------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [3120, 1147]: Comparing 1k0r_A and 1ega_A, based on their crossing files. There are 25 (12 H + 13 S) secondary structure elements in 1k0r_A, of which 6 satisfy the size requirements. There are 19 (9 H + 10 S) secondary structure elements in 1ega_A, of which 7 satisfy the size requirements. 1.00064 [ 1.16707] ((20 . 13) (21 . 14) (22 . 15) (23 . 16) (24 . 17) (25 . 18)) 3.599 {0/12:15} B:0 1.50095 [ 1.75060] ((20 . 13) (21 . 14) (22 . 15) (24 . 16)) 5.386 {0/5:6} B:0 1.50228 [ 1.75144] ((20 . 13) (22 . 15) (24 . 16) (25 . 18)) 6.707 {0/4:6} B:0 3.75985 [ 3.76814] ((20 . 13) (21 . 15) (23 . 16) (24 . 17) (25 . 18)) 5.437 {3/8:10} B:0 4.01995 [ 4.03646] ((20 . 13) (22 . 14) (24 . 16) (25 . 15)) 8.597 {2/5:6} B:1 SIMILARITY (1/min{score1}): 0.9994 [and 1/min{score2}: 0.8568] [3120, 1517]: Comparing 1k0r_A and 1fjg_C, based on their crossing files. There are 25 (12 H + 13 S) secondary structure elements in 1k0r_A, of which 6 satisfy the size requirements. There are 15 (8 H + 7 S) secondary structure elements in 1fjg_C, of which 7 satisfy the size requirements. 1.00383 [ 1.16908] ((20 . 2) (21 . 3) (22 . 4) (23 . 5) (24 . 6) (25 . 7)) 5.637 {0/12:15} B:0 1.20448 [ 1.40283] ((20 . 2) (21 . 3) (22 . 4) (24 . 5) (25 . 7)) 6.721 {0/7:10} B:0 5.01025 [ 5.01881] ((20 . 5) (21 . 4) (23 . 6) (25 . 7)) 8.447 {2/4:6} B:1 2.57801 [ 2.63881] ((20 . 5) (21 . 4) (22 . 7) (23 . 6)) 7.427 {1/4:6} B:2 SIMILARITY (1/min{score1}): 0.9962 [and 1/min{score2}: 0.8554] [3120, 1903]: Comparing 1k0r_A and 1gpm_A, based on their crossing files. There are 25 (12 H + 13 S) secondary structure elements in 1k0r_A, of which 6 satisfy the size requirements. There are 38 (17 H + 21 S) secondary structure elements in 1gpm_A, of which 7 satisfy the size requirements. 1.20116 [ 1.40073] ((20 . 32) (21 . 34) (22 . 35) (24 . 37) (25 . 38)) 4.785 {0/8:10} B:0 3.76004 [ 3.76833] ((20 . 32) (21 . 34) (22 . 35) (24 . 37) (25 . 36)) 7.705 {3/8:10} B:1 SIMILARITY (1/min{score1}): 0.8325 [and 1/min{score2}: 0.7139] [3120, 3005]: Comparing 1k0r_A and 1jos_A, based on their crossing files. There are 25 (12 H + 13 S) secondary structure elements in 1k0r_A, of which 6 satisfy the size requirements. There are 6 (3 H + 3 S) secondary structure elements in 1jos_A, of which 6 satisfy the size requirements. 1.13999 [ 1.13999] ((20 . 1) (21 . 2) (22 . 3) (23 . 4) (24 . 5) (25 . 6)) 4.430 {1/11:15} B:0 1.20164 [ 1.20164] ((20 . 1) (21 . 2) (22 . 3) (24 . 4) (25 . 6)) 5.227 {0/6:10} B:0 2.57790 [ 2.57790] ((20 . 1) (22 . 2) (24 . 4) (25 . 3)) 7.093 {1/4:6} B:1 SIMILARITY (1/min{score1}): 0.8772 [and 1/min{score2}: 0.8772] [3120, 3119]: Comparing 1k0r_A and 1k0r_A, based on their crossing files. There are 25 (12 H + 13 S) secondary structure elements in 1k0r_A, of which 6 satisfy the size requirements. There are 25 (12 H + 13 S) secondary structure elements in 1k0r_A, of which 7 satisfy the size requirements. 1.00019 [ 1.16679] ((20 . 13) (21 . 15) (22 . 16) (23 . 17) (24 . 18) (25 . 19)) 2.666 {0/12:15} B:0 1.50058 [ 1.75036] ((20 . 13) (22 . 16) (24 . 17) (25 . 19)) 4.752 {0/4:6} B:0 5.01015 [ 5.01871] ((20 . 13) (22 . 15) (24 . 17) (25 . 19)) 6.616 {2/4:6} B:0 4.01976 [ 4.03627] ((20 . 13) (22 . 15) (24 . 17) (25 . 16)) 6.799 {2/5:6} B:1 2.57823 [ 2.63901] ((20 . 17) (21 . 16) (22 . 19) (23 . 18)) 7.960 {1/4:6} B:2 SIMILARITY (1/min{score1}): 0.9998 [and 1/min{score2}: 0.8571] [3120, 3120]: Comparing 1k0r_A and 1k0r_A, based on their crossing files. There are 25 (12 H + 13 S) secondary structure elements in 1k0r_A, of which 6 satisfy the size requirements. There are 25 (12 H + 13 S) secondary structure elements in 1k0r_A, of which 6 satisfy the size requirements. 1.00000 [ 1.00000] ((20 . 20) (21 . 21) (22 . 22) (23 . 23) (24 . 24) (25 . 25)) 0.000 {0/12:15} B:0 2.57827 [ 2.57827] ((22 . 21) (23 . 20) (24 . 23) (25 . 22)) 8.042 {1/4:6} B:2 2.57827 [ 2.57827] ((20 . 23) (21 . 22) (22 . 25) (23 . 24)) 8.042 {1/4:6} B:2 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [3120, 6202]: Comparing 1k0r_A and 1v9j_A, based on their crossing files. There are 25 (12 H + 13 S) secondary structure elements in 1k0r_A, of which 6 satisfy the size requirements. There are 8 (5 H + 3 S) secondary structure elements in 1v9j_A, of which 6 satisfy the size requirements. 1.20008 [ 1.20008] ((20 . 1) (21 . 2) (22 . 3) (24 . 5) (25 . 7)) 2.441 {0/5:10} B:0 3.36705 [ 3.36705] ((20 . 1) (22 . 2) (24 . 5) (25 . 3)) 4.978 {1/3:6} B:1 3.36740 [ 3.36740] ((22 . 2) (23 . 1) (24 . 5) (25 . 3)) 7.972 {1/3:6} B:2 SIMILARITY (1/min{score1}): 0.8333 [and 1/min{score2}: 0.8333] [3120, 6590]: Comparing 1k0r_A and 3pro_C, based on their crossing files. There are 25 (12 H + 13 S) secondary structure elements in 1k0r_A, of which 6 satisfy the size requirements. There are 12 (6 H + 6 S) secondary structure elements in 3pro_C, of which 6 satisfy the size requirements. 1.50021 [ 1.50021] ((20 . 3) (21 . 4) (22 . 5) (25 . 6)) 3.675 {0/3:6} B:0 1.50184 [ 1.50184] ((20 . 2) (21 . 4) (22 . 5) (25 . 6)) 6.352 {0/2:6} B:0 6.00243 [ 6.00243] ((20 . 2) (21 . 4) (22 . 5) (23 . 3) (25 . 6)) 6.492 {3/5:10} B:1 SIMILARITY (1/min{score1}): 0.6666 [and 1/min{score2}: 0.6666] -------------------------------------------------------------------------------------------------------------------------