------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [5028, 76]: Comparing 1pja_A and 1a8q, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 18 (10 H + 8 S) secondary structure elements in 1a8q, of which 18 satisfy the size requirements. 1.50638 [ 1.50638] ((1 . 3) (2 . 4) (3 . 5) (5 . 6) (6 . 7) (7 . 8) (8 . 9) (14 . 14) (16 . 15) (17 . 16) (23 . 17) (24 . 18)) 3.025 {2/37:66} B:0 1.78388 [ 1.78388] ((1 . 3) (2 . 4) (3 . 5) (5 . 6) (6 . 7) (7 . 8) (8 . 9) (9 . 10) (16 . 15) (17 . 16) (23 . 17) (24 . 18)) 3.170 {6/40:66} B:0 1.83724 [ 1.83724] ((1 . 3) (2 . 4) (3 . 5) (5 . 6) (6 . 7) (7 . 8) (8 . 9) (9 . 10) (14 . 14) (16 . 15) (17 . 16) (23 . 17) (24 . 18)) 3.410 {8/48:78} B:0 2.00119 [ 2.00119] ((1 . 3) (2 . 4) (3 . 5) (5 . 6) (6 . 7) (7 . 8) (8 . 9) (9 . 10) (15 . 14) (16 . 15) (17 . 16) (23 . 17) (24 . 18)) 3.763 {9/48:78} B:0 2.17838 [ 2.17838] ((1 . 3) (2 . 4) (3 . 5) (5 . 6) (6 . 7) (7 . 8) (8 . 9) (9 . 11) (14 . 14) (16 . 15) (17 . 16) (23 . 17) (24 . 18)) 4.185 {10/48:78} B:0 SIMILARITY (1/min{score1}): 0.6666 [and 1/min{score2}: 0.6666] [5028, 98]: Comparing 1pja_A and 1ac5, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 40 (22 H + 18 S) secondary structure elements in 1ac5, of which 29 satisfy the size requirements. 2.25863 [ 2.61990] ((1 . 7) (2 . 8) (3 . 12) (5 . 14) (6 . 16) (7 . 17) (8 . 18) (10 . 23) (15 . 29) (16 . 30) (17 . 31) (23 . 36) (24 . 38)) 5.562 {10/46:78} B:0 2.91007 [ 3.16828] ((1 . 7) (2 . 8) (3 . 12) (5 . 14) (6 . 16) (7 . 17) (8 . 18) (10 . 19) (14 . 29) (16 . 30) (23 . 36) (24 . 38)) 5.509 {12/42:66} B:0 2.95315 [ 3.13947] ((1 . 7) (2 . 8) (3 . 12) (5 . 14) (6 . 16) (7 . 17) (8 . 18) (10 . 19) (14 . 29) (16 . 30) (17 . 31) (23 . 36) (24 . 38)) 5.466 {14/48:78} B:0 3.60003 [ 5.80001] ((1 . 18) (16 . 30) (17 . 31) (23 . 36) (24 . 38)) 4.309 {0/3:10} B:0 3.60012 [ 5.80003] ((5 . 14) (6 . 16) (7 . 17) (8 . 18) (10 . 21)) 6.230 {0/5:10} B:0 SIMILARITY (1/min{score1}): 0.4654 [and 1/min{score2}: 0.4055] [5028, 211]: Comparing 1pja_A and 1auo_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 19 (8 H + 11 S) secondary structure elements in 1auo_A, of which 17 satisfy the size requirements. 1.50493 [ 1.42251] ((1 . 2) (2 . 3) (3 . 4) (5 . 10) (6 . 12) (7 . 13) (8 . 14) (15 . 15) (16 . 16) (17 . 17) (23 . 18) (24 . 19)) 4.126 {2/40:66} B:0 1.50501 [ 1.42260] ((1 . 2) (2 . 3) (3 . 4) (5 . 10) (6 . 12) (7 . 13) (8 . 14) (15 . 15) (16 . 16) (21 . 17) (23 . 18) (24 . 19)) 4.339 {2/40:66} B:0 1.63648 [ 1.54559] ((1 . 2) (2 . 3) (3 . 4) (5 . 10) (6 . 12) (7 . 13) (8 . 14) (16 . 16) (17 . 17) (23 . 18) (24 . 19)) 3.367 {0/29:55} B:0 1.63649 [ 1.54561] ((1 . 2) (2 . 3) (3 . 4) (5 . 10) (6 . 12) (7 . 13) (8 . 14) (16 . 16) (21 . 17) (23 . 18) (24 . 19)) 3.500 {0/29:55} B:0 2.30799 [ 2.23842] ((5 . 10) (6 . 12) (7 . 13) (8 . 14) (14 . 15) (16 . 16) (17 . 17) (23 . 18) (24 . 19)) 5.654 {3/16:36} B:0 SIMILARITY (1/min{score1}): 0.6645 [and 1/min{score2}: 0.7030] [5028, 303]: Comparing 1pja_A and 1b6g, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 28 (18 H + 10 S) secondary structure elements in 1b6g, of which 21 satisfy the size requirements. 1.83744 [ 1.95247] ((1 . 5) (2 . 7) (3 . 8) (5 . 11) (6 . 12) (7 . 13) (8 . 16) (9 . 18) (14 . 23) (16 . 24) (17 . 25) (23 . 26) (24 . 28)) 4.635 {8/48:78} B:0 2.57145 [ 3.00002] ((1 . 8) (5 . 11) (6 . 12) (7 . 13) (8 . 16) (16 . 24) (24 . 28)) 3.277 {0/11:21} B:0 3.60016 [ 4.20010] ((2 . 6) (3 . 8) (7 . 11) (8 . 12) (23 . 26)) 6.653 {0/6:10} B:0 3.60024 [ 4.20015] ((2 . 6) (3 . 8) (8 . 12) (17 . 23) (23 . 26)) 7.329 {0/5:10} B:0 4.13195 [ 4.56611] ((7 . 7) (10 . 17) (13 . 25) (14 . 27) (15 . 28)) 8.174 {2/6:10} B:0 SIMILARITY (1/min{score1}): 0.6572 [and 1/min{score2}: 0.5670] [5028, 453]: Comparing 1pja_A and 1brt, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 20 (12 H + 8 S) secondary structure elements in 1brt, of which 19 satisfy the size requirements. 2.14132 [ 2.16356] ((1 . 3) (2 . 4) (3 . 5) (5 . 6) (6 . 7) (7 . 8) (8 . 9) (9 . 11) (15 . 15) (16 . 16) (17 . 17) (23 . 18) (24 . 20)) 3.494 {10/49:78} B:0 3.60042 [ 3.80035] ((5 . 4) (8 . 7) (21 . 15) (23 . 16) (24 . 17)) 8.452 {0/3:10} B:0 3.68298 [ 3.87102] ((1 . 1) (7 . 6) (8 . 7) (21 . 15) (23 . 16)) 6.664 {1/5:10} B:0 4.50001 [ 4.75001] ((5 . 15) (6 . 16) (7 . 17) (8 . 18)) 4.206 {0/2:6} B:0 4.50028 [ 4.75024] ((2 . 6) (3 . 7) (16 . 18) (17 . 20)) 9.056 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.5516 [and 1/min{score2}: 0.5315] [5028, 465]: Comparing 1pja_A and 1bu8_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 37 (16 H + 21 S) secondary structure elements in 1bu8_A, of which 20 satisfy the size requirements. 1.80282 [ 2.00206] ((1 . 8) (2 . 9) (3 . 10) (5 . 12) (6 . 14) (7 . 15) (8 . 16) (16 . 19) (23 . 21) (24 . 23)) 3.881 {1/20:45} B:0 1.82046 [ 2.01500] ((1 . 8) (2 . 9) (3 . 10) (5 . 12) (6 . 14) (7 . 15) (8 . 16) (16 . 19) (23 . 21) (24 . 27)) 3.846 {2/24:45} B:0 2.00003 [ 2.22225] ((1 . 8) (2 . 9) (3 . 10) (5 . 12) (6 . 14) (7 . 15) (8 . 16) (16 . 19) (23 . 21)) 2.902 {0/19:36} B:0 2.25005 [ 2.50003] ((1 . 8) (2 . 9) (3 . 10) (5 . 12) (6 . 14) (7 . 15) (8 . 16) (23 . 28)) 3.440 {0/15:28} B:0 2.57227 [ 2.85776] ((2 . 12) (3 . 14) (5 . 15) (6 . 16) (8 . 19) (16 . 21) (23 . 28)) 7.824 {0/8:21} B:0 SIMILARITY (1/min{score1}): 0.5547 [and 1/min{score2}: 0.4995] [5028, 530]: Comparing 1pja_A and 1c4x_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 21 (13 H + 8 S) secondary structure elements in 1c4x_A, of which 18 satisfy the size requirements. 1.65514 [ 1.65514] ((1 . 3) (2 . 4) (3 . 5) (5 . 6) (6 . 7) (7 . 8) (8 . 10) (9 . 11) (16 . 17) (17 . 18) (23 . 19) (24 . 21)) 2.700 {5/40:66} B:0 1.69223 [ 1.69223] ((1 . 3) (2 . 4) (3 . 5) (5 . 6) (6 . 7) (7 . 8) (8 . 10) (9 . 11) (15 . 16) (16 . 17) (17 . 18) (23 . 19) (24 . 21)) 3.337 {7/48:78} B:0 1.80203 [ 1.80203] ((1 . 3) (2 . 4) (3 . 5) (5 . 6) (6 . 7) (7 . 8) (8 . 10) (13 . 12) (23 . 19) (24 . 21)) 6.997 {1/31:45} B:0 1.82537 [ 1.82537] ((1 . 3) (2 . 6) (6 . 7) (7 . 8) (8 . 10) (15 . 16) (16 . 17) (17 . 18) (23 . 19) (24 . 21)) 6.806 {2/23:45} B:0 1.96288 [ 1.96288] ((1 . 3) (2 . 4) (3 . 5) (5 . 6) (6 . 7) (7 . 8) (8 . 10) (9 . 13) (14 . 14) (15 . 16) (16 . 17) (22 . 18) (23 . 19) (24 . 21)) 6.630 {11/59:91} B:0 SIMILARITY (1/min{score1}): 0.6042 [and 1/min{score2}: 0.6042] [5028, 575]: Comparing 1pja_A and 1cex, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 17 (12 H + 5 S) secondary structure elements in 1cex, of which 13 satisfy the size requirements. 1.80010 [ 1.30026] ((1 . 3) (2 . 4) (3 . 5) (5 . 7) (6 . 8) (7 . 9) (8 . 11) (16 . 13) (17 . 14) (24 . 17)) 3.491 {0/22:45} B:0 2.00004 [ 1.44456] ((1 . 3) (2 . 4) (3 . 5) (5 . 7) (6 . 8) (7 . 9) (8 . 11) (16 . 13) (24 . 17)) 3.066 {0/18:36} B:0 3.60003 [ 2.60009] ((1 . 3) (2 . 4) (3 . 5) (7 . 7) (8 . 8)) 4.525 {0/1:10} B:0 3.60008 [ 2.60020] ((1 . 5) (5 . 7) (6 . 8) (8 . 11) (10 . 14)) 5.534 {0/6:10} B:0 3.68298 [ 2.80297] ((6 . 3) (8 . 5) (15 . 10) (16 . 11) (24 . 17)) 6.602 {1/5:10} B:0 SIMILARITY (1/min{score1}): 0.6107 [and 1/min{score2}: 0.8442] [5028, 652]: Comparing 1pja_A and 1cpy, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 31 (17 H + 14 S) secondary structure elements in 1cpy, of which 25 satisfy the size requirements. 1.49461 [ 1.87750] ((1 . 4) (2 . 5) (3 . 9) (5 . 11) (6 . 12) (7 . 13) (8 . 14) (10 . 16) (14 . 22) (16 . 23) (17 . 24) (21 . 25) (23 . 29) (24 . 31)) 4.972 {6/49:91} B:0 3.00007 [ 4.16669] ((5 . 11) (6 . 12) (7 . 13) (8 . 14) (10 . 16) (23 . 23)) 4.734 {0/7:15} B:0 3.20459 [ 4.24874] ((1 . 12) (10 . 18) (16 . 23) (17 . 24) (23 . 29) (24 . 31)) 8.340 {2/9:15} B:0 3.60014 [ 5.00005] ((2 . 11) (6 . 12) (8 . 14) (10 . 16) (23 . 23)) 6.453 {0/7:10} B:0 3.60046 [ 5.00017] ((1 . 12) (2 . 13) (16 . 23) (17 . 24) (24 . 31)) 8.662 {0/4:10} B:0 SIMILARITY (1/min{score1}): 0.6691 [and 1/min{score2}: 0.5326] [5028, 691]: Comparing 1pja_A and 1cvl, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 25 (14 H + 11 S) secondary structure elements in 1cvl, of which 20 satisfy the size requirements. 1.53463 [ 1.69221] ((1 . 1) (2 . 4) (3 . 5) (5 . 6) (6 . 7) (7 . 8) (8 . 10) (10 . 11) (14 . 15) (16 . 17) (23 . 23) (24 . 25)) 3.252 {3/36:66} B:0 1.72175 [ 1.83916] ((1 . 1) (2 . 4) (3 . 5) (5 . 6) (6 . 7) (7 . 8) (8 . 10) (9 . 11) (14 . 15) (16 . 17) (23 . 23) (24 . 25)) 4.062 {5/36:66} B:0 1.77583 [ 1.92401] ((1 . 1) (2 . 4) (3 . 5) (5 . 6) (6 . 7) (7 . 8) (8 . 10) (9 . 11) (16 . 17) (23 . 23) (24 . 25)) 3.776 {4/31:55} B:0 3.60035 [ 4.00025] ((1 . 5) (2 . 6) (6 . 10) (23 . 23) (24 . 25)) 8.085 {0/5:10} B:0 4.50002 [ 5.00002] ((2 . 4) (5 . 8) (6 . 10) (23 . 23)) 4.728 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.6529 [and 1/min{score2}: 0.5917] [5028, 849]: Comparing 1pja_A and 1din, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 17 (8 H + 9 S) secondary structure elements in 1din, of which 15 satisfy the size requirements. 1.50082 [ 1.25142] ((1 . 4) (2 . 5) (3 . 6) (5 . 9) (6 . 10) (7 . 11) (8 . 12) (14 . 13) (16 . 14) (17 . 15) (23 . 16) (24 . 17)) 3.927 {1/34:66} B:0 1.50088 [ 1.25152] ((1 . 4) (2 . 5) (3 . 6) (5 . 9) (6 . 10) (7 . 11) (8 . 12) (14 . 13) (16 . 14) (21 . 15) (23 . 16) (24 . 17)) 4.127 {1/34:66} B:0 1.63750 [ 1.36560] ((1 . 4) (2 . 5) (3 . 6) (5 . 9) (6 . 10) (7 . 11) (8 . 12) (14 . 13) (16 . 14) (17 . 15) (24 . 17)) 3.942 {1/28:55} B:0 1.63753 [ 1.36565] ((1 . 4) (2 . 5) (3 . 6) (5 . 9) (6 . 10) (7 . 11) (8 . 12) (14 . 13) (16 . 14) (21 . 15) (24 . 17)) 4.080 {1/28:55} B:0 2.25020 [ 1.87535] ((1 . 4) (2 . 5) (3 . 6) (5 . 9) (6 . 10) (7 . 11) (8 . 12) (13 . 15)) 4.968 {0/16:28} B:0 SIMILARITY (1/min{score1}): 0.7196 [and 1/min{score2}: 0.8602] [5028, 925]: Comparing 1pja_A and 1dqz_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 19 (11 H + 8 S) secondary structure elements in 1dqz_A, of which 19 satisfy the size requirements. 1.50961 [ 1.59152] ((1 . 3) (2 . 4) (3 . 6) (5 . 7) (6 . 9) (7 . 10) (8 . 11) (14 . 15) (16 . 16) (17 . 17) (23 . 18) (24 . 19)) 5.210 {2/34:66} B:0 1.51492 [ 1.59605] ((1 . 3) (2 . 5) (3 . 6) (5 . 7) (6 . 9) (7 . 10) (8 . 11) (15 . 15) (16 . 16) (17 . 17) (23 . 18) (24 . 19)) 4.607 {2/30:66} B:0 1.51517 [ 1.59627] ((1 . 3) (2 . 5) (3 . 6) (5 . 7) (6 . 9) (7 . 10) (8 . 11) (14 . 15) (16 . 16) (17 . 17) (23 . 18) (24 . 19)) 5.113 {2/30:66} B:0 1.65974 [ 1.74723] ((1 . 3) (3 . 6) (5 . 7) (6 . 9) (7 . 10) (8 . 11) (14 . 15) (16 . 16) (17 . 17) (23 . 18) (24 . 19)) 4.914 {2/25:55} B:0 2.25015 [ 2.37513] ((1 . 3) (3 . 6) (5 . 7) (8 . 9) (16 . 16) (17 . 17) (23 . 18) (24 . 19)) 4.618 {0/13:28} B:0 SIMILARITY (1/min{score1}): 0.6957 [and 1/min{score2}: 0.6712] [5028, 960]: Comparing 1pja_A and 1dx4_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 42 (28 H + 14 S) secondary structure elements in 1dx4_A, of which 33 satisfy the size requirements. 1.50044 [ 2.75007] ((1 . 9) (2 . 11) (3 . 12) (5 . 16) (6 . 19) (7 . 20) (8 . 21) (14 . 27) (16 . 29) (17 . 34) (23 . 35) (24 . 39)) 4.440 {0/40:66} B:0 2.25382 [ 4.12562] ((1 . 9) (2 . 11) (3 . 12) (5 . 16) (6 . 19) (7 . 20) (8 . 21) (17 . 27)) 6.169 {1/16:28} B:0 3.00001 [ 5.50000] ((1 . 12) (5 . 16) (6 . 19) (7 . 20) (8 . 21) (16 . 29)) 2.671 {0/8:15} B:0 3.00015 [ 5.50002] ((2 . 11) (5 . 16) (6 . 19) (7 . 20) (8 . 21) (10 . 23)) 5.702 {0/13:15} B:0 3.03787 [ 5.50625] ((1 . 9) (2 . 11) (3 . 12) (8 . 19) (21 . 27) (23 . 29)) 3.812 {1/7:15} B:0 SIMILARITY (1/min{score1}): 0.7686 [and 1/min{score2}: 0.4362] [5028, 1082]: Comparing 1pja_A and 1ea5_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 39 (24 H + 15 S) secondary structure elements in 1ea5_A, of which 34 satisfy the size requirements. 1.50039 [ 2.83339] ((1 . 9) (2 . 11) (3 . 12) (5 . 14) (6 . 16) (7 . 17) (8 . 19) (14 . 23) (16 . 24) (21 . 29) (23 . 30) (24 . 35)) 4.318 {0/38:66} B:0 1.48496 [ 2.63182] ((1 . 9) (2 . 11) (3 . 12) (5 . 14) (6 . 16) (7 . 17) (8 . 19) (14 . 23) (15 . 18) (16 . 24) (21 . 29) (23 . 30) (24 . 35)) 5.018 {5/48:78} B:1 1.62120 [ 2.49838] ((1 . 9) (2 . 11) (3 . 12) (5 . 14) (6 . 16) (7 . 17) (8 . 19) (9 . 25) (10 . 26) (15 . 23) (16 . 24) (21 . 29) (23 . 30) (24 . 35)) 5.105 {8/56:91} B:1 1.95551 [ 2.75653] ((1 . 9) (2 . 11) (3 . 12) (5 . 14) (6 . 16) (7 . 17) (8 . 19) (15 . 18) (16 . 24) (17 . 28) (22 . 29) (23 . 30) (24 . 35)) 5.972 {8/44:78} B:1 2.57186 [ 4.85721] ((1 . 9) (2 . 11) (3 . 12) (5 . 14) (7 . 17) (8 . 16) (13 . 21)) 6.618 {0/15:21} B:1 SIMILARITY (1/min{score1}): 0.7475 [and 1/min{score2}: 0.4586] [5028, 1165]: Comparing 1pja_A and 1ehy_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 23 (15 H + 8 S) secondary structure elements in 1ehy_A, of which 19 satisfy the size requirements. 1.58376 [ 1.65563] ((1 . 4) (2 . 5) (3 . 7) (5 . 9) (6 . 10) (7 . 11) (8 . 12) (9 . 13) (16 . 19) (17 . 20) (23 . 21) (24 . 23)) 3.002 {4/38:66} B:0 1.65522 [ 1.71884] ((1 . 4) (2 . 6) (3 . 7) (5 . 9) (6 . 10) (7 . 11) (8 . 12) (9 . 13) (16 . 19) (17 . 20) (23 . 21) (24 . 23)) 3.535 {4/32:66} B:0 1.74769 [ 1.82366] ((1 . 4) (2 . 5) (3 . 7) (5 . 9) (6 . 10) (7 . 11) (8 . 12) (9 . 13) (16 . 19) (23 . 21) (24 . 23)) 2.675 {4/33:55} B:0 1.80010 [ 1.90008] ((1 . 4) (3 . 7) (5 . 9) (6 . 10) (7 . 11) (8 . 12) (16 . 19) (21 . 20) (23 . 21) (24 . 23)) 3.510 {0/20:45} B:0 1.82232 [ 1.87084] ((1 . 4) (2 . 6) (3 . 7) (5 . 9) (6 . 10) (7 . 11) (8 . 12) (9 . 15) (16 . 19) (17 . 20) (23 . 21) (24 . 23)) 4.252 {5/32:66} B:0 SIMILARITY (1/min{score1}): 0.6314 [and 1/min{score2}: 0.6040] [5028, 1173]: Comparing 1pja_A and 1ei9_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 25 (17 H + 8 S) secondary structure elements in 1ei9_A, of which 21 satisfy the size requirements. 1.06071 [ 1.23649] ((1 . 1) (2 . 2) (3 . 3) (5 . 5) (6 . 7) (7 . 8) (8 . 9) (10 . 10) (13 . 13) (14 . 14) (15 . 15) (16 . 16) (17 . 17) (21 . 21) (22 . 22) (23 . 23) (24 . 25)) 2.472 {3/99:136} B:0 1.06072 [ 1.23649] ((1 . 1) (2 . 2) (3 . 3) (5 . 5) (6 . 7) (7 . 8) (8 . 9) (10 . 10) (13 . 13) (14 . 14) (15 . 15) (16 . 16) (17 . 17) (21 . 21) (22 . 22) (23 . 23) (24 . 24)) 2.498 {3/99:136} B:0 1.12567 [ 1.31292] ((1 . 1) (2 . 2) (3 . 3) (5 . 5) (6 . 7) (7 . 8) (8 . 9) (10 . 10) (13 . 13) (15 . 15) (16 . 16) (17 . 17) (21 . 21) (22 . 22) (23 . 23) (24 . 24)) 2.519 {2/84:120} B:0 1.20533 [ 1.40337] ((1 . 1) (2 . 2) (3 . 3) (6 . 7) (7 . 8) (8 . 9) (13 . 11) (14 . 14) (15 . 15) (16 . 16) (17 . 17) (21 . 21) (22 . 22) (23 . 23) (24 . 24)) 3.847 {3/70:105} B:0 1.29016 [ 1.50281] ((1 . 1) (2 . 2) (3 . 3) (5 . 5) (6 . 7) (7 . 8) (8 . 9) (10 . 13) (14 . 14) (15 . 15) (16 . 16) (22 . 22) (23 . 23) (24 . 25)) 3.497 {3/69:91} B:0 SIMILARITY (1/min{score1}): 0.9428 [and 1/min{score2}: 0.8087] [5028, 1513]: Comparing 1pja_A and 1fj2_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 19 (10 H + 9 S) secondary structure elements in 1fj2_A, of which 17 satisfy the size requirements. 1.50046 [ 1.41721] ((1 . 3) (2 . 4) (3 . 5) (5 . 9) (6 . 11) (7 . 12) (8 . 13) (14 . 14) (16 . 15) (17 . 16) (23 . 18) (24 . 19)) 3.348 {1/39:66} B:0 1.50057 [ 1.41734] ((1 . 3) (2 . 4) (3 . 5) (5 . 9) (6 . 11) (7 . 12) (8 . 13) (14 . 14) (16 . 15) (21 . 16) (23 . 18) (24 . 19)) 3.713 {1/38:66} B:0 1.63646 [ 1.54557] ((1 . 3) (2 . 4) (3 . 5) (5 . 9) (6 . 11) (7 . 12) (8 . 13) (16 . 15) (17 . 16) (23 . 18) (24 . 19)) 3.246 {0/28:55} B:0 3.49434 [ 3.46324] ((1 . 2) (2 . 4) (3 . 5) (7 . 12) (16 . 15) (17 . 16) (23 . 18) (24 . 19)) 4.924 {5/15:28} B:0 3.60002 [ 3.40002] ((1 . 3) (2 . 4) (3 . 5) (8 . 11) (16 . 18)) 3.888 {0/5:10} B:0 SIMILARITY (1/min{score1}): 0.6665 [and 1/min{score2}: 0.7056] [5028, 1740]: Comparing 1pja_A and 1g66_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 15 (9 H + 6 S) secondary structure elements in 1g66_A, of which 12 satisfy the size requirements. 1.82059 [ 1.26517] ((1 . 1) (2 . 2) (3 . 3) (5 . 5) (6 . 6) (7 . 7) (8 . 10) (15 . 12) (16 . 13) (24 . 15)) 4.501 {2/24:45} B:0 2.00003 [ 1.33343] ((1 . 1) (2 . 2) (3 . 3) (5 . 5) (6 . 6) (7 . 7) (8 . 10) (16 . 13) (24 . 15)) 2.818 {0/15:36} B:0 2.25067 [ 1.50226] ((1 . 1) (2 . 2) (3 . 3) (5 . 5) (6 . 6) (7 . 7) (8 . 10) (14 . 14)) 6.688 {0/12:28} B:0 2.57166 [ 1.71508] ((1 . 1) (2 . 2) (3 . 3) (5 . 5) (6 . 6) (7 . 7) (17 . 15)) 5.688 {0/10:21} B:0 3.00006 [ 2.00019] ((6 . 1) (8 . 3) (16 . 10) (22 . 12) (23 . 13) (24 . 15)) 4.465 {0/6:15} B:0 SIMILARITY (1/min{score1}): 0.5856 [and 1/min{score2}: 0.8331] [5028, 1846]: Comparing 1pja_A and 1gkl_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 18 (10 H + 8 S) secondary structure elements in 1gkl_A, of which 16 satisfy the size requirements. 1.54874 [ 1.40088] ((1 . 4) (2 . 5) (3 . 6) (5 . 7) (6 . 11) (7 . 12) (8 . 13) (15 . 14) (16 . 15) (17 . 16) (23 . 17) (24 . 18)) 4.742 {3/33:66} B:0 1.62587 [ 1.50172] ((1 . 4) (2 . 5) (3 . 6) (5 . 8) (6 . 11) (7 . 12) (8 . 13) (15 . 14) (16 . 15) (17 . 16) (23 . 17) (24 . 18)) 5.012 {4/34:66} B:0 1.62609 [ 1.50201] ((1 . 4) (2 . 5) (3 . 6) (5 . 8) (6 . 11) (7 . 12) (8 . 13) (15 . 14) (16 . 15) (21 . 16) (23 . 17) (24 . 18)) 5.456 {4/34:66} B:0 1.63664 [ 1.45493] ((1 . 4) (2 . 5) (3 . 6) (5 . 8) (6 . 11) (7 . 12) (8 . 13) (16 . 15) (17 . 16) (23 . 17) (24 . 18)) 4.208 {0/26:55} B:0 1.63664 [ 1.45494] ((1 . 4) (2 . 5) (3 . 6) (5 . 7) (6 . 11) (7 . 12) (8 . 13) (16 . 15) (17 . 16) (23 . 17) (24 . 18)) 4.215 {0/26:55} B:0 SIMILARITY (1/min{score1}): 0.7208 [and 1/min{score2}: 0.8099] [5028, 2535]: Comparing 1pja_A and 1imj_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 20 (10 H + 10 S) secondary structure elements in 1imj_A, of which 19 satisfy the size requirements. 1.50803 [ 1.59017] ((1 . 5) (2 . 7) (3 . 8) (5 . 10) (6 . 11) (7 . 12) (8 . 13) (15 . 15) (16 . 16) (17 . 17) (23 . 18) (24 . 20)) 3.648 {2/35:66} B:0 1.53127 [ 1.61008] ((1 . 5) (2 . 6) (3 . 8) (5 . 10) (6 . 11) (7 . 12) (8 . 13) (15 . 15) (16 . 16) (17 . 17) (23 . 18) (24 . 20)) 3.865 {3/37:66} B:0 3.60002 [ 3.80002] ((1 . 11) (3 . 13) (6 . 16) (7 . 17) (8 . 18)) 3.855 {0/3:10} B:0 3.60004 [ 3.80003] ((3 . 11) (5 . 15) (6 . 16) (7 . 17) (8 . 18)) 4.586 {0/4:10} B:0 3.60004 [ 3.80004] ((3 . 13) (5 . 15) (6 . 16) (7 . 17) (8 . 18)) 4.842 {0/3:10} B:0 SIMILARITY (1/min{score1}): 0.6631 [and 1/min{score2}: 0.6289] [5028, 2595]: Comparing 1pja_A and 1isp_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 15 (9 H + 6 S) secondary structure elements in 1isp_A, of which 11 satisfy the size requirements. 1.80000 [ 1.10002] ((1 . 1) (2 . 2) (3 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 9) (16 . 11) (23 . 13) (24 . 15)) 1.552 {0/25:45} B:0 1.82418 [ 1.19505] ((1 . 1) (2 . 2) (3 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 9) (16 . 11) (23 . 13) (24 . 14)) 3.962 {2/23:45} B:0 3.60166 [ 2.20725] ((3 . 1) (5 . 2) (6 . 4) (16 . 13) (17 . 15)) 11.940 {0/4:10} B:0 4.50002 [ 2.75007] ((8 . 1) (16 . 9) (23 . 13) (24 . 15)) 4.455 {0/0:6} B:0 4.50002 [ 2.75009] ((1 . 6) (3 . 9) (6 . 11) (8 . 13)) 4.742 {0/1:6} B:0 SIMILARITY (1/min{score1}): 0.5556 [and 1/min{score2}: 0.9091] [5028, 2616]: Comparing 1pja_A and 1iup_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 23 (15 H + 8 S) secondary structure elements in 1iup_A, of which 20 satisfy the size requirements. 1.83730 [ 1.91047] ((1 . 3) (2 . 4) (3 . 6) (5 . 7) (6 . 8) (7 . 9) (8 . 11) (9 . 12) (14 . 18) (16 . 19) (17 . 20) (23 . 21) (24 . 23)) 3.938 {8/48:78} B:0 1.92273 [ 1.98717] ((1 . 3) (2 . 5) (3 . 6) (5 . 7) (6 . 8) (7 . 9) (8 . 11) (9 . 12) (15 . 18) (16 . 19) (17 . 20) (23 . 21) (24 . 23)) 3.662 {8/45:78} B:0 2.00184 [ 2.22356] ((1 . 3) (3 . 6) (5 . 7) (6 . 8) (7 . 9) (8 . 11) (10 . 13) (16 . 19) (17 . 20)) 5.706 {1/22:36} B:0 2.10618 [ 2.15594] ((1 . 3) (2 . 5) (3 . 6) (5 . 7) (6 . 8) (7 . 9) (8 . 11) (9 . 12) (14 . 18) (16 . 19) (17 . 20) (23 . 21) (24 . 23)) 3.589 {9/45:78} B:0 2.30167 [ 2.34019] ((1 . 3) (2 . 5) (3 . 6) (5 . 7) (6 . 8) (7 . 9) (8 . 11) (9 . 13) (15 . 18) (16 . 19) (17 . 20) (23 . 21) (24 . 23)) 3.916 {10/45:78} B:0 SIMILARITY (1/min{score1}): 0.6665 [and 1/min{score2}: 0.5999] [5028, 2632]: Comparing 1pja_A and 1ivy_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 36 (17 H + 19 S) secondary structure elements in 1ivy_A, of which 30 satisfy the size requirements. 1.50658 [ 2.50143] ((1 . 4) (2 . 5) (3 . 9) (5 . 11) (6 . 13) (7 . 14) (8 . 15) (14 . 28) (16 . 29) (17 . 30) (23 . 34) (24 . 36)) 4.030 {2/37:66} B:0 3.60017 [ 6.00004] ((1 . 13) (2 . 14) (3 . 15) (10 . 23) (14 . 26)) 6.723 {0/4:10} B:0 3.60043 [ 6.00009] ((1 . 9) (2 . 11) (6 . 13) (7 . 14) (8 . 15)) 8.496 {0/5:10} B:0 3.62229 [ 6.00485] ((1 . 13) (2 . 14) (3 . 15) (13 . 23) (15 . 25)) 6.828 {1/7:10} B:0 3.62266 [ 6.00494] ((1 . 13) (2 . 14) (3 . 15) (15 . 25) (24 . 30)) 9.090 {1/7:10} B:0 SIMILARITY (1/min{score1}): 0.6638 [and 1/min{score2}: 0.3998] [5028, 2697]: Comparing 1pja_A and 1j1i_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 20 (12 H + 8 S) secondary structure elements in 1j1i_A, of which 18 satisfy the size requirements. 1.50647 [ 1.50647] ((1 . 3) (2 . 5) (3 . 6) (5 . 7) (6 . 8) (7 . 9) (8 . 11) (15 . 15) (16 . 16) (17 . 17) (23 . 18) (24 . 20)) 3.601 {2/37:66} B:0 1.52547 [ 1.52547] ((1 . 3) (2 . 4) (3 . 6) (5 . 7) (6 . 8) (7 . 9) (8 . 11) (14 . 15) (16 . 16) (17 . 17) (23 . 18) (24 . 20)) 3.611 {3/39:66} B:0 1.53117 [ 1.53117] ((1 . 3) (2 . 5) (3 . 6) (5 . 7) (6 . 8) (7 . 9) (8 . 11) (14 . 15) (16 . 16) (17 . 17) (23 . 18) (24 . 20)) 3.328 {3/37:66} B:0 2.00122 [ 2.00122] ((1 . 3) (2 . 5) (3 . 6) (5 . 7) (6 . 8) (7 . 9) (8 . 11) (9 . 12) (15 . 15) (16 . 16) (17 . 17) (23 . 18) (24 . 20)) 3.993 {9/48:78} B:0 2.28319 [ 2.28319] ((3 . 6) (5 . 7) (6 . 8) (7 . 9) (8 . 11) (10 . 12) (16 . 16) (17 . 17)) 6.150 {2/18:28} B:0 SIMILARITY (1/min{score1}): 0.6665 [and 1/min{score2}: 0.6665] [5028, 2855]: Comparing 1pja_A and 1jfr_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 20 (10 H + 10 S) secondary structure elements in 1jfr_A, of which 17 satisfy the size requirements. 1.63646 [ 1.54557] ((1 . 4) (2 . 6) (3 . 7) (5 . 8) (6 . 11) (7 . 12) (8 . 13) (16 . 14) (17 . 15) (23 . 16) (24 . 18)) 3.272 {0/27:55} B:0 1.63655 [ 1.54567] ((1 . 4) (2 . 6) (3 . 7) (5 . 8) (6 . 11) (7 . 12) (8 . 13) (16 . 14) (21 . 15) (23 . 16) (24 . 18)) 3.818 {0/27:55} B:0 2.30268 [ 2.18700] ((1 . 4) (2 . 6) (3 . 7) (5 . 8) (6 . 11) (7 . 12) (8 . 13) (14 . 17)) 7.351 {2/16:28} B:0 3.00005 [ 2.83339] ((1 . 4) (2 . 6) (5 . 8) (6 . 11) (7 . 12) (8 . 14)) 4.307 {0/8:15} B:0 3.60005 [ 3.40006] ((1 . 11) (3 . 13) (6 . 14) (7 . 15) (8 . 16)) 5.025 {0/1:10} B:0 SIMILARITY (1/min{score1}): 0.6111 [and 1/min{score2}: 0.6470] [5028, 2934]: Comparing 1pja_A and 1jjf_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 17 (9 H + 8 S) secondary structure elements in 1jjf_A, of which 15 satisfy the size requirements. 1.53522 [ 1.30876] ((1 . 3) (2 . 4) (3 . 5) (5 . 6) (6 . 9) (7 . 10) (8 . 11) (15 . 13) (16 . 14) (17 . 15) (23 . 16) (24 . 17)) 5.081 {3/36:66} B:0 1.53526 [ 1.30883] ((1 . 3) (2 . 4) (3 . 5) (5 . 7) (6 . 9) (7 . 10) (8 . 11) (15 . 13) (16 . 14) (17 . 15) (23 . 16) (24 . 17)) 5.159 {3/36:66} B:0 1.53555 [ 1.30929] ((1 . 3) (2 . 4) (3 . 5) (5 . 7) (6 . 9) (7 . 10) (8 . 11) (15 . 13) (16 . 14) (21 . 15) (23 . 16) (24 . 17)) 5.596 {3/36:66} B:0 3.00032 [ 2.50055] ((8 . 3) (13 . 7) (16 . 9) (17 . 10) (23 . 11) (24 . 17)) 6.896 {0/5:15} B:0 3.02250 [ 2.53842] ((1 . 3) (2 . 4) (3 . 5) (5 . 6) (8 . 9) (14 . 15)) 5.658 {1/8:15} B:0 SIMILARITY (1/min{score1}): 0.6663 [and 1/min{score2}: 0.7991] [5028, 2946]: Comparing 1pja_A and 1jkm_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 26 (16 H + 10 S) secondary structure elements in 1jkm_A, of which 20 satisfy the size requirements. 1.66947 [ 1.79673] ((1 . 6) (2 . 7) (3 . 8) (5 . 11) (6 . 12) (7 . 13) (8 . 15) (9 . 18) (16 . 21) (17 . 22) (23 . 23) (24 . 26)) 3.999 {5/39:66} B:0 1.80138 [ 2.00101] ((1 . 6) (2 . 7) (3 . 8) (5 . 11) (6 . 12) (7 . 13) (13 . 18) (16 . 21) (17 . 22) (24 . 26)) 5.868 {1/29:45} B:0 1.81226 [ 1.88826] ((1 . 6) (2 . 7) (3 . 8) (5 . 11) (6 . 12) (7 . 13) (8 . 15) (9 . 18) (14 . 20) (16 . 21) (17 . 22) (23 . 23) (24 . 26)) 4.405 {8/49:78} B:0 3.00043 [ 3.33365] ((5 . 7) (8 . 12) (16 . 21) (17 . 22) (23 . 23) (24 . 26)) 7.433 {0/5:15} B:0 3.60003 [ 4.00002] ((1 . 15) (5 . 20) (6 . 21) (7 . 22) (8 . 23)) 4.465 {0/2:10} B:0 SIMILARITY (1/min{score1}): 0.7000 [and 1/min{score2}: 0.6365] [5028, 2975]: Comparing 1pja_A and 1jmk_C, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 18 (9 H + 9 S) secondary structure elements in 1jmk_C, of which 13 satisfy the size requirements. 1.80005 [ 1.30013] ((1 . 2) (2 . 3) (3 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (16 . 13) (23 . 16) (24 . 18)) 2.922 {0/24:45} B:0 2.57198 [ 1.85860] ((2 . 3) (3 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (17 . 18)) 7.036 {0/12:21} B:0 3.00002 [ 2.16671] ((3 . 2) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (16 . 13)) 3.304 {0/7:15} B:0 3.00035 [ 2.16758] ((1 . 2) (2 . 3) (3 . 4) (6 . 6) (8 . 8) (17 . 18)) 7.032 {0/8:15} B:0 3.00058 [ 2.16820] ((1 . 2) (2 . 3) (6 . 4) (10 . 7) (23 . 16) (24 . 18)) 7.993 {0/9:15} B:0 SIMILARITY (1/min{score1}): 0.5555 [and 1/min{score2}: 0.7692] [5028, 3062]: Comparing 1pja_A and 1ju3_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 46 (19 H + 27 S) secondary structure elements in 1ju3_A, of which 25 satisfy the size requirements. 1.53570 [ 2.09701] ((1 . 4) (2 . 6) (3 . 7) (5 . 8) (6 . 9) (7 . 11) (8 . 12) (14 . 21) (16 . 22) (17 . 23) (23 . 24) (24 . 28)) 5.795 {3/36:66} B:0 1.57737 [ 2.11385] ((1 . 4) (3 . 7) (5 . 8) (6 . 9) (7 . 11) (8 . 12) (10 . 14) (14 . 21) (16 . 22) (17 . 23) (23 . 24) (24 . 28)) 6.133 {4/39:66} B:0 1.65192 [ 2.27860] ((1 . 4) (2 . 6) (3 . 7) (5 . 8) (6 . 9) (7 . 11) (8 . 12) (16 . 22) (17 . 23) (23 . 24) (24 . 28)) 5.720 {2/28:55} B:0 1.86474 [ 2.16801] ((1 . 4) (2 . 6) (3 . 7) (5 . 8) (6 . 9) (7 . 11) (8 . 12) (9 . 15) (14 . 21) (16 . 22) (17 . 23) (23 . 24) (24 . 28)) 6.149 {8/47:78} B:0 1.87000 [ 2.10580] ((1 . 4) (2 . 6) (3 . 7) (5 . 8) (6 . 9) (7 . 11) (8 . 12) (9 . 15) (13 . 20) (14 . 21) (16 . 22) (17 . 23) (23 . 24) (24 . 28)) 6.184 {10/57:91} B:0 SIMILARITY (1/min{score1}): 0.6512 [and 1/min{score2}: 0.4898] [5028, 3218]: Comparing 1pja_A and 1k8q_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 32 (21 H + 11 S) secondary structure elements in 1k8q_A, of which 25 satisfy the size requirements. 1.50679 [ 2.08588] ((1 . 5) (2 . 7) (3 . 8) (5 . 10) (6 . 12) (7 . 13) (8 . 15) (9 . 16) (16 . 27) (17 . 28) (23 . 29) (24 . 32)) 4.620 {2/37:66} B:0 1.58399 [ 2.11661] ((1 . 5) (2 . 7) (3 . 8) (5 . 10) (6 . 12) (7 . 13) (8 . 15) (10 . 16) (16 . 27) (17 . 28) (23 . 29) (24 . 32)) 4.240 {4/38:66} B:0 1.69066 [ 1.98756] ((1 . 5) (2 . 7) (3 . 8) (5 . 11) (6 . 12) (7 . 13) (8 . 15) (13 . 16) (14 . 24) (15 . 25) (16 . 27) (17 . 28) (23 . 29) (24 . 32)) 6.222 {9/59:91} B:0 1.73472 [ 2.08936] ((1 . 5) (2 . 7) (3 . 8) (5 . 11) (6 . 12) (7 . 13) (8 . 15) (10 . 16) (15 . 25) (16 . 27) (17 . 28) (23 . 29) (24 . 32)) 5.835 {7/46:78} B:0 1.80809 [ 2.22397] ((1 . 5) (2 . 7) (3 . 8) (5 . 10) (6 . 12) (7 . 13) (8 . 15) (10 . 16) (15 . 25) (16 . 27) (17 . 28) (23 . 29)) 6.238 {6/39:66} B:0 SIMILARITY (1/min{score1}): 0.7158 [and 1/min{score2}: 0.5187] [5028, 3433]: Comparing 1pja_A and 1ku0_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 34 (23 H + 11 S) secondary structure elements in 1ku0_A, of which 25 satisfy the size requirements. 1.57025 [ 2.11090] ((1 . 1) (2 . 3) (3 . 4) (5 . 5) (6 . 10) (7 . 11) (8 . 14) (10 . 16) (14 . 22) (16 . 23) (23 . 32) (24 . 34)) 5.787 {4/40:66} B:0 1.63722 [ 2.27305] ((1 . 1) (2 . 3) (3 . 4) (5 . 5) (6 . 10) (7 . 11) (8 . 14) (14 . 22) (16 . 23) (23 . 32) (24 . 34)) 2.768 {1/29:55} B:0 1.64254 [ 2.27504] ((1 . 1) (2 . 3) (3 . 4) (5 . 5) (6 . 10) (7 . 11) (8 . 14) (14 . 21) (16 . 23) (23 . 32) (24 . 34)) 3.512 {2/35:55} B:0 1.64763 [ 2.27696] ((1 . 1) (2 . 3) (3 . 4) (5 . 5) (6 . 10) (7 . 11) (8 . 14) (14 . 22) (16 . 23) (23 . 31) (24 . 34)) 3.352 {2/30:55} B:0 1.80004 [ 2.50001] ((1 . 1) (2 . 3) (3 . 4) (5 . 5) (6 . 10) (7 . 11) (8 . 14) (16 . 23) (23 . 32) (24 . 34)) 2.729 {0/25:45} B:0 SIMILARITY (1/min{score1}): 0.6368 [and 1/min{score2}: 0.4737] [5028, 3558]: Comparing 1pja_A and 1l7a_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 22 (12 H + 10 S) secondary structure elements in 1l7a_A, of which 20 satisfy the size requirements. 1.38935 [ 1.54192] ((1 . 7) (2 . 8) (3 . 9) (5 . 10) (6 . 12) (7 . 13) (8 . 14) (9 . 16) (14 . 18) (16 . 19) (17 . 20) (23 . 21) (24 . 22)) 3.960 {2/43:78} B:0 1.48112 [ 1.58080] ((1 . 7) (2 . 8) (3 . 9) (5 . 10) (6 . 12) (7 . 13) (8 . 14) (9 . 16) (10 . 17) (14 . 18) (16 . 19) (17 . 20) (23 . 21) (24 . 22)) 4.482 {6/50:91} B:0 1.80010 [ 2.00007] ((1 . 7) (2 . 8) (3 . 9) (6 . 12) (7 . 13) (8 . 14) (16 . 19) (17 . 20) (23 . 21) (24 . 22)) 3.478 {0/22:45} B:0 3.00002 [ 3.33335] ((1 . 9) (5 . 10) (6 . 12) (7 . 13) (8 . 14) (9 . 16)) 3.638 {0/9:15} B:0 3.00004 [ 3.33336] ((1 . 7) (2 . 8) (3 . 9) (8 . 12) (16 . 19) (17 . 20)) 4.165 {0/8:15} B:0 SIMILARITY (1/min{score1}): 0.7198 [and 1/min{score2}: 0.6485] [5028, 3657]: Comparing 1pja_A and 1llf_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 41 (25 H + 16 S) secondary structure elements in 1llf_A, of which 33 satisfy the size requirements. 1.38562 [ 2.53862] ((1 . 9) (2 . 11) (3 . 12) (5 . 15) (6 . 17) (7 . 18) (8 . 21) (14 . 25) (16 . 26) (17 . 31) (21 . 32) (23 . 33) (24 . 35)) 5.139 {0/44:78} B:0 2.52242 [ 3.10218] ((1 . 9) (2 . 11) (3 . 12) (5 . 15) (6 . 17) (7 . 18) (8 . 21) (14 . 22) (16 . 26) (17 . 31) (23 . 33) (24 . 35)) 6.742 {10/41:66} B:0 2.57187 [ 4.71436] ((1 . 9) (2 . 11) (3 . 12) (5 . 15) (6 . 17) (7 . 18) (13 . 23)) 6.662 {0/14:21} B:0 3.03788 [ 5.50625] ((1 . 9) (2 . 11) (3 . 12) (8 . 17) (21 . 25) (23 . 26)) 4.012 {1/7:15} B:0 3.13837 [ 5.52390] ((5 . 15) (6 . 17) (7 . 18) (8 . 21) (9 . 22) (16 . 26)) 5.066 {2/10:15} B:0 SIMILARITY (1/min{score1}): 0.8306 [and 1/min{score2}: 0.4544] [5028, 3679]: Comparing 1pja_A and 1lns_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 58 (24 H + 34 S) secondary structure elements in 1lns_A, of which 21 satisfy the size requirements. 1.53133 [ 1.77001] ((1 . 14) (2 . 18) (3 . 19) (5 . 20) (6 . 23) (7 . 24) (8 . 25) (14 . 31) (16 . 32) (17 . 33) (23 . 34) (24 . 35)) 4.078 {3/37:66} B:0 1.59262 [ 1.81072] ((1 . 14) (2 . 18) (3 . 19) (5 . 20) (6 . 23) (7 . 24) (8 . 25) (15 . 31) (16 . 32) (17 . 33) (23 . 34) (24 . 35)) 4.273 {4/37:66} B:0 1.59263 [ 1.81073] ((1 . 14) (2 . 18) (3 . 19) (5 . 20) (6 . 23) (7 . 24) (8 . 25) (15 . 31) (16 . 32) (21 . 33) (23 . 34) (24 . 35)) 4.310 {4/37:66} B:0 1.83738 [ 1.95242] ((1 . 14) (2 . 18) (3 . 19) (5 . 20) (6 . 23) (7 . 24) (8 . 25) (14 . 26) (15 . 31) (16 . 32) (21 . 33) (23 . 34) (24 . 35)) 4.392 {7/42:78} B:0 2.00005 [ 2.33336] ((1 . 14) (3 . 19) (5 . 20) (6 . 23) (7 . 24) (8 . 25) (16 . 32) (17 . 33) (23 . 34)) 3.182 {0/19:36} B:0 SIMILARITY (1/min{score1}): 0.6530 [and 1/min{score2}: 0.5650] [5028, 3769]: Comparing 1pja_A and 1lzl_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 20 (11 H + 9 S) secondary structure elements in 1lzl_A, of which 18 satisfy the size requirements. 1.50065 [ 1.50065] ((1 . 5) (2 . 6) (3 . 7) (5 . 8) (6 . 10) (7 . 11) (8 . 12) (10 . 14) (16 . 16) (17 . 17) (23 . 18) (24 . 20)) 4.143 {1/39:66} B:0 1.68511 [ 1.68511] ((1 . 5) (2 . 6) (3 . 7) (5 . 8) (6 . 10) (7 . 11) (8 . 12) (9 . 14) (16 . 16) (17 . 17) (23 . 18) (24 . 20)) 3.840 {5/38:66} B:0 2.25003 [ 2.25003] ((1 . 5) (2 . 6) (3 . 7) (5 . 8) (6 . 10) (7 . 11) (8 . 12) (16 . 18)) 3.137 {0/16:28} B:0 3.00054 [ 3.00054] ((3 . 5) (5 . 6) (8 . 10) (16 . 16) (23 . 18) (24 . 20)) 7.873 {0/7:15} B:0 3.00075 [ 3.00075] ((3 . 5) (5 . 6) (8 . 10) (16 . 16) (17 . 17) (24 . 20)) 8.544 {0/7:15} B:0 SIMILARITY (1/min{score1}): 0.7021 [and 1/min{score2}: 0.7021] [5028, 3814]: Comparing 1pja_A and 1m33_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 20 (13 H + 7 S) secondary structure elements in 1m33_A, of which 17 satisfy the size requirements. 2.28345 [ 2.16448] ((1 . 2) (3 . 5) (5 . 6) (6 . 7) (7 . 8) (8 . 10) (15 . 14) (16 . 16)) 6.878 {2/18:28} B:0 2.45851 [ 2.44091] ((1 . 2) (2 . 4) (3 . 5) (5 . 6) (6 . 7) (7 . 8) (8 . 10) (9 . 12) (14 . 15) (16 . 16) (23 . 18) (24 . 20)) 4.252 {9/38:66} B:0 2.57145 [ 2.42860] ((3 . 2) (5 . 6) (6 . 7) (7 . 8) (8 . 10) (23 . 18) (24 . 20)) 3.246 {0/11:21} B:0 2.69848 [ 2.68522] ((1 . 2) (2 . 4) (3 . 5) (5 . 6) (6 . 7) (7 . 8) (8 . 10) (9 . 12) (15 . 15) (16 . 16) (23 . 18) (24 . 20)) 3.821 {10/38:66} B:0 3.00060 [ 2.83404] ((5 . 3) (6 . 5) (8 . 7) (21 . 15) (23 . 16) (24 . 20)) 8.066 {0/6:15} B:0 SIMILARITY (1/min{score1}): 0.4379 [and 1/min{score2}: 0.4620] [5028, 3943]: Comparing 1pja_A and 1mj5_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 22 (14 H + 8 S) secondary structure elements in 1mj5_A, of which 20 satisfy the size requirements. 1.50105 [ 1.62676] ((1 . 3) (2 . 4) (3 . 6) (5 . 7) (6 . 8) (7 . 9) (8 . 10) (9 . 12) (14 . 17) (16 . 18) (17 . 19) (23 . 20) (24 . 22)) 4.313 {5/46:78} B:0 1.60165 [ 1.70784] ((1 . 3) (2 . 4) (3 . 6) (5 . 7) (6 . 8) (7 . 9) (8 . 10) (9 . 16) (14 . 17) (16 . 18) (17 . 19) (23 . 20) (24 . 22)) 5.152 {6/46:78} B:0 1.90103 [ 1.96756] ((1 . 3) (2 . 5) (3 . 6) (5 . 7) (6 . 8) (7 . 9) (8 . 10) (9 . 12) (14 . 17) (16 . 18) (17 . 19) (23 . 20) (24 . 22)) 4.457 {7/40:78} B:0 2.03066 [ 2.24475] ((1 . 3) (3 . 6) (5 . 7) (6 . 8) (7 . 9) (8 . 10) (15 . 17) (23 . 20) (24 . 22)) 3.984 {2/20:36} B:0 3.02244 [ 3.34976] ((5 . 7) (6 . 8) (7 . 9) (8 . 10) (15 . 17) (17 . 19)) 5.051 {1/8:15} B:0 SIMILARITY (1/min{score1}): 0.6662 [and 1/min{score2}: 0.6228] [5028, 3984]: Comparing 1pja_A and 1mna_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 21 (12 H + 9 S) secondary structure elements in 1mna_A, of which 17 satisfy the size requirements. 1.80112 [ 1.70133] ((1 . 6) (2 . 7) (3 . 8) (5 . 10) (6 . 11) (7 . 12) (8 . 13) (16 . 17) (23 . 19) (24 . 21)) 2.408 {1/25:45} B:0 2.25337 [ 2.12900] ((1 . 6) (2 . 7) (3 . 8) (5 . 10) (6 . 11) (7 . 12) (8 . 13) (16 . 19)) 3.023 {1/16:28} B:0 3.60021 [ 3.40024] ((5 . 7) (8 . 11) (16 . 17) (23 . 19) (24 . 21)) 7.085 {0/4:10} B:0 4.50017 [ 4.25020] ((1 . 8) (2 . 10) (5 . 12) (17 . 21)) 7.988 {0/3:6} B:0 4.50018 [ 4.25022] ((2 . 10) (3 . 11) (5 . 12) (6 . 13)) 8.122 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.6088 [and 1/min{score2}: 0.6440] [5028, 4033]: Comparing 1pja_A and 1mtz_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 21 (13 H + 8 S) secondary structure elements in 1mtz_A, of which 19 satisfy the size requirements. 1.50795 [ 1.59011] ((1 . 3) (2 . 4) (3 . 5) (5 . 7) (6 . 8) (7 . 9) (8 . 10) (14 . 16) (16 . 17) (17 . 18) (23 . 19) (24 . 21)) 3.206 {2/35:66} B:0 2.57874 [ 2.72051] ((2 . 4) (5 . 7) (6 . 8) (7 . 9) (8 . 10) (10 . 13) (16 . 17)) 5.799 {1/12:21} B:0 3.60021 [ 3.80018] ((2 . 4) (6 . 10) (10 . 13) (16 . 17) (17 . 18)) 7.084 {0/6:10} B:0 3.60027 [ 3.80023] ((2 . 13) (5 . 16) (6 . 17) (7 . 18) (8 . 19)) 7.600 {0/5:10} B:0 3.62271 [ 3.81935] ((2 . 7) (3 . 8) (9 . 14) (16 . 19) (17 . 21)) 9.305 {1/7:10} B:0 SIMILARITY (1/min{score1}): 0.6632 [and 1/min{score2}: 0.6289] [5028, 4065]: Comparing 1pja_A and 1mx1_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 41 (22 H + 19 S) secondary structure elements in 1mx1_A, of which 33 satisfy the size requirements. 1.24358 [ 2.20743] ((1 . 11) (2 . 12) (3 . 13) (5 . 15) (6 . 17) (7 . 18) (8 . 20) (9 . 30) (10 . 31) (15 . 19) (16 . 29) (17 . 33) (21 . 34) (23 . 35) (24 . 38)) 6.410 {5/68:105} B:1 1.52026 [ 2.40544] ((1 . 11) (2 . 12) (3 . 13) (5 . 15) (6 . 17) (7 . 18) (8 . 20) (9 . 30) (10 . 31) (15 . 28) (16 . 29) (21 . 34) (23 . 35) (24 . 38)) 4.902 {8/63:91} B:1 1.67891 [ 2.45090] ((1 . 11) (2 . 12) (3 . 13) (5 . 15) (6 . 17) (7 . 18) (8 . 20) (9 . 30) (15 . 19) (16 . 29) (17 . 33) (22 . 34) (23 . 35) (24 . 38)) 6.139 {8/53:91} B:1 2.57145 [ 4.71429] ((1 . 13) (2 . 12) (5 . 15) (6 . 17) (7 . 18) (8 . 20) (16 . 29)) 3.245 {0/13:21} B:1 5.03173 [ 5.32786] ((1 . 10) (2 . 12) (6 . 13) (7 . 15) (8 . 11) (16 . 17) (22 . 19) (23 . 20) (24 . 38)) 5.713 {7/14:36} B:1 SIMILARITY (1/min{score1}): 0.8465 [and 1/min{score2}: 0.4826] [5028, 4422]: Comparing 1pja_A and 1nx9_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 53 (25 H + 28 S) secondary structure elements in 1nx9_A, of which 25 satisfy the size requirements. 1.50101 [ 2.08371] ((1 . 4) (2 . 5) (3 . 8) (5 . 9) (6 . 10) (7 . 11) (8 . 12) (14 . 20) (16 . 21) (21 . 22) (23 . 23) (24 . 27)) 4.623 {1/35:66} B:0 1.62573 [ 2.13458] ((1 . 4) (2 . 7) (3 . 8) (5 . 9) (6 . 10) (7 . 11) (8 . 12) (14 . 20) (16 . 21) (21 . 22) (23 . 23) (24 . 28)) 4.659 {4/34:66} B:0 1.62574 [ 2.13458] ((1 . 4) (2 . 7) (3 . 8) (5 . 9) (6 . 10) (7 . 11) (8 . 12) (14 . 20) (16 . 21) (17 . 22) (23 . 23) (24 . 28)) 4.704 {4/34:66} B:0 1.65537 [ 2.14791] ((1 . 4) (2 . 7) (3 . 8) (5 . 9) (6 . 10) (7 . 11) (8 . 12) (14 . 20) (16 . 21) (21 . 22) (23 . 23) (24 . 27)) 4.262 {4/32:66} B:0 1.89280 [ 2.18605] ((1 . 4) (2 . 7) (3 . 8) (5 . 9) (6 . 10) (7 . 11) (8 . 12) (10 . 15) (14 . 20) (16 . 21) (21 . 22) (23 . 23) (24 . 28)) 5.311 {8/46:78} B:0 SIMILARITY (1/min{score1}): 0.6712 [and 1/min{score2}: 0.5087] [5028, 4769]: Comparing 1pja_A and 1orv_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 62 (17 H + 45 S) secondary structure elements in 1orv_A, of which 17 satisfy the size requirements. 1.40493 [ 1.33167] ((1 . 46) (2 . 47) (3 . 48) (5 . 50) (6 . 52) (7 . 53) (8 . 54) (10 . 56) (15 . 58) (16 . 59) (21 . 60) (23 . 61) (24 . 62)) 4.117 {3/44:78} B:0 1.40519 [ 1.33198] ((1 . 46) (2 . 47) (3 . 48) (5 . 50) (6 . 52) (7 . 53) (8 . 54) (10 . 56) (15 . 58) (16 . 59) (17 . 60) (23 . 61) (24 . 62)) 4.675 {3/44:78} B:0 1.40715 [ 1.33428] ((1 . 46) (2 . 47) (3 . 48) (5 . 50) (6 . 52) (7 . 53) (8 . 54) (10 . 56) (14 . 58) (16 . 59) (21 . 60) (23 . 61) (24 . 62)) 4.822 {3/43:78} B:0 1.44568 [ 1.37906] ((1 . 46) (2 . 47) (3 . 48) (5 . 50) (6 . 52) (7 . 53) (8 . 54) (10 . 56) (14 . 58) (16 . 59) (17 . 60) (23 . 61) (24 . 62)) 5.003 {4/44:78} B:0 1.80887 [ 1.77627] ((1 . 46) (2 . 47) (3 . 48) (5 . 50) (6 . 52) (7 . 53) (8 . 54) (9 . 56) (14 . 58) (16 . 59) (17 . 60) (23 . 61) (24 . 62)) 4.731 {7/43:78} B:0 SIMILARITY (1/min{score1}): 0.7261 [and 1/min{score2}: 0.7574] [5028, 5028]: Comparing 1pja_A and 1pja_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (2 . 2) (3 . 3) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (13 . 13) (14 . 14) (15 . 15) (16 . 16) (17 . 17) (21 . 21) (22 . 22) (23 . 23) (24 . 24)) 0.000 {0/116:153} B:0 1.50003 [ 1.50003] ((1 . 1) (2 . 2) (3 . 3) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (13 . 10) (16 . 16) (17 . 17) (23 . 23) (24 . 24)) 2.356 {0/42:66} B:0 1.63639 [ 1.63639] ((1 . 1) (2 . 2) (3 . 3) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (10 . 13) (16 . 16) (23 . 23) (24 . 24)) 2.319 {0/37:55} B:0 2.46405 [ 2.46405] ((1 . 1) (2 . 2) (3 . 3) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 10) (10 . 13) (14 . 15) (16 . 16) (17 . 17) (21 . 22) (23 . 23) (24 . 24)) 3.976 {17/70:105} B:0 2.46405 [ 2.46405] ((1 . 1) (2 . 2) (3 . 3) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (10 . 9) (13 . 10) (15 . 14) (16 . 16) (17 . 17) (22 . 21) (23 . 23) (24 . 24)) 3.976 {17/70:105} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [5028, 5168]: Comparing 1pja_A and 1q0r_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 21 (13 H + 8 S) secondary structure elements in 1q0r_A, of which 18 satisfy the size requirements. 2.03422 [ 2.03422] ((1 . 3) (2 . 5) (3 . 6) (5 . 7) (6 . 8) (7 . 9) (8 . 11) (10 . 12) (14 . 17) (16 . 18) (17 . 19) (23 . 20) (24 . 21)) 3.539 {9/47:78} B:0 2.05743 [ 2.05743] ((3 . 3) (6 . 8) (7 . 9) (8 . 11) (15 . 17) (16 . 18) (17 . 19) (23 . 20) (24 . 21)) 3.641 {2/17:36} B:0 2.40907 [ 2.40907] ((1 . 3) (2 . 5) (3 . 6) (5 . 7) (6 . 8) (7 . 9) (8 . 11) (10 . 12) (15 . 17) (16 . 18) (17 . 19) (23 . 20) (24 . 21)) 3.627 {11/47:78} B:0 3.60036 [ 3.60036] ((2 . 7) (3 . 8) (6 . 11) (16 . 18) (17 . 19)) 8.171 {0/4:10} B:0 3.60048 [ 3.60048] ((5 . 5) (8 . 8) (21 . 17) (23 . 18) (24 . 19)) 8.743 {0/3:10} B:0 SIMILARITY (1/min{score1}): 0.6056 [and 1/min{score2}: 0.6056] [5028, 5301]: Comparing 1pja_A and 1qe3_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 34 (19 H + 15 S) secondary structure elements in 1qe3_A, of which 31 satisfy the size requirements. 1.38577 [ 2.38484] ((1 . 8) (2 . 10) (3 . 11) (5 . 13) (6 . 15) (7 . 16) (8 . 18) (14 . 22) (16 . 23) (17 . 27) (21 . 28) (23 . 29) (24 . 31)) 5.325 {0/45:78} B:0 1.38718 [ 2.38512] ((1 . 8) (2 . 10) (3 . 11) (5 . 13) (6 . 15) (7 . 16) (8 . 18) (14 . 22) (16 . 23) (17 . 25) (21 . 28) (23 . 29) (24 . 31)) 6.504 {0/44:78} B:0 1.40730 [ 2.38915] ((1 . 8) (2 . 10) (3 . 11) (5 . 13) (6 . 15) (7 . 16) (8 . 18) (14 . 22) (16 . 23) (17 . 24) (21 . 28) (23 . 29) (24 . 31)) 5.049 {3/43:78} B:0 2.25073 [ 3.87514] ((2 . 10) (3 . 11) (5 . 13) (6 . 15) (7 . 16) (8 . 18) (16 . 23) (24 . 28)) 6.834 {0/17:28} B:0 2.57243 [ 4.42877] ((2 . 10) (5 . 13) (6 . 15) (8 . 18) (14 . 22) (16 . 23) (24 . 28)) 8.184 {0/12:21} B:0 SIMILARITY (1/min{score1}): 0.7216 [and 1/min{score2}: 0.4193] [5028, 5315]: Comparing 1pja_A and 1qfm_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 59 (20 H + 39 S) secondary structure elements in 1qfm_A, of which 17 satisfy the size requirements. 1.50660 [ 1.42449] ((1 . 42) (2 . 43) (3 . 44) (5 . 46) (6 . 48) (7 . 49) (8 . 51) (10 . 53) (16 . 56) (21 . 57) (23 . 58) (24 . 59)) 4.094 {2/37:66} B:0 1.50664 [ 1.42454] ((1 . 42) (2 . 43) (3 . 44) (5 . 46) (6 . 48) (7 . 49) (8 . 51) (10 . 53) (16 . 56) (17 . 57) (23 . 58) (24 . 59)) 4.237 {2/37:66} B:0 1.51050 [ 1.45278] ((1 . 42) (2 . 43) (3 . 44) (5 . 46) (6 . 48) (7 . 49) (8 . 51) (10 . 53) (14 . 54) (16 . 56) (21 . 57) (23 . 58) (24 . 59)) 4.462 {5/45:78} B:0 1.60138 [ 1.55354] ((1 . 42) (2 . 43) (3 . 44) (5 . 46) (6 . 48) (7 . 49) (8 . 51) (10 . 53) (14 . 54) (16 . 56) (17 . 57) (23 . 58) (24 . 59)) 4.483 {6/46:78} B:0 1.63782 [ 1.54718] ((1 . 42) (2 . 43) (3 . 44) (5 . 46) (6 . 48) (7 . 49) (8 . 51) (16 . 56) (17 . 57) (23 . 58) (24 . 59)) 3.942 {1/26:55} B:0 SIMILARITY (1/min{score1}): 0.6637 [and 1/min{score2}: 0.7020] [5028, 5352]: Comparing 1pja_A and 1qj4_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 22 (14 H + 8 S) secondary structure elements in 1qj4_A, of which 18 satisfy the size requirements. 1.85483 [ 1.85483] ((1 . 1) (2 . 3) (3 . 4) (5 . 7) (6 . 8) (7 . 9) (8 . 10) (10 . 11) (16 . 18) (17 . 19) (23 . 20) (24 . 22)) 4.475 {5/31:66} B:0 1.92275 [ 1.92275] ((1 . 1) (2 . 3) (3 . 4) (5 . 7) (6 . 8) (7 . 9) (8 . 10) (9 . 14) (14 . 16) (16 . 18) (17 . 19) (23 . 20) (24 . 22)) 3.872 {8/45:78} B:0 2.00014 [ 2.00014] ((1 . 1) (2 . 3) (3 . 4) (5 . 7) (6 . 8) (8 . 10) (16 . 18) (21 . 19) (24 . 22)) 4.132 {0/17:36} B:0 2.91402 [ 2.91402] ((1 . 1) (2 . 3) (3 . 4) (8 . 8) (14 . 14) (23 . 20) (24 . 22)) 6.255 {3/13:21} B:0 3.60028 [ 3.60028] ((2 . 7) (3 . 8) (5 . 9) (6 . 10) (16 . 20)) 7.645 {0/3:10} B:0 SIMILARITY (1/min{score1}): 0.5555 [and 1/min{score2}: 0.5555] [5028, 5380]: Comparing 1pja_A and 1qlw_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 27 (16 H + 11 S) secondary structure elements in 1qlw_A, of which 22 satisfy the size requirements. 1.50549 [ 1.83635] ((1 . 6) (2 . 8) (3 . 9) (5 . 15) (6 . 16) (7 . 18) (8 . 19) (15 . 21) (16 . 22) (17 . 23) (23 . 24) (24 . 27)) 4.334 {2/39:66} B:0 1.50573 [ 1.83648] ((1 . 6) (2 . 8) (3 . 9) (5 . 15) (6 . 16) (7 . 18) (8 . 19) (15 . 21) (16 . 22) (21 . 23) (23 . 24) (24 . 27)) 4.881 {2/39:66} B:0 2.57766 [ 3.14628] ((1 . 6) (2 . 8) (3 . 9) (16 . 22) (17 . 23) (22 . 25) (24 . 27)) 8.387 {1/13:21} B:0 3.60004 [ 4.40002] ((6 . 6) (8 . 9) (16 . 16) (22 . 21) (23 . 22)) 4.819 {0/5:10} B:0 3.60005 [ 4.40003] ((1 . 16) (3 . 19) (6 . 22) (7 . 23) (8 . 24)) 4.883 {0/2:10} B:0 SIMILARITY (1/min{score1}): 0.6642 [and 1/min{score2}: 0.5446] [5028, 5400]: Comparing 1pja_A and 1qo7_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 25 (17 H + 8 S) secondary structure elements in 1qo7_A, of which 22 satisfy the size requirements. 3.00008 [ 3.66671] ((1 . 7) (2 . 8) (3 . 9) (8 . 11) (13 . 16) (23 . 21)) 4.897 {0/10:15} B:0 3.00009 [ 3.66672] ((1 . 11) (6 . 13) (10 . 15) (16 . 21) (17 . 22) (23 . 23)) 5.026 {0/9:15} B:0 3.00663 [ 3.67031] ((2 . 10) (6 . 13) (10 . 16) (16 . 21) (23 . 23) (24 . 25)) 6.962 {1/11:15} B:0 3.60045 [ 4.40024] ((1 . 9) (2 . 10) (6 . 13) (16 . 21) (24 . 25)) 8.597 {0/6:10} B:0 3.60045 [ 4.40025] ((2 . 10) (3 . 11) (6 . 13) (16 . 21) (17 . 22)) 8.604 {0/5:10} B:0 SIMILARITY (1/min{score1}): 0.6128 [and 1/min{score2}: 0.5362] [5028, 5450]: Comparing 1pja_A and 1qtr_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 22 (14 H + 8 S) secondary structure elements in 1qtr_A, of which 21 satisfy the size requirements. 2.00004 [ 2.33336] ((1 . 3) (2 . 4) (3 . 5) (5 . 6) (6 . 7) (7 . 8) (8 . 9) (23 . 19) (24 . 22)) 2.949 {0/19:36} B:0 2.65905 [ 2.69978] ((1 . 3) (2 . 4) (3 . 5) (5 . 6) (6 . 7) (7 . 8) (8 . 9) (9 . 15) (15 . 18) (16 . 19) (17 . 20) (23 . 21) (24 . 22)) 4.271 {12/46:78} B:0 3.09664 [ 3.56218] ((2 . 4) (6 . 9) (9 . 12) (10 . 14) (23 . 21) (24 . 22)) 6.288 {2/11:15} B:0 3.60002 [ 4.20001] ((1 . 5) (6 . 9) (16 . 19) (23 . 21) (24 . 22)) 3.975 {0/3:10} B:0 3.60021 [ 4.20013] ((2 . 4) (3 . 5) (8 . 7) (17 . 17) (23 . 19)) 7.144 {0/6:10} B:0 SIMILARITY (1/min{score1}): 0.5934 [and 1/min{score2}: 0.5331] [5028, 5498]: Comparing 1pja_A and 1qz3_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 22 (13 H + 9 S) secondary structure elements in 1qz3_A, of which 19 satisfy the size requirements. 1.50085 [ 1.58406] ((1 . 5) (2 . 6) (3 . 7) (5 . 8) (6 . 11) (7 . 12) (8 . 13) (10 . 15) (16 . 18) (17 . 19) (23 . 20) (24 . 22)) 4.664 {1/39:66} B:0 1.68515 [ 1.74567] ((1 . 5) (2 . 6) (3 . 7) (5 . 8) (6 . 11) (7 . 12) (8 . 13) (9 . 15) (16 . 18) (17 . 19) (23 . 20) (24 . 22)) 4.073 {5/38:66} B:0 2.25006 [ 2.37505] ((1 . 5) (2 . 6) (3 . 7) (5 . 8) (6 . 11) (7 . 12) (8 . 13) (16 . 20)) 3.695 {0/16:28} B:0 3.00067 [ 3.16724] ((3 . 5) (5 . 6) (8 . 11) (16 . 18) (23 . 20) (24 . 22)) 8.298 {0/8:15} B:0 3.00093 [ 3.16746] ((3 . 5) (5 . 6) (8 . 11) (16 . 18) (17 . 19) (24 . 22)) 9.004 {0/8:15} B:0 SIMILARITY (1/min{score1}): 0.6663 [and 1/min{score2}: 0.6326] [5028, 5522]: Comparing 1pja_A and 1r1d_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 17 (10 H + 7 S) secondary structure elements in 1r1d_A, of which 16 satisfy the size requirements. 1.50052 [ 1.33408] ((1 . 2) (2 . 3) (3 . 4) (5 . 6) (6 . 7) (7 . 8) (8 . 9) (14 . 12) (16 . 13) (17 . 14) (23 . 15) (24 . 17)) 3.491 {1/38:66} B:0 1.56039 [ 1.46029] ((1 . 2) (2 . 3) (3 . 4) (5 . 6) (6 . 7) (7 . 8) (8 . 9) (9 . 10) (14 . 12) (16 . 13) (17 . 14) (23 . 15) (24 . 17)) 4.182 {6/49:78} B:0 1.63650 [ 1.45474] ((1 . 2) (3 . 4) (5 . 6) (6 . 7) (7 . 8) (8 . 9) (14 . 12) (16 . 13) (17 . 14) (23 . 15) (24 . 17)) 3.524 {0/30:55} B:0 2.15194 [ 2.04533] ((1 . 2) (5 . 6) (6 . 7) (7 . 8) (8 . 9) (9 . 12) (16 . 13) (17 . 14) (23 . 15) (24 . 17)) 5.924 {4/22:45} B:0 2.25002 [ 2.00003] ((1 . 2) (2 . 3) (3 . 4) (5 . 6) (6 . 7) (7 . 8) (8 . 9) (16 . 15)) 2.738 {0/14:28} B:0 SIMILARITY (1/min{score1}): 0.6664 [and 1/min{score2}: 0.7496] [5028, 5894]: Comparing 1pja_A and 1tca, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 26 (17 H + 9 S) secondary structure elements in 1tca, of which 22 satisfy the size requirements. 2.25193 [ 2.75106] ((1 . 3) (2 . 5) (3 . 6) (5 . 7) (6 . 8) (7 . 9) (8 . 11) (15 . 17)) 8.713 {0/18:28} B:0 3.00068 [ 3.66704] ((3 . 6) (5 . 7) (6 . 8) (7 . 9) (8 . 11) (21 . 19)) 8.342 {0/9:15} B:0 3.60009 [ 4.40005] ((5 . 1) (6 . 3) (8 . 6) (14 . 10) (24 . 18)) 5.833 {0/5:10} B:0 3.60029 [ 4.40016] ((5 . 5) (6 . 6) (8 . 8) (16 . 15) (24 . 19)) 7.705 {0/3:10} B:0 3.60029 [ 4.40016] ((8 . 3) (16 . 11) (17 . 12) (21 . 14) (23 . 15)) 7.744 {0/0:10} B:0 SIMILARITY (1/min{score1}): 0.6939 [and 1/min{score2}: 0.5899] [5028, 5912]: Comparing 1pja_A and 1tht_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 23 (12 H + 11 S) secondary structure elements in 1tht_A, of which 21 satisfy the size requirements. 1.50102 [ 1.75064] ((1 . 3) (2 . 5) (3 . 6) (5 . 7) (6 . 8) (7 . 9) (8 . 10) (14 . 17) (16 . 18) (21 . 19) (23 . 20) (24 . 21)) 3.716 {1/31:66} B:0 1.51135 [ 1.75718] ((1 . 3) (2 . 5) (3 . 6) (5 . 7) (6 . 8) (7 . 9) (8 . 10) (14 . 17) (16 . 18) (17 . 19) (23 . 20) (24 . 21)) 3.520 {2/32:66} B:0 1.51466 [ 1.75930] ((1 . 3) (2 . 4) (3 . 6) (5 . 7) (6 . 8) (7 . 9) (8 . 10) (14 . 17) (16 . 18) (17 . 19) (23 . 20) (24 . 21)) 3.853 {2/30:66} B:0 2.25001 [ 2.62501] ((1 . 3) (2 . 5) (3 . 6) (5 . 7) (6 . 8) (7 . 9) (8 . 10) (16 . 20)) 2.434 {0/14:28} B:0 2.25767 [ 2.62984] ((1 . 3) (3 . 6) (5 . 7) (6 . 8) (7 . 9) (8 . 10) (14 . 17) (16 . 20)) 2.839 {1/13:28} B:0 SIMILARITY (1/min{score1}): 0.6664 [and 1/min{score2}: 0.5713] [5028, 5913]: Comparing 1pja_A and 1tib, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 23 (13 H + 10 S) secondary structure elements in 1tib, of which 17 satisfy the size requirements. 4.50002 [ 4.25002] ((3 . 13) (5 . 14) (6 . 17) (8 . 20)) 4.591 {0/1:6} B:0 4.50010 [ 4.25011] ((16 . 13) (17 . 14) (22 . 16) (23 . 17)) 6.910 {0/3:6} B:0 4.50013 [ 4.25015] ((2 . 12) (3 . 13) (6 . 15) (8 . 17)) 7.458 {0/2:6} B:0 4.50015 [ 4.25018] ((5 . 4) (9 . 8) (10 . 11) (23 . 20)) 7.737 {0/5:6} B:0 4.50021 [ 4.25025] ((2 . 11) (5 . 14) (6 . 15) (8 . 17)) 8.408 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.4049 [and 1/min{score2}: 0.4110] [5028, 6006]: Comparing 1pja_A and 1ufo_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 17 (9 H + 8 S) secondary structure elements in 1ufo_A, of which 16 satisfy the size requirements. 1.47171 [ 1.34887] ((1 . 3) (2 . 4) (3 . 6) (5 . 7) (6 . 8) (7 . 9) (8 . 10) (14 . 11) (15 . 13) (16 . 14) (21 . 15) (23 . 16) (24 . 17)) 5.669 {5/50:78} B:0 1.50170 [ 1.38734] ((1 . 3) (2 . 5) (3 . 6) (5 . 7) (6 . 8) (7 . 9) (8 . 10) (14 . 11) (15 . 13) (16 . 14) (21 . 15) (23 . 16) (24 . 17)) 5.507 {5/46:78} B:0 1.50590 [ 1.34171] ((1 . 3) (2 . 4) (3 . 6) (5 . 7) (6 . 8) (7 . 9) (8 . 10) (15 . 13) (16 . 14) (17 . 15) (23 . 16) (24 . 17)) 5.180 {2/39:66} B:0 1.50865 [ 1.34559] ((1 . 3) (2 . 5) (3 . 6) (5 . 7) (6 . 8) (7 . 9) (8 . 10) (15 . 13) (16 . 14) (21 . 15) (23 . 16) (24 . 17)) 5.203 {2/35:66} B:0 1.50871 [ 1.34567] ((1 . 3) (2 . 5) (3 . 6) (5 . 7) (6 . 8) (7 . 9) (8 . 10) (15 . 13) (16 . 14) (17 . 15) (23 . 16) (24 . 17)) 5.298 {2/35:66} B:0 SIMILARITY (1/min{score1}): 0.6795 [and 1/min{score2}: 0.7453] [5028, 6129]: Comparing 1pja_A and 1uwc_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 24 (11 H + 13 S) secondary structure elements in 1uwc_A, of which 18 satisfy the size requirements. 3.60087 [ 3.60087] ((3 . 7) (5 . 9) (6 . 11) (7 . 12) (8 . 13)) 10.161 {0/2:10} B:0 4.50005 [ 4.50005] ((6 . 3) (8 . 5) (9 . 6) (16 . 13)) 5.979 {0/3:6} B:0 4.50006 [ 4.50006] ((16 . 11) (17 . 12) (21 . 14) (23 . 15)) 6.024 {0/0:6} B:0 4.50009 [ 4.50009] ((1 . 3) (3 . 5) (8 . 11) (16 . 18)) 6.883 {0/3:6} B:0 4.50012 [ 4.50012] ((2 . 10) (3 . 11) (6 . 13) (8 . 15)) 7.288 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.3911 [and 1/min{score2}: 0.3911] [5028, 6279]: Comparing 1pja_A and 1vj5_A, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 47 (32 H + 15 S) secondary structure elements in 1vj5_A, of which 20 satisfy the size requirements. 2.00004 [ 2.22225] ((1 . 24) (2 . 26) (3 . 27) (5 . 29) (6 . 30) (7 . 31) (8 . 33) (23 . 42) (24 . 47)) 3.095 {0/20:36} B:0 2.52690 [ 2.56705] ((1 . 24) (2 . 26) (3 . 27) (5 . 29) (6 . 30) (7 . 31) (8 . 33) (10 . 34) (14 . 41) (16 . 42) (23 . 45) (24 . 47)) 4.113 {11/45:66} B:0 3.00065 [ 3.33380] ((1 . 27) (2 . 29) (6 . 33) (16 . 42) (23 . 45) (24 . 47)) 8.221 {0/8:15} B:0 3.60072 [ 4.00053] ((1 . 27) (2 . 29) (3 . 30) (6 . 33) (24 . 47)) 9.701 {0/3:10} B:0 4.50023 [ 5.00016] ((13 . 26) (16 . 30) (17 . 31) (23 . 33)) 8.565 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.5497 [and 1/min{score2}: 0.4965] [5028, 6404]: Comparing 1pja_A and 2bce, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 44 (25 H + 19 S) secondary structure elements in 2bce, of which 35 satisfy the size requirements. 1.50178 [ 2.71020] ((1 . 9) (2 . 12) (3 . 13) (5 . 15) (6 . 17) (7 . 18) (8 . 20) (15 . 27) (16 . 28) (17 . 34) (21 . 35) (23 . 36) (24 . 40)) 5.615 {5/46:78} B:0 1.56336 [ 2.92580] ((1 . 9) (2 . 12) (3 . 13) (5 . 15) (6 . 17) (7 . 18) (8 . 20) (15 . 27) (16 . 28) (21 . 35) (23 . 36) (24 . 40)) 4.291 {4/41:66} B:0 1.70279 [ 2.94980] ((1 . 9) (2 . 11) (3 . 13) (5 . 15) (6 . 17) (7 . 18) (8 . 20) (15 . 27) (16 . 28) (17 . 35) (23 . 36) (24 . 37)) 5.016 {5/37:66} B:0 1.92322 [ 2.81223] ((1 . 9) (2 . 12) (3 . 13) (5 . 15) (6 . 17) (7 . 18) (8 . 20) (15 . 27) (16 . 28) (17 . 34) (22 . 35) (23 . 36) (24 . 40)) 5.751 {8/45:78} B:0 2.65014 [ 5.01117] ((1 . 13) (5 . 15) (6 . 17) (7 . 18) (8 . 20) (15 . 27) (16 . 28)) 3.452 {2/13:21} B:0 SIMILARITY (1/min{score1}): 0.7604 [and 1/min{score2}: 0.4232] [5028, 6599]: Comparing 1pja_A and 3tgl, based on their crossing files. There are 24 (16 H + 8 S) secondary structure elements in 1pja_A, of which 18 satisfy the size requirements. There are 24 (11 H + 13 S) secondary structure elements in 3tgl, of which 19 satisfy the size requirements. 3.60062 [ 3.80053] ((5 . 3) (10 . 10) (13 . 11) (14 . 13) (23 . 19)) 9.350 {0/8:10} B:0 4.50010 [ 4.75008] ((1 . 4) (3 . 6) (5 . 10) (8 . 12)) 6.950 {0/2:6} B:0 4.50010 [ 4.75008] ((3 . 4) (7 . 10) (14 . 15) (16 . 16)) 6.979 {0/4:6} B:0 4.50010 [ 4.75009] ((16 . 12) (17 . 13) (22 . 15) (23 . 16)) 7.024 {0/3:6} B:0 4.50012 [ 4.75010] ((1 . 4) (3 . 6) (8 . 12) (16 . 19)) 7.249 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.4333 [and 1/min{score2}: 0.4197] -------------------------------------------------------------------------------------------------------------------------