------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [4767, 39]: Comparing 1oru_A and 1a49_A, based on their crossing files. There are 17 (5 H + 12 S) secondary structure elements in 1oru_A, of which 17 satisfy the size requirements. There are 41 (21 H + 20 S) secondary structure elements in 1a49_A, of which 7 satisfy the size requirements. 3.54555 [ 2.30517] ((6 . 10) (8 . 11) (9 . 12) (11 . 13) (12 . 14)) 4.883 {2/9:10} B:0 4.25008 [ 1.75114] ((10 . 11) (11 . 12) (12 . 13) (15 . 16)) 6.332 {0/5:6} B:0 4.30165 [ 2.24782] ((2 . 12) (4 . 14) (5 . 15) (6 . 16)) 9.972 {1/5:6} B:0 4.91231 [ 4.03630] ((8 . 11) (11 . 12) (12 . 13) (15 . 16)) 7.168 {2/5:6} B:0 3.90513 [ 3.75484] ((1 . 16) (6 . 10) (7 . 11) (9 . 12) (11 . 13) (12 . 14) (15 . 15)) 6.215 {6/16:21} B:1 SIMILARITY (1/min{score1}): 0.3529 [and 1/min{score2}: 0.8555] [4767, 994]: Comparing 1oru_A and 1e0t_A, based on their crossing files. There are 17 (5 H + 12 S) secondary structure elements in 1oru_A, of which 17 satisfy the size requirements. There are 39 (17 H + 22 S) secondary structure elements in 1e0t_A, of which 9 satisfy the size requirements. 1.88893 [ 1.00030] ((3 . 9) (6 . 10) (9 . 11) (10 . 12) (11 . 13) (12 . 14) (15 . 15) (16 . 16) (17 . 17)) 2.982 {0/26:36} B:0 4.25024 [ 2.25165] ((8 . 12) (9 . 13) (11 . 14) (12 . 15)) 8.377 {0/5:6} B:0 4.37191 [ 2.83619] ((12 . 11) (15 . 15) (16 . 16) (17 . 17)) 5.532 {1/4:6} B:0 4.37234 [ 2.83774] ((1 . 9) (2 . 10) (3 . 11) (9 . 17)) 10.052 {1/4:6} B:0 4.37238 [ 2.83791] ((9 . 9) (12 . 11) (15 . 16) (16 . 17)) 10.285 {1/4:6} B:0 SIMILARITY (1/min{score1}): 0.5294 [and 1/min{score2}: 0.9997] [4767, 4507]: Comparing 1oru_A and 1o65_A, based on their crossing files. There are 17 (5 H + 12 S) secondary structure elements in 1oru_A, of which 17 satisfy the size requirements. There are 22 (10 H + 12 S) secondary structure elements in 1o65_A, of which 19 satisfy the size requirements. 1.38705 [ 1.52015] ((1 . 3) (2 . 4) (3 . 5) (6 . 8) (7 . 9) (9 . 11) (11 . 12) (12 . 13) (13 . 14) (14 . 15) (15 . 16) (16 . 17) (17 . 18)) 4.173 {6/64:78} B:0 1.82444 [ 1.94380] ((1 . 3) (2 . 4) (3 . 5) (6 . 8) (9 . 11) (11 . 12) (12 . 13) (13 . 15) (15 . 16) (16 . 17) (17 . 18)) 5.347 {7/46:55} B:0 3.41005 [ 3.80721] ((9 . 3) (11 . 5) (13 . 9) (14 . 10) (17 . 12)) 8.032 {1/9:10} B:0 3.41603 [ 3.81151] ((9 . 3) (11 . 5) (14 . 10) (15 . 11) (17 . 12)) 8.903 {1/8:10} B:0 4.25020 [ 4.75014] ((10 . 1) (11 . 3) (12 . 4) (17 . 11)) 7.934 {0/5:6} B:0 SIMILARITY (1/min{score1}): 0.7210 [and 1/min{score2}: 0.6578] [4767, 4767]: Comparing 1oru_A and 1oru_A, based on their crossing files. There are 17 (5 H + 12 S) secondary structure elements in 1oru_A, of which 17 satisfy the size requirements. There are 17 (5 H + 12 S) secondary structure elements in 1oru_A, of which 17 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) (10 . 10) (11 . 11) (12 . 12) (13 . 13) (14 . 14) (15 . 15) (16 . 16) (17 . 17)) 0.000 {0/118:136} B:0 2.16549 [ 2.16549] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (8 . 8) (9 . 9) (11 . 12) (14 . 13) (15 . 15) (16 . 16) (17 . 17)) 3.324 {14/67:78} B:0 3.54578 [ 3.54578] ((1 . 1) (2 . 2) (3 . 3) (11 . 9) (16 . 15)) 7.535 {2/9:10} B:0 4.25026 [ 4.25026] ((3 . 1) (4 . 2) (10 . 7) (12 . 9)) 8.514 {0/3:6} B:0 4.25026 [ 4.25026] ((1 . 3) (2 . 4) (7 . 10) (9 . 12)) 8.514 {0/3:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [4767, 5038]: Comparing 1oru_A and 1pkl_A, based on their crossing files. There are 17 (5 H + 12 S) secondary structure elements in 1oru_A, of which 17 satisfy the size requirements. There are 45 (23 H + 22 S) secondary structure elements in 1pkl_A, of which 9 satisfy the size requirements. 1.88894 [ 1.00033] ((3 . 9) (6 . 10) (9 . 12) (10 . 13) (11 . 14) (12 . 15) (15 . 16) (16 . 17) (17 . 18)) 3.041 {0/29:36} B:0 1.89777 [ 1.05549] ((1 . 9) (6 . 10) (9 . 12) (10 . 13) (11 . 14) (12 . 15) (15 . 16) (16 . 17) (17 . 18)) 5.589 {2/29:36} B:0 2.21028 [ 1.50112] ((3 . 9) (6 . 10) (8 . 13) (11 . 14) (12 . 15) (15 . 16) (16 . 17) (17 . 18)) 5.868 {3/22:28} B:0 3.54567 [ 2.43078] ((6 . 9) (9 . 12) (10 . 13) (11 . 14) (12 . 15)) 6.583 {2/9:10} B:0 4.25033 [ 2.25225] ((13 . 13) (15 . 16) (16 . 17) (17 . 18)) 9.058 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.5294 [and 1/min{score2}: 0.9997] -------------------------------------------------------------------------------------------------------------------------