------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [1120, 1120]: Comparing 1ee8_A and 1ee8_A, based on their crossing files. There are 20 (9 H + 11 S) secondary structure elements in 1ee8_A, of which 11 satisfy the size requirements. There are 20 (9 H + 11 S) secondary structure elements in 1ee8_A, of which 11 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (2 . 2) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12)) 0.000 {0/44:55} B:0 3.48131 [ 3.48131] ((1 . 1) (2 . 2) (4 . 4) (5 . 6) (12 . 12)) 2.907 {3/9:10} B:0 2.36247 [ 2.36247] ((1 . 1) (4 . 4) (6 . 6) (7 . 5) (9 . 8)) 4.926 {1/6:10} B:1 1.50183 [ 1.50183] ((1 . 4) (2 . 5) (4 . 1) (5 . 2) (6 . 9) (7 . 10) (8 . 11) (9 . 6) (10 . 7) (11 . 8)) 3.946 {4/29:45} B:2 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [1120, 3165]: Comparing 1ee8_A and 1k3x_A, based on their crossing files. There are 20 (9 H + 11 S) secondary structure elements in 1ee8_A, of which 11 satisfy the size requirements. There are 20 (10 H + 10 S) secondary structure elements in 1k3x_A, of which 12 satisfy the size requirements. 1.00144 [ 1.09202] ((1 . 1) (2 . 2) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 13)) 3.123 {1/39:55} B:0 1.10198 [ 1.20152] ((1 . 1) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 13)) 2.860 {1/32:45} B:0 2.75146 [ 3.00113] ((1 . 4) (2 . 6) (5 . 8) (7 . 9)) 9.449 {0/4:6} B:0 7.53378 [ 7.54766] ((2 . 5) (5 . 7) (6 . 8) (8 . 9)) 10.676 {3/4:6} B:0 2.20018 [ 2.40014] ((1 . 1) (4 . 4) (5 . 7) (6 . 6) (12 . 13)) 4.730 {0/7:10} B:1 SIMILARITY (1/min{score1}): 0.9986 [and 1/min{score2}: 0.9157] [1120, 3204]: Comparing 1ee8_A and 1k82_A, based on their crossing files. There are 20 (9 H + 11 S) secondary structure elements in 1ee8_A, of which 11 satisfy the size requirements. There are 19 (8 H + 11 S) secondary structure elements in 1k82_A, of which 10 satisfy the size requirements. 1.16075 [ 1.07816] ((1 . 1) (2 . 2) (4 . 3) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11)) 2.927 {2/26:45} B:0 1.22927 [ 1.12046] ((1 . 1) (2 . 2) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11)) 2.431 {1/21:36} B:0 2.75010 [ 2.50014] ((2 . 7) (6 . 9) (7 . 10) (8 . 11)) 4.871 {0/4:6} B:0 2.75319 [ 2.50424] ((1 . 3) (5 . 7) (8 . 9) (10 . 11)) 11.487 {0/3:6} B:0 3.08065 [ 3.01510] ((1 . 1) (2 . 2) (7 . 7) (8 . 8) (10 . 9)) 3.973 {2/7:10} B:0 SIMILARITY (1/min{score1}): 0.8615 [and 1/min{score2}: 0.9275] [1120, 4324]: Comparing 1ee8_A and 1nnj_A, based on their crossing files. There are 20 (9 H + 11 S) secondary structure elements in 1ee8_A, of which 11 satisfy the size requirements. There are 20 (10 H + 10 S) secondary structure elements in 1nnj_A, of which 11 satisfy the size requirements. 1.14605 [ 1.14605] ((1 . 1) (2 . 2) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11)) 2.613 {2/28:45} B:0 2.36252 [ 2.36252] ((1 . 4) (2 . 7) (6 . 9) (7 . 10) (8 . 11)) 5.249 {1/6:10} B:0 2.75018 [ 2.75018] ((1 . 4) (5 . 6) (6 . 7) (9 . 10)) 5.607 {0/2:6} B:0 3.66664 [ 3.66664] ((1 . 4) (2 . 5) (5 . 8) (7 . 9)) 9.002 {1/3:6} B:0 4.35828 [ 4.35828] ((1 . 4) (2 . 6) (6 . 9) (7 . 10) (8 . 11)) 5.078 {3/7:10} B:0 SIMILARITY (1/min{score1}): 0.8726 [and 1/min{score2}: 0.8726] [1120, 5535]: Comparing 1ee8_A and 1r2z_A, based on their crossing files. There are 20 (9 H + 11 S) secondary structure elements in 1ee8_A, of which 11 satisfy the size requirements. There are 21 (10 H + 11 S) secondary structure elements in 1r2z_A, of which 12 satisfy the size requirements. 1.22234 [ 1.33343] ((1 . 1) (2 . 2) (4 . 5) (6 . 7) (7 . 8) (8 . 9) (9 . 10) (10 . 11) (11 . 12)) 2.752 {0/22:36} B:0 1.31498 [ 1.37740] ((1 . 1) (2 . 2) (4 . 5) (5 . 6) (6 . 7) (7 . 8) (8 . 9) (9 . 10) (10 . 11) (11 . 12)) 3.271 {3/27:45} B:0 2.29210 [ 2.47220] ((1 . 5) (2 . 8) (6 . 10) (7 . 11) (8 . 12)) 5.210 {1/7:10} B:0 2.36252 [ 2.52897] ((1 . 5) (2 . 7) (6 . 10) (7 . 11) (8 . 12)) 5.230 {1/6:10} B:0 2.75007 [ 3.00005] ((1 . 1) (2 . 2) (4 . 5) (10 . 10)) 4.402 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.8181 [and 1/min{score2}: 0.7499] -------------------------------------------------------------------------------------------------------------------------