------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [3038, 454]: Comparing 1jro_B and 1brw_A, based on their crossing files. There are 56 (27 H + 29 S) secondary structure elements in 1jro_B, of which 8 satisfy the size requirements. There are 31 (18 H + 13 S) secondary structure elements in 1brw_A, of which 8 satisfy the size requirements. 1.75207 [ 1.75207] ((3 . 23) (4 . 24) (5 . 25) (6 . 26) (9 . 28) (10 . 29) (11 . 30)) 3.037 {2/12:21} B:0 3.43661 [ 3.43661] ((3 . 24) (5 . 25) (6 . 26) (10 . 29)) 6.398 {1/3:6} B:0 3.43707 [ 3.43707] ((3 . 24) (6 . 26) (9 . 30) (10 . 29)) 9.000 {1/3:6} B:1 5.01306 [ 5.01306] ((3 . 28) (4 . 24) (5 . 25) (9 . 26) (11 . 30)) 2.967 {2/4:10} B:1 7.50985 [ 7.50985] ((3 . 28) (4 . 30) (5 . 29) (6 . 31)) 14.379 {3/4:6} B:1 SIMILARITY (1/min{score1}): 0.5708 [and 1/min{score2}: 0.5708] [3038, 1557]: Comparing 1jro_B and 1fm0_E, based on their crossing files. There are 56 (27 H + 29 S) secondary structure elements in 1jro_B, of which 8 satisfy the size requirements. There are 12 (4 H + 8 S) secondary structure elements in 1fm0_E, of which 12 satisfy the size requirements. 1.28330 [ 1.76217] ((3 . 3) (4 . 4) (5 . 5) (6 . 6) (9 . 8) (10 . 9) (11 . 10)) 4.481 {1/10:21} B:0 1.53886 [ 2.07245] ((3 . 3) (4 . 4) (5 . 5) (9 . 8) (10 . 9) (11 . 10)) 4.445 {1/8:15} B:0 2.00123 [ 3.00037] ((3 . 1) (5 . 5) (9 . 8) (10 . 9)) 7.132 {0/1:6} B:0 2.00328 [ 3.00097] ((3 . 4) (5 . 5) (6 . 6) (10 . 9)) 9.115 {0/2:6} B:0 2.04272 [ 3.01298] ((1 . 5) (4 . 8) (6 . 10) (9 . 11)) 17.440 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.7792 [and 1/min{score2}: 0.5675] [3038, 1586]: Comparing 1jro_B and 1fo4_A, based on their crossing files. There are 56 (27 H + 29 S) secondary structure elements in 1jro_B, of which 8 satisfy the size requirements. There are 96 (51 H + 45 S) secondary structure elements in 1fo4_A, of which 10 satisfy the size requirements. 1.04610 [ 1.27455] ((1 . 44) (3 . 46) (4 . 47) (5 . 48) (6 . 49) (9 . 54) (10 . 55) (11 . 56)) 0.928 {1/15:28} B:0 3.43691 [ 3.57089] ((1 . 44) (3 . 47) (5 . 48) (10 . 55)) 8.380 {1/3:6} B:0 3.43705 [ 3.57101] ((1 . 44) (4 . 46) (5 . 48) (10 . 55)) 8.945 {1/3:6} B:0 SIMILARITY (1/min{score1}): 0.9559 [and 1/min{score2}: 0.7846] [3038, 2906]: Comparing 1jro_B and 1jj2_H, based on their crossing files. There are 56 (27 H + 29 S) secondary structure elements in 1jro_B, of which 8 satisfy the size requirements. There are 11 (3 H + 8 S) secondary structure elements in 1jj2_H, of which 10 satisfy the size requirements. 1.33352 [ 1.66676] ((3 . 3) (4 . 4) (5 . 5) (6 . 6) (9 . 9) (10 . 10)) 3.291 {0/5:15} B:0 1.60009 [ 2.00005] ((3 . 3) (4 . 4) (5 . 5) (6 . 6) (10 . 10)) 3.144 {0/4:10} B:0 2.00121 [ 2.50062] ((3 . 4) (5 . 5) (6 . 6) (10 . 10)) 7.103 {0/1:6} B:0 2.00123 [ 2.50063] ((3 . 2) (4 . 3) (5 . 5) (11 . 9)) 7.126 {0/2:6} B:0 2.00159 [ 2.50081] ((5 . 5) (9 . 9) (10 . 10) (11 . 11)) 7.596 {0/1:6} B:0 SIMILARITY (1/min{score1}): 0.7499 [and 1/min{score2}: 0.6000] [3038, 3038]: Comparing 1jro_B and 1jro_B, based on their crossing files. There are 56 (27 H + 29 S) secondary structure elements in 1jro_B, of which 8 satisfy the size requirements. There are 56 (27 H + 29 S) secondary structure elements in 1jro_B, of which 8 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (9 . 9) (10 . 10) (11 . 11)) 0.000 {0/19:28} B:0 3.43700 [ 3.43700] ((1 . 1) (3 . 4) (5 . 5) (10 . 10)) 8.742 {1/3:6} B:0 3.43700 [ 3.43700] ((1 . 1) (4 . 3) (5 . 5) (10 . 10)) 8.742 {1/3:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [3038, 4137]: Comparing 1jro_B and 1n62_B, based on their crossing files. There are 56 (27 H + 29 S) secondary structure elements in 1jro_B, of which 8 satisfy the size requirements. There are 66 (27 H + 39 S) secondary structure elements in 1n62_B, of which 12 satisfy the size requirements. 1.00001 [ 1.50000] ((1 . 2) (3 . 4) (4 . 5) (5 . 6) (6 . 7) (9 . 12) (10 . 13) (11 . 14)) 1.131 {0/16:28} B:0 2.92529 [ 3.16110] ((1 . 2) (4 . 7) (9 . 12) (10 . 13) (11 . 14)) 6.909 {2/7:10} B:0 3.43706 [ 3.78184] ((1 . 2) (4 . 4) (5 . 6) (10 . 13)) 8.986 {1/3:6} B:0 10.00401 [10.02020] ((4 . 4) (5 . 6) (10 . 13) (11 . 12)) 7.821 {1/1:6} B:1 SIMILARITY (1/min{score1}): 0.9999 [and 1/min{score2}: 0.6667] [3038, 4485]: Comparing 1jro_B and 1o4u_A, based on their crossing files. There are 56 (27 H + 29 S) secondary structure elements in 1jro_B, of which 8 satisfy the size requirements. There are 23 (11 H + 12 S) secondary structure elements in 1o4u_A, of which 9 satisfy the size requirements. 2.00837 [ 2.25589] ((4 . 3) (5 . 5) (9 . 8) (10 . 9)) 11.527 {0/0:6} B:0 2.59887 [ 2.65330] ((3 . 3) (4 . 4) (5 . 5) (6 . 6) (9 . 8)) 3.326 {1/4:10} B:0 10.00043 [10.00069] ((3 . 3) (4 . 7) (5 . 5) (6 . 6) (9 . 8) (10 . 9) (11 . 4)) 6.548 {8/8:21} B:2 10.00167 [10.00265] ((3 . 8) (5 . 5) (6 . 3) (10 . 9) (11 . 4)) 9.218 {3/3:10} B:3 SIMILARITY (1/min{score1}): 0.4979 [and 1/min{score2}: 0.4433] [3038, 5267]: Comparing 1jro_B and 1qap_A, based on their crossing files. There are 56 (27 H + 29 S) secondary structure elements in 1jro_B, of which 8 satisfy the size requirements. There are 26 (12 H + 14 S) secondary structure elements in 1qap_A, of which 6 satisfy the size requirements. 1.60300 [ 1.20706] ((3 . 5) (5 . 7) (6 . 8) (9 . 10) (10 . 11)) 7.538 {0/1:10} B:0 2.00220 [ 1.50519] ((5 . 7) (6 . 10) (9 . 5) (10 . 11)) 8.243 {0/0:6} B:1 10.00405 [10.00131] ((3 . 5) (4 . 8) (5 . 7) (10 . 11)) 10.577 {1/1:6} B:1 SIMILARITY (1/min{score1}): 0.6238 [and 1/min{score2}: 0.8285] [3038, 5411]: Comparing 1jro_B and 1qpo_A, based on their crossing files. There are 56 (27 H + 29 S) secondary structure elements in 1jro_B, of which 8 satisfy the size requirements. There are 23 (11 H + 12 S) secondary structure elements in 1qpo_A, of which 7 satisfy the size requirements. 1.60304 [ 1.40453] ((3 . 3) (5 . 5) (6 . 6) (9 . 8) (10 . 9)) 7.564 {0/1:10} B:0 10.00408 [10.00242] ((1 . 2) (3 . 3) (5 . 5) (10 . 9)) 12.005 {3/3:6} B:0 10.00423 [10.00258] ((1 . 1) (5 . 5) (9 . 8) (10 . 9)) 15.750 {3/3:6} B:0 2.00033 [ 1.75050] ((3 . 3) (6 . 6) (9 . 8) (10 . 5)) 5.148 {0/1:6} B:1 SIMILARITY (1/min{score1}): 0.6238 [and 1/min{score2}: 0.7120] [3038, 6071]: Comparing 1jro_B and 1uou_A, based on their crossing files. There are 56 (27 H + 29 S) secondary structure elements in 1jro_B, of which 8 satisfy the size requirements. There are 32 (19 H + 13 S) secondary structure elements in 1uou_A, of which 8 satisfy the size requirements. 1.28283 [ 1.28283] ((3 . 24) (4 . 25) (5 . 26) (6 . 27) (9 . 29) (10 . 30) (11 . 31)) 3.480 {1/10:21} B:0 3.43704 [ 3.43704] ((6 . 25) (9 . 29) (10 . 30) (11 . 31)) 8.888 {1/3:6} B:0 3.43709 [ 3.43709] ((3 . 25) (6 . 27) (9 . 31) (10 . 30)) 9.076 {1/3:6} B:1 10.00402 [10.00402] ((3 . 25) (6 . 29) (9 . 31) (10 . 30)) 8.786 {3/3:6} B:1 SIMILARITY (1/min{score1}): 0.7795 [and 1/min{score2}: 0.7795] [3038, 6309]: Comparing 1jro_B and 1vlb_A, based on their crossing files. There are 56 (27 H + 29 S) secondary structure elements in 1jro_B, of which 8 satisfy the size requirements. There are 65 (35 H + 30 S) secondary structure elements in 1vlb_A, of which 8 satisfy the size requirements. 1.34062 [ 1.34062] ((3 . 17) (4 . 18) (5 . 19) (6 . 20) (9 . 25) (10 . 26) (11 . 27)) 0.909 {1/9:21} B:0 1.60292 [ 1.60292] ((3 . 18) (5 . 19) (9 . 25) (10 . 26) (11 . 27)) 7.489 {0/2:10} B:0 3.43692 [ 3.43692] ((4 . 20) (9 . 25) (10 . 26) (11 . 27)) 8.395 {1/3:6} B:0 6.67222 [ 6.67222] ((1 . 16) (5 . 19) (9 . 25) (10 . 26) (11 . 27)) 7.253 {4/6:10} B:0 10.00401 [10.00401] ((4 . 17) (5 . 19) (10 . 26) (11 . 25)) 7.737 {1/1:6} B:1 SIMILARITY (1/min{score1}): 0.7459 [and 1/min{score2}: 0.7459] [3038, 6547]: Comparing 1jro_B and 2tpt, based on their crossing files. There are 56 (27 H + 29 S) secondary structure elements in 1jro_B, of which 8 satisfy the size requirements. There are 30 (17 H + 13 S) secondary structure elements in 2tpt, of which 8 satisfy the size requirements. 1.75205 [ 1.75205] ((3 . 22) (4 . 23) (5 . 24) (6 . 25) (9 . 27) (10 . 28) (11 . 29)) 2.855 {2/12:21} B:0 3.43668 [ 3.43668] ((3 . 23) (5 . 24) (6 . 25) (10 . 28)) 7.020 {1/3:6} B:0 3.43726 [ 3.43726] ((3 . 23) (6 . 25) (9 . 29) (10 . 28)) 9.633 {1/3:6} B:1 5.01306 [ 5.01306] ((3 . 27) (4 . 23) (5 . 24) (9 . 25) (11 . 29)) 3.386 {2/4:10} B:1 7.50992 [ 7.50992] ((3 . 27) (4 . 29) (5 . 28) (6 . 30)) 15.013 {3/4:6} B:1 SIMILARITY (1/min{score1}): 0.5708 [and 1/min{score2}: 0.5708] -------------------------------------------------------------------------------------------------------------------------