------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [3373, 65]: Comparing 1ko3_A and 1a7t_A, based on their crossing files. There are 18 (6 H + 12 S) secondary structure elements in 1ko3_A, of which 16 satisfy the size requirements. There are 19 (6 H + 13 S) secondary structure elements in 1a7t_A, of which 17 satisfy the size requirements. 1.01696 [ 1.07671] ((1 . 2) (2 . 3) (3 . 4) (4 . 5) (5 . 6) (6 . 7) (8 . 9) (9 . 10) (10 . 11) (12 . 13) (13 . 14) (14 . 15) (15 . 16) (16 . 17) (17 . 18) (18 . 19)) 2.273 {4/78:120} B:0 1.06846 [ 1.13483] ((1 . 2) (2 . 3) (3 . 4) (4 . 5) (5 . 6) (6 . 7) (8 . 9) (9 . 10) (10 . 11) (13 . 14) (14 . 15) (15 . 16) (16 . 17) (17 . 18) (18 . 19)) 2.086 {2/66:105} B:0 1.23135 [ 1.30818] ((1 . 2) (2 . 3) (3 . 4) (4 . 7) (6 . 10) (9 . 12) (12 . 13) (13 . 14) (14 . 15) (15 . 16) (16 . 17) (17 . 18) (18 . 19)) 3.557 {1/48:78} B:0 3.20002 [ 3.40002] ((5 . 6) (6 . 7) (9 . 12) (16 . 17) (18 . 19)) 3.668 {0/6:10} B:0 3.20047 [ 3.40039] ((1 . 4) (2 . 5) (4 . 7) (6 . 10) (9 . 12)) 7.985 {0/8:10} B:0 SIMILARITY (1/min{score1}): 0.9833 [and 1/min{score2}: 0.9288] [3373, 1041]: Comparing 1ko3_A and 1e5d_A, based on their crossing files. There are 18 (6 H + 12 S) secondary structure elements in 1ko3_A, of which 16 satisfy the size requirements. There are 35 (15 H + 20 S) secondary structure elements in 1e5d_A, of which 19 satisfy the size requirements. 1.04647 [ 1.21619] ((1 . 1) (2 . 2) (3 . 5) (4 . 6) (5 . 7) (6 . 9) (8 . 11) (9 . 12) (10 . 13) (12 . 15) (13 . 16) (14 . 17) (15 . 18) (16 . 22) (17 . 23) (18 . 25)) 3.246 {5/75:120} B:0 1.14367 [ 1.35763] ((1 . 1) (2 . 2) (3 . 5) (4 . 9) (5 . 11) (6 . 12) (9 . 14) (12 . 15) (13 . 16) (14 . 17) (15 . 18) (16 . 22) (17 . 23) (18 . 25)) 4.221 {0/52:91} B:0 1.15261 [ 1.28816] ((1 . 1) (2 . 2) (3 . 5) (4 . 6) (5 . 7) (6 . 9) (8 . 11) (9 . 12) (10 . 13) (12 . 15) (13 . 16) (14 . 17) (15 . 18) (16 . 21) (17 . 23) (18 . 25)) 4.471 {7/75:120} B:0 2.66687 [ 3.16679] ((2 . 6) (4 . 9) (6 . 12) (16 . 22) (17 . 23) (18 . 25)) 5.659 {0/6:15} B:0 3.20001 [ 3.80001] ((1 . 1) (2 . 2) (5 . 7) (9 . 9) (12 . 15)) 3.205 {0/8:10} B:0 SIMILARITY (1/min{score1}): 0.9556 [and 1/min{score2}: 0.8222] [3373, 2933]: Comparing 1ko3_A and 1jje_A, based on their crossing files. There are 18 (6 H + 12 S) secondary structure elements in 1ko3_A, of which 16 satisfy the size requirements. There are 19 (7 H + 12 S) secondary structure elements in 1jje_A, of which 17 satisfy the size requirements. 1.00012 [ 1.06260] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (8 . 8) (9 . 9) (10 . 10) (12 . 12) (13 . 13) (14 . 14) (15 . 15) (16 . 17) (17 . 18) (18 . 19)) 1.949 {1/79:120} B:0 2.85640 [ 2.99487] ((8 . 5) (9 . 6) (12 . 12) (16 . 17) (17 . 18) (18 . 19)) 3.254 {2/10:15} B:0 3.23177 [ 3.42657] ((1 . 3) (2 . 4) (5 . 8) (6 . 9) (9 . 11)) 7.973 {1/7:10} B:0 4.00008 [ 4.25007] ((1 . 14) (2 . 15) (5 . 17) (6 . 18)) 6.108 {0/2:6} B:0 4.00009 [ 4.25007] ((9 . 2) (13 . 6) (15 . 9) (17 . 13)) 6.195 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.9999 [and 1/min{score2}: 0.9411] [3373, 3108]: Comparing 1ko3_A and 1k07_A, based on their crossing files. There are 18 (6 H + 12 S) secondary structure elements in 1ko3_A, of which 16 satisfy the size requirements. There are 21 (9 H + 12 S) secondary structure elements in 1k07_A, of which 18 satisfy the size requirements. 1.14169 [ 1.23160] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 7) (8 . 9) (9 . 10) (10 . 11) (12 . 14) (13 . 15) (14 . 16) (15 . 17) (16 . 18) (17 . 19) (18 . 21)) 5.687 {7/77:120} B:0 2.29593 [ 2.57862] ((5 . 5) (6 . 10) (12 . 14) (13 . 15) (14 . 16) (15 . 17) (17 . 19)) 4.956 {1/12:21} B:0 2.66680 [ 3.00009] ((2 . 2) (5 . 5) (6 . 7) (9 . 10) (15 . 15) (17 . 17)) 5.062 {0/7:15} B:0 3.20002 [ 3.60001] ((5 . 5) (6 . 7) (8 . 9) (10 . 11) (15 . 15)) 3.412 {0/6:10} B:0 3.20004 [ 3.60003] ((9 . 2) (13 . 7) (15 . 10) (16 . 11) (17 . 13)) 4.243 {0/5:10} B:0 SIMILARITY (1/min{score1}): 0.8759 [and 1/min{score2}: 0.8120] [3373, 3373]: Comparing 1ko3_A and 1ko3_A, based on their crossing files. There are 18 (6 H + 12 S) secondary structure elements in 1ko3_A, of which 16 satisfy the size requirements. There are 18 (6 H + 12 S) secondary structure elements in 1ko3_A, of which 16 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (8 . 8) (9 . 9) (10 . 10) (12 . 12) (13 . 13) (14 . 14) (15 . 15) (16 . 16) (17 . 17) (18 . 18)) 0.000 {0/82:120} B:0 3.20000 [ 3.20000] ((5 . 5) (9 . 6) (16 . 16) (17 . 17) (18 . 18)) 2.160 {0/6:10} B:0 3.20000 [ 3.20000] ((5 . 5) (6 . 9) (16 . 16) (17 . 17) (18 . 18)) 2.160 {0/6:10} B:0 3.20052 [ 3.20052] ((12 . 1) (14 . 3) (15 . 4) (16 . 5) (18 . 10)) 8.162 {0/3:10} B:0 3.20052 [ 3.20052] ((1 . 12) (3 . 14) (4 . 15) (5 . 16) (10 . 18)) 8.162 {0/3:10} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [3373, 3812]: Comparing 1ko3_A and 1m2x_A, based on their crossing files. There are 18 (6 H + 12 S) secondary structure elements in 1ko3_A, of which 16 satisfy the size requirements. There are 17 (5 H + 12 S) secondary structure elements in 1m2x_A, of which 17 satisfy the size requirements. 1.00008 [ 1.06256] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (8 . 7) (9 . 8) (10 . 9) (12 . 11) (13 . 12) (14 . 13) (15 . 14) (16 . 15) (17 . 16) (18 . 17)) 2.126 {0/77:120} B:0 1.06674 [ 1.13339] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (8 . 7) (9 . 8) (12 . 11) (13 . 12) (14 . 13) (15 . 14) (16 . 15) (17 . 16) (18 . 17)) 2.169 {0/65:105} B:0 2.66721 [ 2.83379] ((1 . 11) (2 . 12) (3 . 13) (4 . 14) (6 . 16) (10 . 17)) 7.208 {0/7:15} B:0 3.20052 [ 3.40044] ((1 . 3) (2 . 4) (4 . 6) (5 . 7) (9 . 10)) 8.186 {0/7:10} B:0 3.20172 [ 3.40144] ((10 . 7) (12 . 8) (14 . 12) (15 . 13) (18 . 15)) 11.033 {0/6:10} B:0 SIMILARITY (1/min{score1}): 0.9999 [and 1/min{score2}: 0.9411] [3373, 5331]: Comparing 1ko3_A and 1qh5_A, based on their crossing files. There are 18 (6 H + 12 S) secondary structure elements in 1ko3_A, of which 16 satisfy the size requirements. There are 23 (9 H + 14 S) secondary structure elements in 1qh5_A, of which 18 satisfy the size requirements. 1.27395 [ 1.38321] ((2 . 1) (3 . 2) (4 . 3) (5 . 4) (6 . 5) (8 . 7) (9 . 8) (12 . 10) (13 . 11) (14 . 12) (15 . 13) (16 . 16) (17 . 17) (18 . 21)) 4.065 {5/51:91} B:0 2.00007 [ 2.25005] ((5 . 4) (9 . 5) (12 . 10) (13 . 11) (14 . 12) (15 . 13) (16 . 16) (17 . 17)) 3.436 {0/15:28} B:0 3.20007 [ 3.60005] ((13 . 1) (14 . 2) (15 . 3) (16 . 7) (17 . 8)) 4.913 {0/3:10} B:0 3.20010 [ 3.60007] ((13 . 1) (14 . 2) (15 . 3) (16 . 4) (17 . 8)) 5.459 {0/3:10} B:0 3.20021 [ 3.60015] ((1 . 2) (2 . 3) (5 . 7) (6 . 8) (18 . 21)) 6.550 {0/4:10} B:0 SIMILARITY (1/min{score1}): 0.8283 [and 1/min{score2}: 0.7506] [3373, 5827]: Comparing 1ko3_A and 1sml_A, based on their crossing files. There are 18 (6 H + 12 S) secondary structure elements in 1ko3_A, of which 16 satisfy the size requirements. There are 22 (10 H + 12 S) secondary structure elements in 1sml_A, of which 18 satisfy the size requirements. 1.13586 [ 1.22697] ((1 . 2) (2 . 3) (3 . 4) (4 . 5) (5 . 6) (6 . 8) (8 . 10) (9 . 11) (10 . 12) (12 . 14) (13 . 15) (14 . 16) (15 . 17) (16 . 18) (17 . 19) (18 . 22)) 5.683 {7/78:120} B:0 1.25780 [ 1.34597] ((1 . 2) (2 . 3) (3 . 4) (4 . 5) (5 . 6) (6 . 8) (9 . 11) (10 . 12) (12 . 14) (13 . 15) (14 . 16) (15 . 17) (16 . 18) (17 . 19) (18 . 22)) 5.767 {7/67:105} B:0 3.20005 [ 3.60004] ((12 . 4) (13 . 5) (15 . 8) (16 . 10) (17 . 11)) 4.567 {0/3:10} B:0 3.20006 [ 3.60004] ((2 . 3) (5 . 6) (6 . 8) (9 . 11) (15 . 15)) 4.773 {0/5:10} B:0 3.20016 [ 3.60012] ((14 . 4) (15 . 5) (16 . 6) (17 . 8) (18 . 12)) 6.135 {0/2:10} B:0 SIMILARITY (1/min{score1}): 0.8804 [and 1/min{score2}: 0.8150] [3373, 6290]: Comparing 1ko3_A and 1vjn_A, based on their crossing files. There are 18 (6 H + 12 S) secondary structure elements in 1ko3_A, of which 16 satisfy the size requirements. There are 18 (4 H + 14 S) secondary structure elements in 1vjn_A, of which 16 satisfy the size requirements. 2.66671 [ 2.66671] ((6 . 4) (9 . 6) (13 . 10) (15 . 12) (16 . 13) (17 . 14)) 3.760 {0/7:15} B:0 2.66677 [ 2.66677] ((6 . 4) (9 . 6) (12 . 9) (15 . 12) (16 . 13) (17 . 14)) 4.812 {0/8:15} B:0 2.66678 [ 2.66678] ((6 . 4) (9 . 6) (12 . 9) (13 . 10) (15 . 12) (16 . 13)) 4.884 {0/6:15} B:0 2.66687 [ 2.66687] ((4 . 1) (6 . 3) (9 . 6) (12 . 9) (13 . 10) (16 . 13)) 5.626 {0/5:15} B:0 3.20003 [ 3.20003] ((6 . 3) (9 . 6) (15 . 12) (16 . 13) (17 . 14)) 3.928 {0/5:10} B:0 SIMILARITY (1/min{score1}): 0.8020 [and 1/min{score2}: 0.8020] [3373, 6403]: Comparing 1ko3_A and 2bc2_A, based on their crossing files. There are 18 (6 H + 12 S) secondary structure elements in 1ko3_A, of which 16 satisfy the size requirements. There are 18 (6 H + 12 S) secondary structure elements in 2bc2_A, of which 17 satisfy the size requirements. 1.00124 [ 1.06353] ((1 . 2) (2 . 3) (3 . 4) (4 . 5) (5 . 6) (6 . 7) (8 . 9) (9 . 10) (10 . 11) (12 . 12) (13 . 13) (14 . 14) (15 . 15) (16 . 16) (17 . 17) (18 . 18)) 2.289 {2/77:120} B:0 2.66682 [ 2.83346] ((12 . 2) (13 . 3) (14 . 4) (15 . 5) (16 . 6) (17 . 7)) 5.289 {0/7:15} B:0 2.66689 [ 2.83352] ((12 . 2) (13 . 3) (14 . 4) (15 . 5) (16 . 6) (17 . 10)) 5.799 {0/7:15} B:0 3.20007 [ 3.40006] ((13 . 1) (14 . 2) (15 . 3) (16 . 6) (17 . 7)) 5.000 {0/3:10} B:0 3.20048 [ 3.40040] ((9 . 1) (12 . 4) (13 . 5) (15 . 7) (17 . 10)) 8.002 {0/7:10} B:0 SIMILARITY (1/min{score1}): 0.9988 [and 1/min{score2}: 0.9403] -------------------------------------------------------------------------------------------------------------------------