# command:# Seed set to 1216897891 # 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 # 493341 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 888 # BAD_PEPTIDE 2680 # 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= 26.906 sec, elapsed time= 27.061 sec. # command:# Prefix for input files set to # command:# Making conformation for sequence T0503 numbered 1 through 191 Created new target T0503 from T0503.a2m # command:# command:# No conformations to remove in PopConform # command:CPU_time= 37.230 sec, elapsed time= 37.397 sec. # command:# Making generic fragment library # fragment library contains # type length num_fragments num_indexes_used # n-terminus 1 1957 20 (100.000%) # n-terminus 2 1932 333 (83.250%) # middle 1 481122 20 (100.000%) # middle 2 474896 400 (100.000%) # middle 3 468898 7988 (99.850%) # middle 4 463038 120397 (75.248%) # c-terminus 1 1914 20 (100.000%) # c-terminus 2 1887 372 (93.000%) # ss-bonds 1042 # command:CPU_time= 46.901 sec, elapsed time= 47.150 sec. # command:# Prefix for input files set to # command:# reading script from file T0503.undertaker-align.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i6xA/T0503-1i6xA-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 1i6xA expands to /projects/compbio/data/pdb/1i6x.pdb.gz 1i6xA:# T0503 read from 1i6xA/T0503-1i6xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i6xA read from 1i6xA/T0503-1i6xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1i6xA to template set # found chain 1i6xA in template set T0503 18 :EDAGTLSAFFQLKKVRKKETLLKTGEICRINYFVVKGCLRLFFIDEKGIEQTTQFAIENWWLSDYMAFQKQQPADFYIQSVENCELLSITYTEQENLFERIPALERYFRLVYQKSFAAAQLRSKFQHMYSKEEQYHNFSSRF 1i6xA 9 :PTLEWFLSHCHIHKYPSKSTLIHQGEKAETLYYIVKGSVAVLIKHEEGKEMILSYLNQGDFIGELGLFEEGQERSAWVRAKTACEVAEISYKKFRQLIQVNPDILMRLSAQMARRLQVTSEKVGNLAFLDVTGRIAQTLLNL # choosing archetypes in rotamer library T0503 160 :PE 1i6xA 160 :PD T0503 162 :FIQRVPQYLLASYLGFTPEYLSEIRKKYIS 1i6xA 163 :MQIKITRQEIGQIVGCSRETVGRILKMLED Number of specific fragments extracted= 3 number of extra gaps= 0 total=3 # request to SCWRL produces command: ulimit -t 172 ; scwrl3 -i /var/tmp/to_scwrl_1479931547.pdb -s /var/tmp/to_scwrl_1479931547.seq -o /var/tmp/from_scwrl_1479931547.pdb > /var/tmp/scwrl_1479931547.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1479931547.pdb Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fmyA/T0503-2fmyA-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 2fmyA expands to /projects/compbio/data/pdb/2fmy.pdb.gz 2fmyA:# T0503 read from 2fmyA/T0503-2fmyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fmyA read from 2fmyA/T0503-2fmyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2fmyA to template set # found chain 2fmyA in template set T0503 10 :RKFIF 2fmyA 19 :EEYSG T0503 23 :LSAFFQLKKVRKKETLLKTGEICRINYFVVKGCLRLFFIDEK 2fmyA 24 :VLKEFREQRYSKKAILYTPNTERNLVFLVKSGRVRVYLAYED T0503 66 :IEQTTQFAIENWWLS 2fmyA 66 :KEFTLAILEAGDIFC T0503 89 :QPADFYIQSVENCELLSITYTEQENLFERIPALE 2fmyA 81 :THTRAFIQAMEDTTILYTDIRNFQNIVVEFPAFS T0503 124 :YFRLVYQKSFAAAQLRSKF 2fmyA 115 :LNMVKVLGDLLKNSLTIIN T0503 143 :QHMYSKEEQYHNFSSRFPEFIQ 2fmyA 135 :LVFKDARLRLAEFLVQAAMDTG T0503 165 :RVPQYLLASYLGFTPEYLSEIRKK 2fmyA 168 :GLNTEEIALMLGTTRQTVSVLLND T0503 189 :YI 2fmyA 196 :GI Number of specific fragments extracted= 8 number of extra gaps= 0 total=11 # request to SCWRL produces command: ulimit -t 172 ; scwrl3 -i /var/tmp/to_scwrl_581850263.pdb -s /var/tmp/to_scwrl_581850263.seq -o /var/tmp/from_scwrl_581850263.pdb > /var/tmp/scwrl_581850263.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_581850263.pdb Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2pqqA/T0503-2pqqA-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 2pqqA expands to /projects/compbio/data/pdb/2pqq.pdb.gz 2pqqA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 264, because occupancy 0.5 <= existing 0.500 in 2pqqA Skipped atom 268, because occupancy 0.500 <= existing 0.500 in 2pqqA Skipped atom 270, because occupancy 0.500 <= existing 0.500 in 2pqqA Skipped atom 272, because occupancy 0.500 <= existing 0.500 in 2pqqA Skipped atom 274, because occupancy 0.500 <= existing 0.500 in 2pqqA Skipped atom 276, because occupancy 0.500 <= existing 0.500 in 2pqqA Skipped atom 278, because occupancy 0.500 <= existing 0.500 in 2pqqA Skipped atom 280, because occupancy 0.500 <= existing 0.500 in 2pqqA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0503 read from 2pqqA/T0503-2pqqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2pqqA read from 2pqqA/T0503-2pqqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2pqqA to template set # found chain 2pqqA in template set T0503 4 :ALINHIRKFIFLTDEDAGTLSAFFQLKKVRKKETLLKTGEICRINYFVVKGCLRLFFIDEKGIEQTTQFAIENWWLSDY 2pqqA 3 :DVLRRNPLFAALDDEQSAELRASMSEVTLARGDTLFHEGDPGDRLYVVTEGKVKLHRTSPDGRENMLAVVGPSELIGEL T0503 84 :AFQKQQPADFYIQSVENCELLSITYTEQENLFERIPALERYFRLVYQKSFAAA 2pqqA 82 :SLFDPGPRTATGTALTEVKLLALGHGDLQPWLNVRPEVATALLRAVARRLRKT Number of specific fragments extracted= 2 number of extra gaps= 0 total=13 # request to SCWRL produces command: ulimit -t 172 ; scwrl3 -i /var/tmp/to_scwrl_156940231.pdb -s /var/tmp/to_scwrl_156940231.seq -o /var/tmp/from_scwrl_156940231.pdb > /var/tmp/scwrl_156940231.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_156940231.pdb Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2h6bA/T0503-2h6bA-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 2h6bA expands to /projects/compbio/data/pdb/2h6b.pdb.gz 2h6bA:Skipped atom 744, because occupancy 0.500 <= existing 0.500 in 2h6bA Skipped atom 746, because occupancy 0.500 <= existing 0.500 in 2h6bA Skipped atom 748, because occupancy 0.500 <= existing 0.500 in 2h6bA Skipped atom 750, because occupancy 0.500 <= existing 0.500 in 2h6bA Skipped atom 1304, because occupancy 0.500 <= existing 0.500 in 2h6bA Skipped atom 1306, because occupancy 0.500 <= existing 0.500 in 2h6bA Skipped atom 1308, because occupancy 0.500 <= existing 0.500 in 2h6bA Skipped atom 1310, because occupancy 0.500 <= existing 0.500 in 2h6bA Skipped atom 1312, because occupancy 0.500 <= existing 0.500 in 2h6bA Skipped atom 1451, because occupancy 0.500 <= existing 0.500 in 2h6bA Skipped atom 1453, because occupancy 0.500 <= existing 0.500 in 2h6bA # T0503 read from 2h6bA/T0503-2h6bA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2h6bA read from 2h6bA/T0503-2h6bA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2h6bA to template set # found chain 2h6bA in template set Warning: unaligning (T0503)Q71 because of BadResidue code BAD_PEPTIDE in next template residue (2h6bA)Y77 Warning: unaligning (T0503)F72 because of BadResidue code BAD_PEPTIDE at template residue (2h6bA)Y77 Warning: unaligning (T0503)Q89 because of BadResidue code BAD_PEPTIDE in next template residue (2h6bA)G91 Warning: unaligning (T0503)P90 because of BadResidue code BAD_PEPTIDE at template residue (2h6bA)G91 T0503 10 :RKFIFL 2h6bA 23 :EKLRNY T0503 25 :AFFQLKKVRKKETLLKTGEICRINYFVVKGCLRLFFIDEKGIEQTT 2h6bA 30 :QMGLIRDFAKGSAVIMPGEEITSMIFLVEGKIKLDIIFEDGSEKLL T0503 73 :AIENWWLSDY 2h6bA 78 :AGGNSLIGKL T0503 87 :KQ 2h6bA 88 :YP T0503 91 :ADFYIQSVENCELLSITYTEQENLFERIPALERYFRLVYQKSFAAAQLRSKFQHMYSKEEQYHNFSSRFPEFIQ 2h6bA 92 :NNIYATAMEPTRTCWFSEKSLRTVFRTDEDMIFEIFKNYLTKVAYYARQVAEMNTYNPTIRILRLFYELCSSQG T0503 165 :RVPQYLLASYLGFTPEYLSEIRKK 2h6bA 177 :PLSQKSIGEITGVHHVTVSRVLAC Number of specific fragments extracted= 6 number of extra gaps= 2 total=19 # request to SCWRL produces command: ulimit -t 172 ; scwrl3 -i /var/tmp/to_scwrl_325757355.pdb -s /var/tmp/to_scwrl_325757355.seq -o /var/tmp/from_scwrl_325757355.pdb > /var/tmp/scwrl_325757355.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_325757355.pdb Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2zcwA/T0503-2zcwA-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 2zcwA expands to /projects/compbio/data/pdb/2zcw.pdb.gz 2zcwA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0503 read from 2zcwA/T0503-2zcwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2zcwA read from 2zcwA/T0503-2zcwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2zcwA to template set # found chain 2zcwA in template set Warning: unaligning (T0503)Q28 because first residue in template chain is (2zcwA)E5 T0503 29 :LKKVRKKETLLKTGEICR 2zcwA 6 :TVSFKAGDVILYPGVPGP T0503 47 :INYFVVKGCLRLFFIDEKGIEQTTQFAIENWWLSDY 2zcwA 26 :RAYRVLEGLVRLEAVDEEGNALTLRLVRPGGFFGEE T0503 84 :A 2zcwA 62 :A T0503 86 :QKQQPADFYIQSVENCELLSIT 2zcwA 63 :LFGQERIYFAEAATDVRLEPLP T0503 119 :PALERYFRLVYQKSFAAAQLRSKFQHMYSKEEQYHNFSSRFPEFIQ 2zcwA 89 :PELLKDLAQHLSQGLAEAYRRIERLATQRLKNRMAAALLELSETPL T0503 165 :RVPQYLLASYLGFTPEYLSEIRKK 2zcwA 145 :KATHDELAAAVGSVRETVTKVIGE T0503 189 :Y 2zcwA 173 :G Number of specific fragments extracted= 7 number of extra gaps= 0 total=26 # request to SCWRL produces command: ulimit -t 172 ; scwrl3 -i /var/tmp/to_scwrl_1264905884.pdb -s /var/tmp/to_scwrl_1264905884.seq -o /var/tmp/from_scwrl_1264905884.pdb > /var/tmp/scwrl_1264905884.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1264905884.pdb Number of alignments=5 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2z69A/T0503-2z69A-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 2z69A expands to /projects/compbio/data/pdb/2z69.pdb.gz 2z69A:# T0503 read from 2z69A/T0503-2z69A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2z69A read from 2z69A/T0503-2z69A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2z69A to template set # found chain 2z69A in template set Warning: unaligning (T0503)R57 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2z69A)I63 Warning: unaligning (T0503)L58 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2z69A)I63 Warning: unaligning (T0503)E63 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2z69A)I74 Warning: unaligning (T0503)T69 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2z69A)I74 Warning: unaligning (T0503)Q71 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2z69A)V77 Warning: unaligning (T0503)F72 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2z69A)V77 Warning: unaligning (T0503)V98 because of BadResidue code BAD_PEPTIDE in next template residue (2z69A)V104 Warning: unaligning (T0503)E99 because of BadResidue code BAD_PEPTIDE at template residue (2z69A)V104 Warning: unaligning (T0503)L103 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2z69A)F109 Warning: unaligning (T0503)L104 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2z69A)F109 T0503 8 :HIRKFIFLTDEDAGTLSAFFQLKKVRKKETLLKTGEICRINYFVVKGCL 2z69A 13 :SHHLFEPLSPVQLQELLASSDLVNLDKGAYVFRQGEPAHAFYYLISGCV T0503 59 :FFID 2z69A 64 :YRLT T0503 70 :T 2z69A 75 :L T0503 73 :AIENWWLSDYMAFQKQQPADFYIQS 2z69A 78 :TNERNTFAEAMMFMDTPNYVATAQA T0503 100 :NCE 2z69A 105 :PSQ T0503 105 :SITYTEQENLFERIPALERYFRLVYQKS 2z69A 110 :RFSNKAYLRQLQDNTPLALALLAKLSTR Number of specific fragments extracted= 6 number of extra gaps= 4 total=32 # request to SCWRL produces command: ulimit -t 172 ; scwrl3 -i /var/tmp/to_scwrl_668546330.pdb -s /var/tmp/to_scwrl_668546330.seq -o /var/tmp/from_scwrl_668546330.pdb > /var/tmp/scwrl_668546330.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_668546330.pdb Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o5lA/T0503-1o5lA-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 1o5lA expands to /projects/compbio/data/pdb/1o5l.pdb.gz 1o5lA:# T0503 read from 1o5lA/T0503-1o5lA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o5lA read from 1o5lA/T0503-1o5lA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1o5lA to template set # found chain 1o5lA in template set Warning: unaligning (T0503)E75 because of BadResidue code BAD_PEPTIDE in next template residue (1o5lA)V59 Warning: unaligning (T0503)N76 because of BadResidue code BAD_PEPTIDE at template residue (1o5lA)V59 Warning: unaligning (T0503)K87 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o5lA)S70 Warning: unaligning (T0503)Q88 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o5lA)S70 Warning: unaligning (T0503)F93 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1o5lA)N77 Warning: unaligning (T0503)Y94 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1o5lA)N77 Warning: unaligning (T0503)M145 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o5lA)K129 Warning: unaligning (T0503)Y146 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o5lA)K129 T0503 23 :LSAFFQLKKVRKKETLLKTGEICRINYFVVKGCLRLFFIDEKGIEQTTQFAI 1o5lA 6 :LLPCGKVIVFRKGEIVKHQDDPIEDVLILLEGTLKTEHVSENGKTLEIDEIK T0503 77 :WWLSDY 1o5lA 60 :QIIASG T0503 84 :AFQ 1o5lA 66 :FIF T0503 89 :QPA 1o5lA 71 :EPR T0503 92 :D 1o5lA 75 :P T0503 95 :IQSVENCELLSITYTEQENLFERIPALERYFRLVYQKSFAAAQLRSKFQH 1o5lA 78 :VVAGENSKILSIPKEVFLDLLMKDRELLLFFLKDVSEHFRVVSEKLFFLT Number of specific fragments extracted= 6 number of extra gaps= 4 total=38 # request to SCWRL produces command: ulimit -t 172 ; scwrl3 -i /var/tmp/to_scwrl_2081840369.pdb -s /var/tmp/to_scwrl_2081840369.seq -o /var/tmp/from_scwrl_2081840369.pdb > /var/tmp/scwrl_2081840369.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2081840369.pdb Number of alignments=7 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3bpzA/T0503-3bpzA-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 3bpzA expands to /projects/compbio/data/pdb/3bpz.pdb.gz 3bpzA:Skipped atom 241, because occupancy 0.300 <= existing 0.700 in 3bpzA Skipped atom 245, because occupancy 0.300 <= existing 0.700 in 3bpzA Skipped atom 247, because occupancy 0.300 <= existing 0.700 in 3bpzA Skipped atom 249, because occupancy 0.300 <= existing 0.700 in 3bpzA Skipped atom 251, because occupancy 0.300 <= existing 0.700 in 3bpzA Skipped atom 254, because occupancy 0.500 <= existing 0.500 in 3bpzA Skipped atom 258, because occupancy 0.500 <= existing 0.500 in 3bpzA Skipped atom 260, because occupancy 0.500 <= existing 0.500 in 3bpzA Skipped atom 262, because occupancy 0.500 <= existing 0.500 in 3bpzA Skipped atom 264, because occupancy 0.500 <= existing 0.500 in 3bpzA Skipped atom 266, because occupancy 0.500 <= existing 0.500 in 3bpzA Skipped atom 268, because occupancy 0.500 <= existing 0.500 in 3bpzA Skipped atom 1053, because occupancy 0.300 <= existing 0.700 in 3bpzA Skipped atom 1057, because occupancy 0.300 <= existing 0.700 in 3bpzA Skipped atom 1059, because occupancy 0.300 <= existing 0.700 in 3bpzA Skipped atom 1508, because occupancy 0.500 <= existing 0.500 in 3bpzA Skipped atom 1512, because occupancy 0.500 <= existing 0.500 in 3bpzA Skipped atom 1514, because occupancy 0.500 <= existing 0.500 in 3bpzA Skipped atom 1516, because occupancy 0.500 <= existing 0.500 in 3bpzA Skipped atom 1518, because occupancy 0.500 <= existing 0.500 in 3bpzA # T0503 read from 3bpzA/T0503-3bpzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3bpzA read from 3bpzA/T0503-3bpzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3bpzA to template set # found chain 3bpzA in template set T0503 3 :TALINHIRKFIFLTDEDAGTLSAFFQLKKVRKKETLLKTGEICRINYFVVKGCLRL 3bpzA 509 :RKLVASMPLFANADPNFVTAMLTKLKFEVFQPGDYIIREGTIGKKMYFIQHGVVSV T0503 61 :IDEKGIEQTTQ 3bpzA 565 :LTKGNKEMKLS T0503 75 :ENWWLSDY 3bpzA 576 :DGSYFGEI T0503 84 :AFQKQQPADFYIQSVENCELLSITYTEQENLFERIPALERYFRLVYQKSFAA 3bpzA 584 :CLLTRGRRTASVRADTYCRLYSLSVDNFNEVLEEYPMMRRAFETVAIDRLDR Number of specific fragments extracted= 4 number of extra gaps= 0 total=42 # request to SCWRL produces command: ulimit -t 172 ; scwrl3 -i /var/tmp/to_scwrl_1976954410.pdb -s /var/tmp/to_scwrl_1976954410.seq -o /var/tmp/from_scwrl_1976954410.pdb > /var/tmp/scwrl_1976954410.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1976954410.pdb Number of alignments=8 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cx4A/T0503-1cx4A-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 1cx4A expands to /projects/compbio/data/pdb/1cx4.pdb.gz 1cx4A:# T0503 read from 1cx4A/T0503-1cx4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cx4A read from 1cx4A/T0503-1cx4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1cx4A to template set # found chain 1cx4A in template set T0503 2 :HTALINHIRKFIFLTDEDAGTLSAFFQLKKVRKKETLLKTGEICRINYFVVKGCLRLFFIDEK 1cx4A 143 :LQEACKDILLFKNLDPEQMSQVLDAMFEKLVKEGEHVIDQGDDGDNFYVIDRGTFDIYVKCDG T0503 66 :IEQTTQFAIENWWLSDY 1cx4A 206 :VGRCVGNYDNRGSFGEL T0503 84 :AFQKQQPADFYIQSVENCELLSITYTEQENL 1cx4A 223 :ALMYNTPRAATITATSPGALWGLDRVTFRRI T0503 125 :FRLVYQKSFAAAQLRSKF 1cx4A 254 :IVKNNAKKRKMYESFIES T0503 143 :QHMYSKEEQYHNF 1cx4A 275 :LKSLEVSERLKVV Number of specific fragments extracted= 5 number of extra gaps= 0 total=47 # request to SCWRL produces command: ulimit -t 172 ; scwrl3 -i /var/tmp/to_scwrl_52573834.pdb -s /var/tmp/to_scwrl_52573834.seq -o /var/tmp/from_scwrl_52573834.pdb > /var/tmp/scwrl_52573834.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_52573834.pdb Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2oz6A/T0503-2oz6A-t04-global-adpstyle1.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2oz6A expands to /projects/compbio/data/pdb/2oz6.pdb.gz 2oz6A:# T0503 read from 2oz6A/T0503-2oz6A-t04-global-adpstyle1.a2m # 2oz6A read from 2oz6A/T0503-2oz6A-t04-global-adpstyle1.a2m # adding 2oz6A to template set # found chain 2oz6A in template set Warning: unaligning (T0503)L15 because first residue in template chain is (2oz6A)M8 Warning: unaligning (T0503)K87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2oz6A)Q85 Warning: unaligning (T0503)Q89 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2oz6A)Q85 Warning: unaligning (T0503)I190 because last residue in template chain is (2oz6A)T213 T0503 16 :TDEDAGTLSAFFQLKKVRKKETLLKTGEICRINYFVVKGCLRLFFIDEKGIEQTTQFAIENWWLSDY 2oz6A 9 :KLKHLDKLLAHCHRRRYTAKSTIIYAGDRCETLFFIIKGSVTILIEDDDGREMIIGYLNSGDFFGEL T0503 84 :AFQ 2oz6A 76 :GLF T0503 90 :PADFYIQSVENCELLSITYTEQENLFERIPALERYFRLVYQKSFAAAQLRSKFQHMYSKEEQYHNFSSRFPEFIQ 2oz6A 86 :ERSAWVRAKVECEVAEISYAKFRELSQQDSEILYTLGSQMADRLRKTTRKVGDLAFLDVTGRVARTLLDLCQQPD T0503 165 :RVPQYLLASYLGFTPEYLSEIRKK 2oz6A 171 :KITRQEIGRIVGCSREMVGRVLKS T0503 189 :Y 2oz6A 212 :G Number of specific fragments extracted= 5 number of extra gaps= 0 total=52 # request to SCWRL produces command: ulimit -t 172 ; scwrl3 -i /var/tmp/to_scwrl_203211393.pdb -s /var/tmp/to_scwrl_203211393.seq -o /var/tmp/from_scwrl_203211393.pdb > /var/tmp/scwrl_203211393.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_203211393.pdb Number of alignments=10 # command:Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.339 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 1 total_weight= 14790.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 2 total_weight= 14790.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 3 total_weight= 14790.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 4 total_weight= 14790.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 5 total_weight= 14790.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 1.223 rmsd (weighted)= 10.503 (unweighted)= 29.063 superimposing iter= 1 total_weight= 4882.569 rmsd (weighted)= 4.628 (unweighted)= 30.077 superimposing iter= 2 total_weight= 3277.360 rmsd (weighted)= 2.643 (unweighted)= 30.832 superimposing iter= 3 total_weight= 2919.048 rmsd (weighted)= 1.696 (unweighted)= 31.105 superimposing iter= 4 total_weight= 2348.367 rmsd (weighted)= 1.242 (unweighted)= 31.168 superimposing iter= 5 total_weight= 2005.177 rmsd (weighted)= 0.994 (unweighted)= 31.170 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 0.899 rmsd (weighted)= 4.363 (unweighted)= 47.893 superimposing iter= 1 total_weight= 2731.244 rmsd (weighted)= 2.458 (unweighted)= 47.577 superimposing iter= 2 total_weight= 1500.958 rmsd (weighted)= 1.878 (unweighted)= 47.256 superimposing iter= 3 total_weight= 1498.029 rmsd (weighted)= 1.445 (unweighted)= 46.987 superimposing iter= 4 total_weight= 1527.371 rmsd (weighted)= 1.115 (unweighted)= 46.797 superimposing iter= 5 total_weight= 1367.162 rmsd (weighted)= 0.928 (unweighted)= 46.683 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 1.208 rmsd (weighted)= 14.694 (unweighted)= 51.552 superimposing iter= 1 total_weight= 4402.748 rmsd (weighted)= 7.406 (unweighted)= 50.619 superimposing iter= 2 total_weight= 2379.921 rmsd (weighted)= 5.205 (unweighted)= 49.928 superimposing iter= 3 total_weight= 1946.866 rmsd (weighted)= 4.048 (unweighted)= 49.324 superimposing iter= 4 total_weight= 1778.378 rmsd (weighted)= 3.243 (unweighted)= 48.698 superimposing iter= 5 total_weight= 1755.851 rmsd (weighted)= 2.600 (unweighted)= 48.260 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 1.142 rmsd (weighted)= 3.558 (unweighted)= 22.648 superimposing iter= 1 total_weight= 5952.751 rmsd (weighted)= 1.483 (unweighted)= 22.632 superimposing iter= 2 total_weight= 2387.970 rmsd (weighted)= 1.053 (unweighted)= 22.592 superimposing iter= 3 total_weight= 1648.655 rmsd (weighted)= 0.908 (unweighted)= 22.565 superimposing iter= 4 total_weight= 1455.814 rmsd (weighted)= 0.835 (unweighted)= 22.551 superimposing iter= 5 total_weight= 1367.545 rmsd (weighted)= 0.794 (unweighted)= 22.545 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 0.766 rmsd (weighted)= 3.843 (unweighted)= 29.325 superimposing iter= 1 total_weight= 2423.234 rmsd (weighted)= 2.052 (unweighted)= 29.327 superimposing iter= 2 total_weight= 1469.956 rmsd (weighted)= 1.491 (unweighted)= 29.343 superimposing iter= 3 total_weight= 1121.128 rmsd (weighted)= 1.259 (unweighted)= 29.389 superimposing iter= 4 total_weight= 1007.268 rmsd (weighted)= 1.136 (unweighted)= 29.435 superimposing iter= 5 total_weight= 923.235 rmsd (weighted)= 1.077 (unweighted)= 29.471 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 0.881 rmsd (weighted)= 2.856 (unweighted)= 31.864 superimposing iter= 1 total_weight= 2966.072 rmsd (weighted)= 1.531 (unweighted)= 31.806 superimposing iter= 2 total_weight= 1553.640 rmsd (weighted)= 1.167 (unweighted)= 31.776 superimposing iter= 3 total_weight= 1237.584 rmsd (weighted)= 1.011 (unweighted)= 31.726 superimposing iter= 4 total_weight= 1133.193 rmsd (weighted)= 0.920 (unweighted)= 31.665 superimposing iter= 5 total_weight= 1145.838 rmsd (weighted)= 0.832 (unweighted)= 31.613 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 0.853 rmsd (weighted)= 3.951 (unweighted)= 45.005 superimposing iter= 1 total_weight= 3904.179 rmsd (weighted)= 1.755 (unweighted)= 44.912 superimposing iter= 2 total_weight= 1745.984 rmsd (weighted)= 1.242 (unweighted)= 44.789 superimposing iter= 3 total_weight= 1263.856 rmsd (weighted)= 1.046 (unweighted)= 44.690 superimposing iter= 4 total_weight= 1121.583 rmsd (weighted)= 0.941 (unweighted)= 44.601 superimposing iter= 5 total_weight= 1084.165 rmsd (weighted)= 0.862 (unweighted)= 44.524 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 0.969 rmsd (weighted)= 8.437 (unweighted)= 71.963 superimposing iter= 1 total_weight= 2972.866 rmsd (weighted)= 4.646 (unweighted)= 71.061 superimposing iter= 2 total_weight= 1779.294 rmsd (weighted)= 3.295 (unweighted)= 70.111 superimposing iter= 3 total_weight= 1727.972 rmsd (weighted)= 2.354 (unweighted)= 69.295 superimposing iter= 4 total_weight= 1859.848 rmsd (weighted)= 1.634 (unweighted)= 68.800 superimposing iter= 5 total_weight= 1818.016 rmsd (weighted)= 1.187 (unweighted)= 68.583 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 1.294 rmsd (weighted)= 2.882 (unweighted)= 29.807 superimposing iter= 1 total_weight= 9972.894 rmsd (weighted)= 0.822 (unweighted)= 29.860 superimposing iter= 2 total_weight= 3852.841 rmsd (weighted)= 0.489 (unweighted)= 29.861 superimposing iter= 3 total_weight= 1820.926 rmsd (weighted)= 0.430 (unweighted)= 29.862 superimposing iter= 4 total_weight= 1507.127 rmsd (weighted)= 0.417 (unweighted)= 29.862 superimposing iter= 5 total_weight= 1441.554 rmsd (weighted)= 0.413 (unweighted)= 29.862 Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.339 rmsd (weighted)= 4.638 (unweighted)= 23.907 superimposing iter= 1 total_weight= 5371.556 rmsd (weighted)= 2.249 (unweighted)= 23.844 superimposing iter= 2 total_weight= 2248.227 rmsd (weighted)= 1.759 (unweighted)= 23.824 superimposing iter= 3 total_weight= 1832.349 rmsd (weighted)= 1.537 (unweighted)= 23.820 superimposing iter= 4 total_weight= 1852.046 rmsd (weighted)= 1.341 (unweighted)= 23.827 superimposing iter= 5 total_weight= 1871.836 rmsd (weighted)= 1.164 (unweighted)= 23.840 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 1.266 rmsd (weighted)= 8.511 (unweighted)= 26.685 superimposing iter= 1 total_weight= 5444.724 rmsd (weighted)= 3.612 (unweighted)= 26.745 superimposing iter= 2 total_weight= 4114.771 rmsd (weighted)= 1.952 (unweighted)= 26.752 superimposing iter= 3 total_weight= 2700.981 rmsd (weighted)= 1.359 (unweighted)= 26.755 superimposing iter= 4 total_weight= 2025.638 rmsd (weighted)= 1.110 (unweighted)= 26.759 superimposing iter= 5 total_weight= 1735.629 rmsd (weighted)= 0.982 (unweighted)= 26.768 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 1.007 rmsd (weighted)= 3.358 (unweighted)= 41.855 superimposing iter= 1 total_weight= 3257.128 rmsd (weighted)= 1.740 (unweighted)= 41.380 superimposing iter= 2 total_weight= 2109.776 rmsd (weighted)= 1.163 (unweighted)= 41.126 superimposing iter= 3 total_weight= 1903.716 rmsd (weighted)= 0.855 (unweighted)= 41.002 superimposing iter= 4 total_weight= 1546.335 rmsd (weighted)= 0.711 (unweighted)= 40.929 superimposing iter= 5 total_weight= 1336.363 rmsd (weighted)= 0.640 (unweighted)= 40.883 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 1.258 rmsd (weighted)= 11.236 (unweighted)= 38.215 superimposing iter= 1 total_weight= 4635.489 rmsd (weighted)= 5.515 (unweighted)= 37.811 superimposing iter= 2 total_weight= 2638.405 rmsd (weighted)= 3.679 (unweighted)= 37.661 superimposing iter= 3 total_weight= 2103.338 rmsd (weighted)= 2.737 (unweighted)= 37.664 superimposing iter= 4 total_weight= 1934.762 rmsd (weighted)= 2.144 (unweighted)= 37.760 superimposing iter= 5 total_weight= 2005.425 rmsd (weighted)= 1.720 (unweighted)= 37.836 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 1.142 rmsd (weighted)= 4.963 (unweighted)= 16.445 superimposing iter= 1 total_weight= 3689.642 rmsd (weighted)= 2.745 (unweighted)= 16.507 superimposing iter= 2 total_weight= 1851.554 rmsd (weighted)= 2.220 (unweighted)= 16.522 superimposing iter= 3 total_weight= 1459.002 rmsd (weighted)= 2.041 (unweighted)= 16.519 superimposing iter= 4 total_weight= 1335.787 rmsd (weighted)= 1.966 (unweighted)= 16.511 superimposing iter= 5 total_weight= 1309.861 rmsd (weighted)= 1.914 (unweighted)= 16.502 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 0.847 rmsd (weighted)= 2.782 (unweighted)= 24.306 superimposing iter= 1 total_weight= 2300.462 rmsd (weighted)= 1.674 (unweighted)= 24.323 superimposing iter= 2 total_weight= 1418.884 rmsd (weighted)= 1.322 (unweighted)= 24.301 superimposing iter= 3 total_weight= 1189.494 rmsd (weighted)= 1.152 (unweighted)= 24.288 superimposing iter= 4 total_weight= 1081.990 rmsd (weighted)= 1.058 (unweighted)= 24.286 superimposing iter= 5 total_weight= 1013.448 rmsd (weighted)= 1.007 (unweighted)= 24.284 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 0.881 rmsd (weighted)= 1.881 (unweighted)= 31.207 superimposing iter= 1 total_weight= 2938.314 rmsd (weighted)= 1.026 (unweighted)= 30.990 superimposing iter= 2 total_weight= 1406.623 rmsd (weighted)= 0.840 (unweighted)= 30.893 superimposing iter= 3 total_weight= 1114.080 rmsd (weighted)= 0.776 (unweighted)= 30.832 superimposing iter= 4 total_weight= 1030.222 rmsd (weighted)= 0.747 (unweighted)= 30.792 superimposing iter= 5 total_weight= 998.436 rmsd (weighted)= 0.730 (unweighted)= 30.765 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 0.968 rmsd (weighted)= 3.169 (unweighted)= 40.072 superimposing iter= 1 total_weight= 5236.842 rmsd (weighted)= 1.291 (unweighted)= 40.154 superimposing iter= 2 total_weight= 1977.391 rmsd (weighted)= 0.929 (unweighted)= 40.170 superimposing iter= 3 total_weight= 1313.127 rmsd (weighted)= 0.828 (unweighted)= 40.182 superimposing iter= 4 total_weight= 1151.984 rmsd (weighted)= 0.790 (unweighted)= 40.191 superimposing iter= 5 total_weight= 1094.277 rmsd (weighted)= 0.775 (unweighted)= 40.196 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 1.092 rmsd (weighted)= 6.629 (unweighted)= 70.265 superimposing iter= 1 total_weight= 3639.488 rmsd (weighted)= 3.339 (unweighted)= 69.120 superimposing iter= 2 total_weight= 2525.445 rmsd (weighted)= 2.045 (unweighted)= 68.295 superimposing iter= 3 total_weight= 2204.163 rmsd (weighted)= 1.390 (unweighted)= 67.787 superimposing iter= 4 total_weight= 1904.579 rmsd (weighted)= 1.063 (unweighted)= 67.546 superimposing iter= 5 total_weight= 1528.638 rmsd (weighted)= 0.926 (unweighted)= 67.432 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 1.308 rmsd (weighted)= 4.567 (unweighted)= 15.653 superimposing iter= 1 total_weight= 4787.582 rmsd (weighted)= 2.323 (unweighted)= 15.692 superimposing iter= 2 total_weight= 2325.154 rmsd (weighted)= 1.747 (unweighted)= 15.809 superimposing iter= 3 total_weight= 1908.330 rmsd (weighted)= 1.473 (unweighted)= 15.931 superimposing iter= 4 total_weight= 1746.642 rmsd (weighted)= 1.316 (unweighted)= 16.024 superimposing iter= 5 total_weight= 1612.812 rmsd (weighted)= 1.231 (unweighted)= 16.083 Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.339 rmsd (weighted)= 4.731 (unweighted)= 23.997 superimposing iter= 1 total_weight= 5102.948 rmsd (weighted)= 2.363 (unweighted)= 23.930 superimposing iter= 2 total_weight= 2201.534 rmsd (weighted)= 1.871 (unweighted)= 23.903 superimposing iter= 3 total_weight= 1736.856 rmsd (weighted)= 1.687 (unweighted)= 23.895 superimposing iter= 4 total_weight= 1738.277 rmsd (weighted)= 1.524 (unweighted)= 23.903 superimposing iter= 5 total_weight= 1803.000 rmsd (weighted)= 1.350 (unweighted)= 23.926 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 1.266 rmsd (weighted)= 8.526 (unweighted)= 26.769 superimposing iter= 1 total_weight= 5660.370 rmsd (weighted)= 3.548 (unweighted)= 26.816 superimposing iter= 2 total_weight= 4080.714 rmsd (weighted)= 1.926 (unweighted)= 26.819 superimposing iter= 3 total_weight= 2735.345 rmsd (weighted)= 1.329 (unweighted)= 26.822 superimposing iter= 4 total_weight= 2087.160 rmsd (weighted)= 1.067 (unweighted)= 26.825 superimposing iter= 5 total_weight= 1764.431 rmsd (weighted)= 0.936 (unweighted)= 26.834 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 1.007 rmsd (weighted)= 3.354 (unweighted)= 41.881 superimposing iter= 1 total_weight= 3213.578 rmsd (weighted)= 1.756 (unweighted)= 41.426 superimposing iter= 2 total_weight= 2082.793 rmsd (weighted)= 1.182 (unweighted)= 41.184 superimposing iter= 3 total_weight= 1897.761 rmsd (weighted)= 0.869 (unweighted)= 41.063 superimposing iter= 4 total_weight= 1565.610 rmsd (weighted)= 0.718 (unweighted)= 40.991 superimposing iter= 5 total_weight= 1343.977 rmsd (weighted)= 0.645 (unweighted)= 40.942 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 1.258 rmsd (weighted)= 11.174 (unweighted)= 38.176 superimposing iter= 1 total_weight= 4688.107 rmsd (weighted)= 5.424 (unweighted)= 37.747 superimposing iter= 2 total_weight= 2678.199 rmsd (weighted)= 3.586 (unweighted)= 37.587 superimposing iter= 3 total_weight= 2084.687 rmsd (weighted)= 2.685 (unweighted)= 37.589 superimposing iter= 4 total_weight= 1960.699 rmsd (weighted)= 2.096 (unweighted)= 37.681 superimposing iter= 5 total_weight= 1996.719 rmsd (weighted)= 1.693 (unweighted)= 37.750 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 1.142 rmsd (weighted)= 5.017 (unweighted)= 16.497 superimposing iter= 1 total_weight= 3621.205 rmsd (weighted)= 2.806 (unweighted)= 16.571 superimposing iter= 2 total_weight= 1871.839 rmsd (weighted)= 2.257 (unweighted)= 16.597 superimposing iter= 3 total_weight= 1455.212 rmsd (weighted)= 2.079 (unweighted)= 16.603 superimposing iter= 4 total_weight= 1337.896 rmsd (weighted)= 2.003 (unweighted)= 16.600 superimposing iter= 5 total_weight= 1297.156 rmsd (weighted)= 1.960 (unweighted)= 16.595 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 0.847 rmsd (weighted)= 2.773 (unweighted)= 24.192 superimposing iter= 1 total_weight= 2298.844 rmsd (weighted)= 1.673 (unweighted)= 24.200 superimposing iter= 2 total_weight= 1391.680 rmsd (weighted)= 1.339 (unweighted)= 24.178 superimposing iter= 3 total_weight= 1169.502 rmsd (weighted)= 1.176 (unweighted)= 24.165 superimposing iter= 4 total_weight= 1089.366 rmsd (weighted)= 1.074 (unweighted)= 24.165 superimposing iter= 5 total_weight= 1031.638 rmsd (weighted)= 1.013 (unweighted)= 24.167 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 0.881 rmsd (weighted)= 1.836 (unweighted)= 31.309 superimposing iter= 1 total_weight= 2975.648 rmsd (weighted)= 1.001 (unweighted)= 31.107 superimposing iter= 2 total_weight= 1388.665 rmsd (weighted)= 0.825 (unweighted)= 31.013 superimposing iter= 3 total_weight= 1117.617 rmsd (weighted)= 0.761 (unweighted)= 30.952 superimposing iter= 4 total_weight= 1041.090 rmsd (weighted)= 0.728 (unweighted)= 30.912 superimposing iter= 5 total_weight= 1010.179 rmsd (weighted)= 0.708 (unweighted)= 30.884 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 0.968 rmsd (weighted)= 3.132 (unweighted)= 40.333 superimposing iter= 1 total_weight= 5156.220 rmsd (weighted)= 1.285 (unweighted)= 40.408 superimposing iter= 2 total_weight= 1984.350 rmsd (weighted)= 0.922 (unweighted)= 40.407 superimposing iter= 3 total_weight= 1323.581 rmsd (weighted)= 0.819 (unweighted)= 40.411 superimposing iter= 4 total_weight= 1151.124 rmsd (weighted)= 0.782 (unweighted)= 40.415 superimposing iter= 5 total_weight= 1095.714 rmsd (weighted)= 0.766 (unweighted)= 40.418 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 1.092 rmsd (weighted)= 6.515 (unweighted)= 70.354 superimposing iter= 1 total_weight= 3664.618 rmsd (weighted)= 3.265 (unweighted)= 69.238 superimposing iter= 2 total_weight= 2544.802 rmsd (weighted)= 2.003 (unweighted)= 68.476 superimposing iter= 3 total_weight= 2150.601 rmsd (weighted)= 1.386 (unweighted)= 67.990 superimposing iter= 4 total_weight= 1840.148 rmsd (weighted)= 1.079 (unweighted)= 67.742 superimposing iter= 5 total_weight= 1518.490 rmsd (weighted)= 0.943 (unweighted)= 67.616 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 1.308 rmsd (weighted)= 4.625 (unweighted)= 15.584 superimposing iter= 1 total_weight= 4572.616 rmsd (weighted)= 2.420 (unweighted)= 15.629 superimposing iter= 2 total_weight= 2280.134 rmsd (weighted)= 1.840 (unweighted)= 15.753 superimposing iter= 3 total_weight= 1868.158 rmsd (weighted)= 1.568 (unweighted)= 15.887 superimposing iter= 4 total_weight= 1745.534 rmsd (weighted)= 1.399 (unweighted)= 15.995 superimposing iter= 5 total_weight= 1643.654 rmsd (weighted)= 1.296 (unweighted)= 16.067 superimposing iter= 0 total_weight= 1.339 rmsd (weighted)= 4.742 (unweighted)= 24.036 superimposing iter= 1 total_weight= 5073.269 rmsd (weighted)= 2.376 (unweighted)= 23.967 superimposing iter= 2 total_weight= 2201.371 rmsd (weighted)= 1.882 (unweighted)= 23.938 superimposing iter= 3 total_weight= 1732.450 rmsd (weighted)= 1.699 (unweighted)= 23.928 superimposing iter= 4 total_weight= 1732.232 rmsd (weighted)= 1.538 (unweighted)= 23.935 superimposing iter= 5 total_weight= 1791.181 rmsd (weighted)= 1.367 (unweighted)= 23.956 superimposing iter= 0 total_weight= 1.266 rmsd (weighted)= 8.514 (unweighted)= 26.805 superimposing iter= 1 total_weight= 5699.573 rmsd (weighted)= 3.532 (unweighted)= 26.851 superimposing iter= 2 total_weight= 4064.541 rmsd (weighted)= 1.922 (unweighted)= 26.854 superimposing iter= 3 total_weight= 2726.357 rmsd (weighted)= 1.328 (unweighted)= 26.857 superimposing iter= 4 total_weight= 2083.386 rmsd (weighted)= 1.068 (unweighted)= 26.859 superimposing iter= 5 total_weight= 1761.200 rmsd (weighted)= 0.938 (unweighted)= 26.868 superimposing iter= 0 total_weight= 1.007 rmsd (weighted)= 3.360 (unweighted)= 41.912 superimposing iter= 1 total_weight= 3207.213 rmsd (weighted)= 1.761 (unweighted)= 41.460 superimposing iter= 2 total_weight= 2084.279 rmsd (weighted)= 1.185 (unweighted)= 41.219 superimposing iter= 3 total_weight= 1903.345 rmsd (weighted)= 0.869 (unweighted)= 41.098 superimposing iter= 4 total_weight= 1568.750 rmsd (weighted)= 0.718 (unweighted)= 41.025 superimposing iter= 5 total_weight= 1345.630 rmsd (weighted)= 0.645 (unweighted)= 40.977 superimposing iter= 0 total_weight= 1.258 rmsd (weighted)= 11.156 (unweighted)= 38.157 superimposing iter= 1 total_weight= 4691.059 rmsd (weighted)= 5.412 (unweighted)= 37.723 superimposing iter= 2 total_weight= 2677.689 rmsd (weighted)= 3.579 (unweighted)= 37.562 superimposing iter= 3 total_weight= 2081.518 rmsd (weighted)= 2.682 (unweighted)= 37.563 superimposing iter= 4 total_weight= 1964.818 rmsd (weighted)= 2.093 (unweighted)= 37.654 superimposing iter= 5 total_weight= 1994.006 rmsd (weighted)= 1.692 (unweighted)= 37.722 superimposing iter= 0 total_weight= 1.142 rmsd (weighted)= 5.031 (unweighted)= 16.531 superimposing iter= 1 total_weight= 3616.662 rmsd (weighted)= 2.816 (unweighted)= 16.606 superimposing iter= 2 total_weight= 1875.696 rmsd (weighted)= 2.263 (unweighted)= 16.632 superimposing iter= 3 total_weight= 1456.094 rmsd (weighted)= 2.083 (unweighted)= 16.638 superimposing iter= 4 total_weight= 1338.220 rmsd (weighted)= 2.006 (unweighted)= 16.636 superimposing iter= 5 total_weight= 1296.470 rmsd (weighted)= 1.965 (unweighted)= 16.632 superimposing iter= 0 total_weight= 0.847 rmsd (weighted)= 2.769 (unweighted)= 24.204 superimposing iter= 1 total_weight= 2294.116 rmsd (weighted)= 1.673 (unweighted)= 24.212 superimposing iter= 2 total_weight= 1388.593 rmsd (weighted)= 1.340 (unweighted)= 24.190 superimposing iter= 3 total_weight= 1168.227 rmsd (weighted)= 1.178 (unweighted)= 24.178 superimposing iter= 4 total_weight= 1090.688 rmsd (weighted)= 1.076 (unweighted)= 24.178 superimposing iter= 5 total_weight= 1033.042 rmsd (weighted)= 1.013 (unweighted)= 24.180 superimposing iter= 0 total_weight= 0.881 rmsd (weighted)= 1.834 (unweighted)= 31.317 superimposing iter= 1 total_weight= 2975.184 rmsd (weighted)= 1.000 (unweighted)= 31.116 superimposing iter= 2 total_weight= 1387.023 rmsd (weighted)= 0.825 (unweighted)= 31.021 superimposing iter= 3 total_weight= 1117.516 rmsd (weighted)= 0.761 (unweighted)= 30.960 superimposing iter= 4 total_weight= 1041.936 rmsd (weighted)= 0.728 (unweighted)= 30.920 superimposing iter= 5 total_weight= 1009.895 rmsd (weighted)= 0.708 (unweighted)= 30.893 superimposing iter= 0 total_weight= 0.968 rmsd (weighted)= 3.130 (unweighted)= 40.364 superimposing iter= 1 total_weight= 5145.602 rmsd (weighted)= 1.286 (unweighted)= 40.433 superimposing iter= 2 total_weight= 1982.611 rmsd (weighted)= 0.923 (unweighted)= 40.430 superimposing iter= 3 total_weight= 1324.359 rmsd (weighted)= 0.819 (unweighted)= 40.432 superimposing iter= 4 total_weight= 1152.204 rmsd (weighted)= 0.782 (unweighted)= 40.436 superimposing iter= 5 total_weight= 1096.278 rmsd (weighted)= 0.766 (unweighted)= 40.439 superimposing iter= 0 total_weight= 1.092 rmsd (weighted)= 6.509 (unweighted)= 70.384 superimposing iter= 1 total_weight= 3664.951 rmsd (weighted)= 3.262 (unweighted)= 69.269 superimposing iter= 2 total_weight= 2547.512 rmsd (weighted)= 2.001 (unweighted)= 68.510 superimposing iter= 3 total_weight= 2145.161 rmsd (weighted)= 1.388 (unweighted)= 68.024 superimposing iter= 4 total_weight= 1830.621 rmsd (weighted)= 1.085 (unweighted)= 67.774 superimposing iter= 5 total_weight= 1513.694 rmsd (weighted)= 0.950 (unweighted)= 67.643 superimposing iter= 0 total_weight= 1.308 rmsd (weighted)= 4.637 (unweighted)= 15.565 superimposing iter= 1 total_weight= 4558.405 rmsd (weighted)= 2.432 (unweighted)= 15.611 superimposing iter= 2 total_weight= 2276.012 rmsd (weighted)= 1.850 (unweighted)= 15.736 superimposing iter= 3 total_weight= 1867.994 rmsd (weighted)= 1.576 (unweighted)= 15.872 superimposing iter= 4 total_weight= 1747.246 rmsd (weighted)= 1.405 (unweighted)= 15.982 superimposing iter= 5 total_weight= 1648.850 rmsd (weighted)= 1.299 (unweighted)= 16.056 # command:# Printing sheets for alignments to T0503.undertaker-align.sheets # command: