------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [2773, 1327]: Comparing 1j98_A and 1ezv_A, based on their crossing files. There are 9 (5 H + 4 S) secondary structure elements in 1j98_A, of which 8 satisfy the size requirements. There are 32 (20 H + 12 S) secondary structure elements in 1ezv_A, of which 14 satisfy the size requirements. 2.00581 [ 3.50109] ((2 . 1) (3 . 2) (6 . 7) (8 . 11)) 10.520 {0/4:6} B:0 2.37875 [ 3.58988] ((3 . 7) (7 . 11) (8 . 14) (9 . 15)) 5.855 {1/5:6} B:0 1.19890 [ 2.01116] ((2 . 16) (3 . 3) (4 . 5) (5 . 7) (6 . 8) (7 . 10) (8 . 15)) 5.053 {1/13:21} B:1 1.20026 [ 2.01145] ((2 . 16) (3 . 3) (4 . 6) (5 . 7) (6 . 8) (7 . 10) (8 . 15)) 5.963 {1/13:21} B:1 3.19000 [ 3.25266] ((2 . 16) (3 . 3) (4 . 12) (5 . 7) (6 . 8) (7 . 11) (8 . 14) (9 . 15)) 7.853 {7/22:28} B:2 SIMILARITY (1/min{score1}): 0.8341 [and 1/min{score2}: 0.4972] [2773, 1328]: Comparing 1j98_A and 1ezv_A, based on their crossing files. There are 9 (5 H + 4 S) secondary structure elements in 1j98_A, of which 8 satisfy the size requirements. There are 32 (20 H + 12 S) secondary structure elements in 1ezv_A, of which 15 satisfy the size requirements. 2.37873 [ 3.82373] ((3 . 24) (7 . 27) (8 . 29) (9 . 30)) 5.790 {1/5:6} B:0 2.38037 [ 3.82412] ((5 . 21) (6 . 24) (8 . 26) (9 . 27)) 9.111 {1/5:6} B:0 3.43655 [ 4.23353] ((2 . 19) (5 . 24) (6 . 25) (7 . 26)) 5.734 {1/3:6} B:0 1.02065 [ 1.87822] ((2 . 31) (3 . 19) (4 . 20) (5 . 24) (6 . 25) (7 . 27) (8 . 29) (9 . 30)) 6.858 {1/21:28} B:1 1.14381 [ 2.14300] ((2 . 31) (3 . 19) (4 . 20) (5 . 24) (6 . 25) (7 . 26) (8 . 30)) 4.395 {0/13:21} B:1 SIMILARITY (1/min{score1}): 0.9798 [and 1/min{score2}: 0.5324] [2773, 1329]: Comparing 1j98_A and 1ezv_B, based on their crossing files. There are 9 (5 H + 4 S) secondary structure elements in 1j98_A, of which 8 satisfy the size requirements. There are 23 (14 H + 9 S) secondary structure elements in 1ezv_B, of which 12 satisfy the size requirements. 5.03223 [ 5.15517] ((5 . 4) (6 . 5) (7 . 6) (8 . 9)) 11.561 {2/4:6} B:0 1.14804 [ 1.71583] ((2 . 12) (3 . 1) (4 . 2) (5 . 4) (6 . 5) (7 . 6) (8 . 10)) 6.723 {0/11:21} B:1 3.37704 [ 3.53799] ((3 . 1) (4 . 8) (5 . 4) (6 . 5) (8 . 10)) 7.583 {2/6:10} B:1 2.54964 [ 2.72448] ((2 . 12) (3 . 1) (5 . 4) (6 . 5) (7 . 2) (8 . 10)) 6.942 {2/8:15} B:2 SIMILARITY (1/min{score1}): 0.8710 [and 1/min{score2}: 0.5828] [2773, 1330]: Comparing 1j98_A and 1ezv_B, based on their crossing files. There are 9 (5 H + 4 S) secondary structure elements in 1j98_A, of which 8 satisfy the size requirements. There are 23 (14 H + 9 S) secondary structure elements in 1ezv_B, of which 9 satisfy the size requirements. 1.60129 [ 1.80090] ((3 . 15) (4 . 16) (5 . 18) (6 . 19) (7 . 20)) 6.097 {0/4:10} B:0 3.43658 [ 3.49441] ((2 . 18) (3 . 19) (4 . 20) (6 . 22)) 6.096 {1/3:6} B:0 1.33547 [ 1.50150] ((2 . 22) (3 . 15) (4 . 16) (5 . 18) (6 . 19) (7 . 20)) 6.041 {0/7:15} B:1 1.47188 [ 1.60254] ((2 . 18) (3 . 19) (4 . 20) (5 . 22) (6 . 15) (9 . 17)) 4.889 {1/9:15} B:1 SIMILARITY (1/min{score1}): 0.7488 [and 1/min{score2}: 0.6660] [2773, 2265]: Comparing 1j98_A and 1hr6_A, based on their crossing files. There are 9 (5 H + 4 S) secondary structure elements in 1j98_A, of which 8 satisfy the size requirements. There are 32 (20 H + 12 S) secondary structure elements in 1hr6_A, of which 14 satisfy the size requirements. 2.00696 [ 3.50130] ((2 . 1) (3 . 2) (6 . 7) (8 . 10)) 11.005 {0/4:6} B:0 5.03234 [ 5.27691] ((5 . 7) (6 . 8) (7 . 9) (8 . 11)) 12.102 {2/4:6} B:0 1.14632 [ 2.00065] ((2 . 16) (3 . 3) (4 . 5) (5 . 7) (6 . 8) (7 . 9) (8 . 14)) 6.072 {0/11:21} B:1 4.02555 [ 4.22125] ((3 . 3) (4 . 10) (5 . 7) (6 . 8) (8 . 14)) 7.554 {2/5:10} B:1 6.01874 [ 6.16690] ((4 . 9) (5 . 8) (7 . 10) (9 . 14)) 11.467 {3/5:6} B:1 SIMILARITY (1/min{score1}): 0.8724 [and 1/min{score2}: 0.4998] [2773, 2266]: Comparing 1j98_A and 1hr6_A, based on their crossing files. There are 9 (5 H + 4 S) secondary structure elements in 1j98_A, of which 8 satisfy the size requirements. There are 32 (20 H + 12 S) secondary structure elements in 1hr6_A, of which 14 satisfy the size requirements. 2.00071 [ 3.50013] ((2 . 21) (3 . 23) (7 . 26) (8 . 28)) 6.205 {0/4:6} B:0 2.37868 [ 3.58986] ((3 . 23) (7 . 26) (8 . 28) (9 . 29)) 5.522 {1/5:6} B:0 6.68049 [ 6.79017] ((3 . 19) (4 . 20) (5 . 21) (9 . 26)) 12.982 {2/3:6} B:0 1.14617 [ 2.00062] ((2 . 30) (3 . 19) (4 . 22) (5 . 23) (6 . 24) (7 . 25) (8 . 29)) 6.008 {0/13:21} B:1 2.00150 [ 3.50028] ((5 . 21) (6 . 23) (7 . 22) (9 . 26)) 7.495 {0/5:6} B:1 SIMILARITY (1/min{score1}): 0.8725 [and 1/min{score2}: 0.4998] [2773, 2267]: Comparing 1j98_A and 1hr6_B, based on their crossing files. There are 9 (5 H + 4 S) secondary structure elements in 1j98_A, of which 8 satisfy the size requirements. There are 32 (20 H + 12 S) secondary structure elements in 1hr6_B, of which 14 satisfy the size requirements. 2.00753 [ 3.50141] ((2 . 1) (3 . 2) (6 . 7) (8 . 10)) 11.226 {0/4:6} B:0 2.37881 [ 3.58990] ((3 . 7) (7 . 10) (8 . 13) (9 . 14)) 6.113 {1/5:6} B:0 5.03226 [ 5.27684] ((5 . 7) (6 . 8) (7 . 9) (8 . 11)) 11.699 {2/4:6} B:0 1.14517 [ 2.00043] ((2 . 16) (3 . 3) (4 . 5) (5 . 7) (6 . 8) (7 . 9) (8 . 14)) 5.491 {0/11:21} B:1 3.53519 [ 3.58168] ((2 . 16) (3 . 3) (4 . 5) (5 . 7) (6 . 8) (7 . 9) (8 . 14) (9 . 17)) 5.919 {6/17:28} B:1 SIMILARITY (1/min{score1}): 0.8732 [and 1/min{score2}: 0.4999] [2773, 2268]: Comparing 1j98_A and 1hr6_B, based on their crossing files. There are 9 (5 H + 4 S) secondary structure elements in 1j98_A, of which 8 satisfy the size requirements. There are 32 (20 H + 12 S) secondary structure elements in 1hr6_B, of which 14 satisfy the size requirements. 1.73295 [ 2.82766] ((2 . 21) (3 . 23) (7 . 26) (8 . 28) (9 . 29)) 6.279 {1/8:10} B:0 2.00675 [ 3.50127] ((2 . 23) (3 . 24) (4 . 25) (7 . 28)) 10.923 {0/5:6} B:0 2.38017 [ 3.59029] ((5 . 21) (6 . 23) (8 . 25) (9 . 26)) 8.868 {1/5:6} B:0 3.43654 [ 4.06680] ((2 . 19) (5 . 23) (6 . 24) (7 . 25)) 5.590 {1/3:6} B:0 1.14381 [ 2.00018] ((2 . 30) (3 . 19) (4 . 20) (5 . 23) (6 . 24) (7 . 25) (8 . 29)) 4.395 {0/13:21} B:1 SIMILARITY (1/min{score1}): 0.8743 [and 1/min{score2}: 0.5000] [2773, 2750]: Comparing 1j98_A and 1j6w_A, based on their crossing files. There are 9 (5 H + 4 S) secondary structure elements in 1j98_A, of which 8 satisfy the size requirements. There are 12 (7 H + 5 S) secondary structure elements in 1j6w_A, of which 8 satisfy the size requirements. 1.14287 [ 1.14287] ((2 . 3) (3 . 4) (4 . 5) (5 . 6) (6 . 7) (7 . 8) (8 . 10)) 1.371 {0/16:21} B:0 5.03171 [ 5.03171] ((3 . 3) (4 . 5) (7 . 8) (8 . 10)) 4.792 {3/6:6} B:0 5.03172 [ 5.03172] ((2 . 4) (4 . 5) (7 . 8) (8 . 10)) 4.941 {3/6:6} B:0 SIMILARITY (1/min{score1}): 0.8750 [and 1/min{score2}: 0.8750] [2773, 2773]: Comparing 1j98_A and 1j98_A, based on their crossing files. There are 9 (5 H + 4 S) secondary structure elements in 1j98_A, of which 8 satisfy the size requirements. There are 9 (5 H + 4 S) secondary structure elements in 1j98_A, of which 8 satisfy the size requirements. 1.00000 [ 1.00000] ((2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9)) 0.000 {0/23:28} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [2773, 3494]: Comparing 1j98_A and 1l0l_A, based on their crossing files. There are 9 (5 H + 4 S) secondary structure elements in 1j98_A, of which 8 satisfy the size requirements. There are 32 (20 H + 12 S) secondary structure elements in 1l0l_A, of which 14 satisfy the size requirements. 2.00181 [ 3.50034] ((4 . 23) (5 . 24) (6 . 25) (7 . 26)) 7.856 {0/2:6} B:0 2.37878 [ 3.58989] ((3 . 24) (7 . 27) (8 . 29) (9 . 30)) 6.014 {1/5:6} B:0 2.38215 [ 3.59087] ((2 . 22) (3 . 24) (7 . 27) (8 . 30)) 10.723 {1/5:6} B:0 2.72513 [ 3.70883] ((5 . 22) (6 . 24) (8 . 26) (9 . 27)) 8.703 {1/4:6} B:0 1.01742 [ 1.75333] ((2 . 31) (3 . 20) (4 . 21) (5 . 24) (6 . 25) (7 . 27) (8 . 29) (9 . 30)) 6.594 {1/22:28} B:1 SIMILARITY (1/min{score1}): 0.9829 [and 1/min{score2}: 0.5703] [2773, 3495]: Comparing 1j98_A and 1l0l_B, based on their crossing files. There are 9 (5 H + 4 S) secondary structure elements in 1j98_A, of which 8 satisfy the size requirements. There are 30 (19 H + 11 S) secondary structure elements in 1l0l_B, of which 14 satisfy the size requirements. 2.00587 [ 3.50110] ((2 . 1) (3 . 2) (6 . 7) (8 . 10)) 10.544 {0/4:6} B:0 2.72766 [ 3.70984] ((5 . 7) (6 . 8) (7 . 9) (8 . 11)) 11.771 {1/4:6} B:0 6.01875 [ 6.16691] ((4 . 9) (7 . 10) (8 . 13) (9 . 14)) 11.568 {3/5:6} B:0 3.34026 [ 3.39510] ((2 . 16) (3 . 3) (4 . 5) (5 . 7) (6 . 8) (7 . 9) (8 . 14) (9 . 17)) 6.594 {5/15:28} B:1 5.01316 [ 5.11874] ((2 . 3) (3 . 7) (4 . 10) (6 . 8) (7 . 14)) 7.579 {3/6:10} B:1 SIMILARITY (1/min{score1}): 0.4985 [and 1/min{score2}: 0.2945] [2773, 3496]: Comparing 1j98_A and 1l0l_B, based on their crossing files. There are 9 (5 H + 4 S) secondary structure elements in 1j98_A, of which 8 satisfy the size requirements. There are 30 (19 H + 11 S) secondary structure elements in 1l0l_B, of which 12 satisfy the size requirements. 2.00046 [ 3.00014] ((3 . 22) (7 . 25) (8 . 27) (9 . 28)) 5.577 {0/5:6} B:0 2.00969 [ 3.00289] ((2 . 22) (3 . 23) (4 . 24) (7 . 27)) 11.963 {0/5:6} B:0 4.02555 [ 4.12392] ((2 . 19) (4 . 21) (5 . 22) (6 . 23) (7 . 24)) 7.587 {2/5:10} B:0 4.30746 [ 4.38843] ((4 . 21) (5 . 22) (6 . 23) (7 . 24) (8 . 26)) 12.274 {3/7:10} B:0 1.14546 [ 1.71506] ((2 . 29) (3 . 19) (4 . 21) (5 . 22) (6 . 23) (7 . 24) (8 . 28)) 5.651 {0/13:21} B:1 SIMILARITY (1/min{score1}): 0.8730 [and 1/min{score2}: 0.5831] -------------------------------------------------------------------------------------------------------------------------