------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [3175, 611]: Comparing 1k4n_A and 1cjx_A, based on their crossing files. There are 15 (6 H + 9 S) secondary structure elements in 1k4n_A, of which 14 satisfy the size requirements. There are 28 (11 H + 17 S) secondary structure elements in 1cjx_A, of which 12 satisfy the size requirements. 1.40079 [ 1.20125] ((3 . 1) (4 . 2) (5 . 3) (6 . 4) (8 . 5) (9 . 7) (10 . 8) (13 . 9) (14 . 11) (15 . 12)) 3.639 {1/36:45} B:0 1.55678 [ 1.33527] ((3 . 1) (4 . 2) (5 . 3) (6 . 4) (8 . 5) (9 . 7) (10 . 8) (13 . 9) (14 . 11)) 3.435 {1/28:36} B:0 1.66219 [ 1.49075] ((3 . 1) (4 . 2) (5 . 3) (6 . 4) (8 . 5) (9 . 7) (11 . 8) (13 . 9) (14 . 11)) 4.397 {3/26:36} B:0 2.34105 [ 2.01221] ((3 . 1) (4 . 2) (5 . 3) (7 . 4) (9 . 7) (10 . 8)) 7.331 {1/13:15} B:0 3.50026 [ 3.00041] ((2 . 8) (3 . 11) (4 . 12) (5 . 13)) 7.337 {0/6:6} B:0 SIMILARITY (1/min{score1}): 0.7139 [and 1/min{score2}: 0.8325] [3175, 612]: Comparing 1k4n_A and 1cjx_A, based on their crossing files. There are 15 (6 H + 9 S) secondary structure elements in 1k4n_A, of which 14 satisfy the size requirements. There are 28 (11 H + 17 S) secondary structure elements in 1cjx_A, of which 14 satisfy the size requirements. 1.41799 [ 1.41799] ((3 . 14) (4 . 16) (5 . 17) (6 . 18) (8 . 19) (9 . 21) (11 . 24) (12 . 25) (13 . 26) (14 . 27)) 7.516 {2/32:45} B:0 1.55986 [ 1.55986] ((3 . 14) (4 . 16) (5 . 17) (6 . 18) (8 . 19) (9 . 21) (12 . 25) (13 . 26) (14 . 27)) 7.420 {1/27:36} B:0 1.56022 [ 1.56022] ((3 . 14) (4 . 16) (5 . 17) (6 . 18) (8 . 19) (9 . 21) (10 . 22) (13 . 26) (14 . 27)) 7.515 {1/26:36} B:0 2.80006 [ 2.80006] ((4 . 16) (5 . 17) (6 . 18) (9 . 21) (10 . 22)) 4.242 {0/7:10} B:0 2.80008 [ 2.80008] ((4 . 16) (5 . 17) (6 . 18) (8 . 19) (9 . 21)) 4.690 {0/5:10} B:0 SIMILARITY (1/min{score1}): 0.7052 [and 1/min{score2}: 0.7052] [3175, 1105]: Comparing 1k4n_A and 1ecs_A, based on their crossing files. There are 15 (6 H + 9 S) secondary structure elements in 1k4n_A, of which 14 satisfy the size requirements. There are 11 (3 H + 8 S) secondary structure elements in 1ecs_A, of which 10 satisfy the size requirements. 2.80003 [ 2.00007] ((3 . 7) (4 . 8) (5 . 9) (6 . 10) (8 . 11)) 3.534 {0/5:10} B:0 2.88405 [ 2.20686] ((3 . 1) (4 . 2) (5 . 3) (6 . 4) (8 . 5)) 3.795 {1/6:10} B:0 2.96676 [ 2.37849] ((9 . 7) (10 . 8) (12 . 9) (13 . 10) (14 . 11)) 3.989 {1/5:10} B:0 3.36429 [ 3.01509] ((7 . 1) (9 . 7) (12 . 9) (13 . 10) (14 . 11)) 3.784 {2/7:10} B:0 3.50023 [ 2.50064] ((3 . 7) (4 . 8) (7 . 10) (8 . 11)) 7.152 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.4530 [and 1/min{score2}: 0.5384] [3175, 1365]: Comparing 1k4n_A and 1f1u_A, based on their crossing files. There are 15 (6 H + 9 S) secondary structure elements in 1k4n_A, of which 14 satisfy the size requirements. There are 26 (8 H + 18 S) secondary structure elements in 1f1u_A, of which 10 satisfy the size requirements. 1.40106 [ 1.00289] ((3 . 1) (4 . 2) (5 . 3) (6 . 4) (8 . 5) (9 . 6) (10 . 7) (12 . 8) (13 . 9) (14 . 10)) 4.060 {1/34:45} B:0 2.33350 [ 1.66712] ((3 . 1) (4 . 2) (5 . 3) (6 . 4) (10 . 7) (12 . 10)) 4.843 {0/12:15} B:0 2.80034 [ 2.00094] ((3 . 6) (4 . 7) (5 . 8) (7 . 9) (8 . 10)) 6.669 {0/6:10} B:0 2.96676 [ 2.37849] ((9 . 1) (11 . 2) (12 . 3) (13 . 4) (14 . 5)) 4.067 {1/5:10} B:0 3.39493 [ 3.34971] ((3 . 1) (4 . 2) (6 . 3) (9 . 6) (10 . 7) (12 . 8) (13 . 9) (14 . 10)) 3.654 {7/21:28} B:0 SIMILARITY (1/min{score1}): 0.7142 [and 1/min{score2}: 0.9994] [3175, 1366]: Comparing 1k4n_A and 1f1u_A, based on their crossing files. There are 15 (6 H + 9 S) secondary structure elements in 1k4n_A, of which 14 satisfy the size requirements. There are 26 (8 H + 18 S) secondary structure elements in 1f1u_A, of which 12 satisfy the size requirements. 1.40167 [ 1.20265] ((3 . 12) (4 . 13) (5 . 14) (6 . 15) (8 . 16) (9 . 17) (10 . 18) (12 . 20) (13 . 21) (14 . 22)) 4.454 {1/30:45} B:0 1.40232 [ 1.20368] ((3 . 12) (4 . 13) (5 . 14) (6 . 15) (8 . 16) (9 . 17) (11 . 18) (12 . 20) (13 . 21) (14 . 22)) 4.964 {1/28:45} B:0 1.55796 [ 1.33714] ((3 . 12) (4 . 13) (6 . 15) (8 . 16) (9 . 17) (10 . 18) (12 . 20) (13 . 21) (14 . 22)) 4.478 {1/24:36} B:0 2.80044 [ 2.40070] ((3 . 17) (4 . 18) (5 . 20) (7 . 21) (8 . 22)) 7.107 {0/5:10} B:0 2.80060 [ 2.40095] ((3 . 17) (4 . 18) (5 . 20) (6 . 21) (10 . 25)) 7.654 {0/7:10} B:0 SIMILARITY (1/min{score1}): 0.7140 [and 1/min{score2}: 0.8328] [3175, 1451]: Comparing 1k4n_A and 1f9z_A, based on their crossing files. There are 15 (6 H + 9 S) secondary structure elements in 1k4n_A, of which 14 satisfy the size requirements. There are 10 (2 H + 8 S) secondary structure elements in 1f9z_A, of which 10 satisfy the size requirements. 2.37902 [ 2.11995] ((6 . 1) (7 . 5) (9 . 6) (10 . 7) (12 . 8) (13 . 9) (14 . 10)) 6.800 {2/10:21} B:0 2.80003 [ 2.00008] ((3 . 1) (4 . 2) (5 . 3) (6 . 4) (8 . 5)) 3.557 {0/5:10} B:0 2.80004 [ 2.00010] ((9 . 6) (10 . 7) (12 . 8) (13 . 9) (14 . 10)) 3.792 {0/4:10} B:0 2.80006 [ 2.00017] ((9 . 1) (10 . 2) (12 . 3) (13 . 4) (14 . 5)) 4.353 {0/4:10} B:0 2.80040 [ 2.00111] ((8 . 5) (10 . 7) (12 . 8) (13 . 9) (14 . 10)) 6.942 {0/1:10} B:0 SIMILARITY (1/min{score1}): 0.4203 [and 1/min{score2}: 0.5000] [3175, 2819]: Comparing 1k4n_A and 1jc4_A, based on their crossing files. There are 15 (6 H + 9 S) secondary structure elements in 1k4n_A, of which 14 satisfy the size requirements. There are 12 (4 H + 8 S) secondary structure elements in 1jc4_A, of which 11 satisfy the size requirements. 1.55699 [ 1.22517] ((3 . 1) (4 . 2) (5 . 3) (6 . 4) (8 . 5) (9 . 7) (10 . 8) (13 . 10) (14 . 12)) 4.330 {1/28:36} B:0 3.50030 [ 2.75063] ((5 . 4) (6 . 5) (8 . 7) (13 . 12)) 7.647 {0/4:6} B:0 3.50230 [ 2.75473] ((5 . 1) (8 . 3) (10 . 6) (12 . 7)) 12.680 {0/4:6} B:0 3.50322 [ 2.75662] ((2 . 2) (6 . 7) (10 . 11) (12 . 12)) 13.794 {0/4:6} B:0 3.70864 [ 3.13262] ((6 . 3) (8 . 4) (14 . 10) (15 . 11)) 7.464 {1/4:6} B:0 SIMILARITY (1/min{score1}): 0.6423 [and 1/min{score2}: 0.8162] [3175, 2890]: Comparing 1k4n_A and 1jif_A, based on their crossing files. There are 15 (6 H + 9 S) secondary structure elements in 1k4n_A, of which 14 satisfy the size requirements. There are 12 (3 H + 9 S) secondary structure elements in 1jif_A, of which 11 satisfy the size requirements. 2.96694 [ 2.50615] ((3 . 1) (9 . 7) (10 . 8) (13 . 11) (14 . 12)) 6.195 {1/5:10} B:0 3.16648 [ 2.81163] ((9 . 1) (11 . 2) (12 . 3) (13 . 4) (14 . 5)) 4.203 {1/4:10} B:0 3.50048 [ 2.75098] ((9 . 1) (10 . 2) (12 . 5) (15 . 8)) 8.556 {0/2:6} B:0 3.50280 [ 2.75575] ((3 . 3) (5 . 5) (7 . 7) (9 . 10)) 13.319 {0/4:6} B:0 3.70858 [ 3.13253] ((4 . 8) (7 . 10) (8 . 11) (9 . 12)) 6.964 {1/4:6} B:0 SIMILARITY (1/min{score1}): 0.3370 [and 1/min{score2}: 0.3990] [3175, 3175]: Comparing 1k4n_A and 1k4n_A, based on their crossing files. There are 15 (6 H + 9 S) secondary structure elements in 1k4n_A, of which 14 satisfy the size requirements. There are 15 (6 H + 9 S) secondary structure elements in 1k4n_A, of which 14 satisfy the size requirements. 1.00000 [ 1.00000] ((2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12) (13 . 13) (14 . 14) (15 . 15)) 0.000 {0/78:91} B:0 2.41139 [ 2.41139] ((2 . 2) (3 . 3) (4 . 4) (7 . 7) (8 . 9) (15 . 15)) 4.257 {2/14:15} B:0 2.81770 [ 2.81770] ((2 . 2) (4 . 4) (7 . 6) (9 . 9) (15 . 15)) 7.364 {1/9:10} B:0 2.96680 [ 2.96680] ((2 . 2) (4 . 4) (7 . 7) (9 . 8) (15 . 15)) 4.761 {2/10:10} B:0 3.50056 [ 3.50056] ((4 . 2) (12 . 6) (13 . 8) (15 . 10)) 8.902 {0/4:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [3175, 3347]: Comparing 1k4n_A and 1kll_A, based on their crossing files. There are 15 (6 H + 9 S) secondary structure elements in 1k4n_A, of which 14 satisfy the size requirements. There are 12 (5 H + 7 S) secondary structure elements in 1kll_A, of which 11 satisfy the size requirements. 2.59981 [ 2.28664] ((2 . 2) (3 . 8) (4 . 9) (5 . 10) (6 . 11) (8 . 12)) 7.266 {1/5:15} B:0 2.80004 [ 2.20008] ((9 . 8) (10 . 9) (12 . 10) (13 . 11) (14 . 12)) 3.906 {0/3:10} B:0 2.80004 [ 2.20009] ((3 . 8) (4 . 9) (5 . 10) (6 . 11) (8 . 12)) 3.931 {0/4:10} B:0 2.80103 [ 2.20212] ((2 . 7) (3 . 8) (4 . 9) (5 . 10) (6 . 11)) 8.772 {0/7:10} B:0 2.87917 [ 2.66409] ((7 . 4) (9 . 8) (10 . 9) (12 . 10) (13 . 11) (14 . 12)) 5.423 {1/4:15} B:0 SIMILARITY (1/min{score1}): 0.4146 [and 1/min{score2}: 0.4545] [3175, 3456]: Comparing 1k4n_A and 1kw3_B, based on their crossing files. There are 15 (6 H + 9 S) secondary structure elements in 1k4n_A, of which 14 satisfy the size requirements. There are 24 (6 H + 18 S) secondary structure elements in 1kw3_B, of which 10 satisfy the size requirements. 1.57555 [ 1.16327] ((3 . 1) (4 . 2) (5 . 3) (6 . 4) (8 . 5) (9 . 6) (10 . 7) (13 . 10) (14 . 11)) 4.433 {2/27:36} B:0 2.82747 [ 2.07246] ((3 . 1) (4 . 2) (5 . 3) (6 . 4) (12 . 11)) 4.495 {1/8:10} B:0 3.50025 [ 2.50069] ((3 . 6) (4 . 7) (7 . 10) (8 . 11)) 7.287 {0/3:6} B:0 3.50114 [ 2.50312] ((2 . 2) (3 . 3) (5 . 5) (12 . 11)) 10.636 {0/5:6} B:0 3.70869 [ 2.97356] ((10 . 7) (11 . 9) (13 . 10) (14 . 11)) 7.835 {1/4:6} B:0 SIMILARITY (1/min{score1}): 0.6427 [and 1/min{score2}: 0.8993] [3175, 3457]: Comparing 1k4n_A and 1kw3_B, based on their crossing files. There are 15 (6 H + 9 S) secondary structure elements in 1k4n_A, of which 14 satisfy the size requirements. There are 24 (6 H + 18 S) secondary structure elements in 1kw3_B, of which 11 satisfy the size requirements. 1.40284 [ 1.10583] ((3 . 13) (4 . 14) (5 . 15) (6 . 16) (8 . 17) (9 . 18) (10 . 19) (12 . 20) (13 . 21) (14 . 22)) 6.730 {0/31:45} B:0 1.55633 [ 1.22382] ((3 . 13) (4 . 14) (5 . 15) (6 . 16) (8 . 17) (9 . 18) (10 . 19) (13 . 21) (14 . 22)) 5.262 {0/24:36} B:0 1.55931 [ 1.22991] ((3 . 13) (4 . 14) (5 . 15) (6 . 16) (8 . 17) (9 . 18) (11 . 19) (13 . 21) (14 . 22)) 5.501 {1/22:36} B:0 1.75039 [ 1.37580] ((3 . 13) (4 . 14) (5 . 15) (6 . 16) (8 . 17) (9 . 18) (13 . 21) (14 . 22)) 4.836 {0/18:28} B:0 2.80023 [ 2.20047] ((9 . 13) (10 . 14) (12 . 15) (13 . 16) (14 . 17)) 6.020 {0/4:10} B:0 SIMILARITY (1/min{score1}): 0.7128 [and 1/min{score2}: 0.9043] [3175, 4006]: Comparing 1k4n_A and 1mpy_A, based on their crossing files. There are 15 (6 H + 9 S) secondary structure elements in 1k4n_A, of which 14 satisfy the size requirements. There are 23 (6 H + 17 S) secondary structure elements in 1mpy_A, of which 10 satisfy the size requirements. 1.41262 [ 1.03339] ((3 . 1) (4 . 2) (5 . 3) (6 . 4) (8 . 5) (9 . 6) (10 . 7) (12 . 8) (13 . 9) (14 . 10)) 4.356 {2/33:45} B:0 2.80029 [ 2.00079] ((3 . 6) (4 . 7) (5 . 8) (7 . 9) (8 . 10)) 6.389 {0/7:10} B:0 2.82746 [ 2.07244] ((3 . 1) (4 . 2) (5 . 3) (6 . 4) (12 . 10)) 4.418 {1/8:10} B:0 3.50016 [ 2.50044] ((12 . 4) (13 . 5) (14 . 6) (15 . 7)) 6.511 {0/3:6} B:0 3.50049 [ 2.50133] ((3 . 1) (4 . 2) (8 . 6) (12 . 10)) 8.594 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.7141 [and 1/min{score2}: 0.9991] [3175, 4007]: Comparing 1k4n_A and 1mpy_A, based on their crossing files. There are 15 (6 H + 9 S) secondary structure elements in 1k4n_A, of which 14 satisfy the size requirements. There are 23 (6 H + 17 S) secondary structure elements in 1mpy_A, of which 13 satisfy the size requirements. 1.40052 [ 1.30065] ((3 . 11) (4 . 12) (5 . 13) (6 . 14) (8 . 15) (9 . 16) (10 . 17) (12 . 18) (13 . 19) (14 . 20)) 4.406 {0/30:45} B:0 1.42398 [ 1.32969] ((3 . 11) (4 . 12) (5 . 13) (6 . 14) (8 . 15) (9 . 16) (11 . 17) (12 . 18) (13 . 19) (14 . 20)) 5.019 {2/28:45} B:0 1.55594 [ 1.44493] ((3 . 11) (4 . 12) (6 . 14) (8 . 15) (9 . 16) (10 . 17) (12 . 18) (13 . 19) (14 . 20)) 4.424 {0/24:36} B:0 2.80009 [ 2.60012] ((3 . 11) (4 . 12) (5 . 13) (6 . 14) (12 . 20)) 4.809 {0/6:10} B:0 2.80056 [ 2.60070] ((3 . 16) (4 . 17) (5 . 18) (6 . 19) (10 . 23)) 7.550 {0/7:10} B:0 SIMILARITY (1/min{score1}): 0.7140 [and 1/min{score2}: 0.7688] [3175, 4284]: Comparing 1k4n_A and 1nki_A, based on their crossing files. There are 15 (6 H + 9 S) secondary structure elements in 1k4n_A, of which 14 satisfy the size requirements. There are 12 (3 H + 9 S) secondary structure elements in 1nki_A, of which 11 satisfy the size requirements. 2.80002 [ 2.20005] ((3 . 1) (4 . 2) (5 . 3) (6 . 4) (8 . 5)) 3.367 {0/5:10} B:0 2.80009 [ 2.20019] ((3 . 6) (4 . 7) (5 . 8) (6 . 9) (8 . 10)) 4.788 {0/6:10} B:0 2.80078 [ 2.20160] ((3 . 1) (4 . 2) (5 . 3) (6 . 4) (9 . 8)) 8.181 {0/6:10} B:0 3.16649 [ 2.81163] ((9 . 1) (11 . 2) (12 . 3) (13 . 4) (14 . 5)) 4.309 {1/4:10} B:0 3.50047 [ 2.75097] ((2 . 2) (3 . 6) (6 . 9) (8 . 10)) 8.518 {0/1:6} B:0 SIMILARITY (1/min{score1}): 0.4232 [and 1/min{score2}: 0.5283] [3175, 5349]: Comparing 1k4n_A and 1qip_A, based on their crossing files. There are 15 (6 H + 9 S) secondary structure elements in 1k4n_A, of which 14 satisfy the size requirements. There are 16 (8 H + 8 S) secondary structure elements in 1qip_A, of which 15 satisfy the size requirements. 2.80230 [ 3.00187] ((4 . 4) (9 . 11) (10 . 12) (13 . 14) (14 . 15)) 10.730 {0/6:10} B:0 2.82911 [ 3.02375] ((2 . 10) (3 . 11) (4 . 12) (5 . 13) (6 . 14)) 10.031 {1/8:10} B:0 2.84635 [ 3.03791] ((3 . 11) (4 . 12) (5 . 13) (6 . 14) (8 . 15)) 4.661 {1/7:10} B:0 3.50011 [ 3.75009] ((9 . 3) (10 . 4) (14 . 9) (15 . 10)) 5.903 {0/3:6} B:0 3.50139 [ 3.75113] ((3 . 3) (4 . 4) (8 . 9) (11 . 12)) 11.178 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.3568 [and 1/min{score2}: 0.3436] [3175, 5597]: Comparing 1k4n_A and 1r9c_A, based on their crossing files. There are 15 (6 H + 9 S) secondary structure elements in 1k4n_A, of which 14 satisfy the size requirements. There are 11 (4 H + 7 S) secondary structure elements in 1r9c_A, of which 10 satisfy the size requirements. 2.80002 [ 2.00005] ((9 . 1) (10 . 2) (12 . 3) (13 . 5) (14 . 6)) 3.129 {0/4:10} B:0 2.80003 [ 2.00008] ((3 . 1) (4 . 2) (5 . 3) (6 . 5) (8 . 6)) 3.632 {0/4:10} B:0 2.80004 [ 2.00012] ((7 . 1) (9 . 7) (10 . 8) (13 . 9) (14 . 10)) 3.942 {0/5:10} B:0 3.16647 [ 2.72409] ((9 . 1) (11 . 2) (12 . 3) (13 . 5) (14 . 6)) 3.928 {1/4:10} B:0 3.50001 [ 2.50002] ((9 . 7) (10 . 8) (13 . 9) (14 . 10)) 3.102 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.3571 [and 1/min{score2}: 0.5000] -------------------------------------------------------------------------------------------------------------------------