# 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 T0308 numbered 1 through 165 Created new target T0308 from T0308.a2m # command:CPU_time= 6.164 sec, elapsed time= 6.226 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r2qA/T0308-1r2qA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1r2qA/T0308-1r2qA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r2qA read from 1r2qA/T0308-1r2qA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1r2qA in training set Warning: unaligning (T0308)K69 because of BadResidue code BAD_PEPTIDE in next template residue (1r2qA)G92 Warning: unaligning (T0308)E70 because of BadResidue code BAD_PEPTIDE at template residue (1r2qA)G92 T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1r2qA 21 :FKLVLLGESAVGKSSLVLRFVKGQF # choosing archetypes in rotamer library T0308 28 :SQNI 1r2qA 46 :HEFQ T0308 32 :LPTIGFSIEKFKSSS 1r2qA 52 :TIGAAFLTQTVCLDD T0308 47 :LSFTVFDMSGQGRYRNLWEHYY 1r2qA 69 :VKFEIWDTAGQERYHSLAPMYY T0308 71 :GQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1r2qA 93 :AQAAIVVYDITNEESFARAKNWVKELQRQAS T0308 105 :RRIPILFFANKMDLRDAV 1r2qA 124 :PNIVIALSGNKADLANKR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1r2qA 142 :AVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKL Number of specific fragments extracted= 7 number of extra gaps= 1 total=7 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 1r2qA/T0308-1r2qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1r2qA/T0308-1r2qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r2qA read from 1r2qA/T0308-1r2qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1r2qA in training set Warning: unaligning (T0308)K69 because of BadResidue code BAD_PEPTIDE in next template residue (1r2qA)G92 Warning: unaligning (T0308)E70 because of BadResidue code BAD_PEPTIDE at template residue (1r2qA)G92 T0308 2 :VHVLCLGLDNSGKTTIINKLK 1r2qA 21 :FKLVLLGESAVGKSSLVLRFV T0308 24 :SNAQSQNILPTIG 1r2qA 42 :KGQFHEFQESTIG T0308 37 :FSIEKFKSSS 1r2qA 57 :FLTQTVCLDD T0308 47 :LSFTVFDMSGQGRYRNLWEHYY 1r2qA 69 :VKFEIWDTAGQERYHSLAPMYY T0308 71 :GQAIIFVIDSSDRLRMVVAKEELDTLLNH 1r2qA 93 :AQAAIVVYDITNEESFARAKNWVKELQRQ T0308 103 :KHRRIPILFFANKMDLRDAV 1r2qA 122 :ASPNIVIALSGNKADLANKR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1r2qA 142 :AVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKL Number of specific fragments extracted= 7 number of extra gaps= 1 total=14 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 1r2qA/T0308-1r2qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1r2qA/T0308-1r2qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r2qA read from 1r2qA/T0308-1r2qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1r2qA in training set Warning: unaligning (T0308)K69 because of BadResidue code BAD_PEPTIDE in next template residue (1r2qA)G92 Warning: unaligning (T0308)E70 because of BadResidue code BAD_PEPTIDE at template residue (1r2qA)G92 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1r2qA 20 :QFKLVLLGESAVGKSSLVLRFVKGQF T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYY 1r2qA 49 :QESTIGAAFLTQTVCLDDTTVKFEIWDTAGQERYHSLAPMYY T0308 71 :GQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1r2qA 93 :AQAAIVVYDITNEESFARAKNWVKELQRQAS T0308 105 :RRIPILFFANKMDLRDAVTSV 1r2qA 124 :PNIVIALSGNKADLANKRAVD T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1r2qA 145 :FQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKL Number of specific fragments extracted= 5 number of extra gaps= 1 total=19 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 1ek0A/T0308-1ek0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ek0A expands to /projects/compbio/data/pdb/1ek0.pdb.gz 1ek0A:Skipped atom 20, because occupancy 0.16 <= existing 0.840 in 1ek0A Skipped atom 22, because occupancy 0.160 <= existing 0.840 in 1ek0A Skipped atom 80, because occupancy 0.460 <= existing 0.540 in 1ek0A Skipped atom 82, because occupancy 0.460 <= existing 0.540 in 1ek0A Skipped atom 84, because occupancy 0.460 <= existing 0.540 in 1ek0A Skipped atom 86, because occupancy 0.460 <= existing 0.540 in 1ek0A Skipped atom 88, because occupancy 0.460 <= existing 0.540 in 1ek0A Skipped atom 608, because occupancy 0.230 <= existing 0.770 in 1ek0A Skipped atom 610, because occupancy 0.230 <= existing 0.770 in 1ek0A Skipped atom 612, because occupancy 0.230 <= existing 0.770 in 1ek0A Skipped atom 614, because occupancy 0.230 <= existing 0.770 in 1ek0A Skipped atom 842, because occupancy 0.400 <= existing 0.610 in 1ek0A Skipped atom 844, because occupancy 0.400 <= existing 0.610 in 1ek0A Skipped atom 846, because occupancy 0.400 <= existing 0.610 in 1ek0A Skipped atom 848, because occupancy 0.400 <= existing 0.610 in 1ek0A Skipped atom 850, because occupancy 0.400 <= existing 0.610 in 1ek0A Skipped atom 852, because occupancy 0.400 <= existing 0.610 in 1ek0A Skipped atom 1074, because occupancy 0.410 <= existing 0.590 in 1ek0A Skipped atom 1076, because occupancy 0.410 <= existing 0.590 in 1ek0A Skipped atom 1078, because occupancy 0.410 <= existing 0.590 in 1ek0A Skipped atom 1080, because occupancy 0.410 <= existing 0.590 in 1ek0A Skipped atom 1082, because occupancy 0.410 <= existing 0.590 in 1ek0A Skipped atom 1084, because occupancy 0.410 <= existing 0.590 in 1ek0A Skipped atom 1086, because occupancy 0.410 <= existing 0.590 in 1ek0A Skipped atom 1331, because occupancy 0.270 <= existing 0.730 in 1ek0A Skipped atom 1333, because occupancy 0.270 <= existing 0.730 in 1ek0A Skipped atom 1335, because occupancy 0.270 <= existing 0.730 in 1ek0A Skipped atom 1337, because occupancy 0.270 <= existing 0.730 in 1ek0A # T0308 read from 1ek0A/T0308-1ek0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ek0A read from 1ek0A/T0308-1ek0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ek0A to template set # found chain 1ek0A in template set Warning: unaligning (T0308)E65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ek0A)Y76 Warning: unaligning (T0308)Y67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ek0A)Y76 Warning: unaligning (T0308)D117 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ek0A)L125 Warning: unaligning (T0308)R119 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ek0A)L125 T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1ek0A 8 :IKLVLLGEAAVGKSSIVLRFVSNDF T0308 28 :SQNI 1ek0A 33 :AENK T0308 32 :LPTIGFSIEKFKSSS 1ek0A 39 :TIGAAFLTQRVTINE T0308 47 :LSFTVFDMSGQGRYRNLW 1ek0A 56 :VKFEIWDTAGQERFASLA T0308 68 :YKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1ek0A 77 :YRNAQAALVVYDVTKPQSFIKARHWVKELHEQAS T0308 105 :RRIPILFFANKM 1ek0A 111 :KDIIIALVGNKI T0308 120 :DAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1ek0A 126 :QEGGERKVAREEGEKLAEEKGLLFFETSAKTGENVNDVFLGIGEKI Number of specific fragments extracted= 7 number of extra gaps= 0 total=26 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 1ek0A/T0308-1ek0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1ek0A/T0308-1ek0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ek0A read from 1ek0A/T0308-1ek0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ek0A in template set Warning: unaligning (T0308)E65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ek0A)Y76 Warning: unaligning (T0308)Y67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ek0A)Y76 Warning: unaligning (T0308)D117 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ek0A)L125 Warning: unaligning (T0308)R119 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ek0A)L125 T0308 2 :VHVLCLGLDNSGKTTIINKLK 1ek0A 8 :IKLVLLGEAAVGKSSIVLRFV T0308 24 :SNAQSQNILPTIG 1ek0A 29 :SNDFAENKEPTIG T0308 37 :FSIEKFKSSS 1ek0A 44 :FLTQRVTINE T0308 47 :LSFTVFDMSGQGRYRNLW 1ek0A 56 :VKFEIWDTAGQERFASLA T0308 68 :YKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 1ek0A 77 :YRNAQAALVVYDVTKPQSFIKARHWVKELHEQ T0308 103 :KHRRIPILFFANKM 1ek0A 109 :ASKDIIIALVGNKI T0308 120 :DAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1ek0A 126 :QEGGERKVAREEGEKLAEEKGLLFFETSAKTGENVNDVFLGIGEKI Number of specific fragments extracted= 7 number of extra gaps= 0 total=33 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 1ek0A/T0308-1ek0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1ek0A/T0308-1ek0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ek0A read from 1ek0A/T0308-1ek0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ek0A in template set Warning: unaligning (T0308)E65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ek0A)Y76 Warning: unaligning (T0308)Y67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ek0A)Y76 Warning: unaligning (T0308)D117 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ek0A)L125 Warning: unaligning (T0308)R119 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ek0A)L125 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1ek0A 7 :SIKLVLLGEAAVGKSSIVLRFVSNDF T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLW 1ek0A 36 :KEPTIGAAFLTQRVTINEHTVKFEIWDTAGQERFASLA T0308 68 :YKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1ek0A 77 :YRNAQAALVVYDVTKPQSFIKARHWVKELHEQAS T0308 105 :RRIPILFFANKM 1ek0A 111 :KDIIIALVGNKI T0308 120 :DAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1ek0A 126 :QEGGERKVAREEGEKLAEEKGLLFFETSAKTGENVNDVFLGIGEKI Number of specific fragments extracted= 5 number of extra gaps= 0 total=38 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 2bcgY/T0308-2bcgY-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2bcgY expands to /projects/compbio/data/pdb/2bcg.pdb.gz 2bcgY:Skipped atom 4684, because occupancy 0.500 <= existing 0.500 in 2bcgY Skipped atom 4686, because occupancy 0.500 <= existing 0.500 in 2bcgY Skipped atom 4688, because occupancy 0.500 <= existing 0.500 in 2bcgY Skipped atom 4690, because occupancy 0.500 <= existing 0.500 in 2bcgY Skipped atom 4692, because occupancy 0.500 <= existing 0.500 in 2bcgY Skipped atom 4706, because occupancy 0.500 <= existing 0.500 in 2bcgY Skipped atom 4708, because occupancy 0.500 <= existing 0.500 in 2bcgY Skipped atom 4710, because occupancy 0.500 <= existing 0.500 in 2bcgY Skipped atom 4712, because occupancy 0.500 <= existing 0.500 in 2bcgY Skipped atom 4714, because occupancy 0.500 <= existing 0.500 in 2bcgY Skipped atom 4786, because occupancy 0.500 <= existing 0.500 in 2bcgY Skipped atom 4788, because occupancy 0.500 <= existing 0.500 in 2bcgY Skipped atom 4790, because occupancy 0.500 <= existing 0.500 in 2bcgY Skipped atom 4792, because occupancy 0.500 <= existing 0.500 in 2bcgY Skipped atom 4794, because occupancy 0.500 <= existing 0.500 in 2bcgY # T0308 read from 2bcgY/T0308-2bcgY-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bcgY read from 2bcgY/T0308-2bcgY-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2bcgY to template set # found chain 2bcgY in template set T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 2bcgY 9 :FKLLLIGNSGVGKSCLLLRFSDDTY T0308 28 :SQNI 2bcgY 34 :TNDY T0308 32 :LPTIGFSIEKFKSSS 2bcgY 40 :TIGVDFKIKTVELDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 2bcgY 57 :VKLQIWDTAGQERFRTITSSYYRGSHGIIIVYDVTDQESFNGVKMWLQEIDRYAT T0308 105 :RRIPILFFANKMDLRDAV 2bcgY 112 :STVLKLLVGNKCDLKDKR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 2bcgY 130 :VVEYDVAKEFADANKMPFLETSALDSTNVEDAFLTMARQI Number of specific fragments extracted= 6 number of extra gaps= 0 total=44 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 2bcgY/T0308-2bcgY-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 2bcgY/T0308-2bcgY-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bcgY read from 2bcgY/T0308-2bcgY-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bcgY in template set T0308 2 :VHVLCLGLDNSGKTTIINKLK 2bcgY 9 :FKLLLIGNSGVGKSCLLLRFS T0308 24 :SNAQSQNILPTIG 2bcgY 30 :DDTYTNDYISTIG T0308 37 :FSIEKFKSSS 2bcgY 45 :FKIKTVELDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 2bcgY 57 :VKLQIWDTAGQERFRTITSSYYRGSHGIIIVYDVTDQESFNGVKMWLQEIDRY T0308 103 :KHRRIPILFFANKMDLRDAV 2bcgY 110 :ATSTVLKLLVGNKCDLKDKR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 2bcgY 130 :VVEYDVAKEFADANKMPFLETSALDSTNVEDAFLTMARQI Number of specific fragments extracted= 6 number of extra gaps= 0 total=50 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 2bcgY/T0308-2bcgY-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 2bcgY/T0308-2bcgY-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bcgY read from 2bcgY/T0308-2bcgY-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bcgY in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 2bcgY 8 :LFKLLLIGNSGVGKSCLLLRFSDDTY T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 2bcgY 37 :YISTIGVDFKIKTVELDGKTVKLQIWDTAGQERFRTITSSYYRGSHGIIIVYDVTDQESFNGVKMWLQEIDRYAT T0308 105 :RRIPILFFANKMDLRDAVTSV 2bcgY 112 :STVLKLLVGNKCDLKDKRVVE T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 2bcgY 133 :YDVAKEFADANKMPFLETSALDSTNVEDAFLTMARQI Number of specific fragments extracted= 4 number of extra gaps= 0 total=54 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 2a5dA/T0308-2a5dA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2a5dA expands to /projects/compbio/data/pdb/2a5d.pdb.gz 2a5dA:Skipped atom 30, because occupancy 0.400 <= existing 0.600 in 2a5dA Skipped atom 32, because occupancy 0.400 <= existing 0.600 in 2a5dA Skipped atom 34, because occupancy 0.400 <= existing 0.600 in 2a5dA Skipped atom 36, because occupancy 0.400 <= existing 0.600 in 2a5dA Skipped atom 38, because occupancy 0.400 <= existing 0.600 in 2a5dA # T0308 read from 2a5dA/T0308-2a5dA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a5dA read from 2a5dA/T0308-2a5dA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2a5dA to template set # found chain 2a5dA in template set Warning: unaligning (T0308)F37 because of BadResidue code BAD_PEPTIDE in next template residue (2a5dA)N48 Warning: unaligning (T0308)S38 because of BadResidue code BAD_PEPTIDE at template residue (2a5dA)N48 T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNAQ 2a5dA 14 :MRILMLGLDAAGKTTILYKLKLGQSV T0308 30 :NILPTIG 2a5dA 40 :TTIPTVG T0308 39 :IEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 2a5dA 49 :VETVTYKNVKFNVWDVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREM T0308 105 :RRIPILFFANKMDLRDAV 2a5dA 113 :RDAIILIFANKQDLPDAM T0308 128 :SQLLCLENIK 2a5dA 131 :KPHEIQEKLG T0308 138 :DKPWHICASDAIKGEGLQEGVDWLQDQI 2a5dA 146 :DRNWYVQPSCATSGDGLYEGLTWLTSNY Number of specific fragments extracted= 6 number of extra gaps= 1 total=60 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 2a5dA/T0308-2a5dA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 2a5dA/T0308-2a5dA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a5dA read from 2a5dA/T0308-2a5dA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2a5dA in template set Warning: unaligning (T0308)F37 because of BadResidue code BAD_PEPTIDE in next template residue (2a5dA)N48 Warning: unaligning (T0308)S38 because of BadResidue code BAD_PEPTIDE at template residue (2a5dA)N48 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNAQ 2a5dA 13 :EMRILMLGLDAAGKTTILYKLKLGQSV T0308 30 :NILPTIG 2a5dA 40 :TTIPTVG T0308 39 :IEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDIKH 2a5dA 49 :VETVTYKNVKFNVWDVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRD T0308 107 :IPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 2a5dA 115 :AIILIFANKQDLPDAMKPHEIQEKLGLTRIRDRNWYVQPSCATSGDGLYEGLTWLTSNY Number of specific fragments extracted= 4 number of extra gaps= 1 total=64 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 2a5dA/T0308-2a5dA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 2a5dA/T0308-2a5dA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a5dA read from 2a5dA/T0308-2a5dA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2a5dA in template set Warning: unaligning (T0308)F37 because of BadResidue code BAD_PEPTIDE in next template residue (2a5dA)N48 Warning: unaligning (T0308)S38 because of BadResidue code BAD_PEPTIDE at template residue (2a5dA)N48 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 2a5dA 13 :EMRILMLGLDAAGKTTILYKLKLGQS T0308 29 :QNILPTIG 2a5dA 39 :VTTIPTVG T0308 39 :IEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 2a5dA 49 :VETVTYKNVKFNVWDVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDRE T0308 104 :HRRIPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 2a5dA 112 :MRDAIILIFANKQDLPDAMKPHEIQEKLGLTRIRDRNWYVQPSCATSGDGLYEGLTWLTSNY Number of specific fragments extracted= 4 number of extra gaps= 1 total=68 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 1mr3F/T0308-1mr3F-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1mr3F expands to /projects/compbio/data/pdb/1mr3.pdb.gz 1mr3F:Skipped atom 187, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 189, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 191, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 193, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 195, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 197, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 199, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 201, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 203, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 246, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 248, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 250, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 252, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 254, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 256, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 258, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 260, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 262, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 324, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 326, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 328, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 330, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 332, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 334, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 336, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 346, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 348, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 350, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 352, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 354, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 356, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 358, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 360, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 361, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 363, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 364, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 366, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 367, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 369, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 370, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 372, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 373, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 375, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 376, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 378, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 379, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 428, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 430, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 432, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 434, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 436, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 438, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 440, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 495, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 497, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 499, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 501, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 503, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 505, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 853, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 855, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 857, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 859, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 861, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 863, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 865, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 867, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 869, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 871, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 873, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 952, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 954, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 956, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 958, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 960, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 962, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 964, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 966, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 1103, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 1105, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 1107, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 1109, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 1111, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 1113, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 1115, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 1188, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 1190, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 1192, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 1194, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 1196, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 1198, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 1200, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 1202, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 1204, because occupancy 0.500 <= existing 0.500 in 1mr3F # T0308 read from 1mr3F/T0308-1mr3F-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mr3F read from 1mr3F/T0308-1mr3F-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1mr3F to template set # found chain 1mr3F in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNAQSQ 1mr3F 17 :EMRILMVGLDGAGKTTVLYKLKLGEVITT T0308 32 :LPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1mr3F 46 :IPTIGFNVETVQYKNISFTVWDVGGQDRIRSLWRHYYRNTEGVIFVIDSNDRSRIGEAREVMQRMLNEDEL T0308 105 :RRIPILFFANKMDLRDAV 1mr3F 117 :RNAVWLVFANKQDLPEAM T0308 128 :SQLLCLENIK 1mr3F 135 :SAAEITEKLG T0308 138 :DKPWHICASDAIKGEGLQEGVDWLQDQI 1mr3F 150 :NRPWFIQSTCATSGEGLYEGLEWLSNNL Number of specific fragments extracted= 5 number of extra gaps= 0 total=73 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 1mr3F/T0308-1mr3F-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1mr3F/T0308-1mr3F-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mr3F read from 1mr3F/T0308-1mr3F-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mr3F in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNAQSQ 1mr3F 17 :EMRILMVGLDGAGKTTVLYKLKLGEVITT T0308 32 :LPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDIKH 1mr3F 46 :IPTIGFNVETVQYKNISFTVWDVGGQDRIRSLWRHYYRNTEGVIFVIDSNDRSRIGEAREVMQRMLNEDELRN T0308 107 :IPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1mr3F 119 :AVWLVFANKQDLPEAMSAAEITEKLGLHSIRNRPWFIQSTCATSGEGLYEGLEWLSNNL Number of specific fragments extracted= 3 number of extra gaps= 0 total=76 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 1mr3F/T0308-1mr3F-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1mr3F/T0308-1mr3F-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mr3F read from 1mr3F/T0308-1mr3F-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mr3F in template set T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNAQ 1mr3F 18 :MRILMVGLDGAGKTTVLYKLKLGEVI T0308 30 :NILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1mr3F 44 :TTIPTIGFNVETVQYKNISFTVWDVGGQDRIRSLWRHYYRNTEGVIFVIDSNDRSRIGEAREVMQRMLNEDE T0308 104 :HRRIPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1mr3F 116 :LRNAVWLVFANKQDLPEAMSAAEITEKLGLHSIRNRPWFIQSTCATSGEGLYEGLEWLSNNL Number of specific fragments extracted= 3 number of extra gaps= 0 total=79 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 1uptA/T0308-1uptA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1uptA expands to /projects/compbio/data/pdb/1upt.pdb.gz 1uptA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0308 read from 1uptA/T0308-1uptA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1uptA read from 1uptA/T0308-1uptA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1uptA to template set # found chain 1uptA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNAQ 1uptA 17 :EMRILILGLDGAGKTTILYRLQVGEVV T0308 30 :NILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1uptA 44 :TTIPTIGFNVETVTYKNLKFQVWDLGGLTSIRPYWRCYYSNTDAVIYVVDSCDRDRIGISKSELVAMLEEEEL T0308 105 :RRIPILFFANKMDLRDAV 1uptA 117 :RKAILVVFANKQDMEQAM T0308 128 :SQLLCLENIK 1uptA 135 :TSSEMANSLG T0308 138 :DKPWHICASDAIKGEGLQEGVDWLQDQI 1uptA 150 :DRKWQIFKTSATKGTGLDEAMEWLVETL Number of specific fragments extracted= 5 number of extra gaps= 0 total=84 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 1uptA/T0308-1uptA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1uptA/T0308-1uptA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1uptA read from 1uptA/T0308-1uptA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1uptA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNAQS 1uptA 17 :EMRILILGLDGAGKTTILYRLQVGEVVT T0308 31 :ILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDIKH 1uptA 45 :TIPTIGFNVETVTYKNLKFQVWDLGGLTSIRPYWRCYYSNTDAVIYVVDSCDRDRIGISKSELVAMLEEEELRK T0308 107 :IPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1uptA 119 :AILVVFANKQDMEQAMTSSEMANSLGLPALKDRKWQIFKTSATKGTGLDEAMEWLVETL Number of specific fragments extracted= 3 number of extra gaps= 0 total=87 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 1uptA/T0308-1uptA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1uptA/T0308-1uptA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1uptA read from 1uptA/T0308-1uptA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1uptA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNAQ 1uptA 17 :EMRILILGLDGAGKTTILYRLQVGEVV T0308 30 :NILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1uptA 44 :TTIPTIGFNVETVTYKNLKFQVWDLGGLTSIRPYWRCYYSNTDAVIYVVDSCDRDRIGISKSELVAMLEEEE T0308 104 :HRRIPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1uptA 116 :LRKAILVVFANKQDMEQAMTSSEMANSLGLPALKDRKWQIFKTSATKGTGLDEAMEWLVETL Number of specific fragments extracted= 3 number of extra gaps= 0 total=90 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 1x3sA/T0308-1x3sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1x3sA expands to /projects/compbio/data/pdb/1x3s.pdb.gz 1x3sA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0308 read from 1x3sA/T0308-1x3sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1x3sA read from 1x3sA/T0308-1x3sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1x3sA to template set # found chain 1x3sA in template set T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1x3sA 9 :LKILIIGESGVGKSSLLLRFTDDTF T0308 28 :SQNI 1x3sA 34 :DPEL T0308 32 :LPTIGFSIEKFKSSS 1x3sA 40 :TIGVDFKVKTISVDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1x3sA 57 :AKLAIWDTAGQERFRTLTPSYYRGAQGVILVYDVTRRDTFVKLDNWLNELETYCTR T0308 105 :RRIPILFFANKMDLRDA 1x3sA 113 :NDIVNMLVGNKIDKENR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1x3sA 130 :EVDRNEGLKFARKHSMLFIEASAKTCDGVQCAFEELVEKI Number of specific fragments extracted= 6 number of extra gaps= 0 total=96 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 1x3sA/T0308-1x3sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1x3sA/T0308-1x3sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1x3sA read from 1x3sA/T0308-1x3sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1x3sA in template set T0308 2 :VHVLCLGLDNSGKTTIINKLK 1x3sA 9 :LKILIIGESGVGKSSLLLRFT T0308 24 :SNAQSQNILPTIG 1x3sA 30 :DDTFDPELAATIG T0308 37 :FSIEKFKSSS 1x3sA 45 :FKVKTISVDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHP 1x3sA 57 :AKLAIWDTAGQERFRTLTPSYYRGAQGVILVYDVTRRDTFVKLDNWLNELETYC T0308 103 :KHRRIPILFFANKMDLRDA 1x3sA 111 :TRNDIVNMLVGNKIDKENR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1x3sA 130 :EVDRNEGLKFARKHSMLFIEASAKTCDGVQCAFEELVEKI Number of specific fragments extracted= 6 number of extra gaps= 0 total=102 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 1x3sA/T0308-1x3sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1x3sA/T0308-1x3sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1x3sA read from 1x3sA/T0308-1x3sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1x3sA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1x3sA 8 :TLKILIIGESGVGKSSLLLRFTDDTF T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1x3sA 37 :LAATIGVDFKVKTISVDGNKAKLAIWDTAGQERFRTLTPSYYRGAQGVILVYDVTRRDTFVKLDNWLNELETYCT T0308 104 :HRRIPILFFANKMDLRDAVTS 1x3sA 112 :RNDIVNMLVGNKIDKENREVD T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1x3sA 133 :RNEGLKFARKHSMLFIEASAKTCDGVQCAFEELVEKI Number of specific fragments extracted= 4 number of extra gaps= 0 total=106 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 1o3yA/T0308-1o3yA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1o3yA expands to /projects/compbio/data/pdb/1o3y.pdb.gz 1o3yA:# T0308 read from 1o3yA/T0308-1o3yA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o3yA read from 1o3yA/T0308-1o3yA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1o3yA to template set # found chain 1o3yA in template set Warning: unaligning (T0308)I31 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o3yA)I46 Warning: unaligning (T0308)L32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o3yA)I46 T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNAQ 1o3yA 18 :MRILMVGLDAAGKTTILYKLKLGEIV T0308 30 :N 1o3yA 44 :T T0308 33 :PTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1o3yA 47 :PTIGFNVETVEYKNISFTVWDVGGLDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDEL T0308 105 :RRIPILFFANKMDLRDAV 1o3yA 117 :RDAVLLVFANKQDLPNAM T0308 128 :SQLLCLENIK 1o3yA 135 :NAAEITDKLG T0308 138 :DKPWHICASDAIKGEGLQEGVDWLQDQI 1o3yA 150 :HRNWYIQATCATSGDGLYEGLDWLSNQL Number of specific fragments extracted= 6 number of extra gaps= 1 total=112 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 1o3yA/T0308-1o3yA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1o3yA/T0308-1o3yA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o3yA read from 1o3yA/T0308-1o3yA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1o3yA in template set Warning: unaligning (T0308)I31 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o3yA)I46 Warning: unaligning (T0308)L32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o3yA)I46 T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNAQS 1o3yA 18 :MRILMVGLDAAGKTTILYKLKLGEIVT T0308 33 :PTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDIKH 1o3yA 47 :PTIGFNVETVEYKNISFTVWDVGGLDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRD T0308 107 :IPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1o3yA 119 :AVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQL Number of specific fragments extracted= 3 number of extra gaps= 1 total=115 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 1o3yA/T0308-1o3yA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1o3yA/T0308-1o3yA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o3yA read from 1o3yA/T0308-1o3yA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1o3yA in template set Warning: unaligning (T0308)I31 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o3yA)I46 Warning: unaligning (T0308)L32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o3yA)I46 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNAQ 1o3yA 17 :SMRILMVGLDAAGKTTILYKLKLGEIV T0308 30 :N 1o3yA 44 :T T0308 33 :PTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1o3yA 47 :PTIGFNVETVEYKNISFTVWDVGGLDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDE T0308 104 :HRRIPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1o3yA 116 :LRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQL Number of specific fragments extracted= 4 number of extra gaps= 1 total=119 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 2bmeA/T0308-2bmeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2bmeA expands to /projects/compbio/data/pdb/2bme.pdb.gz 2bmeA:Skipped atom 858, because occupancy 0.400 <= existing 0.600 in 2bmeA Skipped atom 860, because occupancy 0.400 <= existing 0.600 in 2bmeA Skipped atom 862, because occupancy 0.400 <= existing 0.600 in 2bmeA Skipped atom 1297, because occupancy 0.500 <= existing 0.500 in 2bmeA Skipped atom 1299, because occupancy 0.500 <= existing 0.500 in 2bmeA Skipped atom 1301, because occupancy 0.500 <= existing 0.500 in 2bmeA Skipped atom 1303, because occupancy 0.500 <= existing 0.500 in 2bmeA Skipped atom 1305, because occupancy 0.500 <= existing 0.500 in 2bmeA # T0308 read from 2bmeA/T0308-2bmeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bmeA read from 2bmeA/T0308-2bmeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2bmeA to template set # found chain 2bmeA in template set Warning: unaligning (T0308)S28 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bmeA)D37 Warning: unaligning (T0308)Q29 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bmeA)D37 Warning: unaligning (T0308)C144 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bmeA)E151 Warning: unaligning (T0308)A145 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bmeA)E151 T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 2bmeA 11 :FKFLVIGNAGTGKSCLLHQFIEKKF T0308 30 :NI 2bmeA 38 :DS T0308 32 :LPTIGFSIEKFKSSS 2bmeA 42 :TIGVEFGSKIINVGG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 2bmeA 59 :VKLQIWDTAGQERFRSVTRSYYRGAAGALLVYDITSRETYNALTNWLTDARMLAS T0308 105 :RRIPILFFANKMDLRDAV 2bmeA 114 :QNIVIILCGNKKDLDADR T0308 126 :KVSQLLCLENIKDKPWHI 2bmeA 132 :EVTFLEASRFAQENELMF T0308 146 :SDAIKGEGLQEGVDWLQDQI 2bmeA 152 :TSALTGENVEEAFVQCARKI Number of specific fragments extracted= 7 number of extra gaps= 2 total=126 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 2bmeA/T0308-2bmeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 2bmeA/T0308-2bmeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bmeA read from 2bmeA/T0308-2bmeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bmeA in template set Warning: unaligning (T0308)S28 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bmeA)D37 Warning: unaligning (T0308)Q29 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bmeA)D37 Warning: unaligning (T0308)C144 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bmeA)E151 Warning: unaligning (T0308)A145 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bmeA)E151 T0308 2 :VHVLCLGLDNSGKTTIINKLK 2bmeA 11 :FKFLVIGNAGTGKSCLLHQFI T0308 24 :SNAQ 2bmeA 32 :EKKF T0308 30 :NILPTIG 2bmeA 38 :DSNHTIG T0308 37 :FSIEKFKSSS 2bmeA 47 :FGSKIINVGG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 2bmeA 59 :VKLQIWDTAGQERFRSVTRSYYRGAAGALLVYDITSRETYNALTNWLTDARML T0308 103 :KHRRIPILFFANKMDLRDAV 2bmeA 112 :ASQNIVIILCGNKKDLDADR T0308 126 :KVSQLLCLENIKDKPWHI 2bmeA 132 :EVTFLEASRFAQENELMF T0308 146 :SDAIKGEGLQEGVDWLQDQI 2bmeA 152 :TSALTGENVEEAFVQCARKI Number of specific fragments extracted= 8 number of extra gaps= 2 total=134 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 2bmeA/T0308-2bmeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 2bmeA/T0308-2bmeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bmeA read from 2bmeA/T0308-2bmeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bmeA in template set Warning: unaligning (T0308)C144 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bmeA)E151 Warning: unaligning (T0308)A145 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bmeA)E151 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 2bmeA 10 :LFKFLVIGNAGTGKSCLLHQFIEKKF T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 2bmeA 39 :SNHTIGVEFGSKIINVGGKYVKLQIWDTAGQERFRSVTRSYYRGAAGALLVYDITSRETYNALTNWLTDARMLAS T0308 105 :RRIPILFFANKMDLRDAVTSV 2bmeA 114 :QNIVIILCGNKKDLDADREVT T0308 129 :QLLCLENIKDKPWHI 2bmeA 135 :FLEASRFAQENELMF T0308 146 :SDAIKGEGLQEGVDWLQDQI 2bmeA 152 :TSALTGENVEEAFVQCARKI Number of specific fragments extracted= 5 number of extra gaps= 1 total=139 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 2f9lA/T0308-2f9lA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2f9lA expands to /projects/compbio/data/pdb/2f9l.pdb.gz 2f9lA:# T0308 read from 2f9lA/T0308-2f9lA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f9lA read from 2f9lA/T0308-2f9lA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2f9lA to template set # found chain 2f9lA in template set Warning: unaligning (T0308)S28 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2f9lA)S42 Warning: unaligning (T0308)Y60 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f9lA)R74 Warning: unaligning (T0308)R61 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f9lA)R74 T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNAQ 2f9lA 12 :FKVVLIGDSGVGKSNLLSRFTRNEFN T0308 32 :LPTIGFSIEKFKSSS 2f9lA 43 :TIGVEFATRSIQVDG T0308 47 :LSFTVFDMSGQGR 2f9lA 60 :IKAQIWDTAGQER T0308 62 :NLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 2f9lA 75 :RITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHAD T0308 105 :RRIPILFFANKMDLRDAV 2f9lA 115 :SNIVIMLVGNKSDLRHLR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 2f9lA 133 :AVPTDEARAFAEKNNLSFIETSALDSTNVEEAFKNILTEI Number of specific fragments extracted= 6 number of extra gaps= 1 total=145 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 2f9lA/T0308-2f9lA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 2f9lA/T0308-2f9lA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f9lA read from 2f9lA/T0308-2f9lA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2f9lA in template set Warning: unaligning (T0308)Q29 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2f9lA)S42 Warning: unaligning (T0308)P33 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2f9lA)S42 Warning: unaligning (T0308)Y60 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f9lA)R74 Warning: unaligning (T0308)R61 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f9lA)R74 T0308 2 :VHVLCLGLDNSGKTTIINKLK 2f9lA 12 :FKVVLIGDSGVGKSNLLSRFT T0308 24 :SNAQS 2f9lA 33 :RNEFN T0308 34 :TIG 2f9lA 43 :TIG T0308 37 :FSIEKFKSSS 2f9lA 48 :FATRSIQVDG T0308 47 :LSFTVFDMSGQGR 2f9lA 60 :IKAQIWDTAGQER T0308 62 :NLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 2f9lA 75 :RITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDH T0308 103 :KHRRIPILFFANKMDLRDAV 2f9lA 113 :ADSNIVIMLVGNKSDLRHLR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 2f9lA 133 :AVPTDEARAFAEKNNLSFIETSALDSTNVEEAFKNILTEI Number of specific fragments extracted= 8 number of extra gaps= 1 total=153 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 2f9lA/T0308-2f9lA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 2f9lA/T0308-2f9lA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f9lA read from 2f9lA/T0308-2f9lA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2f9lA in template set Warning: unaligning (T0308)Q29 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2f9lA)S42 Warning: unaligning (T0308)Y60 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f9lA)R74 Warning: unaligning (T0308)R61 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f9lA)R74 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 2f9lA 11 :LFKVVLIGDSGVGKSNLLSRFTRNEF T0308 30 :NILPTIGFSIEKFKSSSLSFTVFDMSGQGR 2f9lA 43 :TIGVEFATRSIQVDGKTIKAQIWDTAGQER T0308 62 :NLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 2f9lA 75 :RITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHAD T0308 105 :RRIPILFFANKMDLRDAVTSV 2f9lA 115 :SNIVIMLVGNKSDLRHLRAVP T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 2f9lA 136 :TDEARAFAEKNNLSFIETSALDSTNVEEAFKNILTEI Number of specific fragments extracted= 5 number of extra gaps= 1 total=158 Will force an alignment to be made, even if fragment is small Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z0jA/T0308-1z0jA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1z0jA expands to /projects/compbio/data/pdb/1z0j.pdb.gz 1z0jA:# T0308 read from 1z0jA/T0308-1z0jA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z0jA read from 1z0jA/T0308-1z0jA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1z0jA to template set # found chain 1z0jA in template set T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1z0jA 6 :LKVCLLGDTGVGKSSIMWRFVEDSF T0308 28 :SQNI 1z0jA 31 :DPNI T0308 32 :LPTIGFSIEKFKSSS 1z0jA 37 :TIGASFMTKTVQYQN T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1z0jA 54 :HKFLIWDTAGLERFRALAPMYYRGSAAAIIVYDITKEETFSTLKNWVRELRQHGP T0308 105 :RRIPILFFANKMDLRDAV 1z0jA 109 :PSIVVAIAGNKCDLTDVR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1z0jA 127 :EVMERDAKDYADSIHAIFVETSAKNAININELFIEISRRI Number of specific fragments extracted= 6 number of extra gaps= 0 total=164 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 1z0jA/T0308-1z0jA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1z0jA/T0308-1z0jA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z0jA read from 1z0jA/T0308-1z0jA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1z0jA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLK 1z0jA 5 :ELKVCLLGDTGVGKSSIMWRFV T0308 24 :SNAQSQNILPTIG 1z0jA 27 :EDSFDPNINPTIG T0308 37 :FSIEKFKSSS 1z0jA 42 :FMTKTVQYQN T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 1z0jA 54 :HKFLIWDTAGLERFRALAPMYYRGSAAAIIVYDITKEETFSTLKNWVRELRQH T0308 103 :KHRRIPILFFANKMDLRDAV 1z0jA 107 :GPPSIVVAIAGNKCDLTDVR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1z0jA 127 :EVMERDAKDYADSIHAIFVETSAKNAININELFIEISRRI Number of specific fragments extracted= 6 number of extra gaps= 0 total=170 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 1z0jA/T0308-1z0jA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1z0jA/T0308-1z0jA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z0jA read from 1z0jA/T0308-1z0jA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1z0jA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1z0jA 5 :ELKVCLLGDTGVGKSSIMWRFVEDSF T0308 27 :QSQNILPTIGFSIEKFKSSS 1z0jA 32 :PNINPTIGASFMTKTVQYQN T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1z0jA 54 :HKFLIWDTAGLERFRALAPMYYRGSAAAIIVYDITKEETFSTLKNWVRELRQHGP T0308 105 :RRIPILFFANKMDLRDAVTSV 1z0jA 109 :PSIVVAIAGNKCDLTDVREVM T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1z0jA 130 :ERDAKDYADSIHAIFVETSAKNAININELFIEISRRI Number of specific fragments extracted= 5 number of extra gaps= 0 total=175 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 2a5jA/T0308-2a5jA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2a5jA expands to /projects/compbio/data/pdb/2a5j.pdb.gz 2a5jA:# T0308 read from 2a5jA/T0308-2a5jA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a5jA read from 2a5jA/T0308-2a5jA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2a5jA to template set # found chain 2a5jA in template set Warning: unaligning (T0308)Q27 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2a5jA)I44 Warning: unaligning (T0308)P33 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2a5jA)I44 T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 2a5jA 12 :FKYIIIGDTGVGKSCLLLQFTDKRF T0308 34 :TIGFSIEKFKSSS 2a5jA 45 :GVEFGARMVNIDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 2a5jA 60 :IKLQIWDTAGQESFRSITRSYYRGAAGALLVYDITRRETFNHLTSWLEDARQHSS T0308 105 :RRIPILFFANKMDLRDAV 2a5jA 115 :SNMVIMLIGNKSDLESRR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVD 2a5jA 133 :DVKREEGEAFAREHGLIFMETSAKTACNVEEAFI T0308 160 :WLQDQ 2a5jA 171 :EIYRK Number of specific fragments extracted= 6 number of extra gaps= 0 total=181 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 2a5jA/T0308-2a5jA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 2a5jA/T0308-2a5jA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a5jA read from 2a5jA/T0308-2a5jA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2a5jA in template set Warning: unaligning (T0308)Q29 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2a5jA)I44 Warning: unaligning (T0308)I35 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2a5jA)I44 T0308 2 :VHVLCLGLDNSGKTTIINKLK 2a5jA 12 :FKYIIIGDTGVGKSCLLLQFT T0308 24 :SNAQS 2a5jA 33 :DKRFQ T0308 36 :G 2a5jA 45 :G T0308 37 :FSIEKFKSSS 2a5jA 48 :FGARMVNIDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 2a5jA 60 :IKLQIWDTAGQESFRSITRSYYRGAAGALLVYDITRRETFNHLTSWLEDARQH T0308 103 :KHRRIPILFFANKMDLRDAV 2a5jA 113 :SSSNMVIMLIGNKSDLESRR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 2a5jA 133 :DVKREEGEAFAREHGLIFMETSAKTACNVEEAFINTAKEI Number of specific fragments extracted= 7 number of extra gaps= 0 total=188 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 2a5jA/T0308-2a5jA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 2a5jA/T0308-2a5jA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a5jA read from 2a5jA/T0308-2a5jA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2a5jA in template set Warning: unaligning (T0308)I31 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2a5jA)I44 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 2a5jA 11 :LFKYIIIGDTGVGKSCLLLQFTDKRF T0308 32 :LPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 2a5jA 45 :GVEFGARMVNIDGKQIKLQIWDTAGQESFRSITRSYYRGAAGALLVYDITRRETFNHLTSWLEDARQHSS T0308 105 :RRIPILFFANKMDLRDAVTSV 2a5jA 115 :SNMVIMLIGNKSDLESRRDVK T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 2a5jA 136 :REEGEAFAREHGLIFMETSAKTACNVEEAFINTAKEI Number of specific fragments extracted= 4 number of extra gaps= 0 total=192 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 2gf9A/T0308-2gf9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2gf9A expands to /projects/compbio/data/pdb/2gf9.pdb.gz 2gf9A:Skipped atom 705, because occupancy 0.500 <= existing 0.500 in 2gf9A Skipped atom 709, because occupancy 0.500 <= existing 0.500 in 2gf9A Skipped atom 711, because occupancy 0.500 <= existing 0.500 in 2gf9A Skipped atom 713, because occupancy 0.500 <= existing 0.500 in 2gf9A Skipped atom 715, because occupancy 0.500 <= existing 0.500 in 2gf9A Skipped atom 871, because occupancy 0.500 <= existing 0.500 in 2gf9A Skipped atom 875, because occupancy 0.500 <= existing 0.500 in 2gf9A Skipped atom 877, because occupancy 0.500 <= existing 0.500 in 2gf9A Skipped atom 879, because occupancy 0.500 <= existing 0.500 in 2gf9A Skipped atom 881, because occupancy 0.500 <= existing 0.500 in 2gf9A Skipped atom 883, because occupancy 0.500 <= existing 0.500 in 2gf9A Skipped atom 1037, because occupancy 0.500 <= existing 0.500 in 2gf9A Skipped atom 1041, because occupancy 0.500 <= existing 0.500 in 2gf9A Skipped atom 1043, because occupancy 0.500 <= existing 0.500 in 2gf9A Skipped atom 1045, because occupancy 0.500 <= existing 0.500 in 2gf9A Skipped atom 1047, because occupancy 0.500 <= existing 0.500 in 2gf9A Skipped atom 1410, because occupancy 0.500 <= existing 0.500 in 2gf9A Skipped atom 1414, because occupancy 0.500 <= existing 0.500 in 2gf9A Skipped atom 1416, because occupancy 0.500 <= existing 0.500 in 2gf9A Skipped atom 1418, because occupancy 0.500 <= existing 0.500 in 2gf9A Skipped atom 1420, because occupancy 0.500 <= existing 0.500 in 2gf9A # T0308 read from 2gf9A/T0308-2gf9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gf9A read from 2gf9A/T0308-2gf9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2gf9A to template set # found chain 2gf9A in template set Warning: unaligning (T0308)C144 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gf9A)E163 Warning: unaligning (T0308)A145 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gf9A)E163 T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNAQSQNI 2gf9A 23 :FKLLLIGNSSVGKTSFLFRYADDSFTPAFV T0308 32 :LPTIGFSIEKFKSSS 2gf9A 54 :TVGIDFKVKTVYRHD T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 2gf9A 71 :IKLQIWDTAGQERYRTITTAYYRGAMGFLLMYDIANQESFAAVQDWATQIKTYSW T0308 105 :RRIPILFFANKMDLRDAV 2gf9A 126 :DNAQVILVGNKCDLEDER T0308 126 :KVSQLLCLENIKDKPWHI 2gf9A 144 :VVPAEDGRRLADDLGFEF T0308 146 :SDAIKGEGLQEGVDWLQDQI 2gf9A 164 :ASAKENINVKQVFERLVDVI Number of specific fragments extracted= 6 number of extra gaps= 1 total=198 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 2gf9A/T0308-2gf9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 2gf9A/T0308-2gf9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gf9A read from 2gf9A/T0308-2gf9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gf9A in template set Warning: unaligning (T0308)C144 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gf9A)E163 Warning: unaligning (T0308)A145 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gf9A)E163 T0308 2 :VHVLCLGLDNSGKTTIINKLK 2gf9A 23 :FKLLLIGNSSVGKTSFLFRYA T0308 24 :SNAQSQNILPTIG 2gf9A 44 :DDSFTPAFVSTVG T0308 37 :FSIEKFKSSS 2gf9A 59 :FKVKTVYRHD T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 2gf9A 71 :IKLQIWDTAGQERYRTITTAYYRGAMGFLLMYDIANQESFAAVQDWATQIKTY T0308 103 :KHRRIPILFFANKMDLRDAV 2gf9A 124 :SWDNAQVILVGNKCDLEDER T0308 126 :KVSQLLCLENIKDKPWHI 2gf9A 144 :VVPAEDGRRLADDLGFEF T0308 146 :SDAIKGEGLQEGVDWLQDQI 2gf9A 164 :ASAKENINVKQVFERLVDVI Number of specific fragments extracted= 7 number of extra gaps= 1 total=205 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 2gf9A/T0308-2gf9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 2gf9A/T0308-2gf9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gf9A read from 2gf9A/T0308-2gf9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gf9A in template set Warning: unaligning (T0308)C144 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gf9A)E163 Warning: unaligning (T0308)A145 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gf9A)E163 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 2gf9A 22 :MFKLLLIGNSSVGKTSFLFRYADDSF T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 2gf9A 51 :FVSTVGIDFKVKTVYRHDKRIKLQIWDTAGQERYRTITTAYYRGAMGFLLMYDIANQESFAAVQDWATQIKTYSW T0308 105 :RRIPILFFANKMDLRDAVTSV 2gf9A 126 :DNAQVILVGNKCDLEDERVVP T0308 129 :QLLCLENIKDKPWHI 2gf9A 147 :AEDGRRLADDLGFEF T0308 146 :SDAIKGEGLQEGVDWLQDQI 2gf9A 164 :ASAKENINVKQVFERLVDVI Number of specific fragments extracted= 5 number of extra gaps= 1 total=210 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 1fzqA/T0308-1fzqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1fzqA expands to /projects/compbio/data/pdb/1fzq.pdb.gz 1fzqA:Skipped atom 27, because occupancy 0.500 <= existing 0.500 in 1fzqA Skipped atom 139, because occupancy 0.500 <= existing 0.500 in 1fzqA Skipped atom 141, because occupancy 0.500 <= existing 0.500 in 1fzqA Skipped atom 143, because occupancy 0.500 <= existing 0.500 in 1fzqA Skipped atom 145, because occupancy 0.500 <= existing 0.500 in 1fzqA Skipped atom 147, because occupancy 0.500 <= existing 0.500 in 1fzqA Skipped atom 424, because occupancy 0.500 <= existing 0.500 in 1fzqA Skipped atom 426, because occupancy 0.500 <= existing 0.500 in 1fzqA Skipped atom 695, because occupancy 0.500 <= existing 0.500 in 1fzqA Skipped atom 697, because occupancy 0.500 <= existing 0.500 in 1fzqA Skipped atom 699, because occupancy 0.500 <= existing 0.500 in 1fzqA Skipped atom 807, because occupancy 0.500 <= existing 0.500 in 1fzqA Skipped atom 809, because occupancy 0.500 <= existing 0.500 in 1fzqA Skipped atom 811, because occupancy 0.500 <= existing 0.500 in 1fzqA Skipped atom 813, because occupancy 0.500 <= existing 0.500 in 1fzqA Skipped atom 815, because occupancy 0.500 <= existing 0.500 in 1fzqA Skipped atom 817, because occupancy 0.500 <= existing 0.500 in 1fzqA Skipped atom 955, because occupancy 0.500 <= existing 0.500 in 1fzqA Skipped atom 1149, because occupancy 0.500 <= existing 0.500 in 1fzqA Skipped atom 1151, because occupancy 0.500 <= existing 0.500 in 1fzqA Skipped atom 1153, because occupancy 0.500 <= existing 0.500 in 1fzqA Skipped atom 1270, because occupancy 0.500 <= existing 0.500 in 1fzqA # T0308 read from 1fzqA/T0308-1fzqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fzqA read from 1fzqA/T0308-1fzqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1fzqA to template set # found chain 1fzqA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1fzqA 17 :EVRILLLGLDNAGKTTLLKQLASEDI T0308 29 :QNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1fzqA 43 :SHITPTQGFNIKSVQSQGFKLNVWDIGGQRKIRPYWRSYFENTDILIYVIDSADRKRFEETGQELTELLEEEKL T0308 105 :RRIPILFFANKMDLRDAV 1fzqA 117 :SCVPVLIFANKQDLLTAA T0308 128 :SQLLCLENIK 1fzqA 135 :PASEIAEGLN T0308 140 :P 1fzqA 147 :T T0308 141 :WHICASDAIKGEGLQEGVDWLQDQI 1fzqA 153 :WQIQSCSALTGEGVQDGMNWVCKNV Number of specific fragments extracted= 6 number of extra gaps= 0 total=216 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 1fzqA/T0308-1fzqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1fzqA/T0308-1fzqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fzqA read from 1fzqA/T0308-1fzqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fzqA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNAQSQ 1fzqA 17 :EVRILLLGLDNAGKTTLLKQLASEDISHI T0308 32 :LPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDIKH 1fzqA 46 :TPTQGFNIKSVQSQGFKLNVWDIGGQRKIRPYWRSYFENTDILIYVIDSADRKRFEETGQELTELLEEEKLSC T0308 107 :IPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1fzqA 119 :VPVLIFANKQDLLTAAPASEIAEGLNLHTIRDRVWQIQSCSALTGEGVQDGMNWVCKNV Number of specific fragments extracted= 3 number of extra gaps= 0 total=219 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 1fzqA/T0308-1fzqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1fzqA/T0308-1fzqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fzqA read from 1fzqA/T0308-1fzqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fzqA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1fzqA 17 :EVRILLLGLDNAGKTTLLKQLASEDI T0308 30 :NILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1fzqA 44 :HITPTQGFNIKSVQSQGFKLNVWDIGGQRKIRPYWRSYFENTDILIYVIDSADRKRFEETGQELTELLEEEK T0308 104 :HRRIPILFFANKMDLRDAVTSVKVSQL 1fzqA 116 :LSCVPVLIFANKQDLLTAAPASEIAEG T0308 136 :I 1fzqA 143 :L T0308 137 :KDKPWHICASDAIKGEGLQEGVDWLQDQI 1fzqA 149 :RDRVWQIQSCSALTGEGVQDGMNWVCKNV Number of specific fragments extracted= 5 number of extra gaps= 0 total=224 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 1kshA/T0308-1kshA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1kshA expands to /projects/compbio/data/pdb/1ksh.pdb.gz 1kshA:Skipped atom 280, because occupancy 0.400 <= existing 0.600 in 1kshA Skipped atom 282, because occupancy 0.400 <= existing 0.600 in 1kshA Skipped atom 284, because occupancy 0.400 <= existing 0.600 in 1kshA Skipped atom 286, because occupancy 0.400 <= existing 0.600 in 1kshA Skipped atom 288, because occupancy 0.400 <= existing 0.600 in 1kshA Skipped atom 290, because occupancy 0.400 <= existing 0.600 in 1kshA Skipped atom 292, because occupancy 0.400 <= existing 0.600 in 1kshA Skipped atom 294, because occupancy 0.400 <= existing 0.600 in 1kshA Skipped atom 353, because occupancy 0.500 <= existing 0.500 in 1kshA Skipped atom 355, because occupancy 0.500 <= existing 0.500 in 1kshA Skipped atom 357, because occupancy 0.500 <= existing 0.500 in 1kshA Skipped atom 359, because occupancy 0.500 <= existing 0.500 in 1kshA Skipped atom 361, because occupancy 0.500 <= existing 0.500 in 1kshA Skipped atom 1048, because occupancy 0.500 <= existing 0.500 in 1kshA Skipped atom 1050, because occupancy 0.500 <= existing 0.500 in 1kshA Skipped atom 1052, because occupancy 0.500 <= existing 0.500 in 1kshA Skipped atom 1054, because occupancy 0.500 <= existing 0.500 in 1kshA Skipped atom 1091, because occupancy 0.300 <= existing 0.700 in 1kshA Skipped atom 1093, because occupancy 0.300 <= existing 0.700 in 1kshA Skipped atom 1095, because occupancy 0.300 <= existing 0.700 in 1kshA Skipped atom 1097, because occupancy 0.300 <= existing 0.700 in 1kshA Skipped atom 1099, because occupancy 0.300 <= existing 0.700 in 1kshA Skipped atom 1101, because occupancy 0.300 <= existing 0.700 in 1kshA Skipped atom 1150, because occupancy 0.300 <= existing 0.700 in 1kshA Skipped atom 1152, because occupancy 0.300 <= existing 0.700 in 1kshA Skipped atom 1154, because occupancy 0.300 <= existing 0.700 in 1kshA Skipped atom 1156, because occupancy 0.300 <= existing 0.700 in 1kshA # T0308 read from 1kshA/T0308-1kshA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kshA read from 1kshA/T0308-1kshA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1kshA to template set # found chain 1kshA in template set Warning: unaligning (T0308)S128 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1kshA)N136 Warning: unaligning (T0308)L130 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1kshA)N136 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSN 1kshA 16 :ELRLLMLGLDNAGKTTILKKFNGED T0308 28 :SQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1kshA 41 :VDTISPTLGFNIKTLEHRGFKLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADRQRMQDCQRELQSLLVEERL T0308 105 :RRIPILFFANKMDLRDA 1kshA 116 :AGATLLIFANKQDLPGA T0308 127 :V 1kshA 133 :L T0308 131 :LCLENIK 1kshA 137 :AIQEALE T0308 138 :DKPWHICASDAIKGEGLQEGVDWLQDQI 1kshA 149 :SHHWRIQGCSAVTGEDLLPGIDWLLDDI Number of specific fragments extracted= 6 number of extra gaps= 0 total=230 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 1kshA/T0308-1kshA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1kshA/T0308-1kshA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kshA read from 1kshA/T0308-1kshA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kshA in template set Warning: unaligning (T0308)T123 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1kshA)N136 Warning: unaligning (T0308)V125 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1kshA)N136 T0308 1 :EVHVLCLGLDNSGKTTIINKL 1kshA 16 :ELRLLMLGLDNAGKTTILKKF T0308 24 :SNAQSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDIKH 1kshA 37 :NGEDVDTISPTLGFNIKTLEHRGFKLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADRQRMQDCQRELQSLLVEERLAG T0308 107 :IPILFFANKMDLRDAV 1kshA 118 :ATLLIFANKQDLPGAL T0308 126 :KVSQL 1kshA 137 :AIQEA T0308 134 :ENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1kshA 145 :DSIRSHHWRIQGCSAVTGEDLLPGIDWLLDDI Number of specific fragments extracted= 5 number of extra gaps= 0 total=235 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 1kshA/T0308-1kshA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1kshA/T0308-1kshA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kshA read from 1kshA/T0308-1kshA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kshA in template set Warning: unaligning (T0308)T123 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1kshA)N136 Warning: unaligning (T0308)V125 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1kshA)N136 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1kshA 16 :ELRLLMLGLDNAGKTTILKKFNGEDV T0308 29 :QNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1kshA 42 :DTISPTLGFNIKTLEHRGFKLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADRQRMQDCQRELQSLLVEER T0308 104 :HRRIPILFFANKMDLRDAV 1kshA 115 :LAGATLLIFANKQDLPGAL T0308 126 :KVSQ 1kshA 137 :AIQE T0308 135 :NIK 1kshA 141 :ALE T0308 138 :DKPWHICASDAIKGEGLQEGVDWLQDQI 1kshA 149 :SHHWRIQGCSAVTGEDLLPGIDWLLDDI Number of specific fragments extracted= 6 number of extra gaps= 0 total=241 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 1yzqA/T0308-1yzqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1yzqA expands to /projects/compbio/data/pdb/1yzq.pdb.gz 1yzqA:# T0308 read from 1yzqA/T0308-1yzqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yzqA read from 1yzqA/T0308-1yzqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1yzqA to template set # found chain 1yzqA in template set Warning: unaligning (T0308)V2 because first residue in template chain is (1yzqA)F14 Warning: unaligning (T0308)S146 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yzqA)S156 Warning: unaligning (T0308)D147 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yzqA)S156 T0308 3 :HVLCLGLDNSGKTTIINKLKPSNAQSQNI 1yzqA 15 :KLVFLGEQSVGKTSLITRFMYDSFDNTYQ T0308 32 :LPTIGFSIEKFKSSS 1yzqA 45 :TIGIDFLSKTMYLED T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1yzqA 62 :IRLQLWDTAGQERFRSLIPSYIRDSAAAVVVYDITNVNSFQQTTKWIDDVRTERG T0308 105 :RRIPILFFANKMDLRDAV 1yzqA 117 :SDVIIMLVGNKTDLADKR T0308 126 :KVSQLLCLENIKDKPWHICA 1yzqA 135 :QVSIEEGERKAKELNVMFIE T0308 148 :AIKGEGLQEGVDWLQDQI 1yzqA 157 :AKAGYNVKQLFRRVAAAL Number of specific fragments extracted= 6 number of extra gaps= 1 total=247 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 1yzqA/T0308-1yzqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1yzqA/T0308-1yzqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yzqA read from 1yzqA/T0308-1yzqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yzqA in template set Warning: unaligning (T0308)V2 because first residue in template chain is (1yzqA)F14 Warning: unaligning (T0308)S146 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yzqA)S156 Warning: unaligning (T0308)D147 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yzqA)S156 T0308 3 :HVLCLGLDNSGKTTIINKLK 1yzqA 15 :KLVFLGEQSVGKTSLITRFM T0308 24 :SNAQSQNILPTIG 1yzqA 35 :YDSFDNTYQATIG T0308 37 :FSIEKFKSSS 1yzqA 50 :FLSKTMYLED T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 1yzqA 62 :IRLQLWDTAGQERFRSLIPSYIRDSAAAVVVYDITNVNSFQQTTKWIDDVRTE T0308 103 :KHRRIPILFFANKMDLRDAV 1yzqA 115 :RGSDVIIMLVGNKTDLADKR T0308 126 :KVSQLLCLENIKDKPWHICA 1yzqA 135 :QVSIEEGERKAKELNVMFIE T0308 148 :AIKGEGLQEGVDWLQDQI 1yzqA 157 :AKAGYNVKQLFRRVAAAL Number of specific fragments extracted= 7 number of extra gaps= 1 total=254 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 1yzqA/T0308-1yzqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1yzqA/T0308-1yzqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yzqA read from 1yzqA/T0308-1yzqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yzqA in template set Warning: unaligning (T0308)V2 because first residue in template chain is (1yzqA)F14 Warning: unaligning (T0308)S146 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yzqA)S156 Warning: unaligning (T0308)D147 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yzqA)S156 T0308 3 :HVLCLGLDNSGKTTIINKLKPSNA 1yzqA 15 :KLVFLGEQSVGKTSLITRFMYDSF T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1yzqA 42 :YQATIGIDFLSKTMYLEDRTIRLQLWDTAGQERFRSLIPSYIRDSAAAVVVYDITNVNSFQQTTKWIDDVRTERG T0308 105 :RRIPILFFANKMDLRDAVTSV 1yzqA 117 :SDVIIMLVGNKTDLADKRQVS T0308 129 :QLLCLENIKDKPWHICA 1yzqA 138 :IEEGERKAKELNVMFIE T0308 148 :AIKGEGLQEGVDWLQDQI 1yzqA 157 :AKAGYNVKQLFRRVAAAL Number of specific fragments extracted= 5 number of extra gaps= 1 total=259 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 1r8sA/T0308-1r8sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1r8sA expands to /projects/compbio/data/pdb/1r8s.pdb.gz 1r8sA:Skipped atom 270, because occupancy 0.500 <= existing 0.500 in 1r8sA Skipped atom 272, because occupancy 0.500 <= existing 0.500 in 1r8sA Skipped atom 274, because occupancy 0.500 <= existing 0.500 in 1r8sA Skipped atom 552, because occupancy 0.500 <= existing 0.500 in 1r8sA Skipped atom 554, because occupancy 0.500 <= existing 0.500 in 1r8sA Skipped atom 556, because occupancy 0.500 <= existing 0.500 in 1r8sA Skipped atom 684, because occupancy 0.500 <= existing 0.500 in 1r8sA Skipped atom 686, because occupancy 0.500 <= existing 0.500 in 1r8sA Skipped atom 688, because occupancy 0.500 <= existing 0.500 in 1r8sA Skipped atom 690, because occupancy 0.500 <= existing 0.500 in 1r8sA Skipped atom 979, because occupancy 0.500 <= existing 0.500 in 1r8sA Skipped atom 981, because occupancy 0.500 <= existing 0.500 in 1r8sA Skipped atom 983, because occupancy 0.500 <= existing 0.500 in 1r8sA Skipped atom 985, because occupancy 0.500 <= existing 0.500 in 1r8sA Skipped atom 987, because occupancy 0.500 <= existing 0.500 in 1r8sA Skipped atom 1055, because occupancy 0.350 <= existing 0.650 in 1r8sA Skipped atom 1057, because occupancy 0.350 <= existing 0.650 in 1r8sA Skipped atom 1103, because occupancy 0.450 <= existing 0.550 in 1r8sA Skipped atom 1105, because occupancy 0.450 <= existing 0.550 in 1r8sA Skipped atom 1107, because occupancy 0.450 <= existing 0.550 in 1r8sA Skipped atom 1109, because occupancy 0.450 <= existing 0.550 in 1r8sA # T0308 read from 1r8sA/T0308-1r8sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r8sA read from 1r8sA/T0308-1r8sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1r8sA to template set # found chain 1r8sA in template set T0308 3 :HVLCLGLDNSGKTTIINKLKPSNAQSQ 1r8sA 19 :RILMVGLDAAGKTTILYKLKLGEIVTT T0308 32 :LPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1r8sA 46 :IPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDEL T0308 105 :RRIPILFFANKMDLRDAV 1r8sA 117 :RDAVLLVFANKQDLPNAM T0308 128 :SQLLCLENIK 1r8sA 135 :NAAEITDKLG T0308 138 :DKPWHICASDAIKGEGLQEGVDWLQDQI 1r8sA 150 :HRNWYIQATCATSGDGLYEGLDWLSNQL Number of specific fragments extracted= 5 number of extra gaps= 0 total=264 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 1r8sA/T0308-1r8sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1r8sA/T0308-1r8sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r8sA read from 1r8sA/T0308-1r8sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1r8sA in template set T0308 3 :HVLCLGLDNSGKTTIINKLKPSNAQ 1r8sA 19 :RILMVGLDAAGKTTILYKLKLGEIV T0308 30 :NILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDIKH 1r8sA 44 :TTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRD T0308 107 :IPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1r8sA 119 :AVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=267 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 1r8sA/T0308-1r8sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1r8sA/T0308-1r8sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r8sA read from 1r8sA/T0308-1r8sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1r8sA in template set T0308 3 :HVLCLGLDNSGKTTIINKLKPSNA 1r8sA 19 :RILMVGLDAAGKTTILYKLKLGEI T0308 29 :QNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1r8sA 43 :VTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDE T0308 104 :HRRIPILFFANKMDLRDAVTSVKVSQL 1r8sA 116 :LRDAVLLVFANKQDLPNAMNAAEITDK T0308 136 :IK 1r8sA 143 :LG T0308 138 :DKPWHICASDAIKGEGLQEGVDWLQDQI 1r8sA 150 :HRNWYIQATCATSGDGLYEGLDWLSNQL Number of specific fragments extracted= 5 number of extra gaps= 0 total=272 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 1zd9A/T0308-1zd9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zd9A expands to /projects/compbio/data/pdb/1zd9.pdb.gz 1zd9A:# T0308 read from 1zd9A/T0308-1zd9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zd9A read from 1zd9A/T0308-1zd9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zd9A to template set # found chain 1zd9A in template set T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1zd9A 20 :MELTLVGLQYSGKTTFVNVIASGQF T0308 28 :SQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1zd9A 45 :NEDMIPTVGFNMRKITKGNVTIKLWDIGGQPRFRSMWERYCRGVSAIVYMVDAADQEKIEASKNELHNLLDKPQL T0308 105 :RRIPILFFANKMDLRDA 1zd9A 120 :QGIPVLVLGNKRDLPGA T0308 127 :VSQLLCLENIK 1zd9A 137 :LDEKELIEKMN T0308 138 :DKPWHICASDAIKGEGLQEGVDWLQDQI 1zd9A 153 :DREICCYSISCKEKDNIDITLQWLIQHS Number of specific fragments extracted= 5 number of extra gaps= 0 total=277 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 1zd9A/T0308-1zd9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1zd9A/T0308-1zd9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zd9A read from 1zd9A/T0308-1zd9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zd9A in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLK 1zd9A 19 :EMELTLVGLQYSGKTTFVNVIA T0308 24 :SNAQSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDIKH 1zd9A 41 :SGQFNEDMIPTVGFNMRKITKGNVTIKLWDIGGQPRFRSMWERYCRGVSAIVYMVDAADQEKIEASKNELHNLLDKPQLQG T0308 107 :IPILFFANKMDLRDAVTSVKVSQL 1zd9A 122 :IPVLVLGNKRDLPGALDEKELIEK T0308 136 :IK 1zd9A 146 :MN T0308 138 :DKPWHICASDAIKGEGLQEGVDWLQDQI 1zd9A 153 :DREICCYSISCKEKDNIDITLQWLIQHS Number of specific fragments extracted= 5 number of extra gaps= 0 total=282 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 1zd9A/T0308-1zd9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1zd9A/T0308-1zd9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zd9A read from 1zd9A/T0308-1zd9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zd9A in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNAQ 1zd9A 19 :EMELTLVGLQYSGKTTFVNVIASGQFN T0308 29 :QNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1zd9A 46 :EDMIPTVGFNMRKITKGNVTIKLWDIGGQPRFRSMWERYCRGVSAIVYMVDAADQEKIEASKNELHNLLDKPQ T0308 104 :HRRIPILFFANKMDLRDAVTSVKVSQ 1zd9A 119 :LQGIPVLVLGNKRDLPGALDEKELIE T0308 135 :NI 1zd9A 145 :KM T0308 137 :KDKPWHICASDAIKGEGLQEGVDWLQDQ 1zd9A 152 :QDREICCYSISCKEKDNIDITLQWLIQH Number of specific fragments extracted= 5 number of extra gaps= 0 total=287 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 1vg8A/T0308-1vg8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vg8A expands to /projects/compbio/data/pdb/1vg8.pdb.gz 1vg8A:Skipped atom 997, because occupancy 0.500 <= existing 0.500 in 1vg8A Skipped atom 999, because occupancy 0.500 <= existing 0.500 in 1vg8A Skipped atom 1001, because occupancy 0.500 <= existing 0.500 in 1vg8A Skipped atom 1003, because occupancy 0.500 <= existing 0.500 in 1vg8A Skipped atom 1005, because occupancy 0.500 <= existing 0.500 in 1vg8A Skipped atom 1007, because occupancy 0.500 <= existing 0.500 in 1vg8A Skipped atom 1009, because occupancy 0.500 <= existing 0.500 in 1vg8A Skipped atom 1219, because occupancy 0.500 <= existing 0.500 in 1vg8A Skipped atom 1221, because occupancy 0.500 <= existing 0.500 in 1vg8A Skipped atom 1223, because occupancy 0.500 <= existing 0.500 in 1vg8A Skipped atom 1225, because occupancy 0.500 <= existing 0.500 in 1vg8A Skipped atom 1227, because occupancy 0.500 <= existing 0.500 in 1vg8A # T0308 read from 1vg8A/T0308-1vg8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vg8A read from 1vg8A/T0308-1vg8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vg8A to template set # found chain 1vg8A in template set T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1vg8A 1009 :LKVIILGDSGVGKTSLMNQYVNKKF T0308 28 :SQNI 1vg8A 1034 :SNQY T0308 32 :LPTIGFSIEKFKSSS 1vg8A 1040 :TIGADFLTKEVMVDD T0308 47 :LSFTVFDMSGQGRY 1vg8A 1057 :VTMQIWDTAGQERF T0308 66 :HYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1vg8A 1076 :AFYRGADCCVLVFDVTAPNTFKTLDSWRDEFLIQASP T0308 103 :KHRRIPILFFANKMDLRDA 1vg8A 1114 :DPENFPFVVLGNKIDLENR T0308 126 :KVSQLLCLENIKDKP 1vg8A 1133 :QVATKRAQAWCYSKN T0308 141 :WHICASDAIKGEGLQEGVDWLQDQI 1vg8A 1149 :IPYFETSAKEAINVEQAFQTIARNA Number of specific fragments extracted= 8 number of extra gaps= 0 total=295 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 1vg8A/T0308-1vg8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1vg8A/T0308-1vg8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vg8A read from 1vg8A/T0308-1vg8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vg8A in template set T0308 2 :VHVLCLGLDNSGKTTIINKLK 1vg8A 1009 :LKVIILGDSGVGKTSLMNQYV T0308 24 :SNAQSQNILPTIG 1vg8A 1030 :NKKFSNQYKATIG T0308 37 :FSIEKFKSSS 1vg8A 1045 :FLTKEVMVDD T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDIKH 1vg8A 1057 :VTMQIWDTAGQERFQSLGVAFYRGADCCVLVFDVTAPNTFKTLDSWRDEFLIQASPRD T0308 105 :RRIPILFFANKMDLRDA 1vg8A 1116 :ENFPFVVLGNKIDLENR T0308 126 :KVSQLLCLENIKD 1vg8A 1133 :QVATKRAQAWCYS T0308 139 :KPWHICASDAIKGEGLQEGVDWLQDQI 1vg8A 1147 :NNIPYFETSAKEAINVEQAFQTIARNA Number of specific fragments extracted= 7 number of extra gaps= 0 total=302 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 1vg8A/T0308-1vg8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1vg8A/T0308-1vg8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vg8A read from 1vg8A/T0308-1vg8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vg8A in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1vg8A 1008 :LLKVIILGDSGVGKTSLMNQYVNKKF T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDIK 1vg8A 1037 :YKATIGADFLTKEVMVDDRLVTMQIWDTAGQERFQSLGVAFYRGADCCVLVFDVTAPNTFKTLDSWRDEFLIQASPR T0308 104 :HRRIPILFFANKMDLRDAVTSV 1vg8A 1115 :PENFPFVVLGNKIDLENRQVAT T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQ 1vg8A 1137 :KRAQAWCYSKNNIPYFETSAKEAINVEQAFQTIARN Number of specific fragments extracted= 4 number of extra gaps= 0 total=306 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 1z06A/T0308-1z06A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1z06A expands to /projects/compbio/data/pdb/1z06.pdb.gz 1z06A:# T0308 read from 1z06A/T0308-1z06A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z06A read from 1z06A/T0308-1z06A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1z06A to template set # found chain 1z06A in template set T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1z06A 34 :FKIIVIGDSNVGKTCLTYRFCAGRF T0308 27 :QSQN 1z06A 60 :DRTE T0308 32 :LPTIGFSIEKFKSSS 1z06A 65 :TIGVDFRERAVDIDG T0308 47 :LSFTVFDMSGQGRYR 1z06A 82 :IKIQLWDTAGQERFR T0308 62 :NLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1z06A 98 :SMVQHYYRNVHAVVFVYDMTNMASFHSLPAWIEECKQHLLA T0308 105 :RRIPILFFANKMDLRDAV 1z06A 139 :NDIPRILVGNKCDLRSAI T0308 126 :KVSQLLCLENIKDKPWHICASDAI 1z06A 157 :QVPTDLAQKFADTHSMPLFETSAK T0308 150 :KGEGLQEGVDWL 1z06A 184 :DNDHVEAIFMTL Number of specific fragments extracted= 8 number of extra gaps= 0 total=314 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 1z06A/T0308-1z06A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1z06A/T0308-1z06A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z06A read from 1z06A/T0308-1z06A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1z06A in template set T0308 2 :VHVLCLGLDNSGKTTIINKLK 1z06A 34 :FKIIVIGDSNVGKTCLTYRFC T0308 24 :SNAQSQNILPTIG 1z06A 55 :AGRFPDRTEATIG T0308 37 :FSIEKFKSSS 1z06A 70 :FRERAVDIDG T0308 47 :LSFTVFDMSGQGRYR 1z06A 82 :IKIQLWDTAGQERFR T0308 62 :NLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 1z06A 98 :SMVQHYYRNVHAVVFVYDMTNMASFHSLPAWIEECKQH T0308 102 :IKHRRIPILFFANKMDLRDAV 1z06A 136 :LLANDIPRILVGNKCDLRSAI T0308 126 :KVSQLLCLENIKDKPWHICASDAI 1z06A 157 :QVPTDLAQKFADTHSMPLFETSAK T0308 150 :KGEGLQEGVDWL 1z06A 184 :DNDHVEAIFMTL Number of specific fragments extracted= 8 number of extra gaps= 0 total=322 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 1z06A/T0308-1z06A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1z06A/T0308-1z06A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z06A read from 1z06A/T0308-1z06A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1z06A in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1z06A 33 :IFKIIVIGDSNVGKTCLTYRFCAGRF T0308 27 :QSQNILPTIGFSIEKFKSSS 1z06A 60 :DRTEATIGVDFRERAVDIDG T0308 47 :LSFTVFDMSGQGRYRN 1z06A 82 :IKIQLWDTAGQERFRK T0308 63 :LWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1z06A 99 :MVQHYYRNVHAVVFVYDMTNMASFHSLPAWIEECKQHLL T0308 104 :HRRIPILFFANKMDLRDAVTSV 1z06A 138 :ANDIPRILVGNKCDLRSAIQVP T0308 129 :QLLCLENIKDKPWHICASDAI 1z06A 160 :TDLAQKFADTHSMPLFETSAK T0308 150 :KGEGLQEGVDWL 1z06A 184 :DNDHVEAIFMTL Number of specific fragments extracted= 7 number of extra gaps= 0 total=329 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 1zj6A/T0308-1zj6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zj6A expands to /projects/compbio/data/pdb/1zj6.pdb.gz 1zj6A:# T0308 read from 1zj6A/T0308-1zj6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zj6A read from 1zj6A/T0308-1zj6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zj6A to template set # found chain 1zj6A in template set Warning: unaligning (T0308)F37 because of BadResidue code BAD_PEPTIDE in next template residue (1zj6A)N51 Warning: unaligning (T0308)S38 because of BadResidue code BAD_PEPTIDE at template residue (1zj6A)N51 Warning: unaligning (T0308)G56 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1zj6A)R74 Warning: unaligning (T0308)R61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zj6A)R74 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1zj6A 16 :EHKVIIVGLDNAGKTTILYQFSMNEV T0308 27 :QSQ 1zj6A 43 :HTS T0308 33 :PTIG 1zj6A 46 :PTIG T0308 39 :IEKFKSSSLSFTVFDMS 1zj6A 52 :VEEIVINNTRFLMWDIG T0308 62 :NLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1zj6A 75 :SSWNTYYTNTEFVIVVVDSTDRERISVTREELYKMLAHEDL T0308 105 :RRIPILFFANKMDLRDAV 1zj6A 116 :RKAGLLIFANKQDVKECM T0308 128 :SQLLCLENIK 1zj6A 134 :TVAEISQFLK T0308 138 :DKPWHICASDAIKGEGLQEGVDWLQDQI 1zj6A 149 :DHQWHIQACCALTGEGLCQGLEWMMSRL Number of specific fragments extracted= 8 number of extra gaps= 1 total=337 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 1zj6A/T0308-1zj6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1zj6A/T0308-1zj6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zj6A read from 1zj6A/T0308-1zj6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zj6A in template set Warning: unaligning (T0308)F37 because of BadResidue code BAD_PEPTIDE in next template residue (1zj6A)N51 Warning: unaligning (T0308)S38 because of BadResidue code BAD_PEPTIDE at template residue (1zj6A)N51 Warning: unaligning (T0308)G56 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1zj6A)R74 Warning: unaligning (T0308)R61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zj6A)R74 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNAQSQ 1zj6A 16 :EHKVIIVGLDNAGKTTILYQFSMNEVVHT T0308 32 :LPTIG 1zj6A 45 :SPTIG T0308 39 :IEKFKSSSLSFTVFDMS 1zj6A 52 :VEEIVINNTRFLMWDIG T0308 62 :NLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDIKH 1zj6A 75 :SSWNTYYTNTEFVIVVVDSTDRERISVTREELYKMLAHEDLRK T0308 107 :IPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1zj6A 118 :AGLLIFANKQDVKECMTVAEISQFLKLTSIKDHQWHIQACCALTGEGLCQGLEWMMSRL Number of specific fragments extracted= 5 number of extra gaps= 1 total=342 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 1zj6A/T0308-1zj6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1zj6A/T0308-1zj6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zj6A read from 1zj6A/T0308-1zj6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zj6A in template set Warning: unaligning (T0308)F37 because of BadResidue code BAD_PEPTIDE in next template residue (1zj6A)N51 Warning: unaligning (T0308)S38 because of BadResidue code BAD_PEPTIDE at template residue (1zj6A)N51 Warning: unaligning (T0308)G56 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1zj6A)R74 Warning: unaligning (T0308)R61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zj6A)R74 T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1zj6A 17 :HKVIIVGLDNAGKTTILYQFSMNEV T0308 30 :NILPTIG 1zj6A 43 :HTSPTIG T0308 39 :IEKFKSSSLSFTVFDMS 1zj6A 52 :VEEIVINNTRFLMWDIG T0308 62 :NLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1zj6A 75 :SSWNTYYTNTEFVIVVVDSTDRERISVTREELYKMLAHED T0308 104 :HRRIPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1zj6A 115 :LRKAGLLIFANKQDVKECMTVAEISQFLKLTSIKDHQWHIQACCALTGEGLCQGLEWMMSRL Number of specific fragments extracted= 5 number of extra gaps= 1 total=347 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 2g6bA/T0308-2g6bA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2g6bA expands to /projects/compbio/data/pdb/2g6b.pdb.gz 2g6bA:Skipped atom 300, because occupancy 0.500 <= existing 0.500 in 2g6bA Skipped atom 302, because occupancy 0.500 <= existing 0.500 in 2g6bA Skipped atom 304, because occupancy 0.500 <= existing 0.500 in 2g6bA Skipped atom 306, because occupancy 0.500 <= existing 0.500 in 2g6bA Skipped atom 336, because occupancy 0.500 <= existing 0.500 in 2g6bA Skipped atom 340, because occupancy 0.500 <= existing 0.500 in 2g6bA Skipped atom 342, because occupancy 0.500 <= existing 0.500 in 2g6bA Skipped atom 344, because occupancy 0.500 <= existing 0.500 in 2g6bA Skipped atom 346, because occupancy 0.500 <= existing 0.500 in 2g6bA Skipped atom 348, because occupancy 0.500 <= existing 0.500 in 2g6bA Skipped atom 350, because occupancy 0.500 <= existing 0.500 in 2g6bA Skipped atom 352, because occupancy 0.500 <= existing 0.500 in 2g6bA Skipped atom 379, because occupancy 0.500 <= existing 0.500 in 2g6bA Skipped atom 383, because occupancy 0.500 <= existing 0.500 in 2g6bA Skipped atom 385, because occupancy 0.500 <= existing 0.500 in 2g6bA Skipped atom 387, because occupancy 0.500 <= existing 0.500 in 2g6bA Skipped atom 389, because occupancy 0.500 <= existing 0.500 in 2g6bA Skipped atom 392, because occupancy 0.500 <= existing 0.500 in 2g6bA Skipped atom 396, because occupancy 0.500 <= existing 0.500 in 2g6bA Skipped atom 398, because occupancy 0.500 <= existing 0.500 in 2g6bA Skipped atom 400, because occupancy 0.500 <= existing 0.500 in 2g6bA Skipped atom 402, because occupancy 0.500 <= existing 0.500 in 2g6bA # T0308 read from 2g6bA/T0308-2g6bA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2g6bA read from 2g6bA/T0308-2g6bA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2g6bA to template set # found chain 2g6bA in template set Warning: unaligning (T0308)Q57 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2g6bA)A132 Warning: unaligning (T0308)H66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2g6bA)A132 Warning: unaligning (T0308)V77 because of BadResidue code BAD_PEPTIDE in next template residue (2g6bA)Y144 Warning: unaligning (T0308)I78 because of BadResidue code BAD_PEPTIDE at template residue (2g6bA)Y144 T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNAQSQNI 2g6bA 64 :FKVMLVGDSGVGKTCLLVRFKDGAFLAGTF T0308 32 :LPTIGFSIEKFKSSS 2g6bA 96 :TVGIDFRNKVLDVDG T0308 47 :LSFTVFDMSG 2g6bA 113 :VKLQMWDTAG T0308 67 :YYKEGQAIIF 2g6bA 133 :YYRDAHALLL T0308 79 :DSSDRLRMVVAKEELDTLLNHPD 2g6bA 145 :DVTNKASFDNIQAWLTEIHEYAQ T0308 105 :RRIPILFFANKMDLRDAV 2g6bA 168 :HDVALMLLGNKVDSAHER T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 2g6bA 186 :VVKREDGEKLAKEYGLPFMETSAKTGLNVDLAFTAIAKEL Number of specific fragments extracted= 7 number of extra gaps= 1 total=354 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 2g6bA/T0308-2g6bA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 2g6bA/T0308-2g6bA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2g6bA read from 2g6bA/T0308-2g6bA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2g6bA in template set Warning: unaligning (T0308)Q57 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2g6bA)A132 Warning: unaligning (T0308)H66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2g6bA)A132 Warning: unaligning (T0308)V77 because of BadResidue code BAD_PEPTIDE in next template residue (2g6bA)Y144 Warning: unaligning (T0308)I78 because of BadResidue code BAD_PEPTIDE at template residue (2g6bA)Y144 T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNAQSQNILPTIG 2g6bA 64 :FKVMLVGDSGVGKTCLLVRFKDGAFLAGTFISTVG T0308 37 :FSIEKFKSSS 2g6bA 101 :FRNKVLDVDG T0308 47 :LSFTVFDMSG 2g6bA 113 :VKLQMWDTAG T0308 67 :YYKEGQAIIF 2g6bA 133 :YYRDAHALLL T0308 79 :DSSDRLRMVVAKEELDTLLNH 2g6bA 145 :DVTNKASFDNIQAWLTEIHEY T0308 103 :KHRRIPILFFANKMDLRDAV 2g6bA 166 :AQHDVALMLLGNKVDSAHER T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 2g6bA 186 :VVKREDGEKLAKEYGLPFMETSAKTGLNVDLAFTAIAKEL Number of specific fragments extracted= 7 number of extra gaps= 1 total=361 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 2g6bA/T0308-2g6bA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 2g6bA/T0308-2g6bA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2g6bA read from 2g6bA/T0308-2g6bA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2g6bA in template set Warning: unaligning (T0308)Q57 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2g6bA)A132 Warning: unaligning (T0308)H66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2g6bA)A132 Warning: unaligning (T0308)V77 because of BadResidue code BAD_PEPTIDE in next template residue (2g6bA)Y144 Warning: unaligning (T0308)I78 because of BadResidue code BAD_PEPTIDE at template residue (2g6bA)Y144 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 2g6bA 63 :AFKVMLVGDSGVGKTCLLVRFKDGAF T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMSG 2g6bA 93 :FISTVGIDFRNKVLDVDGVKVKLQMWDTAG T0308 67 :YYKEGQAIIF 2g6bA 133 :YYRDAHALLL T0308 79 :DSSDRLRMVVAKEELDTLLNHPD 2g6bA 145 :DVTNKASFDNIQAWLTEIHEYAQ T0308 105 :RRIPILFFANKMDLRDAVTSV 2g6bA 168 :HDVALMLLGNKVDSAHERVVK T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 2g6bA 189 :REDGEKLAKEYGLPFMETSAKTGLNVDLAFTAIAKEL Number of specific fragments extracted= 6 number of extra gaps= 1 total=367 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 1wmsA/T0308-1wmsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1wmsA expands to /projects/compbio/data/pdb/1wms.pdb.gz 1wmsA:# T0308 read from 1wmsA/T0308-1wmsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wmsA read from 1wmsA/T0308-1wmsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1wmsA to template set # found chain 1wmsA in template set Warning: unaligning (T0308)S28 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1wmsA)T39 Warning: unaligning (T0308)L32 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1wmsA)T39 Warning: unaligning (T0308)G56 because of BadResidue code BAD_PEPTIDE in next template residue (1wmsA)Q66 Warning: unaligning (T0308)Q57 because of BadResidue code BAD_PEPTIDE at template residue (1wmsA)Q66 T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNAQ 1wmsA 8 :FKVILLGDGGVGKSSLMNRYVTNKFD T0308 33 :PTIGFSIEKFKSSS 1wmsA 40 :IGVEFLNKDLEVDG T0308 47 :LSFTVFDMS 1wmsA 56 :VTMQIWDTA T0308 58 :GRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDIKH 1wmsA 67 :ERFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFIYYADVKE T0308 105 :RRIPILFFANKMDLRDA 1wmsA 115 :ESFPFVILGNKIDISER T0308 126 :KVSQLLCLENIKDK 1wmsA 132 :QVSTEEAQAWCRDN T0308 140 :PWHICASDAIKGEGLQEGVDWLQDQI 1wmsA 147 :DYPYFETSAKDATNVAAAFEEAVRRV Number of specific fragments extracted= 7 number of extra gaps= 1 total=374 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 1wmsA/T0308-1wmsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1wmsA/T0308-1wmsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wmsA read from 1wmsA/T0308-1wmsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wmsA in template set Warning: unaligning (T0308)Q29 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1wmsA)T39 Warning: unaligning (T0308)T34 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1wmsA)T39 Warning: unaligning (T0308)G56 because of BadResidue code BAD_PEPTIDE in next template residue (1wmsA)Q66 Warning: unaligning (T0308)Q57 because of BadResidue code BAD_PEPTIDE at template residue (1wmsA)Q66 T0308 2 :VHVLCLGLDNSGKTTIINKLK 1wmsA 8 :FKVILLGDGGVGKSSLMNRYV T0308 24 :SNAQS 1wmsA 29 :TNKFD T0308 35 :IG 1wmsA 40 :IG T0308 37 :FSIEKFKSSS 1wmsA 44 :FLNKDLEVDG T0308 47 :LSFTVFDMS 1wmsA 56 :VTMQIWDTA T0308 58 :GRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDIKH 1wmsA 67 :ERFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFIYYADVKE T0308 105 :RRIPILFFANKMDLRDA 1wmsA 115 :ESFPFVILGNKIDISER T0308 126 :KVSQLLCLENIKDK 1wmsA 132 :QVSTEEAQAWCRDN T0308 140 :PWHICASDAIKGEGLQEGVDWLQDQI 1wmsA 147 :DYPYFETSAKDATNVAAAFEEAVRRV Number of specific fragments extracted= 9 number of extra gaps= 1 total=383 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 1wmsA/T0308-1wmsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1wmsA/T0308-1wmsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wmsA read from 1wmsA/T0308-1wmsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wmsA in template set Warning: unaligning (T0308)N30 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1wmsA)T39 Warning: unaligning (T0308)G56 because of BadResidue code BAD_PEPTIDE in next template residue (1wmsA)Q66 Warning: unaligning (T0308)Q57 because of BadResidue code BAD_PEPTIDE at template residue (1wmsA)Q66 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1wmsA 7 :LFKVILLGDGGVGKSSLMNRYVTNKF T0308 31 :ILPTIGFSIEKFKSSSLSFTVFDMS 1wmsA 40 :IGVEFLNKDLEVDGHFVTMQIWDTA T0308 58 :GRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLL 1wmsA 67 :ERFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFI T0308 98 :NHPD 1wmsA 110 :DVKE T0308 104 :HRRIPILFFANKMDLRDAVTSV 1wmsA 114 :PESFPFVILGNKIDISERQVST T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1wmsA 136 :EEAQAWCRDNGDYPYFETSAKDATNVAAAFEEAVRRV Number of specific fragments extracted= 6 number of extra gaps= 1 total=389 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 1z08A/T0308-1z08A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1z08A expands to /projects/compbio/data/pdb/1z08.pdb.gz 1z08A:# T0308 read from 1z08A/T0308-1z08A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z08A read from 1z08A/T0308-1z08A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1z08A to template set # found chain 1z08A in template set Warning: unaligning (T0308)N11 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1z08A)V30 Warning: unaligning (T0308)S12 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1z08A)V30 Warning: unaligning (T0308)Q57 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1z08A)P86 Warning: unaligning (T0308)E65 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1z08A)P86 T0308 2 :VHVLCLGLD 1z08A 20 :FKVVLLGEG T0308 13 :GKTTIINKLKPSNAQSQNI 1z08A 31 :GKTSLVLRYCENKFNDKHI T0308 32 :LPTIGFSIEKFKSSS 1z08A 51 :TLGASFLTKKLNIGG T0308 47 :LSFTVFDMSG 1z08A 68 :VNLAIWDTAG T0308 66 :HYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1z08A 87 :IYYRDSNGAILVYDITDEDSFQKVKNWVKELRKMLG T0308 105 :RRIPILFFANKMDLRDAV 1z08A 123 :NEICLCIVGNKIDLEKER T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1z08A 141 :HVSIQEAESYAESVGAKHYHTSAKQNKGIEELFLDLCKRM Number of specific fragments extracted= 7 number of extra gaps= 1 total=396 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 1z08A/T0308-1z08A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1z08A/T0308-1z08A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z08A read from 1z08A/T0308-1z08A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1z08A in template set Warning: unaligning (T0308)N11 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1z08A)V30 Warning: unaligning (T0308)S12 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1z08A)V30 Warning: unaligning (T0308)Q57 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1z08A)P86 Warning: unaligning (T0308)E65 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1z08A)P86 T0308 2 :VHVLCLGLD 1z08A 20 :FKVVLLGEG T0308 13 :GKTTIINKLK 1z08A 31 :GKTSLVLRYC T0308 24 :SNAQSQNILPTIG 1z08A 41 :ENKFNDKHITTLG T0308 37 :FSIEKFKSSS 1z08A 56 :FLTKKLNIGG T0308 47 :LSFTVFDMSG 1z08A 68 :VNLAIWDTAG T0308 66 :HYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 1z08A 87 :IYYRDSNGAILVYDITDEDSFQKVKNWVKELRKM T0308 103 :KHRRIPILFFANKMDLRDAV 1z08A 121 :LGNEICLCIVGNKIDLEKER T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1z08A 141 :HVSIQEAESYAESVGAKHYHTSAKQNKGIEELFLDLCKRM Number of specific fragments extracted= 8 number of extra gaps= 1 total=404 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 1z08A/T0308-1z08A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1z08A/T0308-1z08A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z08A read from 1z08A/T0308-1z08A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1z08A in template set Warning: unaligning (T0308)N11 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1z08A)V30 Warning: unaligning (T0308)S12 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1z08A)V30 Warning: unaligning (T0308)Q57 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1z08A)P86 Warning: unaligning (T0308)E65 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1z08A)P86 T0308 1 :EVHVLCLGLD 1z08A 19 :SFKVVLLGEG T0308 13 :GKTTIINKLKPSNA 1z08A 31 :GKTSLVLRYCENKF T0308 27 :QSQNILPTIGFSIEKFKSSS 1z08A 46 :DKHITTLGASFLTKKLNIGG T0308 47 :LSFTVFDMSG 1z08A 68 :VNLAIWDTAG T0308 66 :HYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1z08A 87 :IYYRDSNGAILVYDITDEDSFQKVKNWVKELRKMLG T0308 105 :RRIPILFFANKMDLRDAVTSV 1z08A 123 :NEICLCIVGNKIDLEKERHVS T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1z08A 144 :IQEAESYAESVGAKHYHTSAKQNKGIEELFLDLCKRM Number of specific fragments extracted= 7 number of extra gaps= 1 total=411 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 1kao/T0308-1kao-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1kao expands to /projects/compbio/data/pdb/1kao.pdb.gz 1kao:Warning: there is no chain 1kao will retry with 1kaoA # T0308 read from 1kao/T0308-1kao-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kao read from 1kao/T0308-1kao-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1kao to template set # found chain 1kao in template set Warning: unaligning (T0308)Q29 because of BadResidue code BAD_PEPTIDE in next template residue (1kao)K31 Warning: unaligning (T0308)N30 because of BadResidue code BAD_PEPTIDE at template residue (1kao)K31 Warning: unaligning (T0308)I35 because of BadResidue code BAD_PEPTIDE in next template residue (1kao)E37 Warning: unaligning (T0308)R59 because of BadResidue code BAD_PEPTIDE in next template residue (1kao)F64 Warning: unaligning (T0308)Y60 because of BadResidue code BAD_PEPTIDE at template residue (1kao)F64 Warning: unaligning (T0308)S146 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1kao)S146 Warning: unaligning (T0308)D147 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1kao)S146 T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1kao 4 :YKVVVLGSGGVGKSALTVQFVTGTF T0308 28 :S 1kao 29 :I T0308 31 :ILPT 1kao 32 :YDPT T0308 36 :GFSIEKFKSSS 1kao 38 :DFYRKEIEVDS T0308 47 :LSFTVFDMSGQG 1kao 51 :SVLEILDTAGTE T0308 61 :RNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1kao 65 :ASMRDLYIKNGQGFILVYSLVNQQSFQDIKPMRDQIIRVKRY T0308 105 :RRIPILFFANKMDLRDAV 1kao 107 :EKVPVILVGNKVDLESER T0308 126 :KVSQLLCLENIKDKPWHICA 1kao 125 :EVSSSEGRALAEEWGCPFME T0308 148 :AIKGEGLQEGVDWLQDQI 1kao 147 :AKSKTMVDELFAEIVRQM Number of specific fragments extracted= 9 number of extra gaps= 4 total=420 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 1kao/T0308-1kao-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1kao/T0308-1kao-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kao read from 1kao/T0308-1kao-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kao in template set Warning: unaligning (T0308)Q29 because of BadResidue code BAD_PEPTIDE in next template residue (1kao)K31 Warning: unaligning (T0308)N30 because of BadResidue code BAD_PEPTIDE at template residue (1kao)K31 Warning: unaligning (T0308)I35 because of BadResidue code BAD_PEPTIDE in next template residue (1kao)E37 Warning: unaligning (T0308)G36 because of BadResidue code BAD_PEPTIDE at template residue (1kao)E37 Warning: unaligning (T0308)R59 because of BadResidue code BAD_PEPTIDE in next template residue (1kao)F64 Warning: unaligning (T0308)Y60 because of BadResidue code BAD_PEPTIDE at template residue (1kao)F64 Warning: unaligning (T0308)S146 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1kao)S146 Warning: unaligning (T0308)D147 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1kao)S146 T0308 1 :EVHVLCLGLDNSGKTTIINKLK 1kao 3 :EYKVVVLGSGGVGKSALTVQFV T0308 24 :SNAQS 1kao 25 :TGTFI T0308 31 :ILPT 1kao 32 :YDPT T0308 37 :FSIEKFKSSS 1kao 39 :FYRKEIEVDS T0308 47 :LSFTVFDMSGQG 1kao 51 :SVLEILDTAGTE T0308 61 :RNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 1kao 65 :ASMRDLYIKNGQGFILVYSLVNQQSFQDIKPMRDQIIRV T0308 102 :IKHRRIPILFFANKMDLRDAV 1kao 104 :KRYEKVPVILVGNKVDLESER T0308 126 :KVSQLLCLENIKDKPWHICA 1kao 125 :EVSSSEGRALAEEWGCPFME T0308 148 :AIKGEGLQEGVDWLQDQI 1kao 147 :AKSKTMVDELFAEIVRQM Number of specific fragments extracted= 9 number of extra gaps= 4 total=429 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 1kao/T0308-1kao-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1kao/T0308-1kao-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kao read from 1kao/T0308-1kao-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kao in template set Warning: unaligning (T0308)Q27 because of BadResidue code BAD_PEPTIDE at template residue (1kao)K31 Warning: unaligning (T0308)L32 because of BadResidue code BAD_PEPTIDE in next template residue (1kao)E37 Warning: unaligning (T0308)P33 because of BadResidue code BAD_PEPTIDE at template residue (1kao)E37 Warning: unaligning (T0308)R59 because of BadResidue code BAD_PEPTIDE in next template residue (1kao)F64 Warning: unaligning (T0308)Y60 because of BadResidue code BAD_PEPTIDE at template residue (1kao)F64 Warning: unaligning (T0308)S146 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1kao)S146 Warning: unaligning (T0308)D147 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1kao)S146 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1kao 3 :EYKVVVLGSGGVGKSALTVQFVTGTF T0308 28 :SQNI 1kao 32 :YDPT T0308 34 :TIGFSIEKFKSSSLSFTVFDMSGQG 1kao 38 :DFYRKEIEVDSSPSVLEILDTAGTE T0308 61 :RNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1kao 65 :ASMRDLYIKNGQGFILVYSLVNQQSFQDIKPMRDQIIRVKR T0308 104 :HRRIPILFFANKMDLRDAVTSV 1kao 106 :YEKVPVILVGNKVDLESEREVS T0308 129 :QLLCLENIKDKPWHICA 1kao 128 :SSEGRALAEEWGCPFME T0308 148 :AIKGEGLQEGVDWLQDQI 1kao 147 :AKSKTMVDELFAEIVRQM Number of specific fragments extracted= 7 number of extra gaps= 4 total=436 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 1z2aA/T0308-1z2aA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1z2aA expands to /projects/compbio/data/pdb/1z2a.pdb.gz 1z2aA:# T0308 read from 1z2aA/T0308-1z2aA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z2aA read from 1z2aA/T0308-1z2aA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1z2aA to template set # found chain 1z2aA in template set T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNAQSQNI 1z2aA 10 :IKMVVVGNGAVGKSSMIQRYCKGIFTKDYK T0308 32 :LPTIGFSIEKFKSSS 1z2aA 41 :TIGVDFLERQIQVND T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHP 1z2aA 58 :VRLMLWDTAGQEEFDAITKAYYRGAQACVLVFSTTDRESFEAISSWREKVVAEV T0308 105 :RRIPILFFANKMDLRDAV 1z2aA 112 :GDIPTALVQNKIDLLDDS T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQ 1z2aA 130 :CIKNEEAEGLAKRLKLRFYRTSVKEDLNVSEVFKYLAEK Number of specific fragments extracted= 5 number of extra gaps= 0 total=441 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 1z2aA/T0308-1z2aA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1z2aA/T0308-1z2aA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z2aA read from 1z2aA/T0308-1z2aA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1z2aA in template set T0308 2 :VHVLCLGLDNSGKTTIINKLK 1z2aA 10 :IKMVVVGNGAVGKSSMIQRYC T0308 24 :SNAQSQNILPTIG 1z2aA 31 :KGIFTKDYKKTIG T0308 37 :FSIEKFKSSS 1z2aA 46 :FLERQIQVND T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 1z2aA 58 :VRLMLWDTAGQEEFDAITKAYYRGAQACVLVFSTTDRESFEAISSWREKVVAE T0308 103 :K 1z2aA 111 :V T0308 105 :RRIPILFFANKMDLRDAV 1z2aA 112 :GDIPTALVQNKIDLLDDS T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQ 1z2aA 130 :CIKNEEAEGLAKRLKLRFYRTSVKEDLNVSEVFKYLAEK Number of specific fragments extracted= 7 number of extra gaps= 0 total=448 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 1z2aA/T0308-1z2aA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1z2aA/T0308-1z2aA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z2aA read from 1z2aA/T0308-1z2aA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1z2aA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1z2aA 9 :AIKMVVVGNGAVGKSSMIQRYCKGIF T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1z2aA 38 :YKKTIGVDFLERQIQVNDEDVRLMLWDTAGQEEFDAITKAYYRGAQACVLVFSTTDRESFEAISSWREKVVAEVG T0308 106 :RIPILFFANKMDLRDAVTSV 1z2aA 113 :DIPTALVQNKIDLLDDSCIK T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQ 1z2aA 133 :NEEAEGLAKRLKLRFYRTSVKEDLNVSEVFKYLAEK Number of specific fragments extracted= 4 number of extra gaps= 0 total=452 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 1ctqA/T0308-1ctqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ctqA expands to /projects/compbio/data/pdb/1ctq.pdb.gz 1ctqA:Skipped atom 21, because occupancy 0.400 <= existing 0.600 in 1ctqA Skipped atom 23, because occupancy 0.400 <= existing 0.600 in 1ctqA Skipped atom 25, because occupancy 0.400 <= existing 0.600 in 1ctqA Skipped atom 27, because occupancy 0.400 <= existing 0.600 in 1ctqA Skipped atom 29, because occupancy 0.400 <= existing 0.600 in 1ctqA Skipped atom 219, because occupancy 0.390 <= existing 0.610 in 1ctqA Skipped atom 221, because occupancy 0.390 <= existing 0.610 in 1ctqA Skipped atom 223, because occupancy 0.390 <= existing 0.610 in 1ctqA Skipped atom 305, because occupancy 0.470 <= existing 0.530 in 1ctqA Skipped atom 307, because occupancy 0.470 <= existing 0.530 in 1ctqA Skipped atom 350, because occupancy 0.500 <= existing 0.740 in 1ctqA Skipped atom 352, because occupancy 0.500 <= existing 0.740 in 1ctqA Skipped atom 354, because occupancy 0.500 <= existing 0.740 in 1ctqA Skipped atom 356, because occupancy 0.500 <= existing 0.740 in 1ctqA Skipped atom 358, because occupancy 0.500 <= existing 0.740 in 1ctqA Skipped atom 704, because occupancy 0.410 <= existing 0.590 in 1ctqA Skipped atom 706, because occupancy 0.410 <= existing 0.590 in 1ctqA Skipped atom 708, because occupancy 0.410 <= existing 0.590 in 1ctqA Skipped atom 877, because occupancy 0.130 <= existing 0.870 in 1ctqA Skipped atom 879, because occupancy 0.130 <= existing 0.870 in 1ctqA Skipped atom 966, because occupancy 0.330 <= existing 0.670 in 1ctqA Skipped atom 968, because occupancy 0.330 <= existing 0.670 in 1ctqA Skipped atom 1040, because occupancy 0.400 <= existing 0.600 in 1ctqA Skipped atom 1042, because occupancy 0.400 <= existing 0.600 in 1ctqA Skipped atom 1044, because occupancy 0.400 <= existing 0.600 in 1ctqA Skipped atom 1046, because occupancy 0.400 <= existing 0.600 in 1ctqA Skipped atom 1048, because occupancy 0.400 <= existing 0.600 in 1ctqA Skipped atom 1050, because occupancy 0.400 <= existing 0.600 in 1ctqA Skipped atom 1052, because occupancy 0.400 <= existing 0.600 in 1ctqA Skipped atom 1357, because occupancy 0.500 <= existing 0.500 in 1ctqA Skipped atom 1359, because occupancy 0.500 <= existing 0.500 in 1ctqA Skipped atom 1361, because occupancy 0.500 <= existing 0.500 in 1ctqA Skipped atom 1363, because occupancy 0.500 <= existing 0.500 in 1ctqA Skipped atom 1365, because occupancy 0.500 <= existing 0.500 in 1ctqA # T0308 read from 1ctqA/T0308-1ctqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ctqA read from 1ctqA/T0308-1ctqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ctqA to template set # found chain 1ctqA in template set Warning: unaligning (T0308)G56 because of BadResidue code BAD_PEPTIDE in next template residue (1ctqA)Q61 Warning: unaligning (T0308)Q57 because of BadResidue code BAD_PEPTIDE at template residue (1ctqA)Q61 Warning: unaligning (T0308)G58 because of BadResidue code BAD_PEPTIDE at template residue (1ctqA)E62 Warning: unaligning (T0308)R59 because of BadResidue code BAD_PEPTIDE in next template residue (1ctqA)Y64 Warning: unaligning (T0308)Y60 because of BadResidue code BAD_PEPTIDE at template residue (1ctqA)Y64 T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1ctqA 4 :YKLVVVGAGGVGKSALTIQLIQNHF T0308 28 :SQNILPTI 1ctqA 29 :VDEYDPTI T0308 36 :GFSIEKFKSSS 1ctqA 38 :DSYRKQVVIDG T0308 47 :LSFTVFDMS 1ctqA 51 :CLLDILDTA T0308 61 :RNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1ctqA 65 :SAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDS T0308 105 :RRIPILFFANKMDLRDA 1ctqA 107 :DDVPMVLVGNKCDLAAR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1ctqA 124 :TVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREI Number of specific fragments extracted= 7 number of extra gaps= 1 total=459 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 1ctqA/T0308-1ctqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1ctqA/T0308-1ctqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ctqA read from 1ctqA/T0308-1ctqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ctqA in template set Warning: unaligning (T0308)G56 because of BadResidue code BAD_PEPTIDE in next template residue (1ctqA)Q61 Warning: unaligning (T0308)Q57 because of BadResidue code BAD_PEPTIDE at template residue (1ctqA)Q61 Warning: unaligning (T0308)G58 because of BadResidue code BAD_PEPTIDE at template residue (1ctqA)E62 Warning: unaligning (T0308)R59 because of BadResidue code BAD_PEPTIDE in next template residue (1ctqA)Y64 Warning: unaligning (T0308)Y60 because of BadResidue code BAD_PEPTIDE at template residue (1ctqA)Y64 T0308 1 :EVHVLCLGLDNSGKTTIINKLK 1ctqA 3 :EYKLVVVGAGGVGKSALTIQLI T0308 24 :SNAQSQNILPTIG 1ctqA 25 :QNHFVDEYDPTIE T0308 37 :FSIEKFKSSS 1ctqA 39 :SYRKQVVIDG T0308 47 :LSFTVFDMS 1ctqA 51 :CLLDILDTA T0308 61 :RNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 1ctqA 65 :SAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRV T0308 102 :IKHRRIPILFFANKMDLRDAV 1ctqA 104 :KDSDDVPMVLVGNKCDLAART T0308 127 :VSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1ctqA 125 :VESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREI Number of specific fragments extracted= 7 number of extra gaps= 1 total=466 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 1ctqA/T0308-1ctqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1ctqA/T0308-1ctqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ctqA read from 1ctqA/T0308-1ctqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ctqA in template set Warning: unaligning (T0308)G56 because of BadResidue code BAD_PEPTIDE in next template residue (1ctqA)Q61 Warning: unaligning (T0308)Q57 because of BadResidue code BAD_PEPTIDE at template residue (1ctqA)Q61 Warning: unaligning (T0308)G58 because of BadResidue code BAD_PEPTIDE at template residue (1ctqA)E62 Warning: unaligning (T0308)R59 because of BadResidue code BAD_PEPTIDE in next template residue (1ctqA)Y64 Warning: unaligning (T0308)Y60 because of BadResidue code BAD_PEPTIDE at template residue (1ctqA)Y64 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1ctqA 3 :EYKLVVVGAGGVGKSALTIQLIQNHF T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMS 1ctqA 31 :EYDPTIEDSYRKQVVIDGETCLLDILDTA T0308 61 :RNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1ctqA 65 :SAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKD T0308 104 :HRRIPILFFANKMDLRDAVTS 1ctqA 106 :SDDVPMVLVGNKCDLAARTVE T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1ctqA 127 :SRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREI Number of specific fragments extracted= 5 number of extra gaps= 1 total=471 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 1ky3A/T0308-1ky3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ky3A expands to /projects/compbio/data/pdb/1ky3.pdb.gz 1ky3A:Skipped atom 307, because occupancy 0.320 <= existing 0.680 in 1ky3A Skipped atom 309, because occupancy 0.320 <= existing 0.680 in 1ky3A Skipped atom 311, because occupancy 0.320 <= existing 0.680 in 1ky3A # T0308 read from 1ky3A/T0308-1ky3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ky3A read from 1ky3A/T0308-1ky3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ky3A to template set # found chain 1ky3A in template set Warning: unaligning (T0308)I31 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ky3A)I41 Warning: unaligning (T0308)P33 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ky3A)I41 Warning: unaligning (T0308)S44 because of BadResidue code BAD_PEPTIDE in next template residue (1ky3A)D53 Warning: unaligning (T0308)S45 because of BadResidue code BAD_PEPTIDE at template residue (1ky3A)D53 Warning: unaligning (T0308)S46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ky3A)G54 Warning: unaligning (T0308)M54 because of BadResidue code BAD_PEPTIDE in next template residue (1ky3A)A66 Warning: unaligning (T0308)S55 because of BadResidue code BAD_PEPTIDE at template residue (1ky3A)A66 Warning: unaligning (T0308)H66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ky3A)A77 T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1ky3A 9 :LKVIILGDSGVGKTSLMHRYVNDKY T0308 28 :SQN 1ky3A 34 :SQQ T0308 34 :TIGFSIEKFK 1ky3A 42 :GADFLTKEVT T0308 47 :LSFTVFD 1ky3A 58 :ATMQVWD T0308 67 :YYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1ky3A 78 :FYRGADCCVLVYDVTNASSFENIKSWRDEFLVHANV T0308 103 :KHRRIPILFFANKMDLRDAVT 1ky3A 115 :SPETFPFVILGNKIDAEESKK T0308 126 :KVSQLLCLENIKDKP 1ky3A 136 :IVSEKSAQELAKSLG T0308 141 :WHICASDAIKGEGLQEGVDWLQDQ 1ky3A 152 :IPLFLTSAKNAINVDTAFEEIARS Number of specific fragments extracted= 8 number of extra gaps= 2 total=479 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 1ky3A/T0308-1ky3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1ky3A/T0308-1ky3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ky3A read from 1ky3A/T0308-1ky3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ky3A in template set Warning: unaligning (T0308)I31 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ky3A)I41 Warning: unaligning (T0308)I35 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ky3A)I41 Warning: unaligning (T0308)S44 because of BadResidue code BAD_PEPTIDE in next template residue (1ky3A)D53 Warning: unaligning (T0308)S45 because of BadResidue code BAD_PEPTIDE at template residue (1ky3A)D53 Warning: unaligning (T0308)S46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ky3A)G54 Warning: unaligning (T0308)M54 because of BadResidue code BAD_PEPTIDE in next template residue (1ky3A)A66 Warning: unaligning (T0308)S55 because of BadResidue code BAD_PEPTIDE at template residue (1ky3A)A66 Warning: unaligning (T0308)H66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ky3A)A77 T0308 2 :VHVLCLGLDNSGKTTIINKLK 1ky3A 9 :LKVIILGDSGVGKTSLMHRYV T0308 24 :SNAQSQN 1ky3A 30 :NDKYSQQ T0308 36 :G 1ky3A 42 :G T0308 37 :FSIEKFK 1ky3A 45 :FLTKEVT T0308 47 :LSFTVFD 1ky3A 58 :ATMQVWD T0308 67 :YYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1ky3A 78 :FYRGADCCVLVYDVTNASSFENIKSWRDEFLVHANV T0308 103 :KHRRIPILFFANKMDLRDAVT 1ky3A 115 :SPETFPFVILGNKIDAEESKK T0308 126 :KVSQLLCLENIKDK 1ky3A 136 :IVSEKSAQELAKSL T0308 140 :PWHICASDAIKGEGLQEGVDWLQDQ 1ky3A 151 :DIPLFLTSAKNAINVDTAFEEIARS Number of specific fragments extracted= 9 number of extra gaps= 2 total=488 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 1ky3A/T0308-1ky3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1ky3A/T0308-1ky3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ky3A read from 1ky3A/T0308-1ky3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ky3A in template set Warning: unaligning (T0308)Q27 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ky3A)I41 Warning: unaligning (T0308)I31 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ky3A)I41 Warning: unaligning (T0308)F42 because of BadResidue code BAD_PEPTIDE in next template residue (1ky3A)D53 Warning: unaligning (T0308)K43 because of BadResidue code BAD_PEPTIDE at template residue (1ky3A)D53 Warning: unaligning (T0308)S44 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ky3A)G54 Warning: unaligning (T0308)S45 because of BadResidue code BAD_PEPTIDE at template residue (1ky3A)D55 Warning: unaligning (T0308)S46 because of BadResidue code BAD_PEPTIDE at template residue (1ky3A)K56 Warning: unaligning (T0308)M54 because of BadResidue code BAD_PEPTIDE in next template residue (1ky3A)A66 Warning: unaligning (T0308)S55 because of BadResidue code BAD_PEPTIDE at template residue (1ky3A)A66 Warning: unaligning (T0308)H66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ky3A)A77 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1ky3A 8 :ILKVIILGDSGVGKTSLMHRYVNDKY T0308 32 :LPTIGFSIEK 1ky3A 42 :GADFLTKEVT T0308 47 :LSFTVFD 1ky3A 58 :ATMQVWD T0308 67 :YYKEGQAIIFVIDSSDRLRMVVAKEELDTLL 1ky3A 78 :FYRGADCCVLVYDVTNASSFENIKSWRDEFL T0308 98 :NHPD 1ky3A 112 :NVNS T0308 104 :HRRIPILFFANKMDLRDAVTSVK 1ky3A 116 :PETFPFVILGNKIDAEESKKIVS T0308 129 :QLLCLENI 1ky3A 139 :EKSAQELA T0308 137 :KDKPWHICASDAIKGEGLQEGVDWLQDQ 1ky3A 148 :SLGDIPLFLTSAKNAINVDTAFEEIARS Number of specific fragments extracted= 8 number of extra gaps= 2 total=496 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 1u8zA/T0308-1u8zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1u8zA expands to /projects/compbio/data/pdb/1u8z.pdb.gz 1u8zA:# T0308 read from 1u8zA/T0308-1u8zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u8zA read from 1u8zA/T0308-1u8zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1u8zA to template set # found chain 1u8zA in template set Warning: unaligning (T0308)G56 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u8zA)Y75 Warning: unaligning (T0308)Y60 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u8zA)Y75 T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1u8zA 15 :HKVIMVGSGGVGKSALTLQFMYDEF T0308 28 :SQNILPTI 1u8zA 40 :VEDYEPTK T0308 36 :GFSIEKFKSSS 1u8zA 49 :DSYRKKVVLDG T0308 47 :LSFTVFDMS 1u8zA 62 :VQIDILDTA T0308 61 :RNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1u8zA 76 :AAIRDNYFRSGEGFLCVFSITEMESFAATADFREQILRVKED T0308 105 :RRIPILFFANKMDLRDAV 1u8zA 118 :ENVPFLLVGNKSDLEDKR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1u8zA 136 :QVSVEEAKNRADQWNVNYVETSAKTRANVDKVFFDLMREI Number of specific fragments extracted= 7 number of extra gaps= 0 total=503 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 1u8zA/T0308-1u8zA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1u8zA/T0308-1u8zA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u8zA read from 1u8zA/T0308-1u8zA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1u8zA in template set Warning: unaligning (T0308)G56 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u8zA)Y75 Warning: unaligning (T0308)Y60 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u8zA)Y75 T0308 2 :VHVLCLGLDNSGKTTIINKLK 1u8zA 15 :HKVIMVGSGGVGKSALTLQFM T0308 24 :SNAQSQNILPTIG 1u8zA 36 :YDEFVEDYEPTKA T0308 37 :FSIEKFKSSS 1u8zA 50 :SYRKKVVLDG T0308 47 :LSFTVFDMS 1u8zA 62 :VQIDILDTA T0308 61 :RNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 1u8zA 76 :AAIRDNYFRSGEGFLCVFSITEMESFAATADFREQILRV T0308 102 :IKHRRIPILFFANKMDLRDAV 1u8zA 115 :KEDENVPFLLVGNKSDLEDKR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1u8zA 136 :QVSVEEAKNRADQWNVNYVETSAKTRANVDKVFFDLMREI Number of specific fragments extracted= 7 number of extra gaps= 0 total=510 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 1u8zA/T0308-1u8zA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1u8zA/T0308-1u8zA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u8zA read from 1u8zA/T0308-1u8zA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1u8zA in template set Warning: unaligning (T0308)G56 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u8zA)Y75 Warning: unaligning (T0308)Y60 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u8zA)Y75 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1u8zA 14 :LHKVIMVGSGGVGKSALTLQFMYDEF T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMS 1u8zA 42 :DYEPTKADSYRKKVVLDGEEVQIDILDTA T0308 61 :RNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1u8zA 76 :AAIRDNYFRSGEGFLCVFSITEMESFAATADFREQILRVKE T0308 104 :HRRIPILFFANKMDLRDAVTSV 1u8zA 117 :DENVPFLLVGNKSDLEDKRQVS T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1u8zA 139 :VEEAKNRADQWNVNYVETSAKTRANVDKVFFDLMREI Number of specific fragments extracted= 5 number of extra gaps= 0 total=515 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 1kmqA/T0308-1kmqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1kmqA expands to /projects/compbio/data/pdb/1kmq.pdb.gz 1kmqA:# T0308 read from 1kmqA/T0308-1kmqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kmqA read from 1kmqA/T0308-1kmqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1kmqA to template set # found chain 1kmqA in template set Warning: unaligning (T0308)I31 because of BadResidue code BAD_PEPTIDE in next template residue (1kmqA)V35 Warning: unaligning (T0308)L32 because of BadResidue code BAD_PEPTIDE at template residue (1kmqA)V35 T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1kmqA 6 :KKLVIVGDGACGKTCLLIVNSKDQF T0308 28 :SQN 1kmqA 31 :PEV T0308 33 :PTI 1kmqA 36 :PTV T0308 36 :GFSIEKFKSSS 1kmqA 40 :ENYVADIEVDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAK 1kmqA 53 :VELALWDTAGLEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIP T0308 91 :EELDTLLNHP 1kmqA 98 :KWTPEVKHFC T0308 105 :RRIPILFFANKMDLRDAVTSVK 1kmqA 108 :PNVPIILVGNKKDLRNDEHTRR T0308 127 :VSQLLCLENIKDKP 1kmqA 139 :VKPEEGRDMANRIG T0308 141 :WHICASDAIKGEGLQEGVDWLQDQ 1kmqA 154 :FGYMECSAKTKDGVREVFEMATRA Number of specific fragments extracted= 9 number of extra gaps= 1 total=524 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 1kmqA/T0308-1kmqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1kmqA/T0308-1kmqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kmqA read from 1kmqA/T0308-1kmqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kmqA in template set Warning: unaligning (T0308)I31 because of BadResidue code BAD_PEPTIDE in next template residue (1kmqA)V35 Warning: unaligning (T0308)L32 because of BadResidue code BAD_PEPTIDE at template residue (1kmqA)V35 T0308 2 :VHVLCLGLDNSGKTTIINKLK 1kmqA 6 :KKLVIVGDGACGKTCLLIVNS T0308 24 :SNAQSQN 1kmqA 27 :KDQFPEV T0308 33 :PTIG 1kmqA 36 :PTVF T0308 37 :FSIEKFKSSS 1kmqA 41 :NYVADIEVDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKE 1kmqA 53 :VELALWDTAGLEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPE T0308 92 :ELDTLLNH 1kmqA 99 :WTPEVKHF T0308 104 :HRRIPILFFANKMDLRDAVTSVK 1kmqA 107 :CPNVPIILVGNKKDLRNDEHTRR T0308 127 :VSQLLCLENIKDKP 1kmqA 139 :VKPEEGRDMANRIG T0308 141 :WHICASDAIKGEGLQEGVDWLQD 1kmqA 154 :FGYMECSAKTKDGVREVFEMATR Number of specific fragments extracted= 9 number of extra gaps= 1 total=533 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 1kmqA/T0308-1kmqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1kmqA/T0308-1kmqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kmqA read from 1kmqA/T0308-1kmqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kmqA in template set Warning: unaligning (T0308)S28 because of BadResidue code BAD_PEPTIDE in next template residue (1kmqA)V35 Warning: unaligning (T0308)Q29 because of BadResidue code BAD_PEPTIDE at template residue (1kmqA)V35 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1kmqA 5 :RKKLVIVGDGACGKTCLLIVNSKDQF T0308 27 :Q 1kmqA 33 :V T0308 30 :NILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKE 1kmqA 36 :PTVFENYVADIEVDGKQVELALWDTAGLEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPE T0308 92 :ELDTLLNHPD 1kmqA 99 :WTPEVKHFCP T0308 106 :RIPILFFANKMDLRDAVTSV 1kmqA 109 :NVPIILVGNKKDLRNDEHTR T0308 129 :QLLCL 1kmqA 129 :RELAK T0308 134 :ENIKDKPW 1kmqA 146 :DMANRIGA T0308 142 :HICASDAIKGEGLQEGVDWLQD 1kmqA 155 :GYMECSAKTKDGVREVFEMATR Number of specific fragments extracted= 8 number of extra gaps= 1 total=541 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 1i2mA/T0308-1i2mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1i2mA expands to /projects/compbio/data/pdb/1i2m.pdb.gz 1i2mA:# T0308 read from 1i2mA/T0308-1i2mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i2mA read from 1i2mA/T0308-1i2mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1i2mA to template set # found chain 1i2mA in template set Warning: unaligning (T0308)K22 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1i2mA)K37 Warning: unaligning (T0308)Q29 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1i2mA)K37 T0308 2 :VHVLCLGLDNSGKTTIINKL 1i2mA 11 :FKLVLVGDGGTGKTTFVKRH T0308 30 :NILPTIGFSIEKFKS 1i2mA 38 :KYVATLGVEVHPLVF T0308 45 :SS 1i2mA 55 :NR T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHP 1i2mA 59 :IKFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVC T0308 105 :RRIPILFFANKMDLRDAVTSVKVS 1i2mA 113 :ENIPIVLCGNKVDIKDRKVKAKSI T0308 135 :NIKDKP 1i2mA 137 :VFHRKK T0308 141 :WHICASDAIKGEGLQEGVDWLQDQI 1i2mA 144 :LQYYDISAKSNYNFEKPFLWLARKL Number of specific fragments extracted= 7 number of extra gaps= 0 total=548 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 1i2mA/T0308-1i2mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1i2mA/T0308-1i2mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i2mA read from 1i2mA/T0308-1i2mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1i2mA in template set Warning: unaligning (T0308)K22 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1i2mA)K37 Warning: unaligning (T0308)Q29 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1i2mA)K37 T0308 1 :EVHVLCLGLDNSGKTTIINKL 1i2mA 10 :QFKLVLVGDGGTGKTTFVKRH T0308 30 :NILPTIGFSIEKFKS 1i2mA 38 :KYVATLGVEVHPLVF T0308 45 :SS 1i2mA 56 :RG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 1i2mA 59 :IKFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRV T0308 105 :RRIPILFFANKMDLRDAVTSVKVS 1i2mA 113 :ENIPIVLCGNKVDIKDRKVKAKSI T0308 135 :NIKDKP 1i2mA 137 :VFHRKK T0308 141 :WHICASDAIKGEGLQEGVDWLQDQI 1i2mA 144 :LQYYDISAKSNYNFEKPFLWLARKL Number of specific fragments extracted= 7 number of extra gaps= 0 total=555 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 1i2mA/T0308-1i2mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1i2mA/T0308-1i2mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i2mA read from 1i2mA/T0308-1i2mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1i2mA in template set Warning: unaligning (T0308)K22 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1i2mA)K37 T0308 1 :EVHVLCLGLDNSGKTTIINKL 1i2mA 10 :QFKLVLVGDGGTGKTTFVKRH T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1i2mA 39 :YVATLGVEVHPLVFHTNRGPIKFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCE T0308 106 :RIPILFFANKMDLRDAVTSV 1i2mA 114 :NIPIVLCGNKVDIKDRKVKA T0308 133 :LENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1i2mA 136 :IVFHRKKNLQYYDISAKSNYNFEKPFLWLARKL Number of specific fragments extracted= 4 number of extra gaps= 0 total=559 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 2fn4A/T0308-2fn4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2fn4A expands to /projects/compbio/data/pdb/2fn4.pdb.gz 2fn4A:Skipped atom 573, because occupancy 0.500 <= existing 0.500 in 2fn4A Skipped atom 575, because occupancy 0.500 <= existing 0.500 in 2fn4A Skipped atom 577, because occupancy 0.500 <= existing 0.500 in 2fn4A Skipped atom 579, because occupancy 0.500 <= existing 0.500 in 2fn4A Skipped atom 581, because occupancy 0.500 <= existing 0.500 in 2fn4A Skipped atom 1289, because occupancy 0.500 <= existing 0.500 in 2fn4A Skipped atom 1293, because occupancy 0.500 <= existing 0.500 in 2fn4A Skipped atom 1295, because occupancy 0.500 <= existing 0.500 in 2fn4A Skipped atom 1297, because occupancy 0.500 <= existing 0.500 in 2fn4A # T0308 read from 2fn4A/T0308-2fn4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fn4A read from 2fn4A/T0308-2fn4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2fn4A to template set # found chain 2fn4A in template set T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 2fn4A 30 :HKLVVVGGGGVGKSALTIQFIQSYF T0308 28 :SQNILPTI 2fn4A 55 :VSDYDPTI T0308 36 :GFSIEKFKSSS 2fn4A 64 :DSYTKICSVDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 2fn4A 77 :ARLDILDTAGQEEFGAMREQYMRAGHGFLLVFAINDRQSFNEVGKLFTQILRVKDR T0308 105 :RRIPILFFANKMDLRDAV 2fn4A 133 :DDFPVVLVGNKADLESQR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 2fn4A 151 :QVPRSEASAFGASHHVAYFEASAKLRLNVDEAFEQLVRAV Number of specific fragments extracted= 6 number of extra gaps= 0 total=565 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 2fn4A/T0308-2fn4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 2fn4A/T0308-2fn4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fn4A read from 2fn4A/T0308-2fn4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fn4A in template set T0308 2 :VHVLCLGLDNSGKTTIINKLK 2fn4A 30 :HKLVVVGGGGVGKSALTIQFI T0308 24 :SNAQSQNILPTIG 2fn4A 51 :QSYFVSDYDPTIE T0308 37 :FSIEKFKSSS 2fn4A 65 :SYTKICSVDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 2fn4A 77 :ARLDILDTAGQEEFGAMREQYMRAGHGFLLVFAINDRQSFNEVGKLFTQILRV T0308 102 :IKHRRIPILFFANKMDLRDAV 2fn4A 130 :KDRDDFPVVLVGNKADLESQR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 2fn4A 151 :QVPRSEASAFGASHHVAYFEASAKLRLNVDEAFEQLVRAV Number of specific fragments extracted= 6 number of extra gaps= 0 total=571 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 2fn4A/T0308-2fn4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 2fn4A/T0308-2fn4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fn4A read from 2fn4A/T0308-2fn4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fn4A in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 2fn4A 29 :THKLVVVGGGGVGKSALTIQFIQSYF T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 2fn4A 57 :DYDPTIEDSYTKICSVDGIPARLDILDTAGQEEFGAMREQYMRAGHGFLLVFAINDRQSFNEVGKLFTQILRVKD T0308 104 :HRRIPILFFANKMDLRDAVTSV 2fn4A 132 :RDDFPVVLVGNKADLESQRQVP T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQ 2fn4A 154 :RSEASAFGASHHVAYFEASAKLRLNVDEAFEQLVRA Number of specific fragments extracted= 4 number of extra gaps= 0 total=575 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 1mh1/T0308-1mh1-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1mh1 expands to /projects/compbio/data/pdb/1mh1.pdb.gz 1mh1:Warning: there is no chain 1mh1 will retry with 1mh1A WARNING: atom 11 has residue number 1 < previous residue 2A in 1mh1 Skipped atom 60, because occupancy 0.500 <= existing 0.500 in 1mh1 Skipped atom 62, because occupancy 0.500 <= existing 0.500 in 1mh1 Skipped atom 64, because occupancy 0.500 <= existing 0.500 in 1mh1 Skipped atom 325, because occupancy 0.500 <= existing 0.500 in 1mh1 Skipped atom 327, because occupancy 0.500 <= existing 0.500 in 1mh1 Skipped atom 329, because occupancy 0.500 <= existing 0.500 in 1mh1 Skipped atom 1037, because occupancy 0.500 <= existing 0.500 in 1mh1 Skipped atom 1039, because occupancy 0.500 <= existing 0.500 in 1mh1 Skipped atom 1041, because occupancy 0.500 <= existing 0.500 in 1mh1 Skipped atom 1162, because occupancy 0.500 <= existing 0.500 in 1mh1 Skipped atom 1164, because occupancy 0.500 <= existing 0.500 in 1mh1 Skipped atom 1166, because occupancy 0.500 <= existing 0.500 in 1mh1 Skipped atom 1172, because occupancy 0.500 <= existing 0.500 in 1mh1 Skipped atom 1174, because occupancy 0.500 <= existing 0.500 in 1mh1 Skipped atom 1176, because occupancy 0.500 <= existing 0.500 in 1mh1 Skipped atom 1178, because occupancy 0.500 <= existing 0.500 in 1mh1 Skipped atom 1180, because occupancy 0.500 <= existing 0.500 in 1mh1 # T0308 read from 1mh1/T0308-1mh1-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mh1 read from 1mh1/T0308-1mh1-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1mh1 to template set # found chain 1mh1 in template set T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1mh1 4 :IKCVVVGDGAVGKTCLLISYTTNAF T0308 28 :SQNILPTI 1mh1 29 :PGEYIPTV T0308 36 :GFSIEKFKSSS 1mh1 38 :DNYSANVMVDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAK 1mh1 51 :VNLGLWDTAGQEDYDRLRPLSYPQTDVSLICFSLVSPASFENVR T0308 91 :EELDTLLNHP 1mh1 96 :KWYPEVRHHC T0308 105 :RRIPILFFANKMDLRDAVTSVK 1mh1 106 :PNTPIILVGTKLDLRDDKDTIE T0308 127 :VSQLLCLENIKDKP 1mh1 137 :ITYPQGLAMAKEIG T0308 141 :WHICASDAIKGEGLQEGVDWLQDQI 1mh1 152 :VKYLECSALTQRGLKTVFDEAIRAV Number of specific fragments extracted= 8 number of extra gaps= 0 total=583 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 1mh1/T0308-1mh1-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1mh1/T0308-1mh1-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mh1 read from 1mh1/T0308-1mh1-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mh1 in template set T0308 2 :VHVLCLGLDNSGKTTIINKLK 1mh1 4 :IKCVVVGDGAVGKTCLLISYT T0308 24 :SNAQSQNILPTIG 1mh1 25 :TNAFPGEYIPTVF T0308 37 :FSIEKFKSSS 1mh1 39 :NYSANVMVDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKE 1mh1 51 :VNLGLWDTAGQEDYDRLRPLSYPQTDVSLICFSLVSPASFENVRA T0308 92 :ELDTLLNH 1mh1 97 :WYPEVRHH T0308 104 :HRRIPILFFANKMDL 1mh1 105 :CPNTPIILVGTKLDL T0308 119 :RDAV 1mh1 132 :KKLT T0308 126 :KVSQLLCLENIKDKP 1mh1 136 :PITYPQGLAMAKEIG T0308 141 :WHICASDAIKGEGLQEGVDWLQDQ 1mh1 152 :VKYLECSALTQRGLKTVFDEAIRA Number of specific fragments extracted= 9 number of extra gaps= 0 total=592 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 1mh1/T0308-1mh1-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1mh1/T0308-1mh1-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mh1 read from 1mh1/T0308-1mh1-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mh1 in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1mh1 3 :AIKCVVVGDGAVGKTCLLISYTTNAF T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKE 1mh1 31 :EYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDYDRLRPLSYPQTDVSLICFSLVSPASFENVRA T0308 92 :ELDTLLNHPD 1mh1 97 :WYPEVRHHCP T0308 106 :RIPILFFANKMDLRDAVTSV 1mh1 107 :NTPIILVGTKLDLRDDKDTI T0308 129 :QLLCL 1mh1 127 :EKLKE T0308 134 :ENIKDKPW 1mh1 144 :AMAKEIGA T0308 142 :HICASDAIKGEGLQEGVDWLQDQ 1mh1 153 :KYLECSALTQRGLKTVFDEAIRA Number of specific fragments extracted= 7 number of extra gaps= 0 total=599 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 2erxA/T0308-2erxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2erxA expands to /projects/compbio/data/pdb/2erx.pdb.gz 2erxA:Skipped atom 505, because occupancy 0.500 <= existing 0.500 in 2erxA Skipped atom 507, because occupancy 0.500 <= existing 0.500 in 2erxA Skipped atom 509, because occupancy 0.500 <= existing 0.500 in 2erxA Skipped atom 511, because occupancy 0.500 <= existing 0.500 in 2erxA # T0308 read from 2erxA/T0308-2erxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2erxA read from 2erxA/T0308-2erxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2erxA to template set # found chain 2erxA in template set Warning: unaligning (T0308)D101 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2erxA)S113 Warning: unaligning (T0308)R106 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2erxA)S113 T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 2erxA 8 :YRVAVFGAGGVGKSSLVLRFVKGTF T0308 28 :SQNILPTI 2erxA 33 :RESYIPTV T0308 36 :GFSIEKFKSSS 2erxA 42 :DTYRQVISCDK T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHP 2erxA 55 :CTLQITDTTGSHQFPAMQRLSISKGHAFILVYSITSRQSLEELKPIYEQICEIK T0308 107 :IPILFFANKMDLRDAV 2erxA 114 :IPIMLVGNKCDESPSR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 2erxA 130 :EVQSSEAEALARTWKCAFMETSAKLNHNVKELFQELLNLE Number of specific fragments extracted= 6 number of extra gaps= 0 total=605 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 2erxA/T0308-2erxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 2erxA/T0308-2erxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2erxA read from 2erxA/T0308-2erxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2erxA in template set Warning: unaligning (T0308)D101 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2erxA)S113 Warning: unaligning (T0308)R106 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2erxA)S113 T0308 2 :VHVLCLGLDNSGKTTIINKLK 2erxA 8 :YRVAVFGAGGVGKSSLVLRFV T0308 24 :SNAQSQNILPTIG 2erxA 29 :KGTFRESYIPTVE T0308 37 :FSIEKFKSSS 2erxA 43 :TYRQVISCDK T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHP 2erxA 55 :CTLQITDTTGSHQFPAMQRLSISKGHAFILVYSITSRQSLEELKPIYEQICEIK T0308 107 :IPILFFANKMDLRDAV 2erxA 114 :IPIMLVGNKCDESPSR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 2erxA 130 :EVQSSEAEALARTWKCAFMETSAKLNHNVKELFQELLNLE Number of specific fragments extracted= 6 number of extra gaps= 0 total=611 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 2erxA/T0308-2erxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 2erxA/T0308-2erxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2erxA read from 2erxA/T0308-2erxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2erxA in template set Warning: unaligning (T0308)D101 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2erxA)S113 Warning: unaligning (T0308)R106 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2erxA)S113 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNAQSQNILPTIGFSIEKFKSSS 2erxA 7 :DYRVAVFGAGGVGKSSLVLRFVKGTFRESYIPTVEDTYRQVISCDK T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHP 2erxA 55 :CTLQITDTTGSHQFPAMQRLSISKGHAFILVYSITSRQSLEELKPIYEQICEIK T0308 107 :IPILFFANKMDLRDAVTSV 2erxA 114 :IPIMLVGNKCDESPSREVQ T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQ 2erxA 133 :SSEAEALARTWKCAFMETSAKLNHNVKELFQELLNL Number of specific fragments extracted= 4 number of extra gaps= 0 total=615 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 1x1rA/T0308-1x1rA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1x1rA expands to /projects/compbio/data/pdb/1x1r.pdb.gz 1x1rA:# T0308 read from 1x1rA/T0308-1x1rA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1x1rA read from 1x1rA/T0308-1x1rA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1x1rA to template set # found chain 1x1rA in template set T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1x1rA 14 :YKLVVVGDGGVGKSALTIQFFQKIF T0308 28 :SQNILPTI 1x1rA 39 :VPDYDPTI T0308 36 :GFSIEKFKSSS 1x1rA 48 :DSYLKHTEIDN T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1x1rA 61 :AILDVLDTAGQEEFSAMREQYMRTGDGFLIVYSVTDKASFEHVDRFHQLILRVKDR T0308 105 :RRIPILFFANKMDLRDAV 1x1rA 117 :ESFPMILVANKVDLMHLR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKG 1x1rA 135 :KVTRDQGKEMATKYNIPYIETSAKDP T0308 152 :EGLQEGVDWLQDQI 1x1rA 162 :LNVDKTFHDLVRVI Number of specific fragments extracted= 7 number of extra gaps= 0 total=622 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 1x1rA/T0308-1x1rA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1x1rA/T0308-1x1rA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1x1rA read from 1x1rA/T0308-1x1rA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1x1rA in template set T0308 2 :VHVLCLGLDNSGKTTIINKLK 1x1rA 14 :YKLVVVGDGGVGKSALTIQFF T0308 24 :SNAQSQNILPTIG 1x1rA 35 :QKIFVPDYDPTIE T0308 37 :FSIEKFKSSS 1x1rA 49 :SYLKHTEIDN T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 1x1rA 61 :AILDVLDTAGQEEFSAMREQYMRTGDGFLIVYSVTDKASFEHVDRFHQLILRV T0308 102 :IKHRRIPILFFANKMDLRDAV 1x1rA 114 :KDRESFPMILVANKVDLMHLR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKG 1x1rA 135 :KVTRDQGKEMATKYNIPYIETSAKDP T0308 152 :EGLQEGVDWLQDQI 1x1rA 162 :LNVDKTFHDLVRVI Number of specific fragments extracted= 7 number of extra gaps= 0 total=629 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 1x1rA/T0308-1x1rA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1x1rA/T0308-1x1rA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1x1rA read from 1x1rA/T0308-1x1rA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1x1rA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1x1rA 13 :TYKLVVVGDGGVGKSALTIQFFQKIF T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1x1rA 41 :DYDPTIEDSYLKHTEIDNQWAILDVLDTAGQEEFSAMREQYMRTGDGFLIVYSVTDKASFEHVDRFHQLILRVKD T0308 104 :HRRIPILFFANKMDLRDAVTSV 1x1rA 116 :RESFPMILVANKVDLMHLRKVT T0308 129 :QLLCLENIKDKPWHICASDAIKG 1x1rA 138 :RDQGKEMATKYNIPYIETSAKDP T0308 152 :EGLQEGVDWLQDQI 1x1rA 162 :LNVDKTFHDLVRVI Number of specific fragments extracted= 5 number of extra gaps= 0 total=634 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 2eryA/T0308-2eryA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2eryA expands to /projects/compbio/data/pdb/2ery.pdb.gz 2eryA:Skipped atom 53, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 55, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 57, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 59, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 61, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 63, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 328, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 332, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 334, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 336, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 793, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 797, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 799, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 801, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 803, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 805, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 807, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 809, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 842, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 844, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 846, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 848, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 898, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 900, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 902, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 1153, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 1155, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 1157, because occupancy 0.500 <= existing 0.500 in 2eryA # T0308 read from 2eryA/T0308-2eryA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2eryA read from 2eryA/T0308-2eryA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2eryA to template set # found chain 2eryA in template set Warning: unaligning (T0308)L9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2eryA)G23 Warning: unaligning (T0308)D10 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2eryA)G23 Warning: unaligning (T0308)S55 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2eryA)F75 Warning: unaligning (T0308)Y60 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2eryA)F75 T0308 2 :VHVLCLG 2eryA 15 :YRLVVVG T0308 11 :NSGKTTIINKLKPSNA 2eryA 24 :GVGKSALTIQFIQSYF T0308 28 :SQNILPTI 2eryA 40 :VTDYDPTI T0308 36 :GFSIEKFKSSS 2eryA 49 :DSYTKQCVIDD T0308 47 :LSFTVFDM 2eryA 62 :ARLDILDT T0308 61 :RNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 2eryA 76 :GAMREQYMRTGEGFLLVFSVTDRGSFEEIYKFQRQILRVKDR T0308 105 :RRIPILFFANKMDLRDAV 2eryA 118 :DEFPMILIGNKADLDHQR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 2eryA 136 :QVTQEEGQQLARQLKVTYMEASAKIRMNVDQAFHELVRVI Number of specific fragments extracted= 8 number of extra gaps= 1 total=642 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 2eryA/T0308-2eryA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 2eryA/T0308-2eryA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2eryA read from 2eryA/T0308-2eryA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2eryA in template set Warning: unaligning (T0308)L9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2eryA)G23 Warning: unaligning (T0308)D10 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2eryA)G23 Warning: unaligning (T0308)S55 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2eryA)F75 Warning: unaligning (T0308)Y60 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2eryA)F75 T0308 1 :EVHVLCLG 2eryA 14 :KYRLVVVG T0308 11 :NSGKTTIINKLK 2eryA 24 :GVGKSALTIQFI T0308 24 :SNAQSQNILPTIG 2eryA 36 :QSYFVTDYDPTIE T0308 37 :FSIEKFKSSS 2eryA 50 :SYTKQCVIDD T0308 47 :LSFTVFDM 2eryA 62 :ARLDILDT T0308 61 :RNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 2eryA 76 :GAMREQYMRTGEGFLLVFSVTDRGSFEEIYKFQRQILRV T0308 102 :IKHRRIPILFFANKMDLRDAV 2eryA 115 :KDRDEFPMILIGNKADLDHQR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 2eryA 136 :QVTQEEGQQLARQLKVTYMEASAKIRMNVDQAFHELVRVI Number of specific fragments extracted= 8 number of extra gaps= 1 total=650 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 2eryA/T0308-2eryA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 2eryA/T0308-2eryA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2eryA read from 2eryA/T0308-2eryA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2eryA in template set Warning: unaligning (T0308)L9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2eryA)G23 Warning: unaligning (T0308)D10 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2eryA)G23 Warning: unaligning (T0308)S55 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2eryA)F75 Warning: unaligning (T0308)Y60 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2eryA)F75 T0308 1 :EVHVLCLG 2eryA 14 :KYRLVVVG T0308 11 :NSGKTTIINKLKPSNA 2eryA 24 :GVGKSALTIQFIQSYF T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDM 2eryA 42 :DYDPTIEDSYTKQCVIDDRAARLDILDT T0308 61 :RNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 2eryA 76 :GAMREQYMRTGEGFLLVFSVTDRGSFEEIYKFQRQILRVKD T0308 104 :HRRIPILFFANKMDLRDAVTSV 2eryA 117 :RDEFPMILIGNKADLDHQRQVT T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 2eryA 139 :QEEGQQLARQLKVTYMEASAKIRMNVDQAFHELVRVI Number of specific fragments extracted= 6 number of extra gaps= 1 total=656 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 1f6bA/T0308-1f6bA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1f6bA expands to /projects/compbio/data/pdb/1f6b.pdb.gz 1f6bA:# T0308 read from 1f6bA/T0308-1f6bA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f6bA read from 1f6bA/T0308-1f6bA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1f6bA to template set # found chain 1f6bA in template set Warning: unaligning (T0308)S24 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f6bA)P55 Warning: unaligning (T0308)P33 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f6bA)P55 Warning: unaligning (T0308)G56 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f6bA)R83 Warning: unaligning (T0308)R61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f6bA)R83 T0308 2 :VHVLCLGLDNSGKTTIINKLKP 1f6bA 26 :GKLVFLGLDNAGKTTLLHMLKD T0308 34 :TIGFSIEKFKSSSLSFTVFDMS 1f6bA 56 :TLHPTSEELTIAGMTFTTFDLG T0308 62 :NLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1f6bA 84 :RVWKNYLPAINGIVFLVDCADHERLLESKEELDSLMTDETI T0308 105 :RRIPILFFANKMDLRDA 1f6bA 125 :ANVPILILGNKIDRPEA T0308 127 :VSQLLCLENIK 1f6bA 142 :ISEERLREMFG T0308 138 :DKP 1f6bA 167 :ELN T0308 141 :WHICASDAIKGEGLQEGVDWLQDQI 1f6bA 173 :LEVFMCSVLKRQGYGEGFRWMAQYI Number of specific fragments extracted= 7 number of extra gaps= 0 total=663 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 1f6bA/T0308-1f6bA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1f6bA/T0308-1f6bA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f6bA read from 1f6bA/T0308-1f6bA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1f6bA in template set Warning: unaligning (T0308)N25 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f6bA)P55 Warning: unaligning (T0308)P33 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f6bA)P55 Warning: unaligning (T0308)G56 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f6bA)R83 Warning: unaligning (T0308)R61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f6bA)R83 T0308 2 :VHVLCLGLDNSGKTTIINKLK 1f6bA 26 :GKLVFLGLDNAGKTTLLHMLK T0308 24 :S 1f6bA 47 :D T0308 34 :TIGFSIEKFKSSSLSFTVFDMS 1f6bA 56 :TLHPTSEELTIAGMTFTTFDLG T0308 62 :NLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDIKH 1f6bA 84 :RVWKNYLPAINGIVFLVDCADHERLLESKEELDSLMTDETIAN T0308 107 :IPILFFANKMDLRDAVTSVKVSQLL 1f6bA 127 :VPILILGNKIDRPEAISEERLREMF T0308 134 :ENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1f6bA 166 :KELNARPLEVFMCSVLKRQGYGEGFRWMAQYI Number of specific fragments extracted= 6 number of extra gaps= 0 total=669 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 1f6bA/T0308-1f6bA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1f6bA/T0308-1f6bA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f6bA read from 1f6bA/T0308-1f6bA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1f6bA in template set Warning: unaligning (T0308)S24 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f6bA)P55 Warning: unaligning (T0308)P33 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f6bA)P55 Warning: unaligning (T0308)G56 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f6bA)R83 Warning: unaligning (T0308)R61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f6bA)R83 T0308 2 :VHVLCLGLDNSGKTTIINKLKP 1f6bA 26 :GKLVFLGLDNAGKTTLLHMLKD T0308 34 :TIGFSIEKFKSSSLSFTVFDMS 1f6bA 56 :TLHPTSEELTIAGMTFTTFDLG T0308 62 :NLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1f6bA 84 :RVWKNYLPAINGIVFLVDCADHERLLESKEELDSLMTDET T0308 104 :HRRIPILFFANKMDLRDAVTSVKVSQLL 1f6bA 124 :IANVPILILGNKIDRPEAISEERLREMF T0308 134 :ENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1f6bA 166 :KELNARPLEVFMCSVLKRQGYGEGFRWMAQYI Number of specific fragments extracted= 5 number of extra gaps= 0 total=674 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 1xtqA/T0308-1xtqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xtqA expands to /projects/compbio/data/pdb/1xtq.pdb.gz 1xtqA:# T0308 read from 1xtqA/T0308-1xtqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xtqA read from 1xtqA/T0308-1xtqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xtqA to template set # found chain 1xtqA in template set T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1xtqA 7 :RKIAILGYRSVGKSSLTIQFVEGQF T0308 28 :SQNILPTI 1xtqA 32 :VDSYDPTI T0308 36 :GFSIEKFKSSS 1xtqA 41 :NTFTKLITVNG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1xtqA 54 :YHLQLVDTAGQDEYSIFPQTYSIDINGYILVYSVTSIKSFEVIKVIHGKLLDMVGK T0308 105 :RRIPILFFANKMDLRDAV 1xtqA 110 :VQIPIMLVGNKKDLHMER T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQ 1xtqA 128 :VISYEEGKALAESWNAAFLESSAKENQTAVDVFRRII Number of specific fragments extracted= 6 number of extra gaps= 0 total=680 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 1xtqA/T0308-1xtqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1xtqA/T0308-1xtqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xtqA read from 1xtqA/T0308-1xtqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xtqA in template set T0308 2 :VHVLCLGLDNSGKTTIINKLK 1xtqA 7 :RKIAILGYRSVGKSSLTIQFV T0308 24 :SNAQSQNILPTIG 1xtqA 28 :EGQFVDSYDPTIE T0308 37 :FSIEKFKSSS 1xtqA 42 :TFTKLITVNG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 1xtqA 54 :YHLQLVDTAGQDEYSIFPQTYSIDINGYILVYSVTSIKSFEVIKVIHGKLLDM T0308 102 :IKHRRIPILFFANKMDLRDAV 1xtqA 107 :VGKVQIPIMLVGNKKDLHMER T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQD 1xtqA 128 :VISYEEGKALAESWNAAFLESSAKENQTAVDVFRRIIL Number of specific fragments extracted= 6 number of extra gaps= 0 total=686 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 1xtqA/T0308-1xtqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1xtqA/T0308-1xtqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xtqA read from 1xtqA/T0308-1xtqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xtqA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1xtqA 6 :SRKIAILGYRSVGKSSLTIQFVEGQF T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1xtqA 34 :SYDPTIENTFTKLITVNGQEYHLQLVDTAGQDEYSIFPQTYSIDINGYILVYSVTSIKSFEVIKVIHGKLLDMVG T0308 104 :HRRIPILFFANKMDLRDAVTSV 1xtqA 109 :KVQIPIMLVGNKKDLHMERVIS T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQ 1xtqA 131 :YEEGKALAESWNAAFLESSAKENQTAVDVFRRII Number of specific fragments extracted= 4 number of extra gaps= 0 total=690 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 1nf3A/T0308-1nf3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1nf3A expands to /projects/compbio/data/pdb/1nf3.pdb.gz 1nf3A:# T0308 read from 1nf3A/T0308-1nf3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nf3A read from 1nf3A/T0308-1nf3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1nf3A to template set # found chain 1nf3A in template set T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1nf3A 4 :IKCVVVGDGAVGKTCLLISYTTNKF T0308 28 :SQNILPTI 1nf3A 29 :PSEYVPTV T0308 36 :GFSIEKFKSSS 1nf3A 38 :DNYAVTVMIGG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKE 1nf3A 51 :YTLGLFDTAGLEDYDRLRPLSYPQTDVFLVCFSVVSPSSFENVKE T0308 92 :ELDTLLNHP 1nf3A 97 :WVPEITHHC T0308 105 :RRIPILFFANKMDLRDAVTSVK 1nf3A 106 :PKTPFLLVGTQIDLRDDPSTIE T0308 127 :VSQLLCLENIKDKP 1nf3A 137 :ITPETAEKLARDLK T0308 141 :WHICASDAIKGEGLQEGVDWLQDQ 1nf3A 152 :VKYVECSALTQKGLKNVFDEAILA Number of specific fragments extracted= 8 number of extra gaps= 0 total=698 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 1nf3A/T0308-1nf3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1nf3A/T0308-1nf3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nf3A read from 1nf3A/T0308-1nf3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nf3A in template set T0308 2 :VHVLCLGLDNSGKTTIINKLK 1nf3A 4 :IKCVVVGDGAVGKTCLLISYT T0308 24 :SNAQSQNILPTIG 1nf3A 25 :TNKFPSEYVPTVF T0308 37 :FSIEKFKSSS 1nf3A 39 :NYAVTVMIGG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKE 1nf3A 51 :YTLGLFDTAGLEDYDRLRPLSYPQTDVFLVCFSVVSPSSFENVKE T0308 92 :ELDTLLNH 1nf3A 97 :WVPEITHH T0308 104 :HRRIPILFFANKMDLRDAVTSVK 1nf3A 105 :CPKTPFLLVGTQIDLRDDPSTIE T0308 127 :VSQLLCLENIKDKPWH 1nf3A 137 :ITPETAEKLARDLKAV T0308 143 :ICASDAIKGEGLQEGVDWLQDQ 1nf3A 154 :YVECSALTQKGLKNVFDEAILA Number of specific fragments extracted= 8 number of extra gaps= 0 total=706 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 1nf3A/T0308-1nf3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1nf3A/T0308-1nf3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nf3A read from 1nf3A/T0308-1nf3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nf3A in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNAQSQNILPTIGFSIEKFKSSS 1nf3A 3 :TIKCVVVGDGAVGKTCLLISYTTNKFPSEYVPTVFDNYAVTVMIGG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKE 1nf3A 51 :YTLGLFDTAGLEDYDRLRPLSYPQTDVFLVCFSVVSPSSFENVKE T0308 92 :ELDTLLNHPD 1nf3A 97 :WVPEITHHCP T0308 106 :RIPILFFANKMDLRDAVTSVK 1nf3A 107 :KTPFLLVGTQIDLRDDPSTIE T0308 127 :VSQLLCLENIKDKPW 1nf3A 137 :ITPETAEKLARDLKA T0308 142 :HICASDAIKGEGLQEGVDWLQD 1nf3A 153 :KYVECSALTQKGLKNVFDEAIL Number of specific fragments extracted= 6 number of extra gaps= 0 total=712 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 1ukvY/T0308-1ukvY-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ukvY expands to /projects/compbio/data/pdb/1ukv.pdb.gz 1ukvY:Skipped atom 3755, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 3757, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 3759, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 3761, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 3763, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 3765, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 3775, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 3777, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 3779, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 3781, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 3783, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 3785, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 3787, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 3789, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4119, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4121, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4123, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4125, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4127, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4129, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4131, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4133, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4135, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4137, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4139, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4141, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4143, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4145, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4147, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4149, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4151, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4153, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4155, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4157, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4159, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4161, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4163, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4165, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4167, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4169, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4171, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4173, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4175, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4177, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4179, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4181, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4183, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4185, because occupancy 0.500 <= existing 0.500 in 1ukvY # T0308 read from 1ukvY/T0308-1ukvY-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ukvY read from 1ukvY/T0308-1ukvY-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ukvY to template set # found chain 1ukvY in template set T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1ukvY 9 :FKLLLIGNSGVGKSCLLLRFSDDTY T0308 28 :SQNI 1ukvY 34 :TNDY T0308 32 :LPTIGFSIEKFKSSS 1ukvY 40 :TIGVDFKIKTVELDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1ukvY 57 :VKLQIWDTAGQERFRTITSSYYRGSHGIIIVYDVTDQESFNGVKMWLQEIDRYAT T0308 105 :RRIPILFFANKMDLRDAV 1ukvY 112 :STVLKLLVGNKCDLKDKR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1ukvY 130 :VVEYDVAKEFADANKMPFLETSALDSTNVEDAFLTMARQI Number of specific fragments extracted= 6 number of extra gaps= 0 total=718 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 1ukvY/T0308-1ukvY-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1ukvY/T0308-1ukvY-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ukvY read from 1ukvY/T0308-1ukvY-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ukvY in template set T0308 2 :VHVLCLGLDNSGKTTIINKLK 1ukvY 9 :FKLLLIGNSGVGKSCLLLRFS T0308 24 :SNAQSQNILPTIG 1ukvY 30 :DDTYTNDYISTIG T0308 37 :FSIEKFKSSS 1ukvY 45 :FKIKTVELDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 1ukvY 57 :VKLQIWDTAGQERFRTITSSYYRGSHGIIIVYDVTDQESFNGVKMWLQEIDRY T0308 103 :KHRRIPILFFANKMDLRDAV 1ukvY 110 :ATSTVLKLLVGNKCDLKDKR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1ukvY 130 :VVEYDVAKEFADANKMPFLETSALDSTNVEDAFLTMARQI Number of specific fragments extracted= 6 number of extra gaps= 0 total=724 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 1ukvY/T0308-1ukvY-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1ukvY/T0308-1ukvY-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ukvY read from 1ukvY/T0308-1ukvY-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ukvY in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1ukvY 8 :LFKLLLIGNSGVGKSCLLLRFSDDTY T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1ukvY 37 :YISTIGVDFKIKTVELDGKTVKLQIWDTAGQERFRTITSSYYRGSHGIIIVYDVTDQESFNGVKMWLQEIDRYAT T0308 105 :RRIPILFFANKMDLRDAVTSV 1ukvY 112 :STVLKLLVGNKCDLKDKRVVE T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1ukvY 133 :YDVAKEFADANKMPFLETSALDSTNVEDAFLTMARQI Number of specific fragments extracted= 4 number of extra gaps= 0 total=728 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 1huqA/T0308-1huqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1huqA expands to /projects/compbio/data/pdb/1huq.pdb.gz 1huqA:# T0308 read from 1huqA/T0308-1huqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1huqA read from 1huqA/T0308-1huqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1huqA to template set # found chain 1huqA in template set T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1huqA 22 :FKLVLLGESAVGKSSLVLRFVKGQF T0308 27 :QSQN 1huqA 48 :EYQE T0308 32 :LPTIGFSIEKFKSSS 1huqA 53 :TIGAAFLTQTVCLDD T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1huqA 70 :VKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNTDTFARAKNWVKELQRQAS T0308 105 :RRIPILFFANKMDLRDAV 1huqA 125 :PNIVIALAGNKADLASKR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1huqA 143 :AVEFQEAQAYADDNSLLFMETSAKTAMNVNEIFMAIAKKL Number of specific fragments extracted= 6 number of extra gaps= 0 total=734 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 1huqA/T0308-1huqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1huqA/T0308-1huqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1huqA read from 1huqA/T0308-1huqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1huqA in template set T0308 2 :VHVLCLGLDNSGKTTIINKLK 1huqA 22 :FKLVLLGESAVGKSSLVLRFV T0308 24 :SNAQSQNILPTIG 1huqA 43 :KGQFHEYQESTIG T0308 37 :FSIEKFKSSS 1huqA 58 :FLTQTVCLDD T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 1huqA 70 :VKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNTDTFARAKNWVKELQRQ T0308 103 :KHRRIPILFFANKMDLRDAV 1huqA 123 :ASPNIVIALAGNKADLASKR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1huqA 143 :AVEFQEAQAYADDNSLLFMETSAKTAMNVNEIFMAIAKKL Number of specific fragments extracted= 6 number of extra gaps= 0 total=740 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 1huqA/T0308-1huqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1huqA/T0308-1huqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1huqA read from 1huqA/T0308-1huqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1huqA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1huqA 21 :QFKLVLLGESAVGKSSLVLRFVKGQF T0308 27 :QSQNILPTIGFSIEKFKSSS 1huqA 48 :EYQESTIGAAFLTQTVCLDD T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1huqA 70 :VKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNTDTFARAKNWVKELQRQAS T0308 105 :RRIPILFFANKMDLRDAVTSV 1huqA 125 :PNIVIALAGNKADLASKRAVE T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1huqA 146 :FQEAQAYADDNSLLFMETSAKTAMNVNEIFMAIAKKL Number of specific fragments extracted= 5 number of extra gaps= 0 total=745 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 1r4aA/T0308-1r4aA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1r4aA expands to /projects/compbio/data/pdb/1r4a.pdb.gz 1r4aA:# T0308 read from 1r4aA/T0308-1r4aA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r4aA read from 1r4aA/T0308-1r4aA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1r4aA to template set # found chain 1r4aA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNAQ 1r4aA 17 :EMRILILGLDGAGKTTILYRLQVGEVV T0308 30 :NILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1r4aA 44 :TTIPTIGFNVETVTYKNLKFQVWDLGGQTSIRPYWRCYYSNTDAVIYVVDSCDRDRIGISKSELVAMLEEEEL T0308 105 :RRIPILFFANKMDLRDAV 1r4aA 117 :RKAILVVFANKQDMEQAM T0308 128 :SQLLCLENIK 1r4aA 135 :TPSEMANALG T0308 138 :DKPWHICASDAIKGEGLQEGVDWLQDQI 1r4aA 150 :DRKWQIFKTSATKGTGLDEAMEWLVETL Number of specific fragments extracted= 5 number of extra gaps= 0 total=750 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 1r4aA/T0308-1r4aA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1r4aA/T0308-1r4aA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r4aA read from 1r4aA/T0308-1r4aA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1r4aA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNAQS 1r4aA 17 :EMRILILGLDGAGKTTILYRLQVGEVVT T0308 31 :ILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDIKH 1r4aA 45 :TIPTIGFNVETVTYKNLKFQVWDLGGQTSIRPYWRCYYSNTDAVIYVVDSCDRDRIGISKSELVAMLEEEELRK T0308 107 :IPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1r4aA 119 :AILVVFANKQDMEQAMTPSEMANALGLPALKDRKWQIFKTSATKGTGLDEAMEWLVETL Number of specific fragments extracted= 3 number of extra gaps= 0 total=753 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 1r4aA/T0308-1r4aA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1r4aA/T0308-1r4aA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r4aA read from 1r4aA/T0308-1r4aA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1r4aA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNAQ 1r4aA 17 :EMRILILGLDGAGKTTILYRLQVGEVV T0308 30 :NILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1r4aA 44 :TTIPTIGFNVETVTYKNLKFQVWDLGGQTSIRPYWRCYYSNTDAVIYVVDSCDRDRIGISKSELVAMLEEEE T0308 104 :HRRIPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1r4aA 116 :LRKAILVVFANKQDMEQAMTPSEMANALGLPALKDRKWQIFKTSATKGTGLDEAMEWLVETL Number of specific fragments extracted= 3 number of extra gaps= 0 total=756 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 3rabA/T0308-3rabA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3rabA expands to /projects/compbio/data/pdb/3rab.pdb.gz 3rabA:# T0308 read from 3rabA/T0308-3rabA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3rabA read from 3rabA/T0308-3rabA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3rabA to template set # found chain 3rabA in template set T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNAQSQNI 3rabA 23 :FKILIIGNSSVGKTSFLFRYADDSFTPAFV T0308 32 :LPTIGFSIEKFKSSS 3rabA 54 :TVGIDFKVKTIYRND T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 3rabA 71 :IKLQIWDTAGQERYRTITTAYYRGAMGFILMYDITNEESFNAVQDWSTQIKTYSW T0308 105 :RRIPILFFANKMDLRDAV 3rabA 126 :DNAQVLLVGNKCDMEDER T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 3rabA 144 :VVSSERGRQLADHLGFEFFEASAKDNINVKQTFERLVDVI Number of specific fragments extracted= 5 number of extra gaps= 0 total=761 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 3rabA/T0308-3rabA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 3rabA/T0308-3rabA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3rabA read from 3rabA/T0308-3rabA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3rabA in template set T0308 2 :VHVLCLGLDNSGKTTIINKLK 3rabA 23 :FKILIIGNSSVGKTSFLFRYA T0308 24 :SNAQSQNILPTIG 3rabA 44 :DDSFTPAFVSTVG T0308 37 :FSIEKFKSSS 3rabA 59 :FKVKTIYRND T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 3rabA 71 :IKLQIWDTAGQERYRTITTAYYRGAMGFILMYDITNEESFNAVQDWSTQIKTY T0308 103 :KHRRIPILFFANKMDLRDAV 3rabA 124 :SWDNAQVLLVGNKCDMEDER T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 3rabA 144 :VVSSERGRQLADHLGFEFFEASAKDNINVKQTFERLVDVI Number of specific fragments extracted= 6 number of extra gaps= 0 total=767 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 3rabA/T0308-3rabA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 3rabA/T0308-3rabA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3rabA read from 3rabA/T0308-3rabA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3rabA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 3rabA 22 :MFKILIIGNSSVGKTSFLFRYADDSF T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 3rabA 51 :FVSTVGIDFKVKTIYRNDKRIKLQIWDTAGQERYRTITTAYYRGAMGFILMYDITNEESFNAVQDWSTQIKTYSW T0308 105 :RRIPILFFANKMDLRDAVTSV 3rabA 126 :DNAQVLLVGNKCDMEDERVVS T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 3rabA 147 :SERGRQLADHLGFEFFEASAKDNINVKQTFERLVDVI Number of specific fragments extracted= 4 number of extra gaps= 0 total=771 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 1oivA/T0308-1oivA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1oivA expands to /projects/compbio/data/pdb/1oiv.pdb.gz 1oivA:# T0308 read from 1oivA/T0308-1oivA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1oivA read from 1oivA/T0308-1oivA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1oivA to template set # found chain 1oivA in template set T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNAQSQNI 1oivA 12 :FKVVLIGDSGVGKSNLLSRFTRNEFNLESK T0308 32 :LPTIGFSIEKFKSSS 1oivA 43 :TIGVEFATRSIQVDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1oivA 60 :IKAQIWDTAGQERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHAD T0308 105 :RRIPILFFANKMDLRDAV 1oivA 115 :SNIVIMLVGNKSDLRHLR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1oivA 133 :AVPTDEARAFAEKNGLSFIETSALDSTNVEAAFQTILTEI Number of specific fragments extracted= 5 number of extra gaps= 0 total=776 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 1oivA/T0308-1oivA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1oivA/T0308-1oivA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1oivA read from 1oivA/T0308-1oivA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1oivA in template set T0308 2 :VHVLCLGLDNSGKTTIINKLK 1oivA 12 :FKVVLIGDSGVGKSNLLSRFT T0308 24 :SNAQSQNILPTIG 1oivA 33 :RNEFNLESKSTIG T0308 37 :FSIEKFKSSS 1oivA 48 :FATRSIQVDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 1oivA 60 :IKAQIWDTAGQERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDH T0308 103 :KHRRIPILFFANKMDLRDAV 1oivA 113 :ADSNIVIMLVGNKSDLRHLR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1oivA 133 :AVPTDEARAFAEKNGLSFIETSALDSTNVEAAFQTILTEI Number of specific fragments extracted= 6 number of extra gaps= 0 total=782 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 1oivA/T0308-1oivA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1oivA/T0308-1oivA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1oivA read from 1oivA/T0308-1oivA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1oivA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1oivA 11 :LFKVVLIGDSGVGKSNLLSRFTRNEF T0308 27 :QSQNILPTIGFSIEKFKSSS 1oivA 38 :LESKSTIGVEFATRSIQVDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1oivA 60 :IKAQIWDTAGQERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHAD T0308 105 :RRIPILFFANKMDLRDAVTSV 1oivA 115 :SNIVIMLVGNKSDLRHLRAVP T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1oivA 136 :TDEARAFAEKNGLSFIETSALDSTNVEAAFQTILTEI Number of specific fragments extracted= 5 number of extra gaps= 0 total=787 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 1hurA/T0308-1hurA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1hurA expands to /projects/compbio/data/pdb/1hur.pdb.gz 1hurA:# T0308 read from 1hurA/T0308-1hurA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hurA read from 1hurA/T0308-1hurA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1hurA to template set # found chain 1hurA in template set Warning: unaligning (T0308)G56 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1hurA)Q71 Warning: unaligning (T0308)Q57 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1hurA)Q71 Warning: unaligning (T0308)G58 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1hurA)D72 Warning: unaligning (T0308)R59 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1hurA)K73 Warning: unaligning (T0308)Y60 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1hurA)I74 Warning: unaligning (T0308)R61 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1hurA)R75 Warning: unaligning (T0308)N62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1hurA)P76 Warning: unaligning (T0308)L63 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1hurA)L77 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNAQSQ 1hurA 17 :EMRILMVGLDAAGKTTILYKLKLGEIVTT T0308 32 :LPTIGFSIEKFKSSSLSFTVFDMS 1hurA 46 :IPTIGFNVETVEYKNISFTVWDVG T0308 64 :WEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1hurA 78 :WRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDEL T0308 105 :RRIPILFFANKMDLRDAVTS 1hurA 117 :RDAVLLVFANKQDLPNAMNA T0308 130 :LLCLENIK 1hurA 137 :AEITDKLG T0308 138 :DKPWHICASDAIKGEGLQEGVDWLQDQI 1hurA 150 :HRNWYIQATCATSGDGLYEGLDWLSNQL Number of specific fragments extracted= 6 number of extra gaps= 1 total=793 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 1hurA/T0308-1hurA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1hurA/T0308-1hurA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hurA read from 1hurA/T0308-1hurA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1hurA in template set Warning: unaligning (T0308)G56 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1hurA)Q71 Warning: unaligning (T0308)Q57 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1hurA)Q71 Warning: unaligning (T0308)G58 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1hurA)D72 Warning: unaligning (T0308)R59 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1hurA)K73 Warning: unaligning (T0308)Y60 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1hurA)I74 Warning: unaligning (T0308)R61 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1hurA)R75 Warning: unaligning (T0308)N62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1hurA)P76 Warning: unaligning (T0308)L63 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1hurA)L77 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNAQSQ 1hurA 17 :EMRILMVGLDAAGKTTILYKLKLGEIVTT T0308 32 :LPTIGFSIEKFKSSSLSFTVFDMS 1hurA 46 :IPTIGFNVETVEYKNISFTVWDVG T0308 64 :WEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDIKH 1hurA 78 :WRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRD T0308 107 :IPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1hurA 119 :AVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQL Number of specific fragments extracted= 4 number of extra gaps= 1 total=797 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 1hurA/T0308-1hurA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1hurA/T0308-1hurA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hurA read from 1hurA/T0308-1hurA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1hurA in template set Warning: unaligning (T0308)G56 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1hurA)Q71 Warning: unaligning (T0308)Q57 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1hurA)Q71 Warning: unaligning (T0308)G58 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1hurA)D72 Warning: unaligning (T0308)R59 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1hurA)K73 Warning: unaligning (T0308)Y60 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1hurA)I74 Warning: unaligning (T0308)R61 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1hurA)R75 Warning: unaligning (T0308)N62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1hurA)P76 Warning: unaligning (T0308)L63 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1hurA)L77 T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1hurA 18 :MRILMVGLDAAGKTTILYKLKLGEI T0308 30 :NILPTIGFSIEKFKSSSLSFTVFDMS 1hurA 44 :TTIPTIGFNVETVEYKNISFTVWDVG T0308 64 :WEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1hurA 78 :WRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDE T0308 104 :HRRIPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1hurA 116 :LRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQL Number of specific fragments extracted= 4 number of extra gaps= 1 total=801 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 2b6hA/T0308-2b6hA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2b6hA expands to /projects/compbio/data/pdb/2b6h.pdb.gz 2b6hA:Skipped atom 594, because occupancy 0.350 <= existing 0.650 in 2b6hA Skipped atom 596, because occupancy 0.350 <= existing 0.650 in 2b6hA Skipped atom 598, because occupancy 0.350 <= existing 0.650 in 2b6hA Skipped atom 600, because occupancy 0.350 <= existing 0.650 in 2b6hA Skipped atom 957, because occupancy 0.350 <= existing 0.650 in 2b6hA Skipped atom 959, because occupancy 0.350 <= existing 0.650 in 2b6hA Skipped atom 961, because occupancy 0.350 <= existing 0.650 in 2b6hA # T0308 read from 2b6hA/T0308-2b6hA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b6hA read from 2b6hA/T0308-2b6hA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2b6hA to template set # found chain 2b6hA in template set Warning: unaligning (T0308)S55 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b6hA)R75 Warning: unaligning (T0308)R61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b6hA)R75 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNAQSQ 2b6hA 17 :QMRILMVGLDAAGKTTILYKLKLGEIVTT T0308 32 :LPTIGFSIEKFKSSSLSFTVFDM 2b6hA 46 :IPTIGFNVETVEYKNICFTVWDV T0308 62 :NLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 2b6hA 76 :PLWRHYFQNTQGLIFVVDSNDRERVQESADELQKMLQEDEL T0308 105 :RRIPILFFANKMDLRDAV 2b6hA 117 :RDAVLLVFANKQDMPNAM T0308 128 :SQLLCLENIK 2b6hA 135 :PVSELTDKLG T0308 138 :DKPWHICASDAIKGEGLQEGVDWLQDQI 2b6hA 150 :SRTWYVQATCATQGTGLYDGLDWLSHEL Number of specific fragments extracted= 6 number of extra gaps= 0 total=807 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 2b6hA/T0308-2b6hA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 2b6hA/T0308-2b6hA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b6hA read from 2b6hA/T0308-2b6hA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2b6hA in template set Warning: unaligning (T0308)S55 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b6hA)R75 Warning: unaligning (T0308)R61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b6hA)R75 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNAQSQ 2b6hA 17 :QMRILMVGLDAAGKTTILYKLKLGEIVTT T0308 32 :LPTIGFSIEKFKSSSLSFTVFDM 2b6hA 46 :IPTIGFNVETVEYKNICFTVWDV T0308 62 :NLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDIKH 2b6hA 76 :PLWRHYFQNTQGLIFVVDSNDRERVQESADELQKMLQEDELRD T0308 107 :IPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 2b6hA 119 :AVLLVFANKQDMPNAMPVSELTDKLGLQHLRSRTWYVQATCATQGTGLYDGLDWLSHEL Number of specific fragments extracted= 4 number of extra gaps= 0 total=811 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 2b6hA/T0308-2b6hA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 2b6hA/T0308-2b6hA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b6hA read from 2b6hA/T0308-2b6hA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2b6hA in template set Warning: unaligning (T0308)S55 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b6hA)R75 Warning: unaligning (T0308)R61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b6hA)R75 T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNAQ 2b6hA 18 :MRILMVGLDAAGKTTILYKLKLGEIV T0308 30 :NILPTIGFSIEKFKSSSLSFTVFDM 2b6hA 44 :TTIPTIGFNVETVEYKNICFTVWDV T0308 62 :NLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 2b6hA 76 :PLWRHYFQNTQGLIFVVDSNDRERVQESADELQKMLQEDE T0308 104 :HRRIPILFFANKMDLRDAVTSVKVSQL 2b6hA 116 :LRDAVLLVFANKQDMPNAMPVSELTDK T0308 136 :IK 2b6hA 143 :LG T0308 138 :DKPWHICASDAIKGEGLQEGVDWLQDQI 2b6hA 150 :SRTWYVQATCATQGTGLYDGLDWLSHEL Number of specific fragments extracted= 6 number of extra gaps= 0 total=817 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 1yzgA/T0308-1yzgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1yzgA expands to /projects/compbio/data/pdb/1yzg.pdb.gz 1yzgA:# T0308 read from 1yzgA/T0308-1yzgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yzgA read from 1yzgA/T0308-1yzgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1yzgA to template set # found chain 1yzgA in template set Warning: unaligning (T0308)A26 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yzgA)V42 Warning: unaligning (T0308)Q27 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yzgA)V42 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSN 1yzgA 16 :EHKVIIVGLDNAGKTTILYQFLMNE T0308 28 :SQN 1yzgA 43 :HTS T0308 33 :PTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1yzgA 46 :PTIGSNVEEIVVKNTHFLMWDIGGQESLRSSWNTYYSNTEFIILVVDSIDRERLAITKEELYRMLAHEDL T0308 105 :RRIPILFFANKMDLRDAV 1yzgA 116 :RKAAVLIFANKQDMKGCM T0308 128 :SQLLCLENIK 1yzgA 134 :TAAEISKYLT T0308 138 :DKPWHICASDAIKGEGLQEGVDWL 1yzgA 149 :DHPWHIQSCCALTGEGLCQGLEWM Number of specific fragments extracted= 6 number of extra gaps= 1 total=823 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 1yzgA/T0308-1yzgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1yzgA/T0308-1yzgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yzgA read from 1yzgA/T0308-1yzgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yzgA in template set Warning: unaligning (T0308)A26 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yzgA)V42 Warning: unaligning (T0308)Q27 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yzgA)V42 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSN 1yzgA 16 :EHKVIIVGLDNAGKTTILYQFLMNE T0308 28 :SQ 1yzgA 43 :HT T0308 32 :LPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDIKH 1yzgA 45 :SPTIGSNVEEIVVKNTHFLMWDIGGQESLRSSWNTYYSNTEFIILVVDSIDRERLAITKEELYRMLAHEDLRK T0308 107 :IPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWL 1yzgA 118 :AAVLIFANKQDMKGCMTAAEISKYLTLSSIKDHPWHIQSCCALTGEGLCQGLEWM Number of specific fragments extracted= 4 number of extra gaps= 1 total=827 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 1yzgA/T0308-1yzgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1yzgA/T0308-1yzgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yzgA read from 1yzgA/T0308-1yzgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yzgA in template set Warning: unaligning (T0308)A26 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yzgA)V42 Warning: unaligning (T0308)Q27 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yzgA)V42 T0308 3 :HVLCLGLDNSGKTTIINKLKPSN 1yzgA 18 :KVIIVGLDNAGKTTILYQFLMNE T0308 30 :NILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1yzgA 43 :HTSPTIGSNVEEIVVKNTHFLMWDIGGQESLRSSWNTYYSNTEFIILVVDSIDRERLAITKEELYRMLAHED T0308 104 :HRRIPILFFANKMDLRDAVTSVKVSQ 1yzgA 115 :LRKAAVLIFANKQDMKGCMTAAEISK T0308 135 :NIK 1yzgA 141 :YLT T0308 138 :DKPWHICASDAIKGEGLQEGVDWL 1yzgA 149 :DHPWHIQSCCALTGEGLCQGLEWM Number of specific fragments extracted= 5 number of extra gaps= 1 total=832 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 1oixA/T0308-1oixA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1oixA expands to /projects/compbio/data/pdb/1oix.pdb.gz 1oixA:Skipped atom 452, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 454, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 456, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 458, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 460, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 462, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 464, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 466, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 577, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 579, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 581, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 583, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 585, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 587, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 654, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 656, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 658, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 660, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 662, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 664, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 666, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 668, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 935, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 937, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 939, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 941, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 943, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 945, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 947, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 949, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 1219, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 1221, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 1223, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 1225, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 1227, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 1229, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 1231, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 1233, because occupancy 0.500 <= existing 0.500 in 1oixA # T0308 read from 1oixA/T0308-1oixA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1oixA read from 1oixA/T0308-1oixA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1oixA to template set # found chain 1oixA in template set T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNAQSQNI 1oixA 12 :FKVVLIGDSGVGKSNLLSRFTRNEFNLESK T0308 32 :LPTIGFSIEKFKSSS 1oixA 43 :TIGVEFATRSIQVDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1oixA 60 :IKAQIWDTAGLERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHAD T0308 105 :RRIPILFFANKMDLRDAV 1oixA 115 :SNIVIMLVGNKSDLRHLR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1oixA 133 :AVPTDEARAFAEKNGLSFIETSALDSTNVEAAFQTILTEI Number of specific fragments extracted= 5 number of extra gaps= 0 total=837 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 1oixA/T0308-1oixA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1oixA/T0308-1oixA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1oixA read from 1oixA/T0308-1oixA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1oixA in template set T0308 2 :VHVLCLGLDNSGKTTIINKLK 1oixA 12 :FKVVLIGDSGVGKSNLLSRFT T0308 24 :SNAQSQNILPTIG 1oixA 33 :RNEFNLESKSTIG T0308 37 :FSIEKFKSSS 1oixA 48 :FATRSIQVDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 1oixA 60 :IKAQIWDTAGLERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDH T0308 103 :KHRRIPILFFANKMDLRDAV 1oixA 113 :ADSNIVIMLVGNKSDLRHLR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1oixA 133 :AVPTDEARAFAEKNGLSFIETSALDSTNVEAAFQTILTEI Number of specific fragments extracted= 6 number of extra gaps= 0 total=843 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 1oixA/T0308-1oixA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1oixA/T0308-1oixA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1oixA read from 1oixA/T0308-1oixA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1oixA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1oixA 11 :LFKVVLIGDSGVGKSNLLSRFTRNEF T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1oixA 40 :SKSTIGVEFATRSIQVDGKTIKAQIWDTAGLERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHAD T0308 105 :RRIPILFFANKMDLRDAVTSV 1oixA 115 :SNIVIMLVGNKSDLRHLRAVP T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1oixA 136 :TDEARAFAEKNGLSFIETSALDSTNVEAAFQTILTEI Number of specific fragments extracted= 4 number of extra gaps= 0 total=847 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 1s8fA/T0308-1s8fA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1s8fA expands to /projects/compbio/data/pdb/1s8f.pdb.gz 1s8fA:Skipped atom 1223, because occupancy 0.400 <= existing 0.600 in 1s8fA Skipped atom 1225, because occupancy 0.400 <= existing 0.600 in 1s8fA Skipped atom 1227, because occupancy 0.400 <= existing 0.600 in 1s8fA # T0308 read from 1s8fA/T0308-1s8fA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1s8fA read from 1s8fA/T0308-1s8fA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1s8fA to template set # found chain 1s8fA in template set Warning: unaligning (T0308)S28 because of BadResidue code BAD_PEPTIDE in next template residue (1s8fA)T1034 Warning: unaligning (T0308)Q29 because of BadResidue code BAD_PEPTIDE at template residue (1s8fA)T1034 Warning: unaligning (T0308)I102 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1s8fA)P1114 Warning: unaligning (T0308)H104 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1s8fA)P1114 Warning: unaligning (T0308)Q162 because of BadResidue code BAD_PEPTIDE in next template residue (1s8fA)R1170 Warning: unaligning (T0308)D163 because of BadResidue code BAD_PEPTIDE at template residue (1s8fA)R1170 T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1s8fA 1008 :FKVILLGDGGVGKSSLMNRYVTNKF T0308 30 :NILPTIG 1s8fA 1035 :QLFHTIG T0308 37 :FSIEKFKSSS 1s8fA 1044 :FLNKDLEVDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1s8fA 1056 :VTMQIWDTAGQERFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFIYYAD T0308 105 :RRIPILFFANKMDLRDA 1s8fA 1115 :ESFPFVILGNKIDISER T0308 126 :KVSQLLCLENIKDKP 1s8fA 1132 :QVSTEEAQAWCRDNG T0308 141 :WHICASDAIKGEGLQEGVDWL 1s8fA 1148 :YPYFETSAKDATNVAAAFEEA T0308 164 :QI 1s8fA 1171 :RV Number of specific fragments extracted= 8 number of extra gaps= 2 total=855 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 1s8fA/T0308-1s8fA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1s8fA/T0308-1s8fA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1s8fA read from 1s8fA/T0308-1s8fA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1s8fA in template set Warning: unaligning (T0308)S28 because of BadResidue code BAD_PEPTIDE in next template residue (1s8fA)T1034 Warning: unaligning (T0308)Q29 because of BadResidue code BAD_PEPTIDE at template residue (1s8fA)T1034 Warning: unaligning (T0308)H104 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1s8fA)P1114 Warning: unaligning (T0308)Q162 because of BadResidue code BAD_PEPTIDE in next template residue (1s8fA)R1170 Warning: unaligning (T0308)D163 because of BadResidue code BAD_PEPTIDE at template residue (1s8fA)R1170 T0308 2 :VHVLCLGLDNSGKTTIINKLK 1s8fA 1008 :FKVILLGDGGVGKSSLMNRYV T0308 24 :SNAQ 1s8fA 1029 :TNKF T0308 30 :NILPTIG 1s8fA 1035 :QLFHTIG T0308 37 :FSIEKFKSSS 1s8fA 1044 :FLNKDLEVDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 1s8fA 1056 :VTMQIWDTAGQERFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFIYY T0308 105 :RRIPILFFANKMDLRDA 1s8fA 1115 :ESFPFVILGNKIDISER T0308 126 :KVSQLLCLENIKDK 1s8fA 1132 :QVSTEEAQAWCRDN T0308 140 :PWHICASDAIKGEGLQEGVDWL 1s8fA 1147 :DYPYFETSAKDATNVAAAFEEA T0308 164 :QI 1s8fA 1171 :RV Number of specific fragments extracted= 9 number of extra gaps= 2 total=864 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 1s8fA/T0308-1s8fA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1s8fA/T0308-1s8fA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1s8fA read from 1s8fA/T0308-1s8fA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1s8fA in template set Warning: unaligning (T0308)Q27 because of BadResidue code BAD_PEPTIDE at template residue (1s8fA)T1034 Warning: unaligning (T0308)H99 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1s8fA)P1114 Warning: unaligning (T0308)H104 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1s8fA)P1114 Warning: unaligning (T0308)Q162 because of BadResidue code BAD_PEPTIDE in next template residue (1s8fA)R1170 Warning: unaligning (T0308)D163 because of BadResidue code BAD_PEPTIDE at template residue (1s8fA)R1170 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1s8fA 1007 :LFKVILLGDGGVGKSSLMNRYVTNKF T0308 28 :SQNILPTIGFSIEKFKSSS 1s8fA 1035 :QLFHTIGVEFLNKDLEVDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLL 1s8fA 1056 :VTMQIWDTAGQERFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFI T0308 98 :N 1s8fA 1110 :D T0308 105 :RRIPILFFANKMDLRDAVTSV 1s8fA 1115 :ESFPFVILGNKIDISERQVST T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWL 1s8fA 1136 :EEAQAWCRDNGDYPYFETSAKDATNVAAAFEEA T0308 164 :QI 1s8fA 1171 :RV Number of specific fragments extracted= 7 number of extra gaps= 2 total=871 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 1uptC/T0308-1uptC-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1uptC expands to /projects/compbio/data/pdb/1upt.pdb.gz 1uptC:# T0308 read from 1uptC/T0308-1uptC-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1uptC read from 1uptC/T0308-1uptC-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1uptC to template set # found chain 1uptC in template set Warning: unaligning (T0308)H3 because first residue in template chain is (1uptC)R19 Warning: unaligning (T0308)T95 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1uptC)L111 Warning: unaligning (T0308)L97 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uptC)L111 Warning: unaligning (T0308)D117 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1uptC)E131 Warning: unaligning (T0308)R119 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uptC)E131 Warning: unaligning (T0308)A121 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1uptC)T135 Warning: unaligning (T0308)S128 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uptC)T135 Warning: unaligning (T0308)L131 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1uptC)A140 Warning: unaligning (T0308)L133 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uptC)A140 Warning: unaligning (T0308)S146 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1uptC)S159 Warning: unaligning (T0308)D147 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1uptC)S159 Warning: unaligning (T0308)G157 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1uptC)E171 Warning: unaligning (T0308)D159 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uptC)E171 T0308 4 :VLCLGLDNSGKTTIINKLKPSNAQ 1uptC 20 :ILILGLDGAGKTTILYRLQVGEVV T0308 30 :NILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELD 1uptC 44 :TTIPTIGFNVETVTYKNLKFQVWDLGGLTSIRPYWRCYYSNTDAVIYVVDSCDRDRIGISKSELV T0308 98 :NHPDI 1uptC 112 :EEEEL T0308 105 :RRIPILFFANKM 1uptC 117 :RKAILVVFANKQ T0308 120 :D 1uptC 132 :Q T0308 129 :QL 1uptC 136 :SS T0308 134 :ENIK 1uptC 141 :NSLG T0308 141 :WHICA 1uptC 153 :WQIFK T0308 148 :AIKGEGLQE 1uptC 160 :ATKGTGLDE T0308 160 :WLQDQI 1uptC 172 :WLVETL Number of specific fragments extracted= 10 number of extra gaps= 1 total=881 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 1uptC/T0308-1uptC-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1uptC/T0308-1uptC-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1uptC read from 1uptC/T0308-1uptC-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1uptC in template set Warning: unaligning (T0308)H3 because first residue in template chain is (1uptC)R19 Warning: unaligning (T0308)T95 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1uptC)L111 Warning: unaligning (T0308)L97 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uptC)L111 Warning: unaligning (T0308)D117 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1uptC)E131 Warning: unaligning (T0308)R119 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uptC)E131 Warning: unaligning (T0308)A121 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1uptC)T135 Warning: unaligning (T0308)T123 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uptC)T135 Warning: unaligning (T0308)K126 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1uptC)A140 Warning: unaligning (T0308)S128 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uptC)A140 Warning: unaligning (T0308)S146 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1uptC)S159 Warning: unaligning (T0308)D147 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1uptC)S159 Warning: unaligning (T0308)G157 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1uptC)E171 Warning: unaligning (T0308)D159 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uptC)E171 T0308 4 :VLCLGLDNSGKTTIINKLKPSNAQS 1uptC 20 :ILILGLDGAGKTTILYRLQVGEVVT T0308 31 :ILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELD 1uptC 45 :TIPTIGFNVETVTYKNLKFQVWDLGGLTSIRPYWRCYYSNTDAVIYVVDSCDRDRIGISKSELV T0308 98 :NHPDIKH 1uptC 112 :EEEELRK T0308 107 :IPILFFANKM 1uptC 119 :AILVVFANKQ T0308 120 :D 1uptC 132 :Q T0308 124 :SV 1uptC 136 :SS T0308 129 :QLLCLENIKDKPWHICA 1uptC 141 :NSLGLPALKDRKWQIFK T0308 148 :AIKGEGLQE 1uptC 160 :ATKGTGLDE T0308 160 :WLQDQI 1uptC 172 :WLVETL Number of specific fragments extracted= 9 number of extra gaps= 1 total=890 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 1uptC/T0308-1uptC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1uptC/T0308-1uptC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1uptC read from 1uptC/T0308-1uptC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1uptC in template set Warning: unaligning (T0308)H3 because first residue in template chain is (1uptC)R19 Warning: unaligning (T0308)T95 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1uptC)L111 Warning: unaligning (T0308)L97 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uptC)L111 Warning: unaligning (T0308)D117 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1uptC)E131 Warning: unaligning (T0308)R119 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uptC)E131 Warning: unaligning (T0308)A121 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1uptC)T135 Warning: unaligning (T0308)T123 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uptC)T135 Warning: unaligning (T0308)K126 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1uptC)A140 Warning: unaligning (T0308)S128 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uptC)A140 Warning: unaligning (T0308)S146 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1uptC)S159 Warning: unaligning (T0308)D147 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1uptC)S159 Warning: unaligning (T0308)G157 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1uptC)E171 Warning: unaligning (T0308)D159 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uptC)E171 T0308 4 :VLCLGLDNSGKTTIINKLKPSNAQ 1uptC 20 :ILILGLDGAGKTTILYRLQVGEVV T0308 30 :NILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELD 1uptC 44 :TTIPTIGFNVETVTYKNLKFQVWDLGGLTSIRPYWRCYYSNTDAVIYVVDSCDRDRIGISKSELV T0308 98 :NHPD 1uptC 112 :EEEE T0308 104 :HRRIPILFFANKM 1uptC 116 :LRKAILVVFANKQ T0308 120 :D 1uptC 132 :Q T0308 124 :SV 1uptC 136 :SS T0308 129 :QLLCLENIKDKPWHICA 1uptC 141 :NSLGLPALKDRKWQIFK T0308 148 :AIKGEGLQE 1uptC 160 :ATKGTGLDE T0308 160 :WLQDQI 1uptC 172 :WLVETL Number of specific fragments extracted= 9 number of extra gaps= 1 total=899 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 1d5cA/T0308-1d5cA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1d5cA expands to /projects/compbio/data/pdb/1d5c.pdb.gz 1d5cA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0308 read from 1d5cA/T0308-1d5cA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1d5cA read from 1d5cA/T0308-1d5cA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1d5cA to template set # found chain 1d5cA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1d5cA 11 :KYKLVFLGEQAVGKTSIITRFMYDTF T0308 28 :SQNI 1d5cA 37 :DNNY T0308 32 :LPTIGFSIEKFKSSS 1d5cA 43 :TIGIDFLSKTLYLDE T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1d5cA 60 :VRLQLWDTAGQERFRSLIPSYIRDSAAAIVVYDITNRQSFENTTKWIQDILNERG T0308 105 :RRIPILFFANKMDLRDAV 1d5cA 115 :KDVIIALVGNKTDLGDLR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQD 1d5cA 133 :KVTYEEGMQKAQEYNTMFHETSAKAGHNIKVLFKKTAS Number of specific fragments extracted= 6 number of extra gaps= 0 total=905 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 1d5cA/T0308-1d5cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1d5cA/T0308-1d5cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1d5cA read from 1d5cA/T0308-1d5cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1d5cA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLK 1d5cA 11 :KYKLVFLGEQAVGKTSIITRFM T0308 24 :SNAQSQNILPTIG 1d5cA 33 :YDTFDNNYQSTIG T0308 37 :FSIEKFKSSS 1d5cA 48 :FLSKTLYLDE T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 1d5cA 60 :VRLQLWDTAGQERFRSLIPSYIRDSAAAIVVYDITNRQSFENTTKWIQDILNE T0308 103 :KHRRIPILFFANKMDLRDAV 1d5cA 113 :RGKDVIIALVGNKTDLGDLR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQD 1d5cA 133 :KVTYEEGMQKAQEYNTMFHETSAKAGHNIKVLFKKTAS Number of specific fragments extracted= 6 number of extra gaps= 0 total=911 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 1d5cA/T0308-1d5cA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1d5cA/T0308-1d5cA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1d5cA read from 1d5cA/T0308-1d5cA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1d5cA in template set T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1d5cA 12 :YKLVFLGEQAVGKTSIITRFMYDTF T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1d5cA 40 :YQSTIGIDFLSKTLYLDEGPVRLQLWDTAGQERFRSLIPSYIRDSAAAIVVYDITNRQSFENTTKWIQDILNERG T0308 105 :RRIPILFFANKMDLRDAVTSV 1d5cA 115 :KDVIIALVGNKTDLGDLRKVT T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQD 1d5cA 136 :YEEGMQKAQEYNTMFHETSAKAGHNIKVLFKKTAS Number of specific fragments extracted= 4 number of extra gaps= 0 total=915 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 1m2oB/T0308-1m2oB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1m2oB expands to /projects/compbio/data/pdb/1m2o.pdb.gz 1m2oB:# T0308 read from 1m2oB/T0308-1m2oB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m2oB read from 1m2oB/T0308-1m2oB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1m2oB to template set # found chain 1m2oB in template set Warning: unaligning (T0308)V2 because first residue in template chain is (1m2oB)G24 T0308 3 :HVLCLGLDNSGKTTIINKLKPSN 1m2oB 25 :KLLFLGLDNAGKTTLLHMLKNDR T0308 28 :SQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1m2oB 48 :LATLQPTWHPTSEELAIGNIKFTTFDLGGHIQARRLWKDYFPEVNGIVFLVDAADPERFDEARVELDALFNIAEL T0308 105 :RRIPILFFANKMDLRDA 1m2oB 123 :KDVPFVILGNKIDAPNA T0308 127 :VSQLLCLENIKDKP 1m2oB 140 :VSEAELRSALGLLN T0308 141 :WHICASDAIKGEGLQEGVDWLQDQ 1m2oB 166 :VEVFMCSVVMRNGYLEAFQWLSQY Number of specific fragments extracted= 5 number of extra gaps= 0 total=920 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 1m2oB/T0308-1m2oB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1m2oB/T0308-1m2oB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m2oB read from 1m2oB/T0308-1m2oB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1m2oB in template set Warning: unaligning (T0308)V2 because first residue in template chain is (1m2oB)G24 T0308 3 :HVLCLGLDNSGKTTIINKLK 1m2oB 25 :KLLFLGLDNAGKTTLLHMLK T0308 24 :SNAQSQ 1m2oB 45 :NDRLAT T0308 31 :ILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDIKH 1m2oB 51 :LQPTWHPTSEELAIGNIKFTTFDLGGHIQARRLWKDYFPEVNGIVFLVDAADPERFDEARVELDALFNIAELKD T0308 107 :IPILFFANKMDLRDAVT 1m2oB 125 :VPFVILGNKIDAPNAVS T0308 129 :QLLCLENIK 1m2oB 142 :EAELRSALG T0308 138 :DKPWHICASDAIKGEGLQEGVDWLQDQI 1m2oB 163 :QRPVEVFMCSVVMRNGYLEAFQWLSQYI Number of specific fragments extracted= 6 number of extra gaps= 0 total=926 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 1m2oB/T0308-1m2oB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1m2oB/T0308-1m2oB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m2oB read from 1m2oB/T0308-1m2oB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1m2oB in template set T0308 3 :HVLCLGLDNSGKTTIINKLKPSNA 1m2oB 25 :KLLFLGLDNAGKTTLLHMLKNDRL T0308 29 :QNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1m2oB 49 :ATLQPTWHPTSEELAIGNIKFTTFDLGGHIQARRLWKDYFPEVNGIVFLVDAADPERFDEARVELDALFNIAE T0308 104 :HRRIPILFFANKMDLRDAVTSVKVS 1m2oB 122 :LKDVPFVILGNKIDAPNAVSEAELR T0308 134 :ENIK 1m2oB 147 :SALG T0308 138 :DKPWHICASDAIKGEGLQEGVDWLQDQ 1m2oB 163 :QRPVEVFMCSVVMRNGYLEAFQWLSQY Number of specific fragments extracted= 5 number of extra gaps= 0 total=931 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 1agp/T0308-1agp-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1agp expands to /projects/compbio/data/pdb/1agp.pdb.gz 1agp:Warning: there is no chain 1agp will retry with 1agpA # T0308 read from 1agp/T0308-1agp-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1agp read from 1agp/T0308-1agp-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1agp to template set # found chain 1agp in template set T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1agp 4 :YKLVVVGADGVGKSALTIQLIQNHF T0308 28 :SQNILPTI 1agp 29 :VDEYDPTI T0308 36 :GFSIEKFKSSS 1agp 38 :DSYRKQVVIDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1agp 51 :CLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDS T0308 105 :RRIPILFFANKMDLRDA 1agp 107 :DDVPMVLVGNKCDLAAR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1agp 124 :TVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREI Number of specific fragments extracted= 6 number of extra gaps= 0 total=937 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 1agp/T0308-1agp-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1agp/T0308-1agp-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1agp read from 1agp/T0308-1agp-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1agp in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLK 1agp 3 :EYKLVVVGADGVGKSALTIQLI T0308 24 :SNAQSQNILPTIG 1agp 25 :QNHFVDEYDPTIE T0308 37 :FSIEKFKSSS 1agp 39 :SYRKQVVIDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 1agp 51 :CLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRV T0308 102 :IKHRRIPILFFANKMDLRDAV 1agp 104 :KDSDDVPMVLVGNKCDLAART T0308 127 :VSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1agp 125 :VESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREI Number of specific fragments extracted= 6 number of extra gaps= 0 total=943 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 1agp/T0308-1agp-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1agp/T0308-1agp-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1agp read from 1agp/T0308-1agp-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1agp in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1agp 3 :EYKLVVVGADGVGKSALTIQLIQNHF T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1agp 31 :EYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKD T0308 104 :HRRIPILFFANKMDLRDAVTSV 1agp 106 :SDDVPMVLVGNKCDLAARTVES T0308 130 :LLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1agp 128 :RQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREI Number of specific fragments extracted= 4 number of extra gaps= 0 total=947 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 1guaA/T0308-1guaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1guaA expands to /projects/compbio/data/pdb/1gua.pdb.gz 1guaA:# T0308 read from 1guaA/T0308-1guaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1guaA read from 1guaA/T0308-1guaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1guaA to template set # found chain 1guaA in template set T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1guaA 4 :YKLVVLGSGGVGKSALTVQFVQGIF T0308 28 :SQNILPTI 1guaA 29 :VDEYDPTI T0308 36 :GFSIEKFKSSS 1guaA 38 :DSYRKQVEVDC T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1guaA 51 :CMLEILDTAGTEQFTAMRDLYMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDT T0308 105 :RRIPILFFANKMDLRDAV 1guaA 107 :EDVPMILVGNKCDLEDER T0308 126 :KVSQLLCLENIKDKP 1guaA 125 :VVGKEQGQNLARQWC T0308 141 :WHICASDAIKGEGLQEGVDWLQDQI 1guaA 141 :CAFLESSAKSKINVNEIFYDLVRQI Number of specific fragments extracted= 7 number of extra gaps= 0 total=954 Will force an alignment to be made, even if fragment is small Number of alignments=160 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1guaA/T0308-1guaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1guaA/T0308-1guaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1guaA read from 1guaA/T0308-1guaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1guaA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLK 1guaA 3 :EYKLVVLGSGGVGKSALTVQFV T0308 24 :SNAQSQNILPTIG 1guaA 25 :QGIFVDEYDPTIE T0308 37 :FSIEKFKSSS 1guaA 39 :SYRKQVEVDC T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 1guaA 51 :CMLEILDTAGTEQFTAMRDLYMKNGQGFALVYSITAQSTFNDLQDLREQILRV T0308 102 :IKHRRIPILFFANKMDLRDAV 1guaA 104 :KDTEDVPMILVGNKCDLEDER T0308 126 :KVSQLLCLENIKD 1guaA 125 :VVGKEQGQNLARQ T0308 139 :KPWHICASDAIKGEGLQEGVDWLQDQI 1guaA 139 :CNCAFLESSAKSKINVNEIFYDLVRQI Number of specific fragments extracted= 7 number of extra gaps= 0 total=961 Will force an alignment to be made, even if fragment is small Number of alignments=161 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1guaA/T0308-1guaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1guaA/T0308-1guaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1guaA read from 1guaA/T0308-1guaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1guaA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1guaA 3 :EYKLVVLGSGGVGKSALTVQFVQGIF T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1guaA 31 :EYDPTIEDSYRKQVEVDCQQCMLEILDTAGTEQFTAMRDLYMKNGQGFALVYSITAQSTFNDLQDLREQILRVKD T0308 104 :HRRIPILFFANKMDLRDAVTSV 1guaA 106 :TEDVPMILVGNKCDLEDERVVG T0308 129 :QLLCLENIKD 1guaA 128 :KEQGQNLARQ T0308 139 :KPWHICASDAIKGEGLQEGVDWLQDQI 1guaA 139 :CNCAFLESSAKSKINVNEIFYDLVRQI Number of specific fragments extracted= 5 number of extra gaps= 0 total=966 Will force an alignment to be made, even if fragment is small Number of alignments=162 # Reading fragments from alignment file # Attempting to read fragment alignments from file 821p/T0308-821p-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 821p expands to /projects/compbio/data/pdb/821p.pdb.gz 821p:Warning: there is no chain 821p will retry with 821pA # T0308 read from 821p/T0308-821p-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 821p read from 821p/T0308-821p-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 821p to template set # found chain 821p in template set T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 821p 4 :YKLVVVGAPGVGKSALTIQLIQNHF T0308 28 :SQNILPTI 821p 29 :VDEYDPTI T0308 36 :GFSIEKFKSSS 821p 38 :DSYRKQVVIDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 821p 51 :CLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDS T0308 105 :RRIPILFFANKMDLRDA 821p 107 :DDVPMVLVGNKCDLAAR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 821p 124 :TVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREI Number of specific fragments extracted= 6 number of extra gaps= 0 total=972 Will force an alignment to be made, even if fragment is small Number of alignments=163 # Reading fragments from alignment file # Attempting to read fragment alignments from file 821p/T0308-821p-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 821p/T0308-821p-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 821p read from 821p/T0308-821p-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 821p in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLK 821p 3 :EYKLVVVGAPGVGKSALTIQLI T0308 24 :SNAQSQNILPTIG 821p 25 :QNHFVDEYDPTIE T0308 37 :FSIEKFKSSS 821p 39 :SYRKQVVIDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 821p 51 :CLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRV T0308 102 :IKHRRIPILFFANKMDLRDAV 821p 104 :KDSDDVPMVLVGNKCDLAART T0308 127 :VSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 821p 125 :VESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREI Number of specific fragments extracted= 6 number of extra gaps= 0 total=978 Will force an alignment to be made, even if fragment is small Number of alignments=164 # Reading fragments from alignment file # Attempting to read fragment alignments from file 821p/T0308-821p-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 821p/T0308-821p-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 821p read from 821p/T0308-821p-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 821p in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 821p 3 :EYKLVVVGAPGVGKSALTIQLIQNHF T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 821p 31 :EYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKD T0308 104 :HRRIPILFFANKMDLRDAVTS 821p 106 :SDDVPMVLVGNKCDLAARTVE T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 821p 127 :SRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREI Number of specific fragments extracted= 4 number of extra gaps= 0 total=982 Will force an alignment to be made, even if fragment is small Number of alignments=165 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1byuA/T0308-1byuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1byuA expands to /projects/compbio/data/pdb/1byu.pdb.gz 1byuA:# T0308 read from 1byuA/T0308-1byuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1byuA read from 1byuA/T0308-1byuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1byuA to template set # found chain 1byuA in template set Warning: unaligning (T0308)I35 because of BadResidue code BAD_PEPTIDE in next template residue (1byuA)E46 Warning: unaligning (T0308)G36 because of BadResidue code BAD_PEPTIDE at template residue (1byuA)E46 T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNAQSQNI 1byuA 11 :FKLVLVGDGGTGKTTFVKRHLTGEFEKKYV T0308 32 :LPT 1byuA 42 :TLG T0308 37 :FSIEKFKSSS 1byuA 47 :VHPLVFHTNR T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHP 1byuA 59 :IKFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVC T0308 105 :RRIPILFFANKMDLRDAVTSVKVSQLLC 1byuA 113 :ENIPIVLCGNKVDIKDRKVKAKSIVFHR T0308 138 :DKPWHICASDAIKGEGLQEGVDWLQDQI 1byuA 141 :KKNLQYYDISAKSNYNFEKPFLWLARKL Number of specific fragments extracted= 6 number of extra gaps= 1 total=988 Will force an alignment to be made, even if fragment is small Number of alignments=166 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1byuA/T0308-1byuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1byuA/T0308-1byuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1byuA read from 1byuA/T0308-1byuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1byuA in template set Warning: unaligning (T0308)F37 because of BadResidue code BAD_PEPTIDE in next template residue (1byuA)E46 Warning: unaligning (T0308)S38 because of BadResidue code BAD_PEPTIDE at template residue (1byuA)E46 T0308 2 :VHVLCLGLDNSGKTTIINKLK 1byuA 11 :FKLVLVGDGGTGKTTFVKRHL T0308 24 :SNAQ 1byuA 36 :EKKY T0308 32 :LPTIG 1byuA 40 :VPTLG T0308 39 :IEKFKS 1byuA 47 :VHPLVF T0308 45 :SS 1byuA 55 :NR T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 1byuA 59 :IKFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRV T0308 105 :RRIPILFFANKMDLRDAVTSVKVSQLL 1byuA 113 :ENIPIVLCGNKVDIKDRKVKAKSIVFH T0308 137 :KDKPWHICASDAIKGEGLQEGVDWLQDQI 1byuA 140 :RKKNLQYYDISAKSNYNFEKPFLWLARKL Number of specific fragments extracted= 8 number of extra gaps= 1 total=996 Will force an alignment to be made, even if fragment is small Number of alignments=167 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1byuA/T0308-1byuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1byuA/T0308-1byuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1byuA read from 1byuA/T0308-1byuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1byuA in template set Warning: unaligning (T0308)P33 because of BadResidue code BAD_PEPTIDE in next template residue (1byuA)E46 Warning: unaligning (T0308)T34 because of BadResidue code BAD_PEPTIDE at template residue (1byuA)E46 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1byuA 10 :QFKLVLVGDGGTGKTTFVKRHLTGEF T0308 27 :QSQNIL 1byuA 39 :YVPTLG T0308 35 :IGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1byuA 47 :VHPLVFHTNRGPIKFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCE T0308 106 :RIPILFFANKMDLRD 1byuA 114 :NIPIVLCGNKVDIKD T0308 121 :AVTS 1byuA 133 :AKSI T0308 134 :ENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1byuA 137 :VFHRKKNLQYYDISAKSNYNFEKPFLWLARKL Number of specific fragments extracted= 6 number of extra gaps= 1 total=1002 Will force an alignment to be made, even if fragment is small Number of alignments=168 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1n6hA/T0308-1n6hA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1n6hA expands to /projects/compbio/data/pdb/1n6h.pdb.gz 1n6hA:Skipped atom 165, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 167, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 169, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 175, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 177, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 179, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 181, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 187, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 189, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 191, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 193, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 195, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 197, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 199, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 272, because occupancy 0.300 <= existing 0.700 in 1n6hA Skipped atom 274, because occupancy 0.300 <= existing 0.700 in 1n6hA Skipped atom 276, because occupancy 0.300 <= existing 0.700 in 1n6hA Skipped atom 285, because occupancy 0.300 <= existing 0.700 in 1n6hA Skipped atom 362, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 364, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 366, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 874, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 876, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 878, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 880, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 882, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 893, because occupancy 0.300 <= existing 0.700 in 1n6hA Skipped atom 895, because occupancy 0.300 <= existing 0.700 in 1n6hA Skipped atom 1005, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 1007, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 1009, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 1011, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 1068, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 1070, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 1072, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 1074, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 1076, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 1082, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 1084, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 1086, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 1088, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 1090, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 1110, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 1112, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 1272, because occupancy 0.300 <= existing 0.700 in 1n6hA Skipped atom 1274, because occupancy 0.300 <= existing 0.700 in 1n6hA Skipped atom 1276, because occupancy 0.300 <= existing 0.700 in 1n6hA Skipped atom 1278, because occupancy 0.300 <= existing 0.700 in 1n6hA # T0308 read from 1n6hA/T0308-1n6hA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1n6hA read from 1n6hA/T0308-1n6hA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1n6hA to template set # found chain 1n6hA in template set T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1n6hA 21 :FKLVLLGESAVGKSSLVLRFVKGQF T0308 28 :SQNI 1n6hA 46 :HEFQ T0308 32 :LPTIGFSIEKFKSSS 1n6hA 52 :TIGAAFLTQTVCLDD T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1n6hA 69 :VKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQAS T0308 105 :RRIPILFFANKMDLRDAV 1n6hA 124 :PNIVIALSGNKADLANKR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1n6hA 142 :AVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKL Number of specific fragments extracted= 6 number of extra gaps= 0 total=1008 Will force an alignment to be made, even if fragment is small Number of alignments=169 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1n6hA/T0308-1n6hA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1n6hA/T0308-1n6hA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1n6hA read from 1n6hA/T0308-1n6hA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1n6hA in template set T0308 2 :VHVLCLGLDNSGKTTIINKLK 1n6hA 21 :FKLVLLGESAVGKSSLVLRFV T0308 24 :SNAQSQNILPTIG 1n6hA 42 :KGQFHEFQESTIG T0308 37 :FSIEKFKSSS 1n6hA 57 :FLTQTVCLDD T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 1n6hA 69 :VKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQ T0308 103 :KHRRIPILFFANKMDLRDAV 1n6hA 122 :ASPNIVIALSGNKADLANKR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1n6hA 142 :AVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKL Number of specific fragments extracted= 6 number of extra gaps= 0 total=1014 Will force an alignment to be made, even if fragment is small Number of alignments=170 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1n6hA/T0308-1n6hA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0308 read from 1n6hA/T0308-1n6hA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1n6hA read from 1n6hA/T0308-1n6hA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1n6hA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1n6hA 20 :QFKLVLLGESAVGKSSLVLRFVKGQF T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1n6hA 49 :QESTIGAAFLTQTVCLDDTTVKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQAS T0308 105 :RRIPILFFANKMDLRDAVTSV 1n6hA 124 :PNIVIALSGNKADLANKRAVD T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1n6hA 145 :FQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKL Number of specific fragments extracted= 4 number of extra gaps= 0 total=1018 Will force an alignment to be made, even if fragment is small Number of alignments=171 # command:CPU_time= 39.209 sec, elapsed time= 68.969 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 171 Adding 13530 constraints to all_contacts Done adding distance constraints # command:CPU_time= 39.350 sec, elapsed time= 69.120 sec. # command:Reading probabilities from T0308.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 119.525 Optimizing... Probability sum: -267.616, CN propb: -267.616 weights: 0.574 constraints: 415 # command:CPU_time= 52.333 sec, elapsed time= 82.175 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 415 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 415 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 635 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 635 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 11196 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 11196 # command:CPU_time= 52.554 sec, elapsed time= 82.587 sec. # command: