------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [3947, 887]: Comparing 1mjs_A and 1dmz_A, based on their crossing files. There are 17 (5 H + 12 S) secondary structure elements in 1mjs_A, of which 16 satisfy the size requirements. There are 13 (1 H + 12 S) secondary structure elements in 1dmz_A, of which 9 satisfy the size requirements. 3.20009 [ 1.80050] ((9 . 1) (11 . 2) (12 . 3) (15 . 5) (16 . 6)) 5.251 {0/1:10} B:0 4.00004 [ 2.25025] ((1 . 3) (3 . 5) (7 . 9) (9 . 11)) 5.209 {0/2:6} B:0 4.00007 [ 2.25039] ((7 . 1) (11 . 3) (15 . 6) (16 . 9)) 5.829 {0/1:6} B:0 4.00008 [ 2.25046] ((7 . 1) (8 . 2) (15 . 6) (16 . 9)) 6.100 {0/0:6} B:0 4.00012 [ 2.25065] ((1 . 3) (3 . 5) (5 . 6) (7 . 9)) 6.632 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.5000 [and 1/min{score2}: 0.8881] [3947, 1741]: Comparing 1mjs_A and 1g6g_A, based on their crossing files. There are 17 (5 H + 12 S) secondary structure elements in 1mjs_A, of which 16 satisfy the size requirements. There are 14 (3 H + 11 S) secondary structure elements in 1g6g_A, of which 9 satisfy the size requirements. 3.20004 [ 1.80020] ((1 . 1) (3 . 2) (5 . 4) (7 . 6) (8 . 7)) 4.207 {0/4:10} B:0 3.20005 [ 1.80028] ((9 . 1) (11 . 2) (12 . 4) (15 . 6) (16 . 7)) 4.566 {0/4:10} B:0 4.00004 [ 2.25021] ((1 . 4) (3 . 6) (4 . 7) (7 . 13)) 5.020 {0/0:6} B:0 4.00033 [ 2.25183] ((1 . 2) (3 . 4) (9 . 11) (11 . 13)) 8.596 {0/3:6} B:0 4.14466 [ 2.83633] ((7 . 1) (10 . 3) (11 . 4) (15 . 7)) 6.493 {1/4:6} B:0 SIMILARITY (1/min{score1}): 0.4375 [and 1/min{score2}: 0.7773] [3947, 1995]: Comparing 1mjs_A and 1gxc_A, based on their crossing files. There are 17 (5 H + 12 S) secondary structure elements in 1mjs_A, of which 16 satisfy the size requirements. There are 13 (2 H + 11 S) secondary structure elements in 1gxc_A, of which 10 satisfy the size requirements. 1.77779 [ 1.11118] ((1 . 1) (3 . 2) (4 . 3) (7 . 7) (8 . 8) (9 . 9) (12 . 11) (15 . 12) (16 . 13)) 2.192 {0/17:36} B:0 3.20008 [ 2.00033] ((9 . 1) (11 . 2) (12 . 3) (15 . 7) (16 . 8)) 5.131 {0/3:10} B:0 3.20044 [ 2.00180] ((1 . 1) (3 . 2) (4 . 3) (9 . 11) (12 . 13)) 7.839 {0/4:10} B:0 4.00000 [ 2.50002] ((5 . 3) (7 . 7) (8 . 8) (9 . 9)) 3.007 {0/2:6} B:0 4.00001 [ 2.50004] ((8 . 1) (11 . 3) (15 . 8) (16 . 11)) 3.683 {0/1:6} B:0 SIMILARITY (1/min{score1}): 0.5625 [and 1/min{score2}: 0.8999] [3947, 3625]: Comparing 1mjs_A and 1lgp_A, based on their crossing files. There are 17 (5 H + 12 S) secondary structure elements in 1mjs_A, of which 16 satisfy the size requirements. There are 9 (1 H + 8 S) secondary structure elements in 1lgp_A, of which 7 satisfy the size requirements. 4.00041 [ 1.75483] ((1 . 3) (3 . 5) (4 . 6) (8 . 9)) 9.088 {0/1:6} B:0 4.00047 [ 1.75557] ((1 . 3) (5 . 6) (7 . 7) (8 . 9)) 9.417 {0/1:6} B:0 4.00081 [ 1.75959] ((1 . 3) (3 . 5) (4 . 6) (7 . 9)) 10.796 {0/0:6} B:0 4.41365 [ 3.39508] ((4 . 1) (5 . 2) (8 . 5) (9 . 6)) 6.404 {1/3:6} B:0 6.87291 [ 6.67458] ((9 . 1) (12 . 2) (15 . 5) (16 . 6)) 5.245 {2/3:6} B:0 SIMILARITY (1/min{score1}): 0.3125 [and 1/min{score2}: 0.7141] [3947, 3947]: Comparing 1mjs_A and 1mjs_A, based on their crossing files. There are 17 (5 H + 12 S) secondary structure elements in 1mjs_A, of which 16 satisfy the size requirements. There are 17 (5 H + 12 S) secondary structure elements in 1mjs_A, of which 16 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12) (13 . 13) (14 . 14) (15 . 15) (16 . 16) (17 . 17)) 0.000 {0/87:120} B:0 1.77778 [ 1.77778] ((1 . 1) (4 . 5) (6 . 6) (10 . 10) (13 . 13) (14 . 14) (15 . 15) (16 . 16) (17 . 17)) 1.804 {0/26:36} B:0 1.77778 [ 1.77778] ((1 . 1) (5 . 4) (6 . 6) (10 . 10) (13 . 13) (14 . 14) (15 . 15) (16 . 16) (17 . 17)) 1.804 {0/26:36} B:0 3.20005 [ 3.20005] ((3 . 11) (4 . 12) (6 . 14) (7 . 15) (8 . 16)) 4.492 {0/5:10} B:0 3.20005 [ 3.20005] ((11 . 3) (12 . 4) (14 . 6) (15 . 7) (16 . 8)) 4.492 {0/5:10} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [3947, 4084]: Comparing 1mjs_A and 1mzk_A, based on their crossing files. There are 17 (5 H + 12 S) secondary structure elements in 1mjs_A, of which 16 satisfy the size requirements. There are 11 (0 H + 11 S) secondary structure elements in 1mzk_A, of which 7 satisfy the size requirements. 2.28576 [ 1.00051] ((1 . 1) (3 . 2) (4 . 3) (7 . 5) (8 . 6) (15 . 10) (16 . 11)) 3.396 {0/6:21} B:0 2.28577 [ 1.00067] ((1 . 1) (3 . 2) (5 . 3) (7 . 5) (8 . 6) (15 . 10) (16 . 11)) 3.640 {0/6:21} B:0 3.20005 [ 1.40056] ((9 . 1) (11 . 2) (12 . 3) (15 . 5) (16 . 6)) 4.487 {0/3:10} B:0 4.00002 [ 1.75020] ((7 . 2) (8 . 3) (15 . 10) (16 . 11)) 4.069 {0/0:6} B:0 4.00011 [ 1.75130] ((5 . 1) (12 . 5) (15 . 10) (16 . 11)) 6.539 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.4375 [and 1/min{score2}: 0.9995] [3947, 5481]: Comparing 1mjs_A and 1qwt_A, based on their crossing files. There are 17 (5 H + 12 S) secondary structure elements in 1mjs_A, of which 16 satisfy the size requirements. There are 19 (6 H + 13 S) secondary structure elements in 1qwt_A, of which 17 satisfy the size requirements. 1.23118 [ 1.30803] ((1 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 7) (7 . 8) (8 . 9) (9 . 10) (12 . 12) (13 . 13) (15 . 14) (16 . 15) (17 . 16)) 3.117 {1/50:78} B:0 1.60003 [ 1.70003] ((5 . 5) (6 . 7) (7 . 8) (8 . 9) (9 . 10) (12 . 12) (13 . 13) (15 . 14) (16 . 15) (17 . 16)) 2.390 {0/28:45} B:0 2.00241 [ 2.12701] ((1 . 2) (4 . 4) (5 . 5) (6 . 7) (12 . 12) (15 . 14) (16 . 15) (17 . 16)) 2.433 {1/19:28} B:0 2.28573 [ 2.42858] ((4 . 5) (6 . 7) (12 . 12) (13 . 13) (15 . 14) (16 . 15) (17 . 16)) 2.659 {0/14:21} B:0 4.00002 [ 4.25002] ((12 . 5) (14 . 7) (15 . 8) (16 . 9)) 4.344 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.8122 [and 1/min{score2}: 0.7645] [3947, 5527]: Comparing 1mjs_A and 1r21_A, based on their crossing files. There are 17 (5 H + 12 S) secondary structure elements in 1mjs_A, of which 16 satisfy the size requirements. There are 11 (0 H + 11 S) secondary structure elements in 1r21_A, of which 7 satisfy the size requirements. 4.00003 [ 1.75032] ((1 . 3) (3 . 5) (4 . 6) (7 . 11)) 4.602 {0/0:6} B:0 4.00005 [ 1.75065] ((7 . 2) (8 . 3) (15 . 10) (16 . 11)) 5.495 {0/0:6} B:0 4.06112 [ 2.24468] ((9 . 1) (11 . 2) (12 . 3) (16 . 10)) 4.844 {1/5:6} B:0 4.10262 [ 4.00391] ((1 . 1) (3 . 2) (7 . 3) (8 . 5) (12 . 6) (15 . 10) (16 . 11)) 3.853 {4/10:21} B:0 4.10262 [ 4.00392] ((1 . 1) (3 . 2) (4 . 3) (8 . 5) (12 . 6) (15 . 10) (16 . 11)) 4.065 {4/10:21} B:0 SIMILARITY (1/min{score1}): 0.3503 [and 1/min{score2}: 0.5713] [3947, 6022]: Comparing 1mjs_A and 1uht_A, based on their crossing files. There are 17 (5 H + 12 S) secondary structure elements in 1mjs_A, of which 16 satisfy the size requirements. There are 9 (0 H + 9 S) secondary structure elements in 1uht_A, of which 7 satisfy the size requirements. 2.30639 [ 1.18935] ((1 . 1) (4 . 2) (7 . 4) (8 . 5) (12 . 7) (15 . 8) (16 . 9)) 2.795 {1/10:21} B:0 2.30640 [ 1.18944] ((1 . 1) (5 . 2) (7 . 4) (8 . 5) (12 . 7) (15 . 8) (16 . 9)) 3.188 {1/10:21} B:0 4.00002 [ 1.75028] ((5 . 2) (7 . 4) (8 . 5) (9 . 7)) 4.447 {0/3:6} B:0 4.00003 [ 1.75035] ((1 . 2) (3 . 4) (4 . 5) (7 . 9)) 4.717 {0/0:6} B:0 4.00006 [ 1.75077] ((1 . 2) (7 . 7) (8 . 8) (9 . 9)) 5.738 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.4336 [and 1/min{score2}: 0.8560] [3947, 6040]: Comparing 1mjs_A and 1ujx_A, based on their crossing files. There are 17 (5 H + 12 S) secondary structure elements in 1mjs_A, of which 16 satisfy the size requirements. There are 6 (0 H + 6 S) secondary structure elements in 1ujx_A, of which 6 satisfy the size requirements. 3.20005 [ 1.20096] ((4 . 1) (7 . 3) (8 . 4) (12 . 5) (16 . 6)) 4.566 {0/5:10} B:0 4.00001 [ 1.50013] ((8 . 1) (11 . 2) (15 . 4) (16 . 5)) 3.269 {0/2:6} B:0 4.00003 [ 1.50052] ((1 . 2) (3 . 3) (4 . 4) (7 . 6)) 4.642 {0/1:6} B:0 4.41370 [ 3.36726] ((1 . 1) (4 . 2) (7 . 4) (9 . 5)) 7.225 {1/3:6} B:0 4.58195 [ 4.44731] ((3 . 1) (4 . 2) (7 . 3) (8 . 4) (12 . 5) (16 . 6)) 4.381 {4/9:15} B:0 SIMILARITY (1/min{score1}): 0.3749 [and 1/min{score2}: 0.9886] -------------------------------------------------------------------------------------------------------------------------