV 1xfkA 145 :GVKQPRIGI T0325 64 :LTLTLNQAKPILPREMVPSLVDEAG 1xfkA 154 :INFDAHFDLRTFESELAPVRPSSGT T0325 91 :WH 1xfkA 179 :PF T0325 111 :AQIISFMK 1xfkA 181 :NQIHHFCQ T0325 119 :SGRRPDHID 1xfkA 190 :QGWDFHYAC T0325 132 :VHGKNKKLLGVALALARKYQLPLRNASRSIETKDYLEL 1xfkA 199 :LGVSRASNTPALFERADKLGVWYVEDKAFSPLSLKDHL T0325 170 :YQDVRTP 1xfkA 258 :FPAASAP T0325 179 :MLYQFYDKAISTETILQLLDMVVCSEGEVFEINCHPAFID 1xfkA 265 :GVSAPAARGVSLEALAPYFDRILHYKNKLMIADIAEYNPS Number of specific fragments extracted= 10 number of extra gaps= 0 total=1688 Will force an alignment to be made, even if fragment is small Number of alignments=112 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2d13A/T0325-2d13A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2d13A expands to /projects/compbio/data/pdb/2d13.pdb.gz 2d13A:# T0325 read from 2d13A/T0325-2d13A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2d13A read from 2d13A/T0325-2d13A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2d13A to template set # found chain 2d13A in template set Warning: unaligning (T0325)T40 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2d13A)N51 Warning: unaligning (T0325)T67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2d13A)E74 Warning: unaligning (T0325)E97 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2d13A)E74 T0325 2 :SNKKLIINA 2d13A 3 :GLADVAVLY T0325 14 :GYTPAVTQGIIEAHKRG 2d13A 12 :SGGKDSNYALYWALKSG T0325 31 :VVTSTTAL 2d13A 30 :RVRYLVSM T0325 41 :SPYFLEAMESAR 2d13A 52 :VELTSLQARALG T0325 58 :LAI 2d13A 64 :IPI T0325 63 :HLTL 2d13A 67 :IKGF T0325 98 :EKVNLEEVYNEWD 2d13A 75 :KEKEVEDLKNVLE T0325 120 :GRRPDHIDSH 2d13A 88 :GLKVDGIVAG T0325 133 :HGKNKKLLGVALALARKYQLPLRNASRSIETKDYLELY 2d13A 98 :ALASRYQKERIENVARELGLKVYTPAWEKDPYQYMLEI T0325 171 :QD 2d13A 150 :YG T0325 175 :TPDEM 2d13A 152 :LNESW T0325 184 :YDKAISTETILQLLDMVVCSE 2d13A 157 :LGRELNYKNLEELKKLSEKYG Number of specific fragments extracted= 12 number of extra gaps= 0 total=1700 Will force an alignment to be made, even if fragment is small Number of alignments=113 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2d13A/T0325-2d13A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 2d13A/T0325-2d13A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2d13A read from 2d13A/T0325-2d13A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2d13A in template set Warning: unaligning (T0325)T40 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2d13A)N51 Warning: unaligning (T0325)T67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2d13A)E74 Warning: unaligning (T0325)P76 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2d13A)E74 T0325 1 :MSNKKLIINA 2d13A 2 :VGLADVAVLY T0325 14 :GYTPAVTQGIIEAHKRG 2d13A 12 :SGGKDSNYALYWALKSG T0325 31 :VVTSTTALP 2d13A 30 :RVRYLVSMV T0325 41 :SPYFLEAMESAR 2d13A 52 :VELTSLQARALG T0325 58 :LAI 2d13A 64 :IPI T0325 63 :HLTL 2d13A 67 :IKGF T0325 98 :EKVNLEEVYNEWD 2d13A 75 :KEKEVEDLKNVLE T0325 120 :GRRPDHIDSHH 2d13A 88 :GLKVDGIVAGA T0325 134 :GKNKKLLGVALALARKYQLPLRNASRSIETKDYLELY 2d13A 99 :LASRYQKERIENVARELGLKVYTPAWEKDPYQYMLEI T0325 171 :QDVR 2d13A 150 :YGLN T0325 177 :DE 2d13A 154 :ES T0325 183 :FYDKAISTETILQLLDMVVCSE 2d13A 156 :WLGRELNYKNLEELKKLSEKYG Number of specific fragments extracted= 12 number of extra gaps= 0 total=1712 Will force an alignment to be made, even if fragment is small Number of alignments=114 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2d13A/T0325-2d13A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 2d13A/T0325-2d13A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2d13A read from 2d13A/T0325-2d13A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2d13A in template set Warning: unaligning (T0325)Q70 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2d13A)N51 Warning: unaligning (T0325)V80 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2d13A)N51 T0325 3 :NK 2d13A 4 :LA T0325 33 :TSTTALPTSPYFLEAMESARI 2d13A 6 :DVAVLYSGGKDSNYALYWALK T0325 56 :PTLAIGVHLTLTLN 2d13A 27 :SGLRVRYLVSMVSE T0325 81 :P 2d13A 52 :V T0325 87 :AGYFWHQSIFE 2d13A 53 :ELTSLQARALG T0325 98 :EKVNLEEVYNEWD 2d13A 75 :KEKEVEDLKNVLE T0325 120 :GRRPDHIDS 2d13A 88 :GLKVDGIVA T0325 132 :VHGKNKKLLGVALALARKYQLPLRNASRSIETK 2d13A 97 :GALASRYQKERIENVARELGLKVYTPAWEKDPY T0325 195 :QLLDMVVCSEGEVFEINCHPAFIDTILQN 2d13A 130 :QYMLEIIKLGFKVVFVAVSAYGLNESWLG T0325 225 :SGYCMPRIR 2d13A 159 :RELNYKNLE T0325 242 :EVKEAIEERGI 2d13A 168 :ELKKLSEKYGI Number of specific fragments extracted= 11 number of extra gaps= 0 total=1723 Will force an alignment to be made, even if fragment is small Number of alignments=115 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1h1yA/T0325-1h1yA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1h1yA expands to /projects/compbio/data/pdb/1h1y.pdb.gz 1h1yA:# T0325 read from 1h1yA/T0325-1h1yA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1h1yA read from 1h1yA/T0325-1h1yA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1h1yA to template set # found chain 1h1yA in template set T0325 7 :IINADDFGYT 1h1yA 7 :KIAPSMLSSD T0325 17 :PAVTQGIIEAHKRGVVTSTTALPTSPY 1h1yA 18 :ANLAAEADRMVRLGADWLHMDIMDGHF T0325 45 :LEAMESARISA 1h1yA 52 :APVIQSLRKHT T0325 57 :TLAIGVHLTLT 1h1yA 63 :KAYLDCHLMVT T0325 76 :PREMV 1h1yA 74 :NPSDY T0325 113 :IISFMKSG 1h1yA 79 :VEPLAKAG T0325 123 :PDHIDSHHNVHG 1h1yA 87 :ASGFTFHIEVSR T0325 137 :KK 1h1yA 99 :DN T0325 140 :LGVALALARKYQLPLRNASRSIETKDYLELY 1h1yA 101 :WQELIQSIKAKGMRPGVSLRPGTPVEEVFPL T0325 171 :QDVRTPDEM 1h1yA 151 :GGQKFMPEM T0325 190 :TETILQLLDMV 1h1yA 160 :MEKVRALRKKY T0325 204 :EGEVFEINCHPA 1h1yA 171 :PSLDIEVDGGLG T0325 216 :FID 1h1yA 185 :TID T0325 219 :TILQNQSGYCMPRI 1h1yA 201 :SSIFGAAEPGEVIS T0325 242 :EVKEAIEE 1h1yA 215 :ALRKSVEG Number of specific fragments extracted= 15 number of extra gaps= 0 total=1738 Will force an alignment to be made, even if fragment is small Number of alignments=116 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1h1yA/T0325-1h1yA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1h1yA/T0325-1h1yA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1h1yA read from 1h1yA/T0325-1h1yA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1h1yA in template set T0325 5 :K 1h1yA 7 :K T0325 8 :INADDFGYT 1h1yA 8 :IAPSMLSSD T0325 17 :PAVTQGIIEAHKRGVVTSTTALPTSPYF 1h1yA 18 :ANLAAEADRMVRLGADWLHMDIMDGHFV T0325 45 :LEAMESARISA 1h1yA 52 :APVIQSLRKHT T0325 57 :TLAIGVHLTLT 1h1yA 63 :KAYLDCHLMVT T0325 76 :PREMV 1h1yA 74 :NPSDY T0325 113 :IISFMKSG 1h1yA 79 :VEPLAKAG T0325 123 :PDHIDSHHNVHG 1h1yA 87 :ASGFTFHIEVSR T0325 137 :KKLLG 1h1yA 99 :DNWQE T0325 143 :ALALARKYQLPL 1h1yA 104 :LIQSIKAKGMRP T0325 155 :RNASRSIETKDYLEL 1h1yA 117 :VSLRPGTPVEEVFPL T0325 171 :QDVRTPDEML 1h1yA 151 :GGQKFMPEMM T0325 191 :ETILQLLDMV 1h1yA 161 :EKVRALRKKY T0325 204 :EGEVFEIN 1h1yA 171 :PSLDIEVD T0325 212 :CHPAFIDTILQNQS 1h1yA 181 :LGPSTIDVAASAGA T0325 226 :GYCM 1h1yA 205 :GAAE T0325 231 :RIREVE 1h1yA 209 :PGEVIS T0325 242 :EVKEAIEE 1h1yA 215 :ALRKSVEG Number of specific fragments extracted= 18 number of extra gaps= 0 total=1756 Will force an alignment to be made, even if fragment is small Number of alignments=117 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1h1yA/T0325-1h1yA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1h1yA/T0325-1h1yA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1h1yA read from 1h1yA/T0325-1h1yA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1h1yA in template set T0325 32 :VTSTTALPTSPYFLEAMESARI 1h1yA 8 :IAPSMLSSDFANLAAEADRMVR T0325 56 :PTLAI 1h1yA 30 :LGADW T0325 62 :VHLTLTLNQAKPILP 1h1yA 35 :LHMDIMDGHFVPNLT T0325 100 :VNLEEVYN 1h1yA 50 :IGAPVIQS T0325 116 :FMKSGR 1h1yA 58 :LRKHTK T0325 124 :DHIDSHHNVHGK 1h1yA 64 :AYLDCHLMVTNP T0325 137 :KKLLGVALAL 1h1yA 76 :SDYVEPLAKA T0325 147 :ARKYQLPLRNASRSIETKDYLEL 1h1yA 108 :IKAKGMRPGVSLRPGTPVEEVFP T0325 170 :YQDVRTPDEML 1h1yA 146 :VEPGFGGQKFM T0325 190 :TETILQLLDMVVCSEGEVFEIN 1h1yA 157 :PEMMEKVRALRKKYPSLDIEVD T0325 212 :CHPAFID 1h1yA 181 :LGPSTID T0325 219 :TILQNQSG 1h1yA 201 :SSIFGAAE T0325 234 :EVEILT 1h1yA 209 :PGEVIS T0325 242 :EVKEAIEE 1h1yA 215 :ALRKSVEG Number of specific fragments extracted= 14 number of extra gaps= 0 total=1770 Will force an alignment to be made, even if fragment is small Number of alignments=118 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bf6A/T0325-1bf6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1bf6A expands to /projects/compbio/data/pdb/1bf6.pdb.gz 1bf6A:# T0325 read from 1bf6A/T0325-1bf6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bf6A read from 1bf6A/T0325-1bf6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1bf6A to template set # found chain 1bf6A in template set Warning: unaligning (T0325)D127 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1bf6A)E125 Warning: unaligning (T0325)S128 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1bf6A)E125 T0325 18 :AVTQGIIEAHKRG 1bf6A 35 :FICQEMNDLMTRG T0325 32 :VTSTTALPT 1bf6A 48 :VRNVIEMTN T0325 41 :SPYFLEAMESA 1bf6A 63 :AQFMLDVMRET T0325 57 :TLAIGV 1bf6A 74 :GINVVA T0325 66 :LT 1bf6A 80 :CT T0325 73 :PILPREMVPS 1bf6A 82 :GYYQDAFFPE T0325 96 :FEEKVNLEEVYNEWDAQII 1bf6A 92 :HVATRSVQELAQEMVDEIE T0325 119 :S 1bf6A 114 :D T0325 120 :GRRPDHI 1bf6A 117 :ELKAGII T0325 129 :HHNVHG 1bf6A 126 :IGTSEG T0325 135 :KNKK 1bf6A 133 :ITPL T0325 139 :LLGVALALARKYQLPLRNASRSIET 1bf6A 140 :VFIAAALAHNQTGRPISTHTSFSTM T0325 164 :KDYLELY 1bf6A 166 :LEQLALL T0325 171 :QDVRTPDEMLYQ 1bf6A 175 :HGVDLSRVTVGH T0325 184 :YDKAISTETILQLLDM 1bf6A 187 :CDLKDNLDNILKMIDL T0325 206 :EVF 1bf6A 203 :GAY T0325 210 :INCHPAF 1bf6A 206 :VQFDTIG T0325 225 :SGYCMPRIREVEILT 1bf6A 213 :KNSYYPDEKRIAMLH T0325 246 :AIEERGI 1bf6A 228 :ALRDRGL Number of specific fragments extracted= 19 number of extra gaps= 1 total=1789 Will force an alignment to be made, even if fragment is small Number of alignments=119 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bf6A/T0325-1bf6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1bf6A/T0325-1bf6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bf6A read from 1bf6A/T0325-1bf6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1bf6A in template set Warning: unaligning (T0325)D127 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1bf6A)E125 Warning: unaligning (T0325)S128 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1bf6A)E125 T0325 18 :AVTQGIIEAHKRG 1bf6A 35 :FICQEMNDLMTRG T0325 32 :VTSTTALPTSPY 1bf6A 48 :VRNVIEMTNRYM T0325 44 :FLEAMESARI 1bf6A 63 :AQFMLDVMRE T0325 55 :A 1bf6A 73 :T T0325 57 :TLAIGV 1bf6A 74 :GINVVA T0325 66 :LT 1bf6A 80 :CT T0325 73 :PILPREMVPS 1bf6A 82 :GYYQDAFFPE T0325 96 :FEEKVNLEEVYNEWDAQII 1bf6A 92 :HVATRSVQELAQEMVDEIE T0325 119 :S 1bf6A 114 :D T0325 120 :GRRPDHI 1bf6A 117 :ELKAGII T0325 129 :HHNVHG 1bf6A 126 :IGTSEG T0325 135 :KNKK 1bf6A 133 :ITPL T0325 139 :LLGVALALARKYQLPLRNASRSIET 1bf6A 140 :VFIAAALAHNQTGRPISTHTSFSTM T0325 164 :KDYLELY 1bf6A 166 :LEQLALL T0325 171 :QDVRTPDEML 1bf6A 175 :HGVDLSRVTV T0325 182 :QFYDKAISTETILQLLDM 1bf6A 185 :GHCDLKDNLDNILKMIDL T0325 206 :E 1bf6A 203 :G T0325 208 :FEINCHP 1bf6A 204 :AYVQFDT T0325 222 :Q 1bf6A 211 :I T0325 224 :QSGYCMPRIREVEILT 1bf6A 212 :GKNSYYPDEKRIAMLH T0325 246 :AIEERGI 1bf6A 228 :ALRDRGL Number of specific fragments extracted= 21 number of extra gaps= 1 total=1810 Will force an alignment to be made, even if fragment is small Number of alignments=120 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bf6A/T0325-1bf6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1bf6A/T0325-1bf6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bf6A read from 1bf6A/T0325-1bf6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1bf6A in template set Warning: unaligning (T0325)H130 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1bf6A)E125 Warning: unaligning (T0325)N131 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1bf6A)E125 T0325 18 :AVTQGIIEAHKRG 1bf6A 35 :FICQEMNDLMTRG T0325 32 :VTSTTALPTSPY 1bf6A 48 :VRNVIEMTNRYM T0325 44 :FLEAMESARI 1bf6A 63 :AQFMLDVMRE T0325 56 :PTLAIGV 1bf6A 73 :TGINVVA T0325 67 :T 1bf6A 81 :T T0325 72 :KPILPREMVP 1bf6A 82 :GYYQDAFFPE T0325 96 :FEEKVNLEEVYNEWDAQII 1bf6A 92 :HVATRSVQELAQEMVDEIE T0325 119 :SGRRPDH 1bf6A 114 :DGTELKA T0325 127 :DSH 1bf6A 121 :GII T0325 132 :VHGKNKKLLGVA 1bf6A 126 :IGTSEGKITPLE T0325 144 :LALARKYQLPLRNASRSIET 1bf6A 145 :ALAHNQTGRPISTHTSFSTM T0325 164 :KDYLELYQDVRTPDEMLYQFYD 1bf6A 166 :LEQLALLQAHGVDLSRVTVGHC T0325 188 :ISTETILQLLDMVVCS 1bf6A 188 :DLKDNLDNILKMIDLG T0325 208 :FEINCHPA 1bf6A 204 :AYVQFDTI T0325 224 :QSGYCMPRIREVEILT 1bf6A 212 :GKNSYYPDEKRIAMLH T0325 246 :AIEERGI 1bf6A 228 :ALRDRGL Number of specific fragments extracted= 16 number of extra gaps= 1 total=1826 Will force an alignment to be made, even if fragment is small Number of alignments=121 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ur4A/T0325-1ur4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ur4A expands to /projects/compbio/data/pdb/1ur4.pdb.gz 1ur4A:# T0325 read from 1ur4A/T0325-1ur4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ur4A read from 1ur4A/T0325-1ur4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ur4A to template set # found chain 1ur4A in template set T0325 23 :IIEAHKRGVVTSTTALPT 1ur4A 53 :IFKTLKEAGVNYVRVRIW T0325 41 :SPYFLEAMESARI 1ur4A 88 :LEKAIQIGKRATA T0325 56 :PTLAIGVHLTLT 1ur4A 101 :NGMKLLADFHYS T0325 70 :QAKPILPR 1ur4A 113 :DFWADPAK T0325 91 :WHQSIFEEKVNLE 1ur4A 121 :QKAPKAWANLNFE T0325 104 :EVYNEWDAQIISFMKSGRRPDHIDSHHNVHGKN 1ur4A 138 :ALYQYTKQSLKAMKAAGIDIGMVQVGNETNGGL T0325 137 :KKLLGVALALARKY 1ur4A 180 :SQLFNAGSQAVRET T0325 151 :QLPLRNASRSIETKDYLELY 1ur4A 196 :NILVALHFTNPETSGRYAWI T0325 171 :QDVRT 1ur4A 283 :NGQTL T0325 185 :DKAISTETIL 1ur4A 288 :NNPVTVQGQA T0325 195 :QLLDMVVCSEGEVF 1ur4A 302 :DVIQAVSDVGEAGI T0325 209 :EINCHPAFID 1ur4A 317 :VFYWEPAWIP T0325 219 :TILQN 1ur4A 329 :PAHRL T0325 241 :QEVKEAIEER 1ur4A 334 :EKNKALWETY Number of specific fragments extracted= 14 number of extra gaps= 0 total=1840 Will force an alignment to be made, even if fragment is small Number of alignments=122 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ur4A/T0325-1ur4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1ur4A/T0325-1ur4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ur4A read from 1ur4A/T0325-1ur4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ur4A in template set T0325 23 :IIEAHKRGVVTSTTALP 1ur4A 53 :IFKTLKEAGVNYVRVRI T0325 40 :TSPYFLEAMESARI 1ur4A 87 :DLEKAIQIGKRATA T0325 56 :PTLAIGVHLTLT 1ur4A 101 :NGMKLLADFHYS T0325 72 :KPILPREMVPSL 1ur4A 113 :DFWADPAKQKAP T0325 95 :IFEEKVNLE 1ur4A 125 :KAWANLNFE T0325 104 :EVYNEWDAQIISFMKSGRRPDHIDSHHNVHGKN 1ur4A 138 :ALYQYTKQSLKAMKAAGIDIGMVQVGNETNGGL T0325 137 :KKLLGVALALARKY 1ur4A 180 :SQLFNAGSQAVRET T0325 151 :QLPLRNASRSIETKDYLELY 1ur4A 196 :NILVALHFTNPETSGRYAWI T0325 171 :QDVRT 1ur4A 283 :NGQTL T0325 185 :DKAISTETILQ 1ur4A 288 :NNPVTVQGQAN T0325 196 :LLDMVVCSEGEVFEIN 1ur4A 303 :VIQAVSDVGEAGIGVF T0325 212 :CHPAFID 1ur4A 320 :WEPAWIP T0325 219 :TILQN 1ur4A 329 :PAHRL T0325 241 :QEVKEAIEER 1ur4A 334 :EKNKALWETY Number of specific fragments extracted= 14 number of extra gaps= 0 total=1854 Will force an alignment to be made, even if fragment is small Number of alignments=123 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ur4A/T0325-1ur4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1ur4A/T0325-1ur4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ur4A read from 1ur4A/T0325-1ur4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ur4A in template set T0325 23 :IIEAHKRGVVTSTTA 1ur4A 53 :IFKTLKEAGVNYVRV T0325 40 :TSPYFLEAMESARI 1ur4A 87 :DLEKAIQIGKRATA T0325 56 :PTLAIG 1ur4A 101 :NGMKLL T0325 64 :LTLTLNQAKPILPREMVPSLVDEAGYFWH 1ur4A 107 :ADFHYSDFWADPAKQKAPKAWANLNFEDK T0325 102 :LEEVYNEWDAQIISFMKSGRRPDHIDSHHNVHGK 1ur4A 136 :KTALYQYTKQSLKAMKAAGIDIGMVQVGNETNGG T0325 136 :NKKLLGVALALARKYQLPLRN 1ur4A 179 :MSQLFNAGSQAVRETDSNILV T0325 157 :ASRSIETKDYLEL 1ur4A 202 :HFTNPETSGRYAW T0325 171 :QDVRTPDEMLYQ 1ur4A 281 :PKNGQTLNNPVT T0325 186 :KAISTETILQLLDMVVCSEGEVFEINCH 1ur4A 293 :VQGQANAVRDVIQAVSDVGEAGIGVFYW T0325 214 :PAFID 1ur4A 322 :PAWIP T0325 219 :TILQN 1ur4A 329 :PAHRL T0325 241 :QEVKEAIEER 1ur4A 334 :EKNKALWETY Number of specific fragments extracted= 12 number of extra gaps= 0 total=1866 Will force an alignment to be made, even if fragment is small Number of alignments=124 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fuvA/T0325-2fuvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2fuvA expands to /projects/compbio/data/pdb/2fuv.pdb.gz 2fuvA:Skipped atom 75, because occupancy 0.400 <= existing 0.600 in 2fuvA Skipped atom 79, because occupancy 0.400 <= existing 0.600 in 2fuvA Skipped atom 81, because occupancy 0.400 <= existing 0.600 in 2fuvA Skipped atom 83, because occupancy 0.400 <= existing 0.600 in 2fuvA Skipped atom 85, because occupancy 0.400 <= existing 0.600 in 2fuvA Skipped atom 87, because occupancy 0.400 <= existing 0.600 in 2fuvA Skipped atom 90, because occupancy 0.400 <= existing 0.600 in 2fuvA Skipped atom 94, because occupancy 0.400 <= existing 0.600 in 2fuvA Skipped atom 96, because occupancy 0.400 <= existing 0.600 in 2fuvA Skipped atom 98, because occupancy 0.400 <= existing 0.600 in 2fuvA Skipped atom 100, because occupancy 0.400 <= existing 0.600 in 2fuvA Skipped atom 102, because occupancy 0.400 <= existing 0.600 in 2fuvA Skipped atom 232, because occupancy 0.500 <= existing 0.500 in 2fuvA Skipped atom 236, because occupancy 0.500 <= existing 0.500 in 2fuvA Skipped atom 238, because occupancy 0.500 <= existing 0.500 in 2fuvA Skipped atom 240, because occupancy 0.500 <= existing 0.500 in 2fuvA Skipped atom 242, because occupancy 0.500 <= existing 0.500 in 2fuvA Skipped atom 244, because occupancy 0.500 <= existing 0.500 in 2fuvA Skipped atom 1365, because occupancy 0.500 <= existing 0.500 in 2fuvA Skipped atom 1367, because occupancy 0.500 <= existing 0.500 in 2fuvA Skipped atom 1369, because occupancy 0.500 <= existing 0.500 in 2fuvA Skipped atom 1371, because occupancy 0.500 <= existing 0.500 in 2fuvA Skipped atom 1373, because occupancy 0.500 <= existing 0.500 in 2fuvA Skipped atom 1375, because occupancy 0.500 <= existing 0.500 in 2fuvA Skipped atom 1377, because occupancy 0.500 <= existing 0.500 in 2fuvA Skipped atom 1379, because occupancy 0.500 <= existing 0.500 in 2fuvA Skipped atom 1381, because occupancy 0.500 <= existing 0.500 in 2fuvA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1599, because occupancy 0.500 <= existing 0.500 in 2fuvA Skipped atom 1603, because occupancy 0.500 <= existing 0.500 in 2fuvA Skipped atom 1605, because occupancy 0.500 <= existing 0.500 in 2fuvA Skipped atom 1607, because occupancy 0.500 <= existing 0.500 in 2fuvA Skipped atom 1609, because occupancy 0.500 <= existing 0.500 in 2fuvA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2093, because occupancy 0.500 <= existing 0.500 in 2fuvA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2097, because occupancy 0.500 <= existing 0.500 in 2fuvA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2099, because occupancy 0.500 <= existing 0.500 in 2fuvA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2101, because occupancy 0.440 <= existing 0.440 in 2fuvA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2103, because occupancy 0.500 <= existing 0.500 in 2fuvA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 3322, because occupancy 0.500 <= existing 0.500 in 2fuvA Skipped atom 3326, because occupancy 0.500 <= existing 0.500 in 2fuvA Skipped atom 3328, because occupancy 0.500 <= existing 0.500 in 2fuvA Skipped atom 3330, because occupancy 0.500 <= existing 0.500 in 2fuvA Skipped atom 3332, because occupancy 0.500 <= existing 0.500 in 2fuvA Skipped atom 3334, because occupancy 0.500 <= existing 0.500 in 2fuvA Skipped atom 3336, because occupancy 0.500 <= existing 0.500 in 2fuvA Skipped atom 3338, because occupancy 0.500 <= existing 0.500 in 2fuvA Skipped atom 3492, because occupancy 0.400 <= existing 0.600 in 2fuvA Skipped atom 3496, because occupancy 0.400 <= existing 0.600 in 2fuvA Skipped atom 3498, because occupancy 0.400 <= existing 0.600 in 2fuvA Skipped atom 3501, because occupancy 0.500 <= existing 0.500 in 2fuvA Skipped atom 3505, because occupancy 0.500 <= existing 0.500 in 2fuvA Skipped atom 3507, because occupancy 0.500 <= existing 0.500 in 2fuvA Skipped atom 3509, because occupancy 0.500 <= existing 0.500 in 2fuvA Skipped atom 3511, because occupancy 0.500 <= existing 0.500 in 2fuvA Skipped atom 3513, because occupancy 0.500 <= existing 0.500 in 2fuvA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 3968, because occupancy 0.500 <= existing 0.500 in 2fuvA Skipped atom 3972, because occupancy 0.500 <= existing 0.500 in 2fuvA Skipped atom 3974, because occupancy 0.500 <= existing 0.500 in 2fuvA Skipped atom 3976, because occupancy 0.500 <= existing 0.500 in 2fuvA Skipped atom 3978, because occupancy 0.500 <= existing 0.500 in 2fuvA Skipped atom 3980, because occupancy 0.500 <= existing 0.500 in 2fuvA # T0325 read from 2fuvA/T0325-2fuvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fuvA read from 2fuvA/T0325-2fuvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2fuvA to template set # found chain 2fuvA in template set Warning: unaligning (T0325)A157 because of BadResidue code BAD_PEPTIDE in next template residue (2fuvA)N259 Warning: unaligning (T0325)S158 because of BadResidue code BAD_PEPTIDE at template residue (2fuvA)N259 T0325 2 :SNKKLIINADDFGYTPAVTQGIIEAHKRGVVTSTTA 2fuvA 77 :ITGPCYVGKDTHALSEPAFISVLEVLAANGVDVIVQ T0325 38 :LPTSPYFLEAMESARISAPTLAIGV 2fuvA 117 :FTPTPAVSNAILVHNKKGGPLADGI T0325 65 :TLTLNQAKPI 2fuvA 142 :VITPSHNPPE T0325 79 :M 2fuvA 152 :D T0325 83 :LVDEAGYFWHQSI 2fuvA 157 :YNPPNGGPADTNV T0325 100 :VNLEEVYN 2fuvA 191 :ISLDAAMA T0325 113 :IISFM 2fuvA 208 :VQPFV T0325 118 :KSGRRP 2fuvA 226 :KAGLTL T0325 125 :HIDSHHNVH 2fuvA 232 :GVDPLGGSG T0325 140 :LGVALALARKYQLPLRN 2fuvA 241 :IEYWKRIAEHYKLNLTL T0325 159 :RSIETKDYL 2fuvA 260 :DQVDQTFRF T0325 171 :QDVRTPDEMLYQ 2fuvA 316 :AGLMNPNHYLAV T0325 192 :TILQLLDMVVCSEGEVFEINCHP 2fuvA 328 :AINYLFQHRPLWGKDVAVGKTLV T0325 225 :SGYCMPR 2fuvA 351 :SSAMIDR T0325 246 :AIEERGILLANY 2fuvA 358 :VVNDLGRKLVEV Number of specific fragments extracted= 15 number of extra gaps= 1 total=1881 Will force an alignment to be made, even if fragment is small Number of alignments=125 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fuvA/T0325-2fuvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 2fuvA/T0325-2fuvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fuvA read from 2fuvA/T0325-2fuvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fuvA in template set Warning: unaligning (T0325)A157 because of BadResidue code BAD_PEPTIDE in next template residue (2fuvA)N259 Warning: unaligning (T0325)S158 because of BadResidue code BAD_PEPTIDE at template residue (2fuvA)N259 T0325 2 :SNKKLIINADDFGYTPAVTQGIIEAHKRGVVTSTTA 2fuvA 77 :ITGPCYVGKDTHALSEPAFISVLEVLAANGVDVIVQ T0325 38 :LPTSPYFLEAMESARISAPTLAIGV 2fuvA 117 :FTPTPAVSNAILVHNKKGGPLADGI T0325 65 :TLTLNQAKP 2fuvA 142 :VITPSHNPP T0325 78 :EMV 2fuvA 151 :EDG T0325 82 :SLVDEAGYFWH 2fuvA 156 :KYNPPNGGPAD T0325 93 :QSIFEEKVNLEEV 2fuvA 212 :VEGLADIVDMAAI T0325 117 :MKSGRRP 2fuvA 225 :QKAGLTL T0325 125 :HIDSHHNVH 2fuvA 232 :GVDPLGGSG T0325 140 :LGVALALARKYQLPLRN 2fuvA 241 :IEYWKRIAEHYKLNLTL T0325 159 :RSIETKDYLELY 2fuvA 260 :DQVDQTFRFMHL T0325 171 :QDVRTPDEMLYQF 2fuvA 316 :AGLMNPNHYLAVA T0325 193 :ILQLLDMVVCSEGEVFEINC 2fuvA 329 :INYLFQHRPLWGKDVAVGKT T0325 223 :NQSGYCMPR 2fuvA 349 :LVSSAMIDR T0325 246 :AIEERGILLANY 2fuvA 358 :VVNDLGRKLVEV Number of specific fragments extracted= 14 number of extra gaps= 1 total=1895 Will force an alignment to be made, even if fragment is small Number of alignments=126 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fuvA/T0325-2fuvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 2fuvA/T0325-2fuvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fuvA read from 2fuvA/T0325-2fuvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fuvA in template set Warning: unaligning (T0325)V84 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fuvA)Q186 Warning: unaligning (T0325)D85 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fuvA)Q186 Warning: unaligning (T0325)E86 because of BadResidue code BAD_PEPTIDE at template residue (2fuvA)G187 Warning: unaligning (T0325)A157 because of BadResidue code BAD_PEPTIDE in next template residue (2fuvA)N259 Warning: unaligning (T0325)S158 because of BadResidue code BAD_PEPTIDE at template residue (2fuvA)N259 T0325 2 :SNKKLIINADDFGYTPAVTQGIIEAHKRGVVTSTTA 2fuvA 77 :ITGPCYVGKDTHALSEPAFISVLEVLAANGVDVIVQ T0325 38 :LPTSPYFLEAMESARISAPTLAIGV 2fuvA 117 :FTPTPAVSNAILVHNKKGGPLADGI T0325 65 :TLTLNQAKPIL 2fuvA 142 :VITPSHNPPED T0325 76 :PREM 2fuvA 161 :NGGP T0325 81 :PSL 2fuvA 182 :AGG T0325 87 :AG 2fuvA 188 :VK T0325 89 :YFWHQSIFEEKVNLEE 2fuvA 208 :VQPFVEGLADIVDMAA T0325 116 :FMKSGRRPD 2fuvA 224 :IQKAGLTLG T0325 126 :IDSHHNV 2fuvA 233 :VDPLGGS T0325 139 :LLGVALALARKYQLPLRN 2fuvA 240 :GIEYWKRIAEHYKLNLTL T0325 159 :RSIETK 2fuvA 260 :DQVDQT T0325 165 :DYLELYQDVRTPDEMLYQFYDK 2fuvA 267 :RFMHLDKDGAIRMDCSSECAMA T0325 198 :DMVVCSEGEVFEINCHPAFID 2fuvA 289 :GLLALRDKFDLAFANDPDYDR Number of specific fragments extracted= 13 number of extra gaps= 2 total=1908 Will force an alignment to be made, even if fragment is small Number of alignments=127 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1n7kA/T0325-1n7kA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1n7kA expands to /projects/compbio/data/pdb/1n7k.pdb.gz 1n7kA:# T0325 read from 1n7kA/T0325-1n7kA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1n7kA read from 1n7kA/T0325-1n7kA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1n7kA to template set # found chain 1n7kA in template set T0325 17 :PAVTQGIIEAHKRGVVTSTT 1n7kA 37 :EDVRNLVREASDYGFRCAVL T0325 40 :TSPYFLEAMESARIS 1n7kA 57 :TPVYTVKISGLAEKL T0325 57 :TLAIGV 1n7kA 72 :GVKLCS T0325 65 :TLTLNQA 1n7kA 78 :VIGFPLG T0325 76 :P 1n7kA 85 :Q T0325 100 :VNLEEVYNEW 1n7kA 86 :APLEVKLVEA T0325 114 :ISFMKSG 1n7kA 96 :QTVLEAG T0325 123 :PDHIDSHHNVHGKNKKLLGVAL 1n7kA 103 :ATELDVVPHLSLGPEAVYREVS T0325 145 :ALARKYQLPLRNA 1n7kA 128 :KLAKSYGAVVKVI T0325 174 :RTPD 1n7kA 141 :LEAP T0325 187 :AISTETILQLLDMVVCS 1n7kA 145 :LWDDKTLSLLVDSSRRA T0325 206 :EVFEINCHPAFID 1n7kA 162 :GADIVKTSTGVYT T0325 230 :PRIREV 1n7kA 178 :DPVTVF T0325 242 :EVKEAIEERGILLANYESLAM 1n7kA 184 :RLASLAKPLGMGVKASGGIRS Number of specific fragments extracted= 14 number of extra gaps= 0 total=1922 Will force an alignment to be made, even if fragment is small Number of alignments=128 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1n7kA/T0325-1n7kA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1n7kA/T0325-1n7kA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1n7kA read from 1n7kA/T0325-1n7kA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1n7kA in template set T0325 17 :PAVTQGIIEAHKRGVVTSTT 1n7kA 37 :EDVRNLVREASDYGFRCAVL T0325 40 :TSPYFLEAMESARIS 1n7kA 57 :TPVYTVKISGLAEKL T0325 57 :TLAIGV 1n7kA 72 :GVKLCS T0325 65 :TLTLNQA 1n7kA 78 :VIGFPLG T0325 99 :KVNLEEVYNEW 1n7kA 85 :QAPLEVKLVEA T0325 114 :ISFMKSG 1n7kA 96 :QTVLEAG T0325 123 :PDHIDSHHNVHGKNKKLLGVAL 1n7kA 103 :ATELDVVPHLSLGPEAVYREVS T0325 145 :ALARKYQLPLRNASRSIE 1n7kA 128 :KLAKSYGAVVKVILEAPL T0325 188 :ISTETILQLLDMVVCS 1n7kA 146 :WDDKTLSLLVDSSRRA T0325 206 :EVFEINCHPAFID 1n7kA 162 :GADIVKTSTGVYT T0325 230 :PRIREV 1n7kA 178 :DPVTVF T0325 242 :EVKEAIEERGILLANYESLAM 1n7kA 184 :RLASLAKPLGMGVKASGGIRS Number of specific fragments extracted= 12 number of extra gaps= 0 total=1934 Will force an alignment to be made, even if fragment is small Number of alignments=129 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1n7kA/T0325-1n7kA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1n7kA/T0325-1n7kA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1n7kA read from 1n7kA/T0325-1n7kA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1n7kA in template set T0325 17 :PAVTQGIIEAHKRGVVTSTT 1n7kA 37 :EDVRNLVREASDYGFRCAVL T0325 40 :TSPYFLEAMESARI 1n7kA 57 :TPVYTVKISGLAEK T0325 56 :PTLAIGV 1n7kA 71 :LGVKLCS T0325 67 :TLNQAKPI 1n7kA 78 :VIGFPLGQ T0325 100 :VNLEEVYNEW 1n7kA 86 :APLEVKLVEA T0325 114 :ISFMKSG 1n7kA 96 :QTVLEAG T0325 123 :PDHIDSHHNVHGKNKKLLGVA 1n7kA 103 :ATELDVVPHLSLGPEAVYREV T0325 144 :LALARKYQLPLRNA 1n7kA 127 :VKLAKSYGAVVKVI T0325 183 :FYDKAISTETILQLLDMVVCS 1n7kA 141 :LEAPLWDDKTLSLLVDSSRRA T0325 206 :EVFEINCHPAFID 1n7kA 162 :GADIVKTSTGVYT T0325 232 :IREV 1n7kA 180 :VTVF T0325 242 :EVKEAIEERGILLANYESLA 1n7kA 184 :RLASLAKPLGMGVKASGGIR Number of specific fragments extracted= 12 number of extra gaps= 0 total=1946 Will force an alignment to be made, even if fragment is small Number of alignments=130 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1n82A/T0325-1n82A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1n82A expands to /projects/compbio/data/pdb/1n82.pdb.gz 1n82A:Skipped atom 808, because occupancy 0.240 <= existing 0.760 in 1n82A Skipped atom 810, because occupancy 0.240 <= existing 0.760 in 1n82A Skipped atom 919, because occupancy 0.460 <= existing 0.540 in 1n82A Skipped atom 921, because occupancy 0.460 <= existing 0.540 in 1n82A Skipped atom 1506, because occupancy 0.040 <= existing 0.960 in 1n82A Skipped atom 1508, because occupancy 0.040 <= existing 0.960 in 1n82A Skipped atom 1510, because occupancy 0.040 <= existing 0.960 in 1n82A Skipped atom 1512, because occupancy 0.040 <= existing 0.960 in 1n82A Skipped atom 1514, because occupancy 0.040 <= existing 0.960 in 1n82A Skipped atom 1658, because occupancy 0.160 <= existing 0.840 in 1n82A Skipped atom 1660, because occupancy 0.160 <= existing 0.840 in 1n82A Skipped atom 1662, because occupancy 0.160 <= existing 0.840 in 1n82A Skipped atom 1664, because occupancy 0.160 <= existing 0.840 in 1n82A Skipped atom 2137, because occupancy 0.320 <= existing 0.680 in 1n82A Skipped atom 2139, because occupancy 0.320 <= existing 0.680 in 1n82A Skipped atom 2141, because occupancy 0.320 <= existing 0.680 in 1n82A Skipped atom 2143, because occupancy 0.320 <= existing 0.680 in 1n82A Skipped atom 2332, because occupancy 0.150 <= existing 0.850 in 1n82A Skipped atom 2334, because occupancy 0.150 <= existing 0.850 in 1n82A Skipped atom 2336, because occupancy 0.150 <= existing 0.850 in 1n82A Skipped atom 2573, because occupancy 0.050 <= existing 0.950 in 1n82A Skipped atom 2575, because occupancy 0.050 <= existing 0.950 in 1n82A Skipped atom 2577, because occupancy 0.050 <= existing 0.950 in 1n82A Skipped atom 2738, because occupancy 0.200 <= existing 0.800 in 1n82A Skipped atom 2740, because occupancy 0.200 <= existing 0.800 in 1n82A # T0325 read from 1n82A/T0325-1n82A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1n82A read from 1n82A/T0325-1n82A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1n82A to template set # found chain 1n82A in template set Warning: unaligning (T0325)H63 because of BadResidue code BAD_PEPTIDE in next template residue (1n82A)T82 Warning: unaligning (T0325)L64 because of BadResidue code BAD_PEPTIDE at template residue (1n82A)T82 Warning: unaligning (T0325)R155 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1n82A)Y176 Warning: unaligning (T0325)N156 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1n82A)Y176 Warning: unaligning (T0325)E209 because of BadResidue code BAD_PEPTIDE in next template residue (1n82A)T240 Warning: unaligning (T0325)I210 because of BadResidue code BAD_PEPTIDE at template residue (1n82A)T240 Warning: unaligning (T0325)Q224 because of BadResidue code BAD_PEPTIDE in next template residue (1n82A)D255 Warning: unaligning (T0325)S225 because of BadResidue code BAD_PEPTIDE at template residue (1n82A)D255 T0325 4 :KKLIINAD 1n82A 16 :FRIGAAVN T0325 17 :PAVTQGIIEA 1n82A 28 :EMQKQLLIDH T0325 32 :VTSTTA 1n82A 38 :VNSITA T0325 39 :PTSPYFLEAMESARIS 1n82A 59 :FTFQEADRIVDFACSH T0325 57 :TLAIGV 1n82A 75 :RMAVRG T0325 65 :TLTLN 1n82A 83 :LVWHN T0325 74 :ILPREM 1n82A 88 :QTPDWV T0325 83 :LVDEAGYF 1n82A 94 :FQDGQGHF T0325 100 :VNLEEVYNEWDAQIISFMKS 1n82A 102 :VSRDVLLERMKCHISTVVRR T0325 120 :GRRPDHIDSHHNVHG 1n82A 123 :KGKIYCWDVINEAVA T0325 135 :KNKK 1n82A 144 :LRPS T0325 139 :LLGVALALARKY 1n82A 157 :FMEQAFLYAYEA T0325 151 :QLPL 1n82A 171 :DALL T0325 157 :ASRSIETKDYLELY 1n82A 177 :NDYNECFPEKREKI T0325 171 :QDVRTP 1n82A 200 :KGIPIH T0325 179 :MLYQFYDKAISTETILQLLDMVVCSEGEVF 1n82A 209 :MQAHWSLTRPSLDEIRAAIERYASLGVVLH T0325 211 :NCHPAFIDTILQN 1n82A 241 :ELDVSMFEFHDRR T0325 226 :GYCM 1n82A 258 :APTS T0325 230 :PRIREVEILT 1n82A 263 :MIERQAERYG T0325 242 :EVKEAIEERG 1n82A 273 :QIFALFKEYR T0325 252 :ILLANYE 1n82A 285 :IQSVTFW Number of specific fragments extracted= 21 number of extra gaps= 4 total=1967 Will force an alignment to be made, even if fragment is small Number of alignments=131 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1n82A/T0325-1n82A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1n82A/T0325-1n82A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1n82A read from 1n82A/T0325-1n82A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1n82A in template set Warning: unaligning (T0325)H63 because of BadResidue code BAD_PEPTIDE in next template residue (1n82A)T82 Warning: unaligning (T0325)L64 because of BadResidue code BAD_PEPTIDE at template residue (1n82A)T82 Warning: unaligning (T0325)R155 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1n82A)Y176 Warning: unaligning (T0325)N156 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1n82A)Y176 Warning: unaligning (T0325)E209 because of BadResidue code BAD_PEPTIDE in next template residue (1n82A)T240 Warning: unaligning (T0325)I210 because of BadResidue code BAD_PEPTIDE at template residue (1n82A)T240 Warning: unaligning (T0325)Q224 because of BadResidue code BAD_PEPTIDE in next template residue (1n82A)D255 Warning: unaligning (T0325)S225 because of BadResidue code BAD_PEPTIDE at template residue (1n82A)D255 T0325 4 :KKLIINAD 1n82A 16 :FRIGAAVN T0325 17 :PAVTQGIIEA 1n82A 28 :EMQKQLLIDH T0325 32 :VTSTTAL 1n82A 38 :VNSITAE T0325 39 :PTSPYFLEAMESARI 1n82A 59 :FTFQEADRIVDFACS T0325 55 :A 1n82A 74 :H T0325 57 :TLAIGV 1n82A 75 :RMAVRG T0325 65 :TLTLN 1n82A 83 :LVWHN T0325 74 :ILPREM 1n82A 88 :QTPDWV T0325 83 :LVDEAGYF 1n82A 94 :FQDGQGHF T0325 100 :VNLEEVYNEWDAQIISFMKS 1n82A 102 :VSRDVLLERMKCHISTVVRR T0325 120 :GRRPDHIDSHHNVHG 1n82A 123 :KGKIYCWDVINEAVA T0325 135 :KNKK 1n82A 144 :LRPS T0325 139 :LLGVALALARKY 1n82A 157 :FMEQAFLYAYEA T0325 151 :QLPL 1n82A 171 :DALL T0325 157 :ASRSIETKDYLELY 1n82A 177 :NDYNECFPEKREKI T0325 171 :QDVRT 1n82A 200 :KGIPI T0325 179 :MLYQFYDKAISTETILQLLDMVVCSEGEVF 1n82A 209 :MQAHWSLTRPSLDEIRAAIERYASLGVVLH T0325 211 :NCHPAFIDTILQN 1n82A 241 :ELDVSMFEFHDRR T0325 226 :GYCM 1n82A 258 :APTS T0325 230 :PRIREVEILT 1n82A 263 :MIERQAERYG T0325 242 :EVKEAIEERG 1n82A 273 :QIFALFKEYR T0325 252 :ILLANYESL 1n82A 285 :IQSVTFWGI Number of specific fragments extracted= 22 number of extra gaps= 4 total=1989 Will force an alignment to be made, even if fragment is small Number of alignments=132 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1n82A/T0325-1n82A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1n82A/T0325-1n82A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1n82A read from 1n82A/T0325-1n82A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1n82A in template set Warning: unaligning (T0325)H63 because of BadResidue code BAD_PEPTIDE in next template residue (1n82A)T82 Warning: unaligning (T0325)L64 because of BadResidue code BAD_PEPTIDE at template residue (1n82A)T82 Warning: unaligning (T0325)Y166 because of BadResidue code BAD_PEPTIDE in next template residue (1n82A)D255 Warning: unaligning (T0325)Q171 because of BadResidue code BAD_PEPTIDE at template residue (1n82A)D255 T0325 4 :KKLIINA 1n82A 16 :FRIGAAV T0325 17 :PAVTQGIIEA 1n82A 28 :EMQKQLLIDH T0325 32 :VTSTTA 1n82A 38 :VNSITA T0325 39 :PTSPYFLEAMESARI 1n82A 59 :FTFQEADRIVDFACS T0325 56 :PTLAIGV 1n82A 74 :HRMAVRG T0325 65 :TLTLNQAKPIL 1n82A 83 :LVWHNQTPDWV T0325 81 :PSLVDEAGY 1n82A 94 :FQDGQGHFV T0325 90 :FWHQSIF 1n82A 106 :VLLERMK T0325 103 :EEVYNEWDAQIISFMKSGRRPDHIDSHHNVHGKNKKL 1n82A 184 :PEKREKIFALVKSLRDKGIPIHGIGMQAHWSLTRPSL T0325 140 :LGVALALARKYQLP 1n82A 223 :IRAAIERYASLGVV T0325 154 :LRNASRSIETKD 1n82A 242 :LDVSMFEFHDRR T0325 172 :DVRTPDE 1n82A 256 :LAAPTSE T0325 185 :DKAISTETILQLLDMVVCSEGEVFEINCHPAFIDTILQNQSGY 1n82A 263 :MIERQAERYGQIFALFKEYRDVIQSVTFWGIADDHTWLDNFPV Number of specific fragments extracted= 13 number of extra gaps= 2 total=2002 Will force an alignment to be made, even if fragment is small Number of alignments=133 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1eyeA/T0325-1eyeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1eyeA expands to /projects/compbio/data/pdb/1eye.pdb.gz 1eyeA:Skipped atom 461, because occupancy 0.300 <= existing 0.700 in 1eyeA Skipped atom 819, because occupancy 0.500 <= existing 0.500 in 1eyeA Skipped atom 821, because occupancy 0.500 <= existing 0.500 in 1eyeA Skipped atom 823, because occupancy 0.500 <= existing 0.500 in 1eyeA Skipped atom 825, because occupancy 0.500 <= existing 0.500 in 1eyeA Skipped atom 827, because occupancy 0.500 <= existing 0.500 in 1eyeA Skipped atom 829, because occupancy 0.500 <= existing 0.500 in 1eyeA Skipped atom 831, because occupancy 0.500 <= existing 0.500 in 1eyeA Skipped atom 833, because occupancy 0.500 <= existing 0.500 in 1eyeA Skipped atom 835, because occupancy 0.500 <= existing 0.500 in 1eyeA Skipped atom 837, because occupancy 0.500 <= existing 0.500 in 1eyeA Skipped atom 839, because occupancy 0.500 <= existing 0.500 in 1eyeA # T0325 read from 1eyeA/T0325-1eyeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1eyeA read from 1eyeA/T0325-1eyeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1eyeA to template set # found chain 1eyeA in template set Warning: unaligning (T0325)L253 because last residue in template chain is (1eyeA)E274 T0325 17 :PAVTQGIIEAHKRGV 1eyeA 67 :SRVIPVVKELAAQGI T0325 33 :TSTTALPTSPYFLEAME 1eyeA 82 :TVSIDTMRADVARAALQ T0325 50 :SARI 1eyeA 119 :LLAE T0325 55 :A 1eyeA 123 :A T0325 57 :TLAIG 1eyeA 124 :DVPWV T0325 66 :LT 1eyeA 129 :LM T0325 70 :QAKPILPR 1eyeA 131 :HWRAVSAD T0325 85 :DEA 1eyeA 139 :TPH T0325 102 :LEEVYNEWDAQIISFMKSGRRPDHIDSHHNVHGKN 1eyeA 150 :VAEVRADLLASVADAVAAGVDPARLVLDPGLGFAK T0325 137 :KKLLGVALALARKY 1eyeA 186 :AQHNWAILHALPEL T0325 151 :QLPLRNASRSIETKDYLELY 1eyeA 203 :GIPVLVGASRKRFLGALLAG T0325 171 :QDVRTPDEM 1eyeA 225 :GVMRPTDGR T0325 190 :TETILQLLDMVVC 1eyeA 234 :DTATAVISALAAL T0325 205 :GEVFEINCHP 1eyeA 247 :HGAWGVRVHD T0325 231 :RIREVEI 1eyeA 257 :VRASVDA T0325 243 :VKEAIEERGI 1eyeA 264 :IKVVEAWMGA Number of specific fragments extracted= 16 number of extra gaps= 0 total=2018 Will force an alignment to be made, even if fragment is small Number of alignments=134 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1eyeA/T0325-1eyeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1eyeA/T0325-1eyeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1eyeA read from 1eyeA/T0325-1eyeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1eyeA in template set Warning: unaligning (T0325)L253 because last residue in template chain is (1eyeA)E274 T0325 4 :KKLIINAD 1eyeA 81 :ITVSIDTM T0325 19 :VTQGIIEAHKRG 1eyeA 89 :RADVARAALQNG T0325 32 :VTSTTALP 1eyeA 101 :AQMVNDVS T0325 40 :TSPYFLEAMESA 1eyeA 112 :ADPAMGPLLAEA T0325 57 :TLAIGV 1eyeA 124 :DVPWVL T0325 67 :T 1eyeA 130 :M T0325 70 :QAKPILPREM 1eyeA 131 :HWRAVSADTP T0325 87 :A 1eyeA 141 :H T0325 91 :WHQSI 1eyeA 142 :VPVRY T0325 102 :LEEVYNEWDAQIISFMKSGRRPDHIDSHHNVHGK 1eyeA 150 :VAEVRADLLASVADAVAAGVDPARLVLDPGLGFA T0325 136 :NKKLLGVALALARKY 1eyeA 185 :TAQHNWAILHALPEL T0325 151 :QLPLRNASRSIET 1eyeA 203 :GIPVLVGASRKRF T0325 164 :KDYLELYQDVRTPDEML 1eyeA 217 :GALLAGPDGVMRPTDGR T0325 190 :TETILQLLDMVV 1eyeA 234 :DTATAVISALAA T0325 204 :EGEVFEINCHPA 1eyeA 246 :LHGAWGVRVHDV T0325 232 :IREVEI 1eyeA 258 :RASVDA T0325 243 :VKEAIEERGI 1eyeA 264 :IKVVEAWMGA Number of specific fragments extracted= 17 number of extra gaps= 0 total=2035 Will force an alignment to be made, even if fragment is small Number of alignments=135 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1eyeA/T0325-1eyeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1eyeA/T0325-1eyeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1eyeA read from 1eyeA/T0325-1eyeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1eyeA in template set T0325 17 :PAVTQGIIEAHKRGVVTSTT 1eyeA 67 :SRVIPVVKELAAQGITVSID T0325 38 :LPTSPYFLEAME 1eyeA 87 :TMRADVARAALQ T0325 50 :SARI 1eyeA 119 :LLAE T0325 56 :PTL 1eyeA 123 :ADV T0325 64 :LTLTLNQAKPILPREMVPSLVD 1eyeA 127 :WVLMHWRAVSADTPHVPVRYGN T0325 102 :LEEVYNEWDAQIISFMKSGRRPDHIDSHHNVHGKN 1eyeA 150 :VAEVRADLLASVADAVAAGVDPARLVLDPGLGFAK T0325 138 :K 1eyeA 185 :T T0325 139 :LLGVALALARK 1eyeA 188 :HNWAILHALPE T0325 150 :YQLPLRNASRSIET 1eyeA 202 :TGIPVLVGASRKRF T0325 166 :YLEL 1eyeA 216 :LGAL T0325 173 :VRTPDEMLY 1eyeA 220 :LAGPDGVMR T0325 185 :DKAISTETILQLLDMVVCS 1eyeA 229 :PTDGRDTATAVISALAALH T0325 206 :EVFEINCHP 1eyeA 248 :GAWGVRVHD T0325 231 :RIR 1eyeA 257 :VRA T0325 243 :VKEAIEE 1eyeA 260 :SVDAIKV Number of specific fragments extracted= 15 number of extra gaps= 0 total=2050 Will force an alignment to be made, even if fragment is small Number of alignments=136 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v4vA/T0325-1v4vA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1v4vA expands to /projects/compbio/data/pdb/1v4v.pdb.gz 1v4vA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1535, because occupancy 0.500 <= existing 0.500 in 1v4vA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1537, because occupancy 0.500 <= existing 0.500 in 1v4vA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1539, because occupancy 0.500 <= existing 0.500 in 1v4vA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1541, because occupancy 0.500 <= existing 0.500 in 1v4vA Skipped atom 1686, because occupancy 0.500 <= existing 0.500 in 1v4vA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2254, because occupancy 0.500 <= existing 0.500 in 1v4vA Skipped atom 2256, because occupancy 0.500 <= existing 0.500 in 1v4vA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2836, because occupancy 0.500 <= existing 0.500 in 1v4vA Skipped atom 2838, because occupancy 0.500 <= existing 0.500 in 1v4vA # T0325 read from 1v4vA/T0325-1v4vA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v4vA read from 1v4vA/T0325-1v4vA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1v4vA to template set # found chain 1v4vA in template set T0325 3 :NKKLIIN 1v4vA 5 :MKRVVLA T0325 13 :FGYTPAVTQG 1v4vA 12 :FGTRPEATKM T0325 23 :IIEAHKRGVVTSTTALPTSPY 1v4vA 25 :YLALRGIPGLKPLVLLTGQHR T0325 45 :LEAMESARISAPTLA 1v4vA 46 :EQLRQALSLFGIQED T0325 81 :PSL 1v4vA 61 :RNL T0325 94 :SIFEEKVNLEEVYNEWDAQI 1v4vA 64 :DVMQERQALPDLAARILPQA T0325 114 :ISFMKSG 1v4vA 85 :RALKEMG T0325 123 :PDHIDSH 1v4vA 92 :ADYVLVH T0325 135 :KNKKLLGVALALARKYQLPL 1v4vA 99 :GDTLTTFAVAWAAFLEGIPV T0325 155 :RNASRSIETKDYLELY 1v4vA 125 :LRSGNLKEPFPEEANR T0325 171 :QDVR 1v4vA 193 :EGLP T0325 175 :TPDEMLYQF 1v4vA 206 :HRRENWPLL T0325 190 :TETILQLLDMVVCSEGEVFEINCH 1v4vA 215 :SDLAQALKRVAEAFPHLTFVYPVH T0325 239 :TSQEVKEAIEER 1v4vA 239 :LNPVVREAVFPV T0325 251 :GI 1v4vA 253 :GV T0325 253 :LLANYESL 1v4vA 256 :NFVLLDPL Number of specific fragments extracted= 16 number of extra gaps= 0 total=2066 Will force an alignment to be made, even if fragment is small Number of alignments=137 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v4vA/T0325-1v4vA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1v4vA/T0325-1v4vA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v4vA read from 1v4vA/T0325-1v4vA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1v4vA in template set T0325 3 :NKKLIIN 1v4vA 5 :MKRVVLA T0325 13 :FGYTPAVTQG 1v4vA 12 :FGTRPEATKM T0325 23 :IIEAHKRGVVTSTTALPTSP 1v4vA 25 :YLALRGIPGLKPLVLLTGQH T0325 44 :FLEAMESAR 1v4vA 45 :REQLRQALS T0325 54 :SAP 1v4vA 54 :LFG T0325 58 :L 1v4vA 57 :I T0325 78 :EMVPSL 1v4vA 58 :QEDRNL T0325 94 :SIFEEKVNLEEVYNEWDAQI 1v4vA 64 :DVMQERQALPDLAARILPQA T0325 114 :ISFMKSG 1v4vA 85 :RALKEMG T0325 123 :PDHIDSH 1v4vA 92 :ADYVLVH T0325 135 :KNKKLLGVALALARKYQLPL 1v4vA 99 :GDTLTTFAVAWAAFLEGIPV T0325 155 :RNASRSIETKDYLELY 1v4vA 125 :LRSGNLKEPFPEEANR T0325 171 :QDVR 1v4vA 193 :EGLP T0325 175 :TPDEMLYQF 1v4vA 206 :HRRENWPLL T0325 191 :ETILQLLDMVVCSEGEVFEINC 1v4vA 215 :SDLAQALKRVAEAFPHLTFVYP T0325 217 :ID 1v4vA 237 :VH T0325 239 :TSQEVKEAIEER 1v4vA 239 :LNPVVREAVFPV T0325 251 :GI 1v4vA 253 :GV T0325 253 :LLANYESL 1v4vA 256 :NFVLLDPL Number of specific fragments extracted= 19 number of extra gaps= 0 total=2085 Will force an alignment to be made, even if fragment is small Number of alignments=138 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v4vA/T0325-1v4vA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1v4vA/T0325-1v4vA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v4vA read from 1v4vA/T0325-1v4vA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1v4vA in template set Warning: unaligning (T0325)S2 because first residue in template chain is (1v4vA)G4 T0325 3 :NKKLIIN 1v4vA 5 :MKRVVLA T0325 13 :FGYTPAVTQ 1v4vA 12 :FGTRPEATK T0325 22 :GIIEAHKRGVVTSTTALPTSPY 1v4vA 24 :VYLALRGIPGLKPLVLLTGQHR T0325 45 :LEAMESARISAPTLAIG 1v4vA 46 :EQLRQALSLFGIQEDRN T0325 73 :PILP 1v4vA 63 :LDVM T0325 97 :EEKVNLEEVYNEWDAQI 1v4vA 67 :QERQALPDLAARILPQA T0325 114 :ISFMKSG 1v4vA 85 :RALKEMG T0325 123 :PDHIDSHHN 1v4vA 92 :ADYVLVHGD T0325 137 :KKLLGVALALARKYQLPL 1v4vA 101 :TLTTFAVAWAAFLEGIPV T0325 155 :RNASRSIETKDYLEL 1v4vA 124 :GLRSGNLKEPFPEEA T0325 174 :RTPDE 1v4vA 205 :MHRRE T0325 185 :DKAISTETILQLLDMVVCSEGEVFEINCH 1v4vA 210 :NWPLLSDLAQALKRVAEAFPHLTFVYPVH T0325 239 :TSQEVKEAIEE 1v4vA 239 :LNPVVREAVFP T0325 250 :RGILLA 1v4vA 255 :RNFVLL Number of specific fragments extracted= 14 number of extra gaps= 0 total=2099 Will force an alignment to be made, even if fragment is small Number of alignments=139 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wqaA/T0325-1wqaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1wqaA expands to /projects/compbio/data/pdb/1wqa.pdb.gz 1wqaA:# T0325 read from 1wqaA/T0325-1wqaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wqaA read from 1wqaA/T0325-1wqaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1wqaA to template set # found chain 1wqaA in template set T0325 2 :SNKKLIINADDFGYTPAVTQGIIEAHKRGVVTSTTA 1wqaA 40 :KKPLVVVGRDTRVSGEMLKEALISGLLSVGCDVIDV T0325 38 :LPTSPYFLEAME 1wqaA 77 :IAPTPAVQWATK T0325 55 :APTLAIGV 1wqaA 89 :HFNADGGA T0325 65 :TLTL 1wqaA 97 :VITA T0325 73 :PILPREM 1wqaA 101 :SHNPPEY T0325 83 :LVDEAGYFWHQSI 1wqaA 112 :LLEPNGMGLKKER T0325 96 :FEEKVNLEEVYNE 1wqaA 161 :IKSKVDVEAIKKR T0325 122 :RPD 1wqaA 174 :KPF T0325 125 :HIDSHHNVHGKN 1wqaA 178 :VVDTSNGAGSLT T0325 143 :ALALARKYQLPLRNASRSIETK 1wqaA 190 :LPYLLRELGCKVITVNAQPDGY T0325 173 :VRT 1wqaA 212 :FPA T0325 184 :YDKAISTETILQLLDMVVCSEGEVF 1wqaA 215 :RNPEPNEENLKEFMEIVKALGADFG T0325 210 :INCHPAFID 1wqaA 240 :VAQDGDADR T0325 223 :NQSGYCMPRIREVEILT 1wqaA 253 :DENGRFIQGDKTFALVA T0325 243 :VKEAIEERGILLANYE 1wqaA 291 :LDDIAKKHGAKVMRTK Number of specific fragments extracted= 15 number of extra gaps= 0 total=2114 Will force an alignment to be made, even if fragment is small Number of alignments=140 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wqaA/T0325-1wqaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1wqaA/T0325-1wqaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wqaA read from 1wqaA/T0325-1wqaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wqaA in template set T0325 2 :SNKKLIINADDFGYTPAVTQGIIEAHKRGVVTSTTA 1wqaA 40 :KKPLVVVGRDTRVSGEMLKEALISGLLSVGCDVIDV T0325 38 :LPTSPYFLEAME 1wqaA 77 :IAPTPAVQWATK T0325 55 :APTLAIGV 1wqaA 89 :HFNADGGA T0325 65 :TLT 1wqaA 97 :VIT T0325 72 :KPILPREMVP 1wqaA 100 :ASHNPPEYNG T0325 82 :SLVDEAGYFWH 1wqaA 111 :KLLEPNGMGLK T0325 93 :QSIFEEKVNLEEVYNE 1wqaA 158 :IEAIKSKVDVEAIKKR T0325 122 :RPD 1wqaA 174 :KPF T0325 125 :HIDSHHNVHGKN 1wqaA 178 :VVDTSNGAGSLT T0325 143 :ALALARKYQLPLRNASRSIETKDYLELY 1wqaA 190 :LPYLLRELGCKVITVNAQPDGYFPARNP T0325 171 :QDVRTPDEMLY 1wqaA 254 :ENGRFIQGDKT T0325 193 :ILQLLDMVVCSEGE 1wqaA 265 :FALVADAVLKEKGG T0325 208 :FEINCHPAFID 1wqaA 279 :GLLVTTVATSN T0325 220 :I 1wqaA 290 :L T0325 243 :VKEAIEERGILLANYE 1wqaA 291 :LDDIAKKHGAKVMRTK Number of specific fragments extracted= 15 number of extra gaps= 0 total=2129 Will force an alignment to be made, even if fragment is small Number of alignments=141 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wqaA/T0325-1wqaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1wqaA/T0325-1wqaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wqaA read from 1wqaA/T0325-1wqaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wqaA in template set T0325 2 :SNKKLIINADDFGYTPAVTQGIIEAHKRGVVTSTTA 1wqaA 40 :KKPLVVVGRDTRVSGEMLKEALISGLLSVGCDVIDV T0325 38 :LPTSPYFLEAME 1wqaA 77 :IAPTPAVQWATK T0325 55 :APTLAIGVHLTLTLNQ 1wqaA 89 :HFNADGGAVITASHNP T0325 71 :AKPILPREM 1wqaA 138 :DRAKWYEIG T0325 89 :YFWHQSIFEEKVNLEEVYNE 1wqaA 154 :IKPYIEAIKSKVDVEAIKKR T0325 122 :RPD 1wqaA 174 :KPF T0325 125 :HIDSHHNVHGKN 1wqaA 178 :VVDTSNGAGSLT T0325 143 :ALALARKYQLPLRNASRSIETKDYLEL 1wqaA 190 :LPYLLRELGCKVITVNAQPDGYFPARN T0325 179 :MLYQ 1wqaA 257 :RFIQ T0325 188 :ISTETILQLLDMVVCSEGEVFEIN 1wqaA 261 :GDKTFALVADAVLKEKGGGLLVTT T0325 214 :PAF 1wqaA 285 :VAT T0325 218 :DTI 1wqaA 288 :SNL T0325 243 :VKEAIEERGILLANY 1wqaA 291 :LDDIAKKHGAKVMRT Number of specific fragments extracted= 13 number of extra gaps= 0 total=2142 Will force an alignment to be made, even if fragment is small Number of alignments=142 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j5vA/T0325-1j5vA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1j5vA expands to Error: no filename for 1j5vA # T0325 read from 1j5vA/T0325-1j5vA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j5vA read from 1j5vA/T0325-1j5vA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1j5vA to template set Error: can't find template for 1j5vA or 1j5vA, so skipping it. # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j5vA/T0325-1j5vA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1j5vA expands to Error: no filename for 1j5vA # T0325 read from 1j5vA/T0325-1j5vA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j5vA read from 1j5vA/T0325-1j5vA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1j5vA to template set Error: can't find template for 1j5vA or 1j5vA, so skipping it. # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j5vA/T0325-1j5vA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1j5vA expands to Error: no filename for 1j5vA # T0325 read from 1j5vA/T0325-1j5vA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j5vA read from 1j5vA/T0325-1j5vA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1j5vA to template set Error: can't find template for 1j5vA or 1j5vA, so skipping it. # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xmxA/T0325-1xmxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xmxA expands to /projects/compbio/data/pdb/1xmx.pdb.gz 1xmxA:# T0325 read from 1xmxA/T0325-1xmxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xmxA read from 1xmxA/T0325-1xmxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xmxA to template set # found chain 1xmxA in template set Warning: unaligning (T0325)R174 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xmxA)D315 Warning: unaligning (T0325)Y184 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xmxA)D315 T0325 2 :SNKKLIINADD 1xmxA 25 :VSRHIIFIGDH T0325 16 :TPAVTQGIIEAHKRG 1xmxA 37 :QTVIYQRLSDVLNKR T0325 57 :TLAIGV 1xmxA 52 :NISTDF T0325 70 :QAKPIL 1xmxA 58 :FEIPAG T0325 100 :VNLEEVYNEWDAQIISFMKSGRRPDHIDSH 1xmxA 64 :SNTSAIKSAIRELAETLKARGEEVKFNASC T0325 135 :KNKKLLGVALALARKYQLPLRNASRS 1xmxA 94 :GLRHRLLSAYEVFRSYHWPIFVVEPN T0325 171 :QDV 1xmxA 310 :KGM T0325 186 :KAISTETILQLLDMVVCSEGEVFEINCHP 1xmxA 316 :GDDTLYKLESLRDLLGGLQARAMLVSFRP T0325 239 :TSQEVKEAIEERGILLANYESLAM 1xmxA 345 :LRHNDITRAEDLGLALIGPDELKD Number of specific fragments extracted= 9 number of extra gaps= 1 total=2151 Will force an alignment to be made, even if fragment is small Number of alignments=143 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xmxA/T0325-1xmxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1xmxA/T0325-1xmxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xmxA read from 1xmxA/T0325-1xmxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xmxA in template set Warning: unaligning (T0325)Y184 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xmxA)D315 Warning: unaligning (T0325)D185 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xmxA)D315 T0325 2 :SNKKLIINADD 1xmxA 25 :VSRHIIFIGDH T0325 16 :TPAVTQGIIEAHKRG 1xmxA 37 :QTVIYQRLSDVLNKR T0325 57 :TLAIGV 1xmxA 52 :NISTDF T0325 70 :QAKPI 1xmxA 58 :FEIPA T0325 99 :KVNLEEVYNEWDAQIISFMKSGRRPDHIDSH 1xmxA 63 :GSNTSAIKSAIRELAETLKARGEEVKFNASC T0325 135 :KNKKLLGVALALARKYQLPLRNASRS 1xmxA 94 :GLRHRLLSAYEVFRSYHWPIFVVEPN T0325 171 :Q 1xmxA 310 :K T0325 182 :QF 1xmxA 311 :GM T0325 187 :AIS 1xmxA 316 :GDD T0325 190 :TETILQLLDMVVCSEGEVFEINCHP 1xmxA 320 :LYKLESLRDLLGGLQARAMLVSFRP T0325 239 :TSQEVKEAIEERGILLANYESLAM 1xmxA 345 :LRHNDITRAEDLGLALIGPDELKD Number of specific fragments extracted= 11 number of extra gaps= 1 total=2162 Will force an alignment to be made, even if fragment is small Number of alignments=144 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xmxA/T0325-1xmxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1xmxA/T0325-1xmxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xmxA read from 1xmxA/T0325-1xmxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xmxA in template set Warning: unaligning (T0325)I161 because of BadResidue code BAD_PEPTIDE in next template residue (1xmxA)D121 Warning: unaligning (T0325)P176 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xmxA)D315 Warning: unaligning (T0325)D177 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xmxA)D315 T0325 2 :SNKKLIINAD 1xmxA 25 :VSRHIIFIGD T0325 17 :PAVTQGIIEAHKRGVVTSTTA 1xmxA 38 :TVIYQRLSDVLNKRNISTDFF T0325 72 :KPIL 1xmxA 59 :EIPA T0325 99 :KVNLEEVYNEWDAQIISFMKSGRRPDHIDS 1xmxA 63 :GSNTSAIKSAIRELAETLKARGEEVKFNAS T0325 133 :HGK 1xmxA 93 :CGL T0325 137 :KKLLGVALALARKYQLPLRNASRS 1xmxA 96 :RHRLLSAYEVFRSYHWPIFVVEPN T0325 171 :QDVRT 1xmxA 308 :KTKGM T0325 179 :ML 1xmxA 316 :GD T0325 188 :ISTETILQLLDMVVCSEGEVFEINCHP 1xmxA 318 :DTLYKLESLRDLLGGLQARAMLVSFRP T0325 239 :TSQEVKEAIEERGILLANYESLAM 1xmxA 345 :LRHNDITRAEDLGLALIGPDELKD Number of specific fragments extracted= 10 number of extra gaps= 2 total=2172 Will force an alignment to be made, even if fragment is small Number of alignments=145 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1igs/T0325-1igs-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1igs expands to /projects/compbio/data/pdb/1igs.pdb.gz 1igs:Warning: there is no chain 1igs will retry with 1igsA # T0325 read from 1igs/T0325-1igs-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1igs read from 1igs/T0325-1igs-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1igs to template set # found chain 1igs in template set T0325 18 :AVTQGIIEAHKRGVVTSTTALPT 1igs 32 :SLNERILEFNKRNITAIIAEYKR T0325 44 :FLEAMESAR 1igs 66 :PIEYSKFME T0325 57 :TLAIGVHLTLT 1igs 75 :RYAVGLSILTE T0325 81 :PS 1igs 86 :EK T0325 97 :EEKVNLEEVYNEW 1igs 88 :YFNGSYETLRKIA T0325 110 :DAQIISFMKSGRRPDHI 1igs 116 :ESQIDDAYNLGADTVLL T0325 131 :NVHGKNKKLLGVALALARKYQLPLRNASRS 1igs 133 :IVKILTERELESLLEYARSYGMEPLIEIND T0325 164 :KDYLELY 1igs 163 :ENDLDIA T0325 171 :QDVRTPDEMLYQFYDKAISTETILQLL 1igs 172 :IGARFIGINSRDLETLEINKENQRKLI T0325 201 :VCSEGEVFEINCHPA 1igs 199 :SMIPSNVVKVAESGI T0325 218 :DTI 1igs 214 :SER T0325 241 :QEV 1igs 217 :NEI T0325 245 :EAIEERGILLAN 1igs 220 :EELRKLGVNAFL Number of specific fragments extracted= 13 number of extra gaps= 0 total=2185 Will force an alignment to be made, even if fragment is small Number of alignments=146 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1igs/T0325-1igs-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1igs/T0325-1igs-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1igs read from 1igs/T0325-1igs-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1igs in template set T0325 18 :AVTQGIIEAHKRGVVTSTTALPT 1igs 32 :SLNERILEFNKRNITAIIAEYKR T0325 41 :SPY 1igs 56 :SPS T0325 44 :FLEAMESAR 1igs 66 :PIEYSKFME T0325 57 :TLAIGVHLTLT 1igs 75 :RYAVGLSILTE T0325 81 :PSLV 1igs 86 :EKYF T0325 99 :KVNLEEVYNEW 1igs 90 :NGSYETLRKIA T0325 110 :DAQIISFMKSGRRPDHI 1igs 116 :ESQIDDAYNLGADTVLL T0325 131 :NVHGKNKKLLGVALALARKYQLPLRNASRSIETKDYLEL 1igs 133 :IVKILTERELESLLEYARSYGMEPLIEINDENDLDIALR T0325 171 :QDVRTPDEMLYQFYDKAISTETILQLLDMV 1igs 172 :IGARFIGINSRDLETLEINKENQRKLISMI T0325 204 :EGEVFEINCHP 1igs 202 :PSNVVKVAESG T0325 217 :IDT 1igs 213 :ISE T0325 240 :SQEVKE 1igs 216 :RNEIEE T0325 247 :IEERGILLAN 1igs 222 :LRKLGVNAFL Number of specific fragments extracted= 13 number of extra gaps= 0 total=2198 Will force an alignment to be made, even if fragment is small Number of alignments=147 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1igs/T0325-1igs-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1igs/T0325-1igs-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1igs read from 1igs/T0325-1igs-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1igs in template set T0325 19 :VTQGIIEAHKRGVVTSTTALPT 1igs 33 :LNERILEFNKRNITAIIAEYKR T0325 44 :FLEAMESARI 1igs 66 :PIEYSKFMER T0325 58 :LAIGVHLT 1igs 76 :YAVGLSIL T0325 67 :TLN 1igs 84 :TEE T0325 86 :E 1igs 87 :K T0325 97 :EEKVNLEEVYNEW 1igs 88 :YFNGSYETLRKIA T0325 110 :DAQIISFMKSGRRPDHI 1igs 116 :ESQIDDAYNLGADTVLL T0325 131 :NVHGKNKKLLGVALALARKYQLPLRNASRSIETKDYLEL 1igs 133 :IVKILTERELESLLEYARSYGMEPLIEINDENDLDIALR T0325 170 :YQDVRT 1igs 182 :RDLETL T0325 190 :TETILQLLDMVVCSEGEVFEINCHPAFID 1igs 188 :EINKENQRKLISMIPSNVVKVAESGISER T0325 241 :QEVKE 1igs 217 :NEIEE T0325 247 :IEERGILLA 1igs 222 :LRKLGVNAF Number of specific fragments extracted= 12 number of extra gaps= 0 total=2210 Will force an alignment to be made, even if fragment is small Number of alignments=148 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c3zA/T0325-2c3zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2c3zA expands to /projects/compbio/data/pdb/2c3z.pdb.gz 2c3zA:# T0325 read from 2c3zA/T0325-2c3zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c3zA read from 2c3zA/T0325-2c3zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2c3zA to template set # found chain 2c3zA in template set T0325 18 :AVTQGIIEAHKRGVVTSTTALPT 2c3zA 32 :SLNERILEFNKRNITAIIAEYKR T0325 44 :FLEAMESARISA 2c3zA 66 :PIEYSKFMERYA T0325 60 :IGVHL 2c3zA 78 :VGLSI T0325 66 :LT 2c3zA 83 :LT T0325 92 :H 2c3zA 85 :E T0325 95 :IFEEKVNLEEVYNEW 2c3zA 86 :EKYFNGSYETLRKIA T0325 110 :DAQIISFMKSGRRPDHI 2c3zA 116 :ESQIDDAYNLGADTVLL T0325 131 :NVHGKNKKLLGVALALARKYQLPLRNASR 2c3zA 133 :IVKILTERELESLLEYARSYGMEPLIEIN T0325 163 :TKDYLELY 2c3zA 162 :DENDLDIA T0325 171 :QDVRTPDEMLYQFYDKAISTETILQLLD 2c3zA 172 :IGARFIGINSRDLETLEINKENQRKLIS T0325 202 :CSEGEVFEINCHPAFIDTI 2c3zA 200 :MIPSNVVKVAESGISERNE T0325 235 :VE 2c3zA 219 :IE T0325 246 :AIEERGILLA 2c3zA 221 :ELRKLGVNAF Number of specific fragments extracted= 13 number of extra gaps= 0 total=2223 Will force an alignment to be made, even if fragment is small Number of alignments=149 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c3zA/T0325-2c3zA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 2c3zA/T0325-2c3zA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c3zA read from 2c3zA/T0325-2c3zA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2c3zA in template set T0325 18 :AVTQGIIEAHKRGVVTSTTALPTS 2c3zA 32 :SLNERILEFNKRNITAIIAEYKRK T0325 42 :P 2c3zA 57 :P T0325 44 :FLEAMESARISA 2c3zA 66 :PIEYSKFMERYA T0325 60 :IGVHLTLT 2c3zA 78 :VGLSILTE T0325 95 :IFEEKVNLEEVYNEW 2c3zA 86 :EKYFNGSYETLRKIA T0325 110 :DAQIISFMKSGRRPDHI 2c3zA 116 :ESQIDDAYNLGADTVLL T0325 131 :NVHGKNKKLLGVALALARKYQLPLRNASRSIETKDYLEL 2c3zA 133 :IVKILTERELESLLEYARSYGMEPLIEINDENDLDIALR T0325 171 :QDVRTPDEMLYQFYDKAISTETILQLLDMV 2c3zA 172 :IGARFIGINSRDLETLEINKENQRKLISMI T0325 204 :EGEVFEINCHP 2c3zA 202 :PSNVVKVAESG T0325 217 :IDT 2c3zA 213 :ISE T0325 232 :IREVEIL 2c3zA 216 :RNEIEEL T0325 248 :EERGILLA 2c3zA 223 :RKLGVNAF Number of specific fragments extracted= 12 number of extra gaps= 0 total=2235 Will force an alignment to be made, even if fragment is small Number of alignments=150 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c3zA/T0325-2c3zA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 2c3zA/T0325-2c3zA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c3zA read from 2c3zA/T0325-2c3zA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2c3zA in template set T0325 19 :VTQGIIEAHKRGVVTSTTALPTS 2c3zA 33 :LNERILEFNKRNITAIIAEYKRK T0325 44 :FLEAMESARISA 2c3zA 66 :PIEYSKFMERYA T0325 60 :IGVHL 2c3zA 78 :VGLSI T0325 66 :LT 2c3zA 83 :LT T0325 80 :V 2c3zA 85 :E T0325 95 :IFEEKVNLEEVYNEW 2c3zA 86 :EKYFNGSYETLRKIA T0325 110 :DAQIISFMKSGRRPDHI 2c3zA 116 :ESQIDDAYNLGADTVLL T0325 131 :NVHGKNKKLLGVALALARKYQLPLRNASRSIETKDYLEL 2c3zA 133 :IVKILTERELESLLEYARSYGMEPLIEINDENDLDIALR T0325 170 :Y 2c3zA 182 :R T0325 185 :DKAISTETILQLLDMVVCSEGEVFEINCHPAFIDTILQ 2c3zA 183 :DLETLEINKENQRKLISMIPSNVVKVAESGISERNEIE T0325 237 :I 2c3zA 221 :E T0325 247 :IEERGILLA 2c3zA 222 :LRKLGVNAF Number of specific fragments extracted= 12 number of extra gaps= 0 total=2247 Will force an alignment to be made, even if fragment is small Number of alignments=151 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1k1xA/T0325-1k1xA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1k1xA expands to /projects/compbio/data/pdb/1k1x.pdb.gz 1k1xA:# T0325 read from 1k1xA/T0325-1k1xA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1k1xA read from 1k1xA/T0325-1k1xA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1k1xA to template set # found chain 1k1xA in template set T0325 4 :KKLIINADDFGYTPAVTQ 1k1xA 7 :IFGIHNHQPLGNFGWVFE T0325 25 :EAHKR 1k1xA 25 :EAYNR T0325 43 :YFLEAMESAR 1k1xA 30 :SYRPFMEILE T0325 54 :SAPTLAIGVHL 1k1xA 40 :EFPEMKVNVHF T0325 67 :T 1k1xA 51 :S T0325 88 :GY 1k1xA 52 :GP T0325 101 :NLEEVYNE 1k1xA 54 :LLEWIEEN T0325 109 :WDAQIISFMKSGRRPDHIDSHH 1k1xA 65 :YLDLLRSLIKRGQLEIVVAGFY T0325 131 :NVHGKNKK 1k1xA 88 :PVLAAIPK T0325 139 :LLGVALALARKYQL 1k1xA 101 :QIEMLKDYARKLGY T0325 153 :PLRNASRSIETKDYLELY 1k1xA 117 :KGVWLTERVWQPELVKSL T0325 173 :VRTPDEMLYQFY 1k1xA 175 :FPIDEKLRYLIP T0325 187 :AISTETILQLLDMVVCSEGEVFEINCHPAFI 1k1xA 187 :FRPVKKTIEYLESLTSDDPSKVAVFHDDGEK T0325 218 :DTILQNQSGYCMPRI 1k1xA 222 :PGTYEWVYEKGWLRE T0325 243 :VKEAIEERG 1k1xA 237 :FFDAITSNE T0325 252 :ILL 1k1xA 247 :INL Number of specific fragments extracted= 16 number of extra gaps= 0 total=2263 Will force an alignment to be made, even if fragment is small Number of alignments=152 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1k1xA/T0325-1k1xA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1k1xA/T0325-1k1xA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1k1xA read from 1k1xA/T0325-1k1xA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1k1xA in template set T0325 4 :KKLIINADDFGYTPAVTQ 1k1xA 7 :IFGIHNHQPLGNFGWVFE T0325 25 :EAHKR 1k1xA 25 :EAYNR T0325 43 :YFLEAMESAR 1k1xA 30 :SYRPFMEILE T0325 54 :SAPTLAIGVHL 1k1xA 40 :EFPEMKVNVHF T0325 67 :T 1k1xA 51 :S T0325 88 :G 1k1xA 52 :G T0325 102 :LEEVYNE 1k1xA 55 :LEWIEEN T0325 109 :WDAQIISFMKSGRRPDHIDSHH 1k1xA 65 :YLDLLRSLIKRGQLEIVVAGFY T0325 131 :NVHGKNKK 1k1xA 88 :PVLAAIPK T0325 139 :LLGVALALARKYQL 1k1xA 101 :QIEMLKDYARKLGY T0325 153 :PLRNASRSIETKDYLELY 1k1xA 117 :KGVWLTERVWQPELVKSL T0325 173 :VRTPDEMLYQFYD 1k1xA 175 :FPIDEKLRYLIPF T0325 188 :ISTETILQLLDMVVCSEGEVFEINCHPAF 1k1xA 188 :RPVKKTIEYLESLTSDDPSKVAVFHDDGE T0325 217 :IDTILQNQSGYCMPR 1k1xA 221 :WPGTYEWVYEKGWLR T0325 242 :EVKEAIEERG 1k1xA 236 :EFFDAITSNE T0325 252 :ILL 1k1xA 247 :INL Number of specific fragments extracted= 16 number of extra gaps= 0 total=2279 Will force an alignment to be made, even if fragment is small Number of alignments=153 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1k1xA/T0325-1k1xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1k1xA/T0325-1k1xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1k1xA read from 1k1xA/T0325-1k1xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1k1xA in template set T0325 3 :NKKLIINA 1k1xA 2 :ERINFIFG T0325 11 :DDFGYTPAVTQ 1k1xA 14 :QPLGNFGWVFE T0325 25 :EAHKR 1k1xA 25 :EAYNR T0325 43 :YFLEAMESARI 1k1xA 30 :SYRPFMEILEE T0325 55 :APTLAIGVHL 1k1xA 41 :FPEMKVNVHF T0325 89 :YFWH 1k1xA 51 :SGPL T0325 102 :LEEVYNE 1k1xA 55 :LEWIEEN T0325 109 :WDAQIISFMKSGRRPDHIDSHHNVHGKN 1k1xA 65 :YLDLLRSLIKRGQLEIVVAGFYEPVLAA T0325 137 :K 1k1xA 94 :P T0325 139 :LLGVALALARKYQLPLR 1k1xA 101 :QIEMLKDYARKLGYDAK T0325 156 :NASRSIETKDYLEL 1k1xA 120 :WLTERVWQPELVKS T0325 183 :FYDKAISTETILQLLDMVVCSEGEVFEINCHPAFID 1k1xA 183 :YLIPFRPVKKTIEYLESLTSDDPSKVAVFHDDGEKF T0325 219 :TILQNQSGYCMPR 1k1xA 223 :GTYEWVYEKGWLR T0325 242 :EVKEAIEERG 1k1xA 236 :EFFDAITSNE T0325 252 :ILLAN 1k1xA 247 :INLMT Number of specific fragments extracted= 15 number of extra gaps= 0 total=2294 Will force an alignment to be made, even if fragment is small Number of alignments=154 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bp1A/T0325-2bp1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2bp1A expands to /projects/compbio/data/pdb/2bp1.pdb.gz 2bp1A:# T0325 read from 2bp1A/T0325-2bp1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bp1A read from 2bp1A/T0325-2bp1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2bp1A to template set # found chain 2bp1A in template set Warning: unaligning (T0325)N3 because first residue in template chain is (2bp1A)R38 Warning: unaligning (T0325)P73 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bp1A)L115 Warning: unaligning (T0325)V100 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bp1A)L115 Warning: unaligning (T0325)D127 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bp1A)L141 Warning: unaligning (T0325)S128 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bp1A)L141 T0325 4 :KKLIINADDFG 2bp1A 39 :VASVLGTMEMG T0325 17 :PAVTQGIIEAHKRGVVTSTTALPTSPY 2bp1A 55 :PASAAAVRAFLERGHTELDTAFMYSDG T0325 46 :EAMESAR 2bp1A 82 :QSETILG T0325 53 :ISAPTLAIGVHLTLTLNQAK 2bp1A 94 :LGGGDCRVKIATKANPWDGK T0325 101 :NLEEVYNEWDAQIISF 2bp1A 116 :KPDSVRSQLETSLKRL T0325 120 :GRRPDHI 2bp1A 133 :CPQVDLF T0325 129 :HHNVH 2bp1A 142 :HAPDH T0325 135 :KNKK 2bp1A 147 :GTPV T0325 139 :LLGVALALARK 2bp1A 153 :TLHACQRLHQE T0325 151 :QL 2bp1A 164 :GK T0325 154 :LRN 2bp1A 166 :FVE T0325 182 :Q 2bp1A 169 :L T0325 187 :AISTETILQLLDMVVCSEGEVFEINC 2bp1A 173 :NYASWEVAEICTLCKSNGWILPTVYQ T0325 213 :HPAFIDTILQN 2bp1A 201 :YNATTRQVETE T0325 243 :VKEAIEERGILLANY 2bp1A 212 :LFPCLRHFGLRFYAY Number of specific fragments extracted= 15 number of extra gaps= 2 total=2309 Will force an alignment to be made, even if fragment is small Number of alignments=155 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bp1A/T0325-2bp1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 2bp1A/T0325-2bp1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bp1A read from 2bp1A/T0325-2bp1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bp1A in template set Warning: unaligning (T0325)N3 because first residue in template chain is (2bp1A)R38 Warning: unaligning (T0325)P73 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bp1A)L115 Warning: unaligning (T0325)V100 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bp1A)L115 Warning: unaligning (T0325)D127 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bp1A)L141 Warning: unaligning (T0325)S128 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bp1A)L141 T0325 4 :KKLIINADDFG 2bp1A 39 :VASVLGTMEMG T0325 17 :PAVTQGIIEAHKRGVVTSTTALPTSPY 2bp1A 55 :PASAAAVRAFLERGHTELDTAFMYSDG T0325 46 :EAMESARI 2bp1A 82 :QSETILGG T0325 55 :A 2bp1A 90 :L T0325 56 :PTLAIGVHLTLTLNQAK 2bp1A 97 :GDCRVKIATKANPWDGK T0325 101 :NLEEVYNEWDAQIISF 2bp1A 116 :KPDSVRSQLETSLKRL T0325 120 :GRRPDHI 2bp1A 133 :CPQVDLF T0325 129 :HHNVH 2bp1A 142 :HAPDH T0325 135 :KNKK 2bp1A 147 :GTPV T0325 139 :LLGVALALARKY 2bp1A 153 :TLHACQRLHQEG T0325 152 :L 2bp1A 165 :K T0325 154 :LRN 2bp1A 166 :FVE T0325 187 :AISTETILQLLDMVVCSEGEVFEIN 2bp1A 173 :NYASWEVAEICTLCKSNGWILPTVY T0325 212 :CHPAFIDTILQN 2bp1A 200 :MYNATTRQVETE T0325 243 :VKEAIEERGILLANY 2bp1A 212 :LFPCLRHFGLRFYAY Number of specific fragments extracted= 15 number of extra gaps= 2 total=2324 Will force an alignment to be made, even if fragment is small Number of alignments=156 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bp1A/T0325-2bp1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 2bp1A/T0325-2bp1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bp1A read from 2bp1A/T0325-2bp1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bp1A in template set Warning: unaligning (T0325)N3 because first residue in template chain is (2bp1A)R38 Warning: unaligning (T0325)K99 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bp1A)L115 Warning: unaligning (T0325)V100 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bp1A)L115 Warning: unaligning (T0325)D127 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bp1A)L141 Warning: unaligning (T0325)S128 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bp1A)L141 T0325 4 :KKLIINADDFGY 2bp1A 39 :VASVLGTMEMGR T0325 17 :PAVTQGIIEAHKRGVVTSTTALPTSPY 2bp1A 55 :PASAAAVRAFLERGHTELDTAFMYSDG T0325 46 :EAMESARI 2bp1A 82 :QSETILGG T0325 55 :APTLAIGVHLT 2bp1A 96 :GGDCRVKIATK T0325 69 :NQAKPIL 2bp1A 107 :ANPWDGK T0325 101 :NLEEVYNEWDAQIISF 2bp1A 116 :KPDSVRSQLETSLKRL T0325 119 :SGRRPDHI 2bp1A 132 :QCPQVDLF T0325 129 :HHNVHGK 2bp1A 142 :HAPDHGT T0325 137 :K 2bp1A 149 :P T0325 140 :LGVALALARKY 2bp1A 150 :VEETLHACQRL T0325 177 :DEMLYQFYDKAISTETILQLLDMVVCSEGEVFEINC 2bp1A 163 :EGKFVELGLSNYASWEVAEICTLCKSNGWILPTVYQ T0325 213 :HPAFIDTILQN 2bp1A 201 :YNATTRQVETE T0325 243 :VKEAIEERGILLANY 2bp1A 212 :LFPCLRHFGLRFYAY Number of specific fragments extracted= 13 number of extra gaps= 2 total=2337 Will force an alignment to be made, even if fragment is small Number of alignments=157 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i8jA/T0325-1i8jA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1i8jA expands to /projects/compbio/data/pdb/1i8j.pdb.gz 1i8jA:# T0325 read from 1i8jA/T0325-1i8jA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i8jA read from 1i8jA/T0325-1i8jA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1i8jA to template set # found chain 1i8jA in template set T0325 17 :PAVTQGIIEAHKRGVVTSTTALPTSP 1i8jA 58 :KHLAREIERIANAGIRSVMTFGISHH T0325 43 :YFLEAMESARISAPTLAIGVHLTLT 1i8jA 97 :LVARMSRICKQTVPEMIVMSDTCFC T0325 73 :PIL 1i8jA 122 :EYT T0325 86 :EAGYFWHQ 1i8jA 125 :SHGHCGVL T0325 96 :FEEKVNLEEVYNEWDAQIISFMKSG 1i8jA 133 :CEHGVDNDATLENLGKQAVVAAAAG T0325 123 :PDHIDSHH 1i8jA 158 :ADFIAPSA T0325 135 :KNKKLLGVALALARKYQLPLRNA 1i8jA 166 :AMDGQVQAIRQALDAAGFKDTAI T0325 158 :SRSIETKDYLELYQDVRTPDEMLYQFYDKA 1i8jA 194 :KFASSFYGPFREAAGSALKGDRKSYQMNPM T0325 189 :STETILQLLDMVVCSEGEVF 1i8jA 224 :NRREAIRESLLDEAQGADCL T0325 210 :INCHPAFIDTILQNQSGYCM 1i8jA 244 :MVKPAGAYLDIVRELRERTE T0325 232 :IREVEILT 1i8jA 272 :SGEYAMIK T0325 240 :SQEVKEAIEE 1i8jA 290 :EKVVLESLGS T0325 250 :RGILLA 1i8jA 303 :AGADLI Number of specific fragments extracted= 13 number of extra gaps= 0 total=2350 Will force an alignment to be made, even if fragment is small Number of alignments=158 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i8jA/T0325-1i8jA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1i8jA/T0325-1i8jA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i8jA read from 1i8jA/T0325-1i8jA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1i8jA in template set T0325 17 :PAVTQGIIEAHKRGVVTSTTALPTSP 1i8jA 58 :KHLAREIERIANAGIRSVMTFGISHH T0325 43 :YFLEAMESARISAPTLAIGVHLTLT 1i8jA 97 :LVARMSRICKQTVPEMIVMSDTCFC T0325 82 :SLV 1i8jA 122 :EYT T0325 86 :EAGYFWH 1i8jA 125 :SHGHCGV T0325 95 :IFEEKVNLEEVYNEWDAQIISFMKSG 1i8jA 132 :LCEHGVDNDATLENLGKQAVVAAAAG T0325 123 :PDHIDSHH 1i8jA 158 :ADFIAPSA T0325 135 :KNKKLLGVALALARKYQL 1i8jA 166 :AMDGQVQAIRQALDAAGF T0325 153 :PLRN 1i8jA 187 :AIMS T0325 157 :ASRSIETKDYLELYQDVRTPDEMLYQFYDKA 1i8jA 193 :TKFASSFYGPFREAAGSALKGDRKSYQMNPM T0325 189 :STETILQLLDMVVCSEGEVFEIN 1i8jA 224 :NRREAIRESLLDEAQGADCLMVK T0325 213 :HPAF 1i8jA 247 :PAGA T0325 217 :ID 1i8jA 252 :LD T0325 219 :TILQNQS 1i8jA 257 :ELRERTE T0325 226 :GYCMPRIREVEILTS 1i8jA 285 :GAIDEEKVVLESLGS T0325 247 :IEERGILLA 1i8jA 300 :IKRAGADLI Number of specific fragments extracted= 15 number of extra gaps= 0 total=2365 Will force an alignment to be made, even if fragment is small Number of alignments=159 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i8jA/T0325-1i8jA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0325 read from 1i8jA/T0325-1i8jA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i8jA read from 1i8jA/T0325-1i8jA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1i8jA in template set T0325 17 :PAVTQGIIEAHKRGVVTSTTALPTSP 1i8jA 58 :KHLAREIERIANAGIRSVMTFGISHH T0325 43 :YFLEAMESARISAPTLAIGVHLTLTLNQA 1i8jA 97 :LVARMSRICKQTVPEMIVMSDTCFCEYTS T0325 76 :PREMVPSLV 1i8jA 126 :HGHCGVLCE T0325 98 :EKVNLEEVYNEWDAQIISFMKSG 1i8jA 135 :HGVDNDATLENLGKQAVVAAAAG T0325 123 :PDHIDSHHN 1i8jA 158 :ADFIAPSAA T0325 136 :NKKLLGVALALARKYQLPLRNAS 1i8jA 167 :MDGQVQAIRQALDAAGFKDTAIM T0325 159 :RSIETKDYLELYQDVRTPDEM 1i8jA 195 :FASSFYGPFREAAGSALKGDR T0325 181 :YQFYDKAISTETILQLLDMVVCSEGEVFEINCHPAFID 1i8jA 216 :KSYQMNPMNRREAIRESLLDEAQGADCLMVKPAGAYLD T0325 232 :IREVEILT 1i8jA 272 :SGEYAMIK T0325 240 :SQEVKEAIEE 1i8jA 290 :EKVVLESLGS T0325 250 :RGILLA 1i8jA 303 :AGADLI Number of specific fragments extracted= 11 number of extra gaps= 0 total=2376 Will force an alignment to be made, even if fragment is small Number of alignments=160 # command:CPU_time= 47.064 sec, elapsed time= 100.995 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 160 Adding 34191 constraints to all_contacts Done adding distance constraints # command:CPU_time= 47.280 sec, elapsed time= 101.227 sec. # command:Reading probabilities from T0325.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 34.268 Optimizing... Probability sum: -480.793, CN propb: -480.793 weights: 0.181 constraints: 1136 # command:CPU_time= 1041.762 sec, elapsed time= 1096.271 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 1136 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 1136 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 6632 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 6632 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 24363 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 24363 # command:CPU_time= 1042.344 sec, elapsed time= 1097.272 sec. # command: