------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [4985, 34]: Comparing 1pdk_B and 1a3q_A, based on their crossing files. There are 12 (3 H + 9 S) secondary structure elements in 1pdk_B, of which 9 satisfy the size requirements. There are 24 (3 H + 21 S) secondary structure elements in 1a3q_A, of which 10 satisfy the size requirements. 1.50353 [ 1.66924] ((2 . 1) (4 . 3) (6 . 4) (9 . 6) (10 . 7) (12 . 11)) 7.480 {0/7:15} B:0 1.80202 [ 2.00148] ((2 . 1) (4 . 3) (6 . 4) (9 . 6) (12 . 11)) 7.462 {0/5:10} B:0 1.80265 [ 2.00194] ((2 . 1) (4 . 3) (6 . 4) (10 . 8) (12 . 11)) 7.985 {0/4:10} B:0 2.25060 [ 2.50044] ((2 . 4) (4 . 6) (6 . 7) (10 . 11)) 6.512 {0/2:6} B:0 2.25287 [ 2.50210] ((4 . 1) (6 . 3) (9 . 4) (11 . 9)) 9.630 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.6651 [and 1/min{score2}: 0.5991] [4985, 159]: Comparing 1pdk_B and 1amx, based on their crossing files. There are 12 (3 H + 9 S) secondary structure elements in 1pdk_B, of which 9 satisfy the size requirements. There are 14 (2 H + 12 S) secondary structure elements in 1amx, of which 14 satisfy the size requirements. 1.80037 [ 2.80010] ((2 . 1) (4 . 2) (6 . 3) (10 . 11) (12 . 12)) 4.872 {0/2:10} B:0 1.81205 [ 2.80323] ((4 . 2) (6 . 3) (9 . 5) (10 . 9) (12 . 12)) 11.681 {0/2:10} B:0 1.81206 [ 2.80323] ((2 . 2) (4 . 3) (6 . 5) (10 . 12) (12 . 14)) 11.682 {0/1:10} B:0 2.25034 [ 3.50009] ((4 . 1) (6 . 2) (9 . 3) (12 . 11)) 5.651 {0/1:6} B:0 2.25055 [ 3.50015] ((4 . 1) (6 . 2) (10 . 9) (12 . 11)) 6.360 {0/0:6} B:0 SIMILARITY (1/min{score1}): 0.6666 [and 1/min{score2}: 0.4286] [4985, 169]: Comparing 1pdk_B and 1aoh_A, based on their crossing files. There are 12 (3 H + 9 S) secondary structure elements in 1pdk_B, of which 9 satisfy the size requirements. There are 12 (1 H + 11 S) secondary structure elements in 1aoh_A, of which 11 satisfy the size requirements. 1.50196 [ 1.83441] ((2 . 1) (4 . 3) (6 . 4) (9 . 5) (10 . 9) (12 . 10)) 6.453 {0/6:15} B:0 1.80209 [ 2.20114] ((4 . 1) (6 . 3) (9 . 4) (10 . 8) (12 . 9)) 7.518 {0/1:10} B:0 1.80668 [ 2.20367] ((2 . 3) (4 . 4) (6 . 5) (10 . 10) (12 . 12)) 10.066 {0/2:10} B:0 2.25092 [ 2.75050] ((2 . 7) (4 . 8) (6 . 9) (9 . 10)) 7.243 {0/3:6} B:0 2.25272 [ 2.75149] ((4 . 8) (6 . 9) (9 . 10) (10 . 12)) 9.495 {0/1:6} B:0 SIMILARITY (1/min{score1}): 0.6665 [and 1/min{score2}: 0.5454] [4985, 245]: Comparing 1pdk_B and 1ayo_A, based on their crossing files. There are 12 (3 H + 9 S) secondary structure elements in 1pdk_B, of which 9 satisfy the size requirements. There are 11 (2 H + 9 S) secondary structure elements in 1ayo_A, of which 11 satisfy the size requirements. 1.50065 [ 1.83369] ((2 . 1) (4 . 3) (6 . 4) (9 . 5) (10 . 9) (12 . 10)) 4.895 {0/6:15} B:0 2.25120 [ 2.75066] ((2 . 1) (4 . 3) (6 . 4) (9 . 8)) 7.736 {0/3:6} B:0 2.25219 [ 2.75120] ((4 . 5) (6 . 8) (9 . 10) (10 . 11)) 8.999 {0/2:6} B:0 2.25280 [ 2.75153] ((2 . 4) (6 . 8) (9 . 10) (10 . 11)) 9.565 {0/0:6} B:0 2.25754 [ 2.75414] ((6 . 3) (9 . 5) (10 . 8) (12 . 10)) 12.263 {0/1:6} B:0 SIMILARITY (1/min{score1}): 0.6664 [and 1/min{score2}: 0.5581] [4985, 374]: Comparing 1pdk_B and 1bg1_A, based on their crossing files. There are 12 (3 H + 9 S) secondary structure elements in 1pdk_B, of which 9 satisfy the size requirements. There are 35 (20 H + 15 S) secondary structure elements in 1bg1_A, of which 18 satisfy the size requirements. 2.25045 [ 4.50006] ((6 . 10) (9 . 12) (10 . 15) (12 . 18)) 6.070 {0/2:6} B:0 2.25106 [ 4.50013] ((2 . 10) (4 . 13) (6 . 14) (9 . 18)) 7.495 {0/3:6} B:0 2.25106 [ 4.50013] ((4 . 6) (6 . 7) (9 . 10) (12 . 15)) 7.500 {0/3:6} B:0 2.25140 [ 4.50018] ((2 . 6) (4 . 8) (6 . 10) (9 . 13)) 8.041 {0/4:6} B:0 2.25175 [ 4.50022] ((4 . 6) (9 . 10) (10 . 13) (12 . 15)) 8.509 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.4666 [and 1/min{score2}: 0.3186] [4985, 1008]: Comparing 1pdk_B and 1e2w_A, based on their crossing files. There are 12 (3 H + 9 S) secondary structure elements in 1pdk_B, of which 9 satisfy the size requirements. There are 21 (5 H + 16 S) secondary structure elements in 1e2w_A, of which 10 satisfy the size requirements. 1.50333 [ 1.66910] ((2 . 3) (4 . 5) (6 . 8) (9 . 13) (10 . 15) (12 . 16)) 7.376 {0/6:15} B:0 1.80151 [ 2.00110] ((4 . 3) (6 . 5) (9 . 8) (10 . 13) (12 . 15)) 6.933 {0/1:10} B:0 2.25037 [ 2.50027] ((2 . 13) (4 . 15) (6 . 16) (12 . 21)) 5.759 {0/1:6} B:0 2.25235 [ 2.50171] ((9 . 5) (10 . 8) (11 . 11) (12 . 13)) 9.153 {0/2:6} B:0 2.25469 [ 2.50342] ((2 . 5) (6 . 13) (9 . 15) (10 . 16)) 10.884 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.6652 [and 1/min{score2}: 0.5991] [4985, 1040]: Comparing 1pdk_B and 1e5c_A, based on their crossing files. There are 12 (3 H + 9 S) secondary structure elements in 1pdk_B, of which 9 satisfy the size requirements. There are 9 (0 H + 9 S) secondary structure elements in 1e5c_A, of which 8 satisfy the size requirements. 2.25409 [ 2.00582] ((6 . 1) (9 . 4) (10 . 8) (12 . 9)) 10.520 {0/1:6} B:0 6.68825 [ 6.68019] ((2 . 1) (4 . 3) (6 . 4) (9 . 8)) 8.369 {2/3:6} B:0 10.00644 [10.00404] ((4 . 1) (6 . 3) (9 . 5) (10 . 9)) 10.324 {1/1:6} B:0 10.00265 [10.00166] ((2 . 8) (4 . 5) (6 . 3) (9 . 4) (10 . 7)) 8.737 {2/2:10} B:2 10.00641 [10.00401] ((2 . 8) (4 . 5) (9 . 7) (12 . 1)) 7.445 {1/1:6} B:2 SIMILARITY (1/min{score1}): 0.5549 [and 1/min{score2}: 0.6238] [4985, 1087]: Comparing 1pdk_B and 1eaq_A, based on their crossing files. There are 12 (3 H + 9 S) secondary structure elements in 1pdk_B, of which 9 satisfy the size requirements. There are 14 (1 H + 13 S) secondary structure elements in 1eaq_A, of which 11 satisfy the size requirements. 2.25095 [ 2.75052] ((4 . 3) (6 . 4) (9 . 6) (10 . 12)) 7.296 {0/2:6} B:0 2.25290 [ 2.75159] ((4 . 3) (9 . 6) (10 . 12) (12 . 14)) 9.648 {0/3:6} B:0 2.25308 [ 2.75169] ((3 . 1) (6 . 6) (9 . 9) (10 . 13)) 9.797 {0/3:6} B:0 2.25577 [ 2.75317] ((4 . 3) (6 . 4) (9 . 6) (12 . 13)) 11.469 {0/3:6} B:0 5.05079 [ 5.11094] ((5 . 1) (9 . 3) (10 . 6) (12 . 10)) 10.015 {2/4:6} B:0 SIMILARITY (1/min{score1}): 0.4443 [and 1/min{score2}: 0.3636] [4985, 1300]: Comparing 1pdk_B and 1exh, based on their crossing files. There are 12 (3 H + 9 S) secondary structure elements in 1pdk_B, of which 9 satisfy the size requirements. There are 13 (0 H + 13 S) secondary structure elements in 1exh, of which 10 satisfy the size requirements. 2.25279 [ 2.50203] ((2 . 1) (4 . 3) (9 . 8) (10 . 13)) 9.557 {0/3:6} B:0 2.91064 [ 2.93718] ((2 . 1) (4 . 3) (6 . 5) (9 . 8) (10 . 11) (12 . 13)) 8.243 {2/7:15} B:0 3.49550 [ 3.57161] ((2 . 3) (4 . 6) (6 . 8) (9 . 11)) 10.787 {1/3:6} B:0 5.05069 [ 5.07656] ((2 . 5) (4 . 8) (6 . 11) (9 . 13)) 9.108 {2/4:6} B:0 5.05072 [ 5.07659] ((2 . 1) (4 . 5) (6 . 6) (10 . 13)) 9.456 {1/2:6} B:0 SIMILARITY (1/min{score1}): 0.4439 [and 1/min{score2}: 0.3997] [4985, 1351]: Comparing 1pdk_B and 1f0l_A, based on their crossing files. There are 12 (3 H + 9 S) secondary structure elements in 1pdk_B, of which 9 satisfy the size requirements. There are 49 (23 H + 26 S) secondary structure elements in 1f0l_A, of which 16 satisfy the size requirements. 1.50083 [ 2.66681] ((2 . 36) (4 . 37) (6 . 38) (9 . 40) (10 . 46) (12 . 47)) 5.210 {0/4:15} B:0 1.80438 [ 3.20078] ((4 . 34) (6 . 37) (9 . 39) (10 . 44) (12 . 46)) 9.053 {0/3:10} B:0 2.25032 [ 4.00006] ((4 . 37) (6 . 39) (10 . 46) (12 . 47)) 5.580 {0/2:6} B:0 2.25068 [ 4.00012] ((6 . 38) (9 . 41) (10 . 46) (12 . 47)) 6.720 {0/2:6} B:0 2.25092 [ 4.00016] ((2 . 34) (4 . 37) (6 . 39) (10 . 46)) 7.236 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.6663 [and 1/min{score2}: 0.3750] [4985, 1689]: Comparing 1pdk_B and 1g1k_A, based on their crossing files. There are 12 (3 H + 9 S) secondary structure elements in 1pdk_B, of which 9 satisfy the size requirements. There are 15 (3 H + 12 S) secondary structure elements in 1g1k_A, of which 13 satisfy the size requirements. 1.80137 [ 2.60045] ((2 . 1) (4 . 3) (6 . 5) (9 . 6) (10 . 11)) 6.762 {0/4:10} B:0 1.80194 [ 2.60064] ((2 . 1) (4 . 3) (6 . 5) (10 . 11) (12 . 13)) 7.383 {0/2:10} B:0 1.80219 [ 2.60073] ((4 . 1) (6 . 3) (9 . 5) (10 . 9) (12 . 11)) 7.609 {0/1:10} B:0 2.25166 [ 3.25055] ((2 . 9) (4 . 11) (6 . 12) (9 . 15)) 8.393 {0/4:6} B:0 2.25187 [ 3.25062] ((2 . 3) (4 . 5) (6 . 6) (12 . 15)) 8.644 {0/1:6} B:0 SIMILARITY (1/min{score1}): 0.5551 [and 1/min{score2}: 0.3845] [4985, 1760]: Comparing 1pdk_B and 1g87_A, based on their crossing files. There are 12 (3 H + 9 S) secondary structure elements in 1pdk_B, of which 9 satisfy the size requirements. There are 39 (23 H + 16 S) secondary structure elements in 1g87_A, of which 11 satisfy the size requirements. 1.80093 [ 2.20051] ((2 . 24) (4 . 25) (6 . 26) (9 . 29) (10 . 34)) 6.147 {0/4:10} B:0 1.80205 [ 2.20112] ((2 . 24) (4 . 25) (6 . 26) (10 . 34) (12 . 38)) 7.482 {0/3:10} B:0 2.25150 [ 2.75082] ((2 . 31) (4 . 33) (6 . 34) (9 . 38)) 8.188 {0/4:6} B:0 2.25152 [ 2.75083] ((4 . 24) (6 . 25) (9 . 26) (12 . 34)) 8.211 {0/1:6} B:0 2.25175 [ 2.75096] ((4 . 24) (6 . 25) (10 . 33) (12 . 34)) 8.507 {0/1:6} B:0 SIMILARITY (1/min{score1}): 0.5553 [and 1/min{score2}: 0.4544] [4985, 2097]: Comparing 1pdk_B and 1h6f_A, based on their crossing files. There are 12 (3 H + 9 S) secondary structure elements in 1pdk_B, of which 9 satisfy the size requirements. There are 20 (6 H + 14 S) secondary structure elements in 1h6f_A, of which 14 satisfy the size requirements. 2.25052 [ 3.50014] ((2 . 1) (4 . 4) (6 . 5) (12 . 14)) 6.281 {0/2:6} B:0 2.25531 [ 3.50142] ((2 . 5) (4 . 7) (9 . 14) (10 . 16)) 11.233 {0/2:6} B:0 2.25815 [ 3.50218] ((4 . 1) (5 . 2) (9 . 5) (11 . 10)) 12.509 {0/4:6} B:0 2.27007 [ 2.96728] ((2 . 1) (4 . 4) (6 . 5) (9 . 14) (12 . 16)) 7.854 {1/5:10} B:0 2.54064 [ 3.58998] ((4 . 14) (5 . 15) (6 . 16) (9 . 18)) 6.983 {1/5:6} B:0 SIMILARITY (1/min{score1}): 0.4805 [and 1/min{score2}: 0.4203] [4985, 2375]: Comparing 1pdk_B and 1i31_A, based on their crossing files. There are 12 (3 H + 9 S) secondary structure elements in 1pdk_B, of which 9 satisfy the size requirements. There are 19 (2 H + 17 S) secondary structure elements in 1i31_A, of which 17 satisfy the size requirements. 1.50085 [ 2.83346] ((2 . 7) (4 . 8) (6 . 9) (9 . 10) (10 . 14) (12 . 15)) 5.239 {0/4:15} B:0 1.50341 [ 2.83384] ((2 . 1) (4 . 2) (6 . 3) (9 . 4) (10 . 6) (12 . 16)) 7.418 {0/4:15} B:0 2.25137 [ 4.25020] ((2 . 1) (4 . 2) (6 . 3) (9 . 4)) 8.001 {0/2:6} B:0 2.25153 [ 4.25023] ((2 . 7) (4 . 8) (6 . 9) (9 . 13)) 8.230 {0/1:6} B:0 2.25339 [ 4.25050] ((4 . 13) (6 . 14) (9 . 15) (10 . 19)) 10.038 {0/0:6} B:0 SIMILARITY (1/min{score1}): 0.6663 [and 1/min{score2}: 0.3529] [4985, 2769]: Comparing 1pdk_B and 1j8r_A, based on their crossing files. There are 12 (3 H + 9 S) secondary structure elements in 1pdk_B, of which 9 satisfy the size requirements. There are 16 (1 H + 15 S) secondary structure elements in 1j8r_A, of which 14 satisfy the size requirements. 2.25242 [ 3.50064] ((2 . 4) (4 . 7) (10 . 14) (12 . 16)) 9.219 {0/1:6} B:0 2.25351 [ 3.50093] ((2 . 13) (4 . 14) (5 . 15) (6 . 16)) 10.123 {0/4:6} B:0 2.25525 [ 3.50140] ((2 . 9) (4 . 10) (9 . 14) (10 . 16)) 11.197 {0/2:6} B:0 2.25748 [ 3.50200] ((2 . 4) (4 . 6) (10 . 14) (12 . 16)) 12.242 {0/1:6} B:0 2.25886 [ 3.50237] ((2 . 10) (4 . 13) (6 . 14) (9 . 16)) 12.774 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.5533 [and 1/min{score2}: 0.3843] [4985, 3343]: Comparing 1pdk_B and 1klf_B, based on their crossing files. There are 12 (3 H + 9 S) secondary structure elements in 1pdk_B, of which 9 satisfy the size requirements. There are 27 (2 H + 25 S) secondary structure elements in 1klf_B, of which 13 satisfy the size requirements. 1.50138 [ 2.16713] ((2 . 3) (4 . 6) (6 . 7) (9 . 9) (10 . 13) (12 . 15)) 5.913 {0/3:15} B:0 1.50340 [ 2.16780] ((2 . 3) (4 . 4) (6 . 7) (9 . 9) (10 . 13) (12 . 15)) 7.410 {0/5:15} B:0 1.80529 [ 2.60176] ((2 . 1) (4 . 4) (9 . 9) (10 . 13) (12 . 15)) 9.493 {0/3:10} B:0 1.80835 [ 2.60279] ((4 . 7) (6 . 9) (9 . 13) (10 . 15) (12 . 16)) 10.648 {0/1:10} B:0 2.25171 [ 3.25057] ((2 . 11) (4 . 13) (6 . 15) (9 . 16)) 8.450 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.6661 [and 1/min{score2}: 0.4614] [4985, 3344]: Comparing 1pdk_B and 1klf_B, based on their crossing files. There are 12 (3 H + 9 S) secondary structure elements in 1pdk_B, of which 9 satisfy the size requirements. There are 27 (2 H + 25 S) secondary structure elements in 1klf_B, of which 8 satisfy the size requirements. 1.80032 [ 1.60045] ((4 . 20) (6 . 21) (9 . 22) (10 . 26) (12 . 27)) 4.693 {0/4:10} B:0 1.80057 [ 1.60081] ((4 . 19) (6 . 21) (9 . 22) (10 . 26) (12 . 27)) 5.436 {0/4:10} B:0 2.25153 [ 2.00218] ((4 . 18) (6 . 19) (9 . 21) (10 . 24)) 8.223 {0/1:6} B:0 2.25406 [ 2.00577] ((2 . 19) (4 . 21) (6 . 22) (10 . 27)) 10.500 {0/2:6} B:0 4.30174 [ 4.29576] ((2 . 19) (4 . 20) (6 . 21) (9 . 22) (10 . 26) (12 . 27)) 5.371 {3/7:15} B:0 SIMILARITY (1/min{score1}): 0.5555 [and 1/min{score2}: 0.6248] [4985, 3803]: Comparing 1pdk_B and 1m2o_A, based on their crossing files. There are 12 (3 H + 9 S) secondary structure elements in 1pdk_B, of which 9 satisfy the size requirements. There are 52 (25 H + 27 S) secondary structure elements in 1m2o_A, of which 12 satisfy the size requirements. 1.50057 [ 2.00024] ((2 . 3) (4 . 5) (6 . 29) (9 . 30) (10 . 33) (12 . 34)) 4.732 {0/6:15} B:0 2.25154 [ 3.00065] ((2 . 32) (4 . 33) (6 . 34) (9 . 35)) 8.243 {0/4:6} B:0 2.25191 [ 3.00081] ((4 . 29) (6 . 30) (10 . 34) (12 . 35)) 8.696 {0/0:6} B:0 2.25559 [ 3.00237] ((2 . 29) (4 . 30) (9 . 34) (10 . 35)) 11.380 {0/1:6} B:0 5.05075 [ 5.15492] ((6 . 29) (9 . 30) (10 . 32) (12 . 34)) 9.689 {1/2:6} B:0 SIMILARITY (1/min{score1}): 0.6664 [and 1/min{score2}: 0.4999] [4985, 3986]: Comparing 1pdk_B and 1mnn_A, based on their crossing files. There are 12 (3 H + 9 S) secondary structure elements in 1pdk_B, of which 9 satisfy the size requirements. There are 32 (10 H + 22 S) secondary structure elements in 1mnn_A, of which 22 satisfy the size requirements. 2.06607 [ 4.42249] ((2 . 9) (3 . 10) (4 . 13) (6 . 15) (12 . 26)) 4.731 {1/6:10} B:0 2.25086 [ 5.50006] ((2 . 4) (4 . 6) (6 . 9) (9 . 11)) 7.111 {0/3:6} B:0 2.25096 [ 5.50007] ((6 . 4) (9 . 6) (10 . 9) (12 . 13)) 7.323 {0/2:6} B:0 2.25346 [ 5.50024] ((2 . 13) (5 . 19) (10 . 26) (12 . 27)) 10.086 {0/4:6} B:0 2.25358 [ 5.50025] ((2 . 4) (4 . 6) (6 . 9) (10 . 15)) 10.177 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.4840 [and 1/min{score2}: 0.2593] [4985, 4098]: Comparing 1pdk_B and 1n12_A, based on their crossing files. There are 12 (3 H + 9 S) secondary structure elements in 1pdk_B, of which 9 satisfy the size requirements. There are 13 (2 H + 11 S) secondary structure elements in 1n12_A, of which 8 satisfy the size requirements. 1.50039 [ 1.33389] ((2 . 2) (4 . 4) (6 . 5) (9 . 8) (10 . 11) (12 . 13)) 4.304 {0/7:15} B:0 1.80413 [ 1.60588] ((2 . 4) (4 . 7) (6 . 8) (9 . 11) (10 . 13)) 8.924 {0/5:10} B:0 2.25091 [ 2.00130] ((2 . 2) (6 . 7) (10 . 11) (12 . 13)) 7.224 {0/3:6} B:0 2.25127 [ 2.00181] ((4 . 2) (6 . 4) (9 . 5) (12 . 11)) 7.854 {0/2:6} B:0 2.25389 [ 2.00554] ((4 . 2) (6 . 4) (9 . 7) (12 . 11)) 10.391 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.6665 [and 1/min{score2}: 0.7497] [4985, 4141]: Comparing 1pdk_B and 1n67_A, based on their crossing files. There are 12 (3 H + 9 S) secondary structure elements in 1pdk_B, of which 9 satisfy the size requirements. There are 31 (5 H + 26 S) secondary structure elements in 1n67_A, of which 11 satisfy the size requirements. 1.80218 [ 2.20120] ((4 . 2) (6 . 4) (9 . 5) (10 . 9) (12 . 11)) 7.605 {0/2:10} B:0 1.80351 [ 2.20192] ((2 . 2) (4 . 4) (6 . 5) (9 . 7) (10 . 11)) 8.563 {0/4:10} B:0 1.80730 [ 2.20401] ((2 . 2) (4 . 4) (9 . 7) (10 . 11) (12 . 12)) 10.295 {0/3:10} B:0 2.25266 [ 2.75146] ((3 . 10) (4 . 11) (6 . 12) (9 . 13)) 9.447 {0/2:6} B:0 2.25456 [ 2.75250] ((6 . 4) (9 . 7) (10 . 11) (12 . 12)) 10.811 {0/1:6} B:0 SIMILARITY (1/min{score1}): 0.6636 [and 1/min{score2}: 0.5443] [4985, 4142]: Comparing 1pdk_B and 1n67_A, based on their crossing files. There are 12 (3 H + 9 S) secondary structure elements in 1pdk_B, of which 9 satisfy the size requirements. There are 31 (5 H + 26 S) secondary structure elements in 1n67_A, of which 13 satisfy the size requirements. 1.80432 [ 2.60144] ((2 . 15) (4 . 17) (6 . 18) (9 . 20) (12 . 29)) 9.021 {0/4:10} B:0 1.81104 [ 2.60369] ((2 . 17) (4 . 18) (6 . 20) (10 . 29) (12 . 30)) 11.425 {0/2:10} B:0 2.25058 [ 3.25019] ((4 . 15) (6 . 17) (9 . 18) (12 . 28)) 6.451 {0/1:6} B:0 2.25111 [ 3.25037] ((2 . 28) (4 . 29) (6 . 30) (9 . 31)) 7.582 {0/2:6} B:0 2.25115 [ 3.25038] ((2 . 15) (4 . 18) (10 . 28) (12 . 29)) 7.664 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.6658 [and 1/min{score2}: 0.4614] [4985, 4187]: Comparing 1pdk_B and 1nbc_A, based on their crossing files. There are 12 (3 H + 9 S) secondary structure elements in 1pdk_B, of which 9 satisfy the size requirements. There are 18 (2 H + 16 S) secondary structure elements in 1nbc_A, of which 11 satisfy the size requirements. 1.80106 [ 2.20058] ((2 . 1) (4 . 3) (6 . 6) (10 . 14) (12 . 17)) 6.339 {0/4:10} B:0 2.25078 [ 2.75043] ((2 . 7) (4 . 11) (6 . 12) (9 . 14)) 6.954 {0/3:6} B:0 2.25147 [ 2.75080] ((2 . 3) (4 . 6) (6 . 7) (9 . 11)) 8.138 {0/4:6} B:0 2.25196 [ 2.75108] ((2 . 11) (4 . 12) (6 . 14) (9 . 17)) 8.752 {0/4:6} B:0 2.25196 [ 2.75108] ((2 . 1) (4 . 3) (6 . 6) (9 . 8)) 8.752 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.6650 [and 1/min{score2}: 0.5448] [4985, 4232]: Comparing 1pdk_B and 1nfi_A, based on their crossing files. There are 12 (3 H + 9 S) secondary structure elements in 1pdk_B, of which 9 satisfy the size requirements. There are 23 (4 H + 19 S) secondary structure elements in 1nfi_A, of which 8 satisfy the size requirements. 1.80135 [ 1.60192] ((4 . 2) (6 . 3) (9 . 4) (10 . 6) (12 . 8)) 6.743 {0/4:10} B:0 1.80189 [ 1.60270] ((2 . 1) (4 . 2) (6 . 3) (9 . 5) (12 . 8)) 7.339 {0/5:10} B:0 2.25106 [ 2.00151] ((2 . 2) (4 . 4) (6 . 5) (10 . 8)) 7.500 {0/3:6} B:0 2.25137 [ 2.00195] ((2 . 1) (9 . 4) (10 . 6) (12 . 8)) 7.996 {0/4:6} B:0 2.25167 [ 2.00237] ((2 . 3) (4 . 5) (6 . 6) (10 . 8)) 8.404 {0/1:6} B:0 SIMILARITY (1/min{score1}): 0.5551 [and 1/min{score2}: 0.6243] [4985, 4570]: Comparing 1pdk_B and 1o9w_A, based on their crossing files. There are 12 (3 H + 9 S) secondary structure elements in 1pdk_B, of which 9 satisfy the size requirements. There are 18 (1 H + 17 S) secondary structure elements in 1o9w_A, of which 15 satisfy the size requirements. 1.50032 [ 2.50007] ((2 . 2) (4 . 5) (6 . 7) (9 . 10) (10 . 14) (12 . 16)) 4.104 {0/4:15} B:0 1.80277 [ 3.00060] ((4 . 2) (6 . 5) (9 . 7) (10 . 10) (12 . 14)) 8.069 {0/2:10} B:0 1.81309 [ 3.00285] ((2 . 2) (6 . 7) (9 . 10) (10 . 14) (12 . 15)) 11.925 {0/5:10} B:0 2.25074 [ 3.75016] ((2 . 3) (9 . 10) (10 . 14) (12 . 16)) 6.855 {0/3:6} B:0 2.25080 [ 3.75017] ((2 . 9) (4 . 10) (9 . 15) (10 . 18)) 6.996 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.6665 [and 1/min{score2}: 0.4000] [4985, 4910]: Comparing 1pdk_B and 1p5v_B, based on their crossing files. There are 12 (3 H + 9 S) secondary structure elements in 1pdk_B, of which 9 satisfy the size requirements. There are 11 (1 H + 10 S) secondary structure elements in 1p5v_B, of which 7 satisfy the size requirements. 1.50214 [ 1.17119] ((2 . 1) (4 . 3) (6 . 5) (9 . 7) (10 . 10) (12 . 11)) 6.598 {0/7:15} B:0 1.50817 [ 1.18379] ((2 . 1) (4 . 3) (6 . 6) (9 . 7) (10 . 10) (12 . 11)) 9.239 {0/7:15} B:0 1.80213 [ 1.40451] ((2 . 3) (4 . 6) (6 . 7) (9 . 10) (10 . 11)) 7.555 {0/3:10} B:0 1.80525 [ 1.41108] ((4 . 1) (6 . 3) (9 . 5) (10 . 7) (12 . 10)) 9.477 {0/3:10} B:0 1.81310 [ 1.42734] ((4 . 1) (6 . 3) (9 . 6) (10 . 7) (12 . 10)) 11.929 {0/3:10} B:0 SIMILARITY (1/min{score1}): 0.6660 [and 1/min{score2}: 0.8549] [4985, 4922]: Comparing 1pdk_B and 1p7h_L, based on their crossing files. There are 12 (3 H + 9 S) secondary structure elements in 1pdk_B, of which 9 satisfy the size requirements. There are 22 (2 H + 20 S) secondary structure elements in 1p7h_L, of which 11 satisfy the size requirements. 1.80137 [ 2.20075] ((2 . 2) (4 . 3) (6 . 4) (10 . 8) (12 . 11)) 6.767 {0/4:10} B:0 1.80221 [ 2.20121] ((2 . 4) (4 . 6) (6 . 8) (9 . 11) (10 . 12)) 7.631 {0/4:10} B:0 1.80281 [ 2.20154] ((2 . 2) (4 . 3) (6 . 4) (10 . 9) (12 . 11)) 8.102 {0/4:10} B:0 1.80383 [ 2.20210] ((4 . 3) (6 . 4) (9 . 6) (10 . 9) (12 . 11)) 8.756 {0/4:10} B:0 1.80578 [ 2.20317] ((2 . 3) (4 . 4) (9 . 8) (10 . 11) (12 . 12)) 9.706 {0/2:10} B:0 SIMILARITY (1/min{score1}): 0.5551 [and 1/min{score2}: 0.4544] [4985, 4976]: Comparing 1pdk_B and 1pd1_A, based on their crossing files. There are 12 (3 H + 9 S) secondary structure elements in 1pdk_B, of which 9 satisfy the size requirements. There are 58 (29 H + 29 S) secondary structure elements in 1pd1_A, of which 12 satisfy the size requirements. 1.50056 [ 2.00024] ((2 . 5) (4 . 8) (6 . 34) (9 . 35) (10 . 37) (12 . 38)) 4.716 {0/7:15} B:0 1.80028 [ 2.40012] ((4 . 8) (6 . 34) (9 . 35) (10 . 37) (12 . 38)) 4.559 {0/4:10} B:0 2.25249 [ 3.00105] ((2 . 35) (4 . 37) (6 . 38) (9 . 39)) 9.294 {0/4:6} B:0 2.25269 [ 3.00113] ((2 . 34) (4 . 35) (6 . 37) (9 . 38)) 9.468 {0/2:6} B:0 2.25472 [ 3.00199] ((4 . 35) (6 . 36) (9 . 38) (10 . 39)) 10.903 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.6664 [and 1/min{score2}: 0.4999] [4985, 4985]: Comparing 1pdk_B and 1pdk_B, based on their crossing files. There are 12 (3 H + 9 S) secondary structure elements in 1pdk_B, of which 9 satisfy the size requirements. There are 12 (3 H + 9 S) secondary structure elements in 1pdk_B, of which 9 satisfy the size requirements. 1.00000 [ 1.00000] ((2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (9 . 9) (10 . 10) (11 . 11) (12 . 12)) 0.000 {0/25:36} B:0 3.36766 [ 3.36766] ((4 . 2) (5 . 3) (6 . 4) (9 . 6) (10 . 9) (12 . 10)) 9.028 {2/6:15} B:0 3.36766 [ 3.36766] ((2 . 4) (3 . 5) (4 . 6) (6 . 9) (9 . 10) (10 . 12)) 9.028 {2/6:15} B:0 1.54906 [ 1.54906] ((3 . 3) (4 . 6) (5 . 5) (10 . 10) (11 . 11) (12 . 12)) 5.342 {1/11:15} B:1 3.34420 [ 3.34420] ((2 . 4) (3 . 5) (4 . 2) (5 . 3) (6 . 9) (9 . 6) (10 . 12) (12 . 10)) 5.727 {6/18:28} B:3 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [4985, 5278]: Comparing 1pdk_B and 1qba, based on their crossing files. There are 12 (3 H + 9 S) secondary structure elements in 1pdk_B, of which 9 satisfy the size requirements. There are 70 (33 H + 37 S) secondary structure elements in 1qba, of which 11 satisfy the size requirements. 2.25026 [ 2.75014] ((2 . 2) (4 . 5) (6 . 6) (10 . 10)) 5.302 {0/3:6} B:0 2.25120 [ 2.75066] ((2 . 2) (4 . 5) (6 . 6) (9 . 9)) 7.744 {0/4:6} B:0 2.25170 [ 2.75093] ((2 . 6) (4 . 9) (6 . 10) (11 . 16)) 8.437 {0/3:6} B:0 2.96399 [ 3.08100] ((4 . 2) (5 . 3) (9 . 6) (10 . 9) (12 . 10)) 7.320 {2/7:10} B:0 3.49470 [ 3.66649] ((2 . 7) (4 . 9) (6 . 10) (11 . 16)) 8.243 {1/3:6} B:0 SIMILARITY (1/min{score1}): 0.4444 [and 1/min{score2}: 0.3636] [4985, 5520]: Comparing 1pdk_B and 1r17_A, based on their crossing files. There are 12 (3 H + 9 S) secondary structure elements in 1pdk_B, of which 9 satisfy the size requirements. There are 30 (5 H + 25 S) secondary structure elements in 1r17_A, of which 12 satisfy the size requirements. 1.80564 [ 2.40239] ((4 . 5) (6 . 6) (9 . 8) (10 . 12) (12 . 14)) 9.648 {0/2:10} B:0 2.25039 [ 3.00016] ((2 . 3) (4 . 5) (6 . 6) (10 . 12)) 5.826 {0/1:6} B:0 2.25057 [ 3.00024] ((2 . 3) (4 . 5) (6 . 6) (12 . 15)) 6.410 {0/1:6} B:0 2.25104 [ 3.00044] ((2 . 2) (6 . 6) (9 . 8) (10 . 12)) 7.460 {0/3:6} B:0 2.25380 [ 3.00160] ((2 . 2) (9 . 8) (10 . 12) (12 . 14)) 10.325 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.5538 [and 1/min{score2}: 0.4163] [4985, 5521]: Comparing 1pdk_B and 1r17_A, based on their crossing files. There are 12 (3 H + 9 S) secondary structure elements in 1pdk_B, of which 9 satisfy the size requirements. There are 30 (5 H + 25 S) secondary structure elements in 1r17_A, of which 11 satisfy the size requirements. 1.80202 [ 2.20111] ((2 . 17) (4 . 18) (6 . 19) (9 . 20) (12 . 28)) 7.459 {0/3:10} B:0 1.80995 [ 2.20548] ((2 . 18) (4 . 19) (6 . 20) (10 . 28) (12 . 29)) 11.130 {0/1:10} B:0 1.81359 [ 2.20749] ((2 . 18) (4 . 19) (6 . 20) (9 . 24) (12 . 29)) 12.039 {0/4:10} B:0 2.25041 [ 2.75022] ((4 . 17) (6 . 18) (9 . 19) (12 . 26)) 5.909 {0/1:6} B:0 2.25364 [ 2.75200] ((2 . 19) (4 . 20) (6 . 24) (10 . 29)) 10.216 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.5549 [and 1/min{score2}: 0.4543] [4985, 6068]: Comparing 1pdk_B and 1uol_A, based on their crossing files. There are 12 (3 H + 9 S) secondary structure elements in 1pdk_B, of which 9 satisfy the size requirements. There are 13 (2 H + 11 S) secondary structure elements in 1uol_A, of which 13 satisfy the size requirements. 1.80043 [ 2.60014] ((4 . 4) (6 . 5) (9 . 7) (10 . 10) (12 . 11)) 5.075 {0/4:10} B:0 2.25069 [ 3.25023] ((4 . 9) (6 . 10) (9 . 11) (10 . 12)) 6.732 {0/1:6} B:0 2.25135 [ 3.25045] ((2 . 9) (4 . 10) (6 . 11) (9 . 12)) 7.969 {0/4:6} B:0 2.25148 [ 3.25049] ((2 . 4) (4 . 5) (6 . 7) (12 . 12)) 8.160 {0/1:6} B:0 2.25159 [ 3.25053] ((2 . 5) (4 . 7) (10 . 12) (11 . 13)) 8.304 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.7747 [and 1/min{score2}: 0.5380] [4985, 6119]: Comparing 1pdk_B and 1uur_A, based on their crossing files. There are 12 (3 H + 9 S) secondary structure elements in 1pdk_B, of which 9 satisfy the size requirements. There are 31 (12 H + 19 S) secondary structure elements in 1uur_A, of which 15 satisfy the size requirements. 2.25023 [ 3.75005] ((4 . 6) (6 . 7) (10 . 11) (12 . 13)) 5.132 {0/1:6} B:0 2.25529 [ 3.75115] ((4 . 8) (6 . 13) (10 . 14) (11 . 18)) 11.223 {0/3:6} B:0 2.83913 [ 3.92403] ((4 . 11) (6 . 13) (9 . 14) (11 . 18)) 11.670 {1/4:6} B:0 3.49543 [ 4.23412] ((4 . 4) (9 . 7) (10 . 11) (12 . 13)) 10.633 {1/3:6} B:0 5.05126 [ 5.35636] ((4 . 13) (9 . 17) (10 . 20) (11 . 19)) 12.708 {1/2:6} B:1 SIMILARITY (1/min{score1}): 0.4444 [and 1/min{score2}: 0.2667] -------------------------------------------------------------------------------------------------------------------------