------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [2588, 1428]: Comparing 1is1_A and 1f7u_A, based on their crossing files. There are 12 (6 H + 6 S) secondary structure elements in 1is1_A, of which 11 satisfy the size requirements. There are 48 (34 H + 14 S) secondary structure elements in 1f7u_A, of which 10 satisfy the size requirements. 2.75158 [ 2.50210] ((2 . 3) (7 . 7) (8 . 9) (11 . 12)) 9.631 {0/6:6} B:0 2.75245 [ 2.50326] ((8 . 9) (9 . 10) (10 . 11) (11 . 12)) 10.753 {0/3:6} B:0 2.75512 [ 2.50680] ((1 . 4) (2 . 9) (4 . 10) (8 . 12)) 12.934 {0/5:6} B:0 2.75920 [ 2.51221] ((1 . 4) (2 . 9) (4 . 10) (8 . 13)) 14.983 {0/5:6} B:0 3.13235 [ 2.97314] ((2 . 3) (7 . 7) (8 . 9) (10 . 10)) 5.435 {1/4:6} B:0 SIMILARITY (1/min{score1}): 0.5326 [and 1/min{score2}: 0.5799] [2588, 2557]: Comparing 1is1_A and 1iq0_A, based on their crossing files. There are 12 (6 H + 6 S) secondary structure elements in 1is1_A, of which 11 satisfy the size requirements. There are 42 (23 H + 19 S) secondary structure elements in 1iq0_A, of which 7 satisfy the size requirements. 2.20008 [ 1.40030] ((2 . 1) (7 . 3) (8 . 5) (9 . 6) (10 . 7)) 3.829 {0/6:10} B:0 2.75005 [ 1.75018] ((2 . 1) (8 . 5) (9 . 6) (10 . 7)) 3.992 {0/3:6} B:0 2.75298 [ 1.76147] ((2 . 1) (7 . 3) (8 . 5) (11 . 8)) 11.295 {0/6:6} B:0 2.75444 [ 1.76702] ((8 . 5) (9 . 6) (10 . 7) (11 . 8)) 12.480 {0/3:6} B:0 3.13231 [ 2.63831] ((2 . 1) (7 . 3) (8 . 5) (10 . 6)) 4.982 {1/4:6} B:0 SIMILARITY (1/min{score1}): 0.4545 [and 1/min{score2}: 0.7141] [2588, 2588]: Comparing 1is1_A and 1is1_A, based on their crossing files. There are 12 (6 H + 6 S) secondary structure elements in 1is1_A, of which 11 satisfy the size requirements. There are 12 (6 H + 6 S) secondary structure elements in 1is1_A, of which 11 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12)) 0.000 {0/44:55} B:0 1.83454 [ 1.83454] ((1 . 1) (2 . 2) (4 . 6) (8 . 8) (11 . 11) (12 . 12)) 6.652 {0/11:15} B:0 1.83454 [ 1.83454] ((1 . 1) (2 . 2) (6 . 4) (8 . 8) (11 . 11) (12 . 12)) 6.652 {0/11:15} B:0 2.17128 [ 2.17128] ((1 . 1) (2 . 2) (3 . 4) (8 . 8) (11 . 11) (12 . 12)) 2.733 {2/11:15} B:0 2.66473 [ 2.66473] ((1 . 1) (2 . 2) (6 . 3) (8 . 8) (11 . 11) (12 . 12)) 7.978 {3/12:15} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [2588, 5305]: Comparing 1is1_A and 1qf6_A, based on their crossing files. There are 12 (6 H + 6 S) secondary structure elements in 1is1_A, of which 11 satisfy the size requirements. There are 59 (24 H + 35 S) secondary structure elements in 1qf6_A, of which 11 satisfy the size requirements. 2.93222 [ 2.93222] ((2 . 9) (8 . 13) (10 . 14) (11 . 15)) 14.802 {1/5:6} B:0 4.20733 [ 4.20733] ((6 . 14) (8 . 16) (10 . 18) (12 . 23)) 10.054 {2/5:6} B:0 2.75088 [ 2.75088] ((6 . 18) (7 . 17) (9 . 20) (10 . 22)) 8.324 {0/3:6} B:1 3.66731 [ 3.66731] ((4 . 22) (6 . 18) (8 . 16) (12 . 23)) 11.096 {2/6:6} B:2 SIMILARITY (1/min{score1}): 0.3635 [and 1/min{score2}: 0.3635] [2588, 6122]: Comparing 1is1_A and 1uv7_A, based on their crossing files. There are 12 (6 H + 6 S) secondary structure elements in 1is1_A, of which 11 satisfy the size requirements. There are 6 (2 H + 4 S) secondary structure elements in 1uv7_A, of which 6 satisfy the size requirements. 1.83343 [ 1.00060] ((2 . 1) (6 . 2) (7 . 3) (8 . 4) (9 . 5) (10 . 6)) 3.538 {0/5:15} B:0 2.20004 [ 1.20028] ((6 . 2) (7 . 3) (8 . 4) (9 . 5) (10 . 6)) 3.342 {0/2:10} B:0 2.75636 [ 1.53785] ((8 . 1) (9 . 2) (10 . 3) (11 . 4)) 13.656 {0/2:6} B:0 1.83341 [ 1.00049] ((2 . 4) (6 . 5) (7 . 6) (8 . 1) (9 . 2) (10 . 3)) 3.368 {0/5:15} B:1 6.68650 [ 6.66858] ((1 . 4) (6 . 3) (7 . 6) (8 . 1) (10 . 2)) 10.581 {2/3:10} B:2 SIMILARITY (1/min{score1}): 0.5454 [and 1/min{score2}: 0.9995] [2588, 6191]: Comparing 1is1_A and 1v7o_A, based on their crossing files. There are 12 (6 H + 6 S) secondary structure elements in 1is1_A, of which 11 satisfy the size requirements. There are 13 (6 H + 7 S) secondary structure elements in 1v7o_A, of which 10 satisfy the size requirements. 2.92974 [ 2.73000] ((1 . 1) (6 . 6) (9 . 9) (10 . 10)) 13.341 {1/5:6} B:0 3.66886 [ 3.57343] ((8 . 1) (9 . 3) (10 . 4) (11 . 5)) 13.705 {1/3:6} B:0 2.36480 [ 2.20985] ((2 . 5) (7 . 6) (8 . 7) (9 . 10) (10 . 9)) 9.643 {1/6:10} B:1 2.75083 [ 2.50111] ((6 . 10) (7 . 9) (9 . 12) (10 . 13)) 8.210 {0/3:6} B:1 7.53372 [ 7.52310] ((2 . 1) (6 . 4) (7 . 3) (10 . 6)) 8.993 {3/4:6} B:1 SIMILARITY (1/min{score1}): 0.5451 [and 1/min{score2}: 0.5994] -------------------------------------------------------------------------------------------------------------------------