------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [5191, 1389]: Comparing 1q33_A and 1f3y_A, based on their crossing files. There are 21 (8 H + 13 S) secondary structure elements in 1q33_A, of which 11 satisfy the size requirements. There are 12 (5 H + 7 S) secondary structure elements in 1f3y_A, of which 11 satisfy the size requirements. 1.57226 [ 1.57226] ((10 . 1) (11 . 2) (14 . 5) (17 . 6) (18 . 8) (19 . 10) (20 . 12)) 5.388 {0/16:21} B:0 1.83356 [ 1.83356] ((10 . 1) (11 . 2) (14 . 5) (18 . 8) (19 . 10) (20 . 12)) 4.356 {0/12:15} B:0 1.83716 [ 1.83716] ((10 . 1) (11 . 4) (14 . 5) (17 . 6) (18 . 8) (20 . 12)) 8.873 {0/10:15} B:0 2.20196 [ 2.20196] ((10 . 1) (11 . 4) (14 . 5) (17 . 6) (18 . 8)) 8.599 {0/6:10} B:0 2.29233 [ 2.29233] ((11 . 1) (14 . 5) (18 . 8) (19 . 10) (20 . 12)) 6.164 {1/7:10} B:0 SIMILARITY (1/min{score1}): 0.6360 [and 1/min{score2}: 0.6360] [5191, 1669]: Comparing 1q33_A and 1g0s_A, based on their crossing files. There are 21 (8 H + 13 S) secondary structure elements in 1q33_A, of which 11 satisfy the size requirements. There are 17 (7 H + 10 S) secondary structure elements in 1g0s_A, of which 15 satisfy the size requirements. 1.37936 [ 1.87673] ((9 . 4) (10 . 5) (11 . 6) (14 . 10) (17 . 11) (18 . 12) (19 . 14) (20 . 16)) 3.717 {1/22:28} B:0 1.57256 [ 2.14330] ((10 . 5) (11 . 6) (14 . 10) (17 . 11) (18 . 12) (19 . 14) (20 . 17)) 5.825 {0/16:21} B:0 2.25764 [ 3.02336] ((14 . 7) (17 . 11) (18 . 12) (19 . 14) (20 . 16)) 9.247 {1/8:10} B:0 2.83973 [ 3.78662] ((3 . 3) (10 . 9) (11 . 12) (16 . 16)) 9.446 {1/6:6} B:0 2.92608 [ 3.82417] ((11 . 5) (16 . 7) (18 . 8) (20 . 15)) 9.318 {1/5:6} B:0 SIMILARITY (1/min{score1}): 0.7250 [and 1/min{score2}: 0.5385] [5191, 2351]: Comparing 1q33_A and 1hzt_A, based on their crossing files. There are 21 (8 H + 13 S) secondary structure elements in 1q33_A, of which 11 satisfy the size requirements. There are 15 (5 H + 10 S) secondary structure elements in 1hzt_A, of which 13 satisfy the size requirements. 1.58474 [ 1.86526] ((10 . 2) (11 . 3) (14 . 6) (17 . 7) (18 . 10) (19 . 11) (20 . 15)) 5.260 {1/15:21} B:0 2.75081 [ 3.25049] ((10 . 2) (11 . 5) (14 . 6) (20 . 15)) 8.154 {0/4:6} B:0 2.75094 [ 3.25057] ((17 . 7) (18 . 9) (19 . 11) (20 . 14)) 8.463 {0/4:6} B:0 2.75114 [ 3.25069] ((11 . 3) (14 . 6) (17 . 8) (18 . 10)) 8.880 {0/5:6} B:0 2.75142 [ 3.25086] ((17 . 8) (18 . 10) (19 . 11) (20 . 14)) 9.389 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.6310 [and 1/min{score2}: 0.5361] [5191, 2586]: Comparing 1q33_A and 1iry_A, based on their crossing files. There are 21 (8 H + 13 S) secondary structure elements in 1q33_A, of which 11 satisfy the size requirements. There are 11 (2 H + 9 S) secondary structure elements in 1iry_A, of which 9 satisfy the size requirements. 1.57183 [ 1.28645] ((10 . 1) (11 . 3) (14 . 5) (17 . 6) (18 . 7) (19 . 8) (20 . 9)) 4.507 {0/14:21} B:0 2.75057 [ 2.25104] ((10 . 6) (11 . 7) (14 . 9) (17 . 11)) 7.470 {0/1:6} B:0 2.75142 [ 2.25258] ((10 . 6) (11 . 7) (16 . 9) (17 . 11)) 9.375 {0/1:6} B:0 2.75212 [ 2.25386] ((10 . 1) (11 . 3) (14 . 5) (18 . 8)) 10.367 {0/4:6} B:0 2.75294 [ 2.25535] ((10 . 1) (11 . 3) (14 . 5) (19 . 11)) 11.254 {0/5:6} B:0 SIMILARITY (1/min{score1}): 0.6362 [and 1/min{score2}: 0.7773] [5191, 3141]: Comparing 1q33_A and 1k2e_A, based on their crossing files. There are 21 (8 H + 13 S) secondary structure elements in 1q33_A, of which 11 satisfy the size requirements. There are 13 (3 H + 10 S) secondary structure elements in 1k2e_A, of which 11 satisfy the size requirements. 1.58672 [ 1.58672] ((10 . 1) (11 . 3) (14 . 6) (17 . 9) (18 . 10) (19 . 11) (20 . 13)) 7.301 {1/15:21} B:0 2.20047 [ 2.20047] ((10 . 1) (11 . 3) (14 . 6) (18 . 10) (20 . 13)) 6.015 {0/8:10} B:0 2.75281 [ 2.75281] ((10 . 7) (11 . 10) (14 . 12) (16 . 13)) 11.129 {0/4:6} B:0 2.92598 [ 2.92598] ((11 . 1) (14 . 6) (18 . 10) (20 . 13)) 9.124 {1/5:6} B:0 2.92759 [ 2.92759] ((9 . 8) (10 . 9) (11 . 10) (14 . 13)) 11.497 {1/5:6} B:0 SIMILARITY (1/min{score1}): 0.6302 [and 1/min{score2}: 0.6302] [5191, 3428]: Comparing 1q33_A and 1ktg_A, based on their crossing files. There are 21 (8 H + 13 S) secondary structure elements in 1q33_A, of which 11 satisfy the size requirements. There are 12 (4 H + 8 S) secondary structure elements in 1ktg_A, of which 10 satisfy the size requirements. 1.57163 [ 1.42884] ((10 . 1) (11 . 2) (14 . 5) (17 . 8) (18 . 9) (19 . 10) (20 . 12)) 3.783 {0/13:21} B:0 1.57233 [ 1.42977] ((10 . 1) (11 . 2) (14 . 5) (17 . 7) (18 . 9) (19 . 10) (20 . 12)) 5.503 {0/15:21} B:0 2.75133 [ 2.50178] ((10 . 7) (11 . 9) (14 . 11) (16 . 12)) 9.237 {0/3:6} B:0 3.08071 [ 3.01516] ((10 . 1) (11 . 2) (14 . 5) (17 . 9) (20 . 12)) 5.116 {2/7:10} B:0 4.18763 [ 4.18104] ((10 . 1) (11 . 2) (16 . 5) (17 . 8) (18 . 9) (19 . 10) (20 . 12)) 5.570 {5/12:21} B:0 SIMILARITY (1/min{score1}): 0.6363 [and 1/min{score2}: 0.6999] [5191, 4000]: Comparing 1q33_A and 1mp2_A, based on their crossing files. There are 21 (8 H + 13 S) secondary structure elements in 1q33_A, of which 11 satisfy the size requirements. There are 15 (4 H + 11 S) secondary structure elements in 1mp2_A, of which 15 satisfy the size requirements. 1.87693 [ 2.05676] ((3 . 2) (9 . 3) (10 . 4) (11 . 5) (14 . 8) (17 . 10) (18 . 11) (19 . 12) (20 . 14)) 5.161 {5/28:36} B:0 2.75794 [ 3.75314] ((10 . 1) (17 . 10) (18 . 11) (20 . 14)) 14.442 {0/3:6} B:0 2.92061 [ 3.06061] ((3 . 3) (10 . 4) (11 . 5) (14 . 8) (17 . 10) (18 . 11) (20 . 13)) 6.268 {4/14:21} B:0 2.92560 [ 3.82395] ((9 . 3) (10 . 4) (11 . 7) (14 . 8)) 8.152 {1/5:6} B:0 2.92618 [ 3.82421] ((9 . 3) (10 . 4) (14 . 8) (17 . 12)) 9.514 {1/5:6} B:0 SIMILARITY (1/min{score1}): 0.5328 [and 1/min{score2}: 0.4862] [5191, 4044]: Comparing 1q33_A and 1mut, based on their crossing files. There are 21 (8 H + 13 S) secondary structure elements in 1q33_A, of which 11 satisfy the size requirements. There are 11 (2 H + 9 S) secondary structure elements in 1mut, of which 7 satisfy the size requirements. 4.20725 [ 4.03665] ((16 . 6) (18 . 9) (19 . 10) (20 . 11)) 9.672 {2/5:6} B:0 SIMILARITY (1/min{score1}): 0.2377 [and 1/min{score2}: 0.2477] [5191, 4358]: Comparing 1q33_A and 1nqz_A, based on their crossing files. There are 21 (8 H + 13 S) secondary structure elements in 1q33_A, of which 11 satisfy the size requirements. There are 17 (6 H + 11 S) secondary structure elements in 1nqz_A, of which 15 satisfy the size requirements. 1.57202 [ 2.14309] ((10 . 2) (11 . 3) (14 . 6) (17 . 8) (18 . 10) (19 . 12) (20 . 17)) 4.947 {0/15:21} B:0 1.57212 [ 2.14313] ((10 . 2) (11 . 3) (14 . 6) (17 . 9) (18 . 10) (19 . 12) (20 . 17)) 5.145 {0/13:21} B:0 2.07352 [ 2.40532] ((10 . 2) (11 . 3) (14 . 6) (17 . 8) (18 . 10) (19 . 12) (20 . 13)) 6.558 {3/16:21} B:0 2.75040 [ 3.75016] ((10 . 2) (14 . 6) (19 . 16) (20 . 17)) 6.831 {0/5:6} B:0 2.75107 [ 3.75042] ((10 . 2) (11 . 5) (17 . 8) (18 . 10)) 8.739 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.6749 [and 1/min{score2}: 0.5207] [5191, 5185]: Comparing 1q33_A and 1q27_A, based on their crossing files. There are 21 (8 H + 13 S) secondary structure elements in 1q33_A, of which 11 satisfy the size requirements. There are 11 (3 H + 8 S) secondary structure elements in 1q27_A, of which 11 satisfy the size requirements. 1.57179 [ 1.57179] ((10 . 3) (11 . 4) (14 . 6) (17 . 7) (18 . 8) (19 . 9) (20 . 11)) 4.386 {0/14:21} B:0 5.11093 [ 5.11093] ((11 . 1) (16 . 6) (17 . 5) (18 . 7)) 9.888 {2/4:6} B:1 5.04651 [ 5.04651] ((11 . 1) (16 . 6) (17 . 8) (18 . 3) (19 . 2)) 10.079 {3/6:10} B:2 SIMILARITY (1/min{score1}): 0.6362 [and 1/min{score2}: 0.6362] [5191, 5191]: Comparing 1q33_A and 1q33_A, based on their crossing files. There are 21 (8 H + 13 S) secondary structure elements in 1q33_A, of which 11 satisfy the size requirements. There are 21 (8 H + 13 S) secondary structure elements in 1q33_A, of which 11 satisfy the size requirements. 1.00000 [ 1.00000] ((3 . 3) (4 . 4) (9 . 9) (10 . 10) (11 . 11) (14 . 14) (16 . 16) (17 . 17) (18 . 18) (19 . 19) (20 . 20)) 0.000 {0/48:55} B:0 4.20952 [ 4.20952] ((11 . 3) (14 . 4) (18 . 10) (20 . 14)) 15.180 {2/5:6} B:0 4.20952 [ 4.20952] ((3 . 11) (4 . 14) (10 . 18) (14 . 20)) 15.180 {2/5:6} B:0 5.11071 [ 5.11071] ((3 . 3) (4 . 4) (14 . 16) (20 . 20)) 6.498 {3/6:6} B:0 5.11071 [ 5.11071] ((3 . 3) (4 . 4) (16 . 14) (20 . 20)) 6.498 {3/6:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [5191, 5696]: Comparing 1q33_A and 1rrq_A, based on their crossing files. There are 21 (8 H + 13 S) secondary structure elements in 1q33_A, of which 11 satisfy the size requirements. There are 26 (18 H + 8 S) secondary structure elements in 1rrq_A, of which 10 satisfy the size requirements. 1.57160 [ 1.42880] ((10 . 16) (11 . 17) (14 . 20) (17 . 22) (18 . 23) (19 . 24) (20 . 26)) 3.616 {0/14:21} B:0 2.75165 [ 2.50220] ((10 . 21) (11 . 23) (14 . 25) (16 . 26)) 9.742 {0/5:6} B:0 3.87271 [ 3.86436] ((10 . 16) (11 . 17) (16 . 20) (17 . 22) (18 . 23) (19 . 24) (20 . 26)) 4.817 {5/13:21} B:0 4.20686 [ 4.14462] ((10 . 16) (11 . 17) (14 . 20) (17 . 23)) 5.777 {2/5:6} B:0 5.11072 [ 5.07642] ((16 . 20) (18 . 22) (19 . 24) (20 . 26)) 6.865 {2/4:6} B:0 SIMILARITY (1/min{score1}): 0.6363 [and 1/min{score2}: 0.6999] [5191, 5822]: Comparing 1q33_A and 1sjy_A, based on their crossing files. There are 21 (8 H + 13 S) secondary structure elements in 1q33_A, of which 11 satisfy the size requirements. There are 11 (3 H + 8 S) secondary structure elements in 1sjy_A, of which 10 satisfy the size requirements. 1.57182 [ 1.42909] ((10 . 1) (11 . 2) (14 . 5) (17 . 6) (18 . 8) (19 . 9) (20 . 11)) 4.472 {0/16:21} B:0 2.20219 [ 2.00292] ((10 . 1) (11 . 2) (14 . 5) (18 . 9) (20 . 11)) 8.848 {0/7:10} B:0 2.75037 [ 2.50049] ((11 . 1) (18 . 8) (19 . 9) (20 . 11)) 6.698 {0/3:6} B:0 2.75178 [ 2.50237] ((10 . 6) (11 . 8) (14 . 10) (16 . 11)) 9.932 {0/4:6} B:0 4.20687 [ 4.14462] ((16 . 5) (18 . 8) (19 . 9) (20 . 11)) 5.857 {2/5:6} B:0 SIMILARITY (1/min{score1}): 0.6362 [and 1/min{score2}: 0.6997] [5191, 6252]: Comparing 1q33_A and 1vhz_A, based on their crossing files. There are 21 (8 H + 13 S) secondary structure elements in 1q33_A, of which 11 satisfy the size requirements. There are 14 (3 H + 11 S) secondary structure elements in 1vhz_A, of which 14 satisfy the size requirements. 1.82447 [ 1.95821] ((3 . 2) (9 . 3) (10 . 4) (11 . 5) (14 . 8) (17 . 10) (18 . 11) (19 . 12) (20 . 14)) 5.306 {5/29:36} B:0 1.88896 [ 2.07494] ((3 . 2) (10 . 4) (11 . 5) (14 . 8) (17 . 10) (18 . 11) (19 . 12) (20 . 14)) 4.966 {4/23:28} B:0 2.75012 [ 3.50006] ((9 . 1) (11 . 5) (14 . 8) (20 . 14)) 5.071 {0/4:6} B:0 2.81172 [ 3.16655] ((9 . 1) (14 . 8) (17 . 10) (18 . 11) (20 . 14)) 5.434 {2/8:10} B:0 3.08083 [ 3.36444] ((11 . 4) (17 . 10) (18 . 11) (19 . 12) (20 . 14)) 6.352 {2/7:10} B:0 SIMILARITY (1/min{score1}): 0.5481 [and 1/min{score2}: 0.5107] [5191, 6271]: Comparing 1q33_A and 1viu_A, based on their crossing files. There are 21 (8 H + 13 S) secondary structure elements in 1q33_A, of which 11 satisfy the size requirements. There are 14 (4 H + 10 S) secondary structure elements in 1viu_A, of which 14 satisfy the size requirements. 1.37957 [ 1.75222] ((3 . 3) (10 . 4) (11 . 5) (14 . 9) (17 . 10) (18 . 11) (19 . 12) (20 . 14)) 4.267 {1/22:28} B:0 2.12950 [ 2.21768] ((3 . 2) (9 . 3) (10 . 4) (11 . 5) (14 . 9) (17 . 10) (18 . 11) (19 . 12) (20 . 14)) 4.925 {6/29:36} B:0 2.25755 [ 2.82859] ((14 . 6) (17 . 10) (18 . 11) (19 . 12) (20 . 14)) 9.160 {1/8:10} B:0 3.13401 [ 3.70947] ((16 . 6) (17 . 7) (18 . 8) (19 . 10)) 10.932 {1/4:6} B:0 3.66666 [ 4.06713] ((3 . 2) (10 . 8) (11 . 11) (16 . 14)) 9.098 {2/6:6} B:0 SIMILARITY (1/min{score1}): 0.7249 [and 1/min{score2}: 0.5707] [5191, 6305]: Comparing 1q33_A and 1vk6_A, based on their crossing files. There are 21 (8 H + 13 S) secondary structure elements in 1q33_A, of which 11 satisfy the size requirements. There are 23 (6 H + 17 S) secondary structure elements in 1vk6_A, of which 10 satisfy the size requirements. 2.20020 [ 2.00027] ((10 . 2) (11 . 3) (17 . 7) (18 . 8) (20 . 11)) 4.865 {0/6:10} B:0 5.11113 [ 5.07684] ((10 . 3) (11 . 8) (14 . 11) (17 . 13)) 11.346 {2/4:6} B:0 6.06515 [ 6.04474] ((16 . 6) (17 . 7) (18 . 8) (20 . 11)) 6.368 {3/5:6} B:0 SIMILARITY (1/min{score1}): 0.4545 [and 1/min{score2}: 0.4999] [5191, 6306]: Comparing 1q33_A and 1vk6_A, based on their crossing files. There are 21 (8 H + 13 S) secondary structure elements in 1q33_A, of which 11 satisfy the size requirements. There are 23 (6 H + 17 S) secondary structure elements in 1vk6_A, of which 9 satisfy the size requirements. 1.57165 [ 1.28611] ((10 . 15) (11 . 16) (14 . 18) (17 . 19) (18 . 21) (19 . 22) (20 . 23)) 3.863 {0/14:21} B:0 2.20191 [ 1.80348] ((10 . 15) (11 . 16) (14 . 18) (18 . 22) (20 . 23)) 8.544 {0/5:10} B:0 3.87276 [ 3.85819] ((10 . 15) (11 . 16) (16 . 18) (17 . 19) (18 . 21) (19 . 22) (20 . 23)) 5.959 {5/13:21} B:0 5.11070 [ 5.05053] ((16 . 18) (18 . 21) (19 . 22) (20 . 23)) 6.312 {2/4:6} B:0 5.11078 [ 5.05062] ((16 . 18) (18 . 20) (19 . 22) (20 . 23)) 8.132 {1/2:6} B:0 SIMILARITY (1/min{score1}): 0.6363 [and 1/min{score2}: 0.7775] -------------------------------------------------------------------------------------------------------------------------