------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [6169, 844]: Comparing 1v4e_A and 1di1_A, based on their crossing files. There are 17 (15 H + 2 S) secondary structure elements in 1v4e_A, of which 14 satisfy the size requirements. There are 14 (14 H + 0 S) secondary structure elements in 1di1_A, of which 14 satisfy the size requirements. 1.49651 [ 1.49651] ((1 . 1) (3 . 3) (4 . 4) (8 . 5) (9 . 7) (10 . 8) (11 . 9) (12 . 11) (13 . 12) (16 . 13)) 6.590 {3/29:45} B:0 2.80118 [ 2.80118] ((4 . 1) (9 . 4) (10 . 5) (11 . 6) (12 . 7)) 9.081 {0/3:10} B:0 2.80279 [ 2.80279] ((1 . 3) (3 . 4) (4 . 5) (7 . 6) (8 . 7)) 11.262 {0/6:10} B:0 2.80376 [ 2.80376] ((1 . 2) (3 . 4) (4 . 5) (7 . 6) (8 . 7)) 12.137 {0/6:10} B:0 2.82922 [ 2.82922] ((3 . 2) (4 . 4) (9 . 7) (12 . 11) (13 . 12)) 10.196 {1/8:10} B:0 SIMILARITY (1/min{score1}): 0.6682 [and 1/min{score2}: 0.6682] [6169, 1323]: Comparing 1v4e_A and 1ezf_A, based on their crossing files. There are 17 (15 H + 2 S) secondary structure elements in 1v4e_A, of which 14 satisfy the size requirements. There are 20 (20 H + 0 S) secondary structure elements in 1ezf_A, of which 20 satisfy the size requirements. 3.36513 [ 4.23861] ((4 . 1) (9 . 5) (13 . 9) (14 . 11) (15 . 16)) 9.614 {2/7:10} B:0 3.50053 [ 5.00018] ((9 . 1) (13 . 7) (14 . 8) (16 . 9)) 8.783 {0/4:6} B:0 3.50054 [ 5.00019] ((1 . 7) (3 . 9) (4 . 11) (9 . 16)) 8.829 {0/1:6} B:0 3.50055 [ 5.00019] ((4 . 3) (9 . 7) (11 . 8) (16 . 15)) 8.885 {0/0:6} B:0 3.50067 [ 5.00023] ((4 . 3) (8 . 4) (11 . 8) (16 . 15)) 9.321 {0/0:6} B:0 SIMILARITY (1/min{score1}): 0.6415 [and 1/min{score2}: 0.4498] [6169, 3317]: Comparing 1v4e_A and 1kiy_A, based on their crossing files. There are 17 (15 H + 2 S) secondary structure elements in 1v4e_A, of which 14 satisfy the size requirements. There are 20 (20 H + 0 S) secondary structure elements in 1kiy_A, of which 17 satisfy the size requirements. 2.80018 [ 3.40010] ((2 . 10) (4 . 12) (7 . 13) (8 . 14) (9 . 15)) 5.656 {0/6:10} B:0 2.80021 [ 3.40012] ((3 . 11) (4 . 12) (7 . 13) (8 . 14) (9 . 15)) 5.891 {0/5:10} B:0 2.80125 [ 3.40070] ((3 . 8) (4 . 9) (8 . 11) (9 . 12) (13 . 17)) 9.202 {0/5:10} B:0 2.80227 [ 3.40127] ((3 . 8) (4 . 9) (8 . 11) (9 . 12) (12 . 15)) 10.692 {0/2:10} B:0 2.80421 [ 3.40235] ((3 . 2) (4 . 4) (9 . 8) (10 . 9) (12 . 11)) 12.480 {0/5:10} B:0 SIMILARITY (1/min{score1}): 0.6274 [and 1/min{score2}: 0.5495] [6169, 4102]: Comparing 1v4e_A and 1n1b_A, based on their crossing files. There are 17 (15 H + 2 S) secondary structure elements in 1v4e_A, of which 14 satisfy the size requirements. There are 30 (30 H + 0 S) secondary structure elements in 1n1b_A, of which 15 satisfy the size requirements. 1.40366 [ 1.50298] ((1 . 15) (3 . 17) (4 . 18) (8 . 21) (9 . 22) (10 . 23) (11 . 24) (12 . 26) (13 . 27) (16 . 28)) 6.439 {1/29:45} B:0 1.76787 [ 1.88958] ((1 . 15) (3 . 17) (4 . 18) (8 . 21) (9 . 22) (11 . 24) (12 . 26) (16 . 28)) 7.101 {1/13:28} B:0 2.80230 [ 3.00187] ((3 . 17) (4 . 18) (8 . 21) (9 . 22) (12 . 25)) 10.728 {0/3:10} B:0 3.50027 [ 3.75022] ((9 . 18) (10 . 19) (11 . 21) (12 . 22)) 7.451 {0/1:6} B:0 3.50038 [ 3.75031] ((8 . 17) (9 . 18) (11 . 21) (12 . 22)) 8.093 {0/0:6} B:0 SIMILARITY (1/min{score1}): 0.7124 [and 1/min{score2}: 0.6653] [6169, 5092]: Comparing 1v4e_A and 1ps1_A, based on their crossing files. There are 17 (15 H + 2 S) secondary structure elements in 1v4e_A, of which 14 satisfy the size requirements. There are 19 (19 H + 0 S) secondary structure elements in 1ps1_A, of which 17 satisfy the size requirements. 1.28561 [ 1.55271] ((1 . 2) (2 . 3) (3 . 4) (4 . 5) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 13) (13 . 15) (16 . 16)) 6.720 {2/38:55} B:0 1.28650 [ 1.55321] ((1 . 2) (2 . 3) (3 . 4) (4 . 5) (8 . 7) (9 . 9) (10 . 10) (11 . 11) (12 . 13) (13 . 15) (16 . 16)) 7.096 {2/38:55} B:0 1.40345 [ 1.70193] ((1 . 2) (3 . 4) (4 . 5) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 13) (13 . 15) (16 . 16)) 6.146 {1/28:45} B:0 2.80036 [ 3.40020] ((4 . 5) (8 . 7) (9 . 9) (12 . 13) (16 . 16)) 6.744 {0/2:10} B:0 2.80508 [ 3.40284] ((1 . 3) (3 . 5) (4 . 7) (7 . 8) (8 . 9)) 13.082 {0/6:10} B:0 SIMILARITY (1/min{score1}): 0.7778 [and 1/min{score2}: 0.6440] [6169, 5689]: Comparing 1v4e_A and 1rqj_A, based on their crossing files. There are 17 (15 H + 2 S) secondary structure elements in 1v4e_A, of which 14 satisfy the size requirements. There are 19 (17 H + 2 S) secondary structure elements in 1rqj_A, of which 16 satisfy the size requirements. 1.17318 [ 1.33771] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (7 . 7) (8 . 8) (9 . 10) (10 . 11) (11 . 12) (12 . 14) (13 . 17) (16 . 18)) 4.916 {2/47:66} B:0 1.17465 [ 1.33871] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (7 . 7) (8 . 8) (9 . 9) (10 . 11) (11 . 12) (12 . 14) (13 . 17) (16 . 18)) 5.898 {2/47:66} B:0 1.27536 [ 1.45631] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (7 . 7) (8 . 8) (9 . 9) (10 . 11) (11 . 12) (12 . 14) (16 . 18)) 5.727 {1/37:55} B:0 2.80067 [ 3.20045] ((1 . 12) (2 . 13) (3 . 14) (4 . 18) (8 . 19)) 7.879 {0/5:10} B:0 3.50005 [ 4.00003] ((10 . 2) (11 . 3) (12 . 4) (13 . 7)) 4.759 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.8524 [and 1/min{score2}: 0.7475] [6169, 5702]: Comparing 1v4e_A and 1rtr_A, based on their crossing files. There are 17 (15 H + 2 S) secondary structure elements in 1v4e_A, of which 14 satisfy the size requirements. There are 16 (14 H + 2 S) secondary structure elements in 1rtr_A, of which 14 satisfy the size requirements. 1.19092 [ 1.19092] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (7 . 7) (8 . 8) (9 . 10) (10 . 11) (11 . 12) (12 . 13) (13 . 14) (16 . 15)) 4.514 {3/48:66} B:0 1.28279 [ 1.28279] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (8 . 8) (9 . 10) (10 . 11) (11 . 12) (12 . 13) (13 . 14) (16 . 15)) 4.665 {2/38:55} B:0 2.32193 [ 2.32193] ((1 . 1) (3 . 4) (8 . 8) (9 . 10) (10 . 11) (12 . 13) (13 . 14) (16 . 15)) 7.333 {4/19:28} B:0 3.16760 [ 3.16760] ((9 . 2) (10 . 4) (11 . 7) (13 . 10) (14 . 11)) 9.912 {2/8:10} B:0 3.50040 [ 3.50040] ((4 . 11) (7 . 12) (8 . 13) (9 . 15)) 8.168 {0/1:6} B:0 SIMILARITY (1/min{score1}): 0.8397 [and 1/min{score2}: 0.8397] [6169, 5964]: Comparing 1v4e_A and 1uby, based on their crossing files. There are 17 (15 H + 2 S) secondary structure elements in 1v4e_A, of which 14 satisfy the size requirements. There are 19 (17 H + 2 S) secondary structure elements in 1uby, of which 15 satisfy the size requirements. 1.23699 [ 1.30834] ((1 . 1) (2 . 2) (3 . 3) (4 . 5) (8 . 9) (9 . 10) (10 . 11) (11 . 13) (12 . 14) (13 . 15) (15 . 17) (16 . 18)) 4.537 {4/48:66} B:0 1.25713 [ 1.30778] ((1 . 1) (2 . 2) (3 . 3) (4 . 5) (8 . 9) (9 . 10) (10 . 11) (11 . 13) (12 . 14) (13 . 15) (14 . 16) (15 . 17) (16 . 18)) 4.679 {6/58:78} B:0 1.61368 [ 1.64762] ((1 . 1) (2 . 2) (3 . 3) (4 . 5) (8 . 9) (9 . 10) (10 . 11) (11 . 13) (12 . 14) (13 . 15) (15 . 16) (16 . 18)) 4.722 {7/47:66} B:0 2.71127 [ 2.82242] ((3 . 3) (4 . 5) (8 . 9) (9 . 10) (12 . 14) (14 . 15)) 4.886 {2/9:15} B:0 3.50065 [ 3.75053] ((2 . 10) (8 . 14) (9 . 15) (10 . 16)) 9.258 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.8084 [and 1/min{score2}: 0.7647] [6169, 6169]: Comparing 1v4e_A and 1v4e_A, based on their crossing files. There are 17 (15 H + 2 S) secondary structure elements in 1v4e_A, of which 14 satisfy the size requirements. There are 17 (15 H + 2 S) secondary structure elements in 1v4e_A, of which 14 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12) (13 . 13) (14 . 14) (15 . 15) (16 . 16)) 0.000 {0/71:91} B:0 1.59106 [ 1.59106] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12) (13 . 13) (14 . 15) (16 . 16)) 2.729 {9/60:78} B:0 3.50058 [ 3.50058] ((3 . 8) (4 . 9) (8 . 11) (9 . 12)) 8.970 {0/0:6} B:0 3.50058 [ 3.50058] ((8 . 3) (9 . 4) (11 . 8) (12 . 9)) 8.970 {0/0:6} B:0 3.50108 [ 3.50108] ((1 . 8) (3 . 9) (4 . 11) (8 . 12)) 10.507 {0/0:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [6169, 6623]: Comparing 1v4e_A and 5eau, based on their crossing files. There are 17 (15 H + 2 S) secondary structure elements in 1v4e_A, of which 14 satisfy the size requirements. There are 28 (28 H + 0 S) secondary structure elements in 5eau, of which 16 satisfy the size requirements. 1.40313 [ 1.60210] ((1 . 13) (3 . 14) (4 . 15) (8 . 18) (9 . 19) (10 . 20) (11 . 21) (12 . 23) (13 . 25) (16 . 26)) 6.046 {1/29:45} B:0 2.80175 [ 3.20117] ((3 . 14) (4 . 15) (8 . 18) (9 . 19) (12 . 22)) 10.014 {0/3:10} B:0 3.50034 [ 4.00023] ((1 . 16) (3 . 18) (4 . 19) (9 . 23)) 7.866 {0/1:6} B:0 3.50038 [ 4.00026] ((8 . 18) (9 . 19) (10 . 21) (12 . 23)) 8.108 {0/3:6} B:0 3.50042 [ 4.00028] ((9 . 15) (10 . 16) (11 . 18) (12 . 19)) 8.302 {0/1:6} B:0 SIMILARITY (1/min{score1}): 0.7127 [and 1/min{score2}: 0.6242] -------------------------------------------------------------------------------------------------------------------------