------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [4342, 378]: Comparing 1np3_A and 1bg6, based on their crossing files. There are 30 (21 H + 9 S) secondary structure elements in 1np3_A, of which 10 satisfy the size requirements. There are 31 (19 H + 12 S) secondary structure elements in 1bg6, of which 11 satisfy the size requirements. 2.50283 [ 2.75213] ((23 . 19) (24 . 20) (28 . 25) (29 . 26)) 10.380 {0/5:6} B:0 2.72643 [ 2.92686] ((23 . 27) (24 . 28) (26 . 29) (27 . 31)) 10.611 {1/5:6} B:0 2.97353 [ 3.13268] ((23 . 19) (24 . 20) (26 . 23) (27 . 25)) 7.716 {1/4:6} B:0 4.14599 [ 4.20817] ((27 . 20) (28 . 21) (29 . 22) (30 . 23)) 12.785 {2/5:6} B:0 3.57465 [ 3.66999] ((21 . 25) (22 . 26) (23 . 28) (24 . 27)) 14.944 {1/3:6} B:1 SIMILARITY (1/min{score1}): 0.3995 [and 1/min{score2}: 0.3634] [4342, 2726]: Comparing 1np3_A and 1j3v_A, based on their crossing files. There are 30 (21 H + 9 S) secondary structure elements in 1np3_A, of which 10 satisfy the size requirements. There are 22 (13 H + 9 S) secondary structure elements in 1j3v_A, of which 6 satisfy the size requirements. 2.50245 [ 1.51123] ((26 . 18) (27 . 19) (29 . 20) (30 . 21)) 10.012 {0/1:6} B:0 5.07689 [ 5.01065] ((21 . 19) (22 . 21) (26 . 18) (29 . 20)) 11.613 {1/2:6} B:1 SIMILARITY (1/min{score1}): 0.3996 [and 1/min{score2}: 0.6617] [4342, 3415]: Comparing 1np3_A and 1ks9_A, based on their crossing files. There are 30 (21 H + 9 S) secondary structure elements in 1np3_A, of which 10 satisfy the size requirements. There are 24 (13 H + 11 S) secondary structure elements in 1ks9_A, of which 7 satisfy the size requirements. 2.50020 [ 1.75057] ((22 . 20) (27 . 21) (28 . 22) (29 . 23)) 5.332 {0/5:6} B:0 2.50260 [ 1.75754] ((26 . 20) (27 . 21) (28 . 22) (29 . 23)) 10.163 {0/5:6} B:0 2.50665 [ 1.76915] ((24 . 19) (26 . 20) (27 . 21) (29 . 23)) 12.859 {0/5:6} B:0 2.97474 [ 2.64064] ((25 . 20) (26 . 21) (27 . 22) (29 . 23)) 10.432 {1/4:6} B:0 6.04500 [ 6.01112] ((21 . 18) (22 . 20) (24 . 21) (28 . 24)) 11.353 {3/5:6} B:0 SIMILARITY (1/min{score1}): 0.4000 [and 1/min{score2}: 0.5712] [4342, 3638]: Comparing 1np3_A and 1lj8_A, based on their crossing files. There are 30 (21 H + 9 S) secondary structure elements in 1np3_A, of which 10 satisfy the size requirements. There are 40 (27 H + 13 S) secondary structure elements in 1lj8_A, of which 13 satisfy the size requirements. 2.50158 [ 3.25072] ((21 . 28) (22 . 30) (24 . 31) (25 . 32)) 8.977 {0/2:6} B:0 2.50632 [ 3.25288] ((21 . 33) (24 . 35) (25 . 36) (27 . 39)) 12.696 {0/5:6} B:0 2.61579 [ 3.30506] ((24 . 35) (25 . 36) (26 . 37) (27 . 39)) 7.120 {1/6:6} B:0 2.72672 [ 3.36216] ((24 . 27) (26 . 28) (29 . 32) (30 . 33)) 10.916 {1/5:6} B:0 2.72817 [ 3.36294] ((22 . 32) (24 . 34) (26 . 35) (28 . 39)) 12.170 {1/5:6} B:0 SIMILARITY (1/min{score1}): 0.3997 [and 1/min{score2}: 0.3076] [4342, 3855]: Comparing 1np3_A and 1m66_A, based on their crossing files. There are 30 (21 H + 9 S) secondary structure elements in 1np3_A, of which 10 satisfy the size requirements. There are 25 (17 H + 8 S) secondary structure elements in 1m66_A, of which 7 satisfy the size requirements. 2.50561 [ 1.76617] ((22 . 19) (23 . 20) (26 . 21) (30 . 25)) 12.320 {0/5:6} B:0 SIMILARITY (1/min{score1}): 0.3991 [and 1/min{score2}: 0.5662] [4342, 4342]: Comparing 1np3_A and 1np3_A, based on their crossing files. There are 30 (21 H + 9 S) secondary structure elements in 1np3_A, of which 10 satisfy the size requirements. There are 30 (21 H + 9 S) secondary structure elements in 1np3_A, of which 10 satisfy the size requirements. 1.00000 [ 1.00000] ((21 . 21) (22 . 22) (23 . 23) (24 . 24) (25 . 25) (26 . 26) (27 . 27) (28 . 28) (29 . 29) (30 . 30)) 0.000 {0/39:45} B:0 2.72644 [ 2.72644] ((25 . 24) (26 . 25) (28 . 27) (29 . 28)) 10.620 {1/5:6} B:0 2.72693 [ 2.72693] ((22 . 25) (23 . 26) (24 . 27) (26 . 28)) 11.124 {1/5:6} B:0 2.72693 [ 2.72693] ((25 . 22) (26 . 23) (27 . 24) (28 . 26)) 11.124 {1/5:6} B:0 4.14491 [ 4.14491] ((22 . 23) (24 . 25) (25 . 26) (27 . 28)) 8.962 {2/5:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [4342, 5003]: Comparing 1np3_A and 1pgj_A, based on their crossing files. There are 30 (21 H + 9 S) secondary structure elements in 1np3_A, of which 10 satisfy the size requirements. There are 31 (22 H + 9 S) secondary structure elements in 1pgj_A, of which 13 satisfy the size requirements. 2.50277 [ 3.25126] ((26 . 17) (27 . 18) (29 . 20) (30 . 21)) 10.325 {0/3:6} B:0 2.72695 [ 3.36228] ((21 . 23) (24 . 26) (27 . 28) (28 . 29)) 11.141 {1/5:6} B:0 4.14765 [ 4.38120] ((21 . 21) (24 . 23) (27 . 25) (29 . 27)) 15.495 {2/5:6} B:0 4.14504 [ 4.37899] ((22 . 23) (24 . 26) (26 . 25) (27 . 16)) 9.708 {2/5:6} B:2 4.67745 [ 4.69622] ((21 . 23) (22 . 16) (23 . 17) (24 . 25) (25 . 26) (26 . 27) (28 . 20)) 11.123 {7/15:21} B:2 SIMILARITY (1/min{score1}): 0.3996 [and 1/min{score2}: 0.3076] [4342, 5388]: Comparing 1np3_A and 1qmg_A, based on their crossing files. There are 30 (21 H + 9 S) secondary structure elements in 1np3_A, of which 10 satisfy the size requirements. There are 40 (30 H + 10 S) secondary structure elements in 1qmg_A, of which 19 satisfy the size requirements. 1.11936 [ 2.11233] ((21 . 27) (22 . 31) (23 . 32) (24 . 34) (25 . 35) (26 . 36) (27 . 37) (29 . 38) (30 . 39)) 6.484 {1/27:36} B:0 1.16317 [ 2.11920] ((21 . 21) (22 . 22) (23 . 23) (24 . 25) (25 . 26) (26 . 27) (27 . 28) (28 . 29) (30 . 30)) 4.308 {2/27:36} B:0 1.25394 [ 2.37558] ((21 . 27) (22 . 31) (23 . 32) (24 . 33) (25 . 35) (26 . 36) (27 . 37) (30 . 39)) 6.711 {0/21:28} B:0 1.42901 [ 2.71435] ((21 . 21) (22 . 22) (23 . 24) (24 . 25) (27 . 28) (28 . 29) (30 . 30)) 4.279 {0/17:21} B:0 1.66674 [ 3.16668] ((21 . 21) (22 . 22) (23 . 23) (24 . 24) (28 . 29) (30 . 30)) 3.053 {0/12:15} B:0 SIMILARITY (1/min{score1}): 0.8934 [and 1/min{score2}: 0.4734] [4342, 6506]: Comparing 1np3_A and 2pgd, based on their crossing files. There are 30 (21 H + 9 S) secondary structure elements in 1np3_A, of which 10 satisfy the size requirements. There are 30 (22 H + 8 S) secondary structure elements in 2pgd, of which 13 satisfy the size requirements. 2.50294 [ 3.25134] ((26 . 17) (27 . 18) (29 . 20) (30 . 21)) 10.480 {0/3:6} B:0 2.97758 [ 3.50609] ((21 . 22) (22 . 23) (24 . 24) (30 . 29)) 13.319 {1/4:6} B:0 4.14565 [ 4.37951] ((22 . 16) (24 . 17) (29 . 21) (30 . 22)) 11.937 {2/5:6} B:0 7.52316 [ 7.56537] ((21 . 18) (24 . 21) (26 . 22) (29 . 24)) 10.657 {3/4:6} B:0 4.06132 [ 4.16788] ((21 . 18) (23 . 29) (24 . 21) (28 . 17) (30 . 23)) 8.006 {2/5:10} B:2 SIMILARITY (1/min{score1}): 0.3995 [and 1/min{score2}: 0.3076] -------------------------------------------------------------------------------------------------------------------------