------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [3310, 487]: Comparing 1ki1_B and 1by1_A, based on their crossing files. There are 22 (13 H + 9 S) secondary structure elements in 1ki1_B, of which 9 satisfy the size requirements. There are 11 (11 H + 0 S) secondary structure elements in 1by1_A, of which 10 satisfy the size requirements. 1.43887 [ 1.54641] ((1 . 1) (4 . 4) (5 . 5) (6 . 6) (7 . 8) (10 . 10) (11 . 11)) 6.635 {1/9:21} B:0 1.50177 [ 1.66796] ((1 . 1) (4 . 4) (5 . 5) (6 . 6) (10 . 10) (11 . 11)) 6.296 {0/6:15} B:0 1.80112 [ 2.00081] ((1 . 1) (2 . 2) (4 . 4) (10 . 10) (11 . 11)) 6.429 {0/2:10} B:0 1.80774 [ 2.00566] ((1 . 1) (4 . 4) (6 . 5) (10 . 10) (11 . 11)) 10.447 {0/3:10} B:0 2.25348 [ 2.50254] ((3 . 6) (5 . 9) (6 . 10) (7 . 11)) 10.100 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.6950 [and 1/min{score2}: 0.6467] [3310, 782]: Comparing 1ki1_B and 1dbh_A, based on their crossing files. There are 22 (13 H + 9 S) secondary structure elements in 1ki1_B, of which 9 satisfy the size requirements. There are 25 (17 H + 8 S) secondary structure elements in 1dbh_A, of which 14 satisfy the size requirements. 1.26570 [ 1.65053] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 8) (10 . 11) (11 . 12)) 7.253 {2/18:36} B:0 1.71967 [ 1.92039] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 7) (7 . 8) (10 . 11) (11 . 13)) 6.625 {3/18:36} B:0 2.06671 [ 2.88433] ((1 . 1) (4 . 4) (5 . 6) (6 . 7) (10 . 11)) 6.673 {1/6:10} B:0 2.25067 [ 3.50018] ((3 . 10) (4 . 11) (5 . 12) (6 . 14)) 6.691 {0/4:6} B:0 2.25990 [ 3.50265] ((4 . 1) (5 . 3) (6 . 4) (10 . 7)) 13.135 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.7901 [and 1/min{score2}: 0.6059] [3310, 1408]: Comparing 1ki1_B and 1f5x_A, based on their crossing files. There are 22 (13 H + 9 S) secondary structure elements in 1ki1_B, of which 9 satisfy the size requirements. There are 11 (11 H + 0 S) secondary structure elements in 1f5x_A, of which 11 satisfy the size requirements. 1.00479 [ 1.22485] ((1 . 3) (2 . 4) (3 . 5) (4 . 6) (5 . 7) (6 . 8) (7 . 9) (10 . 10) (11 . 11)) 5.962 {0/17:36} B:0 2.25506 [ 2.75278] ((4 . 3) (6 . 6) (10 . 8) (11 . 10)) 11.097 {0/2:6} B:0 1.80814 [ 2.20447] ((1 . 6) (4 . 3) (5 . 10) (10 . 8) (11 . 11)) 10.578 {0/1:10} B:2 3.35375 [ 3.37584] ((1 . 4) (2 . 6) (3 . 7) (4 . 3) (5 . 10) (10 . 8) (11 . 11)) 12.035 {1/3:21} B:2 3.36910 [ 3.40914] ((1 . 4) (3 . 7) (4 . 3) (5 . 10) (10 . 8) (11 . 11)) 12.052 {1/3:15} B:2 SIMILARITY (1/min{score1}): 0.9952 [and 1/min{score2}: 0.8164] [3310, 1592]: Comparing 1ki1_B and 1foe_A, based on their crossing files. There are 22 (13 H + 9 S) secondary structure elements in 1ki1_B, of which 9 satisfy the size requirements. There are 27 (20 H + 7 S) secondary structure elements in 1foe_A, of which 11 satisfy the size requirements. 1.08007 [ 1.26889] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 6) (6 . 8) (7 . 9) (10 . 13) (11 . 14)) 5.147 {1/13:36} B:0 1.08049 [ 1.26915] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 6) (6 . 7) (7 . 9) (10 . 13) (11 . 14)) 5.383 {1/13:36} B:0 1.50248 [ 1.83470] ((1 . 1) (2 . 2) (4 . 4) (5 . 6) (10 . 12) (11 . 14)) 6.852 {0/2:15} B:0 2.26202 [ 2.75661] ((1 . 4) (3 . 7) (5 . 9) (7 . 14)) 13.792 {0/2:6} B:0 2.26622 [ 2.75894] ((1 . 4) (3 . 7) (5 . 12) (7 . 14)) 14.876 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.9259 [and 1/min{score2}: 0.7881] [3310, 3310]: Comparing 1ki1_B and 1ki1_B, based on their crossing files. There are 22 (13 H + 9 S) secondary structure elements in 1ki1_B, of which 9 satisfy the size requirements. There are 22 (13 H + 9 S) secondary structure elements in 1ki1_B, of which 9 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (10 . 10) (11 . 11)) 0.000 {0/18:36} B:0 2.26617 [ 2.26617] ((1 . 4) (3 . 6) (5 . 10) (7 . 11)) 14.863 {0/2:6} B:0 2.26617 [ 2.26617] ((4 . 1) (6 . 3) (10 . 5) (11 . 7)) 14.863 {0/2:6} B:0 2.26977 [ 2.26977] ((2 . 4) (4 . 5) (5 . 7) (10 . 11)) 15.639 {0/0:6} B:0 3.36969 [ 3.36969] ((1 . 4) (2 . 11) (4 . 10) (6 . 3) (10 . 1) (11 . 7)) 12.823 {1/3:15} B:3 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [3310, 3483]: Comparing 1ki1_B and 1kz7_A, based on their crossing files. There are 22 (13 H + 9 S) secondary structure elements in 1ki1_B, of which 9 satisfy the size requirements. There are 21 (13 H + 8 S) secondary structure elements in 1kz7_A, of which 9 satisfy the size requirements. 1.16100 [ 1.16100] ((1 . 1) (3 . 3) (4 . 5) (5 . 6) (6 . 7) (7 . 8) (10 . 9) (11 . 10)) 5.823 {1/15:28} B:0 1.50966 [ 1.50966] ((1 . 1) (2 . 3) (4 . 5) (5 . 6) (6 . 7) (10 . 9) (11 . 10)) 6.033 {1/8:21} B:0 1.74821 [ 1.74821] ((1 . 1) (2 . 3) (4 . 5) (5 . 6) (6 . 7) (7 . 8) (10 . 9) (11 . 10)) 6.209 {2/12:28} B:0 1.81077 [ 1.81077] ((1 . 1) (4 . 5) (5 . 7) (10 . 9) (11 . 10)) 11.354 {0/2:10} B:0 2.25545 [ 2.25545] ((1 . 3) (2 . 5) (4 . 7) (6 . 9)) 11.306 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.8613 [and 1/min{score2}: 0.8613] -------------------------------------------------------------------------------------------------------------------------