------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [2045, 1435]: Comparing 1h2b_A and 1f8f_A, based on their crossing files. There are 31 (14 H + 17 S) secondary structure elements in 1h2b_A, of which 13 satisfy the size requirements. There are 33 (17 H + 16 S) secondary structure elements in 1f8f_A, of which 13 satisfy the size requirements. 1.20589 [ 1.20589] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (7 . 5) (8 . 6) (9 . 7) (11 . 11) (13 . 13) (29 . 31) (30 . 32) (31 . 33)) 3.475 {5/54:66} B:0 1.34092 [ 1.34092] ((1 . 1) (3 . 3) (4 . 4) (7 . 5) (8 . 6) (9 . 7) (11 . 11) (13 . 13) (29 . 31) (30 . 32) (31 . 33)) 3.133 {5/47:55} B:0 2.12948 [ 2.12948] ((2 . 1) (3 . 3) (4 . 4) (7 . 5) (8 . 6) (11 . 11) (13 . 13) (29 . 31) (30 . 32) (31 . 33)) 3.367 {8/39:45} B:0 4.37866 [ 4.37866] ((2 . 5) (3 . 6) (5 . 7) (29 . 33)) 6.323 {2/5:6} B:0 4.37869 [ 4.37869] ((2 . 5) (3 . 6) (5 . 9) (29 . 33)) 6.983 {2/5:6} B:0 SIMILARITY (1/min{score1}): 0.8293 [and 1/min{score2}: 0.8293] [2045, 1707]: Comparing 1h2b_A and 1g31_A, based on their crossing files. There are 31 (14 H + 17 S) secondary structure elements in 1h2b_A, of which 13 satisfy the size requirements. There are 13 (6 H + 7 S) secondary structure elements in 1g31_A, of which 7 satisfy the size requirements. 3.25002 [ 1.75011] ((3 . 2) (7 . 5) (8 . 6) (11 . 11)) 3.499 {0/5:6} B:0 3.25020 [ 1.75126] ((7 . 2) (8 . 5) (11 . 6) (13 . 8)) 6.485 {0/6:6} B:0 3.25125 [ 1.75794] ((1 . 2) (3 . 5) (7 . 8) (8 . 11)) 10.293 {0/4:6} B:0 3.30522 [ 2.03521] ((1 . 5) (2 . 6) (3 . 8) (4 . 9)) 7.980 {1/6:6} B:0 3.50335 [ 2.63830] ((7 . 2) (9 . 4) (11 . 6) (13 . 8)) 4.937 {1/4:6} B:0 SIMILARITY (1/min{score1}): 0.3846 [and 1/min{score2}: 0.7142] [2045, 1955]: Comparing 1h2b_A and 1gu7_A, based on their crossing files. There are 31 (14 H + 17 S) secondary structure elements in 1h2b_A, of which 13 satisfy the size requirements. There are 32 (15 H + 17 S) secondary structure elements in 1gu7_A, of which 12 satisfy the size requirements. 1.30029 [ 1.23471] ((1 . 1) (2 . 3) (3 . 4) (4 . 5) (7 . 7) (8 . 8) (11 . 9) (13 . 11) (29 . 30) (30 . 31) (31 . 32)) 3.344 {4/41:55} B:0 1.83491 [ 1.81289] ((1 . 1) (2 . 3) (3 . 4) (5 . 5) (7 . 7) (8 . 8) (11 . 9) (13 . 11) (29 . 30) (30 . 31) (31 . 32)) 4.513 {7/40:55} B:0 2.20460 [ 2.04778] ((4 . 5) (7 . 7) (9 . 12) (29 . 30) (30 . 31) (31 . 32)) 7.931 {1/9:15} B:0 3.25012 [ 3.00016] ((1 . 1) (2 . 3) (5 . 5) (8 . 7)) 5.791 {0/4:6} B:0 3.36078 [ 3.13835] ((5 . 5) (11 . 9) (13 . 11) (31 . 30)) 4.747 {1/5:6} B:0 SIMILARITY (1/min{score1}): 0.7691 [and 1/min{score2}: 0.8099] [2045, 2045]: Comparing 1h2b_A and 1h2b_A, based on their crossing files. There are 31 (14 H + 17 S) secondary structure elements in 1h2b_A, of which 13 satisfy the size requirements. There are 31 (14 H + 17 S) secondary structure elements in 1h2b_A, of which 13 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (7 . 7) (8 . 8) (9 . 9) (11 . 11) (13 . 13) (29 . 29) (30 . 30) (31 . 31)) 0.000 {0/68:78} B:0 2.29311 [ 2.29311] ((3 . 3) (9 . 9) (13 . 11) (29 . 29) (30 . 30) (31 . 31)) 5.116 {2/13:15} B:0 2.29311 [ 2.29311] ((3 . 3) (9 . 9) (11 . 13) (29 . 29) (30 . 30) (31 . 31)) 5.116 {2/13:15} B:0 3.95009 [ 3.95009] ((5 . 4) (9 . 9) (29 . 29) (30 . 30) (31 . 31)) 4.842 {3/8:10} B:0 3.95009 [ 3.95009] ((4 . 5) (9 . 9) (29 . 29) (30 . 30) (31 . 31)) 4.842 {3/8:10} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [2045, 2193]: Comparing 1h2b_A and 1het_A, based on their crossing files. There are 31 (14 H + 17 S) secondary structure elements in 1h2b_A, of which 13 satisfy the size requirements. There are 34 (15 H + 19 S) secondary structure elements in 1het_A, of which 13 satisfy the size requirements. 1.21962 [ 1.21962] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (7 . 6) (8 . 7) (11 . 11) (13 . 13) (29 . 32) (30 . 33) (31 . 34)) 3.148 {3/42:55} B:0 1.35178 [ 1.35178] ((1 . 1) (3 . 3) (4 . 4) (7 . 6) (8 . 7) (11 . 11) (13 . 13) (29 . 32) (30 . 33) (31 . 34)) 2.623 {3/36:45} B:0 1.74064 [ 1.74064] ((1 . 1) (3 . 3) (4 . 4) (7 . 6) (8 . 7) (13 . 11) (29 . 32) (30 . 33) (31 . 34)) 5.002 {4/27:36} B:0 3.26402 [ 3.26402] ((2 . 1) (3 . 3) (5 . 4) (7 . 6) (8 . 7) (11 . 11) (13 . 13) (29 . 32) (30 . 33) (31 . 34)) 4.506 {12/37:45} B:0 4.16768 [ 4.16768] ((2 . 1) (4 . 4) (29 . 32) (30 . 33) (31 . 34)) 3.633 {2/5:10} B:0 SIMILARITY (1/min{score1}): 0.8199 [and 1/min{score2}: 0.8199] [2045, 2673]: Comparing 1h2b_A and 1iz0_A, based on their crossing files. There are 31 (14 H + 17 S) secondary structure elements in 1h2b_A, of which 13 satisfy the size requirements. There are 29 (13 H + 16 S) secondary structure elements in 1iz0_A, of which 10 satisfy the size requirements. 2.03506 [ 1.97761] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (7 . 5) (8 . 6) (11 . 7) (29 . 27) (30 . 28) (31 . 29)) 2.570 {7/36:45} B:0 2.56699 [ 2.52412] ((2 . 2) (3 . 3) (5 . 4) (7 . 5) (8 . 6) (11 . 7) (29 . 27) (30 . 28) (31 . 29)) 4.314 {7/28:36} B:0 2.63415 [ 2.07249] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (7 . 6)) 4.689 {1/8:10} B:0 3.25091 [ 2.50199] ((7 . 1) (8 . 2) (9 . 4) (11 . 5)) 9.502 {0/4:6} B:0 3.60654 [ 3.43664] ((7 . 2) (8 . 3) (29 . 27) (30 . 28) (31 . 29)) 6.718 {2/6:10} B:0 SIMILARITY (1/min{score1}): 0.4914 [and 1/min{score2}: 0.5057] [2045, 3016]: Comparing 1h2b_A and 1jqb_A, based on their crossing files. There are 31 (14 H + 17 S) secondary structure elements in 1h2b_A, of which 13 satisfy the size requirements. There are 33 (15 H + 18 S) secondary structure elements in 1jqb_A, of which 12 satisfy the size requirements. 1.36539 [ 1.30957] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (7 . 6) (8 . 7) (9 . 8) (11 . 10) (29 . 31) (30 . 32) (31 . 33)) 2.544 {5/45:55} B:0 1.46288 [ 1.35661] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (7 . 6) (8 . 7) (11 . 10) (30 . 32) (31 . 33)) 2.179 {2/29:36} B:0 1.60147 [ 1.55155] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (7 . 6) (8 . 7) (11 . 10) (29 . 31) (30 . 32) (31 . 33)) 2.342 {5/36:45} B:0 2.70346 [ 2.52885] ((4 . 4) (7 . 7) (29 . 31) (30 . 32) (31 . 33)) 3.807 {1/6:10} B:0 3.50438 [ 3.31146] ((3 . 1) (7 . 3) (9 . 4) (11 . 7)) 10.500 {1/4:6} B:0 SIMILARITY (1/min{score1}): 0.7324 [and 1/min{score2}: 0.7636] [2045, 3071]: Comparing 1h2b_A and 1jvb_A, based on their crossing files. There are 31 (14 H + 17 S) secondary structure elements in 1h2b_A, of which 13 satisfy the size requirements. There are 36 (14 H + 22 S) secondary structure elements in 1jvb_A, of which 13 satisfy the size requirements. 1.08710 [ 1.08710] ((1 . 1) (2 . 2) (3 . 3) (4 . 5) (7 . 9) (8 . 10) (9 . 12) (11 . 15) (13 . 17) (29 . 34) (30 . 35) (31 . 36)) 2.324 {2/54:66} B:0 1.08869 [ 1.08869] ((1 . 1) (2 . 2) (3 . 4) (4 . 5) (7 . 9) (8 . 10) (9 . 12) (11 . 15) (13 . 17) (29 . 34) (30 . 35) (31 . 36)) 3.305 {2/50:66} B:0 1.18224 [ 1.18224] ((1 . 1) (2 . 2) (4 . 5) (7 . 9) (8 . 10) (9 . 12) (11 . 15) (13 . 17) (29 . 34) (30 . 35) (31 . 36)) 1.736 {1/44:55} B:0 1.44538 [ 1.44538] ((1 . 1) (2 . 2) (3 . 3) (4 . 5) (8 . 10) (9 . 12) (29 . 34) (30 . 35) (31 . 36)) 2.339 {1/31:36} B:0 3.36075 [ 3.36075] ((4 . 5) (7 . 10) (9 . 12) (30 . 35)) 3.404 {1/5:6} B:0 SIMILARITY (1/min{score1}): 0.9199 [and 1/min{score2}: 0.9199] [2045, 3384]: Comparing 1h2b_A and 1kol_A, based on their crossing files. There are 31 (14 H + 17 S) secondary structure elements in 1h2b_A, of which 13 satisfy the size requirements. There are 35 (17 H + 18 S) secondary structure elements in 1kol_A, of which 13 satisfy the size requirements. 1.26029 [ 1.26029] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (7 . 5) (8 . 6) (9 . 8) (11 . 11) (29 . 33) (30 . 34) (31 . 35)) 2.148 {4/46:55} B:0 1.43347 [ 1.43347] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (7 . 5) (8 . 6) (11 . 11) (29 . 33) (30 . 34) (31 . 35)) 2.145 {4/37:45} B:0 2.62142 [ 2.62142] ((3 . 3) (4 . 4) (9 . 8) (11 . 11) (31 . 33)) 1.991 {1/9:10} B:0 2.70387 [ 2.70387] ((1 . 3) (2 . 5) (29 . 33) (30 . 34) (31 . 35)) 6.949 {1/6:10} B:0 3.03426 [ 3.03426] ((3 . 3) (5 . 4) (7 . 5) (8 . 6) (9 . 8)) 4.048 {2/8:10} B:0 SIMILARITY (1/min{score1}): 0.7935 [and 1/min{score2}: 0.7935] [2045, 4548]: Comparing 1h2b_A and 1o89_A, based on their crossing files. There are 31 (14 H + 17 S) secondary structure elements in 1h2b_A, of which 13 satisfy the size requirements. There are 30 (14 H + 16 S) secondary structure elements in 1o89_A, of which 10 satisfy the size requirements. 1.30867 [ 1.01872] ((1 . 1) (2 . 2) (3 . 4) (4 . 5) (7 . 6) (8 . 7) (11 . 8) (29 . 28) (30 . 29) (31 . 30)) 2.033 {2/38:45} B:0 1.46287 [ 1.15025] ((1 . 1) (2 . 2) (3 . 4) (7 . 6) (8 . 7) (11 . 8) (29 . 28) (30 . 29) (31 . 30)) 1.817 {2/29:36} B:0 3.50353 [ 2.97340] ((1 . 2) (4 . 5) (7 . 7) (29 . 30)) 7.165 {1/4:6} B:0 1.67098 [ 1.34419] ((1 . 1) (2 . 2) (3 . 4) (4 . 5) (7 . 6) (8 . 7) (29 . 30) (30 . 29)) 2.523 {2/21:28} B:1 3.84073 [ 3.82058] ((1 . 1) (2 . 2) (3 . 4) (4 . 29) (7 . 6) (11 . 7) (29 . 28) (31 . 30)) 5.530 {8/21:28} B:1 SIMILARITY (1/min{score1}): 0.7641 [and 1/min{score2}: 0.9816] [2045, 4881]: Comparing 1h2b_A and 1p3h_A, based on their crossing files. There are 31 (14 H + 17 S) secondary structure elements in 1h2b_A, of which 13 satisfy the size requirements. There are 10 (1 H + 9 S) secondary structure elements in 1p3h_A, of which 7 satisfy the size requirements. 3.25022 [ 1.75139] ((7 . 2) (8 . 3) (11 . 6) (13 . 7)) 6.653 {0/6:6} B:0 5.20970 [ 5.01878] ((2 . 1) (3 . 2) (7 . 6) (8 . 7)) 8.126 {2/4:6} B:0 5.20977 [ 5.01886] ((3 . 1) (7 . 3) (8 . 6) (11 . 10)) 9.151 {2/4:6} B:0 2.19327 [ 1.31113] ((1 . 8) (3 . 3) (7 . 2) (8 . 1) (11 . 6) (13 . 7)) 9.055 {1/10:15} B:3 SIMILARITY (1/min{score1}): 0.4559 [and 1/min{score2}: 0.7627] [2045, 5044]: Comparing 1h2b_A and 1pl7_A, based on their crossing files. There are 31 (14 H + 17 S) secondary structure elements in 1h2b_A, of which 13 satisfy the size requirements. There are 33 (13 H + 20 S) secondary structure elements in 1pl7_A, of which 12 satisfy the size requirements. 1.10302 [ 1.02478] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (7 . 8) (8 . 9) (9 . 11) (11 . 14) (13 . 16) (29 . 31) (30 . 32) (31 . 33)) 1.968 {3/53:66} B:0 1.18220 [ 1.09139] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (7 . 8) (8 . 9) (9 . 11) (11 . 14) (13 . 16) (29 . 31) (30 . 32)) 2.054 {1/46:55} B:0 2.96580 [ 2.90616] ((4 . 4) (9 . 11) (11 . 16) (29 . 31) (30 . 32) (31 . 33)) 4.638 {3/11:15} B:0 3.36075 [ 3.13831] ((4 . 4) (7 . 9) (9 . 11) (30 . 32)) 3.704 {1/5:6} B:0 4.37883 [ 4.28484] ((2 . 3) (4 . 4) (7 . 9) (30 . 32)) 8.588 {2/5:6} B:0 SIMILARITY (1/min{score1}): 0.9066 [and 1/min{score2}: 0.9758] [2045, 5405]: Comparing 1h2b_A and 1qor_A, based on their crossing files. There are 31 (14 H + 17 S) secondary structure elements in 1h2b_A, of which 13 satisfy the size requirements. There are 29 (13 H + 16 S) secondary structure elements in 1qor_A, of which 11 satisfy the size requirements. 1.25436 [ 1.11125] ((1 . 1) (2 . 3) (3 . 4) (4 . 5) (7 . 6) (8 . 7) (11 . 8) (13 . 10) (29 . 27) (30 . 28) (31 . 29)) 2.074 {4/47:55} B:0 1.41093 [ 1.26627] ((1 . 1) (2 . 3) (3 . 4) (4 . 5) (7 . 6) (8 . 7) (11 . 8) (29 . 27) (30 . 28) (31 . 29)) 2.152 {4/39:45} B:0 2.26269 [ 1.98328] ((7 . 6) (8 . 7) (11 . 10) (29 . 27) (30 . 28) (31 . 29)) 4.993 {2/14:15} B:0 2.56277 [ 2.38572] ((3 . 1) (11 . 8) (13 . 10) (29 . 27) (30 . 28) (31 . 29)) 5.421 {3/14:15} B:0 2.66443 [ 2.50947] ((1 . 1) (2 . 3) (3 . 4) (4 . 5) (7 . 6) (29 . 29)) 2.472 {3/13:15} B:0 SIMILARITY (1/min{score1}): 0.7972 [and 1/min{score2}: 0.8999] [2045, 6113]: Comparing 1h2b_A and 1uuf_A, based on their crossing files. There are 31 (14 H + 17 S) secondary structure elements in 1h2b_A, of which 13 satisfy the size requirements. There are 32 (14 H + 18 S) secondary structure elements in 1uuf_A, of which 12 satisfy the size requirements. 1.20836 [ 1.12425] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (7 . 5) (8 . 6) (9 . 8) (11 . 11) (29 . 29) (30 . 30) (31 . 31)) 2.128 {3/46:55} B:0 1.91420 [ 1.78566] ((7 . 5) (8 . 6) (9 . 8) (13 . 11) (29 . 29) (30 . 30) (31 . 31)) 4.527 {2/18:21} B:0 2.89342 [ 2.75451] ((8 . 5) (9 . 8) (29 . 29) (30 . 30) (31 . 31)) 3.964 {2/9:10} B:0 2.89342 [ 2.75452] ((1 . 2) (4 . 4) (9 . 8) (11 . 11) (30 . 30)) 3.998 {2/9:10} B:0 2.89364 [ 2.75477] ((1 . 2) (4 . 4) (8 . 7) (11 . 11) (30 . 30)) 6.384 {2/9:10} B:0 SIMILARITY (1/min{score1}): 0.8276 [and 1/min{score2}: 0.8895] [2045, 6273]: Comparing 1h2b_A and 1vj0_A, based on their crossing files. There are 31 (14 H + 17 S) secondary structure elements in 1h2b_A, of which 13 satisfy the size requirements. There are 33 (13 H + 20 S) secondary structure elements in 1vj0_A, of which 13 satisfy the size requirements. 1.15674 [ 1.15674] ((1 . 1) (2 . 2) (3 . 3) (4 . 5) (7 . 6) (8 . 7) (9 . 9) (11 . 12) (13 . 13) (29 . 31) (30 . 32) (31 . 33)) 3.874 {4/50:66} B:0 1.30047 [ 1.30047] ((1 . 1) (2 . 2) (3 . 3) (4 . 5) (7 . 6) (8 . 7) (11 . 12) (13 . 13) (29 . 31) (30 . 32) (31 . 33)) 3.910 {4/41:55} B:0 2.31544 [ 2.31544] ((2 . 1) (3 . 3) (4 . 5) (7 . 6) (8 . 7) (11 . 12) (29 . 31) (30 . 32) (31 . 33)) 3.873 {6/27:36} B:0 2.63409 [ 2.63409] ((4 . 5) (7 . 7) (29 . 31) (30 . 32) (31 . 33)) 3.754 {1/8:10} B:0 3.30618 [ 3.30618] ((1 . 6) (2 . 7) (4 . 9) (7 . 13)) 10.702 {1/6:6} B:0 SIMILARITY (1/min{score1}): 0.8645 [and 1/min{score2}: 0.8645] [2045, 6275]: Comparing 1h2b_A and 1vj1_A, based on their crossing files. There are 31 (14 H + 17 S) secondary structure elements in 1h2b_A, of which 13 satisfy the size requirements. There are 31 (14 H + 17 S) secondary structure elements in 1vj1_A, of which 12 satisfy the size requirements. 1.76348 [ 1.73859] ((1 . 1) (2 . 3) (3 . 4) (4 . 5) (7 . 6) (8 . 7) (11 . 9) (13 . 11) (29 . 29) (30 . 30) (31 . 31)) 4.106 {7/42:55} B:0 2.65742 [ 2.47214] ((2 . 3) (3 . 4) (4 . 5) (7 . 6) (29 . 31)) 4.726 {1/7:10} B:0 3.36145 [ 3.13917] ((4 . 5) (7 . 7) (8 . 9) (9 . 12)) 9.189 {1/5:6} B:0 3.74591 [ 3.71686] ((2 . 1) (3 . 4) (4 . 5) (29 . 29) (30 . 30) (31 . 31)) 3.815 {4/11:15} B:0 4.37878 [ 4.28478] ((2 . 4) (3 . 6) (7 . 7) (8 . 11)) 8.067 {2/5:6} B:0 SIMILARITY (1/min{score1}): 0.5671 [and 1/min{score2}: 0.5752] -------------------------------------------------------------------------------------------------------------------------