------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [499, 499]: Comparing 1c02_A and 1c02_A, based on their crossing files. There are 7 (7 H + 0 S) secondary structure elements in 1c02_A, of which 7 satisfy the size requirements. There are 7 (7 H + 0 S) secondary structure elements in 1c02_A, of which 7 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7)) 0.000 {0/14:21} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [499, 1072]: Comparing 1c02_A and 1e85_A, based on their crossing files. There are 7 (7 H + 0 S) secondary structure elements in 1c02_A, of which 7 satisfy the size requirements. There are 7 (7 H + 0 S) secondary structure elements in 1e85_A, of which 6 satisfy the size requirements. NO SIMILARITY! [499, 1172]: Comparing 1c02_A and 1ei7_A, based on their crossing files. There are 7 (7 H + 0 S) secondary structure elements in 1c02_A, of which 7 satisfy the size requirements. There are 11 (6 H + 5 S) secondary structure elements in 1ei7_A, of which 7 satisfy the size requirements. 1.75124 [ 1.75124] ((2 . 4) (3 . 5) (4 . 7) (7 . 8)) 6.457 {0/1:6} B:0 1.75412 [ 1.75412] ((2 . 4) (3 . 5) (5 . 7) (7 . 8)) 8.731 {0/0:6} B:0 6.00450 [ 6.00450] ((1 . 10) (2 . 4) (3 . 5) (4 . 7) (7 . 8)) 7.584 {3/5:10} B:1 SIMILARITY (1/min{score1}): 0.5710 [and 1/min{score2}: 0.5710] [499, 1724]: Comparing 1c02_A and 1g4u_S, based on their crossing files. There are 7 (7 H + 0 S) secondary structure elements in 1c02_A, of which 7 satisfy the size requirements. There are 23 (14 H + 9 S) secondary structure elements in 1g4u_S, of which 8 satisfy the size requirements. 10.00239 [10.00404] ((1 . 1) (2 . 4) (3 . 5) (5 . 7)) 10.378 {1/1:6} B:0 7.14441 [ 7.14531] ((1 . 8) (2 . 1) (3 . 5) (4 . 6) (5 . 7) (7 . 4)) 12.815 {5/7:15} B:2 SIMILARITY (1/min{score1}): 0.1400 [and 1/min{score2}: 0.1400] [499, 2190]: Comparing 1c02_A and 1he1_A, based on their crossing files. There are 7 (7 H + 0 S) secondary structure elements in 1c02_A, of which 7 satisfy the size requirements. There are 9 (7 H + 2 S) secondary structure elements in 1he1_A, of which 7 satisfy the size requirements. 1.75159 [ 1.75159] ((2 . 1) (3 . 3) (4 . 4) (7 . 9)) 6.876 {0/1:6} B:0 5.01943 [ 5.01943] ((1 . 1) (2 . 2) (3 . 3) (4 . 7)) 12.680 {2/4:6} B:0 2.56255 [ 2.56255] ((1 . 4) (2 . 1) (3 . 3) (4 . 7) (7 . 9)) 10.916 {1/4:10} B:1 7.50256 [ 7.50256] ((1 . 4) (2 . 3) (3 . 7) (4 . 2) (7 . 9)) 13.350 {3/4:10} B:2 SIMILARITY (1/min{score1}): 0.5709 [and 1/min{score2}: 0.5709] [499, 2326]: Comparing 1c02_A and 1hy5_A, based on their crossing files. There are 7 (7 H + 0 S) secondary structure elements in 1c02_A, of which 7 satisfy the size requirements. There are 9 (7 H + 2 S) secondary structure elements in 1hy5_A, of which 7 satisfy the size requirements. 5.01919 [ 5.01919] ((1 . 1) (2 . 2) (3 . 3) (4 . 7)) 11.560 {2/4:6} B:0 4.01595 [ 4.01595] ((1 . 9) (2 . 2) (3 . 3) (4 . 7) (7 . 8)) 11.494 {2/5:10} B:1 SIMILARITY (1/min{score1}): 0.2490 [and 1/min{score2}: 0.2490] [499, 3003]: Comparing 1c02_A and 1jog_A, based on their crossing files. There are 7 (7 H + 0 S) secondary structure elements in 1c02_A, of which 7 satisfy the size requirements. There are 7 (7 H + 0 S) secondary structure elements in 1jog_A, of which 6 satisfy the size requirements. 1.75224 [ 1.50356] ((2 . 1) (3 . 3) (6 . 4) (7 . 7)) 7.496 {0/3:6} B:0 3.39582 [ 3.36792] ((2 . 1) (4 . 3) (6 . 4) (7 . 7)) 9.827 {1/3:6} B:0 3.36160 [ 3.34990] ((2 . 7) (3 . 1) (4 . 3) (5 . 4) (7 . 5)) 12.720 {1/3:10} B:1 SIMILARITY (1/min{score1}): 0.5707 [and 1/min{score2}: 0.6651] [499, 3371]: Comparing 1c02_A and 1kny_A, based on their crossing files. There are 7 (7 H + 0 S) secondary structure elements in 1c02_A, of which 7 satisfy the size requirements. There are 16 (11 H + 5 S) secondary structure elements in 1kny_A, of which 6 satisfy the size requirements. 1.75091 [ 1.50144] ((2 . 12) (3 . 13) (4 . 15) (7 . 16)) 5.982 {0/1:6} B:0 3.39575 [ 3.36785] ((3 . 11) (4 . 12) (6 . 14) (7 . 16)) 9.624 {1/3:6} B:0 3.39656 [ 3.36868] ((1 . 13) (2 . 14) (3 . 15) (4 . 16)) 11.397 {1/3:6} B:0 10.00237 [10.00129] ((2 . 12) (3 . 13) (4 . 14) (7 . 16)) 9.181 {1/1:6} B:0 SIMILARITY (1/min{score1}): 0.5711 [and 1/min{score2}: 0.6660] [499, 4011]: Comparing 1c02_A and 1mqv_A, based on their crossing files. There are 7 (7 H + 0 S) secondary structure elements in 1c02_A, of which 7 satisfy the size requirements. There are 6 (6 H + 0 S) secondary structure elements in 1mqv_A, of which 6 satisfy the size requirements. 1.75413 [ 1.50653] ((2 . 1) (3 . 2) (5 . 5) (7 . 6)) 8.734 {0/0:6} B:0 1.76675 [ 1.52628] ((3 . 1) (4 . 2) (6 . 4) (7 . 6)) 12.429 {0/3:6} B:0 10.00241 [10.00133] ((2 . 1) (3 . 2) (6 . 5) (7 . 6)) 11.402 {1/1:6} B:0 4.01497 [ 4.00812] ((1 . 3) (2 . 1) (3 . 2) (4 . 5) (7 . 6)) 5.335 {2/5:10} B:1 10.00096 [10.00052] ((1 . 3) (2 . 6) (3 . 1) (4 . 2) (7 . 5)) 5.188 {4/4:10} B:1 SIMILARITY (1/min{score1}): 0.5701 [and 1/min{score2}: 0.6638] [499, 5366]: Comparing 1c02_A and 1qkr_A, based on their crossing files. There are 7 (7 H + 0 S) secondary structure elements in 1c02_A, of which 7 satisfy the size requirements. There are 8 (8 H + 0 S) secondary structure elements in 1qkr_A, of which 7 satisfy the size requirements. 1.75927 [ 1.75927] ((2 . 3) (3 . 4) (4 . 5) (7 . 7)) 10.703 {0/0:6} B:0 1.76772 [ 1.76772] ((1 . 2) (2 . 3) (3 . 4) (7 . 7)) 12.609 {0/1:6} B:0 1.77060 [ 1.77060] ((2 . 1) (3 . 2) (4 . 3) (6 . 4)) 13.101 {0/3:6} B:0 2.64120 [ 2.64120] ((1 . 1) (2 . 3) (6 . 6) (7 . 7)) 10.988 {1/4:6} B:0 5.01885 [ 5.01885] ((1 . 1) (2 . 2) (3 . 3) (4 . 4)) 8.971 {2/4:6} B:0 SIMILARITY (1/min{score1}): 0.5713 [and 1/min{score2}: 0.5713] [499, 5741]: Comparing 1c02_A and 1s05_A, based on their crossing files. There are 7 (7 H + 0 S) secondary structure elements in 1c02_A, of which 7 satisfy the size requirements. There are 6 (6 H + 0 S) secondary structure elements in 1s05_A, of which 6 satisfy the size requirements. 1.75556 [ 1.50879] ((2 . 1) (3 . 2) (5 . 4) (7 . 6)) 9.412 {0/0:6} B:0 1.75828 [ 1.51307] ((3 . 1) (4 . 2) (6 . 3) (7 . 6)) 10.403 {0/3:6} B:0 3.39691 [ 3.36904] ((3 . 1) (4 . 2) (6 . 3) (7 . 4)) 11.964 {1/3:6} B:0 5.01896 [ 5.01040] ((2 . 1) (4 . 2) (6 . 3) (7 . 6)) 10.039 {2/4:6} B:0 10.00237 [10.00129] ((2 . 1) (3 . 2) (5 . 3) (7 . 6)) 8.681 {1/1:6} B:0 SIMILARITY (1/min{score1}): 0.5696 [and 1/min{score2}: 0.6628] [499, 6384]: Comparing 1c02_A and 2a0b, based on their crossing files. There are 7 (7 H + 0 S) secondary structure elements in 1c02_A, of which 7 satisfy the size requirements. There are 7 (7 H + 0 S) secondary structure elements in 2a0b, of which 7 satisfy the size requirements. 1.75629 [ 1.75629] ((2 . 3) (3 . 4) (4 . 5) (6 . 6)) 9.707 {0/4:6} B:0 2.11101 [ 2.11101] ((1 . 2) (2 . 3) (3 . 4) (4 . 5) (7 . 6)) 5.835 {1/5:10} B:0 3.35917 [ 3.35917] ((1 . 2) (2 . 3) (3 . 4) (4 . 5) (5 . 6)) 6.689 {2/6:10} B:0 SIMILARITY (1/min{score1}): 0.5694 [and 1/min{score2}: 0.5694] -------------------------------------------------------------------------------------------------------------------------