------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [3807, 141]: Comparing 1m2o_A and 1ak7, based on their crossing files. There are 52 (25 H + 27 S) secondary structure elements in 1m2o_A, of which 8 satisfy the size requirements. There are 10 (6 H + 4 S) secondary structure elements in 1ak7, of which 9 satisfy the size requirements. 1.60021 [ 1.80015] ((43 . 3) (46 . 5) (47 . 6) (49 . 8) (50 . 9)) 3.878 {0/2:10} B:0 2.00041 [ 2.25029] ((43 . 3) (47 . 5) (49 . 8) (50 . 9)) 5.415 {0/1:6} B:0 6.68032 [ 6.68838] ((43 . 3) (49 . 8) (50 . 9) (52 . 10)) 11.122 {2/3:6} B:0 2.00278 [ 2.25195] ((43 . 6) (47 . 9) (48 . 8) (49 . 10)) 8.741 {0/2:6} B:1 SIMILARITY (1/min{score1}): 0.6249 [and 1/min{score2}: 0.5555] [3807, 582]: Comparing 1m2o_A and 1cfy_A, based on their crossing files. There are 52 (25 H + 27 S) secondary structure elements in 1m2o_A, of which 8 satisfy the size requirements. There are 11 (5 H + 6 S) secondary structure elements in 1cfy_A, of which 9 satisfy the size requirements. 1.60149 [ 1.80105] ((43 . 3) (46 . 6) (47 . 7) (49 . 8) (50 . 9)) 6.328 {0/1:10} B:0 2.00052 [ 2.25037] ((43 . 3) (46 . 4) (49 . 8) (50 . 9)) 5.753 {0/1:6} B:0 2.00064 [ 2.25045] ((46 . 3) (47 . 4) (48 . 5) (51 . 8)) 6.050 {0/4:6} B:0 2.00089 [ 2.25062] ((46 . 6) (47 . 7) (49 . 8) (50 . 9)) 6.566 {0/0:6} B:0 2.00091 [ 2.25064] ((43 . 3) (47 . 6) (49 . 8) (50 . 9)) 6.608 {0/1:6} B:0 SIMILARITY (1/min{score1}): 0.6462 [and 1/min{score2}: 0.6015] [3807, 719]: Comparing 1m2o_A and 1d0n_A, based on their crossing files. There are 52 (25 H + 27 S) secondary structure elements in 1m2o_A, of which 8 satisfy the size requirements. There are 64 (30 H + 34 S) secondary structure elements in 1d0n_A, of which 7 satisfy the size requirements. 1.33351 [ 1.16693] ((43 . 22) (46 . 25) (47 . 27) (49 . 29) (50 . 30) (51 . 31)) 3.228 {0/7:15} B:0 2.17952 [ 2.11086] ((43 . 22) (46 . 23) (49 . 29) (50 . 30) (51 . 31)) 5.282 {1/5:10} B:0 SIMILARITY (1/min{score1}): 0.7499 [and 1/min{score2}: 0.8570] [3807, 752]: Comparing 1m2o_A and 1d4x_G, based on their crossing files. There are 52 (25 H + 27 S) secondary structure elements in 1m2o_A, of which 8 satisfy the size requirements. There are 11 (4 H + 7 S) secondary structure elements in 1d4x_G, of which 11 satisfy the size requirements. 1.33354 [ 1.83341] ((43 . 2) (46 . 6) (47 . 7) (49 . 8) (50 . 9) (51 . 10)) 3.352 {0/7:15} B:0 1.60071 [ 2.20027] ((43 . 2) (46 . 3) (49 . 8) (50 . 9) (51 . 10)) 5.248 {0/5:10} B:0 2.17932 [ 2.50585] ((43 . 2) (47 . 6) (49 . 8) (50 . 9) (51 . 10)) 3.918 {1/5:10} B:0 4.02541 [ 4.08857] ((43 . 3) (46 . 6) (47 . 7) (49 . 8) (51 . 10)) 5.488 {2/5:10} B:0 4.06134 [ 4.20703] ((48 . 4) (49 . 8) (50 . 9) (51 . 10)) 8.166 {2/5:6} B:0 SIMILARITY (1/min{score1}): 0.7499 [and 1/min{score2}: 0.5454] [3807, 1426]: Comparing 1m2o_A and 1f7s_A, based on their crossing files. There are 52 (25 H + 27 S) secondary structure elements in 1m2o_A, of which 8 satisfy the size requirements. There are 9 (3 H + 6 S) secondary structure elements in 1f7s_A, of which 8 satisfy the size requirements. 1.60178 [ 1.60178] ((43 . 3) (46 . 6) (47 . 7) (49 . 8) (50 . 9)) 6.610 {0/1:10} B:0 2.00049 [ 2.00049] ((43 . 3) (46 . 4) (49 . 8) (50 . 9)) 5.667 {0/1:6} B:0 2.00058 [ 2.00058] ((46 . 3) (47 . 4) (48 . 5) (51 . 8)) 5.907 {0/4:6} B:0 2.00097 [ 2.00097] ((46 . 6) (47 . 7) (49 . 8) (50 . 9)) 6.724 {0/0:6} B:0 2.00100 [ 2.00100] ((43 . 3) (47 . 6) (49 . 8) (50 . 9)) 6.770 {0/1:6} B:0 SIMILARITY (1/min{score1}): 0.6243 [and 1/min{score2}: 0.6243] [3807, 2263]: Comparing 1m2o_A and 1hqz_1, based on their crossing files. There are 52 (25 H + 27 S) secondary structure elements in 1m2o_A, of which 8 satisfy the size requirements. There are 11 (6 H + 5 S) secondary structure elements in 1hqz_1, of which 10 satisfy the size requirements. 1.60018 [ 2.00009] ((43 . 2) (46 . 5) (47 . 6) (49 . 8) (50 . 9)) 3.753 {0/1:10} B:0 2.00052 [ 2.50026] ((46 . 2) (47 . 3) (48 . 4) (51 . 8)) 5.736 {0/4:6} B:0 2.00117 [ 2.50060] ((43 . 2) (46 . 3) (49 . 7) (50 . 9)) 7.041 {0/1:6} B:0 6.68014 [ 6.69939] ((46 . 5) (47 . 6) (48 . 7) (49 . 8)) 5.235 {2/3:6} B:0 1.33418 [ 1.66710] ((43 . 2) (46 . 5) (47 . 6) (49 . 8) (50 . 9) (51 . 4)) 4.794 {0/3:15} B:1 SIMILARITY (1/min{score1}): 0.7495 [and 1/min{score2}: 0.5998] [3807, 3263]: Comparing 1m2o_A and 1kcq_A, based on their crossing files. There are 52 (25 H + 27 S) secondary structure elements in 1m2o_A, of which 8 satisfy the size requirements. There are 8 (3 H + 5 S) secondary structure elements in 1kcq_A, of which 7 satisfy the size requirements. 1.33339 [ 1.16675] ((43 . 1) (46 . 4) (47 . 5) (49 . 6) (50 . 7) (51 . 8)) 2.448 {0/7:15} B:0 1.60046 [ 1.40068] ((43 . 1) (46 . 2) (49 . 6) (50 . 7) (51 . 8)) 4.703 {0/5:10} B:0 1.60176 [ 1.40262] ((43 . 1) (46 . 4) (47 . 5) (48 . 6) (50 . 7)) 6.595 {0/3:10} B:0 3.43649 [ 3.39496] ((46 . 1) (49 . 6) (50 . 7) (51 . 8)) 4.697 {1/3:6} B:0 3.43676 [ 3.39523] ((47 . 2) (49 . 6) (50 . 7) (51 . 8)) 7.573 {1/3:6} B:0 SIMILARITY (1/min{score1}): 0.7500 [and 1/min{score2}: 0.8571] [3807, 3807]: Comparing 1m2o_A and 1m2o_A, based on their crossing files. There are 52 (25 H + 27 S) secondary structure elements in 1m2o_A, of which 8 satisfy the size requirements. There are 52 (25 H + 27 S) secondary structure elements in 1m2o_A, of which 8 satisfy the size requirements. 1.00000 [ 1.00000] ((43 . 43) (46 . 46) (47 . 47) (48 . 48) (49 . 49) (50 . 50) (51 . 51) (52 . 52)) 0.000 {0/19:28} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [3807, 3831]: Comparing 1m2o_A and 1m4j_A, based on their crossing files. There are 52 (25 H + 27 S) secondary structure elements in 1m2o_A, of which 8 satisfy the size requirements. There are 11 (6 H + 5 S) secondary structure elements in 1m4j_A, of which 9 satisfy the size requirements. 1.60050 [ 1.80035] ((43 . 2) (46 . 5) (47 . 6) (49 . 7) (50 . 9)) 4.823 {0/2:10} B:0 2.00030 [ 2.25021] ((46 . 5) (47 . 6) (49 . 7) (50 . 9)) 5.027 {0/0:6} B:0 2.00047 [ 2.25033] ((43 . 2) (46 . 3) (49 . 7) (50 . 9)) 5.603 {0/1:6} B:0 2.00082 [ 2.25058] ((46 . 2) (47 . 3) (48 . 4) (51 . 7)) 6.445 {0/4:6} B:0 2.00096 [ 2.25068] ((46 . 2) (47 . 3) (49 . 4) (50 . 6)) 6.704 {0/0:6} B:0 SIMILARITY (1/min{score1}): 0.6248 [and 1/min{score2}: 0.5554] [3807, 4932]: Comparing 1m2o_A and 1p8x_A, based on their crossing files. There are 52 (25 H + 27 S) secondary structure elements in 1m2o_A, of which 8 satisfy the size requirements. There are 26 (10 H + 16 S) secondary structure elements in 1p8x_A, of which 10 satisfy the size requirements. 1.33383 [ 1.66692] ((43 . 1) (46 . 5) (47 . 6) (49 . 7) (50 . 8) (51 . 9)) 4.199 {0/6:15} B:0 2.00032 [ 2.50016] ((46 . 2) (49 . 7) (50 . 8) (51 . 9)) 5.082 {0/3:6} B:0 2.17935 [ 2.37850] ((43 . 1) (47 . 5) (49 . 7) (50 . 8) (51 . 9)) 4.194 {1/5:10} B:0 2.17976 [ 2.37882] ((43 . 1) (47 . 4) (49 . 7) (50 . 8) (51 . 9)) 6.144 {1/5:10} B:0 4.02544 [ 4.06116] ((43 . 2) (46 . 5) (47 . 6) (49 . 7) (51 . 9)) 6.071 {2/5:10} B:0 SIMILARITY (1/min{score1}): 0.7497 [and 1/min{score2}: 0.5999] [3807, 4933]: Comparing 1m2o_A and 1p8x_A, based on their crossing files. There are 52 (25 H + 27 S) secondary structure elements in 1m2o_A, of which 8 satisfy the size requirements. There are 26 (10 H + 16 S) secondary structure elements in 1p8x_A, of which 7 satisfy the size requirements. 1.33345 [ 1.16684] ((43 . 11) (46 . 14) (47 . 15) (49 . 16) (50 . 17) (51 . 18)) 2.904 {0/7:15} B:0 1.60055 [ 1.40083] ((43 . 11) (46 . 12) (49 . 16) (50 . 17) (51 . 18)) 4.939 {0/5:10} B:0 2.00080 [ 1.75120] ((43 . 11) (46 . 14) (47 . 15) (48 . 16)) 6.411 {0/2:6} B:0 3.43650 [ 3.39497] ((46 . 11) (49 . 16) (50 . 17) (51 . 18)) 4.823 {1/3:6} B:0 3.43675 [ 3.39522] ((47 . 12) (49 . 16) (50 . 17) (51 . 18)) 7.502 {1/3:6} B:0 SIMILARITY (1/min{score1}): 0.7499 [and 1/min{score2}: 0.8570] [3807, 4934]: Comparing 1m2o_A and 1p8x_A, based on their crossing files. There are 52 (25 H + 27 S) secondary structure elements in 1m2o_A, of which 8 satisfy the size requirements. There are 26 (10 H + 16 S) secondary structure elements in 1p8x_A, of which 6 satisfy the size requirements. 1.33341 [ 1.00018] ((43 . 20) (46 . 22) (47 . 23) (49 . 24) (50 . 25) (51 . 26)) 2.607 {0/7:15} B:0 1.60130 [ 1.20308] ((43 . 20) (46 . 22) (47 . 23) (48 . 24) (50 . 25)) 6.116 {0/3:10} B:0 3.43648 [ 3.36702] ((47 . 22) (49 . 24) (50 . 25) (51 . 26)) 4.116 {1/3:6} B:0 3.43648 [ 3.36703] ((46 . 20) (49 . 24) (50 . 25) (51 . 26)) 4.340 {1/3:6} B:0 SIMILARITY (1/min{score1}): 0.7500 [and 1/min{score2}: 0.9998] [3807, 4980]: Comparing 1m2o_A and 1pd1_A, based on their crossing files. There are 52 (25 H + 27 S) secondary structure elements in 1m2o_A, of which 8 satisfy the size requirements. There are 58 (29 H + 29 S) secondary structure elements in 1pd1_A, of which 8 satisfy the size requirements. 1.21629 [ 1.21629] ((43 . 48) (46 . 50) (47 . 51) (49 . 55) (50 . 56) (51 . 57) (52 . 58)) 2.112 {1/12:21} B:0 1.26060 [ 1.26060] ((43 . 48) (46 . 50) (47 . 51) (48 . 52) (49 . 55) (50 . 56) (51 . 57) (52 . 58)) 2.952 {2/18:28} B:0 SIMILARITY (1/min{score1}): 0.8222 [and 1/min{score2}: 0.8222] [3807, 5865]: Comparing 1m2o_A and 1svy, based on their crossing files. There are 52 (25 H + 27 S) secondary structure elements in 1m2o_A, of which 8 satisfy the size requirements. There are 8 (3 H + 5 S) secondary structure elements in 1svy, of which 7 satisfy the size requirements. 1.33337 [ 1.16672] ((43 . 1) (46 . 4) (47 . 5) (49 . 6) (50 . 7) (51 . 8)) 2.135 {0/7:15} B:0 1.60037 [ 1.40055] ((43 . 1) (46 . 2) (49 . 6) (50 . 7) (51 . 8)) 4.470 {0/5:10} B:0 2.00073 [ 1.75109] ((43 . 1) (46 . 4) (47 . 5) (48 . 6)) 6.250 {0/2:6} B:0 3.43669 [ 3.39516] ((47 . 2) (49 . 6) (50 . 7) (51 . 8)) 7.110 {1/3:6} B:0 SIMILARITY (1/min{score1}): 0.7500 [and 1/min{score2}: 0.8571] -------------------------------------------------------------------------------------------------------------------------