------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [2737, 313]: Comparing 1j5p_A and 1b7g_O, based on their crossing files. There are 21 (10 H + 11 S) secondary structure elements in 1j5p_A, of which 9 satisfy the size requirements. There are 30 (15 H + 15 S) secondary structure elements in 1b7g_O, of which 11 satisfy the size requirements. 2.25003 [ 2.75001] ((12 . 16) (16 . 18) (18 . 19) (19 . 20)) 2.993 {0/0:6} B:0 2.25063 [ 2.75034] ((12 . 20) (13 . 21) (18 . 25) (19 . 28)) 6.580 {0/2:6} B:0 2.25223 [ 2.75122] ((12 . 20) (16 . 23) (18 . 25) (19 . 28)) 9.037 {0/0:6} B:0 2.25475 [ 2.75261] ((12 . 19) (14 . 20) (15 . 21) (20 . 28)) 10.921 {0/1:6} B:0 6.68824 [ 6.71446] ((12 . 20) (14 . 22) (15 . 23) (19 . 28)) 8.169 {2/3:6} B:0 SIMILARITY (1/min{score1}): 0.4444 [and 1/min{score2}: 0.3636] [2737, 848]: Comparing 1j5p_A and 1dih, based on their crossing files. There are 21 (10 H + 11 S) secondary structure elements in 1j5p_A, of which 9 satisfy the size requirements. There are 22 (9 H + 13 S) secondary structure elements in 1dih, of which 7 satisfy the size requirements. 1.50011 [ 1.16689] ((11 . 11) (12 . 12) (16 . 13) (18 . 16) (19 . 17) (20 . 18)) 3.118 {0/3:15} B:0 1.80008 [ 1.40016] ((11 . 11) (12 . 12) (18 . 16) (19 . 17) (20 . 18)) 3.285 {0/2:10} B:0 SIMILARITY (1/min{score1}): 0.6666 [and 1/min{score2}: 0.8570] [2737, 907]: Comparing 1j5p_A and 1dpg_A, based on their crossing files. There are 21 (10 H + 11 S) secondary structure elements in 1j5p_A, of which 9 satisfy the size requirements. There are 36 (21 H + 15 S) secondary structure elements in 1dpg_A, of which 20 satisfy the size requirements. 1.80175 [ 4.00016] ((12 . 23) (14 . 25) (18 . 27) (19 . 28) (20 . 29)) 7.195 {0/2:10} B:0 2.25033 [ 5.00003] ((14 . 27) (18 . 28) (19 . 29) (20 . 30)) 5.612 {0/3:6} B:0 2.25395 [ 5.00036] ((12 . 25) (18 . 29) (19 . 30) (20 . 31)) 10.428 {0/1:6} B:0 2.25903 [ 5.00083] ((12 . 23) (14 . 25) (18 . 28) (20 . 29)) 12.833 {0/1:6} B:0 2.84026 [ 5.07710] ((11 . 22) (12 . 23) (14 . 25) (20 . 29)) 12.612 {1/4:6} B:0 SIMILARITY (1/min{score1}): 0.7776 [and 1/min{score2}: 0.3500] [2737, 1095]: Comparing 1j5p_A and 1ebf_A, based on their crossing files. There are 21 (10 H + 11 S) secondary structure elements in 1j5p_A, of which 9 satisfy the size requirements. There are 30 (18 H + 12 S) secondary structure elements in 1ebf_A, of which 13 satisfy the size requirements. 2.25200 [ 3.25066] ((16 . 23) (18 . 24) (19 . 26) (20 . 28)) 8.789 {0/1:6} B:0 5.05078 [ 5.20985] ((13 . 23) (14 . 24) (18 . 28) (19 . 29)) 9.931 {2/4:6} B:0 7.50162 [ 7.50704] ((11 . 15) (12 . 16) (13 . 17) (16 . 20) (18 . 24) (19 . 28) (20 . 29)) 4.392 {6/8:21} B:0 8.57207 [ 8.57420] ((11 . 15) (12 . 16) (13 . 17) (14 . 26) (16 . 20) (18 . 24) (19 . 28) (20 . 29)) 5.050 {12/14:28} B:1 SIMILARITY (1/min{score1}): 0.4441 [and 1/min{score2}: 0.3076] [2737, 1488]: Comparing 1j5p_A and 1ff9_A, based on their crossing files. There are 21 (10 H + 11 S) secondary structure elements in 1j5p_A, of which 9 satisfy the size requirements. There are 34 (18 H + 16 S) secondary structure elements in 1ff9_A, of which 16 satisfy the size requirements. 2.26384 [ 4.00248] ((13 . 26) (16 . 28) (19 . 29) (20 . 30)) 14.291 {0/1:6} B:0 5.05057 [ 5.44815] ((12 . 17) (13 . 18) (14 . 20) (18 . 22)) 7.233 {2/4:6} B:0 6.02974 [ 6.27684] ((11 . 15) (13 . 18) (14 . 20) (18 . 22)) 11.379 {3/5:6} B:0 10.00641 [10.06341] ((11 . 12) (12 . 13) (18 . 17) (20 . 22)) 7.598 {1/1:6} B:0 2.25684 [ 4.00122] ((13 . 18) (14 . 20) (16 . 23) (18 . 22)) 11.970 {0/3:6} B:1 SIMILARITY (1/min{score1}): 0.4431 [and 1/min{score2}: 0.2499] [2737, 1923]: Comparing 1j5p_A and 1gr0_A, based on their crossing files. There are 21 (10 H + 11 S) secondary structure elements in 1j5p_A, of which 9 satisfy the size requirements. There are 28 (14 H + 14 S) secondary structure elements in 1gr0_A, of which 8 satisfy the size requirements. 1.80252 [ 1.60358] ((12 . 17) (16 . 18) (18 . 20) (19 . 22) (20 . 24)) 7.882 {0/1:10} B:0 2.25110 [ 2.00157] ((16 . 18) (18 . 20) (19 . 22) (20 . 24)) 7.579 {0/1:6} B:0 2.25184 [ 2.00262] ((11 . 16) (12 . 17) (14 . 22) (18 . 24)) 8.614 {0/0:6} B:0 2.25379 [ 2.00539] ((15 . 16) (18 . 20) (19 . 22) (20 . 24)) 10.322 {0/2:6} B:0 2.83804 [ 2.72630] ((11 . 18) (12 . 20) (14 . 22) (18 . 24)) 10.464 {1/4:6} B:0 SIMILARITY (1/min{score1}): 0.5548 [and 1/min{score2}: 0.6236] [2737, 2096]: Comparing 1j5p_A and 1h6d_A, based on their crossing files. There are 21 (10 H + 11 S) secondary structure elements in 1j5p_A, of which 9 satisfy the size requirements. There are 31 (16 H + 15 S) secondary structure elements in 1h6d_A, of which 11 satisfy the size requirements. 2.25010 [ 2.75005] ((14 . 21) (18 . 23) (19 . 24) (20 . 25)) 4.133 {0/2:6} B:0 2.25017 [ 2.75009] ((11 . 16) (12 . 17) (16 . 20) (18 . 21)) 4.728 {0/2:6} B:0 3.49586 [ 3.66749] ((11 . 18) (18 . 24) (19 . 25) (20 . 26)) 11.505 {1/3:6} B:0 5.02092 [ 5.04627] ((11 . 16) (12 . 17) (16 . 20) (19 . 23) (20 . 24)) 6.666 {1/2:10} B:0 3.40275 [ 3.48197] ((13 . 18) (14 . 21) (15 . 20) (18 . 23) (20 . 25)) 9.267 {2/6:10} B:1 SIMILARITY (1/min{score1}): 0.4444 [and 1/min{score2}: 0.3636] [2737, 2737]: Comparing 1j5p_A and 1j5p_A, based on their crossing files. There are 21 (10 H + 11 S) secondary structure elements in 1j5p_A, of which 9 satisfy the size requirements. There are 21 (10 H + 11 S) secondary structure elements in 1j5p_A, of which 9 satisfy the size requirements. 1.00000 [ 1.00000] ((11 . 11) (12 . 12) (13 . 13) (14 . 14) (15 . 15) (16 . 16) (18 . 18) (19 . 19) (20 . 20)) 0.000 {0/22:36} B:0 3.40205 [ 3.40205] ((11 . 11) (12 . 12) (13 . 13) (14 . 14) (19 . 20)) 3.301 {3/9:10} B:0 3.40205 [ 3.40205] ((11 . 11) (12 . 12) (13 . 13) (14 . 14) (20 . 19)) 3.301 {3/9:10} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [2737, 3594]: Comparing 1j5p_A and 1lc0_A, based on their crossing files. There are 21 (10 H + 11 S) secondary structure elements in 1j5p_A, of which 9 satisfy the size requirements. There are 26 (13 H + 13 S) secondary structure elements in 1lc0_A, of which 8 satisfy the size requirements. 2.25002 [ 2.00003] ((11 . 14) (12 . 15) (18 . 22) (19 . 23)) 2.920 {0/0:6} B:0 2.25022 [ 2.00031] ((16 . 18) (18 . 19) (19 . 21) (20 . 22)) 5.041 {0/0:6} B:0 5.02092 [ 5.01311] ((11 . 14) (12 . 15) (16 . 18) (19 . 21) (20 . 22)) 6.542 {1/2:10} B:0 5.05078 [ 5.03199] ((11 . 14) (13 . 17) (18 . 21) (20 . 23)) 9.939 {2/4:6} B:0 6.68823 [ 6.68017] ((13 . 14) (16 . 17) (19 . 19) (20 . 21)) 7.661 {2/3:6} B:0 SIMILARITY (1/min{score1}): 0.6661 [and 1/min{score2}: 0.7490] [2737, 4405]: Comparing 1j5p_A and 1nvm_B, based on their crossing files. There are 21 (10 H + 11 S) secondary structure elements in 1j5p_A, of which 9 satisfy the size requirements. There are 26 (12 H + 14 S) secondary structure elements in 1nvm_B, of which 11 satisfy the size requirements. 2.25252 [ 2.75138] ((12 . 18) (14 . 19) (19 . 23) (20 . 24)) 9.322 {0/2:6} B:0 2.25502 [ 2.75276] ((12 . 18) (14 . 19) (15 . 20) (19 . 25)) 11.077 {0/1:6} B:0 5.01011 [ 5.02246] ((11 . 13) (12 . 14) (16 . 17) (18 . 18) (19 . 19) (20 . 25)) 4.975 {2/4:15} B:0 5.05050 [ 5.11067] ((11 . 13) (12 . 14) (18 . 18) (19 . 19)) 4.554 {1/2:6} B:0 10.00645 [10.01432] ((12 . 18) (14 . 19) (16 . 20) (19 . 22)) 10.865 {1/1:6} B:0 SIMILARITY (1/min{score1}): 0.4439 [and 1/min{score2}: 0.3635] [2737, 4418]: Comparing 1j5p_A and 1nwc_A, based on their crossing files. There are 21 (10 H + 11 S) secondary structure elements in 1j5p_A, of which 9 satisfy the size requirements. There are 30 (16 H + 14 S) secondary structure elements in 1nwc_A, of which 16 satisfy the size requirements. 2.25065 [ 4.00012] ((12 . 23) (13 . 24) (18 . 28) (19 . 29)) 6.640 {0/2:6} B:0 2.25274 [ 4.00049] ((12 . 22) (14 . 23) (19 . 28) (20 . 29)) 9.513 {0/1:6} B:0 2.25496 [ 4.00089] ((12 . 22) (14 . 23) (15 . 24) (20 . 29)) 11.040 {0/1:6} B:0 3.49787 [ 4.41535] ((12 . 15) (13 . 17) (15 . 18) (16 . 19)) 14.150 {1/3:6} B:0 4.09830 [ 4.75794] ((11 . 21) (14 . 22) (16 . 24) (20 . 28)) 13.301 {2/5:6} B:0 SIMILARITY (1/min{score1}): 0.4443 [and 1/min{score2}: 0.3016] [2737, 4589]: Comparing 1j5p_A and 1obf_O, based on their crossing files. There are 21 (10 H + 11 S) secondary structure elements in 1j5p_A, of which 9 satisfy the size requirements. There are 31 (12 H + 19 S) secondary structure elements in 1obf_O, of which 13 satisfy the size requirements. 1.80023 [ 2.60008] ((11 . 17) (12 . 18) (14 . 19) (18 . 22) (19 . 23)) 4.349 {0/4:10} B:0 2.25103 [ 3.25034] ((12 . 18) (14 . 19) (15 . 20) (16 . 21)) 7.445 {0/3:6} B:0 2.25483 [ 3.25161] ((12 . 22) (14 . 23) (15 . 24) (20 . 30)) 10.968 {0/1:6} B:0 3.49498 [ 3.91591] ((12 . 23) (13 . 24) (18 . 29) (19 . 30)) 9.383 {1/3:6} B:0 4.09718 [ 4.37910] ((13 . 21) (14 . 23) (16 . 24) (20 . 27)) 10.296 {2/5:6} B:0 SIMILARITY (1/min{score1}): 0.6666 [and 1/min{score2}: 0.4615] [2737, 4731]: Comparing 1j5p_A and 1ono_A, based on their crossing files. There are 21 (10 H + 11 S) secondary structure elements in 1j5p_A, of which 9 satisfy the size requirements. There are 29 (18 H + 11 S) secondary structure elements in 1ono_A, of which 12 satisfy the size requirements. 1.80012 [ 2.40005] ((12 . 18) (16 . 20) (18 . 22) (19 . 23) (20 . 24)) 3.648 {0/1:10} B:0 3.49494 [ 3.78189] ((13 . 12) (15 . 15) (16 . 16) (18 . 18)) 9.235 {1/3:6} B:0 4.09672 [ 4.28471] ((11 . 13) (12 . 14) (13 . 15) (15 . 17)) 7.280 {2/5:6} B:0 5.05053 [ 5.15471] ((11 . 13) (13 . 15) (15 . 16) (18 . 14)) 6.110 {3/6:6} B:1 2.83811 [ 3.31149] ((11 . 15) (12 . 14) (14 . 18) (15 . 17)) 10.560 {1/4:6} B:2 SIMILARITY (1/min{score1}): 0.5555 [and 1/min{score2}: 0.4167] [2737, 4864]: Comparing 1j5p_A and 1p1j_A, based on their crossing files. There are 21 (10 H + 11 S) secondary structure elements in 1j5p_A, of which 9 satisfy the size requirements. There are 40 (22 H + 18 S) secondary structure elements in 1p1j_A, of which 9 satisfy the size requirements. 1.28713 [ 1.28713] ((11 . 26) (12 . 27) (15 . 29) (16 . 30) (18 . 31) (19 . 33) (20 . 35)) 5.298 {0/2:21} B:0 2.25105 [ 2.25105] ((11 . 30) (12 . 31) (14 . 33) (18 . 35)) 7.479 {0/0:6} B:0 4.44903 [ 4.44903] ((11 . 26) (12 . 27) (13 . 28) (15 . 29) (16 . 30) (18 . 31) (19 . 33) (20 . 35)) 5.140 {4/9:28} B:0 1.80575 [ 1.80575] ((11 . 30) (12 . 27) (14 . 35) (18 . 33) (19 . 31)) 9.693 {0/0:10} B:3 SIMILARITY (1/min{score1}): 0.7769 [and 1/min{score2}: 0.7769] [2737, 4944]: Comparing 1j5p_A and 1p9l_A, based on their crossing files. There are 21 (10 H + 11 S) secondary structure elements in 1j5p_A, of which 9 satisfy the size requirements. There are 19 (8 H + 11 S) secondary structure elements in 1p9l_A, of which 8 satisfy the size requirements. 1.50015 [ 1.33354] ((11 . 10) (12 . 11) (16 . 12) (18 . 14) (19 . 15) (20 . 16)) 3.378 {0/2:15} B:0 1.80008 [ 1.60012] ((11 . 10) (12 . 11) (18 . 14) (19 . 15) (20 . 16)) 3.354 {0/2:10} B:0 2.25357 [ 2.00507] ((13 . 10) (16 . 12) (19 . 13) (20 . 14)) 10.164 {0/2:6} B:0 2.25622 [ 2.00883] ((11 . 10) (12 . 11) (13 . 12) (18 . 14)) 11.685 {0/1:6} B:0 5.05060 [ 5.03181] ((11 . 10) (16 . 12) (18 . 13) (19 . 14)) 7.914 {1/2:6} B:0 SIMILARITY (1/min{score1}): 0.6666 [and 1/min{score2}: 0.7499] [2737, 5363]: Comparing 1j5p_A and 1qki_A, based on their crossing files. There are 21 (10 H + 11 S) secondary structure elements in 1j5p_A, of which 9 satisfy the size requirements. There are 35 (20 H + 15 S) secondary structure elements in 1qki_A, of which 17 satisfy the size requirements. 1.80260 [ 3.40039] ((12 . 22) (14 . 24) (18 . 25) (19 . 26) (20 . 27)) 7.947 {0/3:10} B:0 2.25030 [ 4.25004] ((14 . 25) (18 . 26) (19 . 27) (20 . 28)) 5.478 {0/3:6} B:0 2.25058 [ 4.25009] ((14 . 22) (18 . 24) (19 . 25) (20 . 26)) 6.459 {0/2:6} B:0 2.25429 [ 4.25064] ((12 . 24) (18 . 27) (19 . 28) (20 . 29)) 10.648 {0/1:6} B:0 2.26001 [ 4.25149] ((12 . 22) (14 . 24) (18 . 26) (20 . 27)) 13.170 {0/1:6} B:0 SIMILARITY (1/min{score1}): 0.5562 [and 1/min{score2}: 0.3916] [2737, 6293]: Comparing 1j5p_A and 1vjp_A, based on their crossing files. There are 21 (10 H + 11 S) secondary structure elements in 1j5p_A, of which 9 satisfy the size requirements. There are 29 (17 H + 12 S) secondary structure elements in 1vjp_A, of which 8 satisfy the size requirements. 1.80031 [ 1.60045] ((11 . 15) (12 . 16) (16 . 19) (19 . 23) (20 . 25)) 4.682 {0/1:10} B:0 2.25011 [ 2.00016] ((11 . 15) (12 . 16) (19 . 23) (20 . 25)) 4.286 {0/0:6} B:0 SIMILARITY (1/min{score1}): 0.5555 [and 1/min{score2}: 0.6248] [2737, 6427]: Comparing 1j5p_A and 2dap, based on their crossing files. There are 21 (10 H + 11 S) secondary structure elements in 1j5p_A, of which 9 satisfy the size requirements. There are 27 (13 H + 14 S) secondary structure elements in 2dap, of which 11 satisfy the size requirements. 2.25125 [ 2.75069] ((14 . 17) (15 . 18) (19 . 21) (20 . 22)) 7.823 {0/1:6} B:0 2.25494 [ 2.75271] ((16 . 18) (18 . 19) (19 . 21) (20 . 22)) 11.027 {0/0:6} B:0 2.25927 [ 2.75510] ((12 . 19) (13 . 20) (14 . 21) (18 . 22)) 12.919 {0/3:6} B:0 1.80314 [ 2.20172] ((12 . 12) (14 . 17) (18 . 15) (19 . 21) (20 . 22)) 8.331 {0/0:10} B:1 2.25159 [ 2.75087] ((12 . 15) (16 . 18) (18 . 17) (19 . 19)) 8.303 {0/0:6} B:1 SIMILARITY (1/min{score1}): 0.7716 [and 1/min{score2}: 0.6341] -------------------------------------------------------------------------------------------------------------------------