# command:# Seed set to 1278535025 # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading dunbrack-2191.atoms # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 53157 examples # computed average trans backbone unit before proline from 2010 examples # computed average cis backbone unit from 97 examples # trans (non-proline) backbone unit: # CA= -2.2087 1.0126 -0.0030 # O= -0.1499 2.2440 0.0016 # C= -0.6889 1.1368 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4581 0.0000 0.0000 # cis backbone unit: # CA= -0.1436 2.4534 -0.0002 # O= -2.0284 0.9742 0.0015 # C= -0.8018 1.0771 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4668 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2100 1.0631 -0.0014 # O= -0.1236 2.2458 0.0075 # C= -0.6872 1.1517 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading dunbrack-2191.atoms have 2191 chains in training database # Count of chains,residues,atoms: 2191,500310,3902258 # 493441 residues have no bad marker # 3226 residues lack atoms needed to compute omega # 1453 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 4 # HAS_OXT 1167 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 3052 # HAS_UNKNOWN_ATOMS 9 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 979 # NON_PLANAR_PEPTIDE 55 # BAD_PEPTIDE 2680 # HIGH_B_FACTOR 0 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-2191.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:CPU_time= 23.915 sec, elapsed time= 26.010 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= 37.182 sec, elapsed time= 43.369 sec. # command:# Prefix for input files set to # command:# Making conformation for sequence T0611 numbered 1 through 227 Created new target T0611 from T0611.a2m # command:# command:# No conformations to remove in PopConform # command:CPU_time= 37.184 sec, elapsed time= 43.504 sec. # command:# Prefix for input files set to # command:# reading script from file T0611.undertaker-align.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 3dcfA/T0611-3dcfA-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 3dcfA expands to /projects/compbio/data/pdb/3dcf.pdb.gz 3dcfA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0611 read from 3dcfA/T0611-3dcfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3dcfA read from 3dcfA/T0611-3dcfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3dcfA to template set # found chain 3dcfA in template set Warning: unaligning (T0611)M3 because first residue in template chain is (3dcfA)N29 Warning: unaligning (T0611)Y103 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3dcfA)L135 Warning: unaligning (T0611)S107 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3dcfA)L135 T0611 4 :KTRDKILLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHFRNKSDIIYEIFQEYEKLVDYYLDIPEDRPITL 3dcfA 30 :DRRTQIIKVATELFREKGYYATSLDDIADRIGFTKPAIYYYFKSKEDVLFAIVNSIVDEALERFHAIAAGPGSP # choosing archetypes in rotamer library T0611 78 :EDMTFYLESVFDGLWSYRFFHRDLE 3dcfA 105 :ERIHALLVEHTRTILRNLDANTLFY T0611 108 :DPRLRQDYREFTNRCLAAINRIFAKLADAGIIQPQPEDLRSAMSLNVWLVITNWMAFLKTAHAAEEPASLS 3dcfA 136 :SPEREREMRKREREYTEIMQRLYAEGVATGELLDVDPTVATATLLGAAIWTYRWYDPEGRLSADEVVEQIT T0611 180 :TELKQ 3dcfA 207 :RLLLN Number of specific fragments extracted= 4 number of extra gaps= 0 total=4 # request to SCWRL produces command: ulimit -t 205 ; scwrl4 -t -i /var/tmp/to_scwrl_22553874.pdb -s /var/tmp/to_scwrl_22553874.seq -o /var/tmp/from_scwrl_22553874.pdb > /var/tmp/scwrl_22553874.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_22553874.pdb Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vi0A/T0611-1vi0A-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 # T0611 read from 1vi0A/T0611-1vi0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vi0A read from 1vi0A/T0611-1vi0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vi0A in training set Warning: unaligning (T0611)K4 because first residue in template chain is (1vi0A)P6 Warning: unaligning (T0611)I126 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1vi0A)D131 Warning: unaligning (T0611)N127 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1vi0A)D131 T0611 5 :TRDKILLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHFRNKSDIIYEIFQEYEKLVDYYLDIP 1vi0A 7 :KYMQIIDAAVEVIAENGYHQSQVSKIAKQAGVADGTIYLYFKNKEDILISLFKEKMGQFIERMEED T0611 71 :EDRPITLEDMTFYLESVFDGLWSYRFFHRDLEYLL 1vi0A 74 :KEKATAKEKLALVISKHFSLLAGDHNLAIVTQLEL T0611 106 :DSDPRLRQDYREFTNRCLAA 1vi0A 110 :QSNLELRQKINEILKGYLNI T0611 128 :RIFAKLADAGIIQPQ 1vi0A 132 :GILTEGIQSGEIKEG T0611 143 :PEDLRSAMSLNVWLVITNWMAFLKTAHAAEEPASLSLTELKQG 1vi0A 148 :DVRLARQMIFGTIDETVTTWVMNDQKYDLVALSNSVLELLVSG Number of specific fragments extracted= 5 number of extra gaps= 1 total=9 # request to SCWRL produces command: ulimit -t 205 ; scwrl4 -t -i /var/tmp/to_scwrl_1209026289.pdb -s /var/tmp/to_scwrl_1209026289.seq -o /var/tmp/from_scwrl_1209026289.pdb > /var/tmp/scwrl_1209026289.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1209026289.pdb Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3himA/T0611-3himA-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 3himA expands to /projects/compbio/data/pdb/3him.pdb.gz 3himA:Skipped atom 1125, because occupancy 0.5 <= existing 0.500 in 3himA Skipped atom 1129, because occupancy 0.500 <= existing 0.500 in 3himA Skipped atom 1131, because occupancy 0.500 <= existing 0.500 in 3himA Skipped atom 1133, because occupancy 0.500 <= existing 0.500 in 3himA Skipped atom 1177, because occupancy 0.500 <= existing 0.500 in 3himA Skipped atom 1181, because occupancy 0.500 <= existing 0.500 in 3himA Skipped atom 1183, because occupancy 0.500 <= existing 0.500 in 3himA # T0611 read from 3himA/T0611-3himA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3himA read from 3himA/T0611-3himA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3himA to template set # found chain 3himA in template set Warning: unaligning (T0611)T2 because first residue in template chain is (3himA)T14 T0611 3 :MKTRDKILLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHFRNKSDIIYEIFQEYEKLVDYYLDIPEDRPITL 3himA 15 :SKAAARIRAAAIEVFAAKGYGATTTREIAASLDMSPGAVYPHYKTKESLLYAISLEGHHSVLAAITAADFPDIAA T0611 78 :EDMTFYLESVFDGLWSYRFFHRDLEYLLD 3himA 91 :DRLMSTVTAYVTWHADNRASARVGQYELR T0611 107 :SDPRLRQDYREFTNRCLAAINRIFAKLADAGIIQPQPEDLRSAMSLNVWLVITNWMAFLKTAHAAEEPASLS 3himA 121 :LSPEHFAIIADIRRSTTKVFTRIIEAGATAGDFHPFDIEAAALAITSLGIDVSRWFPSHTYSDPRIIAARYV T0611 180 :TELKQGIYQ 3himA 193 :ELALRMVGC Number of specific fragments extracted= 4 number of extra gaps= 0 total=13 # request to SCWRL produces command: ulimit -t 205 ; scwrl4 -t -i /var/tmp/to_scwrl_1414008768.pdb -s /var/tmp/to_scwrl_1414008768.seq -o /var/tmp/from_scwrl_1414008768.pdb > /var/tmp/scwrl_1414008768.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1414008768.pdb Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3bcgA/T0611-3bcgA-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 3bcgA expands to /projects/compbio/data/pdb/3bcg.pdb.gz 3bcgA:# T0611 read from 3bcgA/T0611-3bcgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3bcgA read from 3bcgA/T0611-3bcgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3bcgA to template set # found chain 3bcgA in template set Warning: unaligning (T0611)Y196 because last residue in template chain is (3bcgA)A212 T0611 2 :TMKTRDKILLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHFRNKSDIIYEIFQ 3bcgA 9 :AQETRQHILDVALRLFSQQGVSSTSLGEIAKAAGVTRGAIYWHFKDKSDLFSEIWE T0611 66 :YLDI 3bcgA 74 :ELEY T0611 71 :EDRPITLEDMTFYLESVFDGLWSYRFFHRDLEYLL 3bcgA 80 :KFPGDPLSVLREILIHVLESTVTEERRRLLMEIIF T0611 106 :DSDPRLRQDYREFTNRCLAAINRIFAKLADAGIIQPQ 3bcgA 121 :GEMAVVQQAQRNLCLESYDRIEQTLKHCIEAKMLPAD T0611 143 :PEDLRSAMSLNVWLVITNWMAFLKTAHAAEEPASLSLTELKQGIYQVLTLEVP 3bcgA 159 :MTRRAAIIMRGYISGLMENWLFAPQSFDLKKEARDYVAILLEMYLLCPTLRNP Number of specific fragments extracted= 5 number of extra gaps= 0 total=18 # request to SCWRL produces command: ulimit -t 205 ; scwrl4 -t -i /var/tmp/to_scwrl_1846801667.pdb -s /var/tmp/to_scwrl_1846801667.seq -o /var/tmp/from_scwrl_1846801667.pdb > /var/tmp/scwrl_1846801667.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1846801667.pdb Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2xdnA/T0611-2xdnA-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 2xdnA expands to /projects/compbio/data/pdb/2xdn.pdb.gz 2xdnA:# T0611 read from 2xdnA/T0611-2xdnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2xdnA read from 2xdnA/T0611-2xdnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2xdnA to template set # found chain 2xdnA in template set T0611 2 :TMKTRDKILLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHFRNKSDIIYEIFQEYEKLVDYYLDIP 2xdnA 9 :AQETRAQIIEAAERAFYKRGVARTTLADIAELAGVTRGAIYWHFNNKAELVQALLDSLAETHDHLARAS T0611 71 :EDRPITLEDMTFYLESVFDGLWSYRFFHRDLEYLL 2xdnA 80 :EDEVDPLGCMRKLLLQVFNELVLDARTRRINEILH T0611 106 :DSDPRLRQDYREFTNRCLAAINRIFAKLADAGIIQPQ 2xdnA 121 :DDMCEIRQQRQSAVLDCHKGITLALANAVRRGQLPGE T0611 143 :PEDLRSAMSLNVWLVITNWMAFLKTAHA 2xdnA 159 :DAERAAVAMFAYVDGLIRRWLLLPDSVD T0611 171 :AEEPASLSLTELK 2xdnA 191 :VEKWVDTGLDMLR Number of specific fragments extracted= 5 number of extra gaps= 0 total=23 # request to SCWRL produces command: ulimit -t 205 ; scwrl4 -t -i /var/tmp/to_scwrl_295457303.pdb -s /var/tmp/to_scwrl_295457303.seq -o /var/tmp/from_scwrl_295457303.pdb > /var/tmp/scwrl_295457303.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_295457303.pdb Number of alignments=5 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ibdA/T0611-2ibdA-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 2ibdA expands to /projects/compbio/data/pdb/2ibd.pdb.gz 2ibdA:Skipped atom 79, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 81, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 83, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 85, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 87, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 89, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 91, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 93, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 153, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 155, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 157, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 159, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 161, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 163, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 165, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 167, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 169, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 171, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 173, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 384, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 386, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 388, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 390, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 392, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 394, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 396, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 398, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 400, because occupancy 0.500 <= existing 0.500 in 2ibdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 579, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 583, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 585, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 587, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 719, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 723, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 725, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 727, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 729, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 731, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 776, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 780, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 782, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 902, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 906, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 908, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 910, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 912, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 914, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 966, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 970, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 972, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 1038, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 1042, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 1044, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 1046, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 1048, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 1050, because occupancy 0.500 <= existing 0.500 in 2ibdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1287, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 1291, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 1293, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 1295, because occupancy 0.500 <= existing 0.500 in 2ibdA Skipped atom 1297, because occupancy 0.500 <= existing 0.500 in 2ibdA # T0611 read from 2ibdA/T0611-2ibdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ibdA read from 2ibdA/T0611-2ibdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2ibdA to template set # found chain 2ibdA in template set T0611 2 :TMKTRDKILLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHFRNKSDIIYEIFQEYEKLVDYYLDIP 2ibdA 12 :KSGRRTELLDIAATLFAERGLRATTVRDIADAAGILSGSLYHHFDSKESMVDEILRGFLDDLFGKYREI T0611 71 :EDRPITLEDMTFYLESVFDGLWSYRFFHRDLEYLL 2ibdA 82 :ASGLDSRATLEALVTTSYEAIDASHSAVAIYQDEV T0611 106 :DSDPRL 2ibdA 120 :VANERF T0611 113 :QDYREFTNRCLAAINRIFAKLADAGIIQPQ 2ibdA 126 :TYLSELNTEFRELWMGVLEAGVKDGSFRSD T0611 143 :PEDLRSAMSLNV 2ibdA 157 :DVELAFRFLRDT T0611 165 :LKTAHAAEEPASLSLTELKQ 2ibdA 178 :PGGSVTVDTVAKQYLSIVLD Number of specific fragments extracted= 6 number of extra gaps= 0 total=29 # request to SCWRL produces command: ulimit -t 205 ; scwrl4 -t -i /var/tmp/to_scwrl_809898591.pdb -s /var/tmp/to_scwrl_809898591.seq -o /var/tmp/from_scwrl_809898591.pdb > /var/tmp/scwrl_809898591.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_809898591.pdb Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3lhqA/T0611-3lhqA-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 3lhqA expands to /projects/compbio/data/pdb/3lhq.pdb.gz 3lhqA:Skipped atom 115, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 119, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 121, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 123, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 125, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 127, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 184, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 188, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 190, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 192, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 194, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 196, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 198, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 200, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 222, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 226, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 228, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 297, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 301, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 303, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 305, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 307, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 309, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 590, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 594, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 596, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 598, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 600, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 602, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 630, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 634, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 636, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 638, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 640, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 642, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 645, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 649, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 651, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 653, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 655, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 657, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 659, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 661, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 663, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 863, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 867, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 869, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 871, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 873, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 875, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 898, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 902, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 904, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 906, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 908, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 910, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 912, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 914, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 916, because occupancy 0.500 <= existing 0.500 in 3lhqA Skipped atom 918, because occupancy 0.500 <= existing 0.500 in 3lhqA Skipped atom 920, because occupancy 0.500 <= existing 0.500 in 3lhqA Skipped atom 922, because occupancy 0.500 <= existing 0.500 in 3lhqA Skipped atom 924, because occupancy 0.500 <= existing 0.500 in 3lhqA Skipped atom 926, because occupancy 0.500 <= existing 0.500 in 3lhqA Skipped atom 928, because occupancy 0.500 <= existing 0.500 in 3lhqA Skipped atom 930, because occupancy 0.500 <= existing 0.500 in 3lhqA Skipped atom 932, because occupancy 0.500 <= existing 0.500 in 3lhqA Skipped atom 934, because occupancy 0.500 <= existing 0.500 in 3lhqA Skipped atom 936, because occupancy 0.500 <= existing 0.500 in 3lhqA Skipped atom 1017, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 1019, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 1021, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 1023, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 1025, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 1027, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 1070, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 1074, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 1076, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 1078, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 1080, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 1161, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 1165, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 1167, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 1450, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 1454, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 1456, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 1715, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 1719, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 1721, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 1723, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 1725, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 1740, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 1744, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 1746, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 1748, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 1750, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 1752, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 1791, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 1795, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 1797, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 1799, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 1801, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 1803, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 1805, because occupancy 0.400 <= existing 0.600 in 3lhqA Skipped atom 1807, because occupancy 0.400 <= existing 0.600 in 3lhqA # T0611 read from 3lhqA/T0611-3lhqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3lhqA read from 3lhqA/T0611-3lhqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3lhqA to template set # found chain 3lhqA in template set Warning: unaligning (T0611)E203 because last residue in template chain is (3lhqA)A210 T0611 3 :MKTRDKILLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHFRNKSDIIYEIFQEYEKLVDYYLDIP 3lhqA 10 :LETRQHILDVALRLFSQQGVSATSLAEIANAAGVTRGAIYWHFKNKSDLFSEIWELSESNIGELEIEY T0611 71 :EDRPITLEDMTFYLESVFDGLWSYRFFHRDLEYLL 3lhqA 80 :KFPDDPLSVLREILVHILEATVTEERRRLLMEIIF T0611 106 :DSDPRLRQDYREFTNRCLAAINRIFAKLADAGIIQPQ 3lhqA 121 :GEMVVVQQAQRSLCLESYDRIEQTLKHCINAKMLPEN T0611 143 :PEDLRSAMSLNVWLVITNWMAFLKTAHAAEEPASLSLTELKQGIYQ 3lhqA 159 :LTRRAAILMRSFISGLMENWLFAPQSFDLKKEARAYVTILLEMYQL T0611 198 :TPEYR 3lhqA 205 :CPTLR Number of specific fragments extracted= 5 number of extra gaps= 0 total=34 # request to SCWRL produces command: ulimit -t 205 ; scwrl4 -t -i /var/tmp/to_scwrl_705247123.pdb -s /var/tmp/to_scwrl_705247123.seq -o /var/tmp/from_scwrl_705247123.pdb > /var/tmp/scwrl_705247123.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_705247123.pdb Number of alignments=7 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2uxuA/T0611-2uxuA-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 2uxuA expands to /projects/compbio/data/pdb/2uxu.pdb.gz 2uxuA:# T0611 read from 2uxuA/T0611-2uxuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2uxuA read from 2uxuA/T0611-2uxuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2uxuA to template set # found chain 2uxuA in template set Warning: unaligning (T0611)S37 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2uxuA)R45 Warning: unaligning (T0611)P38 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2uxuA)R45 Warning: unaligning (T0611)F45 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2uxuA)N53 Warning: unaligning (T0611)R46 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2uxuA)N53 Warning: unaligning (T0611)N47 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2uxuA)N54 Warning: unaligning (T0611)K48 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2uxuA)K55 Warning: unaligning (T0611)D106 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2uxuA)D122 Warning: unaligning (T0611)S107 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2uxuA)D122 T0611 2 :TMKTRDKILLSSLELFNDKGERNITTNHIAAHLAI 2uxuA 9 :AQETRAQIIEAAERAFYKRGVARTTLADIAELAGV T0611 39 :GNLYYH 2uxuA 46 :GAIYWH T0611 49 :SDIIYEIFQEYEKLVDYYLDIP 2uxuA 56 :AELVQALLDSLHETHDHLARAS T0611 71 :EDRPITLEDMTFYLESVFDGLWSYRFFHRDLEYLL 2uxuA 80 :EDEVDPLGCMRKLLLQVFNELVLDARTRRINEILH T0611 108 :DPRLRQDYREFTNRCLAAINRIFAKLADAGIIQPQ 2uxuA 123 :MCEIRQQRQSAVLDCHKGITLALANAVRRGQLPGE T0611 143 :PEDLRSAMSLNVWLVITNWMAFLKTAHA 2uxuA 159 :DAERAAVAMFAYVDGLIRRWLLLPDSVD T0611 171 :AEEPASLSLTELK 2uxuA 191 :VEKWVDTGLDMLR Number of specific fragments extracted= 7 number of extra gaps= 3 total=41 # request to SCWRL produces command: ulimit -t 205 ; scwrl4 -t -i /var/tmp/to_scwrl_973038011.pdb -s /var/tmp/to_scwrl_973038011.seq -o /var/tmp/from_scwrl_973038011.pdb > /var/tmp/scwrl_973038011.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_973038011.pdb Number of alignments=8 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3cdlA/T0611-3cdlA-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 3cdlA expands to /projects/compbio/data/pdb/3cdl.pdb.gz 3cdlA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0611 read from 3cdlA/T0611-3cdlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cdlA read from 3cdlA/T0611-3cdlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3cdlA to template set # found chain 3cdlA in template set Warning: unaligning (T0611)V63 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3cdlA)E70 Warning: unaligning (T0611)D68 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3cdlA)E70 Warning: unaligning (T0611)Y115 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3cdlA)L121 Warning: unaligning (T0611)R116 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3cdlA)L121 Warning: unaligning (T0611)L123 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3cdlA)E128 Warning: unaligning (T0611)I158 because of BadResidue code BAD_PEPTIDE in next template residue (3cdlA)A164 Warning: unaligning (T0611)T159 because of BadResidue code BAD_PEPTIDE at template residue (3cdlA)A164 T0611 2 :TMKTRDKILLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHFRNKSDIIYEIFQEYEKL 3cdlA 4 :TDQKRESIVQAAIAEFGDRGFEITSMDRIAARAEVSKRTVYNHFPSKEELFAEMLQRLWNC T0611 69 :IP 3cdlA 71 :VV T0611 71 :EDRPITLEDMTFYLESVFDGLWSYRFFHRDLEYLL 3cdlA 74 :RPLVSLREQLLELLWGKMRNLTDSSFLDLARVVVG T0611 106 :DSDPRLRQD 3cdlA 111 :IHSPERAQV T0611 124 :AAINRIFAKLADAGIIQPQPEDLRSAMSLNVWLV 3cdlA 129 :ETFSAWIRAAQKDGRLKPVDPGFAATQMHALLKS T0611 160 :NWMAFLK 3cdlA 165 :FWPQVTF T0611 167 :TAHAAEEPASLSLTELKQGI 3cdlA 177 :TPQEQSNVVESALNMFLGWY Number of specific fragments extracted= 7 number of extra gaps= 2 total=48 # request to SCWRL produces command: ulimit -t 205 ; scwrl4 -t -i /var/tmp/to_scwrl_1072389280.pdb -s /var/tmp/to_scwrl_1072389280.seq -o /var/tmp/from_scwrl_1072389280.pdb > /var/tmp/scwrl_1072389280.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1072389280.pdb Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2w53A/T0611-2w53A-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 2w53A expands to /projects/compbio/data/pdb/2w53.pdb.gz 2w53A:Skipped atom 504, because occupancy 0.500 <= existing 0.500 in 2w53A Skipped atom 505, because occupancy 0.500 <= existing 0.500 in 2w53A Skipped atom 506, because occupancy 0.500 <= existing 0.500 in 2w53A Skipped atom 507, because occupancy 0.500 <= existing 0.500 in 2w53A Skipped atom 508, because occupancy 0.500 <= existing 0.500 in 2w53A Skipped atom 509, because occupancy 0.500 <= existing 0.500 in 2w53A Skipped atom 510, because occupancy 0.500 <= existing 0.500 in 2w53A Skipped atom 511, because occupancy 0.500 <= existing 0.500 in 2w53A Skipped atom 846, because occupancy 0.300 <= existing 0.700 in 2w53A Skipped atom 847, because occupancy 0.300 <= existing 0.700 in 2w53A Skipped atom 848, because occupancy 0.300 <= existing 0.700 in 2w53A Skipped atom 849, because occupancy 0.300 <= existing 0.700 in 2w53A Skipped atom 850, because occupancy 0.300 <= existing 0.700 in 2w53A Skipped atom 876, because occupancy 0.500 <= existing 0.500 in 2w53A Skipped atom 877, because occupancy 0.500 <= existing 0.500 in 2w53A Skipped atom 878, because occupancy 0.500 <= existing 0.500 in 2w53A Skipped atom 879, because occupancy 0.500 <= existing 0.500 in 2w53A Skipped atom 880, because occupancy 0.500 <= existing 0.500 in 2w53A Skipped atom 1417, because occupancy 0.500 <= existing 0.500 in 2w53A Skipped atom 1418, because occupancy 0.500 <= existing 0.500 in 2w53A Skipped atom 1419, because occupancy 0.500 <= existing 0.500 in 2w53A Skipped atom 1420, because occupancy 0.500 <= existing 0.500 in 2w53A Skipped atom 1421, because occupancy 0.500 <= existing 0.500 in 2w53A Skipped atom 1590, because occupancy 0.500 <= existing 0.500 in 2w53A Skipped atom 1591, because occupancy 0.500 <= existing 0.500 in 2w53A Skipped atom 1592, because occupancy 0.500 <= existing 0.500 in 2w53A Skipped atom 1593, because occupancy 0.500 <= existing 0.500 in 2w53A Skipped atom 1594, because occupancy 0.500 <= existing 0.500 in 2w53A Skipped atom 1595, because occupancy 0.500 <= existing 0.500 in 2w53A # T0611 read from 2w53A/T0611-2w53A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2w53A read from 2w53A/T0611-2w53A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2w53A to template set # found chain 2w53A in template set Warning: unaligning (T0611)P109 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2w53A)T126 Warning: unaligning (T0611)G224 because last residue in template chain is (2w53A)P217 T0611 6 :RDKILLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHFRNKSDIIYEIFQEYEKLVDYYLDIP 2w53A 13 :REGILDAAEACFHEHGVARTTLEMIGARAGYTRGAVYWHFKNKSEVLAAIVERVHLPFMQELERT T0611 71 :EDRPITLEDMTFYLESVFDGLWSYRFFHRDLEYLL 2w53A 80 :DQRDTPVHDLRAVMIHSFIELSEDERLRKTMEIML T0611 110 :RLR 2w53A 127 :EMQ T0611 116 :REFTNRCLAAINRIFAKLADAGIIQPQ 2w53A 130 :QAGFRDALDRMERALRRARDLGQLREG T0611 143 :PEDLRSAMSLNVWLVITNWMAFLKTAHAAEEP 2w53A 158 :DPKIAARMLHATVLGVLHGAMVEPELMDLKRD T0611 175 :ASLSLTELKQGI 2w53A 191 :MLALDMTLAAYV T0611 210 :EKYRPTLPEAQGIS 2w53A 203 :KDGVFVPGTVPEPL Number of specific fragments extracted= 7 number of extra gaps= 0 total=55 # request to SCWRL produces command: ulimit -t 205 ; scwrl4 -t -i /var/tmp/to_scwrl_916760290.pdb -s /var/tmp/to_scwrl_916760290.seq -o /var/tmp/from_scwrl_916760290.pdb > /var/tmp/scwrl_916760290.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_916760290.pdb Number of alignments=10 # command:Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.149 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 1 total_weight= 14570.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 2 total_weight= 14570.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 3 total_weight= 14570.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 4 total_weight= 14570.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 5 total_weight= 14570.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 1.129 rmsd (weighted)= 4.410 (unweighted)= 72.391 superimposing iter= 1 total_weight= 3474.730 rmsd (weighted)= 2.797 (unweighted)= 72.022 superimposing iter= 2 total_weight= 1602.201 rmsd (weighted)= 2.632 (unweighted)= 71.794 superimposing iter= 3 total_weight= 1519.024 rmsd (weighted)= 2.547 (unweighted)= 71.638 superimposing iter= 4 total_weight= 1506.252 rmsd (weighted)= 2.473 (unweighted)= 71.519 superimposing iter= 5 total_weight= 1493.082 rmsd (weighted)= 2.410 (unweighted)= 71.426 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 1.149 rmsd (weighted)= 3.864 (unweighted)= 53.669 superimposing iter= 1 total_weight= 4335.862 rmsd (weighted)= 2.180 (unweighted)= 53.497 superimposing iter= 2 total_weight= 1948.886 rmsd (weighted)= 1.869 (unweighted)= 53.394 superimposing iter= 3 total_weight= 1595.475 rmsd (weighted)= 1.775 (unweighted)= 53.352 superimposing iter= 4 total_weight= 1496.809 rmsd (weighted)= 1.741 (unweighted)= 53.338 superimposing iter= 5 total_weight= 1462.038 rmsd (weighted)= 1.728 (unweighted)= 53.337 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 1.087 rmsd (weighted)= 5.129 (unweighted)= 46.376 superimposing iter= 1 total_weight= 4605.181 rmsd (weighted)= 2.706 (unweighted)= 46.184 superimposing iter= 2 total_weight= 1732.574 rmsd (weighted)= 2.397 (unweighted)= 46.108 superimposing iter= 3 total_weight= 1459.699 rmsd (weighted)= 2.318 (unweighted)= 46.117 superimposing iter= 4 total_weight= 1441.089 rmsd (weighted)= 2.259 (unweighted)= 46.179 superimposing iter= 5 total_weight= 1431.701 rmsd (weighted)= 2.209 (unweighted)= 46.262 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 1.142 rmsd (weighted)= 5.178 (unweighted)= 31.260 superimposing iter= 1 total_weight= 3935.229 rmsd (weighted)= 3.101 (unweighted)= 30.951 superimposing iter= 2 total_weight= 1638.740 rmsd (weighted)= 2.902 (unweighted)= 30.834 superimposing iter= 3 total_weight= 1544.158 rmsd (weighted)= 2.801 (unweighted)= 30.817 superimposing iter= 4 total_weight= 1563.652 rmsd (weighted)= 2.686 (unweighted)= 30.873 superimposing iter= 5 total_weight= 1583.887 rmsd (weighted)= 2.559 (unweighted)= 30.969 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 1.072 rmsd (weighted)= 5.371 (unweighted)= 68.284 superimposing iter= 1 total_weight= 4158.867 rmsd (weighted)= 2.904 (unweighted)= 67.239 superimposing iter= 2 total_weight= 2111.386 rmsd (weighted)= 2.227 (unweighted)= 66.329 superimposing iter= 3 total_weight= 1853.365 rmsd (weighted)= 1.845 (unweighted)= 65.685 superimposing iter= 4 total_weight= 1691.025 rmsd (weighted)= 1.621 (unweighted)= 65.288 superimposing iter= 5 total_weight= 1549.315 rmsd (weighted)= 1.501 (unweighted)= 65.063 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 1.149 rmsd (weighted)= 4.719 (unweighted)= 63.960 superimposing iter= 1 total_weight= 4341.725 rmsd (weighted)= 2.697 (unweighted)= 64.214 superimposing iter= 2 total_weight= 1656.796 rmsd (weighted)= 2.523 (unweighted)= 64.297 superimposing iter= 3 total_weight= 1506.542 rmsd (weighted)= 2.478 (unweighted)= 64.330 superimposing iter= 4 total_weight= 1487.077 rmsd (weighted)= 2.450 (unweighted)= 64.336 superimposing iter= 5 total_weight= 1478.923 rmsd (weighted)= 2.429 (unweighted)= 64.327 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 1.102 rmsd (weighted)= 5.180 (unweighted)= 52.322 superimposing iter= 1 total_weight= 3888.549 rmsd (weighted)= 3.033 (unweighted)= 51.993 superimposing iter= 2 total_weight= 1819.566 rmsd (weighted)= 2.622 (unweighted)= 51.897 superimposing iter= 3 total_weight= 1660.641 rmsd (weighted)= 2.376 (unweighted)= 51.901 superimposing iter= 4 total_weight= 1594.368 rmsd (weighted)= 2.198 (unweighted)= 51.943 superimposing iter= 5 total_weight= 1523.633 rmsd (weighted)= 2.083 (unweighted)= 51.994 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 1.031 rmsd (weighted)= 5.641 (unweighted)= 74.075 superimposing iter= 1 total_weight= 3953.965 rmsd (weighted)= 3.120 (unweighted)= 73.203 superimposing iter= 2 total_weight= 1756.769 rmsd (weighted)= 2.658 (unweighted)= 72.638 superimposing iter= 3 total_weight= 1445.527 rmsd (weighted)= 2.505 (unweighted)= 72.177 superimposing iter= 4 total_weight= 1405.581 rmsd (weighted)= 2.397 (unweighted)= 71.761 superimposing iter= 5 total_weight= 1407.166 rmsd (weighted)= 2.293 (unweighted)= 71.368 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 1.102 rmsd (weighted)= 4.690 (unweighted)= 50.881 superimposing iter= 1 total_weight= 4957.670 rmsd (weighted)= 2.380 (unweighted)= 50.717 superimposing iter= 2 total_weight= 2064.206 rmsd (weighted)= 1.935 (unweighted)= 50.571 superimposing iter= 3 total_weight= 1599.872 rmsd (weighted)= 1.794 (unweighted)= 50.495 superimposing iter= 4 total_weight= 1483.550 rmsd (weighted)= 1.729 (unweighted)= 50.463 superimposing iter= 5 total_weight= 1434.263 rmsd (weighted)= 1.695 (unweighted)= 50.452 Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.149 rmsd (weighted)= 3.676 (unweighted)= 36.474 superimposing iter= 1 total_weight= 4054.482 rmsd (weighted)= 2.169 (unweighted)= 36.554 superimposing iter= 2 total_weight= 1691.061 rmsd (weighted)= 2.000 (unweighted)= 36.593 superimposing iter= 3 total_weight= 1567.059 rmsd (weighted)= 1.917 (unweighted)= 36.614 superimposing iter= 4 total_weight= 1593.953 rmsd (weighted)= 1.824 (unweighted)= 36.626 superimposing iter= 5 total_weight= 1604.373 rmsd (weighted)= 1.730 (unweighted)= 36.634 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 1.173 rmsd (weighted)= 2.356 (unweighted)= 57.983 superimposing iter= 1 total_weight= 4881.318 rmsd (weighted)= 1.248 (unweighted)= 58.000 superimposing iter= 2 total_weight= 2128.175 rmsd (weighted)= 1.028 (unweighted)= 58.029 superimposing iter= 3 total_weight= 1690.235 rmsd (weighted)= 0.955 (unweighted)= 58.048 superimposing iter= 4 total_weight= 1564.100 rmsd (weighted)= 0.924 (unweighted)= 58.060 superimposing iter= 5 total_weight= 1518.603 rmsd (weighted)= 0.908 (unweighted)= 58.067 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 1.215 rmsd (weighted)= 3.013 (unweighted)= 40.248 superimposing iter= 1 total_weight= 5046.267 rmsd (weighted)= 1.591 (unweighted)= 40.253 superimposing iter= 2 total_weight= 2322.152 rmsd (weighted)= 1.282 (unweighted)= 40.213 superimposing iter= 3 total_weight= 1732.753 rmsd (weighted)= 1.202 (unweighted)= 40.189 superimposing iter= 4 total_weight= 1602.866 rmsd (weighted)= 1.173 (unweighted)= 40.171 superimposing iter= 5 total_weight= 1565.211 rmsd (weighted)= 1.159 (unweighted)= 40.157 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 1.208 rmsd (weighted)= 2.359 (unweighted)= 35.794 superimposing iter= 1 total_weight= 6211.559 rmsd (weighted)= 1.090 (unweighted)= 35.695 superimposing iter= 2 total_weight= 2719.869 rmsd (weighted)= 0.799 (unweighted)= 35.651 superimposing iter= 3 total_weight= 1925.005 rmsd (weighted)= 0.701 (unweighted)= 35.645 superimposing iter= 4 total_weight= 1656.188 rmsd (weighted)= 0.664 (unweighted)= 35.650 superimposing iter= 5 total_weight= 1552.498 rmsd (weighted)= 0.651 (unweighted)= 35.656 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 1.194 rmsd (weighted)= 2.392 (unweighted)= 28.046 superimposing iter= 1 total_weight= 4345.504 rmsd (weighted)= 1.342 (unweighted)= 28.060 superimposing iter= 2 total_weight= 2322.939 rmsd (weighted)= 1.064 (unweighted)= 28.012 superimposing iter= 3 total_weight= 1832.821 rmsd (weighted)= 0.957 (unweighted)= 27.971 superimposing iter= 4 total_weight= 1672.243 rmsd (weighted)= 0.903 (unweighted)= 27.949 superimposing iter= 5 total_weight= 1583.677 rmsd (weighted)= 0.876 (unweighted)= 27.940 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 1.124 rmsd (weighted)= 3.934 (unweighted)= 55.016 superimposing iter= 1 total_weight= 3745.001 rmsd (weighted)= 2.360 (unweighted)= 54.932 superimposing iter= 2 total_weight= 1795.409 rmsd (weighted)= 2.081 (unweighted)= 54.893 superimposing iter= 3 total_weight= 1521.135 rmsd (weighted)= 1.998 (unweighted)= 54.855 superimposing iter= 4 total_weight= 1473.070 rmsd (weighted)= 1.950 (unweighted)= 54.813 superimposing iter= 5 total_weight= 1469.044 rmsd (weighted)= 1.906 (unweighted)= 54.769 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 1.256 rmsd (weighted)= 2.135 (unweighted)= 46.555 superimposing iter= 1 total_weight= 5617.893 rmsd (weighted)= 1.080 (unweighted)= 46.699 superimposing iter= 2 total_weight= 2459.461 rmsd (weighted)= 0.849 (unweighted)= 46.751 superimposing iter= 3 total_weight= 1893.849 rmsd (weighted)= 0.765 (unweighted)= 46.764 superimposing iter= 4 total_weight= 1690.925 rmsd (weighted)= 0.731 (unweighted)= 46.765 superimposing iter= 5 total_weight= 1607.948 rmsd (weighted)= 0.717 (unweighted)= 46.764 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 1.142 rmsd (weighted)= 2.351 (unweighted)= 48.861 superimposing iter= 1 total_weight= 4279.402 rmsd (weighted)= 1.297 (unweighted)= 48.937 superimposing iter= 2 total_weight= 2191.971 rmsd (weighted)= 1.037 (unweighted)= 48.925 superimposing iter= 3 total_weight= 1685.956 rmsd (weighted)= 0.951 (unweighted)= 48.909 superimposing iter= 4 total_weight= 1562.543 rmsd (weighted)= 0.909 (unweighted)= 48.896 superimposing iter= 5 total_weight= 1511.928 rmsd (weighted)= 0.884 (unweighted)= 48.885 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 1.094 rmsd (weighted)= 3.555 (unweighted)= 54.764 superimposing iter= 1 total_weight= 4928.518 rmsd (weighted)= 1.787 (unweighted)= 54.648 superimposing iter= 2 total_weight= 2246.489 rmsd (weighted)= 1.374 (unweighted)= 54.612 superimposing iter= 3 total_weight= 1733.589 rmsd (weighted)= 1.214 (unweighted)= 54.608 superimposing iter= 4 total_weight= 1553.610 rmsd (weighted)= 1.137 (unweighted)= 54.613 superimposing iter= 5 total_weight= 1477.085 rmsd (weighted)= 1.095 (unweighted)= 54.618 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 1.230 rmsd (weighted)= 2.327 (unweighted)= 38.526 superimposing iter= 1 total_weight= 5648.199 rmsd (weighted)= 1.168 (unweighted)= 38.557 superimposing iter= 2 total_weight= 2317.701 rmsd (weighted)= 0.943 (unweighted)= 38.588 superimposing iter= 3 total_weight= 1868.356 rmsd (weighted)= 0.856 (unweighted)= 38.608 superimposing iter= 4 total_weight= 1688.417 rmsd (weighted)= 0.819 (unweighted)= 38.618 superimposing iter= 5 total_weight= 1600.395 rmsd (weighted)= 0.806 (unweighted)= 38.624 Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.149 rmsd (weighted)= 3.684 (unweighted)= 36.461 superimposing iter= 1 total_weight= 3996.366 rmsd (weighted)= 2.192 (unweighted)= 36.535 superimposing iter= 2 total_weight= 1668.796 rmsd (weighted)= 2.036 (unweighted)= 36.571 superimposing iter= 3 total_weight= 1554.541 rmsd (weighted)= 1.961 (unweighted)= 36.590 superimposing iter= 4 total_weight= 1571.968 rmsd (weighted)= 1.879 (unweighted)= 36.602 superimposing iter= 5 total_weight= 1611.675 rmsd (weighted)= 1.779 (unweighted)= 36.611 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 1.173 rmsd (weighted)= 2.353 (unweighted)= 58.002 superimposing iter= 1 total_weight= 4863.559 rmsd (weighted)= 1.250 (unweighted)= 58.022 superimposing iter= 2 total_weight= 2093.950 rmsd (weighted)= 1.040 (unweighted)= 58.054 superimposing iter= 3 total_weight= 1667.842 rmsd (weighted)= 0.973 (unweighted)= 58.076 superimposing iter= 4 total_weight= 1556.274 rmsd (weighted)= 0.945 (unweighted)= 58.089 superimposing iter= 5 total_weight= 1518.777 rmsd (weighted)= 0.929 (unweighted)= 58.097 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 1.215 rmsd (weighted)= 3.038 (unweighted)= 40.237 superimposing iter= 1 total_weight= 5000.567 rmsd (weighted)= 1.610 (unweighted)= 40.264 superimposing iter= 2 total_weight= 2353.764 rmsd (weighted)= 1.289 (unweighted)= 40.232 superimposing iter= 3 total_weight= 1738.372 rmsd (weighted)= 1.207 (unweighted)= 40.209 superimposing iter= 4 total_weight= 1609.520 rmsd (weighted)= 1.176 (unweighted)= 40.191 superimposing iter= 5 total_weight= 1570.144 rmsd (weighted)= 1.159 (unweighted)= 40.175 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 1.208 rmsd (weighted)= 2.348 (unweighted)= 35.769 superimposing iter= 1 total_weight= 6309.356 rmsd (weighted)= 1.071 (unweighted)= 35.681 superimposing iter= 2 total_weight= 2805.451 rmsd (weighted)= 0.770 (unweighted)= 35.639 superimposing iter= 3 total_weight= 1951.470 rmsd (weighted)= 0.668 (unweighted)= 35.634 superimposing iter= 4 total_weight= 1661.044 rmsd (weighted)= 0.629 (unweighted)= 35.637 superimposing iter= 5 total_weight= 1549.977 rmsd (weighted)= 0.613 (unweighted)= 35.640 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 1.194 rmsd (weighted)= 2.378 (unweighted)= 28.029 superimposing iter= 1 total_weight= 4376.607 rmsd (weighted)= 1.328 (unweighted)= 28.056 superimposing iter= 2 total_weight= 2339.780 rmsd (weighted)= 1.047 (unweighted)= 28.011 superimposing iter= 3 total_weight= 1844.404 rmsd (weighted)= 0.937 (unweighted)= 27.973 superimposing iter= 4 total_weight= 1670.342 rmsd (weighted)= 0.882 (unweighted)= 27.957 superimposing iter= 5 total_weight= 1575.396 rmsd (weighted)= 0.856 (unweighted)= 27.951 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 1.124 rmsd (weighted)= 3.929 (unweighted)= 55.061 superimposing iter= 1 total_weight= 3762.330 rmsd (weighted)= 2.352 (unweighted)= 54.975 superimposing iter= 2 total_weight= 1800.474 rmsd (weighted)= 2.071 (unweighted)= 54.936 superimposing iter= 3 total_weight= 1522.897 rmsd (weighted)= 1.988 (unweighted)= 54.903 superimposing iter= 4 total_weight= 1474.597 rmsd (weighted)= 1.939 (unweighted)= 54.867 superimposing iter= 5 total_weight= 1465.528 rmsd (weighted)= 1.899 (unweighted)= 54.830 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 1.256 rmsd (weighted)= 2.124 (unweighted)= 46.599 superimposing iter= 1 total_weight= 5674.804 rmsd (weighted)= 1.067 (unweighted)= 46.739 superimposing iter= 2 total_weight= 2518.905 rmsd (weighted)= 0.827 (unweighted)= 46.787 superimposing iter= 3 total_weight= 1915.760 rmsd (weighted)= 0.740 (unweighted)= 46.795 superimposing iter= 4 total_weight= 1700.016 rmsd (weighted)= 0.705 (unweighted)= 46.793 superimposing iter= 5 total_weight= 1607.821 rmsd (weighted)= 0.692 (unweighted)= 46.791 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 1.142 rmsd (weighted)= 2.341 (unweighted)= 48.869 superimposing iter= 1 total_weight= 4318.647 rmsd (weighted)= 1.284 (unweighted)= 48.960 superimposing iter= 2 total_weight= 2215.623 rmsd (weighted)= 1.021 (unweighted)= 48.948 superimposing iter= 3 total_weight= 1701.806 rmsd (weighted)= 0.932 (unweighted)= 48.932 superimposing iter= 4 total_weight= 1568.694 rmsd (weighted)= 0.888 (unweighted)= 48.922 superimposing iter= 5 total_weight= 1508.700 rmsd (weighted)= 0.864 (unweighted)= 48.917 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 1.094 rmsd (weighted)= 3.551 (unweighted)= 54.794 superimposing iter= 1 total_weight= 4961.970 rmsd (weighted)= 1.776 (unweighted)= 54.674 superimposing iter= 2 total_weight= 2271.056 rmsd (weighted)= 1.356 (unweighted)= 54.635 superimposing iter= 3 total_weight= 1748.124 rmsd (weighted)= 1.191 (unweighted)= 54.628 superimposing iter= 4 total_weight= 1564.792 rmsd (weighted)= 1.109 (unweighted)= 54.630 superimposing iter= 5 total_weight= 1472.652 rmsd (weighted)= 1.067 (unweighted)= 54.632 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 1.230 rmsd (weighted)= 2.297 (unweighted)= 38.541 superimposing iter= 1 total_weight= 5862.553 rmsd (weighted)= 1.120 (unweighted)= 38.627 superimposing iter= 2 total_weight= 2699.336 rmsd (weighted)= 0.829 (unweighted)= 38.660 superimposing iter= 3 total_weight= 2227.487 rmsd (weighted)= 0.676 (unweighted)= 38.682 superimposing iter= 4 total_weight= 1885.829 rmsd (weighted)= 0.598 (unweighted)= 38.685 superimposing iter= 5 total_weight= 1728.128 rmsd (weighted)= 0.553 (unweighted)= 38.675 superimposing iter= 0 total_weight= 1.149 rmsd (weighted)= 3.684 (unweighted)= 36.462 superimposing iter= 1 total_weight= 3995.900 rmsd (weighted)= 2.192 (unweighted)= 36.537 superimposing iter= 2 total_weight= 1668.093 rmsd (weighted)= 2.036 (unweighted)= 36.573 superimposing iter= 3 total_weight= 1554.152 rmsd (weighted)= 1.962 (unweighted)= 36.592 superimposing iter= 4 total_weight= 1570.920 rmsd (weighted)= 1.881 (unweighted)= 36.603 superimposing iter= 5 total_weight= 1610.010 rmsd (weighted)= 1.781 (unweighted)= 36.612 superimposing iter= 0 total_weight= 1.173 rmsd (weighted)= 2.353 (unweighted)= 58.023 superimposing iter= 1 total_weight= 4863.939 rmsd (weighted)= 1.250 (unweighted)= 58.044 superimposing iter= 2 total_weight= 2093.047 rmsd (weighted)= 1.040 (unweighted)= 58.076 superimposing iter= 3 total_weight= 1667.314 rmsd (weighted)= 0.974 (unweighted)= 58.098 superimposing iter= 4 total_weight= 1556.678 rmsd (weighted)= 0.945 (unweighted)= 58.112 superimposing iter= 5 total_weight= 1519.036 rmsd (weighted)= 0.929 (unweighted)= 58.120 superimposing iter= 0 total_weight= 1.215 rmsd (weighted)= 3.039 (unweighted)= 40.239 superimposing iter= 1 total_weight= 4999.772 rmsd (weighted)= 1.611 (unweighted)= 40.266 superimposing iter= 2 total_weight= 2355.747 rmsd (weighted)= 1.289 (unweighted)= 40.233 superimposing iter= 3 total_weight= 1738.776 rmsd (weighted)= 1.207 (unweighted)= 40.211 superimposing iter= 4 total_weight= 1609.876 rmsd (weighted)= 1.175 (unweighted)= 40.192 superimposing iter= 5 total_weight= 1570.357 rmsd (weighted)= 1.159 (unweighted)= 40.176 superimposing iter= 0 total_weight= 1.208 rmsd (weighted)= 2.348 (unweighted)= 35.755 superimposing iter= 1 total_weight= 6316.263 rmsd (weighted)= 1.070 (unweighted)= 35.668 superimposing iter= 2 total_weight= 2807.852 rmsd (weighted)= 0.769 (unweighted)= 35.627 superimposing iter= 3 total_weight= 1950.878 rmsd (weighted)= 0.668 (unweighted)= 35.622 superimposing iter= 4 total_weight= 1660.798 rmsd (weighted)= 0.629 (unweighted)= 35.625 superimposing iter= 5 total_weight= 1551.251 rmsd (weighted)= 0.613 (unweighted)= 35.628 superimposing iter= 0 total_weight= 1.194 rmsd (weighted)= 2.378 (unweighted)= 28.028 superimposing iter= 1 total_weight= 4376.895 rmsd (weighted)= 1.328 (unweighted)= 28.056 superimposing iter= 2 total_weight= 2339.210 rmsd (weighted)= 1.047 (unweighted)= 28.010 superimposing iter= 3 total_weight= 1843.871 rmsd (weighted)= 0.937 (unweighted)= 27.973 superimposing iter= 4 total_weight= 1670.123 rmsd (weighted)= 0.882 (unweighted)= 27.957 superimposing iter= 5 total_weight= 1575.003 rmsd (weighted)= 0.856 (unweighted)= 27.951 superimposing iter= 0 total_weight= 1.124 rmsd (weighted)= 3.929 (unweighted)= 55.084 superimposing iter= 1 total_weight= 3763.044 rmsd (weighted)= 2.352 (unweighted)= 54.999 superimposing iter= 2 total_weight= 1800.355 rmsd (weighted)= 2.071 (unweighted)= 54.961 superimposing iter= 3 total_weight= 1522.641 rmsd (weighted)= 1.988 (unweighted)= 54.928 superimposing iter= 4 total_weight= 1474.347 rmsd (weighted)= 1.940 (unweighted)= 54.893 superimposing iter= 5 total_weight= 1464.821 rmsd (weighted)= 1.900 (unweighted)= 54.856 superimposing iter= 0 total_weight= 1.256 rmsd (weighted)= 2.125 (unweighted)= 46.619 superimposing iter= 1 total_weight= 5677.196 rmsd (weighted)= 1.067 (unweighted)= 46.760 superimposing iter= 2 total_weight= 2529.244 rmsd (weighted)= 0.825 (unweighted)= 46.809 superimposing iter= 3 total_weight= 1924.496 rmsd (weighted)= 0.736 (unweighted)= 46.816 superimposing iter= 4 total_weight= 1706.215 rmsd (weighted)= 0.700 (unweighted)= 46.814 superimposing iter= 5 total_weight= 1611.599 rmsd (weighted)= 0.685 (unweighted)= 46.811 superimposing iter= 0 total_weight= 1.142 rmsd (weighted)= 2.341 (unweighted)= 48.888 superimposing iter= 1 total_weight= 4321.451 rmsd (weighted)= 1.283 (unweighted)= 48.980 superimposing iter= 2 total_weight= 2216.034 rmsd (weighted)= 1.020 (unweighted)= 48.968 superimposing iter= 3 total_weight= 1701.514 rmsd (weighted)= 0.931 (unweighted)= 48.952 superimposing iter= 4 total_weight= 1567.544 rmsd (weighted)= 0.888 (unweighted)= 48.943 superimposing iter= 5 total_weight= 1507.862 rmsd (weighted)= 0.864 (unweighted)= 48.938 superimposing iter= 0 total_weight= 1.094 rmsd (weighted)= 3.551 (unweighted)= 54.788 superimposing iter= 1 total_weight= 4964.273 rmsd (weighted)= 1.775 (unweighted)= 54.667 superimposing iter= 2 total_weight= 2273.178 rmsd (weighted)= 1.355 (unweighted)= 54.628 superimposing iter= 3 total_weight= 1749.045 rmsd (weighted)= 1.189 (unweighted)= 54.620 superimposing iter= 4 total_weight= 1564.866 rmsd (weighted)= 1.108 (unweighted)= 54.622 superimposing iter= 5 total_weight= 1472.263 rmsd (weighted)= 1.065 (unweighted)= 54.624 superimposing iter= 0 total_weight= 1.230 rmsd (weighted)= 2.297 (unweighted)= 38.557 superimposing iter= 1 total_weight= 5854.429 rmsd (weighted)= 1.120 (unweighted)= 38.647 superimposing iter= 2 total_weight= 2660.490 rmsd (weighted)= 0.837 (unweighted)= 38.685 superimposing iter= 3 total_weight= 2250.351 rmsd (weighted)= 0.679 (unweighted)= 38.716 superimposing iter= 4 total_weight= 1902.702 rmsd (weighted)= 0.599 (unweighted)= 38.724 superimposing iter= 5 total_weight= 1740.645 rmsd (weighted)= 0.553 (unweighted)= 38.718 # command:# Printing sheets for alignments to T0611.undertaker-align.sheets # command: