------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [6515, 25]: Comparing 2prg_A and 1a28_A, based on their crossing files. There are 17 (13 H + 4 S) secondary structure elements in 2prg_A, of which 15 satisfy the size requirements. There are 16 (12 H + 4 S) secondary structure elements in 1a28_A, of which 14 satisfy the size requirements. 1.50093 [ 1.40114] ((1 . 1) (5 . 2) (7 . 5) (9 . 6) (10 . 7) (13 . 9) (14 . 10) (15 . 12) (16 . 13) (17 . 14)) 4.816 {1/39:45} B:0 1.56949 [ 1.48377] ((1 . 1) (5 . 2) (7 . 4) (9 . 6) (10 . 7) (13 . 9) (14 . 10) (15 . 12) (16 . 13) (17 . 14)) 4.329 {4/40:45} B:0 1.65650 [ 1.58483] ((1 . 1) (5 . 2) (7 . 4) (9 . 6) (10 . 7) (12 . 9) (14 . 10) (15 . 12) (16 . 13) (17 . 14)) 6.398 {5/40:45} B:0 3.00044 [ 2.80055] ((5 . 2) (7 . 5) (15 . 12) (16 . 13) (17 . 15)) 7.487 {0/9:10} B:0 3.75122 [ 3.50150] ((4 . 9) (7 . 13) (12 . 14) (13 . 15)) 11.389 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.6663 [and 1/min{score2}: 0.7137] [6515, 1472]: Comparing 2prg_A and 1fcy_A, based on their crossing files. There are 17 (13 H + 4 S) secondary structure elements in 2prg_A, of which 15 satisfy the size requirements. There are 14 (11 H + 3 S) secondary structure elements in 1fcy_A, of which 11 satisfy the size requirements. 1.36719 [ 1.00892] ((1 . 1) (5 . 3) (7 . 5) (9 . 7) (10 . 8) (11 . 9) (13 . 10) (14 . 11) (15 . 12) (16 . 13) (17 . 14)) 2.275 {2/46:55} B:0 1.50042 [ 1.10107] ((5 . 3) (7 . 5) (9 . 7) (10 . 8) (11 . 9) (13 . 10) (14 . 11) (15 . 12) (16 . 13) (17 . 14)) 2.242 {1/37:45} B:0 1.73377 [ 1.37277] ((1 . 1) (5 . 3) (7 . 5) (12 . 9) (13 . 10) (14 . 11) (15 . 12) (16 . 13) (17 . 14)) 3.373 {3/28:36} B:0 1.87658 [ 1.37899] ((2 . 1) (5 . 3) (7 . 5) (13 . 10) (14 . 11) (15 . 12) (16 . 13) (17 . 14)) 7.230 {0/23:28} B:0 3.75068 [ 2.75171] ((7 . 1) (13 . 3) (16 . 11) (17 . 12)) 9.834 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.7314 [and 1/min{score2}: 0.9912] [6515, 1701]: Comparing 2prg_A and 1g2n_A, based on their crossing files. There are 17 (13 H + 4 S) secondary structure elements in 2prg_A, of which 15 satisfy the size requirements. There are 13 (11 H + 2 S) secondary structure elements in 1g2n_A, of which 12 satisfy the size requirements. 1.41337 [ 1.18155] ((1 . 1) (5 . 2) (7 . 4) (9 . 5) (10 . 6) (11 . 7) (12 . 8) (13 . 9) (14 . 10) (15 . 11) (16 . 12)) 4.790 {4/47:55} B:0 1.50512 [ 1.20992] ((1 . 1) (5 . 2) (7 . 4) (9 . 5) (10 . 6) (12 . 8) (13 . 9) (14 . 10) (15 . 11) (16 . 12)) 4.617 {2/40:45} B:0 1.52551 [ 1.24814] ((1 . 1) (5 . 2) (7 . 4) (9 . 5) (10 . 6) (11 . 7) (13 . 9) (14 . 10) (15 . 11) (16 . 12)) 3.808 {3/39:45} B:0 1.57627 [ 1.33585] ((1 . 1) (5 . 2) (7 . 4) (9 . 5) (10 . 6) (12 . 7) (13 . 9) (14 . 10) (15 . 11) (16 . 12)) 4.089 {4/39:45} B:0 1.67734 [ 1.35390] ((5 . 2) (7 . 4) (9 . 5) (10 . 6) (11 . 7) (13 . 8) (14 . 10) (15 . 11) (16 . 12)) 3.398 {2/30:36} B:0 SIMILARITY (1/min{score1}): 0.7075 [and 1/min{score2}: 0.8463] [6515, 2467]: Comparing 2prg_A and 1ie9_A, based on their crossing files. There are 17 (13 H + 4 S) secondary structure elements in 2prg_A, of which 15 satisfy the size requirements. There are 18 (15 H + 3 S) secondary structure elements in 1ie9_A, of which 14 satisfy the size requirements. 1.52822 [ 1.43441] ((1 . 1) (5 . 4) (7 . 6) (9 . 9) (11 . 12) (13 . 13) (14 . 14) (15 . 15) (16 . 16) (17 . 18)) 3.870 {3/38:45} B:0 1.57384 [ 1.51740] ((1 . 1) (4 . 3) (5 . 4) (7 . 6) (9 . 9) (11 . 12) (13 . 13) (14 . 14) (15 . 15) (16 . 16) (17 . 18)) 6.141 {6/47:55} B:0 1.70255 [ 1.63701] ((1 . 1) (5 . 4) (7 . 7) (9 . 9) (12 . 12) (13 . 13) (14 . 14) (15 . 15) (16 . 16) (17 . 18)) 4.244 {5/37:45} B:0 2.17453 [ 2.03869] ((1 . 1) (4 . 3) (5 . 4) (7 . 7) (13 . 13) (14 . 14) (16 . 16)) 7.434 {2/19:21} B:0 2.50039 [ 2.33381] ((5 . 4) (9 . 9) (12 . 13) (15 . 15) (16 . 16) (17 . 18)) 6.305 {0/14:15} B:0 SIMILARITY (1/min{score1}): 0.6544 [and 1/min{score2}: 0.6971] [6515, 3446]: Comparing 2prg_A and 1kv6_A, based on their crossing files. There are 17 (13 H + 4 S) secondary structure elements in 2prg_A, of which 15 satisfy the size requirements. There are 13 (11 H + 2 S) secondary structure elements in 1kv6_A, of which 13 satisfy the size requirements. 1.58794 [ 1.48410] ((1 . 1) (5 . 2) (7 . 3) (9 . 5) (10 . 6) (11 . 7) (13 . 8) (14 . 9) (15 . 10) (16 . 12) (17 . 13)) 4.453 {6/46:55} B:0 2.50883 [ 2.18017] ((5 . 2) (11 . 7) (12 . 8) (15 . 10) (16 . 12) (17 . 13)) 8.296 {1/12:15} B:0 3.00109 [ 2.60167] ((2 . 1) (5 . 2) (7 . 4) (16 . 12) (17 . 13)) 9.367 {0/8:10} B:0 3.07039 [ 2.70541] ((7 . 1) (11 . 2) (12 . 4) (16 . 9) (17 . 10)) 10.077 {1/6:10} B:0 3.75054 [ 3.25083] ((1 . 2) (7 . 9) (11 . 10) (13 . 11)) 9.287 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.6297 [and 1/min{score2}: 0.6738] [6515, 3743]: Comparing 2prg_A and 1lv2_A, based on their crossing files. There are 17 (13 H + 4 S) secondary structure elements in 2prg_A, of which 15 satisfy the size requirements. There are 14 (12 H + 2 S) secondary structure elements in 1lv2_A, of which 14 satisfy the size requirements. 1.41447 [ 1.33423] ((1 . 1) (5 . 2) (7 . 5) (9 . 6) (10 . 7) (12 . 8) (13 . 9) (14 . 10) (15 . 11) (16 . 13) (17 . 14)) 6.056 {4/47:55} B:0 1.41630 [ 1.33641] ((1 . 1) (5 . 2) (7 . 5) (9 . 6) (10 . 7) (12 . 8) (13 . 9) (14 . 10) (15 . 11) (16 . 12) (17 . 14)) 7.214 {4/47:55} B:0 1.52947 [ 1.43593] ((1 . 1) (5 . 2) (7 . 5) (9 . 6) (12 . 8) (13 . 9) (14 . 10) (15 . 11) (16 . 13) (17 . 14)) 6.115 {3/38:45} B:0 2.02840 [ 2.00295] ((1 . 1) (5 . 2) (7 . 5) (9 . 6) (10 . 7) (11 . 8) (13 . 9) (14 . 10) (15 . 11) (16 . 13) (17 . 14)) 6.374 {9/47:55} B:0 3.00005 [ 2.80006] ((5 . 2) (13 . 8) (14 . 10) (15 . 11) (17 . 14)) 4.230 {0/9:10} B:0 SIMILARITY (1/min{score1}): 0.7070 [and 1/min{score2}: 0.7495] [6515, 4121]: Comparing 2prg_A and 1n46_A, based on their crossing files. There are 17 (13 H + 4 S) secondary structure elements in 2prg_A, of which 15 satisfy the size requirements. There are 15 (12 H + 3 S) secondary structure elements in 1n46_A, of which 12 satisfy the size requirements. 1.37950 [ 1.12116] ((1 . 1) (5 . 3) (7 . 6) (9 . 7) (10 . 8) (11 . 9) (13 . 10) (14 . 11) (15 . 12) (16 . 13) (17 . 15)) 5.199 {3/48:55} B:0 1.37996 [ 1.12201] ((1 . 1) (5 . 4) (7 . 6) (9 . 7) (10 . 8) (11 . 9) (13 . 10) (14 . 11) (15 . 12) (16 . 13) (17 . 15)) 3.587 {3/47:55} B:0 1.50433 [ 1.20840] ((1 . 1) (5 . 4) (7 . 6) (9 . 7) (10 . 8) (13 . 10) (14 . 11) (15 . 12) (16 . 13) (17 . 15)) 3.406 {2/41:45} B:0 1.57263 [ 1.42081] ((1 . 1) (5 . 4) (7 . 6) (9 . 7) (10 . 8) (12 . 9) (13 . 10) (14 . 11) (15 . 12) (16 . 13) (17 . 15)) 3.728 {6/47:55} B:0 2.67821 [ 2.57773] ((1 . 1) (5 . 4) (7 . 6) (11 . 10) (14 . 11) (15 . 12) (16 . 13) (17 . 15)) 6.477 {6/24:28} B:0 SIMILARITY (1/min{score1}): 0.7249 [and 1/min{score2}: 0.8919] [6515, 4352]: Comparing 2prg_A and 1nq7_A, based on their crossing files. There are 17 (13 H + 4 S) secondary structure elements in 2prg_A, of which 15 satisfy the size requirements. There are 17 (14 H + 3 S) secondary structure elements in 1nq7_A, of which 16 satisfy the size requirements. 1.46178 [ 1.51622] ((1 . 1) (2 . 2) (5 . 4) (7 . 6) (9 . 9) (10 . 10) (11 . 11) (13 . 12) (14 . 13) (15 . 14) (16 . 15) (17 . 17)) 3.702 {7/58:66} B:0 1.58589 [ 1.62916] ((1 . 1) (2 . 2) (5 . 4) (7 . 7) (9 . 9) (10 . 10) (12 . 11) (13 . 12) (14 . 13) (15 . 14) (16 . 15) (17 . 17)) 3.979 {8/57:66} B:0 2.50160 [ 2.66799] ((2 . 1) (5 . 4) (11 . 11) (15 . 14) (16 . 15) (17 . 17)) 9.002 {0/13:15} B:0 3.20475 [ 3.37235] ((1 . 1) (5 . 4) (7 . 7) (13 . 13) (17 . 17)) 8.877 {2/9:10} B:0 3.75050 [ 4.00041] ((1 . 6) (2 . 7) (3 . 10) (7 . 14)) 9.097 {0/5:6} B:0 SIMILARITY (1/min{score1}): 0.6841 [and 1/min{score2}: 0.6595] [6515, 4370]: Comparing 2prg_A and 1nrl_A, based on their crossing files. There are 17 (13 H + 4 S) secondary structure elements in 2prg_A, of which 15 satisfy the size requirements. There are 19 (14 H + 5 S) secondary structure elements in 1nrl_A, of which 16 satisfy the size requirements. 3.00091 [ 3.20075] ((1 . 1) (4 . 2) (15 . 16) (16 . 18) (17 . 19)) 8.967 {0/9:10} B:0 3.75104 [ 4.00086] ((2 . 9) (5 . 15) (7 . 16) (13 . 19)) 10.954 {0/3:6} B:0 3.75130 [ 4.00107] ((1 . 8) (2 . 9) (5 . 15) (13 . 19)) 11.584 {0/5:6} B:0 3.78675 [ 4.03038] ((4 . 1) (7 . 6) (11 . 8) (17 . 18)) 9.967 {1/6:6} B:0 3.82620 [ 4.06321] ((4 . 14) (5 . 16) (7 . 18) (12 . 19)) 13.904 {1/5:6} B:0 SIMILARITY (1/min{score1}): 0.4221 [and 1/min{score2}: 0.4198] [6515, 4773]: Comparing 2prg_A and 1osh_A, based on their crossing files. There are 17 (13 H + 4 S) secondary structure elements in 2prg_A, of which 15 satisfy the size requirements. There are 11 (11 H + 0 S) secondary structure elements in 1osh_A, of which 10 satisfy the size requirements. 1.66705 [ 1.11240] ((1 . 1) (5 . 2) (7 . 5) (11 . 6) (13 . 7) (14 . 8) (15 . 9) (16 . 10) (17 . 11)) 4.640 {0/29:36} B:0 1.66748 [ 1.11386] ((1 . 1) (5 . 2) (7 . 4) (11 . 6) (13 . 7) (14 . 8) (15 . 9) (16 . 10) (17 . 11)) 3.684 {1/30:36} B:0 1.87647 [ 1.25495] ((5 . 2) (7 . 4) (11 . 6) (13 . 7) (14 . 8) (15 . 9) (16 . 10) (17 . 11)) 3.802 {1/23:28} B:0 2.50807 [ 1.69339] ((5 . 2) (11 . 6) (12 . 7) (15 . 9) (16 . 10) (17 . 11)) 6.334 {1/12:15} B:0 3.00029 [ 2.00097] ((7 . 1) (11 . 2) (12 . 4) (13 . 5) (16 . 8)) 6.715 {0/4:10} B:0 SIMILARITY (1/min{score1}): 0.5999 [and 1/min{score2}: 0.8990] [6515, 4988]: Comparing 2prg_A and 1pdu_A, based on their crossing files. There are 17 (13 H + 4 S) secondary structure elements in 2prg_A, of which 15 satisfy the size requirements. There are 15 (13 H + 2 S) secondary structure elements in 1pdu_A, of which 14 satisfy the size requirements. 1.36770 [ 1.27772] ((1 . 1) (5 . 3) (7 . 6) (9 . 7) (10 . 8) (11 . 9) (13 . 10) (14 . 11) (15 . 12) (16 . 14) (17 . 15)) 4.395 {2/46:55} B:0 1.41722 [ 1.33750] ((1 . 1) (5 . 3) (7 . 5) (9 . 7) (10 . 8) (11 . 9) (13 . 10) (14 . 11) (15 . 12) (16 . 14) (17 . 15)) 4.161 {4/46:55} B:0 1.50497 [ 1.40610] ((1 . 1) (5 . 3) (7 . 6) (9 . 7) (10 . 8) (13 . 10) (14 . 11) (15 . 12) (16 . 14) (17 . 15)) 4.228 {2/40:45} B:0 1.60388 [ 1.52415] ((2 . 1) (5 . 3) (7 . 6) (9 . 7) (12 . 9) (13 . 10) (14 . 11) (15 . 12) (16 . 14) (17 . 15)) 6.698 {4/36:45} B:0 1.88456 [ 1.85261] ((1 . 1) (5 . 3) (7 . 5) (9 . 7) (10 . 8) (12 . 9) (13 . 10) (14 . 11) (15 . 12) (16 . 14) (17 . 15)) 4.746 {8/46:55} B:0 SIMILARITY (1/min{score1}): 0.7312 [and 1/min{score2}: 0.7826] [6515, 5034]: Comparing 2prg_A and 1pk5_A, based on their crossing files. There are 17 (13 H + 4 S) secondary structure elements in 2prg_A, of which 15 satisfy the size requirements. There are 15 (13 H + 2 S) secondary structure elements in 1pk5_A, of which 14 satisfy the size requirements. 1.40977 [ 1.32862] ((1 . 1) (5 . 3) (7 . 6) (9 . 7) (10 . 8) (11 . 9) (13 . 10) (14 . 11) (15 . 12) (16 . 14) (17 . 15)) 5.054 {4/48:55} B:0 1.46801 [ 1.39715] ((1 . 1) (5 . 3) (7 . 5) (9 . 7) (10 . 8) (11 . 9) (13 . 10) (14 . 11) (15 . 12) (16 . 14) (17 . 15)) 4.948 {5/48:55} B:0 1.78672 [ 1.76034] ((1 . 1) (4 . 2) (5 . 3) (7 . 6) (9 . 7) (10 . 8) (11 . 9) (13 . 10) (14 . 11) (15 . 12) (16 . 14) (17 . 15)) 6.859 {9/54:66} B:0 3.75068 [ 3.50083] ((1 . 3) (7 . 11) (11 . 12) (13 . 13)) 9.837 {0/4:6} B:0 3.75092 [ 3.50113] ((4 . 5) (7 . 11) (11 . 12) (13 . 13)) 10.628 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.7093 [and 1/min{score2}: 0.7527] [6515, 5079]: Comparing 2prg_A and 1pq9_A, based on their crossing files. There are 17 (13 H + 4 S) secondary structure elements in 2prg_A, of which 15 satisfy the size requirements. There are 12 (9 H + 3 S) secondary structure elements in 1pq9_A, of which 11 satisfy the size requirements. 1.36671 [ 1.00774] ((1 . 1) (5 . 2) (7 . 3) (9 . 5) (10 . 6) (11 . 7) (13 . 8) (14 . 9) (15 . 10) (16 . 11) (17 . 12)) 2.962 {2/48:55} B:0 1.50569 [ 1.11424] ((5 . 2) (7 . 3) (9 . 5) (10 . 6) (11 . 7) (13 . 8) (14 . 9) (15 . 10) (16 . 11) (17 . 12)) 2.443 {2/38:45} B:0 1.55861 [ 1.36223] ((1 . 1) (5 . 2) (7 . 3) (9 . 5) (10 . 6) (12 . 7) (13 . 8) (14 . 9) (15 . 10) (16 . 11) (17 . 12)) 3.428 {6/48:55} B:0 2.01846 [ 1.89885] ((2 . 1) (5 . 2) (7 . 3) (9 . 5) (12 . 7) (13 . 8) (14 . 9) (15 . 10) (16 . 11) (17 . 12)) 6.142 {7/38:45} B:0 2.61578 [ 2.08921] ((5 . 2) (7 . 3) (14 . 8) (15 . 10) (16 . 11) (17 . 12)) 7.080 {2/12:15} B:0 SIMILARITY (1/min{score1}): 0.7317 [and 1/min{score2}: 0.9923] [6515, 5365]: Comparing 2prg_A and 1qkm_A, based on their crossing files. There are 17 (13 H + 4 S) secondary structure elements in 2prg_A, of which 15 satisfy the size requirements. There are 15 (13 H + 2 S) secondary structure elements in 1qkm_A, of which 12 satisfy the size requirements. 1.50110 [ 1.20214] ((1 . 1) (5 . 2) (7 . 5) (9 . 6) (10 . 7) (11 . 8) (13 . 9) (14 . 10) (15 . 12) (16 . 13)) 4.997 {1/37:45} B:0 1.58405 [ 1.34855] ((1 . 1) (5 . 2) (7 . 4) (9 . 6) (10 . 7) (11 . 8) (13 . 9) (14 . 10) (15 . 12) (16 . 13)) 4.445 {4/38:45} B:0 3.75053 [ 3.00103] ((1 . 4) (2 . 5) (7 . 12) (14 . 15)) 9.249 {0/4:6} B:0 3.75096 [ 3.00188] ((7 . 1) (13 . 4) (15 . 9) (16 . 10)) 10.743 {0/4:6} B:0 3.75140 [ 3.00274] ((7 . 1) (11 . 2) (13 . 4) (16 . 10)) 11.807 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.6662 [and 1/min{score2}: 0.8318] [6515, 5525]: Comparing 2prg_A and 1r1k_D, based on their crossing files. There are 17 (13 H + 4 S) secondary structure elements in 2prg_A, of which 15 satisfy the size requirements. There are 14 (11 H + 3 S) secondary structure elements in 1r1k_D, of which 12 satisfy the size requirements. 1.36389 [ 1.09141] ((1 . 1) (5 . 3) (7 . 5) (9 . 7) (10 . 8) (11 . 9) (13 . 10) (14 . 11) (15 . 12) (16 . 13) (17 . 14)) 2.605 {1/48:55} B:0 1.50003 [ 1.20007] ((1 . 1) (5 . 3) (7 . 5) (9 . 7) (10 . 8) (13 . 10) (14 . 11) (15 . 12) (16 . 13) (17 . 14)) 2.352 {0/41:45} B:0 1.50037 [ 1.20071] ((5 . 3) (7 . 5) (9 . 7) (10 . 8) (11 . 9) (13 . 10) (14 . 11) (15 . 12) (16 . 13) (17 . 14)) 2.518 {1/39:45} B:0 1.76275 [ 1.60683] ((1 . 1) (5 . 3) (7 . 5) (9 . 7) (10 . 8) (11 . 10) (14 . 11) (15 . 12) (16 . 13) (17 . 14)) 4.513 {6/41:45} B:0 2.61571 [ 2.20756] ((5 . 3) (7 . 5) (13 . 11) (15 . 12) (16 . 13) (17 . 14)) 6.836 {2/12:15} B:0 SIMILARITY (1/min{score1}): 0.7332 [and 1/min{score2}: 0.9162] [6515, 6515]: Comparing 2prg_A and 2prg_A, based on their crossing files. There are 17 (13 H + 4 S) secondary structure elements in 2prg_A, of which 15 satisfy the size requirements. There are 17 (13 H + 4 S) secondary structure elements in 2prg_A, of which 15 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (7 . 7) (9 . 9) (10 . 10) (11 . 11) (12 . 12) (13 . 13) (14 . 14) (15 . 15) (16 . 16) (17 . 17)) 0.000 {0/94:105} B:0 1.87651 [ 1.87651] ((3 . 3) (4 . 4) (5 . 5) (7 . 7) (13 . 12) (15 . 15) (16 . 16) (17 . 17)) 5.867 {1/26:28} B:0 1.87651 [ 1.87651] ((3 . 3) (4 . 4) (5 . 5) (7 . 7) (12 . 13) (15 . 15) (16 . 16) (17 . 17)) 5.867 {1/26:28} B:0 2.50092 [ 2.50092] ((2 . 1) (5 . 5) (7 . 7) (15 . 15) (16 . 16) (17 . 17)) 7.829 {0/13:15} B:0 2.50092 [ 2.50092] ((1 . 2) (5 . 5) (7 . 7) (15 . 15) (16 . 16) (17 . 17)) 7.829 {0/13:15} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] -------------------------------------------------------------------------------------------------------------------------