# command:# Seed set to 1274346319 # 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= 24.114 sec, elapsed time= 27.803 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= 37.096 sec, elapsed time= 44.410 sec. # command:# Prefix for input files set to # command:# Making conformation for sequence T0529 numbered 1 through 569 Created new target T0529 from T0529.a2m # command:# command:# No conformations to remove in PopConform # command:CPU_time= 37.099 sec, elapsed time= 44.425 sec. # command:# Prefix for input files set to # command:# reading script from file T0529.undertaker-align.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 3crvA/T0529-3crvA-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 3crvA expands to /projects/compbio/data/pdb/3crv.pdb.gz 3crvA:# T0529 read from 3crvA/T0529-3crvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3crvA read from 3crvA/T0529-3crvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3crvA to template set # found chain 3crvA in template set T0529 51 :QRLMRKERRDDNDLKRLRDLNQAVNNLV 3crvA 201 :IQMAIKQSKSEESRRILSKLLNQLREVV # choosing archetypes in rotamer library T0529 83 :TQQKSILR 3crvA 229 :LPDEKYIK T0529 91 :VGTLTSDDLLILAADLEKLKSKVIRTERPLS 3crvA 240 :VPKLSKEELEILADDYEDIRKDSLKQGKVNK T0529 133 :QLDQRRALLNMIGM 3crvA 272 :HIGSILRFFSLLSI T0529 158 :DGVVRVWDVK 3crvA 286 :GSFIPFSYSK T0529 207 :LIYTAKYPNTSD 3crvA 296 :RLVIKNPEISYY T0529 229 :LNMIDTKKSSL 3crvA 308 :LNLLNDNELSI T0529 240 :NISGYNFSLGAAVKA 3crvA 320 :LMSGTLPPREYMEKV T0529 260 :DGGNMLET 3crvA 337 :IKRNMLYL T0529 284 :KVKKALG 3crvA 345 :DVEREIQ T0529 299 :ERNP 3crvA 352 :KRVS T0529 314 :G 3crvA 356 :G T0529 345 :QKADSN 3crvA 364 :VDVTSK T0529 362 :TAGLTYSQLMTLKDAMLQLDPNAKTWMDIEGRP 3crvA 370 :YDMRSDNMWKRYADYLLKIYFQAKANVLVVFPS T0529 420 :LKQFKQDAKY 3crvA 406 :MDRVMSRISL T0529 430 :SHGIDVTDLFATQPG 3crvA 421 :SEDSSVEDLYSAISA T0529 454 :PRNMVITCQGS 3crvA 436 :NNKVLIGSVGK T0529 474 :QGRKDIKLIDI 3crvA 458 :NDRSLISDVVI T0529 490 :DSRKYENAVWDQ 3crvA 475 :PPDDYLKILAQR T0529 509 :HTG 3crvA 487 :VSL T0529 519 :RGGKEEITPHCALMDCIMFDAAVSGGLN 3crvA 490 :KMNRENEEFLFKIPALVTIKQAIGRAIR Number of specific fragments extracted= 21 number of extra gaps= 0 total=21 # request to SCWRL produces command: ulimit -t 513 ; scwrl4 -t -i /var/tmp/to_scwrl_177696832.pdb -s /var/tmp/to_scwrl_177696832.seq -o /var/tmp/from_scwrl_177696832.pdb > /var/tmp/scwrl_177696832.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_177696832.pdb Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2pt7A/T0529-2pt7A-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 2pt7A expands to /projects/compbio/data/pdb/2pt7.pdb.gz 2pt7A:# T0529 read from 2pt7A/T0529-2pt7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2pt7A read from 2pt7A/T0529-2pt7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2pt7A to template set # found chain 2pt7A in template set Warning: unaligning (T0529)D60 because first residue in template chain is (2pt7A)L6 T0529 61 :DNDLKRLRDLNQAVNNLV 2pt7A 7 :SAEDKKFLEVERALKEAA T0529 114 :I 2pt7A 25 :L T0529 131 :SQQLDQRRALLNMIGMSGGNQGARAGRDGVVRVWDVKN 2pt7A 26 :NPLRHATEELFGDFLKMENITEICYNGNKVVWVLKNNG T0529 193 :V 2pt7A 64 :E T0529 208 :IYTAKY 2pt7A 65 :WQPFDV T0529 224 :QSHPILN 2pt7A 71 :RDRKAFS T0529 272 :PQTMDGILKSILKVK 2pt7A 78 :LSRLMHFARCCASFK T0529 290 :GMFISDTP 2pt7A 93 :KKTIDNYE T0529 305 :NILYKICLSGD 2pt7A 101 :NPILSSNLANG T0529 322 :SRTSIT 2pt7A 112 :ERVQIV T0529 328 :GRAWENTVVDLE 2pt7A 122 :TVNDETISISIR T0529 345 :QKADSNNSSKSLQSAGFTAGL 2pt7A 134 :IPSKTTYPHSFFEEQGFYNLL T0529 366 :TYSQLMTLKDAMLQ 2pt7A 157 :KEQAISAIKDGIAI T0529 384 :AKTWMDIEG 2pt7A 171 :GKNVIVCGG T0529 394 :PEDP 2pt7A 180 :TGSG T0529 442 :QPGLTSAVIDALPRNM 2pt7A 184 :KTTYIKSIMEFIPKEE T0529 458 :VITCQGSDD 2pt7A 201 :IISIEDTEE T0529 467 :IRKLLESQGRKDIKLIDI 2pt7A 229 :SADCLKSCLRMRPDRIIL T0529 485 :ALSKTDSRKY 2pt7A 248 :ELRSSEAYDF T0529 502 :YKDLCHMHTGVVVEKKKR 2pt7A 258 :YNVLCSGHKGTLTTLHAG T0529 526 :TPHCALMDCIMFD 2pt7A 276 :SSEEAFIRLANMS T0529 541 :VS 2pt7A 289 :SS T0529 543 :GGLNT 2pt7A 295 :RNIKF T0529 548 :SVLRAVLPR 2pt7A 304 :EGFKDLIDM T0529 558 :MVFRTSTPRV 2pt7A 313 :IVHINHHKQC Number of specific fragments extracted= 25 number of extra gaps= 0 total=46 # request to SCWRL produces command: ulimit -t 513 ; scwrl4 -t -i /var/tmp/to_scwrl_1860368611.pdb -s /var/tmp/to_scwrl_1860368611.seq -o /var/tmp/from_scwrl_1860368611.pdb > /var/tmp/scwrl_1860368611.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1860368611.pdb Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3kk1A/T0529-3kk1A-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 3kk1A expands to /projects/compbio/data/pdb/3kk1.pdb.gz 3kk1A:# T0529 read from 3kk1A/T0529-3kk1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3kk1A read from 3kk1A/T0529-3kk1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3kk1A to template set # found chain 3kk1A in template set Warning: unaligning (T0529)L182 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3kk1A)N136 Warning: unaligning (T0529)K189 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3kk1A)N136 Warning: unaligning (T0529)V193 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3kk1A)G141 Warning: unaligning (T0529)D194 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3kk1A)G141 Warning: unaligning (T0529)D295 because of BadResidue code BAD_PEPTIDE in next template residue (3kk1A)K219 Warning: unaligning (T0529)T296 because of BadResidue code BAD_PEPTIDE at template residue (3kk1A)K219 Warning: unaligning (T0529)N301 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3kk1A)P225 Warning: unaligning (T0529)P302 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3kk1A)P225 Warning: unaligning (T0529)P405 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3kk1A)P345 Warning: unaligning (T0529)S406 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3kk1A)P345 T0529 93 :TLTSDDLLILAADLEKLKSK 3kk1A 25 :PLTEEKIKALVEICTEMEKE T0529 116 :TERPLSAGVYMGNLS 3kk1A 64 :KKKDSTKWRKLVDFR T0529 136 :QRRAL 3kk1A 79 :ELNKR T0529 146 :MSGGNQGARAGRDGVVRVWDVK 3kk1A 91 :QLGIPHPAGLKKKKSVTVLDVG T0529 168 :NAELLNNQFGTMPS 3kk1A 121 :DEDFRKYTAFTIPS T0529 190 :QGQ 3kk1A 137 :NET T0529 195 :LNDAVQALTD 3kk1A 156 :SPAIFQSSMT T0529 217 :SDLDRLTQSHP 3kk1A 166 :KILEPFRKQNP T0529 238 :SLNISGY 3kk1A 177 :DIVIYQY T0529 261 :GGNMLETIKVSPQTMDGILKSILKVKKALGMFIS 3kk1A 184 :MDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTP T0529 297 :PGER 3kk1A 220 :KHQK T0529 318 :PYIASR 3kk1A 226 :PFLWMG T0529 336 :VDLESDG 3kk1A 232 :YELHPDK T0529 343 :KPQKADSNNSS 3kk1A 240 :TVQPIVLPEKD T0529 354 :KSLQSAGFTAGLTYSQLMTLKDAMLQL 3kk1A 284 :RGTKALTEVIPLTEEAELELAENREIL T0529 381 :DPNAKTWMDIEGRPEDPVEIALYQ 3kk1A 320 :DPSKDLIAEIQKQGQGQWTYQIYQ T0529 407 :SGC 3kk1A 346 :FKN T0529 410 :YIHFFRE 3kk1A 350 :KTGKYAR T0529 427 :AKYSHGIDVTDLFATQPGLTSAVIDALPRNMVITCQGS 3kk1A 357 :MRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQ T0529 465 :DDIRKLLESQGRK 3kk1A 396 :ETWETWWTEYWQA Number of specific fragments extracted= 20 number of extra gaps= 5 total=66 # request to SCWRL produces command: ulimit -t 513 ; scwrl4 -t -i /var/tmp/to_scwrl_23127877.pdb -s /var/tmp/to_scwrl_23127877.seq -o /var/tmp/from_scwrl_23127877.pdb > /var/tmp/scwrl_23127877.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_23127877.pdb Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3e2qA/T0529-3e2qA-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 3e2qA expands to /projects/compbio/data/pdb/3e2q.pdb.gz 3e2qA:Skipped atom 2112, because occupancy 0.5 <= existing 0.500 in 3e2qA Skipped atom 2116, because occupancy 0.500 <= existing 0.500 in 3e2qA Skipped atom 2118, because occupancy 0.500 <= existing 0.500 in 3e2qA Skipped atom 2120, because occupancy 0.500 <= existing 0.500 in 3e2qA Skipped atom 2122, because occupancy 0.500 <= existing 0.500 in 3e2qA Skipped atom 2124, because occupancy 0.500 <= existing 0.500 in 3e2qA Skipped atom 2126, because occupancy 0.500 <= existing 0.500 in 3e2qA Skipped atom 2128, because occupancy 0.500 <= existing 0.500 in 3e2qA Skipped atom 2556, because occupancy 0.500 <= existing 0.500 in 3e2qA Skipped atom 2560, because occupancy 0.500 <= existing 0.500 in 3e2qA Skipped atom 2562, because occupancy 0.500 <= existing 0.500 in 3e2qA Skipped atom 2564, because occupancy 0.500 <= existing 0.500 in 3e2qA Skipped atom 2566, because occupancy 0.500 <= existing 0.500 in 3e2qA Skipped atom 2723, because occupancy 0.500 <= existing 0.500 in 3e2qA Skipped atom 2725, because occupancy 0.500 <= existing 0.500 in 3e2qA Skipped atom 2727, because occupancy 0.500 <= existing 0.500 in 3e2qA Skipped atom 2729, because occupancy 0.500 <= existing 0.500 in 3e2qA Skipped atom 2731, because occupancy 0.500 <= existing 0.500 in 3e2qA Skipped atom 2733, because occupancy 0.500 <= existing 0.500 in 3e2qA Skipped atom 2735, because occupancy 0.500 <= existing 0.500 in 3e2qA Skipped atom 2737, because occupancy 0.500 <= existing 0.500 in 3e2qA Skipped atom 2739, because occupancy 0.500 <= existing 0.500 in 3e2qA Skipped atom 2741, because occupancy 0.500 <= existing 0.500 in 3e2qA Skipped atom 2743, because occupancy 0.500 <= existing 0.500 in 3e2qA Skipped atom 2745, because occupancy 0.500 <= existing 0.500 in 3e2qA Skipped atom 2747, because occupancy 0.500 <= existing 0.500 in 3e2qA Skipped atom 2749, because occupancy 0.500 <= existing 0.500 in 3e2qA Skipped atom 2751, because occupancy 0.500 <= existing 0.500 in 3e2qA Skipped atom 2753, because occupancy 0.500 <= existing 0.500 in 3e2qA Skipped atom 2755, because occupancy 0.500 <= existing 0.500 in 3e2qA # T0529 read from 3e2qA/T0529-3e2qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3e2qA read from 3e2qA/T0529-3e2qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3e2qA to template set # found chain 3e2qA in template set Warning: unaligning (T0529)K112 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3e2qA)G240 Warning: unaligning (T0529)N168 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3e2qA)G240 T0529 8 :KSFLWTQSLRRELS 3e2qA 102 :PETEAVSMLLEQAR T0529 23 :YCSNIKLQVVKDAQALLHGL 3e2qA 116 :LPQPVAEQAHKLAYQLADKL T0529 43 :DFSEVSNVQRLMRKERRDDNDLKRLRDLNQAVNNL 3e2qA 141 :ASGRAGMVQGLLQEFSLSSQEGVALMCLAEALLRI T0529 95 :TSDD 3e2qA 177 :DKAT T0529 105 :D 3e2qA 181 :R T0529 110 :KS 3e2qA 182 :DA T0529 169 :AELLNNQF 3e2qA 241 :EPLIRKGV T0529 181 :SLTLACLTKQ 3e2qA 249 :DMAMRLMGEQ T0529 191 :GQVDLNDAVQ 3e2qA 261 :TGETIAEALA T0529 201 :ALTDLGLIYTA 3e2qA 274 :KLEEKGFRYSY T0529 212 :KYPNTSDLDRLTQ 3e2qA 290 :AALTAADAQAYMV T0529 247 :SL 3e2qA 303 :SY T0529 276 :DGILKSILKVKKALGMF 3e2qA 305 :QQAIHAIGKASNGRGIY T0529 304 :ENI 3e2qA 322 :EGP T0529 335 :VVDL 3e2qA 325 :GISI T0529 353 :SKSLQSAGF 3e2qA 329 :KLSALHPRY T0529 363 :AGLTYSQ 3e2qA 338 :SRAQYDR T0529 370 :LMTLKDAMLQL 3e2qA 346 :MEELYPRLKSL T0529 385 :KTWMDIEGRP 3e2qA 364 :DIGINIDAEE T0529 436 :TDLFATQPGLTSAVIDA 3e2qA 374 :SDRLEISLDLLEKLCFE T0529 455 :RN 3e2qA 391 :PE T0529 457 :MVITCQG 3e2qA 399 :IGFVIQA T0529 465 :DDIRKLLESQGRK 3e2qA 415 :DYLIDLATRSRRR T0529 479 :IKLIDIAL 3e2qA 428 :LMIRLVKG T0529 494 :YENAVWDQYKDL 3e2qA 437 :YWDSEIKRAQMD T0529 520 :GGKE 3e2qA 449 :GLEG T0529 524 :EITPHCALMDCIMFDAAV 3e2qA 454 :PVYTRKVYTDVSYLACAK Number of specific fragments extracted= 27 number of extra gaps= 0 total=93 # request to SCWRL produces command: ulimit -t 513 ; scwrl4 -t -i /var/tmp/to_scwrl_1466158786.pdb -s /var/tmp/to_scwrl_1466158786.seq -o /var/tmp/from_scwrl_1466158786.pdb > /var/tmp/scwrl_1466158786.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1466158786.pdb Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2nwrA/T0529-2nwrA-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 2nwrA expands to /projects/compbio/data/pdb/2nwr.pdb.gz 2nwrA:# T0529 read from 2nwrA/T0529-2nwrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2nwrA read from 2nwrA/T0529-2nwrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2nwrA to template set # found chain 2nwrA in template set Warning: unaligning (T0529)D419 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2nwrA)G1199 Warning: unaligning (T0529)I433 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2nwrA)G1199 Warning: unaligning (T0529)V512 because last residue in template chain is (2nwrA)I1264 T0529 95 :TSDDLLILAADLEKLKSKVIR 2nwrA 1015 :SEELLLKVGEEIKRLSEKFKE T0529 116 :TERPLSAGVYMGNLSSQQLDQRRALLNMIGMS 2nwrA 1046 :KANRSSIHSFRGHGLEYGVKALRKVKEEFGLK T0529 162 :RVWDVKNAELLNNQFGTMPSLTLACLTK 2nwrA 1078 :ITTDIHESWQAEPVAEVADIIQIPAFLC T0529 191 :GQ 2nwrA 1106 :RQ T0529 196 :NDAVQALTDLGLIYTAKYPNT 2nwrA 1108 :TDLLLAAAKTGRAVNVKKGQF T0529 270 :VSPQTMDGILKSILK 2nwrA 1129 :LAPWDTKNVVEKLKF T0529 289 :LG 2nwrA 1144 :GG T0529 330 :AWENTVVD 2nwrA 1146 :AKEIYLTE T0529 338 :LESDGKPQKAD 2nwrA 1156 :TTFGYNNLVVD T0529 363 :AG 2nwrA 1167 :FR T0529 376 :AMLQLDPNAKTWMDIE 2nwrA 1169 :SLPIMKQWAKVIYDAT T0529 403 :Y 2nwrA 1187 :V T0529 415 :REPT 2nwrA 1188 :QLPG T0529 434 :DVTDLFA 2nwrA 1200 :MREFIFP T0529 445 :LTSAVIDALPR 2nwrA 1207 :LIRAAVAVGCD T0529 457 :MVITCQGSD 2nwrA 1218 :GVFMETHPE T0529 486 :LSKTDSRKYENAVWDQYKDLCHMHTG 2nwrA 1238 :LPLSQLEGIIEAILEIREVASKYYET Number of specific fragments extracted= 17 number of extra gaps= 0 total=110 # request to SCWRL produces command: ulimit -t 513 ; scwrl4 -t -i /var/tmp/to_scwrl_1351065079.pdb -s /var/tmp/to_scwrl_1351065079.seq -o /var/tmp/from_scwrl_1351065079.pdb > /var/tmp/scwrl_1351065079.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1351065079.pdb Number of alignments=5 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pe1A/T0529-1pe1A-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 # T0529 read from 1pe1A/T0529-1pe1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pe1A read from 1pe1A/T0529-1pe1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1pe1A in training set Warning: unaligning (T0529)T418 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1pe1A)G1198 Warning: unaligning (T0529)D419 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1pe1A)G1198 Warning: unaligning (T0529)V512 because last residue in template chain is (1pe1A)I1264 T0529 95 :TSDDLLILAADLEKLKSKVIR 1pe1A 1015 :SEELLLKVGEEIKRLSEKFKE T0529 116 :TERPLSAGVYMGNLSSQQLDQRRALLNMIGMS 1pe1A 1046 :KANRSSIHSFRGHGLEYGVKALRKVKEEFGLK T0529 162 :RVWDVKNAELLNNQFGTMPSLTLACLTKQG 1pe1A 1078 :ITTDIHESWQAEPVAEVADIIQIPAFLCRQ T0529 196 :NDAVQALTDLGLIYTAKYPNT 1pe1A 1108 :TDLLLAAAKTGRAVNVKKGQF T0529 270 :VSPQTMDGILKSILK 1pe1A 1129 :LAPWDTKNVVEKLKF T0529 289 :LG 1pe1A 1144 :GG T0529 293 :ISD 1pe1A 1146 :AKE T0529 319 :YIASR 1pe1A 1150 :YLTER T0529 344 :PQKADS 1pe1A 1155 :GTTFGY T0529 357 :QSAGFTAG 1pe1A 1161 :NNLVVDFR T0529 376 :AMLQLDPNAKTWMDIE 1pe1A 1169 :SLPIMKQWAKVIYDAT T0529 413 :FFREP 1pe1A 1186 :SVQLP T0529 433 :IDVTDLFA 1pe1A 1199 :GMREFIFP T0529 445 :LTSAVIDALP 1pe1A 1207 :LIRAAVAVGC T0529 456 :NMVITCQGSD 1pe1A 1217 :DGVFMETHPE T0529 486 :LSKTDSRKYENAVWDQYKDLCHMHTG 1pe1A 1238 :LPLSQLEGIIEAILEIREVASKYYET Number of specific fragments extracted= 16 number of extra gaps= 1 total=126 # request to SCWRL produces command: ulimit -t 513 ; scwrl4 -t -i /var/tmp/to_scwrl_1087869132.pdb -s /var/tmp/to_scwrl_1087869132.seq -o /var/tmp/from_scwrl_1087869132.pdb > /var/tmp/scwrl_1087869132.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1087869132.pdb Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zhaA/T0529-1zhaA-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 1zhaA expands to /projects/compbio/data/pdb/1zha.pdb.gz 1zhaA:# T0529 read from 1zhaA/T0529-1zhaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zhaA read from 1zhaA/T0529-1zhaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zhaA to template set # found chain 1zhaA in template set Warning: unaligning (T0529)T418 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1zhaA)G1199 Warning: unaligning (T0529)D419 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zhaA)G1199 Warning: unaligning (T0529)V512 because last residue in template chain is (1zhaA)I1264 T0529 95 :TSDDLLILAADLEKLKSKVIR 1zhaA 1015 :SEELLLKVGEEIKRLSEKFKE T0529 116 :TERPLSAGVYMGNLSSQQLDQRRALLNMIGMS 1zhaA 1046 :KANRSSIHSFRGHGLEYGVKALRKVKEEFGLK T0529 162 :RVWDVKNAELLNNQFGTMPSLTLACLT 1zhaA 1078 :ITTDIHESWQAEPVAEVADIIQIPAFL T0529 190 :QGQ 1zhaA 1105 :CGQ T0529 196 :NDAVQALTDLGLIYTAKYPNT 1zhaA 1108 :TDLLLAAAKTGRAVNVKKGQF T0529 270 :VSPQTMDGILKSILK 1zhaA 1129 :LAPWDTKNVVEKLKF T0529 293 :ISD 1zhaA 1146 :AKE T0529 319 :YIASR 1zhaA 1150 :YLTER T0529 333 :N 1zhaA 1155 :G T0529 338 :LESDGK 1zhaA 1156 :TTFGYN T0529 358 :SAGFTAG 1zhaA 1162 :NLVVDFR T0529 376 :AMLQLDPNAKTWMDIE 1zhaA 1169 :SLPIMKQWAKVIYDAT T0529 414 :FREP 1zhaA 1187 :VQLP T0529 434 :DVTDLFA 1zhaA 1200 :MREFIFP T0529 445 :LTSAVIDALP 1zhaA 1207 :LIRAAVAVGC T0529 456 :NMVITCQGSD 1zhaA 1217 :DGVFMETHPE T0529 486 :LSKTDSRKYENAVWDQYKDLCHMHTG 1zhaA 1238 :LPLSQLEGIIEAILEIREVASKYYET Number of specific fragments extracted= 17 number of extra gaps= 1 total=143 # request to SCWRL produces command: ulimit -t 513 ; scwrl4 -t -i /var/tmp/to_scwrl_1460281835.pdb -s /var/tmp/to_scwrl_1460281835.seq -o /var/tmp/from_scwrl_1460281835.pdb > /var/tmp/scwrl_1460281835.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1460281835.pdb Number of alignments=7 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2wadA/T0529-2wadA-t2k-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 2wadA expands to /projects/compbio/data/pdb/2wad.pdb.gz 2wadA:Skipped atom 3305, because occupancy 0.500 <= existing 0.500 in 2wadA Skipped atom 3306, because occupancy 0.500 <= existing 0.500 in 2wadA Skipped atom 3307, because occupancy 0.500 <= existing 0.500 in 2wadA Skipped atom 3308, because occupancy 0.500 <= existing 0.500 in 2wadA Skipped atom 3309, because occupancy 0.500 <= existing 0.500 in 2wadA Skipped atom 3310, because occupancy 0.500 <= existing 0.500 in 2wadA Skipped atom 3311, because occupancy 0.500 <= existing 0.500 in 2wadA Skipped atom 3312, because occupancy 0.500 <= existing 0.500 in 2wadA Skipped atom 3942, because occupancy 0.300 <= existing 0.700 in 2wadA Skipped atom 3943, because occupancy 0.300 <= existing 0.700 in 2wadA Skipped atom 3944, because occupancy 0.300 <= existing 0.700 in 2wadA Skipped atom 3945, because occupancy 0.300 <= existing 0.700 in 2wadA Skipped atom 3946, because occupancy 0.300 <= existing 0.700 in 2wadA Skipped atom 3947, because occupancy 0.300 <= existing 0.700 in 2wadA Skipped atom 3948, because occupancy 0.300 <= existing 0.700 in 2wadA Skipped atom 3949, because occupancy 0.300 <= existing 0.700 in 2wadA Skipped atom 3950, because occupancy 0.300 <= existing 0.700 in 2wadA # T0529 read from 2wadA/T0529-2wadA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2wadA read from 2wadA/T0529-2wadA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2wadA to template set # found chain 2wadA in template set Warning: unaligning (T0529)E117 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2wadA)E149 Warning: unaligning (T0529)L239 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2wadA)D222 Warning: unaligning (T0529)N240 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2wadA)D222 T0529 28 :KLQVVKDAQALLHGLDF 2wadA 90 :ATDLKEIAKKLLTYVSI T0529 81 :KS 2wadA 107 :SS T0529 92 :GTLTSDDLLILA 2wadA 109 :PNLTERQLADYY T0529 105 :DLEKLKSKVIRT 2wadA 123 :DPEIYKKTVEAL T0529 131 :SQQLDQRRA 2wadA 151 :ELYNNAVDS T0529 147 :SGGNQ 2wadA 160 :VPTSQ T0529 153 :AR 2wadA 165 :LN T0529 166 :V 2wadA 167 :Y T0529 168 :NAELLNNQ 2wadA 168 :TEDEKKEI T0529 197 :DAVQALTDLGLIYTAKYP 2wadA 176 :YLFSQLNAVGNFATGTIA T0529 215 :NTSDLDRLTQSHPILNMID 2wadA 198 :NDSQVAVIASISKEMPGIS T0529 241 :ISGYNFSLGAAVK 2wadA 223 :RKILETSLSSIVG T0529 257 :C 2wadA 236 :S T0529 259 :LDGGNM 2wadA 237 :VSSEKA T0529 269 :KVSPQTMDGILKS 2wadA 243 :GLPAEEAESYLKK T0529 294 :SDTPGERNPYENILYKICLSGD 2wadA 258 :SLNDRVGTSYLEKQYEEVLQGK T0529 331 :WENTVVDLESDGKPQKADSNNSSKSLQ 2wadA 280 :RPVKEIHLDKHGDMESVENIEEGSKGK T0529 364 :GLTYSQLMTLKDAMLQ 2wadA 311 :TIDLAFQDSVDALLKS T0529 392 :GRPEDPVEIALYQPSSGCYIHFFR 2wadA 337 :AKYSEGVYAVALNPQTGAVLSMSG T0529 418 :T 2wadA 363 :H T0529 507 :HMHTGVVVEK 2wadA 364 :DLKTGELTPD T0529 523 :EEITPHCALMDCIMFDAAVSGGLNTSVLRAVLPR 2wadA 380 :NVFVPGSVVKAATISSGWENGVLSGNQTLTDQPI T0529 560 :FRTSTPRVV 2wadA 414 :VFQGSAPIY Number of specific fragments extracted= 23 number of extra gaps= 1 total=166 # request to SCWRL produces command: ulimit -t 513 ; scwrl4 -t -i /var/tmp/to_scwrl_1927525551.pdb -s /var/tmp/to_scwrl_1927525551.seq -o /var/tmp/from_scwrl_1927525551.pdb > /var/tmp/scwrl_1927525551.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1927525551.pdb Number of alignments=8 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j7nA/T0529-1j7nA-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 1j7nA expands to /projects/compbio/data/pdb/1j7n.pdb.gz 1j7nA:# T0529 read from 1j7nA/T0529-1j7nA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j7nA read from 1j7nA/T0529-1j7nA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1j7nA to template set # found chain 1j7nA in template set Warning: unaligning (T0529)M146 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1j7nA)L368 Warning: unaligning (T0529)A211 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1j7nA)L368 T0529 12 :WTQSLRR 1j7nA 229 :HRDVLQL T0529 19 :ELSGYCSNIKLQVVKDAQALLHGLDFSEVSNVQRLMRK 1j7nA 239 :EAFNYMDKFNEQEINLSLEELKDQRMLSRYEKWEKIKQ T0529 57 :ERRDDNDLKRLRDLN 1j7nA 283 :DSLSEEGRGLLKKLQ T0529 92 :GTLTSDDLLI 1j7nA 300 :IEPKKDDIIH T0529 110 :KSKVIRTERPLS 1j7nA 316 :KELLKRIQIDSS T0529 127 :GNLSSQQLDQRRALL 1j7nA 328 :DFLSTEEKEFLKKLQ T0529 144 :IG 1j7nA 343 :ID T0529 212 :KYPNTSDLDRLT 1j7nA 369 :SEKEKEFLKKLK T0529 239 :LNIS 1j7nA 381 :LDIQ T0529 245 :NFSLGAAVKAGACMLDGGN 1j7nA 385 :PYDINQRLQDTGGLIDSPS T0529 270 :VSPQTMDGILKSILKVKKALGMFISDTPGERN 1j7nA 404 :INLDVRKQYKRDIQNIDALLHQSIGSTLYNKI T0529 319 :YIASRTSITGRA 1j7nA 436 :YLYENMNINNLT T0529 351 :NSSKSLQSAGFTAGLTYSQLMTLKD 1j7nA 449 :TLGADLVDSTDNTKINRGIFNEFKK T0529 379 :QLDPNAKTWMDIEGRPEDP 1j7nA 492 :PALDNERLKWRIQLSPDTR T0529 398 :VEIAL 1j7nA 525 :IGLEI T0529 403 :YQPSSGCYIHFFREPTDLKQFKQ 1j7nA 535 :IKQSEKEYIRIDAKVVPKSKIDT T0529 437 :DLFATQPGLTSAVIDA 1j7nA 558 :KIQEAQLNINQEWNKA T0529 453 :LPRN 1j7nA 576 :LPKY T0529 457 :MVITCQGS 1j7nA 583 :ITFNVHNR T0529 468 :RKLL 1j7nA 593 :SNIV T0529 493 :KYENAVWDQYKDLCHM 1j7nA 597 :ESAYLILNEWKNNIQS T0529 531 :LMDCIMFDAAVSGGLN 1j7nA 613 :DLIKKVTNYLVDGNGR T0529 547 :TSVLRAVLPRDMVFRTSTPRVV 1j7nA 646 :QDEIYEQVHSKGLYVPESRSIL Number of specific fragments extracted= 23 number of extra gaps= 0 total=189 # request to SCWRL produces command: ulimit -t 513 ; scwrl4 -t -i /var/tmp/to_scwrl_917572072.pdb -s /var/tmp/to_scwrl_917572072.seq -o /var/tmp/from_scwrl_917572072.pdb > /var/tmp/scwrl_917572072.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_917572072.pdb Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vlwA/T0529-1vlwA-t2k-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 1vlwA expands to /projects/compbio/data/pdb/1vlw.pdb.gz 1vlwA:# T0529 read from 1vlwA/T0529-1vlwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vlwA read from 1vlwA/T0529-1vlwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vlwA to template set # found chain 1vlwA in template set Warning: unaligning (T0529)I144 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1vlwA)K11 Warning: unaligning (T0529)G159 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1vlwA)K11 Warning: unaligning (T0529)D194 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1vlwA)T44 Warning: unaligning (T0529)T460 because of BadResidue code BAD_PEPTIDE in next template residue (1vlwA)T156 Warning: unaligning (T0529)C461 because of BadResidue code BAD_PEPTIDE at template residue (1vlwA)T156 T0529 137 :RRALLNM 1vlwA 3 :MEELFKK T0529 160 :VVRVWDVKNAELLNNQF 1vlwA 12 :IVAVLRANSVEEAKEKA T0529 185 :ACLTKQG 1vlwA 29 :LAVFEGG T0529 195 :LNDAVQALTDLG 1vlwA 45 :VPDADTVIKELS T0529 207 :LIYTAKYPNTSDLDR 1vlwA 64 :IIGAGTVTSVEQCRK T0529 251 :AVKAGACML 1vlwA 79 :AVESGAEFI T0529 270 :VSPQTMDGILKSI 1vlwA 88 :VSPHLDEEISQFC T0529 287 :KALGMFI 1vlwA 101 :KEKGVFY T0529 320 :IAS 1vlwA 108 :MPG T0529 365 :LTYSQLMTLKD 1vlwA 112 :MTPTELVKAMK T0529 382 :PNAKTWMDIEG 1vlwA 123 :LGHTILKLFPG T0529 439 :FATQPGLTSAVIDALPRNMVI 1vlwA 134 :EVVGPQFVKAMKGPFPNVKFV T0529 462 :QG 1vlwA 157 :GG T0529 464 :SDDIRKLLES 1vlwA 161 :LDNVCEWFKA T0529 478 :DIKLIDI 1vlwA 171 :GVLAVGV T0529 485 :ALSKTDSRKYENAVWDQYKD 1vlwA 183 :KGTPDEVREKAKAFVEKIRG Number of specific fragments extracted= 16 number of extra gaps= 3 total=205 # request to SCWRL produces command: ulimit -t 513 ; scwrl4 -t -i /var/tmp/to_scwrl_420231705.pdb -s /var/tmp/to_scwrl_420231705.seq -o /var/tmp/from_scwrl_420231705.pdb > /var/tmp/scwrl_420231705.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_420231705.pdb Number of alignments=10 # command:Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 0.745 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 1 total_weight= 21740.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 2 total_weight= 21740.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 3 total_weight= 21740.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 4 total_weight= 21740.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 5 total_weight= 21740.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 0.383 rmsd (weighted)= 17.820 (unweighted)= 60.449 superimposing iter= 1 total_weight= 2821.138 rmsd (weighted)= 10.604 (unweighted)= 60.672 superimposing iter= 2 total_weight= 1695.743 rmsd (weighted)= 8.185 (unweighted)= 60.909 superimposing iter= 3 total_weight= 1600.617 rmsd (weighted)= 6.639 (unweighted)= 61.030 superimposing iter= 4 total_weight= 1364.129 rmsd (weighted)= 5.891 (unweighted)= 61.077 superimposing iter= 5 total_weight= 1240.908 rmsd (weighted)= 5.502 (unweighted)= 61.107 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 0.369 rmsd (weighted)= 23.690 (unweighted)= 89.314 superimposing iter= 1 total_weight= 2578.267 rmsd (weighted)= 14.889 (unweighted)= 88.171 superimposing iter= 2 total_weight= 1324.930 rmsd (weighted)= 13.215 (unweighted)= 87.265 superimposing iter= 3 total_weight= 1152.755 rmsd (weighted)= 12.534 (unweighted)= 86.231 superimposing iter= 4 total_weight= 1197.133 rmsd (weighted)= 11.631 (unweighted)= 85.511 superimposing iter= 5 total_weight= 1234.391 rmsd (weighted)= 10.643 (unweighted)= 85.365 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 0.382 rmsd (weighted)= 21.647 (unweighted)= 75.294 superimposing iter= 1 total_weight= 2401.491 rmsd (weighted)= 14.551 (unweighted)= 75.151 superimposing iter= 2 total_weight= 1302.081 rmsd (weighted)= 13.443 (unweighted)= 74.936 superimposing iter= 3 total_weight= 1168.771 rmsd (weighted)= 13.122 (unweighted)= 74.535 superimposing iter= 4 total_weight= 1139.465 rmsd (weighted)= 12.968 (unweighted)= 73.875 superimposing iter= 5 total_weight= 1131.999 rmsd (weighted)= 12.846 (unweighted)= 72.914 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 0.309 rmsd (weighted)= 21.568 (unweighted)= 70.408 superimposing iter= 1 total_weight= 2445.923 rmsd (weighted)= 12.677 (unweighted)= 70.860 superimposing iter= 2 total_weight= 1237.804 rmsd (weighted)= 10.747 (unweighted)= 71.440 superimposing iter= 3 total_weight= 968.666 rmsd (weighted)= 10.326 (unweighted)= 71.971 superimposing iter= 4 total_weight= 916.233 rmsd (weighted)= 10.207 (unweighted)= 72.493 superimposing iter= 5 total_weight= 903.367 rmsd (weighted)= 10.160 (unweighted)= 73.023 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 0.316 rmsd (weighted)= 21.418 (unweighted)= 66.090 superimposing iter= 1 total_weight= 2512.175 rmsd (weighted)= 12.603 (unweighted)= 67.155 superimposing iter= 2 total_weight= 1272.869 rmsd (weighted)= 10.636 (unweighted)= 68.011 superimposing iter= 3 total_weight= 1011.423 rmsd (weighted)= 10.096 (unweighted)= 68.714 superimposing iter= 4 total_weight= 947.036 rmsd (weighted)= 9.908 (unweighted)= 69.284 superimposing iter= 5 total_weight= 925.975 rmsd (weighted)= 9.833 (unweighted)= 69.780 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 0.296 rmsd (weighted)= 20.482 (unweighted)= 79.636 superimposing iter= 1 total_weight= 1856.109 rmsd (weighted)= 13.474 (unweighted)= 81.510 superimposing iter= 2 total_weight= 1204.915 rmsd (weighted)= 11.253 (unweighted)= 82.578 superimposing iter= 3 total_weight= 1023.965 rmsd (weighted)= 10.251 (unweighted)= 83.249 superimposing iter= 4 total_weight= 963.301 rmsd (weighted)= 9.643 (unweighted)= 83.698 superimposing iter= 5 total_weight= 928.750 rmsd (weighted)= 9.244 (unweighted)= 84.005 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 0.325 rmsd (weighted)= 26.123 (unweighted)= 87.016 superimposing iter= 1 total_weight= 2183.143 rmsd (weighted)= 16.672 (unweighted)= 86.455 superimposing iter= 2 total_weight= 1146.630 rmsd (weighted)= 14.967 (unweighted)= 85.941 superimposing iter= 3 total_weight= 967.319 rmsd (weighted)= 14.668 (unweighted)= 85.428 superimposing iter= 4 total_weight= 946.016 rmsd (weighted)= 14.547 (unweighted)= 84.938 superimposing iter= 5 total_weight= 948.518 rmsd (weighted)= 14.416 (unweighted)= 84.497 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 0.455 rmsd (weighted)= 24.495 (unweighted)= 132.054 superimposing iter= 1 total_weight= 2947.457 rmsd (weighted)= 15.731 (unweighted)= 133.944 superimposing iter= 2 total_weight= 1902.691 rmsd (weighted)= 12.843 (unweighted)= 134.852 superimposing iter= 3 total_weight= 1689.780 rmsd (weighted)= 11.262 (unweighted)= 135.253 superimposing iter= 4 total_weight= 1528.813 rmsd (weighted)= 10.406 (unweighted)= 135.307 superimposing iter= 5 total_weight= 1475.385 rmsd (weighted)= 9.791 (unweighted)= 135.198 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 0.248 rmsd (weighted)= 17.948 (unweighted)= 84.852 superimposing iter= 1 total_weight= 1154.428 rmsd (weighted)= 14.162 (unweighted)= 84.409 superimposing iter= 2 total_weight= 761.211 rmsd (weighted)= 13.791 (unweighted)= 84.050 superimposing iter= 3 total_weight= 745.452 rmsd (weighted)= 13.579 (unweighted)= 83.713 superimposing iter= 4 total_weight= 746.517 rmsd (weighted)= 13.368 (unweighted)= 83.394 superimposing iter= 5 total_weight= 745.301 rmsd (weighted)= 13.177 (unweighted)= 83.116 Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 0.745 rmsd (weighted)= 13.375 (unweighted)= 57.312 superimposing iter= 1 total_weight= 5572.414 rmsd (weighted)= 8.085 (unweighted)= 57.729 superimposing iter= 2 total_weight= 2982.607 rmsd (weighted)= 6.749 (unweighted)= 57.996 superimposing iter= 3 total_weight= 2483.151 rmsd (weighted)= 6.176 (unweighted)= 58.125 superimposing iter= 4 total_weight= 2290.096 rmsd (weighted)= 5.879 (unweighted)= 58.177 superimposing iter= 5 total_weight= 2193.271 rmsd (weighted)= 5.715 (unweighted)= 58.196 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 0.749 rmsd (weighted)= 14.439 (unweighted)= 45.681 superimposing iter= 1 total_weight= 4560.160 rmsd (weighted)= 9.808 (unweighted)= 45.444 superimposing iter= 2 total_weight= 2660.129 rmsd (weighted)= 8.818 (unweighted)= 45.331 superimposing iter= 3 total_weight= 2336.881 rmsd (weighted)= 8.478 (unweighted)= 45.279 superimposing iter= 4 total_weight= 2237.669 rmsd (weighted)= 8.336 (unweighted)= 45.256 superimposing iter= 5 total_weight= 2196.191 rmsd (weighted)= 8.275 (unweighted)= 45.248 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 0.741 rmsd (weighted)= 17.537 (unweighted)= 69.804 superimposing iter= 1 total_weight= 4138.984 rmsd (weighted)= 12.420 (unweighted)= 69.634 superimposing iter= 2 total_weight= 2486.370 rmsd (weighted)= 11.452 (unweighted)= 69.607 superimposing iter= 3 total_weight= 2232.641 rmsd (weighted)= 11.159 (unweighted)= 69.654 superimposing iter= 4 total_weight= 2184.891 rmsd (weighted)= 10.994 (unweighted)= 69.715 superimposing iter= 5 total_weight= 2168.452 rmsd (weighted)= 10.875 (unweighted)= 69.772 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 0.731 rmsd (weighted)= 16.378 (unweighted)= 61.812 superimposing iter= 1 total_weight= 4170.065 rmsd (weighted)= 11.477 (unweighted)= 61.921 superimposing iter= 2 total_weight= 2527.889 rmsd (weighted)= 10.454 (unweighted)= 61.973 superimposing iter= 3 total_weight= 2304.834 rmsd (weighted)= 10.010 (unweighted)= 61.951 superimposing iter= 4 total_weight= 2234.196 rmsd (weighted)= 9.749 (unweighted)= 61.858 superimposing iter= 5 total_weight= 2206.550 rmsd (weighted)= 9.561 (unweighted)= 61.715 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 0.575 rmsd (weighted)= 11.871 (unweighted)= 55.300 superimposing iter= 1 total_weight= 3986.276 rmsd (weighted)= 7.453 (unweighted)= 56.111 superimposing iter= 2 total_weight= 2191.115 rmsd (weighted)= 6.425 (unweighted)= 56.649 superimposing iter= 3 total_weight= 1848.076 rmsd (weighted)= 6.068 (unweighted)= 56.979 superimposing iter= 4 total_weight= 1749.978 rmsd (weighted)= 5.903 (unweighted)= 57.175 superimposing iter= 5 total_weight= 1707.525 rmsd (weighted)= 5.818 (unweighted)= 57.289 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 0.579 rmsd (weighted)= 11.899 (unweighted)= 56.057 superimposing iter= 1 total_weight= 4144.277 rmsd (weighted)= 7.290 (unweighted)= 56.893 superimposing iter= 2 total_weight= 2252.136 rmsd (weighted)= 6.226 (unweighted)= 57.330 superimposing iter= 3 total_weight= 1852.410 rmsd (weighted)= 5.906 (unweighted)= 57.528 superimposing iter= 4 total_weight= 1734.642 rmsd (weighted)= 5.798 (unweighted)= 57.613 superimposing iter= 5 total_weight= 1699.398 rmsd (weighted)= 5.753 (unweighted)= 57.647 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 0.568 rmsd (weighted)= 11.760 (unweighted)= 55.883 superimposing iter= 1 total_weight= 4071.826 rmsd (weighted)= 7.218 (unweighted)= 56.853 superimposing iter= 2 total_weight= 2171.777 rmsd (weighted)= 6.221 (unweighted)= 57.355 superimposing iter= 3 total_weight= 1809.377 rmsd (weighted)= 5.906 (unweighted)= 57.597 superimposing iter= 4 total_weight= 1721.642 rmsd (weighted)= 5.758 (unweighted)= 57.704 superimposing iter= 5 total_weight= 1676.082 rmsd (weighted)= 5.691 (unweighted)= 57.749 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 0.744 rmsd (weighted)= 21.454 (unweighted)= 74.113 superimposing iter= 1 total_weight= 5047.944 rmsd (weighted)= 13.731 (unweighted)= 73.751 superimposing iter= 2 total_weight= 2538.982 rmsd (weighted)= 12.580 (unweighted)= 73.638 superimposing iter= 3 total_weight= 2210.699 rmsd (weighted)= 12.365 (unweighted)= 73.584 superimposing iter= 4 total_weight= 2159.043 rmsd (weighted)= 12.301 (unweighted)= 73.564 superimposing iter= 5 total_weight= 2144.498 rmsd (weighted)= 12.277 (unweighted)= 73.562 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 0.900 rmsd (weighted)= 17.909 (unweighted)= 104.273 superimposing iter= 1 total_weight= 6051.074 rmsd (weighted)= 11.545 (unweighted)= 104.091 superimposing iter= 2 total_weight= 3140.324 rmsd (weighted)= 10.486 (unweighted)= 103.995 superimposing iter= 3 total_weight= 2765.818 rmsd (weighted)= 10.173 (unweighted)= 103.907 superimposing iter= 4 total_weight= 2679.226 rmsd (weighted)= 10.033 (unweighted)= 103.824 superimposing iter= 5 total_weight= 2649.199 rmsd (weighted)= 9.951 (unweighted)= 103.751 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 0.459 rmsd (weighted)= 13.919 (unweighted)= 59.050 superimposing iter= 1 total_weight= 3358.404 rmsd (weighted)= 8.605 (unweighted)= 59.222 superimposing iter= 2 total_weight= 1675.260 rmsd (weighted)= 7.609 (unweighted)= 59.381 superimposing iter= 3 total_weight= 1449.908 rmsd (weighted)= 7.249 (unweighted)= 59.497 superimposing iter= 4 total_weight= 1385.498 rmsd (weighted)= 7.071 (unweighted)= 59.576 superimposing iter= 5 total_weight= 1355.488 rmsd (weighted)= 6.975 (unweighted)= 59.628 Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 0.745 rmsd (weighted)= 13.831 (unweighted)= 57.254 superimposing iter= 1 total_weight= 5367.925 rmsd (weighted)= 8.555 (unweighted)= 57.494 superimposing iter= 2 total_weight= 2850.106 rmsd (weighted)= 7.316 (unweighted)= 57.740 superimposing iter= 3 total_weight= 2402.358 rmsd (weighted)= 6.810 (unweighted)= 57.885 superimposing iter= 4 total_weight= 2239.796 rmsd (weighted)= 6.559 (unweighted)= 57.955 superimposing iter= 5 total_weight= 2161.403 rmsd (weighted)= 6.426 (unweighted)= 57.987 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 0.749 rmsd (weighted)= 13.790 (unweighted)= 45.861 superimposing iter= 1 total_weight= 4364.096 rmsd (weighted)= 9.572 (unweighted)= 45.579 superimposing iter= 2 total_weight= 2624.221 rmsd (weighted)= 8.662 (unweighted)= 45.493 superimposing iter= 3 total_weight= 2302.142 rmsd (weighted)= 8.386 (unweighted)= 45.481 superimposing iter= 4 total_weight= 2217.323 rmsd (weighted)= 8.277 (unweighted)= 45.497 superimposing iter= 5 total_weight= 2192.196 rmsd (weighted)= 8.218 (unweighted)= 45.522 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 0.741 rmsd (weighted)= 16.970 (unweighted)= 68.849 superimposing iter= 1 total_weight= 4399.455 rmsd (weighted)= 11.601 (unweighted)= 68.752 superimposing iter= 2 total_weight= 2640.013 rmsd (weighted)= 10.373 (unweighted)= 68.716 superimposing iter= 3 total_weight= 2340.922 rmsd (weighted)= 9.865 (unweighted)= 68.702 superimposing iter= 4 total_weight= 2257.105 rmsd (weighted)= 9.559 (unweighted)= 68.706 superimposing iter= 5 total_weight= 2193.945 rmsd (weighted)= 9.395 (unweighted)= 68.717 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 0.731 rmsd (weighted)= 16.259 (unweighted)= 63.044 superimposing iter= 1 total_weight= 4679.019 rmsd (weighted)= 10.634 (unweighted)= 63.069 superimposing iter= 2 total_weight= 2680.863 rmsd (weighted)= 9.390 (unweighted)= 62.993 superimposing iter= 3 total_weight= 2331.623 rmsd (weighted)= 8.934 (unweighted)= 62.791 superimposing iter= 4 total_weight= 2333.673 rmsd (weighted)= 8.502 (unweighted)= 62.483 superimposing iter= 5 total_weight= 2319.944 rmsd (weighted)= 8.104 (unweighted)= 62.194 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 0.575 rmsd (weighted)= 11.219 (unweighted)= 55.854 superimposing iter= 1 total_weight= 4098.134 rmsd (weighted)= 6.858 (unweighted)= 56.665 superimposing iter= 2 total_weight= 2252.837 rmsd (weighted)= 5.810 (unweighted)= 57.211 superimposing iter= 3 total_weight= 1878.601 rmsd (weighted)= 5.444 (unweighted)= 57.506 superimposing iter= 4 total_weight= 1757.538 rmsd (weighted)= 5.292 (unweighted)= 57.652 superimposing iter= 5 total_weight= 1701.913 rmsd (weighted)= 5.232 (unweighted)= 57.727 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 0.579 rmsd (weighted)= 11.060 (unweighted)= 56.523 superimposing iter= 1 total_weight= 4208.865 rmsd (weighted)= 6.627 (unweighted)= 57.291 superimposing iter= 2 total_weight= 2399.898 rmsd (weighted)= 5.473 (unweighted)= 57.657 superimposing iter= 3 total_weight= 1870.331 rmsd (weighted)= 5.167 (unweighted)= 57.802 superimposing iter= 4 total_weight= 1721.292 rmsd (weighted)= 5.093 (unweighted)= 57.872 superimposing iter= 5 total_weight= 1688.143 rmsd (weighted)= 5.070 (unweighted)= 57.914 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 0.568 rmsd (weighted)= 11.063 (unweighted)= 56.484 superimposing iter= 1 total_weight= 4263.638 rmsd (weighted)= 6.539 (unweighted)= 57.328 superimposing iter= 2 total_weight= 2305.541 rmsd (weighted)= 5.466 (unweighted)= 57.746 superimposing iter= 3 total_weight= 1797.342 rmsd (weighted)= 5.217 (unweighted)= 57.939 superimposing iter= 4 total_weight= 1685.061 rmsd (weighted)= 5.151 (unweighted)= 58.040 superimposing iter= 5 total_weight= 1659.664 rmsd (weighted)= 5.125 (unweighted)= 58.099 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 0.744 rmsd (weighted)= 21.249 (unweighted)= 73.859 superimposing iter= 1 total_weight= 5250.949 rmsd (weighted)= 13.293 (unweighted)= 73.802 superimposing iter= 2 total_weight= 2551.976 rmsd (weighted)= 12.136 (unweighted)= 73.828 superimposing iter= 3 total_weight= 2220.746 rmsd (weighted)= 11.897 (unweighted)= 73.829 superimposing iter= 4 total_weight= 2168.996 rmsd (weighted)= 11.805 (unweighted)= 73.812 superimposing iter= 5 total_weight= 2155.232 rmsd (weighted)= 11.751 (unweighted)= 73.786 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 0.900 rmsd (weighted)= 17.685 (unweighted)= 103.476 superimposing iter= 1 total_weight= 6208.960 rmsd (weighted)= 11.189 (unweighted)= 103.309 superimposing iter= 2 total_weight= 3261.190 rmsd (weighted)= 9.924 (unweighted)= 103.229 superimposing iter= 3 total_weight= 2792.098 rmsd (weighted)= 9.539 (unweighted)= 103.173 superimposing iter= 4 total_weight= 2668.710 rmsd (weighted)= 9.385 (unweighted)= 103.131 superimposing iter= 5 total_weight= 2625.562 rmsd (weighted)= 9.312 (unweighted)= 103.101 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 0.459 rmsd (weighted)= 13.081 (unweighted)= 58.300 superimposing iter= 1 total_weight= 3368.771 rmsd (weighted)= 8.101 (unweighted)= 58.398 superimposing iter= 2 total_weight= 1541.209 rmsd (weighted)= 7.508 (unweighted)= 58.474 superimposing iter= 3 total_weight= 1385.481 rmsd (weighted)= 7.350 (unweighted)= 58.523 superimposing iter= 4 total_weight= 1366.820 rmsd (weighted)= 7.248 (unweighted)= 58.558 superimposing iter= 5 total_weight= 1352.489 rmsd (weighted)= 7.187 (unweighted)= 58.582 superimposing iter= 0 total_weight= 0.745 rmsd (weighted)= 14.129 (unweighted)= 57.113 superimposing iter= 1 total_weight= 5358.239 rmsd (weighted)= 8.738 (unweighted)= 57.275 superimposing iter= 2 total_weight= 2880.604 rmsd (weighted)= 7.431 (unweighted)= 57.504 superimposing iter= 3 total_weight= 2407.240 rmsd (weighted)= 6.908 (unweighted)= 57.647 superimposing iter= 4 total_weight= 2234.900 rmsd (weighted)= 6.656 (unweighted)= 57.719 superimposing iter= 5 total_weight= 2155.658 rmsd (weighted)= 6.524 (unweighted)= 57.752 superimposing iter= 0 total_weight= 0.749 rmsd (weighted)= 13.502 (unweighted)= 45.901 superimposing iter= 1 total_weight= 4424.568 rmsd (weighted)= 9.295 (unweighted)= 45.592 superimposing iter= 2 total_weight= 2630.462 rmsd (weighted)= 8.397 (unweighted)= 45.469 superimposing iter= 3 total_weight= 2297.604 rmsd (weighted)= 8.136 (unweighted)= 45.418 superimposing iter= 4 total_weight= 2217.202 rmsd (weighted)= 8.030 (unweighted)= 45.392 superimposing iter= 5 total_weight= 2192.596 rmsd (weighted)= 7.972 (unweighted)= 45.375 superimposing iter= 0 total_weight= 0.741 rmsd (weighted)= 16.797 (unweighted)= 68.180 superimposing iter= 1 total_weight= 4734.929 rmsd (weighted)= 10.989 (unweighted)= 68.047 superimposing iter= 2 total_weight= 2818.494 rmsd (weighted)= 9.488 (unweighted)= 68.003 superimposing iter= 3 total_weight= 2328.350 rmsd (weighted)= 9.049 (unweighted)= 68.002 superimposing iter= 4 total_weight= 2177.084 rmsd (weighted)= 8.930 (unweighted)= 68.011 superimposing iter= 5 total_weight= 2139.643 rmsd (weighted)= 8.890 (unweighted)= 68.022 superimposing iter= 0 total_weight= 0.731 rmsd (weighted)= 16.206 (unweighted)= 63.604 superimposing iter= 1 total_weight= 4645.858 rmsd (weighted)= 10.637 (unweighted)= 63.636 superimposing iter= 2 total_weight= 2645.550 rmsd (weighted)= 9.465 (unweighted)= 63.591 superimposing iter= 3 total_weight= 2297.043 rmsd (weighted)= 9.078 (unweighted)= 63.417 superimposing iter= 4 total_weight= 2284.161 rmsd (weighted)= 8.740 (unweighted)= 63.149 superimposing iter= 5 total_weight= 2357.714 rmsd (weighted)= 8.283 (unweighted)= 62.841 superimposing iter= 0 total_weight= 0.575 rmsd (weighted)= 11.173 (unweighted)= 56.553 superimposing iter= 1 total_weight= 4028.222 rmsd (weighted)= 6.889 (unweighted)= 57.340 superimposing iter= 2 total_weight= 2267.710 rmsd (weighted)= 5.810 (unweighted)= 57.868 superimposing iter= 3 total_weight= 1915.069 rmsd (weighted)= 5.390 (unweighted)= 58.156 superimposing iter= 4 total_weight= 1759.517 rmsd (weighted)= 5.235 (unweighted)= 58.311 superimposing iter= 5 total_weight= 1699.484 rmsd (weighted)= 5.177 (unweighted)= 58.404 superimposing iter= 0 total_weight= 0.579 rmsd (weighted)= 10.823 (unweighted)= 57.095 superimposing iter= 1 total_weight= 4138.646 rmsd (weighted)= 6.553 (unweighted)= 57.864 superimposing iter= 2 total_weight= 2374.132 rmsd (weighted)= 5.432 (unweighted)= 58.245 superimposing iter= 3 total_weight= 1891.712 rmsd (weighted)= 5.097 (unweighted)= 58.410 superimposing iter= 4 total_weight= 1733.250 rmsd (weighted)= 5.006 (unweighted)= 58.496 superimposing iter= 5 total_weight= 1690.720 rmsd (weighted)= 4.980 (unweighted)= 58.551 superimposing iter= 0 total_weight= 0.568 rmsd (weighted)= 10.942 (unweighted)= 57.158 superimposing iter= 1 total_weight= 4193.933 rmsd (weighted)= 6.518 (unweighted)= 57.959 superimposing iter= 2 total_weight= 2295.899 rmsd (weighted)= 5.449 (unweighted)= 58.381 superimposing iter= 3 total_weight= 1826.309 rmsd (weighted)= 5.154 (unweighted)= 58.595 superimposing iter= 4 total_weight= 1697.882 rmsd (weighted)= 5.066 (unweighted)= 58.717 superimposing iter= 5 total_weight= 1663.411 rmsd (weighted)= 5.032 (unweighted)= 58.796 superimposing iter= 0 total_weight= 0.744 rmsd (weighted)= 21.109 (unweighted)= 73.667 superimposing iter= 1 total_weight= 5246.276 rmsd (weighted)= 13.147 (unweighted)= 73.778 superimposing iter= 2 total_weight= 2642.782 rmsd (weighted)= 11.777 (unweighted)= 73.887 superimposing iter= 3 total_weight= 2267.946 rmsd (weighted)= 11.420 (unweighted)= 73.959 superimposing iter= 4 total_weight= 2185.896 rmsd (weighted)= 11.286 (unweighted)= 74.000 superimposing iter= 5 total_weight= 2160.791 rmsd (weighted)= 11.219 (unweighted)= 74.020 superimposing iter= 0 total_weight= 0.900 rmsd (weighted)= 17.716 (unweighted)= 103.569 superimposing iter= 1 total_weight= 6181.593 rmsd (weighted)= 11.215 (unweighted)= 103.403 superimposing iter= 2 total_weight= 3350.657 rmsd (weighted)= 9.813 (unweighted)= 103.332 superimposing iter= 3 total_weight= 2819.638 rmsd (weighted)= 9.385 (unweighted)= 103.297 superimposing iter= 4 total_weight= 2674.028 rmsd (weighted)= 9.221 (unweighted)= 103.279 superimposing iter= 5 total_weight= 2625.466 rmsd (weighted)= 9.145 (unweighted)= 103.267 superimposing iter= 0 total_weight= 0.459 rmsd (weighted)= 12.723 (unweighted)= 57.699 superimposing iter= 1 total_weight= 3341.023 rmsd (weighted)= 7.886 (unweighted)= 57.788 superimposing iter= 2 total_weight= 1578.235 rmsd (weighted)= 7.212 (unweighted)= 57.761 superimposing iter= 3 total_weight= 1397.845 rmsd (weighted)= 7.023 (unweighted)= 57.745 superimposing iter= 4 total_weight= 1366.044 rmsd (weighted)= 6.924 (unweighted)= 57.745 superimposing iter= 5 total_weight= 1350.958 rmsd (weighted)= 6.868 (unweighted)= 57.751 # command:# Printing sheets for alignments to T0529.undertaker-align.sheets # command: