# command:# Seed set to 1279154612 # 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= 24.194 sec, elapsed time= 25.709 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= 37.325 sec, elapsed time= 42.935 sec. # command:# Prefix for input files set to # command:# Making conformation for sequence T0632 numbered 1 through 168 Created new target T0632 from T0632.a2m # command:# command:# No conformations to remove in PopConform # command:CPU_time= 37.327 sec, elapsed time= 42.938 sec. # command:# Prefix for input files set to # command:# reading script from file T0632.undertaker-align.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b6eA/T0632-2b6eA-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 2b6eA expands to /projects/compbio/data/pdb/2b6e.pdb.gz 2b6eA: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 # T0632 read from 2b6eA/T0632-2b6eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b6eA read from 2b6eA/T0632-2b6eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2b6eA to template set # found chain 2b6eA in template set Warning: unaligning (T0632)R165 because last residue in template chain is (2b6eA)N137 T0632 34 :DGLLAKQER 2b6eA 8 :TLENLNQLC # choosing archetypes in rotamer library T0632 45 :ATYLASLTQIESQEREDGRFEVRLPIGPLVNNPLNMVHGGITATLLDTAMGQMVNRQLPDGQSAVTSELNIHYVKPGMGTYLRAVASIVHQGKQRIVVEGKVYTDQGETVAMGTGSFFVL 2b6eA 17 :SNSAVSHLGIEISAFGEDWIEATMPVDHRTMQPFGVLHGGVSVALAETIGSLAGSLCLEEGKTVVGLDINANHLRPVRSGKVTARATPINLGRNIQVWQIDIRTEENKLCCVSRLTLSVI Number of specific fragments extracted= 2 number of extra gaps= 0 total=2 # request to SCWRL produces command: ulimit -t 152 ; scwrl4 -t -i /var/tmp/to_scwrl_529063302.pdb -s /var/tmp/to_scwrl_529063302.seq -o /var/tmp/from_scwrl_529063302.pdb > /var/tmp/scwrl_529063302.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_529063302.pdb Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3f5oA/T0632-3f5oA-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 3f5oA expands to /projects/compbio/data/pdb/3f5o.pdb.gz 3f5oA:Skipped atom 471, because occupancy 0.5 <= existing 0.500 in 3f5oA Skipped atom 475, because occupancy 0.500 <= existing 0.500 in 3f5oA Skipped atom 477, because occupancy 0.500 <= existing 0.500 in 3f5oA Skipped atom 479, because occupancy 0.500 <= existing 0.500 in 3f5oA Skipped atom 481, because occupancy 0.500 <= existing 0.500 in 3f5oA Skipped atom 622, because occupancy 0.500 <= existing 0.500 in 3f5oA Skipped atom 624, because occupancy 0.500 <= existing 0.500 in 3f5oA Skipped atom 626, because occupancy 0.500 <= existing 0.500 in 3f5oA Skipped atom 628, because occupancy 0.500 <= existing 0.500 in 3f5oA Skipped atom 630, because occupancy 0.500 <= existing 0.500 in 3f5oA Skipped atom 632, because occupancy 0.500 <= existing 0.500 in 3f5oA Skipped atom 634, because occupancy 0.500 <= existing 0.500 in 3f5oA Skipped atom 636, because occupancy 0.500 <= existing 0.500 in 3f5oA Skipped atom 674, because occupancy 0.500 <= existing 0.500 in 3f5oA Skipped atom 678, because occupancy 0.500 <= existing 0.500 in 3f5oA Skipped atom 680, because occupancy 0.500 <= existing 0.500 in 3f5oA Skipped atom 682, because occupancy 0.500 <= existing 0.500 in 3f5oA Skipped atom 684, because occupancy 0.500 <= existing 0.500 in 3f5oA # T0632 read from 3f5oA/T0632-3f5oA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3f5oA read from 3f5oA/T0632-3f5oA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3f5oA to template set # found chain 3f5oA in template set Warning: unaligning (T0632)L164 because last residue in template chain is (3f5oA)G139 T0632 6 :QQDRIVDKMERFLSTANEEEK 3f5oA 4 :MTQSLREVIKAMTKARNFERV T0632 51 :LTQIESQEREDGRFEVRLPIGPLVNNPLNMVHGGITATLLDTAMGQMVNRQ 3f5oA 25 :LGKITLVSAAPGKVICEMKVEEEHTNAIGTLHGGLTATLVDNISTMALLCT T0632 103 :PDGQSAVTSELNIHYVKPGM 3f5oA 76 :ERGAPGVSVDMNITYMSPAK T0632 123 :GTYLRAVASIVHQGKQRIVVEGKVYT 3f5oA 97 :GEDIVITAHVLKQGKTLAFTSVDLTN T0632 149 :DQGETVAMGTGSFFV 3f5oA 124 :ATGKLIAQGRHTKHL Number of specific fragments extracted= 5 number of extra gaps= 0 total=7 # request to SCWRL produces command: ulimit -t 152 ; scwrl4 -t -i /var/tmp/to_scwrl_1578033515.pdb -s /var/tmp/to_scwrl_1578033515.seq -o /var/tmp/from_scwrl_1578033515.pdb > /var/tmp/scwrl_1578033515.log sh: line 1: 9114 Killed scwrl4 -t -i /var/tmp/to_scwrl_1578033515.pdb -s /var/tmp/to_scwrl_1578033515.seq -o /var/tmp/from_scwrl_1578033515.pdb > /var/tmp/scwrl_1578033515.log Error: Couldn't open file /var/tmp/from_scwrl_1578033515.pdb or /var/tmp/from_scwrl_1578033515.pdb.gz for input Warning: Couldn't open file /var/tmp/from_scwrl_1578033515_b.pdb or /var/tmp/from_scwrl_1578033515_b.pdb.gz for input Trying /var/tmp/from_scwrl_1578033515_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_1578033515_b.pdb or /var/tmp/from_scwrl_1578033515_b.pdb.gz for input Warning: Couldn't open file /var/tmp/from_scwrl_1578033515_a.pdb or /var/tmp/from_scwrl_1578033515_a.pdb.gz for input Trying /var/tmp/from_scwrl_1578033515_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_1578033515_a.pdb or /var/tmp/from_scwrl_1578033515_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_1578033515.pdb or /var/tmp/from_scwrl_1578033515_b.pdb or /var/tmp/from_scwrl_1578033515_a.pdb Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3e1eA/T0632-3e1eA-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 3e1eA expands to /projects/compbio/data/pdb/3e1e.pdb.gz 3e1eA:# T0632 read from 3e1eA/T0632-3e1eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3e1eA read from 3e1eA/T0632-3e1eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3e1eA to template set # found chain 3e1eA in template set Warning: unaligning (T0632)D34 because first residue in template chain is (3e1eA)G6 T0632 35 :GLLAKQERRYATYLASLTQIESQEREDGRFEVRLPIGPLVNNPLNMVHGGITATLLDTAMGQMVNRQLPDGQSAVTSELNIHYVKPGMGTYLRAVASIVHQGKQRIVVEGKVYT 3e1eA 7 :YAQKVRDSFARQPVMATLGARIDTLLPGRVELCMPYDRALTQQHGFLHAGIVSTVLDSACGYAAFSLMEEEAAVLTVEFKVNFLNPAEGERFAFRAEVVKPGRTLTVATATAYA T0632 149 :DQGE 3e1eA 122 :RDGE T0632 153 :TVAMGTGSFFVL 3e1eA 128 :AIATMTATLMAL Number of specific fragments extracted= 3 number of extra gaps= 0 total=10 # request to SCWRL produces command: ulimit -t 152 ; scwrl4 -t -i /var/tmp/to_scwrl_1724713562.pdb -s /var/tmp/to_scwrl_1724713562.seq -o /var/tmp/from_scwrl_1724713562.pdb > /var/tmp/scwrl_1724713562.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1724713562.pdb Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3dkzA/T0632-3dkzA-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 3dkzA expands to /projects/compbio/data/pdb/3dkz.pdb.gz 3dkzA: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 # T0632 read from 3dkzA/T0632-3dkzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3dkzA read from 3dkzA/T0632-3dkzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3dkzA to template set # found chain 3dkzA in template set Warning: unaligning (T0632)R165 because last residue in template chain is (3dkzA)Q163 T0632 42 :RRYATYLASLTQIESQEREDGRFEVRLPIGPLVNNPLNMVHGGITATLLDTAMGQMVNRQ 3dkzA 42 :FGLTIPFMQLLGVVPEHSGNGTARTRLPARADLVNSRGDIHGGTLMSVLDFTLGAAIRGD T0632 103 :PDGQSAVTSELNIHYVKPGMGT 3dkzA 102 :TPEVGVATIDMNTSFMSPGRGD T0632 126 :LRAVASIVHQGKQRIVVEGKVYTDQGETVAMGTGSFFVL 3dkzA 124 :LVIETRCLRRGASIAFCEGEIRDSAGELVAKATATFKII Number of specific fragments extracted= 3 number of extra gaps= 0 total=13 # request to SCWRL produces command: ulimit -t 152 ; scwrl4 -t -i /var/tmp/to_scwrl_640897878.pdb -s /var/tmp/to_scwrl_640897878.seq -o /var/tmp/from_scwrl_640897878.pdb > /var/tmp/scwrl_640897878.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_640897878.pdb Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3e29A/T0632-3e29A-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 3e29A expands to /projects/compbio/data/pdb/3e29.pdb.gz 3e29A: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 Skipped atom 829, because occupancy 0.500 <= existing 0.500 in 3e29A Skipped atom 833, because occupancy 0.500 <= existing 0.500 in 3e29A Skipped atom 835, because occupancy 0.500 <= existing 0.500 in 3e29A Skipped atom 837, because occupancy 0.500 <= existing 0.500 in 3e29A Skipped atom 839, because occupancy 0.500 <= existing 0.500 in 3e29A Skipped atom 841, because occupancy 0.500 <= existing 0.500 in 3e29A Skipped atom 843, because occupancy 0.500 <= existing 0.500 in 3e29A Skipped atom 845, because occupancy 0.500 <= existing 0.500 in 3e29A 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 # T0632 read from 3e29A/T0632-3e29A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3e29A read from 3e29A/T0632-3e29A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3e29A to template set # found chain 3e29A in template set T0632 34 :DGLLAKQERRYATYLASLTQIESQEREDGRFEVRLPIGPLVNNPL 3e29A 4 :TALEMASRFVNRSPFNRWLGMSVLEAGEQGIVLGIKWREELISSP T0632 79 :NMVHGGITATLLDTAMGQMVNRQL 3e29A 51 :RSTHGGILATLVDAAGDYAVALKT T0632 105 :GQSAVTSELNIHYVKPGMGTYLRAVASIVHQGKQRIVVEGKVYTDQGETVAMGTGSFFV 3e29A 75 :GHPVPTMDMHVDYHRVATPGDLRAEGQVIHFGKRFATAHARVLDMDGNLVASGRALYLI Number of specific fragments extracted= 3 number of extra gaps= 0 total=16 # request to SCWRL produces command: ulimit -t 152 ; scwrl4 -t -i /var/tmp/to_scwrl_140377024.pdb -s /var/tmp/to_scwrl_140377024.seq -o /var/tmp/from_scwrl_140377024.pdb > /var/tmp/scwrl_140377024.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_140377024.pdb Number of alignments=5 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3f1tA/T0632-3f1tA-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 3f1tA expands to /projects/compbio/data/pdb/3f1t.pdb.gz 3f1tA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 436, because occupancy 0.500 <= existing 0.500 in 3f1tA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 438, because occupancy 0.500 <= existing 0.500 in 3f1tA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 440, because occupancy 0.500 <= existing 0.500 in 3f1tA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 442, because occupancy 0.500 <= existing 0.500 in 3f1tA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 444, because occupancy 0.500 <= existing 0.500 in 3f1tA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 446, because occupancy 0.500 <= existing 0.500 in 3f1tA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 448, because occupancy 0.500 <= existing 0.500 in 3f1tA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 450, because occupancy 0.500 <= existing 0.500 in 3f1tA 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 # T0632 read from 3f1tA/T0632-3f1tA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3f1tA read from 3f1tA/T0632-3f1tA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3f1tA to template set # found chain 3f1tA in template set Warning: unaligning (T0632)V33 because first residue in template chain is (3f1tA)N4 Warning: unaligning (T0632)E60 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (3f1tA)E32 Warning: unaligning (T0632)D61 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (3f1tA)E32 Warning: unaligning (T0632)N79 because of BadResidue code BAD_PEPTIDE in next template residue (3f1tA)V53 Warning: unaligning (T0632)M80 because of BadResidue code BAD_PEPTIDE at template residue (3f1tA)V53 Warning: unaligning (T0632)F162 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3f1tA)R138 Warning: unaligning (T0632)V163 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3f1tA)R138 T0632 34 :DGLLAKQERRYATYLASLTQIESQER 3f1tA 5 :PLLERARRFLSALRHCQVLGLTVEAA T0632 62 :GRFEVRLPIGPLVNNPL 3f1tA 33 :KGLTLRLPYSQAIIGNP T0632 81 :VHGGITATLLDTAMGQMVNRQLPDGQSAVTSELNIHYVKPGM 3f1tA 54 :VHGGAITTLMDTTCGISTVCVLPDFEICPTLDLRIDYMHPAE T0632 123 :GTYLRAVASIVHQGKQRIVVEGKVY 3f1tA 97 :HKDVYGFAECYRVTPNVIFTRGFAY T0632 148 :TDQG 3f1tA 124 :DPGQ T0632 153 :TVAMGTGSF 3f1tA 128 :PIAHVVGAF Number of specific fragments extracted= 6 number of extra gaps= 3 total=22 # request to SCWRL produces command: ulimit -t 152 ; scwrl4 -t -i /var/tmp/to_scwrl_1306836185.pdb -s /var/tmp/to_scwrl_1306836185.seq -o /var/tmp/from_scwrl_1306836185.pdb > /var/tmp/scwrl_1306836185.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1306836185.pdb Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3e8pA/T0632-3e8pA-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 3e8pA expands to /projects/compbio/data/pdb/3e8p.pdb.gz 3e8pA: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 # T0632 read from 3e8pA/T0632-3e8pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3e8pA read from 3e8pA/T0632-3e8pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3e8pA to template set # found chain 3e8pA in template set Warning: unaligning (T0632)A21 because first residue in template chain is (3e8pA)S12 T0632 22 :NEEEKDVLS 3e8pA 13 :NPIQAEVLK T0632 37 :LAKQERRYATYLASLTQIESQEREDGRFEVRLPIGPLVN 3e8pA 22 :RVAEVFDQHVPFHNLLGLDIKRYDIDGVEVAINMKPELI T0632 76 :NPL 3e8pA 62 :NIH T0632 79 :NMVHGGITATLLDTAMGQMVNRQL 3e8pA 66 :QILHGGVTATVLDVVGGLTAFAGL T0632 110 :TSELNIHYVKPGMGTYLRAVASIVHQGKQRIVVEGKVYTDQGETVAMGTGSFFV 3e8pA 110 :TIDMRVDYLRPGRGQIFTGTGSVIRAGNRVSVCRMELHNEQGTHIAFGTGTYMV Number of specific fragments extracted= 5 number of extra gaps= 0 total=27 # request to SCWRL produces command: ulimit -t 152 ; scwrl4 -t -i /var/tmp/to_scwrl_1290664640.pdb -s /var/tmp/to_scwrl_1290664640.seq -o /var/tmp/from_scwrl_1290664640.pdb > /var/tmp/scwrl_1290664640.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1290664640.pdb Number of alignments=7 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2pimA/T0632-2pimA-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 2pimA expands to /projects/compbio/data/pdb/2pim.pdb.gz 2pimA: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 Skipped atom 656, because occupancy 0.500 <= existing 0.500 in 2pimA Skipped atom 658, because occupancy 0.500 <= existing 0.500 in 2pimA Skipped atom 660, because occupancy 0.500 <= existing 0.500 in 2pimA Skipped atom 662, because occupancy 0.500 <= existing 0.500 in 2pimA Skipped atom 664, because occupancy 0.500 <= existing 0.500 in 2pimA Skipped atom 666, because occupancy 0.500 <= existing 0.500 in 2pimA Skipped atom 668, because occupancy 0.500 <= existing 0.500 in 2pimA Skipped atom 670, because occupancy 0.500 <= existing 0.500 in 2pimA Skipped atom 672, because occupancy 0.500 <= existing 0.500 in 2pimA Skipped atom 730, because occupancy 0.500 <= existing 0.500 in 2pimA Skipped atom 732, because occupancy 0.500 <= existing 0.500 in 2pimA Skipped atom 734, because occupancy 0.500 <= existing 0.500 in 2pimA Skipped atom 736, because occupancy 0.500 <= existing 0.500 in 2pimA Skipped atom 738, because occupancy 0.500 <= existing 0.500 in 2pimA Skipped atom 740, because occupancy 0.500 <= existing 0.500 in 2pimA Skipped atom 742, because occupancy 0.500 <= existing 0.500 in 2pimA Skipped atom 744, because occupancy 0.500 <= existing 0.500 in 2pimA Skipped atom 746, because occupancy 0.500 <= existing 0.500 in 2pimA Skipped atom 748, because occupancy 0.500 <= existing 0.500 in 2pimA Skipped atom 750, because occupancy 0.500 <= existing 0.500 in 2pimA 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 # T0632 read from 2pimA/T0632-2pimA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2pimA read from 2pimA/T0632-2pimA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2pimA to template set # found chain 2pimA in template set Warning: unaligning (T0632)V33 because first residue in template chain is (2pimA)N5 Warning: unaligning (T0632)Y117 because of BadResidue code BAD_PEPTIDE in next template residue (2pimA)L92 Warning: unaligning (T0632)V118 because of BadResidue code BAD_PEPTIDE at template residue (2pimA)L92 Warning: unaligning (T0632)V163 because last residue in template chain is (2pimA)V136 T0632 34 :DGLLAKQERRYATYLASLTQIESQER 2pimA 6 :YFSRMLRGEAPVPAVAGTLGGVIRAV T0632 60 :EDGRFEVRLPIGPLVNNPLNMVHGGITATLLDTAMGQMVNRQLPDGQSAVTSELNIH 2pimA 34 :EAGSLESDYVATDAFLNPVGQVQGGMLGAMLDDVTAMLVTATLEDGASCSTLNLNLS T0632 119 :KPGMGTYLRAVASIVHQGKQRIVVEGKVY 2pimA 93 :RPAQAGLLRGRARLERRGRNVCNVVGELS T0632 149 :DQGETVAMGTGSFF 2pimA 122 :QDGKLVATATATCM Number of specific fragments extracted= 4 number of extra gaps= 1 total=31 # request to SCWRL produces command: ulimit -t 152 ; scwrl4 -t -i /var/tmp/to_scwrl_1097318579.pdb -s /var/tmp/to_scwrl_1097318579.seq -o /var/tmp/from_scwrl_1097318579.pdb > /var/tmp/scwrl_1097318579.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1097318579.pdb Number of alignments=8 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3hduA/T0632-3hduA-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 3hduA expands to /projects/compbio/data/pdb/3hdu.pdb.gz 3hduA:Skipped atom 171, because occupancy 0.500 <= existing 0.500 in 3hduA Skipped atom 175, because occupancy 0.500 <= existing 0.500 in 3hduA Skipped atom 177, because occupancy 0.500 <= existing 0.500 in 3hduA Skipped atom 179, because occupancy 0.500 <= existing 0.500 in 3hduA Skipped atom 181, because occupancy 0.500 <= existing 0.500 in 3hduA Skipped atom 276, because occupancy 0.500 <= existing 0.500 in 3hduA Skipped atom 278, because occupancy 0.500 <= existing 0.500 in 3hduA Skipped atom 280, because occupancy 0.500 <= existing 0.500 in 3hduA Skipped atom 282, because occupancy 0.500 <= existing 0.500 in 3hduA Skipped atom 284, because occupancy 0.500 <= existing 0.500 in 3hduA Skipped atom 286, because occupancy 0.500 <= existing 0.500 in 3hduA Skipped atom 288, because occupancy 0.500 <= existing 0.500 in 3hduA Skipped atom 290, because occupancy 0.500 <= existing 0.500 in 3hduA Skipped atom 292, because occupancy 0.500 <= existing 0.500 in 3hduA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 804, because occupancy 0.500 <= existing 0.500 in 3hduA Skipped atom 808, because occupancy 0.500 <= existing 0.500 in 3hduA Skipped atom 810, because occupancy 0.500 <= existing 0.500 in 3hduA Skipped atom 812, because occupancy 0.500 <= existing 0.500 in 3hduA Skipped atom 814, because occupancy 0.500 <= existing 0.500 in 3hduA Skipped atom 816, because occupancy 0.500 <= existing 0.500 in 3hduA 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 1047, because occupancy 0.500 <= existing 0.500 in 3hduA 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 1051, because occupancy 0.500 <= existing 0.500 in 3hduA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1053, because occupancy 0.500 <= existing 0.500 in 3hduA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1055, because occupancy 0.370 <= existing 0.380 in 3hduA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1057, because occupancy 0.500 <= existing 0.500 in 3hduA # T0632 read from 3hduA/T0632-3hduA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3hduA read from 3hduA/T0632-3hduA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3hduA to template set # found chain 3hduA in template set Warning: unaligning (T0632)L164 because last residue in template chain is (3hduA)V156 T0632 31 :SIVDGLLAKQERRYATYLASLTQIESQEREDGRFEVRLPIGPLVNNPL 3hduA 8 :EEVLFSAVNEIFEEKIPFNKIIGLKVRFISPEQVKLSFEMRDELIGNA T0632 79 :NMVHGGITATLLDTAMGQMVNRQL 3hduA 58 :RMLYGGVISSAIDMTAGLAAFMGF T0632 103 :P 3hduA 86 :S T0632 105 :G 3hduA 87 :G T0632 106 :QSAVTSELNIHYVKPGMGTYLRAVASIVHQGKQRIVVEGKVYTDQGETVAMGTGSFFV 3hduA 98 :GRLSTMSLHVEYLRPGLGREFVCTGYNVRTGNKVAVIRTELMNDQDELIAVGSVSYIL Number of specific fragments extracted= 5 number of extra gaps= 0 total=36 # request to SCWRL produces command: ulimit -t 152 ; scwrl4 -t -i /var/tmp/to_scwrl_2078063416.pdb -s /var/tmp/to_scwrl_2078063416.seq -o /var/tmp/from_scwrl_2078063416.pdb > /var/tmp/scwrl_2078063416.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2078063416.pdb Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3gekA/T0632-3gekA-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 3gekA expands to /projects/compbio/data/pdb/3gek.pdb.gz 3gekA: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 Skipped atom 520, because occupancy 0.500 <= existing 0.500 in 3gekA Skipped atom 524, because occupancy 0.500 <= existing 0.500 in 3gekA Skipped atom 526, because occupancy 0.500 <= existing 0.500 in 3gekA Skipped atom 799, because occupancy 0.500 <= existing 0.500 in 3gekA Skipped atom 803, because occupancy 0.500 <= existing 0.500 in 3gekA Skipped atom 805, because occupancy 0.500 <= existing 0.500 in 3gekA Skipped atom 807, because occupancy 0.500 <= existing 0.500 in 3gekA Skipped atom 809, because occupancy 0.500 <= existing 0.500 in 3gekA Skipped atom 811, because occupancy 0.500 <= existing 0.500 in 3gekA Skipped atom 813, because occupancy 0.500 <= existing 0.500 in 3gekA Skipped atom 815, because occupancy 0.500 <= existing 0.500 in 3gekA # T0632 read from 3gekA/T0632-3gekA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3gekA read from 3gekA/T0632-3gekA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3gekA to template set # found chain 3gekA in template set Warning: unaligning (T0632)R165 because last residue in template chain is (3gekA)P132 T0632 45 :ATYLASLTQIESQERED 3gekA 3 :MIDQLNITDFQVFTDEN T0632 63 :RFEVRLPIGPLVNNPLNMVHGGITATLLDTAMGQMVNRQLPDGQSAVTSELNIHYVKPGM 3gekA 29 :KFSSKMILSDFHAQPQGFLNGGASLALAEITAGMASNAIGSGQYFAFGQSINANHLNPKK T0632 123 :GTYLRAVASIVHQGKQRIVVEGKVYTDQGETVAMGTGSFFVL 3gekA 90 :EGFVNARGLLLKNGKRNHVWEIKITDENETLISQITVVNALV Number of specific fragments extracted= 3 number of extra gaps= 0 total=39 # request to SCWRL produces command: ulimit -t 152 ; scwrl4 -t -i /var/tmp/to_scwrl_2114984873.pdb -s /var/tmp/to_scwrl_2114984873.seq -o /var/tmp/from_scwrl_2114984873.pdb > /var/tmp/scwrl_2114984873.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2114984873.pdb Number of alignments=10 # command:Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.144 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 1 total_weight= 9820.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 2 total_weight= 9820.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 3 total_weight= 9820.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 4 total_weight= 9820.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 5 total_weight= 9820.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 0.993 rmsd (weighted)= 2.473 (unweighted)= 46.503 superimposing iter= 1 total_weight= 3570.096 rmsd (weighted)= 1.123 (unweighted)= 46.388 superimposing iter= 2 total_weight= 1468.505 rmsd (weighted)= 0.839 (unweighted)= 46.315 superimposing iter= 3 total_weight= 1027.215 rmsd (weighted)= 0.756 (unweighted)= 46.260 superimposing iter= 4 total_weight= 903.967 rmsd (weighted)= 0.727 (unweighted)= 46.220 superimposing iter= 5 total_weight= 862.558 rmsd (weighted)= 0.716 (unweighted)= 46.191 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 1.135 rmsd (weighted)= 2.926 (unweighted)= 37.767 superimposing iter= 1 total_weight= 5039.527 rmsd (weighted)= 1.131 (unweighted)= 37.537 superimposing iter= 2 total_weight= 1911.506 rmsd (weighted)= 0.790 (unweighted)= 37.405 superimposing iter= 3 total_weight= 1231.008 rmsd (weighted)= 0.698 (unweighted)= 37.345 superimposing iter= 4 total_weight= 1032.986 rmsd (weighted)= 0.673 (unweighted)= 37.319 superimposing iter= 5 total_weight= 984.836 rmsd (weighted)= 0.666 (unweighted)= 37.309 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 1.053 rmsd (weighted)= 2.336 (unweighted)= 42.458 superimposing iter= 1 total_weight= 4612.767 rmsd (weighted)= 0.946 (unweighted)= 42.671 superimposing iter= 2 total_weight= 1550.857 rmsd (weighted)= 0.713 (unweighted)= 42.698 superimposing iter= 3 total_weight= 1009.742 rmsd (weighted)= 0.670 (unweighted)= 42.704 superimposing iter= 4 total_weight= 918.164 rmsd (weighted)= 0.660 (unweighted)= 42.709 superimposing iter= 5 total_weight= 899.374 rmsd (weighted)= 0.658 (unweighted)= 42.713 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 1.118 rmsd (weighted)= 2.697 (unweighted)= 52.277 superimposing iter= 1 total_weight= 4561.519 rmsd (weighted)= 1.125 (unweighted)= 51.891 superimposing iter= 2 total_weight= 1790.477 rmsd (weighted)= 0.807 (unweighted)= 51.745 superimposing iter= 3 total_weight= 1153.248 rmsd (weighted)= 0.730 (unweighted)= 51.670 superimposing iter= 4 total_weight= 1009.073 rmsd (weighted)= 0.708 (unweighted)= 51.622 superimposing iter= 5 total_weight= 971.505 rmsd (weighted)= 0.699 (unweighted)= 51.588 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 1.068 rmsd (weighted)= 3.372 (unweighted)= 55.032 superimposing iter= 1 total_weight= 3904.308 rmsd (weighted)= 1.489 (unweighted)= 54.204 superimposing iter= 2 total_weight= 1539.429 rmsd (weighted)= 1.125 (unweighted)= 53.937 superimposing iter= 3 total_weight= 1076.529 rmsd (weighted)= 1.024 (unweighted)= 53.785 superimposing iter= 4 total_weight= 1001.445 rmsd (weighted)= 0.970 (unweighted)= 53.679 superimposing iter= 5 total_weight= 968.306 rmsd (weighted)= 0.935 (unweighted)= 53.602 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 1.054 rmsd (weighted)= 2.433 (unweighted)= 67.396 superimposing iter= 1 total_weight= 4004.873 rmsd (weighted)= 1.068 (unweighted)= 67.136 superimposing iter= 2 total_weight= 1594.247 rmsd (weighted)= 0.798 (unweighted)= 67.039 superimposing iter= 3 total_weight= 1038.105 rmsd (weighted)= 0.742 (unweighted)= 66.983 superimposing iter= 4 total_weight= 945.056 rmsd (weighted)= 0.724 (unweighted)= 66.949 superimposing iter= 5 total_weight= 918.580 rmsd (weighted)= 0.717 (unweighted)= 66.930 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 1.098 rmsd (weighted)= 3.289 (unweighted)= 55.154 superimposing iter= 1 total_weight= 5052.960 rmsd (weighted)= 1.256 (unweighted)= 54.969 superimposing iter= 2 total_weight= 1874.041 rmsd (weighted)= 0.863 (unweighted)= 54.823 superimposing iter= 3 total_weight= 1246.254 rmsd (weighted)= 0.739 (unweighted)= 54.736 superimposing iter= 4 total_weight= 1049.667 rmsd (weighted)= 0.694 (unweighted)= 54.681 superimposing iter= 5 total_weight= 984.037 rmsd (weighted)= 0.676 (unweighted)= 54.645 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 1.126 rmsd (weighted)= 3.430 (unweighted)= 91.516 superimposing iter= 1 total_weight= 4573.351 rmsd (weighted)= 1.418 (unweighted)= 91.929 superimposing iter= 2 total_weight= 1993.920 rmsd (weighted)= 0.959 (unweighted)= 92.120 superimposing iter= 3 total_weight= 1299.121 rmsd (weighted)= 0.816 (unweighted)= 92.221 superimposing iter= 4 total_weight= 1099.827 rmsd (weighted)= 0.757 (unweighted)= 92.281 superimposing iter= 5 total_weight= 1018.954 rmsd (weighted)= 0.731 (unweighted)= 92.317 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 1.057 rmsd (weighted)= 3.752 (unweighted)= 52.376 superimposing iter= 1 total_weight= 4760.194 rmsd (weighted)= 1.278 (unweighted)= 52.310 superimposing iter= 2 total_weight= 2141.810 rmsd (weighted)= 0.797 (unweighted)= 52.293 superimposing iter= 3 total_weight= 1219.546 rmsd (weighted)= 0.679 (unweighted)= 52.281 superimposing iter= 4 total_weight= 1014.133 rmsd (weighted)= 0.639 (unweighted)= 52.273 superimposing iter= 5 total_weight= 947.588 rmsd (weighted)= 0.623 (unweighted)= 52.269 Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.144 rmsd (weighted)= 1.906 (unweighted)= 35.732 superimposing iter= 1 total_weight= 4088.192 rmsd (weighted)= 0.854 (unweighted)= 35.741 superimposing iter= 2 total_weight= 1748.485 rmsd (weighted)= 0.628 (unweighted)= 35.738 superimposing iter= 3 total_weight= 1160.680 rmsd (weighted)= 0.572 (unweighted)= 35.730 superimposing iter= 4 total_weight= 1033.014 rmsd (weighted)= 0.554 (unweighted)= 35.722 superimposing iter= 5 total_weight= 1004.312 rmsd (weighted)= 0.544 (unweighted)= 35.714 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 1.193 rmsd (weighted)= 3.303 (unweighted)= 28.388 superimposing iter= 1 total_weight= 6147.673 rmsd (weighted)= 1.094 (unweighted)= 28.603 superimposing iter= 2 total_weight= 3057.420 rmsd (weighted)= 0.582 (unweighted)= 28.643 superimposing iter= 3 total_weight= 2156.291 rmsd (weighted)= 0.374 (unweighted)= 28.647 superimposing iter= 4 total_weight= 1792.770 rmsd (weighted)= 0.264 (unweighted)= 28.649 superimposing iter= 5 total_weight= 1627.357 rmsd (weighted)= 0.196 (unweighted)= 28.651 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 1.159 rmsd (weighted)= 1.917 (unweighted)= 43.503 superimposing iter= 1 total_weight= 4745.626 rmsd (weighted)= 0.781 (unweighted)= 43.355 superimposing iter= 2 total_weight= 2159.170 rmsd (weighted)= 0.513 (unweighted)= 43.303 superimposing iter= 3 total_weight= 1405.797 rmsd (weighted)= 0.425 (unweighted)= 43.290 superimposing iter= 4 total_weight= 1147.657 rmsd (weighted)= 0.392 (unweighted)= 43.290 superimposing iter= 5 total_weight= 1047.430 rmsd (weighted)= 0.380 (unweighted)= 43.294 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 1.076 rmsd (weighted)= 1.861 (unweighted)= 38.255 superimposing iter= 1 total_weight= 4461.910 rmsd (weighted)= 0.760 (unweighted)= 38.187 superimposing iter= 2 total_weight= 1943.711 rmsd (weighted)= 0.513 (unweighted)= 38.154 superimposing iter= 3 total_weight= 1166.801 rmsd (weighted)= 0.453 (unweighted)= 38.141 superimposing iter= 4 total_weight= 983.939 rmsd (weighted)= 0.437 (unweighted)= 38.135 superimposing iter= 5 total_weight= 938.037 rmsd (weighted)= 0.431 (unweighted)= 38.131 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 1.141 rmsd (weighted)= 1.574 (unweighted)= 40.104 superimposing iter= 1 total_weight= 4091.210 rmsd (weighted)= 0.707 (unweighted)= 39.879 superimposing iter= 2 total_weight= 1724.286 rmsd (weighted)= 0.524 (unweighted)= 39.803 superimposing iter= 3 total_weight= 1168.698 rmsd (weighted)= 0.477 (unweighted)= 39.756 superimposing iter= 4 total_weight= 1052.169 rmsd (weighted)= 0.457 (unweighted)= 39.726 superimposing iter= 5 total_weight= 1019.042 rmsd (weighted)= 0.447 (unweighted)= 39.706 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 1.092 rmsd (weighted)= 2.594 (unweighted)= 47.270 superimposing iter= 1 total_weight= 4376.089 rmsd (weighted)= 1.079 (unweighted)= 47.067 superimposing iter= 2 total_weight= 1780.377 rmsd (weighted)= 0.757 (unweighted)= 46.933 superimposing iter= 3 total_weight= 1262.835 rmsd (weighted)= 0.639 (unweighted)= 46.853 superimposing iter= 4 total_weight= 1116.805 rmsd (weighted)= 0.578 (unweighted)= 46.803 superimposing iter= 5 total_weight= 1039.903 rmsd (weighted)= 0.543 (unweighted)= 46.770 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 1.161 rmsd (weighted)= 3.406 (unweighted)= 56.229 superimposing iter= 1 total_weight= 6183.192 rmsd (weighted)= 1.098 (unweighted)= 56.162 superimposing iter= 2 total_weight= 2704.392 rmsd (weighted)= 0.643 (unweighted)= 56.189 superimposing iter= 3 total_weight= 1578.234 rmsd (weighted)= 0.501 (unweighted)= 56.197 superimposing iter= 4 total_weight= 1258.808 rmsd (weighted)= 0.438 (unweighted)= 56.193 superimposing iter= 5 total_weight= 1127.254 rmsd (weighted)= 0.406 (unweighted)= 56.187 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 1.121 rmsd (weighted)= 2.511 (unweighted)= 35.884 superimposing iter= 1 total_weight= 5216.183 rmsd (weighted)= 0.933 (unweighted)= 35.903 superimposing iter= 2 total_weight= 2147.801 rmsd (weighted)= 0.611 (unweighted)= 35.912 superimposing iter= 3 total_weight= 1234.251 rmsd (weighted)= 0.536 (unweighted)= 35.921 superimposing iter= 4 total_weight= 1046.453 rmsd (weighted)= 0.512 (unweighted)= 35.929 superimposing iter= 5 total_weight= 1012.805 rmsd (weighted)= 0.497 (unweighted)= 35.936 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 1.175 rmsd (weighted)= 2.634 (unweighted)= 76.438 superimposing iter= 1 total_weight= 5284.321 rmsd (weighted)= 0.997 (unweighted)= 76.454 superimposing iter= 2 total_weight= 2463.880 rmsd (weighted)= 0.614 (unweighted)= 76.459 superimposing iter= 3 total_weight= 1467.894 rmsd (weighted)= 0.502 (unweighted)= 76.458 superimposing iter= 4 total_weight= 1164.909 rmsd (weighted)= 0.463 (unweighted)= 76.456 superimposing iter= 5 total_weight= 1065.103 rmsd (weighted)= 0.448 (unweighted)= 76.453 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 1.057 rmsd (weighted)= 3.273 (unweighted)= 42.474 superimposing iter= 1 total_weight= 4904.481 rmsd (weighted)= 1.122 (unweighted)= 42.291 superimposing iter= 2 total_weight= 2204.174 rmsd (weighted)= 0.697 (unweighted)= 42.261 superimposing iter= 3 total_weight= 1209.407 rmsd (weighted)= 0.597 (unweighted)= 42.251 superimposing iter= 4 total_weight= 983.959 rmsd (weighted)= 0.569 (unweighted)= 42.248 superimposing iter= 5 total_weight= 920.401 rmsd (weighted)= 0.562 (unweighted)= 42.247 Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.144 rmsd (weighted)= 1.915 (unweighted)= 35.783 superimposing iter= 1 total_weight= 4100.844 rmsd (weighted)= 0.856 (unweighted)= 35.784 superimposing iter= 2 total_weight= 1755.326 rmsd (weighted)= 0.628 (unweighted)= 35.779 superimposing iter= 3 total_weight= 1161.715 rmsd (weighted)= 0.572 (unweighted)= 35.770 superimposing iter= 4 total_weight= 1036.487 rmsd (weighted)= 0.553 (unweighted)= 35.761 superimposing iter= 5 total_weight= 1006.458 rmsd (weighted)= 0.543 (unweighted)= 35.753 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 1.193 rmsd (weighted)= 3.302 (unweighted)= 28.380 superimposing iter= 1 total_weight= 6126.396 rmsd (weighted)= 1.097 (unweighted)= 28.600 superimposing iter= 2 total_weight= 3058.805 rmsd (weighted)= 0.583 (unweighted)= 28.643 superimposing iter= 3 total_weight= 2162.713 rmsd (weighted)= 0.374 (unweighted)= 28.643 superimposing iter= 4 total_weight= 1792.874 rmsd (weighted)= 0.264 (unweighted)= 28.642 superimposing iter= 5 total_weight= 1627.165 rmsd (weighted)= 0.196 (unweighted)= 28.642 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 1.159 rmsd (weighted)= 1.910 (unweighted)= 43.577 superimposing iter= 1 total_weight= 4726.477 rmsd (weighted)= 0.780 (unweighted)= 43.420 superimposing iter= 2 total_weight= 2158.421 rmsd (weighted)= 0.512 (unweighted)= 43.365 superimposing iter= 3 total_weight= 1407.276 rmsd (weighted)= 0.424 (unweighted)= 43.352 superimposing iter= 4 total_weight= 1148.910 rmsd (weighted)= 0.391 (unweighted)= 43.352 superimposing iter= 5 total_weight= 1047.087 rmsd (weighted)= 0.378 (unweighted)= 43.355 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 1.076 rmsd (weighted)= 1.857 (unweighted)= 38.282 superimposing iter= 1 total_weight= 4444.255 rmsd (weighted)= 0.760 (unweighted)= 38.214 superimposing iter= 2 total_weight= 1943.188 rmsd (weighted)= 0.513 (unweighted)= 38.180 superimposing iter= 3 total_weight= 1167.573 rmsd (weighted)= 0.453 (unweighted)= 38.167 superimposing iter= 4 total_weight= 984.925 rmsd (weighted)= 0.436 (unweighted)= 38.160 superimposing iter= 5 total_weight= 938.866 rmsd (weighted)= 0.431 (unweighted)= 38.156 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 1.141 rmsd (weighted)= 1.565 (unweighted)= 40.055 superimposing iter= 1 total_weight= 4101.215 rmsd (weighted)= 0.704 (unweighted)= 39.841 superimposing iter= 2 total_weight= 1711.787 rmsd (weighted)= 0.524 (unweighted)= 39.767 superimposing iter= 3 total_weight= 1163.526 rmsd (weighted)= 0.478 (unweighted)= 39.719 superimposing iter= 4 total_weight= 1051.111 rmsd (weighted)= 0.459 (unweighted)= 39.689 superimposing iter= 5 total_weight= 1020.966 rmsd (weighted)= 0.447 (unweighted)= 39.668 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 1.092 rmsd (weighted)= 2.594 (unweighted)= 47.198 superimposing iter= 1 total_weight= 4397.818 rmsd (weighted)= 1.076 (unweighted)= 47.005 superimposing iter= 2 total_weight= 1786.888 rmsd (weighted)= 0.753 (unweighted)= 46.876 superimposing iter= 3 total_weight= 1262.372 rmsd (weighted)= 0.636 (unweighted)= 46.798 superimposing iter= 4 total_weight= 1112.965 rmsd (weighted)= 0.576 (unweighted)= 46.748 superimposing iter= 5 total_weight= 1038.628 rmsd (weighted)= 0.542 (unweighted)= 46.715 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 1.161 rmsd (weighted)= 3.412 (unweighted)= 56.196 superimposing iter= 1 total_weight= 6183.906 rmsd (weighted)= 1.099 (unweighted)= 56.130 superimposing iter= 2 total_weight= 2701.212 rmsd (weighted)= 0.642 (unweighted)= 56.152 superimposing iter= 3 total_weight= 1570.315 rmsd (weighted)= 0.500 (unweighted)= 56.159 superimposing iter= 4 total_weight= 1254.458 rmsd (weighted)= 0.437 (unweighted)= 56.157 superimposing iter= 5 total_weight= 1123.283 rmsd (weighted)= 0.404 (unweighted)= 56.153 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 1.121 rmsd (weighted)= 2.513 (unweighted)= 35.814 superimposing iter= 1 total_weight= 5207.198 rmsd (weighted)= 0.934 (unweighted)= 35.837 superimposing iter= 2 total_weight= 2148.506 rmsd (weighted)= 0.612 (unweighted)= 35.848 superimposing iter= 3 total_weight= 1234.348 rmsd (weighted)= 0.537 (unweighted)= 35.859 superimposing iter= 4 total_weight= 1046.304 rmsd (weighted)= 0.513 (unweighted)= 35.869 superimposing iter= 5 total_weight= 1013.699 rmsd (weighted)= 0.498 (unweighted)= 35.877 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 1.175 rmsd (weighted)= 2.634 (unweighted)= 76.461 superimposing iter= 1 total_weight= 5277.017 rmsd (weighted)= 0.995 (unweighted)= 76.480 superimposing iter= 2 total_weight= 2553.396 rmsd (weighted)= 0.601 (unweighted)= 76.485 superimposing iter= 3 total_weight= 1552.311 rmsd (weighted)= 0.476 (unweighted)= 76.483 superimposing iter= 4 total_weight= 1232.078 rmsd (weighted)= 0.426 (unweighted)= 76.481 superimposing iter= 5 total_weight= 1084.751 rmsd (weighted)= 0.406 (unweighted)= 76.480 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 1.057 rmsd (weighted)= 3.272 (unweighted)= 42.469 superimposing iter= 1 total_weight= 4895.452 rmsd (weighted)= 1.123 (unweighted)= 42.286 superimposing iter= 2 total_weight= 2200.543 rmsd (weighted)= 0.698 (unweighted)= 42.256 superimposing iter= 3 total_weight= 1213.978 rmsd (weighted)= 0.597 (unweighted)= 42.245 superimposing iter= 4 total_weight= 986.015 rmsd (weighted)= 0.568 (unweighted)= 42.242 superimposing iter= 5 total_weight= 923.431 rmsd (weighted)= 0.559 (unweighted)= 42.241 superimposing iter= 0 total_weight= 1.144 rmsd (weighted)= 1.915 (unweighted)= 35.820 superimposing iter= 1 total_weight= 4101.873 rmsd (weighted)= 0.856 (unweighted)= 35.820 superimposing iter= 2 total_weight= 1756.319 rmsd (weighted)= 0.627 (unweighted)= 35.814 superimposing iter= 3 total_weight= 1162.037 rmsd (weighted)= 0.571 (unweighted)= 35.805 superimposing iter= 4 total_weight= 1036.890 rmsd (weighted)= 0.552 (unweighted)= 35.796 superimposing iter= 5 total_weight= 1006.757 rmsd (weighted)= 0.542 (unweighted)= 35.788 superimposing iter= 0 total_weight= 1.193 rmsd (weighted)= 3.300 (unweighted)= 28.376 superimposing iter= 1 total_weight= 6097.674 rmsd (weighted)= 1.102 (unweighted)= 28.599 superimposing iter= 2 total_weight= 3062.110 rmsd (weighted)= 0.586 (unweighted)= 28.645 superimposing iter= 3 total_weight= 2154.292 rmsd (weighted)= 0.377 (unweighted)= 28.641 superimposing iter= 4 total_weight= 1804.197 rmsd (weighted)= 0.265 (unweighted)= 28.637 superimposing iter= 5 total_weight= 1631.830 rmsd (weighted)= 0.196 (unweighted)= 28.636 superimposing iter= 0 total_weight= 1.159 rmsd (weighted)= 1.910 (unweighted)= 43.632 superimposing iter= 1 total_weight= 4726.274 rmsd (weighted)= 0.780 (unweighted)= 43.473 superimposing iter= 2 total_weight= 2158.505 rmsd (weighted)= 0.512 (unweighted)= 43.418 superimposing iter= 3 total_weight= 1407.729 rmsd (weighted)= 0.424 (unweighted)= 43.405 superimposing iter= 4 total_weight= 1149.072 rmsd (weighted)= 0.391 (unweighted)= 43.405 superimposing iter= 5 total_weight= 1047.342 rmsd (weighted)= 0.378 (unweighted)= 43.408 superimposing iter= 0 total_weight= 1.076 rmsd (weighted)= 1.856 (unweighted)= 38.321 superimposing iter= 1 total_weight= 4440.551 rmsd (weighted)= 0.760 (unweighted)= 38.253 superimposing iter= 2 total_weight= 1943.416 rmsd (weighted)= 0.513 (unweighted)= 38.218 superimposing iter= 3 total_weight= 1167.800 rmsd (weighted)= 0.453 (unweighted)= 38.205 superimposing iter= 4 total_weight= 985.000 rmsd (weighted)= 0.436 (unweighted)= 38.198 superimposing iter= 5 total_weight= 938.921 rmsd (weighted)= 0.431 (unweighted)= 38.194 superimposing iter= 0 total_weight= 1.141 rmsd (weighted)= 1.564 (unweighted)= 40.028 superimposing iter= 1 total_weight= 4101.447 rmsd (weighted)= 0.703 (unweighted)= 39.815 superimposing iter= 2 total_weight= 1711.102 rmsd (weighted)= 0.524 (unweighted)= 39.741 superimposing iter= 3 total_weight= 1163.307 rmsd (weighted)= 0.477 (unweighted)= 39.693 superimposing iter= 4 total_weight= 1052.842 rmsd (weighted)= 0.458 (unweighted)= 39.662 superimposing iter= 5 total_weight= 1021.175 rmsd (weighted)= 0.447 (unweighted)= 39.642 superimposing iter= 0 total_weight= 1.092 rmsd (weighted)= 2.594 (unweighted)= 47.152 superimposing iter= 1 total_weight= 4399.033 rmsd (weighted)= 1.076 (unweighted)= 46.960 superimposing iter= 2 total_weight= 1787.705 rmsd (weighted)= 0.753 (unweighted)= 46.832 superimposing iter= 3 total_weight= 1262.653 rmsd (weighted)= 0.636 (unweighted)= 46.755 superimposing iter= 4 total_weight= 1112.827 rmsd (weighted)= 0.576 (unweighted)= 46.706 superimposing iter= 5 total_weight= 1038.530 rmsd (weighted)= 0.542 (unweighted)= 46.673 superimposing iter= 0 total_weight= 1.161 rmsd (weighted)= 3.416 (unweighted)= 56.162 superimposing iter= 1 total_weight= 6183.707 rmsd (weighted)= 1.100 (unweighted)= 56.098 superimposing iter= 2 total_weight= 2703.301 rmsd (weighted)= 0.641 (unweighted)= 56.117 superimposing iter= 3 total_weight= 1567.372 rmsd (weighted)= 0.499 (unweighted)= 56.124 superimposing iter= 4 total_weight= 1253.804 rmsd (weighted)= 0.436 (unweighted)= 56.122 superimposing iter= 5 total_weight= 1119.800 rmsd (weighted)= 0.404 (unweighted)= 56.118 superimposing iter= 0 total_weight= 1.121 rmsd (weighted)= 2.513 (unweighted)= 35.758 superimposing iter= 1 total_weight= 5205.697 rmsd (weighted)= 0.935 (unweighted)= 35.782 superimposing iter= 2 total_weight= 2148.946 rmsd (weighted)= 0.612 (unweighted)= 35.793 superimposing iter= 3 total_weight= 1234.900 rmsd (weighted)= 0.537 (unweighted)= 35.804 superimposing iter= 4 total_weight= 1046.434 rmsd (weighted)= 0.513 (unweighted)= 35.814 superimposing iter= 5 total_weight= 1013.489 rmsd (weighted)= 0.498 (unweighted)= 35.822 superimposing iter= 0 total_weight= 1.175 rmsd (weighted)= 2.634 (unweighted)= 76.480 superimposing iter= 1 total_weight= 5276.513 rmsd (weighted)= 0.995 (unweighted)= 76.499 superimposing iter= 2 total_weight= 2551.855 rmsd (weighted)= 0.601 (unweighted)= 76.507 superimposing iter= 3 total_weight= 1546.193 rmsd (weighted)= 0.477 (unweighted)= 76.507 superimposing iter= 4 total_weight= 1234.747 rmsd (weighted)= 0.426 (unweighted)= 76.507 superimposing iter= 5 total_weight= 1086.899 rmsd (weighted)= 0.406 (unweighted)= 76.506 superimposing iter= 0 total_weight= 1.057 rmsd (weighted)= 3.272 (unweighted)= 42.462 superimposing iter= 1 total_weight= 4895.643 rmsd (weighted)= 1.123 (unweighted)= 42.279 superimposing iter= 2 total_weight= 2199.751 rmsd (weighted)= 0.698 (unweighted)= 42.248 superimposing iter= 3 total_weight= 1213.924 rmsd (weighted)= 0.597 (unweighted)= 42.238 superimposing iter= 4 total_weight= 985.906 rmsd (weighted)= 0.568 (unweighted)= 42.235 superimposing iter= 5 total_weight= 924.110 rmsd (weighted)= 0.559 (unweighted)= 42.234 # command:# Printing sheets for alignments to T0632.undertaker-align.sheets # command: