------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [3202, 513]: Comparing 1k7w_A and 1c3c_A, based on their crossing files. There are 30 (22 H + 8 S) secondary structure elements in 1k7w_A, of which 24 satisfy the size requirements. There are 27 (21 H + 6 S) secondary structure elements in 1c3c_A, of which 22 satisfy the size requirements. 1.33504 [ 1.22443] ((3 . 3) (4 . 4) (5 . 6) (6 . 7) (7 . 8) (8 . 9) (9 . 10) (10 . 11) (12 . 13) (15 . 15) (20 . 17) (21 . 18) (23 . 20) (24 . 21) (25 . 22) (28 . 25) (29 . 26) (30 . 27)) 4.173 {4/122:153} B:0 1.58066 [ 1.50092] ((3 . 3) (4 . 4) (5 . 6) (6 . 7) (7 . 8) (8 . 9) (9 . 10) (10 . 11) (12 . 13) (15 . 15) (20 . 17) (21 . 18) (23 . 20) (25 . 21) (28 . 25) (29 . 26) (30 . 27)) 4.757 {13/106:136} B:0 4.00011 [ 3.66681] ((4 . 5) (7 . 8) (10 . 11) (15 . 15) (20 . 17) (21 . 18)) 6.519 {0/8:15} B:0 4.41359 [ 4.17633] ((7 . 8) (9 . 9) (10 . 11) (15 . 15) (20 . 17) (21 . 18)) 4.090 {3/9:15} B:0 5.83077 [ 5.62316] ((7 . 8) (10 . 11) (12 . 13) (15 . 15) (25 . 23)) 5.202 {3/6:10} B:0 SIMILARITY (1/min{score1}): 0.7490 [and 1/min{score2}: 0.8167] [3202, 895]: Comparing 1k7w_A and 1dof_A, based on their crossing files. There are 30 (22 H + 8 S) secondary structure elements in 1k7w_A, of which 24 satisfy the size requirements. There are 21 (17 H + 4 S) secondary structure elements in 1dof_A, of which 18 satisfy the size requirements. 1.60057 [ 1.20135] ((3 . 3) (4 . 4) (5 . 5) (7 . 6) (8 . 7) (9 . 8) (10 . 9) (12 . 11) (15 . 12) (20 . 14) (21 . 15) (23 . 17) (24 . 18) (25 . 19) (30 . 21)) 4.556 {2/87:105} B:0 1.69779 [ 1.39882] ((3 . 3) (4 . 4) (6 . 5) (7 . 6) (8 . 7) (9 . 8) (10 . 9) (12 . 11) (15 . 12) (20 . 14) (21 . 15) (23 . 17) (24 . 18) (25 . 19) (30 . 21)) 5.004 {10/87:105} B:0 1.71462 [ 1.28651] ((3 . 3) (4 . 4) (5 . 5) (7 . 6) (8 . 7) (9 . 8) (10 . 9) (12 . 11) (15 . 12) (20 . 14) (21 . 15) (24 . 18) (25 . 19) (30 . 21)) 4.532 {1/74:91} B:0 4.00004 [ 3.00008] ((2 . 2) (3 . 3) (7 . 6) (10 . 9) (12 . 11) (15 . 12)) 4.923 {0/6:15} B:0 4.61536 [ 4.08608] ((7 . 6) (9 . 7) (10 . 9) (15 . 12) (20 . 14) (21 . 15)) 4.017 {3/8:15} B:0 SIMILARITY (1/min{score1}): 0.6248 [and 1/min{score2}: 0.8324] [3202, 1847]: Comparing 1k7w_A and 1gkm_A, based on their crossing files. There are 30 (22 H + 8 S) secondary structure elements in 1k7w_A, of which 24 satisfy the size requirements. There are 34 (25 H + 9 S) secondary structure elements in 1gkm_A, of which 29 satisfy the size requirements. 2.67826 [ 3.22882] ((3 . 8) (4 . 9) (5 . 12) (6 . 16) (7 . 17) (10 . 24) (15 . 27) (20 . 30) (21 . 31)) 7.994 {2/21:36} B:0 3.02294 [ 3.63808] ((3 . 8) (4 . 9) (5 . 12) (7 . 17) (10 . 24) (15 . 27) (20 . 30) (21 . 31)) 8.066 {2/16:28} B:0 4.80084 [ 5.80048] ((3 . 19) (4 . 20) (7 . 27) (10 . 30) (15 . 31)) 12.496 {0/2:10} B:0 4.81751 [ 5.80995] ((3 . 9) (6 . 15) (7 . 17) (15 . 27) (20 . 30)) 8.305 {1/6:10} B:0 4.94412 [ 5.88362] ((3 . 8) (4 . 9) (5 . 12) (7 . 17) (21 . 30)) 7.323 {2/7:10} B:0 SIMILARITY (1/min{score1}): 0.3847 [and 1/min{score2}: 0.3441] [3202, 3202]: Comparing 1k7w_A and 1k7w_A, based on their crossing files. There are 30 (22 H + 8 S) secondary structure elements in 1k7w_A, of which 24 satisfy the size requirements. There are 30 (22 H + 8 S) secondary structure elements in 1k7w_A, of which 24 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (12 . 12) (14 . 14) (15 . 15) (18 . 18) (19 . 19) (20 . 20) (21 . 21) (23 . 23) (24 . 24) (25 . 25) (27 . 27) (28 . 28) (29 . 29) (30 . 30)) 0.000 {0/236:276} B:0 4.41358 [ 4.41358] ((7 . 7) (8 . 9) (10 . 10) (15 . 15) (20 . 20) (21 . 21)) 3.603 {3/9:15} B:0 6.00001 [ 6.00001] ((3 . 24) (4 . 25) (5 . 27) (6 . 28)) 4.883 {0/5:6} B:0 6.00013 [ 6.00013] ((4 . 3) (9 . 8) (25 . 24) (27 . 25)) 9.229 {0/4:6} B:0 6.00014 [ 6.00014] ((24 . 3) (25 . 4) (27 . 5) (30 . 7)) 9.428 {0/5:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [3202, 5214]: Comparing 1k7w_A and 1q5n_A, based on their crossing files. There are 30 (22 H + 8 S) secondary structure elements in 1k7w_A, of which 24 satisfy the size requirements. There are 27 (23 H + 4 S) secondary structure elements in 1q5n_A, of which 22 satisfy the size requirements. 1.43256 [ 1.32088] ((3 . 3) (4 . 4) (5 . 7) (6 . 8) (7 . 9) (8 . 10) (9 . 11) (10 . 12) (12 . 14) (15 . 15) (20 . 17) (21 . 18) (23 . 20) (24 . 21) (25 . 22) (28 . 25) (30 . 27)) 4.280 {8/115:136} B:0 1.61069 [ 1.55198] ((3 . 3) (4 . 4) (5 . 7) (6 . 8) (7 . 9) (8 . 10) (9 . 11) (10 . 12) (12 . 14) (15 . 15) (20 . 17) (21 . 18) (23 . 20) (24 . 21) (25 . 22) (27 . 24) (28 . 25) (30 . 27)) 4.357 {18/131:153} B:0 3.64878 [ 3.41893] ((6 . 7) (7 . 9) (10 . 12) (12 . 14) (15 . 15) (20 . 17) (21 . 18)) 4.442 {3/12:21} B:0 4.06116 [ 3.74534] ((6 . 7) (7 . 9) (10 . 12) (20 . 17) (21 . 18) (30 . 27)) 6.040 {2/10:15} B:0 4.80553 [ 4.40718] ((2 . 20) (3 . 21) (4 . 22) (5 . 23) (6 . 25)) 5.123 {1/8:10} B:0 SIMILARITY (1/min{score1}): 0.6980 [and 1/min{score2}: 0.7571] [3202, 6210]: Comparing 1k7w_A and 1vdk_A, based on their crossing files. There are 30 (22 H + 8 S) secondary structure elements in 1k7w_A, of which 24 satisfy the size requirements. There are 28 (20 H + 8 S) secondary structure elements in 1vdk_A, of which 23 satisfy the size requirements. 2.05426 [ 2.03101] ((3 . 4) (4 . 5) (5 . 7) (7 . 10) (8 . 11) (9 . 12) (10 . 13) (12 . 15) (14 . 17) (15 . 18) (20 . 20) (21 . 21) (23 . 23) (24 . 24) (28 . 26) (29 . 28)) 5.663 {17/90:120} B:0 4.88599 [ 4.69724] ((3 . 4) (4 . 5) (5 . 7) (10 . 13) (27 . 25)) 5.400 {2/8:10} B:0 4.94408 [ 4.76241] ((1 . 3) (3 . 4) (4 . 5) (10 . 13) (27 . 25)) 6.234 {2/7:10} B:0 6.00041 [ 5.75046] ((14 . 8) (15 . 9) (21 . 13) (30 . 20)) 12.329 {0/3:6} B:0 6.00065 [ 5.75074] ((4 . 13) (7 . 18) (10 . 20) (15 . 21)) 13.860 {0/0:6} B:0 SIMILARITY (1/min{score1}): 0.4868 [and 1/min{score2}: 0.4924] -------------------------------------------------------------------------------------------------------------------------