------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [5600, 1344]: Comparing 1r9w_A and 1f08_A, based on their crossing files. There are 12 (7 H + 5 S) secondary structure elements in 1r9w_A, of which 10 satisfy the size requirements. There are 12 (7 H + 5 S) secondary structure elements in 1f08_A, of which 10 satisfy the size requirements. 1.00002 [ 1.00002] ((1 . 1) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (9 . 9) (10 . 10) (11 . 11) (12 . 12)) 1.415 {0/32:45} B:0 2.50255 [ 2.50255] ((3 . 5) (5 . 6) (9 . 11) (10 . 12)) 10.116 {0/3:6} B:0 2.50348 [ 2.50348] ((3 . 6) (4 . 7) (5 . 9) (6 . 11)) 10.930 {0/0:6} B:0 2.50372 [ 2.50372] ((6 . 3) (7 . 4) (9 . 5) (11 . 6)) 11.120 {0/0:6} B:0 5.07669 [ 5.07669] ((3 . 5) (7 . 10) (9 . 11) (10 . 12)) 10.305 {2/4:6} B:0 SIMILARITY (1/min{score1}): 0.9999 [and 1/min{score2}: 0.9999] [5600, 3539]: Comparing 1r9w_A and 1l5i_A, based on their crossing files. There are 12 (7 H + 5 S) secondary structure elements in 1r9w_A, of which 10 satisfy the size requirements. There are 10 (2 H + 8 S) secondary structure elements in 1l5i_A, of which 8 satisfy the size requirements. 1.60328 [ 1.42717] ((3 . 1) (4 . 2) (5 . 3) (6 . 4) (9 . 8) (10 . 9) (11 . 10)) 3.008 {1/8:21} B:0 1.66671 [ 1.33342] ((3 . 1) (4 . 2) (5 . 3) (6 . 4) (9 . 8) (11 . 10)) 2.695 {0/3:15} B:0 2.50042 [ 2.00082] ((1 . 2) (3 . 3) (5 . 5) (9 . 10)) 6.448 {0/2:6} B:0 2.50052 [ 2.00101] ((6 . 1) (7 . 2) (9 . 3) (11 . 5)) 6.788 {0/3:6} B:0 5.07646 [ 5.03180] ((3 . 1) (4 . 2) (9 . 5) (12 . 9)) 7.646 {1/2:6} B:0 SIMILARITY (1/min{score1}): 0.6237 [and 1/min{score2}: 0.7500] [5600, 3840]: Comparing 1r9w_A and 1m55_A, based on their crossing files. There are 12 (7 H + 5 S) secondary structure elements in 1r9w_A, of which 10 satisfy the size requirements. There are 14 (8 H + 6 S) secondary structure elements in 1m55_A, of which 10 satisfy the size requirements. 2.07248 [ 2.07248] ((3 . 1) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (9 . 8) (10 . 10) (11 . 11)) 4.622 {2/10:28} B:0 2.50076 [ 2.50076] ((3 . 5) (5 . 6) (9 . 11) (12 . 14)) 7.479 {0/3:6} B:0 2.50086 [ 2.50086] ((3 . 5) (5 . 6) (10 . 10) (12 . 14)) 7.703 {0/3:6} B:0 2.50210 [ 2.50210] ((3 . 6) (4 . 7) (5 . 8) (10 . 14)) 9.629 {0/1:6} B:0 4.06112 [ 4.06112] ((4 . 4) (5 . 6) (7 . 7) (9 . 8) (11 . 11)) 4.824 {2/5:10} B:0 SIMILARITY (1/min{score1}): 0.4998 [and 1/min{score2}: 0.4998] [5600, 4712]: Comparing 1r9w_A and 1omh_A, based on their crossing files. There are 12 (7 H + 5 S) secondary structure elements in 1r9w_A, of which 10 satisfy the size requirements. There are 22 (11 H + 11 S) secondary structure elements in 1omh_A, of which 20 satisfy the size requirements. 2.50159 [ 5.00020] ((7 . 15) (9 . 17) (10 . 19) (12 . 20)) 8.987 {0/4:6} B:0 2.50201 [ 5.00025] ((5 . 1) (6 . 3) (7 . 5) (11 . 6)) 9.528 {0/3:6} B:0 2.50669 [ 5.00084] ((3 . 6) (4 . 8) (6 . 9) (9 . 12)) 12.880 {0/0:6} B:0 2.51093 [ 5.00137] ((3 . 6) (4 . 8) (5 . 9) (6 . 10)) 14.570 {0/0:6} B:0 2.72737 [ 5.03223] ((3 . 12) (9 . 18) (10 . 20) (12 . 21)) 11.531 {1/5:6} B:0 SIMILARITY (1/min{score1}): 0.3997 [and 1/min{score2}: 0.3250] [5600, 4888]: Comparing 1r9w_A and 1p4d_A, based on their crossing files. There are 12 (7 H + 5 S) secondary structure elements in 1r9w_A, of which 10 satisfy the size requirements. There are 24 (11 H + 13 S) secondary structure elements in 1p4d_A, of which 19 satisfy the size requirements. 2.51159 [ 4.75170] ((3 . 9) (4 . 11) (5 . 12) (6 . 13)) 14.787 {0/0:6} B:0 5.07649 [ 5.80318] ((3 . 1) (7 . 6) (9 . 9) (10 . 11)) 8.153 {2/4:6} B:0 5.07688 [ 5.80344] ((1 . 6) (6 . 12) (9 . 14) (12 . 18)) 11.576 {3/6:6} B:0 1.48834 [ 2.41973] ((1 . 2) (3 . 9) (4 . 11) (5 . 14) (6 . 15) (7 . 18) (11 . 4) (12 . 5)) 6.301 {2/16:28} B:1 2.50103 [ 4.75015] ((1 . 10) (3 . 9) (4 . 11) (6 . 14)) 8.069 {0/3:6} B:1 SIMILARITY (1/min{score1}): 0.6719 [and 1/min{score2}: 0.4133] [5600, 5600]: Comparing 1r9w_A and 1r9w_A, based on their crossing files. There are 12 (7 H + 5 S) secondary structure elements in 1r9w_A, of which 10 satisfy the size requirements. There are 12 (7 H + 5 S) secondary structure elements in 1r9w_A, of which 10 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (9 . 9) (10 . 10) (11 . 11) (12 . 12)) 0.000 {0/32:45} B:0 2.50218 [ 2.50218] ((6 . 3) (7 . 4) (9 . 5) (12 . 10)) 9.722 {0/3:6} B:0 2.50218 [ 2.50218] ((3 . 6) (4 . 7) (5 . 9) (10 . 12)) 9.722 {0/3:6} B:0 2.50301 [ 2.50301] ((3 . 6) (4 . 7) (5 . 9) (6 . 11)) 10.544 {0/0:6} B:0 2.50301 [ 2.50301] ((6 . 3) (7 . 4) (9 . 5) (11 . 6)) 10.544 {0/0:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [5600, 6539]: Comparing 1r9w_A and 2tbd, based on their crossing files. There are 12 (7 H + 5 S) secondary structure elements in 1r9w_A, of which 10 satisfy the size requirements. There are 10 (4 H + 6 S) secondary structure elements in 2tbd, of which 10 satisfy the size requirements. 1.33037 [ 1.33037] ((3 . 2) (4 . 3) (5 . 4) (6 . 5) (7 . 7) (9 . 8) (10 . 9) (11 . 10)) 4.795 {1/11:28} B:0 1.66676 [ 1.66676] ((3 . 2) (4 . 3) (5 . 4) (6 . 5) (7 . 7) (9 . 8)) 3.249 {0/5:15} B:0 2.50037 [ 2.50037] ((6 . 2) (7 . 3) (9 . 4) (11 . 6)) 6.230 {0/3:6} B:0 2.50045 [ 2.50045] ((4 . 1) (5 . 2) (9 . 5) (11 . 8)) 6.538 {0/1:6} B:0 2.50025 [ 2.50025] ((3 . 4) (4 . 3) (6 . 5) (9 . 10)) 5.645 {0/1:6} B:1 SIMILARITY (1/min{score1}): 0.7517 [and 1/min{score2}: 0.7517] -------------------------------------------------------------------------------------------------------------------------