------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [6553, 483]: Comparing 2uag_A and 1bx4_A, based on their crossing files. There are 40 (20 H + 20 S) secondary structure elements in 2uag_A, of which 15 satisfy the size requirements. There are 29 (15 H + 14 S) secondary structure elements in 1bx4_A, of which 28 satisfy the size requirements. 2.50008 [ 4.66668] ((17 . 19) (23 . 25) (24 . 26) (25 . 27) (27 . 28) (28 . 29)) 4.311 {0/11:15} B:0 2.50020 [ 4.66670] ((11 . 16) (15 . 19) (17 . 22) (20 . 25) (27 . 28) (28 . 29)) 5.369 {0/5:15} B:0 2.50028 [ 4.66671] ((16 . 18) (17 . 19) (24 . 26) (25 . 27) (27 . 28) (28 . 29)) 5.817 {0/10:15} B:0 2.50037 [ 4.66672] ((13 . 16) (23 . 25) (24 . 26) (25 . 27) (27 . 28) (28 . 29)) 6.255 {0/11:15} B:0 2.52424 [ 4.67044] ((13 . 16) (15 . 19) (16 . 20) (17 . 22) (27 . 28) (28 . 29)) 5.430 {1/9:15} B:0 SIMILARITY (1/min{score1}): 0.9276 [and 1/min{score2}: 0.4997] [6553, 830]: Comparing 2uag_A and 1dgm_A, based on their crossing files. There are 40 (20 H + 20 S) secondary structure elements in 2uag_A, of which 15 satisfy the size requirements. There are 28 (14 H + 14 S) secondary structure elements in 1dgm_A, of which 28 satisfy the size requirements. 1.25265 [ 2.33374] ((11 . 1) (12 . 7) (13 . 10) (17 . 15) (19 . 17) (20 . 18) (22 . 21) (23 . 24) (24 . 25) (25 . 26) (27 . 27) (28 . 28)) 5.821 {1/42:66} B:0 2.50030 [ 4.66671] ((11 . 15) (15 . 18) (16 . 20) (17 . 21) (27 . 27) (28 . 28)) 5.928 {0/6:15} B:0 2.50057 [ 4.66675] ((11 . 15) (16 . 20) (17 . 21) (23 . 26) (27 . 27) (28 . 28)) 6.942 {0/8:15} B:0 2.61544 [ 4.68557] ((11 . 15) (16 . 20) (17 . 21) (20 . 24) (27 . 27) (28 . 28)) 5.539 {1/6:15} B:0 2.82248 [ 4.72557] ((13 . 15) (15 . 18) (16 . 19) (17 . 21) (27 . 27) (28 . 28)) 5.570 {2/9:15} B:0 SIMILARITY (1/min{score1}): 0.9894 [and 1/min{score2}: 0.5352] [6553, 1076]: Comparing 2uag_A and 1e8c_A, based on their crossing files. There are 40 (20 H + 20 S) secondary structure elements in 2uag_A, of which 15 satisfy the size requirements. There are 43 (19 H + 24 S) secondary structure elements in 1e8c_A, of which 18 satisfy the size requirements. 1.66678 [ 2.00007] ((13 . 16) (15 . 18) (17 . 21) (20 . 23) (22 . 24) (24 . 26) (25 . 27) (27 . 28) (28 . 29)) 3.441 {0/24:36} B:0 1.66835 [ 2.00097] ((13 . 16) (16 . 17) (17 . 18) (19 . 20) (20 . 21) (22 . 23) (23 . 24) (27 . 28) (28 . 29)) 2.868 {1/24:36} B:0 2.21903 [ 2.61671] ((15 . 16) (16 . 17) (17 . 18) (19 . 20) (20 . 21) (22 . 23) (25 . 25)) 3.075 {2/15:21} B:0 2.50004 [ 3.00002] ((13 . 16) (15 . 18) (20 . 23) (23 . 25) (27 . 28) (28 . 29)) 3.607 {0/10:15} B:0 2.97302 [ 3.31019] ((11 . 11) (12 . 12) (15 . 16) (17 . 18) (19 . 20) (22 . 21)) 2.630 {1/4:15} B:0 SIMILARITY (1/min{score1}): 0.9976 [and 1/min{score2}: 0.8324] [6553, 1819]: Comparing 2uag_A and 1gg4_A, based on their crossing files. There are 40 (20 H + 20 S) secondary structure elements in 2uag_A, of which 15 satisfy the size requirements. There are 39 (17 H + 22 S) secondary structure elements in 1gg4_A, of which 16 satisfy the size requirements. 1.50009 [ 1.60007] ((13 . 16) (17 . 18) (19 . 19) (20 . 20) (22 . 22) (23 . 23) (24 . 24) (25 . 25) (27 . 26) (28 . 27)) 2.987 {0/29:45} B:0 1.87503 [ 2.00003] ((11 . 12) (12 . 13) (13 . 14) (15 . 16) (17 . 18) (19 . 19) (20 . 20) (25 . 23)) 2.737 {0/11:28} B:0 1.87513 [ 2.00011] ((13 . 16) (19 . 21) (22 . 22) (23 . 23) (24 . 24) (25 . 25) (27 . 26) (28 . 27)) 3.892 {0/18:28} B:0 1.87558 [ 2.00048] ((11 . 14) (13 . 16) (19 . 21) (20 . 22) (24 . 24) (25 . 25) (27 . 26) (28 . 27)) 5.629 {0/16:28} B:0 2.14294 [ 2.28578] ((11 . 12) (12 . 13) (15 . 14) (17 . 16) (19 . 17) (20 . 18) (22 . 20)) 3.839 {0/7:21} B:0 SIMILARITY (1/min{score1}): 0.9984 [and 1/min{score2}: 0.9364] [6553, 2740]: Comparing 2uag_A and 1j5v_A, based on their crossing files. There are 40 (20 H + 20 S) secondary structure elements in 2uag_A, of which 15 satisfy the size requirements. There are 28 (14 H + 14 S) secondary structure elements in 1j5v_A, of which 24 satisfy the size requirements. 1.15771 [ 1.84710] ((11 . 1) (12 . 5) (13 . 6) (15 . 8) (17 . 14) (19 . 16) (20 . 17) (22 . 19) (23 . 22) (24 . 23) (25 . 24) (27 . 26) (28 . 27)) 6.170 {1/49:78} B:0 1.25164 [ 2.00040] ((11 . 1) (12 . 5) (15 . 6) (17 . 14) (19 . 16) (20 . 17) (22 . 19) (23 . 22) (24 . 23) (25 . 24) (27 . 26) (28 . 27)) 4.969 {1/41:66} B:0 2.50035 [ 4.00009] ((11 . 14) (15 . 17) (17 . 19) (25 . 25) (27 . 26) (28 . 27)) 6.162 {0/7:15} B:0 2.50038 [ 4.00009] ((13 . 14) (15 . 17) (17 . 19) (25 . 25) (27 . 26) (28 . 27)) 6.273 {0/8:15} B:0 2.50046 [ 4.00011] ((11 . 6) (12 . 7) (13 . 8) (19 . 13) (20 . 14) (22 . 17)) 6.579 {0/7:15} B:0 SIMILARITY (1/min{score1}): 0.9312 [and 1/min{score2}: 0.5831] [6553, 2748]: Comparing 2uag_A and 1j6u_A, based on their crossing files. There are 40 (20 H + 20 S) secondary structure elements in 2uag_A, of which 15 satisfy the size requirements. There are 37 (16 H + 21 S) secondary structure elements in 1j6u_A, of which 17 satisfy the size requirements. 1.00037 [ 1.13359] ((10 . 9) (11 . 10) (12 . 11) (13 . 12) (15 . 14) (16 . 15) (17 . 16) (19 . 18) (20 . 19) (22 . 21) (23 . 22) (24 . 23) (25 . 24) (27 . 25) (28 . 26)) 2.773 {1/64:105} B:0 1.07177 [ 1.21452] ((10 . 9) (11 . 10) (12 . 11) (13 . 12) (15 . 14) (17 . 16) (19 . 18) (20 . 19) (22 . 21) (23 . 22) (24 . 23) (25 . 24) (27 . 25) (28 . 26)) 2.692 {1/58:91} B:0 1.50006 [ 1.70004] ((10 . 9) (11 . 10) (12 . 11) (13 . 12) (15 . 14) (17 . 16) (19 . 18) (20 . 21) (27 . 25) (28 . 26)) 2.693 {0/19:45} B:0 1.87505 [ 2.12504] ((10 . 9) (11 . 10) (12 . 11) (13 . 14) (19 . 18) (20 . 21) (27 . 25) (28 . 26)) 3.103 {0/14:28} B:0 2.14302 [ 2.42868] ((10 . 9) (11 . 10) (12 . 11) (15 . 12) (17 . 14) (22 . 19) (25 . 22)) 4.526 {0/10:21} B:0 SIMILARITY (1/min{score1}): 0.9996 [and 1/min{score2}: 0.8822] [6553, 2817]: Comparing 2uag_A and 1jbw_A, based on their crossing files. There are 40 (20 H + 20 S) secondary structure elements in 2uag_A, of which 15 satisfy the size requirements. There are 32 (16 H + 16 S) secondary structure elements in 1jbw_A, of which 19 satisfy the size requirements. 1.15402 [ 1.46163] ((11 . 4) (12 . 5) (13 . 6) (15 . 12) (17 . 13) (19 . 15) (20 . 16) (22 . 18) (23 . 19) (24 . 20) (25 . 21) (27 . 22) (28 . 23)) 2.904 {0/50:78} B:0 1.66678 [ 2.11117] ((13 . 12) (19 . 15) (20 . 16) (22 . 18) (23 . 19) (24 . 20) (25 . 21) (27 . 22) (28 . 23)) 3.437 {0/25:36} B:0 1.87514 [ 2.37507] ((13 . 12) (15 . 13) (19 . 17) (20 . 18) (24 . 20) (25 . 21) (27 . 22) (28 . 23)) 3.965 {0/17:28} B:0 2.14324 [ 2.71448] ((13 . 12) (17 . 16) (19 . 17) (20 . 18) (22 . 19) (27 . 22) (28 . 23)) 5.624 {0/11:21} B:0 2.14335 [ 2.71453] ((13 . 12) (15 . 13) (19 . 17) (22 . 19) (25 . 21) (27 . 22) (28 . 23)) 5.963 {0/13:21} B:0 SIMILARITY (1/min{score1}): 0.9831 [and 1/min{score2}: 0.7842] [6553, 3480]: Comparing 2uag_A and 1kyh_A, based on their crossing files. There are 40 (20 H + 20 S) secondary structure elements in 2uag_A, of which 15 satisfy the size requirements. There are 23 (14 H + 9 S) secondary structure elements in 1kyh_A, of which 19 satisfy the size requirements. 1.16006 [ 1.46461] ((11 . 2) (12 . 3) (15 . 4) (16 . 7) (17 . 8) (19 . 9) (20 . 10) (22 . 12) (23 . 16) (24 . 17) (25 . 18) (27 . 20) (28 . 21)) 4.398 {2/47:78} B:0 1.25067 [ 1.58366] ((11 . 2) (12 . 3) (15 . 4) (17 . 8) (19 . 9) (20 . 10) (22 . 12) (23 . 16) (24 . 17) (25 . 18) (27 . 20) (28 . 21)) 4.299 {0/38:66} B:0 1.49088 [ 1.66746] ((11 . 2) (12 . 3) (15 . 4) (16 . 7) (17 . 8) (19 . 9) (20 . 10) (22 . 12) (23 . 16) (24 . 17) (25 . 18) (27 . 20) (28 . 23)) 4.698 {6/45:78} B:0 1.57603 [ 1.77885] ((11 . 2) (12 . 3) (15 . 4) (17 . 8) (19 . 9) (20 . 10) (22 . 12) (23 . 16) (24 . 17) (25 . 18) (27 . 20) (28 . 23)) 4.637 {5/36:66} B:0 2.50002 [ 3.16667] ((11 . 2) (12 . 3) (15 . 4) (17 . 8) (19 . 9) (20 . 10)) 2.829 {0/2:15} B:0 SIMILARITY (1/min{score1}): 0.9137 [and 1/min{score2}: 0.7306] [6553, 3629]: Comparing 2uag_A and 1lhp_A, based on their crossing files. There are 40 (20 H + 20 S) secondary structure elements in 2uag_A, of which 15 satisfy the size requirements. There are 20 (10 H + 10 S) secondary structure elements in 1lhp_A, of which 17 satisfy the size requirements. 2.50013 [ 2.83342] ((11 . 1) (12 . 2) (13 . 3) (17 . 6) (19 . 7) (20 . 8)) 4.830 {0/2:15} B:0 2.50043 [ 2.83363] ((10 . 5) (11 . 6) (22 . 14) (24 . 15) (27 . 17) (28 . 18)) 6.466 {0/7:15} B:0 2.50095 [ 2.83399] ((11 . 6) (16 . 9) (19 . 13) (20 . 14) (27 . 17) (28 . 18)) 7.909 {0/7:15} B:0 2.50128 [ 2.83421] ((11 . 6) (13 . 8) (19 . 13) (20 . 14) (27 . 17) (28 . 18)) 8.503 {0/6:15} B:0 3.00010 [ 3.40007] ((11 . 1) (12 . 2) (15 . 3) (19 . 7) (22 . 8)) 5.210 {0/2:10} B:0 SIMILARITY (1/min{score1}): 0.7981 [and 1/min{score2}: 0.7049] [6553, 4470]: Comparing 2uag_A and 1o14_A, based on their crossing files. There are 40 (20 H + 20 S) secondary structure elements in 2uag_A, of which 15 satisfy the size requirements. There are 25 (10 H + 15 S) secondary structure elements in 1o14_A, of which 23 satisfy the size requirements. 2.14313 [ 3.28579] ((15 . 12) (17 . 14) (23 . 18) (24 . 19) (25 . 20) (27 . 22) (28 . 23)) 5.132 {0/11:21} B:0 2.50021 [ 3.83339] ((11 . 5) (12 . 6) (13 . 7) (19 . 11) (20 . 12) (22 . 14)) 5.392 {0/8:15} B:0 3.00005 [ 4.60001] ((13 . 12) (15 . 14) (19 . 17) (20 . 18) (22 . 20)) 4.340 {0/5:10} B:0 3.00014 [ 4.60004] ((13 . 12) (15 . 14) (19 . 17) (20 . 18) (23 . 20)) 5.570 {0/5:10} B:0 3.00019 [ 4.60005] ((16 . 4) (17 . 5) (19 . 6) (20 . 8) (27 . 11)) 6.042 {0/2:10} B:0 SIMILARITY (1/min{score1}): 0.8643 [and 1/min{score2}: 0.5649] [6553, 4504]: Comparing 2uag_A and 1o5z_A, based on their crossing files. There are 40 (20 H + 20 S) secondary structure elements in 2uag_A, of which 15 satisfy the size requirements. There are 36 (19 H + 17 S) secondary structure elements in 1o5z_A, of which 20 satisfy the size requirements. 1.07177 [ 1.42872] ((10 . 2) (11 . 4) (12 . 5) (13 . 6) (15 . 13) (17 . 15) (19 . 16) (20 . 17) (22 . 19) (23 . 20) (24 . 21) (25 . 22) (27 . 23) (28 . 24)) 3.251 {0/57:91} B:0 1.15398 [ 1.53852] ((11 . 4) (12 . 5) (13 . 6) (15 . 13) (17 . 15) (19 . 16) (20 . 17) (22 . 19) (23 . 20) (24 . 21) (25 . 22) (27 . 23) (28 . 24)) 2.690 {0/50:78} B:0 1.87508 [ 2.50003] ((15 . 13) (17 . 15) (19 . 18) (20 . 19) (24 . 21) (25 . 22) (27 . 23) (28 . 24)) 3.388 {0/16:28} B:0 2.50002 [ 3.33334] ((13 . 13) (17 . 17) (19 . 18) (20 . 19) (27 . 23) (28 . 24)) 2.883 {0/7:15} B:0 2.50025 [ 3.33344] ((13 . 13) (19 . 18) (20 . 19) (22 . 20) (27 . 23) (28 . 24)) 5.651 {0/9:15} B:0 SIMILARITY (1/min{score1}): 0.9330 [and 1/min{score2}: 0.6999] [6553, 4879]: Comparing 2uag_A and 1p3d_A, based on their crossing files. There are 40 (20 H + 20 S) secondary structure elements in 2uag_A, of which 15 satisfy the size requirements. There are 40 (18 H + 22 S) secondary structure elements in 1p3d_A, of which 18 satisfy the size requirements. 1.07160 [ 1.28581] ((10 . 10) (11 . 11) (12 . 12) (13 . 13) (15 . 15) (17 . 17) (19 . 19) (20 . 20) (22 . 22) (23 . 23) (24 . 25) (25 . 26) (27 . 27) (28 . 28)) 2.713 {0/51:91} B:0 1.87511 [ 2.25007] ((10 . 10) (11 . 11) (12 . 12) (15 . 15) (17 . 17) (19 . 19) (20 . 20) (25 . 24)) 3.737 {0/11:28} B:0 1.87518 [ 2.25010] ((15 . 17) (19 . 19) (20 . 20) (22 . 22) (24 . 25) (25 . 26) (27 . 27) (28 . 28)) 4.172 {0/16:28} B:0 2.14296 [ 2.57149] ((13 . 15) (15 . 17) (20 . 22) (22 . 23) (25 . 26) (27 . 27) (28 . 28)) 4.035 {0/13:21} B:0 2.14303 [ 2.57153] ((15 . 17) (19 . 21) (23 . 24) (24 . 25) (25 . 26) (27 . 27) (28 . 28)) 4.592 {0/12:21} B:0 SIMILARITY (1/min{score1}): 0.9772 [and 1/min{score2}: 0.8239] [6553, 4945]: Comparing 2uag_A and 1p9o_A, based on their crossing files. There are 40 (20 H + 20 S) secondary structure elements in 2uag_A, of which 15 satisfy the size requirements. There are 26 (11 H + 15 S) secondary structure elements in 1p9o_A, of which 21 satisfy the size requirements. 2.50028 [ 3.50010] ((13 . 12) (17 . 14) (23 . 22) (24 . 23) (25 . 24) (27 . 26)) 5.823 {0/9:15} B:0 2.50029 [ 3.50011] ((13 . 12) (17 . 14) (20 . 20) (23 . 22) (24 . 23) (27 . 26)) 5.895 {0/8:15} B:0 2.50036 [ 3.50013] ((12 . 13) (17 . 20) (19 . 21) (20 . 22) (22 . 24) (27 . 26)) 6.196 {0/7:15} B:0 3.00018 [ 4.20007] ((11 . 6) (15 . 12) (16 . 13) (17 . 14) (22 . 20)) 5.970 {0/3:10} B:0 3.00027 [ 4.20010] ((15 . 14) (19 . 21) (20 . 22) (23 . 24) (27 . 26)) 6.641 {0/6:10} B:0 SIMILARITY (1/min{score1}): 0.7945 [and 1/min{score2}: 0.5704] [6553, 5656]: Comparing 2uag_A and 1rkd, based on their crossing files. There are 40 (20 H + 20 S) secondary structure elements in 2uag_A, of which 15 satisfy the size requirements. There are 28 (14 H + 14 S) secondary structure elements in 1rkd, of which 24 satisfy the size requirements. 1.36535 [ 2.18224] ((11 . 1) (12 . 4) (15 . 5) (17 . 14) (19 . 15) (20 . 16) (23 . 21) (24 . 23) (25 . 24) (27 . 25) (28 . 26)) 4.927 {1/33:55} B:0 1.38486 [ 2.03757] ((11 . 1) (12 . 4) (15 . 5) (16 . 12) (17 . 14) (19 . 15) (20 . 16) (23 . 21) (24 . 23) (25 . 24) (27 . 25) (28 . 26)) 4.922 {4/38:66} B:0 2.14325 [ 3.42867] ((10 . 6) (17 . 16) (23 . 21) (24 . 23) (25 . 24) (27 . 25) (28 . 26)) 5.654 {0/13:21} B:0 3.00016 [ 4.80004] ((11 . 5) (12 . 6) (13 . 8) (20 . 14) (22 . 16)) 5.798 {0/5:10} B:0 3.00022 [ 4.80005] ((12 . 4) (13 . 5) (15 . 8) (20 . 14) (22 . 16)) 6.264 {0/6:10} B:0 SIMILARITY (1/min{score1}): 0.8581 [and 1/min{score2}: 0.5408] [6553, 5945]: Comparing 2uag_A and 1ua4_A, based on their crossing files. There are 40 (20 H + 20 S) secondary structure elements in 2uag_A, of which 15 satisfy the size requirements. There are 39 (21 H + 18 S) secondary structure elements in 1ua4_A, of which 33 satisfy the size requirements. 2.72463 [ 5.52396] ((13 . 7) (15 . 19) (19 . 22) (20 . 26) (27 . 27) (28 . 29)) 7.468 {2/10:15} B:0 3.00061 [ 6.60006] ((10 . 27) (11 . 28) (15 . 32) (23 . 38) (27 . 39)) 8.115 {0/4:10} B:0 3.03833 [ 6.60367] ((15 . 23) (19 . 27) (20 . 28) (27 . 31) (28 . 34)) 7.732 {1/7:10} B:0 3.06907 [ 6.60670] ((15 . 23) (17 . 26) (19 . 27) (20 . 28) (28 . 34)) 4.163 {1/6:10} B:0 3.06932 [ 6.60673] ((10 . 12) (17 . 23) (19 . 25) (20 . 26) (28 . 34)) 6.855 {1/6:10} B:0 SIMILARITY (1/min{score1}): 0.9307 [and 1/min{score2}: 0.4242] [6553, 5955]: Comparing 2uag_A and 1ub0_A, based on their crossing files. There are 40 (20 H + 20 S) secondary structure elements in 2uag_A, of which 15 satisfy the size requirements. There are 19 (8 H + 11 S) secondary structure elements in 1ub0_A, of which 17 satisfy the size requirements. 2.50008 [ 2.83339] ((17 . 9) (23 . 14) (24 . 16) (25 . 17) (27 . 18) (28 . 19)) 4.248 {0/8:15} B:0 2.50015 [ 2.83344] ((17 . 9) (22 . 14) (24 . 16) (25 . 17) (27 . 18) (28 . 19)) 4.966 {0/8:15} B:0 3.00013 [ 3.40009] ((11 . 1) (12 . 2) (17 . 7) (19 . 8) (25 . 14)) 5.457 {0/4:10} B:0 3.00014 [ 3.40009] ((17 . 9) (19 . 10) (23 . 14) (27 . 18) (28 . 19)) 5.575 {0/5:10} B:0 3.00017 [ 3.40012] ((13 . 7) (15 . 9) (20 . 14) (27 . 18) (28 . 19)) 5.890 {0/5:10} B:0 SIMILARITY (1/min{score1}): 0.7993 [and 1/min{score2}: 0.7055] [6553, 6155]: Comparing 2uag_A and 1v1a_A, based on their crossing files. There are 40 (20 H + 20 S) secondary structure elements in 2uag_A, of which 15 satisfy the size requirements. There are 27 (14 H + 13 S) secondary structure elements in 1v1a_A, of which 24 satisfy the size requirements. 1.25154 [ 2.00038] ((11 . 1) (12 . 5) (15 . 6) (17 . 13) (19 . 15) (20 . 16) (22 . 18) (23 . 21) (24 . 23) (25 . 24) (27 . 25) (28 . 26)) 4.863 {1/41:66} B:0 1.36535 [ 2.18224] ((11 . 1) (12 . 5) (15 . 6) (17 . 13) (19 . 15) (20 . 16) (22 . 18) (23 . 21) (24 . 23) (27 . 25) (28 . 26)) 4.566 {1/31:55} B:0 2.14387 [ 3.42882] ((10 . 7) (17 . 16) (19 . 17) (24 . 23) (25 . 24) (27 . 25) (28 . 26)) 7.149 {0/13:21} B:0 2.50005 [ 4.00001] ((13 . 13) (15 . 16) (17 . 18) (19 . 20) (20 . 21) (22 . 24)) 3.737 {0/7:15} B:0 2.50025 [ 4.00006] ((15 . 13) (16 . 15) (17 . 16) (19 . 17) (27 . 25) (28 . 26)) 5.642 {0/5:15} B:0 SIMILARITY (1/min{score1}): 0.8650 [and 1/min{score2}: 0.5415] [6553, 6194]: Comparing 2uag_A and 1v8a_A, based on their crossing files. There are 40 (20 H + 20 S) secondary structure elements in 2uag_A, of which 15 satisfy the size requirements. There are 21 (12 H + 9 S) secondary structure elements in 1v8a_A, of which 21 satisfy the size requirements. 2.50020 [ 3.50007] ((11 . 2) (16 . 7) (17 . 8) (24 . 14) (25 . 15) (27 . 17)) 5.382 {0/9:15} B:0 2.50038 [ 3.50014] ((12 . 3) (16 . 7) (17 . 8) (23 . 13) (27 . 17) (28 . 18)) 6.286 {0/8:15} B:0 3.00008 [ 4.20003] ((11 . 2) (12 . 3) (16 . 7) (17 . 8) (19 . 9)) 4.903 {0/3:10} B:0 3.00013 [ 4.20005] ((11 . 2) (12 . 3) (13 . 4) (22 . 10) (25 . 13)) 5.555 {0/7:10} B:0 3.00025 [ 4.20009] ((12 . 7) (15 . 8) (17 . 10) (20 . 13) (22 . 15)) 6.474 {0/5:10} B:0 SIMILARITY (1/min{score1}): 0.8655 [and 1/min{score2}: 0.6188] [6553, 6261]: Comparing 2uag_A and 1vi9_A, based on their crossing files. There are 40 (20 H + 20 S) secondary structure elements in 2uag_A, of which 15 satisfy the size requirements. There are 26 (13 H + 13 S) secondary structure elements in 1vi9_A, of which 19 satisfy the size requirements. 1.25222 [ 1.58443] ((11 . 1) (12 . 2) (15 . 3) (16 . 7) (17 . 9) (19 . 10) (20 . 11) (22 . 19) (24 . 21) (25 . 22) (27 . 23) (28 . 24)) 4.263 {1/30:66} B:0 2.14346 [ 2.71458] ((10 . 7) (15 . 11) (22 . 19) (24 . 21) (25 . 22) (27 . 23) (28 . 24)) 6.277 {0/8:21} B:0 2.14346 [ 2.71458] ((10 . 7) (11 . 9) (15 . 11) (22 . 19) (25 . 22) (27 . 23) (28 . 24)) 6.284 {0/8:21} B:0 2.50003 [ 3.16668] ((11 . 1) (12 . 2) (13 . 3) (17 . 9) (19 . 10) (20 . 11)) 3.278 {0/3:15} B:0 2.50026 [ 3.16679] ((10 . 7) (11 . 9) (20 . 19) (23 . 22) (27 . 23) (28 . 24)) 5.689 {0/6:15} B:0 SIMILARITY (1/min{score1}): 0.7993 [and 1/min{score2}: 0.6314] [6553, 6304]: Comparing 2uag_A and 1vk4_A, based on their crossing files. There are 40 (20 H + 20 S) secondary structure elements in 2uag_A, of which 15 satisfy the size requirements. There are 28 (13 H + 15 S) secondary structure elements in 1vk4_A, of which 27 satisfy the size requirements. 2.14317 [ 3.85720] ((17 . 14) (19 . 18) (23 . 22) (24 . 23) (25 . 24) (27 . 26) (28 . 27)) 5.341 {0/14:21} B:0 2.15531 [ 3.85930] ((15 . 12) (17 . 14) (19 . 18) (20 . 19) (25 . 24) (27 . 26) (28 . 27)) 5.331 {1/12:21} B:0 3.00006 [ 5.40001] ((11 . 5) (13 . 8) (17 . 12) (19 . 13) (20 . 14)) 4.480 {0/2:10} B:0 3.00010 [ 5.40002] ((12 . 4) (15 . 8) (19 . 11) (20 . 12) (22 . 14)) 5.207 {0/5:10} B:0 3.00011 [ 5.40002] ((12 . 4) (13 . 5) (15 . 8) (19 . 13) (20 . 14)) 5.267 {0/3:10} B:0 SIMILARITY (1/min{score1}): 0.9314 [and 1/min{score2}: 0.5184] [6553, 6553]: Comparing 2uag_A and 2uag_A, based on their crossing files. There are 40 (20 H + 20 S) secondary structure elements in 2uag_A, of which 15 satisfy the size requirements. There are 40 (20 H + 20 S) secondary structure elements in 2uag_A, of which 15 satisfy the size requirements. 1.00000 [ 1.00000] ((10 . 10) (11 . 11) (12 . 12) (13 . 13) (15 . 15) (16 . 16) (17 . 17) (19 . 19) (20 . 20) (22 . 22) (23 . 23) (24 . 24) (25 . 25) (27 . 27) (28 . 28)) 0.000 {0/73:105} B:0 1.36364 [ 1.36364] ((10 . 10) (11 . 11) (12 . 12) (13 . 13) (15 . 15) (16 . 16) (17 . 17) (19 . 19) (20 . 22) (27 . 27) (28 . 28)) 1.428 {0/29:55} B:0 1.36364 [ 1.36364] ((10 . 10) (11 . 11) (12 . 12) (13 . 13) (15 . 15) (16 . 16) (17 . 17) (19 . 19) (22 . 20) (27 . 27) (28 . 28)) 1.428 {0/29:55} B:0 3.00112 [ 3.00112] ((12 . 10) (15 . 13) (19 . 19) (22 . 20) (25 . 23)) 9.433 {0/7:10} B:0 3.00112 [ 3.00112] ((10 . 12) (13 . 15) (19 . 19) (20 . 22) (23 . 25)) 9.433 {0/7:10} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] -------------------------------------------------------------------------------------------------------------------------