# command:# Seed set to 1273998660 # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading dunbrack-2191.atoms # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 53157 examples # computed average trans backbone unit before proline from 2010 examples # computed average cis backbone unit from 97 examples # trans (non-proline) backbone unit: # CA= -2.2087 1.0126 -0.0030 # O= -0.1499 2.2440 0.0016 # C= -0.6889 1.1368 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4581 0.0000 0.0000 # cis backbone unit: # CA= -0.1436 2.4534 -0.0002 # O= -2.0284 0.9742 0.0015 # C= -0.8018 1.0771 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4668 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2100 1.0631 -0.0014 # O= -0.1236 2.2458 0.0075 # C= -0.6872 1.1517 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading dunbrack-2191.atoms have 2191 chains in training database # Count of chains,residues,atoms: 2191,500310,3902258 # 493441 residues have no bad marker # 3226 residues lack atoms needed to compute omega # 1453 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 4 # HAS_OXT 1167 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 3052 # HAS_UNKNOWN_ATOMS 9 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 979 # NON_PLANAR_PEPTIDE 55 # BAD_PEPTIDE 2680 # HIGH_B_FACTOR 0 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-2191.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:CPU_time= 24.383 sec, elapsed time= 25.335 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= 37.429 sec, elapsed time= 41.893 sec. # command:# Prefix for input files set to # command:# Making conformation for sequence T0538 numbered 1 through 54 Created new target T0538 from T0538.a2m # command:# command:# No conformations to remove in PopConform # command:CPU_time= 37.429 sec, elapsed time= 42.155 sec. # command:# Prefix for input files set to # command:# reading script from file T0538.undertaker-align.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2kruA/T0538-2kruA-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 2kruA expands to /projects/compbio/data/pdb/2kru.pdb.gz 2kruA:# T0538 read from 2kruA/T0538-2kruA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2kruA read from 2kruA/T0538-2kruA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2kruA to template set # found chain 2kruA in template set T0538 1 :MNLRWTSEAKTKLKNIPFFARSQAKARIEQLARQAEQDIVTPELVEQARLEFGQ 2kruA 2 :GELSWTAEAEKMLGKVPFFVRKKVRKNTDNYAREIGEPVVTADVFRKAKEHLGG # choosing archetypes in rotamer library Number of specific fragments extracted= 1 number of extra gaps= 0 total=1 # request to SCWRL produces command: ulimit -t 49 ; scwrl4 -t -i /var/tmp/to_scwrl_807341095.pdb -s /var/tmp/to_scwrl_807341095.seq -o /var/tmp/from_scwrl_807341095.pdb > /var/tmp/scwrl_807341095.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_807341095.pdb Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3aetB/T0538-3aetB-t04-local-adpstyle1.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 3aetB expands to /projects/compbio/data/pdb/3aet.pdb.gz 3aetB:# T0538 read from 3aetB/T0538-3aetB-t04-local-adpstyle1.a2m # 3aetB read from 3aetB/T0538-3aetB-t04-local-adpstyle1.a2m # adding 3aetB to template set # found chain 3aetB in template set Number of specific fragments extracted= 0 number of extra gaps= 0 total=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3aeuB/T0538-3aeuB-t04-local-adpstyle1.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 3aeuB expands to /projects/compbio/data/pdb/3aeu.pdb.gz 3aeuB:# T0538 read from 3aeuB/T0538-3aeuB-t04-local-adpstyle1.a2m # 3aeuB read from 3aeuB/T0538-3aeuB-t04-local-adpstyle1.a2m # adding 3aeuB to template set # found chain 3aeuB in template set Number of specific fragments extracted= 0 number of extra gaps= 0 total=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3aekB/T0538-3aekB-t04-local-adpstyle1.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 3aekB expands to /projects/compbio/data/pdb/3aek.pdb.gz 3aekB:Skipped atom 5757, because occupancy 0.5 <= existing 0.500 in 3aekB Skipped atom 5759, because occupancy 0.500 <= existing 0.500 in 3aekB Skipped atom 5761, because occupancy 0.500 <= existing 0.500 in 3aekB Skipped atom 5763, because occupancy 0.500 <= existing 0.500 in 3aekB Skipped atom 5765, because occupancy 0.500 <= existing 0.500 in 3aekB Skipped atom 5767, because occupancy 0.500 <= existing 0.500 in 3aekB Skipped atom 5769, because occupancy 0.500 <= existing 0.500 in 3aekB Skipped atom 5771, because occupancy 0.500 <= existing 0.500 in 3aekB Skipped atom 5773, because occupancy 0.500 <= existing 0.500 in 3aekB # T0538 read from 3aekB/T0538-3aekB-t04-local-adpstyle1.a2m # 3aekB read from 3aekB/T0538-3aekB-t04-local-adpstyle1.a2m # adding 3aekB to template set # found chain 3aekB in template set Number of specific fragments extracted= 0 number of extra gaps= 0 total=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a7wA/T0538-1a7wA-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 1a7wA expands to /projects/compbio/data/pdb/1a7w.pdb.gz 1a7wA:Skipped atom 265, because occupancy 0.500 <= existing 0.500 in 1a7wA Skipped atom 267, because occupancy 0.500 <= existing 0.500 in 1a7wA Skipped atom 269, because occupancy 0.500 <= existing 0.500 in 1a7wA Skipped atom 312, because occupancy 0.500 <= existing 0.500 in 1a7wA # T0538 read from 1a7wA/T0538-1a7wA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1a7wA read from 1a7wA/T0538-1a7wA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1a7wA to template set # found chain 1a7wA in template set Warning: unaligning (T0538)G53 because last residue in template chain is (1a7wA)K68 T0538 4 :RWTSEAKTKLKNIPFFARSQAKARIEQLARQAEQDIVTPELVEQARLEF 1a7wA 19 :RVSDDARITLAKILEEMGRDIASEAIKLARHAGRKTIKAEDIELAVRRF Number of specific fragments extracted= 1 number of extra gaps= 0 total=2 # request to SCWRL produces command: ulimit -t 49 ; scwrl4 -t -i /var/tmp/to_scwrl_1800383025.pdb -s /var/tmp/to_scwrl_1800383025.seq -o /var/tmp/from_scwrl_1800383025.pdb > /var/tmp/scwrl_1800383025.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1800383025.pdb Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a7w/T0538-1a7w-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 1a7w expands to /projects/compbio/data/pdb/1a7w.pdb.gz 1a7w:Warning: there is no chain 1a7w will retry with 1a7wA Skipped atom 265, because occupancy 0.500 <= existing 0.500 in 1a7w Skipped atom 267, because occupancy 0.500 <= existing 0.500 in 1a7w Skipped atom 269, because occupancy 0.500 <= existing 0.500 in 1a7w Skipped atom 312, because occupancy 0.500 <= existing 0.500 in 1a7w # T0538 read from 1a7w/T0538-1a7w-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1a7w read from 1a7w/T0538-1a7w-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1a7w to template set # found chain 1a7w in template set Warning: unaligning (T0538)G53 because last residue in template chain is (1a7w)K68 T0538 4 :RWTSEAKTKLKNIPFFARSQAKARIEQLARQAEQDIVTPELVEQARLEF 1a7w 19 :RVSDDARITLAKILEEMGRDIASEAIKLARHAGRKTIKAEDIELAVRRF Number of specific fragments extracted= 1 number of extra gaps= 0 total=3 # request to SCWRL produces command: ulimit -t 49 ; scwrl4 -t -i /var/tmp/to_scwrl_1070410715.pdb -s /var/tmp/to_scwrl_1070410715.seq -o /var/tmp/from_scwrl_1070410715.pdb > /var/tmp/scwrl_1070410715.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1070410715.pdb Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g8iA/T0538-1g8iA-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 1g8iA expands to /projects/compbio/data/pdb/1g8i.pdb.gz 1g8iA:Skipped atom 300, because occupancy 0.500 <= existing 0.500 in 1g8iA Skipped atom 565, because occupancy 0.500 <= existing 0.500 in 1g8iA Skipped atom 567, because occupancy 0.500 <= existing 0.500 in 1g8iA Skipped atom 670, because occupancy 0.500 <= existing 0.500 in 1g8iA Skipped atom 733, because occupancy 0.500 <= existing 0.500 in 1g8iA Skipped atom 735, because occupancy 0.500 <= existing 0.500 in 1g8iA Skipped atom 749, because occupancy 0.500 <= existing 0.500 in 1g8iA Skipped atom 963, because occupancy 0.500 <= existing 0.500 in 1g8iA Skipped atom 965, because occupancy 0.500 <= existing 0.500 in 1g8iA Skipped atom 967, because occupancy 0.500 <= existing 0.500 in 1g8iA Skipped atom 969, because occupancy 0.500 <= existing 0.500 in 1g8iA Skipped atom 1451, because occupancy 0.500 <= existing 0.500 in 1g8iA # T0538 read from 1g8iA/T0538-1g8iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1g8iA read from 1g8iA/T0538-1g8iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1g8iA to template set # found chain 1g8iA in template set T0538 1 :MNLRWTSEAKTKLKNIPFFARSQAKARIEQLARQAEQDIVTPELVEQARLEF 1g8iA 4 :SNSKLKPEVVEELTRKTYFTEKEVQQWYKGFIKDCPSGQLDAAGFQKIYKQF Number of specific fragments extracted= 1 number of extra gaps= 0 total=4 # request to SCWRL produces command: ulimit -t 49 ; scwrl4 -t -i /var/tmp/to_scwrl_907585786.pdb -s /var/tmp/to_scwrl_907585786.seq -o /var/tmp/from_scwrl_907585786.pdb > /var/tmp/scwrl_907585786.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_907585786.pdb Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2da4A/T0538-2da4A-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 2da4A expands to /projects/compbio/data/pdb/2da4.pdb.gz 2da4A:# T0538 read from 2da4A/T0538-2da4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2da4A read from 2da4A/T0538-2da4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2da4A to template set # found chain 2da4A in template set T0538 1 :MNLRWTSEAKTKLKN 2da4A 11 :DRTQFSDRDLATLKK T0538 22 :SQAKARIEQLARQAEQ 2da4A 36 :SVCREKIEAVATELNV T0538 41 :TPELVEQARLEF 2da4A 52 :DCEIVRTWIGNR Number of specific fragments extracted= 3 number of extra gaps= 0 total=7 # request to SCWRL produces command: ulimit -t 49 ; scwrl4 -t -i /var/tmp/to_scwrl_1938579466.pdb -s /var/tmp/to_scwrl_1938579466.seq -o /var/tmp/from_scwrl_1938579466.pdb > /var/tmp/scwrl_1938579466.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1938579466.pdb Number of alignments=5 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c9oA/T0538-2c9oA-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 2c9oA expands to /projects/compbio/data/pdb/2c9o.pdb.gz 2c9oA:# T0538 read from 2c9oA/T0538-2c9oA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c9oA read from 2c9oA/T0538-2c9oA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2c9oA to template set # found chain 2c9oA in template set T0538 2 :NLRWTSEAKTKLKN 2c9oA 383 :GINISEEALNHLGE T0538 16 :IPFFARSQAKARIEQLARQAEQDIVTPELVEQARLEF 2c9oA 401 :TTLRYSVQLLTPANLLAKINGKDSIEKEHVEEISELF Number of specific fragments extracted= 2 number of extra gaps= 0 total=9 # request to SCWRL produces command: ulimit -t 49 ; scwrl4 -t -i /var/tmp/to_scwrl_1747735430.pdb -s /var/tmp/to_scwrl_1747735430.seq -o /var/tmp/from_scwrl_1747735430.pdb > /var/tmp/scwrl_1747735430.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1747735430.pdb Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jfiB/T0538-1jfiB-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 1jfiB expands to /projects/compbio/data/pdb/1jfi.pdb.gz 1jfiB:# T0538 read from 1jfiB/T0538-1jfiB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jfiB read from 1jfiB/T0538-1jfiB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1jfiB to template set # found chain 1jfiB in template set T0538 2 :NLRWTSEAKTKLKN 1jfiB 128 :NVRVANDARELVVN T0538 20 :ARSQAKARIEQLARQAEQDIVTPELVEQARLEFG 1jfiB 146 :FIHLISSEANEICNKSEKKTISPEHVIQALESLG Number of specific fragments extracted= 2 number of extra gaps= 0 total=11 # request to SCWRL produces command: ulimit -t 49 ; scwrl4 -t -i /var/tmp/to_scwrl_1850235212.pdb -s /var/tmp/to_scwrl_1850235212.seq -o /var/tmp/from_scwrl_1850235212.pdb > /var/tmp/scwrl_1850235212.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1850235212.pdb Number of alignments=7 # command:Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.489 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 1 total_weight= 4420.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 2 total_weight= 4420.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 3 total_weight= 4420.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 4 total_weight= 4420.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 5 total_weight= 4420.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 1.360 rmsd (weighted)= 10.905 (unweighted)= 12.017 superimposing iter= 1 total_weight= 1261.135 rmsd (weighted)= 5.121 (unweighted)= 12.979 superimposing iter= 2 total_weight= 826.307 rmsd (weighted)= 3.174 (unweighted)= 13.841 superimposing iter= 3 total_weight= 705.412 rmsd (weighted)= 2.272 (unweighted)= 14.247 superimposing iter= 4 total_weight= 514.146 rmsd (weighted)= 1.971 (unweighted)= 14.362 superimposing iter= 5 total_weight= 437.334 rmsd (weighted)= 1.876 (unweighted)= 14.408 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 1.360 rmsd (weighted)= 10.905 (unweighted)= 12.017 superimposing iter= 1 total_weight= 1261.135 rmsd (weighted)= 5.121 (unweighted)= 12.979 superimposing iter= 2 total_weight= 826.307 rmsd (weighted)= 3.174 (unweighted)= 13.841 superimposing iter= 3 total_weight= 705.412 rmsd (weighted)= 2.272 (unweighted)= 14.247 superimposing iter= 4 total_weight= 514.146 rmsd (weighted)= 1.971 (unweighted)= 14.362 superimposing iter= 5 total_weight= 437.334 rmsd (weighted)= 1.876 (unweighted)= 14.408 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 1.441 rmsd (weighted)= 7.267 (unweighted)= 7.944 superimposing iter= 1 total_weight= 997.702 rmsd (weighted)= 4.540 (unweighted)= 8.158 superimposing iter= 2 total_weight= 656.060 rmsd (weighted)= 3.541 (unweighted)= 8.498 superimposing iter= 3 total_weight= 579.438 rmsd (weighted)= 2.966 (unweighted)= 8.833 superimposing iter= 4 total_weight= 518.461 rmsd (weighted)= 2.646 (unweighted)= 9.133 superimposing iter= 5 total_weight= 489.443 rmsd (weighted)= 2.436 (unweighted)= 9.410 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 1.188 rmsd (weighted)= 10.664 (unweighted)= 13.027 superimposing iter= 1 total_weight= 999.846 rmsd (weighted)= 5.920 (unweighted)= 13.405 superimposing iter= 2 total_weight= 617.675 rmsd (weighted)= 4.309 (unweighted)= 13.686 superimposing iter= 3 total_weight= 516.333 rmsd (weighted)= 3.448 (unweighted)= 13.952 superimposing iter= 4 total_weight= 507.137 rmsd (weighted)= 2.772 (unweighted)= 14.253 superimposing iter= 5 total_weight= 535.242 rmsd (weighted)= 2.161 (unweighted)= 14.532 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 1.414 rmsd (weighted)= 2.794 (unweighted)= 12.872 superimposing iter= 1 total_weight= 1438.842 rmsd (weighted)= 1.425 (unweighted)= 12.927 superimposing iter= 2 total_weight= 728.377 rmsd (weighted)= 1.055 (unweighted)= 12.969 superimposing iter= 3 total_weight= 538.787 rmsd (weighted)= 0.913 (unweighted)= 13.002 superimposing iter= 4 total_weight= 476.290 rmsd (weighted)= 0.844 (unweighted)= 13.028 superimposing iter= 5 total_weight= 447.858 rmsd (weighted)= 0.805 (unweighted)= 13.048 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 1.312 rmsd (weighted)= 13.084 (unweighted)= 44.967 superimposing iter= 1 total_weight= 1220.199 rmsd (weighted)= 5.981 (unweighted)= 43.950 superimposing iter= 2 total_weight= 977.732 rmsd (weighted)= 3.202 (unweighted)= 43.449 superimposing iter= 3 total_weight= 789.676 rmsd (weighted)= 2.089 (unweighted)= 43.258 superimposing iter= 4 total_weight= 543.148 rmsd (weighted)= 1.730 (unweighted)= 43.216 superimposing iter= 5 total_weight= 421.575 rmsd (weighted)= 1.645 (unweighted)= 43.214 Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.489 rmsd (weighted)= 5.253 (unweighted)= 5.491 superimposing iter= 1 total_weight= 1218.038 rmsd (weighted)= 2.928 (unweighted)= 5.656 superimposing iter= 2 total_weight= 709.602 rmsd (weighted)= 2.223 (unweighted)= 5.844 superimposing iter= 3 total_weight= 603.812 rmsd (weighted)= 1.850 (unweighted)= 5.991 superimposing iter= 4 total_weight= 531.804 rmsd (weighted)= 1.651 (unweighted)= 6.100 superimposing iter= 5 total_weight= 512.520 rmsd (weighted)= 1.510 (unweighted)= 6.174 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 1.360 rmsd (weighted)= 6.540 (unweighted)= 8.308 superimposing iter= 1 total_weight= 1316.061 rmsd (weighted)= 3.080 (unweighted)= 8.794 superimposing iter= 2 total_weight= 795.500 rmsd (weighted)= 2.058 (unweighted)= 9.084 superimposing iter= 3 total_weight= 571.958 rmsd (weighted)= 1.695 (unweighted)= 9.208 superimposing iter= 4 total_weight= 464.952 rmsd (weighted)= 1.568 (unweighted)= 9.257 superimposing iter= 5 total_weight= 425.569 rmsd (weighted)= 1.521 (unweighted)= 9.281 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 1.360 rmsd (weighted)= 6.540 (unweighted)= 8.308 superimposing iter= 1 total_weight= 1316.061 rmsd (weighted)= 3.080 (unweighted)= 8.794 superimposing iter= 2 total_weight= 795.500 rmsd (weighted)= 2.058 (unweighted)= 9.084 superimposing iter= 3 total_weight= 571.958 rmsd (weighted)= 1.695 (unweighted)= 9.208 superimposing iter= 4 total_weight= 464.952 rmsd (weighted)= 1.568 (unweighted)= 9.257 superimposing iter= 5 total_weight= 425.569 rmsd (weighted)= 1.521 (unweighted)= 9.281 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 1.441 rmsd (weighted)= 7.019 (unweighted)= 7.875 superimposing iter= 1 total_weight= 772.297 rmsd (weighted)= 5.009 (unweighted)= 8.052 superimposing iter= 2 total_weight= 599.932 rmsd (weighted)= 4.109 (unweighted)= 8.295 superimposing iter= 3 total_weight= 607.361 rmsd (weighted)= 3.369 (unweighted)= 8.552 superimposing iter= 4 total_weight= 610.515 rmsd (weighted)= 2.763 (unweighted)= 8.768 superimposing iter= 5 total_weight= 566.268 rmsd (weighted)= 2.359 (unweighted)= 8.917 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 1.188 rmsd (weighted)= 10.225 (unweighted)= 12.419 superimposing iter= 1 total_weight= 547.389 rmsd (weighted)= 8.024 (unweighted)= 12.675 superimposing iter= 2 total_weight= 454.636 rmsd (weighted)= 6.887 (unweighted)= 13.019 superimposing iter= 3 total_weight= 448.419 rmsd (weighted)= 6.002 (unweighted)= 13.257 superimposing iter= 4 total_weight= 399.503 rmsd (weighted)= 5.575 (unweighted)= 13.427 superimposing iter= 5 total_weight= 376.057 rmsd (weighted)= 5.333 (unweighted)= 13.634 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 1.414 rmsd (weighted)= 5.546 (unweighted)= 14.312 superimposing iter= 1 total_weight= 1128.668 rmsd (weighted)= 3.083 (unweighted)= 14.365 superimposing iter= 2 total_weight= 794.867 rmsd (weighted)= 2.133 (unweighted)= 14.437 superimposing iter= 3 total_weight= 615.266 rmsd (weighted)= 1.735 (unweighted)= 14.470 superimposing iter= 4 total_weight= 488.509 rmsd (weighted)= 1.594 (unweighted)= 14.490 superimposing iter= 5 total_weight= 448.082 rmsd (weighted)= 1.532 (unweighted)= 14.501 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 1.312 rmsd (weighted)= 9.014 (unweighted)= 42.517 superimposing iter= 1 total_weight= 1295.066 rmsd (weighted)= 4.041 (unweighted)= 41.868 superimposing iter= 2 total_weight= 893.249 rmsd (weighted)= 2.407 (unweighted)= 41.587 superimposing iter= 3 total_weight= 628.515 rmsd (weighted)= 1.833 (unweighted)= 41.484 superimposing iter= 4 total_weight= 452.903 rmsd (weighted)= 1.677 (unweighted)= 41.426 superimposing iter= 5 total_weight= 406.170 rmsd (weighted)= 1.628 (unweighted)= 41.387 Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.489 rmsd (weighted)= 5.601 (unweighted)= 5.837 superimposing iter= 1 total_weight= 1250.862 rmsd (weighted)= 3.088 (unweighted)= 5.990 superimposing iter= 2 total_weight= 637.834 rmsd (weighted)= 2.498 (unweighted)= 6.180 superimposing iter= 3 total_weight= 494.680 rmsd (weighted)= 2.316 (unweighted)= 6.360 superimposing iter= 4 total_weight= 473.121 rmsd (weighted)= 2.206 (unweighted)= 6.520 superimposing iter= 5 total_weight= 466.014 rmsd (weighted)= 2.124 (unweighted)= 6.653 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 1.360 rmsd (weighted)= 6.214 (unweighted)= 7.953 superimposing iter= 1 total_weight= 1448.761 rmsd (weighted)= 2.735 (unweighted)= 8.403 superimposing iter= 2 total_weight= 925.458 rmsd (weighted)= 1.667 (unweighted)= 8.730 superimposing iter= 3 total_weight= 697.714 rmsd (weighted)= 1.230 (unweighted)= 8.875 superimposing iter= 4 total_weight= 544.589 rmsd (weighted)= 1.047 (unweighted)= 8.942 superimposing iter= 5 total_weight= 461.661 rmsd (weighted)= 0.973 (unweighted)= 8.975 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 1.360 rmsd (weighted)= 6.214 (unweighted)= 7.953 superimposing iter= 1 total_weight= 1448.761 rmsd (weighted)= 2.735 (unweighted)= 8.403 superimposing iter= 2 total_weight= 925.458 rmsd (weighted)= 1.667 (unweighted)= 8.730 superimposing iter= 3 total_weight= 697.714 rmsd (weighted)= 1.230 (unweighted)= 8.875 superimposing iter= 4 total_weight= 544.589 rmsd (weighted)= 1.047 (unweighted)= 8.942 superimposing iter= 5 total_weight= 461.661 rmsd (weighted)= 0.973 (unweighted)= 8.975 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 1.441 rmsd (weighted)= 6.770 (unweighted)= 7.616 superimposing iter= 1 total_weight= 764.672 rmsd (weighted)= 4.935 (unweighted)= 7.733 superimposing iter= 2 total_weight= 532.907 rmsd (weighted)= 4.358 (unweighted)= 7.866 superimposing iter= 3 total_weight= 495.855 rmsd (weighted)= 4.008 (unweighted)= 7.996 superimposing iter= 4 total_weight= 482.510 rmsd (weighted)= 3.741 (unweighted)= 8.120 superimposing iter= 5 total_weight= 477.120 rmsd (weighted)= 3.514 (unweighted)= 8.223 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 1.188 rmsd (weighted)= 10.161 (unweighted)= 12.245 superimposing iter= 1 total_weight= 535.736 rmsd (weighted)= 8.078 (unweighted)= 12.455 superimposing iter= 2 total_weight= 427.740 rmsd (weighted)= 7.146 (unweighted)= 12.980 superimposing iter= 3 total_weight= 458.335 rmsd (weighted)= 6.108 (unweighted)= 13.544 superimposing iter= 4 total_weight= 442.374 rmsd (weighted)= 5.332 (unweighted)= 13.910 superimposing iter= 5 total_weight= 443.484 rmsd (weighted)= 4.659 (unweighted)= 14.141 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 1.414 rmsd (weighted)= 5.925 (unweighted)= 14.200 superimposing iter= 1 total_weight= 1143.758 rmsd (weighted)= 3.325 (unweighted)= 14.223 superimposing iter= 2 total_weight= 667.638 rmsd (weighted)= 2.533 (unweighted)= 14.274 superimposing iter= 3 total_weight= 528.662 rmsd (weighted)= 2.217 (unweighted)= 14.311 superimposing iter= 4 total_weight= 464.098 rmsd (weighted)= 2.087 (unweighted)= 14.336 superimposing iter= 5 total_weight= 435.118 rmsd (weighted)= 2.034 (unweighted)= 14.354 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 1.312 rmsd (weighted)= 8.634 (unweighted)= 42.611 superimposing iter= 1 total_weight= 1444.852 rmsd (weighted)= 3.610 (unweighted)= 41.931 superimposing iter= 2 total_weight= 999.973 rmsd (weighted)= 1.975 (unweighted)= 41.613 superimposing iter= 3 total_weight= 807.862 rmsd (weighted)= 1.289 (unweighted)= 41.500 superimposing iter= 4 total_weight= 598.821 rmsd (weighted)= 1.016 (unweighted)= 41.468 superimposing iter= 5 total_weight= 470.377 rmsd (weighted)= 0.914 (unweighted)= 41.461 superimposing iter= 0 total_weight= 1.489 rmsd (weighted)= 5.594 (unweighted)= 5.834 superimposing iter= 1 total_weight= 1336.751 rmsd (weighted)= 2.964 (unweighted)= 5.981 superimposing iter= 2 total_weight= 653.517 rmsd (weighted)= 2.364 (unweighted)= 6.180 superimposing iter= 3 total_weight= 491.729 rmsd (weighted)= 2.195 (unweighted)= 6.363 superimposing iter= 4 total_weight= 466.870 rmsd (weighted)= 2.107 (unweighted)= 6.518 superimposing iter= 5 total_weight= 454.995 rmsd (weighted)= 2.055 (unweighted)= 6.653 superimposing iter= 0 total_weight= 1.360 rmsd (weighted)= 6.252 (unweighted)= 8.140 superimposing iter= 1 total_weight= 1500.349 rmsd (weighted)= 2.684 (unweighted)= 8.553 superimposing iter= 2 total_weight= 950.115 rmsd (weighted)= 1.604 (unweighted)= 8.860 superimposing iter= 3 total_weight= 720.752 rmsd (weighted)= 1.151 (unweighted)= 9.021 superimposing iter= 4 total_weight= 586.173 rmsd (weighted)= 0.935 (unweighted)= 9.104 superimposing iter= 5 total_weight= 505.715 rmsd (weighted)= 0.823 (unweighted)= 9.158 superimposing iter= 0 total_weight= 1.360 rmsd (weighted)= 6.252 (unweighted)= 8.140 superimposing iter= 1 total_weight= 1500.349 rmsd (weighted)= 2.684 (unweighted)= 8.553 superimposing iter= 2 total_weight= 950.115 rmsd (weighted)= 1.604 (unweighted)= 8.860 superimposing iter= 3 total_weight= 720.752 rmsd (weighted)= 1.151 (unweighted)= 9.021 superimposing iter= 4 total_weight= 586.173 rmsd (weighted)= 0.935 (unweighted)= 9.104 superimposing iter= 5 total_weight= 505.715 rmsd (weighted)= 0.823 (unweighted)= 9.158 superimposing iter= 0 total_weight= 1.441 rmsd (weighted)= 6.773 (unweighted)= 7.502 superimposing iter= 1 total_weight= 752.418 rmsd (weighted)= 4.975 (unweighted)= 7.626 superimposing iter= 2 total_weight= 541.027 rmsd (weighted)= 4.360 (unweighted)= 7.761 superimposing iter= 3 total_weight= 499.500 rmsd (weighted)= 4.001 (unweighted)= 7.882 superimposing iter= 4 total_weight= 474.992 rmsd (weighted)= 3.770 (unweighted)= 7.992 superimposing iter= 5 total_weight= 466.049 rmsd (weighted)= 3.587 (unweighted)= 8.080 superimposing iter= 0 total_weight= 1.188 rmsd (weighted)= 10.259 (unweighted)= 12.415 superimposing iter= 1 total_weight= 549.402 rmsd (weighted)= 8.032 (unweighted)= 12.651 superimposing iter= 2 total_weight= 432.108 rmsd (weighted)= 7.040 (unweighted)= 13.241 superimposing iter= 3 total_weight= 471.029 rmsd (weighted)= 5.892 (unweighted)= 13.863 superimposing iter= 4 total_weight= 487.985 rmsd (weighted)= 4.876 (unweighted)= 14.204 superimposing iter= 5 total_weight= 473.437 rmsd (weighted)= 4.112 (unweighted)= 14.394 superimposing iter= 0 total_weight= 1.414 rmsd (weighted)= 5.957 (unweighted)= 13.958 superimposing iter= 1 total_weight= 1159.728 rmsd (weighted)= 3.325 (unweighted)= 13.985 superimposing iter= 2 total_weight= 647.385 rmsd (weighted)= 2.568 (unweighted)= 14.053 superimposing iter= 3 total_weight= 517.008 rmsd (weighted)= 2.272 (unweighted)= 14.102 superimposing iter= 4 total_weight= 455.997 rmsd (weighted)= 2.156 (unweighted)= 14.140 superimposing iter= 5 total_weight= 433.796 rmsd (weighted)= 2.103 (unweighted)= 14.172 superimposing iter= 0 total_weight= 1.312 rmsd (weighted)= 8.706 (unweighted)= 42.676 superimposing iter= 1 total_weight= 1468.079 rmsd (weighted)= 3.579 (unweighted)= 42.004 superimposing iter= 2 total_weight= 1033.841 rmsd (weighted)= 1.891 (unweighted)= 41.692 superimposing iter= 3 total_weight= 882.955 rmsd (weighted)= 1.169 (unweighted)= 41.586 superimposing iter= 4 total_weight= 675.027 rmsd (weighted)= 0.863 (unweighted)= 41.551 superimposing iter= 5 total_weight= 512.500 rmsd (weighted)= 0.742 (unweighted)= 41.539 # command:# Printing sheets for alignments to T0538.undertaker-align.sheets # command: