# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 1600 examples # computed average trans backbone unit before proline from 52 examples # trans (non-proline) backbone unit: # CA= -2.2097 1.0151 -0.0046 # O= -0.1488 2.2425 0.0020 # C= -0.6903 1.1357 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4580 -0.0000 -0.0000 # cis backbone unit: # CA= -0.1462 2.4515 0.0018 # O= -2.0272 0.9713 0.0022 # C= -0.8006 1.0755 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4659 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2063 1.0654 0.0002 # O= -0.1193 2.2442 0.0054 # C= -0.6842 1.1479 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4661 -0.0000 0.0000 # After reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz have 408 chains in training database # Count of chains,residues,atoms: 408,82795,639989 # 81291 residues have no bad marker # 565 residues lack atoms needed to compute omega # 313 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 1 # HAS_OXT 265 # TOO_MANY_ATOMS 0 # TOO_FEW_ATOMS 378 # HAS_UNKNOWN_ATOMS 0 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 139 # NON_PLANAR_PEPTIDE 424 # BAD_PEPTIDE 803 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-40pc-3157.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to # command:# Making conformation for sequence T0514 numbered 1 through 145 Created new target T0514 from T0514.a2m # command:CPU_time= 6.586 sec, elapsed time= 6.755 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 3cbnA/T0514-3cbnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3cbnA expands to /projects/compbio/data/pdb/3cbn.pdb.gz 3cbnA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0514 read from 3cbnA/T0514-3cbnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cbnA read from 3cbnA/T0514-3cbnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3cbnA to template set # found chain 3cbnA in template set Warning: unaligning (T0514)E120 because last residue in template chain is (3cbnA)H165 T0514 12 :INCGIQEG 3cbnA 28 :LRARGHPN # choosing archetypes in rotamer library T0514 20 :KKVCFMHRQE 3cbnA 41 :RTTFEVTVDP T0514 30 :VNDQNR 3cbnA 52 :IGETAD T0514 36 :VV 3cbnA 59 :II T0514 39 :AMSVVLNADGV 3cbnA 85 :LVRVILRTENG T0514 50 :VSGNLTVPFGILVSKPVRLQVDEGKAV 3cbnA 97 :DEIRGYGHPELTLDHPTDIVCRKSDYI T0514 85 :VPAGCIVPI 3cbnA 124 :CSRTLMIRA T0514 94 :VFDKNYVAALRAGKHLKLAMT 3cbnA 138 :DLDENLVRDLRKGRELKVEII T0514 115 :IAAPG 3cbnA 160 :EYEGH Number of specific fragments extracted= 9 number of extra gaps= 0 total=9 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 3cbnA/T0514-3cbnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0514 read from 3cbnA/T0514-3cbnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cbnA read from 3cbnA/T0514-3cbnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3cbnA in template set Warning: unaligning (T0514)P121 because last residue in template chain is (3cbnA)H165 T0514 20 :KKVCFMH 3cbnA 41 :RTTFEVT T0514 27 :RQEVNDQNRVV 3cbnA 49 :DPEIGETADCI T0514 38 :VAMSVV 3cbnA 86 :VRVILR T0514 48 :GVVSGNLTVPFG 3cbnA 93 :ENGYDEIRGYGH T0514 60 :ILVSKPVRLQVDEGKAVIETGIRT 3cbnA 107 :LTLDHPTDIVCRKSDYICSRTLMI T0514 93 :IVFDKNYVAALRAGKHLKLAMTIAAPGE 3cbnA 137 :FDLDENLVRDLRKGRELKVEIIVEYEGH Number of specific fragments extracted= 6 number of extra gaps= 0 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 3cbnA/T0514-3cbnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0514 read from 3cbnA/T0514-3cbnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cbnA read from 3cbnA/T0514-3cbnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3cbnA in template set Warning: unaligning (T0514)P121 because last residue in template chain is (3cbnA)H165 T0514 37 :VVAMSV 3cbnA 85 :LVRVIL T0514 45 :NADG 3cbnA 91 :RTEN T0514 49 :VVSGNLTVPFGILVSKPVRLQVDEGKAV 3cbnA 96 :YDEIRGYGHPELTLDHPTDIVCRKSDYI T0514 78 :ETGIRTCVPAG 3cbnA 124 :CSRTLMIRADK T0514 95 :FDKNYVAALRAGKHLKLAMTIAAPGE 3cbnA 139 :LDENLVRDLRKGRELKVEIIVEYEGH Number of specific fragments extracted= 5 number of extra gaps= 0 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 1x3cA/T0514-1x3cA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1x3cA expands to /projects/compbio/data/pdb/1x3c.pdb.gz 1x3cA:# T0514 read from 1x3cA/T0514-1x3cA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1x3cA read from 1x3cA/T0514-1x3cA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1x3cA to template set # found chain 1x3cA in template set T0514 82 :RTCVPAGCIVPIVFDKNYVAALR 1x3cA 28 :YRCVHQGCFAAFTIQQNLILHYQ Number of specific fragments extracted= 1 number of extra gaps= 0 total=21 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 1x3cA/T0514-1x3cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0514 read from 1x3cA/T0514-1x3cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1x3cA read from 1x3cA/T0514-1x3cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1x3cA in template set T0514 73 :GKAV 1x3cA 20 :TRYS T0514 78 :ETGIRTCVPAGCIVPIVFDKNYVAALRA 1x3cA 24 :PYRPYRCVHQGCFAAFTIQQNLILHYQA Number of specific fragments extracted= 2 number of extra gaps= 0 total=23 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 1x3cA/T0514-1x3cA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0514 read from 1x3cA/T0514-1x3cA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1x3cA read from 1x3cA/T0514-1x3cA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1x3cA in template set T0514 72 :EGKAV 1x3cA 19 :PTRYS T0514 78 :ETGIRTCVPAGCIVPIVFDKNYVAALRA 1x3cA 24 :PYRPYRCVHQGCFAAFTIQQNLILHYQA Number of specific fragments extracted= 2 number of extra gaps= 0 total=25 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 1x6oA/T0514-1x6oA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1x6oA expands to /projects/compbio/data/pdb/1x6o.pdb.gz 1x6oA:# T0514 read from 1x6oA/T0514-1x6oA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1x6oA read from 1x6oA/T0514-1x6oA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1x6oA to template set # found chain 1x6oA in template set Warning: unaligning (T0514)Q33 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1x6oA)H56 T0514 8 :GLWSIN 1x6oA 31 :GGYVCI T0514 19 :GKKVCFMHRQEVND 1x6oA 37 :NGRPCKVIDLSVSK T0514 38 :VAMSVVLNADGV 1x6oA 59 :VSIVATDIFTGN T0514 51 :SGNLTVPFGILV 1x6oA 71 :RLEDQAPSTHNV T0514 63 :SKPVRLQV 1x6oA 87 :VKTYTYSV T0514 71 :DEGKAV 1x6oA 102 :DPSLPA T0514 78 :ETGIR 1x6oA 108 :HLSLM T0514 85 :VPAGCI 1x6oA 113 :DDEGES T0514 91 :VPIVFDKNYVA 1x6oA 122 :LDMPPDPALAT T0514 102 :ALRAGKHLKLAMTI 1x6oA 137 :QFDSGKDVLVVVVS T0514 117 :APGEPPLNDLF 1x6oA 151 :AMGTEQVLQTK Number of specific fragments extracted= 11 number of extra gaps= 0 total=36 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 1x6oA/T0514-1x6oA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0514 read from 1x6oA/T0514-1x6oA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1x6oA read from 1x6oA/T0514-1x6oA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1x6oA in template set Warning: unaligning (T0514)Q33 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1x6oA)H56 T0514 6 :TYGLWSIN 1x6oA 29 :KKGGYVCI T0514 19 :GKKVCFMHRQEVND 1x6oA 37 :NGRPCKVIDLSVSK T0514 38 :VAMSVVLNADGVVS 1x6oA 59 :VSIVATDIFTGNRL T0514 52 :GNLTVP 1x6oA 80 :HNVEVP T0514 59 :GILV 1x6oA 91 :TYSV T0514 66 :VRLQVDEGKAVIE 1x6oA 109 :LSLMDDEGESRED T0514 91 :VPIVFDKNYVA 1x6oA 122 :LDMPPDPALAT T0514 102 :ALRAGKHLKLAMTI 1x6oA 137 :QFDSGKDVLVVVVS T0514 117 :APGEPPL 1x6oA 151 :AMGTEQV T0514 126 :LFV 1x6oA 158 :LQT Number of specific fragments extracted= 10 number of extra gaps= 0 total=46 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 1x6oA/T0514-1x6oA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0514 read from 1x6oA/T0514-1x6oA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1x6oA read from 1x6oA/T0514-1x6oA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1x6oA in template set Warning: unaligning (T0514)R35 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1x6oA)H56 T0514 17 :QEG 1x6oA 29 :KKG T0514 20 :KKVCFMHRQEVN 1x6oA 38 :GRPCKVIDLSVS T0514 36 :VVVAMSVVLNADG 1x6oA 57 :AKVSIVATDIFTG T0514 49 :VVS 1x6oA 71 :RLE T0514 60 :ILVSKPVRLQVDEGKAV 1x6oA 74 :DQAPSTHNVEVPFVKTY T0514 78 :ETGIRTCV 1x6oA 91 :TYSVLDIQ T0514 86 :PAGCIVPIV 1x6oA 104 :SLPAHLSLM T0514 95 :FD 1x6oA 126 :PD T0514 97 :KNYVAALRAGKHLKLAMT 1x6oA 132 :TQIKEQFDSGKDVLVVVV T0514 116 :AAP 1x6oA 150 :SAM T0514 121 :PPLNDLFV 1x6oA 153 :GTEQVLQT Number of specific fragments extracted= 11 number of extra gaps= 0 total=57 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 2pz4A/T0514-2pz4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2pz4A expands to /projects/compbio/data/pdb/2pz4.pdb.gz 2pz4A:Skipped atom 1366, because occupancy 0.5 <= existing 0.500 in 2pz4A Skipped atom 1370, because occupancy 0.500 <= existing 0.500 in 2pz4A Skipped atom 1372, because occupancy 0.500 <= existing 0.500 in 2pz4A Skipped atom 1374, because occupancy 0.500 <= existing 0.500 in 2pz4A Skipped atom 1376, because occupancy 0.500 <= existing 0.500 in 2pz4A Skipped atom 1378, because occupancy 0.500 <= existing 0.500 in 2pz4A Skipped atom 1380, because occupancy 0.500 <= existing 0.500 in 2pz4A # T0514 read from 2pz4A/T0514-2pz4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2pz4A read from 2pz4A/T0514-2pz4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2pz4A to template set # found chain 2pz4A in template set T0514 6 :TYGLWSINCGI 2pz4A 29 :PIEGVLYQLYQ T0514 17 :QEG 2pz4A 45 :DGD T0514 24 :FMHRQEVNDQNRVV 2pz4A 66 :QVFEATTNQQGKAT T0514 39 :AMSVVLNADGV 2pz4A 87 :IYYGLAVKAGE T0514 50 :VSGNL 2pz4A 105 :FLVDL T0514 55 :TVPFGILVSKP 2pz4A 114 :VIYPKIIWSTG T0514 66 :VRLQV 2pz4A 126 :LDLLK T0514 72 :EGKAV 2pz4A 134 :DGDTK T0514 78 :ETGIR 2pz4A 145 :VFELY T0514 85 :VPAG 2pz4A 150 :EKNG T0514 89 :CIVPIVFDK 2pz4A 170 :AAKHLETDS T0514 108 :HLKLAMTIAAPG 2pz4A 191 :DYVLKEIETQSG T0514 120 :E 2pz4A 208 :A T0514 123 :LNDLFVQLNG 2pz4A 209 :ETAVTIEKSK Number of specific fragments extracted= 14 number of extra gaps= 0 total=71 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 2pz4A/T0514-2pz4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0514 read from 2pz4A/T0514-2pz4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2pz4A read from 2pz4A/T0514-2pz4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2pz4A in template set Warning: unaligning (T0514)V49 because of BadResidue code BAD_PEPTIDE in next template residue (2pz4A)I182 Warning: unaligning (T0514)V50 because of BadResidue code BAD_PEPTIDE at template residue (2pz4A)I182 T0514 2 :SLTETYGLWSINCGIQEGKKVCFMH 2pz4A 136 :DTKKPLAGVVFELYEKNGRTPIRVK T0514 27 :RQEVNDQNR 2pz4A 162 :GVHSQDIDA T0514 42 :VVLNADG 2pz4A 174 :LETDSSG T0514 51 :SGN 2pz4A 183 :RIS T0514 61 :LVSKP 2pz4A 186 :GLIHG T0514 66 :VRLQVDEGK 2pz4A 192 :YVLKEIETQ T0514 79 :TGIRT 2pz4A 201 :SGYQI T0514 85 :VPAGCIVPIV 2pz4A 206 :GQAETAVTIE T0514 105 :AGKHLKLAMTIA 2pz4A 216 :KSKTVTVTIENK Number of specific fragments extracted= 9 number of extra gaps= 1 total=80 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 2pz4A/T0514-2pz4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0514 read from 2pz4A/T0514-2pz4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2pz4A read from 2pz4A/T0514-2pz4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2pz4A in template set Warning: unaligning (T0514)V49 because of BadResidue code BAD_PEPTIDE in next template residue (2pz4A)I182 Warning: unaligning (T0514)V50 because of BadResidue code BAD_PEPTIDE at template residue (2pz4A)I182 T0514 1 :SSLTETYGLWSINCGIQEGKKVCFMHRQEVN 2pz4A 135 :GDTKKPLAGVVFELYEKNGRTPIRVKNGVHS T0514 32 :DQNRV 2pz4A 167 :DIDAA T0514 42 :VVLNADG 2pz4A 174 :LETDSSG T0514 51 :SGN 2pz4A 183 :RIS T0514 55 :TVPFG 2pz4A 186 :GLIHG T0514 65 :PVRLQVDE 2pz4A 191 :DYVLKEIE T0514 73 :GKAVIETG 2pz4A 201 :SGYQIGQA T0514 90 :IVPIVFD 2pz4A 209 :ETAVTIE T0514 105 :AGKHLKLAMTIAAPGEPPLN 2pz4A 216 :KSKTVTVTIENKKVPTPKVP Number of specific fragments extracted= 9 number of extra gaps= 1 total=89 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 2awfA/T0514-2awfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2awfA expands to /projects/compbio/data/pdb/2awf.pdb.gz 2awfA:# T0514 read from 2awfA/T0514-2awfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2awfA read from 2awfA/T0514-2awfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2awfA to template set # found chain 2awfA in template set T0514 25 :MHRQEVNDQNRVVVAMSVVLNAD 2awfA 25 :FSAGLIDDNDLYRWEVLIIGPPD T0514 48 :GV 2awfA 52 :GG T0514 50 :VSGNLTVPFGILVSKP 2awfA 55 :FKAHLTFPKDYPLRPP T0514 66 :VRL 2awfA 72 :MKF T0514 70 :VDEGKA 2awfA 83 :VDKNGD Number of specific fragments extracted= 5 number of extra gaps= 0 total=94 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 2awfA/T0514-2awfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0514 read from 2awfA/T0514-2awfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2awfA read from 2awfA/T0514-2awfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2awfA in template set T0514 25 :MHRQEVNDQNRVVVAMSVVLNAD 2awfA 25 :FSAGLIDDNDLYRWEVLIIGPPD T0514 48 :GV 2awfA 52 :GG T0514 50 :VSGNLTVPFGILVSKP 2awfA 55 :FKAHLTFPKDYPLRPP T0514 66 :VRLQ 2awfA 72 :MKFI T0514 70 :VDEGKAV 2awfA 83 :VDKNGDV T0514 78 :ETGIRT 2awfA 90 :CISILH Number of specific fragments extracted= 6 number of extra gaps= 0 total=100 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 2awfA/T0514-2awfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0514 read from 2awfA/T0514-2awfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2awfA read from 2awfA/T0514-2awfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2awfA in template set T0514 27 :RQEVN 2awfA 26 :SAGLI T0514 32 :DQNRVVVAMSVVLNADG 2awfA 32 :DNDLYRWEVLIIGPPDT T0514 49 :VVSGNLTVPFGIL 2awfA 54 :VFKAHLTFPKDYP T0514 63 :SKPVRLQ 2awfA 67 :LRPPKMK T0514 70 :VDEGKAV 2awfA 83 :VDKNGDV Number of specific fragments extracted= 5 number of extra gaps= 0 total=105 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 2hqhE/T0514-2hqhE-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2hqhE expands to /projects/compbio/data/pdb/2hqh.pdb.gz 2hqhE:# T0514 read from 2hqhE/T0514-2hqhE-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2hqhE read from 2hqhE/T0514-2hqhE-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2hqhE to template set # found chain 2hqhE in template set T0514 116 :AAPGE 2hqhE 1421 :CNDDE Number of specific fragments extracted= 1 number of extra gaps= 0 total=106 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 2hqhE/T0514-2hqhE-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0514 read from 2hqhE/T0514-2hqhE-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2hqhE read from 2hqhE/T0514-2hqhE-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2hqhE in template set T0514 116 :AAPGEP 2hqhE 1421 :CNDDET Number of specific fragments extracted= 1 number of extra gaps= 0 total=107 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 2hqhE/T0514-2hqhE-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0514 read from 2hqhE/T0514-2hqhE-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2hqhE read from 2hqhE/T0514-2hqhE-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2hqhE in template set T0514 5 :ETYGLWSINCGIQE 2hqhE 1412 :EMFGHWATNCNDDE Number of specific fragments extracted= 1 number of extra gaps= 0 total=108 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 2vqeI/T0514-2vqeI-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2vqeI expands to /projects/compbio/data/pdb/2vqe.pdb.gz 2vqeI:# T0514 read from 2vqeI/T0514-2vqeI-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2vqeI read from 2vqeI/T0514-2vqeI-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2vqeI to template set # found chain 2vqeI in template set T0514 38 :VAMSVVLNADGV 2vqeI 13 :AVARVFLRPGNG T0514 50 :VS 2vqeI 26 :VT T0514 62 :VSKPVRLQVD 2vqeI 55 :ALGRFDAYIT Number of specific fragments extracted= 3 number of extra gaps= 0 total=111 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 2vqeI/T0514-2vqeI-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0514 read from 2vqeI/T0514-2vqeI-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2vqeI read from 2vqeI/T0514-2vqeI-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2vqeI in template set T0514 36 :VVVAMSVVLN 2vqeI 13 :AVARVFLRPG T0514 48 :GV 2vqeI 23 :NG T0514 67 :RLQVDEGKA 2vqeI 25 :KVTVNGQDF Number of specific fragments extracted= 3 number of extra gaps= 0 total=114 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 2vqeI/T0514-2vqeI-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0514 read from 2vqeI/T0514-2vqeI-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2vqeI read from 2vqeI/T0514-2vqeI-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2vqeI in template set Number of specific fragments extracted= 0 number of extra gaps= 0 total=114 Will force an alignment to be made, even if fragment is small # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fzyA/T0514-1fzyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1fzyA expands to /projects/compbio/data/pdb/1fzy.pdb.gz 1fzyA:# T0514 read from 1fzyA/T0514-1fzyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fzyA read from 1fzyA/T0514-1fzyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1fzyA to template set # found chain 1fzyA in template set T0514 25 :MHRQEVNDQNRVVVAMSVVLNAD 1fzyA 22 :ITLEFVSESDIHHLKGTFLGPPG T0514 48 :GV 1fzyA 49 :GG T0514 50 :VSGNLTVPFGIL 1fzyA 52 :FVVDIEVPMEYP T0514 63 :SKPVRLQVD 1fzyA 64 :FKPPKMQFD Number of specific fragments extracted= 4 number of extra gaps= 0 total=118 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 1fzyA/T0514-1fzyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0514 read from 1fzyA/T0514-1fzyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fzyA read from 1fzyA/T0514-1fzyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fzyA in template set T0514 26 :HRQEVNDQNRVVVAMSVVLNAD 1fzyA 23 :TLEFVSESDIHHLKGTFLGPPG T0514 48 :GV 1fzyA 49 :GG T0514 50 :VSGNLTVPFGILV 1fzyA 52 :FVVDIEVPMEYPF T0514 64 :KPVRLQV 1fzyA 65 :KPPKMQF T0514 72 :EGKAVI 1fzyA 84 :TGAICL T0514 91 :VPIVFDK 1fzyA 92 :LKNAWSP T0514 98 :N 1fzyA 104 :S T0514 99 :YVAALR 1fzyA 109 :LQALLQ T0514 116 :AAPGEPPL 1fzyA 116 :PEPNDPQD T0514 134 :SNALNRLIA 1fzyA 124 :AEVAQHYLR Number of specific fragments extracted= 10 number of extra gaps= 0 total=128 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 1fzyA/T0514-1fzyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0514 read from 1fzyA/T0514-1fzyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fzyA read from 1fzyA/T0514-1fzyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fzyA in template set T0514 25 :MHRQEVNDQNRVVVAMSVVLNADG 1fzyA 22 :ITLEFVSESDIHHLKGTFLGPPGT T0514 49 :VVSGNLTVPFGI 1fzyA 51 :KFVVDIEVPMEY T0514 62 :VSKPVRLQV 1fzyA 63 :PFKPPKMQF Number of specific fragments extracted= 3 number of extra gaps= 0 total=131 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 1e5rA/T0514-1e5rA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1e5rA expands to /projects/compbio/data/pdb/1e5r.pdb.gz 1e5rA:# T0514 read from 1e5rA/T0514-1e5rA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1e5rA read from 1e5rA/T0514-1e5rA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1e5rA to template set # found chain 1e5rA in template set Warning: unaligning (T0514)Q17 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1e5rA)A67 Warning: unaligning (T0514)E18 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1e5rA)A67 T0514 6 :TYGLWSINCGI 1e5rA 37 :SNGFWKHVPLW T0514 37 :V 1e5rA 68 :P T0514 38 :VAMSVVLNADGVVS 1e5rA 92 :QMARSRNLKNAIVI T0514 52 :GNLTVPFGI 1e5rA 121 :FRTFMVLED T0514 63 :SKPVRLQVDEG 1e5rA 130 :SPLAFHSNEDT T0514 78 :ETGIR 1e5rA 141 :VIHMR T0514 85 :VPAGCIVPIVF 1e5rA 146 :PGEIWFLDAAT T0514 109 :L 1e5rA 157 :V T0514 111 :LAMTIAAPGEPP 1e5rA 158 :HSAVNFSEISRQ T0514 125 :DLFVQ 1e5rA 170 :SLCVD Number of specific fragments extracted= 10 number of extra gaps= 1 total=141 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 1e5rA/T0514-1e5rA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0514 read from 1e5rA/T0514-1e5rA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1e5rA read from 1e5rA/T0514-1e5rA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1e5rA in template set Warning: unaligning (T0514)Q17 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1e5rA)A67 Warning: unaligning (T0514)E18 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1e5rA)A67 T0514 6 :TYGLWSINCGI 1e5rA 37 :SNGFWKHVPLW T0514 30 :VND 1e5rA 68 :PTA T0514 34 :NRVVVAMSVVLNADGVVS 1e5rA 88 :GTHLQMARSRNLKNAIVI T0514 52 :GNLTVPFGI 1e5rA 121 :FRTFMVLED T0514 63 :SKPVRLQVDEGKAVIET 1e5rA 130 :SPLAFHSNEDTVIHMRP T0514 80 :GIRTCVPAGCIVP 1e5rA 148 :EIWFLDAATVHSA T0514 94 :V 1e5rA 163 :F T0514 105 :AGKHLKLAMTIAAPGEPPLND 1e5rA 164 :SEISRQSLCVDFAFDGPFDEK Number of specific fragments extracted= 8 number of extra gaps= 1 total=149 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 1e5rA/T0514-1e5rA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0514 read from 1e5rA/T0514-1e5rA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1e5rA read from 1e5rA/T0514-1e5rA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1e5rA in template set T0514 36 :VVVAMSVVLNADGVVSGN 1e5rA 90 :HLQMARSRNLKNAIVIPH T0514 54 :LTVPFGI 1e5rA 123 :TFMVLED T0514 63 :SKPVRLQVDEGKAVIETGIRTCVPA 1e5rA 130 :SPLAFHSNEDTVIHMRPGEIWFLDA Number of specific fragments extracted= 3 number of extra gaps= 0 total=152 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 1eejA/T0514-1eejA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1eejA expands to /projects/compbio/data/pdb/1eej.pdb.gz 1eejA:# T0514 read from 1eejA/T0514-1eejA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1eejA read from 1eejA/T0514-1eejA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1eejA to template set # found chain 1eejA in template set T0514 25 :MHRQEVNDQNRVVVAM 1eejA 17 :SDIQPAPVAGMKTVLT T0514 41 :SVVLNADGVVS 1eejA 36 :VLYITDDGKHI T0514 55 :TVPFGILVSKP 1eejA 47 :IQGPMYDVSGT T0514 74 :KAVI 1eejA 58 :APVN T0514 79 :T 1eejA 78 :M T0514 81 :IRTCVPAG 1eejA 79 :IVYKAPQE T0514 89 :CIVPIVFDKNYVA 1eejA 91 :TVFTDITCGYCHK T0514 102 :ALRAGKHLKLAMTIA 1eejA 111 :YNALGITVRYLAFPR T0514 118 :PGEPP 1eejA 126 :QGLDS T0514 135 :NALNRLI 1eejA 131 :DAEKEMK Number of specific fragments extracted= 10 number of extra gaps= 0 total=162 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 1eejA/T0514-1eejA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0514 read from 1eejA/T0514-1eejA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1eejA read from 1eejA/T0514-1eejA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1eejA in template set T0514 25 :MHR 1eejA 16 :SSD T0514 28 :QEVNDQNRVVVAM 1eejA 20 :QPAPVAGMKTVLT T0514 41 :SVVLNADGVVS 1eejA 36 :VLYITDDGKHI T0514 66 :VRLQVDEGKAV 1eejA 79 :IVYKAPQEKHV T0514 81 :IRTCVPAGC 1eejA 90 :ITVFTDITC T0514 97 :KNYVAA 1eejA 99 :GYCHKL T0514 103 :LRAGKHLKLAMTIA 1eejA 112 :NALGITVRYLAFPR T0514 118 :P 1eejA 126 :Q T0514 120 :EPP 1eejA 127 :GLD T0514 134 :SNALNRLIA 1eejA 130 :SDAEKEMKA Number of specific fragments extracted= 10 number of extra gaps= 0 total=172 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 1eejA/T0514-1eejA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0514 read from 1eejA/T0514-1eejA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1eejA read from 1eejA/T0514-1eejA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1eejA in template set T0514 22 :VCFMH 1eejA 16 :SSDIQ T0514 29 :EVNDQNRVVVAM 1eejA 21 :PAPVAGMKTVLT T0514 41 :SVVLN 1eejA 36 :VLYIT T0514 46 :ADGVVSGNLTVPFGI 1eejA 84 :PQEKHVITVFTDITC T0514 97 :KNYVA 1eejA 109 :ADYNA T0514 107 :KHLKLAMTIAAPGEPPL 1eejA 114 :LGITVRYLAFPRQGLDS T0514 135 :NALNRLIAL 1eejA 131 :DAEKEMKAI Number of specific fragments extracted= 7 number of extra gaps= 0 total=179 Will force an alignment to be made, even if fragment is small Number of alignments=29 # command:CPU_time= 11.745 sec, elapsed time= 14.626 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 29 Adding 1550 constraints to all_contacts Done adding distance constraints # command:CPU_time= 11.770 sec, elapsed time= 14.652 sec. # command:Reading probabilities from T0514.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 6.403 Optimizing... Probability sum: -272.472, CN propb: -272.472 weights: 0.200 constraints: 543 # command:CPU_time= 27.281 sec, elapsed time= 30.162 sec. # command:Found ConstraintSet # PrintContacts align.constraints Number of constraints in align 543 # command:Found ConstraintSet # PrintContacts align_bonus.constraints Number of constraints in align.bonus 543 # command:Found ConstraintSet # PrintContacts rejected.constraints Number of constraints in rejected 1007 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints Number of constraints in rejected.bonus 1007 # 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= 27.309 sec, elapsed time= 31.319 sec. # command: