------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [790, 22]: Comparing 1dce_A and 1a25_A, based on their crossing files. There are 36 (22 H + 14 S) secondary structure elements in 1dce_A, of which 7 satisfy the size requirements. There are 11 (3 H + 8 S) secondary structure elements in 1a25_A, of which 9 satisfy the size requirements. 1.00127 [ 1.28631] ((12 . 1) (13 . 2) (14 . 3) (16 . 5) (18 . 7) (19 . 8) (20 . 10)) 4.276 {0/10:21} B:0 1.75062 [ 2.25029] ((12 . 1) (13 . 2) (14 . 3) (19 . 7)) 5.426 {0/2:6} B:0 1.75473 [ 2.25223] ((12 . 3) (14 . 5) (16 . 8) (18 . 10)) 9.039 {0/4:6} B:0 3.39515 [ 3.49451] ((12 . 1) (13 . 2) (14 . 3) (20 . 8)) 7.048 {1/3:6} B:0 6.00216 [ 6.00587] ((12 . 1) (13 . 2) (16 . 5) (18 . 3) (19 . 7) (20 . 8)) 5.450 {3/5:15} B:1 SIMILARITY (1/min{score1}): 0.9987 [and 1/min{score2}: 0.7774] [790, 357]: Comparing 1dce_A and 1bdy_A, based on their crossing files. There are 36 (22 H + 14 S) secondary structure elements in 1dce_A, of which 7 satisfy the size requirements. There are 10 (2 H + 8 S) secondary structure elements in 1bdy_A, of which 10 satisfy the size requirements. 1.17015 [ 1.66786] ((13 . 1) (14 . 2) (16 . 5) (18 . 6) (19 . 7) (20 . 9)) 6.176 {0/7:15} B:0 1.40750 [ 2.00259] ((12 . 2) (14 . 5) (16 . 7) (18 . 9) (19 . 10)) 8.589 {0/6:10} B:0 1.75075 [ 2.50026] ((16 . 4) (18 . 5) (19 . 6) (20 . 7)) 5.705 {0/4:6} B:0 1.75227 [ 2.50078] ((12 . 2) (13 . 4) (14 . 5) (16 . 7)) 7.522 {0/3:6} B:0 1.75690 [ 2.50238] ((12 . 4) (13 . 5) (14 . 6) (18 . 10)) 9.937 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.9973 [and 1/min{score2}: 0.6995] [790, 613]: Comparing 1dce_A and 1cjy_A, based on their crossing files. There are 36 (22 H + 14 S) secondary structure elements in 1dce_A, of which 7 satisfy the size requirements. There are 53 (28 H + 25 S) secondary structure elements in 1cjy_A, of which 8 satisfy the size requirements. 1.40860 [ 1.60578] ((12 . 3) (14 . 5) (16 . 7) (18 . 8) (19 . 9)) 8.889 {0/6:10} B:0 1.75316 [ 2.00212] ((13 . 5) (14 . 6) (16 . 8) (18 . 9)) 8.168 {0/2:6} B:0 3.39516 [ 3.43668] ((12 . 6) (13 . 7) (14 . 8) (16 . 9)) 7.060 {1/3:6} B:0 1.00345 [ 1.14517] ((12 . 9) (13 . 1) (14 . 3) (16 . 5) (18 . 6) (19 . 7) (20 . 8)) 5.490 {0/9:21} B:1 6.36462 [ 6.36530] ((12 . 3) (13 . 6) (14 . 8) (16 . 7) (18 . 9) (19 . 1) (20 . 5)) 5.483 {7/11:21} B:2 SIMILARITY (1/min{score1}): 0.9966 [and 1/min{score2}: 0.8732] [790, 755]: Comparing 1dce_A and 1d5r_A, based on their crossing files. There are 36 (22 H + 14 S) secondary structure elements in 1dce_A, of which 7 satisfy the size requirements. There are 23 (8 H + 15 S) secondary structure elements in 1d5r_A, of which 10 satisfy the size requirements. 1.16791 [ 1.66709] ((13 . 11) (14 . 12) (16 . 15) (18 . 17) (19 . 18) (20 . 20)) 4.767 {0/7:15} B:0 1.40169 [ 2.00058] ((14 . 11) (16 . 13) (18 . 15) (19 . 17) (20 . 18)) 5.909 {0/6:10} B:0 1.40644 [ 2.00222] ((12 . 11) (13 . 12) (14 . 13) (16 . 17) (19 . 20)) 8.265 {0/5:10} B:0 1.75100 [ 2.50034] ((16 . 16) (18 . 17) (19 . 18) (20 . 20)) 6.120 {0/4:6} B:0 1.75136 [ 2.50047] ((16 . 11) (18 . 12) (19 . 13) (20 . 15)) 6.608 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.9990 [and 1/min{score2}: 0.6998] [790, 790]: Comparing 1dce_A and 1dce_A, based on their crossing files. There are 36 (22 H + 14 S) secondary structure elements in 1dce_A, of which 7 satisfy the size requirements. There are 36 (22 H + 14 S) secondary structure elements in 1dce_A, of which 7 satisfy the size requirements. 1.00000 [ 1.00000] ((12 . 12) (13 . 13) (14 . 14) (16 . 16) (18 . 18) (19 . 19) (20 . 20)) 0.000 {0/11:21} B:0 1.75399 [ 1.75399] ((14 . 12) (16 . 14) (19 . 16) (20 . 18)) 8.660 {0/4:6} B:0 1.75399 [ 1.75399] ((12 . 14) (14 . 16) (16 . 19) (18 . 20)) 8.660 {0/4:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [790, 1068]: Comparing 1dce_A and 1e7u_A, based on their crossing files. There are 36 (22 H + 14 S) secondary structure elements in 1dce_A, of which 7 satisfy the size requirements. There are 61 (37 H + 24 S) secondary structure elements in 1e7u_A, of which 8 satisfy the size requirements. 1.16905 [ 1.33493] ((13 . 13) (14 . 14) (16 . 17) (18 . 19) (19 . 20) (20 . 21)) 5.614 {0/7:15} B:0 1.40884 [ 1.60594] ((12 . 13) (13 . 14) (14 . 15) (16 . 19) (19 . 21)) 8.951 {0/6:10} B:0 1.41225 [ 1.60825] ((12 . 13) (13 . 14) (14 . 15) (16 . 19) (18 . 20)) 9.721 {0/5:10} B:0 1.75040 [ 2.00027] ((12 . 17) (13 . 19) (14 . 20) (19 . 24)) 4.881 {0/2:6} B:0 1.75093 [ 2.00063] ((16 . 15) (18 . 17) (19 . 19) (20 . 20)) 6.019 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.9993 [and 1/min{score2}: 0.8746] [790, 1874]: Comparing 1dce_A and 1gmi_A, based on their crossing files. There are 36 (22 H + 14 S) secondary structure elements in 1dce_A, of which 7 satisfy the size requirements. There are 10 (2 H + 8 S) secondary structure elements in 1gmi_A, of which 9 satisfy the size requirements. 1.40084 [ 1.80040] ((14 . 3) (16 . 5) (18 . 6) (19 . 7) (20 . 9)) 4.959 {0/6:10} B:0 1.40513 [ 1.80242] ((13 . 3) (14 . 4) (16 . 6) (19 . 9) (20 . 10)) 7.806 {0/5:10} B:0 1.40619 [ 1.80292] ((12 . 3) (14 . 5) (16 . 7) (18 . 9) (19 . 10)) 8.182 {0/6:10} B:0 1.40871 [ 1.80412] ((12 . 1) (13 . 3) (14 . 4) (16 . 6) (18 . 7)) 8.917 {0/5:10} B:0 1.75079 [ 2.25037] ((16 . 1) (18 . 3) (19 . 4) (20 . 5)) 5.771 {0/1:6} B:0 SIMILARITY (1/min{score1}): 0.9993 [and 1/min{score2}: 0.7776] [790, 3187]: Comparing 1dce_A and 1k5w_A, based on their crossing files. There are 36 (22 H + 14 S) secondary structure elements in 1dce_A, of which 7 satisfy the size requirements. There are 10 (2 H + 8 S) secondary structure elements in 1k5w_A, of which 10 satisfy the size requirements. 1.17807 [ 1.67062] ((13 . 1) (14 . 2) (16 . 4) (18 . 5) (19 . 6) (20 . 7)) 8.330 {0/7:15} B:0 1.40021 [ 2.00007] ((12 . 1) (13 . 2) (14 . 3) (16 . 5) (18 . 6)) 3.526 {0/5:10} B:0 1.40714 [ 2.00246] ((12 . 2) (13 . 3) (14 . 4) (16 . 6) (18 . 7)) 8.483 {0/4:10} B:0 1.75084 [ 2.50029] ((16 . 2) (18 . 3) (19 . 4) (20 . 5)) 5.860 {0/2:6} B:0 1.75086 [ 2.50030] ((12 . 5) (13 . 6) (14 . 7) (18 . 9)) 5.897 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.9996 [and 1/min{score2}: 0.6999] [790, 3534]: Comparing 1dce_A and 1l4i_A, based on their crossing files. There are 36 (22 H + 14 S) secondary structure elements in 1dce_A, of which 7 satisfy the size requirements. There are 19 (2 H + 17 S) secondary structure elements in 1l4i_A, of which 7 satisfy the size requirements. 1.75129 [ 1.75129] ((14 . 12) (16 . 14) (18 . 16) (19 . 17)) 6.522 {0/4:6} B:0 3.39503 [ 3.39503] ((12 . 12) (13 . 13) (14 . 14) (18 . 19)) 5.826 {1/3:6} B:0 3.39513 [ 3.39513] ((13 . 12) (14 . 14) (16 . 17) (18 . 18)) 6.860 {1/3:6} B:0 3.39524 [ 3.39524] ((12 . 12) (13 . 13) (14 . 14) (16 . 18)) 7.628 {1/3:6} B:0 5.01870 [ 5.01870] ((12 . 13) (13 . 14) (14 . 16) (16 . 19)) 6.413 {2/4:6} B:0 SIMILARITY (1/min{score1}): 0.5710 [and 1/min{score2}: 0.5710] [790, 4909]: Comparing 1dce_A and 1p5v_A, based on their crossing files. There are 36 (22 H + 14 S) secondary structure elements in 1dce_A, of which 7 satisfy the size requirements. There are 18 (1 H + 17 S) secondary structure elements in 1p5v_A, of which 7 satisfy the size requirements. 1.16731 [ 1.16731] ((12 . 11) (13 . 12) (14 . 13) (16 . 16) (18 . 17) (19 . 18)) 4.047 {0/8:15} B:0 3.35904 [ 3.35904] ((12 . 11) (13 . 12) (14 . 13) (16 . 16) (18 . 18)) 5.165 {2/6:10} B:0 3.39519 [ 3.39519] ((12 . 11) (13 . 12) (14 . 13) (16 . 17)) 7.312 {1/3:6} B:0 7.50562 [ 7.50562] ((14 . 11) (16 . 13) (19 . 17) (20 . 18)) 9.262 {3/4:6} B:0 8.33500 [ 8.33500] ((12 . 11) (13 . 12) (14 . 17) (16 . 16) (18 . 18)) 4.843 {5/6:10} B:1 SIMILARITY (1/min{score1}): 0.8567 [and 1/min{score2}: 0.8567] [790, 5270]: Comparing 1dce_A and 1qas_A, based on their crossing files. There are 36 (22 H + 14 S) secondary structure elements in 1dce_A, of which 7 satisfy the size requirements. There are 41 (21 H + 20 S) secondary structure elements in 1qas_A, of which 9 satisfy the size requirements. 1.16860 [ 1.50091] ((13 . 31) (14 . 32) (16 . 34) (18 . 36) (19 . 37) (20 . 39)) 5.331 {0/6:15} B:0 1.40853 [ 1.80404] ((12 . 31) (13 . 32) (14 . 33) (16 . 36) (18 . 37)) 8.872 {0/4:10} B:0 1.75068 [ 2.25032] ((16 . 31) (18 . 32) (19 . 33) (20 . 34)) 5.557 {0/1:6} B:0 1.75105 [ 2.25049] ((12 . 32) (13 . 33) (14 . 34) (16 . 37)) 6.196 {0/2:6} B:0 1.75129 [ 2.25061] ((12 . 33) (13 . 34) (14 . 36) (16 . 39)) 6.530 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.9998 [and 1/min{score2}: 0.7777] [790, 5414]: Comparing 1dce_A and 1qpx_A, based on their crossing files. There are 36 (22 H + 14 S) secondary structure elements in 1dce_A, of which 7 satisfy the size requirements. There are 22 (4 H + 18 S) secondary structure elements in 1qpx_A, of which 9 satisfy the size requirements. 1.00103 [ 1.28620] ((12 . 14) (13 . 15) (14 . 16) (16 . 19) (18 . 20) (19 . 21) (20 . 22)) 4.056 {0/11:21} B:0 1.75064 [ 2.25030] ((16 . 15) (18 . 16) (19 . 18) (20 . 19)) 5.484 {0/3:6} B:0 1.75193 [ 2.25091] ((14 . 15) (18 . 19) (19 . 20) (20 . 21)) 7.219 {0/3:6} B:0 1.75289 [ 2.25136] ((14 . 14) (16 . 16) (19 . 19) (20 . 20)) 7.988 {0/5:6} B:0 3.35901 [ 3.40208] ((12 . 14) (13 . 15) (14 . 16) (16 . 19) (19 . 22)) 4.639 {2/6:10} B:0 SIMILARITY (1/min{score1}): 0.9993 [and 1/min{score2}: 0.7776] [790, 5631]: Comparing 1dce_A and 1rh8_A, based on their crossing files. There are 36 (22 H + 14 S) secondary structure elements in 1dce_A, of which 7 satisfy the size requirements. There are 12 (4 H + 8 S) secondary structure elements in 1rh8_A, of which 11 satisfy the size requirements. 1.75970 [ 2.75252] ((13 . 7) (14 . 9) (16 . 10) (18 . 12)) 10.828 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.5683 [and 1/min{score2}: 0.3633] [790, 5700]: Comparing 1dce_A and 1rsy, based on their crossing files. There are 36 (22 H + 14 S) secondary structure elements in 1dce_A, of which 7 satisfy the size requirements. There are 11 (3 H + 8 S) secondary structure elements in 1rsy, of which 9 satisfy the size requirements. 1.00145 [ 1.28640] ((12 . 2) (13 . 3) (14 . 4) (16 . 6) (18 . 8) (19 . 9) (20 . 11)) 4.416 {0/10:21} B:0 1.75065 [ 2.25031] ((12 . 2) (13 . 3) (14 . 4) (19 . 8)) 5.503 {0/2:6} B:0 1.75356 [ 2.25168] ((14 . 2) (16 . 4) (19 . 6) (20 . 8)) 8.417 {0/3:6} B:0 1.75952 [ 2.25450] ((14 . 2) (18 . 4) (19 . 6) (20 . 8)) 10.777 {0/2:6} B:0 3.39524 [ 3.49459] ((12 . 2) (13 . 3) (14 . 4) (20 . 9)) 7.616 {1/3:6} B:0 SIMILARITY (1/min{score1}): 0.9986 [and 1/min{score2}: 0.7774] [790, 6015]: Comparing 1dce_A and 1ugk_A, based on their crossing files. There are 36 (22 H + 14 S) secondary structure elements in 1dce_A, of which 7 satisfy the size requirements. There are 10 (2 H + 8 S) secondary structure elements in 1ugk_A, of which 9 satisfy the size requirements. 1.40074 [ 1.80035] ((14 . 4) (16 . 6) (18 . 8) (19 . 9) (20 . 10)) 4.808 {0/6:10} B:0 1.40096 [ 1.80045] ((12 . 1) (13 . 3) (14 . 4) (16 . 6) (18 . 8)) 5.130 {0/4:10} B:0 1.40522 [ 1.80247] ((13 . 1) (14 . 3) (16 . 5) (19 . 8) (20 . 9)) 7.839 {0/5:10} B:0 1.40696 [ 1.80329] ((14 . 1) (16 . 4) (18 . 5) (19 . 6) (20 . 8)) 8.428 {0/4:10} B:0 1.41016 [ 1.80481] ((12 . 3) (13 . 4) (14 . 5) (16 . 8) (18 . 9)) 9.271 {0/4:10} B:0 SIMILARITY (1/min{score1}): 0.9996 [and 1/min{score2}: 0.7777] [790, 6156]: Comparing 1dce_A and 1v27_A, based on their crossing files. There are 36 (22 H + 14 S) secondary structure elements in 1dce_A, of which 7 satisfy the size requirements. There are 9 (2 H + 7 S) secondary structure elements in 1v27_A, of which 7 satisfy the size requirements. 1.16814 [ 1.16814] ((12 . 1) (13 . 2) (14 . 3) (18 . 6) (19 . 7) (20 . 9)) 4.982 {0/4:15} B:0 1.75065 [ 1.75065] ((12 . 1) (13 . 2) (14 . 3) (19 . 6)) 5.501 {0/1:6} B:0 1.75273 [ 1.75273] ((12 . 2) (13 . 3) (19 . 7) (20 . 9)) 7.874 {0/0:6} B:0 5.00771 [ 5.00771] ((12 . 1) (13 . 2) (14 . 3) (18 . 6) (20 . 7)) 6.193 {1/2:10} B:0 5.00772 [ 5.00772] ((12 . 1) (13 . 2) (18 . 3) (19 . 6) (20 . 7)) 6.355 {1/2:10} B:0 SIMILARITY (1/min{score1}): 0.8561 [and 1/min{score2}: 0.8561] [790, 6331]: Comparing 1dce_A and 1who, based on their crossing files. There are 36 (22 H + 14 S) secondary structure elements in 1dce_A, of which 7 satisfy the size requirements. There are 10 (0 H + 10 S) secondary structure elements in 1who, of which 6 satisfy the size requirements. 1.16782 [ 1.00183] ((12 . 1) (13 . 2) (14 . 3) (16 . 6) (18 . 7) (19 . 8)) 4.686 {0/8:15} B:0 1.40068 [ 1.20108] ((12 . 1) (14 . 3) (16 . 6) (18 . 7) (19 . 8)) 4.701 {0/7:10} B:0 1.75195 [ 1.50309] ((13 . 1) (16 . 6) (18 . 7) (19 . 8)) 7.236 {0/2:6} B:0 1.75258 [ 1.50408] ((14 . 1) (16 . 3) (19 . 6) (20 . 7)) 7.761 {0/4:6} B:0 3.35912 [ 3.34740] ((12 . 1) (13 . 2) (14 . 3) (16 . 6) (18 . 8)) 6.251 {2/6:10} B:0 SIMILARITY (1/min{score1}): 0.8571 [and 1/min{score2}: 0.9998] [790, 6594]: Comparing 1dce_A and 3rpb_A, based on their crossing files. There are 36 (22 H + 14 S) secondary structure elements in 1dce_A, of which 7 satisfy the size requirements. There are 9 (2 H + 7 S) secondary structure elements in 3rpb_A, of which 9 satisfy the size requirements. 1.00158 [ 1.28646] ((12 . 1) (13 . 2) (14 . 3) (16 . 4) (18 . 6) (19 . 7) (20 . 9)) 4.511 {0/9:21} B:0 1.75077 [ 2.25036] ((12 . 4) (13 . 6) (14 . 7) (18 . 9)) 5.732 {0/2:6} B:0 2.11080 [ 2.26903] ((12 . 2) (14 . 3) (16 . 4) (18 . 6) (19 . 7)) 5.010 {1/5:10} B:0 3.39621 [ 3.49548] ((13 . 4) (14 . 6) (16 . 7) (19 . 9)) 10.735 {1/3:6} B:0 5.01876 [ 5.05059] ((12 . 1) (13 . 2) (14 . 3) (20 . 7)) 7.695 {1/2:6} B:0 SIMILARITY (1/min{score1}): 0.9984 [and 1/min{score2}: 0.7773] -------------------------------------------------------------------------------------------------------------------------