------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [4265, 1910]: Comparing 1ni4_B and 1gpu_A, based on their crossing files. There are 31 (17 H + 14 S) secondary structure elements in 1ni4_B, of which 12 satisfy the size requirements. There are 51 (31 H + 20 S) secondary structure elements in 1gpu_A, of which 12 satisfy the size requirements. 1.20229 [ 1.20229] ((20 . 41) (21 . 42) (22 . 43) (23 . 44) (25 . 46) (26 . 47) (27 . 48) (29 . 49) (30 . 50) (31 . 51)) 3.276 {1/29:45} B:0 1.33346 [ 1.33346] ((20 . 41) (21 . 42) (22 . 43) (23 . 44) (25 . 46) (26 . 47) (27 . 48) (29 . 49) (31 . 51)) 2.980 {0/22:36} B:0 1.33929 [ 1.33929] ((20 . 41) (21 . 42) (22 . 43) (23 . 44) (25 . 45) (26 . 47) (27 . 48) (29 . 49) (31 . 51)) 4.340 {1/21:36} B:0 1.50040 [ 1.50040] ((21 . 42) (22 . 43) (23 . 44) (25 . 45) (26 . 47) (27 . 48) (29 . 49) (31 . 51)) 4.326 {0/13:28} B:0 1.71492 [ 1.71492] ((21 . 42) (22 . 43) (23 . 44) (26 . 47) (27 . 48) (29 . 49) (31 . 50)) 5.379 {0/11:21} B:0 SIMILARITY (1/min{score1}): 0.8317 [and 1/min{score2}: 0.8317] [4265, 2605]: Comparing 1ni4_B and 1itz_A, based on their crossing files. There are 31 (17 H + 14 S) secondary structure elements in 1ni4_B, of which 12 satisfy the size requirements. There are 49 (32 H + 17 S) secondary structure elements in 1itz_A, of which 12 satisfy the size requirements. 1.20222 [ 1.20222] ((20 . 39) (21 . 40) (22 . 41) (23 . 42) (25 . 44) (26 . 45) (27 . 46) (29 . 47) (30 . 48) (31 . 49)) 2.998 {1/29:45} B:0 1.33337 [ 1.33337] ((20 . 39) (21 . 40) (22 . 41) (23 . 42) (26 . 45) (27 . 46) (29 . 47) (30 . 48) (31 . 49)) 2.193 {0/23:36} B:0 3.00011 [ 3.00011] ((21 . 45) (22 . 46) (23 . 47) (27 . 49)) 5.273 {0/1:6} B:0 3.00020 [ 3.00020] ((21 . 42) (23 . 45) (25 . 46) (26 . 47)) 6.143 {0/1:6} B:0 3.00032 [ 3.00032] ((22 . 43) (25 . 46) (26 . 47) (27 . 49)) 6.894 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.8318 [and 1/min{score2}: 0.8318] [4265, 3276]: Comparing 1ni4_B and 1kek_A, based on their crossing files. There are 31 (17 H + 14 S) secondary structure elements in 1ni4_B, of which 12 satisfy the size requirements. There are 87 (51 H + 36 S) secondary structure elements in 1kek_A, of which 10 satisfy the size requirements. 1.20016 [ 1.00028] ((20 . 21) (21 . 22) (22 . 23) (23 . 24) (24 . 25) (25 . 26) (26 . 27) (27 . 28) (29 . 29) (31 . 31)) 2.935 {0/29:45} B:0 1.33338 [ 1.11119] ((20 . 21) (21 . 22) (22 . 23) (23 . 24) (24 . 25) (26 . 27) (27 . 28) (29 . 29) (31 . 31)) 2.341 {0/24:36} B:0 1.33347 [ 1.11135] ((20 . 21) (21 . 22) (22 . 23) (23 . 24) (25 . 26) (26 . 27) (27 . 28) (29 . 29) (31 . 31)) 3.037 {0/20:36} B:0 2.40032 [ 2.00055] ((22 . 23) (23 . 25) (25 . 26) (27 . 28) (29 . 29)) 5.821 {0/6:10} B:0 3.00021 [ 2.50036] ((25 . 23) (26 . 24) (27 . 26) (29 . 27)) 6.205 {0/0:6} B:0 SIMILARITY (1/min{score1}): 0.8332 [and 1/min{score2}: 0.9997] [4265, 3568]: Comparing 1ni4_B and 1l8a_A, based on their crossing files. There are 31 (17 H + 14 S) secondary structure elements in 1ni4_B, of which 12 satisfy the size requirements. There are 58 (40 H + 18 S) secondary structure elements in 1l8a_A, of which 13 satisfy the size requirements. 1.20311 [ 1.30245] ((20 . 46) (21 . 47) (22 . 48) (23 . 49) (25 . 51) (26 . 52) (27 . 53) (29 . 55) (30 . 56) (31 . 57)) 4.316 {1/28:45} B:0 1.33378 [ 1.44479] ((20 . 46) (21 . 47) (22 . 48) (23 . 49) (25 . 51) (26 . 52) (27 . 53) (29 . 55) (31 . 57)) 4.076 {0/21:36} B:0 1.33737 [ 1.44762] ((20 . 46) (21 . 47) (22 . 48) (23 . 49) (25 . 51) (26 . 52) (29 . 55) (30 . 56) (31 . 57)) 3.654 {1/23:36} B:0 2.00015 [ 2.16679] ((20 . 46) (21 . 47) (22 . 48) (23 . 49) (27 . 51) (29 . 55)) 4.234 {0/9:15} B:0 2.00016 [ 2.16679] ((20 . 46) (21 . 47) (22 . 48) (23 . 49) (27 . 51) (29 . 52)) 4.277 {0/8:15} B:0 SIMILARITY (1/min{score1}): 0.8312 [and 1/min{score2}: 0.7678] [4265, 4265]: Comparing 1ni4_B and 1ni4_B, based on their crossing files. There are 31 (17 H + 14 S) secondary structure elements in 1ni4_B, of which 12 satisfy the size requirements. There are 31 (17 H + 14 S) secondary structure elements in 1ni4_B, of which 12 satisfy the size requirements. 1.00000 [ 1.00000] ((20 . 20) (21 . 21) (22 . 22) (23 . 23) (24 . 24) (25 . 25) (26 . 26) (27 . 27) (28 . 28) (29 . 29) (30 . 30) (31 . 31)) 0.000 {0/50:66} B:0 1.09091 [ 1.09091] ((20 . 20) (21 . 21) (22 . 22) (23 . 23) (24 . 24) (25 . 25) (26 . 26) (27 . 27) (29 . 29) (30 . 30) (31 . 31)) 0.000 {0/41:55} B:0 2.40075 [ 2.40075] ((22 . 22) (25 . 25) (26 . 26) (29 . 29) (30 . 31)) 7.231 {0/6:10} B:0 2.40075 [ 2.40075] ((22 . 22) (25 . 25) (26 . 26) (29 . 29) (31 . 30)) 7.231 {0/6:10} B:0 2.40082 [ 2.40082] ((23 . 21) (25 . 22) (26 . 23) (29 . 26) (31 . 27)) 7.395 {0/3:10} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [4265, 4704]: Comparing 1ni4_B and 1ols_B, based on their crossing files. There are 31 (17 H + 14 S) secondary structure elements in 1ni4_B, of which 12 satisfy the size requirements. There are 29 (15 H + 14 S) secondary structure elements in 1ols_B, of which 11 satisfy the size requirements. 1.09100 [ 1.00012] ((20 . 19) (21 . 20) (22 . 21) (23 . 22) (24 . 23) (25 . 24) (26 . 25) (27 . 26) (29 . 27) (30 . 28) (31 . 29)) 2.371 {0/35:55} B:0 1.20007 [ 1.10009] ((20 . 19) (21 . 20) (22 . 21) (23 . 22) (24 . 23) (25 . 24) (26 . 25) (27 . 26) (29 . 27) (31 . 29)) 2.399 {0/30:45} B:0 3.00007 [ 2.75009] ((26 . 20) (27 . 21) (29 . 22) (31 . 26)) 4.666 {0/0:6} B:0 3.00018 [ 2.75024] ((21 . 25) (22 . 26) (23 . 27) (27 . 29)) 6.004 {0/1:6} B:0 3.00081 [ 2.75105] ((22 . 24) (25 . 26) (26 . 27) (27 . 29)) 8.696 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.9166 [and 1/min{score2}: 0.9999] -------------------------------------------------------------------------------------------------------------------------