------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [3805, 204]: Comparing 1m2o_A and 1atz_A, based on their crossing files. There are 52 (25 H + 27 S) secondary structure elements in 1m2o_A, of which 15 satisfy the size requirements. There are 14 (8 H + 6 S) secondary structure elements in 1atz_A, of which 14 satisfy the size requirements. 1.26960 [ 1.19060] ((12 . 1) (13 . 2) (14 . 3) (15 . 4) (20 . 5) (21 . 6) (22 . 7) (24 . 8) (25 . 9) (26 . 10) (27 . 12) (28 . 13)) 4.069 {1/16:66} B:0 1.26973 [ 1.19076] ((12 . 1) (13 . 2) (14 . 3) (15 . 4) (20 . 5) (21 . 6) (22 . 7) (24 . 8) (25 . 9) (26 . 10) (27 . 12) (28 . 14)) 4.309 {1/16:66} B:0 3.00004 [ 2.80005] ((12 . 1) (13 . 2) (14 . 3) (15 . 4) (21 . 8)) 4.192 {0/2:10} B:0 3.00007 [ 2.80009] ((14 . 1) (20 . 5) (21 . 6) (22 . 7) (25 . 12)) 4.755 {0/1:10} B:0 3.00022 [ 2.80027] ((12 . 1) (13 . 2) (14 . 3) (15 . 4) (21 . 10)) 6.285 {0/2:10} B:0 SIMILARITY (1/min{score1}): 0.7876 [and 1/min{score2}: 0.8399] [3805, 2514]: Comparing 1m2o_A and 1ijb_A, based on their crossing files. There are 52 (25 H + 27 S) secondary structure elements in 1m2o_A, of which 15 satisfy the size requirements. There are 13 (7 H + 6 S) secondary structure elements in 1ijb_A, of which 12 satisfy the size requirements. 1.26943 [ 1.03676] ((12 . 1) (13 . 2) (14 . 3) (15 . 4) (20 . 5) (21 . 6) (22 . 7) (24 . 9) (25 . 10) (26 . 11) (27 . 12) (28 . 13)) 3.663 {1/16:66} B:0 2.50008 [ 2.00015] ((12 . 1) (13 . 2) (14 . 3) (15 . 4) (21 . 9) (22 . 10)) 4.245 {0/3:15} B:0 3.00008 [ 2.40016] ((14 . 1) (20 . 5) (21 . 6) (22 . 7) (24 . 11)) 4.916 {0/0:10} B:0 3.00011 [ 2.40021] ((12 . 1) (13 . 2) (14 . 3) (15 . 4) (17 . 6)) 5.237 {0/3:10} B:0 3.00017 [ 2.40034] ((14 . 1) (16 . 3) (20 . 5) (21 . 6) (22 . 10)) 5.908 {0/3:10} B:0 SIMILARITY (1/min{score1}): 0.7878 [and 1/min{score2}: 0.9645] [3805, 2842]: Comparing 1m2o_A and 1jey_A, based on their crossing files. There are 52 (25 H + 27 S) secondary structure elements in 1m2o_A, of which 15 satisfy the size requirements. There are 37 (18 H + 19 S) secondary structure elements in 1jey_A, of which 12 satisfy the size requirements. 1.55878 [ 1.40190] ((12 . 1) (13 . 3) (14 . 4) (15 . 5) (20 . 6) (21 . 8) (22 . 9) (24 . 10) (25 . 11) (26 . 12) (28 . 13)) 4.215 {1/8:55} B:0 1.87649 [ 1.50290] ((12 . 1) (13 . 3) (14 . 4) (15 . 5) (20 . 6) (22 . 9) (24 . 12) (26 . 13)) 7.125 {0/2:28} B:0 2.50024 [ 2.00047] ((12 . 1) (14 . 4) (15 . 5) (21 . 8) (22 . 9) (24 . 12)) 5.609 {0/2:15} B:0 3.00010 [ 2.40019] ((12 . 1) (13 . 3) (21 . 8) (22 . 9) (24 . 12)) 5.125 {0/0:10} B:0 3.00012 [ 2.40024] ((12 . 1) (20 . 6) (21 . 8) (22 . 9) (24 . 12)) 5.433 {0/0:10} B:0 SIMILARITY (1/min{score1}): 0.6659 [and 1/min{score2}: 0.8309] [3805, 2844]: Comparing 1m2o_A and 1jey_B, based on their crossing files. There are 52 (25 H + 27 S) secondary structure elements in 1m2o_A, of which 15 satisfy the size requirements. There are 41 (20 H + 21 S) secondary structure elements in 1jey_B, of which 14 satisfy the size requirements. 1.25091 [ 1.16778] ((12 . 1) (13 . 3) (14 . 4) (15 . 5) (20 . 6) (21 . 7) (22 . 8) (24 . 9) (25 . 10) (26 . 11) (27 . 13) (28 . 14)) 4.645 {0/14:66} B:0 1.25124 [ 1.16820] ((12 . 1) (13 . 3) (14 . 4) (15 . 5) (20 . 6) (21 . 7) (22 . 8) (24 . 9) (25 . 10) (26 . 11) (27 . 13) (28 . 15)) 5.025 {0/15:66} B:0 2.14315 [ 2.00037] ((12 . 1) (13 . 3) (20 . 6) (21 . 7) (22 . 10) (24 . 11) (28 . 15)) 5.262 {0/0:21} B:0 2.50011 [ 2.33347] ((14 . 1) (20 . 6) (21 . 7) (22 . 8) (26 . 11) (27 . 13)) 4.588 {0/2:15} B:0 2.50015 [ 2.33351] ((14 . 1) (20 . 6) (21 . 7) (22 . 8) (24 . 11) (27 . 13)) 4.950 {0/2:15} B:0 SIMILARITY (1/min{score1}): 0.7994 [and 1/min{score2}: 0.8563] [3805, 3795]: Comparing 1m2o_A and 1m1x_B, based on their crossing files. There are 52 (25 H + 27 S) secondary structure elements in 1m2o_A, of which 15 satisfy the size requirements. There are 42 (14 H + 28 S) secondary structure elements in 1m1x_B, of which 16 satisfy the size requirements. 1.45517 [ 1.53157] ((12 . 6) (13 . 8) (14 . 9) (20 . 12) (21 . 13) (22 . 15) (24 . 18) (25 . 19) (26 . 20) (27 . 21) (28 . 22)) 6.435 {1/10:55} B:0 1.56991 [ 1.65848] ((12 . 6) (13 . 7) (14 . 9) (20 . 12) (21 . 13) (22 . 15) (24 . 18) (25 . 19) (27 . 21) (28 . 22)) 5.285 {1/10:45} B:0 1.57011 [ 1.65864] ((12 . 6) (13 . 7) (14 . 9) (20 . 12) (21 . 13) (22 . 15) (24 . 18) (25 . 19) (26 . 20) (27 . 21)) 5.593 {1/10:45} B:0 1.71855 [ 1.82096] ((12 . 6) (13 . 7) (14 . 9) (20 . 12) (21 . 13) (22 . 15) (24 . 18) (25 . 19) (27 . 21)) 4.550 {1/10:36} B:0 3.00001 [ 3.20001] ((12 . 6) (14 . 9) (20 . 12) (22 . 15) (25 . 21)) 3.192 {0/3:10} B:0 SIMILARITY (1/min{score1}): 0.6872 [and 1/min{score2}: 0.6529] [3805, 3805]: Comparing 1m2o_A and 1m2o_A, based on their crossing files. There are 52 (25 H + 27 S) secondary structure elements in 1m2o_A, of which 15 satisfy the size requirements. There are 52 (25 H + 27 S) secondary structure elements in 1m2o_A, of which 15 satisfy the size requirements. 1.00000 [ 1.00000] ((12 . 12) (13 . 13) (14 . 14) (15 . 15) (16 . 16) (17 . 17) (20 . 20) (21 . 21) (22 . 22) (23 . 23) (24 . 24) (25 . 25) (26 . 26) (27 . 27) (28 . 28)) 0.000 {0/57:105} B:0 1.07143 [ 1.07143] ((12 . 12) (13 . 13) (14 . 14) (15 . 15) (16 . 16) (17 . 17) (20 . 20) (21 . 21) (22 . 22) (24 . 24) (25 . 25) (26 . 26) (27 . 27) (28 . 28)) 0.000 {0/43:91} B:0 2.14291 [ 2.14291] ((12 . 12) (13 . 13) (17 . 17) (20 . 20) (21 . 21) (22 . 22) (24 . 26)) 3.405 {0/6:21} B:0 2.14291 [ 2.14291] ((12 . 12) (13 . 13) (17 . 17) (20 . 20) (21 . 21) (22 . 22) (26 . 24)) 3.405 {0/6:21} B:0 3.00035 [ 3.00035] ((12 . 12) (13 . 13) (24 . 26) (25 . 27) (26 . 28)) 7.035 {0/3:10} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [3805, 3917]: Comparing 1m2o_A and 1mf7_A, based on their crossing files. There are 52 (25 H + 27 S) secondary structure elements in 1m2o_A, of which 15 satisfy the size requirements. There are 16 (10 H + 6 S) secondary structure elements in 1mf7_A, of which 13 satisfy the size requirements. 1.25083 [ 1.08460] ((12 . 1) (13 . 2) (14 . 3) (15 . 4) (20 . 6) (21 . 7) (22 . 9) (24 . 10) (25 . 11) (26 . 13) (27 . 15) (28 . 16)) 4.538 {0/18:66} B:0 2.50007 [ 2.16678] ((12 . 1) (13 . 2) (14 . 3) (15 . 4) (21 . 10) (22 . 11)) 4.150 {0/3:15} B:0 3.00007 [ 2.60010] ((14 . 1) (20 . 6) (21 . 7) (22 . 9) (25 . 15)) 4.654 {0/1:10} B:0 3.00012 [ 2.60019] ((12 . 1) (13 . 2) (14 . 3) (15 . 4) (17 . 7)) 5.411 {0/4:10} B:0 3.00041 [ 2.60063] ((12 . 1) (13 . 2) (14 . 3) (15 . 4) (21 . 13)) 7.333 {0/2:10} B:0 SIMILARITY (1/min{score1}): 0.7995 [and 1/min{score2}: 0.9220] [3805, 3946]: Comparing 1m2o_A and 1mjn_A, based on their crossing files. There are 52 (25 H + 27 S) secondary structure elements in 1m2o_A, of which 15 satisfy the size requirements. There are 18 (12 H + 6 S) secondary structure elements in 1mjn_A, of which 13 satisfy the size requirements. 1.37614 [ 1.20083] ((12 . 1) (13 . 2) (14 . 3) (15 . 4) (20 . 6) (21 . 7) (22 . 9) (24 . 10) (25 . 11) (27 . 16) (28 . 18)) 4.913 {1/17:55} B:0 1.51179 [ 1.31795] ((12 . 1) (13 . 2) (14 . 3) (15 . 4) (21 . 7) (22 . 9) (24 . 10) (25 . 11) (27 . 16) (28 . 18)) 4.846 {1/16:45} B:0 3.00010 [ 2.60016] ((12 . 1) (13 . 2) (14 . 3) (15 . 4) (22 . 16)) 5.193 {0/3:10} B:0 3.00010 [ 2.60016] ((12 . 1) (13 . 2) (14 . 3) (15 . 4) (17 . 7)) 5.197 {0/4:10} B:0 3.57087 [ 3.47348] ((12 . 1) (21 . 2) (22 . 3) (25 . 9) (26 . 10) (27 . 11)) 8.274 {1/3:15} B:0 SIMILARITY (1/min{score1}): 0.7267 [and 1/min{score2}: 0.8328] [3805, 4978]: Comparing 1m2o_A and 1pd1_A, based on their crossing files. There are 52 (25 H + 27 S) secondary structure elements in 1m2o_A, of which 15 satisfy the size requirements. There are 58 (29 H + 29 S) secondary structure elements in 1pd1_A, of which 15 satisfy the size requirements. 1.15682 [ 1.15682] ((12 . 18) (13 . 20) (14 . 21) (15 . 22) (16 . 24) (20 . 26) (21 . 27) (22 . 28) (24 . 29) (25 . 30) (26 . 31) (27 . 32) (28 . 33)) 3.420 {1/28:78} B:0 1.87510 [ 1.87510] ((12 . 18) (13 . 20) (14 . 21) (15 . 22) (16 . 24) (20 . 26) (21 . 27) (22 . 30)) 3.638 {0/11:28} B:0 2.46781 [ 2.46781] ((14 . 18) (22 . 28) (24 . 29) (25 . 30) (26 . 31) (27 . 32) (28 . 33)) 4.034 {1/5:21} B:0 2.50013 [ 2.50013] ((12 . 18) (20 . 26) (21 . 27) (22 . 28) (24 . 31) (25 . 32)) 4.840 {0/0:15} B:0 2.50014 [ 2.50014] ((12 . 18) (13 . 20) (20 . 26) (21 . 27) (24 . 31) (25 . 32)) 4.864 {0/1:15} B:0 SIMILARITY (1/min{score1}): 0.8644 [and 1/min{score2}: 0.8644] [3805, 5104]: Comparing 1m2o_A and 1pt6_A, based on their crossing files. There are 52 (25 H + 27 S) secondary structure elements in 1m2o_A, of which 15 satisfy the size requirements. There are 15 (9 H + 6 S) secondary structure elements in 1pt6_A, of which 13 satisfy the size requirements. 1.26550 [ 1.10681] ((12 . 1) (13 . 2) (14 . 3) (15 . 4) (20 . 5) (21 . 6) (22 . 8) (24 . 9) (25 . 10) (26 . 12) (27 . 14) (28 . 15)) 3.918 {1/17:66} B:0 3.00001 [ 2.60002] ((12 . 1) (13 . 2) (14 . 3) (15 . 4) (22 . 10)) 3.184 {0/3:10} B:0 3.00005 [ 2.60008] ((14 . 1) (20 . 5) (21 . 6) (22 . 8) (25 . 14)) 4.344 {0/1:10} B:0 3.00012 [ 2.60018] ((12 . 1) (13 . 2) (14 . 3) (15 . 4) (17 . 6)) 5.389 {0/4:10} B:0 3.00073 [ 2.60112] ((21 . 2) (22 . 3) (26 . 6) (27 . 8) (28 . 9)) 8.474 {0/0:10} B:0 SIMILARITY (1/min{score1}): 0.7902 [and 1/min{score2}: 0.9035] [3805, 5167]: Comparing 1m2o_A and 1q0p_A, based on their crossing files. There are 52 (25 H + 27 S) secondary structure elements in 1m2o_A, of which 15 satisfy the size requirements. There are 14 (8 H + 6 S) secondary structure elements in 1q0p_A, of which 12 satisfy the size requirements. 1.36410 [ 1.09181] ((12 . 1) (13 . 2) (14 . 3) (15 . 4) (20 . 6) (21 . 7) (22 . 9) (24 . 10) (25 . 12) (26 . 13) (27 . 14)) 4.183 {0/13:55} B:0 2.50005 [ 2.00010] ((12 . 1) (13 . 2) (14 . 3) (15 . 4) (21 . 10) (22 . 12)) 3.835 {0/4:15} B:0 3.00012 [ 2.40024] ((12 . 1) (13 . 2) (21 . 10) (24 . 13) (25 . 14)) 5.416 {0/3:10} B:0 3.00013 [ 2.40025] ((14 . 1) (20 . 6) (21 . 7) (22 . 9) (24 . 13)) 5.461 {0/0:10} B:0 3.00017 [ 2.40034] ((14 . 1) (16 . 3) (22 . 9) (24 . 13) (25 . 14)) 5.905 {0/3:10} B:0 SIMILARITY (1/min{score1}): 0.7331 [and 1/min{score2}: 0.9159] [3805, 5817]: Comparing 1m2o_A and 1shu_X, based on their crossing files. There are 52 (25 H + 27 S) secondary structure elements in 1m2o_A, of which 15 satisfy the size requirements. There are 14 (8 H + 6 S) secondary structure elements in 1shu_X, of which 13 satisfy the size requirements. 1.25043 [ 1.08400] ((12 . 1) (13 . 3) (14 . 4) (15 . 5) (20 . 6) (21 . 7) (22 . 8) (24 . 9) (25 . 10) (26 . 11) (27 . 13) (28 . 14)) 3.863 {0/14:66} B:0 1.36382 [ 1.18211] ((12 . 1) (13 . 3) (14 . 4) (15 . 5) (20 . 6) (21 . 7) (22 . 8) (24 . 9) (25 . 10) (27 . 13) (28 . 14)) 3.340 {0/13:55} B:0 3.00010 [ 2.60016] ((12 . 1) (13 . 3) (14 . 4) (15 . 5) (21 . 9)) 5.206 {0/0:10} B:0 3.00038 [ 2.60058] ((12 . 1) (13 . 3) (14 . 4) (15 . 5) (21 . 11)) 7.185 {0/1:10} B:0 3.00057 [ 2.60088] ((21 . 3) (24 . 7) (25 . 8) (26 . 9) (27 . 10)) 7.983 {0/2:10} B:0 SIMILARITY (1/min{score1}): 0.7997 [and 1/min{score2}: 0.9225] -------------------------------------------------------------------------------------------------------------------------