------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [210, 210]: Comparing 1auk and 1auk, based on their crossing files. There are 38 (19 H + 19 S) secondary structure elements in 1auk, of which 28 satisfy the size requirements. There are 38 (19 H + 19 S) secondary structure elements in 1auk, of which 28 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (3 . 3) (4 . 4) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (11 . 11) (12 . 12) (13 . 13) (15 . 15) (16 . 16) (17 . 17) (18 . 18) (19 . 19) (21 . 21) (22 . 22) (24 . 24) (25 . 25) (27 . 27) (28 . 28) (29 . 29) (30 . 30) (31 . 31) (32 . 32) (34 . 34) (35 . 35) (36 . 36)) 0.000 {0/299:378} B:0 1.03704 [ 1.03704] ((1 . 1) (3 . 3) (4 . 4) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (11 . 11) (12 . 12) (13 . 13) (15 . 15) (16 . 16) (17 . 17) (18 . 18) (19 . 19) (21 . 21) (22 . 22) (24 . 24) (25 . 25) (27 . 27) (28 . 28) (29 . 29) (30 . 30) (31 . 31) (34 . 34) (35 . 35) (36 . 36)) 0.000 {0/273:351} B:0 1.03704 [ 1.03704] ((1 . 1) (3 . 3) (4 . 4) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (12 . 12) (13 . 13) (15 . 15) (16 . 16) (17 . 17) (18 . 18) (19 . 19) (21 . 21) (22 . 22) (24 . 24) (25 . 25) (27 . 27) (28 . 28) (29 . 29) (30 . 30) (31 . 31) (32 . 32) (34 . 34) (35 . 35) (36 . 36)) 0.000 {0/276:351} B:0 4.00190 [ 4.00190] ((1 . 1) (9 . 12) (17 . 17) (19 . 19) (21 . 21) (34 . 35) (36 . 36)) 4.272 {1/12:21} B:0 4.00190 [ 4.00190] ((1 . 1) (12 . 9) (17 . 17) (19 . 19) (21 . 21) (35 . 34) (36 . 36)) 4.272 {1/12:21} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [210, 1108]: Comparing 1auk and 1ed8_A, based on their crossing files. There are 38 (19 H + 19 S) secondary structure elements in 1auk, of which 28 satisfy the size requirements. There are 35 (17 H + 18 S) secondary structure elements in 1ed8_A, of which 29 satisfy the size requirements. 1.89304 [ 1.94310] ((1 . 2) (4 . 4) (6 . 7) (8 . 8) (9 . 9) (11 . 13) (12 . 14) (15 . 19) (16 . 17) (17 . 24) (18 . 25) (19 . 27) (21 . 28) (24 . 32) (25 . 34) (27 . 35)) 4.373 {6/44:120} B:1 2.05332 [ 2.11966] ((1 . 2) (4 . 4) (6 . 7) (8 . 8) (9 . 9) (12 . 14) (15 . 19) (16 . 17) (17 . 24) (18 . 25) (19 . 27) (21 . 28) (24 . 32) (27 . 35)) 3.763 {3/26:91} B:1 2.10158 [ 2.16371] ((1 . 14) (3 . 16) (4 . 17) (6 . 18) (8 . 24) (9 . 25) (11 . 27) (12 . 28) (15 . 2) (16 . 4) (17 . 7) (18 . 9) (19 . 13) (21 . 19)) 7.525 {3/22:91} B:1 2.11107 [ 2.15809] ((1 . 2) (4 . 4) (6 . 7) (8 . 8) (9 . 9) (11 . 13) (12 . 14) (15 . 19) (16 . 17) (17 . 24) (18 . 25) (19 . 27) (21 . 28) (24 . 32) (27 . 35)) 4.045 {5/30:105} B:1 1.90522 [ 1.95438] ((1 . 2) (4 . 4) (6 . 10) (8 . 8) (9 . 9) (11 . 13) (12 . 14) (15 . 19) (16 . 17) (17 . 24) (18 . 25) (19 . 27) (21 . 28) (24 . 32) (25 . 34) (27 . 35)) 4.494 {6/43:120} B:2 SIMILARITY (1/min{score1}): 0.5293 [and 1/min{score2}: 0.5146] [210, 1171]: Comparing 1auk and 1ei6_A, based on their crossing files. There are 38 (19 H + 19 S) secondary structure elements in 1auk, of which 28 satisfy the size requirements. There are 39 (20 H + 19 S) secondary structure elements in 1ei6_A, of which 30 satisfy the size requirements. 2.00011 [ 2.14295] ((1 . 3) (3 . 5) (4 . 6) (6 . 7) (8 . 12) (9 . 13) (11 . 14) (12 . 15) (17 . 18) (18 . 19) (19 . 21) (21 . 22) (24 . 38) (27 . 39)) 3.904 {0/35:91} B:0 2.15392 [ 2.30775] ((1 . 3) (3 . 5) (4 . 6) (6 . 7) (8 . 12) (9 . 13) (12 . 15) (17 . 18) (18 . 19) (19 . 21) (21 . 22) (24 . 38) (27 . 39)) 3.676 {0/27:78} B:0 5.60000 [ 6.00000] ((12 . 13) (17 . 18) (18 . 19) (19 . 21) (21 . 22)) 3.512 {0/1:10} B:0 5.60002 [ 6.00002] ((8 . 7) (17 . 18) (18 . 19) (19 . 21) (21 . 22)) 5.487 {0/0:10} B:0 5.60004 [ 6.00003] ((1 . 13) (8 . 18) (9 . 19) (11 . 21) (12 . 22)) 6.340 {0/0:10} B:0 SIMILARITY (1/min{score1}): 0.5000 [and 1/min{score2}: 0.4681] [210, 1280]: Comparing 1auk and 1ew2_A, based on their crossing files. There are 38 (19 H + 19 S) secondary structure elements in 1auk, of which 28 satisfy the size requirements. There are 37 (22 H + 15 S) secondary structure elements in 1ew2_A, of which 28 satisfy the size requirements. 2.03743 [ 2.03743] ((1 . 3) (4 . 6) (6 . 7) (8 . 9) (9 . 10) (12 . 15) (15 . 21) (16 . 19) (17 . 23) (18 . 24) (19 . 26) (21 . 27) (24 . 34) (27 . 37)) 4.076 {2/19:91} B:1 2.06203 [ 2.06203] ((1 . 3) (4 . 6) (6 . 11) (8 . 9) (9 . 10) (12 . 15) (15 . 21) (17 . 23) (18 . 24) (19 . 26) (21 . 27) (24 . 34) (25 . 36) (27 . 37)) 4.402 {3/25:91} B:1 4.39571 [ 4.39571] ((1 . 3) (4 . 6) (6 . 7) (8 . 9) (9 . 10) (11 . 14) (12 . 15) (17 . 23) (18 . 24) (19 . 26) (21 . 27) (24 . 34) (27 . 37) (28 . 35)) 3.720 {10/23:91} B:1 1.89975 [ 1.89975] ((1 . 3) (4 . 6) (6 . 11) (8 . 9) (9 . 10) (12 . 15) (15 . 21) (16 . 19) (17 . 23) (18 . 24) (19 . 26) (21 . 27) (24 . 34) (25 . 36) (27 . 37)) 4.612 {3/31:105} B:2 1.90422 [ 1.90422] ((1 . 3) (4 . 6) (6 . 11) (8 . 9) (9 . 10) (11 . 14) (12 . 15) (15 . 21) (16 . 19) (17 . 23) (18 . 24) (19 . 26) (21 . 27) (24 . 34) (27 . 37)) 4.627 {2/20:105} B:2 SIMILARITY (1/min{score1}): 0.5564 [and 1/min{score2}: 0.5564] [210, 1621]: Comparing 1auk and 1fsu, based on their crossing files. There are 38 (19 H + 19 S) secondary structure elements in 1auk, of which 28 satisfy the size requirements. There are 36 (18 H + 18 S) secondary structure elements in 1fsu, of which 24 satisfy the size requirements. 1.33356 [ 1.14321] ((1 . 1) (3 . 3) (4 . 4) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (12 . 12) (17 . 18) (18 . 19) (19 . 21) (21 . 23) (24 . 26) (25 . 27) (27 . 29) (28 . 30) (29 . 31) (30 . 32) (31 . 33) (35 . 34) (36 . 35)) 2.290 {3/148:210} B:0 1.37111 [ 1.23504] ((1 . 1) (3 . 3) (4 . 4) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (12 . 12) (13 . 13) (17 . 18) (18 . 19) (19 . 21) (21 . 23) (24 . 26) (25 . 27) (27 . 29) (28 . 30) (29 . 31) (30 . 32) (31 . 33) (35 . 34) (36 . 35)) 4.121 {16/164:231} B:0 3.44146 [ 3.41467] ((1 . 1) (3 . 3) (6 . 6) (8 . 8) (9 . 9) (12 . 12) (13 . 13) (17 . 18) (18 . 19) (19 . 21) (21 . 23) (24 . 26) (27 . 29) (29 . 32) (31 . 33) (34 . 34)) 5.322 {23/68:120} B:0 3.50001 [ 3.00001] ((12 . 9) (17 . 18) (18 . 19) (19 . 21) (21 . 23) (27 . 29) (28 . 30) (36 . 35)) 3.194 {0/15:28} B:0 4.00000 [ 3.42858] ((1 . 1) (4 . 4) (8 . 8) (9 . 12) (19 . 21) (21 . 23) (36 . 35)) 2.765 {0/10:21} B:0 SIMILARITY (1/min{score1}): 0.7499 [and 1/min{score2}: 0.8747] [210, 2182]: Comparing 1auk and 1hdh_A, based on their crossing files. There are 38 (19 H + 19 S) secondary structure elements in 1auk, of which 28 satisfy the size requirements. There are 41 (23 H + 18 S) secondary structure elements in 1hdh_A, of which 27 satisfy the size requirements. 1.33348 [ 1.28588] ((1 . 1) (3 . 3) (4 . 4) (6 . 6) (7 . 7) (8 . 9) (9 . 10) (12 . 12) (15 . 14) (17 . 16) (18 . 17) (19 . 21) (21 . 23) (24 . 30) (27 . 33) (28 . 36) (29 . 37) (30 . 38) (31 . 39) (35 . 40) (36 . 41)) 3.079 {0/132:210} B:0 1.40013 [ 1.35014] ((1 . 1) (3 . 3) (4 . 4) (6 . 6) (7 . 7) (8 . 9) (9 . 10) (12 . 12) (17 . 16) (18 . 17) (19 . 21) (21 . 23) (24 . 30) (27 . 33) (28 . 36) (29 . 37) (30 . 38) (31 . 39) (35 . 40) (36 . 41)) 3.092 {0/123:190} B:0 1.40013 [ 1.35014] ((1 . 1) (3 . 3) (4 . 4) (6 . 6) (7 . 7) (8 . 9) (9 . 10) (12 . 12) (15 . 14) (17 . 16) (18 . 17) (19 . 21) (21 . 23) (24 . 30) (27 . 33) (29 . 37) (30 . 38) (31 . 39) (35 . 40) (36 . 41)) 3.105 {0/113:190} B:0 1.40014 [ 1.35015] ((1 . 1) (3 . 3) (4 . 4) (6 . 6) (7 . 7) (9 . 10) (12 . 12) (15 . 14) (17 . 16) (18 . 17) (19 . 21) (21 . 23) (24 . 30) (27 . 33) (28 . 36) (29 . 37) (30 . 38) (31 . 39) (35 . 40) (36 . 41)) 3.143 {0/124:190} B:0 2.80015 [ 2.70017] ((1 . 1) (4 . 4) (6 . 9) (9 . 10) (12 . 12) (15 . 14) (17 . 16) (18 . 17) (19 . 21) (21 . 23)) 5.424 {0/7:45} B:0 SIMILARITY (1/min{score1}): 0.7499 [and 1/min{score2}: 0.7777] [210, 4563]: Comparing 1auk and 1o98_A, based on their crossing files. There are 38 (19 H + 19 S) secondary structure elements in 1auk, of which 28 satisfy the size requirements. There are 37 (21 H + 16 S) secondary structure elements in 1o98_A, of which 16 satisfy the size requirements. 2.00012 [ 1.14352] ((1 . 1) (3 . 3) (4 . 4) (6 . 6) (8 . 25) (9 . 26) (11 . 27) (12 . 28) (17 . 30) (18 . 31) (19 . 33) (21 . 34) (24 . 35) (27 . 37)) 4.021 {0/35:91} B:0 5.60002 [ 3.20009] ((12 . 26) (15 . 28) (17 . 30) (18 . 31) (19 . 33)) 5.211 {0/0:10} B:0 5.60004 [ 3.20020] ((9 . 31) (11 . 33) (12 . 34) (15 . 35) (17 . 37)) 6.455 {0/0:10} B:0 5.60004 [ 3.20022] ((17 . 27) (19 . 33) (21 . 34) (24 . 35) (27 . 37)) 6.604 {0/1:10} B:0 5.60010 [ 3.20055] ((1 . 1) (3 . 3) (4 . 4) (6 . 6) (27 . 27)) 8.273 {0/6:10} B:0 SIMILARITY (1/min{score1}): 0.5000 [and 1/min{score2}: 0.8745] [210, 4886]: Comparing 1auk and 1p49_A, based on their crossing files. There are 38 (19 H + 19 S) secondary structure elements in 1auk, of which 28 satisfy the size requirements. There are 36 (19 H + 17 S) secondary structure elements in 1p49_A, of which 25 satisfy the size requirements. 1.27293 [ 1.13665] ((1 . 1) (3 . 3) (4 . 4) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (12 . 11) (15 . 16) (16 . 17) (17 . 18) (18 . 19) (19 . 20) (21 . 22) (24 . 24) (27 . 27) (28 . 28) (29 . 29) (30 . 30) (31 . 31) (35 . 32) (36 . 33)) 2.140 {3/157:231} B:0 2.41953 [ 2.40247] ((1 . 1) (3 . 3) (4 . 4) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (12 . 11) (15 . 16) (16 . 17) (17 . 18) (18 . 19) (19 . 20) (21 . 22) (24 . 24) (27 . 27) (28 . 28) (29 . 29) (31 . 30) (34 . 31) (35 . 32) (36 . 33)) 3.298 {37/156:231} B:0 3.11158 [ 2.77843] ((17 . 18) (18 . 19) (19 . 20) (21 . 22) (24 . 24) (27 . 27) (28 . 28) (34 . 32) (36 . 33)) 4.143 {1/21:36} B:0 3.50000 [ 3.12501] ((9 . 11) (17 . 18) (18 . 19) (19 . 20) (21 . 22) (27 . 27) (28 . 28) (36 . 33)) 2.647 {0/13:28} B:0 4.00000 [ 3.57143] ((9 . 11) (17 . 18) (18 . 19) (19 . 20) (21 . 22) (30 . 30) (36 . 33)) 2.952 {0/11:21} B:0 SIMILARITY (1/min{score1}): 0.7856 [and 1/min{score2}: 0.8798] -------------------------------------------------------------------------------------------------------------------------