# 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 T0379 numbered 1 through 208 Created new target T0379 from T0379.a2m # command:CPU_time= 6.461 sec, elapsed time= 6.507 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fdrA/T0379-2fdrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2fdrA expands to /projects/compbio/data/pdb/2fdr.pdb.gz 2fdrA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 600, because occupancy 0.5 <= existing 0.500 in 2fdrA Skipped atom 602, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 604, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 606, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 608, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 610, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 612, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 614, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 616, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 618, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 620, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 709, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 711, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 713, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 715, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 717, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 719, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 721, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 723, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 725, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 751, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 753, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 755, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 757, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 759, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 761, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 763, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 765, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 767, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 769, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 771, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 773, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 775, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 777, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 779, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 781, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 783, because occupancy 0.500 <= existing 0.500 in 2fdrA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1330, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 1332, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 1334, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 1336, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 1338, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 1340, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 1342, because occupancy 0.500 <= existing 0.500 in 2fdrA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0379 read from 2fdrA/T0379-2fdrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fdrA read from 2fdrA/T0379-2fdrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2fdrA to template set # found chain 2fdrA in template set Warning: unaligning (T0379)F7 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fdrA)D10 Warning: unaligning (T0379)D8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fdrA)D10 T0379 2 :IRNIV 2fdrA 4 :FDLII # choosing archetypes in rotamer library T0379 9 :LGGVLIHLN 2fdrA 11 :CDGVLVDSE T0379 18 :REESIRRFKAIGVADIE 2fdrA 23 :AQVESRLLTEAGYPISV T0379 44 :GLFLDLESGRKSEE 2fdrA 40 :EEMGERFAGMTWKN T0379 59 :FRTELSRYIGKELT 2fdrA 54 :ILLQVESEASIPLS T0379 73 :YQQVYDALLGFL 2fdrA 71 :LDKSEKLLDMRL T0379 85 :EEISAEKFDYIDSLR 2fdrA 86 :VKIIDGVKFALSRLT T0379 102 :YRLFLLSNTNPYVLDLAMSPRF 2fdrA 101 :TPRCICSNSSSHRLDMMLTKVG T0379 130 :LDSFF 2fdrA 123 :LKPYF T0379 135 :DKVYASCQMG 2fdrA 129 :PHIYSAKDLG T0379 145 :KYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGENWIPAITRLLRE 2fdrA 141 :RVKPKPDIFLHGAAQFGVSPDRVVVVEDSVHGIHGARAAGMRVIGFTGASHTYPSHADRLTD Number of specific fragments extracted= 11 number of extra gaps= 1 total=11 Will force an alignment to be made, even if fragment is small Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fdrA/T0379-2fdrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 2fdrA/T0379-2fdrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fdrA read from 2fdrA/T0379-2fdrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fdrA in template set Warning: unaligning (T0379)F7 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fdrA)D10 Warning: unaligning (T0379)D8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fdrA)D10 T0379 2 :IRNIV 2fdrA 4 :FDLII T0379 9 :LGGVLIHLNREESIRRFKAIGVADIEEMLDPYLQKG 2fdrA 11 :CDGVLVDSEIIAAQVESRLLTEAGYPISVEEMGERF T0379 45 :LFLDLESGRKSEEEF 2fdrA 48 :GMTWKNILLQVESEA T0379 61 :TELS 2fdrA 63 :SIPL T0379 66 :YIGKELTYQQVYDALLGFLEEISAEKFDYIDSLR 2fdrA 67 :SASLLDKSEKLLDMRLERDVKIIDGVKFALSRLT T0379 102 :YRLFLLSNTNPYVLDLAMSPRF 2fdrA 101 :TPRCICSNSSSHRLDMMLTKVG T0379 130 :LDSFF 2fdrA 123 :LKPYF T0379 135 :DKVYASCQMGK 2fdrA 129 :PHIYSAKDLGA T0379 146 :YKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGENWIP 2fdrA 142 :VKPKPDIFLHGAAQFGVSPDRVVVVEDSVHGIHGARAAGMRVIGFTGASHTYP Number of specific fragments extracted= 9 number of extra gaps= 1 total=20 Will force an alignment to be made, even if fragment is small Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fdrA/T0379-2fdrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 2fdrA/T0379-2fdrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fdrA read from 2fdrA/T0379-2fdrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fdrA in template set Warning: unaligning (T0379)F7 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fdrA)D10 Warning: unaligning (T0379)D8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fdrA)D10 T0379 1 :MIRNIV 2fdrA 3 :GFDLII T0379 9 :LGGVLIHLNREESIRRFKAIGVADIEEMLDPYLQKGLFLDLESGRKSEEEFRTE 2fdrA 11 :CDGVLVDSEIIAAQVESRLLTEAGYPISVEEMGERFAGMTWKNILLQVESEASI T0379 67 :IGKELTYQQVYDALLGFLEEISAEKFDYIDSLR 2fdrA 68 :ASLLDKSEKLLDMRLERDVKIIDGVKFALSRLT T0379 103 :RLFLLSNTNPYVLDLAMS 2fdrA 102 :PRCICSNSSSHRLDMMLT T0379 127 :GRTLDSFF 2fdrA 120 :KVGLKPYF T0379 135 :DKVYASCQMGK 2fdrA 129 :PHIYSAKDLGA T0379 146 :YKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGENWIPAITRL 2fdrA 142 :VKPKPDIFLHGAAQFGVSPDRVVVVEDSVHGIHGARAAGMRVIGFTGASHTYPSHADR Number of specific fragments extracted= 7 number of extra gaps= 1 total=27 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 1x42A/T0379-1x42A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1x42A expands to /projects/compbio/data/pdb/1x42.pdb.gz 1x42A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0379 read from 1x42A/T0379-1x42A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1x42A read from 1x42A/T0379-1x42A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1x42A to template set # found chain 1x42A in template set T0379 1 :MIRNIVFDLGGVLIHLN 1x42A 1 :MIRAVFFDFVGTLLSVE T0379 18 :REESIRRFKAI 1x42A 38 :PKTLLDEYEKL T0379 44 :GLFLDLESGRK 1x42A 50 :REAFSNYAGKP T0379 55 :SEEEFRTELSRYIGKELT 1x42A 67 :IEEEVMRKLAEKYGFKYP T0379 73 :YQQVYDALLGF 1x42A 88 :WEIHLRMHQRY T0379 85 :EEISAEKFDYIDSLRPDYRLFLLSNTNPYVLDLAMSPRF 1x42A 99 :GELYPEVVEVLKSLKGKYHVGMITDSDTEYLMAHLDALG T0379 130 :LDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPA 1x42A 138 :IKDLFDSITTSEEAGFFKPHPRIFELALKKAGVKGEEAVYVGDNPV T0379 176 :NVATAERLGFHTYCPDNGENWIPAI 1x42A 185 :DCGGSKNLGMTSILLDRKGEKREFW T0379 201 :TRLLREQ 1x42A 223 :IKIVDEL Number of specific fragments extracted= 9 number of extra gaps= 0 total=36 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 1x42A/T0379-1x42A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1x42A/T0379-1x42A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1x42A read from 1x42A/T0379-1x42A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1x42A in template set T0379 1 :MIRNIVFDLGGVLI 1x42A 1 :MIRAVFFDFVGTLL T0379 16 :LNREESIRRFKAIGVA 1x42A 15 :SVEGEAKTHLKIMEEV T0379 32 :DIEEMLDPYLQKG 1x42A 33 :DYPLNPKTLLDEY T0379 49 :LESGRKSEEEF 1x42A 46 :EKLTREAFSNY T0379 60 :RTELSRYIGKELT 1x42A 65 :RDIEEEVMRKLAE T0379 73 :YQQVYDALLGFLEEISAEKFDYIDSLRPDYRLFLLSNTNPYVLDLAMSPRF 1x42A 87 :FWEIHLRMHQRYGELYPEVVEVLKSLKGKYHVGMITDSDTEYLMAHLDALG T0379 130 :LDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGP 1x42A 138 :IKDLFDSITTSEEAGFFKPHPRIFELALKKAGVKGEEAVYVGDNP T0379 175 :ANVATAERLGFHTYCPDNGENWIP 1x42A 184 :KDCGGSKNLGMTSILLDRKGEKRE T0379 199 :AITRLLRE 1x42A 221 :EVIKIVDE Number of specific fragments extracted= 9 number of extra gaps= 0 total=45 Will force an alignment to be made, even if fragment is small Number of alignments=5 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1x42A/T0379-1x42A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1x42A/T0379-1x42A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1x42A read from 1x42A/T0379-1x42A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1x42A in template set T0379 1 :MIRNIVFDLGGVLIHLNREESIRRFKAIGVAD 1x42A 1 :MIRAVFFDFVGTLLSVEGEAKTHLKIMEEVLG T0379 33 :IEEMLDPYLQKGLFLDLESGRKSEEEFRTELSRY 1x42A 45 :YEKLTREAFSNYAGKPYRPIRDIEEEVMRKLAEK T0379 67 :IGKELTYQQVYDALLGFLEEISAEKFDYIDSLRPDYRLFLLSNTNPYVLDLAMS 1x42A 81 :FKYPENFWEIHLRMHQRYGELYPEVVEVLKSLKGKYHVGMITDSDTEYLMAHLD T0379 127 :GRTLDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGP 1x42A 135 :ALGIKDLFDSITTSEEAGFFKPHPRIFELALKKAGVKGEEAVYVGDNP T0379 175 :ANVATAERLGFHTYCPDNGENWIPAI 1x42A 184 :KDCGGSKNLGMTSILLDRKGEKREFW Number of specific fragments extracted= 5 number of extra gaps= 0 total=50 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 1zrn/T0379-1zrn-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zrn expands to /projects/compbio/data/pdb/1zrn.pdb.gz 1zrn:Warning: there is no chain 1zrn will retry with 1zrnA # T0379 read from 1zrn/T0379-1zrn-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zrn read from 1zrn/T0379-1zrn-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zrn to template set # found chain 1zrn in template set T0379 2 :IRNIVFDLGGVLIHLN 1zrn 4 :IKGIAFDLYGTLFDVH T0379 18 :REESIRRFKAI 1zrn 33 :GREISALWRQK T0379 44 :GLFLDLESGRK 1zrn 47 :YTWLRSLMNRY T0379 55 :SEEEFRTELSRYIGKELTYQQ 1zrn 63 :ATEDALRFTCRHLGLDLDART T0379 77 :YDALLGFL 1zrn 84 :RSTLCDAY T0379 85 :EEISAEKFDYIDSLR 1zrn 94 :LAPFSEVPDSLRELK T0379 100 :PDYRLFLLSNTNPYVLDLAMSPRF 1zrn 110 :RGLKLAILSNGSPQSIDAVVSHAG T0379 130 :LDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGENWIPAI 1zrn 134 :LRDGFDHLLSVDPVQVYKPDNRVYELAEQALGLDRSAILFVASNAWDATGARYFGFPTCWINRTGNVFEEM T0379 201 :TRLLREQ 1zrn 215 :LRAVVEL Number of specific fragments extracted= 9 number of extra gaps= 0 total=59 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 1zrn/T0379-1zrn-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1zrn/T0379-1zrn-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zrn read from 1zrn/T0379-1zrn-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zrn in template set T0379 2 :IRNIVFDLGGVLIHLNRE 1zrn 4 :IKGIAFDLYGTLFDVHSV T0379 20 :ESIRRFKAIGV 1zrn 33 :GREISALWRQK T0379 36 :MLDPYLQKGLFLDLESGRKSEEEFRTELSRYIGK 1zrn 44 :QLEYTWLRSLMNRYVNFQQATEDALRFTCRHLGL T0379 70 :ELTYQQVYDALLGFL 1zrn 80 :DARTRSTLCDAYLRL T0379 86 :EISAEKFDYIDSLRP 1zrn 95 :APFSEVPDSLRELKR T0379 101 :DYRLFLLSNTNPYVLDLAMSPRF 1zrn 111 :GLKLAILSNGSPQSIDAVVSHAG T0379 130 :LDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGENWIP 1zrn 134 :LRDGFDHLLSVDPVQVYKPDNRVYELAEQALGLDRSAILFVASNAWDATGARYFGFPTCWINRTGNVFE T0379 199 :AITRLLRE 1zrn 214 :SLRAVVEL Number of specific fragments extracted= 8 number of extra gaps= 0 total=67 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 1zrn/T0379-1zrn-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1zrn/T0379-1zrn-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zrn read from 1zrn/T0379-1zrn-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zrn in template set T0379 1 :MIRNIVFDLGGVLIHLNREESIRRFKAIGVAD 1zrn 3 :YIKGIAFDLYGTLFDVHSVVGRCDEAFPGRGR T0379 33 :IEEMLDPYLQKGLFLDLES 1zrn 36 :ISALWRQKQLEYTWLRSLM T0379 52 :GRKSEEEFRTELSRY 1zrn 60 :FQQATEDALRFTCRH T0379 67 :IGKELTYQQVYDA 1zrn 78 :DLDARTRSTLCDA T0379 82 :GFLEEISAEKFDYIDSLR 1zrn 91 :YLRLAPFSEVPDSLRELK T0379 100 :PDYRLFLLSNTNPYVLDLAMS 1zrn 110 :RGLKLAILSNGSPQSIDAVVS T0379 127 :GRTLDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGEN 1zrn 131 :HAGLRDGFDHLLSVDPVQVYKPDNRVYELAEQALGLDRSAILFVASNAWDATGARYFGFPTCWINRTGN Number of specific fragments extracted= 7 number of extra gaps= 0 total=74 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 2gfhA/T0379-2gfhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2gfhA expands to /projects/compbio/data/pdb/2gfh.pdb.gz 2gfhA:Skipped atom 62, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 66, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 68, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 70, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 72, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 74, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 76, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 78, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 789, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 793, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 795, because occupancy 0.500 <= existing 0.500 in 2gfhA # T0379 read from 2gfhA/T0379-2gfhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gfhA read from 2gfhA/T0379-2gfhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2gfhA to template set # found chain 2gfhA in template set Warning: unaligning (T0379)F7 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gfhA)D12 Warning: unaligning (T0379)D8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gfhA)D12 Warning: unaligning (T0379)K54 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gfhA)C67 T0379 2 :IRNIV 2gfhA 6 :VRAVF T0379 9 :LGGVLIHLN 2gfhA 13 :LDNTLIDTA T0379 18 :REESIRRFKAI 2gfhA 28 :MLEVIKLLQSK T0379 29 :GVA 2gfhA 40 :HYK T0379 44 :GLF 2gfhA 43 :EEA T0379 55 :SEEEFRTELSRYIG 2gfhA 68 :ITDVRTSHWEEAIQ T0379 69 :KELTYQ 2gfhA 86 :GADNRK T0379 75 :QVYDALLGFL 2gfhA 95 :ECYFLWKSTR T0379 85 :EEISAEKFDYIDSLRPDYRLFLLSNTNPYVLDLAMSPRF 2gfhA 108 :MILADDVKAMLTELRKEVRLLLLTNGDRQTQREKIEACA T0379 130 :LDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPA 2gfhA 147 :CQSYFDAIVIGGEQKEEKPAPSIFYHCCDLLGVQPGDCVMVGDTLE T0379 176 :NVATAERLGF 2gfhA 194 :DIQGGLNAGL T0379 186 :HTYCPDNGENWIPAI 2gfhA 205 :ATVWINKSGRVPLTS Number of specific fragments extracted= 12 number of extra gaps= 1 total=86 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 2gfhA/T0379-2gfhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 2gfhA/T0379-2gfhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gfhA read from 2gfhA/T0379-2gfhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gfhA in template set Warning: unaligning (T0379)F7 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gfhA)D12 Warning: unaligning (T0379)D8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gfhA)D12 Warning: unaligning (T0379)E50 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gfhA)C67 T0379 2 :IRNIV 2gfhA 6 :VRAVF T0379 9 :LGGVLIHLNREESIRRFKAIGVA 2gfhA 13 :LDNTLIDTAGASRRGMLEVIKLL T0379 32 :DIEEMLDPYLQKGLF 2gfhA 40 :HYKEEAEIICDKVQV T0379 51 :SGRKSEEEFRTELSRYI 2gfhA 68 :ITDVRTSHWEEAIQETK T0379 68 :GKELTYQQVYDALLGFLEEISAEKFDYIDSLRPDYRLFLLSNTNPYVLDLAMSPRF 2gfhA 91 :KLAEECYFLWKSTRLQHMILADDVKAMLTELRKEVRLLLLTNGDRQTQREKIEACA T0379 130 :LDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGP 2gfhA 147 :CQSYFDAIVIGGEQKEEKPAPSIFYHCCDLLGVQPGDCVMVGDTL T0379 175 :ANVATAERLGF 2gfhA 193 :TDIQGGLNAGL T0379 186 :HTYCPDNGENWIP 2gfhA 205 :ATVWINKSGRVPL T0379 199 :AITRLLRE 2gfhA 232 :ELPALLQS Number of specific fragments extracted= 9 number of extra gaps= 1 total=95 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 2gfhA/T0379-2gfhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 2gfhA/T0379-2gfhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gfhA read from 2gfhA/T0379-2gfhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gfhA in template set Warning: unaligning (T0379)F7 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gfhA)D12 Warning: unaligning (T0379)D8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gfhA)D12 Warning: unaligning (T0379)E50 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gfhA)C67 T0379 1 :MIRNIV 2gfhA 5 :RVRAVF T0379 9 :LGGVLIHLNREESIRRFKAIG 2gfhA 13 :LDNTLIDTAGASRRGMLEVIK T0379 30 :VADIEEMLDPYLQKGLFLDL 2gfhA 38 :KYHYKEEAEIICDKVQVKLS T0379 51 :SGRKSEEEFRTELSRY 2gfhA 68 :ITDVRTSHWEEAIQET T0379 67 :IGKELTYQQVYDALLGFLEEISAEKFDYIDSLRPDYRLFLLSNTNPYVLDLAMS 2gfhA 90 :RKLAEECYFLWKSTRLQHMILADDVKAMLTELRKEVRLLLLTNGDRQTQREKIE T0379 127 :GRTLDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGP 2gfhA 144 :ACACQSYFDAIVIGGEQKEEKPAPSIFYHCCDLLGVQPGDCVMVGDTL T0379 175 :ANVATAERLGFHTYCPDNGEN 2gfhA 193 :TDIQGGLNAGLKATVWINKSG Number of specific fragments extracted= 7 number of extra gaps= 1 total=102 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 1te2A/T0379-1te2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1te2A expands to /projects/compbio/data/pdb/1te2.pdb.gz 1te2A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 75, because occupancy 0.500 <= existing 0.500 in 1te2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 79, because occupancy 0.470 <= existing 0.530 in 1te2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 83, because occupancy 0.490 <= existing 0.510 in 1te2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 87, because occupancy 0.440 <= existing 0.560 in 1te2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 89, because occupancy 0.420 <= existing 0.580 in 1te2A Skipped atom 203, because occupancy 0.500 <= existing 0.500 in 1te2A Skipped atom 205, because occupancy 0.500 <= existing 0.500 in 1te2A Skipped atom 207, because occupancy 0.500 <= existing 0.500 in 1te2A Skipped atom 209, because occupancy 0.500 <= existing 0.500 in 1te2A Skipped atom 213, because occupancy 0.450 <= existing 0.550 in 1te2A Skipped atom 215, because occupancy 0.480 <= existing 0.520 in 1te2A Skipped atom 217, because occupancy 0.480 <= existing 0.520 in 1te2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 412, because occupancy 0.500 <= existing 0.500 in 1te2A Skipped atom 416, because occupancy 0.500 <= existing 0.500 in 1te2A Skipped atom 418, because occupancy 0.500 <= existing 0.500 in 1te2A Skipped atom 420, because occupancy 0.480 <= existing 0.520 in 1te2A Skipped atom 424, because occupancy 0.500 <= existing 0.500 in 1te2A Skipped atom 426, because occupancy 0.490 <= existing 0.510 in 1te2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 538, because occupancy 0.500 <= existing 0.500 in 1te2A Skipped atom 540, because occupancy 0.500 <= existing 0.500 in 1te2A Skipped atom 542, because occupancy 0.500 <= existing 0.500 in 1te2A Skipped atom 544, because occupancy 0.490 <= existing 0.510 in 1te2A Skipped atom 546, because occupancy 0.500 <= existing 0.500 in 1te2A Skipped atom 552, because occupancy 0.480 <= existing 0.520 in 1te2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 996, because occupancy 0.500 <= existing 0.500 in 1te2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 998, because occupancy 0.490 <= existing 0.510 in 1te2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1000, because occupancy 0.500 <= existing 0.500 in 1te2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0379 read from 1te2A/T0379-1te2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1te2A read from 1te2A/T0379-1te2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1te2A to template set # found chain 1te2A in template set Warning: unaligning (T0379)P121 because of BadResidue code BAD_PEPTIDE in next template residue (1te2A)F129 Warning: unaligning (T0379)R122 because of BadResidue code BAD_PEPTIDE at template residue (1te2A)F129 T0379 2 :IRNIVFDLGGVLIHLN 1te2A 7 :ILAAIFDMDGLLIDSE T0379 18 :REESIRRFKAIGVADIEEMLDPY 1te2A 26 :DRAELDVMASLGVDISRRNELPD T0379 50 :ESGRKSEE 1te2A 49 :TLGLRIDM T0379 59 :FRTELSRYIG 1te2A 57 :VVDLWYARQP T0379 69 :KELTYQQVYDALLGFL 1te2A 68 :NGPSRQEVVERVIARA T0379 85 :EEISAEKFDYIDSLR 1te2A 91 :RPLLPGVREAVALCK T0379 100 :PDYRLFLLSNTNPYVLDLAMS 1te2A 107 :QGLLVGLASASPLHMLEKVLT T0379 123 :F 1te2A 130 :D T0379 130 :LDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPD 1te2A 131 :LRDSFDALASAEKLPYSKPHPQVYLDCAAKLGVDPLTCVALEDSVNGMIASKAARMRSIVVP T0379 192 :NGENWIPAI 1te2A 194 :PEAQNDPRF T0379 201 :TRLLREQK 1te2A 209 :LSSLTELT Number of specific fragments extracted= 11 number of extra gaps= 1 total=113 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 1te2A/T0379-1te2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1te2A/T0379-1te2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1te2A read from 1te2A/T0379-1te2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1te2A in template set Warning: unaligning (T0379)P121 because of BadResidue code BAD_PEPTIDE in next template residue (1te2A)F129 Warning: unaligning (T0379)R122 because of BadResidue code BAD_PEPTIDE at template residue (1te2A)F129 T0379 2 :IRNIVFDLGGVLIHLNREESIRRFKAIGVADIEEM 1te2A 7 :ILAAIFDMDGLLIDSEPLWDRAELDVMASLGVDIS T0379 37 :LDPYLQKGLFLDLESGRKSEEEFRTELSRYIGKELTYQQVYDALLGFLEEISAEKFDYIDSLRP 1te2A 43 :RNELPDTLGLRIDMVVDLWYARQPWNGPSRQEVVERVIARAISLVEETRPLLPGVREAVALCKE T0379 101 :DYRLFLLSNTNPYVLDLAMS 1te2A 108 :GLLVGLASASPLHMLEKVLT T0379 123 :F 1te2A 130 :D T0379 130 :LDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGENWIP 1te2A 131 :LRDSFDALASAEKLPYSKPHPQVYLDCAAKLGVDPLTCVALEDSVNGMIASKAARMRSIVVPAPEAQND T0379 200 :ITRLLR 1te2A 209 :LSSLTE Number of specific fragments extracted= 6 number of extra gaps= 1 total=119 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 1te2A/T0379-1te2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1te2A/T0379-1te2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1te2A read from 1te2A/T0379-1te2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1te2A in template set Warning: unaligning (T0379)G127 because of BadResidue code BAD_PEPTIDE in next template residue (1te2A)F129 Warning: unaligning (T0379)R128 because of BadResidue code BAD_PEPTIDE at template residue (1te2A)F129 T0379 1 :MIRNIVFDLGGVLIHLNREESIRRFKAIGVADIEEMLDPYLQKGLFLD 1te2A 6 :QILAAIFDMDGLLIDSEPLWDRAELDVMASLGVDISRRNELPDTLGLR T0379 52 :GRKSEEEFRTELSRY 1te2A 54 :IDMVVDLWYARQPWN T0379 67 :IGKELTYQQVYDALLGFLEEISAEKFDYIDSLR 1te2A 73 :QEVVERVIARAISLVEETRPLLPGVREAVALCK T0379 100 :PDYRLFLLSNTNPYVLDLAMS 1te2A 107 :QGLLVGLASASPLHMLEKVLT T0379 129 :TLDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNG 1te2A 130 :DLRDSFDALASAEKLPYSKPHPQVYLDCAAKLGVDPLTCVALEDSVNGMIASKAARMRSIVVPAP Number of specific fragments extracted= 5 number of extra gaps= 1 total=124 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 1o08A/T0379-1o08A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1o08A/T0379-1o08A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o08A read from 1o08A/T0379-1o08A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1o08A in training set Warning: unaligning (T0379)F7 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o08A)D1008 Warning: unaligning (T0379)D8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o08A)D1008 T0379 1 :MIRNIV 1o08A 1001 :MFKAVL T0379 9 :LGGVLIHLN 1o08A 1009 :LDGVITDTA T0379 18 :REESIRRFKAIGVADI 1o08A 1021 :FRAWKALAEEIGINGV T0379 44 :GLFLDLESGRKSEEEFRTELSRYIGKELTYQQ 1o08A 1037 :DRQFNEQLKGVSREDSLQKILDLADKKVSAEE T0379 76 :VYDALLGFL 1o08A 1072 :LAKRKNDNY T0379 85 :EEISAEKFDYIDSLR 1o08A 1090 :ADVYPGILQLLKDLR T0379 100 :PDYRLFLLSNT 1o08A 1106 :NKIKIALASAS T0379 113 :YVLDLAMSPRF 1o08A 1117 :KNGPFLLERMN T0379 130 :LDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGENWIPAI 1o08A 1128 :LTGYFDAIADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQAGIQAIKDSGALPIGVGRPEDLGDDI T0379 201 :TRLLRE 1o08A 1209 :LEFLKE Number of specific fragments extracted= 10 number of extra gaps= 1 total=134 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 1o08A/T0379-1o08A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1o08A/T0379-1o08A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o08A read from 1o08A/T0379-1o08A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1o08A in training set Warning: unaligning (T0379)F7 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o08A)D1008 Warning: unaligning (T0379)D8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o08A)D1008 T0379 1 :MIRNIV 1o08A 1001 :MFKAVL T0379 9 :LGGVLIHLNREESIRRFKAIGVADIEEMLDPYLQKG 1o08A 1009 :LDGVITDTAEYHFRAWKALAEEIGINGVDRQFNEQL T0379 45 :LFLDLESGRKSEEEF 1o08A 1046 :GVSREDSLQKILDLA T0379 62 :ELSRYIGKELTYQQVYDALLGFL 1o08A 1065 :SAEEFKELAKRKNDNYVKMIQDV T0379 85 :EEISAEKFDYIDSLRP 1o08A 1090 :ADVYPGILQLLKDLRS T0379 101 :DYRLFLLSNT 1o08A 1107 :KIKIALASAS T0379 113 :YVLDLAMSPRF 1o08A 1117 :KNGPFLLERMN T0379 130 :LDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGENWIP 1o08A 1128 :LTGYFDAIADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQAGIQAIKDSGALPIGVGRPEDLGD T0379 199 :AITRLLR 1o08A 1211 :FLKEVWL Number of specific fragments extracted= 9 number of extra gaps= 1 total=143 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 1o08A/T0379-1o08A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1o08A/T0379-1o08A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o08A read from 1o08A/T0379-1o08A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1o08A in training set Warning: unaligning (T0379)F7 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o08A)D1008 Warning: unaligning (T0379)D8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o08A)D1008 T0379 1 :MIRNIV 1o08A 1001 :MFKAVL T0379 9 :LGGVLIHLNREESIRRFKAIGVADIEEMLDPYLQKGLFLDLESGRKSEEEFRTELSRYIGKELTYQQVYDALLGFLEE 1o08A 1009 :LDGVITDTAEYHFRAWKALAEEIGINGVDRQFNEQLKGVSREDSLQKILDLADKKVSAEEFKELAKRKNDNYVKMIQD T0379 87 :ISAEKFDYIDSLR 1o08A 1092 :VYPGILQLLKDLR T0379 100 :PDYRLFLLSNTNP 1o08A 1106 :NKIKIALASASKN T0379 115 :LDLAMS 1o08A 1119 :GPFLLE T0379 127 :GRTLDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGENWIP 1o08A 1125 :RMNLTGYFDAIADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQAGIQAIKDSGALPIGVGRPEDLGD Number of specific fragments extracted= 6 number of extra gaps= 1 total=149 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 1jud/T0379-1jud-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1jud expands to /projects/compbio/data/pdb/1jud.pdb.gz 1jud:Warning: there is no chain 1jud will retry with 1judA # T0379 read from 1jud/T0379-1jud-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jud read from 1jud/T0379-1jud-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1jud to template set # found chain 1jud in template set T0379 2 :IRNIVFDLGGVLIHLN 1jud 4 :IKGIAFDLYGTLFDVH T0379 18 :REESIRRFKAI 1jud 33 :GREISALWRQK T0379 44 :GLFLDLESGRK 1jud 47 :YTWLRSLMNRY T0379 55 :SEEEFRTELSRYIGKELTYQQ 1jud 63 :ATEDALRFTCRHLGLDLDART T0379 77 :YDALLGFL 1jud 84 :RSTLCDAY T0379 85 :EEISAEKFDYIDSLR 1jud 94 :LAPFSEVPDSLRELK T0379 100 :PDYRLFLLSNTNPYVLDLAMSPRF 1jud 110 :RGLKLAILSNGSPQSIDAVVSHAG T0379 130 :LDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGENWIPAI 1jud 134 :LRDGFDHLLSVDPVQVYKPDNRVYELAEQALGLDRSAILFVSSNAWDATGARYFGFPTCWINRTGNVFEEM T0379 201 :TRLLREQK 1jud 215 :LRAVVELF Number of specific fragments extracted= 9 number of extra gaps= 0 total=158 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 1jud/T0379-1jud-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1jud/T0379-1jud-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jud read from 1jud/T0379-1jud-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jud in template set Warning: unaligning (T0379)Q207 because last residue in template chain is (1jud)F222 T0379 2 :IRNIVFDLGGVLIHLNREESIRRFK 1jud 4 :IKGIAFDLYGTLFDVHSVVGRCDEA T0379 33 :IEEMLDPYLQKGLFLDLESGRKSEEEF 1jud 29 :FPGRGREISALWRQKQLEYTWLRSLMN T0379 60 :RTELSRYIGK 1jud 68 :LRFTCRHLGL T0379 70 :ELTYQQVYDALLGFL 1jud 80 :DARTRSTLCDAYLRL T0379 86 :EISAEKFDYIDSLRP 1jud 95 :APFSEVPDSLRELKR T0379 101 :DYRLFLLSNTNPYVLDLAMSPRF 1jud 111 :GLKLAILSNGSPQSIDAVVSHAG T0379 130 :LDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGENWIP 1jud 134 :LRDGFDHLLSVDPVQVYKPDNRVYELAEQALGLDRSAILFVSSNAWDATGARYFGFPTCWINRTGNVFE T0379 199 :AITRLLRE 1jud 214 :SLRAVVEL Number of specific fragments extracted= 8 number of extra gaps= 0 total=166 Will force an alignment to be made, even if fragment is small Number of alignments=20 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jud/T0379-1jud-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1jud/T0379-1jud-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jud read from 1jud/T0379-1jud-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jud in template set T0379 1 :MIRNIVFDLGGVLIHLNREESIRR 1jud 3 :YIKGIAFDLYGTLFDVHSVVGRCD T0379 26 :KAIGVAD 1jud 27 :EAFPGRG T0379 33 :IEEMLDPYLQKGLFLDLESG 1jud 36 :ISALWRQKQLEYTWLRSLMN T0379 53 :RKSEEEFRTE 1jud 61 :QQATEDALRF T0379 67 :IGKELTYQQVYDA 1jud 78 :DLDARTRSTLCDA T0379 82 :GFLEEISAEKFDYIDSLR 1jud 91 :YLRLAPFSEVPDSLRELK T0379 100 :PDYRLFLLSNTNPYVLDLAMS 1jud 110 :RGLKLAILSNGSPQSIDAVVS T0379 127 :GRTLDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGEN 1jud 131 :HAGLRDGFDHLLSVDPVQVYKPDNRVYELAEQALGLDRSAILFVSSNAWDATGARYFGFPTCWINRTGN Number of specific fragments extracted= 8 number of extra gaps= 0 total=174 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 2ah5A/T0379-2ah5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2ah5A expands to /projects/compbio/data/pdb/2ah5.pdb.gz 2ah5A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0379 read from 2ah5A/T0379-2ah5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ah5A read from 2ah5A/T0379-2ah5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2ah5A to template set # found chain 2ah5A in template set Warning: unaligning (T0379)N109 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ah5A)K108 Warning: unaligning (T0379)T110 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ah5A)K108 T0379 1 :M 2ah5A 1 :M T0379 2 :IRNIVFDLGGVLIHLN 2ah5A 4 :ITAIFFDLDGTLVDSS T0379 18 :REESIRRFKAI 2ah5A 22 :IHNAFTYTFKE T0379 29 :GVADIE 2ah5A 34 :GVPSPD T0379 44 :GLFLDLESGRK 2ah5A 40 :AKTIRGFMGPP T0379 59 :FRTELSRYIG 2ah5A 51 :LESSFATCLS T0379 70 :ELTYQQVYDALLGFL 2ah5A 61 :KDQISEAVQIYRSYY T0379 85 :EEISAEKFDYIDSLRPDYRLFLLS 2ah5A 83 :AQLFPQIIDLLEELSSSYPLYITT T0379 111 :NPYVLDLAMSPRF 2ah5A 109 :DTSTAQDMAKNLE T0379 130 :LDSFFDKVYASCQMGKYK 2ah5A 122 :IHHFFDGIYGSSPEAPHK T0379 150 :EDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGENWIPAI 2ah5A 140 :ADVIHQALQTHQLAPEQAIIIGDTKFDMLGARETGIQKLAITWGFGEQADL Number of specific fragments extracted= 11 number of extra gaps= 1 total=185 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 2ah5A/T0379-2ah5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 2ah5A/T0379-2ah5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ah5A read from 2ah5A/T0379-2ah5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ah5A in template set Warning: unaligning (T0379)N109 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ah5A)K108 Warning: unaligning (T0379)T110 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ah5A)K108 T0379 1 :M 2ah5A 1 :M T0379 2 :IRNIVFDLGGVLIHLNREESIRRFKAIGVADIE 2ah5A 4 :ITAIFFDLDGTLVDSSIGIHNAFTYTFKELGVP T0379 35 :EMLDPYLQKGLFLDLESGRKSEEE 2ah5A 38 :PDAKTIRGFMGPPLESSFATCLSK T0379 64 :SRYIGKELTYQQVYDALLGFLEEISAEKFDYIDSLRPDYRLFLLS 2ah5A 62 :DQISEAVQIYRSYYKAKGIYEAQLFPQIIDLLEELSSSYPLYITT T0379 111 :NPYVLDLAMSPRF 2ah5A 109 :DTSTAQDMAKNLE T0379 130 :LDSFFDKVYASCQMGKYK 2ah5A 122 :IHHFFDGIYGSSPEAPHK T0379 150 :EDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGENWIPAITR 2ah5A 140 :ADVIHQALQTHQLAPEQAIIIGDTKFDMLGARETGIQKLAITWGFGEQADLLN Number of specific fragments extracted= 7 number of extra gaps= 1 total=192 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 2ah5A/T0379-2ah5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 2ah5A/T0379-2ah5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ah5A read from 2ah5A/T0379-2ah5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ah5A in template set Warning: unaligning (T0379)N109 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ah5A)K108 Warning: unaligning (T0379)T110 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ah5A)K108 T0379 2 :IRNIVFDLGGVLIHLNREESIRRFKAIGVADIEEMLDPYLQKGLFLDLESGRKS 2ah5A 4 :ITAIFFDLDGTLVDSSIGIHNAFTYTFKELGVPSPDAKTIRGFMGPPLESSFAT T0379 62 :ELSRY 2ah5A 58 :CLSKD T0379 67 :IGKELTYQQVYDALLGFLEEISAEKFDYIDSLRPDYRLFLLS 2ah5A 65 :SEAVQIYRSYYKAKGIYEAQLFPQIIDLLEELSSSYPLYITT T0379 111 :NPYVLDLAMS 2ah5A 109 :DTSTAQDMAK T0379 127 :GRTLDSFFDKVYASCQMGKYK 2ah5A 119 :NLEIHHFFDGIYGSSPEAPHK T0379 150 :EDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGENWIPAITRLL 2ah5A 140 :ADVIHQALQTHQLAPEQAIIIGDTKFDMLGARETGIQKLAITWGFGEQADLLNYQ 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=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b0cA/T0379-2b0cA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2b0cA expands to /projects/compbio/data/pdb/2b0c.pdb.gz 2b0cA:# T0379 read from 2b0cA/T0379-2b0cA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b0cA read from 2b0cA/T0379-2b0cA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2b0cA to template set # found chain 2b0cA in template set T0379 3 :RNIVFDLGGVLIHLNREESIRRFKAI 2b0cA 8 :MLYIFDLGNVIVDIDFNRVLGAWSDL T0379 29 :GVADIEEMLDPYLQ 2b0cA 35 :RIPLASLKKSFHMG T0379 44 :GLFLDLESGRKSEEEFRTELSRYIGKELTYQQVYDALLGFLEEISAEKFDYIDSLR 2b0cA 49 :EAFHQHERGEISDEAFAEALCHEMALPLSYEQFSHGWQAVFVALRPEVIAIMHKLR T0379 100 :PDYRLFLLSNTNP 2b0cA 106 :QGHRVVVLSNTNR T0379 119 :MSPRFLPSGR 2b0cA 119 :LHTTFWPEEY T0379 129 :TLDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGENWI 2b0cA 130 :EIRDAADHIYLSQDLGMRKPEARIYQHVLQAEGFSPSDTVFFDDNADNIEGANQLGITSILVKDKTTIP T0379 202 :RLL 2b0cA 199 :DYF Number of specific fragments extracted= 7 number of extra gaps= 0 total=205 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 2b0cA/T0379-2b0cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 2b0cA/T0379-2b0cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b0cA read from 2b0cA/T0379-2b0cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2b0cA in template set Warning: unaligning (T0379)Q207 because last residue in template chain is (2b0cA)V204 T0379 3 :RNIVFDLGGVLIHLNRE 2b0cA 8 :MLYIFDLGNVIVDIDFN T0379 22 :IRRFKAIGVA 2b0cA 25 :RVLGAWSDLT T0379 34 :EEMLDPYLQKGLFLDLESGRK 2b0cA 35 :RIPLASLKKSFHMGEAFHQHE T0379 55 :SEEEFRTELSRYIGK 2b0cA 60 :SDEAFAEALCHEMAL T0379 70 :E 2b0cA 78 :Y T0379 75 :QVYDALLGFL 2b0cA 79 :EQFSHGWQAV T0379 85 :EEISAEKFDYIDSLRP 2b0cA 90 :VALRPEVIAIMHKLRE T0379 101 :DYRLFLLSNTNP 2b0cA 107 :GHRVVVLSNTNR T0379 119 :MSPRFLP 2b0cA 119 :LHTTFWP T0379 126 :SGRTLDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGEN 2b0cA 127 :EYPEIRDAADHIYLSQDLGMRKPEARIYQHVLQAEGFSPSDTVFFDDNADNIEGANQLGITSILVKDKTT T0379 200 :ITRLLRE 2b0cA 197 :IPDYFAK Number of specific fragments extracted= 11 number of extra gaps= 0 total=216 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 2b0cA/T0379-2b0cA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 2b0cA/T0379-2b0cA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b0cA read from 2b0cA/T0379-2b0cA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2b0cA in template set T0379 4 :NIVFDLGGVLIHLNREESIRRFKAIGVADIEEMLDPYLQKGLFLDLESGRKSEEEFRTELSRYIGKELTYQQVYDALLGFLEEISAEKFDYIDSLR 2b0cA 9 :LYIFDLGNVIVDIDFNRVLGAWSDLTRIPLASLKKSFHMGEAFHQHERGEISDEAFAEALCHEMALPLSYEQFSHGWQAVFVALRPEVIAIMHKLR T0379 100 :PDYRLFLLSNTNPYV 2b0cA 106 :QGHRVVVLSNTNRLH T0379 120 :SPRFLPSGRTLDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGENWIPAIT 2b0cA 121 :TTFWPEEYPEIRDAADHIYLSQDLGMRKPEARIYQHVLQAEGFSPSDTVFFDDNADNIEGANQLGITSILVKDKTTIPDYFA 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=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qq5A/T0379-1qq5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1qq5A expands to /projects/compbio/data/pdb/1qq5.pdb.gz 1qq5A:Skipped atom 187, because occupancy 0.500 <= existing 0.500 in 1qq5A Skipped atom 189, because occupancy 0.500 <= existing 0.500 in 1qq5A Skipped atom 191, because occupancy 0.500 <= existing 0.500 in 1qq5A Skipped atom 193, because occupancy 0.500 <= existing 0.500 in 1qq5A Skipped atom 195, because occupancy 0.500 <= existing 0.500 in 1qq5A Skipped atom 197, because occupancy 0.500 <= existing 0.500 in 1qq5A Skipped atom 199, because occupancy 0.500 <= existing 0.500 in 1qq5A Skipped atom 646, because occupancy 0.450 <= existing 0.550 in 1qq5A Skipped atom 648, because occupancy 0.450 <= existing 0.550 in 1qq5A Skipped atom 650, because occupancy 0.450 <= existing 0.550 in 1qq5A Skipped atom 652, because occupancy 0.450 <= existing 0.550 in 1qq5A Skipped atom 654, because occupancy 0.450 <= existing 0.550 in 1qq5A Skipped atom 764, because occupancy 0.440 <= existing 0.560 in 1qq5A Skipped atom 766, because occupancy 0.440 <= existing 0.560 in 1qq5A Skipped atom 768, because occupancy 0.440 <= existing 0.560 in 1qq5A Skipped atom 883, because occupancy 0.500 <= existing 0.500 in 1qq5A Skipped atom 885, because occupancy 0.500 <= existing 0.500 in 1qq5A Skipped atom 887, because occupancy 0.500 <= existing 0.500 in 1qq5A Skipped atom 889, because occupancy 0.500 <= existing 0.500 in 1qq5A Skipped atom 891, because occupancy 0.500 <= existing 0.500 in 1qq5A Skipped atom 1361, because occupancy 0.510 <= existing 0.530 in 1qq5A Skipped atom 1363, because occupancy 0.510 <= existing 0.530 in 1qq5A Skipped atom 1463, because occupancy 0.510 <= existing 0.530 in 1qq5A Skipped atom 1465, because occupancy 0.510 <= existing 0.530 in 1qq5A Skipped atom 1752, because occupancy 0.280 <= existing 0.720 in 1qq5A Skipped atom 1754, because occupancy 0.280 <= existing 0.720 in 1qq5A Skipped atom 1756, because occupancy 0.280 <= existing 0.720 in 1qq5A Skipped atom 1758, because occupancy 0.280 <= existing 0.720 in 1qq5A Skipped atom 1793, because occupancy 0.490 <= existing 0.510 in 1qq5A Skipped atom 1795, because occupancy 0.490 <= existing 0.510 in 1qq5A Skipped atom 1797, because occupancy 0.490 <= existing 0.510 in 1qq5A Skipped atom 1820, because occupancy 0.460 <= existing 0.540 in 1qq5A Skipped atom 1822, because occupancy 0.460 <= existing 0.540 in 1qq5A Skipped atom 1824, because occupancy 0.460 <= existing 0.540 in 1qq5A Skipped atom 1826, because occupancy 0.460 <= existing 0.540 in 1qq5A Skipped atom 1828, because occupancy 0.460 <= existing 0.540 in 1qq5A # T0379 read from 1qq5A/T0379-1qq5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qq5A read from 1qq5A/T0379-1qq5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1qq5A to template set # found chain 1qq5A in template set T0379 1 :MIRNIVFDLGGVLIHLN 1qq5A 1 :MIKAVVFDAYGTLFDVQ T0379 18 :REESIRRFKA 1qq5A 35 :TQVWRQKQLE T0379 44 :GLFLDLESGRKSE 1qq5A 45 :YSWLRALMGRYAD T0379 57 :EEFRTELSRYIGKELTYQQVYDALLGFL 1qq5A 63 :REALAYTLGTLGLEPDESFLADMAQAYN T0379 85 :EEISAEKFDYIDSL 1qq5A 92 :LTPYPDAAQCLAEL T0379 100 :PDYRLFLLSNTNPYVLDLAMSPRF 1qq5A 106 :APLKRAILSNGAPDMLQALVANAG T0379 130 :LDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGEN 1qq5A 130 :LTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGFDVGGAKNFGFSVARVARLSQ Number of specific fragments extracted= 7 number of extra gaps= 0 total=226 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 1qq5A/T0379-1qq5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1qq5A/T0379-1qq5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qq5A read from 1qq5A/T0379-1qq5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qq5A in template set T0379 1 :MIRNIVFDLGGVLIH 1qq5A 1 :MIKAVVFDAYGTLFD T0379 18 :REESIRRFKA 1qq5A 32 :EYITQVWRQK T0379 36 :MLDPYLQKGLFLDLESGRKSEEEFRTELSRYIGK 1qq5A 42 :QLEYSWLRALMGRYADFWSVTREALAYTLGTLGL T0379 70 :ELT 1qq5A 79 :ESF T0379 77 :YDALLGFL 1qq5A 82 :LADMAQAY T0379 85 :EEISAEKFDYIDSLR 1qq5A 92 :LTPYPDAAQCLAELA T0379 101 :DYRLFLLSNTNPYVLDLAMSPRF 1qq5A 107 :PLKRAILSNGAPDMLQALVANAG T0379 130 :LDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGEN 1qq5A 130 :LTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGFDVGGAKNFGFSVARVARLSQ Number of specific fragments extracted= 8 number of extra gaps= 0 total=234 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 1qq5A/T0379-1qq5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1qq5A/T0379-1qq5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qq5A read from 1qq5A/T0379-1qq5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qq5A in template set T0379 1 :MIRNIVFDLGGVLIHLNRE 1qq5A 1 :MIKAVVFDAYGTLFDVQSV T0379 22 :IRRFKAIGVADIEEMLDPYLQKGLFLDLESGRKSEEE 1qq5A 20 :ADATERAYPGRGEYITQVWRQKQLEYSWLRALMGRYA T0379 63 :LSRY 1qq5A 57 :DFWS T0379 67 :IGKELTYQQVYDA 1qq5A 76 :EPDESFLADMAQA T0379 82 :GFLEEISAEKFDYIDSLR 1qq5A 89 :YNRLTPYPDAAQCLAELA T0379 101 :DYRLFLLSNTNPYVLDLAMS 1qq5A 107 :PLKRAILSNGAPDMLQALVA T0379 127 :GRTLDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGEN 1qq5A 127 :NAGLTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGFDVGGAKNFGFSVARVARLSQ Number of specific fragments extracted= 7 number of extra gaps= 0 total=241 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 1aq6A/T0379-1aq6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1aq6A expands to /projects/compbio/data/pdb/1aq6.pdb.gz 1aq6A:# T0379 read from 1aq6A/T0379-1aq6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1aq6A read from 1aq6A/T0379-1aq6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1aq6A to template set # found chain 1aq6A in template set T0379 1 :MIRNIVFDLGGVLIHLN 1aq6A 1 :MIKAVVFDAYGTLFDVQ T0379 18 :REESIRRFKA 1aq6A 35 :TQVWRQKQLE T0379 44 :GLFLDLESGRK 1aq6A 45 :YSWLRALMGRY T0379 55 :SEEEFRTELSRYIGKELTYQQVYDALLGF 1aq6A 61 :VTREALAYTLGTLGLEPDESFLADMAQAY T0379 85 :EEISAEKFDYIDSL 1aq6A 92 :LTPYPDAAQCLAEL T0379 100 :PDYRLFLLSNTNPYVLDLAMSPRF 1aq6A 106 :APLKRAILSNGAPDMLQALVANAG T0379 130 :LDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGEN 1aq6A 130 :LTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGFDVGGAKNFGFSVARVARLSQ Number of specific fragments extracted= 7 number of extra gaps= 0 total=248 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 1aq6A/T0379-1aq6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1aq6A/T0379-1aq6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1aq6A read from 1aq6A/T0379-1aq6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1aq6A in template set T0379 1 :MIRNIVFDLGGVLIHLN 1aq6A 1 :MIKAVVFDAYGTLFDVQ T0379 18 :REESIRR 1aq6A 20 :ADATERA T0379 33 :IEEMLDPYLQKGLFLDLESGRKSEEEF 1aq6A 27 :YPGRGEYITQVWRQKQLEYSWLRALMG T0379 60 :RTELSRYIGK 1aq6A 66 :LAYTLGTLGL T0379 70 :EL 1aq6A 79 :ES T0379 76 :VYDALLGFL 1aq6A 81 :FLADMAQAY T0379 85 :EEISAEKFDYIDSLR 1aq6A 92 :LTPYPDAAQCLAELA T0379 101 :DYRLFLLSNTNPYVLDLAMSPRF 1aq6A 107 :PLKRAILSNGAPDMLQALVANAG T0379 130 :LDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGENW 1aq6A 130 :LTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGFDVGGAKNFGFSVARVARLSQE T0379 199 :AITRLLR 1aq6A 197 :ALARELV Number of specific fragments extracted= 10 number of extra gaps= 0 total=258 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 1aq6A/T0379-1aq6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1aq6A/T0379-1aq6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1aq6A read from 1aq6A/T0379-1aq6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1aq6A in template set T0379 1 :MIRNIVFDLGGVLIHLNRE 1aq6A 1 :MIKAVVFDAYGTLFDVQSV T0379 22 :IRRFKAIGVADIEEMLDPYLQKGLFLDLESGRKSE 1aq6A 20 :ADATERAYPGRGEYITQVWRQKQLEYSWLRALMGR T0379 61 :TELSRY 1aq6A 55 :YADFWG T0379 67 :IGKELTYQQVYD 1aq6A 76 :EPDESFLADMAQ T0379 81 :LGFLEEISAEKFDYIDSLR 1aq6A 88 :AYNRLTPYPDAAQCLAELA T0379 101 :DYRLFLLSNTNPYVLDLAMS 1aq6A 107 :PLKRAILSNGAPDMLQALVA T0379 127 :GRTLDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGEN 1aq6A 127 :NAGLTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGFDVGGAKNFGFSVARVARLSQ Number of specific fragments extracted= 7 number of extra gaps= 0 total=265 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 1qq7A/T0379-1qq7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1qq7A expands to /projects/compbio/data/pdb/1qq7.pdb.gz 1qq7A:Bad short name: C2 for alphabet: pdb_atoms Bad short name: C1 for alphabet: pdb_atoms Bad short name: O1 for alphabet: pdb_atoms Bad short name: O2 for alphabet: pdb_atoms Skipped atom 191, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 193, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 195, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 197, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 199, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 201, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 203, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 763, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 765, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 767, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 882, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 884, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 886, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 888, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 890, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1206, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1208, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1357, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1359, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1459, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1461, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1619, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1621, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1623, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1625, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1627, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1629, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1631, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1633, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1635, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1637, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1639, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1641, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1643, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1645, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1647, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1649, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1651, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1653, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1655, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1657, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1659, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1661, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1663, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1665, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1667, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1669, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1671, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1673, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1675, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1677, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1679, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1681, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1683, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1685, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1687, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1689, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1691, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1693, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1695, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1697, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1699, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1701, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1703, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1705, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1707, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1709, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1748, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1750, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1752, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1754, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1789, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1791, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1793, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1816, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1818, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1820, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1822, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1824, because occupancy 0.500 <= existing 0.500 in 1qq7A # T0379 read from 1qq7A/T0379-1qq7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qq7A read from 1qq7A/T0379-1qq7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1qq7A to template set # found chain 1qq7A in template set Warning: unaligning (T0379)F7 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qq7A)A9 Warning: unaligning (T0379)L9 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qq7A)A9 T0379 1 :MIRNIV 1qq7A 1 :MIKAVV T0379 10 :GGVLIHLN 1qq7A 10 :YGTLFDVQ T0379 18 :REESIRRFKA 1qq7A 35 :TQVWRQKQLE T0379 44 :GLFLDLESGRK 1qq7A 45 :YSWLRALMGRY T0379 55 :SEEEFRTELSRYIGKELTYQQVYDALLGFL 1qq7A 61 :VTREALAYTLGTLGLEPDESFLADMAQAYN T0379 85 :EEISAEKFDYIDSL 1qq7A 92 :LTPYPDAAQCLAEL T0379 100 :PDYRLFLLSNTNPYVLDLAMSPRF 1qq7A 106 :APLKRAILSNGAPDMLQALVANAG T0379 130 :LDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGEN 1qq7A 130 :LTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGFDVGGAKNFGFSVARVARLSQ Number of specific fragments extracted= 8 number of extra gaps= 0 total=273 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 1qq7A/T0379-1qq7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1qq7A/T0379-1qq7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qq7A read from 1qq7A/T0379-1qq7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qq7A in template set Warning: unaligning (T0379)F7 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qq7A)A9 Warning: unaligning (T0379)L9 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qq7A)A9 T0379 1 :MIRNIV 1qq7A 1 :MIKAVV T0379 10 :GGVLIHLN 1qq7A 10 :YGTLFDVQ T0379 18 :REESIRR 1qq7A 20 :ADATERA T0379 25 :FKAIGV 1qq7A 36 :QVWRQK T0379 36 :MLDPYLQKGLFLDLESGRKSEEEFRTELSRYIGK 1qq7A 42 :QLEYSWLRALMGRYADFWSVTREALAYTLGTLGL T0379 70 :E 1qq7A 79 :E T0379 75 :QVYDALLGFL 1qq7A 80 :SFLADMAQAY T0379 85 :EEISAEKFDYIDSLR 1qq7A 92 :LTPYPDAAQCLAELA T0379 101 :DYRLFLLSNTNPYVLDLAMSPRF 1qq7A 107 :PLKRAILSNGAPDMLQALVANAG T0379 130 :LDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGEN 1qq7A 130 :LTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGFDVGGAKNFGFSVARVARLSQ Number of specific fragments extracted= 10 number of extra gaps= 0 total=283 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 1qq7A/T0379-1qq7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1qq7A/T0379-1qq7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qq7A read from 1qq7A/T0379-1qq7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qq7A in template set Warning: unaligning (T0379)F7 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qq7A)A9 Warning: unaligning (T0379)L9 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qq7A)A9 T0379 1 :MIRNIV 1qq7A 1 :MIKAVV T0379 10 :GGVLIHLNRE 1qq7A 10 :YGTLFDVQSV T0379 22 :IRRFKAIGVADIEEMLDPYLQKGLFLDLESGRKSEEEFRTEL 1qq7A 20 :ADATERAYPGRGEYITQVWRQKQLEYSWLRALMGRYADFWSV T0379 67 :IGKELTY 1qq7A 76 :EPDESFL T0379 78 :DALLG 1qq7A 83 :ADMAQ T0379 83 :FLEEISAEKFDYIDSLR 1qq7A 90 :NRLTPYPDAAQCLAELA T0379 101 :DYRLFLLSNTNPYVLDLAMS 1qq7A 107 :PLKRAILSNGAPDMLQALVA T0379 127 :GRTLDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGEN 1qq7A 127 :NAGLTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGFDVGGAKNFGFSVARVARLSQ Number of specific fragments extracted= 8 number of extra gaps= 0 total=291 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 2go7A/T0379-2go7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2go7A expands to /projects/compbio/data/pdb/2go7.pdb.gz 2go7A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0379 read from 2go7A/T0379-2go7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2go7A read from 2go7A/T0379-2go7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2go7A to template set # found chain 2go7A in template set Warning: unaligning (T0379)I2 because first residue in template chain is (2go7A)K3 Warning: unaligning (T0379)F7 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)D9 Warning: unaligning (T0379)D8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)D9 Warning: unaligning (T0379)L106 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)Y106 Warning: unaligning (T0379)L107 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)Y106 T0379 3 :RNIV 2go7A 4 :TAFI T0379 9 :LGGVLIHLN 2go7A 10 :LDGTLLDSY T0379 18 :REESIRRFKAI 2go7A 21 :ILSGIEETFAQ T0379 29 :GVADI 2go7A 33 :SIPYD T0379 44 :GLFLDLESGRKSEEEFRTELSRYI 2go7A 38 :KEKVREFIFKYSVQDLLVRVAEDR T0379 70 :ELTYQQVYDALLGFL 2go7A 62 :NLDVEVLNQVRAQSL T0379 85 :EEISAEKFDYIDSLR 2go7A 83 :VVLMPGAREVLAWAD T0379 100 :PDYRLF 2go7A 99 :SGIQQF T0379 108 :SNTNPY 2go7A 107 :THKGNN T0379 115 :LDLAMSPRF 2go7A 113 :AFTILKDLG T0379 130 :LDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGE 2go7A 122 :VESYFTEILTSQSGFVRKPSPEAATYLLDKYQLNSDNTYYIGDRTLDVEFAQNSGIQSINFLEST Number of specific fragments extracted= 11 number of extra gaps= 2 total=302 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 2go7A/T0379-2go7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 2go7A/T0379-2go7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2go7A read from 2go7A/T0379-2go7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2go7A in template set Warning: unaligning (T0379)I2 because first residue in template chain is (2go7A)K3 Warning: unaligning (T0379)F7 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)D9 Warning: unaligning (T0379)D8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)D9 Warning: unaligning (T0379)L106 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)Y106 Warning: unaligning (T0379)L107 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)Y106 T0379 3 :RNIV 2go7A 4 :TAFI T0379 9 :LGGVLIHLNREESIRRFKAIGVADIEEMLDPYLQKG 2go7A 10 :LDGTLLDSYEAILSGIEETFAQFSIPYDKEKVREFI T0379 45 :LFLDLESGRKSEEE 2go7A 47 :KYSVQDLLVRVAED T0379 62 :ELSR 2go7A 61 :RNLD T0379 70 :ELTYQQVYDALLGFLEE 2go7A 65 :VEVLNQVRAQSLAEKNA T0379 87 :ISAEKFDYIDSLRP 2go7A 85 :LMPGAREVLAWADE T0379 101 :DYRLF 2go7A 100 :GIQQF T0379 108 :SNTNP 2go7A 107 :THKGN T0379 114 :VLDLAMSPRF 2go7A 112 :NAFTILKDLG T0379 130 :LDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGENW 2go7A 122 :VESYFTEILTSQSGFVRKPSPEAATYLLDKYQLNSDNTYYIGDRTLDVEFAQNSGIQSINFLESTYE T0379 199 :AITRLL 2go7A 198 :DISRIF Number of specific fragments extracted= 11 number of extra gaps= 2 total=313 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 2go7A/T0379-2go7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 2go7A/T0379-2go7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2go7A read from 2go7A/T0379-2go7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2go7A in template set Warning: unaligning (T0379)F7 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)D9 Warning: unaligning (T0379)D8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)D9 Warning: unaligning (T0379)L106 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)Y106 Warning: unaligning (T0379)L107 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)Y106 T0379 3 :RNIV 2go7A 4 :TAFI T0379 9 :LGGVLIHLNREESIRRFKAIGVADIEEMLDPYLQKGLFLDLESGRKSEEEFRT 2go7A 10 :LDGTLLDSYEAILSGIEETFAQFSIPYDKEKVREFIFKYSVQDLLVRVAEDRN T0379 68 :GKELTYQQVYDALLGF 2go7A 63 :LDVEVLNQVRAQSLAE T0379 84 :LEEISAEKFDYIDSLR 2go7A 82 :QVVLMPGAREVLAWAD T0379 100 :PDYRLF 2go7A 99 :SGIQQF T0379 108 :SNTNPYVLDLAMS 2go7A 107 :THKGNNAFTILKD T0379 128 :RTLDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGE 2go7A 120 :LGVESYFTEILTSQSGFVRKPSPEAATYLLDKYQLNSDNTYYIGDRTLDVEFAQNSGIQSINFLEST Number of specific fragments extracted= 7 number of extra gaps= 2 total=320 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 2fi1A/T0379-2fi1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2fi1A expands to /projects/compbio/data/pdb/2fi1.pdb.gz 2fi1A:# T0379 read from 2fi1A/T0379-2fi1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fi1A read from 2fi1A/T0379-2fi1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2fi1A to template set # found chain 2fi1A in template set T0379 1 :M 2fi1A 4 :M T0379 2 :IRNIVFDLGGVLIHLN 2fi1A 6 :YHDYIWDLGGTLLDNY T0379 18 :REESIRRFKAIGVADIE 2fi1A 25 :TAAFVETLALYGITQDH T0379 44 :GLFLDLES 2fi1A 42 :DSVYQALK T0379 54 :KSEEEFRTELSRYI 2fi1A 50 :VSTPFAIETFAPNL T0379 70 :ELTYQQVYDALLGFL 2fi1A 64 :ENFLEKYKENEAREL T0379 85 :EEISAEKFDYIDSLR 2fi1A 81 :PILFEGVSDLLEDIS T0379 100 :PDYRLFLLSNTNPY 2fi1A 97 :QGGRHFLVSHRNDQ T0379 115 :LDLAMSPRF 2fi1A 111 :VLEILEKTS T0379 130 :LDSFFDKVYASCQMGKYKPNEDIFLEMIADSGM 2fi1A 120 :IAAYFTEVVTSSSGFKRKPNPESMLYLREKYQI T0379 165 :EETLFIDDGPANVATAERLGFHTYCPDNGENW 2fi1A 153 :SSGLVIGDRPIDIEAGQAAGLDTHLFTSIVNL Number of specific fragments extracted= 11 number of extra gaps= 0 total=331 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 2fi1A/T0379-2fi1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 2fi1A/T0379-2fi1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fi1A read from 2fi1A/T0379-2fi1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fi1A in template set T0379 1 :M 2fi1A 4 :M T0379 2 :IRNIVFDLGGVLIHLNREESIRRFKAIGVADIEEMLDPYLQKGLFLDLESGRKSEEEF 2fi1A 6 :YHDYIWDLGGTLLDNYETSTAAFVETLALYGITQDHDSVYQALKVSTPFAIETFAPNL T0379 67 :IGKELTYQQVYDALLGFL 2fi1A 64 :ENFLEKYKENEARELEHP T0379 86 :EISAEKFDYIDSLRP 2fi1A 82 :ILFEGVSDLLEDISN T0379 101 :DYRLFLLSNTNPY 2fi1A 98 :GGRHFLVSHRNDQ T0379 115 :LDLAMSPRF 2fi1A 111 :VLEILEKTS T0379 130 :LDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMK 2fi1A 120 :IAAYFTEVVTSSSGFKRKPNPESMLYLREKYQIS T0379 166 :ETLFIDDGPANVATAERLGFHTYCPDN 2fi1A 154 :SGLVIGDRPIDIEAGQAAGLDTHLFTS T0379 200 :ITRLLRE 2fi1A 181 :IVNLRQV Number of specific fragments extracted= 9 number of extra gaps= 0 total=340 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 2fi1A/T0379-2fi1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 2fi1A/T0379-2fi1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fi1A read from 2fi1A/T0379-2fi1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fi1A in template set T0379 1 :MIRNIVFDLGGVLIHLNREESIRRFKAIGVADIEEMLDPYLQKG 2fi1A 5 :KYHDYIWDLGGTLLDNYETSTAAFVETLALYGITQDHDSVYQAL T0379 53 :RKSEEEFRTELSRY 2fi1A 49 :KVSTPFAIETFAPN T0379 67 :IGKELTYQQVYDALLG 2fi1A 64 :ENFLEKYKENEARELE T0379 84 :LEEISAEKFDYIDSLR 2fi1A 80 :HPILFEGVSDLLEDIS T0379 100 :PDYRLFLLSNTNPYVLDLAMS 2fi1A 97 :QGGRHFLVSHRNDQVLEILEK T0379 128 :RTLDSFFDKVYASCQMGKYKPNEDIFLEMIADSGM 2fi1A 118 :TSIAAYFTEVVTSSSGFKRKPNPESMLYLREKYQI T0379 165 :EETLFIDDGPANVATAERLGFHTYCPDNGENWIPAI 2fi1A 153 :SSGLVIGDRPIDIEAGQAAGLDTHLFTSIVNLRQVL Number of specific fragments extracted= 7 number of extra gaps= 0 total=347 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 1swvA/T0379-1swvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1swvA expands to /projects/compbio/data/pdb/1swv.pdb.gz 1swvA:# T0379 read from 1swvA/T0379-1swvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1swvA read from 1swvA/T0379-1swvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1swvA to template set # found chain 1swvA in template set T0379 2 :IRNIVFDLGGVLIHLN 1swvA 6 :IEAVIFAWAGTTVDYG T0379 18 :REESIRRFKAIGVADIEEMLDPYLQ 1swvA 26 :LEVFMEIFHKRGVAITAEEARKPMG T0379 44 :GLFLDLESGRKSEEEFRTELSRYIGKELTYQ 1swvA 51 :LLKIDHVRALTEMPRIASEWNRVFRQLPTEA T0379 75 :QVYDALLGFL 1swvA 85 :EMYEEFEEIL T0379 85 :EEISAEKFDYIDSLR 1swvA 102 :ASPINGVKEVIASLR T0379 100 :PDYRLFLLSNTNPYVLDLAMS 1swvA 118 :RGIKIGSTTGYTREMMDIVAK T0379 121 :PRF 1swvA 142 :LQG T0379 130 :LD 1swvA 145 :YK T0379 134 :FDKVYASCQMGKYKPNEDIFLEMIADSGM 1swvA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMELGV T0379 163 :KPEETLFIDDGPANVATAERLGFHTYCPDNG 1swvA 177 :PMNHMIKVGDTVSDMKEGRNAGMWTVGVILG Number of specific fragments extracted= 10 number of extra gaps= 0 total=357 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 1swvA/T0379-1swvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1swvA/T0379-1swvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1swvA read from 1swvA/T0379-1swvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1swvA in template set T0379 2 :IRNIVFDLGGVLIHL 1swvA 6 :IEAVIFAWAGTTVDY T0379 17 :NREESIRRFKAIGVADIEEMLDPYLQKGLFLDLESGRKSEEEF 1swvA 22 :CFAPLEVFMEIFHKRGVAITAEEARKPMGLLKIDHVRALTEMP T0379 60 :RTEL 1swvA 71 :NRVF T0379 64 :SRYIGKELTYQQVYDALLGFLEEISAEKFDYIDSLRP 1swvA 81 :ADIQEMYEEFEEILFAILPRYASPINGVKEVIASLRE T0379 101 :DYRLFLLSNTNPYVLDLAMSPRF 1swvA 119 :GIKIGSTTGYTREMMDIVAKEAA T0379 130 :LDSF 1swvA 142 :LQGY T0379 134 :FDKVYASCQMGKYKPNEDIFLEMIADSGM 1swvA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMELGV T0379 163 :KPEETLFIDDGPANVATAERLGFHTYCPDNGENWIP 1swvA 177 :PMNHMIKVGDTVSDMKEGRNAGMWTVGVILGSSELG T0379 200 :ITRLLRE 1swvA 226 :LREKIEV Number of specific fragments extracted= 9 number of extra gaps= 0 total=366 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 1swvA/T0379-1swvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1swvA/T0379-1swvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1swvA read from 1swvA/T0379-1swvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1swvA in template set T0379 1 :MIRNIVFDLGGVLIHLN 1swvA 5 :KIEAVIFAWAGTTVDYG T0379 20 :ESIRRFKAIGVADIEEMLDPYLQ 1swvA 25 :PLEVFMEIFHKRGVAITAEEARK T0379 43 :KGLFLDLESGRKSEEEFRTELSRY 1swvA 54 :IDHVRALTEMPRIASEWNRVFRQL T0379 67 :IGKELTYQQVYDALLGFLEEISAEKFDYIDSLR 1swvA 84 :QEMYEEFEEILFAILPRYASPINGVKEVIASLR T0379 100 :PDYRLFLLSNTNPYVLDLAMS 1swvA 118 :RGIKIGSTTGYTREMMDIVAK T0379 127 :GRTLDSFF 1swvA 139 :EAALQGYK T0379 135 :DKVYASCQMGKYKPNEDIFLEMIADSGMKP 1swvA 148 :DFLVTPDDVPAGRPYPWMCYKNAMELGVYP T0379 165 :EETLFIDDGPANVATAERLGFHTYCPDNG 1swvA 179 :NHMIKVGDTVSDMKEGRNAGMWTVGVILG T0379 197 :IPAITRLLRE 1swvA 215 :EEEVENMDSV Number of specific fragments extracted= 9 number of extra gaps= 0 total=375 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 1rdfA/T0379-1rdfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1rdfA expands to /projects/compbio/data/pdb/1rdf.pdb.gz 1rdfA:# T0379 read from 1rdfA/T0379-1rdfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rdfA read from 1rdfA/T0379-1rdfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1rdfA to template set # found chain 1rdfA in template set Warning: unaligning (T0379)K163 because of BadResidue code BAD_PEPTIDE at template residue (1rdfA)P177 T0379 2 :IRNIVFDLGGVLIHLN 1rdfA 6 :IEAVIFDWAGTTVDYG T0379 18 :REESIRRFKAIGVADIEEMLDPYLQ 1rdfA 26 :LEVFMEIFHKRGVAITAEEARKPMP T0379 44 :GLFLDLESGRKSEEEFRTELSRYIGKELTYQ 1rdfA 51 :LLKIDHVRALTEMPRIASEWNRVFRQLPTEA T0379 75 :QVYDALLGFL 1rdfA 89 :EFEEILFAIL T0379 85 :EEISAEKFDYIDSLR 1rdfA 102 :ASPINAVKEVIASLR T0379 100 :PDYRLFLLSNTNPYVLDLAMSPRF 1rdfA 118 :RGIKIGSTTGYTREMMDIVAKEAA T0379 130 :LDSF 1rdfA 142 :LQGY T0379 134 :FDKVYASCQMGKYKPNEDIFLEMIADSGM 1rdfA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMELGV T0379 164 :PEETLFIDDGPANVATAERLGFHTYCPDNG 1rdfA 178 :MNHMIKVGDTVSDMKEGRNAGMWTVGVILG Number of specific fragments extracted= 9 number of extra gaps= 1 total=384 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 1rdfA/T0379-1rdfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1rdfA/T0379-1rdfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rdfA read from 1rdfA/T0379-1rdfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rdfA in template set Warning: unaligning (T0379)K163 because of BadResidue code BAD_PEPTIDE at template residue (1rdfA)P177 T0379 2 :IRNIVFDLGGVLIHL 1rdfA 6 :IEAVIFDWAGTTVDY T0379 17 :NREESIRRFKAIGVADIEEMLDPYLQ 1rdfA 22 :CFAPLEVFMEIFHKRGVAITAEEARK T0379 43 :KGLFLDLESGRKSEEEF 1rdfA 58 :RALTEMPRIASEWNRVF T0379 60 :RTELSRYIGKELTYQQVYDALLGFLEEISAEKFDYIDSLRP 1rdfA 77 :LPTEADIQEMYEEFEEILFAILPRYASPINAVKEVIASLRE T0379 101 :DYRLFLLSNTNPYVLDLAMSPRF 1rdfA 119 :GIKIGSTTGYTREMMDIVAKEAA T0379 130 :LDSF 1rdfA 142 :LQGY T0379 134 :FDKVYASCQMGKYKPNEDIFLEMIADSGM 1rdfA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMELGV T0379 164 :PEETLFIDDGPANVATAERLGFHTYCPDNGENWIP 1rdfA 178 :MNHMIKVGDTVSDMKEGRNAGMWTVGVILGSSELG T0379 200 :ITRLLRE 1rdfA 226 :LREKIEV Number of specific fragments extracted= 9 number of extra gaps= 1 total=393 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 1rdfA/T0379-1rdfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1rdfA/T0379-1rdfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rdfA read from 1rdfA/T0379-1rdfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rdfA in template set Warning: unaligning (T0379)K163 because of BadResidue code BAD_PEPTIDE at template residue (1rdfA)P177 T0379 1 :MIRNIVFDLGGVLIHLN 1rdfA 5 :KIEAVIFDWAGTTVDYG T0379 18 :REESIRRFKAIGVADIEEMLDPYLQ 1rdfA 23 :FAPLEVFMEIFHKRGVAITAEEARK T0379 43 :KGLFLDLESGRKSEEEFRTELSRY 1rdfA 54 :IDHVRALTEMPRIASEWNRVFRQL T0379 67 :IGKELTYQQVYDALLGFLEEISAEKFDYIDSLR 1rdfA 84 :QEMYEEFEEILFAILPRYASPINAVKEVIASLR T0379 100 :PDYRLFLLSNTNPYVLDLAMS 1rdfA 118 :RGIKIGSTTGYTREMMDIVAK T0379 127 :GRTLDSFF 1rdfA 139 :EAALQGYK T0379 135 :DKVYASCQMGKYKPNEDIFLEMIADSGM 1rdfA 148 :DFLVTPDDVPAGRPYPWMCYKNAMELGV T0379 164 :PEETLFIDDGPANVATAERLGFHTYCPD 1rdfA 178 :MNHMIKVGDTVSDMKEGRNAGMWTVGVI Number of specific fragments extracted= 8 number of extra gaps= 1 total=401 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 1fezA/T0379-1fezA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1fezA expands to /projects/compbio/data/pdb/1fez.pdb.gz 1fezA:# T0379 read from 1fezA/T0379-1fezA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fezA read from 1fezA/T0379-1fezA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1fezA to template set # found chain 1fezA in template set T0379 2 :IRNIVFDLGGVLIHLN 1fezA 6 :IEAVIFDWAGTTVDYG T0379 18 :REESIRRFKAIGVADIEEMLDPYLQKGLFLDLESGRKSEE 1fezA 26 :LEVFMEIFHKRGVAITAEEARKPMGLLKIDHVRALTEMPR T0379 59 :FRTELSRYIGKELT 1fezA 66 :IASEWNRVFRQLPT T0379 73 :YQQVYDALLGFL 1fezA 83 :IQEMYEEFEEIL T0379 85 :EEISAEKFDYIDSLR 1fezA 102 :ASPINAVKEVIASLR T0379 100 :PDYRLFLLSNTNPYVLDLAMS 1fezA 118 :RGIKIGSTTGYTREMMDIVAK T0379 121 :PRF 1fezA 142 :LQG T0379 130 :LD 1fezA 145 :YK T0379 134 :FDKVYASCQMGKYKPNEDIFLEMIADSGM 1fezA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMELGV T0379 163 :KPEETLFIDDGPANVATAERLGFHTYCPDNGENWIPAI 1fezA 177 :PMNHMIKVGDTVSDMKEGRNAGMWTVGVILGSSELGLT T0379 201 :TRL 1fezA 230 :IEV Number of specific fragments extracted= 11 number of extra gaps= 0 total=412 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 1fezA/T0379-1fezA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1fezA/T0379-1fezA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fezA read from 1fezA/T0379-1fezA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fezA in template set T0379 2 :IRNIVFDLGGVLIHL 1fezA 6 :IEAVIFDWAGTTVDY T0379 17 :NREESIRRFKAIGVADIEEMLDPYLQKGLFLDLESGRKSEEEF 1fezA 22 :CFAPLEVFMEIFHKRGVAITAEEARKPMGLLKIDHVRALTEMP T0379 60 :RTELSRYIGKELTYQQVYDALLGFLEEISAEKFDYIDSLRP 1fezA 77 :LPTEADIQEMYEEFEEILFAILPRYASPINAVKEVIASLRE T0379 101 :DYRLFLLSNTNPYVLDLAMSPRF 1fezA 119 :GIKIGSTTGYTREMMDIVAKEAA T0379 130 :LDSF 1fezA 142 :LQGY T0379 134 :FDKVYASCQMGKYKPNEDIFLEMIADSGM 1fezA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMELGV T0379 163 :KPEETLFIDDGPANVATAERLGFHTYCPDNGENWIP 1fezA 177 :PMNHMIKVGDTVSDMKEGRNAGMWTVGVILGSSELG T0379 199 :AITRLLREQ 1fezA 225 :ELREKIEVV Number of specific fragments extracted= 8 number of extra gaps= 0 total=420 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 1fezA/T0379-1fezA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1fezA/T0379-1fezA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fezA read from 1fezA/T0379-1fezA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fezA in template set T0379 1 :MIRNIVFDLGGVLIHLN 1fezA 5 :KIEAVIFDWAGTTVDYG T0379 18 :REESIRRFKAIGVADIEEMLDPYLQ 1fezA 23 :FAPLEVFMEIFHKRGVAITAEEARK T0379 43 :KGLFLDLESGRKSEEEFRTELSRY 1fezA 54 :IDHVRALTEMPRIASEWNRVFRQL T0379 67 :IGKELTYQQVYDALLGFLEEISAEKFDYIDSLR 1fezA 84 :QEMYEEFEEILFAILPRYASPINAVKEVIASLR T0379 100 :PDYRLFLLSNTNPYVLDLAMS 1fezA 118 :RGIKIGSTTGYTREMMDIVAK T0379 127 :GRTLDSFF 1fezA 139 :EAALQGYK T0379 135 :DKVYASCQMGKYKPNEDIFLEMIADSGMKP 1fezA 148 :DFLVTPDDVPAGRPYPWMCYKNAMELGVYP T0379 165 :EETLFIDDGPANVATAERLGFHTYCPD 1fezA 179 :NHMIKVGDTVSDMKEGRNAGMWTVGVI Number of specific fragments extracted= 8 number of extra gaps= 0 total=428 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 1rqlA/T0379-1rqlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1rqlA expands to /projects/compbio/data/pdb/1rql.pdb.gz 1rqlA:# T0379 read from 1rqlA/T0379-1rqlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rqlA read from 1rqlA/T0379-1rqlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1rqlA to template set # found chain 1rqlA in template set T0379 2 :IRNIVFDLGGVLIHLN 1rqlA 6 :IEAVIFDWAGTTVDYG T0379 18 :REESIRRFKAIGVADIEEMLDPYLQKGLFLDLESGRKSEE 1rqlA 26 :LEVFMEIFHKRGVAITAEEARKPMGLLKIDHVRALTEMPR T0379 59 :FRTELSRYIGKELT 1rqlA 66 :IASEWNRVFRQLPT T0379 73 :YQQVYDALLGFL 1rqlA 83 :IQEMYEEFEEIL T0379 85 :EEISAEKFDYIDSLR 1rqlA 102 :ASPINAVKEVIASLR T0379 100 :PDYRLFLLSNTNPYVLDLAMSPRF 1rqlA 118 :RGIKIGSTTGYTREMMDIVAKEAA T0379 130 :LDSF 1rqlA 142 :LQGY T0379 134 :FDKVYASCQMGKYKPNEDIFLEMIADSGM 1rqlA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMELGV T0379 163 :KPEETLFIDDGPANVATAERLGFHTYCPDNGENWIPAI 1rqlA 177 :PMNHMIKVGDTVSDMKEGRNAGMWTVGVILGSSELGLT Number of specific fragments extracted= 9 number of extra gaps= 0 total=437 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 1rqlA/T0379-1rqlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1rqlA/T0379-1rqlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rqlA read from 1rqlA/T0379-1rqlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rqlA in template set T0379 2 :IRNIVFDLGGVLIHL 1rqlA 6 :IEAVIFDWAGTTVDY T0379 17 :NREESIRRFKAIGVADIEEMLDPYLQKGLFLDLESGRKSE 1rqlA 22 :CFAPLEVFMEIFHKRGVAITAEEARKPMGLLKIDHVRALT T0379 57 :EEF 1rqlA 64 :PRI T0379 60 :RTELSRYIGKELTYQQVYDALLGFLEEISAEKFDYIDSLRP 1rqlA 77 :LPTEADIQEMYEEFEEILFAILPRYASPINAVKEVIASLRE T0379 101 :DYRLFLLSNTNPYVLDLAMSPRF 1rqlA 119 :GIKIGSTTGYTREMMDIVAKEAA T0379 130 :LDSF 1rqlA 142 :LQGY T0379 134 :FDKVYASCQMGKYKPNEDIFLEMIADSGM 1rqlA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMELGV T0379 163 :KPEETLFIDDGPANVATAERLGFHTYCPDNGENWIP 1rqlA 177 :PMNHMIKVGDTVSDMKEGRNAGMWTVGVILGSSELG Number of specific fragments extracted= 8 number of extra gaps= 0 total=445 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 1rqlA/T0379-1rqlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1rqlA/T0379-1rqlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rqlA read from 1rqlA/T0379-1rqlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rqlA in template set T0379 1 :MIRNIVFDLGGVLIHLN 1rqlA 5 :KIEAVIFDWAGTTVDYG T0379 18 :REESIRRFKAIGVADIEEMLDPYLQ 1rqlA 23 :FAPLEVFMEIFHKRGVAITAEEARK T0379 43 :KGLFLDLESGRKSEEEFRTELSRY 1rqlA 54 :IDHVRALTEMPRIASEWNRVFRQL T0379 67 :IGKELTYQQVYDALLGFLEEISAEKFDYIDSLR 1rqlA 84 :QEMYEEFEEILFAILPRYASPINAVKEVIASLR T0379 100 :PDYRLFLLSNTNPYVLDLAMS 1rqlA 118 :RGIKIGSTTGYTREMMDIVAK T0379 127 :GRTLDSFF 1rqlA 139 :EAALQGYK T0379 135 :DKVYASCQMGKYKPNEDIFLEMIADSGMKP 1rqlA 148 :DFLVTPDDVPAGRPYPWMCYKNAMELGVYP T0379 165 :EETLFIDDGPANVATAERLGFHTYCPDNG 1rqlA 179 :NHMIKVGDTVSDMKEGRNAGMWTVGVILG T0379 196 :WIPAITRLLRE 1rqlA 214 :TEEEVENMDSV Number of specific fragments extracted= 9 number of extra gaps= 0 total=454 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 1zd3A/T0379-1zd3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zd3A expands to /projects/compbio/data/pdb/1zd3.pdb.gz 1zd3A:# T0379 read from 1zd3A/T0379-1zd3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zd3A read from 1zd3A/T0379-1zd3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zd3A to template set # found chain 1zd3A in template set T0379 2 :IRNIVFDLGGVLIHLN 1zd3A 3 :LRAAVFDLDGVLALPA T0379 18 :REESIRRFKAIGVAD 1zd3A 20 :FGVLGRTEEALALPR T0379 33 :IEEMLDPY 1zd3A 40 :AFQKGGPE T0379 44 :GLFLDLESGRKSEEEFRTELSR 1zd3A 48 :GATTRLMKGEITLSQWIPLMEE T0379 69 :KELTYQQV 1zd3A 84 :KNFSIKEI T0379 77 :YDALLG 1zd3A 93 :DKAISA T0379 85 :EEISAEKFDYIDSLR 1zd3A 99 :RKINRPMLQAALMLR T0379 100 :PDYRLFLLSN 1zd3A 115 :KGFTTAILTN T0379 110 :TNPYVLDLAMSP 1zd3A 131 :AERDGLAQLMCE T0379 130 :LDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGENWIPAI 1zd3A 143 :LKMHFDFLIESCQVGMVKPEPQIYKFLLDTLKASPSEVVFLDDIGANLKPARDLGMVTILVQDTDTALKEL Number of specific fragments extracted= 10 number of extra gaps= 0 total=464 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 1zd3A/T0379-1zd3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1zd3A/T0379-1zd3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zd3A read from 1zd3A/T0379-1zd3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zd3A in template set T0379 2 :IRNIVFDLGGVLIHL 1zd3A 3 :LRAAVFDLDGVLALP T0379 19 :EESIRRFKAIGVADIEEM 1zd3A 18 :AVFGVLGRTEEALALPRG T0379 37 :L 1zd3A 37 :L T0379 38 :DPYLQKGLFLDLESGRKSEEEFRTELSRY 1zd3A 50 :TTRLMKGEITLSQWIPLMEENCRKCSETA T0379 68 :G 1zd3A 79 :K T0379 73 :YQQVYDALLGFL 1zd3A 88 :IKEIFDKAISAR T0379 86 :EISAEKFDYIDSLRP 1zd3A 100 :KINRPMLQAALMLRK T0379 101 :DYRLFLLSNTN 1zd3A 116 :GFTTAILTNTW T0379 112 :PYVLDLAMSP 1zd3A 133 :RDGLAQLMCE T0379 130 :LDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGENW 1zd3A 143 :LKMHFDFLIESCQVGMVKPEPQIYKFLLDTLKASPSEVVFLDDIGANLKPARDLGMVTILVQDTDTA T0379 200 :ITRLLR 1zd3A 210 :LKELEK Number of specific fragments extracted= 11 number of extra gaps= 0 total=475 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 1zd3A/T0379-1zd3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1zd3A/T0379-1zd3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zd3A read from 1zd3A/T0379-1zd3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zd3A in template set T0379 1 :MIRNIVFDLGGVLIHLNRE 1zd3A 2 :TLRAAVFDLDGVLALPAVF T0379 22 :IRRFKAIGVADIEEMLDPYLQKG 1zd3A 21 :GVLGRTEEALALPRGLLNDAFQK T0379 45 :LFLDLESGRKSEEEFRTELSRY 1zd3A 49 :ATTRLMKGEITLSQWIPLMEEN T0379 67 :IGKELTYQQVYDALLGFL 1zd3A 82 :LPKNFSIKEIFDKAISAR T0379 86 :EISAEKFDYIDSLR 1zd3A 100 :KINRPMLQAALMLR T0379 100 :PDYRLFLLSNTN 1zd3A 115 :KGFTTAILTNTW T0379 112 :PYVLDLA 1zd3A 133 :RDGLAQL T0379 127 :GRTLDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGENWIPAITRL 1zd3A 140 :MCELKMHFDFLIESCQVGMVKPEPQIYKFLLDTLKASPSEVVFLDDIGANLKPARDLGMVTILVQDTDTALKELEKV Number of specific fragments extracted= 8 number of extra gaps= 0 total=483 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 1l7mA/T0379-1l7mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1l7mA expands to /projects/compbio/data/pdb/1l7m.pdb.gz 1l7mA:Skipped atom 73, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 75, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 77, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 79, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 81, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 83, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 85, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 87, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 108, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 110, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 112, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 114, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 116, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 118, because occupancy 0.500 <= existing 0.500 in 1l7mA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 465, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 467, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 469, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 471, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 473, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 475, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 785, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 787, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 789, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 791, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 793, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 795, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 797, because occupancy 0.500 <= existing 0.500 in 1l7mA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1526, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 1528, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 1530, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 1532, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 1534, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 1536, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 1538, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 1540, because occupancy 0.500 <= existing 0.500 in 1l7mA # T0379 read from 1l7mA/T0379-1l7mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1l7mA read from 1l7mA/T0379-1l7mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1l7mA to template set # found chain 1l7mA in template set T0379 2 :IRNIVFDLGGVLIHLN 1l7mA 5 :KKLILFDFDSTLVNNE T0379 18 :REESI 1l7mA 32 :EEEVK T0379 44 :GLFLDLESGRKSEEEFRTELSRYIG 1l7mA 37 :KITKEAMEGKLNFEQSLRKRVSLLK T0379 70 :ELTYQQVYDALLG 1l7mA 62 :DLPIEKVEKAIKR T0379 85 :EEISAEKFDYIDSLR 1l7mA 75 :ITPTEGAEETIKELK T0379 100 :PDYRLFLLSNTNPYVLDLAMSPRF 1l7mA 91 :RGYVVAVVSGGFDIAVNKIKEKLG T0379 130 :LDSFFDKVYASCQM 1l7mA 115 :LDYAFANRLIVKDG T0379 145 :KYK 1l7mA 142 :NAK T0379 150 :EDIFLEMIADSGMKPEETLFIDDGPANVATAERLG 1l7mA 145 :GEILEKIAKIEGINLEDTVAVGDGANDISMFKKAG T0379 186 :HTYCP 1l7mA 180 :LKIAF T0379 192 :NGE 1l7mA 185 :CAK T0379 202 :RLLRE 1l7mA 188 :PILKE Number of specific fragments extracted= 12 number of extra gaps= 0 total=495 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 1l7mA/T0379-1l7mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1l7mA/T0379-1l7mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1l7mA read from 1l7mA/T0379-1l7mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1l7mA in template set T0379 2 :IRNIVFDLGGVLIHLNR 1l7mA 5 :KKLILFDFDSTLVNNET T0379 24 :RFKAIGVADIEEMLDPYLQKG 1l7mA 22 :IDEIAREAGVEEEVKKITKEA T0379 45 :LFLDLESGRKSEEEFRTELSRY 1l7mA 46 :KLNFEQSLRKRVSLLKDLPIEK T0379 77 :YDALLGFL 1l7mA 68 :VEKAIKRI T0379 86 :EISAEKFDYIDSLRP 1l7mA 76 :TPTEGAEETIKELKN T0379 101 :DYRLFLLSNTNPYVLDLAMSPRF 1l7mA 92 :GYVVAVVSGGFDIAVNKIKEKLG T0379 134 :FDKVYAS 1l7mA 115 :LDYAFAN T0379 141 :CQMGK 1l7mA 136 :GEVLK T0379 150 :EDIFLEMIADSGMKPEETLFIDDGPANVATAERLG 1l7mA 145 :GEILEKIAKIEGINLEDTVAVGDGANDISMFKKAG T0379 186 :HTYCPDN 1l7mA 180 :LKIAFCA Number of specific fragments extracted= 10 number of extra gaps= 0 total=505 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 1l7mA/T0379-1l7mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1l7mA/T0379-1l7mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1l7mA read from 1l7mA/T0379-1l7mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1l7mA in template set T0379 1 :MIRNIVFDLGGVLIHLNRE 1l7mA 4 :KKKLILFDFDSTLVNNETI T0379 25 :FKAIGVADIEEMLDPYLQKGLFLDLESGRKSEE 1l7mA 23 :DEIAREAGVEEEVKKITKEAMEGKLNFEQSLRK T0379 59 :FRTELS 1l7mA 56 :RVSLLK T0379 67 :IGKELTYQQVYD 1l7mA 62 :DLPIEKVEKAIK T0379 84 :LEEISAEKFDYIDSLR 1l7mA 74 :RITPTEGAEETIKELK T0379 100 :PDYRLFLLSNTNPYVLDLAMS 1l7mA 91 :RGYVVAVVSGGFDIAVNKIKE T0379 127 :GRTL 1l7mA 112 :KLGL T0379 135 :DKVYA 1l7mA 116 :DYAFA T0379 150 :EDIFLEMIADSGMKPEETLFIDDGPANVATAERLG 1l7mA 145 :GEILEKIAKIEGINLEDTVAVGDGANDISMFKKAG T0379 186 :HTYCPD 1l7mA 180 :LKIAFC T0379 196 :WIPAITRL 1l7mA 186 :AKPILKEK Number of specific fragments extracted= 11 number of extra gaps= 0 total=516 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 1l7pA/T0379-1l7pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1l7pA expands to /projects/compbio/data/pdb/1l7p.pdb.gz 1l7pA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0379 read from 1l7pA/T0379-1l7pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1l7pA read from 1l7pA/T0379-1l7pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1l7pA to template set # found chain 1l7pA in template set T0379 2 :IRNIVFDLGGVLIHLN 1l7pA 5 :KKLILFNFDSTLVNNE T0379 20 :ESIRRFKAIGV 1l7pA 21 :TIDEIAREAGV T0379 31 :ADIE 1l7pA 33 :EEVK T0379 44 :GLFLDLESGRKSEEEFRTELSRYIG 1l7pA 37 :KITKEAMEGKLNFEQSLRKRVSLLK T0379 70 :ELTYQQVYDALLG 1l7pA 62 :DLPIEKVEKAIKR T0379 85 :EEISAEKFDYIDSLR 1l7pA 75 :ITPTEGAEETIKELK T0379 100 :PDYRLFLLSNTNPYVLDLAMSPRF 1l7pA 91 :RGYVVAVVSGGFDIAVNKIKEKLG T0379 130 :LDSFFDKVYASCQMG 1l7pA 115 :LDYAFANRLIVKDGK T0379 145 :KYK 1l7pA 142 :NAK T0379 150 :EDIFLEMIADSGMKPEETLFIDDGPANVATAERLG 1l7pA 145 :GEILEKIAKIEGINLEDTVAVGDGANDISMFKKAG T0379 186 :HTYCP 1l7pA 180 :LKIAF T0379 192 :NGE 1l7pA 185 :CAK T0379 202 :RLLRE 1l7pA 188 :PILKE Number of specific fragments extracted= 13 number of extra gaps= 0 total=529 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 1l7pA/T0379-1l7pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1l7pA/T0379-1l7pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1l7pA read from 1l7pA/T0379-1l7pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1l7pA in template set T0379 2 :IRNIVFDLGGVLIHLNR 1l7pA 5 :KKLILFNFDSTLVNNET T0379 24 :RFKAIGVADIEEMLDPYLQKG 1l7pA 22 :IDEIAREAGVEEEVKKITKEA T0379 45 :LFLDLESGRKSEEEFRTELSRY 1l7pA 46 :KLNFEQSLRKRVSLLKDLPIEK T0379 77 :YDALLGFL 1l7pA 68 :VEKAIKRI T0379 86 :EISAEKFDYIDSLRP 1l7pA 76 :TPTEGAEETIKELKN T0379 101 :DYRLFLLSNTNPYVLDLAMSPRF 1l7pA 92 :GYVVAVVSGGFDIAVNKIKEKLG T0379 134 :FDKVYAS 1l7pA 115 :LDYAFAN T0379 141 :CQMGKY 1l7pA 136 :GEVLKE T0379 150 :EDIFLEMIADSGMKPEETLFIDDGPANVATAERLG 1l7pA 145 :GEILEKIAKIEGINLEDTVAVGDGANDISMFKKAG T0379 186 :HTYCPD 1l7pA 180 :LKIAFC Number of specific fragments extracted= 10 number of extra gaps= 0 total=539 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 1l7pA/T0379-1l7pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1l7pA/T0379-1l7pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1l7pA read from 1l7pA/T0379-1l7pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1l7pA in template set T0379 1 :MIRNIVFDLGGVLIHLNRE 1l7pA 4 :KKKLILFNFDSTLVNNETI T0379 25 :FKAIGVADIEEMLDPYLQKGLFLDLESGRKSEEEFRT 1l7pA 23 :DEIAREAGVEEEVKKITKEAMEGKLNFEQSLRKRVSL T0379 66 :Y 1l7pA 60 :L T0379 67 :IGKELTYQQVYD 1l7pA 62 :DLPIEKVEKAIK T0379 84 :LEEISAEKFDYIDSLR 1l7pA 74 :RITPTEGAEETIKELK T0379 100 :PDYRLFLLSNTNPYVLDLAMS 1l7pA 91 :RGYVVAVVSGGFDIAVNKIKE T0379 127 :GRTL 1l7pA 112 :KLGL T0379 135 :DKVYA 1l7pA 116 :DYAFA T0379 150 :EDIFLEMIADSGMKPEETLFIDDGPANVATAERLG 1l7pA 145 :GEILEKIAKIEGINLEDTVAVGDGANDISMFKKAG T0379 186 :HTYCPD 1l7pA 180 :LKIAFC T0379 196 :WIPAITRL 1l7pA 186 :AKPILKEK Number of specific fragments extracted= 11 number of extra gaps= 0 total=550 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 1vj5A/T0379-1vj5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vj5A expands to /projects/compbio/data/pdb/1vj5.pdb.gz 1vj5A:# T0379 read from 1vj5A/T0379-1vj5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vj5A read from 1vj5A/T0379-1vj5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vj5A to template set # found chain 1vj5A in template set T0379 2 :IRNIVFDLGGVLIHLN 1vj5A 3 :LRAAVFDLDGVLALPA T0379 18 :REESIRRFKAIGVADIEEMLDPYLQ 1vj5A 20 :FGVLGRTEEALALPRGLLNDAFQKG T0379 43 :KGLFLDLESGRKSEEEFRTELSR 1vj5A 47 :EGATTRLMKGEITLSQWIPLMEE T0379 69 :KELTYQQV 1vj5A 84 :KNFSIKEI T0379 77 :YDALLG 1vj5A 93 :DKAISA T0379 85 :EEISAEKFDYIDSLR 1vj5A 99 :RKINRPMLQAALMLR T0379 100 :PDYRLFLLSN 1vj5A 115 :KGFTTAILTN T0379 110 :TNPYVLDLAMSP 1vj5A 131 :AERDGLAQLMCE T0379 130 :LDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGENWIPAI 1vj5A 143 :LKMHFDFLIESCQVGMVKPEPQIYKFLLDTLKASPSEVVFLDDIGANLKPARDLGMVTILVQDTDTALKEL Number of specific fragments extracted= 9 number of extra gaps= 0 total=559 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 1vj5A/T0379-1vj5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1vj5A/T0379-1vj5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vj5A read from 1vj5A/T0379-1vj5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vj5A in template set T0379 2 :IRNIVFDLGGVLIHL 1vj5A 3 :LRAAVFDLDGVLALP T0379 19 :EESIRRFKAIGVADIEEM 1vj5A 18 :AVFGVLGRTEEALALPRG T0379 37 :LDPYLQKGLF 1vj5A 37 :LNDAFQKGGP T0379 47 :LDLESGRKSEEEFRTELSRY 1vj5A 59 :TLSQWIPLMEENCRKCSETA T0379 68 :GK 1vj5A 79 :KV T0379 73 :YQQVYDALLGFLEE 1vj5A 88 :IKEIFDKAISARKI T0379 88 :SAEKFDYIDSLRP 1vj5A 102 :NRPMLQAALMLRK T0379 101 :DYRLFLLSNTN 1vj5A 116 :GFTTAILTNTW T0379 112 :PYVLDLAMSP 1vj5A 133 :RDGLAQLMCE T0379 130 :LDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGENW 1vj5A 143 :LKMHFDFLIESCQVGMVKPEPQIYKFLLDTLKASPSEVVFLDDIGANLKPARDLGMVTILVQDTDTA T0379 200 :ITRLLR 1vj5A 210 :LKELEK Number of specific fragments extracted= 11 number of extra gaps= 0 total=570 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 1vj5A/T0379-1vj5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1vj5A/T0379-1vj5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vj5A read from 1vj5A/T0379-1vj5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vj5A in template set T0379 1 :MIRNIVFDLGGVLIHLNRE 1vj5A 2 :TLRAAVFDLDGVLALPAVF T0379 22 :IRRFKAIGVADIEEMLDPYLQKG 1vj5A 21 :GVLGRTEEALALPRGLLNDAFQK T0379 45 :LFLDLESGRKSEEEFRTELSRY 1vj5A 49 :ATTRLMKGEITLSQWIPLMEEN T0379 67 :IGKELTYQQVYDALLGFL 1vj5A 82 :LPKNFSIKEIFDKAISAR T0379 86 :EISAEKFDYIDSLR 1vj5A 100 :KINRPMLQAALMLR T0379 100 :PDYRLFLLSNTN 1vj5A 115 :KGFTTAILTNTW T0379 112 :PYVLDLAM 1vj5A 133 :RDGLAQLM T0379 128 :RTLDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGENWIPAITRL 1vj5A 141 :CELKMHFDFLIESCQVGMVKPEPQIYKFLLDTLKASPSEVVFLDDIGANLKPARDLGMVTILVQDTDTALKELEKV Number of specific fragments extracted= 8 number of extra gaps= 0 total=578 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 1lvhA/T0379-1lvhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1lvhA expands to /projects/compbio/data/pdb/1lvh.pdb.gz 1lvhA:Bad short name: P for alphabet: pdb_atoms Bad short name: OP1 for alphabet: pdb_atoms Bad short name: OP2 for alphabet: pdb_atoms Bad short name: OP3 for alphabet: pdb_atoms # T0379 read from 1lvhA/T0379-1lvhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lvhA read from 1lvhA/T0379-1lvhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1lvhA to template set # found chain 1lvhA in template set Warning: unaligning (T0379)F7 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1lvhA)L9 Warning: unaligning (T0379)L9 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lvhA)L9 T0379 1 :MIRNIV 1lvhA 1 :MFKAVL T0379 10 :GGVLIHLN 1lvhA 10 :DGVITDTA T0379 18 :REESIRRFKAIGVADIE 1lvhA 21 :FRAWKALAEEIGINGVD T0379 44 :GLFLDLESGRKSEE 1lvhA 38 :RQFNEQLKGVSRED T0379 59 :FRTELSRYIGKELTYQ 1lvhA 52 :SLQKILDLADKKVSAE T0379 75 :QVYDALLGFL 1lvhA 71 :ELAKRKNDNY T0379 85 :EEISAEKFDYIDSLR 1lvhA 90 :ADVYPGILQLLKDLR T0379 100 :PDYRLFLLSNT 1lvhA 106 :NKIKIALASAS T0379 113 :YVLDLAMSPRF 1lvhA 117 :KNGPFLLERMN T0379 130 :LDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGENWIPAI 1lvhA 128 :LTGYFDAIADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQAGIQAIKDSGALPIGVGRPEDLGDDI T0379 201 :TRLLRE 1lvhA 209 :LEFLKE Number of specific fragments extracted= 11 number of extra gaps= 0 total=589 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 1lvhA/T0379-1lvhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1lvhA/T0379-1lvhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lvhA read from 1lvhA/T0379-1lvhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lvhA in template set Warning: unaligning (T0379)F7 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1lvhA)L9 Warning: unaligning (T0379)L9 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lvhA)L9 T0379 1 :MIRNIV 1lvhA 1 :MFKAVL T0379 10 :GGVLIHLNREESIRRFKAIGVADIE 1lvhA 10 :DGVITDTAEYHFRAWKALAEEIGIN T0379 35 :EMLDPYLQKGLFLDLESGRKSEEEF 1lvhA 36 :VDRQFNEQLKGVSREDSLQKILDLA T0379 61 :T 1lvhA 61 :D T0379 62 :ELSRYIGKELTYQQVYDALLGFL 1lvhA 65 :SAEEFKELAKRKNDNYVKMIQDV T0379 85 :E 1lvhA 90 :A T0379 87 :ISAEKFDYIDSLRP 1lvhA 92 :VYPGILQLLKDLRS T0379 101 :DYRLFLLSNT 1lvhA 107 :KIKIALASAS T0379 113 :YVLDLAMSPRF 1lvhA 117 :KNGPFLLERMN T0379 130 :LDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGENWIP 1lvhA 128 :LTGYFDAIADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQAGIQAIKDSGALPIGVGRPEDLGD T0379 199 :AITRLLREQ 1lvhA 211 :FLKEVWLQK Number of specific fragments extracted= 11 number of extra gaps= 0 total=600 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 1lvhA/T0379-1lvhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1lvhA/T0379-1lvhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lvhA read from 1lvhA/T0379-1lvhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lvhA in template set Warning: unaligning (T0379)F7 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1lvhA)L9 Warning: unaligning (T0379)L9 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lvhA)L9 T0379 1 :MIRNIV 1lvhA 1 :MFKAVL T0379 10 :GGVLIHLNREESIRRFKAIGVADIEEMLDPYLQKGLFLDLESGRKSEEEFRTELSRYIGKELTYQQVYDALLGFLEEIS 1lvhA 10 :DGVITDTAEYHFRAWKALAEEIGINGVDRQFNEQLKGVSREDSLQKILDLADKKVSAEEFKELAKRKNDNYVKMIQDVS T0379 89 :AEKFDYIDSLR 1lvhA 94 :PGILQLLKDLR T0379 100 :PDYRLFLLSNTNP 1lvhA 106 :NKIKIALASASKN T0379 115 :LDLAMS 1lvhA 119 :GPFLLE T0379 127 :GRTLDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGENWIP 1lvhA 125 :RMNLTGYFDAIADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQAGIQAIKDSGALPIGVGRPEDLGD Number of specific fragments extracted= 6 number of extra gaps= 0 total=606 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 1cr6A/T0379-1cr6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1cr6A expands to /projects/compbio/data/pdb/1cr6.pdb.gz 1cr6A:# T0379 read from 1cr6A/T0379-1cr6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cr6A read from 1cr6A/T0379-1cr6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1cr6A to template set # found chain 1cr6A in template set Warning: unaligning (T0379)R3 because first residue in template chain is (1cr6A)R4 Warning: unaligning (T0379)E70 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cr6A)Q90 T0379 4 :NIVFDLGGVLIHLN 1cr6A 5 :VAAFDLDGVLALPS T0379 71 :LTYQQVYD 1cr6A 91 :IFSQAMAA T0379 85 :EEISAEKFDYIDSLR 1cr6A 99 :RSINRPMLQAAIALK T0379 100 :PDYRLFLLSN 1cr6A 115 :KGFTTCIVTN T0379 110 :TNPYVLDLAMSP 1cr6A 131 :DKRDSLAQMMCE T0379 130 :LDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGENWIPAI 1cr6A 143 :LSQHFDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGSNLKPARDMGMVTILVHNTASALREL Number of specific fragments extracted= 6 number of extra gaps= 0 total=612 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 1cr6A/T0379-1cr6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1cr6A/T0379-1cr6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cr6A read from 1cr6A/T0379-1cr6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cr6A in template set Warning: unaligning (T0379)R3 because first residue in template chain is (1cr6A)R4 Warning: unaligning (T0379)G68 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cr6A)Q90 T0379 4 :NIVFDLGGVLI 1cr6A 5 :VAAFDLDGVLA T0379 69 :KELT 1cr6A 91 :IFSQ T0379 79 :A 1cr6A 95 :A T0379 81 :LGFL 1cr6A 96 :MAAR T0379 86 :EISAEKFDYIDSLRP 1cr6A 100 :SINRPMLQAAIALKK T0379 101 :DYRLFLLSN 1cr6A 116 :GFTTCIVTN T0379 110 :TNPYVLDLAMSP 1cr6A 131 :DKRDSLAQMMCE T0379 130 :LDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNG 1cr6A 143 :LSQHFDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGSNLKPARDMGMVTILVHNT T0379 200 :ITRLLRE 1cr6A 207 :ASALREL Number of specific fragments extracted= 9 number of extra gaps= 0 total=621 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 1cr6A/T0379-1cr6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1cr6A/T0379-1cr6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cr6A read from 1cr6A/T0379-1cr6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cr6A in template set Warning: unaligning (T0379)R3 because first residue in template chain is (1cr6A)R4 Warning: unaligning (T0379)R18 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cr6A)G48 Warning: unaligning (T0379)L47 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cr6A)G48 Warning: unaligning (T0379)E62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cr6A)Q90 Warning: unaligning (T0379)G68 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cr6A)Q90 T0379 4 :NIVFDLGGVLIHLN 1cr6A 5 :VAAFDLDGVLALPS T0379 48 :DLESGRKSEEEFRT 1cr6A 49 :PTEQLMKGKITFSQ T0379 69 :KELTYQ 1cr6A 91 :IFSQAM T0379 83 :FLEEISAEKFDYIDSLR 1cr6A 97 :AARSINRPMLQAAIALK T0379 100 :PDYRLFLLSN 1cr6A 115 :KGFTTCIVTN T0379 110 :TNPYVLDLAMS 1cr6A 131 :DKRDSLAQMMC T0379 129 :TLDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNG 1cr6A 142 :ELSQHFDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGSNLKPARDMGMVTILVHNT T0379 194 :ENWIPAITRLLREQ 1cr6A 208 :SALRELEKVTGTQF Number of specific fragments extracted= 8 number of extra gaps= 0 total=629 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 2c4nA/T0379-2c4nA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2c4nA expands to /projects/compbio/data/pdb/2c4n.pdb.gz 2c4nA:# T0379 read from 2c4nA/T0379-2c4nA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c4nA read from 2c4nA/T0379-2c4nA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2c4nA to template set # found chain 2c4nA in template set Warning: unaligning (T0379)I14 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c4nA)H16 Warning: unaligning (T0379)H15 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c4nA)H16 T0379 1 :M 2c4nA 1 :M T0379 2 :IRNIVFDLGGVL 2c4nA 3 :IKNVICDIDGVL T0379 16 :LN 2c4nA 17 :DN T0379 18 :REESIRRFKAIGVADIEEMLDP 2c4nA 24 :AAEFLHGIMDKGLPLVLLTNYP T0379 70 :ELTYQQVYDALLGFL 2c4nA 46 :SQTGQDLANRFATAG T0379 85 :EEISAEKFDYIDSLR 2c4nA 120 :RSYNWDMMHKAAYFV T0379 100 :PDYR 2c4nA 136 :NGAR T0379 105 :FLLSNTNP 2c4nA 140 :FIATNPDT T0379 122 :RFLPSGRTLDSFFDKVYASCQMG 2c4nA 148 :HGRGFYPACGALCAGIEKISGRK T0379 145 :KYKPNEDIFLEMIADSGMKPEETLFIDDGPA 2c4nA 174 :VGKPSPWIIRAALNKMQAHSEETVIVGDNLR T0379 176 :NVATAERLGFHTYCPDNGENWIPAI 2c4nA 206 :DILAGFQAGLETILVLSGVSSLDDI T0379 202 :RLLRE 2c4nA 242 :PSVAE Number of specific fragments extracted= 12 number of extra gaps= 1 total=641 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 2c4nA/T0379-2c4nA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 2c4nA/T0379-2c4nA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c4nA read from 2c4nA/T0379-2c4nA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2c4nA in template set Warning: unaligning (T0379)I14 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c4nA)H16 Warning: unaligning (T0379)H15 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c4nA)H16 T0379 1 :M 2c4nA 1 :M T0379 2 :IRNIVFDLGGVL 2c4nA 3 :IKNVICDIDGVL T0379 16 :LNREESIRRFKAIGV 2c4nA 20 :AVPGAAEFLHGIMDK T0379 32 :DIE 2c4nA 35 :GLP T0379 44 :GLFLDLE 2c4nA 44 :YPSQTGQ T0379 54 :KSEEEF 2c4nA 51 :DLANRF T0379 83 :FLEEISAEKFDYIDS 2c4nA 118 :ETRSYNWDMMHKAAY T0379 98 :LRPDYRL 2c4nA 134 :VANGARF T0379 106 :LLSNTNP 2c4nA 141 :IATNPDT T0379 122 :RFLPSGRTLDSFFDKVYASCQMG 2c4nA 148 :HGRGFYPACGALCAGIEKISGRK T0379 145 :KYKPNEDIFLEMIADSGMKPEETLFIDDGP 2c4nA 174 :VGKPSPWIIRAALNKMQAHSEETVIVGDNL T0379 175 :ANVATAERLGFHTYCPDNGENWIPAITR 2c4nA 205 :TDILAGFQAGLETILVLSGVSSLDDIDS Number of specific fragments extracted= 12 number of extra gaps= 1 total=653 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 2c4nA/T0379-2c4nA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 2c4nA/T0379-2c4nA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c4nA read from 2c4nA/T0379-2c4nA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2c4nA in template set Warning: unaligning (T0379)I14 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c4nA)H16 Warning: unaligning (T0379)H15 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c4nA)H16 T0379 1 :MIRNIVFDLGGVL 2c4nA 2 :TIKNVICDIDGVL T0379 84 :LEEISAEKFDYIDSLR 2c4nA 17 :DNVAVPGAAEFLHGIM T0379 100 :PDYRLFLLSN 2c4nA 34 :KGLPLVLLTN T0379 110 :TNPYVLDLAMS 2c4nA 47 :QTGQDLANRFA T0379 127 :GRTL 2c4nA 58 :TAGV T0379 131 :DSF 2c4nA 65 :DSV T0379 137 :VYASCQM 2c4nA 68 :FYTSAMA T0379 145 :KYKPNEDIFLEMIADSGMKPEETLFIDDGP 2c4nA 174 :VGKPSPWIIRAALNKMQAHSEETVIVGDNL T0379 175 :ANVATAERLGFHTYCPDNGENWIPAI 2c4nA 205 :TDILAGFQAGLETILVLSGVSSLDDI Number of specific fragments extracted= 9 number of extra gaps= 1 total=662 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 1qyiA/T0379-1qyiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1qyiA expands to /projects/compbio/data/pdb/1qyi.pdb.gz 1qyiA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0379 read from 1qyiA/T0379-1qyiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qyiA read from 1qyiA/T0379-1qyiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1qyiA to template set # found chain 1qyiA in template set T0379 1 :M 1qyiA 1 :M T0379 3 :RNIVFDLGGVLIHLN 1qyiA 2 :KKILFDVDGVFLSEE T0379 18 :REESIRRFKAIGVADIEEML 1qyiA 62 :KDKILNKLKSLGLNSNWDML T0379 47 :LDLESGRKSEEEFRTELSR 1qyiA 89 :LIDILKKLSHDEIEAFMYQ T0379 66 :YIG 1qyiA 136 :FLD T0379 69 :KELTYQQVYDALLGFL 1qyiA 140 :VKVGKNNIYAALEEFA T0379 85 :EEISAEKFDYIDSLR 1qyiA 214 :LRPVDEVKVLLNDLK T0379 100 :PDYRLFLLSNTNPYVLDLAMSPRF 1qyiA 230 :AGFELGIATGRPYTETVVPFENLG T0379 130 :LDSFF 1qyiA 254 :LLPYF T0379 135 :DKVYA 1qyiA 261 :DFIAT T0379 150 :EDIFLEMIADS 1qyiA 266 :ASDVLEAENMY T0379 162 :MKPEETLFIDDGPANVATAERLGFHTYCPDNGENWIPAI 1qyiA 313 :VNKDDVFIVGDSLADLLSAQKIGATFIGTLTGLKGKDAA T0379 202 :RLLREQ 1qyiA 352 :GELEAH Number of specific fragments extracted= 13 number of extra gaps= 0 total=675 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 1qyiA/T0379-1qyiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1qyiA/T0379-1qyiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qyiA read from 1qyiA/T0379-1qyiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qyiA in template set T0379 1 :M 1qyiA 1 :M T0379 3 :RNIVFDLGGVLI 1qyiA 2 :KKILFDVDGVFL T0379 16 :LNREESIRRFKAIGVA 1qyiA 14 :SEERCFDVSALTVYEL T0379 32 :DIE 1qyiA 37 :GLH T0379 35 :EMLD 1qyiA 42 :IDWE T0379 46 :FLDLESGRKSEEEF 1qyiA 46 :TLTDNDIQDIRNRI T0379 60 :RTELSRYIGKELTYQQVYDALLGFL 1qyiA 174 :WTLAQEVYQEWYLGSKLYEDVEKKI T0379 85 :EE 1qyiA 201 :TT T0379 87 :ISAEKFDYIDSLRP 1qyiA 216 :PVDEVKVLLNDLKG T0379 101 :DYRLFLLSNTNPYVLDLAMSPRF 1qyiA 231 :GFELGIATGRPYTETVVPFENLG T0379 130 :LDSFF 1qyiA 254 :LLPYF T0379 135 :DKVYASCQM 1qyiA 261 :DFIATASDV T0379 144 :GK 1qyiA 277 :PQ T0379 146 :YKPNEDIFLEMIA 1qyiA 283 :GKPNPFSYIAALY T0379 161 :G 1qyiA 296 :G T0379 162 :MKPEETLFIDDGPANVATAERLGFHTYCPDNGENWIPAITRLLREQ 1qyiA 313 :VNKDDVFIVGDSLADLLSAQKIGATFIGTLTGLKGKDAAGELEAHH Number of specific fragments extracted= 16 number of extra gaps= 0 total=691 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 1qyiA/T0379-1qyiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1qyiA/T0379-1qyiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qyiA read from 1qyiA/T0379-1qyiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qyiA in template set T0379 3 :RNIVFDLGGVLIHLNREESIRRFKAIGVAD 1qyiA 2 :KKILFDVDGVFLSEERCFDVSALTVYELLM T0379 33 :IEEMLDPYLQKGLFLDLESGRKSEEEFRTELSRY 1qyiA 44 :WETLTDNDIQDIRNRIFQKDKILNKLKSLGLNSN T0379 67 :IGKELTYQQVYDALLGFLEEIS 1qyiA 181 :YQEWYLGSKLYEDVEKKIARTT T0379 89 :AEKFDYIDSLR 1qyiA 218 :DEVKVLLNDLK T0379 100 :PDYRLFLLSNTNPYVLDLAMS 1qyiA 230 :AGFELGIATGRPYTETVVPFE T0379 127 :GRTLDSFF 1qyiA 251 :NLGLLPYF T0379 135 :DKVYASCQMG 1qyiA 261 :DFIATASDVL T0379 145 :KYKPNEDIFLEMIA 1qyiA 282 :LGKPNPFSYIAALY T0379 162 :MKPEETLFIDDGPANVATAERLGFHTYCPDN 1qyiA 313 :VNKDDVFIVGDSLADLLSAQKIGATFIGTLT T0379 193 :GENWIPAITRL 1qyiA 347 :GKDAAGELEAH Number of specific fragments extracted= 10 number of extra gaps= 0 total=701 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 1zs9A/T0379-1zs9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zs9A expands to /projects/compbio/data/pdb/1zs9.pdb.gz 1zs9A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0379 read from 1zs9A/T0379-1zs9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zs9A read from 1zs9A/T0379-1zs9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zs9A to template set # found chain 1zs9A in template set T0379 2 :IRNIVFDLGGVLIHLN 1zs9A 10 :VTVILLDIEGTTTPIA T0379 56 :EEEFRTELSR 1zs9A 52 :CQQDVSLLRK T0379 69 :KELTYQQVYDALLGFL 1zs9A 79 :SGNGVDDLQQMIQAVV T0379 85 :EEISAEKFDYIDSLR 1zs9A 129 :AEFFADVVPAVRKWR T0379 100 :PDYRLFLLSNTNPYVLDLAMSPRFLPS 1zs9A 145 :AGMKVYIYSSGSVEAQKLLFGHSTEGD T0379 130 :LDSFFDKVYA 1zs9A 172 :ILELVDGHFD T0379 142 :QMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGEN 1zs9A 182 :TKIGHKVESESYRKIADSIGCSTNNILFLTDVTREASAAEEADVHVAVVVRPGN T0379 198 :PAITRL 1zs9A 236 :AGLTDD Number of specific fragments extracted= 8 number of extra gaps= 0 total=709 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 1zs9A/T0379-1zs9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1zs9A/T0379-1zs9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zs9A read from 1zs9A/T0379-1zs9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zs9A in template set Warning: unaligning (T0379)L63 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1zs9A)K106 Warning: unaligning (T0379)R65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zs9A)K106 T0379 2 :IRNIVFDLGGVLIH 1zs9A 10 :VTVILLDIEGTTTP T0379 16 :LNREESIRRFKAIGVA 1zs9A 31 :LFPYIEENVKEYLQTH T0379 32 :DIE 1zs9A 48 :EEE T0379 47 :LDLESGRKSEEEF 1zs9A 51 :ECQQDVSLLRKQA T0379 60 :RTE 1zs9A 101 :MSL T0379 66 :YIGKELTYQQVYDALLGFL 1zs9A 107 :TTALKQLQGHMWRAAFTAG T0379 85 :EEISAEKFDYIDSLRP 1zs9A 129 :AEFFADVVPAVRKWRE T0379 101 :DYRLFLLSNTNPYVLDLAMSPRF 1zs9A 146 :GMKVYIYSSGSVEAQKLLFGHST T0379 127 :GRTLDSFFDKVY 1zs9A 169 :EGDILELVDGHF T0379 141 :CQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGENWI 1zs9A 181 :DTKIGHKVESESYRKIADSIGCSTNNILFLTDVTREASAAEEADVHVAVVVRPGNAG T0379 200 :ITRLLRE 1zs9A 238 :LTDDEKT Number of specific fragments extracted= 11 number of extra gaps= 0 total=720 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 1zs9A/T0379-1zs9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1zs9A/T0379-1zs9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zs9A read from 1zs9A/T0379-1zs9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zs9A in template set T0379 2 :IRNIVFDLGGVLIHLNRE 1zs9A 10 :VTVILLDIEGTTTPIAFV T0379 30 :VADIEEMLDPYLQKGLFLDL 1zs9A 28 :KDILFPYIEENVKEYLQTHW T0379 50 :ESGRKSEEEFRTELSRY 1zs9A 50 :EECQQDVSLLRKQAEED T0379 67 :IGKELTYQQVYDALLGFLE 1zs9A 108 :TALKQLQGHMWRAAFTAGR T0379 86 :EISAEKFDYIDSLR 1zs9A 130 :EFFADVVPAVRKWR T0379 100 :PDYRLFLLSNTNPYVLDLAMS 1zs9A 145 :AGMKVYIYSSGSVEAQKLLFG T0379 124 :LPSGRTLDSFFDKVYA 1zs9A 166 :HSTEGDILELVDGHFD T0379 142 :QMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGE 1zs9A 182 :TKIGHKVESESYRKIADSIGCSTNNILFLTDVTREASAAEEADVHVAVVVRPG Number of specific fragments extracted= 8 number of extra gaps= 0 total=728 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 1cqzA/T0379-1cqzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1cqzA expands to /projects/compbio/data/pdb/1cqz.pdb.gz 1cqzA:# T0379 read from 1cqzA/T0379-1cqzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cqzA read from 1cqzA/T0379-1cqzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1cqzA to template set # found chain 1cqzA in template set Warning: unaligning (T0379)R3 because first residue in template chain is (1cqzA)R4 Warning: unaligning (T0379)R53 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cqzA)Q90 T0379 4 :NIVFDLGGVLIHLN 1cqzA 5 :VAAFDLDGVLALPS T0379 54 :KSE 1cqzA 91 :IFS T0379 78 :DALLG 1cqzA 94 :QAMAA T0379 85 :EEISAEKFDYIDSLR 1cqzA 99 :RSINRPMLQAAIALK T0379 100 :PDYRLFLLSN 1cqzA 115 :KGFTTCIVTN T0379 110 :TNPYVLDLAMSP 1cqzA 131 :DKRDSLAQMMCE T0379 130 :LDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGENWIPA 1cqzA 143 :LSQHFDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGSNLKPARDMGMVTILVHNTASALRE Number of specific fragments extracted= 7 number of extra gaps= 0 total=735 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 1cqzA/T0379-1cqzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1cqzA/T0379-1cqzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cqzA read from 1cqzA/T0379-1cqzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cqzA in template set Warning: unaligning (T0379)R3 because first residue in template chain is (1cqzA)R4 Warning: unaligning (T0379)R18 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cqzA)G48 T0379 4 :NIVFDLGGVLIHLN 1cqzA 5 :VAAFDLDGVLALPS T0379 78 :DALLGF 1cqzA 94 :QAMAAR T0379 86 :EISAEKFDYIDSLRP 1cqzA 100 :SINRPMLQAAIALKK T0379 101 :DYRLFLLSN 1cqzA 116 :GFTTCIVTN T0379 110 :TNPYVLDLAMSP 1cqzA 131 :DKRDSLAQMMCE T0379 130 :LDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGEN 1cqzA 143 :LSQHFDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGSNLKPARDMGMVTILVHNTAS T0379 202 :RLL 1cqzA 209 :ALR Number of specific fragments extracted= 7 number of extra gaps= 0 total=742 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 1cqzA/T0379-1cqzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1cqzA/T0379-1cqzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cqzA read from 1cqzA/T0379-1cqzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cqzA in template set Warning: unaligning (T0379)R3 because first residue in template chain is (1cqzA)R4 Warning: unaligning (T0379)R18 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cqzA)G48 Warning: unaligning (T0379)L47 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cqzA)G48 Warning: unaligning (T0379)E62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cqzA)Q90 Warning: unaligning (T0379)I67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cqzA)Q90 T0379 4 :NIVFDLGGVLIHLN 1cqzA 5 :VAAFDLDGVLALPS T0379 48 :DLESGRKSEEEFRT 1cqzA 49 :PTEQLMKGKITFSQ T0379 68 :GKELTY 1cqzA 91 :IFSQAM T0379 83 :FLEEISAEKFDYIDSLR 1cqzA 97 :AARSINRPMLQAAIALK T0379 100 :PDYRLFLLSN 1cqzA 115 :KGFTTCIVTN T0379 110 :TNPYVLDLAMS 1cqzA 131 :DKRDSLAQMMC T0379 129 :TLDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNG 1cqzA 142 :ELSQHFDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGSNLKPARDMGMVTILVHNT T0379 194 :ENWIPAITRLLREQK 1cqzA 208 :SALRELEKVTGTQFP Number of specific fragments extracted= 8 number of extra gaps= 0 total=750 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 1j97A/T0379-1j97A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1j97A expands to /projects/compbio/data/pdb/1j97.pdb.gz 1j97A:Bad short name: BE for alphabet: pdb_atoms Bad short name: F1 for alphabet: pdb_atoms Bad short name: F2 for alphabet: pdb_atoms Bad short name: F3 for alphabet: pdb_atoms # T0379 read from 1j97A/T0379-1j97A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j97A read from 1j97A/T0379-1j97A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1j97A to template set # found chain 1j97A in template set Warning: unaligning (T0379)F7 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1j97A)F12 Warning: unaligning (T0379)L9 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1j97A)F12 T0379 2 :IRNIV 1j97A 5 :KKLIL T0379 10 :GGVLIHLN 1j97A 13 :DSTLVNNE T0379 20 :ESIRRFKAIGV 1j97A 21 :TIDEIAREAGV T0379 31 :ADIE 1j97A 33 :EEVK T0379 44 :GLFLDLESGRKSEEEFRTELSRYIG 1j97A 37 :KITKEAMEGKLNFEQSLRKRVSLLK T0379 70 :ELTYQQVYDALLG 1j97A 62 :DLPIEKVEKAIKR T0379 85 :EEISAEKFDYIDSLR 1j97A 75 :ITPTEGAEETIKELK T0379 100 :PDYRLFLLSNTNPYVLDLAMSPRF 1j97A 91 :RGYVVAVVSGGFDIAVNKIKEKLG T0379 130 :LDSFFDKVYASCQ 1j97A 115 :LDYAFANRLIVKD T0379 145 :KYK 1j97A 142 :NAK T0379 150 :EDIFLEMIADSGMKPEETLFIDDGPANVATAERLG 1j97A 145 :GEILEKIAKIEGINLEDTVAVGDGANDISMFKKAG T0379 186 :HTYCP 1j97A 180 :LKIAF T0379 192 :NGE 1j97A 185 :CAK T0379 202 :RLLRE 1j97A 188 :PILKE Number of specific fragments extracted= 14 number of extra gaps= 0 total=764 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 1j97A/T0379-1j97A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1j97A/T0379-1j97A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j97A read from 1j97A/T0379-1j97A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1j97A in template set Warning: unaligning (T0379)F7 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1j97A)F12 Warning: unaligning (T0379)L9 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1j97A)F12 T0379 2 :IRNIV 1j97A 5 :KKLIL T0379 10 :GGVLIHLNR 1j97A 13 :DSTLVNNET T0379 24 :RFKAIGVADIEEMLDPYLQKG 1j97A 22 :IDEIAREAGVEEEVKKITKEA T0379 45 :LFLDLESGRKSEEEFRTELSRY 1j97A 46 :KLNFEQSLRKRVSLLKDLPIEK T0379 77 :YDALLGFL 1j97A 68 :VEKAIKRI T0379 86 :EISAEKFDYIDSLRP 1j97A 76 :TPTEGAEETIKELKN T0379 101 :DYRLFLLSNTNPYVLDLAMSPRF 1j97A 92 :GYVVAVVSGGFDIAVNKIKEKLG T0379 134 :FDKVYAS 1j97A 115 :LDYAFAN T0379 141 :CQMGKY 1j97A 136 :GEVLKE T0379 150 :EDIFLEMIADSGMKPEETLFIDDGPANVATAERLG 1j97A 145 :GEILEKIAKIEGINLEDTVAVGDGANDISMFKKAG T0379 186 :HTYCPDN 1j97A 180 :LKIAFCA Number of specific fragments extracted= 11 number of extra gaps= 0 total=775 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 1j97A/T0379-1j97A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1j97A/T0379-1j97A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j97A read from 1j97A/T0379-1j97A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1j97A in template set Warning: unaligning (T0379)F7 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1j97A)F12 Warning: unaligning (T0379)L9 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1j97A)F12 T0379 1 :MIRNIV 1j97A 4 :KKKLIL T0379 10 :GGVLIHLNRE 1j97A 13 :DSTLVNNETI T0379 25 :FKAIGVADIEEMLDPYLQKGLFLDLESGRKSEEEFRT 1j97A 23 :DEIAREAGVEEEVKKITKEAMEGKLNFEQSLRKRVSL T0379 63 :L 1j97A 60 :L T0379 67 :IGKELTYQQVYD 1j97A 62 :DLPIEKVEKAIK T0379 84 :LEEISAEKFDYIDSLR 1j97A 74 :RITPTEGAEETIKELK T0379 100 :PDYRLFLLSNTNPYVLDLAMS 1j97A 91 :RGYVVAVVSGGFDIAVNKIKE T0379 127 :GRTL 1j97A 112 :KLGL T0379 135 :DKVYA 1j97A 116 :DYAFA T0379 150 :EDIFLEMIADSGMKPEETLFIDDGPANVATAERLG 1j97A 145 :GEILEKIAKIEGINLEDTVAVGDGANDISMFKKAG T0379 186 :HTYCPD 1j97A 180 :LKIAFC T0379 196 :WIPAITR 1j97A 186 :AKPILKE Number of specific fragments extracted= 12 number of extra gaps= 0 total=787 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 1cr6B/T0379-1cr6B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1cr6B expands to /projects/compbio/data/pdb/1cr6.pdb.gz 1cr6B:# T0379 read from 1cr6B/T0379-1cr6B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cr6B read from 1cr6B/T0379-1cr6B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1cr6B to template set # found chain 1cr6B in template set Warning: unaligning (T0379)R3 because first residue in template chain is (1cr6B)R4 T0379 4 :NIVFDLGGVLIHLNREESIRRFKAI 1cr6B 5 :VAAFDLDGVLALPSIAGAFRRSEEA T0379 29 :GVADIEEMLDPYLQ 1cr6B 31 :ALPRDFLLGAYQTE T0379 43 :KGLFLDLESGRKSEEEFRTELSRYIG 1cr6B 47 :EGPTEQLMKGKITFSQWVPLMDESYR T0379 69 :KELT 1cr6B 80 :ANLP T0379 73 :YQQVYDALLG 1cr6B 89 :SQIFSQAMAA T0379 85 :EEISAEKFDYIDSLR 1cr6B 99 :RSINRPMLQAAIALK T0379 100 :PDYRLFLLSN 1cr6B 115 :KGFTTCIVTN T0379 112 :PYVLDLAMSP 1cr6B 133 :RDSLAQMMCE T0379 130 :LDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGENWIPA 1cr6B 143 :LSQHFDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGSNLKPARDMGMVTILVHNTASALRE Number of specific fragments extracted= 9 number of extra gaps= 0 total=796 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 1cr6B/T0379-1cr6B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1cr6B/T0379-1cr6B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cr6B read from 1cr6B/T0379-1cr6B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cr6B in template set Warning: unaligning (T0379)R3 because first residue in template chain is (1cr6B)R4 T0379 4 :NIVFDLGGVLI 1cr6B 5 :VAAFDLDGVLA T0379 17 :NREESIRRFKAIGVA 1cr6B 16 :LPSIAGAFRRSEEAL T0379 32 :DIEEMLDPYL 1cr6B 45 :FPEGPTEQLM T0379 43 :KGLFLDLESGRKSEEEFRTEL 1cr6B 55 :KGKITFSQWVPLMDESYRKSS T0379 73 :YQQVYDALLGFL 1cr6B 88 :ISQIFSQAMAAR T0379 86 :EISAEKFDYIDSLRP 1cr6B 100 :SINRPMLQAAIALKK T0379 101 :DYRLFLLSNTN 1cr6B 116 :GFTTCIVTNNW T0379 112 :PYVLDLAMSP 1cr6B 133 :RDSLAQMMCE T0379 130 :LDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGENW 1cr6B 143 :LSQHFDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGSNLKPARDMGMVTILVHNTASA Number of specific fragments extracted= 9 number of extra gaps= 0 total=805 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 1cr6B/T0379-1cr6B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1cr6B/T0379-1cr6B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cr6B read from 1cr6B/T0379-1cr6B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cr6B in template set Warning: unaligning (T0379)R3 because first residue in template chain is (1cr6B)R4 T0379 4 :NIVFDLGGVLIHLNRE 1cr6B 5 :VAAFDLDGVLALPSIA T0379 22 :IRRFKAIGVADIEEM 1cr6B 21 :GAFRRSEEALALPRD T0379 39 :PYLQKGLFLDLESGRKSEEEFRTELSRY 1cr6B 47 :EGPTEQLMKGKITFSQWVPLMDESYRKS T0379 67 :IGKELTYQQVYDALLGF 1cr6B 82 :LPENFSISQIFSQAMAA T0379 85 :EEISAEKFDYIDSLR 1cr6B 99 :RSINRPMLQAAIALK T0379 100 :PDYRLFLLSNTN 1cr6B 115 :KGFTTCIVTNNW T0379 112 :PYVLDLAMS 1cr6B 133 :RDSLAQMMC T0379 129 :TLDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGE 1cr6B 142 :ELSQHFDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGSNLKPARDMGMVTILVHNTA Number of specific fragments extracted= 8 number of extra gaps= 0 total=813 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 1zjjA/T0379-1zjjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zjjA expands to /projects/compbio/data/pdb/1zjj.pdb.gz 1zjjA:# T0379 read from 1zjjA/T0379-1zjjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zjjA read from 1zjjA/T0379-1zjjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zjjA to template set # found chain 1zjjA in template set T0379 3 :RNIVFDLGGVLIHLN 1zjjA 2 :VAIIFDMDGVLYRGN T0379 18 :REESIRRFKAIGVADIEEMLDPY 1zjjA 22 :VRELIEFLKERGIPFAFLTNNST T0379 54 :KSEEEFRTELSR 1zjjA 45 :KTPEMYREKLLK T0379 85 :EEISAEKFDYIDSLR 1zjjA 128 :PDLTYEKLKYATLAI T0379 100 :PDYR 1zjjA 144 :NGAT T0379 105 :FLLSN 1zjjA 148 :FIGTN T0379 110 :TNPYVLDLAMSPRF 1zjjA 166 :GAGSIIAALKVATN T0379 130 :LD 1zjjA 180 :VE T0379 134 :FDKV 1zjjA 182 :PIII T0379 146 :YKPNEDIFLEMIADS 1zjjA 186 :GKPNEPMYEVVREMF T0379 161 :G 1zjjA 202 :G T0379 165 :EETLFIDDGPA 1zjjA 203 :EELWMVGDRLD T0379 176 :NVATAERLGFHTYCPDNGENWIPAI 1zjjA 215 :DIAFAKKFGMKAIMVLTGVSSLEDI T0379 201 :TRLL 1zjjA 257 :IDYL Number of specific fragments extracted= 14 number of extra gaps= 0 total=827 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 1zjjA/T0379-1zjjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1zjjA/T0379-1zjjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zjjA read from 1zjjA/T0379-1zjjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zjjA in template set T0379 3 :RNIVFDLGGVLIH 1zjjA 2 :VAIIFDMDGVLYR T0379 16 :LNRE 1zjjA 18 :AIPG T0379 21 :SIRRFKAIGVADIE 1zjjA 22 :VRELIEFLKERGIP T0379 35 :EMLDPYLQKGLF 1zjjA 45 :KTPEMYREKLLK T0379 83 :FLEEISAEKFDYIDSLRP 1zjjA 126 :LDPDLTYEKLKYATLAIR T0379 101 :DYRL 1zjjA 145 :GATF T0379 106 :LLSNTNP 1zjjA 149 :IGTNPDA T0379 113 :YVLDLAMSPRF 1zjjA 172 :AALKVATNVEP T0379 138 :YAS 1zjjA 183 :III T0379 146 :YKPNEDIFLEMIADSG 1zjjA 186 :GKPNEPMYEVVREMFP T0379 164 :PEETLFIDDGP 1zjjA 202 :GEELWMVGDRL T0379 175 :ANVATAERLGFHTYCPDNGENWIP 1zjjA 214 :TDIAFAKKFGMKAIMVLTGVSSLE T0379 199 :AITRLL 1zjjA 252 :SVYELI Number of specific fragments extracted= 13 number of extra gaps= 0 total=840 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 1zjjA/T0379-1zjjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1zjjA/T0379-1zjjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zjjA read from 1zjjA/T0379-1zjjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zjjA in template set T0379 3 :RNIVFDLGGVLIH 1zjjA 2 :VAIIFDMDGVLYR T0379 84 :LEEISAEKFDYIDSLR 1zjjA 15 :GNRAIPGVRELIEFLK T0379 100 :PDYRLFLLSN 1zjjA 32 :RGIPFAFLTN T0379 110 :TNPYVLDLAMSPRFLPSGRTL 1zjjA 45 :KTPEMYREKLLKMGIDVSSSI T0379 137 :VYASCQMG 1zjjA 66 :IITSGLAT T0379 145 :KYKPN 1zjjA 185 :IGKPN T0379 151 :DIFLEMIADS 1zjjA 190 :EPMYEVVREM T0379 165 :EETLFIDDGP 1zjjA 203 :EELWMVGDRL T0379 175 :ANVATAERLGFHTYCPDNGENWIPAITR 1zjjA 214 :TDIAFAKKFGMKAIMVLTGVSSLEDIKK Number of specific fragments extracted= 9 number of extra gaps= 0 total=849 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 1u7pA/T0379-1u7pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1u7pA expands to /projects/compbio/data/pdb/1u7p.pdb.gz 1u7pA:# T0379 read from 1u7pA/T0379-1u7pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u7pA read from 1u7pA/T0379-1u7pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1u7pA to template set # found chain 1u7pA in template set T0379 1 :M 1u7pA 1 :M T0379 2 :IRNIVFDLGGVLIHLN 1u7pA 5 :PKLAVFDLDYTLWPFW T0379 30 :VADIE 1u7pA 29 :FHKSS T0379 44 :GLFLDLESGRK 1u7pA 34 :DGTVRDRRGQN T0379 85 :EEISAEKFDYIDSLR 1u7pA 45 :IQLYPEVPEVLGRLQ T0379 100 :PDYRLFLLSN 1u7pA 61 :LGVPVAAASR T0379 110 :TNPYVLDLAMSPRF 1u7pA 72 :SEIQGANQLLELFD T0379 130 :LDSFFDKVYA 1u7pA 86 :LGKYFIQREI T0379 143 :MGKYK 1u7pA 96 :YPGSK T0379 150 :EDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNG 1u7pA 101 :VTHFERLHHKTGVPFSQMVFFDDENRNIIDVGRLGVTCIHIRDG T0379 195 :NWIPAI 1u7pA 145 :MSLQTL Number of specific fragments extracted= 11 number of extra gaps= 0 total=860 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 1u7pA/T0379-1u7pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1u7pA/T0379-1u7pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u7pA read from 1u7pA/T0379-1u7pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1u7pA in template set T0379 1 :M 1u7pA 1 :M T0379 2 :IRNIVFDLGGVLIHLNR 1u7pA 5 :PKLAVFDLDYTLWPFWV T0379 30 :VADIEEM 1u7pA 22 :DTHVDPP T0379 61 :T 1u7pA 35 :G T0379 82 :GFL 1u7pA 40 :RRG T0379 85 :EEISAEKFDYIDSLRP 1u7pA 45 :IQLYPEVPEVLGRLQS T0379 101 :DYRLFLLSN 1u7pA 62 :GVPVAAASR T0379 110 :TNPYVLDLAMSPRF 1u7pA 72 :SEIQGANQLLELFD T0379 130 :LDSFFDKVYA 1u7pA 86 :LGKYFIQREI T0379 145 :KYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNG 1u7pA 96 :YPGSKVTHFERLHHKTGVPFSQMVFFDDENRNIIDVGRLGVTCIHIRDG T0379 195 :NWIPAITRLLRE 1u7pA 145 :MSLQTLTQGLET Number of specific fragments extracted= 11 number of extra gaps= 0 total=871 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 1u7pA/T0379-1u7pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1u7pA/T0379-1u7pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u7pA read from 1u7pA/T0379-1u7pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1u7pA in template set T0379 2 :IRNIVFDLGGVLIHLNRE 1u7pA 5 :PKLAVFDLDYTLWPFWVD T0379 65 :RY 1u7pA 23 :TH T0379 85 :EEISAEKFDYIDSLR 1u7pA 45 :IQLYPEVPEVLGRLQ T0379 100 :PDYRLFLLSN 1u7pA 61 :LGVPVAAASR T0379 110 :TNPYVLDLAMS 1u7pA 72 :SEIQGANQLLE T0379 127 :GRTLDSFFDKVYA 1u7pA 83 :LFDLGKYFIQREI T0379 145 :KYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNG 1u7pA 96 :YPGSKVTHFERLHHKTGVPFSQMVFFDDENRNIIDVGRLGVTCIHIRDG T0379 194 :ENWIP 1u7pA 151 :TQGLE Number of specific fragments extracted= 8 number of extra gaps= 0 total=879 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 1yv9A/T0379-1yv9A-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1yv9A expands to /projects/compbio/data/pdb/1yv9.pdb.gz 1yv9A:# T0379 read from 1yv9A/T0379-1yv9A-t06-local-adpstyle5.a2m # 1yv9A read from 1yv9A/T0379-1yv9A-t06-local-adpstyle5.a2m # adding 1yv9A to template set # found chain 1yv9A in template set T0379 2 :IRNIVFDLGGVLIHLN 1yv9A 5 :YQGYLIDLDGTIYLGK T0379 18 :REESIRRFKAIGVADIEEMLDPYLQKGLF 1yv9A 26 :GKRFVERLQEKDLPFLFVTNNTTKSPETV T0379 47 :LDLESGRKSEEEFRTELSRYI 1yv9A 91 :VFVIGEAGLIDLILEAGFEWD T0379 70 :ELTYQQVYDALLG 1yv9A 112 :ETNPDYVVVGLDT T0379 85 :EEISAEK 1yv9A 125 :ELSYEKV T0379 94 :YIDSLR 1yv9A 132 :VLATLA T0379 100 :PDYRLFLLSNTNPYVLDLAMSPRFLPS 1yv9A 139 :QKGALFIGTNPDKNIPTERGLLPGAGS T0379 130 :LDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPA 1yv9A 166 :VVTFVETATQTKPVYIGKPKAIIMERAIAHLGVEKEQVIMVGDNYE T0379 176 :NVATAERLGFHTYCPDNGENWIPAI 1yv9A 213 :DIQSGIQNGIDSLLVTSGFTPKSAV T0379 201 :TRLL 1yv9A 244 :PTYV Number of specific fragments extracted= 10 number of extra gaps= 0 total=889 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 1ys9A/T0379-1ys9A-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ys9A expands to /projects/compbio/data/pdb/1ys9.pdb.gz 1ys9A:# T0379 read from 1ys9A/T0379-1ys9A-t06-local-adpstyle5.a2m # 1ys9A read from 1ys9A/T0379-1ys9A-t06-local-adpstyle5.a2m # adding 1ys9A to template set # found chain 1ys9A in template set T0379 2 :IRNIVFDLGGVLIHLN 1ys9A 3 :YKGYLIDLDGTIYQGK T0379 18 :REESIRRFKAIGVADIEEMLDPYLQKGLF 1ys9A 24 :GERFIKRLQERGIPYLLVTNNTTRTPEMV T0379 47 :LDL 1ys9A 88 :TAY T0379 85 :EEISAEKF 1ys9A 122 :SQVTYEML T0379 94 :YIDSLR 1ys9A 130 :AIATLA T0379 100 :PDYRLFLLSNTNPYVLDLAMSPRFLPS 1ys9A 137 :QKGALFIGTNPDLNIPTERGLMPGAGA T0379 130 :LDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPA 1ys9A 164 :LNALLEAATRVKPVFIGKPNAIIMNKSLEVLGIQRSEAVMVGDNYL T0379 176 :NVATAERLGFHTYCPDNGENWIPAI 1ys9A 211 :DIMAGIQNDIATILVTTGFTRPEEV T0379 201 :TRLL 1ys9A 242 :PDHV Number of specific fragments extracted= 9 number of extra gaps= 0 total=898 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 1pw5A/T0379-1pw5A-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1pw5A expands to /projects/compbio/data/pdb/1pw5.pdb.gz 1pw5A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0379 read from 1pw5A/T0379-1pw5A-t06-local-adpstyle5.a2m # 1pw5A read from 1pw5A/T0379-1pw5A-t06-local-adpstyle5.a2m # adding 1pw5A to template set # found chain 1pw5A in template set T0379 1 :M 1pw5A 1 :M T0379 2 :IRNIVFDLGGVLIHLN 1pw5A 5 :IELFILDMDGTFYLDD T0379 18 :REESIRRFKAIGVADIEEMLDPYLQKGLF 1pw5A 26 :SLEFLETLKEKNKRFVFFTNNSSLGAQDY T0379 81 :LGFL 1pw5A 86 :GRCR T0379 85 :EEISAEKFDYIDSLRPD 1pw5A 124 :TLTYERLKKACILLRKG T0379 103 :RLFLLSNTNPYVLDLAMSPRFLPS 1pw5A 141 :KFYIATHPDINCPSKEGPVPDAGS T0379 130 :LDSFFDKVYAS 1pw5A 165 :IMAAIEASTGR T0379 141 :CQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPA 1pw5A 177 :PDLIAGKPNPLVVDVISEKFGVPKERMAMVGDRLY T0379 176 :NVATAERLGFHTYCPDNGENWIPAI 1pw5A 213 :DVKLGKNAGIVSILVLTGETTPEDL T0379 201 :TRLL 1pw5A 244 :PDFV Number of specific fragments extracted= 10 number of extra gaps= 0 total=908 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 1vjrA/T0379-1vjrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vjrA expands to /projects/compbio/data/pdb/1vjr.pdb.gz 1vjrA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 172, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 173, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 177, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 178, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 180, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 181, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 183, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 184, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 186, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 187, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 237, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 241, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 243, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 245, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 247, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 249, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 271, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 275, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 277, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 279, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 281, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 283, because occupancy 0.500 <= existing 0.500 in 1vjrA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1601, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1605, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1607, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1609, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1611, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1613, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1616, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1620, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1622, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1624, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1626, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1628, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1630, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1632, because occupancy 0.500 <= existing 0.500 in 1vjrA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1868, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1872, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1874, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1876, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1878, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1880, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1912, because occupancy 0.350 <= existing 0.650 in 1vjrA Skipped atom 1914, because occupancy 0.350 <= existing 0.650 in 1vjrA Skipped atom 1916, because occupancy 0.350 <= existing 0.650 in 1vjrA Skipped atom 1918, because occupancy 0.350 <= existing 0.650 in 1vjrA Skipped atom 1920, because occupancy 0.350 <= existing 0.650 in 1vjrA Skipped atom 1922, because occupancy 0.350 <= existing 0.650 in 1vjrA Skipped atom 1930, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1934, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1936, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1938, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1940, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1942, because occupancy 0.500 <= existing 0.500 in 1vjrA # T0379 read from 1vjrA/T0379-1vjrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vjrA read from 1vjrA/T0379-1vjrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vjrA to template set # found chain 1vjrA in template set T0379 2 :IRNIVFDLGGVLIHLN 1vjrA 5 :IELFILDMDGTFYLDD T0379 18 :REESIRRFKAIGVADIEEMLDPY 1vjrA 26 :SLEFLETLKEKNKRFVFFTNNSS T0379 54 :KSEEEFRTELSR 1vjrA 49 :LGAQDYVRKLRN T0379 73 :YQQVYDALLGFL 1vjrA 95 :TPQLKKVFEAYG T0379 85 :EEISAEKFDYIDSLR 1vjrA 123 :KTLTYERLKKACILL T0379 100 :PDYR 1vjrA 139 :KGKF T0379 105 :FLLSN 1vjrA 143 :YIATH T0379 110 :TNPYVLDLAMSPRF 1vjrA 161 :DAGSIMAAIEASTG T0379 130 :LD 1vjrA 175 :RK T0379 134 :FDKVY 1vjrA 177 :PDLIA T0379 146 :YKPNEDIFLEMIADSGMKPEETLFIDDGPA 1vjrA 182 :GKPNPLVVDVISEKFGVPKERMAMVGDRLY T0379 176 :NVATAERLGFHTYCPDNGENWIPAI 1vjrA 213 :DVKLGKNAGIVSILVLTGETTPEDL T0379 201 :TRLLRE 1vjrA 248 :FKNLGE Number of specific fragments extracted= 13 number of extra gaps= 0 total=921 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 1vjrA/T0379-1vjrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1vjrA/T0379-1vjrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vjrA read from 1vjrA/T0379-1vjrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vjrA in template set T0379 2 :IRNIVFDLGGVLI 1vjrA 5 :IELFILDMDGTFY T0379 16 :LNRE 1vjrA 22 :LLPG T0379 21 :SIRRFKAIGVADIE 1vjrA 26 :SLEFLETLKEKNKR T0379 44 :GLFLDLESGRKSEEEF 1vjrA 47 :SSLGAQDYVRKLRNMG T0379 60 :RTELSRYIGK 1vjrA 78 :AEHMLKRFGR T0379 70 :ELTYQQVYDAL 1vjrA 95 :TPQLKKVFEAY T0379 84 :LEEISAEKFDYIDSLRP 1vjrA 122 :DKTLTYERLKKACILLR T0379 101 :DYRL 1vjrA 140 :GKFY T0379 106 :LLSNTNP 1vjrA 144 :IATHPDI T0379 113 :YVLDLAMSPRF 1vjrA 164 :SIMAAIEASTG T0379 130 :LD 1vjrA 175 :RK T0379 134 :FDKV 1vjrA 177 :PDLI T0379 145 :KYKPNEDIFLEMIADSGMKPEETLFIDDGP 1vjrA 181 :AGKPNPLVVDVISEKFGVPKERMAMVGDRL T0379 175 :ANVATAERLGFHTYCPDNGENWIP 1vjrA 212 :TDVKLGKNAGIVSILVLTGETTPE T0379 199 :AITRLLRE 1vjrA 250 :NLGELAKA Number of specific fragments extracted= 15 number of extra gaps= 0 total=936 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 1vjrA/T0379-1vjrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1vjrA/T0379-1vjrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vjrA read from 1vjrA/T0379-1vjrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vjrA in template set T0379 2 :IRNIVFDLGGVLIH 1vjrA 5 :IELFILDMDGTFYL T0379 84 :LEEISAEKFDYIDSLR 1vjrA 19 :DDSLLPGSLEFLETLK T0379 100 :PDYRLFLLSN 1vjrA 36 :KNKRFVFFTN T0379 110 :TNPYVLDLAMS 1vjrA 49 :LGAQDYVRKLR T0379 127 :GRTLD 1vjrA 60 :NMGVD T0379 134 :F 1vjrA 65 :V T0379 135 :DKVYASCQMG 1vjrA 68 :DAVVTSGEIT T0379 145 :KYKPNEDIFLEMIADSGMKPEETLFIDDGP 1vjrA 181 :AGKPNPLVVDVISEKFGVPKERMAMVGDRL T0379 175 :ANVATAERLGFHTYCPDNGENWIPAITRL 1vjrA 212 :TDVKLGKNAGIVSILVLTGETTPEDLERA Number of specific fragments extracted= 9 number of extra gaps= 0 total=945 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 1ek1A/T0379-1ek1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ek1A expands to /projects/compbio/data/pdb/1ek1.pdb.gz 1ek1A:# T0379 read from 1ek1A/T0379-1ek1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ek1A read from 1ek1A/T0379-1ek1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ek1A to template set # found chain 1ek1A in template set Warning: unaligning (T0379)R3 because first residue in template chain is (1ek1A)R4 Warning: unaligning (T0379)G44 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ek1A)G48 Warning: unaligning (T0379)S55 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ek1A)Q90 T0379 4 :NIVFDLGGVLIHLN 1ek1A 5 :VAAFDLDGVLALPS T0379 45 :LFLDLESGRK 1ek1A 49 :PTEQLMKGKI T0379 85 :EEISAEKFDYIDSLR 1ek1A 99 :RSINRPMLQAAIALK T0379 100 :PDYRLFLLSN 1ek1A 115 :KGFTTCIVTN T0379 110 :TNPYVLDLAMSP 1ek1A 131 :DKRDSLAQMMCE T0379 130 :LDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGENWIPAI 1ek1A 143 :LSQHFDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGSNLKPARDMGMVTILVHNTASALREL Number of specific fragments extracted= 6 number of extra gaps= 0 total=951 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 1ek1A/T0379-1ek1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1ek1A/T0379-1ek1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ek1A read from 1ek1A/T0379-1ek1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ek1A in template set Warning: unaligning (T0379)R3 because first residue in template chain is (1ek1A)R4 Warning: unaligning (T0379)D38 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ek1A)G48 Warning: unaligning (T0379)K54 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ek1A)Q90 Warning: unaligning (T0379)F83 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ek1A)Q90 T0379 4 :NIVFDLGGVLI 1ek1A 5 :VAAFDLDGVLA T0379 39 :PYLQKG 1ek1A 49 :PTEQLM T0379 45 :LFLDLESGR 1ek1A 57 :KITFSQWVP T0379 84 :L 1ek1A 91 :I T0379 85 :E 1ek1A 93 :S T0379 87 :ISAEKFDYIDSLRP 1ek1A 101 :INRPMLQAAIALKK T0379 101 :DYRLFLLSNTN 1ek1A 116 :GFTTCIVTNNW T0379 112 :PYVLDLAMSP 1ek1A 133 :RDSLAQMMCE T0379 130 :LDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNGENW 1ek1A 143 :LSQHFDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGSNLKPARDMGMVTILVHNTASA Number of specific fragments extracted= 9 number of extra gaps= 0 total=960 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 1ek1A/T0379-1ek1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1ek1A/T0379-1ek1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ek1A read from 1ek1A/T0379-1ek1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ek1A in template set Warning: unaligning (T0379)R3 because first residue in template chain is (1ek1A)R4 Warning: unaligning (T0379)R18 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ek1A)G48 Warning: unaligning (T0379)L47 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ek1A)G48 Warning: unaligning (T0379)R65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ek1A)Q90 T0379 4 :NIVFDLGGVLIHLN 1ek1A 5 :VAAFDLDGVLALPS T0379 48 :DLESGRKSEEEFRTELS 1ek1A 49 :PTEQLMKGKITFSQWVP T0379 81 :LGFLEEISAEKFDYIDSLR 1ek1A 95 :AMAARSINRPMLQAAIALK T0379 100 :PDYRLFLLSNTN 1ek1A 115 :KGFTTCIVTNNW T0379 112 :PYVLDLAMS 1ek1A 133 :RDSLAQMMC T0379 129 :TLDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTYCPDNG 1ek1A 142 :ELSQHFDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGSNLKPARDMGMVTILVHNT T0379 194 :ENWIPAITRL 1ek1A 208 :SALRELEKVT Number of specific fragments extracted= 7 number of extra gaps= 0 total=967 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 1wviA/T0379-1wviA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1wviA expands to /projects/compbio/data/pdb/1wvi.pdb.gz 1wviA:# T0379 read from 1wviA/T0379-1wviA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wviA read from 1wviA/T0379-1wviA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1wviA to template set # found chain 1wviA in template set T0379 2 :IRNIVFDLGGVLIHLN 1wviA 1003 :YKGYLIDLDGTIYKGK T0379 18 :REESIRRFKAIGVADIEEMLDP 1wviA 1024 :GEDFVKRLQERQLPYILVTNNT T0379 53 :RKSEEEFRTELSRYIGKELTY 1wviA 1046 :TRTPEMVQEMLATSFNIKTPL T0379 74 :QQVYDALLGFL 1wviA 1095 :TGLKKAVAEAG T0379 85 :EEISAEKFDYIDSLR 1wviA 1122 :TNLTYEKLTLATLAI T0379 100 :PDYR 1wviA 1138 :KGAV T0379 105 :FLLSN 1wviA 1142 :FIGTN T0379 110 :TNPYVLDLAMSPRF 1wviA 1160 :GAGAILFLLEKATR T0379 130 :LD 1wviA 1174 :VK T0379 134 :F 1wviA 1176 :P T0379 145 :KYKPNEDIFLEMIADSGMKPEETLFIDDGPA 1wviA 1179 :IGKPEAVIMNKALDRLGVKRHEAIMVGDNYL T0379 176 :NVATAERLGFHTYCPDNGENWIPAI 1wviA 1211 :DITAGIKNDIATLLVTTGFTKPEEV Number of specific fragments extracted= 12 number of extra gaps= 0 total=979 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 1wviA/T0379-1wviA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1wviA/T0379-1wviA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wviA read from 1wviA/T0379-1wviA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wviA in template set T0379 2 :IRNIVFDLGGVLIH 1wviA 1003 :YKGYLIDLDGTIYK T0379 16 :LNREESIRRFKAIGVA 1wviA 1020 :RIPAGEDFVKRLQERQ T0379 32 :DIEEMLDPYLQK 1wviA 1044 :NTTRTPEMVQEM T0379 55 :SEEEF 1wviA 1056 :LATSF T0379 71 :LTYQQVYDAL 1wviA 1095 :TGLKKAVAEA T0379 83 :FLEEISAEKFDYIDSLRP 1wviA 1120 :LDTNLTYEKLTLATLAIQ T0379 101 :DYRL 1wviA 1139 :GAVF T0379 106 :LLSNTNP 1wviA 1143 :IGTNPDL T0379 113 :YVLDLAMSPRF 1wviA 1166 :FLLEKATRVKP T0379 138 :YA 1wviA 1177 :II T0379 145 :KYKPNEDIFLEMIADSGMKPEETLFIDDGP 1wviA 1179 :IGKPEAVIMNKALDRLGVKRHEAIMVGDNY T0379 175 :ANVATAERLGFHTYCPDNGENWIPAITR 1wviA 1210 :TDITAGIKNDIATLLVTTGFTKPEEVPA Number of specific fragments extracted= 12 number of extra gaps= 0 total=991 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 1wviA/T0379-1wviA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1wviA/T0379-1wviA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wviA read from 1wviA/T0379-1wviA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wviA in template set T0379 1 :MIRNIVFDLGGVLIH 1wviA 1002 :TYKGYLIDLDGTIYK T0379 84 :LEEISAEKFDYIDSLR 1wviA 1017 :GKDRIPAGEDFVKRLQ T0379 100 :PDYRLFLLSN 1wviA 1034 :RQLPYILVTN T0379 110 :TNPYVLDLAMSPR 1wviA 1047 :RTPEMVQEMLATS T0379 124 :LPS 1wviA 1060 :FNI T0379 127 :GRTLDSFFDKVYASCQMG 1wviA 1079 :YMNDMKRGKTAYVIGETG T0379 145 :KYKPNEDIFLEMIADSGMKPEETLFIDDGP 1wviA 1179 :IGKPEAVIMNKALDRLGVKRHEAIMVGDNY T0379 175 :ANVATAERLGFHTYCPDNGENWIPAI 1wviA 1210 :TDITAGIKNDIATLLVTTGFTKPEEV Number of specific fragments extracted= 8 number of extra gaps= 0 total=999 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 1ydfA/T0379-1ydfA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ydfA expands to /projects/compbio/data/pdb/1ydf.pdb.gz 1ydfA:# T0379 read from 1ydfA/T0379-1ydfA-t06-local-adpstyle5.a2m # 1ydfA read from 1ydfA/T0379-1ydfA-t06-local-adpstyle5.a2m # adding 1ydfA to template set # found chain 1ydfA in template set T0379 2 :IRNIVFDLGGVLIHLN 1ydfA 4 :YKGYLIDLDGTIYKGK T0379 18 :REESIRRFKAIGVADIEEMLDPYLQKGLF 1ydfA 25 :GETFVHELQKRDIPYLFVTNNTTRTPESV T0379 47 :LDLESGRKSE 1ydfA 78 :IDYMNDLGLE T0379 83 :FL 1ydfA 88 :KT T0379 85 :EEISAEKFDY 1ydfA 123 :WQVDYEKFAT T0379 96 :DSLR 1ydfA 133 :ATLA T0379 100 :PDYRLFLLSNTNPYVLDLAMSPRFLPS 1ydfA 138 :QKGAHFIGTNPDLNIPTERGLLPGAGS T0379 130 :LDSFFDKVYASCQMGKYKPNEDIFLEMIADSGMKPEETLFIDDGPA 1ydfA 165 :LITLLEVATRVKPVYIGKPNAIIMDKAVEHLGLEREELIMVGDNYL T0379 176 :NVATAERLGFHTYCPDNGENWIPAI 1ydfA 212 :DIRAGIDNGIPTLLVTTGFTKAEEV T0379 201 :TRLL 1ydfA 243 :PTHV Number of specific fragments extracted= 10 number of extra gaps= 0 total=1009 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 1nnlA/T0379-1nnlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1nnlA expands to /projects/compbio/data/pdb/1nnl.pdb.gz 1nnlA:# T0379 read from 1nnlA/T0379-1nnlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nnlA read from 1nnlA/T0379-1nnlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1nnlA to template set # found chain 1nnlA in template set Warning: unaligning (T0379)E34 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1nnlA)P57 Warning: unaligning (T0379)S55 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1nnlA)P57 T0379 2 :IRNIVFDLGGVLIHLN 1nnlA 14 :ADAVCFDVDSTVIREE T0379 21 :SIRRFKAI 1nnlA 30 :GIDELAKI T0379 29 :GVADI 1nnlA 39 :GVEDA T0379 56 :EEEFRTELSRYI 1nnlA 58 :FKAALTERLALI T0379 70 :ELTYQQVYDALLGFLEEISAEKFDYIDSLR 1nnlA 70 :QPSREQVQRLIAEQPPHLTPGIRELVSRLQ T0379 100 :PDYRLFLLSNTNPYVLDLAMSPRF 1nnlA 101 :RNVQVFLISGGFRSIVEHVASKLN T0379 130 :LD 1nnlA 125 :IP T0379 134 :FDKVYASCQMG 1nnlA 127 :ATNVFANRLKF T0379 145 :KYK 1nnlA 156 :GGK T0379 150 :EDIFLEMIADS 1nnlA 159 :GKVIKLLKEKF T0379 163 :KPEETLFIDDGPANVATAERLG 1nnlA 170 :HFKKIIMIGDGATDMEACPPAD T0379 186 :HTYCP 1nnlA 192 :AFIGF T0379 192 :NGENWIPAI 1nnlA 197 :GGNVIRQQV Number of specific fragments extracted= 13 number of extra gaps= 0 total=1022 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 1nnlA/T0379-1nnlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1nnlA/T0379-1nnlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nnlA read from 1nnlA/T0379-1nnlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nnlA in template set Warning: unaligning (T0379)L37 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1nnlA)P57 Warning: unaligning (T0379)E50 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1nnlA)P57 T0379 2 :IRNIVFDLGGVLIHLNR 1nnlA 14 :ADAVCFDVDSTVIREEG T0379 24 :RFKAIGVADIEEM 1nnlA 31 :IDELAKICGVEDA T0379 51 :SGRKSEEEF 1nnlA 58 :FKAALTERL T0379 68 :GKELTYQQVYDALLGFL 1nnlA 67 :ALIQPSREQVQRLIAEQ T0379 85 :EEISAEKFDYIDSLRP 1nnlA 85 :PHLTPGIRELVSRLQE T0379 101 :DYRLFLLSNTNPYVLDLAMSPRF 1nnlA 102 :NVQVFLISGGFRSIVEHVASKLN T0379 130 :LDSFF 1nnlA 125 :IPATN T0379 137 :VYAS 1nnlA 130 :VFAN T0379 141 :CQMGKY 1nnlA 136 :KFYFNG T0379 150 :EDIFLEMIADS 1nnlA 155 :SGGKGKVIKLL T0379 163 :KPEETLFIDDGPANVA 1nnlA 170 :HFKKIIMIGDGATDME T0379 184 :GF 1nnlA 189 :PA T0379 186 :HTYCPDNGENWIP 1nnlA 192 :AFIGFGGNVIRQQ Number of specific fragments extracted= 13 number of extra gaps= 0 total=1035 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 1nnlA/T0379-1nnlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1nnlA/T0379-1nnlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nnlA read from 1nnlA/T0379-1nnlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nnlA in template set Warning: unaligning (T0379)L37 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1nnlA)P57 Warning: unaligning (T0379)E50 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1nnlA)P57 T0379 2 :IRNIVFDLGGVLIHLNRE 1nnlA 14 :ADAVCFDVDSTVIREEGI T0379 25 :FKAIGVADIEEM 1nnlA 32 :DELAKICGVEDA T0379 51 :SGRKSEEEFRTELSRY 1nnlA 58 :FKAALTERLALIQPSR T0379 75 :QVYDALLGFLE 1nnlA 74 :EQVQRLIAEQP T0379 86 :EISAEKFDYIDSLR 1nnlA 86 :HLTPGIRELVSRLQ T0379 100 :PDYRLFLLSNTNPYVLDLAMS 1nnlA 101 :RNVQVFLISGGFRSIVEHVAS T0379 127 :GRTLDS 1nnlA 122 :KLNIPA T0379 151 :DIFLEMIADS 1nnlA 160 :KVIKLLKEKF T0379 163 :KPEETLFIDDGPANV 1nnlA 170 :HFKKIIMIGDGATDM T0379 186 :HTYCPDNG 1nnlA 192 :AFIGFGGN T0379 195 :NWIPAITR 1nnlA 200 :VIRQQVKD Number of specific fragments extracted= 11 number of extra gaps= 0 total=1046 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 1rkuA/T0379-1rkuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1rkuA expands to /projects/compbio/data/pdb/1rku.pdb.gz 1rkuA:Skipped atom 759, because occupancy 0.500 <= existing 0.500 in 1rkuA Skipped atom 761, because occupancy 0.500 <= existing 0.500 in 1rkuA Skipped atom 763, because occupancy 0.500 <= existing 0.500 in 1rkuA Skipped atom 765, because occupancy 0.500 <= existing 0.500 in 1rkuA Skipped atom 767, because occupancy 0.500 <= existing 0.500 in 1rkuA Skipped atom 769, because occupancy 0.500 <= existing 0.500 in 1rkuA Skipped atom 771, because occupancy 0.500 <= existing 0.500 in 1rkuA Skipped atom 1094, because occupancy 0.500 <= existing 0.500 in 1rkuA Skipped atom 1096, because occupancy 0.500 <= existing 0.500 in 1rkuA Skipped atom 1098, because occupancy 0.500 <= existing 0.500 in 1rkuA Skipped atom 1256, because occupancy 0.500 <= existing 0.500 in 1rkuA Skipped atom 1258, because occupancy 0.500 <= existing 0.500 in 1rkuA # T0379 read from 1rkuA/T0379-1rkuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rkuA read from 1rkuA/T0379-1rkuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1rkuA to template set # found chain 1rkuA in template set Warning: unaligning (T0379)F7 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rkuA)D7 Warning: unaligning (T0379)D8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rkuA)D7 T0379 1 :M 1rkuA 1 :M T0379 3 :RNIV 1rkuA 2 :EIAC T0379 9 :LGGVLIHL 1rkuA 8 :LEGVLVPE T0379 21 :SIRRFKAI 1rkuA 16 :IWIAFAEK T0379 29 :GVADIEEM 1rkuA 25 :GIDALKAT T0379 50 :ESGRKSEEEFRTELSRYIG 1rkuA 33 :TRDIPDYDVLMKQRLRILD T0379 69 :KELTYQQVYDALLG 1rkuA 53 :HGLKLGDIQEVIAT T0379 85 :EEISAEKFDYIDSLRPDYRLFLLSNTNPYVLDLAMSPRF 1rkuA 67 :LKPLEGAVEFVDWLRERFQVVILSDTFYEFSQPLMRQLG T0379 130 :LDSFFDKVYASCQMG 1rkuA 106 :FPTLLCHKLEIDDSD T0379 145 :KYK 1rkuA 128 :RQK T0379 151 :DIFLEMIADS 1rkuA 131 :DPKRQSVIAF T0379 161 :GM 1rkuA 144 :YY T0379 166 :ETLFIDDGPANVATAERLG 1rkuA 146 :RVIAAGDSYNDTTMLSEAH T0379 186 :HTYCPDNGENWIPAI 1rkuA 165 :AGILFHAPENVIREF T0379 201 :TRLL 1rkuA 188 :YEDL Number of specific fragments extracted= 15 number of extra gaps= 1 total=1061 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 1rkuA/T0379-1rkuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1rkuA/T0379-1rkuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rkuA read from 1rkuA/T0379-1rkuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rkuA in template set Warning: unaligning (T0379)F7 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rkuA)D7 Warning: unaligning (T0379)D8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rkuA)D7 T0379 1 :M 1rkuA 1 :M T0379 3 :RNIV 1rkuA 2 :EIAC T0379 9 :LGGVLIH 1rkuA 8 :LEGVLVP T0379 22 :IRRFKAIGVADIEEMLDP 1rkuA 15 :EIWIAFAEKTGIDALKAT T0379 42 :QKGLFLDLESGRKSEEEFRTELSRYIG 1rkuA 33 :TRDIPDYDVLMKQRLRILDEHGLKLGD T0379 77 :YDALLGFL 1rkuA 60 :IQEVIATL T0379 86 :EISAEKFDYIDSLRPDYRLFLLSNTNPYVLDLAMSPRFL 1rkuA 68 :KPLEGAVEFVDWLRERFQVVILSDTFYEFSQPLMRQLGF T0379 130 :LD 1rkuA 107 :PT T0379 137 :VYAS 1rkuA 109 :LLCH T0379 145 :KYK 1rkuA 128 :RQK T0379 151 :DIFLEMIADS 1rkuA 131 :DPKRQSVIAF T0379 161 :GM 1rkuA 144 :YY T0379 166 :ETLFIDDGPANVATAERLG 1rkuA 146 :RVIAAGDSYNDTTMLSEAH T0379 186 :HTYCPDNGENWIP 1rkuA 165 :AGILFHAPENVIR T0379 200 :ITRLLR 1rkuA 188 :YEDLKR Number of specific fragments extracted= 15 number of extra gaps= 1 total=1076 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 1rkuA/T0379-1rkuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1rkuA/T0379-1rkuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rkuA read from 1rkuA/T0379-1rkuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rkuA in template set Warning: unaligning (T0379)F7 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rkuA)D7 Warning: unaligning (T0379)D8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rkuA)D7 T0379 3 :RNIV 1rkuA 2 :EIAC T0379 9 :LGGVLIHLN 1rkuA 8 :LEGVLVPEI T0379 24 :RFKAIGVADIEEMLDP 1rkuA 17 :WIAFAEKTGIDALKAT T0379 46 :FLDLESGRKSEEEFRTELSRYIGKELTYQQVY 1rkuA 33 :TRDIPDYDVLMKQRLRILDEHGLKLGDIQEVI T0379 83 :FLEEISAEKFDYIDSLRPDYRLFLLSNTNPYVLDLAMS 1rkuA 65 :ATLKPLEGAVEFVDWLRERFQVVILSDTFYEFSQPLMR T0379 127 :GRTL 1rkuA 103 :QLGF T0379 145 :KYKPNEDIFLEMIA 1rkuA 129 :QKDPKRQSVIAFKS T0379 160 :SGM 1rkuA 143 :LYY T0379 166 :ETLFIDDGPANVATAERLG 1rkuA 146 :RVIAAGDSYNDTTMLSEAH T0379 186 :HTYCPDNGENWIPAITRL 1rkuA 165 :AGILFHAPENVIREFPQF Number of specific fragments extracted= 10 number of extra gaps= 1 total=1086 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 1f5sA/T0379-1f5sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1f5sA expands to /projects/compbio/data/pdb/1f5s.pdb.gz 1f5sA:Skipped atom 82, because occupancy 0.500 <= existing 0.500 in 1f5sA Skipped atom 84, because occupancy 0.500 <= existing 0.500 in 1f5sA Skipped atom 86, because occupancy 0.500 <= existing 0.500 in 1f5sA Skipped atom 88, because occupancy 0.500 <= existing 0.500 in 1f5sA Skipped atom 90, because occupancy 0.500 <= existing 0.500 in 1f5sA Skipped atom 92, because occupancy 0.500 <= existing 0.500 in 1f5sA Skipped atom 94, because occupancy 0.500 <= existing 0.500 in 1f5sA Skipped atom 96, because occupancy 0.500 <= existing 0.500 in 1f5sA # T0379 read from 1f5sA/T0379-1f5sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f5sA read from 1f5sA/T0379-1f5sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1f5sA to template set # found chain 1f5sA in template set T0379 2 :IRNIVFDLGGVLIHLN 1f5sA 5 :KKLILFDFDSTLVNNE T0379 20 :ESIRRFKAIGV 1f5sA 21 :TIDEIAREAGV T0379 31 :ADIE 1f5sA 33 :EEVK T0379 44 :GLFLDLESGRKSEEEFRTELSRYIG 1f5sA 37 :KITKEAMEGKLNFEQSLRKRVSLLK T0379 70 :ELTYQQVYDALLG 1f5sA 62 :DLPIEKVEKAIKR T0379 85 :EEISAEKFDYIDSLR 1f5sA 75 :ITPTEGAEETIKELK T0379 100 :PDYRLFLLSNTNPYVLDLAMSPRF 1f5sA 91 :RGYVVAVVSGGFDIAVNKIKEKLG T0379 130 :LDSFFDKVYASCQ 1f5sA 115 :LDYAFANRLIVKD T0379 145 :KYK 1f5sA 142 :NAK T0379 150 :EDIFLEMIADSGMKPEETLFIDDGPANVATAERLG 1f5sA 145 :GEILEKIAKIEGINLEDTVAVGDGANDISMFKKAG T0379 186 :HTYCP 1f5sA 180 :LKIAF T0379 192 :NGE 1f5sA 185 :CAK T0379 202 :RLLRE 1f5sA 188 :PILKE Number of specific fragments extracted= 13 number of extra gaps= 0 total=1099 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 1f5sA/T0379-1f5sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1f5sA/T0379-1f5sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f5sA read from 1f5sA/T0379-1f5sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1f5sA in template set T0379 2 :IRNIVFDLGGVLIHLNR 1f5sA 5 :KKLILFDFDSTLVNNET T0379 24 :RFKAIGVADIEEMLDPYLQKG 1f5sA 22 :IDEIAREAGVEEEVKKITKEA T0379 45 :LFLDLESGRKSEEEFRTELSRY 1f5sA 46 :KLNFEQSLRKRVSLLKDLPIEK T0379 77 :YDALLGFL 1f5sA 68 :VEKAIKRI T0379 86 :EISAEKFDYIDSLRP 1f5sA 76 :TPTEGAEETIKELKN T0379 101 :DYRLFLLSNTNPYVLDLAMSPRF 1f5sA 92 :GYVVAVVSGGFDIAVNKIKEKLG T0379 134 :FDKVYAS 1f5sA 115 :LDYAFAN T0379 141 :CQMGKY 1f5sA 136 :GEVLKE T0379 150 :EDIFLEMIADSGMKPEETLFIDDGPANVATAERLG 1f5sA 145 :GEILEKIAKIEGINLEDTVAVGDGANDISMFKKAG T0379 186 :HTYCPDN 1f5sA 180 :LKIAFCA Number of specific fragments extracted= 10 number of extra gaps= 0 total=1109 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 1f5sA/T0379-1f5sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1f5sA/T0379-1f5sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f5sA read from 1f5sA/T0379-1f5sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1f5sA in template set T0379 1 :MIRNIVFDLGGVLIHLNRE 1f5sA 4 :KKKLILFDFDSTLVNNETI T0379 25 :FKAIGVADIEEMLDPYLQKGLFLDLESGRKSEEEFRT 1f5sA 23 :DEIAREAGVEEEVKKITKEAMEGKLNFEQSLRKRVSL T0379 63 :L 1f5sA 60 :L T0379 67 :IGKELTYQQVYD 1f5sA 62 :DLPIEKVEKAIK T0379 84 :LEEISAEKFDYIDSLR 1f5sA 74 :RITPTEGAEETIKELK T0379 100 :PDYRLFLLSNTNPYVLDLAMS 1f5sA 91 :RGYVVAVVSGGFDIAVNKIKE T0379 127 :GRTL 1f5sA 112 :KLGL T0379 135 :DKVYA 1f5sA 116 :DYAFA T0379 150 :EDIFLEMIADSGMKPEETLFIDDGPANVATAERLG 1f5sA 145 :GEILEKIAKIEGINLEDTVAVGDGANDISMFKKAG T0379 186 :HTYCPD 1f5sA 180 :LKIAFC T0379 196 :WIPAITR 1f5sA 186 :AKPILKE Number of specific fragments extracted= 11 number of extra gaps= 0 total=1120 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 2g80A/T0379-2g80A-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2g80A expands to /projects/compbio/data/pdb/2g80.pdb.gz 2g80A:Skipped atom 115, because occupancy 0.500 <= existing 0.500 in 2g80A Skipped atom 119, because occupancy 0.500 <= existing 0.500 in 2g80A Skipped atom 121, because occupancy 0.500 <= existing 0.500 in 2g80A # T0379 read from 2g80A/T0379-2g80A-t06-local-adpstyle5.a2m # 2g80A read from 2g80A/T0379-2g80A-t06-local-adpstyle5.a2m # adding 2g80A to template set # found chain 2g80A in template set T0379 2 :IRNIVFDLGGVLIHLN 2g80A 19 :YSTYLLDIEGTVCPIS T0379 24 :RFKAIGVADIEEMLDPYLQKGLFLDLESGRKSEEEFRTELSRYIGKELTYQQVYDALLGFL 2g80A 44 :FTNKVPQLVQQDTRDSPVSNILSQFHIDNKEQLQAHILELVAKDVKDPILKQLQGYVWAHG T0379 85 :EEISAEKFDYID 2g80A 112 :APVYADAIDFIK T0379 100 :PDYRLFLLSNTNPYVLDLAMSPRFL 2g80A 124 :RKKRVFIYSSGSVKAQKLLFGYVQD T0379 125 :PSGRTLDSFFDKVYASCQMG 2g80A 154 :HDSLDLNSYIDGYFDINTSG T0379 146 :YKPNEDIFLEMIADSGMKPEETLFIDDGPANVATAERLGF 2g80A 174 :KKTETQSYANILRDIGAKASEVLFLSDNPLELDAAAGVGI T0379 186 :HTYCPDNGENWIPAI 2g80A 215 :TGLASRPGNAPVPDG Number of specific fragments extracted= 7 number of extra gaps= 0 total=1127 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 1wr8A/T0379-1wr8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1wr8A expands to /projects/compbio/data/pdb/1wr8.pdb.gz 1wr8A:# T0379 read from 1wr8A/T0379-1wr8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wr8A read from 1wr8A/T0379-1wr8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1wr8A to template set # found chain 1wr8A in template set T0379 2 :IRNIVFDLGGVLIHLN 1wr8A 3 :IKAISIDIDGTITYPN T0379 85 :EEISAEKFDYIDSLR 1wr8A 19 :RMIHEKALEAIRRAE T0379 100 :PDYRLFLLSN 1wr8A 35 :LGIPIMLVTG T0379 110 :TNPYVLDLAMSPRF 1wr8A 120 :INVETVREIINELN T0379 130 :LD 1wr8A 134 :LN T0379 134 :FDKVYASCQMGKYK 1wr8A 141 :SGFAIHVKKPWINK T0379 150 :EDIFLEMIADSGMKPEETLFIDDGPANVATAERLG 1wr8A 155 :GSGIEKASEFLGIKPKEVAHVGDGENDLDAFKVVG T0379 186 :HTYCPDNGENWIPAI 1wr8A 190 :YKVAVAQAPKILKEN T0379 201 :TRLLRE 1wr8A 221 :IYHILE Number of specific fragments extracted= 9 number of extra gaps= 0 total=1136 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 1wr8A/T0379-1wr8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1wr8A/T0379-1wr8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wr8A read from 1wr8A/T0379-1wr8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wr8A in template set T0379 2 :IRNIVFDLGGVLI 1wr8A 3 :IKAISIDIDGTIT T0379 16 :LNREESIRRFKAI 1wr8A 21 :IHEKALEAIRRAE T0379 30 :VADIE 1wr8A 34 :SLGIP T0379 45 :LFLDLESGRKSEEEF 1wr8A 43 :TGNTVQFAEAASILI T0379 61 :TEL 1wr8A 84 :DEE T0379 71 :LTYQQVYDALLGFL 1wr8A 87 :WILWNEIRKRFPNA T0379 86 :EISAEK 1wr8A 101 :RTSYTM T0379 110 :TNPYVLDLAMSPRF 1wr8A 120 :INVETVREIINELN T0379 130 :LD 1wr8A 134 :LN T0379 134 :FDKVYASCQMGKYK 1wr8A 141 :SGFAIHVKKPWINK T0379 150 :EDIFLEMIADSGMKPEETLFIDDGPANVATAERLG 1wr8A 155 :GSGIEKASEFLGIKPKEVAHVGDGENDLDAFKVVG T0379 186 :HTYCPDNGENWIP 1wr8A 190 :YKVAVAQAPKILK T0379 199 :AITRLLRE 1wr8A 220 :AIYHILEK Number of specific fragments extracted= 13 number of extra gaps= 0 total=1149 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 1wr8A/T0379-1wr8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1wr8A/T0379-1wr8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wr8A read from 1wr8A/T0379-1wr8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wr8A in template set T0379 1 :MIRNIVFDLGGVLI 1wr8A 2 :KIKAISIDIDGTIT T0379 82 :GFLEEISAEKFDYIDSLR 1wr8A 16 :YPNRMIHEKALEAIRRAE T0379 100 :PDYRLFLLSNTNPYVLDLAMS 1wr8A 35 :LGIPIMLVTGNTVQFAEAASI T0379 127 :GRTL 1wr8A 56 :LIGT T0379 135 :DKVYASCQMG 1wr8A 60 :SGPVVAEDGG T0379 150 :EDIFLEMIADSGMKPEETLFIDDGPANVATAERLGFHTY 1wr8A 155 :GSGIEKASEFLGIKPKEVAHVGDGENDLDAFKVVGYKVA T0379 193 :GENWIPAITR 1wr8A 194 :VAQAPKILKE Number of specific fragments extracted= 7 number of extra gaps= 0 total=1156 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 1q92A/T0379-1q92A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1q92A expands to /projects/compbio/data/pdb/1q92.pdb.gz 1q92A:# T0379 read from 1q92A/T0379-1q92A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q92A read from 1q92A/T0379-1q92A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1q92A to template set # found chain 1q92A in template set Warning: unaligning (T0379)I28 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)F61 Warning: unaligning (T0379)E35 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)E70 Warning: unaligning (T0379)M36 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)E70 Warning: unaligning (T0379)P39 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)G74 Warning: unaligning (T0379)Y40 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)G74 Warning: unaligning (T0379)S64 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)R83 Warning: unaligning (T0379)R65 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)R83 Warning: unaligning (T0379)S88 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)P109 Warning: unaligning (T0379)A89 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)P109 Warning: unaligning (T0379)L98 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)A119 Warning: unaligning (T0379)R99 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)A119 Warning: unaligning (T0379)R122 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)F151 Warning: unaligning (T0379)F123 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)F151 Warning: unaligning (T0379)F185 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1q92A)E190 Warning: unaligning (T0379)H186 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1q92A)E190 Warning: unaligning (T0379)D191 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)A196 Warning: unaligning (T0379)N192 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)A196 T0379 4 :NIVFDLGGVLIHL 1q92A 37 :RVLVDMDGVLADF T0379 18 :REESIRRFKA 1q92A 50 :EGGFLRKFRA T0379 29 :GVADIE 1q92A 63 :DQPFIA T0379 37 :LD 1q92A 71 :DR T0379 41 :LQ 1q92A 75 :FW T0379 59 :FRTEL 1q92A 77 :VSEQY T0379 66 :YIG 1q92A 84 :LRP T0379 71 :LTYQQ 1q92A 87 :GLSEK T0379 80 :LLGFL 1q92A 92 :AISIW T0379 85 :EEI 1q92A 105 :LEP T0379 90 :EKFDYIDS 1q92A 110 :GAVEAVKE T0379 100 :PDYRLFLLSN 1q92A 122 :QNTDVFICTS T0379 110 :TNPYVLDLAMSP 1q92A 138 :YCPYEKYAWVEK T0379 130 :LDSFFDKVYASCQMGKYKPN 1q92A 152 :GPDFLEQIVLTRDKTVVSAD T0379 168 :LFIDDGPA 1q92A 172 :LLIDDRPD T0379 187 :TYCP 1q92A 191 :HVLF T0379 193 :GENWIPAI 1q92A 197 :CHNQHLQL Number of specific fragments extracted= 17 number of extra gaps= 9 total=1173 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 1q92A/T0379-1q92A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1q92A/T0379-1q92A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q92A read from 1q92A/T0379-1q92A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1q92A in template set Warning: unaligning (T0379)A27 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)F61 Warning: unaligning (T0379)I28 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)F61 Warning: unaligning (T0379)L37 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)E70 Warning: unaligning (T0379)D38 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)E70 Warning: unaligning (T0379)G44 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)G74 Warning: unaligning (T0379)L45 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)G74 Warning: unaligning (T0379)R53 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)R83 Warning: unaligning (T0379)K54 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)R83 Warning: unaligning (T0379)S88 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)P109 Warning: unaligning (T0379)A89 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)P109 Warning: unaligning (T0379)L98 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)A119 Warning: unaligning (T0379)R99 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)A119 Warning: unaligning (T0379)R122 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)F151 Warning: unaligning (T0379)F123 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)F151 Warning: unaligning (T0379)F185 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1q92A)E190 Warning: unaligning (T0379)H186 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1q92A)E190 Warning: unaligning (T0379)D191 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)A196 T0379 4 :NIVFDLGGVLIHLNREESIRRFK 1q92A 37 :RVLVDMDGVLADFEGGFLRKFRA T0379 29 :GVADI 1q92A 62 :PDQPF T0379 34 :E 1q92A 68 :A T0379 39 :P 1q92A 71 :D T0379 43 :K 1q92A 72 :R T0379 46 :FLDLESG 1q92A 75 :FWVSEQY T0379 55 :SEEEFRTELSRYIGK 1q92A 84 :LRPGLSEKAISIWES T0379 80 :LLGF 1q92A 101 :FFFE T0379 85 :EEI 1q92A 105 :LEP T0379 90 :EKFDYIDS 1q92A 110 :GAVEAVKE T0379 100 :P 1q92A 120 :S T0379 101 :DYRLFLLSN 1q92A 123 :NTDVFICTS T0379 110 :TNPYVLDLAMSP 1q92A 138 :YCPYEKYAWVEK T0379 130 :LDSFFDKVYASCQMGKYKPN 1q92A 152 :GPDFLEQIVLTRDKTVVSAD T0379 168 :LFIDDGP 1q92A 172 :LLIDDRP T0379 184 :G 1q92A 188 :S T0379 187 :TYCP 1q92A 191 :HVLF T0379 192 :NGENWIP 1q92A 197 :CHNQHLQ T0379 199 :AITRLLR 1q92A 217 :DWKAILD Number of specific fragments extracted= 19 number of extra gaps= 9 total=1192 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 1q92A/T0379-1q92A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1q92A/T0379-1q92A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q92A read from 1q92A/T0379-1q92A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1q92A in template set Warning: unaligning (T0379)A27 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)F61 Warning: unaligning (T0379)I28 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)F61 Warning: unaligning (T0379)I33 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)E70 Warning: unaligning (T0379)E34 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)E70 Warning: unaligning (T0379)L37 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)G74 Warning: unaligning (T0379)L45 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)R83 Warning: unaligning (T0379)F46 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)R83 Warning: unaligning (T0379)S88 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)P109 Warning: unaligning (T0379)A89 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)P109 Warning: unaligning (T0379)L98 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)A119 Warning: unaligning (T0379)R99 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)A119 Warning: unaligning (T0379)P125 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)F151 Warning: unaligning (T0379)S126 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)F151 Warning: unaligning (T0379)F185 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1q92A)E190 Warning: unaligning (T0379)H186 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1q92A)E190 Warning: unaligning (T0379)D191 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)A196 Warning: unaligning (T0379)N192 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)A196 T0379 4 :NIVFDLGGVLIHLNREESIRRFK 1q92A 37 :RVLVDMDGVLADFEGGFLRKFRA T0379 29 :GVAD 1q92A 62 :PDQP T0379 35 :EM 1q92A 71 :DR T0379 38 :DPYLQKG 1q92A 75 :FWVSEQY T0379 47 :LDLESGRKSEEEFRTEL 1q92A 84 :LRPGLSEKAISIWESKN T0379 81 :LGFLEEI 1q92A 101 :FFFELEP T0379 90 :EKFDYIDS 1q92A 110 :GAVEAVKE T0379 100 :PDYRLFLLSN 1q92A 122 :QNTDVFICTS T0379 110 :TNPYVLDLAMS 1q92A 138 :YCPYEKYAWVE T0379 124 :L 1q92A 149 :K T0379 127 :GRTLDSF 1q92A 152 :GPDFLEQ T0379 137 :VYASCQMGKYKPN 1q92A 159 :IVLTRDKTVVSAD T0379 168 :LFIDDGP 1q92A 172 :LLIDDRP T0379 184 :G 1q92A 188 :S T0379 187 :TYCP 1q92A 191 :HVLF Number of specific fragments extracted= 15 number of extra gaps= 9 total=1207 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 1mh9A/T0379-1mh9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1mh9A expands to /projects/compbio/data/pdb/1mh9.pdb.gz 1mh9A:# T0379 read from 1mh9A/T0379-1mh9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mh9A read from 1mh9A/T0379-1mh9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1mh9A to template set # found chain 1mh9A in template set T0379 4 :NIVFDLGGVLIHL 1mh9A 37 :RVLVDMDGVLADF T0379 18 :REESIRRFKAI 1mh9A 50 :EGGFLRKFRAR T0379 29 :GVADIEEMLDPYLQ 1mh9A 63 :DQPFIALEDRRGFW T0379 59 :FRTELSRYIG 1mh9A 77 :VSEQYGRLRP T0379 71 :LTYQQVYDALL 1mh9A 87 :GLSEKAISIWE T0379 85 :EEISAEKFDYIDSLR 1mh9A 105 :LEPLPGAVEAVKEMA T0379 100 :PDYRLFLLSNTN 1mh9A 122 :QNTDVFICTSPI T0379 112 :PYVLDLAMSPRF 1mh9A 140 :PYEKYAWVEKYF T0379 130 :LDSFFDKVYASCQMGKYKPN 1mh9A 152 :GPDFLEQIVLTRDKTVVSAD T0379 168 :LFIDDGPA 1mh9A 172 :LLIDDRPD T0379 185 :FHTYCPDNGENWIPAI 1mh9A 189 :WEHVLFTACHNQHLQL Number of specific fragments extracted= 11 number of extra gaps= 0 total=1218 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 1mh9A/T0379-1mh9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1mh9A/T0379-1mh9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mh9A read from 1mh9A/T0379-1mh9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mh9A in template set T0379 4 :NIVFDLGGVLIHLNREESIRRFKAIGVADI 1mh9A 37 :RVLVDMDGVLADFEGGFLRKFRARFPDQPF T0379 34 :E 1mh9A 68 :A T0379 37 :LDP 1mh9A 69 :LED T0379 43 :KGLFLDLESGRKSEEEFRTELSRYIGK 1mh9A 72 :RRGFWVSEQYGRLRPGLSEKAISIWES T0379 80 :LLGF 1mh9A 101 :FFFE T0379 85 :EEISAEKFDYIDSLRP 1mh9A 105 :LEPLPGAVEAVKEMAS T0379 101 :DYRLFLLSNTN 1mh9A 123 :NTDVFICTSPI T0379 112 :PYVLDLAMSPRF 1mh9A 140 :PYEKYAWVEKYF T0379 130 :LDSFFDKVYASCQMGKYKPN 1mh9A 152 :GPDFLEQIVLTRDKTVVSAD T0379 168 :LFIDDGP 1mh9A 172 :LLIDDRP T0379 184 :GFHTYCPD 1mh9A 188 :SWEHVLFT T0379 192 :NGENWIP 1mh9A 197 :CHNQHLQ T0379 199 :AITRLLR 1mh9A 217 :DWKAILD Number of specific fragments extracted= 13 number of extra gaps= 0 total=1231 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 1mh9A/T0379-1mh9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0379 read from 1mh9A/T0379-1mh9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mh9A read from 1mh9A/T0379-1mh9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mh9A in template set T0379 4 :NIVFDLGGVLIHLNREESIRRFKAIGVADIEEM 1mh9A 37 :RVLVDMDGVLADFEGGFLRKFRARFPDQPFIAL T0379 37 :LDPYLQKGLFLDLESGRKSEEEFRTEL 1mh9A 74 :GFWVSEQYGRLRPGLSEKAISIWESKN T0379 81 :LGFLEEISAEKFDYIDSLR 1mh9A 101 :FFFELEPLPGAVEAVKEMA T0379 100 :PDYRLFLLSNTN 1mh9A 122 :QNTDVFICTSPI T0379 112 :PYVLDLAMSPR 1mh9A 140 :PYEKYAWVEKY T0379 126 :SGRTLDSF 1mh9A 151 :FGPDFLEQ T0379 137 :VYASCQMGKYKPN 1mh9A 159 :IVLTRDKTVVSAD T0379 168 :LFIDDGP 1mh9A 172 :LLIDDRP T0379 184 :GFHTYCPDN 1mh9A 188 :SWEHVLFTA Number of specific fragments extracted= 9 number of extra gaps= 0 total=1240 Will force an alignment to be made, even if fragment is small Number of alignments=128 # command:CPU_time= 37.276 sec, elapsed time= 39.765 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 128 Adding 21528 constraints to all_contacts Done adding distance constraints # command:CPU_time= 37.430 sec, elapsed time= 39.924 sec. # command:Reading probabilities from T0379.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 80.615 Optimizing... Probability sum: -350.339, CN propb: -350.339 weights: 0.399 constraints: 457 # command:CPU_time= 113.812 sec, elapsed time= 116.426 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 457 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 457 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 2887 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 2887 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 16556 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 16556 # command:CPU_time= 114.171 sec, elapsed time= 117.042 sec. # command: