------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [1158, 84]: Comparing 1ehi_A and 1a9x_A, based on their crossing files. There are 26 (14 H + 12 S) secondary structure elements in 1ehi_A, of which 9 satisfy the size requirements. There are 84 (46 H + 38 S) secondary structure elements in 1a9x_A, of which 9 satisfy the size requirements. 1.28592 [ 1.28592] ((1 . 1) (2 . 2) (3 . 3) (6 . 7) (7 . 8) (8 . 10) (9 . 12)) 3.281 {0/5:21} B:0 1.28610 [ 1.28610] ((1 . 1) (2 . 2) (3 . 3) (6 . 7) (7 . 8) (8 . 9) (9 . 12)) 3.833 {0/7:21} B:0 1.50016 [ 1.50016] ((1 . 1) (2 . 2) (3 . 3) (6 . 7) (7 . 8) (8 . 9)) 3.458 {0/6:15} B:0 1.80025 [ 1.80025] ((3 . 1) (6 . 7) (7 . 8) (8 . 9) (9 . 12)) 4.403 {0/4:10} B:0 2.25044 [ 2.25044] ((1 . 1) (2 . 2) (3 . 3) (6 . 9)) 6.016 {0/1:6} B:0 SIMILARITY (1/min{score1}): 0.7777 [and 1/min{score2}: 0.7777] [1158, 304]: Comparing 1ehi_A and 1b6r_A, based on their crossing files. There are 26 (14 H + 12 S) secondary structure elements in 1ehi_A, of which 9 satisfy the size requirements. There are 31 (15 H + 16 S) secondary structure elements in 1b6r_A, of which 6 satisfy the size requirements. 2.25049 [ 1.50164] ((1 . 1) (2 . 2) (3 . 3) (5 . 6)) 6.175 {0/3:6} B:0 4.04085 [ 4.00855] ((1 . 3) (2 . 2) (3 . 1) (5 . 6) (6 . 7)) 9.462 {2/5:10} B:2 SIMILARITY (1/min{score1}): 0.4443 [and 1/min{score2}: 0.6659] [1158, 947]: Comparing 1ehi_A and 1dv1_A, based on their crossing files. There are 26 (14 H + 12 S) secondary structure elements in 1ehi_A, of which 9 satisfy the size requirements. There are 37 (18 H + 19 S) secondary structure elements in 1dv1_A, of which 9 satisfy the size requirements. 1.28596 [ 1.28596] ((1 . 1) (2 . 2) (3 . 3) (6 . 8) (7 . 9) (8 . 10) (9 . 12)) 3.433 {0/7:21} B:0 1.80003 [ 1.80003] ((3 . 1) (6 . 8) (7 . 9) (8 . 10) (9 . 12)) 2.695 {0/3:10} B:0 2.25061 [ 2.25061] ((1 . 1) (2 . 2) (4 . 8) (6 . 10)) 6.527 {0/0:6} B:0 2.25061 [ 2.25061] ((1 . 1) (2 . 5) (4 . 8) (6 . 10)) 6.545 {0/0:6} B:0 2.25108 [ 2.25108] ((1 . 1) (2 . 2) (5 . 8) (6 . 10)) 7.533 {0/0:6} B:0 SIMILARITY (1/min{score1}): 0.7776 [and 1/min{score2}: 0.7776] [1158, 1031]: Comparing 1ehi_A and 1e4e_A, based on their crossing files. There are 26 (14 H + 12 S) secondary structure elements in 1ehi_A, of which 9 satisfy the size requirements. There are 28 (11 H + 17 S) secondary structure elements in 1e4e_A, of which 10 satisfy the size requirements. 1.50001 [ 1.66667] ((1 . 1) (2 . 2) (3 . 3) (7 . 8) (8 . 9) (9 . 10)) 1.662 {0/6:15} B:0 2.25064 [ 2.50047] ((1 . 5) (3 . 8) (4 . 9) (5 . 10)) 6.616 {0/2:6} B:0 5.01017 [ 5.01544] ((1 . 1) (2 . 2) (3 . 3) (6 . 9) (7 . 8) (8 . 10)) 7.137 {2/4:15} B:1 5.05063 [ 5.07650] ((1 . 3) (2 . 2) (6 . 9) (8 . 10)) 8.294 {1/2:6} B:1 4.30175 [ 4.31006] ((1 . 3) (3 . 1) (4 . 9) (5 . 10) (6 . 2) (7 . 4)) 5.717 {3/7:15} B:2 SIMILARITY (1/min{score1}): 0.6667 [and 1/min{score2}: 0.6000] [1158, 1158]: Comparing 1ehi_A and 1ehi_A, based on their crossing files. There are 26 (14 H + 12 S) secondary structure elements in 1ehi_A, of which 9 satisfy the size requirements. There are 26 (14 H + 12 S) secondary structure elements in 1ehi_A, 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) (8 . 8) (9 . 9)) 0.000 {0/24:36} B:0 2.25099 [ 2.25099] ((1 . 3) (2 . 4) (4 . 6) (6 . 8)) 7.383 {0/3:6} B:0 2.25099 [ 2.25099] ((3 . 1) (4 . 2) (6 . 4) (8 . 6)) 7.383 {0/3:6} B:0 2.52559 [ 2.52559] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (7 . 7) (8 . 6) (9 . 8)) 6.163 {4/16:28} B:1 2.52559 [ 2.52559] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 8) (7 . 7) (8 . 9)) 6.163 {4/16:28} B:1 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [1158, 1932]: Comparing 1ehi_A and 1gsa, based on their crossing files. There are 26 (14 H + 12 S) secondary structure elements in 1ehi_A, of which 9 satisfy the size requirements. There are 31 (14 H + 17 S) secondary structure elements in 1gsa, of which 10 satisfy the size requirements. 1.50037 [ 1.66694] ((1 . 1) (2 . 3) (3 . 4) (7 . 10) (8 . 11) (9 . 13)) 4.250 {0/3:15} B:0 5.05051 [ 5.07638] ((1 . 1) (2 . 3) (6 . 11) (7 . 12)) 5.459 {1/2:6} B:0 3.36704 [ 3.38429] ((1 . 10) (2 . 11) (3 . 12) (4 . 13) (7 . 1) (8 . 3)) 4.698 {1/3:15} B:1 3.49450 [ 3.57067] ((1 . 4) (2 . 3) (6 . 11) (7 . 12)) 6.938 {1/3:6} B:1 3.49501 [ 3.57115] ((1 . 4) (2 . 3) (5 . 11) (7 . 12)) 9.484 {1/3:6} B:1 SIMILARITY (1/min{score1}): 0.6665 [and 1/min{score2}: 0.5999] [1158, 1940]: Comparing 1ehi_A and 1gso_A, based on their crossing files. There are 26 (14 H + 12 S) secondary structure elements in 1ehi_A, of which 9 satisfy the size requirements. There are 37 (16 H + 21 S) secondary structure elements in 1gso_A, of which 10 satisfy the size requirements. 1.27058 [ 1.36246] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (6 . 6) (7 . 7) (8 . 9) (9 . 11)) 4.123 {1/10:28} B:0 1.28585 [ 1.42867] ((1 . 1) (2 . 2) (3 . 3) (6 . 6) (7 . 7) (8 . 9) (9 . 11)) 2.963 {0/8:21} B:0 1.50874 [ 1.60366] ((1 . 1) (2 . 2) (3 . 3) (6 . 6) (7 . 7) (8 . 8) (9 . 11)) 4.702 {1/8:21} B:0 1.80038 [ 2.00028] ((3 . 1) (6 . 6) (7 . 7) (8 . 8) (9 . 11)) 4.925 {0/5:10} B:0 2.14247 [ 2.20695] ((1 . 1) (2 . 2) (3 . 3) (6 . 6) (7 . 7) (8 . 8)) 4.652 {1/5:15} B:0 SIMILARITY (1/min{score1}): 0.7870 [and 1/min{score2}: 0.7340] [1158, 2422]: Comparing 1ehi_A and 1i7n_A, based on their crossing files. There are 26 (14 H + 12 S) secondary structure elements in 1ehi_A, of which 9 satisfy the size requirements. There are 27 (10 H + 17 S) secondary structure elements in 1i7n_A, of which 8 satisfy the size requirements. 1.80026 [ 1.60037] ((1 . 1) (2 . 2) (3 . 4) (7 . 9) (8 . 10)) 4.452 {0/2:10} B:0 2.25036 [ 2.00051] ((1 . 1) (2 . 2) (3 . 4) (6 . 10)) 5.719 {0/0:6} B:0 SIMILARITY (1/min{score1}): 0.5555 [and 1/min{score2}: 0.6249] [1158, 2552]: Comparing 1ehi_A and 1iow, based on their crossing files. There are 26 (14 H + 12 S) secondary structure elements in 1ehi_A, of which 9 satisfy the size requirements. There are 25 (12 H + 13 S) secondary structure elements in 1iow, of which 7 satisfy the size requirements. 1.62066 [ 1.50761] ((1 . 1) (2 . 2) (3 . 3) (6 . 4) (7 . 5) (8 . 6) (9 . 7)) 2.937 {1/7:21} B:0 2.25030 [ 1.75064] ((1 . 1) (2 . 2) (3 . 3) (6 . 6)) 5.487 {0/0:6} B:0 2.25105 [ 1.75222] ((2 . 2) (3 . 3) (5 . 4) (6 . 6)) 7.479 {0/0:6} B:0 10.00262 [10.00096] ((3 . 1) (6 . 4) (7 . 5) (8 . 6) (9 . 7)) 3.197 {1/1:10} B:0 10.00263 [10.00097] ((1 . 1) (2 . 2) (3 . 3) (6 . 4) (8 . 7)) 6.982 {2/2:10} B:0 SIMILARITY (1/min{score1}): 0.7765 [and 1/min{score2}: 0.9954] [1158, 3322]: Comparing 1ehi_A and 1kjq_A, based on their crossing files. There are 26 (14 H + 12 S) secondary structure elements in 1ehi_A, of which 9 satisfy the size requirements. There are 36 (14 H + 22 S) secondary structure elements in 1kjq_A, of which 9 satisfy the size requirements. 1.28606 [ 1.28606] ((1 . 1) (2 . 2) (3 . 3) (6 . 6) (7 . 7) (8 . 8) (9 . 10)) 3.734 {0/4:21} B:0 1.80008 [ 1.80008] ((3 . 1) (6 . 6) (7 . 7) (8 . 8) (9 . 10)) 3.284 {0/3:10} B:0 2.25044 [ 2.25044] ((1 . 1) (2 . 2) (3 . 3) (6 . 8)) 6.017 {0/0:6} B:0 3.36708 [ 3.36708] ((1 . 1) (2 . 2) (3 . 3) (6 . 6) (7 . 7) (8 . 10)) 5.420 {1/3:15} B:0 10.00644 [10.00644] ((1 . 3) (2 . 4) (4 . 8) (5 . 10)) 10.239 {1/1:6} B:0 SIMILARITY (1/min{score1}): 0.7776 [and 1/min{score2}: 0.7776] [1158, 3776]: Comparing 1ehi_A and 1m0w_A, based on their crossing files. There are 26 (14 H + 12 S) secondary structure elements in 1ehi_A, of which 9 satisfy the size requirements. There are 43 (20 H + 23 S) secondary structure elements in 1m0w_A, of which 10 satisfy the size requirements. 2.25015 [ 2.50011] ((3 . 15) (7 . 21) (8 . 23) (9 . 25)) 4.584 {0/2:6} B:0 2.25045 [ 2.50032] ((3 . 15) (4 . 16) (7 . 21) (9 . 25)) 6.039 {0/3:6} B:0 2.57741 [ 2.61531] ((1 . 15) (2 . 16) (3 . 17) (6 . 18) (7 . 21) (9 . 25)) 4.211 {1/4:15} B:0 3.49479 [ 3.57094] ((1 . 15) (2 . 16) (3 . 17) (4 . 18)) 8.641 {1/3:6} B:0 4.01066 [ 4.01620] ((1 . 15) (2 . 16) (3 . 17) (6 . 18) (7 . 21) (8 . 23) (9 . 25)) 4.652 {2/5:21} B:0 SIMILARITY (1/min{score1}): 0.5560 [and 1/min{score2}: 0.5385] [1158, 5967]: Comparing 1ehi_A and 1uc8_A, based on their crossing files. There are 26 (14 H + 12 S) secondary structure elements in 1ehi_A, of which 9 satisfy the size requirements. There are 24 (11 H + 13 S) secondary structure elements in 1uc8_A, of which 7 satisfy the size requirements. 1.39056 [ 1.19017] ((1 . 1) (2 . 2) (3 . 3) (6 . 6) (7 . 7) (8 . 8) (9 . 10)) 4.536 {1/10:21} B:0 1.74325 [ 1.56672] ((1 . 1) (2 . 2) (3 . 3) (6 . 6) (7 . 7) (8 . 8)) 4.710 {1/7:15} B:0 1.80025 [ 1.40054] ((3 . 1) (6 . 6) (7 . 7) (8 . 8) (9 . 10)) 4.441 {0/5:10} B:0 2.25031 [ 1.75067] ((1 . 1) (2 . 2) (3 . 3) (6 . 8)) 5.531 {0/1:6} B:0 2.25055 [ 1.75116] ((1 . 3) (2 . 6) (4 . 8) (5 . 10)) 6.354 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.7753 [and 1/min{score2}: 0.9914] -------------------------------------------------------------------------------------------------------------------------