------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [2297, 470]: Comparing 1hv2_A and 1buo_A, based on their crossing files. There are 7 (4 H + 3 S) secondary structure elements in 1hv2_A, of which 7 satisfy the size requirements. There are 9 (6 H + 3 S) secondary structure elements in 1buo_A, of which 9 satisfy the size requirements. 1.00020 [ 1.28581] ((1 . 2) (2 . 3) (3 . 4) (4 . 5) (5 . 6) (6 . 7) (7 . 8)) 2.693 {0/18:21} B:0 1.16677 [ 1.50005] ((1 . 2) (2 . 3) (3 . 4) (4 . 5) (5 . 6) (6 . 7)) 2.538 {0/12:15} B:0 3.39503 [ 3.49440] ((4 . 4) (5 . 6) (6 . 7) (7 . 8)) 5.857 {2/6:6} B:0 1.76085 [ 2.25513] ((3 . 5) (4 . 7) (5 . 6) (6 . 8)) 11.137 {0/6:6} B:1 4.03626 [ 4.09667] ((1 . 3) (2 . 2) (3 . 5) (4 . 4)) 6.747 {2/5:6} B:2 SIMILARITY (1/min{score1}): 0.9998 [and 1/min{score2}: 0.7777] [2297, 2297]: Comparing 1hv2_A and 1hv2_A, based on their crossing files. There are 7 (4 H + 3 S) secondary structure elements in 1hv2_A, of which 7 satisfy the size requirements. There are 7 (4 H + 3 S) secondary structure elements in 1hv2_A, of which 7 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7)) 0.000 {0/19:21} B:0 2.63821 [ 2.63821] ((1 . 2) (5 . 5) (6 . 6) (7 . 7)) 3.427 {1/4:6} B:0 2.63821 [ 2.63821] ((2 . 1) (5 . 5) (6 . 6) (7 . 7)) 3.427 {1/4:6} B:0 4.03616 [ 4.03616] ((1 . 2) (4 . 4) (6 . 6) (7 . 7)) 3.968 {2/5:6} B:0 6.01087 [ 6.01087] ((2 . 5) (3 . 4) (6 . 6) (7 . 7)) 7.144 {3/5:6} B:1 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [2297, 3663]: Comparing 1hv2_A and 1lm8_C, based on their crossing files. There are 7 (4 H + 3 S) secondary structure elements in 1hv2_A, of which 7 satisfy the size requirements. There are 7 (4 H + 3 S) secondary structure elements in 1lm8_C, of which 7 satisfy the size requirements. 1.00009 [ 1.00009] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7)) 2.220 {0/17:21} B:0 2.63824 [ 2.63824] ((2 . 1) (5 . 5) (6 . 6) (7 . 7)) 4.179 {1/4:6} B:0 3.39500 [ 3.39500] ((3 . 4) (5 . 5) (6 . 6) (7 . 7)) 5.400 {2/6:6} B:0 4.03619 [ 4.03619] ((4 . 3) (5 . 5) (6 . 6) (7 . 7)) 5.321 {2/5:6} B:0 2.25256 [ 2.25256] ((4 . 3) (5 . 2) (6 . 4) (7 . 6)) 12.451 {1/5:6} B:1 SIMILARITY (1/min{score1}): 0.9999 [and 1/min{score2}: 0.9999] [2297, 4319]: Comparing 1hv2_A and 1nn7_A, based on their crossing files. There are 7 (4 H + 3 S) secondary structure elements in 1hv2_A, of which 7 satisfy the size requirements. There are 10 (6 H + 4 S) secondary structure elements in 1nn7_A, of which 8 satisfy the size requirements. 1.02330 [ 1.15869] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 7) (6 . 8) (7 . 9)) 3.011 {1/18:21} B:0 1.16676 [ 1.33340] ((1 . 1) (2 . 2) (3 . 3) (5 . 7) (6 . 8) (7 . 9)) 2.509 {0/12:15} B:0 1.23630 [ 1.38164] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 7) (6 . 8)) 3.010 {1/12:15} B:0 3.39503 [ 3.43656] ((4 . 3) (5 . 7) (6 . 8) (7 . 9)) 5.858 {2/6:6} B:0 1.40030 [ 1.60020] ((1 . 2) (2 . 1) (3 . 3) (5 . 7) (6 . 8)) 3.824 {0/5:10} B:1 SIMILARITY (1/min{score1}): 0.9772 [and 1/min{score2}: 0.8630] [2297, 5529]: Comparing 1hv2_A and 1r29_A, based on their crossing files. There are 7 (4 H + 3 S) secondary structure elements in 1hv2_A, of which 7 satisfy the size requirements. There are 9 (6 H + 3 S) secondary structure elements in 1r29_A, of which 9 satisfy the size requirements. 1.00031 [ 1.28586] ((1 . 2) (2 . 3) (3 . 4) (4 . 5) (5 . 6) (6 . 7) (7 . 8)) 3.012 {0/18:21} B:0 1.16683 [ 1.50007] ((1 . 2) (2 . 3) (3 . 4) (4 . 5) (5 . 6) (6 . 7)) 2.852 {0/12:15} B:0 3.39505 [ 3.49442] ((4 . 4) (5 . 6) (6 . 7) (7 . 8)) 6.111 {2/6:6} B:0 1.65271 [ 1.80737] ((1 . 3) (3 . 4) (4 . 5) (5 . 2) (6 . 7) (7 . 8)) 4.478 {2/13:15} B:1 2.25187 [ 2.54518] ((4 . 4) (5 . 3) (6 . 5) (7 . 7)) 12.174 {1/5:6} B:1 SIMILARITY (1/min{score1}): 0.9997 [and 1/min{score2}: 0.7777] [2297, 5875]: Comparing 1hv2_A and 1t1d_A, based on their crossing files. There are 7 (4 H + 3 S) secondary structure elements in 1hv2_A, of which 7 satisfy the size requirements. There are 9 (5 H + 4 S) secondary structure elements in 1t1d_A, of which 8 satisfy the size requirements. 1.02894 [ 1.16259] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 6) (6 . 7) (7 . 8)) 2.944 {1/17:21} B:0 1.16674 [ 1.33338] ((1 . 1) (2 . 2) (3 . 3) (5 . 6) (6 . 7) (7 . 8)) 2.353 {0/11:15} B:0 1.40004 [ 1.60002] ((1 . 1) (2 . 2) (3 . 3) (5 . 6) (6 . 7)) 2.276 {0/6:10} B:0 2.63823 [ 2.72409] ((2 . 1) (5 . 6) (6 . 7) (7 . 8)) 3.934 {1/4:6} B:0 3.39503 [ 3.43656] ((4 . 3) (5 . 6) (6 . 7) (7 . 8)) 5.825 {2/6:6} B:0 SIMILARITY (1/min{score1}): 0.9719 [and 1/min{score2}: 0.8602] [2297, 6575]: Comparing 1hv2_A and 3kvt, based on their crossing files. There are 7 (4 H + 3 S) secondary structure elements in 1hv2_A, of which 7 satisfy the size requirements. There are 10 (6 H + 4 S) secondary structure elements in 3kvt, of which 6 satisfy the size requirements. 1.16679 [ 1.00019] ((1 . 1) (2 . 2) (3 . 3) (5 . 5) (6 . 6) (7 . 7)) 2.671 {0/11:15} B:0 1.58359 [ 1.45816] ((1 . 2) (3 . 3) (5 . 5) (6 . 6) (7 . 7)) 4.418 {1/8:10} B:0 1.75023 [ 1.50037] ((1 . 1) (2 . 2) (5 . 5) (7 . 6)) 4.260 {0/2:6} B:0 2.63825 [ 2.57742] ((2 . 1) (5 . 5) (6 . 6) (7 . 7)) 4.342 {1/4:6} B:0 3.39504 [ 3.36713] ((4 . 3) (5 . 5) (6 . 6) (7 . 7)) 6.057 {2/6:6} B:0 SIMILARITY (1/min{score1}): 0.8571 [and 1/min{score2}: 0.9998] -------------------------------------------------------------------------------------------------------------------------