------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [2960, 31]: Comparing 1jlr_A and 1a3c, based on their crossing files. There are 23 (9 H + 14 S) secondary structure elements in 1jlr_A, of which 17 satisfy the size requirements. There are 13 (4 H + 9 S) secondary structure elements in 1a3c, of which 12 satisfy the size requirements. 1.88898 [ 1.33360] ((4 . 2) (7 . 3) (8 . 4) (9 . 5) (10 . 6) (12 . 7) (14 . 8) (16 . 9) (19 . 10)) 3.576 {0/21:36} B:0 2.12503 [ 1.50008] ((4 . 2) (7 . 3) (8 . 4) (9 . 5) (10 . 6) (12 . 7) (14 . 8) (16 . 9)) 2.897 {0/17:28} B:0 3.40005 [ 2.40014] ((7 . 3) (8 . 4) (16 . 7) (18 . 8) (19 . 9)) 4.708 {0/6:10} B:0 3.49780 [ 2.64885] ((11 . 2) (12 . 3) (14 . 4) (16 . 5) (19 . 7)) 7.659 {1/5:10} B:0 4.25005 [ 3.00013] ((12 . 5) (16 . 7) (18 . 8) (19 . 9)) 5.531 {0/1:6} B:0 SIMILARITY (1/min{score1}): 0.5294 [and 1/min{score2}: 0.7499] [2960, 497]: Comparing 1jlr_A and 1bzy_A, based on their crossing files. There are 23 (9 H + 14 S) secondary structure elements in 1jlr_A, of which 17 satisfy the size requirements. There are 18 (7 H + 11 S) secondary structure elements in 1bzy_A, of which 15 satisfy the size requirements. 1.70139 [ 1.50202] ((4 . 5) (7 . 6) (8 . 7) (9 . 8) (10 . 10) (11 . 11) (12 . 12) (14 . 13) (16 . 14) (19 . 15)) 4.851 {1/27:45} B:0 1.88903 [ 1.66687] ((4 . 5) (7 . 6) (8 . 7) (9 . 8) (10 . 10) (11 . 11) (12 . 12) (14 . 13) (16 . 14)) 3.947 {0/23:36} B:0 1.88922 [ 1.66715] ((4 . 5) (7 . 6) (8 . 7) (9 . 8) (10 . 10) (12 . 12) (14 . 13) (16 . 14) (19 . 15)) 4.925 {0/19:36} B:0 2.12510 [ 1.87515] ((4 . 5) (7 . 6) (8 . 7) (9 . 8) (10 . 10) (12 . 12) (14 . 13) (16 . 14)) 4.025 {0/16:28} B:0 2.12511 [ 1.87517] ((4 . 5) (8 . 7) (9 . 8) (10 . 10) (11 . 11) (12 . 12) (14 . 13) (16 . 14)) 4.121 {0/19:28} B:0 SIMILARITY (1/min{score1}): 0.5878 [and 1/min{score2}: 0.6658] [2960, 863]: Comparing 1jlr_A and 1dkr_A, based on their crossing files. There are 23 (9 H + 14 S) secondary structure elements in 1jlr_A, of which 17 satisfy the size requirements. There are 26 (10 H + 16 S) secondary structure elements in 1dkr_A, of which 12 satisfy the size requirements. 2.83345 [ 2.00032] ((9 . 5) (12 . 7) (14 . 8) (16 . 9) (18 . 10) (19 . 11)) 5.094 {0/5:15} B:0 3.40010 [ 2.40028] ((8 . 2) (9 . 5) (12 . 7) (18 . 8) (19 . 9)) 5.661 {0/5:10} B:0 3.40015 [ 2.40042] ((2 . 5) (4 . 8) (7 . 9) (8 . 10) (9 . 11)) 6.234 {0/7:10} B:0 3.40031 [ 2.40087] ((2 . 1) (8 . 6) (12 . 9) (14 . 10) (16 . 11)) 7.492 {0/7:10} B:0 3.40033 [ 2.40094] ((1 . 2) (4 . 6) (7 . 9) (8 . 10) (9 . 11)) 7.647 {0/7:10} B:0 SIMILARITY (1/min{score1}): 0.7057 [and 1/min{score2}: 0.9988] [2960, 864]: Comparing 1jlr_A and 1dkr_A, based on their crossing files. There are 23 (9 H + 14 S) secondary structure elements in 1jlr_A, of which 17 satisfy the size requirements. There are 26 (10 H + 16 S) secondary structure elements in 1dkr_A, of which 11 satisfy the size requirements. 2.83336 [ 1.83342] ((7 . 13) (8 . 14) (9 . 15) (14 . 19) (16 . 23) (19 . 24)) 3.424 {0/10:15} B:0 2.83336 [ 1.83345] ((7 . 13) (8 . 14) (9 . 15) (12 . 20) (16 . 23) (19 . 24)) 3.675 {0/9:15} B:0 3.40024 [ 2.20090] ((1 . 14) (2 . 15) (4 . 19) (7 . 23) (9 . 24)) 7.088 {0/8:10} B:0 3.40035 [ 2.20129] ((9 . 13) (11 . 14) (14 . 19) (16 . 20) (19 . 23)) 7.753 {0/7:10} B:0 3.42625 [ 2.29207] ((8 . 14) (11 . 19) (12 . 20) (16 . 23) (19 . 24)) 4.992 {1/7:10} B:0 SIMILARITY (1/min{score1}): 0.6470 [and 1/min{score2}: 0.9992] [2960, 920]: Comparing 1jlr_A and 1dqn_A, based on their crossing files. There are 23 (9 H + 14 S) secondary structure elements in 1jlr_A, of which 17 satisfy the size requirements. There are 18 (8 H + 10 S) secondary structure elements in 1dqn_A, of which 17 satisfy the size requirements. 3.40083 [ 3.40083] ((4 . 4) (6 . 8) (12 . 13) (14 . 14) (16 . 15)) 9.624 {0/5:10} B:0 4.00490 [ 4.00490] ((1 . 6) (7 . 13) (8 . 14) (9 . 15) (14 . 18)) 10.217 {2/6:10} B:0 4.25000 [ 4.25000] ((12 . 7) (16 . 11) (18 . 12) (19 . 13)) 2.910 {0/1:6} B:0 4.25010 [ 4.25010] ((8 . 4) (16 . 11) (18 . 12) (19 . 13)) 6.613 {0/0:6} B:0 4.25011 [ 4.25011] ((11 . 4) (14 . 6) (16 . 7) (23 . 12)) 6.823 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.6703 [and 1/min{score2}: 0.6703] [2960, 1101]: Comparing 1jlr_A and 1ecf_A, based on their crossing files. There are 23 (9 H + 14 S) secondary structure elements in 1jlr_A, of which 17 satisfy the size requirements. There are 38 (17 H + 21 S) secondary structure elements in 1ecf_A, of which 14 satisfy the size requirements. 1.55368 [ 1.28732] ((4 . 24) (7 . 25) (8 . 26) (9 . 27) (10 . 28) (11 . 29) (12 . 30) (14 . 31) (16 . 32) (18 . 34) (19 . 35)) 3.639 {2/34:55} B:0 3.40046 [ 2.80082] ((7 . 30) (8 . 31) (9 . 32) (14 . 34) (16 . 35)) 8.300 {0/5:10} B:0 3.40048 [ 2.80087] ((1 . 26) (2 . 27) (4 . 31) (8 . 34) (9 . 35)) 8.406 {0/8:10} B:0 4.25002 [ 3.50004] ((4 . 24) (12 . 32) (18 . 34) (19 . 35)) 4.601 {0/2:6} B:0 4.25005 [ 3.50008] ((8 . 24) (9 . 25) (18 . 31) (19 . 32)) 5.510 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.6808 [and 1/min{score2}: 0.7968] [2960, 1619]: Comparing 1jlr_A and 1fsg_A, based on their crossing files. There are 23 (9 H + 14 S) secondary structure elements in 1jlr_A, of which 17 satisfy the size requirements. There are 19 (8 H + 11 S) secondary structure elements in 1fsg_A, of which 14 satisfy the size requirements. 1.88910 [ 1.55593] ((4 . 7) (7 . 8) (8 . 9) (9 . 10) (10 . 11) (11 . 12) (12 . 13) (14 . 14) (16 . 15)) 4.375 {0/23:36} B:0 2.83342 [ 2.33349] ((4 . 7) (7 . 8) (8 . 9) (16 . 13) (18 . 14) (19 . 15)) 4.813 {0/7:15} B:0 3.40015 [ 2.80027] ((7 . 8) (12 . 10) (16 . 13) (18 . 14) (19 . 15)) 6.269 {0/3:10} B:0 4.25008 [ 3.50014] ((14 . 7) (16 . 8) (18 . 9) (19 . 10)) 6.331 {0/1:6} B:0 4.25010 [ 3.50019] ((4 . 7) (11 . 14) (12 . 15) (16 . 16)) 6.755 {0/0:6} B:0 SIMILARITY (1/min{score1}): 0.5294 [and 1/min{score2}: 0.6427] [2960, 1703]: Comparing 1jlr_A and 1g2q_A, based on their crossing files. There are 23 (9 H + 14 S) secondary structure elements in 1jlr_A, of which 17 satisfy the size requirements. There are 14 (5 H + 9 S) secondary structure elements in 1g2q_A, of which 14 satisfy the size requirements. 1.88915 [ 1.55603] ((3 . 1) (4 . 5) (8 . 7) (9 . 9) (10 . 10) (12 . 11) (14 . 12) (16 . 13) (19 . 14)) 4.656 {0/26:36} B:0 2.12506 [ 1.75011] ((3 . 1) (8 . 7) (9 . 8) (10 . 10) (12 . 11) (14 . 12) (16 . 13) (19 . 14)) 3.565 {0/20:28} B:0 3.40008 [ 2.80014] ((7 . 6) (9 . 8) (16 . 11) (18 . 12) (19 . 13)) 5.339 {0/6:10} B:0 3.40026 [ 2.80046] ((1 . 1) (4 . 5) (8 . 7) (12 . 13) (16 . 14)) 7.163 {0/4:10} B:0 3.40040 [ 2.80072] ((1 . 7) (2 . 8) (4 . 12) (7 . 13) (9 . 14)) 8.028 {0/7:10} B:0 SIMILARITY (1/min{score1}): 0.6454 [and 1/min{score2}: 0.7813] [2960, 2209]: Comparing 1jlr_A and 1hgx_A, based on their crossing files. There are 23 (9 H + 14 S) secondary structure elements in 1jlr_A, of which 17 satisfy the size requirements. There are 12 (3 H + 9 S) secondary structure elements in 1hgx_A, of which 11 satisfy the size requirements. 1.88918 [ 1.22330] ((4 . 2) (7 . 3) (8 . 4) (9 . 5) (10 . 6) (12 . 7) (14 . 8) (16 . 9) (19 . 10)) 4.772 {0/19:36} B:0 2.12510 [ 1.37536] ((4 . 2) (7 . 3) (8 . 4) (9 . 5) (10 . 6) (12 . 7) (14 . 8) (16 . 9)) 3.970 {0/16:28} B:0 3.40034 [ 2.20124] ((11 . 4) (12 . 5) (16 . 7) (18 . 8) (19 . 9)) 7.675 {0/4:10} B:0 3.62537 [ 2.81214] ((11 . 2) (12 . 3) (14 . 4) (16 . 5) (19 . 7)) 7.585 {1/4:10} B:0 4.23107 [ 4.04355] ((4 . 2) (7 . 3) (8 . 4) (9 . 7) (11 . 8) (12 . 9)) 6.869 {2/5:15} B:0 SIMILARITY (1/min{score1}): 0.5293 [and 1/min{score2}: 0.8175] [2960, 2755]: Comparing 1jlr_A and 1j7j_A, based on their crossing files. There are 23 (9 H + 14 S) secondary structure elements in 1jlr_A, of which 17 satisfy the size requirements. There are 12 (4 H + 8 S) secondary structure elements in 1j7j_A, of which 10 satisfy the size requirements. 2.12524 [ 1.25117] ((4 . 2) (7 . 3) (8 . 4) (9 . 5) (12 . 6) (14 . 7) (16 . 8) (19 . 10)) 4.950 {0/14:28} B:0 2.42868 [ 1.42911] ((4 . 2) (7 . 3) (8 . 4) (9 . 5) (12 . 6) (14 . 7) (16 . 8)) 4.515 {0/11:21} B:0 3.40013 [ 2.00065] ((8 . 2) (9 . 3) (12 . 6) (14 . 7) (16 . 8)) 6.088 {0/2:10} B:0 3.40016 [ 2.00080] ((4 . 2) (8 . 4) (9 . 5) (12 . 8) (16 . 10)) 6.406 {0/6:10} B:0 3.40030 [ 2.00147] ((8 . 2) (12 . 3) (14 . 4) (16 . 5) (19 . 6)) 7.451 {0/4:10} B:0 SIMILARITY (1/min{score1}): 0.5291 [and 1/min{score2}: 0.8962] [2960, 2960]: Comparing 1jlr_A and 1jlr_A, based on their crossing files. There are 23 (9 H + 14 S) secondary structure elements in 1jlr_A, of which 17 satisfy the size requirements. There are 23 (9 H + 14 S) secondary structure elements in 1jlr_A, of which 17 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12) (14 . 14) (16 . 16) (18 . 18) (19 . 19) (23 . 23)) 0.000 {0/109:136} B:0 3.40038 [ 3.40038] ((8 . 1) (9 . 2) (16 . 7) (18 . 8) (19 . 9)) 7.905 {0/6:10} B:0 3.40038 [ 3.40038] ((1 . 8) (2 . 9) (7 . 16) (8 . 18) (9 . 19)) 7.905 {0/6:10} B:0 3.41545 [ 3.41545] ((6 . 5) (8 . 8) (18 . 14) (19 . 16) (23 . 23)) 4.084 {1/8:10} B:0 3.41545 [ 3.41545] ((5 . 6) (8 . 8) (14 . 18) (16 . 19) (23 . 23)) 4.084 {1/8:10} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [2960, 3517]: Comparing 1jlr_A and 1l1q_A, based on their crossing files. There are 23 (9 H + 14 S) secondary structure elements in 1jlr_A, of which 17 satisfy the size requirements. There are 18 (9 H + 9 S) secondary structure elements in 1l1q_A, of which 14 satisfy the size requirements. 1.54566 [ 1.27309] ((3 . 1) (4 . 5) (7 . 6) (8 . 7) (9 . 8) (10 . 10) (12 . 12) (14 . 13) (16 . 15) (18 . 17) (19 . 18)) 3.749 {0/33:55} B:0 3.40006 [ 2.80011] ((2 . 8) (4 . 13) (7 . 15) (8 . 17) (9 . 18)) 4.961 {0/5:10} B:0 3.40042 [ 2.80075] ((4 . 5) (6 . 8) (12 . 15) (14 . 17) (16 . 18)) 8.099 {0/5:10} B:0 4.25003 [ 3.50005] ((12 . 8) (16 . 12) (18 . 13) (19 . 15)) 4.765 {0/1:6} B:0 4.25006 [ 3.50011] ((4 . 7) (12 . 15) (14 . 17) (16 . 18)) 5.931 {0/1:6} B:0 SIMILARITY (1/min{score1}): 0.6470 [and 1/min{score2}: 0.7855] [2960, 3628]: Comparing 1jlr_A and 1lh0_A, based on their crossing files. There are 23 (9 H + 14 S) secondary structure elements in 1jlr_A, of which 17 satisfy the size requirements. There are 16 (8 H + 8 S) secondary structure elements in 1lh0_A, of which 15 satisfy the size requirements. 1.54569 [ 1.36397] ((3 . 1) (4 . 5) (7 . 6) (8 . 7) (9 . 8) (10 . 9) (12 . 10) (14 . 11) (16 . 12) (18 . 13) (19 . 14)) 3.869 {0/37:55} B:0 3.40011 [ 3.00016] ((4 . 5) (9 . 10) (12 . 12) (14 . 13) (16 . 14)) 5.784 {0/3:10} B:0 3.40032 [ 3.00047] ((1 . 7) (2 . 8) (4 . 11) (7 . 12) (9 . 14)) 7.591 {0/7:10} B:0 4.25009 [ 3.75014] ((12 . 6) (14 . 7) (16 . 8) (23 . 11)) 6.610 {0/3:6} B:0 4.25014 [ 3.75020] ((7 . 10) (8 . 11) (9 . 12) (11 . 13)) 7.277 {0/0:6} B:0 SIMILARITY (1/min{score1}): 0.7055 [and 1/min{score2}: 0.7993] [2960, 4398]: Comparing 1jlr_A and 1nul_A, based on their crossing files. There are 23 (9 H + 14 S) secondary structure elements in 1jlr_A, of which 17 satisfy the size requirements. There are 14 (6 H + 8 S) secondary structure elements in 1nul_A, of which 12 satisfy the size requirements. 1.70009 [ 1.20026] ((4 . 2) (7 . 4) (8 . 5) (9 . 6) (10 . 7) (12 . 8) (14 . 9) (16 . 10) (18 . 11) (19 . 12)) 3.297 {0/27:45} B:0 1.88895 [ 1.33350] ((4 . 2) (7 . 4) (8 . 5) (9 . 6) (10 . 7) (12 . 8) (14 . 9) (16 . 10) (18 . 11)) 3.179 {0/22:36} B:0 2.83345 [ 2.00035] ((8 . 2) (9 . 4) (12 . 8) (14 . 9) (16 . 10) (18 . 11)) 5.189 {0/8:15} B:0 2.83347 [ 2.00038] ((4 . 2) (8 . 5) (9 . 6) (12 . 10) (14 . 11) (16 . 12)) 5.297 {0/9:15} B:0 3.40002 [ 2.40007] ((9 . 4) (14 . 9) (16 . 10) (18 . 11) (19 . 12)) 3.978 {0/4:10} B:0 SIMILARITY (1/min{score1}): 0.5882 [and 1/min{score2}: 0.8332] [2960, 4494]: Comparing 1jlr_A and 1o57_A, based on their crossing files. There are 23 (9 H + 14 S) secondary structure elements in 1jlr_A, of which 17 satisfy the size requirements. There are 22 (10 H + 12 S) secondary structure elements in 1o57_A, of which 12 satisfy the size requirements. 1.70160 [ 1.20453] ((3 . 6) (4 . 10) (7 . 11) (8 . 12) (9 . 13) (10 . 15) (12 . 17) (14 . 18) (16 . 19) (19 . 20)) 5.372 {1/27:45} B:0 1.88906 [ 1.33382] ((3 . 6) (4 . 10) (7 . 11) (8 . 12) (9 . 13) (10 . 15) (12 . 17) (14 . 18) (16 . 19)) 4.174 {0/23:36} B:0 2.12524 [ 1.50067] ((3 . 6) (4 . 10) (8 . 12) (9 . 14) (10 . 15) (12 . 17) (14 . 18) (16 . 19)) 4.939 {0/18:28} B:0 2.83346 [ 2.00035] ((7 . 11) (8 . 12) (9 . 13) (16 . 17) (18 . 18) (19 . 19)) 5.220 {0/9:15} B:0 3.40012 [ 2.40034] ((8 . 10) (12 . 11) (16 . 17) (18 . 18) (19 . 19)) 5.936 {0/5:10} B:0 SIMILARITY (1/min{score1}): 0.5877 [and 1/min{score2}: 0.8302] [2960, 4502]: Comparing 1jlr_A and 1o5o_A, based on their crossing files. There are 23 (9 H + 14 S) secondary structure elements in 1jlr_A, of which 17 satisfy the size requirements. There are 21 (6 H + 15 S) secondary structure elements in 1o5o_A, of which 15 satisfy the size requirements. 1.13680 [ 1.00503] ((2 . 1) (3 . 2) (4 . 3) (5 . 4) (6 . 5) (7 . 6) (8 . 7) (9 . 9) (10 . 10) (12 . 11) (14 . 13) (16 . 14) (18 . 16) (19 . 17) (23 . 21)) 2.407 {3/80:105} B:0 1.21440 [ 1.07160] ((2 . 1) (3 . 2) (4 . 3) (5 . 4) (7 . 6) (8 . 7) (9 . 9) (10 . 10) (12 . 11) (14 . 13) (16 . 14) (18 . 16) (19 . 17) (23 . 21)) 2.200 {1/68:91} B:0 3.40001 [ 3.00001] ((8 . 7) (12 . 14) (14 . 16) (16 . 17) (23 . 21)) 2.987 {0/7:10} B:0 3.40005 [ 3.00007] ((6 . 4) (8 . 7) (18 . 13) (19 . 14) (23 . 21)) 4.772 {0/7:10} B:0 3.40036 [ 3.00052] ((1 . 7) (4 . 13) (7 . 14) (8 . 16) (9 . 17)) 7.790 {0/5:10} B:0 SIMILARITY (1/min{score1}): 0.8797 [and 1/min{score2}: 0.9950] [2960, 5277]: Comparing 1jlr_A and 1qb7_A, based on their crossing files. There are 23 (9 H + 14 S) secondary structure elements in 1jlr_A, of which 17 satisfy the size requirements. There are 23 (12 H + 11 S) secondary structure elements in 1qb7_A, of which 16 satisfy the size requirements. 1.41700 [ 1.33373] ((2 . 2) (3 . 3) (4 . 8) (7 . 9) (8 . 10) (9 . 11) (10 . 14) (12 . 15) (14 . 16) (16 . 17) (18 . 19) (19 . 20)) 3.968 {0/44:66} B:0 3.40008 [ 3.20010] ((7 . 9) (9 . 11) (16 . 15) (18 . 16) (19 . 17)) 5.422 {0/5:10} B:0 3.40012 [ 3.20014] ((3 . 3) (7 . 9) (9 . 11) (16 . 15) (18 . 16)) 5.917 {0/6:10} B:0 3.40026 [ 3.20031] ((1 . 10) (2 . 11) (4 . 16) (7 . 17) (8 . 19)) 7.186 {0/7:10} B:0 4.25002 [ 4.00002] ((2 . 11) (7 . 17) (8 . 19) (9 . 20)) 4.257 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.7643 [and 1/min{score2}: 0.8120] [2960, 5892]: Comparing 1jlr_A and 1tc1_A, based on their crossing files. There are 23 (9 H + 14 S) secondary structure elements in 1jlr_A, of which 17 satisfy the size requirements. There are 12 (3 H + 9 S) secondary structure elements in 1tc1_A, of which 12 satisfy the size requirements. 1.88911 [ 1.33396] ((4 . 2) (7 . 3) (8 . 4) (9 . 5) (10 . 6) (12 . 7) (14 . 8) (16 . 9) (19 . 10)) 4.441 {0/20:36} B:0 2.12509 [ 1.50026] ((4 . 2) (7 . 3) (8 . 4) (9 . 5) (10 . 6) (12 . 7) (14 . 8) (16 . 9)) 3.878 {0/16:28} B:0 3.40040 [ 2.40113] ((8 . 2) (12 . 3) (14 . 4) (16 . 5) (19 . 7)) 8.002 {0/4:10} B:0 3.62542 [ 2.91599] ((11 . 2) (12 . 3) (14 . 4) (16 . 5) (19 . 7)) 7.937 {1/4:10} B:0 4.25003 [ 3.00008] ((12 . 5) (16 . 7) (18 . 8) (19 . 9)) 4.848 {0/1:6} B:0 SIMILARITY (1/min{score1}): 0.5294 [and 1/min{score2}: 0.7496] -------------------------------------------------------------------------------------------------------------------------