------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [829, 153]: Comparing 1dg6_A and 1aly, based on their crossing files. There are 13 (1 H + 12 S) secondary structure elements in 1dg6_A, of which 10 satisfy the size requirements. There are 12 (1 H + 11 S) secondary structure elements in 1aly, of which 9 satisfy the size requirements. 1.11113 [ 1.00003] ((1 . 1) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (13 . 12)) 1.711 {0/11:36} B:0 2.00195 [ 1.80267] ((7 . 6) (8 . 7) (9 . 8) (10 . 9) (13 . 10)) 7.999 {0/1:10} B:0 2.00284 [ 1.80389] ((6 . 7) (7 . 8) (8 . 9) (9 . 10) (10 . 12)) 8.791 {0/0:10} B:0 2.00495 [ 1.80678] ((5 . 4) (7 . 8) (8 . 9) (9 . 10) (10 . 12)) 10.104 {0/1:10} B:0 2.00584 [ 1.80800] ((4 . 1) (8 . 6) (9 . 7) (10 . 8) (13 . 9)) 10.533 {0/2:10} B:0 SIMILARITY (1/min{score1}): 0.9000 [and 1/min{score2}: 0.9999] [829, 517]: Comparing 1dg6_A and 1c3h_A, based on their crossing files. There are 13 (1 H + 12 S) secondary structure elements in 1dg6_A, of which 10 satisfy the size requirements. There are 10 (0 H + 10 S) secondary structure elements in 1c3h_A, of which 9 satisfy the size requirements. 1.11221 [ 1.00151] ((1 . 1) (3 . 2) (5 . 4) (6 . 5) (7 . 6) (8 . 7) (9 . 8) (10 . 9) (13 . 10)) 4.460 {0/5:36} B:0 1.25048 [ 1.12566] ((1 . 1) (5 . 4) (6 . 5) (7 . 6) (8 . 7) (9 . 8) (10 . 9) (13 . 10)) 3.965 {0/5:28} B:0 2.00004 [ 1.80006] ((1 . 1) (5 . 4) (6 . 5) (7 . 6) (13 . 10)) 3.075 {0/0:10} B:0 2.00042 [ 1.80058] ((4 . 1) (8 . 7) (9 . 8) (10 . 9) (13 . 10)) 5.462 {0/3:10} B:0 2.00525 [ 1.80718] ((1 . 5) (4 . 7) (5 . 8) (6 . 9) (7 . 10)) 10.253 {0/4:10} B:0 SIMILARITY (1/min{score1}): 0.8991 [and 1/min{score2}: 0.9985] [829, 829]: Comparing 1dg6_A and 1dg6_A, based on their crossing files. There are 13 (1 H + 12 S) secondary structure elements in 1dg6_A, of which 10 satisfy the size requirements. There are 13 (1 H + 12 S) secondary structure elements in 1dg6_A, of which 10 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (13 . 13)) 0.000 {0/17:45} B:0 2.00269 [ 2.00269] ((7 . 6) (8 . 7) (9 . 8) (10 . 9) (13 . 10)) 8.671 {0/0:10} B:0 2.00269 [ 2.00269] ((6 . 7) (7 . 8) (8 . 9) (9 . 10) (10 . 13)) 8.671 {0/0:10} B:0 2.00675 [ 2.00675] ((1 . 4) (6 . 8) (7 . 9) (8 . 10) (9 . 13)) 10.922 {0/2:10} B:0 2.00675 [ 2.00675] ((4 . 1) (8 . 6) (9 . 7) (10 . 8) (13 . 9)) 10.922 {0/2:10} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [829, 2565]: Comparing 1dg6_A and 1iqa_A, based on their crossing files. There are 13 (1 H + 12 S) secondary structure elements in 1dg6_A, of which 10 satisfy the size requirements. There are 14 (2 H + 12 S) secondary structure elements in 1iqa_A, of which 10 satisfy the size requirements. 1.00008 [ 1.00008] ((1 . 1) (3 . 4) (4 . 5) (5 . 6) (6 . 7) (7 . 9) (8 . 10) (9 . 11) (10 . 12) (13 . 14)) 2.129 {0/12:45} B:0 2.00409 [ 2.00409] ((6 . 9) (7 . 10) (8 . 11) (9 . 12) (10 . 14)) 9.633 {0/0:10} B:0 2.00434 [ 2.00434] ((7 . 7) (8 . 9) (9 . 10) (10 . 11) (13 . 12)) 9.776 {0/0:10} B:0 2.00465 [ 2.00465] ((5 . 7) (6 . 9) (7 . 10) (8 . 11) (9 . 12)) 9.948 {0/0:10} B:0 2.00729 [ 2.00729] ((4 . 1) (8 . 7) (9 . 9) (10 . 10) (13 . 11)) 11.135 {0/2:10} B:0 SIMILARITY (1/min{score1}): 0.9999 [and 1/min{score2}: 0.9999] [829, 3467]: Comparing 1dg6_A and 1kxg_A, based on their crossing files. There are 13 (1 H + 12 S) secondary structure elements in 1dg6_A, of which 10 satisfy the size requirements. There are 13 (0 H + 13 S) secondary structure elements in 1kxg_A, of which 12 satisfy the size requirements. 1.05990 [ 1.23623] ((1 . 1) (3 . 4) (4 . 5) (5 . 6) (6 . 7) (7 . 8) (8 . 9) (9 . 10) (10 . 11) (13 . 13)) 3.234 {1/14:45} B:0 1.15591 [ 1.36006] ((1 . 1) (4 . 5) (5 . 6) (6 . 7) (7 . 8) (8 . 9) (9 . 10) (10 . 11) (13 . 13)) 2.677 {1/14:36} B:0 1.42909 [ 1.71459] ((1 . 1) (5 . 4) (7 . 8) (8 . 9) (9 . 10) (10 . 11) (13 . 13)) 4.464 {0/5:21} B:0 2.00197 [ 2.40114] ((6 . 8) (7 . 9) (8 . 10) (9 . 11) (10 . 13)) 8.015 {0/0:10} B:0 2.00198 [ 2.40115] ((7 . 7) (8 . 8) (9 . 9) (10 . 10) (13 . 11)) 8.031 {0/0:10} B:0 SIMILARITY (1/min{score1}): 0.9952 [and 1/min{score2}: 0.8314] [829, 4556]: Comparing 1dg6_A and 1o91_A, based on their crossing files. There are 13 (1 H + 12 S) secondary structure elements in 1dg6_A, of which 10 satisfy the size requirements. There are 12 (1 H + 11 S) secondary structure elements in 1o91_A, of which 10 satisfy the size requirements. 1.11140 [ 1.11140] ((1 . 1) (3 . 2) (5 . 4) (6 . 5) (7 . 6) (8 . 7) (9 . 8) (10 . 9) (13 . 12)) 3.204 {0/4:36} B:0 1.66718 [ 1.66718] ((5 . 2) (7 . 6) (8 . 7) (9 . 8) (10 . 9) (13 . 12)) 4.986 {0/2:15} B:0 1.66735 [ 1.66735] ((4 . 1) (5 . 2) (7 . 6) (8 . 7) (9 . 8) (13 . 12)) 5.357 {0/3:15} B:0 2.00033 [ 2.00033] ((1 . 1) (3 . 2) (5 . 4) (6 . 5) (8 . 8)) 5.126 {0/0:10} B:0 2.00062 [ 2.00062] ((7 . 5) (8 . 7) (9 . 8) (10 . 9) (13 . 12)) 6.001 {0/1:10} B:0 SIMILARITY (1/min{score1}): 0.8998 [and 1/min{score2}: 0.8998] [829, 5035]: Comparing 1dg6_A and 1pk6_A, based on their crossing files. There are 13 (1 H + 12 S) secondary structure elements in 1dg6_A, of which 10 satisfy the size requirements. There are 13 (0 H + 13 S) secondary structure elements in 1pk6_A, of which 10 satisfy the size requirements. 1.11194 [ 1.11194] ((1 . 1) (3 . 3) (5 . 5) (6 . 6) (7 . 7) (8 . 9) (9 . 10) (10 . 11) (13 . 13)) 4.154 {0/4:36} B:0 1.25044 [ 1.25044] ((1 . 1) (5 . 5) (6 . 6) (7 . 7) (8 . 9) (9 . 10) (10 . 11) (13 . 13)) 3.873 {0/4:28} B:0 1.66754 [ 1.66754] ((4 . 1) (5 . 3) (7 . 7) (9 . 10) (10 . 11) (13 . 13)) 5.708 {0/3:15} B:0 1.66757 [ 1.66757] ((5 . 3) (7 . 7) (8 . 9) (9 . 10) (10 . 11) (13 . 13)) 5.757 {0/3:15} B:0 2.00111 [ 2.00111] ((1 . 1) (3 . 3) (5 . 5) (6 . 6) (9 . 11)) 6.943 {0/0:10} B:0 SIMILARITY (1/min{score1}): 0.8993 [and 1/min{score2}: 0.8993] [829, 5036]: Comparing 1dg6_A and 1pk6_C, based on their crossing files. There are 13 (1 H + 12 S) secondary structure elements in 1dg6_A, of which 10 satisfy the size requirements. There are 10 (0 H + 10 S) secondary structure elements in 1pk6_C, of which 9 satisfy the size requirements. 1.25017 [ 1.12524] ((1 . 1) (5 . 4) (6 . 5) (7 . 6) (8 . 7) (9 . 8) (10 . 9) (13 . 10)) 3.072 {0/7:28} B:0 2.00162 [ 1.80222] ((7 . 5) (8 . 6) (9 . 7) (10 . 8) (13 . 9)) 7.635 {0/1:10} B:0 2.00523 [ 1.80716] ((1 . 5) (4 . 7) (5 . 8) (6 . 9) (7 . 10)) 10.243 {0/3:10} B:0 2.50032 [ 2.25044] ((7 . 1) (9 . 5) (10 . 6) (13 . 7)) 6.023 {0/1:6} B:0 2.50037 [ 2.25051] ((5 . 7) (6 . 8) (7 . 9) (8 . 10)) 6.238 {0/1:6} B:0 SIMILARITY (1/min{score1}): 0.8936 [and 1/min{score2}: 0.9893] [829, 5649]: Comparing 1dg6_A and 1rj8_A, based on their crossing files. There are 13 (1 H + 12 S) secondary structure elements in 1dg6_A, of which 10 satisfy the size requirements. There are 14 (2 H + 12 S) secondary structure elements in 1rj8_A, of which 12 satisfy the size requirements. 1.00027 [ 1.20016] ((1 . 1) (3 . 5) (4 . 6) (5 . 7) (6 . 8) (7 . 9) (8 . 10) (9 . 11) (10 . 12) (13 . 14)) 2.898 {0/11:45} B:0 1.66669 [ 2.00001] ((1 . 1) (6 . 8) (7 . 9) (8 . 10) (9 . 11) (13 . 14)) 2.177 {0/4:15} B:0 1.66713 [ 2.00027] ((1 . 1) (5 . 5) (8 . 10) (9 . 11) (10 . 12) (13 . 14)) 4.864 {0/4:15} B:0 2.00267 [ 2.40155] ((4 . 5) (7 . 10) (8 . 11) (9 . 12) (10 . 14)) 8.655 {0/3:10} B:0 2.00366 [ 2.40212] ((3 . 1) (7 . 8) (8 . 9) (9 . 10) (10 . 11)) 9.369 {0/0:10} B:0 SIMILARITY (1/min{score1}): 0.9997 [and 1/min{score2}: 0.8332] [829, 5922]: Comparing 1dg6_A and 1tnr_A, based on their crossing files. There are 13 (1 H + 12 S) secondary structure elements in 1dg6_A, of which 10 satisfy the size requirements. There are 13 (2 H + 11 S) secondary structure elements in 1tnr_A, of which 11 satisfy the size requirements. 1.00005 [ 1.10003] ((1 . 1) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 8) (8 . 9) (9 . 10) (10 . 11) (13 . 13)) 1.865 {0/13:45} B:0 2.00260 [ 2.20196] ((6 . 8) (7 . 9) (8 . 10) (9 . 11) (10 . 13)) 8.600 {0/0:10} B:0 2.00275 [ 2.20207] ((7 . 6) (8 . 8) (9 . 9) (10 . 10) (13 . 11)) 8.717 {0/0:10} B:0 2.00327 [ 2.20246] ((3 . 1) (8 . 8) (9 . 9) (10 . 10) (13 . 11)) 9.106 {0/0:10} B:0 2.00377 [ 2.20284] ((3 . 1) (7 . 6) (8 . 8) (9 . 9) (10 . 10)) 9.438 {0/0:10} B:0 SIMILARITY (1/min{score1}): 0.9999 [and 1/min{score2}: 0.9091] [829, 6544]: Comparing 1dg6_A and 2tnf_A, based on their crossing files. There are 13 (1 H + 12 S) secondary structure elements in 1dg6_A, of which 10 satisfy the size requirements. There are 12 (1 H + 11 S) secondary structure elements in 2tnf_A, of which 10 satisfy the size requirements. 1.00001 [ 1.00001] ((1 . 1) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (13 . 12)) 1.353 {0/15:45} B:0 2.00257 [ 2.00257] ((7 . 6) (8 . 7) (9 . 8) (10 . 9) (13 . 10)) 8.572 {0/0:10} B:0 2.00279 [ 2.00279] ((6 . 7) (7 . 8) (8 . 9) (9 . 10) (10 . 12)) 8.748 {0/0:10} B:0 2.00611 [ 2.00611] ((4 . 5) (6 . 7) (7 . 8) (8 . 9) (9 . 10)) 10.653 {0/2:10} B:0 2.00653 [ 2.00653] ((1 . 4) (6 . 8) (7 . 9) (8 . 10) (9 . 12)) 10.829 {0/2:10} B:0 SIMILARITY (1/min{score1}): 0.9999 [and 1/min{score2}: 0.9999] -------------------------------------------------------------------------------------------------------------------------