# 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: 408,82794,639987 # 79931 residues have no bad marker # 573 residues lack atoms needed to compute omega # 313 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 0 # HAS_OXT 264 # TOO_MANY_ATOMS 0 # TOO_FEW_ATOMS 378 # HAS_UNKNOWN_ATOMS 0 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 148 # NON_PLANAR_PEPTIDE 17 # BAD_PEPTIDE 812 # HIGH_B_FACTOR 1566 # 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 T0618 numbered 1 through 182 Created new target T0618 from T0618.a2m # command:CPU_time= 5.769 sec, elapsed time= 9.105 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hf8A/T0618-1hf8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1hf8A expands to /projects/compbio/data/pdb/1hf8.pdb.gz 1hf8A:# T0618 read from 1hf8A/T0618-1hf8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hf8A read from 1hf8A/T0618-1hf8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1hf8A to template set # found chain 1hf8A in template set T0618 31 :ESMKR 1hf8A 115 :LQGYD # choosing archetypes in rotamer library T0618 36 :STFVDTTLKILPLLYLKASMLPKC 1hf8A 121 :STFIRRYSRYLNEKAVSYRQVAFD T0618 60 :EMIGDESPETYVTEE 1hf8A 148 :VKRGADGVMRTMNTE T0618 75 :IYE 1hf8A 164 :LLK T0618 79 :LRINLASILA 1hf8A 167 :TVPIIQNQMD T0618 95 :EV 1hf8A 180 :DF T0618 106 :EPIKKNISEDLAD 1hf8A 182 :NVNSNELTNGVIN T0618 119 :IYQDIKDFIFVFQLGL 1hf8A 207 :LFAAYNEGIINLLEKY T0618 135 :NETMNDSLAICQENFGL 1hf8A 227 :KNQCKEGLDIYKKFLTR T0618 154 :GQKLVNTMRALHDVKYSPK 1hf8A 244 :MTRISEFLKVAEQVGIDRG T0618 173 :ARLEHHHH 1hf8A 265 :PDLSQAPS Number of specific fragments extracted= 11 number of extra gaps= 0 total=11 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 1hf8A/T0618-1hf8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0618 read from 1hf8A/T0618-1hf8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hf8A read from 1hf8A/T0618-1hf8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1hf8A in template set T0618 10 :DKNVIEF 1hf8A 114 :GLQGYDM T0618 36 :STFVDTTLKILPLLYLKASMLPK 1hf8A 121 :STFIRRYSRYLNEKAVSYRQVAF T0618 59 :CEMIGDESPETYVTEEIYEVLR 1hf8A 148 :VKRGADGVMRTMNTEKLLKTVP T0618 82 :NLASILA 1hf8A 170 :IIQNQMD T0618 92 :D 1hf8A 180 :D T0618 105 :DEPIKKNISEDLAD 1hf8A 181 :FNVNSNELTNGVIN T0618 119 :IYQDIKDFIFVFQLG 1hf8A 207 :LFAAYNEGIINLLEK T0618 134 :LNETMNDSLAICQENFGLL 1hf8A 226 :KKNQCKEGLDIYKKFLTRM T0618 155 :QKLVNTMRALHDVKYSPKARLEHHHH 1hf8A 245 :TRISEFLKVAEQVGIDRGDIPDLSQA Number of specific fragments extracted= 9 number of extra gaps= 0 total=20 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 1hf8A/T0618-1hf8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0618 read from 1hf8A/T0618-1hf8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hf8A read from 1hf8A/T0618-1hf8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1hf8A in template set T0618 8 :IFDKNVIEFVTVAAEFCAF 1hf8A 112 :KSGLQGYDMSTFIRRYSRY T0618 39 :VDTTLKILPLL 1hf8A 131 :LNEKAVSYRQV T0618 54 :SMLPKCEMIGDESPETYVTEEIYEVLR 1hf8A 143 :FDFTKVKRGADGVMRTMNTEKLLKTVP T0618 82 :NLASILA 1hf8A 170 :IIQNQMD T0618 92 :DYLEVF 1hf8A 177 :ALLDFN T0618 107 :PIKKNISEDLA 1hf8A 183 :VNSNELTNGVI T0618 118 :DIYQDIKDFIFVFQLGLNET 1hf8A 206 :RLFAAYNEGIINLLEKYFDM T0618 138 :MNDSLAICQENFGLL 1hf8A 230 :CKEGLDIYKKFLTRM T0618 155 :QKLVNTMRALHDVKYSPKARLEHHHHHH 1hf8A 245 :TRISEFLKVAEQVGIDRGDIPDLSQAPS Number of specific fragments extracted= 9 number of extra gaps= 0 total=29 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 1i9gA/T0618-1i9gA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1i9gA expands to /projects/compbio/data/pdb/1i9g.pdb.gz 1i9gA:# T0618 read from 1i9gA/T0618-1i9gA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i9gA read from 1i9gA/T0618-1i9gA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1i9gA to template set # found chain 1i9gA in template set T0618 41 :TTLKILPL 1i9gA 86 :KDAAQIVH T0618 49 :LYLKASML 1i9gA 113 :LTLSLLRA T0618 57 :PKC 1i9gA 122 :GPA T0618 60 :EM 1i9gA 126 :QV T0618 70 :YVTEEIYEVLRINLASILAEKDDYLEVFLPDMAYSDEPIK 1i9gA 131 :EQRADHAEHARRNVSGCYGQPPDNWRLVVSDLADSELPDG T0618 110 :KNISE 1i9gA 180 :LAPWE T0618 119 :I 1i9gA 185 :V T0618 123 :IKDFIFV 1i9gA 186 :LDAVSRL T0618 132 :LGLNETMNDSLAICQEN 1i9gA 203 :VATVTQLSRIVEALRAK Number of specific fragments extracted= 9 number of extra gaps= 0 total=38 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 1i9gA/T0618-1i9gA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0618 read from 1i9gA/T0618-1i9gA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i9gA read from 1i9gA/T0618-1i9gA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1i9gA in template set T0618 37 :TFVDTTLKI 1i9gA 86 :KDAAQIVHE T0618 49 :LYLKASMLP 1i9gA 113 :LTLSLLRAV T0618 62 :IGDESP 1i9gA 122 :GPAGQV T0618 70 :YVTEEIYEVLRINLASILAEKDDYLEVFLPDMAYSDEPIK 1i9gA 131 :EQRADHAEHARRNVSGCYGQPPDNWRLVVSDLADSELPDG T0618 110 :KNISEDLADIYQDIK 1i9gA 180 :LAPWEVLDAVSRLLV T0618 127 :IFVFQL 1i9gA 199 :LMVYVA T0618 134 :LNETMNDSLAICQEN 1i9gA 205 :TVTQLSRIVEALRAK Number of specific fragments extracted= 7 number of extra gaps= 0 total=45 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 1i9gA/T0618-1i9gA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0618 read from 1i9gA/T0618-1i9gA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i9gA read from 1i9gA/T0618-1i9gA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1i9gA in template set T0618 37 :TFVDTTLKIL 1i9gA 86 :KDAAQIVHEG T0618 47 :PLLYLKASMLPKCEM 1i9gA 112 :ALTLSLLRAVGPAGQ T0618 70 :YVTEEIYEVLRINLASILAEKDDYLEVFL 1i9gA 131 :EQRADHAEHARRNVSGCYGQPPDNWRLVV T0618 99 :PDMAYSDE 1i9gA 163 :ADSELPDG T0618 107 :PIKKNISEDLADI 1i9gA 180 :LAPWEVLDAVSRL T0618 129 :VFQLGLNETMNDSLAICQE 1i9gA 200 :MVYVATVTQLSRIVEALRA Number of specific fragments extracted= 6 number of extra gaps= 0 total=51 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 2fl7A/T0618-2fl7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2fl7A expands to /projects/compbio/data/pdb/2fl7.pdb.gz 2fl7A:# T0618 read from 2fl7A/T0618-2fl7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fl7A read from 2fl7A/T0618-2fl7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2fl7A to template set # found chain 2fl7A in template set Warning: unaligning (T0618)P67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fl7A)I166 Warning: unaligning (T0618)L87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fl7A)I166 T0618 21 :AEFCAFLER 2fl7A 99 :KLYYEQFRP T0618 31 :ESMKRSTFVDTTLKILPL 2fl7A 108 :DLIKEDHPLEFYKDKFFN T0618 58 :KC 2fl7A 144 :KD T0618 60 :EMIGDES 2fl7A 151 :QILPESQ T0618 89 :EKDDY 2fl7A 167 :EDRDF T0618 94 :LEVFLPD 2fl7A 173 :VRYACEP T0618 103 :YSDEPIKKNISEDLADI 2fl7A 180 :TAEKFVPIDIFQIIRRV T0618 124 :K 2fl7A 197 :K T0618 131 :Q 2fl7A 198 :E T0618 134 :LNE 2fl7A 199 :MEP T0618 139 :NDSLAICQEN 2fl7A 202 :KQSDEYLKRV Number of specific fragments extracted= 11 number of extra gaps= 0 total=62 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 2fl7A/T0618-2fl7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0618 read from 2fl7A/T0618-2fl7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fl7A read from 2fl7A/T0618-2fl7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fl7A in template set Warning: unaligning (T0618)P67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fl7A)I166 Warning: unaligning (T0618)L87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fl7A)I166 T0618 21 :AEFCAFLER 2fl7A 99 :KLYYEQFRP T0618 31 :ESMKRSTFVDTTLKILPL 2fl7A 108 :DLIKEDHPLEFYKDKFFN T0618 57 :PK 2fl7A 144 :KD T0618 59 :CEMIGDES 2fl7A 150 :GQILPESQ T0618 88 :AEKDDYLEVFLPDM 2fl7A 167 :EDRDFLVRYACEPT T0618 104 :SDEPIKKNIS 2fl7A 181 :AEKFVPIDIF T0618 118 :DIYQDIKD 2fl7A 191 :QIIRRVKE T0618 132 :LGL 2fl7A 199 :MEP T0618 139 :NDSLAICQEN 2fl7A 202 :KQSDEYLKRV Number of specific fragments extracted= 9 number of extra gaps= 0 total=71 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 2fl7A/T0618-2fl7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0618 read from 2fl7A/T0618-2fl7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fl7A read from 2fl7A/T0618-2fl7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fl7A in template set Warning: unaligning (T0618)P67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fl7A)I166 Warning: unaligning (T0618)E74 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fl7A)I166 T0618 21 :AEFCAFLERA 2fl7A 99 :KLYYEQFRPD T0618 31 :ESMKRSTFVDTTLK 2fl7A 112 :EDHPLEFYKDKFFN T0618 57 :PKCEMIGDES 2fl7A 148 :AVGQILPESQ T0618 88 :AEKDDYLEVFLP 2fl7A 167 :EDRDFLVRYACE T0618 102 :AYSDEPIKKNISE 2fl7A 179 :PTAEKFVPIDIFQ T0618 126 :FIFVFQLGL 2fl7A 192 :IIRRVKEME T0618 138 :MNDSLAICQEN 2fl7A 201 :PKQSDEYLKRV Number of specific fragments extracted= 7 number of extra gaps= 0 total=78 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 3cf6E/T0618-3cf6E-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3cf6E expands to /projects/compbio/data/pdb/3cf6.pdb.gz 3cf6E:# T0618 read from 3cf6E/T0618-3cf6E-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cf6E read from 3cf6E/T0618-3cf6E-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3cf6E to template set # found chain 3cf6E in template set Warning: unaligning (T0618)A102 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3cf6E)P900 Warning: unaligning (T0618)Y103 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3cf6E)P900 Warning: unaligning (T0618)S104 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3cf6E)P901 T0618 11 :KNVIEFVTVAAEFCAFLERAESMKR 3cf6E 817 :SQLSKRVQLLKKFIKIAAHCKEYKN T0618 39 :VDTTLKILPLL 3cf6E 842 :LNSFFAIVMGL T0618 52 :KASMLPKC 3cf6E 856 :AVSRLALT T0618 69 :TYVTEEIYEV 3cf6E 865 :EKLPSKFKKF T0618 80 :RINLASILAEKDDY 3cf6E 875 :YAEFESLMDPSRNH T0618 94 :LEVF 3cf6E 892 :RLTA T0618 99 :PDM 3cf6E 896 :AKL T0618 105 :DEP 3cf6E 902 :LIP T0618 115 :DLADIYQDIKDF 3cf6E 905 :FMPLLIKDMTFT T0618 131 :QLGLNET 3cf6E 917 :HEGNKTF T0618 149 :FGL 3cf6E 930 :FEK T0618 154 :GQKLVNTMRALHDVKYSPK 3cf6E 933 :MRMIANTARTVRYYRSQPF Number of specific fragments extracted= 12 number of extra gaps= 1 total=90 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 3cf6E/T0618-3cf6E-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0618 read from 3cf6E/T0618-3cf6E-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cf6E read from 3cf6E/T0618-3cf6E-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3cf6E in template set Warning: unaligning (T0618)A102 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3cf6E)P900 Warning: unaligning (T0618)Y103 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3cf6E)P900 Warning: unaligning (T0618)S104 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3cf6E)P901 Warning: unaligning (T0618)A173 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3cf6E)H962 T0618 11 :KNVIEFVTVAAEFCAFLERA 3cf6E 817 :SQLSKRVQLLKKFIKIAAHC T0618 34 :KRSTFVDTTLKILPLL 3cf6E 837 :KEYKNLNSFFAIVMGL T0618 52 :KASMLPKC 3cf6E 856 :AVSRLALT T0618 69 :TYVTEEIYEVL 3cf6E 865 :EKLPSKFKKFY T0618 81 :INLASILA 3cf6E 876 :AEFESLMD T0618 89 :EKDDYLEVF 3cf6E 887 :NHRAYRLTA T0618 99 :PDM 3cf6E 896 :AKL T0618 105 :DEPI 3cf6E 902 :LIPF T0618 116 :LADIYQDIKDF 3cf6E 906 :MPLLIKDMTFT T0618 131 :QLGLNE 3cf6E 917 :HEGNKT T0618 149 :FGLL 3cf6E 930 :FEKM T0618 155 :QKLVNTMRALHDVKYSPK 3cf6E 934 :RMIANTARTVRYYRSQPF Number of specific fragments extracted= 12 number of extra gaps= 1 total=102 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 3cf6E/T0618-3cf6E-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0618 read from 3cf6E/T0618-3cf6E-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cf6E read from 3cf6E/T0618-3cf6E-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3cf6E in template set Warning: unaligning (T0618)S104 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3cf6E)P900 Warning: unaligning (T0618)D105 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3cf6E)P900 Warning: unaligning (T0618)E106 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3cf6E)P901 T0618 11 :K 3cf6E 820 :S T0618 15 :EFVTVAAEFCAFLERAESMKRSTFVDTTLKILP 3cf6E 821 :KRVQLLKKFIKIAAHCKEYKNLNSFFAIVMGLS T0618 52 :KASML 3cf6E 856 :AVSRL T0618 70 :YVTEEIYEVLR 3cf6E 866 :KLPSKFKKFYA T0618 82 :NLASILAEKDDYLEVFLPDMAY 3cf6E 877 :EFESLMDPSRNHRAYRLTAAKL T0618 107 :PIK 3cf6E 902 :LIP T0618 115 :DLADIYQDIKDF 3cf6E 905 :FMPLLIKDMTFT T0618 130 :FQLGL 3cf6E 917 :HEGNK T0618 149 :FGLL 3cf6E 930 :FEKM T0618 155 :QKLVNTMRALHDV 3cf6E 934 :RMIANTARTVRYY Number of specific fragments extracted= 10 number of extra gaps= 1 total=112 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 1qfjA/T0618-1qfjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1qfjA expands to /projects/compbio/data/pdb/1qfj.pdb.gz 1qfjA:# T0618 read from 1qfjA/T0618-1qfjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qfjA read from 1qfjA/T0618-1qfjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1qfjA to template set # found chain 1qfjA in template set T0618 40 :DTTLKILPLLYL 1qfjA 115 :SYARSILLTALA T0618 55 :MLPKCEM 1qfjA 127 :RNPNRDI T0618 66 :SPETYV 1qfjA 140 :REEQHL T0618 76 :YE 1qfjA 148 :LC T0618 82 :NLASILAEKDDYLEVF 1qfjA 150 :ELEALSLKHPGLQVVP T0618 98 :LPDMAYSDEPIKKNISEDLADI 1qfjA 167 :VEQPEAGWRGRTGTVLTAVLQD Number of specific fragments extracted= 6 number of extra gaps= 0 total=118 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 1qfjA/T0618-1qfjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0618 read from 1qfjA/T0618-1qfjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qfjA read from 1qfjA/T0618-1qfjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qfjA in template set T0618 44 :KILPLLYLKASMLPK 1qfjA 115 :SYARSILLTALARNP T0618 59 :CEM 1qfjA 137 :WGG T0618 65 :ESP 1qfjA 140 :REE T0618 69 :TYV 1qfjA 143 :QHL T0618 76 :YE 1qfjA 148 :LC T0618 82 :NLASILAEKDDY 1qfjA 150 :ELEALSLKHPGL T0618 94 :LEVFLPDMAYSDEPIKKNISEDLADI 1qfjA 163 :VVPVVEQPEAGWRGRTGTVLTAVLQD Number of specific fragments extracted= 7 number of extra gaps= 0 total=125 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 1qfjA/T0618-1qfjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0618 read from 1qfjA/T0618-1qfjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qfjA read from 1qfjA/T0618-1qfjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qfjA in template set T0618 42 :TLKILPLLYLKASML 1qfjA 117 :ARSILLTALARNPNR T0618 57 :PKCEMI 1qfjA 141 :EEQHLY T0618 78 :VLR 1qfjA 147 :DLC T0618 82 :NLASILAEKDDYLEVFLP 1qfjA 150 :ELEALSLKHPGLQVVPVV T0618 101 :MAYSDEP 1qfjA 168 :EQPEAGW T0618 108 :IKKNISEDLADI 1qfjA 177 :RTGTVLTAVLQD Number of specific fragments extracted= 6 number of extra gaps= 0 total=131 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 1m4zA/T0618-1m4zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1m4zA expands to /projects/compbio/data/pdb/1m4z.pdb.gz 1m4zA:# T0618 read from 1m4zA/T0618-1m4zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m4zA read from 1m4zA/T0618-1m4zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1m4zA to template set # found chain 1m4zA in template set T0618 21 :AEFCAF 1m4zA 99 :LAHYRQ T0618 29 :RAESMKRSTF 1m4zA 105 :FNPDANILNR T0618 39 :VDTTLKILPL 1m4zA 116 :LNYYNKLFSE T0618 58 :KC 1m4zA 142 :QL T0618 60 :EMIG 1m4zA 145 :NFIR T0618 69 :TYVTEEIYEV 1m4zA 151 :NVMDGSKWEV T0618 86 :ILAEKDDYLEVFLPDMAYSDEPIKKNI 1m4zA 161 :LKGNVDPERDFTVRYICEPTGEKFVDI T0618 115 :DLADIYQDI 1m4zA 188 :NIEDVKAYI T0618 132 :LGLN 1m4zA 197 :KKVE T0618 138 :MNDSLAICQENFG 1m4zA 201 :PREAQEYLKDLTL Number of specific fragments extracted= 10 number of extra gaps= 0 total=141 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 1m4zA/T0618-1m4zA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0618 read from 1m4zA/T0618-1m4zA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m4zA read from 1m4zA/T0618-1m4zA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1m4zA in template set T0618 21 :AEFCAF 1m4zA 99 :LAHYRQ T0618 29 :RAESMKRS 1m4zA 105 :FNPDANIL T0618 37 :TFVDTTLKILPL 1m4zA 114 :RPLNYYNKLFSE T0618 58 :KCEMIGDESPETYV 1m4zA 137 :ELAELQLFNFIRVA T0618 72 :TEEIYEVL 1m4zA 154 :DGSKWEVL T0618 84 :ASILAEKDDY 1m4zA 162 :KGNVDPERDF T0618 94 :LEVFLPDMAYS 1m4zA 173 :VRYICEPTGEK T0618 107 :PIK 1m4zA 184 :FVD T0618 112 :I 1m4zA 187 :I T0618 115 :DLADIYQDI 1m4zA 188 :NIEDVKAYI T0618 132 :LGLN 1m4zA 197 :KKVE T0618 138 :MNDSLAICQEN 1m4zA 201 :PREAQEYLKDL Number of specific fragments extracted= 12 number of extra gaps= 0 total=153 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 1m4zA/T0618-1m4zA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0618 read from 1m4zA/T0618-1m4zA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m4zA read from 1m4zA/T0618-1m4zA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1m4zA in template set T0618 88 :AEKDDYLEVFLP 1m4zA 167 :PERDFTVRYICE T0618 102 :AYSDEPIKKNIS 1m4zA 179 :PTGEKFVDINIE T0618 118 :DIYQDIKD 1m4zA 191 :DVKAYIKK T0618 133 :GL 1m4zA 199 :VE T0618 138 :MNDSLAICQE 1m4zA 201 :PREAQEYLKD Number of specific fragments extracted= 5 number of extra gaps= 0 total=158 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 2okuA/T0618-2okuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2okuA expands to /projects/compbio/data/pdb/2oku.pdb.gz 2okuA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 799, because occupancy 0.5 <= existing 0.500 in 2okuA Skipped atom 801, because occupancy 0.500 <= existing 0.500 in 2okuA Skipped atom 803, because occupancy 0.500 <= existing 0.500 in 2okuA Skipped atom 805, because occupancy 0.500 <= existing 0.500 in 2okuA Skipped atom 807, because occupancy 0.500 <= existing 0.500 in 2okuA Skipped atom 809, because occupancy 0.500 <= existing 0.500 in 2okuA Skipped atom 811, because occupancy 0.500 <= existing 0.500 in 2okuA Skipped atom 813, because occupancy 0.500 <= existing 0.500 in 2okuA Skipped atom 815, because occupancy 0.500 <= existing 0.500 in 2okuA Skipped atom 817, because occupancy 0.500 <= existing 0.500 in 2okuA Skipped atom 819, because occupancy 0.500 <= existing 0.500 in 2okuA # T0618 read from 2okuA/T0618-2okuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2okuA read from 2okuA/T0618-2okuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2okuA to template set # found chain 2okuA in template set T0618 4 :ESQVIFDKNVI 2okuA 464 :YQQTEVKPELQ T0618 15 :EFVTVAAEFCAFLERAESMKRSTFVDTTLKILPL 2okuA 479 :ALARMTDRAEALIAFVTEQKDQELLDFQARRLVE T0618 49 :LYLKASML 2okuA 517 :AVFGHLLM T0618 57 :PKC 2okuA 530 :DDS T0618 72 :TEEIYEVLRINLASILA 2okuA 537 :AEVYLRYGQAEQEKIDS T0618 92 :D 2okuA 557 :A T0618 97 :F 2okuA 558 :F T0618 99 :P 2okuA 559 :R Number of specific fragments extracted= 8 number of extra gaps= 0 total=166 Will force an alignment to be made, even if fragment is small Number of alignments=19 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2okuA/T0618-2okuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0618 read from 2okuA/T0618-2okuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2okuA read from 2okuA/T0618-2okuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2okuA in template set Warning: unaligning (T0618)A102 because last residue in template chain is (2okuA)T564 T0618 3 :KESQVIFDKNVI 2okuA 463 :EYQQTEVKPELQ T0618 15 :EFVTVAAEFCAFLERAESMKRSTFVDTTLKILPL 2okuA 479 :ALARMTDRAEALIAFVTEQKDQELLDFQARRLVE T0618 49 :LYLKASML 2okuA 517 :AVFGHLLM T0618 57 :PK 2okuA 530 :DD T0618 61 :MI 2okuA 532 :SF T0618 72 :TEE 2okuA 534 :RQS T0618 75 :IYEVLRINLASILA 2okuA 540 :YLRYGQAEQEKIDS T0618 89 :EKDD 2okuA 557 :AFRP T0618 99 :PDM 2okuA 561 :EEL Number of specific fragments extracted= 9 number of extra gaps= 0 total=175 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 2okuA/T0618-2okuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0618 read from 2okuA/T0618-2okuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2okuA read from 2okuA/T0618-2okuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2okuA in template set Warning: unaligning (T0618)Y103 because last residue in template chain is (2okuA)T564 T0618 6 :QVIFDKNVIEFVTVAAEFCAFLERAESMKR 2okuA 470 :KPELQPMKEALARMTDRAEALIAFVTEQKD T0618 36 :STFVDTTLKILPLLYLKASML 2okuA 504 :DFQARRLVEMTAHAVFGHLLM T0618 57 :PKC 2okuA 531 :DSF T0618 72 :TEEIYEVLR 2okuA 534 :RQSAEVYLR T0618 82 :NLASILAEKDDYLEVFLPDMA 2okuA 543 :YGQAEQEKIDSYVRAFRPEEL Number of specific fragments extracted= 5 number of extra gaps= 0 total=180 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 1ad2A/T0618-1ad2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ad2A expands to /projects/compbio/data/pdb/1ad2.pdb.gz 1ad2A:# T0618 read from 1ad2A/T0618-1ad2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ad2A read from 1ad2A/T0618-1ad2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ad2A to template set # found chain 1ad2A in template set T0618 29 :RAESMKR 1ad2A 82 :KIKEAEE T0618 36 :STFVDTTLK 1ad2A 97 :EEIIQKILD T0618 65 :ESPETYV 1ad2A 106 :GWMDFDA T0618 72 :TEEIYEVLRINLASILAEKDDY 1ad2A 116 :TPDVMGAVGSKLGRILGPRGLL T0618 98 :LPD 1ad2A 138 :PNP T0618 108 :IKKNISEDLADIYQDIKD 1ad2A 141 :KAGTVGFNIGEIIREIKA T0618 131 :QLGLNE 1ad2A 177 :KACFPP T0618 151 :LLWGQKLVNTMRALHDV 1ad2A 183 :EKLADNIRAFIRALEAH T0618 169 :YSPKARLE 1ad2A 200 :KPEGAKGT Number of specific fragments extracted= 9 number of extra gaps= 0 total=189 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 1ad2A/T0618-1ad2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0618 read from 1ad2A/T0618-1ad2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ad2A read from 1ad2A/T0618-1ad2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ad2A in template set T0618 36 :STFVDTTL 1ad2A 97 :EEIIQKIL T0618 64 :DESPETYV 1ad2A 105 :DGWMDFDA T0618 72 :TEEIYEVLRINLASILAEKD 1ad2A 116 :TPDVMGAVGSKLGRILGPRG T0618 100 :DMAYSDE 1ad2A 136 :LLPNPKA T0618 110 :KNISEDLADIYQDIKDF 1ad2A 143 :GTVGFNIGEIIREIKAG T0618 131 :QLGLNE 1ad2A 177 :KACFPP T0618 151 :LLWGQKLVNTMRALHDVK 1ad2A 183 :EKLADNIRAFIRALEAHK T0618 170 :SPKAR 1ad2A 201 :PEGAK Number of specific fragments extracted= 8 number of extra gaps= 0 total=197 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 1ad2A/T0618-1ad2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0618 read from 1ad2A/T0618-1ad2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ad2A read from 1ad2A/T0618-1ad2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ad2A in template set T0618 74 :EIYEVLRINLASILAEKDD 1ad2A 118 :DVMGAVGSKLGRILGPRGL T0618 96 :VFLP 1ad2A 137 :LPNP T0618 108 :IKKNISEDLADIYQDIKDF 1ad2A 141 :KAGTVGFNIGEIIREIKAG T0618 128 :FVFQLGLN 1ad2A 174 :PVGKACFP T0618 138 :MNDSL 1ad2A 182 :PEKLA T0618 155 :QKLVNTMRALHDVK 1ad2A 187 :DNIRAFIRALEAHK Number of specific fragments extracted= 6 number of extra gaps= 0 total=203 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 1umkA/T0618-1umkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1umkA expands to /projects/compbio/data/pdb/1umk.pdb.gz 1umkA:Skipped atom 218, because occupancy 0.300 <= existing 0.700 in 1umkA Skipped atom 220, because occupancy 0.300 <= existing 0.700 in 1umkA Skipped atom 492, because occupancy 0.500 <= existing 0.500 in 1umkA Skipped atom 494, because occupancy 0.500 <= existing 0.500 in 1umkA Skipped atom 636, because occupancy 0.300 <= existing 0.700 in 1umkA Skipped atom 638, because occupancy 0.300 <= existing 0.700 in 1umkA Skipped atom 934, because occupancy 0.300 <= existing 0.400 in 1umkA Skipped atom 935, because occupancy 0.300 <= existing 0.400 in 1umkA # T0618 read from 1umkA/T0618-1umkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1umkA read from 1umkA/T0618-1umkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1umkA to template set # found chain 1umkA in template set Warning: unaligning (T0618)E95 because of BadResidue code BAD_PEPTIDE in next template residue (1umkA)T237 Warning: unaligning (T0618)V96 because of BadResidue code BAD_PEPTIDE at template residue (1umkA)T237 T0618 43 :LKILPLLYLKASMLPKC 1umkA 183 :ITPMLQVIRAIMKDPDD T0618 60 :E 1umkA 202 :V T0618 66 :SPETYV 1umkA 210 :QTEKDI T0618 73 :EEIYEV 1umkA 218 :RPELEE T0618 83 :LASILAEKDDYL 1umkA 224 :LRNKHSARFKLW T0618 97 :F 1umkA 238 :L T0618 99 :PDMAYSDEPIKKNISEDLA 1umkA 239 :DRAPEAWDYGQGFVNEEMI Number of specific fragments extracted= 7 number of extra gaps= 1 total=210 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 1umkA/T0618-1umkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0618 read from 1umkA/T0618-1umkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1umkA read from 1umkA/T0618-1umkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1umkA in template set Warning: unaligning (T0618)E95 because of BadResidue code BAD_PEPTIDE in next template residue (1umkA)T237 Warning: unaligning (T0618)V96 because of BadResidue code BAD_PEPTIDE at template residue (1umkA)T237 T0618 43 :LKILPLLYLKASM 1umkA 183 :ITPMLQVIRAIMK T0618 57 :PKCEMI 1umkA 196 :DPDDHT T0618 66 :SPETYV 1umkA 210 :QTEKDI T0618 76 :YEVLRI 1umkA 218 :RPELEE T0618 83 :LASILAEKDDYL 1umkA 224 :LRNKHSARFKLW T0618 97 :F 1umkA 238 :L T0618 99 :PDMAYSDEPIKKNISEDLA 1umkA 239 :DRAPEAWDYGQGFVNEEMI Number of specific fragments extracted= 7 number of extra gaps= 1 total=217 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 1umkA/T0618-1umkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0618 read from 1umkA/T0618-1umkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1umkA read from 1umkA/T0618-1umkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1umkA in template set Warning: unaligning (T0618)L98 because of BadResidue code BAD_PEPTIDE in next template residue (1umkA)T237 Warning: unaligning (T0618)P99 because of BadResidue code BAD_PEPTIDE at template residue (1umkA)T237 T0618 40 :DTTLKILPLLY 1umkA 184 :TPMLQVIRAIM T0618 62 :IGDESPET 1umkA 195 :KDPDDHTV T0618 70 :YVTEEI 1umkA 209 :NQTEKD T0618 79 :LRINLASILAEKDDYLEVF 1umkA 217 :LRPELEELRNKHSARFKLW T0618 100 :DMAYSDEP 1umkA 238 :LDRAPEAW T0618 108 :IKKNISEDLAD 1umkA 248 :GQGFVNEEMIR Number of specific fragments extracted= 6 number of extra gaps= 1 total=223 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 2ksmA/T0618-2ksmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2ksmA expands to /projects/compbio/data/pdb/2ksm.pdb.gz 2ksmA:# T0618 read from 2ksmA/T0618-2ksmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ksmA read from 2ksmA/T0618-2ksmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2ksmA to template set # found chain 2ksmA in template set T0618 37 :TFVDTTLKILPL 2ksmA 101 :AAKAALMTALNG T0618 49 :LYLKASMLPKC 2ksmA 141 :VFTASVPIPDF T0618 64 :DESP 2ksmA 156 :ERDT T0618 68 :ETYV 2ksmA 163 :TGTA T0618 72 :TEEIYEVLRINLASILAEKDDYLEVFLPDMAYSDE 2ksmA 168 :SSEHKDAVKRAATSTWPDMKIVNNIEVTGQAPPGP Number of specific fragments extracted= 5 number of extra gaps= 0 total=228 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 2ksmA/T0618-2ksmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0618 read from 2ksmA/T0618-2ksmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ksmA read from 2ksmA/T0618-2ksmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ksmA in template set Warning: unaligning (T0618)P107 because last residue in template chain is (2ksmA)P203 T0618 49 :LYLKASMLPKC 2ksmA 141 :VFTASVPIPDF T0618 62 :IGD 2ksmA 156 :ERD T0618 69 :TYVTEEIYEVLRINLASILAEKDDYLEVFLPDMAYSDE 2ksmA 165 :TAPSSEHKDAVKRAATSTWPDMKIVNNIEVTGQAPPGP Number of specific fragments extracted= 3 number of extra gaps= 0 total=231 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 2ksmA/T0618-2ksmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0618 read from 2ksmA/T0618-2ksmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ksmA read from 2ksmA/T0618-2ksmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ksmA in template set T0618 70 :YVTEEIYEVLRINLASILAEKDDYLEVFLPDMAYSD 2ksmA 166 :APSSEHKDAVKRAATSTWPDMKIVNNIEVTGQAPPG Number of specific fragments extracted= 1 number of extra gaps= 0 total=232 Will force an alignment to be made, even if fragment is small Number of alignments=30 # command:CPU_time= 11.461 sec, elapsed time= 22.256 sec. # command:DEBUG: alignment library has 30 conformations DEBUG: current conformations has 0 conformations # in ExtractAlignmentsContacts extracting from alignment library using radius 8.000 separation >= 9 style evalue NUMB_ALIGNS: 30 # Adding 1130 constraints to all_contacts Done adding distance constraints # command:CPU_time= 11.497 sec, elapsed time= 22.295 sec. # command:Reading probabilities from T0618.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 6.900 Optimizing... Probability sum: -316.535, CN propb: -316.535 weights: 0.285 constraints: 251 # command:CPU_time= 16.340 sec, elapsed time= 27.178 sec. # command:Found ConstraintSet # PrintContacts align.constraints Number of constraints in align 251 # command:Found ConstraintSet # PrintContacts align_bonus.constraints Number of constraints in align.bonus 251 # command:Found ConstraintSet # PrintContacts rejected.constraints Number of constraints in rejected 879 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints Number of constraints in rejected.bonus 879 # command:Found ConstraintSet # PrintContacts noncontact.constraints Number of constraints in noncontact 0 # command:Found ConstraintSet # PrintContacts noncontact_bonus.constraints Number of constraints in noncontact.bonus 0 # command:CPU_time= 16.361 sec, elapsed time= 27.938 sec. # command: