# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 1600 examples # computed average trans backbone unit before proline from 52 examples # trans (non-proline) backbone unit: # CA= -2.2097 1.0151 -0.0046 # O= -0.1488 2.2425 0.0020 # C= -0.6903 1.1357 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4580 -0.0000 -0.0000 # cis backbone unit: # CA= -0.1462 2.4515 0.0018 # O= -2.0272 0.9713 0.0022 # C= -0.8006 1.0755 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4659 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2063 1.0654 0.0002 # O= -0.1193 2.2442 0.0054 # C= -0.6842 1.1479 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4661 -0.0000 0.0000 # After reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz have 408 chains in training database # Count of chains,residues,atoms: 408,82794,639987 # 79931 residues have no bad marker # 573 residues lack atoms needed to compute omega # 313 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 0 # HAS_OXT 264 # TOO_MANY_ATOMS 0 # TOO_FEW_ATOMS 378 # HAS_UNKNOWN_ATOMS 0 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 148 # NON_PLANAR_PEPTIDE 17 # BAD_PEPTIDE 812 # HIGH_B_FACTOR 1566 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-40pc-3157.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to # command:# Making conformation for sequence T0615 numbered 1 through 179 Created new target T0615 from T0615.a2m # command:CPU_time= 5.849 sec, elapsed time= 7.424 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vj7A/T0615-1vj7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vj7A expands to /projects/compbio/data/pdb/1vj7.pdb.gz 1vj7A:# T0615 read from 1vj7A/T0615-1vj7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vj7A read from 1vj7A/T0615-1vj7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vj7A to template set # found chain 1vj7A in template set Warning: unaligning (T0615)T51 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1vj7A)D67 Warning: unaligning (T0615)D52 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1vj7A)D67 Warning: unaligning (T0615)K94 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1vj7A)H124 Warning: unaligning (T0615)L131 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vj7A)K159 Warning: unaligning (T0615)Q132 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vj7A)K159 Warning: unaligning (T0615)T140 because of BadResidue code BAD_PEPTIDE at template residue (1vj7A)Q160 T0615 2 :ATYPSAKFMECLQYAAFKHRQQRRKD 1vj7A 21 :NETDAAFVKKALDYATAAHFYQVRKS # choosing archetypes in rotamer library T0615 30 :ETPYVNHVINVSTILSVEA 1vj7A 47 :GEPYIVHPIQVAGILADLH T0615 53 :EGVLMAALLHDVVEDTDASFEDVEKLFGPDVCGLVREVTDD 1vj7A 68 :AVTVACGFLHDVVEDTDITLDNIEFDFGKDVRDIVDGVTKL T0615 113 :SCRAKLIKLADKLDNLRD 1vj7A 134 :DIRVILVKLADRLHNMRT T0615 141 :QERRDQYFVWAKKVVD 1vj7A 161 :ERISRETMEIYAPLAH T0615 157 :NLRGTNANLE 1vj7A 179 :GISRIKWELE T0615 170 :DEIFR 1vj7A 189 :DLAFR Number of specific fragments extracted= 7 number of extra gaps= 2 total=7 Will force an alignment to be made, even if fragment is small Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vj7A/T0615-1vj7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0615 read from 1vj7A/T0615-1vj7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vj7A read from 1vj7A/T0615-1vj7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vj7A in template set Warning: unaligning (T0615)I50 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1vj7A)D67 Warning: unaligning (T0615)D52 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1vj7A)D67 Warning: unaligning (T0615)K94 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1vj7A)H124 Warning: unaligning (T0615)L131 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vj7A)K159 Warning: unaligning (T0615)Q132 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vj7A)K159 T0615 2 :ATYPSAKFMECLQYAAFKHRQQRRKDPQ 1vj7A 21 :NETDAAFVKKALDYATAAHFYQVRKSGE T0615 32 :PYVNHVINVSTILS 1vj7A 49 :PYIVHPIQVAGILA T0615 47 :EAC 1vj7A 63 :DLH T0615 53 :EGVLMAALLHDVVEDTDASFEDVEKLFGPDVCGLVREVTDD 1vj7A 68 :AVTVACGFLHDVVEDTDITLDNIEFDFGKDVRDIVDGVTKL T0615 112 :SSCRAKLIKLADKLDNLRD 1vj7A 133 :KDIRVILVKLADRLHNMRT T0615 139 :WTQERRDQYFVWAKKV 1vj7A 163 :ISRETMEIYAPLAHRL T0615 155 :VDNLRGTNANLELK 1vj7A 180 :ISRIKWELEDLAFR T0615 169 :LDEIFRQRGL 1vj7A 200 :FYKISHMMNE Number of specific fragments extracted= 8 number of extra gaps= 2 total=15 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 1vj7A/T0615-1vj7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0615 read from 1vj7A/T0615-1vj7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vj7A read from 1vj7A/T0615-1vj7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vj7A in template set Warning: unaligning (T0615)C49 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1vj7A)D67 Warning: unaligning (T0615)D52 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1vj7A)D67 Warning: unaligning (T0615)K94 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1vj7A)H124 Warning: unaligning (T0615)L131 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vj7A)K159 Warning: unaligning (T0615)Q132 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vj7A)K159 Warning: unaligning (T0615)T140 because of BadResidue code BAD_PEPTIDE at template residue (1vj7A)Q160 T0615 2 :ATYPSAKFMECLQYAAFKHRQQRRK 1vj7A 21 :NETDAAFVKKALDYATAAHFYQVRK T0615 29 :QETPYVNHVINVSTILSVEA 1vj7A 46 :SGEPYIVHPIQVAGILADLH T0615 53 :EGVLMAALLHDVVEDTDASFEDVEKLFGPDVCGLVREVTDD 1vj7A 68 :AVTVACGFLHDVVEDTDITLDNIEFDFGKDVRDIVDGVTKL T0615 108 :NAAKSSCRAKLIKLADKLDNLRD 1vj7A 129 :MAMSKDIRVILVKLADRLHNMRT T0615 141 :QERRDQYFVWAKKVVDNLRGTNANLELKLDEIFRQRGL 1vj7A 161 :ERISRETMEIYAPLAHRLGISRIKWELEDLAFRYLNET Number of specific fragments extracted= 5 number of extra gaps= 2 total=20 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 2qgsA/T0615-2qgsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2qgsA expands to /projects/compbio/data/pdb/2qgs.pdb.gz 2qgsA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0615 read from 2qgsA/T0615-2qgsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qgsA read from 2qgsA/T0615-2qgsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2qgsA to template set # found chain 2qgsA in template set Warning: unaligning (T0615)D93 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2qgsA)H109 T0615 4 :YPSAKFMECLQYAAFKHRQQ 2qgsA 2 :NSRMKIKKAYEYMKSFHQHD T0615 29 :QETPYVNHVINVSTILS 2qgsA 22 :TTGHDIAHVERVYNNAC T0615 46 :VEACITDEGVLMAALLHDVVEDTDASFED 2qgsA 43 :RENITDTLVIELSSLLHDTVDSKLTDEIL T0615 75 :VEKL 2qgsA 80 :LSTL T0615 79 :FGPDVCGLVREVTD 2qgsA 85 :LSSEISQQVLYIIK T0615 94 :KSLEKQERKRLQIENAAKS 2qgsA 110 :VKLSIDGEIVRDADRLDAI T0615 113 :SCRA 2qgsA 167 :DNSA T0615 120 :KLADKLDNLRDLQVNTPTG 2qgsA 171 :IKHFYEKLFKLKDLMHTPT T0615 140 :TQERRDQYFV 2qgsA 190 :AKKLAEERHQ T0615 164 :NLELKLDEIFRQRGL 2qgsA 200 :FMIQYLKQFMSEWNF Number of specific fragments extracted= 10 number of extra gaps= 0 total=30 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 2qgsA/T0615-2qgsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0615 read from 2qgsA/T0615-2qgsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qgsA read from 2qgsA/T0615-2qgsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2qgsA in template set Warning: unaligning (T0615)T91 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2qgsA)H109 Warning: unaligning (T0615)D93 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2qgsA)H109 T0615 5 :PSAKFMECLQYAAFKHRQQ 2qgsA 3 :SRMKIKKAYEYMKSFHQHD T0615 28 :PQE 2qgsA 22 :TTG T0615 32 :PYVNHVINVSTILSV 2qgsA 25 :HDIAHVERVYNNACY T0615 47 :EACITD 2qgsA 43 :RENITD T0615 53 :EGVLMAALLHDVVEDTDASFED 2qgsA 50 :LVIELSSLLHDTVDSKLTDEIL T0615 75 :VEKLFG 2qgsA 76 :LKQFLS T0615 81 :PDVCGLVREV 2qgsA 91 :QQVLYIIKHM T0615 94 :KSLEKQ 2qgsA 110 :VKLSID T0615 100 :ERKRLQIENAAK 2qgsA 134 :ARTFQFSGHFGE T0615 112 :SSC 2qgsA 167 :DNS T0615 120 :KLADKLDNLRDL 2qgsA 170 :AIKHFYEKLFKL T0615 132 :QVNTP 2qgsA 183 :DLMHT T0615 145 :DQYFVWAKKVVDN 2qgsA 188 :PTAKKLAEERHQF T0615 165 :LELKLDEIFRQRG 2qgsA 201 :MIQYLKQFMSEWN Number of specific fragments extracted= 14 number of extra gaps= 0 total=44 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 2qgsA/T0615-2qgsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0615 read from 2qgsA/T0615-2qgsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qgsA read from 2qgsA/T0615-2qgsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2qgsA in template set Warning: unaligning (T0615)T91 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2qgsA)H109 T0615 6 :SAKFMECLQYAAFKHRQQRRK 2qgsA 4 :RMKIKKAYEYMKSFHQHDTTG T0615 33 :YVNHVINVSTILSVEACITD 2qgsA 29 :HVERVYNNACYIAKRENITD T0615 53 :EGVLMAALLHDVVEDTDASFEDVEKL 2qgsA 50 :LVIELSSLLHDTVDSKLTDEILAYDQ T0615 79 :FGPDVCGLVREV 2qgsA 89 :ISQQVLYIIKHM T0615 100 :ERKRLQIENAAKSSCR 2qgsA 131 :IGIARTFQFSGHFGEP T0615 120 :KLADKLDNLRD 2qgsA 173 :HFYEKLFKLKD T0615 133 :VNTP 2qgsA 184 :LMHT T0615 138 :GWTQERRDQYFVWAKKVVDNL 2qgsA 188 :PTAKKLAEERHQFMIQYLKQF Number of specific fragments extracted= 8 number of extra gaps= 0 total=52 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 3b57A/T0615-3b57A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3b57A expands to /projects/compbio/data/pdb/3b57.pdb.gz 3b57A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0615 read from 3b57A/T0615-3b57A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3b57A read from 3b57A/T0615-3b57A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3b57A to template set # found chain 3b57A in template set Warning: unaligning (T0615)R24 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3b57A)H25 Warning: unaligning (T0615)P32 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3b57A)H25 Warning: unaligning (T0615)D69 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3b57A)Q70 Warning: unaligning (T0615)S95 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3b57A)A111 Warning: unaligning (T0615)V133 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3b57A)P153 Warning: unaligning (T0615)T135 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3b57A)P153 T0615 13 :LQYAAFKHRQQ 3b57A 7 :ILSAKNWMHSH T0615 33 :YVNHVINVSTILS 3b57A 26 :DWSHIKRVWKLSK T0615 46 :VEA 3b57A 43 :KEG T0615 51 :TDEGVL 3b57A 46 :GDLFTI T0615 57 :MAALLHDV 3b57A 53 :LAALFHDY T0615 70 :ASFEDVEKL 3b57A 71 :EATKTLINW T0615 80 :GPDVCGLVREVTD 3b57A 86 :PSELIKKIIRIIQ T0615 96 :LE 3b57A 112 :LT T0615 98 :KQERKRLQIENAAKS 3b57A 129 :GAIGIARTFTYGGAH T0615 132 :Q 3b57A 150 :Q T0615 136 :PTG 3b57A 154 :KNT T0615 140 :TQERRDQ 3b57A 157 :TLQHFYD T0615 147 :YFVWAKKV 3b57A 165 :LLLIKDQL T0615 155 :VD 3b57A 177 :AK T0615 157 :NLRGTNANLELKLDEIFRQR 3b57A 180 :IAKEKQKIMQDFIQALEKEL Number of specific fragments extracted= 15 number of extra gaps= 0 total=67 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 3b57A/T0615-3b57A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0615 read from 3b57A/T0615-3b57A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3b57A read from 3b57A/T0615-3b57A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3b57A in template set Warning: unaligning (T0615)R24 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3b57A)H25 Warning: unaligning (T0615)Q29 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3b57A)H25 Warning: unaligning (T0615)D69 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3b57A)Q70 Warning: unaligning (T0615)T91 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3b57A)A111 Warning: unaligning (T0615)T137 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3b57A)P153 T0615 5 :PSA 3b57A 2 :NKE T0615 11 :ECLQYAAFKHRQQ 3b57A 5 :EIILSAKNWMHSH T0615 30 :ETPYVNHVINVSTILSVEACI 3b57A 26 :DWSHIKRVWKLSKEIQSKEGG T0615 52 :DEG 3b57A 47 :DLF T0615 55 :VLMAALLHDV 3b57A 51 :IELAALFHDY T0615 70 :ASFEDVEKL 3b57A 71 :EATKTLINW T0615 79 :FG 3b57A 83 :KE T0615 81 :PDVCGLVREV 3b57A 91 :KKIIRIIQSV T0615 100 :ERKRLQIENAAKSSCR 3b57A 131 :IGIARTFTYGGAHNRE T0615 133 :VNTP 3b57A 147 :IANQ T0615 139 :WTQERRDQYFVWAKKV 3b57A 157 :TLQHFYDKLLLIKDQL T0615 155 :VDNLRGTNANLELKLDEIFRQ 3b57A 174 :TETAKTIAKEKQKIMQDFIQA T0615 176 :RGL 3b57A 199 :LKV Number of specific fragments extracted= 13 number of extra gaps= 0 total=80 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 3b57A/T0615-3b57A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0615 read from 3b57A/T0615-3b57A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3b57A read from 3b57A/T0615-3b57A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3b57A in template set Warning: unaligning (T0615)Y4 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3b57A)H25 Warning: unaligning (T0615)E66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3b57A)Q70 Warning: unaligning (T0615)T91 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3b57A)A111 T0615 5 :PSAKFMECLQYAAFKHRQQRRK 3b57A 26 :DWSHIKRVWKLSKEIQSKEGGD T0615 52 :DEGVLMAALLHDVV 3b57A 48 :LFTIELAALFHDYS T0615 71 :SFEDVEKL 3b57A 72 :ATKTLINW T0615 79 :FGPDVCGLVREV 3b57A 89 :LIKKIIRIIQSV T0615 99 :QERKRLQIENAAKSSCR 3b57A 130 :AIGIARTFTYGGAHNRE T0615 124 :KLDNLRDLQV 3b57A 165 :LLLIKDQLNT T0615 138 :GWTQERRDQYFVWAKKVVDNL 3b57A 175 :ETAKTIAKEKQKIMQDFIQAL T0615 172 :IFRQRGLL 3b57A 196 :EKELKVLE Number of specific fragments extracted= 8 number of extra gaps= 0 total=88 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 2ogiA/T0615-2ogiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2ogiA expands to /projects/compbio/data/pdb/2ogi.pdb.gz 2ogiA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 827, because occupancy 0.5 <= existing 0.500 in 2ogiA Skipped atom 829, because occupancy 0.500 <= existing 0.500 in 2ogiA Skipped atom 831, because occupancy 0.500 <= existing 0.500 in 2ogiA Skipped atom 833, because occupancy 0.500 <= existing 0.500 in 2ogiA Skipped atom 835, because occupancy 0.500 <= existing 0.500 in 2ogiA Skipped atom 837, because occupancy 0.500 <= existing 0.500 in 2ogiA Skipped atom 839, because occupancy 0.500 <= existing 0.500 in 2ogiA Skipped atom 841, because occupancy 0.500 <= existing 0.500 in 2ogiA Skipped atom 953, because occupancy 0.500 <= existing 0.500 in 2ogiA Skipped atom 955, because occupancy 0.500 <= existing 0.500 in 2ogiA Skipped atom 957, because occupancy 0.500 <= existing 0.500 in 2ogiA Skipped atom 959, because occupancy 0.500 <= existing 0.500 in 2ogiA Skipped atom 961, because occupancy 0.500 <= existing 0.500 in 2ogiA Skipped atom 963, because occupancy 0.500 <= existing 0.500 in 2ogiA Skipped atom 965, because occupancy 0.500 <= existing 0.500 in 2ogiA Skipped atom 967, because occupancy 0.500 <= existing 0.500 in 2ogiA Skipped atom 969, because occupancy 0.500 <= existing 0.500 in 2ogiA Skipped atom 971, because occupancy 0.500 <= existing 0.500 in 2ogiA Skipped atom 973, because occupancy 0.500 <= existing 0.500 in 2ogiA Skipped atom 975, because occupancy 0.500 <= existing 0.500 in 2ogiA Skipped atom 977, because occupancy 0.500 <= existing 0.500 in 2ogiA Skipped atom 979, because occupancy 0.500 <= existing 0.500 in 2ogiA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0615 read from 2ogiA/T0615-2ogiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ogiA read from 2ogiA/T0615-2ogiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2ogiA to template set # found chain 2ogiA in template set Warning: unaligning (T0615)L61 because of BadResidue code BAD_PEPTIDE in next template residue (2ogiA)H58 Warning: unaligning (T0615)H62 because of BadResidue code BAD_PEPTIDE at template residue (2ogiA)H58 Warning: unaligning (T0615)D126 because of BadResidue code BAD_PEPTIDE in next template residue (2ogiA)H139 Warning: unaligning (T0615)V133 because of BadResidue code BAD_PEPTIDE at template residue (2ogiA)H139 T0615 2 :ATYPSAKFMECLQYAAF 2ogiA 23 :SDKRFNHVLGVERAAIE T0615 44 :LSVEACITDEGVLMAAL 2ogiA 40 :LAERYGYDKEKAGLAAL T0615 63 :DVV 2ogiA 59 :DYA T0615 68 :TDASFEDVEKLFGPD 2ogiA 62 :KELSDDEFLRLIDKY T0615 83 :VCGLVREVT 2ogiA 95 :GIYKIQEDL T0615 95 :SLEKQE 2ogiA 104 :AIKDQD T0615 105 :QIENAAKS 2ogiA 110 :ILAAIAKH T0615 113 :SCRAKLIKLADKL 2ogiA 125 :STLDKIVYVADYI T0615 134 :NTPTGWTQERRD 2ogiA 140 :NRDFPGVEEARE T0615 147 :Y 2ogiA 152 :L T0615 158 :LRGTNANLE 2ogiA 153 :AKVDLNKAV T0615 170 :DEIFR 2ogiA 162 :AYETA T0615 175 :QRG 2ogiA 173 :ASK Number of specific fragments extracted= 13 number of extra gaps= 2 total=101 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 2ogiA/T0615-2ogiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0615 read from 2ogiA/T0615-2ogiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ogiA read from 2ogiA/T0615-2ogiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ogiA in template set Warning: unaligning (T0615)L61 because of BadResidue code BAD_PEPTIDE in next template residue (2ogiA)H58 Warning: unaligning (T0615)H62 because of BadResidue code BAD_PEPTIDE at template residue (2ogiA)H58 Warning: unaligning (T0615)S112 because of BadResidue code BAD_PEPTIDE at template residue (2ogiA)A122 Warning: unaligning (T0615)D126 because of BadResidue code BAD_PEPTIDE in next template residue (2ogiA)H139 Warning: unaligning (T0615)Q132 because of BadResidue code BAD_PEPTIDE at template residue (2ogiA)H139 T0615 4 :YPSAK 2ogiA 9 :LDRTE T0615 16 :AAFKHRQQRRKD 2ogiA 14 :LLSKVRHMMSDK T0615 30 :ETPYVNHVINVSTILSVEACITDEGVLMAAL 2ogiA 26 :RFNHVLGVERAAIELAERYGYDKEKAGLAAL T0615 63 :DVVE 2ogiA 59 :DYAK T0615 69 :DASFEDVEKLFGPD 2ogiA 63 :ELSDDEFLRLIDKY T0615 92 :DDKSLE 2ogiA 79 :DPDLKK T0615 98 :KQ 2ogiA 87 :NN T0615 106 :IENAAK 2ogiA 96 :IYKIQE T0615 113 :SCR 2ogiA 123 :QMS T0615 116 :AKLIKLADKL 2ogiA 128 :DKIVYVADYI T0615 133 :VNTPTG 2ogiA 140 :NRDFPG T0615 139 :WTQERRDQYFVWAKKVVD 2ogiA 149 :ARELAKVDLNKAVAYETA T0615 160 :GTNANLELK 2ogiA 167 :RTVAFLASK T0615 169 :LDEIFRQ 2ogiA 183 :TIETYNA Number of specific fragments extracted= 14 number of extra gaps= 3 total=115 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 2ogiA/T0615-2ogiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0615 read from 2ogiA/T0615-2ogiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ogiA read from 2ogiA/T0615-2ogiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ogiA in template set Warning: unaligning (T0615)L61 because of BadResidue code BAD_PEPTIDE in next template residue (2ogiA)H58 Warning: unaligning (T0615)H62 because of BadResidue code BAD_PEPTIDE at template residue (2ogiA)H58 Warning: unaligning (T0615)D93 because of BadResidue code BAD_PEPTIDE in next template residue (2ogiA)A122 Warning: unaligning (T0615)K94 because of BadResidue code BAD_PEPTIDE at template residue (2ogiA)A122 T0615 4 :YPSAKFMECLQYA 2ogiA 22 :MSDKRFNHVLGVE T0615 39 :NVSTILSVEACITDEGVLMAAL 2ogiA 35 :RAAIELAERYGYDKEKAGLAAL T0615 63 :DVVE 2ogiA 59 :DYAK T0615 69 :DASFEDVEKL 2ogiA 63 :ELSDDEFLRL T0615 80 :GPDVCGLVREVTD 2ogiA 107 :DQDILAAIAKHTV T0615 95 :SLEK 2ogiA 123 :QMST T0615 99 :QE 2ogiA 147 :EE T0615 106 :IENAAKSS 2ogiA 149 :ARELAKVD T0615 148 :FVWAKKVV 2ogiA 157 :LNKAVAYE T0615 167 :LK 2ogiA 165 :TA Number of specific fragments extracted= 10 number of extra gaps= 2 total=125 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 2gz4A/T0615-2gz4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2gz4A expands to /projects/compbio/data/pdb/2gz4.pdb.gz 2gz4A:# T0615 read from 2gz4A/T0615-2gz4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gz4A read from 2gz4A/T0615-2gz4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2gz4A to template set # found chain 2gz4A in template set T0615 7 :AK 2gz4A 32 :AD T0615 16 :AAFKHRQQRR 2gz4A 34 :IAHGLARVAR T0615 26 :KDPQETPYVNHVINVSTILSVEACITDEGVLMAALLHDVVED 2gz4A 49 :RGDHAFTVAQHCLIVETIFCRMCPGATPDEMQMALLHDAPEY T0615 70 :ASFED 2gz4A 103 :VGGGY T0615 76 :EKL 2gz4A 108 :KTV T0615 80 :GPDVCGLVREVTD 2gz4A 111 :EKRLEAAVHLRFG T0615 93 :DKSLEKQE 2gz4A 125 :PPHASREL T0615 103 :RLQIENAAKS 2gz4A 133 :KDRIKKADTV T0615 113 :SCR 2gz4A 168 :GIT T0615 128 :LRDLQVNTPTG 2gz4A 171 :RDMFDIIPLPS T0615 141 :QERRDQYFVWAKKV 2gz4A 182 :TEAQRLFIARFEAI T0615 170 :DEIFRQ 2gz4A 196 :ETLRVT Number of specific fragments extracted= 12 number of extra gaps= 0 total=137 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 2gz4A/T0615-2gz4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0615 read from 2gz4A/T0615-2gz4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gz4A read from 2gz4A/T0615-2gz4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gz4A in template set T0615 22 :QQRRKDPQETPYVNHVINVSTILSVEA 2gz4A 45 :NGQTRGDHAFTVAQHCLIVETIFCRMC T0615 49 :CI 2gz4A 73 :GA T0615 52 :DEGVLMAALLHDVVED 2gz4A 75 :TPDEMQMALLHDAPEY T0615 70 :ASFED 2gz4A 103 :VGGGY T0615 76 :EKL 2gz4A 108 :KTV T0615 81 :PDVCGLVREVTD 2gz4A 112 :KRLEAAVHLRFG T0615 93 :DKSLEKQE 2gz4A 125 :PPHASREL T0615 103 :RLQIENAAK 2gz4A 133 :KDRIKKADT T0615 112 :SSC 2gz4A 167 :RGI T0615 130 :DLQVNTPTG 2gz4A 170 :TRDMFDIIP T0615 139 :WTQERRDQYFVWAKKVVDNLRGT 2gz4A 180 :PSTEAQRLFIARFEAIETLRVTR Number of specific fragments extracted= 11 number of extra gaps= 0 total=148 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 2gz4A/T0615-2gz4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0615 read from 2gz4A/T0615-2gz4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gz4A read from 2gz4A/T0615-2gz4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gz4A in template set T0615 4 :YPSAKFMECL 2gz4A 29 :VEIADIAHGL T0615 20 :HRQQRRK 2gz4A 44 :WNGQTRG T0615 30 :ETPYVN 2gz4A 51 :DHAFTV T0615 36 :HVINVSTILSVEACITDEGVLMAALLHDVVED 2gz4A 59 :HCLIVETIFCRMCPGATPDEMQMALLHDAPEY T0615 95 :SL 2gz4A 94 :DM T0615 97 :EKQERKRLQIENAAKS 2gz4A 105 :GGYKTVEKRLEAAVHL T0615 128 :LRDLQVNTP 2gz4A 121 :RFGLPPHAS T0615 138 :GWTQERRDQYFVWAKKVVDN 2gz4A 130 :RELKDRIKKADTVAAFFEAT Number of specific fragments extracted= 8 number of extra gaps= 0 total=156 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 2o08A/T0615-2o08A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2o08A expands to /projects/compbio/data/pdb/2o08.pdb.gz 2o08A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 270, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 274, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 276, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 278, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 280, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 282, because occupancy 0.500 <= existing 0.500 in 2o08A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 743, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 747, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 749, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 751, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 753, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 755, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 757, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 759, because occupancy 0.500 <= existing 0.500 in 2o08A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1106, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 1110, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 1112, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 1114, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 1116, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 1118, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 1120, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 1122, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 1267, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 1271, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 1273, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 1291, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 1295, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 1297, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 1299, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 1301, because occupancy 0.500 <= existing 0.500 in 2o08A # T0615 read from 2o08A/T0615-2o08A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2o08A read from 2o08A/T0615-2o08A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2o08A to template set # found chain 2o08A in template set T0615 2 :ATYPSAKFMECLQYAAF 2o08A 15 :TEHRYQHTIGVMETAID T0615 44 :LSVEACITDEGVLMAALLHDVV 2o08A 32 :LAKLYGADQQKAELAAIFHDYA T0615 68 :TDASFEDVEKLFGPD 2o08A 54 :KFRDKNEMRTLIREK T0615 83 :VCGLVREVTDDKSLEKQE 2o08A 84 :APCGAYYVREEVGIEDED T0615 105 :QIENAAKS 2o08A 102 :VLQAIRFH T0615 113 :SCRAKLIKLADKL 2o08A 117 :SLLEKIIFLADYI T0615 131 :LQVNTPTG 2o08A 130 :EPNRQFPG T0615 140 :TQERRDQY 2o08A 138 :VEKVRTQA T0615 159 :RGTNANLELKL 2o08A 146 :KTDLNGAIISS T0615 170 :DEIFR 2o08A 158 :VNTIT T0615 175 :QRGL 2o08A 165 :LKKN Number of specific fragments extracted= 11 number of extra gaps= 0 total=167 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 2o08A/T0615-2o08A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0615 read from 2o08A/T0615-2o08A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2o08A read from 2o08A/T0615-2o08A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2o08A in template set T0615 16 :AAFKHRQQRRKDPQ 2o08A 6 :ALQLVKPHLTEHRY T0615 32 :PYVNHVINVSTILSVEACI 2o08A 20 :QHTIGVMETAIDLAKLYGA T0615 52 :DEG 2o08A 39 :DQQ T0615 55 :VLMAALLHDVVED 2o08A 43 :AELAAIFHDYAKF T0615 70 :ASFEDVEKLFGPD 2o08A 56 :RDKNEMRTLIREK T0615 91 :TDDKSLEKQ 2o08A 72 :QDILFYGDE T0615 100 :ERKRLQIENAAK 2o08A 82 :LHAPCGAYYVRE T0615 112 :SSCR 2o08A 114 :PNMS T0615 116 :AKLIKLADKLDNL 2o08A 120 :EKIIFLADYIEPN T0615 133 :VNTPTG 2o08A 133 :RQFPGV T0615 139 :WTQERRDQYFVWAKKVVDN 2o08A 141 :VRTQAKTDLNGAIISSLVN T0615 161 :TNANLELK 2o08A 160 :TITFLLKK T0615 169 :LDEIFRQ 2o08A 175 :TLATYNQ Number of specific fragments extracted= 13 number of extra gaps= 0 total=180 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 2o08A/T0615-2o08A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0615 read from 2o08A/T0615-2o08A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2o08A read from 2o08A/T0615-2o08A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2o08A in template set T0615 4 :YPSAKFMECLQY 2o08A 14 :LTEHRYQHTIGV T0615 38 :INVSTILSVEACITDEGVLMAALLHDVVE 2o08A 26 :METAIDLAKLYGADQQKAELAAIFHDYAK T0615 69 :DASFEDVEKL 2o08A 55 :FRDKNEMRTL T0615 79 :FGPDVCGLVREVT 2o08A 98 :EDEDVLQAIRFHT T0615 93 :DKSLEKQE 2o08A 113 :RPNMSLLE T0615 117 :KLIKLADKLDNLRDLQV 2o08A 121 :KIIFLADYIEPNRQFPG T0615 136 :P 2o08A 138 :V T0615 138 :GWTQ 2o08A 139 :EKVR T0615 142 :ERRDQYFVWAKKVVDNLRGTNANLELKLDEIFR 2o08A 151 :GAIISSLVNTITFLLKKNQPIYPDTLATYNQLL Number of specific fragments extracted= 9 number of extra gaps= 0 total=189 Will force an alignment to be made, even if fragment is small Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2pq7A/T0615-2pq7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2pq7A expands to /projects/compbio/data/pdb/2pq7.pdb.gz 2pq7A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 4, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 6, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 8, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 10, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 12, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 14, because occupancy 0.370 <= existing 0.370 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 16, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 56, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 58, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 60, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 62, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 64, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 66, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 68, because occupancy 0.370 <= existing 0.370 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 70, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 145, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 147, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 149, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 151, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 153, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 155, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 157, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 159, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 161, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 163, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 165, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 167, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 169, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 171, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 173, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 175, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 352, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 354, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 356, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 358, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 360, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 362, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 364, because occupancy 0.370 <= existing 0.370 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 366, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 396, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 398, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 400, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 402, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 404, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 406, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 498, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 500, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 502, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 504, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 506, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 508, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 510, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 512, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 674, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 676, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 678, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 680, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 682, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 684, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 686, because occupancy 0.250 <= existing 0.250 in 2pq7A Skipped atom 689, because occupancy 0.250 <= existing 0.250 in 2pq7A Skipped atom 692, because occupancy 0.250 <= existing 0.250 in 2pq7A Skipped atom 695, because occupancy 0.250 <= existing 0.250 in 2pq7A Skipped atom 698, because occupancy 0.250 <= existing 0.250 in 2pq7A Skipped atom 701, because occupancy 0.250 <= existing 0.250 in 2pq7A Skipped atom 739, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 741, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 743, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 745, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 747, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 749, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 870, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 874, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 876, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 909, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 911, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 913, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 915, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 917, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 919, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1253, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1255, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1257, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1259, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1261, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1263, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1265, because occupancy 0.370 <= existing 0.370 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1267, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 1311, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 1313, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 1315, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 1317, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 1319, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 1321, because occupancy 0.500 <= existing 0.500 in 2pq7A # T0615 read from 2pq7A/T0615-2pq7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2pq7A read from 2pq7A/T0615-2pq7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2pq7A to template set # found chain 2pq7A in template set Warning: unaligning (T0615)Y4 because first residue in template chain is (2pq7A)M1 Warning: unaligning (T0615)S113 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2pq7A)T118 T0615 5 :PSAKFME 2pq7A 2 :NLTELME T0615 12 :CLQYAAFKHRQQRRKD 2pq7A 16 :ILNIVREAFKDYDDPA T0615 32 :PYVNHVINVSTILS 2pq7A 32 :HDISHTFRVMENAS T0615 46 :VEA 2pq7A 50 :REK T0615 51 :TDEG 2pq7A 53 :CDLQ T0615 55 :VLMAALLHDVVED 2pq7A 58 :AIIAALLHDIKRP T0615 74 :DVEKL 2pq7A 71 :HEALT T0615 79 :FGPDVCGLVREVTDDKSLE 2pq7A 79 :HAESGAEYASGLLPTMGFD T0615 99 :QERKRLQIENAAKS 2pq7A 98 :ISFVAEVSKAIRSH T0615 114 :CR 2pq7A 119 :PT T0615 116 :AKLIKLADKLDNLRD 2pq7A 124 :GKILQDADRLDAIGA T0615 140 :TQERRDQY 2pq7A 139 :VAIARVFS Number of specific fragments extracted= 12 number of extra gaps= 0 total=201 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 2pq7A/T0615-2pq7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0615 read from 2pq7A/T0615-2pq7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2pq7A read from 2pq7A/T0615-2pq7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2pq7A in template set Warning: unaligning (T0615)T91 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2pq7A)T118 Warning: unaligning (T0615)E97 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2pq7A)T118 Warning: unaligning (T0615)A110 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2pq7A)P186 Warning: unaligning (T0615)P136 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2pq7A)P186 Warning: unaligning (T0615)G177 because last residue in template chain is (2pq7A)G217 T0615 9 :FMECLQYAAFKHRQQRRKDPQE 2pq7A 13 :LREILNIVREAFKDYDDPAHDI T0615 32 :PYVNHVINVSTILSVEACI 2pq7A 35 :SHTFRVMENASEIASREKC T0615 52 :DEG 2pq7A 54 :DLQ T0615 55 :VLMAALLHDV 2pq7A 58 :AIIAALLHDI T0615 65 :VEDTDASFEDV 2pq7A 91 :LPTMGFDISFV T0615 81 :PDVCGLVREV 2pq7A 102 :AEVSKAIRSH T0615 100 :ERK 2pq7A 139 :VAI T0615 105 :QIENA 2pq7A 142 :ARVFS T0615 137 :TG 2pq7A 187 :ET T0615 149 :VWAKKVVDNLRGTNANLE 2pq7A 192 :ETARKMAEDRYSFVVEFV T0615 170 :DEIFRQR 2pq7A 210 :QRFLAEW Number of specific fragments extracted= 11 number of extra gaps= 0 total=212 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 2pq7A/T0615-2pq7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0615 read from 2pq7A/T0615-2pq7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2pq7A read from 2pq7A/T0615-2pq7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2pq7A in template set Warning: unaligning (T0615)K111 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2pq7A)T118 Warning: unaligning (T0615)Y147 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2pq7A)P186 T0615 9 :FMECLQYAAFKHRQQRRK 2pq7A 13 :LREILNIVREAFKDYDDP T0615 29 :QET 2pq7A 31 :AHD T0615 35 :NHVINVSTILSVEAC 2pq7A 35 :SHTFRVMENASEIAS T0615 50 :ITDEG 2pq7A 52 :KCDLQ T0615 55 :VLMAALLHDV 2pq7A 58 :AIIAALLHDI T0615 74 :DVEKL 2pq7A 71 :HEALT T0615 79 :FGPDVCGLVREVTDDKSL 2pq7A 79 :HAESGAEYASGLLPTMGF T0615 97 :EKQERKRLQIENAA 2pq7A 98 :ISFVAEVSKAIRSH T0615 116 :AKLIKLADKLDNLR 2pq7A 124 :GKILQDADRLDAIG T0615 138 :GWTQERRDQ 2pq7A 138 :AVAIARVFS Number of specific fragments extracted= 10 number of extra gaps= 0 total=222 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 2parA/T0615-2parA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2parA expands to /projects/compbio/data/pdb/2par.pdb.gz 2parA:# T0615 read from 2parA/T0615-2parA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2parA read from 2parA/T0615-2parA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2parA to template set # found chain 2parA in template set Warning: unaligning (T0615)A70 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2parA)E92 Warning: unaligning (T0615)E97 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2parA)E92 Warning: unaligning (T0615)K98 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (2parA)Y93 Warning: unaligning (T0615)Q132 because of BadResidue code BAD_PEPTIDE in next template residue (2parA)E122 Warning: unaligning (T0615)V133 because of BadResidue code BAD_PEPTIDE at template residue (2parA)E122 Warning: unaligning (T0615)N134 because of BadResidue code BAD_PEPTIDE at template residue (2parA)H123 T0615 9 :FMECLQYAAFK 2parA 30 :VSEHSLQVAMV T0615 37 :VINVSTILSVEA 2parA 41 :AHALAAIKNRKF T0615 49 :CITDEGVLMAALLHDVVE 2parA 55 :NVNAERIALLAMYHDASA T0615 67 :DTD 2parA 77 :DLP T0615 99 :QERKRLQIENAAKS 2parA 94 :KAIEKIAQQKLVDM T0615 125 :LDNLRDL 2parA 114 :DIFAPLI T0615 135 :TPTGWTQERRDQYFVWAKKVVD 2parA 124 :AYSDEEKSLVKQADALCAYLKC T0615 157 :NLRGTNANLELKLD 2parA 155 :EFLLAKTRLEATLE Number of specific fragments extracted= 8 number of extra gaps= 1 total=230 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 2parA/T0615-2parA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0615 read from 2parA/T0615-2parA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2parA read from 2parA/T0615-2parA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2parA in template set Warning: unaligning (T0615)T3 because of BadResidue code BAD_PEPTIDE at template residue (2parA)Q3 Warning: unaligning (T0615)E97 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2parA)E92 Warning: unaligning (T0615)K98 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (2parA)Y93 T0615 4 :YPSAKFM 2parA 4 :SHFFAHL T0615 18 :FKHRQQRRKDPQE 2parA 11 :SRLKLINRWPLMR T0615 31 :TPYVNHVINVSTILSV 2parA 28 :ENVSEHSLQVAMVAHA T0615 58 :AALLHDVVEDTDASFEDVEKLF 2parA 44 :LAAIKNRKFGGNVNAERIALLA T0615 99 :QERKRLQIENAAK 2parA 94 :KAIEKIAQQKLVD T0615 136 :PTG 2parA 110 :EEL T0615 139 :WTQERRDQYFVWAKKV 2parA 128 :EEKSLVKQADALCAYL T0615 155 :VDNLRGTNANLELK 2parA 146 :LEELAAGNNEFLLA T0615 169 :LDEIFRQ 2parA 163 :LEATLEA Number of specific fragments extracted= 9 number of extra gaps= 1 total=239 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 2parA/T0615-2parA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0615 read from 2parA/T0615-2parA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2parA read from 2parA/T0615-2parA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2parA in template set Warning: unaligning (T0615)S95 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2parA)E92 Warning: unaligning (T0615)L96 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (2parA)Y93 Warning: unaligning (T0615)Q132 because of BadResidue code BAD_PEPTIDE in next template residue (2parA)E122 Warning: unaligning (T0615)V133 because of BadResidue code BAD_PEPTIDE at template residue (2parA)E122 Warning: unaligning (T0615)N134 because of BadResidue code BAD_PEPTIDE at template residue (2parA)H123 T0615 21 :RQQRRK 2parA 20 :PLMRNV T0615 29 :QETPYVNHVINVSTILS 2parA 26 :RTENVSEHSLQVAMVAH T0615 57 :MAALLHDVVEDTDASFEDVEKL 2parA 43 :ALAAIKNRKFGGNVNAERIALL T0615 97 :EKQERKRLQIENAAKSS 2parA 94 :KAIEKIAQQKLVDMVPE T0615 124 :KLDNLRDL 2parA 113 :RDIFAPLI T0615 135 :TPTGWTQERRDQYFVWAKKVVD 2parA 124 :AYSDEEKSLVKQADALCAYLKC T0615 157 :NLRGTNAN 2parA 150 :AAGNNEFL Number of specific fragments extracted= 7 number of extra gaps= 1 total=246 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 3ccgA/T0615-3ccgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3ccgA expands to /projects/compbio/data/pdb/3ccg.pdb.gz 3ccgA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 34, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 36, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 38, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 40, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 42, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 44, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 46, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 48, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 50, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 52, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 54, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 56, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 90, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 92, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 94, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 96, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 98, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 100, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 102, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 104, because occupancy 0.500 <= existing 0.500 in 3ccgA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 126, because occupancy 0.300 <= existing 0.700 in 3ccgA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 128, because occupancy 0.300 <= existing 0.700 in 3ccgA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 130, because occupancy 0.300 <= existing 0.700 in 3ccgA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 132, because occupancy 0.300 <= existing 0.700 in 3ccgA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 134, because occupancy 0.300 <= existing 0.700 in 3ccgA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 136, because occupancy 0.300 <= existing 0.700 in 3ccgA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 138, because occupancy 0.250 <= existing 0.500 in 3ccgA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 140, because occupancy 0.300 <= existing 0.700 in 3ccgA Skipped atom 142, because occupancy 0.300 <= existing 0.700 in 3ccgA Skipped atom 144, because occupancy 0.300 <= existing 0.700 in 3ccgA Skipped atom 146, because occupancy 0.300 <= existing 0.700 in 3ccgA Skipped atom 148, because occupancy 0.300 <= existing 0.700 in 3ccgA Skipped atom 150, because occupancy 0.300 <= existing 0.700 in 3ccgA Skipped atom 152, because occupancy 0.300 <= existing 0.700 in 3ccgA Skipped atom 154, because occupancy 0.300 <= existing 0.700 in 3ccgA Skipped atom 156, because occupancy 0.300 <= existing 0.700 in 3ccgA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 337, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 339, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 341, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 343, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 345, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 347, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 349, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 351, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 400, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 402, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 404, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 406, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 408, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 410, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 412, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 414, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 416, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 418, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 420, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 554, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 556, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 558, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 560, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 562, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 564, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 566, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 568, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 570, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 673, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 675, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 677, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 679, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 681, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 683, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 685, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 687, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 689, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 691, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 693, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 706, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 708, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 710, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 712, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 714, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 716, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 718, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 720, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 722, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 724, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 726, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 728, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 869, because occupancy 0.300 <= existing 0.700 in 3ccgA Skipped atom 871, because occupancy 0.300 <= existing 0.700 in 3ccgA Skipped atom 873, because occupancy 0.300 <= existing 0.700 in 3ccgA Skipped atom 875, because occupancy 0.300 <= existing 0.700 in 3ccgA Skipped atom 877, because occupancy 0.300 <= existing 0.700 in 3ccgA Skipped atom 879, because occupancy 0.300 <= existing 0.700 in 3ccgA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1289, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 1291, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 1293, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 1295, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 1297, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 1299, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 1301, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 1303, because occupancy 0.500 <= existing 0.500 in 3ccgA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1313, because occupancy 0.500 <= existing 0.500 in 3ccgA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1315, because occupancy 0.500 <= existing 0.500 in 3ccgA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1317, because occupancy 0.500 <= existing 0.500 in 3ccgA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1319, because occupancy 0.500 <= existing 0.500 in 3ccgA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1321, because occupancy 0.500 <= existing 0.500 in 3ccgA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1323, because occupancy 0.500 <= existing 0.500 in 3ccgA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1325, because occupancy 0.370 <= existing 0.380 in 3ccgA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1327, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 1354, because occupancy 0.300 <= existing 0.700 in 3ccgA Skipped atom 1356, because occupancy 0.300 <= existing 0.700 in 3ccgA Skipped atom 1358, because occupancy 0.300 <= existing 0.700 in 3ccgA Skipped atom 1360, because occupancy 0.300 <= existing 0.700 in 3ccgA Skipped atom 1362, because occupancy 0.300 <= existing 0.700 in 3ccgA Skipped atom 1364, because occupancy 0.300 <= existing 0.700 in 3ccgA Skipped atom 1366, because occupancy 0.300 <= existing 0.700 in 3ccgA Skipped atom 1368, because occupancy 0.300 <= existing 0.700 in 3ccgA Skipped atom 1420, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 1422, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 1424, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 1426, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 1428, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 1430, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 1432, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 1434, because occupancy 0.500 <= existing 0.500 in 3ccgA # T0615 read from 3ccgA/T0615-3ccgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ccgA read from 3ccgA/T0615-3ccgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3ccgA to template set # found chain 3ccgA in template set T0615 5 :PSA 3ccgA 3 :SYD T0615 11 :ECLQYAAFKHRQQR 3ccgA 6 :KITDYLMNNLGEKR T0615 34 :VNHVINVSTI 3ccgA 20 :YKHSLGVMDT T0615 44 :LSVEAC 3ccgA 33 :LAGIYN T0615 51 :TDEGVL 3ccgA 39 :EDTEKA T0615 57 :MAALLHDVVE 3ccgA 46 :IAGLVHDCAK T0615 69 :DASFEDVEKLFGP 3ccgA 56 :KLPGEKIIEICTN T0615 82 :D 3ccgA 76 :E T0615 83 :VCGLVREVTDDKSLEKQE 3ccgA 86 :GLAGRILAKKVIGIDDED T0615 105 :QIENAAKS 3ccgA 104 :VLNAIEFH T0615 113 :SCR 3ccgA 117 :NMS T0615 116 :AKLIKLADKL 3ccgA 122 :EKIIYIADYI T0615 131 :LQVNTPTGWT 3ccgA 132 :EPGREFKGVD T0615 141 :QERR 3ccgA 144 :RKAA T0615 145 :DQYFVWAKKVVD 3ccgA 153 :KALLMSFDNTIK T0615 175 :QRGL 3ccgA 168 :DKGG Number of specific fragments extracted= 16 number of extra gaps= 0 total=262 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 3ccgA/T0615-3ccgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0615 read from 3ccgA/T0615-3ccgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ccgA read from 3ccgA/T0615-3ccgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3ccgA in template set T0615 4 :YPSA 3ccgA 2 :WSYD T0615 11 :ECLQYAAFKHRQQRR 3ccgA 6 :KITDYLMNNLGEKRY T0615 32 :PYVNHVINVSTILSVEACI 3ccgA 21 :KHSLGVMDTAVRLAGIYNE T0615 52 :DEG 3ccgA 40 :DTE T0615 55 :VLMAALLHDVVED 3ccgA 44 :ARIAGLVHDCAKK T0615 70 :ASFEDVEKL 3ccgA 57 :LPGEKIIEI T0615 90 :VTDDK 3ccgA 66 :CTNEG T0615 95 :SLEKQ 3ccgA 72 :ELGDE T0615 100 :ERKRLQIENAAK 3ccgA 102 :EDVLNAIEFHTT T0615 112 :SSCR 3ccgA 116 :PNMS T0615 120 :KLADKLDNLRDL 3ccgA 120 :LLEKIIYIADYI T0615 132 :QVNTPTG 3ccgA 133 :PGREFKG T0615 139 :WTQERRD 3ccgA 142 :ELRKAAD T0615 146 :QYFVWAKKVVDNLRGTNANLELKLDEIFRQ 3ccgA 154 :ALLMSFDNTIKFVIDKGGFLHHNTIEARNY Number of specific fragments extracted= 14 number of extra gaps= 0 total=276 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 3ccgA/T0615-3ccgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0615 read from 3ccgA/T0615-3ccgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ccgA read from 3ccgA/T0615-3ccgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3ccgA in template set Warning: unaligning (T0615)A2 because first residue in template chain is (3ccgA)G0 T0615 3 :TYPSAKFME 3ccgA 1 :MWSYDKITD T0615 15 :YAAFKHRQQRRK 3ccgA 10 :YLMNNLGEKRYK T0615 36 :HVINVSTILSVEAC 3ccgA 22 :HSLGVMDTAVRLAG T0615 50 :ITDEGVLMAALLHDVVE 3ccgA 39 :EDTEKARIAGLVHDCAK T0615 69 :DASFEDVEKL 3ccgA 56 :KLPGEKIIEI T0615 79 :FG 3ccgA 97 :IG T0615 81 :PDVCGLVREVT 3ccgA 102 :EDVLNAIEFHT T0615 93 :DKSLEKQE 3ccgA 115 :RPNMSLLE T0615 117 :KLIKLADKLDN 3ccgA 123 :KIIYIADYIEP T0615 133 :VNTPT 3ccgA 134 :GREFK T0615 138 :GWTQERRDQ 3ccgA 141 :DELRKAADE T0615 147 :YFVWAKK 3ccgA 158 :SFDNTIK Number of specific fragments extracted= 12 number of extra gaps= 0 total=288 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 1vqrA/T0615-1vqrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vqrA expands to /projects/compbio/data/pdb/1vqr.pdb.gz 1vqrA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1584, because occupancy 0.350 <= existing 0.650 in 1vqrA Skipped atom 1586, because occupancy 0.350 <= existing 0.650 in 1vqrA Skipped atom 1588, because occupancy 0.350 <= existing 0.650 in 1vqrA Skipped atom 1590, because occupancy 0.350 <= existing 0.650 in 1vqrA # T0615 read from 1vqrA/T0615-1vqrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vqrA read from 1vqrA/T0615-1vqrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vqrA to template set # found chain 1vqrA in template set T0615 5 :PSAKFMECL 1vqrA 82 :GVGNIINIV T0615 24 :RRKDPQETPYV 1vqrA 91 :MADSIRDNFKI T0615 35 :NHVINVSTILSVEACITDEG 1vqrA 115 :KTCNEEATFIANWLNDEDKK T0615 55 :VLMAALLHDV 1vqrA 139 :LVPCAMLLRL T0615 65 :VEDTD 1vqrA 157 :LIQNH T0615 75 :VEKL 1vqrA 195 :LLHR T0615 79 :FGPDVCGLVREVTDDKSLE 1vqrA 201 :FDDVLIESICFVRTPHAAR T0615 105 :QIEN 1vqrA 224 :KSAY T0615 118 :LIKLADKLDNLRDLQ 1vqrA 228 :ALAITDHLFAPHDGS T0615 140 :TQERRDQYFVWAKKVVD 1vqrA 243 :SPFNAKAAVALLKEAKT T0615 157 :NLRGTNANLELKL 1vqrA 261 :GINFDLNNLLSKL T0615 170 :DEIFRQRGL 1vqrA 275 :NKAKENLNK Number of specific fragments extracted= 12 number of extra gaps= 0 total=300 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 1vqrA/T0615-1vqrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0615 read from 1vqrA/T0615-1vqrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vqrA read from 1vqrA/T0615-1vqrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vqrA in template set T0615 5 :PSAKF 1vqrA 82 :GVGNI T0615 17 :AFKHR 1vqrA 87 :INIVM T0615 24 :RRKDPQET 1vqrA 92 :ADSIRDNF T0615 32 :P 1vqrA 104 :S T0615 33 :YVNHVINVSTILSVEACITDEG 1vqrA 113 :FLKTCNEEATFIANWLNDEDKK T0615 55 :VLMAALLHDV 1vqrA 139 :LVPCAMLLRL T0615 65 :VEDTDA 1vqrA 157 :LIQNHK T0615 85 :GLVREVTDDKSLEKQ 1vqrA 165 :DFLAFLNKNENLALA T0615 100 :ERKRLQIENAAKSSCR 1vqrA 187 :DHISFLGFLLHRWNFD T0615 120 :KLADKLDNLRDLQVNTPTG 1vqrA 204 :VLIESICFVRTPHAAREKV T0615 142 :ERRDQYFVWAKKV 1vqrA 223 :KKSAYALAITDHL T0615 155 :VDNL 1vqrA 238 :PHDG T0615 159 :RGTNANLELKLDEIFRQ 1vqrA 244 :PFNAKAAVALLKEAKTQ Number of specific fragments extracted= 13 number of extra gaps= 0 total=313 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 1vqrA/T0615-1vqrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0615 read from 1vqrA/T0615-1vqrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vqrA read from 1vqrA/T0615-1vqrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vqrA in template set T0615 4 :YPSAKFME 1vqrA 108 :LNTQNFLK T0615 36 :HVINVSTILSVEACITDEG 1vqrA 116 :TCNEEATFIANWLNDEDKK T0615 55 :VLMAALLHDVVE 1vqrA 139 :LVPCAMLLRLGI T0615 79 :FGPDVCGLVREVTDDKSL 1vqrA 159 :QNHKDKDFLAFLNKNENL T0615 99 :QERKRLQIENAAKSSC 1vqrA 188 :HISFLGFLLHRWNFDD T0615 120 :KLADKLDNLRDLQVNTPTGW 1vqrA 204 :VLIESICFVRTPHAAREKVK T0615 143 :RRDQYFVWAKKVVDNLRGTNANLELKLDEIF 1vqrA 224 :KSAYALAITDHLFAPHDGSSPFNAKAAVALL Number of specific fragments extracted= 7 number of extra gaps= 0 total=320 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 1xx7A/T0615-1xx7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xx7A expands to /projects/compbio/data/pdb/1xx7.pdb.gz 1xx7A:# T0615 read from 1xx7A/T0615-1xx7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xx7A read from 1xx7A/T0615-1xx7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xx7A to template set # found chain 1xx7A in template set Warning: unaligning (T0615)L61 because of BadResidue code BAD_PEPTIDE in next template residue (1xx7A)H67 Warning: unaligning (T0615)H62 because of BadResidue code BAD_PEPTIDE at template residue (1xx7A)H67 T0615 9 :FMECLQYAAFK 1xx7A 30 :VADHSYRVAFI T0615 37 :VINVSTILSVEACITDEG 1xx7A 41 :TLLLAEELKKKGVEIDVE T0615 55 :VLMAAL 1xx7A 60 :ALKIAI T0615 63 :DVVE 1xx7A 68 :DLGE T0615 67 :D 1xx7A 76 :D T0615 70 :ASFED 1xx7A 77 :LPLSA T0615 79 :FGPDVCGLVREVTD 1xx7A 87 :KEEAEAKALKDVLP T0615 97 :EKQE 1xx7A 101 :EYTE T0615 105 :QIENAAKS 1xx7A 105 :LFEEYSKA T0615 113 :SCRAKLIKLADKLD 1xx7A 114 :TLEGQLVKIADKLD T0615 140 :TQERRDQYF 1xx7A 128 :MIIQAYEYE T0615 149 :VWAKKVVD 1xx7A 148 :NALEDLEK T0615 157 :NLRGTNANLELKLDE 1xx7A 157 :EISRYLREIIEEVRR Number of specific fragments extracted= 13 number of extra gaps= 1 total=333 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 1xx7A/T0615-1xx7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0615 read from 1xx7A/T0615-1xx7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xx7A read from 1xx7A/T0615-1xx7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xx7A in template set Warning: unaligning (T0615)L61 because of BadResidue code BAD_PEPTIDE in next template residue (1xx7A)H67 Warning: unaligning (T0615)H62 because of BadResidue code BAD_PEPTIDE at template residue (1xx7A)H67 T0615 16 :AAFKHRQQRR 1xx7A 7 :LAGKLKRIPR T0615 26 :KDPQETPYVNHVINVSTILSV 1xx7A 23 :GVPNPESVADHSYRVAFITLL T0615 47 :EACI 1xx7A 50 :KKGV T0615 52 :D 1xx7A 54 :E T0615 53 :EGVLMAAL 1xx7A 58 :EKALKIAI T0615 63 :DVVED 1xx7A 68 :DLGEA T0615 70 :ASF 1xx7A 77 :LPL T0615 91 :TDDKSLEKQERKRLQIENAAK 1xx7A 80 :SAQKYLNKEEAEAKALKDVLP T0615 112 :SSCRAKLIKLADKLDNLRDL 1xx7A 113 :LTLEGQLVKIADKLDMIIQA T0615 132 :QVNTPTGWTQERRDQ 1xx7A 139 :GAKNLSEFWNALEDL T0615 160 :GTNANLELKLDEIFR 1xx7A 157 :EISRYLREIIEEVRR Number of specific fragments extracted= 11 number of extra gaps= 1 total=344 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 1xx7A/T0615-1xx7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0615 read from 1xx7A/T0615-1xx7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xx7A read from 1xx7A/T0615-1xx7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xx7A in template set Warning: unaligning (T0615)L61 because of BadResidue code BAD_PEPTIDE in next template residue (1xx7A)H67 Warning: unaligning (T0615)H62 because of BadResidue code BAD_PEPTIDE at template residue (1xx7A)H67 T0615 6 :SAKFMECLQYAAF 1xx7A 31 :ADHSYRVAFITLL T0615 40 :VSTILSVEACITDEG 1xx7A 44 :LAEELKKKGVEIDVE T0615 55 :VLMAAL 1xx7A 60 :ALKIAI T0615 63 :DVVE 1xx7A 68 :DLGE T0615 70 :AS 1xx7A 85 :LN T0615 72 :FEDVEKL 1xx7A 88 :EEAEAKA T0615 79 :FGPDVCGLVREVTDDKSL 1xx7A 98 :VLPEYTELFEEYSKALTL T0615 115 :RAKLIKLADKLDNL 1xx7A 116 :EGQLVKIADKLDMI T0615 150 :WAKKVVDNLRGTNANLELKLD 1xx7A 130 :IQAYEYELSGAKNLSEFWNAL Number of specific fragments extracted= 9 number of extra gaps= 1 total=353 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 3kh1A/T0615-3kh1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3kh1A expands to /projects/compbio/data/pdb/3kh1.pdb.gz 3kh1A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2, because occupancy 0.500 <= existing 0.500 in 3kh1A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 4, because occupancy 0.500 <= existing 0.500 in 3kh1A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 6, because occupancy 0.500 <= existing 0.500 in 3kh1A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 8, because occupancy 0.500 <= existing 0.500 in 3kh1A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 10, because occupancy 0.500 <= existing 0.500 in 3kh1A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 12, because occupancy 0.500 <= existing 0.500 in 3kh1A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 14, because occupancy 0.370 <= existing 0.380 in 3kh1A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 16, because occupancy 0.500 <= existing 0.500 in 3kh1A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 389, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 393, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 395, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 397, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 399, because occupancy 0.500 <= existing 0.500 in 3kh1A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 485, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 489, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 491, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 493, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 495, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 508, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 512, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 514, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 516, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 528, because occupancy 0.400 <= existing 0.600 in 3kh1A Skipped atom 532, because occupancy 0.400 <= existing 0.600 in 3kh1A Skipped atom 534, because occupancy 0.400 <= existing 0.600 in 3kh1A Skipped atom 536, because occupancy 0.400 <= existing 0.600 in 3kh1A Skipped atom 538, because occupancy 0.400 <= existing 0.600 in 3kh1A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 722, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 726, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 728, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 730, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 732, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 770, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 774, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 776, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 778, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 780, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 782, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 784, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 786, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 941, because occupancy 0.330 <= existing 0.330 in 3kh1A Skipped atom 942, because occupancy 0.330 <= existing 0.330 in 3kh1A Skipped atom 946, because occupancy 0.330 <= existing 0.330 in 3kh1A Skipped atom 947, because occupancy 0.330 <= existing 0.330 in 3kh1A Skipped atom 949, because occupancy 0.330 <= existing 0.330 in 3kh1A Skipped atom 950, because occupancy 0.330 <= existing 0.330 in 3kh1A Skipped atom 980, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 984, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 986, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 988, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 990, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 992, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 1265, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 1269, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 1271, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 1273, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 1275, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 1277, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 1315, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 1319, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 1321, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 1323, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 1325, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 1327, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 1329, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 1331, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 1442, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 1446, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 1448, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 1450, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 1452, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 1454, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 1456, because occupancy 0.500 <= existing 0.500 in 3kh1A Skipped atom 1458, because occupancy 0.500 <= existing 0.500 in 3kh1A # T0615 read from 3kh1A/T0615-3kh1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3kh1A read from 3kh1A/T0615-3kh1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3kh1A to template set # found chain 3kh1A in template set Warning: unaligning (T0615)S71 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3kh1A)D94 T0615 27 :DPQETPYVN 3kh1A 31 :LTDSSRREN T0615 36 :HVINVSTILSVEA 3kh1A 43 :HSWHIATMAFLLA T0615 49 :CITDEG 3kh1A 60 :EAVQIG T0615 55 :VLMAALLHDVVE 3kh1A 67 :VARMLLIHDIVE T0615 72 :FEDVEK 3kh1A 95 :KEERER T0615 85 :GLVREVTDDKSLEKQERKRLQIENAAKS 3kh1A 101 :KAAARLFGLLPPDQAAEYSALWQEYEAR T0615 113 :SCRAKLIKLADKLDNLRDL 3kh1A 130 :TADARFADALDRLQPLLHN T0615 132 :QVNTPTG 3kh1A 155 :TWKPHGV T0615 140 :TQERRDQYFVWAKKVVDNLRGTNANLE 3kh1A 162 :TRAKVDKLLPRIEAGSKRLGAYARALV T0615 170 :DEIFR 3kh1A 189 :DEAVR T0615 176 :R 3kh1A 194 :R Number of specific fragments extracted= 11 number of extra gaps= 0 total=364 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 3kh1A/T0615-3kh1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0615 read from 3kh1A/T0615-3kh1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3kh1A read from 3kh1A/T0615-3kh1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3kh1A in template set Warning: unaligning (T0615)S71 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3kh1A)D94 T0615 23 :QRRKDPQETPYVNHVINVSTILSV 3kh1A 30 :LLTDSSRRENDAEHSWHIATMAFL T0615 48 :A 3kh1A 54 :L T0615 49 :CITDEGVLMAALLHDVVED 3kh1A 61 :AVQIGRVARMLLIHDIVEI T0615 72 :FED 3kh1A 95 :KEE T0615 82 :DVCGLVREVTDDKSLEKQERKRLQIENAAK 3kh1A 98 :RERKAAARLFGLLPPDQAAEYSALWQEYEA T0615 112 :SSCRAKLIKLADKLDNLRDL 3kh1A 129 :ETADARFADALDRLQPLLHN T0615 132 :QVNTP 3kh1A 155 :TWKPH T0615 139 :WTQERRDQYFVWAKKVVDNLRGTNANLELK 3kh1A 165 :KVDKLLPRIEAGSKRLGAYARALVDEAVRR Number of specific fragments extracted= 8 number of extra gaps= 0 total=372 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 3kh1A/T0615-3kh1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0615 read from 3kh1A/T0615-3kh1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3kh1A read from 3kh1A/T0615-3kh1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3kh1A in template set Warning: unaligning (T0615)S71 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3kh1A)D94 T0615 26 :KDPQETPYVNHVINVSTILSVEAC 3kh1A 33 :DSSRRENDAEHSWHIATMAFLLAE T0615 50 :ITDEGVLMAALLHDVVE 3kh1A 62 :VQIGRVARMLLIHDIVE T0615 68 :T 3kh1A 89 :E T0615 72 :FEDVEK 3kh1A 95 :KEERER T0615 85 :GLVREVTDDKSLEKQERKRLQIENAAKSS 3kh1A 101 :KAAARLFGLLPPDQAAEYSALWQEYEARE T0615 114 :CRAKLIKLADKLDNLRDL 3kh1A 131 :ADARFADALDRLQPLLHN T0615 132 :QVNTPTGWTQERRDQYFVWAKKVVDNL 3kh1A 158 :PHGVTRAKVDKLLPRIEAGSKRLGAYA Number of specific fragments extracted= 7 number of extra gaps= 0 total=379 Will force an alignment to be made, even if fragment is small Number of alignments=36 # command:CPU_time= 14.014 sec, elapsed time= 19.371 sec. # command:DEBUG: alignment library has 36 conformations DEBUG: current conformations has 0 conformations # in ExtractAlignmentsContacts extracting from alignment library using radius 8.000 separation >= 9 style evalue NUMB_ALIGNS: 36 # Adding 2121 constraints to all_contacts Done adding distance constraints # command:CPU_time= 14.056 sec, elapsed time= 19.414 sec. # command:Reading probabilities from T0615.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 19.662 Optimizing... Probability sum: -314.456, CN propb: -314.456 weights: 0.215 constraints: 397 # command:CPU_time= 36.442 sec, elapsed time= 41.884 sec. # command:Found ConstraintSet # PrintContacts align.constraints Number of constraints in align 397 # command:Found ConstraintSet # PrintContacts align_bonus.constraints Number of constraints in align.bonus 397 # command:Found ConstraintSet # PrintContacts rejected.constraints Number of constraints in rejected 1724 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints Number of constraints in rejected.bonus 1724 # command:Found ConstraintSet # PrintContacts noncontact.constraints Number of constraints in noncontact 0 # command:Found ConstraintSet # PrintContacts noncontact_bonus.constraints Number of constraints in noncontact.bonus 0 # command:CPU_time= 36.474 sec, elapsed time= 42.950 sec. # command: