------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [3652, 100]: Comparing 1ll8_A and 1acf, based on their crossing files. There are 9 (3 H + 6 S) secondary structure elements in 1ll8_A, of which 7 satisfy the size requirements. There are 12 (5 H + 7 S) secondary structure elements in 1acf, of which 12 satisfy the size requirements. 1.75073 [ 3.00015] ((3 . 2) (5 . 5) (6 . 7) (7 . 8)) 5.667 {0/4:6} B:0 1.75115 [ 3.00023] ((3 . 1) (5 . 5) (6 . 7) (7 . 8)) 6.345 {0/4:6} B:0 6.01088 [ 6.09168] ((1 . 3) (2 . 4) (3 . 5) (6 . 10)) 7.424 {3/5:6} B:0 2.89804 [ 3.16128] ((1 . 3) (2 . 4) (3 . 5) (5 . 12) (9 . 11)) 7.811 {2/7:10} B:1 7.50110 [ 7.50947] ((1 . 11) (2 . 3) (5 . 5) (6 . 7) (7 . 8) (9 . 10)) 5.041 {9/12:15} B:1 SIMILARITY (1/min{score1}): 0.5712 [and 1/min{score2}: 0.3333] [3652, 496]: Comparing 1ll8_A and 1byw_A, based on their crossing files. There are 9 (3 H + 6 S) secondary structure elements in 1ll8_A, of which 7 satisfy the size requirements. There are 9 (4 H + 5 S) secondary structure elements in 1byw_A, of which 8 satisfy the size requirements. 1.00276 [ 1.14471] ((1 . 1) (2 . 2) (3 . 3) (5 . 6) (6 . 7) (7 . 8) (9 . 9)) 5.192 {0/14:21} B:0 1.16694 [ 1.33352] ((1 . 1) (2 . 2) (3 . 3) (5 . 6) (6 . 7) (9 . 9)) 3.276 {0/11:15} B:0 2.63902 [ 2.72481] ((1 . 2) (3 . 4) (6 . 8) (7 . 9)) 7.977 {1/4:6} B:0 4.29787 [ 4.30639] ((1 . 1) (2 . 2) (3 . 3) (7 . 7) (9 . 9)) 3.848 {3/7:10} B:0 5.01884 [ 5.03188] ((2 . 1) (3 . 3) (5 . 4) (9 . 8)) 8.879 {3/6:6} B:0 SIMILARITY (1/min{score1}): 0.9972 [and 1/min{score2}: 0.8736] [3652, 1279]: Comparing 1ll8_A and 1ew0_A, based on their crossing files. There are 9 (3 H + 6 S) secondary structure elements in 1ll8_A, of which 7 satisfy the size requirements. There are 11 (6 H + 5 S) secondary structure elements in 1ew0_A, of which 10 satisfy the size requirements. 1.00269 [ 1.42950] ((1 . 3) (2 . 4) (3 . 5) (5 . 8) (6 . 9) (7 . 10) (9 . 11)) 5.161 {0/16:21} B:0 1.75294 [ 2.50101] ((1 . 4) (3 . 6) (6 . 10) (7 . 11)) 8.021 {0/3:6} B:0 4.03634 [ 4.14474] ((2 . 3) (3 . 5) (5 . 8) (9 . 10)) 7.612 {2/5:6} B:0 4.03662 [ 4.14500] ((2 . 3) (5 . 6) (7 . 9) (9 . 10)) 9.539 {2/5:6} B:0 5.01899 [ 5.07669] ((1 . 4) (3 . 6) (5 . 8) (6 . 10)) 10.313 {2/4:6} B:0 SIMILARITY (1/min{score1}): 0.9973 [and 1/min{score2}: 0.6995] [3652, 1402]: Comparing 1ll8_A and 1f5m_A, based on their crossing files. There are 9 (3 H + 6 S) secondary structure elements in 1ll8_A, of which 7 satisfy the size requirements. There are 12 (6 H + 6 S) secondary structure elements in 1f5m_A, of which 11 satisfy the size requirements. 1.40148 [ 2.20038] ((1 . 4) (2 . 5) (6 . 8) (7 . 10) (9 . 11)) 5.713 {0/4:10} B:0 1.40191 [ 2.20049] ((1 . 4) (2 . 5) (5 . 7) (7 . 10) (9 . 11)) 6.088 {0/5:10} B:0 3.39531 [ 3.66645] ((1 . 4) (2 . 5) (5 . 7) (7 . 11)) 7.991 {1/3:6} B:0 5.01893 [ 5.11092] ((2 . 4) (3 . 3) (5 . 7) (9 . 10)) 9.816 {2/4:6} B:1 SIMILARITY (1/min{score1}): 0.7135 [and 1/min{score2}: 0.4545] [3652, 1985]: Comparing 1ll8_A and 1gw5_M, based on their crossing files. There are 9 (3 H + 6 S) secondary structure elements in 1ll8_A, of which 7 satisfy the size requirements. There are 29 (6 H + 23 S) secondary structure elements in 1gw5_M, of which 9 satisfy the size requirements. NO SIMILARITY! [3652, 1986]: Comparing 1ll8_A and 1gw5_S, based on their crossing files. There are 9 (3 H + 6 S) secondary structure elements in 1ll8_A, of which 7 satisfy the size requirements. There are 12 (5 H + 7 S) secondary structure elements in 1gw5_S, of which 10 satisfy the size requirements. NO SIMILARITY! [3652, 2072]: Comparing 1ll8_A and 1h3q_A, based on their crossing files. There are 9 (3 H + 6 S) secondary structure elements in 1ll8_A, of which 7 satisfy the size requirements. There are 9 (3 H + 6 S) secondary structure elements in 1h3q_A, of which 9 satisfy the size requirements. NO SIMILARITY! [3652, 2139]: Comparing 1ll8_A and 1h8m_A, based on their crossing files. There are 9 (3 H + 6 S) secondary structure elements in 1ll8_A, of which 7 satisfy the size requirements. There are 9 (4 H + 5 S) secondary structure elements in 1h8m_A, of which 8 satisfy the size requirements. NO SIMILARITY! [3652, 2472]: Comparing 1ll8_A and 1ifq_A, based on their crossing files. There are 9 (3 H + 6 S) secondary structure elements in 1ll8_A, of which 7 satisfy the size requirements. There are 8 (3 H + 5 S) secondary structure elements in 1ifq_A, of which 8 satisfy the size requirements. NO SIMILARITY! [3652, 2727]: Comparing 1ll8_A and 1j3w_A, based on their crossing files. There are 9 (3 H + 6 S) secondary structure elements in 1ll8_A, of which 7 satisfy the size requirements. There are 8 (3 H + 5 S) secondary structure elements in 1j3w_A, of which 8 satisfy the size requirements. 1.40063 [ 1.60042] ((1 . 2) (2 . 3) (6 . 5) (7 . 6) (9 . 7)) 4.610 {0/4:10} B:0 1.40241 [ 1.60162] ((1 . 2) (2 . 3) (5 . 4) (7 . 6) (9 . 7)) 6.456 {0/5:10} B:0 1.75402 [ 2.00269] ((1 . 2) (2 . 3) (5 . 4) (7 . 7)) 8.674 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.7140 [and 1/min{score2}: 0.6248] [3652, 3527]: Comparing 1ll8_A and 1l3l_A, based on their crossing files. There are 9 (3 H + 6 S) secondary structure elements in 1ll8_A, of which 7 satisfy the size requirements. There are 19 (13 H + 6 S) secondary structure elements in 1l3l_A, of which 12 satisfy the size requirements. 1.16829 [ 2.00032] ((1 . 3) (2 . 4) (5 . 7) (6 . 8) (7 . 11) (9 . 13)) 5.100 {0/10:15} B:0 2.63836 [ 3.31027] ((1 . 3) (2 . 4) (5 . 9) (9 . 13)) 5.423 {1/4:6} B:0 6.01096 [ 6.09176] ((1 . 8) (2 . 11) (3 . 10) (5 . 14)) 9.409 {3/5:6} B:1 SIMILARITY (1/min{score1}): 0.8560 [and 1/min{score2}: 0.4999] [3652, 3652]: Comparing 1ll8_A and 1ll8_A, based on their crossing files. There are 9 (3 H + 6 S) secondary structure elements in 1ll8_A, of which 7 satisfy the size requirements. There are 9 (3 H + 6 S) secondary structure elements in 1ll8_A, of which 7 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (2 . 2) (3 . 3) (5 . 5) (6 . 6) (7 . 7) (9 . 9)) 0.000 {0/17:21} B:0 2.24458 [ 2.24458] ((2 . 1) (3 . 3) (5 . 5) (9 . 9)) 4.049 {1/5:6} B:0 2.24458 [ 2.24458] ((1 . 2) (3 . 3) (5 . 5) (9 . 9)) 4.049 {1/5:6} B:0 2.63828 [ 2.63828] ((1 . 2) (3 . 3) (5 . 5) (6 . 7)) 4.646 {1/4:6} B:0 2.63828 [ 2.63828] ((2 . 1) (3 . 3) (5 . 5) (7 . 6)) 4.646 {1/4:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [3652, 3903]: Comparing 1ll8_A and 1mc0_A, based on their crossing files. There are 9 (3 H + 6 S) secondary structure elements in 1ll8_A, of which 7 satisfy the size requirements. There are 25 (11 H + 14 S) secondary structure elements in 1mc0_A, of which 12 satisfy the size requirements. 1.40144 [ 2.40029] ((1 . 3) (2 . 4) (5 . 7) (7 . 11) (9 . 12)) 5.673 {0/6:10} B:0 2.24654 [ 3.13904] ((1 . 4) (2 . 5) (5 . 10) (6 . 11)) 8.825 {1/5:6} B:0 2.63915 [ 3.31068] ((5 . 1) (6 . 3) (7 . 4) (9 . 6)) 8.278 {1/4:6} B:0 2.63979 [ 3.31100] ((1 . 4) (2 . 6) (5 . 10) (6 . 11)) 9.394 {1/4:6} B:0 5.01876 [ 5.15477] ((1 . 4) (2 . 6) (3 . 7) (5 . 10)) 7.685 {2/4:6} B:0 SIMILARITY (1/min{score1}): 0.7136 [and 1/min{score2}: 0.4166] [3652, 3904]: Comparing 1ll8_A and 1mc0_A, based on their crossing files. There are 9 (3 H + 6 S) secondary structure elements in 1ll8_A, of which 7 satisfy the size requirements. There are 25 (11 H + 14 S) secondary structure elements in 1mc0_A, of which 9 satisfy the size requirements. 1.75014 [ 2.25007] ((1 . 16) (2 . 17) (5 . 20) (9 . 24)) 3.740 {0/4:6} B:0 3.35905 [ 3.40212] ((1 . 16) (2 . 17) (5 . 20) (7 . 21) (9 . 24)) 5.322 {2/6:10} B:0 5.01892 [ 5.05075] ((1 . 17) (3 . 20) (5 . 22) (6 . 24)) 9.689 {3/6:6} B:0 2.26388 [ 2.33008] ((1 . 16) (2 . 17) (3 . 15) (6 . 21) (7 . 23) (9 . 24)) 6.547 {2/9:15} B:1 4.03634 [ 4.09675] ((2 . 16) (3 . 15) (6 . 21) (9 . 23)) 7.623 {2/5:6} B:1 SIMILARITY (1/min{score1}): 0.5714 [and 1/min{score2}: 0.4444] [3652, 3961]: Comparing 1ll8_A and 1mkm_A, based on their crossing files. There are 9 (3 H + 6 S) secondary structure elements in 1ll8_A, of which 7 satisfy the size requirements. There are 18 (10 H + 8 S) secondary structure elements in 1mkm_A, of which 11 satisfy the size requirements. NO SIMILARITY! [3652, 4177]: Comparing 1ll8_A and 1n9l_A, based on their crossing files. There are 9 (3 H + 6 S) secondary structure elements in 1ll8_A, of which 7 satisfy the size requirements. There are 9 (4 H + 5 S) secondary structure elements in 1n9l_A, of which 8 satisfy the size requirements. 1.00242 [ 1.14448] ((1 . 1) (2 . 2) (3 . 3) (5 . 6) (6 . 7) (7 . 8) (9 . 9)) 5.023 {0/14:21} B:0 1.16691 [ 1.33350] ((1 . 1) (2 . 2) (3 . 3) (5 . 6) (6 . 7) (9 . 9)) 3.181 {0/11:15} B:0 2.63899 [ 2.72478] ((1 . 2) (3 . 4) (6 . 8) (7 . 9)) 7.905 {1/4:6} B:0 4.03664 [ 4.06158] ((2 . 1) (5 . 4) (7 . 7) (9 . 8)) 9.637 {2/5:6} B:0 6.01095 [ 6.01856] ((1 . 2) (3 . 4) (5 . 6) (6 . 8)) 9.161 {3/5:6} B:0 SIMILARITY (1/min{score1}): 0.9976 [and 1/min{score2}: 0.8738] [3652, 4366]: Comparing 1ll8_A and 1nrj_A, based on their crossing files. There are 9 (3 H + 6 S) secondary structure elements in 1ll8_A, of which 7 satisfy the size requirements. There are 12 (6 H + 6 S) secondary structure elements in 1nrj_A, of which 10 satisfy the size requirements. 2.63864 [ 2.97334] ((1 . 8) (2 . 9) (3 . 10) (5 . 11)) 6.868 {1/4:6} B:0 2.89759 [ 3.01518] ((1 . 1) (2 . 2) (3 . 3) (6 . 7) (9 . 9)) 5.365 {2/7:10} B:0 3.39507 [ 3.57061] ((1 . 1) (2 . 2) (3 . 3) (6 . 8)) 6.341 {1/3:6} B:0 4.03620 [ 4.14461] ((1 . 1) (2 . 2) (3 . 3) (6 . 7)) 5.602 {2/5:6} B:0 SIMILARITY (1/min{score1}): 0.3790 [and 1/min{score2}: 0.3363] [3652, 4420]: Comparing 1ll8_A and 1nwz_A, based on their crossing files. There are 9 (3 H + 6 S) secondary structure elements in 1ll8_A, of which 7 satisfy the size requirements. There are 12 (7 H + 5 S) secondary structure elements in 1nwz_A, of which 11 satisfy the size requirements. 1.00101 [ 1.57169] ((1 . 3) (2 . 4) (3 . 5) (5 . 9) (6 . 10) (7 . 11) (9 . 12)) 4.037 {0/13:21} B:0 1.16727 [ 1.83349] ((1 . 3) (2 . 4) (3 . 5) (5 . 9) (7 . 11) (9 . 12)) 3.978 {0/9:15} B:0 2.63900 [ 3.13273] ((2 . 3) (3 . 5) (5 . 7) (9 . 12)) 7.934 {1/4:6} B:0 3.01706 [ 3.09959] ((1 . 3) (2 . 4) (3 . 5) (5 . 9) (7 . 10) (9 . 12)) 4.387 {3/10:15} B:0 3.39503 [ 3.66623] ((1 . 3) (2 . 4) (3 . 6) (5 . 9)) 5.934 {1/3:6} B:0 SIMILARITY (1/min{score1}): 0.9990 [and 1/min{score2}: 0.6363] [3652, 4674]: Comparing 1ll8_A and 1oj5_A, based on their crossing files. There are 9 (3 H + 6 S) secondary structure elements in 1ll8_A, of which 7 satisfy the size requirements. There are 9 (3 H + 6 S) secondary structure elements in 1oj5_A, of which 9 satisfy the size requirements. 1.00640 [ 1.28874] ((1 . 1) (2 . 2) (3 . 3) (5 . 5) (6 . 7) (7 . 8) (9 . 9)) 6.415 {0/13:21} B:0 1.16871 [ 1.50096] ((1 . 1) (2 . 2) (3 . 3) (5 . 5) (6 . 7) (9 . 9)) 5.406 {0/10:15} B:0 4.03674 [ 4.09713] ((2 . 1) (5 . 4) (7 . 7) (9 . 8)) 10.052 {2/5:6} B:0 SIMILARITY (1/min{score1}): 0.9936 [and 1/min{score2}: 0.7760] [3652, 4676]: Comparing 1ll8_A and 1ojg_A, based on their crossing files. There are 9 (3 H + 6 S) secondary structure elements in 1ll8_A, of which 7 satisfy the size requirements. There are 10 (6 H + 4 S) secondary structure elements in 1ojg_A, of which 9 satisfy the size requirements. 1.75150 [ 2.25071] ((3 . 4) (5 . 6) (6 . 7) (7 . 8)) 6.775 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.5709 [and 1/min{score2}: 0.4443] [3652, 4856]: Comparing 1ll8_A and 1p0z_A, based on their crossing files. There are 9 (3 H + 6 S) secondary structure elements in 1ll8_A, of which 7 satisfy the size requirements. There are 11 (6 H + 5 S) secondary structure elements in 1p0z_A, of which 10 satisfy the size requirements. 2.63845 [ 2.97321] ((1 . 4) (2 . 5) (3 . 6) (5 . 7)) 6.023 {1/4:6} B:0 2.63883 [ 2.97347] ((5 . 6) (6 . 8) (7 . 9) (9 . 10)) 7.489 {1/4:6} B:0 6.67459 [ 6.69940] ((1 . 4) (3 . 6) (7 . 8) (9 . 9)) 6.255 {2/3:6} B:0 SIMILARITY (1/min{score1}): 0.3790 [and 1/min{score2}: 0.3363] [3652, 4938]: Comparing 1ll8_A and 1p97_A, based on their crossing files. There are 9 (3 H + 6 S) secondary structure elements in 1ll8_A, of which 7 satisfy the size requirements. There are 9 (4 H + 5 S) secondary structure elements in 1p97_A, of which 7 satisfy the size requirements. 1.17121 [ 1.17121] ((1 . 1) (3 . 3) (5 . 6) (6 . 7) (7 . 8) (9 . 9)) 6.603 {0/8:15} B:0 1.40289 [ 1.40289] ((1 . 1) (3 . 3) (5 . 6) (7 . 8) (9 . 9)) 6.755 {0/4:10} B:0 2.63836 [ 2.63836] ((1 . 1) (3 . 4) (5 . 6) (9 . 9)) 5.413 {1/4:6} B:0 3.39503 [ 3.39503] ((1 . 1) (3 . 3) (7 . 7) (9 . 8)) 5.885 {1/3:6} B:0 4.03636 [ 4.03636] ((1 . 1) (3 . 4) (5 . 6) (6 . 8)) 7.856 {2/5:6} B:0 SIMILARITY (1/min{score1}): 0.8538 [and 1/min{score2}: 0.8538] [3652, 5065]: Comparing 1ll8_A and 1pne, based on their crossing files. There are 9 (3 H + 6 S) secondary structure elements in 1ll8_A, of which 7 satisfy the size requirements. There are 12 (5 H + 7 S) secondary structure elements in 1pne, of which 11 satisfy the size requirements. 1.75011 [ 2.75003] ((1 . 2) (2 . 3) (6 . 9) (9 . 11)) 3.497 {0/4:6} B:0 1.75254 [ 2.75066] ((2 . 2) (6 . 8) (7 . 9) (9 . 10)) 7.732 {0/4:6} B:0 2.63851 [ 3.13243] ((1 . 2) (2 . 3) (3 . 5) (9 . 11)) 6.319 {1/4:6} B:0 1.16736 [ 1.83351] ((1 . 10) (2 . 11) (5 . 5) (6 . 7) (7 . 8) (9 . 9)) 4.122 {0/12:15} B:1 SIMILARITY (1/min{score1}): 0.8566 [and 1/min{score2}: 0.5454] [3652, 6238]: Comparing 1ll8_A and 1vhm_A, based on their crossing files. There are 9 (3 H + 6 S) secondary structure elements in 1ll8_A, of which 7 satisfy the size requirements. There are 11 (5 H + 6 S) secondary structure elements in 1vhm_A, of which 10 satisfy the size requirements. 1.35735 [ 1.74433] ((1 . 3) (2 . 4) (5 . 6) (6 . 7) (7 . 8) (9 . 9)) 5.830 {1/9:15} B:0 1.40140 [ 2.00048] ((1 . 3) (2 . 4) (6 . 7) (7 . 8) (9 . 9)) 5.640 {0/5:10} B:0 3.39533 [ 3.57083] ((1 . 3) (2 . 4) (5 . 6) (7 . 9)) 8.074 {1/3:6} B:0 1.75276 [ 2.50095] ((1 . 4) (2 . 3) (6 . 8) (7 . 9)) 7.894 {0/3:6} B:1 1.75194 [ 2.50066] ((1 . 4) (6 . 8) (7 . 7) (9 . 5)) 7.224 {0/4:6} B:2 SIMILARITY (1/min{score1}): 0.7367 [and 1/min{score2}: 0.5733] [3652, 6584]: Comparing 1ll8_A and 3nul, based on their crossing files. There are 9 (3 H + 6 S) secondary structure elements in 1ll8_A, of which 7 satisfy the size requirements. There are 10 (3 H + 7 S) secondary structure elements in 3nul, of which 10 satisfy the size requirements. 5.01878 [ 5.07648] ((1 . 2) (2 . 3) (3 . 4) (6 . 8)) 8.039 {2/4:6} B:0 6.01084 [ 6.04472] ((5 . 4) (6 . 5) (7 . 6) (9 . 8)) 5.478 {3/5:6} B:0 7.77877 [ 7.78189] ((1 . 9) (2 . 2) (5 . 4) (6 . 5) (7 . 7) (9 . 8)) 6.024 {7/9:15} B:1 8.18267 [ 8.18534] ((1 . 9) (2 . 2) (5 . 4) (6 . 5) (7 . 6) (9 . 8)) 4.917 {9/11:15} B:1 SIMILARITY (1/min{score1}): 0.1993 [and 1/min{score2}: 0.1970] -------------------------------------------------------------------------------------------------------------------------