------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [914, 268]: Comparing 1dq3_A and 1b24_A, based on their crossing files. There are 44 (14 H + 30 S) secondary structure elements in 1dq3_A, of which 9 satisfy the size requirements. There are 15 (8 H + 7 S) secondary structure elements in 1b24_A, of which 8 satisfy the size requirements. 1.30341 [ 1.16776] ((24 . 1) (25 . 2) (26 . 3) (27 . 5) (28 . 6) (29 . 7) (30 . 8)) 2.849 {1/16:21} B:0 1.54829 [ 1.40027] ((25 . 2) (26 . 3) (27 . 5) (28 . 6) (29 . 7) (30 . 8)) 2.888 {1/11:15} B:0 1.80030 [ 1.60043] ((24 . 1) (25 . 2) (26 . 3) (27 . 4) (30 . 8)) 4.646 {0/8:10} B:0 1.29917 [ 1.22434] ((23 . 4) (24 . 1) (25 . 2) (26 . 3) (27 . 5) (28 . 6) (29 . 7) (30 . 8)) 5.964 {2/19:28} B:1 1.30006 [ 1.22540] ((23 . 5) (24 . 1) (25 . 2) (26 . 3) (27 . 4) (28 . 6) (29 . 7) (30 . 8)) 6.492 {2/19:28} B:1 SIMILARITY (1/min{score1}): 0.7697 [and 1/min{score2}: 0.8563] [914, 269]: Comparing 1dq3_A and 1b24_A, based on their crossing files. There are 44 (14 H + 30 S) secondary structure elements in 1dq3_A, of which 9 satisfy the size requirements. There are 15 (8 H + 7 S) secondary structure elements in 1b24_A, of which 6 satisfy the size requirements. 1.50003 [ 1.00011] ((24 . 10) (26 . 11) (27 . 12) (28 . 13) (29 . 14) (30 . 15)) 2.312 {0/10:15} B:0 2.83616 [ 2.57750] ((24 . 10) (27 . 12) (28 . 14) (30 . 15)) 5.172 {1/4:6} B:0 2.83660 [ 2.57808] ((23 . 10) (24 . 12) (25 . 13) (26 . 14)) 7.612 {1/4:6} B:0 2.96360 [ 2.87915] ((24 . 10) (26 . 11) (27 . 12) (29 . 13) (30 . 15)) 3.763 {2/7:10} B:0 2.54017 [ 2.14242] ((24 . 10) (26 . 13) (27 . 12) (30 . 15)) 4.271 {1/5:6} B:1 SIMILARITY (1/min{score1}): 0.6667 [and 1/min{score2}: 0.9999] [914, 913]: Comparing 1dq3_A and 1dq3_A, based on their crossing files. There are 44 (14 H + 30 S) secondary structure elements in 1dq3_A, of which 9 satisfy the size requirements. There are 44 (14 H + 30 S) secondary structure elements in 1dq3_A, of which 6 satisfy the size requirements. 1.80716 [ 1.60301] ((24 . 15) (25 . 16) (26 . 17) (27 . 18) (29 . 20) (30 . 21)) 2.887 {2/13:15} B:0 5.01016 [ 5.00206] ((24 . 21) (26 . 20) (27 . 15) (28 . 16) (29 . 17) (30 . 18)) 6.716 {5/10:15} B:2 SIMILARITY (1/min{score1}): 0.5534 [and 1/min{score2}: 0.6238] [914, 914]: Comparing 1dq3_A and 1dq3_A, based on their crossing files. There are 44 (14 H + 30 S) secondary structure elements in 1dq3_A, of which 9 satisfy the size requirements. There are 44 (14 H + 30 S) secondary structure elements in 1dq3_A, of which 9 satisfy the size requirements. 1.00000 [ 1.00000] ((23 . 23) (24 . 24) (25 . 25) (26 . 26) (27 . 27) (28 . 28) (29 . 29) (30 . 30) (31 . 31)) 0.000 {0/27:36} B:0 2.25174 [ 2.25174] ((27 . 23) (28 . 25) (29 . 26) (30 . 27)) 8.490 {0/3:6} B:0 2.25174 [ 2.25174] ((23 . 27) (25 . 28) (26 . 29) (27 . 30)) 8.490 {0/3:6} B:0 2.32990 [ 2.32990] ((24 . 27) (25 . 28) (26 . 29) (27 . 30) (28 . 25) (29 . 26)) 5.913 {2/9:15} B:1 2.32990 [ 2.32990] ((25 . 28) (26 . 29) (27 . 24) (28 . 25) (29 . 26) (30 . 27)) 5.913 {2/9:15} B:1 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [914, 1785]: Comparing 1dq3_A and 1g9z_A, based on their crossing files. There are 44 (14 H + 30 S) secondary structure elements in 1dq3_A, of which 9 satisfy the size requirements. There are 10 (6 H + 4 S) secondary structure elements in 1g9z_A, of which 10 satisfy the size requirements. 1.23004 [ 1.32997] ((24 . 1) (25 . 2) (26 . 3) (27 . 4) (28 . 5) (29 . 6) (30 . 7) (31 . 8)) 4.105 {2/22:28} B:0 2.83631 [ 2.97325] ((27 . 1) (28 . 2) (29 . 3) (30 . 4)) 6.341 {1/4:6} B:0 4.09675 [ 4.14475] ((24 . 1) (25 . 2) (26 . 3) (31 . 7)) 7.680 {2/5:6} B:0 5.05051 [ 5.07638] ((27 . 4) (28 . 6) (30 . 7) (31 . 8)) 5.010 {2/4:6} B:0 2.54545 [ 2.72840] ((24 . 7) (25 . 6) (27 . 8) (30 . 10)) 12.332 {1/5:6} B:1 SIMILARITY (1/min{score1}): 0.8130 [and 1/min{score2}: 0.7519] [914, 3069]: Comparing 1dq3_A and 1jva_A, based on their crossing files. There are 44 (14 H + 30 S) secondary structure elements in 1dq3_A, of which 9 satisfy the size requirements. There are 42 (13 H + 29 S) secondary structure elements in 1jva_A, of which 7 satisfy the size requirements. 1.56964 [ 1.30048] ((24 . 22) (26 . 23) (27 . 24) (28 . 25) (29 . 26) (30 . 27)) 4.742 {1/10:15} B:0 1.80029 [ 1.40062] ((24 . 22) (26 . 23) (27 . 24) (28 . 25) (29 . 26)) 4.587 {0/5:10} B:0 2.25044 [ 1.75093] ((24 . 22) (27 . 24) (28 . 26) (30 . 27)) 6.013 {0/4:6} B:0 2.83667 [ 2.63897] ((23 . 22) (24 . 24) (25 . 25) (26 . 26)) 7.856 {1/4:6} B:0 4.09664 [ 4.03623] ((24 . 22) (26 . 23) (27 . 24) (31 . 27)) 6.254 {2/5:6} B:0 SIMILARITY (1/min{score1}): 0.6371 [and 1/min{score2}: 0.7689] [914, 3070]: Comparing 1dq3_A and 1jva_A, based on their crossing files. There are 44 (14 H + 30 S) secondary structure elements in 1dq3_A, of which 9 satisfy the size requirements. There are 42 (13 H + 29 S) secondary structure elements in 1jva_A, of which 8 satisfy the size requirements. 1.14558 [ 1.02885] ((23 . 30) (24 . 31) (25 . 32) (26 . 33) (27 . 34) (28 . 35) (29 . 36) (30 . 37)) 2.649 {1/17:28} B:0 1.31533 [ 1.18420] ((24 . 31) (25 . 32) (26 . 33) (27 . 34) (28 . 35) (29 . 36) (30 . 37)) 2.062 {1/14:21} B:0 1.80034 [ 1.60048] ((23 . 30) (24 . 31) (27 . 34) (28 . 36) (30 . 37)) 4.775 {0/6:10} B:0 2.06611 [ 1.94389] ((23 . 30) (24 . 31) (27 . 34) (29 . 35) (30 . 37)) 4.938 {1/6:10} B:0 2.83742 [ 2.72561] ((24 . 30) (27 . 31) (30 . 34) (31 . 37)) 9.541 {1/4:6} B:0 SIMILARITY (1/min{score1}): 0.8729 [and 1/min{score2}: 0.9720] [914, 3845]: Comparing 1dq3_A and 1m5x_A, based on their crossing files. There are 44 (14 H + 30 S) secondary structure elements in 1dq3_A, of which 9 satisfy the size requirements. There are 10 (6 H + 4 S) secondary structure elements in 1m5x_A, of which 10 satisfy the size requirements. 1.27075 [ 1.36259] ((24 . 1) (25 . 2) (26 . 3) (27 . 4) (28 . 5) (29 . 6) (30 . 7) (31 . 8)) 4.414 {2/20:28} B:0 1.31607 [ 1.45097] ((25 . 2) (26 . 3) (27 . 4) (28 . 5) (29 . 6) (30 . 7) (31 . 8)) 4.636 {1/14:21} B:0 2.83616 [ 2.97313] ((27 . 4) (28 . 6) (30 . 7) (31 . 8)) 5.238 {1/4:6} B:0 2.83633 [ 2.97327] ((27 . 1) (28 . 2) (29 . 3) (30 . 4)) 6.479 {1/4:6} B:0 4.09675 [ 4.14474] ((24 . 1) (25 . 2) (26 . 3) (31 . 7)) 7.603 {2/5:6} B:0 SIMILARITY (1/min{score1}): 0.7869 [and 1/min{score2}: 0.7339] [914, 4480]: Comparing 1dq3_A and 1o2f_B, based on their crossing files. There are 44 (14 H + 30 S) secondary structure elements in 1dq3_A, of which 9 satisfy the size requirements. There are 8 (4 H + 4 S) secondary structure elements in 1o2f_B, of which 7 satisfy the size requirements. 1.50020 [ 1.16709] ((25 . 2) (26 . 3) (27 . 5) (28 . 6) (29 . 7) (30 . 8)) 3.644 {0/9:15} B:0 2.06651 [ 1.84475] ((23 . 1) (26 . 3) (27 . 5) (28 . 6) (30 . 8)) 6.254 {1/6:10} B:0 2.25029 [ 1.75062] ((27 . 1) (28 . 2) (29 . 3) (30 . 5)) 5.432 {0/1:6} B:0 2.36146 [ 2.32785] ((24 . 1) (25 . 2) (26 . 3) (27 . 5) (28 . 6) (29 . 7) (30 . 8)) 4.038 {3/13:21} B:0 2.96360 [ 2.89750] ((24 . 1) (25 . 2) (26 . 3) (27 . 5) (30 . 8)) 3.926 {2/7:10} B:0 SIMILARITY (1/min{score1}): 0.6666 [and 1/min{score2}: 0.8568] [914, 4930]: Comparing 1dq3_A and 1p8k_Z, based on their crossing files. There are 44 (14 H + 30 S) secondary structure elements in 1dq3_A, of which 9 satisfy the size requirements. There are 20 (12 H + 8 S) secondary structure elements in 1p8k_Z, of which 9 satisfy the size requirements. 1.54983 [ 1.54983] ((24 . 1) (25 . 2) (26 . 3) (27 . 4) (28 . 5) (29 . 6) (30 . 8) (31 . 9)) 3.683 {3/21:28} B:0 1.55821 [ 1.55821] ((24 . 1) (26 . 3) (27 . 4) (28 . 5) (29 . 6) (30 . 8) (31 . 9)) 3.476 {2/15:21} B:0 2.83613 [ 2.83613] ((27 . 4) (28 . 6) (30 . 8) (31 . 9)) 4.858 {1/4:6} B:0 5.05063 [ 5.05063] ((24 . 1) (27 . 4) (28 . 3) (31 . 8)) 8.348 {2/4:6} B:1 4.29448 [ 4.29448] ((24 . 8) (25 . 5) (26 . 6) (27 . 1) (28 . 2) (29 . 3) (30 . 4)) 6.920 {6/14:21} B:2 SIMILARITY (1/min{score1}): 0.6452 [and 1/min{score2}: 0.6452] [914, 4931]: Comparing 1dq3_A and 1p8k_Z, based on their crossing files. There are 44 (14 H + 30 S) secondary structure elements in 1dq3_A, of which 9 satisfy the size requirements. There are 20 (12 H + 8 S) secondary structure elements in 1p8k_Z, of which 9 satisfy the size requirements. 1.30333 [ 1.30333] ((24 . 12) (25 . 13) (26 . 14) (27 . 15) (29 . 17) (30 . 18) (31 . 19)) 2.106 {1/16:21} B:0 2.06598 [ 2.06598] ((26 . 14) (27 . 15) (28 . 17) (30 . 18) (31 . 19)) 4.168 {1/6:10} B:0 2.25220 [ 2.25220] ((23 . 12) (24 . 15) (30 . 19) (31 . 20)) 9.004 {0/5:6} B:0 3.49453 [ 3.49453] ((24 . 11) (27 . 12) (28 . 13) (29 . 14)) 7.219 {1/3:6} B:0 2.14243 [ 2.14243] ((24 . 12) (27 . 15) (28 . 14) (29 . 17) (30 . 18) (31 . 19)) 4.370 {2/10:15} B:1 SIMILARITY (1/min{score1}): 0.7673 [and 1/min{score2}: 0.7673] -------------------------------------------------------------------------------------------------------------------------