------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [3410, 75]: Comparing 1krh_A and 1a8p, based on their crossing files. There are 30 (11 H + 19 S) secondary structure elements in 1krh_A, of which 9 satisfy the size requirements. There are 23 (11 H + 12 S) secondary structure elements in 1a8p, of which 12 satisfy the size requirements. 1.12513 [ 1.50006] ((19 . 10) (20 . 11) (21 . 13) (23 . 15) (24 . 18) (28 . 21) (29 . 22) (30 . 23)) 2.650 {0/9:28} B:0 1.28581 [ 1.71432] ((19 . 10) (20 . 11) (21 . 13) (23 . 15) (24 . 18) (28 . 21) (29 . 22)) 2.675 {0/7:21} B:0 1.50054 [ 2.00023] ((19 . 13) (20 . 15) (21 . 18) (28 . 21) (29 . 22) (30 . 23)) 4.673 {0/3:15} B:0 1.50138 [ 2.00058] ((19 . 10) (20 . 11) (21 . 13) (23 . 15) (29 . 20) (30 . 21)) 5.918 {0/6:15} B:0 1.80004 [ 2.40002] ((19 . 13) (24 . 18) (28 . 21) (29 . 22) (30 . 23)) 2.727 {0/4:10} B:0 SIMILARITY (1/min{score1}): 0.8888 [and 1/min{score2}: 0.6666] [3410, 658]: Comparing 1krh_A and 1cqx_A, based on their crossing files. There are 30 (11 H + 19 S) secondary structure elements in 1krh_A, of which 9 satisfy the size requirements. There are 26 (14 H + 12 S) secondary structure elements in 1cqx_A, of which 8 satisfy the size requirements. 1.12517 [ 1.00024] ((19 . 15) (20 . 16) (21 . 17) (23 . 18) (24 . 19) (28 . 23) (29 . 24) (30 . 26)) 2.822 {0/8:28} B:0 1.28578 [ 1.14296] ((19 . 15) (21 . 17) (23 . 18) (24 . 19) (28 . 23) (29 . 24) (30 . 26)) 2.504 {0/6:21} B:0 1.80033 [ 1.60047] ((19 . 15) (27 . 16) (28 . 17) (29 . 18) (30 . 19)) 4.746 {0/0:10} B:0 2.25014 [ 2.00020] ((27 . 16) (28 . 17) (29 . 18) (30 . 19)) 4.537 {0/0:6} B:0 2.25020 [ 2.00029] ((24 . 15) (28 . 17) (29 . 18) (30 . 19)) 4.946 {0/0:6} B:0 SIMILARITY (1/min{score1}): 0.8888 [and 1/min{score2}: 0.9998] [3410, 806]: Comparing 1krh_A and 1ddg_A, based on their crossing files. There are 30 (11 H + 19 S) secondary structure elements in 1krh_A, of which 9 satisfy the size requirements. There are 30 (15 H + 15 S) secondary structure elements in 1ddg_A, of which 11 satisfy the size requirements. 1.02313 [ 1.23513] ((19 . 19) (20 . 20) (21 . 21) (23 . 23) (24 . 24) (27 . 26) (28 . 27) (29 . 28) (30 . 30)) 2.434 {1/18:36} B:0 1.18205 [ 1.40753] ((19 . 19) (20 . 20) (21 . 21) (23 . 23) (24 . 24) (27 . 26) (28 . 27) (30 . 30)) 2.192 {1/13:28} B:0 1.50005 [ 1.83336] ((19 . 19) (20 . 20) (21 . 21) (23 . 23) (24 . 24) (30 . 27)) 2.625 {0/4:15} B:0 1.80163 [ 2.20089] ((19 . 21) (20 . 23) (21 . 24) (23 . 26) (24 . 27)) 7.068 {0/2:10} B:0 1.80318 [ 2.20175] ((19 . 21) (20 . 23) (21 . 24) (24 . 27) (30 . 30)) 8.357 {0/0:10} B:0 SIMILARITY (1/min{score1}): 0.9774 [and 1/min{score2}: 0.8096] [3410, 1233]: Comparing 1krh_A and 1ep3_B, based on their crossing files. There are 30 (11 H + 19 S) secondary structure elements in 1krh_A, of which 9 satisfy the size requirements. There are 25 (8 H + 17 S) secondary structure elements in 1ep3_B, of which 11 satisfy the size requirements. 1.28582 [ 1.57149] ((19 . 11) (20 . 13) (21 . 14) (23 . 16) (24 . 17) (28 . 20) (30 . 22)) 2.753 {0/4:21} B:0 1.50012 [ 1.83340] ((19 . 11) (20 . 13) (21 . 14) (23 . 16) (24 . 17) (28 . 22)) 3.184 {0/3:15} B:0 1.50013 [ 1.83341] ((21 . 11) (23 . 16) (24 . 17) (28 . 20) (29 . 21) (30 . 22)) 3.300 {0/4:15} B:0 1.54971 [ 1.66798] ((19 . 11) (20 . 13) (21 . 14) (23 . 16) (24 . 17) (28 . 20) (29 . 21) (30 . 22)) 2.790 {1/7:28} B:0 1.80029 [ 2.20016] ((21 . 11) (23 . 13) (24 . 14) (28 . 20) (30 . 22)) 4.592 {0/1:10} B:0 SIMILARITY (1/min{score1}): 0.8880 [and 1/min{score2}: 0.7269] [3410, 1476]: Comparing 1krh_A and 1fdr, based on their crossing files. There are 30 (11 H + 19 S) secondary structure elements in 1krh_A, of which 9 satisfy the size requirements. There are 20 (8 H + 12 S) secondary structure elements in 1fdr, of which 11 satisfy the size requirements. 1.12504 [ 1.37502] ((19 . 9) (20 . 10) (21 . 11) (23 . 13) (24 . 14) (28 . 18) (29 . 19) (30 . 20)) 1.997 {0/11:28} B:0 1.28784 [ 1.57259] ((19 . 9) (20 . 10) (21 . 11) (23 . 13) (24 . 14) (29 . 17) (30 . 18)) 5.870 {0/9:21} B:0 1.50031 [ 1.83350] ((19 . 11) (21 . 14) (24 . 15) (28 . 18) (29 . 19) (30 . 20)) 4.057 {0/5:15} B:0 1.50035 [ 1.83352] ((19 . 11) (20 . 13) (21 . 14) (28 . 18) (29 . 19) (30 . 20)) 4.189 {0/3:15} B:0 1.80280 [ 2.20153] ((19 . 11) (20 . 13) (21 . 14) (24 . 18) (30 . 20)) 8.092 {0/0:10} B:0 SIMILARITY (1/min{score1}): 0.8889 [and 1/min{score2}: 0.7273] [3410, 1972]: Comparing 1krh_A and 1gvh_A, based on their crossing files. There are 30 (11 H + 19 S) secondary structure elements in 1krh_A, of which 9 satisfy the size requirements. There are 27 (15 H + 12 S) secondary structure elements in 1gvh_A, of which 9 satisfy the size requirements. 1.12503 [ 1.12503] ((19 . 16) (20 . 17) (21 . 18) (23 . 19) (24 . 20) (28 . 24) (29 . 25) (30 . 27)) 1.886 {0/9:28} B:0 1.80061 [ 1.80061] ((19 . 16) (27 . 17) (28 . 18) (29 . 19) (30 . 20)) 5.518 {0/0:10} B:0 2.25027 [ 2.25027] ((24 . 16) (28 . 18) (29 . 19) (30 . 20)) 5.304 {0/0:6} B:0 2.25044 [ 2.25044] ((27 . 17) (28 . 18) (29 . 19) (30 . 20)) 6.010 {0/0:6} B:0 10.00265 [10.00265] ((19 . 18) (20 . 19) (21 . 20) (23 . 21) (24 . 24)) 9.296 {1/1:10} B:0 SIMILARITY (1/min{score1}): 0.8889 [and 1/min{score2}: 0.8889] [3410, 2425]: Comparing 1krh_A and 1i7p_A, based on their crossing files. There are 30 (11 H + 19 S) secondary structure elements in 1krh_A, of which 9 satisfy the size requirements. There are 24 (9 H + 15 S) secondary structure elements in 1i7p_A, of which 12 satisfy the size requirements. 1.12522 [ 1.50009] ((19 . 11) (20 . 12) (21 . 13) (23 . 15) (24 . 17) (28 . 20) (29 . 22) (30 . 24)) 3.017 {0/8:28} B:0 1.12556 [ 1.50024] ((19 . 11) (20 . 12) (21 . 13) (23 . 15) (24 . 17) (28 . 20) (29 . 21) (30 . 24)) 3.798 {0/11:28} B:0 1.80087 [ 2.40037] ((19 . 11) (27 . 12) (28 . 13) (29 . 15) (30 . 17)) 6.046 {0/0:10} B:0 2.14248 [ 2.37856] ((20 . 12) (21 . 13) (23 . 15) (24 . 17) (29 . 19) (30 . 20)) 4.738 {1/5:15} B:0 2.25040 [ 3.00017] ((24 . 11) (28 . 13) (29 . 15) (30 . 17)) 5.883 {0/0:6} B:0 SIMILARITY (1/min{score1}): 0.8887 [and 1/min{score2}: 0.6666] [3410, 2807]: Comparing 1krh_A and 1jb9_A, based on their crossing files. There are 30 (11 H + 19 S) secondary structure elements in 1krh_A, of which 9 satisfy the size requirements. There are 23 (10 H + 13 S) secondary structure elements in 1jb9_A, of which 11 satisfy the size requirements. 1.01272 [ 1.22926] ((19 . 11) (20 . 12) (21 . 14) (23 . 16) (24 . 17) (27 . 19) (28 . 20) (29 . 21) (30 . 23)) 2.292 {1/21:36} B:0 1.16818 [ 1.39939] ((19 . 11) (20 . 12) (21 . 14) (23 . 16) (24 . 17) (27 . 19) (28 . 20) (30 . 23)) 1.688 {1/14:28} B:0 1.50002 [ 1.83335] ((19 . 11) (20 . 12) (21 . 14) (23 . 16) (24 . 17) (30 . 20)) 2.121 {0/5:15} B:0 1.65519 [ 1.92530] ((19 . 14) (21 . 17) (27 . 19) (28 . 20) (29 . 21) (30 . 23)) 3.319 {1/8:15} B:0 1.80043 [ 2.20023] ((19 . 14) (20 . 16) (21 . 17) (28 . 20) (30 . 23)) 5.056 {0/1:10} B:0 SIMILARITY (1/min{score1}): 0.9874 [and 1/min{score2}: 0.8135] [3410, 3410]: Comparing 1krh_A and 1krh_A, based on their crossing files. There are 30 (11 H + 19 S) secondary structure elements in 1krh_A, of which 9 satisfy the size requirements. There are 30 (11 H + 19 S) secondary structure elements in 1krh_A, of which 9 satisfy the size requirements. 1.00000 [ 1.00000] ((19 . 19) (20 . 20) (21 . 21) (23 . 23) (24 . 24) (27 . 27) (28 . 28) (29 . 29) (30 . 30)) 0.000 {0/21:36} B:0 2.25033 [ 2.25033] ((24 . 19) (28 . 21) (29 . 23) (30 . 24)) 5.614 {0/0:6} B:0 2.25033 [ 2.25033] ((19 . 24) (21 . 28) (23 . 29) (24 . 30)) 5.614 {0/0:6} B:0 10.00641 [10.00641] ((27 . 20) (28 . 21) (29 . 23) (30 . 24)) 6.557 {1/1:6} B:0 10.00641 [10.00641] ((20 . 27) (21 . 28) (23 . 29) (24 . 30)) 6.557 {1/1:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [3410, 5313]: Comparing 1krh_A and 1qfj_A, based on their crossing files. There are 30 (11 H + 19 S) secondary structure elements in 1krh_A, of which 9 satisfy the size requirements. There are 20 (8 H + 12 S) secondary structure elements in 1qfj_A, of which 9 satisfy the size requirements. 1.28573 [ 1.28573] ((19 . 8) (20 . 9) (21 . 10) (23 . 12) (24 . 13) (28 . 16) (29 . 17)) 1.832 {0/7:21} B:0 1.50005 [ 1.50005] ((19 . 8) (20 . 9) (21 . 10) (23 . 12) (24 . 13) (30 . 16)) 2.558 {0/2:15} B:0 2.25024 [ 2.25024] ((24 . 8) (28 . 10) (29 . 12) (30 . 13)) 5.170 {0/0:6} B:0 2.14295 [ 2.14295] ((19 . 8) (20 . 20) (27 . 9) (28 . 10) (29 . 12) (30 . 13)) 6.442 {1/5:15} B:1 1.80015 [ 1.80015] ((20 . 9) (21 . 8) (23 . 12) (24 . 10) (30 . 16)) 3.916 {0/1:10} B:2 SIMILARITY (1/min{score1}): 0.7778 [and 1/min{score2}: 0.7778] [3410, 6508]: Comparing 1krh_A and 2pia, based on their crossing files. There are 30 (11 H + 19 S) secondary structure elements in 1krh_A, of which 9 satisfy the size requirements. There are 26 (7 H + 19 S) secondary structure elements in 2pia, of which 9 satisfy the size requirements. 1.22967 [ 1.22967] ((19 . 9) (20 . 10) (21 . 11) (23 . 13) (24 . 14) (28 . 16) (29 . 17) (30 . 18)) 3.194 {1/11:28} B:0 1.50019 [ 1.50019] ((19 . 9) (20 . 10) (21 . 11) (23 . 13) (24 . 14) (28 . 18)) 3.599 {0/4:15} B:0 1.50062 [ 1.50062] ((21 . 9) (23 . 10) (24 . 11) (28 . 16) (29 . 17) (30 . 18)) 4.833 {0/4:15} B:0 1.80229 [ 1.80229] ((19 . 9) (20 . 10) (21 . 11) (23 . 15) (28 . 18)) 7.695 {0/1:10} B:0 1.80270 [ 1.80270] ((19 . 11) (20 . 13) (21 . 16) (23 . 17) (24 . 18)) 8.020 {0/2:10} B:0 SIMILARITY (1/min{score1}): 0.8132 [and 1/min{score2}: 0.8132] -------------------------------------------------------------------------------------------------------------------------