------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [327, 77]: Comparing 1b9l_A and 1a8r_A, based on their crossing files. There are 9 (4 H + 5 S) secondary structure elements in 1b9l_A, of which 8 satisfy the size requirements. There are 17 (10 H + 7 S) secondary structure elements in 1a8r_A, of which 13 satisfy the size requirements. 1.33360 [ 2.16673] ((1 . 7) (3 . 8) (5 . 10) (7 . 12) (8 . 13) (9 . 15)) 3.579 {0/8:15} B:0 2.01881 [ 3.25444] ((1 . 8) (3 . 9) (5 . 12) (8 . 15)) 14.142 {0/3:6} B:0 2.59892 [ 3.03427] ((3 . 7) (5 . 10) (7 . 12) (8 . 13) (9 . 15)) 4.340 {1/4:10} B:0 3.43913 [ 3.91723] ((1 . 7) (3 . 9) (5 . 12) (8 . 15)) 13.004 {1/3:6} B:0 4.06190 [ 4.37924] ((2 . 1) (5 . 2) (7 . 3) (9 . 7)) 10.941 {2/5:6} B:0 SIMILARITY (1/min{score1}): 0.7499 [and 1/min{score2}: 0.4615] [327, 298]: Comparing 1b9l_A and 1b66_A, based on their crossing files. There are 9 (4 H + 5 S) secondary structure elements in 1b9l_A, of which 8 satisfy the size requirements. There are 11 (6 H + 5 S) secondary structure elements in 1b66_A, of which 8 satisfy the size requirements. 1.33355 [ 1.33355] ((1 . 1) (3 . 3) (5 . 5) (7 . 9) (8 . 10) (9 . 11)) 3.420 {0/8:15} B:0 1.33364 [ 1.33364] ((1 . 1) (3 . 3) (5 . 4) (7 . 9) (8 . 10) (9 . 11)) 3.729 {0/9:15} B:0 1.60164 [ 1.60164] ((4 . 4) (5 . 5) (7 . 9) (8 . 10) (9 . 11)) 6.478 {0/7:10} B:0 2.73222 [ 2.73222] ((1 . 3) (2 . 4) (4 . 5) (8 . 11)) 14.443 {1/4:6} B:0 2.87535 [ 2.87535] ((1 . 1) (2 . 2) (3 . 3) (5 . 5) (7 . 9) (8 . 10) (9 . 11)) 4.859 {4/14:21} B:0 SIMILARITY (1/min{score1}): 0.7499 [and 1/min{score2}: 0.7499] [327, 327]: Comparing 1b9l_A and 1b9l_A, based on their crossing files. There are 9 (4 H + 5 S) secondary structure elements in 1b9l_A, of which 8 satisfy the size requirements. There are 9 (4 H + 5 S) secondary structure elements in 1b9l_A, of which 8 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (7 . 7) (8 . 8) (9 . 9)) 0.000 {0/22:28} B:0 2.73732 [ 2.73732] ((3 . 1) (5 . 2) (7 . 4) (9 . 8)) 16.317 {1/4:6} B:0 2.73732 [ 2.73732] ((1 . 3) (2 . 5) (4 . 7) (8 . 9)) 16.317 {1/4:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [327, 841]: Comparing 1b9l_A and 1dhn, based on their crossing files. There are 9 (4 H + 5 S) secondary structure elements in 1b9l_A, of which 8 satisfy the size requirements. There are 9 (5 H + 4 S) secondary structure elements in 1dhn, of which 8 satisfy the size requirements. 1.56919 [ 1.56919] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 6) (7 . 7) (8 . 8) (9 . 9)) 2.635 {3/20:28} B:0 SIMILARITY (1/min{score1}): 0.6373 [and 1/min{score2}: 0.6373] [327, 2593]: Comparing 1b9l_A and 1is8_A, based on their crossing files. There are 9 (4 H + 5 S) secondary structure elements in 1b9l_A, of which 8 satisfy the size requirements. There are 15 (8 H + 7 S) secondary structure elements in 1is8_A, of which 12 satisfy the size requirements. 1.33343 [ 2.00003] ((1 . 5) (3 . 6) (5 . 8) (7 . 10) (8 . 11) (9 . 13)) 2.759 {0/7:15} B:0 2.00101 [ 3.00030] ((1 . 11) (2 . 12) (3 . 13) (5 . 15)) 6.782 {0/2:6} B:0 2.18215 [ 2.64977] ((2 . 3) (5 . 8) (7 . 10) (8 . 11) (9 . 13)) 9.435 {1/5:10} B:0 2.72613 [ 3.31135] ((1 . 6) (2 . 10) (3 . 11) (7 . 15)) 10.260 {1/4:6} B:0 3.37674 [ 3.53773] ((3 . 5) (5 . 8) (7 . 10) (8 . 11) (9 . 13)) 4.087 {1/3:10} B:0 SIMILARITY (1/min{score1}): 0.7499 [and 1/min{score2}: 0.5000] [327, 4190]: Comparing 1b9l_A and 1nbu_A, based on their crossing files. There are 9 (4 H + 5 S) secondary structure elements in 1b9l_A, of which 8 satisfy the size requirements. There are 9 (5 H + 4 S) secondary structure elements in 1nbu_A, of which 8 satisfy the size requirements. 1.16207 [ 1.16207] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 6) (7 . 7) (8 . 8) (9 . 9)) 2.754 {2/21:28} B:0 1.17473 [ 1.17473] ((1 . 1) (2 . 2) (3 . 3) (5 . 6) (7 . 7) (8 . 8) (9 . 9)) 2.742 {1/15:21} B:0 2.72418 [ 2.72418] ((1 . 1) (2 . 2) (3 . 3) (5 . 7)) 5.215 {1/4:6} B:0 SIMILARITY (1/min{score1}): 0.8605 [and 1/min{score2}: 0.8605] [327, 5554]: Comparing 1b9l_A and 1r51_A, based on their crossing files. There are 9 (4 H + 5 S) secondary structure elements in 1b9l_A, of which 8 satisfy the size requirements. There are 20 (8 H + 12 S) secondary structure elements in 1r51_A, of which 9 satisfy the size requirements. 1.33384 [ 1.50036] ((1 . 1) (3 . 2) (5 . 5) (7 . 6) (8 . 7) (9 . 10)) 4.220 {0/7:15} B:0 2.29120 [ 2.32975] ((1 . 1) (3 . 2) (4 . 3) (5 . 5) (7 . 6) (8 . 7)) 5.217 {2/9:15} B:0 2.52700 [ 2.54276] ((1 . 1) (3 . 2) (4 . 3) (5 . 5) (7 . 6) (8 . 7) (9 . 10)) 4.959 {3/12:21} B:0 6.68018 [ 6.68824] ((1 . 1) (3 . 2) (7 . 5) (9 . 7)) 7.951 {2/3:6} B:0 5.03241 [ 5.05119] ((1 . 2) (3 . 7) (4 . 6) (8 . 10)) 12.415 {1/2:6} B:1 SIMILARITY (1/min{score1}): 0.7497 [and 1/min{score2}: 0.6665] [327, 5555]: Comparing 1b9l_A and 1r51_A, based on their crossing files. There are 9 (4 H + 5 S) secondary structure elements in 1b9l_A, of which 8 satisfy the size requirements. There are 20 (8 H + 12 S) secondary structure elements in 1r51_A, of which 9 satisfy the size requirements. 1.18433 [ 1.31542] ((1 . 11) (3 . 12) (4 . 13) (5 . 14) (7 . 15) (8 . 16) (9 . 20)) 2.934 {1/14:21} B:0 1.33342 [ 1.50006] ((1 . 11) (3 . 12) (5 . 14) (7 . 15) (8 . 16) (9 . 20)) 2.719 {0/8:15} B:0 1.42831 [ 1.56923] ((1 . 11) (3 . 12) (4 . 13) (5 . 14) (7 . 15) (8 . 16)) 3.089 {1/10:15} B:0 1.60990 [ 1.80698] ((1 . 11) (3 . 12) (5 . 14) (7 . 15) (8 . 17)) 10.177 {0/4:10} B:0 5.03228 [ 5.05107] ((1 . 12) (2 . 13) (5 . 15) (9 . 19)) 11.825 {2/4:6} B:0 SIMILARITY (1/min{score1}): 0.8444 [and 1/min{score2}: 0.7602] -------------------------------------------------------------------------------------------------------------------------