------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [2043, 968]: Comparing 1h21_A and 1dxr_C, based on their crossing files. There are 11 (11 H + 0 S) secondary structure elements in 1h21_A, of which 9 satisfy the size requirements. There are 21 (19 H + 2 S) secondary structure elements in 1dxr_C, of which 12 satisfy the size requirements. 2.25363 [ 3.00153] ((1 . 9) (5 . 11) (9 . 16) (10 . 19)) 10.207 {0/5:6} B:0 5.05073 [ 5.15490] ((3 . 3) (6 . 5) (7 . 7) (10 . 9)) 9.479 {2/4:6} B:0 4.09682 [ 4.28480] ((2 . 9) (3 . 3) (6 . 5) (7 . 7)) 8.283 {2/5:6} B:1 3.40270 [ 3.53830] ((1 . 19) (2 . 9) (3 . 3) (6 . 5) (7 . 7)) 9.094 {3/9:10} B:2 SIMILARITY (1/min{score1}): 0.4437 [and 1/min{score2}: 0.3332] [2043, 1497]: Comparing 1h21_A and 1fgj_A, based on their crossing files. There are 11 (11 H + 0 S) secondary structure elements in 1h21_A, of which 9 satisfy the size requirements. There are 33 (31 H + 2 S) secondary structure elements in 1fgj_A, of which 27 satisfy the size requirements. 2.25190 [ 6.75007] ((1 . 12) (3 . 15) (5 . 17) (6 . 19)) 8.683 {0/3:6} B:0 2.25333 [ 6.75012] ((1 . 12) (3 . 15) (5 . 16) (9 . 21)) 9.992 {0/3:6} B:0 2.25897 [ 6.75033] ((2 . 9) (3 . 10) (7 . 12) (10 . 19)) 12.813 {0/3:6} B:0 2.26398 [ 6.75052] ((1 . 5) (6 . 11) (9 . 16) (10 . 19)) 14.328 {0/4:6} B:0 2.26636 [ 6.75061] ((1 . 20) (5 . 24) (9 . 27) (10 . 28)) 14.907 {0/6:6} B:0 SIMILARITY (1/min{score1}): 0.5524 [and 1/min{score2}: 0.1852] [2043, 1617]: Comparing 1h21_A and 1fs7_A, based on their crossing files. There are 11 (11 H + 0 S) secondary structure elements in 1h21_A, of which 9 satisfy the size requirements. There are 33 (27 H + 6 S) secondary structure elements in 1fs7_A, of which 27 satisfy the size requirements. 2.25459 [ 6.75017] ((6 . 13) (7 . 14) (9 . 17) (10 . 20)) 10.831 {0/3:6} B:0 2.25800 [ 6.75030] ((1 . 17) (2 . 20) (9 . 26) (10 . 27)) 12.447 {0/4:6} B:0 2.40674 [ 6.75643] ((1 . 8) (3 . 10) (7 . 14) (10 . 20)) 10.789 {1/6:6} B:0 2.54266 [ 6.76311] ((2 . 20) (3 . 21) (6 . 25) (7 . 26)) 10.258 {1/5:6} B:0 2.55096 [ 6.76355] ((1 . 13) (3 . 14) (6 . 17) (10 . 26)) 14.726 {1/5:6} B:0 SIMILARITY (1/min{score1}): 0.7511 [and 1/min{score2}: 0.2591] [2043, 1623]: Comparing 1h21_A and 1ft5_A, based on their crossing files. There are 11 (11 H + 0 S) secondary structure elements in 1h21_A, of which 9 satisfy the size requirements. There are 16 (14 H + 2 S) secondary structure elements in 1ft5_A, of which 10 satisfy the size requirements. 2.25457 [ 2.50334] ((1 . 6) (5 . 9) (6 . 11) (9 . 14)) 10.818 {0/3:6} B:0 2.26070 [ 2.50782] ((5 . 5) (6 . 6) (9 . 11) (11 . 14)) 13.394 {0/4:6} B:0 2.26975 [ 2.51446] ((1 . 5) (6 . 9) (7 . 11) (11 . 16)) 15.634 {0/4:6} B:0 4.09689 [ 4.14488] ((1 . 9) (2 . 11) (3 . 12) (7 . 16)) 8.808 {2/5:6} B:0 5.05061 [ 5.07647] ((5 . 5) (6 . 6) (7 . 8) (11 . 14)) 7.943 {2/4:6} B:0 SIMILARITY (1/min{score1}): 0.4435 [and 1/min{score2}: 0.3995] [2043, 2043]: Comparing 1h21_A and 1h21_A, based on their crossing files. There are 11 (11 H + 0 S) secondary structure elements in 1h21_A, of which 9 satisfy the size requirements. There are 11 (11 H + 0 S) secondary structure elements in 1h21_A, of which 9 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (2 . 2) (3 . 3) (5 . 5) (6 . 6) (7 . 7) (9 . 9) (10 . 10) (11 . 11)) 0.000 {0/32:36} B:0 2.25381 [ 2.25381] ((1 . 5) (2 . 6) (5 . 7) (7 . 9)) 10.333 {0/4:6} B:0 2.25381 [ 2.25381] ((5 . 1) (6 . 2) (7 . 5) (9 . 7)) 10.333 {0/4:6} B:0 2.83616 [ 2.83616] ((7 . 6) (9 . 9) (10 . 10) (11 . 11)) 5.224 {1/4:6} B:0 2.83616 [ 2.83616] ((6 . 7) (9 . 9) (10 . 10) (11 . 11)) 5.224 {1/4:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [2043, 2044]: Comparing 1h21_A and 1h29_A, based on their crossing files. There are 11 (11 H + 0 S) secondary structure elements in 1h21_A, of which 9 satisfy the size requirements. There are 37 (25 H + 12 S) secondary structure elements in 1h29_A, of which 25 satisfy the size requirements. 2.25806 [ 6.25038] ((5 . 25) (6 . 27) (7 . 28) (10 . 32)) 12.473 {0/3:6} B:0 2.54555 [ 6.26668] ((2 . 24) (3 . 25) (10 . 34) (11 . 36)) 12.386 {1/5:6} B:0 2.56184 [ 6.26779] ((1 . 19) (5 . 23) (10 . 28) (11 . 32)) 17.540 {1/5:6} B:0 4.09815 [ 6.49750] ((1 . 23) (5 . 25) (7 . 27) (10 . 32)) 13.004 {2/5:6} B:0 4.10103 [ 6.49822] ((1 . 17) (3 . 18) (9 . 24) (10 . 26)) 16.853 {2/5:6} B:0 SIMILARITY (1/min{score1}): 0.4437 [and 1/min{score2}: 0.1682] [2043, 4579]: Comparing 1h21_A and 1oah_A, based on their crossing files. There are 11 (11 H + 0 S) secondary structure elements in 1h21_A, of which 9 satisfy the size requirements. There are 34 (26 H + 8 S) secondary structure elements in 1oah_A, of which 22 satisfy the size requirements. 2.25140 [ 5.50010] ((1 . 16) (3 . 21) (7 . 25) (11 . 28)) 8.046 {0/6:6} B:0 2.25218 [ 5.50015] ((1 . 16) (3 . 21) (7 . 25) (10 . 26)) 8.981 {0/5:6} B:0 2.25304 [ 5.50021] ((3 . 5) (6 . 7) (10 . 13) (11 . 16)) 9.769 {0/3:6} B:0 2.25331 [ 5.50023] ((5 . 11) (6 . 13) (9 . 21) (11 . 25)) 9.975 {0/6:6} B:0 2.25744 [ 5.50051] ((5 . 7) (6 . 8) (7 . 11) (10 . 16)) 12.223 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.4442 [and 1/min{score2}: 0.2551] [2043, 4635]: Comparing 1h21_A and 1ofw_A, based on their crossing files. There are 11 (11 H + 0 S) secondary structure elements in 1h21_A, of which 9 satisfy the size requirements. There are 20 (16 H + 4 S) secondary structure elements in 1ofw_A, of which 15 satisfy the size requirements. 2.30079 [ 3.76130] ((2 . 7) (3 . 8) (7 . 11) (11 . 20)) 19.901 {0/5:6} B:0 2.54133 [ 3.82402] ((2 . 16) (3 . 17) (5 . 18) (7 . 20)) 8.546 {1/5:6} B:0 2.55889 [ 3.82921] ((2 . 7) (3 . 8) (7 . 11) (11 . 18)) 16.905 {1/5:6} B:0 4.09817 [ 4.61648] ((1 . 3) (5 . 8) (7 . 10) (10 . 16)) 13.058 {2/5:6} B:0 2.25371 [ 3.75080] ((5 . 8) (6 . 16) (7 . 18) (9 . 7)) 10.266 {0/3:6} B:1 SIMILARITY (1/min{score1}): 0.4437 [and 1/min{score2}: 0.2666] [2043, 4772]: Comparing 1h21_A and 1os6_A, based on their crossing files. There are 11 (11 H + 0 S) secondary structure elements in 1h21_A, of which 9 satisfy the size requirements. There are 8 (6 H + 2 S) secondary structure elements in 1os6_A, of which 7 satisfy the size requirements. NO SIMILARITY! -------------------------------------------------------------------------------------------------------------------------