------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [2273, 2273]: Comparing 1hru_A and 1hru_A, based on their crossing files. There are 15 (8 H + 7 S) secondary structure elements in 1hru_A, of which 14 satisfy the size requirements. There are 15 (8 H + 7 S) secondary structure elements in 1hru_A, of which 14 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) (13 . 13) (14 . 14) (15 . 15)) 0.000 {0/78:91} B:0 3.16660 [ 3.16660] ((1 . 1) (4 . 4) (6 . 6) (7 . 8) (15 . 15)) 5.973 {2/8:10} B:0 4.06725 [ 4.06725] ((4 . 1) (6 . 2) (8 . 4) (9 . 6)) 9.702 {2/6:6} B:0 4.06725 [ 4.06725] ((1 . 4) (2 . 6) (4 . 8) (6 . 9)) 9.702 {2/6:6} B:0 4.48939 [ 4.48939] ((7 . 1) (8 . 4) (13 . 9) (15 . 13)) 9.911 {2/5:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [2273, 2825]: Comparing 1hru_A and 1jcu_A, based on their crossing files. There are 15 (8 H + 7 S) secondary structure elements in 1hru_A, of which 14 satisfy the size requirements. There are 16 (6 H + 10 S) secondary structure elements in 1jcu_A, of which 14 satisfy the size requirements. 1.45698 [ 1.45698] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (6 . 5) (8 . 7) (9 . 8) (10 . 9) (11 . 10) (12 . 11) (13 . 12) (14 . 13) (15 . 15)) 2.622 {8/60:78} B:0 3.58989 [ 3.58989] ((11 . 5) (12 . 7) (13 . 8) (15 . 12)) 6.045 {1/5:6} B:0 3.59039 [ 3.59039] ((6 . 2) (11 . 5) (13 . 8) (15 . 12)) 9.284 {1/5:6} B:0 4.06687 [ 4.06687] ((1 . 7) (2 . 8) (3 . 10) (8 . 13)) 6.900 {1/3:6} B:0 4.06738 [ 4.06738] ((4 . 7) (8 . 11) (9 . 12) (13 . 15)) 10.285 {1/3:6} B:0 SIMILARITY (1/min{score1}): 0.6864 [and 1/min{score2}: 0.6864] [2273, 3173]: Comparing 1hru_A and 1k4i_A, based on their crossing files. There are 15 (8 H + 7 S) secondary structure elements in 1hru_A, of which 14 satisfy the size requirements. There are 22 (10 H + 12 S) secondary structure elements in 1k4i_A, of which 16 satisfy the size requirements. 1.40111 [ 1.60074] ((1 . 1) (2 . 2) (3 . 3) (4 . 5) (6 . 6) (7 . 7) (11 . 12) (12 . 14) (13 . 15) (14 . 20)) 3.067 {1/31:45} B:0 1.75772 [ 1.83740] ((1 . 1) (2 . 2) (3 . 3) (4 . 5) (6 . 6) (7 . 7) (9 . 11) (11 . 12) (12 . 14) (13 . 15) (14 . 20)) 4.533 {6/37:55} B:0 2.84637 [ 3.23138] ((1 . 1) (2 . 2) (3 . 3) (7 . 7) (9 . 8)) 4.916 {1/7:10} B:0 3.04408 [ 3.37183] ((1 . 1) (4 . 5) (6 . 6) (7 . 7) (9 . 8)) 5.601 {2/9:10} B:0 3.70862 [ 4.14472] ((4 . 1) (9 . 6) (10 . 7) (15 . 12)) 7.351 {1/4:6} B:0 SIMILARITY (1/min{score1}): 0.7137 [and 1/min{score2}: 0.6247] [2273, 3200]: Comparing 1hru_A and 1k7j_A, based on their crossing files. There are 15 (8 H + 7 S) secondary structure elements in 1hru_A, of which 14 satisfy the size requirements. There are 19 (9 H + 10 S) secondary structure elements in 1k7j_A, of which 16 satisfy the size requirements. 1.11451 [ 1.25648] ((1 . 2) (2 . 3) (3 . 4) (4 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (11 . 11) (12 . 12) (13 . 13) (14 . 14) (15 . 16)) 2.110 {4/60:78} B:0 1.22219 [ 1.37159] ((1 . 2) (2 . 3) (3 . 4) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (11 . 11) (12 . 12) (13 . 13) (14 . 14) (15 . 16)) 2.022 {4/51:66} B:0 3.50043 [ 4.00029] ((3 . 6) (4 . 7) (12 . 14) (13 . 15)) 8.360 {0/3:6} B:0 3.59027 [ 4.06142] ((1 . 5) (2 . 6) (4 . 8) (6 . 9)) 8.769 {1/5:6} B:0 4.48930 [ 4.75709] ((3 . 1) (4 . 2) (8 . 5) (9 . 6)) 9.303 {2/5:6} B:0 SIMILARITY (1/min{score1}): 0.8973 [and 1/min{score2}: 0.7959] [2273, 5134]: Comparing 1hru_A and 1pvy_A, based on their crossing files. There are 15 (8 H + 7 S) secondary structure elements in 1hru_A, of which 14 satisfy the size requirements. There are 20 (12 H + 8 S) secondary structure elements in 1pvy_A, of which 19 satisfy the size requirements. 1.40152 [ 1.90061] ((1 . 1) (2 . 2) (3 . 3) (4 . 5) (6 . 6) (8 . 9) (11 . 14) (12 . 16) (13 . 17) (14 . 18)) 4.833 {1/33:45} B:0 2.76737 [ 2.81823] ((1 . 1) (2 . 2) (3 . 3) (4 . 5) (6 . 6) (8 . 8) (9 . 10) (10 . 11) (11 . 14) (12 . 16) (13 . 17) (14 . 18)) 5.343 {14/51:66} B:0 2.84813 [ 2.88233] ((1 . 1) (2 . 2) (3 . 3) (4 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 10) (10 . 11) (11 . 14) (12 . 16) (13 . 17) (14 . 18)) 5.304 {17/60:78} B:0 3.50042 [ 4.75017] ((2 . 14) (4 . 16) (6 . 17) (7 . 18)) 8.267 {0/5:6} B:0 3.50045 [ 4.75018] ((8 . 11) (11 . 14) (12 . 16) (13 . 17)) 8.454 {0/5:6} B:0 SIMILARITY (1/min{score1}): 0.7135 [and 1/min{score2}: 0.5261] -------------------------------------------------------------------------------------------------------------------------