------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [784, 493]: Comparing 1dbq_A and 1byk_A, based on their crossing files. There are 21 (10 H + 11 S) secondary structure elements in 1dbq_A, of which 20 satisfy the size requirements. There are 21 (10 H + 11 S) secondary structure elements in 1byk_A, of which 19 satisfy the size requirements. 1.22238 [ 1.17053] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (14 . 15) (15 . 16) (16 . 17) (17 . 18) (18 . 19) (19 . 20) (20 . 21)) 2.464 {6/80:136} B:0 1.25583 [ 1.19429] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (14 . 15) (15 . 16) (16 . 17) (17 . 18) (18 . 19) (19 . 20) (20 . 21)) 2.376 {3/65:120} B:0 1.43515 [ 1.36481] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (9 . 9) (10 . 10) (11 . 11) (14 . 15) (15 . 16) (16 . 17) (17 . 18) (18 . 19) (19 . 20) (20 . 21)) 2.458 {3/57:91} B:0 2.07232 [ 1.98339] ((6 . 4) (7 . 5) (9 . 9) (10 . 10) (14 . 15) (15 . 16) (16 . 17) (17 . 18) (18 . 19) (19 . 20)) 3.146 {3/24:45} B:0 2.85717 [ 2.71432] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 7) (7 . 8) (16 . 19)) 3.612 {0/6:21} B:0 SIMILARITY (1/min{score1}): 0.8181 [and 1/min{score2}: 0.8543] [784, 784]: Comparing 1dbq_A and 1dbq_A, based on their crossing files. There are 21 (10 H + 11 S) secondary structure elements in 1dbq_A, of which 20 satisfy the size requirements. There are 21 (10 H + 11 S) secondary structure elements in 1dbq_A, of which 20 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) (13 . 13) (14 . 14) (15 . 15) (16 . 16) (17 . 17) (18 . 18) (19 . 19) (20 . 20) (21 . 21)) 0.000 {0/129:190} B:0 2.85997 [ 2.85997] ((2 . 2) (3 . 5) (4 . 6) (5 . 7) (9 . 9) (11 . 11) (16 . 18)) 3.992 {1/14:21} B:0 3.33354 [ 3.33354] ((3 . 5) (4 . 6) (5 . 7) (11 . 13) (14 . 16) (16 . 18)) 6.683 {0/9:15} B:0 3.33354 [ 3.33354] ((5 . 3) (6 . 4) (7 . 5) (13 . 11) (16 . 14) (18 . 16)) 6.683 {0/9:15} B:0 4.00001 [ 4.00001] ((14 . 3) (15 . 4) (16 . 5) (17 . 6) (18 . 7)) 3.233 {0/1:10} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [784, 903]: Comparing 1dbq_A and 1dp4_A, based on their crossing files. There are 21 (10 H + 11 S) secondary structure elements in 1dbq_A, of which 20 satisfy the size requirements. There are 27 (12 H + 15 S) secondary structure elements in 1dp4_A, of which 26 satisfy the size requirements. 2.00149 [ 2.60068] ((9 . 10) (10 . 11) (11 . 12) (13 . 14) (14 . 15) (15 . 16) (16 . 17) (18 . 19) (19 . 20) (21 . 25)) 4.253 {1/22:45} B:0 3.76175 [ 3.89408] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 9) (19 . 21) (20 . 24)) 4.557 {7/19:45} B:0 5.42325 [ 5.49285] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (19 . 21) (20 . 24)) 3.990 {7/13:36} B:0 1.55530 [ 2.00774] ((6 . 4) (8 . 9) (9 . 10) (10 . 11) (11 . 12) (13 . 14) (14 . 15) (15 . 16) (16 . 17) (18 . 19) (19 . 2) (20 . 7) (21 . 25)) 5.330 {3/43:78} B:1 1.67132 [ 2.16879] ((6 . 4) (8 . 7) (9 . 10) (10 . 11) (11 . 12) (13 . 14) (14 . 15) (15 . 16) (16 . 17) (18 . 19) (19 . 2) (21 . 25)) 5.031 {2/38:66} B:1 SIMILARITY (1/min{score1}): 0.7485 [and 1/min{score2}: 0.6540] [784, 928]: Comparing 1dbq_A and 1drk, based on their crossing files. There are 21 (10 H + 11 S) secondary structure elements in 1dbq_A, of which 20 satisfy the size requirements. There are 21 (9 H + 12 S) secondary structure elements in 1drk, of which 21 satisfy the size requirements. 1.35144 [ 1.37276] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (13 . 13) (14 . 14) (15 . 15) (16 . 16) (17 . 17) (18 . 18) (19 . 19) (20 . 20) (21 . 21)) 3.466 {11/89:190} B:0 1.82912 [ 1.91856] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (11 . 17) (19 . 19) (20 . 20)) 4.276 {2/28:55} B:0 2.50006 [ 2.62505] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (9 . 9) (16 . 14)) 4.004 {0/9:28} B:0 2.50195 [ 2.62668] ((1 . 3) (9 . 9) (11 . 11) (13 . 13) (14 . 14) (15 . 15) (16 . 18) (19 . 19)) 3.382 {1/17:28} B:0 3.33336 [ 3.50002] ((10 . 1) (11 . 2) (13 . 4) (14 . 5) (16 . 8) (19 . 9)) 3.843 {0/6:15} B:0 SIMILARITY (1/min{score1}): 0.7988 [and 1/min{score2}: 0.7683] [784, 1286]: Comparing 1dbq_A and 1ewk_A, based on their crossing files. There are 21 (10 H + 11 S) secondary structure elements in 1dbq_A, of which 20 satisfy the size requirements. There are 32 (16 H + 16 S) secondary structure elements in 1ewk_A, of which 30 satisfy the size requirements. 1.80301 [ 2.06972] ((1 . 2) (2 . 4) (3 . 5) (4 . 6) (5 . 7) (8 . 9) (9 . 12) (10 . 13) (11 . 14) (13 . 16) (14 . 17) (15 . 18) (16 . 19) (17 . 20) (18 . 22) (19 . 25) (21 . 30)) 5.689 {12/70:136} B:0 2.28314 [ 2.40337] ((1 . 2) (2 . 4) (3 . 5) (4 . 6) (5 . 7) (6 . 8) (7 . 9) (8 . 11) (9 . 12) (10 . 13) (11 . 14) (13 . 16) (14 . 17) (15 . 18) (16 . 19) (18 . 22) (19 . 25) (21 . 32)) 5.978 {18/80:153} B:0 2.57658 [ 2.64657] ((1 . 2) (2 . 4) (3 . 5) (4 . 6) (5 . 7) (6 . 8) (7 . 9) (8 . 11) (9 . 12) (10 . 13) (11 . 14) (13 . 16) (14 . 17) (15 . 18) (16 . 19) (17 . 20) (18 . 22) (19 . 25) (21 . 30)) 6.054 {22/86:171} B:0 2.86238 [ 2.96271] ((1 . 2) (2 . 4) (3 . 5) (4 . 6) (5 . 7) (9 . 12) (10 . 13) (11 . 14) (13 . 16) (14 . 17) (15 . 18) (16 . 19) (18 . 22) (19 . 25) (20 . 29) (21 . 32)) 5.690 {19/67:120} B:0 1.92765 [ 2.08214] ((1 . 2) (2 . 4) (3 . 5) (4 . 6) (5 . 7) (6 . 8) (8 . 11) (9 . 12) (10 . 13) (11 . 14) (13 . 16) (14 . 17) (15 . 18) (16 . 19) (17 . 20) (18 . 22) (19 . 25) (20 . 9) (21 . 30)) 6.358 {16/85:171} B:1 SIMILARITY (1/min{score1}): 0.7846 [and 1/min{score2}: 0.5566] [784, 1791]: Comparing 1dbq_A and 1gca, based on their crossing files. There are 21 (10 H + 11 S) secondary structure elements in 1dbq_A, of which 20 satisfy the size requirements. There are 25 (13 H + 12 S) secondary structure elements in 1gca, of which 22 satisfy the size requirements. 1.56457 [ 1.60051] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 9) (9 . 10) (10 . 12) (11 . 13) (13 . 15) (14 . 17) (15 . 18) (17 . 20) (18 . 21) (19 . 22) (20 . 23) (21 . 24)) 3.286 {13/88:171} B:0 2.22225 [ 2.44446] ((9 . 10) (10 . 12) (11 . 13) (13 . 15) (14 . 17) (15 . 18) (17 . 20) (18 . 21) (19 . 22)) 2.856 {0/13:36} B:0 2.22441 [ 2.44609] ((2 . 2) (9 . 10) (10 . 12) (11 . 13) (13 . 15) (14 . 17) (15 . 18) (17 . 20) (19 . 22)) 2.890 {1/18:36} B:0 2.50192 [ 2.75145] ((1 . 3) (11 . 13) (13 . 15) (14 . 17) (15 . 18) (19 . 22) (20 . 23) (21 . 24)) 2.493 {1/17:28} B:0 2.86444 [ 3.14835] ((1 . 3) (10 . 14) (14 . 17) (15 . 18) (19 . 22) (20 . 23) (21 . 24)) 2.710 {1/11:21} B:0 SIMILARITY (1/min{score1}): 0.6783 [and 1/min{score2}: 0.6428] [784, 1957]: Comparing 1dbq_A and 1gud_A, based on their crossing files. There are 21 (10 H + 11 S) secondary structure elements in 1dbq_A, of which 20 satisfy the size requirements. There are 22 (10 H + 12 S) secondary structure elements in 1gud_A, of which 22 satisfy the size requirements. 1.61995 [ 1.68283] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 9) (9 . 12) (14 . 15) (15 . 16) (16 . 17) (17 . 18) (18 . 19) (19 . 20) (20 . 21)) 4.266 {9/62:120} B:0 1.93244 [ 1.94832] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 9) (9 . 10) (10 . 11) (11 . 12) (13 . 14) (14 . 15) (15 . 16) (16 . 17) (17 . 18) (18 . 19) (19 . 20) (20 . 21) (21 . 22)) 4.697 {22/116:190} B:0 2.00146 [ 2.20110] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 9) (9 . 10) (16 . 15)) 4.069 {1/22:45} B:0 2.86095 [ 3.14572] ((1 . 3) (9 . 10) (11 . 12) (13 . 14) (14 . 15) (15 . 16) (19 . 20)) 4.427 {1/13:21} B:0 2.86786 [ 3.15092] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (6 . 6) (16 . 15) (18 . 17)) 4.372 {1/10:21} B:0 SIMILARITY (1/min{score1}): 0.6556 [and 1/min{score2}: 0.6074] [784, 2830]: Comparing 1dbq_A and 1jdp_A, based on their crossing files. There are 21 (10 H + 11 S) secondary structure elements in 1dbq_A, of which 20 satisfy the size requirements. There are 27 (12 H + 15 S) secondary structure elements in 1jdp_A, of which 26 satisfy the size requirements. 2.22230 [ 2.88892] ((9 . 10) (10 . 11) (11 . 12) (13 . 14) (14 . 15) (15 . 16) (16 . 17) (18 . 19) (21 . 25)) 3.836 {0/20:36} B:0 2.50003 [ 3.25001] ((9 . 10) (10 . 11) (11 . 12) (13 . 14) (14 . 15) (15 . 16) (16 . 17) (18 . 19)) 3.200 {0/13:28} B:0 3.33337 [ 4.33335] ((10 . 1) (11 . 2) (14 . 3) (15 . 4) (17 . 6) (18 . 7)) 4.228 {0/7:15} B:0 3.33339 [ 4.33336] ((1 . 11) (2 . 12) (3 . 13) (4 . 14) (5 . 15) (11 . 20)) 4.872 {0/3:15} B:0 5.23053 [ 5.59170] ((1 . 11) (2 . 12) (3 . 13) (4 . 14) (5 . 15) (13 . 20)) 6.554 {1/2:15} B:0 SIMILARITY (1/min{score1}): 0.7583 [and 1/min{score2}: 0.6276] [784, 3084]: Comparing 1dbq_A and 1jx6_A, based on their crossing files. There are 21 (10 H + 11 S) secondary structure elements in 1dbq_A, of which 20 satisfy the size requirements. There are 25 (13 H + 12 S) secondary structure elements in 1jx6_A, of which 24 satisfy the size requirements. 2.00002 [ 2.40001] ((9 . 12) (10 . 13) (11 . 14) (13 . 16) (14 . 17) (15 . 18) (18 . 21) (19 . 22) (20 . 23) (21 . 24)) 2.414 {0/20:45} B:0 2.01090 [ 2.40633] ((1 . 3) (2 . 4) (8 . 11) (9 . 12) (11 . 14) (13 . 16) (14 . 17) (15 . 18) (19 . 22) (20 . 23)) 3.172 {2/26:45} B:0 2.01494 [ 2.40870] ((2 . 4) (8 . 11) (9 . 12) (10 . 13) (11 . 14) (13 . 16) (14 . 17) (15 . 18) (19 . 22) (20 . 23)) 3.040 {2/24:45} B:0 2.22224 [ 2.66668] ((9 . 12) (10 . 13) (11 . 14) (13 . 16) (14 . 17) (15 . 18) (17 . 20) (18 . 21) (19 . 22)) 2.675 {0/14:36} B:0 2.25621 [ 2.68657] ((1 . 3) (2 . 4) (5 . 7) (8 . 11) (9 . 12) (11 . 14) (14 . 17) (15 . 18) (19 . 22)) 3.550 {2/18:36} B:0 SIMILARITY (1/min{score1}): 0.6737 [and 1/min{score2}: 0.5901] [784, 3091]: Comparing 1dbq_A and 1jye_A, based on their crossing files. There are 21 (10 H + 11 S) secondary structure elements in 1dbq_A, of which 20 satisfy the size requirements. There are 21 (9 H + 12 S) secondary structure elements in 1jye_A, of which 21 satisfy the size requirements. 1.07835 [ 1.11896] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (13 . 13) (14 . 14) (15 . 15) (16 . 16) (17 . 17) (18 . 18) (19 . 19) (20 . 20) (21 . 21)) 3.404 {8/104:190} B:0 1.87888 [ 1.96197] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (11 . 17) (19 . 19) (20 . 20)) 5.047 {3/27:55} B:0 1.88794 [ 1.96994] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (13 . 17) (19 . 19) (20 . 20)) 3.923 {3/26:55} B:0 2.11728 [ 2.15978] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (11 . 15) (13 . 17) (19 . 19) (20 . 20)) 6.044 {6/32:66} B:0 2.22400 [ 2.33487] ((2 . 2) (8 . 7) (9 . 9) (10 . 10) (11 . 11) (13 . 13) (14 . 14) (15 . 15) (17 . 17)) 3.127 {1/19:36} B:0 SIMILARITY (1/min{score1}): 0.9273 [and 1/min{score2}: 0.8937] [784, 5396]: Comparing 1dbq_A and 1qo0_A, based on their crossing files. There are 21 (10 H + 11 S) secondary structure elements in 1dbq_A, of which 20 satisfy the size requirements. There are 28 (13 H + 15 S) secondary structure elements in 1qo0_A, of which 27 satisfy the size requirements. 2.60617 [ 2.65476] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (13 . 13) (14 . 14) (15 . 15) (16 . 16) (18 . 19) (19 . 21) (20 . 24) (21 . 26)) 4.596 {23/89:153} B:0 2.72378 [ 2.75838] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (13 . 13) (14 . 14) (15 . 15) (16 . 16) (18 . 19) (19 . 21) (20 . 24) (21 . 26)) 5.089 {26/96:171} B:0 2.84126 [ 2.86623] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (13 . 13) (14 . 14) (15 . 15) (16 . 16) (17 . 17) (18 . 19) (19 . 21) (20 . 24) (21 . 26)) 5.042 {30/106:190} B:0 3.33796 [ 4.50188] ((1 . 1) (2 . 2) (3 . 3) (9 . 9) (11 . 11) (16 . 14)) 4.065 {1/11:15} B:0 4.00002 [ 5.40001] ((11 . 2) (13 . 4) (14 . 5) (15 . 6) (16 . 8)) 4.478 {0/4:10} B:0 SIMILARITY (1/min{score1}): 0.6681 [and 1/min{score2}: 0.5521] [784, 6095]: Comparing 1dbq_A and 1usg_A, based on their crossing files. There are 21 (10 H + 11 S) secondary structure elements in 1dbq_A, of which 20 satisfy the size requirements. There are 29 (15 H + 14 S) secondary structure elements in 1usg_A, of which 26 satisfy the size requirements. 2.22228 [ 2.88892] ((9 . 10) (10 . 11) (11 . 12) (13 . 14) (14 . 15) (15 . 16) (16 . 17) (18 . 21) (21 . 28)) 3.608 {0/20:36} B:0 2.50003 [ 3.25002] ((9 . 10) (10 . 11) (11 . 12) (13 . 14) (14 . 15) (15 . 16) (16 . 17) (18 . 21)) 3.442 {0/13:28} B:0 5.76770 [ 5.78627] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 9) (10 . 17) (11 . 20) (19 . 24) (20 . 27)) 6.765 {19/33:66} B:0 2.50003 [ 3.25002] ((1 . 15) (2 . 16) (3 . 17) (4 . 10) (5 . 11) (6 . 12) (7 . 13) (19 . 14)) 3.427 {0/6:28} B:1 3.26347 [ 3.40050] ((1 . 11) (2 . 12) (3 . 13) (4 . 14) (5 . 15) (6 . 16) (7 . 17) (8 . 21) (18 . 9) (19 . 10) (20 . 28)) 4.201 {7/22:55} B:1 SIMILARITY (1/min{score1}): 0.5836 [and 1/min{score2}: 0.4788] [784, 6645]: Comparing 1dbq_A and 8abp, based on their crossing files. There are 21 (10 H + 11 S) secondary structure elements in 1dbq_A, of which 20 satisfy the size requirements. There are 25 (13 H + 12 S) secondary structure elements in 8abp, of which 22 satisfy the size requirements. 1.41216 [ 1.45167] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 11) (11 . 12) (13 . 15) (14 . 16) (15 . 17) (16 . 19) (17 . 20) (18 . 21) (19 . 22) (20 . 23) (21 . 24)) 3.910 {13/99:190} B:0 1.54209 [ 1.69504] ((1 . 3) (9 . 9) (10 . 11) (11 . 12) (13 . 15) (14 . 16) (15 . 17) (16 . 19) (17 . 20) (18 . 21) (19 . 22) (20 . 23) (21 . 24)) 3.215 {2/42:78} B:0 2.22236 [ 2.44455] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (8 . 8) (9 . 9) (16 . 16)) 4.456 {0/15:36} B:0 3.33337 [ 3.66669] ((10 . 1) (11 . 2) (13 . 4) (14 . 5) (16 . 8) (19 . 9)) 4.327 {0/6:15} B:0 3.33368 [ 3.66693] ((10 . 1) (13 . 2) (14 . 3) (16 . 5) (17 . 6) (18 . 7)) 7.610 {0/3:15} B:0 SIMILARITY (1/min{score1}): 0.7081 [and 1/min{score2}: 0.6889] -------------------------------------------------------------------------------------------------------------------------