------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [208, 208]: Comparing 1aui_A and 1aui_A, based on their crossing files. There are 29 (15 H + 14 S) secondary structure elements in 1aui_A, of which 25 satisfy the size requirements. There are 29 (15 H + 14 S) secondary structure elements in 1aui_A, of which 25 satisfy the size requirements. 1.00000 [ 1.00000] ((2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12) (13 . 13) (14 . 14) (15 . 15) (16 . 16) (18 . 18) (19 . 19) (20 . 20) (21 . 21) (22 . 22) (23 . 23) (25 . 25) (26 . 26) (28 . 28) (29 . 29)) 0.000 {0/243:300} B:0 5.00490 [ 5.00490] ((2 . 15) (3 . 16) (7 . 21) (9 . 23) (15 . 29)) 5.339 {1/8:10} B:0 5.00490 [ 5.00490] ((15 . 2) (16 . 3) (21 . 7) (23 . 9) (29 . 15)) 5.339 {1/8:10} B:0 6.25012 [ 6.25012] ((5 . 18) (8 . 20) (9 . 22) (16 . 29)) 9.285 {0/4:6} B:0 6.25012 [ 6.25012] ((18 . 5) (20 . 8) (22 . 9) (29 . 16)) 9.285 {0/4:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [208, 1730]: Comparing 1aui_A and 1g5b_A, based on their crossing files. There are 29 (15 H + 14 S) secondary structure elements in 1aui_A, of which 25 satisfy the size requirements. There are 20 (10 H + 10 S) secondary structure elements in 1g5b_A, of which 18 satisfy the size requirements. 1.61495 [ 1.25025] ((4 . 1) (5 . 3) (6 . 4) (7 . 5) (8 . 6) (9 . 7) (10 . 9) (11 . 10) (12 . 11) (13 . 12) (14 . 13) (16 . 14) (21 . 16) (22 . 17) (23 . 18) (25 . 20)) 2.962 {9/94:120} B:0 4.23770 [ 3.17864] ((6 . 4) (7 . 5) (8 . 6) (9 . 7) (16 . 14) (21 . 18)) 2.488 {3/14:15} B:0 5.00840 [ 3.62236] ((18 . 3) (20 . 4) (21 . 5) (23 . 7) (29 . 14)) 7.478 {1/7:10} B:0 5.00852 [ 3.62266] ((2 . 8) (7 . 13) (8 . 15) (9 . 16) (13 . 20)) 9.090 {1/7:10} B:0 5.15469 [ 3.97226] ((6 . 4) (7 . 5) (8 . 6) (12 . 10) (16 . 14)) 5.082 {3/10:10} B:0 SIMILARITY (1/min{score1}): 0.6350 [and 1/min{score2}: 0.8641] [208, 2253]: Comparing 1aui_A and 1hp1_A, based on their crossing files. There are 29 (15 H + 14 S) secondary structure elements in 1aui_A, of which 25 satisfy the size requirements. There are 49 (18 H + 31 S) secondary structure elements in 1hp1_A, of which 21 satisfy the size requirements. 5.00003 [ 4.20006] ((5 . 1) (6 . 2) (7 . 3) (20 . 15) (26 . 23)) 5.778 {0/8:10} B:0 5.00006 [ 4.20011] ((6 . 5) (7 . 6) (8 . 8) (22 . 24) (23 . 25)) 6.721 {0/7:10} B:0 5.00007 [ 4.20013] ((6 . 2) (7 . 3) (9 . 6) (20 . 18) (26 . 23)) 7.030 {0/7:10} B:0 5.00835 [ 4.21405] ((6 . 5) (7 . 6) (21 . 23) (22 . 24) (23 . 25)) 5.930 {1/7:10} B:0 5.07640 [ 4.32610] ((6 . 5) (14 . 16) (21 . 23) (22 . 24) (23 . 25)) 6.337 {1/4:10} B:0 SIMILARITY (1/min{score1}): 0.4956 [and 1/min{score2}: 0.5296] [208, 2504]: Comparing 1aui_A and 1ii7_A, based on their crossing files. There are 29 (15 H + 14 S) secondary structure elements in 1aui_A, of which 25 satisfy the size requirements. There are 30 (11 H + 19 S) secondary structure elements in 1ii7_A, of which 26 satisfy the size requirements. 4.29569 [ 4.44877] ((6 . 5) (7 . 6) (8 . 7) (15 . 16) (22 . 24) (23 . 25)) 7.128 {3/12:15} B:0 4.42222 [ 4.56332] ((5 . 4) (6 . 5) (7 . 6) (8 . 7) (12 . 13) (23 . 25)) 6.568 {3/10:15} B:0 5.00004 [ 5.20004] ((6 . 5) (7 . 6) (8 . 7) (19 . 20) (23 . 25)) 5.993 {0/7:10} B:0 5.00493 [ 5.20438] ((6 . 3) (7 . 4) (9 . 6) (15 . 13) (21 . 18)) 6.437 {1/8:10} B:0 5.07639 [ 5.26813] ((7 . 4) (8 . 5) (9 . 6) (13 . 11) (21 . 20)) 5.589 {2/8:10} B:0 SIMILARITY (1/min{score1}): 0.4780 [and 1/min{score2}: 0.4678] [208, 2942]: Comparing 1aui_A and 1jk7_A, based on their crossing files. There are 29 (15 H + 14 S) secondary structure elements in 1aui_A, of which 25 satisfy the size requirements. There are 25 (11 H + 14 S) secondary structure elements in 1jk7_A, of which 24 satisfy the size requirements. 1.09013 [ 1.04706] ((2 . 1) (3 . 2) (4 . 3) (5 . 4) (6 . 5) (7 . 6) (8 . 7) (9 . 8) (10 . 9) (11 . 10) (12 . 11) (13 . 12) (14 . 13) (15 . 14) (16 . 15) (18 . 17) (19 . 18) (20 . 19) (21 . 20) (22 . 21) (23 . 22) (25 . 24) (26 . 25)) 1.504 {7/196:253} B:0 1.13743 [ 1.09211] ((3 . 2) (4 . 3) (5 . 4) (6 . 5) (7 . 6) (8 . 7) (9 . 8) (10 . 9) (11 . 10) (12 . 11) (13 . 12) (14 . 13) (15 . 14) (16 . 15) (18 . 17) (19 . 18) (20 . 19) (21 . 20) (22 . 21) (23 . 22) (25 . 24) (26 . 25)) 1.056 {5/178:231} B:0 3.57976 [ 3.43799] ((3 . 2) (6 . 5) (7 . 6) (8 . 7) (9 . 8) (20 . 19) (21 . 22)) 1.888 {2/18:21} B:0 3.61305 [ 3.47547] ((2 . 1) (3 . 2) (7 . 4) (20 . 19) (23 . 22) (25 . 24) (26 . 25)) 2.775 {2/12:21} B:0 4.16668 [ 4.00002] ((7 . 6) (8 . 7) (9 . 8) (20 . 19) (21 . 22) (23 . 25)) 4.228 {0/12:15} B:0 SIMILARITY (1/min{score1}): 0.9173 [and 1/min{score2}: 0.9551] [208, 4329]: Comparing 1aui_A and 1nnw_A, based on their crossing files. There are 29 (15 H + 14 S) secondary structure elements in 1aui_A, of which 25 satisfy the size requirements. There are 19 (9 H + 10 S) secondary structure elements in 1nnw_A, of which 19 satisfy the size requirements. 1.69693 [ 1.33224] ((5 . 1) (6 . 2) (7 . 3) (8 . 4) (9 . 5) (11 . 8) (12 . 9) (13 . 10) (14 . 11) (20 . 12) (21 . 13) (22 . 14) (23 . 15) (25 . 16) (26 . 17)) 4.048 {6/69:105} B:0 4.16668 [ 3.16671] ((7 . 1) (9 . 3) (20 . 12) (23 . 15) (25 . 16) (26 . 17)) 4.312 {0/11:15} B:0 4.16669 [ 3.16672] ((5 . 1) (6 . 2) (7 . 3) (8 . 4) (9 . 5) (23 . 17)) 4.633 {0/7:15} B:0 4.16670 [ 3.16673] ((7 . 1) (9 . 3) (20 . 12) (22 . 14) (23 . 15) (26 . 17)) 4.856 {0/11:15} B:0 4.16670 [ 3.16675] ((8 . 2) (9 . 3) (20 . 12) (21 . 13) (22 . 14) (23 . 15)) 5.090 {0/10:15} B:0 SIMILARITY (1/min{score1}): 0.5893 [and 1/min{score2}: 0.7506] [208, 5998]: Comparing 1aui_A and 1uf3_A, based on their crossing files. There are 29 (15 H + 14 S) secondary structure elements in 1aui_A, of which 25 satisfy the size requirements. There are 20 (6 H + 14 S) secondary structure elements in 1uf3_A, of which 19 satisfy the size requirements. 4.16671 [ 3.16677] ((5 . 1) (6 . 2) (7 . 3) (9 . 5) (20 . 14) (23 . 20)) 5.388 {0/8:15} B:0 4.17510 [ 3.18575] ((6 . 2) (7 . 3) (8 . 4) (9 . 5) (20 . 14) (21 . 17)) 4.261 {1/8:15} B:0 4.22092 [ 3.28580] ((5 . 1) (6 . 2) (7 . 3) (9 . 5) (13 . 8) (20 . 14)) 4.674 {1/5:15} B:0 4.29557 [ 3.43746] ((5 . 1) (6 . 2) (7 . 3) (9 . 5) (20 . 14) (21 . 17)) 3.609 {2/8:15} B:0 5.00001 [ 3.80002] ((7 . 1) (9 . 3) (20 . 14) (25 . 19) (26 . 20)) 3.842 {0/5:10} B:0 SIMILARITY (1/min{score1}): 0.4817 [and 1/min{score2}: 0.5397] [208, 6109]: Comparing 1aui_A and 1ute_A, based on their crossing files. There are 29 (15 H + 14 S) secondary structure elements in 1aui_A, of which 25 satisfy the size requirements. There are 24 (10 H + 14 S) secondary structure elements in 1ute_A, of which 22 satisfy the size requirements. 4.16670 [ 3.66671] ((6 . 2) (7 . 3) (9 . 6) (13 . 10) (14 . 11) (20 . 16)) 4.984 {0/8:15} B:0 4.22092 [ 3.74528] ((5 . 15) (6 . 16) (7 . 17) (9 . 19) (13 . 22) (14 . 23)) 4.768 {1/5:15} B:0 5.00002 [ 4.40003] ((7 . 6) (8 . 8) (10 . 12) (22 . 22) (23 . 23)) 4.978 {0/7:10} B:0 5.00002 [ 4.40003] ((5 . 15) (6 . 16) (7 . 17) (9 . 19) (13 . 23)) 5.121 {0/3:10} B:0 5.44809 [ 5.01159] ((5 . 3) (21 . 19) (23 . 21) (25 . 22) (26 . 23)) 4.258 {2/5:10} B:0 SIMILARITY (1/min{score1}): 0.3870 [and 1/min{score2}: 0.3940] [208, 6613]: Comparing 1aui_A and 4kbp_A, based on their crossing files. There are 29 (15 H + 14 S) secondary structure elements in 1aui_A, of which 25 satisfy the size requirements. There are 35 (12 H + 23 S) secondary structure elements in 4kbp_A, of which 18 satisfy the size requirements. 3.57143 [ 2.57144] ((5 . 10) (6 . 11) (7 . 12) (8 . 15) (20 . 26) (21 . 27) (22 . 28)) 2.740 {0/11:21} B:0 3.57335 [ 2.57657] ((5 . 10) (6 . 11) (7 . 12) (8 . 15) (21 . 27) (22 . 28) (23 . 31)) 2.367 {1/13:21} B:0 4.16668 [ 3.00004] ((5 . 10) (6 . 11) (7 . 12) (20 . 25) (21 . 27) (22 . 28)) 4.019 {0/12:15} B:0 4.18099 [ 3.03785] ((6 . 11) (7 . 12) (8 . 15) (20 . 26) (23 . 31) (25 . 33)) 2.746 {1/7:15} B:0 4.29557 [ 3.31019] ((6 . 11) (7 . 12) (8 . 15) (13 . 21) (23 . 31) (25 . 33)) 3.088 {2/8:15} B:0 SIMILARITY (1/min{score1}): 0.3712 [and 1/min{score2}: 0.3889] -------------------------------------------------------------------------------------------------------------------------