------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [1768, 1607]: Comparing 1g8k_B and 1fqt_A, based on their crossing files. There are 12 (2 H + 10 S) secondary structure elements in 1g8k_B, of which 11 satisfy the size requirements. There are 11 (1 H + 10 S) secondary structure elements in 1fqt_A, of which 9 satisfy the size requirements. 1.22239 [ 1.00031] ((1 . 1) (3 . 3) (4 . 4) (5 . 5) (7 . 7) (8 . 8) (10 . 9) (11 . 10) (12 . 11)) 2.997 {0/29:36} B:0 1.37511 [ 1.12520] ((1 . 1) (3 . 3) (4 . 4) (5 . 5) (8 . 8) (10 . 9) (11 . 10) (12 . 11)) 2.951 {0/24:28} B:0 2.20155 [ 1.80282] ((5 . 4) (6 . 5) (8 . 7) (10 . 8) (12 . 10)) 8.107 {0/9:10} B:0 2.20311 [ 1.80566] ((5 . 1) (6 . 3) (7 . 4) (8 . 5) (11 . 7)) 9.658 {0/6:10} B:0 2.75006 [ 2.25011] ((1 . 1) (3 . 3) (6 . 8) (7 . 9)) 4.227 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.8181 [and 1/min{score2}: 0.9997] [1768, 1768]: Comparing 1g8k_B and 1g8k_B, based on their crossing files. There are 12 (2 H + 10 S) secondary structure elements in 1g8k_B, of which 11 satisfy the size requirements. There are 12 (2 H + 10 S) secondary structure elements in 1g8k_B, of which 11 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12)) 0.000 {0/46:55} B:0 2.75189 [ 2.75189] ((5 . 1) (6 . 3) (7 . 4) (11 . 6)) 10.075 {0/1:6} B:0 2.75189 [ 2.75189] ((1 . 5) (3 . 6) (4 . 7) (6 . 11)) 10.075 {0/1:6} B:0 2.75244 [ 2.75244] ((1 . 4) (5 . 7) (8 . 11) (10 . 12)) 10.741 {0/5:6} B:0 2.75244 [ 2.75244] ((4 . 1) (7 . 5) (11 . 8) (12 . 10)) 10.741 {0/5:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [1768, 2966]: Comparing 1g8k_B and 1jm1_A, based on their crossing files. There are 12 (2 H + 10 S) secondary structure elements in 1g8k_B, of which 11 satisfy the size requirements. There are 19 (5 H + 14 S) secondary structure elements in 1jm1_A, of which 17 satisfy the size requirements. 1.10001 [ 1.70000] ((1 . 1) (3 . 3) (4 . 4) (5 . 9) (6 . 11) (7 . 12) (8 . 13) (10 . 15) (11 . 16) (12 . 17)) 1.443 {0/35:45} B:0 1.83335 [ 2.83334] ((5 . 9) (6 . 10) (8 . 13) (10 . 15) (11 . 16) (12 . 17)) 2.331 {0/15:15} B:0 2.20024 [ 3.40007] ((3 . 8) (4 . 9) (6 . 12) (7 . 13) (11 . 17)) 5.104 {0/5:10} B:0 2.20057 [ 3.40016] ((3 . 1) (4 . 3) (5 . 4) (10 . 8) (11 . 9)) 6.330 {0/7:10} B:0 2.20067 [ 3.40018] ((4 . 3) (5 . 4) (6 . 6) (7 . 8) (12 . 11)) 6.580 {0/4:10} B:0 SIMILARITY (1/min{score1}): 0.9091 [and 1/min{score2}: 0.5882] [1768, 4440]: Comparing 1g8k_B and 1nyk_A, based on their crossing files. There are 12 (2 H + 10 S) secondary structure elements in 1g8k_B, of which 11 satisfy the size requirements. There are 18 (7 H + 11 S) secondary structure elements in 1nyk_A, of which 12 satisfy the size requirements. 1.05051 [ 1.13064] ((1 . 2) (3 . 4) (4 . 6) (5 . 9) (6 . 10) (7 . 12) (8 . 13) (9 . 14) (10 . 15) (11 . 17) (12 . 18)) 3.283 {3/44:55} B:0 1.17365 [ 1.25830] ((3 . 4) (4 . 6) (5 . 9) (6 . 10) (7 . 12) (8 . 13) (9 . 14) (10 . 15) (11 . 17) (12 . 18)) 2.909 {3/37:45} B:0 1.17376 [ 1.25839] ((1 . 2) (3 . 4) (4 . 6) (5 . 9) (7 . 12) (8 . 13) (9 . 14) (10 . 15) (11 . 17) (12 . 18)) 3.298 {3/37:45} B:0 2.23538 [ 2.42744] ((1 . 2) (3 . 4) (4 . 6) (8 . 10) (9 . 14)) 5.977 {1/9:10} B:0 2.75008 [ 3.00006] ((3 . 4) (4 . 6) (8 . 10) (10 . 12)) 4.622 {0/5:6} B:0 SIMILARITY (1/min{score1}): 0.9519 [and 1/min{score2}: 0.8845] [1768, 4541]: Comparing 1g8k_B and 1o7n_A, based on their crossing files. There are 12 (2 H + 10 S) secondary structure elements in 1g8k_B, of which 11 satisfy the size requirements. There are 41 (19 H + 22 S) secondary structure elements in 1o7n_A, of which 13 satisfy the size requirements. 1.10045 [ 1.30028] ((1 . 5) (3 . 7) (4 . 8) (5 . 9) (6 . 10) (7 . 11) (8 . 12) (10 . 13) (11 . 16) (12 . 17)) 3.549 {0/35:45} B:0 2.20003 [ 2.60002] ((1 . 5) (3 . 7) (6 . 12) (11 . 16) (12 . 17)) 3.010 {0/6:10} B:0 2.20079 [ 2.60048] ((5 . 5) (6 . 7) (7 . 8) (8 . 9) (10 . 10)) 6.862 {0/6:10} B:0 2.20247 [ 2.60150] ((5 . 5) (6 . 7) (7 . 8) (8 . 9) (12 . 12)) 9.117 {0/6:10} B:0 2.75019 [ 3.25012] ((4 . 5) (5 . 7) (8 . 10) (10 . 11)) 5.676 {0/5:6} B:0 SIMILARITY (1/min{score1}): 0.9087 [and 1/min{score2}: 0.7691] [1768, 5622]: Comparing 1g8k_B and 1rfs, based on their crossing files. There are 12 (2 H + 10 S) secondary structure elements in 1g8k_B, of which 11 satisfy the size requirements. There are 11 (2 H + 9 S) secondary structure elements in 1rfs, of which 9 satisfy the size requirements. 1.37504 [ 1.12507] ((3 . 2) (4 . 4) (5 . 5) (7 . 7) (8 . 8) (10 . 9) (11 . 10) (12 . 11)) 2.247 {0/23:28} B:0 2.75015 [ 2.25028] ((6 . 2) (7 . 4) (11 . 7) (12 . 8)) 5.385 {0/4:6} B:0 2.75017 [ 2.25031] ((3 . 4) (4 . 5) (7 . 10) (8 . 11)) 5.495 {0/4:6} B:0 2.75017 [ 2.25031] ((1 . 4) (3 . 5) (6 . 10) (7 . 11)) 5.528 {0/3:6} B:0 2.75041 [ 2.25074] ((6 . 4) (7 . 5) (11 . 8) (12 . 9)) 6.859 {0/5:6} B:0 SIMILARITY (1/min{score1}): 0.7273 [and 1/min{score2}: 0.8888] [1768, 5644]: Comparing 1g8k_B and 1rie, based on their crossing files. There are 12 (2 H + 10 S) secondary structure elements in 1g8k_B, of which 11 satisfy the size requirements. There are 14 (4 H + 10 S) secondary structure elements in 1rie, of which 10 satisfy the size requirements. 1.22237 [ 1.11130] ((1 . 1) (3 . 3) (4 . 4) (5 . 8) (7 . 10) (8 . 11) (10 . 12) (11 . 13) (12 . 14)) 2.877 {0/26:36} B:0 1.37511 [ 1.25015] ((1 . 1) (3 . 3) (4 . 4) (5 . 8) (7 . 10) (8 . 11) (11 . 13) (12 . 14)) 2.954 {0/18:28} B:0 2.20083 [ 2.00110] ((3 . 1) (4 . 3) (5 . 4) (8 . 8) (11 . 10)) 6.939 {0/5:10} B:0 2.20091 [ 2.00121] ((3 . 1) (4 . 3) (5 . 4) (11 . 10) (12 . 11)) 7.096 {0/6:10} B:0 2.20195 [ 2.00259] ((1 . 1) (3 . 3) (4 . 4) (11 . 11) (12 . 12)) 8.587 {0/9:10} B:0 SIMILARITY (1/min{score1}): 0.8181 [and 1/min{score2}: 0.8998] -------------------------------------------------------------------------------------------------------------------------