------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [2223, 417]: Comparing 1hkk_A and 1bkf, based on their crossing files. There are 32 (17 H + 15 S) secondary structure elements in 1hkk_A, of which 7 satisfy the size requirements. There are 9 (3 H + 6 S) secondary structure elements in 1bkf, of which 7 satisfy the size requirements. 2.24653 [ 2.24653] ((22 . 3) (23 . 5) (24 . 7) (28 . 9)) 8.822 {1/5:6} B:0 6.01094 [ 6.01094] ((22 . 1) (23 . 2) (26 . 5) (28 . 7)) 8.935 {3/5:6} B:0 1.16695 [ 1.16695] ((22 . 2) (23 . 3) (24 . 5) (26 . 1) (27 . 7) (28 . 9)) 3.306 {0/10:15} B:1 SIMILARITY (1/min{score1}): 0.8569 [and 1/min{score2}: 0.8569] [2223, 1114]: Comparing 1hkk_A and 1edq_A, based on their crossing files. There are 32 (17 H + 15 S) secondary structure elements in 1hkk_A, of which 7 satisfy the size requirements. There are 45 (20 H + 25 S) secondary structure elements in 1edq_A, of which 6 satisfy the size requirements. 1.16667 [ 1.00000] ((22 . 34) (24 . 37) (25 . 38) (26 . 39) (27 . 40) (28 . 41)) 0.862 {0/12:15} B:0 1.40063 [ 1.20100] ((22 . 34) (23 . 37) (26 . 39) (27 . 40) (28 . 41)) 4.611 {0/7:10} B:0 4.03616 [ 4.01965] ((22 . 34) (24 . 37) (25 . 38) (28 . 40)) 4.095 {2/5:6} B:0 5.01866 [ 5.01011] ((22 . 34) (24 . 37) (25 . 38) (27 . 39)) 4.386 {3/6:6} B:0 6.01092 [ 6.00595] ((23 . 34) (26 . 37) (27 . 39) (28 . 40)) 8.650 {3/5:6} B:0 SIMILARITY (1/min{score1}): 0.8571 [and 1/min{score2}: 0.9999] [2223, 1243]: Comparing 1hkk_A and 1eq3_A, based on their crossing files. There are 32 (17 H + 15 S) secondary structure elements in 1hkk_A, of which 7 satisfy the size requirements. There are 7 (3 H + 4 S) secondary structure elements in 1eq3_A, of which 7 satisfy the size requirements. 3.39519 [ 3.39519] ((23 . 4) (25 . 5) (27 . 6) (28 . 7)) 7.330 {1/3:6} B:0 SIMILARITY (1/min{score1}): 0.2945 [and 1/min{score2}: 0.2945] [2223, 1474]: Comparing 1hkk_A and 1fd9_A, based on their crossing files. There are 32 (17 H + 15 S) secondary structure elements in 1hkk_A, of which 7 satisfy the size requirements. There are 14 (7 H + 7 S) secondary structure elements in 1fd9_A, of which 11 satisfy the size requirements. 2.24470 [ 2.92502] ((22 . 6) (24 . 9) (25 . 11) (28 . 14)) 4.981 {1/5:6} B:0 2.24562 [ 2.92544] ((22 . 6) (23 . 9) (25 . 11) (28 . 14)) 7.604 {1/5:6} B:0 4.03639 [ 4.20702] ((23 . 4) (24 . 5) (27 . 6) (28 . 7)) 8.041 {2/5:6} B:0 4.03651 [ 4.20713] ((22 . 7) (23 . 9) (24 . 12) (28 . 14)) 8.910 {2/5:6} B:0 4.03663 [ 4.20724] ((22 . 4) (23 . 5) (24 . 6) (27 . 9)) 9.567 {2/5:6} B:0 SIMILARITY (1/min{score1}): 0.7692 [and 1/min{score2}: 0.5340] [2223, 1890]: Comparing 1hkk_A and 1goi_A, based on their crossing files. There are 32 (17 H + 15 S) secondary structure elements in 1hkk_A, of which 7 satisfy the size requirements. There are 36 (19 H + 17 S) secondary structure elements in 1goi_A, of which 7 satisfy the size requirements. 1.16670 [ 1.16670] ((22 . 23) (24 . 25) (25 . 26) (26 . 27) (27 . 28) (28 . 29)) 1.867 {0/13:15} B:0 1.16804 [ 1.16804] ((22 . 23) (23 . 25) (25 . 26) (26 . 27) (27 . 28) (28 . 29)) 4.896 {0/13:15} B:0 1.40067 [ 1.40067] ((23 . 25) (25 . 26) (26 . 27) (27 . 28) (28 . 29)) 4.688 {0/9:10} B:0 4.03617 [ 4.03617] ((22 . 23) (24 . 25) (25 . 26) (28 . 28)) 4.454 {2/5:6} B:0 5.01866 [ 5.01866] ((22 . 23) (24 . 25) (25 . 26) (27 . 27)) 4.284 {3/6:6} B:0 SIMILARITY (1/min{score1}): 0.8571 [and 1/min{score2}: 0.8571] [2223, 2223]: Comparing 1hkk_A and 1hkk_A, based on their crossing files. There are 32 (17 H + 15 S) secondary structure elements in 1hkk_A, of which 7 satisfy the size requirements. There are 32 (17 H + 15 S) secondary structure elements in 1hkk_A, of which 7 satisfy the size requirements. 1.00000 [ 1.00000] ((22 . 22) (23 . 23) (24 . 24) (25 . 25) (26 . 26) (27 . 27) (28 . 28)) 0.000 {0/19:21} B:0 1.75011 [ 1.75011] ((24 . 23) (26 . 26) (27 . 27) (28 . 28)) 3.524 {0/5:6} B:0 1.75011 [ 1.75011] ((23 . 24) (26 . 26) (27 . 27) (28 . 28)) 3.524 {0/5:6} B:0 4.03616 [ 4.03616] ((22 . 22) (23 . 23) (25 . 25) (27 . 28)) 4.150 {2/5:6} B:0 4.03616 [ 4.03616] ((22 . 22) (23 . 23) (25 . 25) (28 . 27)) 4.150 {2/5:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [2223, 2604]: Comparing 1hkk_A and 1itx_A, based on their crossing files. There are 32 (17 H + 15 S) secondary structure elements in 1hkk_A, of which 7 satisfy the size requirements. There are 36 (19 H + 17 S) secondary structure elements in 1itx_A, of which 7 satisfy the size requirements. 1.16667 [ 1.16667] ((22 . 25) (24 . 28) (25 . 29) (26 . 30) (27 . 31) (28 . 32)) 1.168 {0/13:15} B:0 4.03616 [ 4.03616] ((22 . 25) (24 . 28) (25 . 29) (28 . 31)) 4.253 {2/5:6} B:0 5.01866 [ 5.01866] ((22 . 25) (24 . 28) (25 . 29) (27 . 30)) 3.998 {3/6:6} B:0 SIMILARITY (1/min{score1}): 0.8571 [and 1/min{score2}: 0.8571] [2223, 2642]: Comparing 1hkk_A and 1ix5_A, based on their crossing files. There are 32 (17 H + 15 S) secondary structure elements in 1hkk_A, of which 7 satisfy the size requirements. There are 13 (3 H + 10 S) secondary structure elements in 1ix5_A, of which 10 satisfy the size requirements. 1.76215 [ 2.50420] ((22 . 7) (26 . 12) (27 . 11) (28 . 13)) 11.460 {0/3:6} B:1 SIMILARITY (1/min{score1}): 0.5675 [and 1/min{score2}: 0.3993] [2223, 2992]: Comparing 1hkk_A and 1jnd_A, based on their crossing files. There are 32 (17 H + 15 S) secondary structure elements in 1hkk_A, of which 7 satisfy the size requirements. There are 31 (17 H + 14 S) secondary structure elements in 1jnd_A, of which 6 satisfy the size requirements. 1.16669 [ 1.00004] ((22 . 20) (24 . 22) (25 . 23) (26 . 25) (27 . 26) (28 . 27)) 1.787 {0/13:15} B:0 1.16822 [ 1.00246] ((22 . 20) (23 . 22) (25 . 23) (26 . 25) (27 . 26) (28 . 27)) 5.042 {0/13:15} B:0 1.75037 [ 1.50058] ((22 . 20) (24 . 22) (25 . 23) (28 . 25)) 4.770 {0/5:6} B:0 5.01867 [ 5.01011] ((22 . 20) (24 . 22) (25 . 23) (27 . 25)) 4.467 {3/6:6} B:0 5.01888 [ 5.01032] ((22 . 22) (24 . 25) (26 . 26) (28 . 27)) 9.318 {2/4:6} B:0 SIMILARITY (1/min{score1}): 0.8571 [and 1/min{score2}: 0.9999] [2223, 2998]: Comparing 1hkk_A and 1jnt_A, based on their crossing files. There are 32 (17 H + 15 S) secondary structure elements in 1hkk_A, of which 7 satisfy the size requirements. There are 8 (4 H + 4 S) secondary structure elements in 1jnt_A, of which 6 satisfy the size requirements. 1.75046 [ 1.50072] ((22 . 1) (25 . 6) (27 . 7) (28 . 8)) 5.032 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.5713 [and 1/min{score2}: 0.6663] [2223, 3075]: Comparing 1hkk_A and 1jvw_A, based on their crossing files. There are 32 (17 H + 15 S) secondary structure elements in 1hkk_A, of which 7 satisfy the size requirements. There are 14 (7 H + 7 S) secondary structure elements in 1jvw_A, of which 11 satisfy the size requirements. 2.24466 [ 2.92500] ((22 . 4) (24 . 7) (25 . 9) (28 . 12)) 4.710 {1/5:6} B:0 4.03638 [ 4.20701] ((23 . 2) (24 . 3) (27 . 4) (28 . 5)) 7.972 {2/5:6} B:0 4.03643 [ 4.20706] ((22 . 5) (23 . 7) (24 . 10) (28 . 12)) 8.369 {2/5:6} B:0 4.03660 [ 4.20721] ((22 . 2) (23 . 3) (24 . 4) (27 . 7)) 9.436 {2/5:6} B:0 1.40082 [ 2.20021] ((22 . 10) (24 . 3) (26 . 5) (27 . 4) (28 . 12)) 4.923 {0/5:10} B:2 SIMILARITY (1/min{score1}): 0.7139 [and 1/min{score2}: 0.4545] [2223, 3289]: Comparing 1hkk_A and 1kfw_A, based on their crossing files. There are 32 (17 H + 15 S) secondary structure elements in 1hkk_A, of which 7 satisfy the size requirements. There are 35 (17 H + 18 S) secondary structure elements in 1kfw_A, of which 6 satisfy the size requirements. 1.16669 [ 1.00003] ((22 . 25) (24 . 27) (25 . 28) (26 . 29) (27 . 30) (28 . 31)) 1.665 {0/12:15} B:0 1.16792 [ 1.00199] ((22 . 25) (23 . 27) (25 . 28) (26 . 29) (27 . 30) (28 . 31)) 4.782 {0/12:15} B:0 1.40001 [ 1.20001] ((22 . 25) (24 . 27) (25 . 28) (27 . 30) (28 . 31)) 1.413 {0/8:10} B:0 4.03616 [ 4.01964] ((22 . 25) (24 . 27) (25 . 28) (27 . 31)) 3.964 {2/5:6} B:0 6.01091 [ 6.00594] ((23 . 25) (26 . 27) (27 . 29) (28 . 30)) 8.417 {3/5:6} B:0 SIMILARITY (1/min{score1}): 0.8571 [and 1/min{score2}: 0.9999] [2223, 3423]: Comparing 1hkk_A and 1kt1_A, based on their crossing files. There are 32 (17 H + 15 S) secondary structure elements in 1hkk_A, of which 7 satisfy the size requirements. There are 23 (12 H + 11 S) secondary structure elements in 1kt1_A, of which 7 satisfy the size requirements. 4.03637 [ 4.03637] ((22 . 9) (23 . 10) (25 . 11) (27 . 13)) 7.940 {2/5:6} B:0 5.01906 [ 5.01906] ((22 . 8) (23 . 9) (24 . 10) (27 . 13)) 10.750 {2/4:6} B:0 1.30106 [ 1.30106] ((22 . 9) (23 . 10) (25 . 12) (26 . 8) (27 . 13) (28 . 15)) 5.383 {1/10:15} B:1 1.40076 [ 1.40076] ((22 . 9) (23 . 10) (26 . 8) (27 . 13) (28 . 15)) 4.843 {0/5:10} B:1 SIMILARITY (1/min{score1}): 0.7686 [and 1/min{score2}: 0.7686] [2223, 3847]: Comparing 1hkk_A and 1m5y_A, based on their crossing files. There are 32 (17 H + 15 S) secondary structure elements in 1hkk_A, of which 7 satisfy the size requirements. There are 28 (17 H + 11 S) secondary structure elements in 1m5y_A, of which 8 satisfy the size requirements. 1.68360 [ 1.81057] ((22 . 9) (23 . 13) (25 . 15) (27 . 16) (28 . 17)) 6.537 {1/7:10} B:0 1.75016 [ 2.00011] ((22 . 9) (24 . 13) (27 . 16) (28 . 17)) 3.869 {0/4:6} B:0 2.63846 [ 2.72430] ((24 . 13) (25 . 15) (27 . 16) (28 . 17)) 6.053 {1/4:6} B:0 2.63852 [ 2.72435] ((23 . 13) (25 . 15) (27 . 16) (28 . 17)) 6.374 {1/4:6} B:0 1.75016 [ 2.00011] ((22 . 16) (26 . 13) (27 . 9) (28 . 17)) 3.889 {0/4:6} B:2 SIMILARITY (1/min{score1}): 0.5940 [and 1/min{score2}: 0.5523] [2223, 3848]: Comparing 1hkk_A and 1m5y_A, based on their crossing files. There are 32 (17 H + 15 S) secondary structure elements in 1hkk_A, of which 7 satisfy the size requirements. There are 28 (17 H + 11 S) secondary structure elements in 1m5y_A, of which 7 satisfy the size requirements. NO SIMILARITY! [2223, 4690]: Comparing 1hkk_A and 1okg_A, based on their crossing files. There are 32 (17 H + 15 S) secondary structure elements in 1hkk_A, of which 7 satisfy the size requirements. There are 32 (14 H + 18 S) secondary structure elements in 1okg_A, of which 6 satisfy the size requirements. 2.24569 [ 2.14366] ((22 . 28) (23 . 29) (24 . 31) (26 . 32)) 7.718 {1/5:6} B:0 5.01880 [ 5.01024] ((23 . 27) (26 . 28) (27 . 29) (28 . 31)) 8.367 {2/4:6} B:0 7.50557 [ 7.50301] ((22 . 27) (25 . 30) (26 . 31) (27 . 32)) 6.314 {3/4:6} B:0 1.23717 [ 1.10485] ((22 . 28) (24 . 29) (25 . 30) (26 . 27) (27 . 31) (28 . 32)) 4.763 {1/12:15} B:1 1.40033 [ 1.20053] ((22 . 28) (24 . 29) (26 . 27) (27 . 31) (28 . 32)) 3.930 {0/7:10} B:1 SIMILARITY (1/min{score1}): 0.8083 [and 1/min{score2}: 0.9051] [2223, 5022]: Comparing 1hkk_A and 1pin_A, based on their crossing files. There are 32 (17 H + 15 S) secondary structure elements in 1hkk_A, of which 7 satisfy the size requirements. There are 11 (4 H + 7 S) secondary structure elements in 1pin_A, of which 7 satisfy the size requirements. NO SIMILARITY! [2223, 5222]: Comparing 1hkk_A and 1q6h_A, based on their crossing files. There are 32 (17 H + 15 S) secondary structure elements in 1hkk_A, of which 7 satisfy the size requirements. There are 14 (7 H + 7 S) secondary structure elements in 1q6h_A, of which 12 satisfy the size requirements. 2.24464 [ 3.13834] ((22 . 6) (24 . 9) (25 . 11) (28 . 14)) 4.531 {1/5:6} B:0 4.03647 [ 4.28484] ((22 . 7) (23 . 9) (24 . 12) (28 . 14)) 8.636 {2/5:6} B:0 4.03649 [ 4.28486] ((22 . 4) (23 . 5) (25 . 8) (26 . 9)) 8.806 {2/5:6} B:0 6.01095 [ 6.09175] ((22 . 5) (23 . 6) (26 . 9) (28 . 12)) 9.180 {3/5:6} B:0 1.29982 [ 2.03060] ((22 . 6) (23 . 7) (24 . 9) (26 . 5) (27 . 12) (28 . 14)) 3.331 {1/10:15} B:1 SIMILARITY (1/min{score1}): 0.7693 [and 1/min{score2}: 0.4925] [2223, 6565]: Comparing 1hkk_A and 3eip_A, based on their crossing files. There are 32 (17 H + 15 S) secondary structure elements in 1hkk_A, of which 7 satisfy the size requirements. There are 7 (3 H + 4 S) secondary structure elements in 3eip_A, of which 7 satisfy the size requirements. 1.40026 [ 1.40026] ((22 . 1) (23 . 2) (25 . 3) (27 . 5) (28 . 7)) 3.694 {0/7:10} B:0 1.40164 [ 1.40164] ((22 . 1) (24 . 2) (25 . 3) (27 . 5) (28 . 7)) 5.864 {0/7:10} B:0 1.75011 [ 1.75011] ((22 . 1) (23 . 2) (25 . 3) (27 . 5)) 3.529 {0/5:6} B:0 2.03525 [ 2.03525] ((22 . 2) (23 . 5) (25 . 6) (27 . 7)) 8.026 {1/6:6} B:0 2.24665 [ 2.24665] ((23 . 1) (24 . 2) (25 . 3) (27 . 5)) 8.943 {1/5:6} B:0 SIMILARITY (1/min{score1}): 0.7142 [and 1/min{score2}: 0.7142] -------------------------------------------------------------------------------------------------------------------------