------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [5300, 203]: Comparing 1qe0_A and 1ati_A, based on their crossing files. There are 33 (17 H + 16 S) secondary structure elements in 1qe0_A, of which 9 satisfy the size requirements. There are 41 (18 H + 23 S) secondary structure elements in 1ati_A, of which 9 satisfy the size requirements. 1.12506 [ 1.12506] ((25 . 33) (26 . 34) (27 . 35) (28 . 36) (29 . 37) (31 . 39) (32 . 40) (33 . 41)) 2.137 {0/14:28} B:0 1.16199 [ 1.16199] ((25 . 33) (26 . 34) (27 . 35) (28 . 36) (29 . 37) (30 . 38) (31 . 39) (32 . 40) (33 . 41)) 2.285 {2/21:36} B:0 2.25011 [ 2.25011] ((25 . 33) (28 . 34) (29 . 35) (30 . 36)) 4.289 {0/0:6} B:0 2.25033 [ 2.25033] ((27 . 33) (28 . 34) (29 . 35) (30 . 36)) 5.590 {0/0:6} B:0 2.25044 [ 2.25044] ((27 . 33) (28 . 34) (31 . 35) (33 . 36)) 6.018 {0/0:6} B:0 SIMILARITY (1/min{score1}): 0.8888 [and 1/min{score2}: 0.8888] [5300, 665]: Comparing 1qe0_A and 1crz_A, based on their crossing files. There are 33 (17 H + 16 S) secondary structure elements in 1qe0_A, of which 9 satisfy the size requirements. There are 34 (4 H + 30 S) secondary structure elements in 1crz_A, of which 8 satisfy the size requirements. 1.12768 [ 1.00381] ((25 . 1) (26 . 3) (27 . 4) (28 . 6) (29 . 7) (31 . 8) (32 . 9) (33 . 10)) 5.631 {0/12:28} B:0 1.28692 [ 1.14457] ((25 . 1) (26 . 3) (27 . 4) (28 . 6) (31 . 8) (32 . 9) (33 . 10)) 5.093 {0/10:21} B:0 1.28736 [ 1.14520] ((25 . 1) (26 . 3) (27 . 4) (29 . 7) (31 . 8) (32 . 9) (33 . 10)) 5.504 {0/10:21} B:0 2.25029 [ 2.00041] ((27 . 1) (28 . 3) (29 . 4) (33 . 6)) 5.412 {0/2:6} B:0 2.25425 [ 2.00604] ((26 . 6) (27 . 7) (29 . 9) (33 . 10)) 10.619 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.8868 [and 1/min{score2}: 0.9962] [5300, 1129]: Comparing 1qe0_A and 1eex_B, based on their crossing files. There are 33 (17 H + 16 S) secondary structure elements in 1qe0_A, of which 9 satisfy the size requirements. There are 12 (5 H + 7 S) secondary structure elements in 1eex_B, of which 11 satisfy the size requirements. 1.12568 [ 1.37537] ((25 . 2) (26 . 3) (27 . 4) (28 . 5) (29 . 6) (31 . 7) (32 . 8) (33 . 10)) 3.993 {0/10:28} B:0 2.25130 [ 2.75071] ((25 . 2) (28 . 3) (29 . 4) (32 . 6)) 7.894 {0/1:6} B:0 2.25134 [ 2.75073] ((25 . 6) (27 . 8) (28 . 10) (33 . 11)) 7.956 {0/1:6} B:0 2.25225 [ 2.75124] ((25 . 1) (28 . 3) (29 . 4) (32 . 6)) 9.060 {0/2:6} B:0 2.25250 [ 2.75137] ((25 . 4) (26 . 5) (27 . 6) (33 . 10)) 9.303 {0/1:6} B:0 SIMILARITY (1/min{score1}): 0.8884 [and 1/min{score2}: 0.7271] [5300, 1296]: Comparing 1qe0_A and 1ex2_A, based on their crossing files. There are 33 (17 H + 16 S) secondary structure elements in 1qe0_A, of which 9 satisfy the size requirements. There are 15 (8 H + 7 S) secondary structure elements in 1ex2_A, of which 13 satisfy the size requirements. 2.25142 [ 3.25047] ((27 . 6) (28 . 7) (29 . 8) (31 . 9)) 8.068 {0/3:6} B:0 3.49757 [ 3.91774] ((27 . 9) (28 . 10) (30 . 14) (33 . 15)) 13.842 {1/3:6} B:0 5.05071 [ 5.20978] ((26 . 4) (27 . 6) (29 . 8) (31 . 9)) 9.277 {2/4:6} B:0 4.04068 [ 4.16793] ((25 . 5) (27 . 6) (29 . 8) (30 . 15) (31 . 9)) 8.383 {2/5:10} B:1 SIMILARITY (1/min{score1}): 0.4442 [and 1/min{score2}: 0.3076] [5300, 1734]: Comparing 1qe0_A and 1g5h_A, based on their crossing files. There are 33 (17 H + 16 S) secondary structure elements in 1qe0_A, of which 9 satisfy the size requirements. There are 37 (17 H + 20 S) secondary structure elements in 1g5h_A, of which 9 satisfy the size requirements. 1.00296 [ 1.00296] ((25 . 28) (26 . 29) (27 . 30) (28 . 32) (29 . 33) (30 . 34) (31 . 35) (32 . 36) (33 . 37)) 5.285 {0/22:36} B:0 1.12502 [ 1.12502] ((25 . 28) (26 . 29) (27 . 30) (28 . 32) (29 . 33) (30 . 34) (31 . 35) (32 . 36)) 1.639 {0/18:28} B:0 2.25016 [ 2.25016] ((27 . 28) (28 . 29) (29 . 30) (33 . 32)) 4.661 {0/0:6} B:0 2.25216 [ 2.25216] ((27 . 28) (28 . 29) (29 . 30) (32 . 33)) 8.966 {0/2:6} B:0 2.25249 [ 2.25249] ((25 . 30) (26 . 32) (27 . 33) (29 . 36)) 9.290 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.9970 [and 1/min{score2}: 0.9970] [5300, 2082]: Comparing 1qe0_A and 1h4v_B, based on their crossing files. There are 33 (17 H + 16 S) secondary structure elements in 1qe0_A, of which 9 satisfy the size requirements. There are 33 (17 H + 16 S) secondary structure elements in 1h4v_B, of which 9 satisfy the size requirements. 1.01056 [ 1.01056] ((25 . 25) (26 . 26) (27 . 27) (28 . 28) (29 . 29) (30 . 30) (31 . 31) (32 . 32) (33 . 33)) 1.927 {1/22:36} B:0 2.25011 [ 2.25011] ((25 . 25) (26 . 26) (27 . 29) (33 . 33)) 4.232 {0/1:6} B:0 2.25178 [ 2.25178] ((25 . 27) (26 . 28) (27 . 29) (29 . 32)) 8.545 {0/2:6} B:0 2.25194 [ 2.25194] ((27 . 25) (28 . 26) (29 . 27) (32 . 29)) 8.726 {0/2:6} B:0 10.00641 [10.00641] ((27 . 25) (28 . 26) (31 . 27) (33 . 28)) 6.471 {1/1:6} B:0 SIMILARITY (1/min{score1}): 0.9896 [and 1/min{score2}: 0.9896] [5300, 2167]: Comparing 1qe0_A and 1hc7_A, based on their crossing files. There are 33 (17 H + 16 S) secondary structure elements in 1qe0_A, of which 9 satisfy the size requirements. There are 37 (14 H + 23 S) secondary structure elements in 1hc7_A, of which 9 satisfy the size requirements. 1.14384 [ 1.14384] ((25 . 23) (26 . 24) (27 . 25) (28 . 26) (29 . 27) (30 . 28) (31 . 29) (32 . 30) (33 . 31)) 6.593 {2/22:36} B:0 1.32972 [ 1.32972] ((25 . 23) (26 . 24) (27 . 25) (28 . 26) (29 . 27) (30 . 28) (31 . 29) (32 . 30)) 2.321 {2/18:28} B:0 1.47933 [ 1.47933] ((25 . 23) (26 . 24) (27 . 25) (28 . 26) (29 . 27) (30 . 28) (31 . 29) (33 . 31)) 6.481 {2/15:28} B:0 2.25242 [ 2.25242] ((25 . 25) (26 . 26) (27 . 27) (33 . 31)) 9.228 {0/2:6} B:0 5.00546 [ 5.00546] ((25 . 23) (26 . 24) (27 . 25) (28 . 26) (29 . 27) (30 . 28) (32 . 29)) 3.272 {6/12:21} B:0 SIMILARITY (1/min{score1}): 0.8742 [and 1/min{score2}: 0.8742] [5300, 2290]: Comparing 1qe0_A and 1htt_A, based on their crossing files. There are 33 (17 H + 16 S) secondary structure elements in 1qe0_A, of which 9 satisfy the size requirements. There are 30 (14 H + 16 S) secondary structure elements in 1htt_A, of which 9 satisfy the size requirements. 1.01061 [ 1.01061] ((25 . 22) (26 . 23) (27 . 24) (28 . 25) (29 . 26) (30 . 27) (31 . 28) (32 . 29) (33 . 30)) 2.285 {1/22:36} B:0 2.25018 [ 2.25018] ((25 . 22) (26 . 25) (27 . 26) (28 . 27)) 4.845 {0/0:6} B:0 2.25101 [ 2.25101] ((25 . 26) (26 . 27) (27 . 29) (28 . 30)) 7.408 {0/0:6} B:0 2.25194 [ 2.25194] ((25 . 24) (26 . 25) (27 . 26) (29 . 29)) 8.727 {0/2:6} B:0 10.00641 [10.00641] ((27 . 22) (28 . 23) (31 . 24) (33 . 25)) 6.082 {1/1:6} B:0 SIMILARITY (1/min{score1}): 0.9895 [and 1/min{score2}: 0.9895] [5300, 3201]: Comparing 1qe0_A and 1k7k_A, based on their crossing files. There are 33 (17 H + 16 S) secondary structure elements in 1qe0_A, of which 9 satisfy the size requirements. There are 18 (11 H + 7 S) secondary structure elements in 1k7k_A, of which 12 satisfy the size requirements. 1.13273 [ 1.50328] ((25 . 1) (26 . 2) (27 . 3) (28 . 4) (29 . 5) (31 . 10) (32 . 11) (33 . 18)) 7.347 {0/11:28} B:0 1.29012 [ 1.71615] ((25 . 1) (26 . 2) (27 . 3) (28 . 4) (29 . 5) (31 . 10) (33 . 18)) 7.049 {0/7:21} B:0 2.25051 [ 3.00022] ((25 . 1) (26 . 2) (27 . 3) (32 . 5)) 6.253 {0/3:6} B:0 2.25109 [ 3.00046] ((27 . 1) (28 . 2) (29 . 3) (33 . 4)) 7.560 {0/2:6} B:0 2.54092 [ 3.13873] ((27 . 10) (30 . 12) (32 . 13) (33 . 17)) 7.722 {1/5:6} B:0 SIMILARITY (1/min{score1}): 0.8828 [and 1/min{score2}: 0.6652] [5300, 4194]: Comparing 1qe0_A and 1nbw_B, based on their crossing files. There are 33 (17 H + 16 S) secondary structure elements in 1qe0_A, of which 9 satisfy the size requirements. There are 8 (3 H + 5 S) secondary structure elements in 1nbw_B, of which 8 satisfy the size requirements. 1.12594 [ 1.00134] ((25 . 1) (26 . 2) (27 . 3) (28 . 4) (29 . 5) (31 . 6) (32 . 7) (33 . 8)) 4.330 {0/12:28} B:0 1.28613 [ 1.14345] ((25 . 1) (26 . 2) (27 . 3) (29 . 5) (31 . 6) (32 . 7) (33 . 8)) 3.907 {0/10:21} B:0 2.25018 [ 2.00026] ((25 . 1) (26 . 2) (31 . 5) (33 . 8)) 4.840 {0/1:6} B:0 2.25024 [ 2.00034] ((25 . 1) (26 . 2) (29 . 3) (33 . 8)) 5.165 {0/2:6} B:0 2.25044 [ 2.00062] ((27 . 1) (28 . 2) (29 . 3) (33 . 4)) 6.004 {0/1:6} B:0 SIMILARITY (1/min{score1}): 0.8881 [and 1/min{score2}: 0.9987] [5300, 4275]: Comparing 1qe0_A and 1nj8_A, based on their crossing files. There are 33 (17 H + 16 S) secondary structure elements in 1qe0_A, of which 9 satisfy the size requirements. There are 36 (15 H + 21 S) secondary structure elements in 1nj8_A, of which 9 satisfy the size requirements. 1.14340 [ 1.14340] ((25 . 21) (26 . 22) (27 . 23) (28 . 24) (29 . 25) (30 . 26) (31 . 27) (32 . 28) (33 . 29)) 6.436 {2/22:36} B:0 1.32969 [ 1.32969] ((25 . 21) (26 . 22) (27 . 23) (28 . 24) (29 . 25) (30 . 26) (31 . 27) (32 . 28)) 1.690 {2/18:28} B:0 2.25224 [ 2.25224] ((27 . 21) (28 . 22) (29 . 23) (32 . 25)) 9.050 {0/2:6} B:0 2.25251 [ 2.25251] ((25 . 23) (26 . 24) (27 . 25) (33 . 29)) 9.313 {0/2:6} B:0 1.80013 [ 1.80013] ((25 . 21) (26 . 24) (27 . 25) (28 . 22) (29 . 23)) 3.763 {0/1:10} B:1 SIMILARITY (1/min{score1}): 0.8746 [and 1/min{score2}: 0.8746] [5300, 5300]: Comparing 1qe0_A and 1qe0_A, based on their crossing files. There are 33 (17 H + 16 S) secondary structure elements in 1qe0_A, of which 9 satisfy the size requirements. There are 33 (17 H + 16 S) secondary structure elements in 1qe0_A, of which 9 satisfy the size requirements. 1.00000 [ 1.00000] ((25 . 25) (26 . 26) (27 . 27) (28 . 28) (29 . 29) (30 . 30) (31 . 31) (32 . 32) (33 . 33)) 0.000 {0/23:36} B:0 2.25050 [ 2.25050] ((25 . 27) (26 . 28) (27 . 31) (28 . 33)) 6.228 {0/0:6} B:0 2.25050 [ 2.25050] ((27 . 25) (28 . 26) (31 . 27) (33 . 28)) 6.228 {0/0:6} B:0 2.25197 [ 2.25197] ((27 . 25) (28 . 26) (29 . 27) (32 . 29)) 8.757 {0/2:6} B:0 2.25197 [ 2.25197] ((25 . 27) (26 . 28) (27 . 29) (29 . 32)) 8.757 {0/2:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [5300, 5307]: Comparing 1qe0_A and 1qf6_A, based on their crossing files. There are 33 (17 H + 16 S) secondary structure elements in 1qe0_A, of which 9 satisfy the size requirements. There are 59 (24 H + 35 S) secondary structure elements in 1qf6_A, of which 9 satisfy the size requirements. 1.15834 [ 1.15834] ((25 . 51) (26 . 52) (27 . 53) (28 . 54) (29 . 55) (31 . 57) (32 . 58) (33 . 59)) 2.838 {1/15:28} B:0 1.93998 [ 1.93998] ((25 . 51) (26 . 52) (27 . 53) (28 . 54) (29 . 55) (30 . 56) (31 . 57) (32 . 58) (33 . 59)) 2.813 {4/21:36} B:0 2.25039 [ 2.25039] ((27 . 51) (28 . 52) (31 . 53) (33 . 54)) 5.853 {0/0:6} B:0 2.25187 [ 2.25187] ((27 . 51) (28 . 52) (29 . 53) (32 . 55)) 8.643 {0/2:6} B:0 5.05051 [ 5.05051] ((25 . 51) (26 . 52) (29 . 57) (33 . 59)) 5.254 {1/2:6} B:0 SIMILARITY (1/min{score1}): 0.8633 [and 1/min{score2}: 0.8633] [5300, 6192]: Comparing 1qe0_A and 1v7r_A, based on their crossing files. There are 33 (17 H + 16 S) secondary structure elements in 1qe0_A, of which 9 satisfy the size requirements. There are 16 (10 H + 6 S) secondary structure elements in 1v7r_A, of which 13 satisfy the size requirements. 1.28989 [ 1.85853] ((25 . 1) (26 . 2) (27 . 3) (29 . 5) (31 . 10) (32 . 11) (33 . 16)) 6.955 {0/10:21} B:0 2.25048 [ 3.25016] ((25 . 1) (26 . 2) (27 . 3) (32 . 5)) 6.143 {0/3:6} B:0 2.25052 [ 3.25017] ((25 . 1) (26 . 2) (27 . 3) (28 . 4)) 6.270 {0/0:6} B:0 2.25091 [ 3.25030] ((25 . 1) (26 . 2) (28 . 4) (29 . 5)) 7.223 {0/1:6} B:0 2.25119 [ 3.25039] ((27 . 1) (28 . 2) (29 . 3) (33 . 4)) 7.715 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.7753 [and 1/min{score2}: 0.5381] -------------------------------------------------------------------------------------------------------------------------