------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [4249, 133]: Comparing 1nh2_A and 1ais_A, based on their crossing files. There are 14 (4 H + 10 S) secondary structure elements in 1nh2_A, of which 6 satisfy the size requirements. There are 13 (4 H + 9 S) secondary structure elements in 1ais_A, of which 6 satisfy the size requirements. 1.00003 [ 1.00003] ((8 . 1) (9 . 2) (11 . 3) (12 . 4) (13 . 5) (14 . 6)) 1.607 {0/8:15} B:0 1.50068 [ 1.50068] ((8 . 1) (9 . 2) (13 . 3) (14 . 6)) 4.957 {0/3:6} B:0 2.57743 [ 2.57743] ((8 . 1) (9 . 2) (11 . 5) (14 . 6)) 4.544 {1/4:6} B:0 2.57748 [ 2.57748] ((8 . 1) (9 . 2) (12 . 5) (14 . 6)) 5.052 {1/4:6} B:0 SIMILARITY (1/min{score1}): 0.9999 [and 1/min{score2}: 0.9999] [4249, 1211]: Comparing 1nh2_A and 1em2_A, based on their crossing files. There are 14 (4 H + 10 S) secondary structure elements in 1nh2_A, of which 6 satisfy the size requirements. There are 17 (5 H + 12 S) secondary structure elements in 1em2_A, of which 13 satisfy the size requirements. 10.00132 [10.02783] ((8 . 11) (11 . 14) (12 . 15) (14 . 17)) 10.918 {2/2:6} B:0 1.50633 [ 3.25063] ((8 . 5) (9 . 7) (11 . 9) (12 . 8)) 8.665 {0/3:6} B:1 SIMILARITY (1/min{score1}): 0.6639 [and 1/min{score2}: 0.3076] [4249, 1396]: Comparing 1nh2_A and 1f46_A, based on their crossing files. There are 14 (4 H + 10 S) secondary structure elements in 1nh2_A, of which 6 satisfy the size requirements. There are 12 (4 H + 8 S) secondary structure elements in 1f46_A, of which 9 satisfy the size requirements. 1.00260 [ 1.50077] ((8 . 1) (9 . 3) (11 . 6) (12 . 7) (13 . 9) (14 . 10)) 5.114 {0/8:15} B:0 1.20018 [ 1.80005] ((9 . 3) (11 . 6) (12 . 7) (13 . 9) (14 . 10)) 3.016 {0/5:10} B:0 SIMILARITY (1/min{score1}): 0.9974 [and 1/min{score2}: 0.6663] [4249, 1558]: Comparing 1nh2_A and 1fm4_A, based on their crossing files. There are 14 (4 H + 10 S) secondary structure elements in 1nh2_A, of which 6 satisfy the size requirements. There are 10 (3 H + 7 S) secondary structure elements in 1fm4_A, of which 10 satisfy the size requirements. 1.19291 [ 1.71946] ((8 . 1) (9 . 2) (11 . 7) (12 . 8) (13 . 9) (14 . 10)) 6.366 {1/10:15} B:0 3.36703 [ 3.57051] ((9 . 3) (11 . 5) (12 . 6) (13 . 7)) 4.370 {1/3:6} B:0 5.01016 [ 5.07643] ((9 . 3) (11 . 4) (12 . 5) (13 . 6)) 6.925 {1/2:6} B:0 4.00403 [ 4.02993] ((8 . 9) (9 . 3) (11 . 5) (12 . 6) (13 . 7) (14 . 10)) 6.795 {4/10:15} B:1 7.00076 [ 7.00565] ((8 . 7) (9 . 3) (11 . 5) (12 . 6) (13 . 8) (14 . 10)) 7.227 {7/10:15} B:1 SIMILARITY (1/min{score1}): 0.8383 [and 1/min{score2}: 0.5816] [4249, 3050]: Comparing 1nh2_A and 1jss_A, based on their crossing files. There are 14 (4 H + 10 S) secondary structure elements in 1nh2_A, of which 6 satisfy the size requirements. There are 17 (5 H + 12 S) secondary structure elements in 1jss_A, of which 13 satisfy the size requirements. 1.20826 [ 2.60082] ((8 . 5) (11 . 9) (12 . 10) (13 . 11) (14 . 17)) 7.842 {0/6:10} B:0 1.50236 [ 3.25023] ((8 . 5) (11 . 9) (12 . 10) (13 . 11)) 6.766 {0/3:6} B:0 3.36727 [ 3.91559] ((9 . 7) (11 . 8) (12 . 9) (13 . 10)) 7.267 {1/3:6} B:0 3.36768 [ 3.91585] ((9 . 6) (11 . 8) (12 . 9) (13 . 10)) 9.118 {1/3:6} B:0 6.00621 [ 6.12550] ((9 . 1) (12 . 3) (13 . 4) (14 . 6)) 11.952 {3/5:6} B:0 SIMILARITY (1/min{score1}): 0.8276 [and 1/min{score2}: 0.3845] [4249, 3262]: Comparing 1nh2_A and 1kcm_A, based on their crossing files. There are 14 (4 H + 10 S) secondary structure elements in 1nh2_A, of which 6 satisfy the size requirements. There are 20 (11 H + 9 S) secondary structure elements in 1kcm_A, of which 16 satisfy the size requirements. 1.50475 [ 4.00025] ((8 . 3) (12 . 8) (13 . 9) (14 . 10)) 8.062 {0/3:6} B:0 1.50874 [ 4.00046] ((8 . 4) (12 . 8) (13 . 9) (14 . 10)) 9.397 {0/3:6} B:0 10.00130 [10.06343] ((8 . 4) (11 . 8) (12 . 9) (13 . 11)) 9.831 {2/2:6} B:0 1.52679 [ 4.00145] ((8 . 5) (11 . 9) (12 . 8) (13 . 11)) 12.491 {0/0:6} B:1 1.20578 [ 3.20031] ((8 . 3) (11 . 9) (12 . 8) (13 . 5) (14 . 10)) 7.166 {0/5:10} B:2 SIMILARITY (1/min{score1}): 0.8293 [and 1/min{score2}: 0.3125] [4249, 3673]: Comparing 1nh2_A and 1ln1_A, based on their crossing files. There are 14 (4 H + 10 S) secondary structure elements in 1nh2_A, of which 6 satisfy the size requirements. There are 16 (6 H + 10 S) secondary structure elements in 1ln1_A, of which 15 satisfy the size requirements. 1.20542 [ 3.00035] ((8 . 5) (11 . 9) (12 . 10) (13 . 11) (14 . 16)) 7.052 {0/6:10} B:0 1.50204 [ 3.75013] ((8 . 5) (11 . 9) (12 . 10) (13 . 11)) 6.521 {0/3:6} B:0 4.02022 [ 4.61574] ((9 . 1) (11 . 4) (12 . 5) (14 . 6)) 9.999 {2/5:6} B:0 5.01035 [ 5.35592] ((9 . 6) (11 . 8) (12 . 9) (13 . 10)) 9.574 {2/4:6} B:0 6.00615 [ 6.21711] ((9 . 1) (12 . 3) (13 . 4) (14 . 6)) 11.402 {3/5:6} B:0 SIMILARITY (1/min{score1}): 0.8296 [and 1/min{score2}: 0.3333] [4249, 3819]: Comparing 1nh2_A and 1m3q_A, based on their crossing files. There are 14 (4 H + 10 S) secondary structure elements in 1nh2_A, of which 6 satisfy the size requirements. There are 23 (16 H + 7 S) secondary structure elements in 1m3q_A, of which 9 satisfy the size requirements. 1.00673 [ 1.50201] ((8 . 2) (9 . 3) (11 . 5) (12 . 6) (13 . 7) (14 . 8)) 6.496 {0/11:15} B:0 1.20009 [ 1.80003] ((9 . 3) (11 . 5) (12 . 6) (13 . 7) (14 . 8)) 2.527 {0/8:10} B:0 5.00204 [ 5.01014] ((8 . 7) (9 . 3) (11 . 5) (12 . 6) (13 . 2) (14 . 8)) 6.230 {5/10:15} B:2 SIMILARITY (1/min{score1}): 0.9933 [and 1/min{score2}: 0.6658] [4249, 4002]: Comparing 1nh2_A and 1mpg_A, based on their crossing files. There are 14 (4 H + 10 S) secondary structure elements in 1nh2_A, of which 6 satisfy the size requirements. There are 20 (15 H + 5 S) secondary structure elements in 1mpg_A, of which 10 satisfy the size requirements. 1.00944 [ 1.66873] ((8 . 1) (9 . 2) (11 . 4) (12 . 5) (13 . 6) (14 . 8)) 7.078 {0/11:15} B:0 3.64176 [ 3.67604] ((8 . 1) (9 . 2) (11 . 3) (12 . 5) (13 . 6) (14 . 8)) 7.190 {4/11:15} B:0 SIMILARITY (1/min{score1}): 0.9906 [and 1/min{score2}: 0.5993] [4249, 4248]: Comparing 1nh2_A and 1nh2_A, based on their crossing files. There are 14 (4 H + 10 S) secondary structure elements in 1nh2_A, of which 6 satisfy the size requirements. There are 14 (4 H + 10 S) secondary structure elements in 1nh2_A, of which 8 satisfy the size requirements. 1.18926 [ 1.42822] ((8 . 1) (9 . 2) (11 . 4) (12 . 5) (13 . 6) (14 . 7)) 2.215 {1/10:15} B:0 2.57749 [ 2.72417] ((8 . 1) (9 . 2) (13 . 4) (14 . 7)) 5.087 {1/4:6} B:0 2.57749 [ 2.72417] ((8 . 1) (9 . 2) (11 . 5) (14 . 7)) 5.088 {1/4:6} B:0 2.57749 [ 2.72418] ((8 . 1) (9 . 2) (11 . 6) (14 . 7)) 5.155 {1/4:6} B:0 2.57759 [ 2.72426] ((8 . 1) (9 . 2) (12 . 6) (14 . 7)) 5.818 {1/4:6} B:0 SIMILARITY (1/min{score1}): 0.8409 [and 1/min{score2}: 0.7002] [4249, 4249]: Comparing 1nh2_A and 1nh2_A, based on their crossing files. There are 14 (4 H + 10 S) secondary structure elements in 1nh2_A, of which 6 satisfy the size requirements. There are 14 (4 H + 10 S) secondary structure elements in 1nh2_A, of which 6 satisfy the size requirements. 1.00000 [ 1.00000] ((8 . 8) (9 . 9) (11 . 11) (12 . 12) (13 . 13) (14 . 14)) 0.000 {0/11:15} B:0 2.57742 [ 2.57742] ((8 . 8) (9 . 9) (11 . 13) (14 . 14)) 4.443 {1/4:6} B:0 2.57742 [ 2.57742] ((8 . 8) (9 . 9) (13 . 11) (14 . 14)) 4.443 {1/4:6} B:0 2.57748 [ 2.57748] ((8 . 8) (9 . 9) (13 . 12) (14 . 14)) 5.074 {1/4:6} B:0 2.57748 [ 2.57748] ((8 . 8) (9 . 9) (12 . 13) (14 . 14)) 5.074 {1/4:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [4249, 4542]: Comparing 1nh2_A and 1o7n_A, based on their crossing files. There are 14 (4 H + 10 S) secondary structure elements in 1nh2_A, of which 6 satisfy the size requirements. There are 41 (19 H + 22 S) secondary structure elements in 1o7n_A, of which 23 satisfy the size requirements. 1.00877 [ 3.83349] ((8 . 20) (9 . 22) (11 . 31) (12 . 32) (13 . 33) (14 . 34)) 6.947 {0/9:15} B:0 4.02019 [ 6.06073] ((9 . 35) (12 . 36) (13 . 38) (14 . 39)) 9.873 {2/5:6} B:0 8.00256 [ 8.48746] ((9 . 24) (12 . 26) (13 . 27) (14 . 28)) 10.520 {4/5:6} B:0 SIMILARITY (1/min{score1}): 0.9913 [and 1/min{score2}: 0.2609] [4249, 4904]: Comparing 1nh2_A and 1p5d_X, based on their crossing files. There are 14 (4 H + 10 S) secondary structure elements in 1nh2_A, of which 6 satisfy the size requirements. There are 37 (15 H + 22 S) secondary structure elements in 1p5d_X, of which 7 satisfy the size requirements. 1.01667 [ 1.17729] ((8 . 31) (9 . 32) (11 . 34) (12 . 35) (13 . 36) (14 . 37)) 8.182 {0/9:15} B:0 2.14248 [ 2.24466] ((9 . 32) (12 . 33) (13 . 34) (14 . 37)) 4.735 {1/5:6} B:0 1.22241 [ 1.41429] ((8 . 31) (9 . 32) (11 . 34) (12 . 33) (14 . 37)) 10.108 {0/8:10} B:1 2.86841 [ 2.87740] ((8 . 34) (9 . 32) (11 . 33) (12 . 35) (13 . 36) (14 . 37)) 7.834 {2/7:15} B:1 6.67119 [ 6.67482] ((8 . 33) (9 . 32) (11 . 36) (14 . 37)) 11.845 {2/3:6} B:1 SIMILARITY (1/min{score1}): 0.9836 [and 1/min{score2}: 0.8494] [4249, 5264]: Comparing 1nh2_A and 1q9u_A, based on their crossing files. There are 14 (4 H + 10 S) secondary structure elements in 1nh2_A, of which 6 satisfy the size requirements. There are 11 (6 H + 5 S) secondary structure elements in 1q9u_A, of which 11 satisfy the size requirements. 5.01045 [ 5.11099] ((8 . 5) (11 . 8) (12 . 9) (14 . 11)) 10.397 {1/2:6} B:0 SIMILARITY (1/min{score1}): 0.1996 [and 1/min{score2}: 0.1957] [4249, 6046]: Comparing 1nh2_A and 1ul7_A, based on their crossing files. There are 14 (4 H + 10 S) secondary structure elements in 1nh2_A, of which 6 satisfy the size requirements. There are 7 (3 H + 4 S) secondary structure elements in 1ul7_A, of which 6 satisfy the size requirements. 1.20053 [ 1.20053] ((9 . 1) (11 . 3) (12 . 5) (13 . 6) (14 . 7)) 3.940 {0/5:10} B:0 5.01019 [ 5.01019] ((9 . 1) (11 . 3) (13 . 5) (14 . 7)) 7.512 {2/4:6} B:0 5.01021 [ 5.01021] ((9 . 1) (11 . 2) (12 . 3) (13 . 5)) 7.788 {1/2:6} B:0 SIMILARITY (1/min{score1}): 0.8330 [and 1/min{score2}: 0.8330] [4249, 6196]: Comparing 1nh2_A and 1v8c_A, based on their crossing files. There are 14 (4 H + 10 S) secondary structure elements in 1nh2_A, of which 6 satisfy the size requirements. There are 19 (7 H + 12 S) secondary structure elements in 1v8c_A, of which 7 satisfy the size requirements. 1.01357 [ 1.17529] ((8 . 13) (9 . 14) (11 . 16) (12 . 17) (13 . 18) (14 . 19)) 7.762 {0/8:15} B:0 1.20646 [ 1.40409] ((8 . 13) (9 . 14) (11 . 16) (13 . 18) (14 . 19)) 7.371 {0/6:10} B:0 SIMILARITY (1/min{score1}): 0.9866 [and 1/min{score2}: 0.8509] [4249, 6284]: Comparing 1nh2_A and 1vjh_A, based on their crossing files. There are 14 (4 H + 10 S) secondary structure elements in 1nh2_A, of which 6 satisfy the size requirements. There are 8 (3 H + 5 S) secondary structure elements in 1vjh_A, of which 8 satisfy the size requirements. 1.00334 [ 1.33475] ((8 . 1) (9 . 2) (11 . 4) (12 . 6) (13 . 7) (14 . 8)) 5.448 {0/9:15} B:0 5.01025 [ 5.03185] ((9 . 2) (11 . 3) (12 . 4) (13 . 6)) 8.397 {1/2:6} B:0 7.50304 [ 7.50950] ((9 . 2) (12 . 3) (13 . 4) (14 . 5)) 8.213 {3/4:6} B:0 SIMILARITY (1/min{score1}): 0.9967 [and 1/min{score2}: 0.7492] [4249, 6588]: Comparing 1nh2_A and 3pmg_A, based on their crossing files. There are 14 (4 H + 10 S) secondary structure elements in 1nh2_A, of which 6 satisfy the size requirements. There are 48 (22 H + 26 S) secondary structure elements in 3pmg_A, of which 9 satisfy the size requirements. 1.36419 [ 1.65630] ((8 . 37) (9 . 38) (11 . 43) (12 . 44) (13 . 45) (14 . 46)) 6.162 {1/8:15} B:0 2.57881 [ 2.83714] ((8 . 37) (9 . 38) (12 . 40) (13 . 43)) 9.017 {1/4:6} B:0 SIMILARITY (1/min{score1}): 0.7330 [and 1/min{score2}: 0.6038] -------------------------------------------------------------------------------------------------------------------------