------------------------------------------------------------------------------------------------------------------------- Will print the top 5 alignments (based on backbone shifts) for each pairing of chains, as measured by a combination of score and contiguity. Some relevant parameters: HELIX min length: 5 STRAND min length: 3 shift-tolerance = -10 permissible-violations = 4 max-breaks = NIL retain-m = 100 best-n = 100 anglethresh = 0.5 septhresh = 5 min_length = 4 rmsd-tol = 9.9999999999999E12 Legend: score1 [score2] pairings L2ERR {Xbad/Xsig:Xtot} Breaks (score2 is the score from protein2's perspective, not the minimum of the two perspectives as in some earlier printouts.) Recall that "SIMILARITY" refers to similarities over all alignments not just the top ones. ------------------------------------------------------------------------------------------------------------------------- [5367, 533]: Comparing 1qks_A and 1c52, based on their crossing files. There are 50 (15 H + 35 S) secondary structure elements in 1qks_A, of which 7 satisfy the size requirements. There are 9 (7 H + 2 S) secondary structure elements in 1c52, of which 8 satisfy the size requirements. 1.52591 [ 1.68877] ((1 . 1) (2 . 2) (3 . 3) (6 . 6) (7 . 8)) 7.775 {1/9:10} B:0 1.75004 [ 2.00003] ((3 . 1) (5 . 2) (6 . 3) (7 . 6)) 2.767 {0/6:6} B:0 1.75007 [ 2.00005] ((4 . 1) (5 . 2) (6 . 3) (7 . 6)) 3.133 {0/6:6} B:0 1.75246 [ 2.00165] ((2 . 2) (3 . 3) (6 . 6) (7 . 8)) 7.671 {0/5:6} B:0 1.75660 [ 2.00443] ((2 . 1) (3 . 3) (6 . 6) (7 . 8)) 9.826 {0/5:6} B:0 SIMILARITY (1/min{score1}): 0.6553 [and 1/min{score2}: 0.5921] [5367, 644]: Comparing 1qks_A and 1cot, based on their crossing files. There are 50 (15 H + 35 S) secondary structure elements in 1qks_A, of which 7 satisfy the size requirements. There are 7 (5 H + 2 S) secondary structure elements in 1cot, of which 6 satisfy the size requirements. NO SIMILARITY! [5367, 1005]: Comparing 1qks_A and 1e29_A, based on their crossing files. There are 50 (15 H + 35 S) secondary structure elements in 1qks_A, of which 7 satisfy the size requirements. There are 8 (6 H + 2 S) secondary structure elements in 1e29_A, of which 7 satisfy the size requirements. 1.40019 [ 1.40019] ((3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 8)) 3.409 {0/9:10} B:0 SIMILARITY (1/min{score1}): 0.7142 [and 1/min{score2}: 0.7142] [5367, 1333]: Comparing 1qks_A and 1ezv_D, based on their crossing files. There are 50 (15 H + 35 S) secondary structure elements in 1qks_A, of which 7 satisfy the size requirements. There are 14 (9 H + 5 S) secondary structure elements in 1ezv_D, of which 8 satisfy the size requirements. NO SIMILARITY! [5367, 2054]: Comparing 1qks_A and 1h32_A, based on their crossing files. There are 50 (15 H + 35 S) secondary structure elements in 1qks_A, of which 7 satisfy the size requirements. There are 25 (14 H + 11 S) secondary structure elements in 1h32_A, of which 12 satisfy the size requirements. 1.40016 [ 2.40003] ((3 . 9) (4 . 10) (5 . 12) (6 . 15) (7 . 16)) 3.250 {0/9:10} B:0 1.75048 [ 3.00010] ((3 . 9) (4 . 10) (5 . 11) (6 . 12)) 5.093 {0/6:6} B:0 1.75076 [ 3.00015] ((3 . 10) (5 . 12) (6 . 15) (7 . 16)) 5.712 {0/6:6} B:0 1.75411 [ 3.00082] ((1 . 9) (2 . 10) (4 . 15) (6 . 16)) 8.725 {0/5:6} B:0 1.75457 [ 3.00091] ((1 . 9) (2 . 10) (4 . 15) (5 . 16)) 8.962 {0/5:6} B:0 SIMILARITY (1/min{score1}): 0.7142 [and 1/min{score2}: 0.4167] [5367, 2055]: Comparing 1qks_A and 1h32_A, based on their crossing files. There are 50 (15 H + 35 S) secondary structure elements in 1qks_A, of which 7 satisfy the size requirements. There are 25 (14 H + 11 S) secondary structure elements in 1h32_A, of which 7 satisfy the size requirements. 1.75018 [ 1.75018] ((3 . 17) (4 . 18) (6 . 23) (7 . 24)) 4.013 {0/5:6} B:0 1.75451 [ 1.75451] ((1 . 17) (2 . 18) (4 . 23) (6 . 24)) 8.929 {0/5:6} B:0 1.75490 [ 1.75490] ((1 . 17) (2 . 18) (4 . 23) (5 . 24)) 9.118 {0/5:6} B:0 SIMILARITY (1/min{score1}): 0.5714 [and 1/min{score2}: 0.5714] [5367, 2566]: Comparing 1qks_A and 1iqc_A, based on their crossing files. There are 50 (15 H + 35 S) secondary structure elements in 1qks_A, of which 7 satisfy the size requirements. There are 21 (17 H + 4 S) secondary structure elements in 1iqc_A, of which 6 satisfy the size requirements. 1.75830 [ 1.51310] ((2 . 7) (3 . 8) (5 . 10) (6 . 11)) 10.410 {0/4:6} B:0 2.24998 [ 2.14860] ((2 . 7) (4 . 9) (5 . 10) (6 . 11)) 11.306 {1/5:6} B:0 2.63905 [ 2.57827] ((1 . 1) (4 . 7) (5 . 8) (6 . 9)) 8.038 {1/4:6} B:0 4.03654 [ 4.02003] ((1 . 1) (3 . 11) (5 . 8) (6 . 9)) 9.066 {2/5:6} B:1 SIMILARITY (1/min{score1}): 0.5687 [and 1/min{score2}: 0.6609] [5367, 2567]: Comparing 1qks_A and 1iqc_A, based on their crossing files. There are 50 (15 H + 35 S) secondary structure elements in 1qks_A, of which 7 satisfy the size requirements. There are 21 (17 H + 4 S) secondary structure elements in 1iqc_A, of which 10 satisfy the size requirements. 1.40010 [ 2.00004] ((3 . 13) (4 . 14) (5 . 19) (6 . 20) (7 . 21)) 2.927 {0/9:10} B:0 1.75006 [ 2.50002] ((3 . 13) (5 . 19) (6 . 20) (7 . 21)) 3.026 {0/5:6} B:0 1.75068 [ 2.50023] ((3 . 14) (5 . 19) (6 . 20) (7 . 21)) 5.552 {0/6:6} B:0 3.39505 [ 3.57060] ((1 . 14) (4 . 19) (5 . 20) (6 . 21)) 6.131 {2/6:6} B:0 3.39533 [ 3.57084] ((4 . 16) (5 . 19) (6 . 20) (7 . 21)) 8.101 {2/6:6} B:0 SIMILARITY (1/min{score1}): 0.7142 [and 1/min{score2}: 0.5000] [5367, 3450]: Comparing 1qks_A and 1kv9_A, based on their crossing files. There are 50 (15 H + 35 S) secondary structure elements in 1qks_A, of which 7 satisfy the size requirements. There are 59 (20 H + 39 S) secondary structure elements in 1kv9_A, of which 6 satisfy the size requirements. 1.40129 [ 1.20204] ((3 . 52) (4 . 53) (5 . 56) (6 . 57) (7 . 59)) 5.518 {0/7:10} B:0 1.75014 [ 1.50023] ((3 . 52) (4 . 53) (6 . 56) (7 . 59)) 3.759 {0/4:6} B:0 2.64012 [ 2.57942] ((2 . 53) (3 . 56) (4 . 57) (6 . 59)) 9.832 {1/4:6} B:0 3.39595 [ 3.36805] ((3 . 53) (5 . 57) (6 . 58) (7 . 59)) 10.147 {2/6:6} B:0 1.23789 [ 1.10586] ((1 . 58) (3 . 52) (4 . 53) (5 . 56) (6 . 57) (7 . 59)) 5.433 {1/12:15} B:1 SIMILARITY (1/min{score1}): 0.8078 [and 1/min{score2}: 0.9043] [5367, 4964]: Comparing 1qks_A and 1pby_A, based on their crossing files. There are 50 (15 H + 35 S) secondary structure elements in 1qks_A, of which 7 satisfy the size requirements. There are 43 (15 H + 28 S) secondary structure elements in 1pby_A, of which 7 satisfy the size requirements. 1.75040 [ 1.75040] ((3 . 1) (5 . 3) (6 . 5) (7 . 6)) 4.860 {0/5:6} B:0 1.75080 [ 1.75080] ((3 . 2) (5 . 3) (6 . 5) (7 . 6)) 5.789 {0/5:6} B:0 1.52428 [ 1.52428] ((1 . 3) (3 . 1) (4 . 2) (6 . 5) (7 . 6)) 6.795 {1/9:10} B:1 SIMILARITY (1/min{score1}): 0.6560 [and 1/min{score2}: 0.6560] [5367, 4965]: Comparing 1qks_A and 1pby_A, based on their crossing files. There are 50 (15 H + 35 S) secondary structure elements in 1qks_A, of which 7 satisfy the size requirements. There are 43 (15 H + 28 S) secondary structure elements in 1pby_A, of which 7 satisfy the size requirements. 2.03447 [ 2.03447] ((3 . 9) (5 . 12) (6 . 13) (7 . 15)) 7.008 {1/6:6} B:0 2.24830 [ 2.24830] ((2 . 9) (3 . 12) (4 . 13) (6 . 15)) 10.315 {1/5:6} B:0 2.63835 [ 2.63835] ((3 . 9) (4 . 10) (5 . 12) (7 . 14)) 5.346 {1/4:6} B:0 3.39515 [ 3.39515] ((3 . 9) (4 . 10) (5 . 12) (7 . 15)) 7.045 {2/6:6} B:0 SIMILARITY (1/min{score1}): 0.4915 [and 1/min{score2}: 0.4915] [5367, 5367]: Comparing 1qks_A and 1qks_A, based on their crossing files. There are 50 (15 H + 35 S) secondary structure elements in 1qks_A, of which 7 satisfy the size requirements. There are 50 (15 H + 35 S) secondary structure elements in 1qks_A, of which 7 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7)) 0.000 {0/20:21} B:0 2.03397 [ 2.03397] ((1 . 1) (2 . 2) (5 . 6) (7 . 7)) 6.019 {1/6:6} B:0 2.03491 [ 2.03491] ((1 . 1) (4 . 3) (6 . 5) (7 . 7)) 7.632 {1/6:6} B:0 5.01883 [ 5.01883] ((1 . 3) (4 . 4) (5 . 1) (7 . 6)) 8.704 {3/6:6} B:1 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [5367, 6494]: Comparing 1qks_A and 2mta_C, based on their crossing files. There are 50 (15 H + 35 S) secondary structure elements in 1qks_A, of which 7 satisfy the size requirements. There are 9 (9 H + 0 S) secondary structure elements in 2mta_C, of which 6 satisfy the size requirements. 1.42334 [ 1.23632] ((2 . 3) (3 . 4) (4 . 5) (6 . 7) (7 . 8)) 11.455 {0/9:10} B:0 2.03465 [ 1.89228] ((4 . 4) (5 . 5) (6 . 7) (7 . 8)) 7.290 {1/6:6} B:0 SIMILARITY (1/min{score1}): 0.7026 [and 1/min{score2}: 0.8088] -------------------------------------------------------------------------------------------------------------------------