------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [768, 768]: Comparing 1d7y_A and 1d7y_A, based on their crossing files. There are 41 (15 H + 26 S) secondary structure elements in 1d7y_A, of which 8 satisfy the size requirements. There are 41 (15 H + 26 S) secondary structure elements in 1d7y_A, of which 8 satisfy the size requirements. 1.00000 [ 1.00000] ((34 . 34) (35 . 35) (36 . 36) (37 . 37) (38 . 38) (39 . 39) (40 . 40) (41 . 41)) 0.000 {0/7:28} B:0 2.00023 [ 2.00023] ((38 . 37) (39 . 39) (40 . 40) (41 . 41)) 4.711 {0/1:6} B:0 10.00164 [10.00164] ((36 . 35) (37 . 36) (38 . 37) (40 . 39) (41 . 40)) 5.871 {1/1:10} B:0 10.00164 [10.00164] ((35 . 36) (36 . 37) (37 . 38) (39 . 40) (40 . 41)) 5.871 {1/1:10} B:0 1.60048 [ 1.60048] ((35 . 36) (36 . 35) (37 . 38) (38 . 37) (39 . 40)) 4.763 {0/0:10} B:2 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [768, 1480]: Comparing 1d7y_A and 1fec_A, based on their crossing files. There are 41 (15 H + 26 S) secondary structure elements in 1d7y_A, of which 8 satisfy the size requirements. There are 43 (17 H + 26 S) secondary structure elements in 1fec_A, of which 12 satisfy the size requirements. 1.14327 [ 1.71441] ((34 . 32) (35 . 33) (36 . 35) (37 . 37) (38 . 38) (39 . 39) (40 . 40)) 3.561 {0/2:21} B:0 1.33347 [ 2.00004] ((34 . 32) (35 . 33) (36 . 35) (37 . 37) (38 . 38) (39 . 39)) 3.061 {0/1:15} B:0 2.00018 [ 3.00005] ((34 . 32) (35 . 33) (36 . 35) (38 . 37)) 4.377 {0/1:6} B:0 2.00323 [ 3.00096] ((34 . 32) (35 . 33) (36 . 35) (40 . 39)) 9.078 {0/1:6} B:0 2.00670 [ 3.00199] ((34 . 35) (36 . 37) (37 . 38) (39 . 39)) 10.901 {0/0:6} B:0 SIMILARITY (1/min{score1}): 0.8747 [and 1/min{score2}: 0.5833] [768, 1585]: Comparing 1d7y_A and 1fo4_A, based on their crossing files. There are 41 (15 H + 26 S) secondary structure elements in 1d7y_A, of which 8 satisfy the size requirements. There are 96 (51 H + 45 S) secondary structure elements in 1fo4_A, of which 6 satisfy the size requirements. 2.00010 [ 1.50024] ((36 . 35) (37 . 36) (38 . 37) (41 . 39)) 3.808 {0/0:6} B:0 2.00062 [ 1.50147] ((36 . 35) (37 . 36) (38 . 37) (40 . 39)) 6.005 {0/0:6} B:0 2.00591 [ 1.51387] ((34 . 35) (36 . 36) (37 . 37) (39 . 39)) 10.562 {0/0:6} B:0 5.03172 [ 5.01011] ((36 . 35) (37 . 36) (38 . 37) (41 . 40)) 5.005 {1/2:6} B:0 10.00164 [10.00052] ((36 . 35) (37 . 36) (38 . 37) (39 . 39) (40 . 41)) 5.991 {1/1:10} B:0 SIMILARITY (1/min{score1}): 0.5000 [and 1/min{score2}: 0.6666] [768, 2114]: Comparing 1d7y_A and 1h6v_A, based on their crossing files. There are 41 (15 H + 26 S) secondary structure elements in 1d7y_A, of which 8 satisfy the size requirements. There are 40 (18 H + 22 S) secondary structure elements in 1h6v_A, of which 11 satisfy the size requirements. 1.14369 [ 1.57175] ((34 . 28) (35 . 29) (36 . 32) (37 . 34) (38 . 36) (39 . 37) (41 . 38)) 4.255 {0/2:21} B:0 1.33342 [ 1.83337] ((34 . 28) (35 . 29) (36 . 32) (37 . 34) (38 . 36) (39 . 37)) 2.739 {0/1:15} B:0 1.33350 [ 1.83340] ((35 . 29) (36 . 32) (37 . 34) (38 . 36) (39 . 37) (40 . 38)) 3.191 {0/0:15} B:0 1.60002 [ 2.20001] ((34 . 28) (35 . 29) (36 . 32) (37 . 34) (38 . 36)) 2.031 {0/1:10} B:0 2.00014 [ 2.75006] ((34 . 28) (35 . 29) (36 . 32) (38 . 34)) 4.164 {0/1:6} B:0 SIMILARITY (1/min{score1}): 0.8744 [and 1/min{score2}: 0.6362] [768, 3037]: Comparing 1d7y_A and 1jro_A, based on their crossing files. There are 41 (15 H + 26 S) secondary structure elements in 1d7y_A, of which 8 satisfy the size requirements. There are 39 (22 H + 17 S) secondary structure elements in 1jro_A, of which 6 satisfy the size requirements. 2.00268 [ 1.50631] ((35 . 32) (36 . 33) (37 . 34) (39 . 36)) 8.659 {0/0:6} B:0 2.00513 [ 1.51205] ((34 . 32) (36 . 33) (37 . 34) (39 . 36)) 10.193 {0/0:6} B:0 5.00636 [ 5.00205] ((36 . 32) (37 . 33) (38 . 34) (39 . 36) (40 . 38) (41 . 37)) 6.351 {2/4:15} B:1 10.00080 [10.00026] ((35 . 32) (37 . 34) (38 . 33) (39 . 38) (40 . 36) (41 . 37)) 6.364 {1/1:15} B:2 SIMILARITY (1/min{score1}): 0.4993 [and 1/min{score2}: 0.6639] [768, 3861]: Comparing 1d7y_A and 1m6i_A, based on their crossing files. There are 41 (15 H + 26 S) secondary structure elements in 1d7y_A, of which 8 satisfy the size requirements. There are 46 (17 H + 29 S) secondary structure elements in 1m6i_A, of which 8 satisfy the size requirements. 1.33335 [ 1.33335] ((34 . 38) (35 . 39) (36 . 40) (37 . 43) (38 . 44) (39 . 45)) 1.697 {0/2:15} B:0 2.00012 [ 2.00012] ((34 . 38) (35 . 39) (36 . 40) (41 . 45)) 3.971 {0/1:6} B:0 2.00389 [ 2.00389] ((34 . 40) (36 . 43) (37 . 44) (39 . 45)) 9.512 {0/0:6} B:0 2.00469 [ 2.00469] ((34 . 39) (35 . 40) (38 . 43) (40 . 45)) 9.965 {0/0:6} B:0 10.00401 [10.00401] ((34 . 39) (36 . 40) (38 . 43) (41 . 45)) 7.728 {1/1:6} B:0 SIMILARITY (1/min{score1}): 0.7500 [and 1/min{score2}: 0.7500] [768, 3991]: Comparing 1d7y_A and 1mo9_A, based on their crossing files. There are 41 (15 H + 26 S) secondary structure elements in 1d7y_A, of which 8 satisfy the size requirements. There are 42 (17 H + 25 S) secondary structure elements in 1mo9_A, of which 11 satisfy the size requirements. 1.60326 [ 2.20125] ((34 . 35) (37 . 38) (38 . 39) (39 . 40) (40 . 41)) 7.695 {0/0:10} B:0 2.00032 [ 2.75012] ((34 . 32) (35 . 33) (36 . 35) (41 . 40)) 5.082 {0/1:6} B:0 2.00251 [ 2.75097] ((34 . 33) (36 . 35) (38 . 38) (41 . 40)) 8.522 {0/0:6} B:0 2.00417 [ 2.75161] ((34 . 35) (36 . 38) (37 . 39) (39 . 40)) 9.679 {0/0:6} B:0 2.00547 [ 2.75211] ((34 . 33) (35 . 35) (38 . 38) (40 . 40)) 10.358 {0/0:6} B:0 SIMILARITY (1/min{score1}): 0.6237 [and 1/min{score2}: 0.4543] [768, 4140]: Comparing 1d7y_A and 1n62_C, based on their crossing files. There are 41 (15 H + 26 S) secondary structure elements in 1d7y_A, of which 8 satisfy the size requirements. There are 27 (13 H + 14 S) secondary structure elements in 1n62_C, of which 6 satisfy the size requirements. 2.00223 [ 1.50526] ((35 . 21) (36 . 22) (37 . 23) (39 . 25)) 8.272 {0/0:6} B:0 2.00550 [ 1.51293] ((34 . 21) (36 . 22) (37 . 23) (39 . 25)) 10.375 {0/0:6} B:0 5.01307 [ 5.00416] ((36 . 21) (37 . 22) (38 . 23) (39 . 25) (41 . 26)) 4.953 {1/2:10} B:0 7.50189 [ 7.50061] ((36 . 21) (37 . 22) (38 . 23) (39 . 25) (40 . 27) (41 . 26)) 6.310 {3/4:15} B:1 SIMILARITY (1/min{score1}): 0.4994 [and 1/min{score2}: 0.6643] [768, 4259]: Comparing 1d7y_A and 1nhp, based on their crossing files. There are 41 (15 H + 26 S) secondary structure elements in 1d7y_A, of which 8 satisfy the size requirements. There are 40 (15 H + 25 S) secondary structure elements in 1nhp, of which 9 satisfy the size requirements. 1.14300 [ 1.28581] ((34 . 32) (35 . 33) (36 . 35) (37 . 36) (38 . 37) (39 . 38) (40 . 39)) 2.712 {0/2:21} B:0 2.00009 [ 2.25007] ((34 . 32) (35 . 33) (36 . 35) (38 . 36)) 3.753 {0/1:6} B:0 2.00054 [ 2.25038] ((35 . 35) (38 . 37) (39 . 38) (40 . 39)) 5.807 {0/0:6} B:0 2.00142 [ 2.25100] ((36 . 33) (37 . 35) (38 . 36) (41 . 38)) 7.394 {0/0:6} B:0 2.00614 [ 2.25432] ((34 . 35) (36 . 36) (37 . 37) (39 . 38)) 10.665 {0/0:6} B:0 SIMILARITY (1/min{score1}): 0.8749 [and 1/min{score2}: 0.7777] [768, 4681]: Comparing 1d7y_A and 1ojt, based on their crossing files. There are 41 (15 H + 26 S) secondary structure elements in 1d7y_A, of which 8 satisfy the size requirements. There are 42 (17 H + 25 S) secondary structure elements in 1ojt, of which 10 satisfy the size requirements. 1.14320 [ 1.42875] ((34 . 32) (35 . 33) (36 . 35) (37 . 38) (38 . 39) (39 . 40) (40 . 41)) 3.410 {0/2:21} B:0 2.00010 [ 2.50005] ((34 . 32) (35 . 33) (36 . 35) (38 . 38)) 3.825 {0/1:6} B:0 2.00136 [ 2.50070] ((36 . 33) (37 . 35) (38 . 38) (41 . 40)) 7.311 {0/1:6} B:0 2.00237 [ 2.50121] ((34 . 33) (36 . 35) (38 . 38) (39 . 40)) 8.400 {0/0:6} B:0 2.00466 [ 2.50239] ((34 . 35) (36 . 38) (37 . 39) (39 . 40)) 9.953 {0/0:6} B:0 SIMILARITY (1/min{score1}): 0.8747 [and 1/min{score2}: 0.6999] [768, 5183]: Comparing 1d7y_A and 1q1r_A, based on their crossing files. There are 41 (15 H + 26 S) secondary structure elements in 1d7y_A, of which 8 satisfy the size requirements. There are 41 (15 H + 26 S) secondary structure elements in 1q1r_A, of which 8 satisfy the size requirements. 1.00008 [ 1.00008] ((34 . 34) (35 . 35) (36 . 36) (37 . 37) (38 . 38) (39 . 39) (40 . 40) (41 . 41)) 2.158 {0/5:28} B:0 1.60463 [ 1.60463] ((34 . 35) (35 . 36) (37 . 38) (39 . 40) (40 . 41)) 8.404 {0/0:10} B:0 2.00040 [ 2.00040] ((38 . 37) (39 . 39) (40 . 40) (41 . 41)) 5.392 {0/0:6} B:0 10.00164 [10.00164] ((36 . 35) (37 . 36) (38 . 37) (40 . 39) (41 . 40)) 5.961 {1/1:10} B:0 10.00165 [10.00165] ((35 . 36) (36 . 37) (37 . 38) (39 . 40) (40 . 41)) 6.652 {1/1:10} B:0 SIMILARITY (1/min{score1}): 0.9999 [and 1/min{score2}: 0.9999] [768, 6574]: Comparing 1d7y_A and 3grs, based on their crossing files. There are 41 (15 H + 26 S) secondary structure elements in 1d7y_A, of which 8 satisfy the size requirements. There are 41 (18 H + 23 S) secondary structure elements in 3grs, of which 10 satisfy the size requirements. 1.14354 [ 1.42892] ((34 . 31) (35 . 32) (36 . 35) (37 . 37) (38 . 38) (39 . 39) (41 . 41)) 4.039 {0/2:21} B:0 1.33344 [ 1.66672] ((34 . 31) (35 . 32) (36 . 35) (37 . 37) (38 . 38) (39 . 39)) 2.846 {0/1:15} B:0 1.60002 [ 2.00001] ((34 . 31) (35 . 32) (36 . 35) (37 . 37) (38 . 38)) 2.126 {0/1:10} B:0 2.00014 [ 2.50007] ((34 . 31) (35 . 32) (36 . 35) (38 . 37)) 4.152 {0/1:6} B:0 2.00138 [ 2.50071] ((36 . 32) (37 . 35) (38 . 37) (41 . 39)) 7.342 {0/0:6} B:0 SIMILARITY (1/min{score1}): 0.8745 [and 1/min{score2}: 0.6998] [768, 6578]: Comparing 1d7y_A and 3lad_A, based on their crossing files. There are 41 (15 H + 26 S) secondary structure elements in 1d7y_A, of which 8 satisfy the size requirements. There are 41 (16 H + 25 S) secondary structure elements in 3lad_A, of which 10 satisfy the size requirements. 2.00009 [ 2.50005] ((34 . 31) (35 . 32) (36 . 34) (38 . 37)) 3.743 {0/1:6} B:0 2.00168 [ 2.50086] ((36 . 32) (37 . 34) (38 . 37) (41 . 39)) 7.701 {0/1:6} B:0 2.00466 [ 2.50239] ((34 . 34) (36 . 37) (37 . 38) (39 . 39)) 9.954 {0/0:6} B:0 3.34480 [ 3.36111] ((34 . 31) (35 . 32) (36 . 34) (37 . 37) (38 . 38) (39 . 39) (40 . 40)) 3.317 {1/3:21} B:0 3.43708 [ 3.57104] ((36 . 34) (39 . 39) (40 . 40) (41 . 41)) 9.062 {1/3:6} B:0 SIMILARITY (1/min{score1}): 0.7452 [and 1/min{score2}: 0.5984] -------------------------------------------------------------------------------------------------------------------------