------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [5608, 2634]: Comparing 1rcw_A and 1iw0_A, based on their crossing files. There are 12 (12 H + 0 S) secondary structure elements in 1rcw_A, of which 11 satisfy the size requirements. There are 13 (13 H + 0 S) secondary structure elements in 1iw0_A, of which 10 satisfy the size requirements. 1.10161 [ 1.00214] ((1 . 1) (3 . 2) (4 . 3) (6 . 5) (7 . 6) (8 . 7) (9 . 8) (10 . 9) (11 . 12) (12 . 13)) 4.872 {0/22:45} B:0 2.75041 [ 2.50055] ((1 . 6) (4 . 8) (6 . 12) (8 . 13)) 6.885 {0/0:6} B:0 2.75118 [ 2.50157] ((1 . 1) (3 . 2) (4 . 3) (5 . 5)) 8.957 {0/3:6} B:0 2.75173 [ 2.50230] ((5 . 1) (10 . 5) (11 . 7) (12 . 9)) 9.851 {0/0:6} B:0 2.75179 [ 2.50238] ((5 . 6) (7 . 8) (8 . 9) (11 . 13)) 9.938 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.9078 [and 1/min{score2}: 0.9979] [5608, 2753]: Comparing 1rcw_A and 1j77_A, based on their crossing files. There are 12 (12 H + 0 S) secondary structure elements in 1rcw_A, of which 11 satisfy the size requirements. There are 11 (11 H + 0 S) secondary structure elements in 1j77_A, of which 10 satisfy the size requirements. 1.90538 [ 1.87928] ((1 . 1) (3 . 2) (4 . 3) (5 . 5) (6 . 6) (9 . 7) (10 . 8) (11 . 10) (12 . 11)) 6.061 {2/11:36} B:0 2.75007 [ 2.50010] ((1 . 1) (4 . 3) (5 . 5) (6 . 6)) 4.455 {0/0:6} B:0 2.75050 [ 2.50067] ((7 . 1) (8 . 2) (10 . 3) (11 . 6)) 7.239 {0/3:6} B:0 2.75056 [ 2.50074] ((6 . 5) (9 . 7) (11 . 10) (12 . 11)) 7.432 {0/3:6} B:0 2.75097 [ 2.50129] ((6 . 3) (8 . 6) (10 . 7) (11 . 8)) 8.527 {0/1:6} B:0 SIMILARITY (1/min{score1}): 0.8151 [and 1/min{score2}: 0.8950] [5608, 4120]: Comparing 1rcw_A and 1n45_A, based on their crossing files. There are 12 (12 H + 0 S) secondary structure elements in 1rcw_A, of which 11 satisfy the size requirements. There are 13 (13 H + 0 S) secondary structure elements in 1n45_A, of which 11 satisfy the size requirements. 1.10178 [ 1.10178] ((1 . 1) (3 . 2) (4 . 3) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 12) (12 . 13)) 4.996 {0/22:45} B:0 1.37877 [ 1.37877] ((1 . 1) (3 . 2) (4 . 3) (5 . 6) (8 . 8) (9 . 9) (10 . 10) (12 . 13)) 7.125 {0/10:28} B:0 2.75111 [ 2.75111] ((3 . 8) (4 . 9) (6 . 12) (8 . 13)) 8.825 {0/2:6} B:0 2.75143 [ 2.75143] ((5 . 7) (7 . 9) (8 . 10) (11 . 13)) 9.399 {0/3:6} B:0 2.75869 [ 2.75869] ((1 . 3) (4 . 6) (5 . 8) (11 . 13)) 14.771 {0/0:6} B:0 SIMILARITY (1/min{score1}): 0.9076 [and 1/min{score2}: 0.9076] [5608, 4786]: Comparing 1rcw_A and 1otv_A, based on their crossing files. There are 12 (12 H + 0 S) secondary structure elements in 1rcw_A, of which 11 satisfy the size requirements. There are 12 (12 H + 0 S) secondary structure elements in 1otv_A, of which 11 satisfy the size requirements. 1.07151 [ 1.07151] ((1 . 1) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12)) 5.791 {2/27:55} B:0 1.10156 [ 1.10156] ((1 . 1) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (11 . 11) (12 . 12)) 4.829 {0/25:45} B:0 1.38078 [ 1.38078] ((4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (10 . 9) (11 . 11) (12 . 12)) 7.935 {0/9:28} B:0 1.83401 [ 1.83401] ((1 . 1) (3 . 3) (4 . 4) (5 . 5) (11 . 10) (12 . 12)) 5.757 {0/5:15} B:0 2.75072 [ 2.75072] ((1 . 4) (5 . 8) (10 . 11) (11 . 12)) 7.904 {0/1:6} B:0 SIMILARITY (1/min{score1}): 0.9333 [and 1/min{score2}: 0.9333] [5608, 5207]: Comparing 1rcw_A and 1q4m_A, based on their crossing files. There are 12 (12 H + 0 S) secondary structure elements in 1rcw_A, of which 11 satisfy the size requirements. There are 13 (11 H + 2 S) secondary structure elements in 1q4m_A, of which 12 satisfy the size requirements. 1.37733 [ 1.50179] ((1 . 1) (4 . 5) (6 . 6) (8 . 8) (9 . 9) (10 . 11) (11 . 12) (12 . 13)) 6.315 {0/9:28} B:0 1.37806 [ 1.50236] ((1 . 1) (4 . 5) (5 . 6) (8 . 8) (9 . 9) (10 . 10) (11 . 12) (12 . 13)) 6.762 {0/8:28} B:0 1.40377 [ 1.52236] ((3 . 2) (4 . 5) (6 . 6) (8 . 8) (9 . 9) (10 . 11) (11 . 12) (12 . 13)) 7.502 {1/14:28} B:0 2.20099 [ 2.40076] ((4 . 6) (5 . 8) (9 . 11) (10 . 12) (11 . 13)) 7.248 {0/0:10} B:0 2.20149 [ 2.40115] ((3 . 8) (4 . 9) (5 . 11) (6 . 12) (8 . 13)) 8.037 {0/4:10} B:0 SIMILARITY (1/min{score1}): 0.7260 [and 1/min{score2}: 0.6659] [5608, 5608]: Comparing 1rcw_A and 1rcw_A, based on their crossing files. There are 12 (12 H + 0 S) secondary structure elements in 1rcw_A, of which 11 satisfy the size requirements. There are 12 (12 H + 0 S) secondary structure elements in 1rcw_A, of which 11 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12)) 0.000 {0/30:55} B:0 1.22686 [ 1.22686] ((1 . 1) (3 . 3) (4 . 4) (5 . 6) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12)) 6.872 {0/16:36} B:0 1.98598 [ 1.98598] ((1 . 1) (3 . 3) (4 . 4) (9 . 10) (11 . 11) (12 . 12)) 8.858 {1/7:15} B:0 2.20409 [ 2.20409] ((1 . 7) (3 . 8) (4 . 9) (6 . 11) (8 . 12)) 10.344 {0/3:10} B:0 2.20409 [ 2.20409] ((7 . 1) (8 . 3) (9 . 4) (11 . 6) (12 . 8)) 10.344 {0/3:10} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [5608, 5704]: Comparing 1rcw_A and 1rtw_A, based on their crossing files. There are 12 (12 H + 0 S) secondary structure elements in 1rcw_A, of which 11 satisfy the size requirements. There are 10 (10 H + 0 S) secondary structure elements in 1rtw_A, of which 10 satisfy the size requirements. 1.24669 [ 1.14324] ((1 . 1) (3 . 3) (4 . 4) (6 . 5) (8 . 6) (9 . 7) (10 . 8) (11 . 9) (12 . 10)) 6.741 {1/16:36} B:0 1.25476 [ 1.15367] ((1 . 1) (3 . 3) (4 . 4) (5 . 5) (8 . 6) (9 . 7) (10 . 8) (11 . 9) (12 . 10)) 7.556 {1/15:36} B:0 2.75036 [ 2.50048] ((4 . 5) (9 . 8) (10 . 9) (11 . 10)) 6.645 {0/0:6} B:0 2.75042 [ 2.50056] ((6 . 5) (10 . 7) (11 . 9) (12 . 10)) 6.924 {0/1:6} B:0 2.75069 [ 2.50092] ((4 . 5) (5 . 6) (10 . 9) (11 . 10)) 7.835 {0/0:6} B:0 SIMILARITY (1/min{score1}): 0.8021 [and 1/min{score2}: 0.8747] -------------------------------------------------------------------------------------------------------------------------