# command:# Seed set to 1277388821 # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading dunbrack-2191.atoms # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 53157 examples # computed average trans backbone unit before proline from 2010 examples # computed average cis backbone unit from 97 examples # trans (non-proline) backbone unit: # CA= -2.2087 1.0126 -0.0030 # O= -0.1499 2.2440 0.0016 # C= -0.6889 1.1368 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4581 0.0000 0.0000 # cis backbone unit: # CA= -0.1436 2.4534 -0.0002 # O= -2.0284 0.9742 0.0015 # C= -0.8018 1.0771 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4668 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2100 1.0631 -0.0014 # O= -0.1236 2.2458 0.0075 # C= -0.6872 1.1517 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading dunbrack-2191.atoms have 2191 chains in training database # Count of chains,residues,atoms: 2191,500310,3902258 # 493441 residues have no bad marker # 3226 residues lack atoms needed to compute omega # 1453 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 4 # HAS_OXT 1167 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 3052 # HAS_UNKNOWN_ATOMS 9 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 979 # NON_PLANAR_PEPTIDE 55 # BAD_PEPTIDE 2680 # HIGH_B_FACTOR 0 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-2191.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:CPU_time= 23.675 sec, elapsed time= 30.506 sec. # command:# Making generic fragment library # fragment library contains # type length num_fragments num_indexes_used # n-terminus 1 1963 20 (100.000%) # n-terminus 2 1934 333 (83.250%) # middle 1 483679 20 (100.000%) # middle 2 477517 400 (100.000%) # middle 3 471578 7988 (99.850%) # middle 4 465793 120683 (75.427%) # c-terminus 1 1917 20 (100.000%) # c-terminus 2 1889 372 (93.000%) # ss-bonds 1052 # command:CPU_time= 37.089 sec, elapsed time= 48.054 sec. # command:# Prefix for input files set to # command:# Making conformation for sequence T0588 numbered 1 through 400 Created new target T0588 from T0588.a2m # command:# command:# No conformations to remove in PopConform # command:CPU_time= 37.091 sec, elapsed time= 48.058 sec. # command:# Prefix for input files set to # command:# reading script from file T0588.undertaker-align.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qazA/T0588-1qazA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0588 read from 1qazA/T0588-1qazA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qazA read from 1qazA/T0588-1qazA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qazA in training set T0588 32 :LAKVKEKADSPLYAPAVKTL 1qazA 23 :VKARRTFLQSGQLDDRLKAA # choosing archetypes in rotamer library T0588 72 :TADSGDKHDYMSMG 1qazA 43 :LPKEYDCTTEATPN T0588 90 :PDPSKPD 1qazA 57 :PQQGEMV T0588 97 :GLPYIRKD 1qazA 65 :PRRYLSGN T0588 105 :GQRNPE 1qazA 74 :GPVNPD T0588 112 :DKLDRNKLGDMSKAVTTLGLAYYFSGDEKYAQKAVDFLNVW 1qazA 80 :YEPVVTLYRDFEKISATLGNLYVATGKPVYATCLLNMLDKW T0588 154 :LDAKTKMN 1qazA 121 :AKADALLN T0588 173 :KNKG 1qazA 129 :YDPK T0588 178 :GRGAGMIDI 1qazA 133 :SQSWYQVEW T0588 188 :SFTEMIDAMTLMENSKAFTPKVKKGMKEWFTQLVEWMQTSPVAA 1qazA 142 :SAATAAFALSTMMAEPNVDTAQRERVVKWLNRVARHQTSFPGGD T0588 234 :QRAKNNHGLAYDVQLTAYALYTGNQDLAMKTIQEF 1qazA 186 :TSCCNNHSYWRGQEATIIGVISKDDELFRWGLGRY T0588 271 :KRLFAQIEPDGKQPLELAR 1qazA 221 :VQAMGLINEDGSFVHEMTR T0588 290 :TTALGYTIFNLGHMLDMCSIASTLGQDIYNATSQ 1qazA 241 :EQSLHYQNYAMLPLTMIAETASRQGIDLYAYKEN T0588 325 :GRSITAALKFLIPYIGKPQSE 1qazA 275 :GRDIHSARKFVFAAVKNPDLI T0588 347 :PYQQIKEWDKKQEE 1qazA 301 :EPQDTRAFKPGRGD T0588 361 :ACWILRRASFFDPKA 1qazA 316 :NWIEYQRARFGFADE Number of specific fragments extracted= 16 number of extra gaps= 0 total=16 # request to SCWRL produces command: ulimit -t 360 ; scwrl4 -t -i /var/tmp/to_scwrl_1211053249.pdb -s /var/tmp/to_scwrl_1211053249.seq -o /var/tmp/from_scwrl_1211053249.pdb > /var/tmp/scwrl_1211053249.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1211053249.pdb Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3ew4A/T0588-3ew4A-t04-global-adpstyle1.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 3ew4A expands to /projects/compbio/data/pdb/3ew4.pdb.gz 3ew4A:# T0588 read from 3ew4A/T0588-3ew4A-t04-global-adpstyle1.a2m # 3ew4A read from 3ew4A/T0588-3ew4A-t04-global-adpstyle1.a2m # adding 3ew4A to template set # found chain 3ew4A in template set Warning: unaligning (T0588)V35 because first residue in template chain is (3ew4A)G4 Warning: unaligning (T0588)K36 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3ew4A)H6 Warning: unaligning (T0588)E37 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ew4A)H6 Warning: unaligning (T0588)A236 because of BadResidue code BAD_PEPTIDE in next template residue (3ew4A)C189 Warning: unaligning (T0588)K237 because of BadResidue code BAD_PEPTIDE at template residue (3ew4A)C189 Warning: unaligning (T0588)Y338 because of BadResidue code BAD_PEPTIDE in next template residue (3ew4A)V289 Warning: unaligning (T0588)I339 because of BadResidue code BAD_PEPTIDE at template residue (3ew4A)V289 T0588 38 :KADSPLYAPAVKTLL 3ew4A 7 :PFDQAVVKDPTASYV T0588 53 :RDADKALKMTPPSVMDKTMTADSGDKHDYMSMGPY 3ew4A 24 :KARRTFLQSGQLDDRLKAALPKEYDCTTEATPNPQ T0588 91 :DPSKPDGLPYIRKD 3ew4A 59 :QGEMVIPRRYLSGN T0588 105 :GQRNP 3ew4A 74 :GPVNP T0588 112 :DKLDRNKLGDMS 3ew4A 79 :DYEPVVTLYRDF T0588 124 :KAVTTLGLAYYFSGDEKYAQKAVDFLNVW 3ew4A 92 :KISATLGNLYVATGKPVYATCLLNMLDKW T0588 154 :LDAKTKMNPHLT 3ew4A 121 :AKADALLNYDPK T0588 178 :GRGAGMIDI 3ew4A 133 :SQSWYQVEW T0588 188 :SFTEMIDAMTLMENSKAFTPKVKKGMKEWFTQLVEWMQTSPVAA 3ew4A 142 :SAATAAFALSTMMAEPNVDTAQRERVVKWLNRVARHQTSFPGGD T0588 234 :QR 3ew4A 186 :TS T0588 238 :NNHGLAYDVQLTAYALYTGNQDLAMKTIQEFP 3ew4A 190 :NNHSYWRGQEATIIGVISKDDELFRWGLGRYV T0588 272 :RLFAQIEPDGKQPLELAR 3ew4A 222 :QAMGLINEDGSFVHEMTR T0588 290 :TTALGYTIFNLGHMLDMCSIASTLGQDIYNAT 3ew4A 241 :EQSLHFQNYAMLPLTMIAETASRQGIDLYAYK T0588 323 :QDGRSITAALKFLIP 3ew4A 273 :ENGRDIHSARKFVFA T0588 340 :GKPQSE 3ew4A 290 :KNPDLI T0588 346 :WPYQQIKEWDKKQEEA 3ew4A 300 :SEPQDTRAFKPGRGDL T0588 362 :CWILRRASFFDPKAGYEAIGAQFRETPANKRIHLIYSLE 3ew4A 317 :WIEYQRARFGFADELGFMTVPIFDPRTGGSATLLAYKPQ Number of specific fragments extracted= 17 number of extra gaps= 2 total=33 # request to SCWRL produces command: ulimit -t 360 ; scwrl4 -t -i /var/tmp/to_scwrl_484046130.pdb -s /var/tmp/to_scwrl_484046130.seq -o /var/tmp/from_scwrl_484046130.pdb > /var/tmp/scwrl_484046130.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_484046130.pdb Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3evhA/T0588-3evhA-t04-global-adpstyle1.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 3evhA expands to /projects/compbio/data/pdb/3evh.pdb.gz 3evhA:Skipped atom 2546, because occupancy 0.5 <= existing 0.500 in 3evhA Skipped atom 2548, because occupancy 0.500 <= existing 0.500 in 3evhA Skipped atom 2550, because occupancy 0.500 <= existing 0.500 in 3evhA Skipped atom 2552, because occupancy 0.500 <= existing 0.500 in 3evhA Skipped atom 2554, because occupancy 0.500 <= existing 0.500 in 3evhA Skipped atom 2556, because occupancy 0.500 <= existing 0.500 in 3evhA Skipped atom 2558, because occupancy 0.500 <= existing 0.500 in 3evhA Skipped atom 2628, because occupancy 0.170 <= existing 0.830 in 3evhA Skipped atom 2630, because occupancy 0.170 <= existing 0.830 in 3evhA Skipped atom 2632, because occupancy 0.170 <= existing 0.830 in 3evhA Skipped atom 2634, because occupancy 0.170 <= existing 0.830 in 3evhA # T0588 read from 3evhA/T0588-3evhA-t04-global-adpstyle1.a2m # 3evhA read from 3evhA/T0588-3evhA-t04-global-adpstyle1.a2m # adding 3evhA to template set # found chain 3evhA in template set Warning: unaligning (T0588)V35 because first residue in template chain is (3evhA)G4 Warning: unaligning (T0588)A236 because of BadResidue code BAD_PEPTIDE in next template residue (3evhA)C189 Warning: unaligning (T0588)K237 because of BadResidue code BAD_PEPTIDE at template residue (3evhA)C189 Warning: unaligning (T0588)S311 because of BadResidue code BAD_PEPTIDE in next template residue (3evhA)R263 Warning: unaligning (T0588)T312 because of BadResidue code BAD_PEPTIDE at template residue (3evhA)R263 T0588 36 :KEKADSPLYAPAVKTLL 3evhA 5 :SHPFDQAVVKDPTASYV T0588 53 :RDADKALKMTPPSVMDKTMTADSGDKHDYMSMGPY 3evhA 24 :KARRTFLQSGQLDDRLKAALPKEYDCTTEATPNPQ T0588 91 :DPSKPDGLPYIRKD 3evhA 59 :QGEMVIPRRYLSGN T0588 105 :GQRNP 3evhA 74 :GPVNP T0588 112 :DKLDRNKLGDMS 3evhA 79 :DYEPVVTLYRDF T0588 124 :KAVTTLGLAYYFSGDEKYAQKAVDFLNVW 3evhA 92 :KISATLGNLYVATGKPVYATCLLNMLDKW T0588 154 :LDAKTKMNPHLT 3evhA 121 :AKADALLNYDPK T0588 178 :GRGAGMIDI 3evhA 133 :SQSWYQVEW T0588 188 :SFTEMIDAMTLMENSKAFTPKVKKGMKEWFTQLVEWMQTSPVAA 3evhA 142 :SAATAAFALSTMMAEPNVDTAQRERVVKWLNRVARHQTSFPGGD T0588 234 :QR 3evhA 186 :TS T0588 238 :NNHGLAYDVQLTAYALYTGNQDLAMKTIQEFP 3evhA 190 :NNASYWRGQEATIIGVISKDDELFRWGLGRYV T0588 272 :RLFAQIEPDGKQPLELAR 3evhA 222 :QAMGLINEDGSFVHEMTR T0588 290 :TTALGYTIFNLGHMLDMCSIA 3evhA 241 :EQSLHYQNYAMLPLTMIAETA T0588 313 :LGQDIYNAT 3evhA 264 :QGIDLYAYK T0588 323 :QDGRSITAALKFLIPYIGKPQSE 3evhA 273 :ENGRDIHSARKFVFAAVKNPDLI T0588 346 :WPYQQIKEWDKKQEEA 3evhA 300 :SEPQDTRAFKPGRGDL T0588 362 :CWILRRASFFDPKAGYEAIGAQFRETPANKRIHLIYSLE 3evhA 317 :WIEYQRARFGFADELGFMTVPIFDPRTGGSATLLAYKPQ Number of specific fragments extracted= 17 number of extra gaps= 2 total=50 # request to SCWRL produces command: ulimit -t 360 ; scwrl4 -t -i /var/tmp/to_scwrl_116362446.pdb -s /var/tmp/to_scwrl_116362446.seq -o /var/tmp/from_scwrl_116362446.pdb > /var/tmp/scwrl_116362446.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_116362446.pdb Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3a0oA/T0588-3a0oA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 3a0oA expands to /projects/compbio/data/pdb/3a0o.pdb.gz 3a0oA:Skipped atom 80, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 82, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 84, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 86, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 88, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 90, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 951, because occupancy 0.300 <= existing 0.700 in 3a0oA Skipped atom 953, because occupancy 0.300 <= existing 0.700 in 3a0oA Skipped atom 955, because occupancy 0.300 <= existing 0.700 in 3a0oA Skipped atom 957, because occupancy 0.300 <= existing 0.700 in 3a0oA Skipped atom 959, because occupancy 0.300 <= existing 0.700 in 3a0oA Skipped atom 961, because occupancy 0.300 <= existing 0.700 in 3a0oA Skipped atom 963, because occupancy 0.300 <= existing 0.700 in 3a0oA Skipped atom 965, because occupancy 0.300 <= existing 0.700 in 3a0oA Skipped atom 967, because occupancy 0.300 <= existing 0.700 in 3a0oA Skipped atom 969, because occupancy 0.300 <= existing 0.700 in 3a0oA Skipped atom 971, because occupancy 0.300 <= existing 0.700 in 3a0oA Skipped atom 1020, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 1022, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 1024, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 1026, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 1028, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 1030, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 1032, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 1034, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 1036, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 4093, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 4095, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 4097, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 4099, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 4101, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 4103, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 4105, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 4107, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 4109, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 4111, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 4113, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 5320, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 5322, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 5324, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 5326, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 5328, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 5330, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 5332, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 5334, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 5336, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 5338, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 5340, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 5922, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 5924, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 5926, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 5928, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 5930, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 5932, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 5934, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 5936, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 5938, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 5940, because occupancy 0.500 <= existing 0.500 in 3a0oA Skipped atom 5942, because occupancy 0.500 <= existing 0.500 in 3a0oA # T0588 read from 3a0oA/T0588-3a0oA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3a0oA read from 3a0oA/T0588-3a0oA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3a0oA to template set # found chain 3a0oA in template set Warning: unaligning (T0588)L273 because of BadResidue code BAD_PEPTIDE in next template residue (3a0oA)S350 Warning: unaligning (T0588)F274 because of BadResidue code BAD_PEPTIDE at template residue (3a0oA)S350 T0588 23 :NTRIYAAEKLAKVKEKADSPL 3a0oA 140 :PRLWLNSEQLSAFADAVAKDP T0588 44 :YAPAVKTLLRDAD 3a0oA 165 :WAEFYEKSVEPWL T0588 94 :KPDGLPYI 3a0oA 178 :ERPVMPEP T0588 106 :QRNPEL 3a0oA 186 :QPYPNN T0588 112 :DKLDRNKLGDMSKAVTTLGLAYYFSGDEKYAQKAVDFLNV 3a0oA 198 :WRQMYIDCQEVIYAIRHLAIAGRVLGRDDLLDASRKWLLA T0588 153 :FLD 3a0oA 238 :VAA T0588 173 :KNKGM 3a0oA 241 :WDTKG T0588 178 :GRGAGMID 3a0oA 248 :SRAYNDEA T0588 186 :IYSFTEMIDAMTLM 3a0oA 257 :FRVVVALAWGYDWL T0588 202 :SKAFTPKVKKGMKEWFTQLVEWMQTSPVAAEEQR 3a0oA 271 :YDHLSEDERRTVRSVLLERTREVADHVIAHARIH T0588 236 :AKNNHGLAYDVQLTAYAL 3a0oA 310 :SHAVRSLSAVLTPACIAL T0588 255 :TGN 3a0oA 328 :QGE T0588 258 :QD 3a0oA 332 :DE T0588 260 :LAMKTIQEFP 3a0oA 337 :WLDYTVEFLA T0588 271 :KR 3a0oA 347 :TL T0588 275 :AQIEPDGK 3a0oA 351 :PWAGTDGG T0588 284 :PLE 3a0oA 359 :WAE T0588 292 :ALGYTIFNLGHMLDMCSIASTL 3a0oA 362 :GPHYWMTGMAYLIEAANLIRSY T0588 314 :GQDIYN 3a0oA 385 :GYDLYQ T0588 325 :GRSITAALKFLIPYIGKPQSEWPYQQIKEW 3a0oA 391 :RPFFQNTGRFPLYTKAPGTRRANFGDDSTL T0588 355 :DKKQEEACWILRRASFFDPKAGYEAIGAQFRE 3a0oA 422 :DLPGLKLGYNVRQFAGVTGNGHYQWYFDHIKA Number of specific fragments extracted= 21 number of extra gaps= 1 total=71 # request to SCWRL produces command: ulimit -t 360 ; scwrl4 -t -i /var/tmp/to_scwrl_1077736296.pdb -s /var/tmp/to_scwrl_1077736296.seq -o /var/tmp/from_scwrl_1077736296.pdb > /var/tmp/scwrl_1077736296.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1077736296.pdb Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fuqA/T0588-2fuqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fuqA expands to /projects/compbio/data/pdb/2fuq.pdb.gz 2fuqA:Bad short name: OE for alphabet: pdb_atoms # T0588 read from 2fuqA/T0588-2fuqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fuqA read from 2fuqA/T0588-2fuqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2fuqA to template set # found chain 2fuqA in template set Warning: unaligning (T0588)Y244 because of BadResidue code BAD_PEPTIDE in next template residue (2fuqA)D211 Warning: unaligning (T0588)D245 because of BadResidue code BAD_PEPTIDE at template residue (2fuqA)D211 T0588 30 :EKLAKVKE 2fuqA 59 :PDLKNRMN T0588 45 :APAVKTLLRDADKALKM 2fuqA 67 :DPKLKKVWADMIKMQED T0588 89 :W 2fuqA 84 :W T0588 91 :DPSKPDGLP 2fuqA 85 :KPADIPEVK T0588 112 :DKLDRNKLGDMSKAVTTLGLAYYFSGDEKYAQKAVDFLN 2fuqA 94 :DFRFYFNQKGLTVRVELMALNYLMTKDPKVGREAITSII T0588 153 :FLD 2fuqA 135 :LET T0588 161 :N 2fuqA 138 :A T0588 169 :TIP 2fuqA 139 :TFK T0588 173 :KNKGMGRGAGM 2fuqA 142 :PAGDISRGIGL T0588 188 :SFTEMIDAMTLM 2fuqA 153 :FMVTGAIVYDWC T0588 202 :SKAFTPKVKKGMKEWFTQLVEWMQTS 2fuqA 165 :YDQLKPEEKTRFVKAFVRLAKMLECG T0588 230 :AAEEQRAKNNHGLA 2fuqA 196 :DKSIVGHASEWMIM T0588 246 :VQLTAYALYTGNQDLAMKTIQEFPEK 2fuqA 212 :LLSVGIAIYDEFPEMYNLAAGRFFKE T0588 272 :RLFAQIEPD 2fuqA 240 :VARNWFYPS T0588 283 :QPLE 2fuqA 249 :HNYH T0588 291 :TALGYTIFNLGHMLDMCSIASTLG 2fuqA 253 :QGMSYLNVRFTNDLFALWILDRMG T0588 315 :QDIYNATSQD 2fuqA 278 :GNVFNPGQQF T0588 332 :LKFLIPYIGKPQSEWPYQQIKEWDKKQEEACWILRRASFFDPKAGYEAIGAQFRETPAN 2fuqA 289 :LYDAIYKRRPDGQILAGGDVDYSRKKPKYYTMPALLAGSYYKDEYLNYEFLKDPNVEPH T0588 391 :KRI 2fuqA 349 :KLF T0588 394 :HLI 2fuqA 353 :FLW Number of specific fragments extracted= 20 number of extra gaps= 1 total=91 # request to SCWRL produces command: ulimit -t 360 ; scwrl4 -t -i /var/tmp/to_scwrl_570596875.pdb -s /var/tmp/to_scwrl_570596875.seq -o /var/tmp/from_scwrl_570596875.pdb > /var/tmp/scwrl_570596875.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_570596875.pdb Number of alignments=5 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3e7jA/T0588-3e7jA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 3e7jA expands to /projects/compbio/data/pdb/3e7j.pdb.gz 3e7jA:# T0588 read from 3e7jA/T0588-3e7jA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3e7jA read from 3e7jA/T0588-3e7jA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3e7jA to template set # found chain 3e7jA in template set T0588 25 :RIYAAEKLAKVKEKADSPLYAPAVKTLLRD 3e7jA 51 :LYLREQQVPDLKNRMNDPKLKKVWADMIKM T0588 60 :KMTP 3e7jA 81 :QEDW T0588 91 :DPSKPDGLP 3e7jA 85 :KPADIPEVK T0588 112 :DKLDRNKLGDMSKAVTTLGLAYYFSGDEKYAQKAVDFLNVWFLD 3e7jA 94 :DFRFYFNQKGLTVRVELMALNYLMTKDPKVGREAITSIIDTLET T0588 167 :G 3e7jA 138 :A T0588 169 :TIP 3e7jA 139 :TFK T0588 173 :KNKGMGRGAGM 3e7jA 142 :PAGDISRGIGL T0588 188 :SFTEMIDAMTLM 3e7jA 153 :FMVTGAIVYDWC T0588 202 :SKAFTPKVKKGMKEWFTQLVEWMQTSPV 3e7jA 165 :YDQLKPEEKTRFVKAFVRLAKMLECGYP T0588 230 :AAEEQRAKNNHGLAYDVQLTAYALYTGNQDLAMKTIQEFPEKRL 3e7jA 196 :DKSIVGAASEWMIMRDLLSVGIAIYDEFPEMYNLAAGRFFKEHL T0588 274 :FAQIEPD 3e7jA 242 :RNWFYPS T0588 283 :QPLE 3e7jA 249 :HNYH T0588 291 :TALGYTIFNLGHMLDMCSIASTLG 3e7jA 253 :QGMSALNVRFTNDLFALWILDRMG T0588 315 :QDIYNATSQD 3e7jA 278 :GNVFNPGQQF T0588 332 :LKFLIPYIGKPQSEWPYQQIKEWDKKQEEACWILRRASFFDPKAGYEAIGAQFRETPAN 3e7jA 289 :LYDAIYKRRPDGQILAGGDVDYSRKKPKYYTMPALLAGSYYKDEYLNYEFLKDPNVEPH T0588 391 :KRI 3e7jA 349 :KLF Number of specific fragments extracted= 16 number of extra gaps= 0 total=107 # request to SCWRL produces command: ulimit -t 360 ; scwrl4 -t -i /var/tmp/to_scwrl_1456154054.pdb -s /var/tmp/to_scwrl_1456154054.seq -o /var/tmp/from_scwrl_1456154054.pdb > /var/tmp/scwrl_1456154054.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1456154054.pdb Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3e80A/T0588-3e80A-t04-local-adpstyle1.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 3e80A expands to /projects/compbio/data/pdb/3e80.pdb.gz 3e80A:Bad short name: OE for alphabet: pdb_atoms # T0588 read from 3e80A/T0588-3e80A-t04-local-adpstyle1.a2m # 3e80A read from 3e80A/T0588-3e80A-t04-local-adpstyle1.a2m # adding 3e80A to template set # found chain 3e80A in template set T0588 63 :PPSVMDKTMTADSGDKHDYMSMGPYWWPDPSK 3e80A 32 :VWKDVDGVSMPIPPKTHPRLYLREQQVPDLKN T0588 95 :PDGLPYIRKDGQR 3e80A 74 :WADMIKMQEDWKP T0588 108 :NPEL 3e80A 89 :IPEV T0588 112 :DKLDRNKLGDMSKAVTTLGLAYYFSGDEKYAQKAVDFLNV 3e80A 94 :DFRFYFNQKGLTVRVELMALNYLMTKDPKVGREAITSIID T0588 158 :TKMNPHLT 3e80A 134 :TLETATFK T0588 173 :KNKGMGRGAGM 3e80A 142 :PAGDISRGIGL T0588 188 :SFTEMIDAMTLM 3e80A 153 :FMVTGAIVYDWC T0588 202 :SKAFTPKVKKGMKEWFTQLVEWMQTSPVAAEEQRAKNN 3e80A 165 :YDQLKPEEKTRFVKAFVRLAKMLECGYPPVKDKSIVGH T0588 240 :HGLAYDVQLTAYALYTGNQDLAMKTIQEFP 3e80A 206 :WMIMRDLLSVGIAIYDEFPEMYNLAAGRFF T0588 270 :EKRLFAQIEP 3e80A 238 :HLVARNWFYP T0588 282 :KQPLE 3e80A 248 :SHNYH T0588 291 :TALGYTIFNLGHMLDMCSIASTLGQ 3e80A 253 :QGMSYLNVRFTNDLFALWILDRMGA T0588 325 :GRSITAALKFLIPYIG 3e80A 278 :GNVFNPGQQFILYDAI T0588 341 :KPQSEWPYQQIKEWDKKQEEACWILRRASFFDPKA 3e80A 298 :PDGQILAGGDVDYSRKKPKYYTMPALLAGSYYKDE Number of specific fragments extracted= 14 number of extra gaps= 0 total=121 # request to SCWRL produces command: ulimit -t 360 ; scwrl4 -t -i /var/tmp/to_scwrl_1630347395.pdb -s /var/tmp/to_scwrl_1630347395.seq -o /var/tmp/from_scwrl_1630347395.pdb > /var/tmp/scwrl_1630347395.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1630347395.pdb Number of alignments=7 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2futA/T0588-2futA-t04-local-adpstyle1.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2futA expands to /projects/compbio/data/pdb/2fut.pdb.gz 2futA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0588 read from 2futA/T0588-2futA-t04-local-adpstyle1.a2m # 2futA read from 2futA/T0588-2futA-t04-local-adpstyle1.a2m # adding 2futA to template set # found chain 2futA in template set Warning: unaligning (T0588)E110 because of BadResidue code BAD_PEPTIDE in next template residue (2futA)V92 Warning: unaligning (T0588)L111 because of BadResidue code BAD_PEPTIDE at template residue (2futA)V92 T0588 63 :PPSVMDKTMTADSGDKHDYMSMGPYWWPDPSK 2futA 32 :VWKDVDGVSMPIPPKTHPRLYLREQQVPDLKN T0588 95 :PDGLPYIRKDGQR 2futA 74 :WADMIKMQEDWKP T0588 108 :NP 2futA 89 :IP T0588 112 :DKLDRNKLGDMSKAVTTLGLAYYFSGDEKYAQKAVDFLNV 2futA 94 :DFRFYFNQKGLTVRVELMALNYLMTKDPKVGREAITSIID T0588 158 :TKMNPHLT 2futA 134 :TLETATFK T0588 173 :KNKGMGRGAGM 2futA 142 :PAGDISRGIGL T0588 188 :SFTEMIDAMTLM 2futA 153 :FMVTGAIVYDWC T0588 202 :SKAFTPKVKKGMKEWFTQLVEWMQTSPVAAEEQRAKNN 2futA 165 :YDQLKPEEKTRFVKAFVRLAKMLECGYPPVKDKSIVGH T0588 240 :HGLAYDVQLTAYALYTGNQDLAMKTIQEFP 2futA 206 :WMIMRDLLSVGIAIYDEFPEMYNLAAGRFF T0588 270 :EKRLFAQIEP 2futA 238 :HLVARNWFYP T0588 282 :KQPLE 2futA 248 :SHNYH T0588 291 :TALGYTIFNLGHMLDMCSIASTLGQ 2futA 253 :QGMSYLNVRFTNDLFALWILDRMGA T0588 325 :GRSITAALKFLIPYIG 2futA 278 :GNVFNPGQQFILYDAI T0588 341 :KPQSEWPYQQIKEWDKKQEEACWILRRASFFDPKA 2futA 298 :PDGQILAGGDVDYSRKKPKYYTMPALLAGSYYKDE Number of specific fragments extracted= 14 number of extra gaps= 1 total=135 # request to SCWRL produces command: ulimit -t 360 ; scwrl4 -t -i /var/tmp/to_scwrl_186838115.pdb -s /var/tmp/to_scwrl_186838115.seq -o /var/tmp/from_scwrl_186838115.pdb > /var/tmp/scwrl_186838115.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_186838115.pdb Number of alignments=8 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3aflA/T0588-3aflA-t04-local-adpstyle1.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 3aflA expands to /projects/compbio/data/pdb/3afl.pdb.gz 3aflA:Skipped atom 3602, because occupancy 0.500 <= existing 0.500 in 3aflA Skipped atom 3604, because occupancy 0.500 <= existing 0.500 in 3aflA Skipped atom 3606, because occupancy 0.500 <= existing 0.500 in 3aflA Skipped atom 3608, because occupancy 0.500 <= existing 0.500 in 3aflA Skipped atom 3610, because occupancy 0.500 <= existing 0.500 in 3aflA Skipped atom 3612, because occupancy 0.500 <= existing 0.500 in 3aflA Skipped atom 3614, because occupancy 0.500 <= existing 0.500 in 3aflA Skipped atom 3616, because occupancy 0.500 <= existing 0.500 in 3aflA Skipped atom 3618, because occupancy 0.500 <= existing 0.500 in 3aflA Skipped atom 4328, because occupancy 0.500 <= existing 0.500 in 3aflA Skipped atom 4330, because occupancy 0.500 <= existing 0.500 in 3aflA Skipped atom 4332, because occupancy 0.500 <= existing 0.500 in 3aflA Skipped atom 4334, because occupancy 0.500 <= existing 0.500 in 3aflA Skipped atom 4336, because occupancy 0.500 <= existing 0.500 in 3aflA Skipped atom 4338, because occupancy 0.500 <= existing 0.500 in 3aflA Skipped atom 4340, because occupancy 0.500 <= existing 0.500 in 3aflA Skipped atom 4342, because occupancy 0.500 <= existing 0.500 in 3aflA # T0588 read from 3aflA/T0588-3aflA-t04-local-adpstyle1.a2m # 3aflA read from 3aflA/T0588-3aflA-t04-local-adpstyle1.a2m # adding 3aflA to template set # found chain 3aflA in template set Warning: unaligning (T0588)L273 because of BadResidue code BAD_PEPTIDE in next template residue (3aflA)S350 Warning: unaligning (T0588)F274 because of BadResidue code BAD_PEPTIDE at template residue (3aflA)S350 T0588 75 :SGDKHDYMSMGPYWWPDPSKPDGL 3aflA 174 :EPWLERPVMPEPQPYPNNTRVATL T0588 112 :DKLDRNKLGDMSKAVTTLGLAYYFSGDEKYAQKAVDFLN 3aflA 198 :WRQMYIDCQEVIYAIRHLAIAGRVLGRDDLLDASRKWLL T0588 151 :VWFLD 3aflA 240 :AWDTK T0588 167 :GQTIPGKNK 3aflA 245 :GATSRAYND T0588 178 :GRGAG 3aflA 254 :EAGFR T0588 188 :SFTEMIDAMTLM 3aflA 259 :VVVALAWGYDWL T0588 202 :SKAFTPKVKKGMKEWFTQLV 3aflA 271 :YDHLSEDERRTVRSVLLERT T0588 222 :EWMQTSPVAAEEQRAKNNHGLAYDVQLTAYALYTGNQD 3aflA 296 :HVIAHARIHVFPYDSHAVRSLSAVLTPACIALQGESDE T0588 260 :LAMKTIQEFP 3aflA 337 :WLDYTVEFLA T0588 271 :KR 3aflA 347 :TL T0588 275 :AQIEPDGK 3aflA 351 :PWAGTDGG T0588 284 :PLE 3aflA 359 :WAE T0588 292 :ALGYTIFNLGHMLDMCSIASTL 3aflA 362 :GPHYWMTGMAYLIEAANLIRSY T0588 314 :GQDIYN 3aflA 385 :GYDLYQ T0588 325 :GRSITAALKFLIPYIGKPQSEWPYQQ 3aflA 391 :RPFFQNTGRFPLYTKAPGTRRANFGD T0588 351 :IKEWDKKQEEACWILRRASFFDPKAGYEAIGAQFRE 3aflA 418 :STLGDLPGLKLGYNVRQFAGVTGNGHYQWYFDHIKA T0588 387 :TPANKRIHLIYSL 3aflA 455 :ATGTEMAFYNYGW Number of specific fragments extracted= 17 number of extra gaps= 1 total=152 # request to SCWRL produces command: ulimit -t 360 ; scwrl4 -t -i /var/tmp/to_scwrl_327854445.pdb -s /var/tmp/to_scwrl_327854445.seq -o /var/tmp/from_scwrl_327854445.pdb > /var/tmp/scwrl_327854445.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_327854445.pdb Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rwhA/T0588-1rwhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0588 read from 1rwhA/T0588-1rwhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rwhA read from 1rwhA/T0588-1rwhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rwhA in training set Warning: unaligning (T0588)Y27 because first residue in template chain is (1rwhA)P4 T0588 28 :AAEKLAKVKEKA 1rwhA 5 :GAAEFAALRNRW T0588 40 :DSPL 1rwhA 27 :QAGD T0588 44 :YAPAVKTLLRDADKALKM 1rwhA 33 :FAKAITALNNKAADSLAK T0588 62 :T 1rwhA 52 :D T0588 90 :PDPSKPD 1rwhA 53 :AAAGRTS T0588 107 :RNPELDKLDRNKLGDMSKAVTTLGLAYYFS 1rwhA 60 :VFTDLSLAKDAEMVTTYTRLSQLATAWATP T0588 137 :GDEKYAQKAVDFLNV 1rwhA 95 :GDAAVLAAIKAGLAD T0588 153 :FLD 1rwhA 110 :ANT T0588 158 :TKMNPHLT 1rwhA 113 :LCYNDRKE T0588 172 :GK 1rwhA 121 :EV T0588 178 :GRGAGM 1rwhA 123 :GNWWSW T0588 185 :DIYSFTEMIDAMTLM 1rwhA 129 :EIGVPRALADAMVLL T0588 202 :SKAFTPKVKKGMKEWFTQLV 1rwhA 144 :HAELSAAERTAYCAAIDHFV T0588 237 :KNNHGLAYDVQLTAYALYTGNQDLAMKTIQEF 1rwhA 180 :VGANRVDLCQGIIIRSLAGEDPTKLNHAVAGL T0588 271 :KRLFAQIE 1rwhA 212 :SQVWQYVT T0588 279 :PDGKQPLELARTTALGYTIFNLGHMLDMCSIA 1rwhA 226 :RDGSFIQHSTTPYTGSYGVVLLTGLSKLFSLL T0588 313 :LGQD 1rwhA 258 :GGTA T0588 318 :YNATSQDGRSITAALKFLIPYI 1rwhA 262 :FEVSDPTRSIFFDAVEGSFAPV T0588 342 :PQ 1rwhA 286 :NG T0588 355 :DKKQEEACWILRRASFFDP 1rwhA 307 :DLGASAIEAILLLARAMDP T0588 375 :AGYEAIGAQ 1rwhA 326 :ATAARWRGL Number of specific fragments extracted= 21 number of extra gaps= 0 total=173 # request to SCWRL produces command: ulimit -t 360 ; scwrl4 -t -i /var/tmp/to_scwrl_1770078374.pdb -s /var/tmp/to_scwrl_1770078374.seq -o /var/tmp/from_scwrl_1770078374.pdb > /var/tmp/scwrl_1770078374.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1770078374.pdb Number of alignments=10 # command:Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.117 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 1 total_weight= 23570.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 2 total_weight= 23570.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 3 total_weight= 23570.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 4 total_weight= 23570.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 5 total_weight= 23570.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 1.049 rmsd (weighted)= 7.182 (unweighted)= 29.008 superimposing iter= 1 total_weight= 15117.273 rmsd (weighted)= 1.466 (unweighted)= 28.914 superimposing iter= 2 total_weight= 13910.037 rmsd (weighted)= 0.458 (unweighted)= 28.905 superimposing iter= 3 total_weight= 5781.259 rmsd (weighted)= 0.277 (unweighted)= 28.908 superimposing iter= 4 total_weight= 2830.639 rmsd (weighted)= 0.244 (unweighted)= 28.909 superimposing iter= 5 total_weight= 2328.699 rmsd (weighted)= 0.237 (unweighted)= 28.910 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 1.060 rmsd (weighted)= 7.541 (unweighted)= 27.842 superimposing iter= 1 total_weight= 15165.903 rmsd (weighted)= 1.505 (unweighted)= 27.926 superimposing iter= 2 total_weight= 13329.073 rmsd (weighted)= 0.466 (unweighted)= 27.970 superimposing iter= 3 total_weight= 6674.050 rmsd (weighted)= 0.260 (unweighted)= 27.974 superimposing iter= 4 total_weight= 3084.755 rmsd (weighted)= 0.220 (unweighted)= 27.975 superimposing iter= 5 total_weight= 2374.739 rmsd (weighted)= 0.213 (unweighted)= 27.975 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 0.953 rmsd (weighted)= 7.144 (unweighted)= 27.224 superimposing iter= 1 total_weight= 8175.023 rmsd (weighted)= 3.282 (unweighted)= 27.189 superimposing iter= 2 total_weight= 2981.616 rmsd (weighted)= 2.668 (unweighted)= 27.196 superimposing iter= 3 total_weight= 2183.084 rmsd (weighted)= 2.550 (unweighted)= 27.207 superimposing iter= 4 total_weight= 2051.043 rmsd (weighted)= 2.517 (unweighted)= 27.217 superimposing iter= 5 total_weight= 2028.421 rmsd (weighted)= 2.499 (unweighted)= 27.223 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 0.886 rmsd (weighted)= 7.289 (unweighted)= 63.404 superimposing iter= 1 total_weight= 5602.405 rmsd (weighted)= 4.057 (unweighted)= 63.653 superimposing iter= 2 total_weight= 2361.411 rmsd (weighted)= 3.582 (unweighted)= 63.723 superimposing iter= 3 total_weight= 1950.187 rmsd (weighted)= 3.494 (unweighted)= 63.742 superimposing iter= 4 total_weight= 1908.627 rmsd (weighted)= 3.449 (unweighted)= 63.738 superimposing iter= 5 total_weight= 1910.440 rmsd (weighted)= 3.404 (unweighted)= 63.721 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 0.933 rmsd (weighted)= 7.388 (unweighted)= 33.205 superimposing iter= 1 total_weight= 6040.672 rmsd (weighted)= 4.085 (unweighted)= 33.174 superimposing iter= 2 total_weight= 2511.840 rmsd (weighted)= 3.598 (unweighted)= 33.190 superimposing iter= 3 total_weight= 2044.796 rmsd (weighted)= 3.521 (unweighted)= 33.216 superimposing iter= 4 total_weight= 1988.810 rmsd (weighted)= 3.495 (unweighted)= 33.249 superimposing iter= 5 total_weight= 1983.619 rmsd (weighted)= 3.474 (unweighted)= 33.287 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 0.954 rmsd (weighted)= 11.954 (unweighted)= 65.293 superimposing iter= 1 total_weight= 7932.317 rmsd (weighted)= 5.327 (unweighted)= 64.855 superimposing iter= 2 total_weight= 3730.768 rmsd (weighted)= 3.779 (unweighted)= 64.830 superimposing iter= 3 total_weight= 2650.128 rmsd (weighted)= 3.258 (unweighted)= 64.950 superimposing iter= 4 total_weight= 2302.741 rmsd (weighted)= 3.025 (unweighted)= 65.062 superimposing iter= 5 total_weight= 2209.602 rmsd (weighted)= 2.869 (unweighted)= 65.152 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 0.950 rmsd (weighted)= 11.964 (unweighted)= 99.734 superimposing iter= 1 total_weight= 7846.206 rmsd (weighted)= 5.374 (unweighted)= 100.282 superimposing iter= 2 total_weight= 3605.494 rmsd (weighted)= 3.866 (unweighted)= 100.481 superimposing iter= 3 total_weight= 2630.152 rmsd (weighted)= 3.335 (unweighted)= 100.610 superimposing iter= 4 total_weight= 2285.677 rmsd (weighted)= 3.102 (unweighted)= 100.710 superimposing iter= 5 total_weight= 2191.075 rmsd (weighted)= 2.949 (unweighted)= 100.797 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 0.895 rmsd (weighted)= 6.079 (unweighted)= 23.876 superimposing iter= 1 total_weight= 6753.185 rmsd (weighted)= 3.074 (unweighted)= 23.838 superimposing iter= 2 total_weight= 2777.585 rmsd (weighted)= 2.514 (unweighted)= 23.831 superimposing iter= 3 total_weight= 2088.603 rmsd (weighted)= 2.381 (unweighted)= 23.828 superimposing iter= 4 total_weight= 1948.174 rmsd (weighted)= 2.337 (unweighted)= 23.827 superimposing iter= 5 total_weight= 1908.863 rmsd (weighted)= 2.317 (unweighted)= 23.827 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 0.883 rmsd (weighted)= 6.755 (unweighted)= 52.718 superimposing iter= 1 total_weight= 7107.754 rmsd (weighted)= 3.141 (unweighted)= 52.655 superimposing iter= 2 total_weight= 3276.644 rmsd (weighted)= 2.318 (unweighted)= 52.693 superimposing iter= 3 total_weight= 2287.903 rmsd (weighted)= 2.064 (unweighted)= 52.725 superimposing iter= 4 total_weight= 2078.064 rmsd (weighted)= 1.935 (unweighted)= 52.739 superimposing iter= 5 total_weight= 1962.721 rmsd (weighted)= 1.868 (unweighted)= 52.744 Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.117 rmsd (weighted)= 5.581 (unweighted)= 18.190 superimposing iter= 1 total_weight= 9895.569 rmsd (weighted)= 2.491 (unweighted)= 18.306 superimposing iter= 2 total_weight= 4105.979 rmsd (weighted)= 1.853 (unweighted)= 18.333 superimposing iter= 3 total_weight= 2751.141 rmsd (weighted)= 1.699 (unweighted)= 18.337 superimposing iter= 4 total_weight= 2448.375 rmsd (weighted)= 1.653 (unweighted)= 18.336 superimposing iter= 5 total_weight= 2363.113 rmsd (weighted)= 1.637 (unweighted)= 18.335 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 1.254 rmsd (weighted)= 7.974 (unweighted)= 25.222 superimposing iter= 1 total_weight= 13307.918 rmsd (weighted)= 3.157 (unweighted)= 25.173 superimposing iter= 2 total_weight= 5559.840 rmsd (weighted)= 2.131 (unweighted)= 25.171 superimposing iter= 3 total_weight= 3308.339 rmsd (weighted)= 1.887 (unweighted)= 25.164 superimposing iter= 4 total_weight= 2808.563 rmsd (weighted)= 1.818 (unweighted)= 25.158 superimposing iter= 5 total_weight= 2674.745 rmsd (weighted)= 1.796 (unweighted)= 25.154 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 1.265 rmsd (weighted)= 8.201 (unweighted)= 24.018 superimposing iter= 1 total_weight= 13524.689 rmsd (weighted)= 3.217 (unweighted)= 24.024 superimposing iter= 2 total_weight= 5747.768 rmsd (weighted)= 2.146 (unweighted)= 24.043 superimposing iter= 3 total_weight= 3345.521 rmsd (weighted)= 1.900 (unweighted)= 24.047 superimposing iter= 4 total_weight= 2824.427 rmsd (weighted)= 1.834 (unweighted)= 24.044 superimposing iter= 5 total_weight= 2694.361 rmsd (weighted)= 1.813 (unweighted)= 24.041 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 1.082 rmsd (weighted)= 5.049 (unweighted)= 20.700 superimposing iter= 1 total_weight= 9863.058 rmsd (weighted)= 2.184 (unweighted)= 20.505 superimposing iter= 2 total_weight= 4019.485 rmsd (weighted)= 1.630 (unweighted)= 20.477 superimposing iter= 3 total_weight= 2546.981 rmsd (weighted)= 1.541 (unweighted)= 20.467 superimposing iter= 4 total_weight= 2336.571 rmsd (weighted)= 1.522 (unweighted)= 20.463 superimposing iter= 5 total_weight= 2297.902 rmsd (weighted)= 1.517 (unweighted)= 20.460 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 1.061 rmsd (weighted)= 4.524 (unweighted)= 60.074 superimposing iter= 1 total_weight= 6372.955 rmsd (weighted)= 2.542 (unweighted)= 60.039 superimposing iter= 2 total_weight= 3251.028 rmsd (weighted)= 2.066 (unweighted)= 60.028 superimposing iter= 3 total_weight= 2556.136 rmsd (weighted)= 1.918 (unweighted)= 60.022 superimposing iter= 4 total_weight= 2315.995 rmsd (weighted)= 1.877 (unweighted)= 60.019 superimposing iter= 5 total_weight= 2266.890 rmsd (weighted)= 1.860 (unweighted)= 60.016 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 1.102 rmsd (weighted)= 4.847 (unweighted)= 28.819 superimposing iter= 1 total_weight= 7178.300 rmsd (weighted)= 2.604 (unweighted)= 28.701 superimposing iter= 2 total_weight= 3395.254 rmsd (weighted)= 2.103 (unweighted)= 28.662 superimposing iter= 3 total_weight= 2761.153 rmsd (weighted)= 1.907 (unweighted)= 28.655 superimposing iter= 4 total_weight= 2477.578 rmsd (weighted)= 1.836 (unweighted)= 28.662 superimposing iter= 5 total_weight= 2377.568 rmsd (weighted)= 1.809 (unweighted)= 28.672 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 1.050 rmsd (weighted)= 8.017 (unweighted)= 63.723 superimposing iter= 1 total_weight= 9434.481 rmsd (weighted)= 3.293 (unweighted)= 63.529 superimposing iter= 2 total_weight= 4581.760 rmsd (weighted)= 2.180 (unweighted)= 63.510 superimposing iter= 3 total_weight= 3231.065 rmsd (weighted)= 1.777 (unweighted)= 63.547 superimposing iter= 4 total_weight= 2565.685 rmsd (weighted)= 1.638 (unweighted)= 63.573 superimposing iter= 5 total_weight= 2339.753 rmsd (weighted)= 1.585 (unweighted)= 63.588 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 1.042 rmsd (weighted)= 7.981 (unweighted)= 97.199 superimposing iter= 1 total_weight= 9273.117 rmsd (weighted)= 3.313 (unweighted)= 97.905 superimposing iter= 2 total_weight= 4250.022 rmsd (weighted)= 2.277 (unweighted)= 98.157 superimposing iter= 3 total_weight= 3048.444 rmsd (weighted)= 1.906 (unweighted)= 98.291 superimposing iter= 4 total_weight= 2545.662 rmsd (weighted)= 1.762 (unweighted)= 98.369 superimposing iter= 5 total_weight= 2341.449 rmsd (weighted)= 1.702 (unweighted)= 98.423 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 1.048 rmsd (weighted)= 6.227 (unweighted)= 17.162 superimposing iter= 1 total_weight= 9100.128 rmsd (weighted)= 2.697 (unweighted)= 17.452 superimposing iter= 2 total_weight= 3733.251 rmsd (weighted)= 2.036 (unweighted)= 17.547 superimposing iter= 3 total_weight= 2631.957 rmsd (weighted)= 1.855 (unweighted)= 17.591 superimposing iter= 4 total_weight= 2416.397 rmsd (weighted)= 1.770 (unweighted)= 17.619 superimposing iter= 5 total_weight= 2338.840 rmsd (weighted)= 1.719 (unweighted)= 17.637 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 1.001 rmsd (weighted)= 6.735 (unweighted)= 51.667 superimposing iter= 1 total_weight= 7886.526 rmsd (weighted)= 3.251 (unweighted)= 51.299 superimposing iter= 2 total_weight= 3489.345 rmsd (weighted)= 2.477 (unweighted)= 51.201 superimposing iter= 3 total_weight= 2613.204 rmsd (weighted)= 2.200 (unweighted)= 51.174 superimposing iter= 4 total_weight= 2328.556 rmsd (weighted)= 2.073 (unweighted)= 51.165 superimposing iter= 5 total_weight= 2218.688 rmsd (weighted)= 2.001 (unweighted)= 51.161 Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.117 rmsd (weighted)= 5.587 (unweighted)= 18.195 superimposing iter= 1 total_weight= 9878.138 rmsd (weighted)= 2.496 (unweighted)= 18.312 superimposing iter= 2 total_weight= 4091.944 rmsd (weighted)= 1.861 (unweighted)= 18.339 superimposing iter= 3 total_weight= 2740.615 rmsd (weighted)= 1.710 (unweighted)= 18.343 superimposing iter= 4 total_weight= 2443.041 rmsd (weighted)= 1.666 (unweighted)= 18.343 superimposing iter= 5 total_weight= 2363.099 rmsd (weighted)= 1.650 (unweighted)= 18.342 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 1.254 rmsd (weighted)= 8.005 (unweighted)= 25.218 superimposing iter= 1 total_weight= 13298.526 rmsd (weighted)= 3.170 (unweighted)= 25.168 superimposing iter= 2 total_weight= 5569.869 rmsd (weighted)= 2.138 (unweighted)= 25.169 superimposing iter= 3 total_weight= 3292.124 rmsd (weighted)= 1.898 (unweighted)= 25.166 superimposing iter= 4 total_weight= 2796.262 rmsd (weighted)= 1.833 (unweighted)= 25.164 superimposing iter= 5 total_weight= 2666.995 rmsd (weighted)= 1.813 (unweighted)= 25.161 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 1.265 rmsd (weighted)= 8.234 (unweighted)= 24.012 superimposing iter= 1 total_weight= 13516.653 rmsd (weighted)= 3.230 (unweighted)= 24.018 superimposing iter= 2 total_weight= 5767.374 rmsd (weighted)= 2.152 (unweighted)= 24.039 superimposing iter= 3 total_weight= 3319.326 rmsd (weighted)= 1.913 (unweighted)= 24.047 superimposing iter= 4 total_weight= 2804.832 rmsd (weighted)= 1.853 (unweighted)= 24.047 superimposing iter= 5 total_weight= 2685.178 rmsd (weighted)= 1.834 (unweighted)= 24.044 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 1.082 rmsd (weighted)= 5.042 (unweighted)= 20.711 superimposing iter= 1 total_weight= 9888.571 rmsd (weighted)= 2.178 (unweighted)= 20.519 superimposing iter= 2 total_weight= 4026.939 rmsd (weighted)= 1.620 (unweighted)= 20.493 superimposing iter= 3 total_weight= 2565.906 rmsd (weighted)= 1.521 (unweighted)= 20.486 superimposing iter= 4 total_weight= 2323.537 rmsd (weighted)= 1.502 (unweighted)= 20.484 superimposing iter= 5 total_weight= 2281.549 rmsd (weighted)= 1.498 (unweighted)= 20.483 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 1.061 rmsd (weighted)= 4.536 (unweighted)= 60.099 superimposing iter= 1 total_weight= 6406.427 rmsd (weighted)= 2.537 (unweighted)= 60.063 superimposing iter= 2 total_weight= 3263.269 rmsd (weighted)= 2.059 (unweighted)= 60.054 superimposing iter= 3 total_weight= 2548.840 rmsd (weighted)= 1.915 (unweighted)= 60.052 superimposing iter= 4 total_weight= 2313.160 rmsd (weighted)= 1.876 (unweighted)= 60.049 superimposing iter= 5 total_weight= 2268.990 rmsd (weighted)= 1.857 (unweighted)= 60.046 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 1.102 rmsd (weighted)= 4.847 (unweighted)= 28.776 superimposing iter= 1 total_weight= 7191.956 rmsd (weighted)= 2.599 (unweighted)= 28.659 superimposing iter= 2 total_weight= 3406.918 rmsd (weighted)= 2.095 (unweighted)= 28.623 superimposing iter= 3 total_weight= 2767.914 rmsd (weighted)= 1.898 (unweighted)= 28.618 superimposing iter= 4 total_weight= 2478.232 rmsd (weighted)= 1.827 (unweighted)= 28.626 superimposing iter= 5 total_weight= 2367.180 rmsd (weighted)= 1.804 (unweighted)= 28.637 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 1.050 rmsd (weighted)= 8.000 (unweighted)= 63.665 superimposing iter= 1 total_weight= 9447.830 rmsd (weighted)= 3.278 (unweighted)= 63.470 superimposing iter= 2 total_weight= 4586.131 rmsd (weighted)= 2.173 (unweighted)= 63.457 superimposing iter= 3 total_weight= 3207.790 rmsd (weighted)= 1.778 (unweighted)= 63.496 superimposing iter= 4 total_weight= 2558.235 rmsd (weighted)= 1.642 (unweighted)= 63.522 superimposing iter= 5 total_weight= 2338.882 rmsd (weighted)= 1.588 (unweighted)= 63.537 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 1.042 rmsd (weighted)= 7.965 (unweighted)= 97.199 superimposing iter= 1 total_weight= 9283.830 rmsd (weighted)= 3.298 (unweighted)= 97.901 superimposing iter= 2 total_weight= 4259.560 rmsd (weighted)= 2.268 (unweighted)= 98.150 superimposing iter= 3 total_weight= 3029.020 rmsd (weighted)= 1.905 (unweighted)= 98.282 superimposing iter= 4 total_weight= 2538.783 rmsd (weighted)= 1.764 (unweighted)= 98.361 superimposing iter= 5 total_weight= 2338.291 rmsd (weighted)= 1.705 (unweighted)= 98.414 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 1.048 rmsd (weighted)= 6.219 (unweighted)= 17.159 superimposing iter= 1 total_weight= 9146.108 rmsd (weighted)= 2.685 (unweighted)= 17.448 superimposing iter= 2 total_weight= 3727.593 rmsd (weighted)= 2.029 (unweighted)= 17.549 superimposing iter= 3 total_weight= 2674.496 rmsd (weighted)= 1.831 (unweighted)= 17.604 superimposing iter= 4 total_weight= 2465.487 rmsd (weighted)= 1.726 (unweighted)= 17.631 superimposing iter= 5 total_weight= 2349.049 rmsd (weighted)= 1.668 (unweighted)= 17.645 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 1.001 rmsd (weighted)= 6.736 (unweighted)= 51.671 superimposing iter= 1 total_weight= 7897.582 rmsd (weighted)= 3.251 (unweighted)= 51.306 superimposing iter= 2 total_weight= 3480.110 rmsd (weighted)= 2.480 (unweighted)= 51.209 superimposing iter= 3 total_weight= 2616.440 rmsd (weighted)= 2.200 (unweighted)= 51.183 superimposing iter= 4 total_weight= 2332.237 rmsd (weighted)= 2.071 (unweighted)= 51.175 superimposing iter= 5 total_weight= 2221.062 rmsd (weighted)= 1.999 (unweighted)= 51.172 superimposing iter= 0 total_weight= 1.117 rmsd (weighted)= 5.588 (unweighted)= 18.194 superimposing iter= 1 total_weight= 9874.297 rmsd (weighted)= 2.497 (unweighted)= 18.310 superimposing iter= 2 total_weight= 4089.789 rmsd (weighted)= 1.863 (unweighted)= 18.337 superimposing iter= 3 total_weight= 2741.940 rmsd (weighted)= 1.711 (unweighted)= 18.342 superimposing iter= 4 total_weight= 2442.967 rmsd (weighted)= 1.667 (unweighted)= 18.342 superimposing iter= 5 total_weight= 2362.936 rmsd (weighted)= 1.651 (unweighted)= 18.341 superimposing iter= 0 total_weight= 1.254 rmsd (weighted)= 8.007 (unweighted)= 25.214 superimposing iter= 1 total_weight= 13294.170 rmsd (weighted)= 3.171 (unweighted)= 25.164 superimposing iter= 2 total_weight= 5567.974 rmsd (weighted)= 2.139 (unweighted)= 25.166 superimposing iter= 3 total_weight= 3289.772 rmsd (weighted)= 1.900 (unweighted)= 25.164 superimposing iter= 4 total_weight= 2795.939 rmsd (weighted)= 1.834 (unweighted)= 25.161 superimposing iter= 5 total_weight= 2666.710 rmsd (weighted)= 1.814 (unweighted)= 25.159 superimposing iter= 0 total_weight= 1.265 rmsd (weighted)= 8.236 (unweighted)= 24.008 superimposing iter= 1 total_weight= 13512.283 rmsd (weighted)= 3.231 (unweighted)= 24.014 superimposing iter= 2 total_weight= 5768.571 rmsd (weighted)= 2.153 (unweighted)= 24.036 superimposing iter= 3 total_weight= 3319.052 rmsd (weighted)= 1.914 (unweighted)= 24.043 superimposing iter= 4 total_weight= 2803.815 rmsd (weighted)= 1.853 (unweighted)= 24.044 superimposing iter= 5 total_weight= 2683.628 rmsd (weighted)= 1.835 (unweighted)= 24.042 superimposing iter= 0 total_weight= 1.082 rmsd (weighted)= 5.043 (unweighted)= 20.721 superimposing iter= 1 total_weight= 9889.273 rmsd (weighted)= 2.178 (unweighted)= 20.529 superimposing iter= 2 total_weight= 4026.821 rmsd (weighted)= 1.620 (unweighted)= 20.504 superimposing iter= 3 total_weight= 2568.341 rmsd (weighted)= 1.521 (unweighted)= 20.498 superimposing iter= 4 total_weight= 2324.525 rmsd (weighted)= 1.502 (unweighted)= 20.496 superimposing iter= 5 total_weight= 2281.984 rmsd (weighted)= 1.497 (unweighted)= 20.495 superimposing iter= 0 total_weight= 1.061 rmsd (weighted)= 4.537 (unweighted)= 60.115 superimposing iter= 1 total_weight= 6409.555 rmsd (weighted)= 2.537 (unweighted)= 60.078 superimposing iter= 2 total_weight= 3263.844 rmsd (weighted)= 2.059 (unweighted)= 60.070 superimposing iter= 3 total_weight= 2548.545 rmsd (weighted)= 1.914 (unweighted)= 60.068 superimposing iter= 4 total_weight= 2312.643 rmsd (weighted)= 1.875 (unweighted)= 60.065 superimposing iter= 5 total_weight= 2269.372 rmsd (weighted)= 1.856 (unweighted)= 60.062 superimposing iter= 0 total_weight= 1.102 rmsd (weighted)= 4.848 (unweighted)= 28.784 superimposing iter= 1 total_weight= 7191.702 rmsd (weighted)= 2.599 (unweighted)= 28.667 superimposing iter= 2 total_weight= 3406.137 rmsd (weighted)= 2.095 (unweighted)= 28.631 superimposing iter= 3 total_weight= 2768.668 rmsd (weighted)= 1.898 (unweighted)= 28.627 superimposing iter= 4 total_weight= 2478.313 rmsd (weighted)= 1.827 (unweighted)= 28.634 superimposing iter= 5 total_weight= 2368.231 rmsd (weighted)= 1.803 (unweighted)= 28.645 superimposing iter= 0 total_weight= 1.050 rmsd (weighted)= 7.999 (unweighted)= 63.661 superimposing iter= 1 total_weight= 9451.145 rmsd (weighted)= 3.277 (unweighted)= 63.464 superimposing iter= 2 total_weight= 4586.205 rmsd (weighted)= 2.172 (unweighted)= 63.452 superimposing iter= 3 total_weight= 3206.112 rmsd (weighted)= 1.778 (unweighted)= 63.491 superimposing iter= 4 total_weight= 2557.812 rmsd (weighted)= 1.642 (unweighted)= 63.517 superimposing iter= 5 total_weight= 2338.827 rmsd (weighted)= 1.588 (unweighted)= 63.532 superimposing iter= 0 total_weight= 1.042 rmsd (weighted)= 7.964 (unweighted)= 97.211 superimposing iter= 1 total_weight= 9286.072 rmsd (weighted)= 3.296 (unweighted)= 97.911 superimposing iter= 2 total_weight= 4259.937 rmsd (weighted)= 2.267 (unweighted)= 98.160 superimposing iter= 3 total_weight= 3027.550 rmsd (weighted)= 1.905 (unweighted)= 98.292 superimposing iter= 4 total_weight= 2538.237 rmsd (weighted)= 1.764 (unweighted)= 98.370 superimposing iter= 5 total_weight= 2338.057 rmsd (weighted)= 1.705 (unweighted)= 98.424 superimposing iter= 0 total_weight= 1.048 rmsd (weighted)= 6.219 (unweighted)= 17.161 superimposing iter= 1 total_weight= 9149.253 rmsd (weighted)= 2.684 (unweighted)= 17.449 superimposing iter= 2 total_weight= 3721.483 rmsd (weighted)= 2.031 (unweighted)= 17.550 superimposing iter= 3 total_weight= 2679.493 rmsd (weighted)= 1.831 (unweighted)= 17.606 superimposing iter= 4 total_weight= 2467.528 rmsd (weighted)= 1.725 (unweighted)= 17.634 superimposing iter= 5 total_weight= 2351.680 rmsd (weighted)= 1.667 (unweighted)= 17.648 superimposing iter= 0 total_weight= 1.001 rmsd (weighted)= 6.736 (unweighted)= 51.678 superimposing iter= 1 total_weight= 7897.793 rmsd (weighted)= 3.250 (unweighted)= 51.313 superimposing iter= 2 total_weight= 3479.105 rmsd (weighted)= 2.480 (unweighted)= 51.216 superimposing iter= 3 total_weight= 2616.555 rmsd (weighted)= 2.200 (unweighted)= 51.190 superimposing iter= 4 total_weight= 2332.701 rmsd (weighted)= 2.071 (unweighted)= 51.182 superimposing iter= 5 total_weight= 2221.875 rmsd (weighted)= 1.998 (unweighted)= 51.179 # command:# Printing sheets for alignments to T0588.undertaker-align.sheets # command: