------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [608, 7]: Comparing 1cja_A and 1a06, based on their crossing files. There are 22 (14 H + 8 S) secondary structure elements in 1cja_A, of which 18 satisfy the size requirements. There are 22 (14 H + 8 S) secondary structure elements in 1a06, of which 18 satisfy the size requirements. 1.80032 [ 1.80032] ((4 . 3) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (11 . 9) (14 . 11) (16 . 13) (17 . 14) (18 . 20)) 4.708 {0/26:45} B:0 3.60003 [ 3.60003] ((8 . 6) (11 . 9) (14 . 11) (16 . 13) (17 . 14)) 4.343 {0/4:10} B:0 3.60004 [ 3.60004] ((8 . 6) (14 . 11) (16 . 13) (17 . 14) (19 . 16)) 4.803 {0/6:10} B:0 3.60923 [ 3.60923] ((7 . 4) (16 . 13) (18 . 15) (19 . 16) (20 . 17)) 10.768 {1/9:10} B:0 3.79370 [ 3.79370] ((12 . 5) (14 . 7) (16 . 8) (18 . 11) (21 . 16)) 9.218 {2/8:10} B:0 SIMILARITY (1/min{score1}): 0.5555 [and 1/min{score2}: 0.5555] [608, 608]: Comparing 1cja_A and 1cja_A, based on their crossing files. There are 22 (14 H + 8 S) secondary structure elements in 1cja_A, of which 18 satisfy the size requirements. There are 22 (14 H + 8 S) secondary structure elements in 1cja_A, of which 18 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12) (14 . 14) (16 . 16) (17 . 17) (18 . 18) (19 . 19) (20 . 20) (21 . 21) (22 . 22)) 0.000 {0/125:153} B:0 2.57179 [ 2.57179] ((4 . 4) (5 . 5) (6 . 6) (8 . 8) (11 . 11) (21 . 14) (22 . 19)) 6.353 {0/14:21} B:0 2.57179 [ 2.57179] ((4 . 4) (5 . 5) (6 . 6) (8 . 8) (11 . 11) (14 . 21) (19 . 22)) 6.353 {0/14:21} B:0 3.61346 [ 3.61346] ((4 . 5) (5 . 6) (9 . 10) (16 . 17) (19 . 20)) 8.621 {1/8:10} B:0 3.61346 [ 3.61346] ((5 . 4) (6 . 5) (10 . 9) (17 . 16) (20 . 19)) 8.621 {1/8:10} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [608, 675]: Comparing 1cja_A and 1csn, based on their crossing files. There are 22 (14 H + 8 S) secondary structure elements in 1cja_A, of which 18 satisfy the size requirements. There are 21 (11 H + 10 S) secondary structure elements in 1csn, of which 16 satisfy the size requirements. 2.07940 [ 2.00007] ((4 . 2) (5 . 3) (6 . 4) (7 . 5) (8 . 6) (11 . 7) (14 . 9) (16 . 12) (17 . 13) (19 . 16) (20 . 20)) 5.199 {7/38:55} B:0 3.00084 [ 2.66786] ((4 . 2) (5 . 3) (6 . 4) (7 . 5) (8 . 6) (22 . 20)) 8.779 {0/12:15} B:0 3.28704 [ 3.26791] ((4 . 2) (5 . 3) (6 . 4) (7 . 5) (8 . 6) (11 . 7) (14 . 9) (16 . 12) (17 . 13) (18 . 19) (20 . 20)) 4.935 {11/34:55} B:0 3.60005 [ 3.20007] ((8 . 4) (11 . 7) (14 . 9) (16 . 12) (17 . 13)) 5.021 {0/4:10} B:0 3.60033 [ 3.20047] ((5 . 2) (6 . 3) (18 . 15) (20 . 17) (22 . 19)) 7.960 {0/9:10} B:0 SIMILARITY (1/min{score1}): 0.4809 [and 1/min{score2}: 0.5146] [608, 1070]: Comparing 1cja_A and 1e7u_A, based on their crossing files. There are 22 (14 H + 8 S) secondary structure elements in 1cja_A, of which 18 satisfy the size requirements. There are 61 (37 H + 24 S) secondary structure elements in 1e7u_A, of which 21 satisfy the size requirements. 3.60006 [ 4.20004] ((4 . 41) (19 . 56) (20 . 57) (21 . 58) (22 . 59)) 5.166 {0/8:10} B:0 3.60012 [ 4.20008] ((4 . 41) (11 . 48) (12 . 49) (19 . 56) (20 . 57)) 6.245 {0/8:10} B:0 3.60019 [ 4.20012] ((5 . 44) (6 . 45) (11 . 48) (12 . 49) (22 . 60)) 6.929 {0/8:10} B:0 3.60121 [ 4.20076] ((4 . 40) (14 . 50) (20 . 57) (21 . 58) (22 . 59)) 11.028 {0/8:10} B:0 3.61308 [ 4.20826] ((4 . 40) (19 . 56) (20 . 57) (21 . 58) (22 . 59)) 5.468 {1/8:10} B:0 SIMILARITY (1/min{score1}): 0.8251 [and 1/min{score2}: 0.7104] [608, 1385]: Comparing 1cja_A and 1f3m_C, based on their crossing files. There are 22 (14 H + 8 S) secondary structure elements in 1cja_A, of which 18 satisfy the size requirements. There are 25 (15 H + 10 S) secondary structure elements in 1f3m_C, of which 18 satisfy the size requirements. 2.39397 [ 2.39397] ((4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (11 . 9) (14 . 12) (16 . 15) (17 . 16) (20 . 22)) 5.453 {5/23:45} B:0 3.13697 [ 3.13697] ((4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (11 . 9) (14 . 12) (16 . 15) (17 . 16) (18 . 21) (20 . 22)) 6.885 {8/26:55} B:0 3.60002 [ 3.60002] ((6 . 4) (8 . 6) (14 . 12) (16 . 15) (17 . 16)) 4.096 {0/3:10} B:0 3.60011 [ 3.60011] ((6 . 4) (8 . 6) (11 . 9) (14 . 12) (19 . 18)) 6.098 {0/4:10} B:0 4.50002 [ 4.50002] ((5 . 8) (6 . 9) (14 . 18) (18 . 21)) 4.458 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.4177 [and 1/min{score2}: 0.4177] [608, 1498]: Comparing 1cja_A and 1fgk_A, based on their crossing files. There are 22 (14 H + 8 S) secondary structure elements in 1cja_A, of which 18 satisfy the size requirements. There are 20 (13 H + 7 S) secondary structure elements in 1fgk_A, of which 15 satisfy the size requirements. 2.07432 [ 1.78842] ((4 . 2) (5 . 3) (6 . 4) (7 . 5) (8 . 6) (11 . 7) (14 . 9) (18 . 18) (22 . 20)) 8.307 {3/24:36} B:0 2.43386 [ 2.38708] ((4 . 2) (5 . 3) (6 . 4) (7 . 5) (8 . 6) (11 . 7) (14 . 9) (16 . 11) (17 . 12) (18 . 15) (19 . 16) (20 . 20)) 6.253 {11/47:66} B:0 3.13682 [ 3.10631] ((4 . 2) (5 . 3) (6 . 4) (7 . 5) (8 . 6) (11 . 7) (14 . 9) (16 . 11) (17 . 12) (18 . 15) (20 . 16)) 5.658 {12/39:55} B:0 3.60008 [ 3.00015] ((8 . 4) (14 . 9) (16 . 11) (17 . 12) (19 . 16)) 5.671 {0/6:10} B:0 4.50004 [ 3.75008] ((16 . 2) (17 . 3) (21 . 8) (22 . 9)) 5.677 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.4821 [and 1/min{score2}: 0.5592] [608, 1563]: Comparing 1cja_A and 1fmk, based on their crossing files. There are 22 (14 H + 8 S) secondary structure elements in 1cja_A, of which 18 satisfy the size requirements. There are 37 (18 H + 19 S) secondary structure elements in 1fmk, of which 16 satisfy the size requirements. 2.07939 [ 2.00006] ((4 . 18) (5 . 19) (6 . 20) (7 . 21) (8 . 22) (11 . 23) (14 . 26) (16 . 28) (17 . 30) (19 . 33) (20 . 37)) 5.165 {7/38:55} B:0 2.51718 [ 2.45294] ((4 . 18) (5 . 19) (6 . 20) (7 . 21) (8 . 22) (11 . 23) (14 . 26) (16 . 28) (17 . 30) (20 . 37)) 4.725 {7/30:45} B:0 3.00020 [ 2.66695] ((4 . 18) (5 . 19) (6 . 20) (7 . 21) (8 . 22) (20 . 35)) 6.128 {0/13:15} B:0 3.60006 [ 3.20009] ((8 . 20) (11 . 23) (14 . 26) (16 . 28) (17 . 30)) 5.209 {0/4:10} B:0 3.60016 [ 3.20022] ((4 . 18) (7 . 21) (8 . 22) (11 . 23) (20 . 35)) 6.626 {0/7:10} B:0 SIMILARITY (1/min{score1}): 0.4809 [and 1/min{score2}: 0.5000] [608, 2018]: Comparing 1cja_A and 1gz8_A, based on their crossing files. There are 22 (14 H + 8 S) secondary structure elements in 1cja_A, of which 18 satisfy the size requirements. There are 21 (13 H + 8 S) secondary structure elements in 1gz8_A, of which 18 satisfy the size requirements. 2.15268 [ 2.15268] ((4 . 1) (5 . 2) (6 . 3) (7 . 4) (8 . 5) (11 . 6) (14 . 9) (16 . 11) (17 . 12) (19 . 15) (20 . 20)) 4.974 {7/36:55} B:0 3.00040 [ 3.00040] ((4 . 1) (5 . 2) (6 . 3) (7 . 4) (8 . 5) (22 . 20)) 7.291 {0/11:15} B:0 3.60004 [ 3.60004] ((8 . 3) (11 . 6) (14 . 9) (16 . 11) (17 . 12)) 4.707 {0/4:10} B:0 3.60008 [ 3.60008] ((8 . 3) (14 . 9) (16 . 11) (17 . 12) (19 . 15)) 5.552 {0/6:10} B:0 3.60039 [ 3.60039] ((5 . 1) (6 . 2) (18 . 14) (20 . 16) (22 . 19)) 8.314 {0/8:10} B:0 SIMILARITY (1/min{score1}): 0.5389 [and 1/min{score2}: 0.5389] [608, 2439]: Comparing 1cja_A and 1ia9_A, based on their crossing files. There are 22 (14 H + 8 S) secondary structure elements in 1cja_A, of which 18 satisfy the size requirements. There are 23 (9 H + 14 S) secondary structure elements in 1ia9_A, of which 18 satisfy the size requirements. 1.80085 [ 1.80085] ((4 . 6) (5 . 7) (6 . 9) (7 . 11) (8 . 13) (11 . 14) (14 . 16) (16 . 18) (18 . 22) (20 . 23)) 5.999 {0/32:45} B:0 2.00049 [ 2.00049] ((5 . 7) (6 . 9) (7 . 11) (8 . 13) (11 . 14) (14 . 16) (16 . 18) (18 . 22) (20 . 23)) 5.654 {0/25:36} B:0 2.29135 [ 2.29135] ((5 . 7) (6 . 9) (7 . 11) (11 . 14) (14 . 16) (17 . 18) (18 . 22) (20 . 23)) 6.089 {2/17:28} B:0 3.06926 [ 3.06926] ((5 . 7) (6 . 9) (14 . 16) (16 . 18) (19 . 22) (20 . 23)) 6.517 {2/12:15} B:0 3.60013 [ 3.60013] ((4 . 2) (5 . 6) (6 . 7) (11 . 9) (20 . 22)) 6.310 {0/8:10} B:0 SIMILARITY (1/min{score1}): 0.5553 [and 1/min{score2}: 0.5553] [608, 2446]: Comparing 1cja_A and 1ias_A, based on their crossing files. There are 22 (14 H + 8 S) secondary structure elements in 1cja_A, of which 18 satisfy the size requirements. There are 26 (16 H + 10 S) secondary structure elements in 1ias_A, of which 20 satisfy the size requirements. 3.00013 [ 3.33343] ((5 . 4) (8 . 5) (11 . 9) (14 . 11) (16 . 14) (17 . 15)) 5.476 {0/6:15} B:0 3.72691 [ 4.09415] ((5 . 3) (6 . 4) (19 . 20) (21 . 22) (22 . 24)) 13.960 {2/9:10} B:0 4.50015 [ 5.00011] ((5 . 3) (6 . 4) (18 . 20) (22 . 24)) 7.794 {0/5:6} B:0 4.50018 [ 5.00013] ((5 . 3) (18 . 20) (20 . 22) (22 . 24)) 8.044 {0/5:6} B:0 4.50038 [ 5.00028] ((14 . 2) (16 . 4) (17 . 5) (19 . 10)) 9.764 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.6652 [and 1/min{score2}: 0.5991] [608, 2756]: Comparing 1cja_A and 1j7l_A, based on their crossing files. There are 22 (14 H + 8 S) secondary structure elements in 1cja_A, of which 18 satisfy the size requirements. There are 21 (11 H + 10 S) secondary structure elements in 1j7l_A, of which 19 satisfy the size requirements. 3.00003 [ 3.16669] ((4 . 2) (5 . 3) (6 . 4) (7 . 6) (8 . 7) (19 . 19)) 3.723 {0/11:15} B:0 3.02251 [ 3.18585] ((4 . 2) (5 . 3) (6 . 4) (8 . 7) (11 . 8) (14 . 12)) 5.833 {1/8:15} B:0 4.50004 [ 4.75004] ((8 . 8) (14 . 19) (19 . 20) (20 . 21)) 5.655 {0/6:6} B:0 4.50024 [ 4.75020] ((8 . 8) (17 . 16) (19 . 20) (20 . 21)) 8.680 {0/5:6} B:0 4.50028 [ 4.75024] ((5 . 16) (6 . 17) (7 . 19) (9 . 20)) 9.042 {0/6:6} B:0 SIMILARITY (1/min{score1}): 0.6759 [and 1/min{score2}: 0.6478] [608, 2947]: Comparing 1cja_A and 1jks_A, based on their crossing files. There are 22 (14 H + 8 S) secondary structure elements in 1cja_A, of which 18 satisfy the size requirements. There are 22 (13 H + 9 S) secondary structure elements in 1jks_A, of which 16 satisfy the size requirements. 2.14656 [ 2.07496] ((4 . 2) (5 . 3) (6 . 4) (7 . 5) (8 . 6) (11 . 7) (14 . 9) (16 . 12) (17 . 13) (18 . 20) (22 . 22)) 6.527 {6/31:55} B:0 2.25007 [ 2.00010] ((4 . 2) (5 . 3) (6 . 4) (7 . 5) (8 . 6) (11 . 7) (12 . 13) (19 . 17)) 3.838 {0/19:28} B:0 3.00707 [ 2.67671] ((4 . 2) (5 . 3) (6 . 4) (7 . 5) (8 . 6) (20 . 19)) 8.591 {1/11:15} B:0 3.60004 [ 3.20006] ((8 . 4) (11 . 7) (14 . 9) (16 . 12) (17 . 13)) 4.680 {0/3:10} B:0 4.50009 [ 4.00012] ((12 . 3) (14 . 5) (16 . 6) (17 . 7)) 6.760 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.6109 [and 1/min{score2}: 0.6871] [608, 3143]: Comparing 1cja_A and 1k2p_A, based on their crossing files. There are 22 (14 H + 8 S) secondary structure elements in 1cja_A, of which 18 satisfy the size requirements. There are 20 (12 H + 8 S) secondary structure elements in 1k2p_A, of which 14 satisfy the size requirements. 2.90619 [ 2.79685] ((5 . 2) (6 . 3) (7 . 4) (8 . 5) (11 . 6) (14 . 10) (16 . 12) (17 . 13) (20 . 20)) 5.029 {6/22:36} B:0 3.40220 [ 3.35914] ((5 . 2) (6 . 3) (7 . 4) (8 . 5) (11 . 6) (14 . 10) (16 . 12) (17 . 13) (18 . 15) (20 . 16)) 6.399 {9/27:45} B:0 3.60004 [ 2.80008] ((8 . 3) (11 . 6) (14 . 10) (16 . 12) (17 . 13)) 4.649 {0/4:10} B:0 3.60008 [ 2.80016] ((8 . 3) (14 . 10) (16 . 12) (17 . 13) (19 . 16)) 5.529 {0/5:10} B:0 3.60016 [ 2.80035] ((5 . 2) (6 . 3) (7 . 4) (8 . 5) (20 . 18)) 6.684 {0/9:10} B:0 SIMILARITY (1/min{score1}): 0.3887 [and 1/min{score2}: 0.4994] [608, 3379]: Comparing 1cja_A and 1kob_A, based on their crossing files. There are 22 (14 H + 8 S) secondary structure elements in 1cja_A, of which 18 satisfy the size requirements. There are 29 (18 H + 11 S) secondary structure elements in 1kob_A, of which 21 satisfy the size requirements. 2.11453 [ 2.26038] ((4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (11 . 9) (14 . 11) (16 . 14) (17 . 15) (19 . 20) (20 . 24)) 5.165 {7/37:55} B:0 2.57403 [ 3.00164] ((4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (11 . 9) (20 . 21)) 6.319 {1/16:21} B:0 3.00009 [ 3.50006] ((5 . 5) (8 . 6) (11 . 9) (14 . 11) (16 . 14) (17 . 15)) 5.054 {0/9:15} B:0 3.60005 [ 4.20003] ((8 . 6) (14 . 11) (16 . 14) (17 . 15) (19 . 20)) 4.924 {0/7:10} B:0 4.50008 [ 5.25005] ((12 . 5) (16 . 8) (17 . 9) (18 . 11)) 6.567 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.4729 [and 1/min{score2}: 0.4424] [608, 3778]: Comparing 1cja_A and 1m14_A, based on their crossing files. There are 22 (14 H + 8 S) secondary structure elements in 1cja_A, of which 18 satisfy the size requirements. There are 25 (14 H + 11 S) secondary structure elements in 1m14_A, of which 15 satisfy the size requirements. 2.07940 [ 1.96747] ((4 . 2) (5 . 3) (6 . 4) (7 . 5) (8 . 6) (11 . 7) (14 . 9) (16 . 12) (17 . 13) (19 . 19) (20 . 23)) 5.230 {7/38:55} B:0 3.60005 [ 3.00009] ((8 . 4) (11 . 7) (14 . 9) (16 . 12) (17 . 13)) 4.993 {0/4:10} B:0 3.60007 [ 3.00012] ((8 . 4) (14 . 9) (16 . 12) (17 . 13) (19 . 19)) 5.425 {0/6:10} B:0 4.50025 [ 3.75043] ((4 . 4) (6 . 6) (7 . 8) (11 . 12)) 8.763 {0/4:6} B:0 4.50026 [ 3.75044] ((1 . 5) (5 . 12) (6 . 13) (14 . 21)) 8.846 {0/5:6} B:0 SIMILARITY (1/min{score1}): 0.4809 [and 1/min{score2}: 0.5083] [608, 3808]: Comparing 1cja_A and 1m2r_A, based on their crossing files. There are 22 (14 H + 8 S) secondary structure elements in 1cja_A, of which 18 satisfy the size requirements. There are 27 (18 H + 9 S) secondary structure elements in 1m2r_A, of which 19 satisfy the size requirements. 1.64247 [ 1.73247] ((4 . 5) (5 . 6) (6 . 7) (7 . 8) (8 . 9) (11 . 10) (14 . 12) (16 . 15) (17 . 16) (19 . 20) (20 . 27)) 5.330 {2/36:55} B:0 3.60005 [ 3.80004] ((8 . 7) (11 . 10) (14 . 12) (16 . 15) (17 . 16)) 4.935 {0/3:10} B:0 3.60008 [ 3.80007] ((8 . 7) (14 . 12) (16 . 15) (17 . 16) (19 . 20)) 5.597 {0/5:10} B:0 3.60036 [ 3.80031] ((5 . 5) (6 . 6) (18 . 19) (20 . 21) (22 . 25)) 8.152 {0/9:10} B:0 3.96843 [ 3.97534] ((4 . 5) (5 . 6) (6 . 7) (7 . 8) (8 . 9) (11 . 10) (14 . 12) (16 . 15) (17 . 16) (19 . 25) (20 . 26)) 4.965 {13/33:55} B:0 SIMILARITY (1/min{score1}): 0.6643 [and 1/min{score2}: 0.6298] [608, 4001]: Comparing 1cja_A and 1mp8_A, based on their crossing files. There are 22 (14 H + 8 S) secondary structure elements in 1cja_A, of which 18 satisfy the size requirements. There are 20 (12 H + 8 S) secondary structure elements in 1mp8_A, of which 15 satisfy the size requirements. 2.07951 [ 1.96759] ((4 . 2) (5 . 3) (6 . 4) (7 . 5) (8 . 6) (11 . 7) (14 . 10) (16 . 12) (17 . 13) (19 . 16) (20 . 20)) 5.612 {7/38:55} B:0 3.00647 [ 2.51114] ((4 . 2) (5 . 3) (6 . 4) (7 . 5) (8 . 6) (18 . 17)) 5.840 {1/11:15} B:0 3.60006 [ 3.00011] ((8 . 4) (11 . 7) (14 . 10) (16 . 12) (17 . 13)) 5.271 {0/4:10} B:0 3.60008 [ 3.00014] ((6 . 2) (8 . 4) (14 . 10) (16 . 12) (17 . 13)) 5.648 {0/5:10} B:0 3.60009 [ 3.00016] ((12 . 3) (14 . 5) (16 . 6) (17 . 7) (21 . 16)) 5.776 {0/6:10} B:0 SIMILARITY (1/min{score1}): 0.4809 [and 1/min{score2}: 0.5082] [608, 4008]: Comparing 1cja_A and 1mq4_A, based on their crossing files. There are 22 (14 H + 8 S) secondary structure elements in 1cja_A, of which 18 satisfy the size requirements. There are 23 (14 H + 9 S) secondary structure elements in 1mq4_A, of which 17 satisfy the size requirements. 1.80022 [ 1.70027] ((4 . 2) (5 . 3) (6 . 4) (7 . 6) (8 . 7) (11 . 8) (14 . 10) (16 . 13) (17 . 14) (19 . 18)) 4.307 {0/31:45} B:0 2.07934 [ 2.03733] ((4 . 2) (5 . 3) (6 . 4) (7 . 6) (8 . 7) (11 . 8) (14 . 10) (16 . 13) (17 . 14) (19 . 18) (20 . 22)) 4.949 {7/38:55} B:0 2.73131 [ 2.71853] ((4 . 2) (5 . 3) (6 . 4) (7 . 6) (8 . 7) (11 . 8) (14 . 10) (16 . 13) (17 . 14) (18 . 17) (19 . 18) (20 . 22)) 6.167 {12/45:66} B:0 3.60005 [ 3.40006] ((8 . 4) (11 . 8) (14 . 10) (16 . 13) (17 . 14)) 5.053 {0/4:10} B:0 4.50001 [ 4.25001] ((5 . 7) (6 . 8) (14 . 18) (18 . 20)) 3.984 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.5555 [and 1/min{score2}: 0.5881] [608, 4200]: Comparing 1cja_A and 1nd4_A, based on their crossing files. There are 22 (14 H + 8 S) secondary structure elements in 1cja_A, of which 18 satisfy the size requirements. There are 21 (11 H + 10 S) secondary structure elements in 1nd4_A, of which 17 satisfy the size requirements. 1.63732 [ 1.54658] ((4 . 2) (5 . 3) (6 . 4) (7 . 5) (8 . 6) (11 . 7) (14 . 9) (16 . 16) (17 . 17) (19 . 19) (20 . 20)) 5.752 {0/38:55} B:0 3.01440 [ 2.85040] ((4 . 2) (5 . 3) (6 . 4) (7 . 5) (8 . 6) (14 . 11)) 7.254 {1/9:15} B:0 3.18780 [ 3.17111] ((4 . 2) (5 . 3) (6 . 4) (7 . 5) (8 . 6) (11 . 7) (14 . 9) (16 . 16) (17 . 17) (19 . 20)) 4.533 {9/29:45} B:0 3.87993 [ 3.86586] ((5 . 3) (6 . 4) (7 . 5) (8 . 6) (11 . 7) (14 . 9) (16 . 16) (17 . 17) (19 . 20)) 4.713 {8/21:36} B:0 4.50001 [ 4.25001] ((12 . 6) (16 . 7) (21 . 9) (22 . 19)) 4.031 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.6471 [and 1/min{score2}: 0.6803] [608, 4408]: Comparing 1cja_A and 1nvr_A, based on their crossing files. There are 22 (14 H + 8 S) secondary structure elements in 1cja_A, of which 18 satisfy the size requirements. There are 24 (11 H + 13 S) secondary structure elements in 1nvr_A, of which 16 satisfy the size requirements. 2.00021 [ 1.77807] ((5 . 3) (6 . 4) (7 . 5) (8 . 6) (11 . 7) (14 . 10) (16 . 13) (17 . 14) (18 . 24)) 4.573 {0/17:36} B:0 2.12040 [ 1.94133] ((4 . 1) (5 . 3) (6 . 4) (7 . 5) (8 . 6) (11 . 7) (14 . 10) (18 . 23) (22 . 24)) 7.559 {3/21:36} B:0 2.84742 [ 2.82660] ((4 . 1) (5 . 3) (6 . 4) (7 . 5) (8 . 6) (11 . 7) (14 . 10) (16 . 13) (17 . 14) (18 . 19) (19 . 20) (20 . 24)) 6.091 {12/43:66} B:0 3.60004 [ 3.20006] ((8 . 4) (11 . 7) (14 . 10) (16 . 13) (17 . 14)) 4.740 {0/5:10} B:0 4.50014 [ 4.00019] ((4 . 3) (5 . 4) (12 . 13) (18 . 21)) 7.552 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.4999 [and 1/min{score2}: 0.5624] [608, 4411]: Comparing 1cja_A and 1nw1_A, based on their crossing files. There are 22 (14 H + 8 S) secondary structure elements in 1cja_A, of which 18 satisfy the size requirements. There are 33 (19 H + 14 S) secondary structure elements in 1nw1_A, of which 22 satisfy the size requirements. 3.01705 [ 3.41935] ((4 . 6) (5 . 7) (6 . 8) (11 . 11) (14 . 15) (18 . 19) (19 . 30)) 8.309 {3/12:21} B:0 3.20467 [ 3.78492] ((4 . 6) (5 . 7) (6 . 8) (7 . 9) (14 . 15) (18 . 19)) 8.614 {2/9:15} B:0 3.60008 [ 4.40004] ((5 . 10) (6 . 11) (19 . 29) (21 . 31) (22 . 32)) 5.618 {0/8:10} B:0 4.50007 [ 5.50004] ((5 . 10) (6 . 11) (21 . 31) (22 . 33)) 6.370 {0/4:6} B:0 4.50008 [ 5.50005] ((16 . 7) (17 . 8) (20 . 14) (21 . 15)) 6.679 {0/5:6} B:0 SIMILARITY (1/min{score1}): 0.4881 [and 1/min{score2}: 0.4410] [608, 4428]: Comparing 1cja_A and 1nxk_A, based on their crossing files. There are 22 (14 H + 8 S) secondary structure elements in 1cja_A, of which 18 satisfy the size requirements. There are 26 (14 H + 12 S) secondary structure elements in 1nxk_A, of which 18 satisfy the size requirements. 1.80130 [ 1.80130] ((4 . 5) (5 . 6) (6 . 7) (7 . 8) (8 . 9) (11 . 10) (14 . 13) (16 . 16) (17 . 17) (18 . 24)) 4.860 {1/26:45} B:0 3.60004 [ 3.60004] ((8 . 7) (11 . 10) (14 . 13) (16 . 16) (17 . 17)) 4.837 {0/4:10} B:0 4.50003 [ 4.50003] ((5 . 9) (6 . 10) (14 . 20) (18 . 22)) 5.013 {0/3:6} B:0 4.50006 [ 4.50006] ((6 . 5) (8 . 7) (11 . 10) (14 . 13)) 6.178 {0/2:6} B:0 4.50013 [ 4.50013] ((1 . 8) (5 . 16) (6 . 17) (14 . 22)) 7.431 {0/5:6} B:0 SIMILARITY (1/min{score1}): 0.6108 [and 1/min{score2}: 0.6108] [608, 4511]: Comparing 1cja_A and 1o6l_A, based on their crossing files. There are 22 (14 H + 8 S) secondary structure elements in 1cja_A, of which 18 satisfy the size requirements. There are 24 (15 H + 9 S) secondary structure elements in 1o6l_A, of which 17 satisfy the size requirements. 1.80025 [ 1.70029] ((4 . 2) (5 . 3) (6 . 4) (7 . 6) (8 . 7) (11 . 8) (14 . 10) (16 . 12) (17 . 13) (19 . 17)) 4.409 {0/30:45} B:0 2.11450 [ 2.07463] ((4 . 2) (5 . 3) (6 . 4) (7 . 6) (8 . 7) (11 . 8) (14 . 10) (16 . 12) (17 . 13) (19 . 17) (20 . 20)) 5.021 {7/37:55} B:0 3.60004 [ 3.40005] ((8 . 4) (11 . 8) (14 . 10) (16 . 12) (17 . 13)) 4.685 {0/4:10} B:0 4.50001 [ 4.25001] ((5 . 7) (6 . 8) (14 . 17) (18 . 19)) 3.771 {0/2:6} B:0 4.50007 [ 4.25008] ((8 . 4) (11 . 8) (14 . 10) (19 . 17)) 6.405 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.5715 [and 1/min{score2}: 0.5964] [608, 4519]: Comparing 1cja_A and 1o6y_A, based on their crossing files. There are 22 (14 H + 8 S) secondary structure elements in 1cja_A, of which 18 satisfy the size requirements. There are 22 (11 H + 11 S) secondary structure elements in 1o6y_A, of which 16 satisfy the size requirements. 2.32974 [ 2.29119] ((4 . 2) (5 . 3) (6 . 4) (7 . 5) (8 . 6) (11 . 7) (12 . 8) (14 . 10) (16 . 13) (17 . 14) (19 . 17) (20 . 22)) 5.137 {10/45:66} B:0 3.00006 [ 2.66675] ((8 . 4) (11 . 7) (12 . 8) (14 . 10) (16 . 13) (17 . 14)) 4.535 {0/7:15} B:0 4.50002 [ 4.00003] ((5 . 6) (6 . 7) (14 . 17) (18 . 20)) 4.632 {0/4:6} B:0 4.50003 [ 4.00004] ((6 . 3) (11 . 7) (12 . 8) (14 . 10)) 4.993 {0/2:6} B:0 4.50012 [ 4.00018] ((12 . 3) (14 . 5) (16 . 6) (17 . 7)) 7.376 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.4443 [and 1/min{score2}: 0.4998] [608, 4717]: Comparing 1cja_A and 1omw_A, based on their crossing files. There are 22 (14 H + 8 S) secondary structure elements in 1cja_A, of which 18 satisfy the size requirements. There are 45 (28 H + 17 S) secondary structure elements in 1omw_A, of which 19 satisfy the size requirements. 3.36720 [ 3.37518] ((4 . 11) (5 . 12) (6 . 13) (7 . 15) (8 . 16) (11 . 17) (14 . 19) (16 . 22) (17 . 23) (19 . 27) (20 . 30) (21 . 33)) 6.767 {16/48:66} B:0 3.60023 [ 3.80020] ((8 . 13) (14 . 19) (16 . 22) (17 . 23) (22 . 30)) 7.307 {0/6:10} B:0 3.61313 [ 3.81117] ((4 . 11) (5 . 12) (6 . 13) (11 . 17) (20 . 28)) 6.134 {1/8:10} B:0 4.50001 [ 4.75001] ((5 . 16) (6 . 17) (14 . 27) (18 . 29)) 4.219 {0/4:6} B:0 4.50006 [ 4.75005] ((8 . 13) (11 . 17) (14 . 19) (19 . 27)) 6.086 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.6233 [and 1/min{score2}: 0.5974] [608, 4889]: Comparing 1cja_A and 1p4o_A, based on their crossing files. There are 22 (14 H + 8 S) secondary structure elements in 1cja_A, of which 18 satisfy the size requirements. There are 24 (15 H + 9 S) secondary structure elements in 1p4o_A, of which 17 satisfy the size requirements. 2.28840 [ 2.26650] ((4 . 2) (5 . 3) (6 . 4) (7 . 5) (8 . 6) (11 . 7) (14 . 9) (16 . 11) (17 . 12) (18 . 18) (19 . 19) (20 . 23)) 6.502 {10/46:66} B:0 3.00091 [ 2.83441] ((4 . 2) (5 . 3) (6 . 4) (7 . 5) (11 . 7) (22 . 23)) 8.958 {0/13:15} B:0 3.60008 [ 3.40009] ((8 . 4) (14 . 9) (16 . 11) (17 . 12) (19 . 19)) 5.545 {0/7:10} B:0 3.60133 [ 3.40158] ((12 . 4) (16 . 7) (18 . 8) (21 . 13) (22 . 19)) 11.306 {0/7:10} B:0 3.60585 [ 3.59436] ((5 . 2) (6 . 4) (7 . 5) (8 . 6) (11 . 7) (14 . 9) (16 . 11) (17 . 12) (19 . 19) (20 . 23)) 6.346 {11/31:45} B:0 SIMILARITY (1/min{score1}): 0.6648 [and 1/min{score2}: 0.7034] [608, 5013]: Comparing 1cja_A and 1phk, based on their crossing files. There are 22 (14 H + 8 S) secondary structure elements in 1cja_A, of which 18 satisfy the size requirements. There are 22 (13 H + 9 S) secondary structure elements in 1phk, of which 16 satisfy the size requirements. 1.80031 [ 1.60044] ((4 . 1) (5 . 2) (6 . 3) (7 . 4) (8 . 5) (11 . 6) (14 . 8) (16 . 11) (17 . 12) (19 . 16)) 4.655 {0/31:45} B:0 1.85651 [ 1.74090] ((4 . 1) (5 . 2) (6 . 3) (7 . 4) (8 . 5) (11 . 6) (14 . 8) (16 . 11) (17 . 12) (18 . 19) (22 . 21)) 6.781 {5/34:55} B:0 2.07942 [ 2.00009] ((4 . 1) (5 . 2) (6 . 3) (7 . 4) (8 . 5) (11 . 6) (14 . 8) (16 . 11) (17 . 12) (19 . 16) (20 . 21)) 5.282 {7/38:55} B:0 3.00054 [ 2.66743] ((4 . 1) (5 . 2) (6 . 3) (11 . 6) (19 . 16) (22 . 21)) 7.862 {0/12:15} B:0 3.60005 [ 3.20007] ((8 . 3) (11 . 6) (14 . 8) (16 . 11) (17 . 12)) 4.943 {0/4:10} B:0 SIMILARITY (1/min{score1}): 0.5555 [and 1/min{score2}: 0.6248] [608, 5201]: Comparing 1cja_A and 1q41_A, based on their crossing files. There are 22 (14 H + 8 S) secondary structure elements in 1cja_A, of which 18 satisfy the size requirements. There are 29 (17 H + 12 S) secondary structure elements in 1q41_A, of which 21 satisfy the size requirements. 1.69713 [ 1.94832] ((4 . 3) (5 . 4) (6 . 5) (7 . 6) (8 . 7) (11 . 8) (14 . 11) (16 . 14) (17 . 15) (19 . 19) (20 . 26)) 5.957 {4/39:55} B:0 2.11455 [ 2.26040] ((4 . 3) (5 . 4) (6 . 5) (7 . 6) (8 . 7) (11 . 8) (14 . 11) (16 . 14) (17 . 15) (19 . 19) (20 . 25)) 5.261 {7/37:55} B:0 3.60004 [ 4.20002] ((8 . 5) (11 . 8) (14 . 11) (16 . 14) (17 . 15)) 4.556 {0/3:10} B:0 3.60007 [ 4.20004] ((8 . 5) (14 . 11) (16 . 14) (17 . 15) (19 . 19)) 5.406 {0/5:10} B:0 3.60007 [ 4.20005] ((4 . 2) (7 . 6) (8 . 7) (11 . 8) (19 . 19)) 5.494 {0/9:10} B:0 SIMILARITY (1/min{score1}): 0.6451 [and 1/min{score2}: 0.5611] [608, 5248]: Comparing 1cja_A and 1q8y_A, based on their crossing files. There are 22 (14 H + 8 S) secondary structure elements in 1cja_A, of which 18 satisfy the size requirements. There are 26 (15 H + 11 S) secondary structure elements in 1q8y_A, of which 20 satisfy the size requirements. 3.00006 [ 3.33338] ((5 . 3) (6 . 4) (7 . 5) (11 . 8) (16 . 14) (19 . 19)) 4.591 {0/10:15} B:0 3.60881 [ 4.00643] ((5 . 2) (6 . 3) (17 . 14) (19 . 18) (20 . 19)) 9.550 {1/9:10} B:0 3.75457 [ 3.78030] ((5 . 3) (6 . 4) (7 . 5) (8 . 7) (11 . 8) (12 . 14) (16 . 15) (18 . 18) (19 . 19) (20 . 24)) 7.735 {10/27:45} B:0 3.91911 [ 3.93463] ((4 . 2) (5 . 3) (6 . 4) (7 . 5) (8 . 7) (11 . 8) (14 . 11) (16 . 14) (17 . 15) (19 . 24) (20 . 25)) 6.223 {14/36:55} B:0 4.50011 [ 5.00008] ((12 . 3) (14 . 5) (16 . 7) (17 . 8)) 7.196 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.3333 [and 1/min{score2}: 0.3000] [608, 5510]: Comparing 1cja_A and 1r0p_A, based on their crossing files. There are 22 (14 H + 8 S) secondary structure elements in 1cja_A, of which 18 satisfy the size requirements. There are 23 (15 H + 8 S) secondary structure elements in 1r0p_A, of which 17 satisfy the size requirements. 1.98310 [ 1.94907] ((1 . 2) (4 . 5) (5 . 6) (6 . 7) (7 . 8) (8 . 9) (11 . 10) (14 . 12) (16 . 14) (17 . 15) (19 . 19) (20 . 23)) 6.369 {7/39:66} B:0 2.28856 [ 2.25736] ((4 . 5) (5 . 6) (6 . 7) (7 . 8) (8 . 9) (11 . 10) (14 . 12) (16 . 14) (17 . 15) (19 . 19) (20 . 23)) 5.648 {7/33:55} B:0 2.57152 [ 2.42867] ((4 . 4) (5 . 6) (6 . 7) (7 . 8) (8 . 9) (11 . 10) (19 . 19)) 4.436 {0/14:21} B:0 3.45978 [ 3.45352] ((1 . 2) (4 . 5) (5 . 6) (6 . 7) (7 . 8) (8 . 9) (11 . 10) (14 . 12) (16 . 14) (17 . 15) (18 . 21) (20 . 23)) 7.058 {12/35:66} B:0 3.60004 [ 3.40004] ((6 . 5) (8 . 7) (14 . 12) (16 . 14) (17 . 15)) 4.583 {0/5:10} B:0 SIMILARITY (1/min{score1}): 0.5043 [and 1/min{score2}: 0.5131] [608, 5539]: Comparing 1cja_A and 1r3c_A, based on their crossing files. There are 22 (14 H + 8 S) secondary structure elements in 1cja_A, of which 18 satisfy the size requirements. There are 28 (18 H + 10 S) secondary structure elements in 1r3c_A, of which 22 satisfy the size requirements. 1.80054 [ 2.20030] ((4 . 3) (5 . 4) (6 . 5) (7 . 6) (8 . 7) (11 . 8) (14 . 11) (16 . 13) (17 . 14) (18 . 25)) 5.360 {0/25:45} B:0 3.60003 [ 4.40002] ((8 . 5) (11 . 8) (14 . 11) (16 . 13) (17 . 14)) 4.384 {0/3:10} B:0 3.60005 [ 4.40003] ((8 . 5) (14 . 11) (16 . 13) (17 . 14) (19 . 18)) 5.057 {0/5:10} B:0 4.50002 [ 5.50001] ((4 . 1) (5 . 2) (6 . 3) (8 . 5)) 4.668 {0/5:6} B:0 4.50005 [ 5.50003] ((8 . 5) (11 . 8) (14 . 11) (19 . 18)) 5.874 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.6108 [and 1/min{score2}: 0.4999] [608, 5609]: Comparing 1cja_A and 1rdq_E, based on their crossing files. There are 22 (14 H + 8 S) secondary structure elements in 1cja_A, of which 18 satisfy the size requirements. There are 25 (15 H + 10 S) secondary structure elements in 1rdq_E, of which 18 satisfy the size requirements. 3.60004 [ 3.60004] ((8 . 5) (11 . 9) (14 . 11) (16 . 14) (17 . 15)) 4.694 {0/4:10} B:0 3.60023 [ 3.60023] ((14 . 11) (16 . 14) (17 . 15) (19 . 20) (22 . 23)) 7.282 {0/6:10} B:0 4.50008 [ 4.50008] ((12 . 4) (16 . 8) (17 . 9) (18 . 11)) 6.621 {0/3:6} B:0 4.50014 [ 4.50014] ((1 . 10) (7 . 20) (9 . 21) (14 . 25)) 7.540 {0/5:6} B:0 4.50022 [ 4.50022] ((1 . 7) (5 . 14) (6 . 15) (14 . 22)) 8.558 {0/5:6} B:0 SIMILARITY (1/min{score1}): 0.4178 [and 1/min{score2}: 0.4178] [608, 5917]: Comparing 1cja_A and 1tki_A, based on their crossing files. There are 22 (14 H + 8 S) secondary structure elements in 1cja_A, of which 18 satisfy the size requirements. There are 28 (16 H + 12 S) secondary structure elements in 1tki_A, of which 20 satisfy the size requirements. 3.60004 [ 4.00003] ((8 . 3) (11 . 6) (14 . 8) (16 . 11) (17 . 12)) 4.759 {0/4:10} B:0 3.60005 [ 4.00004] ((8 . 3) (14 . 8) (16 . 11) (17 . 12) (19 . 18)) 4.979 {0/6:10} B:0 3.78146 [ 3.96409] ((4 . 1) (5 . 2) (6 . 3) (7 . 4) (8 . 5) (19 . 19)) 5.737 {4/12:15} B:0 4.50008 [ 5.00006] ((12 . 2) (16 . 5) (17 . 6) (18 . 8)) 6.603 {0/3:6} B:0 4.50016 [ 5.00011] ((5 . 5) (6 . 6) (18 . 21) (21 . 27)) 7.831 {0/0:6} B:0 SIMILARITY (1/min{score1}): 0.6108 [and 1/min{score2}: 0.5498] [608, 6112]: Comparing 1cja_A and 1uu3_A, based on their crossing files. There are 22 (14 H + 8 S) secondary structure elements in 1cja_A, of which 18 satisfy the size requirements. There are 26 (16 H + 10 S) secondary structure elements in 1uu3_A, of which 18 satisfy the size requirements. 2.27575 [ 2.27575] ((4 . 2) (5 . 3) (6 . 4) (7 . 6) (8 . 7) (11 . 8) (14 . 11) (16 . 14) (17 . 15) (19 . 19) (20 . 24)) 4.880 {8/38:55} B:0 3.28710 [ 3.28710] ((4 . 2) (5 . 3) (6 . 4) (7 . 6) (8 . 7) (11 . 8) (14 . 11) (16 . 14) (17 . 15) (18 . 18) (20 . 19)) 5.828 {11/34:55} B:0 3.60004 [ 3.60004] ((8 . 4) (11 . 8) (14 . 11) (16 . 14) (17 . 15)) 4.651 {0/5:10} B:0 4.50008 [ 4.50008] ((12 . 3) (16 . 7) (17 . 8) (18 . 11)) 6.636 {0/3:6} B:0 4.50014 [ 4.50014] ((1 . 10) (7 . 19) (9 . 20) (14 . 25)) 7.570 {0/5:6} B:0 SIMILARITY (1/min{score1}): 0.5554 [and 1/min{score2}: 0.5554] [608, 6130]: Comparing 1cja_A and 1uwh_A, based on their crossing files. There are 22 (14 H + 8 S) secondary structure elements in 1cja_A, of which 18 satisfy the size requirements. There are 20 (12 H + 8 S) secondary structure elements in 1uwh_A, of which 16 satisfy the size requirements. 1.63800 [ 1.45688] ((4 . 1) (5 . 2) (6 . 3) (7 . 4) (8 . 5) (11 . 6) (12 . 7) (14 . 9) (16 . 11) (17 . 12) (18 . 20)) 5.855 {1/31:55} B:0 2.06661 [ 2.01049] ((4 . 1) (5 . 2) (6 . 3) (7 . 4) (8 . 5) (11 . 6) (12 . 7) (14 . 9) (16 . 11) (17 . 12) (19 . 15) (20 . 20)) 5.574 {8/42:66} B:0 3.00004 [ 2.66673] ((8 . 3) (11 . 6) (12 . 7) (14 . 9) (16 . 11) (17 . 12)) 4.218 {0/8:15} B:0 3.45236 [ 3.44075] ((4 . 1) (5 . 2) (6 . 3) (7 . 4) (8 . 5) (11 . 6) (12 . 7) (14 . 9) (16 . 11) (17 . 12) (18 . 18) (20 . 20)) 6.125 {13/38:66} B:0 3.60003 [ 3.20004] ((6 . 1) (8 . 3) (14 . 9) (16 . 11) (17 . 12)) 4.418 {0/4:10} B:0 SIMILARITY (1/min{score1}): 0.6105 [and 1/min{score2}: 0.6864] -------------------------------------------------------------------------------------------------------------------------