# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 1600 examples # computed average trans backbone unit before proline from 52 examples # trans (non-proline) backbone unit: # CA= -2.2097 1.0151 -0.0046 # O= -0.1488 2.2425 0.0020 # C= -0.6903 1.1357 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4580 -0.0000 -0.0000 # cis backbone unit: # CA= -0.1462 2.4515 0.0018 # O= -2.0272 0.9713 0.0022 # C= -0.8006 1.0755 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4659 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2063 1.0654 0.0002 # O= -0.1193 2.2442 0.0054 # C= -0.6842 1.1479 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4661 -0.0000 0.0000 # After reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz have 408 chains in training database # Count of chains,residues,atoms: 408,82794,639987 # 79931 residues have no bad marker # 573 residues lack atoms needed to compute omega # 313 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 0 # HAS_OXT 264 # TOO_MANY_ATOMS 0 # TOO_FEW_ATOMS 378 # HAS_UNKNOWN_ATOMS 0 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 148 # NON_PLANAR_PEPTIDE 17 # BAD_PEPTIDE 812 # HIGH_B_FACTOR 1566 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-40pc-3157.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to # command:# Making conformation for sequence T0561 numbered 1 through 161 Created new target T0561 from T0561.a2m # command:CPU_time= 5.742 sec, elapsed time= 9.193 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2dwkA/T0561-2dwkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2dwkA expands to /projects/compbio/data/pdb/2dwk.pdb.gz 2dwkA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0561 read from 2dwkA/T0561-2dwkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2dwkA read from 2dwkA/T0561-2dwkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2dwkA to template set # found chain 2dwkA in template set Warning: unaligning (T0561)K81 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2dwkA)N144 Warning: unaligning (T0561)E89 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2dwkA)N144 T0561 18 :AQLLDMWKQARARW 2dwkA 88 :MNLMNMAKLSIKGL # choosing archetypes in rotamer library T0561 39 :WAHMLALNP 2dwkA 102 :IESALNLGR T0561 52 :FLWKNQ 2dwkA 111 :TLDSDY T0561 62 :SAFFDLCEVGKQVMLGLLG 2dwkA 117 :APLQQFFVVMEHCLKHGLK T0561 90 :QAFWIMYAVHLSA 2dwkA 145 :KSFWGPLELVEKL Number of specific fragments extracted= 5 number of extra gaps= 0 total=5 Will force an alignment to be made, even if fragment is small Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2dwkA/T0561-2dwkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0561 read from 2dwkA/T0561-2dwkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2dwkA read from 2dwkA/T0561-2dwkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2dwkA in template set Warning: unaligning (T0561)K81 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2dwkA)N144 Warning: unaligning (T0561)E89 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2dwkA)N144 T0561 18 :AQLLDMWKQARARW 2dwkA 88 :MNLMNMAKLSIKGL T0561 39 :WAHMLALNPERK 2dwkA 102 :IESALNLGRTLD T0561 59 :EMNSAFFDLCEVGKQVMLGLLG 2dwkA 114 :SDYAPLQQFFVVMEHCLKHGLK T0561 90 :QAFWIMYAVHLSA 2dwkA 145 :KSFWGPLELVEKL Number of specific fragments extracted= 4 number of extra gaps= 0 total=9 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 2dwkA/T0561-2dwkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0561 read from 2dwkA/T0561-2dwkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2dwkA read from 2dwkA/T0561-2dwkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2dwkA in template set Warning: unaligning (T0561)K81 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2dwkA)N144 Warning: unaligning (T0561)E89 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2dwkA)N144 T0561 24 :WKQARARWLELVGKEWAHMLALNPERKD 2dwkA 87 :RMNLMNMAKLSIKGLIESALNLGRTLDS T0561 60 :MNSAFFDLCEVGKQVMLGLLG 2dwkA 115 :DYAPLQQFFVVMEHCLKHGLK T0561 90 :QAFWIMYAVHLSA 2dwkA 145 :KSFWGPLELVEKL Number of specific fragments extracted= 3 number of extra gaps= 0 total=12 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 1uj2A/T0561-1uj2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1uj2A expands to /projects/compbio/data/pdb/1uj2.pdb.gz 1uj2A:# T0561 read from 1uj2A/T0561-1uj2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1uj2A read from 1uj2A/T0561-1uj2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1uj2A to template set # found chain 1uj2A in template set Warning: unaligning (T0561)G77 because last residue in template chain is (1uj2A)G231 T0561 8 :DSEFLLHCISAQLLDM 1uj2A 158 :DADTRLSRRVLRDISE T0561 25 :KQARARWLELVGKEWAHMLALNPERKDFLWKNQSEMNSAFFDLCEVGKQVML 1uj2A 179 :EQILSQYITFVKPAFEEFCLPTKKYADVIIPRGADNLVAINLIVQHIQDILN Number of specific fragments extracted= 2 number of extra gaps= 0 total=14 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 1uj2A/T0561-1uj2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0561 read from 1uj2A/T0561-1uj2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1uj2A read from 1uj2A/T0561-1uj2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1uj2A in template set T0561 8 :DSEFLLHCISAQLLD 1uj2A 158 :DADTRLSRRVLRDIS T0561 25 :KQARARWLELVGKEWAHMLALNPERKDFLWKNQSEMNSAFFDLCEVGKQVML 1uj2A 179 :EQILSQYITFVKPAFEEFCLPTKKYADVIIPRGADNLVAINLIVQHIQDILN Number of specific fragments extracted= 2 number of extra gaps= 0 total=16 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 1uj2A/T0561-1uj2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0561 read from 1uj2A/T0561-1uj2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1uj2A read from 1uj2A/T0561-1uj2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1uj2A in template set Warning: unaligning (T0561)G77 because last residue in template chain is (1uj2A)G231 T0561 8 :DSEFLLHCISAQLLD 1uj2A 158 :DADTRLSRRVLRDIS T0561 24 :WKQARARWLELVGKEWAHMLALNPERKDFLWKNQSEMNSAFFDLCEVGKQVML 1uj2A 178 :LEQILSQYITFVKPAFEEFCLPTKKYADVIIPRGADNLVAINLIVQHIQDILN Number of specific fragments extracted= 2 number of extra gaps= 0 total=18 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 1xrjA/T0561-1xrjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xrjA expands to /projects/compbio/data/pdb/1xrj.pdb.gz 1xrjA:# T0561 read from 1xrjA/T0561-1xrjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xrjA read from 1xrjA/T0561-1xrjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xrjA to template set # found chain 1xrjA in template set Warning: unaligning (T0561)L76 because last residue in template chain is (1xrjA)N230 T0561 7 :LDSEFLLHCISAQLLD 1xrjA 157 :TDADTRLSRRVLRDIS T0561 25 :KQARARWLELVGKEWAHMLALNPERKDFLWKNQSEMNSAFFDLCEVGKQVM 1xrjA 179 :EQILSQYITFVKPAFEEFCLPTKKYADVIIPRGADNLVAINLIVQHIQDIL Number of specific fragments extracted= 2 number of extra gaps= 0 total=20 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 1xrjA/T0561-1xrjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0561 read from 1xrjA/T0561-1xrjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xrjA read from 1xrjA/T0561-1xrjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xrjA in template set T0561 8 :DSEFLLHCISAQLLD 1xrjA 158 :DADTRLSRRVLRDIS T0561 25 :KQARARWLELVGKEWAHMLALNPERKDFLWKNQSEMNSAFFDLCEVGKQVM 1xrjA 179 :EQILSQYITFVKPAFEEFCLPTKKYADVIIPRGADNLVAINLIVQHIQDIL Number of specific fragments extracted= 2 number of extra gaps= 0 total=22 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 1xrjA/T0561-1xrjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0561 read from 1xrjA/T0561-1xrjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xrjA read from 1xrjA/T0561-1xrjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xrjA in template set Warning: unaligning (T0561)G80 because last residue in template chain is (1xrjA)N230 T0561 8 :DSEFLLHCISAQLLDM 1xrjA 158 :DADTRLSRRVLRDISE T0561 25 :KQARARWLELVGKEWAHMLALNPERKDFLWKNQSEMNS 1xrjA 179 :EQILSQYITFVKPAFEEFCLPTKKYADVIIPRGADNLV T0561 67 :LCEVGKQVMLGLL 1xrjA 217 :AINLIVQHIQDIL Number of specific fragments extracted= 3 number of extra gaps= 0 total=25 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 2oa4A/T0561-2oa4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2oa4A expands to /projects/compbio/data/pdb/2oa4.pdb.gz 2oa4A:# T0561 read from 2oa4A/T0561-2oa4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2oa4A read from 2oa4A/T0561-2oa4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2oa4A to template set # found chain 2oa4A in template set T0561 67 :LCEVGKQVMLGLLG 2oa4A 39 :KIAVVRGVIYGLIT T0561 82 :EVALPKEEQAFWI 2oa4A 59 :TYGLSDEEFNSWV Number of specific fragments extracted= 2 number of extra gaps= 0 total=27 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 2oa4A/T0561-2oa4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0561 read from 2oa4A/T0561-2oa4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2oa4A read from 2oa4A/T0561-2oa4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2oa4A in template set T0561 67 :LCEVGKQVMLGLLG 2oa4A 39 :KIAVVRGVIYGLIT T0561 81 :KEVALPKEEQAFWI 2oa4A 58 :QTYGLSDEEFNSWV Number of specific fragments extracted= 2 number of extra gaps= 0 total=29 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 2oa4A/T0561-2oa4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0561 read from 2oa4A/T0561-2oa4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2oa4A read from 2oa4A/T0561-2oa4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2oa4A in template set T0561 67 :LCEVGKQVMLGLLG 2oa4A 39 :KIAVVRGVIYGLIT T0561 81 :KEVALPKEEQAFWI 2oa4A 58 :QTYGLSDEEFNSWV Number of specific fragments extracted= 2 number of extra gaps= 0 total=31 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 3a7sA/T0561-3a7sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3a7sA expands to /projects/compbio/data/pdb/3a7s.pdb.gz 3a7sA:# T0561 read from 3a7sA/T0561-3a7sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3a7sA read from 3a7sA/T0561-3a7sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3a7sA to template set # found chain 3a7sA in template set Warning: unaligning (T0561)G80 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3a7sA)A162 Warning: unaligning (T0561)S115 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3a7sA)A162 T0561 34 :LVGKEWAHMLALNPER 3a7sA 110 :TLSEFKEFSQSFDAAM T0561 61 :NSAFFDLCEVGKQVMLGLL 3a7sA 126 :KGLALSNSDVIRQVHNSFA T0561 116 :LRKLNVKLKD 3a7sA 163 :FHFVSYVPVN T0561 126 :FNFGGTRYFKDMPPEE 3a7sA 180 :GLREGPIDLGACNQDD T0561 142 :KKRRMER 3a7sA 201 :RPVIEKR T0561 152 :IEEARRHGMP 3a7sA 208 :IQKYSEGEIR Number of specific fragments extracted= 6 number of extra gaps= 0 total=37 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 3a7sA/T0561-3a7sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0561 read from 3a7sA/T0561-3a7sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3a7sA read from 3a7sA/T0561-3a7sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3a7sA in template set Warning: unaligning (T0561)G80 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3a7sA)A162 Warning: unaligning (T0561)S115 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3a7sA)A162 T0561 34 :LVGKEWAHMLALNPER 3a7sA 110 :TLSEFKEFSQSFDAAM T0561 61 :NSAFFDLCEVGKQVMLGLL 3a7sA 126 :KGLALSNSDVIRQVHNSFA T0561 116 :LRKLNVKLKD 3a7sA 163 :FHFVSYVPVN T0561 126 :FNFGGTRYFKDMPPEE 3a7sA 180 :GLREGPIDLGACNQDD T0561 142 :KKRRMERKQRIEE 3a7sA 201 :RPVIEKRIQKYSE Number of specific fragments extracted= 5 number of extra gaps= 0 total=42 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 3a7sA/T0561-3a7sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0561 read from 3a7sA/T0561-3a7sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3a7sA read from 3a7sA/T0561-3a7sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3a7sA in template set Warning: unaligning (T0561)A84 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3a7sA)A162 Warning: unaligning (T0561)S115 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3a7sA)A162 T0561 34 :LVGKEWAHMLALNPERKDFLWKNQSEMNSAFFDL 3a7sA 110 :TLSEFKEFSQSFDAAMKGLALSNSDVIRQVHNSF T0561 83 :V 3a7sA 144 :A T0561 116 :LRKLNVKLKD 3a7sA 163 :FHFVSYVPVN T0561 126 :FNFGGTRYFKDMPPEE 3a7sA 180 :GLREGPIDLGACNQDD T0561 142 :KKRR 3a7sA 201 :RPVI T0561 149 :KQRIEEARRHGMP 3a7sA 205 :EKRIQKYSEGEIR Number of specific fragments extracted= 6 number of extra gaps= 0 total=48 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 2avwA/T0561-2avwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2avwA expands to /projects/compbio/data/pdb/2avw.pdb.gz 2avwA:# T0561 read from 2avwA/T0561-2avwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2avwA read from 2avwA/T0561-2avwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2avwA to template set # found chain 2avwA in template set T0561 31 :WLELVGKEWAHMLALNPERKDFLWKNQS 2avwA 106 :WFDQNKDQIKRYLEEHPEKQKINFNGEQ T0561 59 :EMNSAF 2avwA 136 :DVKEAI T0561 77 :GLLGKEVA 2avwA 142 :DTKNHQLD Number of specific fragments extracted= 3 number of extra gaps= 0 total=51 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 2avwA/T0561-2avwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0561 read from 2avwA/T0561-2avwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2avwA read from 2avwA/T0561-2avwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2avwA in template set T0561 31 :WLELVGKEWAHMLALNPERKDFLWKNQSE 2avwA 106 :WFDQNKDQIKRYLEEHPEKQKINFNGEQM T0561 65 :FDL 2avwA 135 :FDV T0561 73 :QVMLGLLGKEVAL 2avwA 138 :KEAIDTKNHQLDS T0561 91 :AFWIMY 2avwA 151 :KLFEYF Number of specific fragments extracted= 4 number of extra gaps= 0 total=55 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 2avwA/T0561-2avwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0561 read from 2avwA/T0561-2avwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2avwA read from 2avwA/T0561-2avwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2avwA in template set T0561 31 :WLELVGKEWAHMLALNPERKDFLWKNQS 2avwA 106 :WFDQNKDQIKRYLEEHPEKQKINFNGEQ T0561 64 :FFDL 2avwA 134 :MFDV T0561 73 :QVMLGLLGKE 2avwA 138 :KEAIDTKNHQ Number of specific fragments extracted= 3 number of extra gaps= 0 total=58 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 1okcA/T0561-1okcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1okcA expands to /projects/compbio/data/pdb/1okc.pdb.gz 1okcA:# T0561 read from 1okcA/T0561-1okcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1okcA read from 1okcA/T0561-1okcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1okcA to template set # found chain 1okcA in template set T0561 9 :SEFLLHCISAQL 1okcA 156 :LGNCITKIFKSD T0561 21 :LDMWKQARARWLELVGKEWAHMLALNPERKDFL 1okcA 176 :FNVSVQGIIIYRAAYFGVYDTAKGMLPDPKNVH Number of specific fragments extracted= 2 number of extra gaps= 0 total=60 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 1okcA/T0561-1okcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0561 read from 1okcA/T0561-1okcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1okcA read from 1okcA/T0561-1okcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1okcA in template set T0561 11 :FLLHCISAQL 1okcA 158 :NCITKIFKSD T0561 21 :LDMWKQARARWLELVGKEWAHMLALNPERKDFL 1okcA 176 :FNVSVQGIIIYRAAYFGVYDTAKGMLPDPKNVH T0561 54 :WKNQSEMNSAFFDLCEVGKQVMLGLLG 1okcA 217 :QTVTAVAGLVSYPFDTVRRRMMMQSGR T0561 81 :KEVALPKE 1okcA 246 :ADIMYTGT T0561 102 :AACAEELHMEVAMS 1okcA 254 :VDCWRKIAKDEGPK Number of specific fragments extracted= 5 number of extra gaps= 0 total=65 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 1okcA/T0561-1okcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0561 read from 1okcA/T0561-1okcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1okcA read from 1okcA/T0561-1okcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1okcA in template set Number of specific fragments extracted= 0 number of extra gaps= 0 total=65 Will force an alignment to be made, even if fragment is small # Reading fragments from alignment file # Attempting to read fragment alignments from file 1svmA/T0561-1svmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1svmA expands to /projects/compbio/data/pdb/1svm.pdb.gz 1svmA:# T0561 read from 1svmA/T0561-1svmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1svmA read from 1svmA/T0561-1svmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1svmA to template set # found chain 1svmA in template set T0561 2 :EKKKYLDS 1svmA 332 :NQKTICQQ T0561 10 :EFLLHCISAQLLDM 1svmA 342 :DTVLAKKRVDSLQL T0561 24 :WKQARARWLELVGKEWAHMLAL 1svmA 357 :REQMLTNRFNDLLDRMDIMFGS T0561 57 :QSEMNSAFF 1svmA 379 :TGSADIEEW T0561 70 :VGKQVMLGLL 1svmA 388 :MAGVAWLHCL T0561 85 :LPKEEQAFWIMYAVHLS 1svmA 398 :LPKMDSVVYDFLKCMVY Number of specific fragments extracted= 6 number of extra gaps= 0 total=71 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 1svmA/T0561-1svmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0561 read from 1svmA/T0561-1svmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1svmA read from 1svmA/T0561-1svmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1svmA in template set T0561 3 :KKKYLDS 1svmA 333 :QKTICQQ T0561 10 :EFLLHCISAQLLDM 1svmA 342 :DTVLAKKRVDSLQL T0561 24 :WKQARARWLELVGKEWAHMLA 1svmA 357 :REQMLTNRFNDLLDRMDIMFG T0561 56 :NQSEM 1svmA 378 :STGSA T0561 62 :SAFFDLC 1svmA 383 :DIEEWMA T0561 71 :GKQVMLGLL 1svmA 390 :GVAWLHCLL T0561 86 :PKEEQAFWIMY 1svmA 399 :PKMDSVVYDFL Number of specific fragments extracted= 7 number of extra gaps= 0 total=78 Will force an alignment to be made, even if fragment is small Number of alignments=22 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1svmA/T0561-1svmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0561 read from 1svmA/T0561-1svmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1svmA read from 1svmA/T0561-1svmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1svmA in template set T0561 13 :LHCISAQLLDMWKQARA 1svmA 333 :QKTICQQAVDTVLAKKR T0561 40 :AHMLALN 1svmA 350 :VDSLQLT T0561 60 :MNSAFFDLCEVGKQVMLGLLGKEVALPK 1svmA 357 :REQMLTNRFNDLLDRMDIMFGSTGSADI T0561 91 :AFWIMYAVHLSA 1svmA 385 :EEWMAGVAWLHC Number of specific fragments extracted= 4 number of extra gaps= 0 total=82 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 2wa0A/T0561-2wa0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2wa0A expands to /projects/compbio/data/pdb/2wa0.pdb.gz 2wa0A:Skipped atom 111, because occupancy 0.5 <= existing 0.500 in 2wa0A Skipped atom 112, because occupancy 0.500 <= existing 0.500 in 2wa0A Skipped atom 198, because occupancy 0.500 <= existing 0.500 in 2wa0A Skipped atom 199, because occupancy 0.500 <= existing 0.500 in 2wa0A Skipped atom 200, because occupancy 0.500 <= existing 0.500 in 2wa0A Skipped atom 201, because occupancy 0.500 <= existing 0.500 in 2wa0A Skipped atom 202, because occupancy 0.500 <= existing 0.500 in 2wa0A Skipped atom 350, because occupancy 0.500 <= existing 0.500 in 2wa0A Skipped atom 351, because occupancy 0.500 <= existing 0.500 in 2wa0A Skipped atom 352, because occupancy 0.500 <= existing 0.500 in 2wa0A Skipped atom 353, because occupancy 0.500 <= existing 0.500 in 2wa0A # T0561 read from 2wa0A/T0561-2wa0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2wa0A read from 2wa0A/T0561-2wa0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2wa0A to template set # found chain 2wa0A in template set Warning: unaligning (T0561)P86 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2wa0A)S174 T0561 2 :EKKKYLDSEFLLHCI 2wa0A 0 :MDAESLFREALSNKV T0561 18 :AQLLDMWKQARA 2wa0A 115 :DELAHFLLRKYR T0561 36 :GKEWAHML 2wa0A 133 :KAEMLERV T0561 57 :QSEMNSAFFDLCEVGKQVMLGLLG 2wa0A 141 :IKNYKRCFPVIFGKASESLKMIFG T0561 81 :KEVAL 2wa0A 166 :DVKEV Number of specific fragments extracted= 5 number of extra gaps= 0 total=87 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 2wa0A/T0561-2wa0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0561 read from 2wa0A/T0561-2wa0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2wa0A read from 2wa0A/T0561-2wa0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2wa0A in template set Warning: unaligning (T0561)P86 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2wa0A)S174 T0561 13 :LHCISAQLLDMWKQARARWLELVGKE 2wa0A 103 :ESLFREALSNKVDELAHFLLRKYRAK T0561 39 :WAHMLAL 2wa0A 133 :KAEMLER T0561 56 :NQSEMNSAFFDLCEVGKQVMLGLLG 2wa0A 140 :VIKNYKRCFPVIFGKASESLKMIFG T0561 81 :KEVAL 2wa0A 166 :DVKEV Number of specific fragments extracted= 4 number of extra gaps= 0 total=91 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 2wa0A/T0561-2wa0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0561 read from 2wa0A/T0561-2wa0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2wa0A read from 2wa0A/T0561-2wa0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2wa0A in template set T0561 13 :LHCISAQLLDMWKQARARWLELVGK 2wa0A 103 :ESLFREALSNKVDELAHFLLRKYRA T0561 39 :WAHMLAL 2wa0A 133 :KAEMLER T0561 56 :NQSEMNSAFFDLCEVGKQVMLGLL 2wa0A 140 :VIKNYKRCFPVIFGKASESLKMIF Number of specific fragments extracted= 3 number of extra gaps= 0 total=94 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 2ap3A/T0561-2ap3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2ap3A expands to /projects/compbio/data/pdb/2ap3.pdb.gz 2ap3A:# T0561 read from 2ap3A/T0561-2ap3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ap3A read from 2ap3A/T0561-2ap3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2ap3A to template set # found chain 2ap3A in template set Warning: unaligning (T0561)L45 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ap3A)D104 Warning: unaligning (T0561)K50 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ap3A)D104 Warning: unaligning (T0561)D51 because of BadResidue code BAD_PEPTIDE at template residue (2ap3A)N105 T0561 8 :DSEFLLHCISAQL 2ap3A 60 :DTAVRGKAVKDLI T0561 21 :LDMWKQARARWLELVGKEWAHMLA 2ap3A 75 :ADDRLKEFEKEEDAIKKSEQDFKK T0561 52 :FL 2ap3A 106 :ID T0561 57 :QSEMNSAFFDLCEVGKQVMLGL 2ap3A 108 :NDVKRKEVKQLDDVLKEKYKLH T0561 90 :QAFWIMYAVHLSAA 2ap3A 130 :SDYAKAYKKAVNSE T0561 105 :AEELHM 2ap3A 144 :KTLFKY T0561 124 :K 2ap3A 151 :N T0561 134 :FKDMPPEEKKRRMERKQRIEEARRH 2ap3A 152 :QNDATQQGVNEKSKAIEQNYKKLKE Number of specific fragments extracted= 8 number of extra gaps= 0 total=102 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 2ap3A/T0561-2ap3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0561 read from 2ap3A/T0561-2ap3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ap3A read from 2ap3A/T0561-2ap3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ap3A in template set Warning: unaligning (T0561)R49 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ap3A)D104 Warning: unaligning (T0561)W54 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ap3A)D104 Warning: unaligning (T0561)K55 because of BadResidue code BAD_PEPTIDE at template residue (2ap3A)N105 T0561 9 :SEFLLH 2ap3A 61 :TAVRGK T0561 16 :ISAQLLDMWKQARAR 2ap3A 67 :AVKDLIKNADDRLKE T0561 32 :LELVGKEWAHMLALNPE 2ap3A 82 :FEKEEDAIKKSEQDFKK T0561 56 :N 2ap3A 106 :I T0561 57 :QSEMNSAFFDLCEVGKQVM 2ap3A 108 :NDVKRKEVKQLDDVLKEKY T0561 91 :AFWIM 2ap3A 127 :KLHSD T0561 100 :LSAACAEELHMEVAM 2ap3A 132 :YAKAYKKAVNSEKTL T0561 115 :SL 2ap3A 148 :KY T0561 123 :LK 2ap3A 150 :LN T0561 134 :FKDMPPEEKKRRME 2ap3A 152 :QNDATQQGVNEKSK T0561 148 :RKQRIEEARR 2ap3A 170 :NYKKLKEVSD Number of specific fragments extracted= 11 number of extra gaps= 0 total=113 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 2ap3A/T0561-2ap3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0561 read from 2ap3A/T0561-2ap3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ap3A read from 2ap3A/T0561-2ap3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ap3A in template set Warning: unaligning (T0561)L45 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ap3A)D104 Warning: unaligning (T0561)K50 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ap3A)D104 Warning: unaligning (T0561)D51 because of BadResidue code BAD_PEPTIDE at template residue (2ap3A)N105 T0561 10 :EFLLHCISA 2ap3A 62 :AVRGKAVKD T0561 19 :QLLDMWKQARARWLELVGKEWAHMLA 2ap3A 73 :KNADDRLKEFEKEEDAIKKSEQDFKK T0561 52 :FL 2ap3A 106 :ID T0561 57 :QSEMNSAFFDLCEVGKQVML 2ap3A 108 :NDVKRKEVKQLDDVLKEKYK T0561 88 :EEQAF 2ap3A 128 :LHSDY T0561 101 :SAACAEELHMEV 2ap3A 133 :AKAYKKAVNSEK T0561 113 :AMSLR 2ap3A 146 :LFKYL T0561 133 :YFKDMPPEEKKRRME 2ap3A 151 :NQNDATQQGVNEKSK T0561 148 :RKQRIEEARRH 2ap3A 170 :NYKKLKEVSDK Number of specific fragments extracted= 9 number of extra gaps= 0 total=122 Will force an alignment to be made, even if fragment is small Number of alignments=29 # command:CPU_time= 10.892 sec, elapsed time= 26.351 sec. # command:DEBUG: alignment library has 29 conformations DEBUG: current conformations has 0 conformations # in ExtractAlignmentsContacts extracting from alignment library using radius 8.000 separation >= 9 style evalue NUMB_ALIGNS: 29 # Adding 563 constraints to all_contacts Done adding distance constraints # command:CPU_time= 10.920 sec, elapsed time= 26.379 sec. # command:Reading probabilities from T0561.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 5.228 Optimizing... Probability sum: -290.574, CN propb: -290.574 weights: 0.206 constraints: 188 # command:CPU_time= 12.156 sec, elapsed time= 27.619 sec. # command:Found ConstraintSet # PrintContacts align.constraints Number of constraints in align 188 # command:Found ConstraintSet # PrintContacts align_bonus.constraints Number of constraints in align.bonus 188 # command:Found ConstraintSet # PrintContacts rejected.constraints Number of constraints in rejected 375 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints Number of constraints in rejected.bonus 375 # command:Found ConstraintSet # PrintContacts noncontact.constraints Number of constraints in noncontact 0 # command:Found ConstraintSet # PrintContacts noncontact_bonus.constraints Number of constraints in noncontact.bonus 0 # command:CPU_time= 12.165 sec, elapsed time= 28.111 sec. # command: