------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [6385, 532]: Comparing 2aak and 1c4z_D, based on their crossing files. There are 9 (5 H + 4 S) secondary structure elements in 2aak, of which 9 satisfy the size requirements. There are 8 (4 H + 4 S) secondary structure elements in 1c4z_D, of which 8 satisfy the size requirements. 1.12505 [ 1.00007] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (7 . 6) (8 . 7) (9 . 8)) 2.103 {0/21:28} B:0 3.49452 [ 3.43669] ((2 . 4) (3 . 5) (6 . 6) (8 . 8)) 7.108 {1/3:6} B:0 4.09668 [ 4.06121] ((2 . 4) (3 . 5) (6 . 7) (7 . 8)) 6.871 {2/5:6} B:0 5.05063 [ 5.03184] ((2 . 3) (3 . 4) (4 . 5) (8 . 8)) 8.356 {1/2:6} B:0 SIMILARITY (1/min{score1}): 0.8888 [and 1/min{score2}: 0.9999] [6385, 2787]: Comparing 2aak and 1jat_A, based on their crossing files. There are 9 (5 H + 4 S) secondary structure elements in 2aak, of which 9 satisfy the size requirements. There are 10 (5 H + 5 S) secondary structure elements in 1jat_A, of which 9 satisfy the size requirements. 1.00001 [ 1.00001] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9)) 1.320 {0/26:36} B:0 2.83638 [ 2.83638] ((4 . 2) (5 . 3) (8 . 6) (9 . 7)) 6.741 {1/4:6} B:0 4.09672 [ 4.09672] ((2 . 4) (3 . 5) (6 . 8) (7 . 9)) 7.319 {2/5:6} B:0 5.05060 [ 5.05060] ((4 . 2) (5 . 3) (7 . 6) (9 . 8)) 7.858 {1/2:6} B:0 5.05070 [ 5.05070] ((2 . 3) (3 . 4) (4 . 5) (8 . 9)) 9.224 {1/2:6} B:0 SIMILARITY (1/min{score1}): 0.9999 [and 1/min{score2}: 0.9999] [6385, 2788]: Comparing 2aak and 1jat_B, based on their crossing files. There are 9 (5 H + 4 S) secondary structure elements in 2aak, of which 9 satisfy the size requirements. There are 8 (4 H + 4 S) secondary structure elements in 1jat_B, of which 8 satisfy the size requirements. 1.50000 [ 1.33334] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (7 . 7)) 1.293 {0/10:15} B:0 1.69912 [ 1.64419] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7)) 1.596 {2/13:21} B:0 SIMILARITY (1/min{score1}): 0.6667 [and 1/min{score2}: 0.7500] [6385, 5160]: Comparing 2aak and 1pzv_A, based on their crossing files. There are 9 (5 H + 4 S) secondary structure elements in 2aak, of which 9 satisfy the size requirements. There are 10 (6 H + 4 S) secondary structure elements in 1pzv_A, of which 9 satisfy the size requirements. 1.12501 [ 1.12501] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 6) (7 . 8) (8 . 9) (9 . 10)) 1.442 {0/21:28} B:0 2.25114 [ 2.25114] ((1 . 1) (2 . 3) (3 . 4) (4 . 6)) 7.643 {0/1:6} B:0 2.43040 [ 2.43040] ((1 . 1) (4 . 6) (7 . 8) (8 . 9) (9 . 10)) 4.601 {2/9:10} B:0 3.49463 [ 3.49463] ((2 . 4) (3 . 6) (6 . 8) (8 . 10)) 7.866 {1/3:6} B:0 5.05069 [ 5.05069] ((3 . 2) (4 . 3) (5 . 4) (9 . 9)) 9.121 {1/2:6} B:0 SIMILARITY (1/min{score1}): 0.8889 [and 1/min{score2}: 0.8889] [6385, 5749]: Comparing 2aak and 1s1q_A, based on their crossing files. There are 9 (5 H + 4 S) secondary structure elements in 2aak, of which 9 satisfy the size requirements. There are 10 (4 H + 6 S) secondary structure elements in 1s1q_A, of which 8 satisfy the size requirements. 1.74297 [ 1.64526] ((1 . 2) (3 . 4) (4 . 5) (5 . 6) (6 . 8) (7 . 9)) 3.276 {1/7:15} B:0 1.79824 [ 1.75237] ((1 . 2) (2 . 3) (3 . 4) (4 . 5) (5 . 6) (6 . 8) (7 . 9)) 4.764 {2/12:21} B:0 2.54130 [ 2.37989] ((4 . 3) (5 . 4) (8 . 8) (9 . 9)) 8.497 {1/5:6} B:0 3.49432 [ 3.43648] ((1 . 2) (3 . 5) (6 . 8) (7 . 9)) 4.203 {1/3:6} B:0 5.05051 [ 5.03172] ((1 . 2) (2 . 4) (6 . 8) (7 . 9)) 5.038 {2/4:6} B:0 SIMILARITY (1/min{score1}): 0.5737 [and 1/min{score2}: 0.6078] [6385, 5944]: Comparing 2aak and 1u9a_A, based on their crossing files. There are 9 (5 H + 4 S) secondary structure elements in 2aak, of which 9 satisfy the size requirements. There are 10 (5 H + 5 S) secondary structure elements in 1u9a_A, of which 8 satisfy the size requirements. 1.12503 [ 1.00004] ((1 . 1) (2 . 2) (3 . 4) (4 . 5) (5 . 6) (7 . 8) (8 . 9) (9 . 10)) 1.749 {0/21:28} B:0 2.25219 [ 2.00311] ((3 . 2) (4 . 4) (5 . 5) (8 . 8)) 8.994 {0/3:6} B:0 3.49458 [ 3.43676] ((2 . 5) (3 . 6) (6 . 8) (8 . 10)) 7.572 {1/3:6} B:0 4.09668 [ 4.06121] ((2 . 5) (3 . 6) (6 . 9) (7 . 10)) 6.840 {2/5:6} B:0 5.05066 [ 5.03187] ((1 . 1) (2 . 4) (3 . 5) (4 . 6)) 8.684 {1/2:6} B:0 SIMILARITY (1/min{score1}): 0.8889 [and 1/min{score2}: 0.9999] [6385, 6153]: Comparing 2aak and 1uzx_A, based on their crossing files. There are 9 (5 H + 4 S) secondary structure elements in 2aak, of which 9 satisfy the size requirements. There are 9 (5 H + 4 S) secondary structure elements in 1uzx_A, of which 8 satisfy the size requirements. 1.56947 [ 1.42862] ((1 . 2) (2 . 3) (3 . 4) (4 . 5) (5 . 6) (7 . 9)) 4.261 {1/10:15} B:0 SIMILARITY (1/min{score1}): 0.6372 [and 1/min{score2}: 0.7000] [6385, 6385]: Comparing 2aak and 2aak, based on their crossing files. There are 9 (5 H + 4 S) secondary structure elements in 2aak, of which 9 satisfy the size requirements. There are 9 (5 H + 4 S) secondary structure elements in 2aak, of which 9 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9)) 0.000 {0/27:36} B:0 4.09670 [ 4.09670] ((2 . 4) (3 . 5) (6 . 8) (7 . 9)) 7.062 {2/5:6} B:0 4.09670 [ 4.09670] ((4 . 2) (5 . 3) (8 . 6) (9 . 7)) 7.062 {2/5:6} B:0 5.05071 [ 5.05071] ((3 . 2) (4 . 3) (5 . 4) (9 . 8)) 9.302 {1/2:6} B:0 5.05071 [ 5.05071] ((2 . 3) (3 . 4) (4 . 5) (8 . 9)) 9.302 {1/2:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [6385, 6434]: Comparing 2aak and 2e2c, based on their crossing files. There are 9 (5 H + 4 S) secondary structure elements in 2aak, of which 9 satisfy the size requirements. There are 9 (5 H + 4 S) secondary structure elements in 2e2c, of which 9 satisfy the size requirements. 1.00469 [ 1.00469] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9)) 1.454 {1/27:36} B:0 4.09666 [ 4.09666] ((2 . 4) (3 . 5) (6 . 8) (7 . 9)) 6.597 {2/5:6} B:0 4.09668 [ 4.09668] ((4 . 2) (5 . 3) (8 . 6) (9 . 7)) 6.833 {2/5:6} B:0 5.05067 [ 5.05067] ((3 . 2) (4 . 3) (5 . 4) (9 . 8)) 8.882 {1/2:6} B:0 5.05069 [ 5.05069] ((2 . 3) (3 . 4) (4 . 5) (8 . 9)) 9.079 {1/2:6} B:0 SIMILARITY (1/min{score1}): 0.9953 [and 1/min{score2}: 0.9953] -------------------------------------------------------------------------------------------------------------------------