------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [119, 119]: Comparing 1afr_A and 1afr_A, based on their crossing files. There are 19 (17 H + 2 S) secondary structure elements in 1afr_A, of which 17 satisfy the size requirements. There are 19 (17 H + 2 S) secondary structure elements in 1afr_A, of which 17 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (2 . 2) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12) (13 . 13) (14 . 14) (15 . 15) (16 . 16) (17 . 17) (18 . 18) (19 . 19)) 0.000 {0/108:136} B:0 2.83443 [ 2.83443] ((8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12) (16 . 15)) 8.991 {0/4:15} B:0 2.83443 [ 2.83443] ((8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12) (15 . 16)) 8.991 {0/4:15} B:0 4.25016 [ 4.25016] ((9 . 8) (10 . 10) (11 . 11) (12 . 12)) 7.484 {0/2:6} B:0 4.25074 [ 4.25074] ((8 . 5) (9 . 6) (10 . 8) (18 . 13)) 11.055 {0/3:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [119, 2032]: Comparing 1afr_A and 1h0o_A, based on their crossing files. There are 19 (17 H + 2 S) secondary structure elements in 1afr_A, of which 17 satisfy the size requirements. There are 15 (15 H + 0 S) secondary structure elements in 1h0o_A, of which 13 satisfy the size requirements. 2.83393 [ 2.16801] ((6 . 4) (8 . 6) (9 . 7) (10 . 9) (11 . 11) (14 . 14)) 7.734 {0/5:15} B:0 4.25023 [ 3.25051] ((7 . 4) (8 . 6) (9 . 7) (14 . 14)) 8.221 {0/1:6} B:0 4.25054 [ 3.25121] ((7 . 1) (9 . 5) (10 . 6) (15 . 14)) 10.208 {0/0:6} B:0 4.25071 [ 3.25158] ((6 . 1) (8 . 4) (11 . 9) (14 . 12)) 10.916 {0/2:6} B:0 4.25086 [ 3.25192] ((7 . 3) (9 . 6) (10 . 7) (13 . 11)) 11.468 {0/1:6} B:0 SIMILARITY (1/min{score1}): 0.6294 [and 1/min{score2}: 0.7860] [119, 2948]: Comparing 1afr_A and 1jkv_A, based on their crossing files. There are 19 (17 H + 2 S) secondary structure elements in 1afr_A, of which 17 satisfy the size requirements. There are 15 (12 H + 3 S) secondary structure elements in 1jkv_A, of which 13 satisfy the size requirements. 2.83374 [ 2.16757] ((6 . 2) (7 . 3) (8 . 4) (10 . 9) (11 . 10) (14 . 13)) 7.009 {0/4:15} B:0 3.40020 [ 2.60046] ((6 . 2) (8 . 4) (10 . 9) (11 . 10) (15 . 13)) 6.775 {0/0:10} B:0 3.40066 [ 2.60148] ((5 . 2) (6 . 3) (8 . 4) (10 . 9) (11 . 10)) 9.087 {0/1:10} B:0 3.40066 [ 2.60148] ((6 . 3) (8 . 4) (10 . 9) (11 . 10) (15 . 13)) 9.096 {0/1:10} B:0 3.40289 [ 2.60644] ((6 . 3) (8 . 4) (9 . 6) (10 . 9) (11 . 10)) 13.135 {0/1:10} B:0 SIMILARITY (1/min{score1}): 0.4115 [and 1/min{score2}: 0.5376] [119, 3294]: Comparing 1afr_A and 1kgn_A, based on their crossing files. There are 19 (17 H + 2 S) secondary structure elements in 1afr_A, of which 17 satisfy the size requirements. There are 16 (16 H + 0 S) secondary structure elements in 1kgn_A, of which 14 satisfy the size requirements. 2.98577 [ 2.91899] ((2 . 2) (6 . 5) (7 . 6) (8 . 7) (9 . 9) (10 . 10) (11 . 12) (13 . 13) (14 . 14)) 9.105 {2/7:36} B:0 3.40159 [ 2.80284] ((7 . 5) (8 . 7) (10 . 10) (11 . 12) (14 . 14)) 11.311 {0/2:10} B:0 4.25021 [ 3.50037] ((12 . 2) (13 . 5) (14 . 6) (15 . 7)) 8.040 {0/1:6} B:0 4.25039 [ 3.50070] ((10 . 11) (11 . 12) (12 . 13) (14 . 16)) 9.424 {0/3:6} B:0 4.25040 [ 3.50072] ((6 . 7) (8 . 9) (10 . 12) (11 . 13)) 9.476 {0/0:6} B:0 SIMILARITY (1/min{score1}): 0.5768 [and 1/min{score2}: 0.6856] [119, 3587]: Comparing 1afr_A and 1lb3_A, based on their crossing files. There are 19 (17 H + 2 S) secondary structure elements in 1afr_A, of which 17 satisfy the size requirements. There are 6 (6 H + 0 S) secondary structure elements in 1lb3_A, of which 6 satisfy the size requirements. 4.25004 [ 1.50098] ((6 . 1) (8 . 2) (10 . 3) (11 . 5)) 5.432 {0/1:6} B:0 4.25019 [ 1.50438] ((7 . 1) (8 . 2) (10 . 3) (11 . 5)) 7.899 {0/0:6} B:0 5.55753 [ 5.01546] ((1 . 2) (5 . 3) (7 . 5) (8 . 6)) 20.512 {1/2:6} B:0 3.40135 [ 1.22960] ((7 . 2) (8 . 4) (9 . 1) (10 . 3) (11 . 5)) 10.860 {0/0:10} B:1 3.70348 [ 3.34155] ((1 . 6) (6 . 1) (7 . 2) (8 . 4) (10 . 3) (11 . 5)) 10.971 {2/6:15} B:2 SIMILARITY (1/min{score1}): 0.2940 [and 1/min{score2}: 0.8133] [119, 4030]: Comparing 1afr_A and 1mty_B, based on their crossing files. There are 19 (17 H + 2 S) secondary structure elements in 1afr_A, of which 17 satisfy the size requirements. There are 20 (20 H + 0 S) secondary structure elements in 1mty_B, of which 18 satisfy the size requirements. 3.40010 [ 3.60009] ((6 . 7) (8 . 9) (9 . 10) (11 . 15) (14 . 18)) 5.694 {0/3:10} B:0 3.40015 [ 3.60013] ((6 . 7) (8 . 9) (10 . 13) (11 . 15) (14 . 18)) 6.301 {0/2:10} B:0 3.40017 [ 3.60014] ((6 . 6) (7 . 7) (8 . 9) (11 . 15) (14 . 18)) 6.470 {0/5:10} B:0 4.00484 [ 4.13224] ((5 . 10) (6 . 11) (8 . 15) (10 . 17) (11 . 18)) 9.989 {2/6:10} B:0 4.25018 [ 4.50015] ((11 . 4) (12 . 7) (14 . 9) (15 . 11)) 7.788 {0/0:6} B:0 SIMILARITY (1/min{score1}): 0.5301 [and 1/min{score2}: 0.5098] [119, 4031]: Comparing 1afr_A and 1mty_D, based on their crossing files. There are 19 (17 H + 2 S) secondary structure elements in 1afr_A, of which 17 satisfy the size requirements. There are 31 (27 H + 4 S) secondary structure elements in 1mty_D, of which 24 satisfy the size requirements. 2.93273 [ 3.64940] ((5 . 3) (6 . 4) (8 . 5) (10 . 10) (11 . 12) (14 . 13) (15 . 17)) 9.556 {1/4:21} B:0 3.40016 [ 4.80006] ((8 . 5) (10 . 11) (11 . 12) (14 . 14) (15 . 17)) 6.361 {0/1:10} B:0 3.40028 [ 4.80010] ((6 . 4) (8 . 5) (10 . 11) (11 . 12) (14 . 15)) 7.342 {0/3:10} B:0 3.40030 [ 4.80011] ((6 . 9) (7 . 11) (8 . 12) (9 . 13) (17 . 25)) 7.433 {0/6:10} B:0 3.40030 [ 4.80011] ((6 . 13) (8 . 14) (9 . 17) (12 . 21) (13 . 26)) 7.472 {0/6:10} B:0 SIMILARITY (1/min{score1}): 0.5876 [and 1/min{score2}: 0.4457] [119, 4077]: Comparing 1afr_A and 1mxr_A, based on their crossing files. There are 19 (17 H + 2 S) secondary structure elements in 1afr_A, of which 17 satisfy the size requirements. There are 18 (16 H + 2 S) secondary structure elements in 1mxr_A, of which 17 satisfy the size requirements. 1.93459 [ 1.93459] ((2 . 1) (5 . 3) (6 . 4) (8 . 6) (9 . 7) (10 . 13) (11 . 14) (12 . 16) (14 . 17)) 7.558 {2/19:36} B:0 1.99767 [ 1.99767] ((2 . 1) (5 . 3) (6 . 4) (7 . 5) (8 . 6) (9 . 8) (10 . 13) (11 . 14) (14 . 17)) 6.934 {2/15:36} B:0 2.09621 [ 2.09621] ((2 . 1) (5 . 3) (6 . 4) (7 . 5) (8 . 6) (9 . 7) (10 . 13) (11 . 14) (12 . 15) (14 . 17)) 6.530 {4/22:45} B:0 2.95027 [ 2.95027] ((2 . 1) (6 . 4) (8 . 6) (9 . 7) (10 . 13) (11 . 14) (12 . 15) (15 . 17)) 7.418 {3/11:28} B:0 3.07493 [ 3.07493] ((2 . 1) (5 . 3) (6 . 4) (7 . 5) (8 . 6) (9 . 7) (10 . 13) (11 . 14) (13 . 16) (14 . 17)) 7.526 {6/20:45} B:0 SIMILARITY (1/min{score1}): 0.5577 [and 1/min{score2}: 0.5577] [119, 4270]: Comparing 1afr_A and 1nig_A, based on their crossing files. There are 19 (17 H + 2 S) secondary structure elements in 1afr_A, of which 17 satisfy the size requirements. There are 8 (6 H + 2 S) secondary structure elements in 1nig_A, of which 8 satisfy the size requirements. 4.25007 [ 2.00063] ((6 . 3) (8 . 4) (10 . 7) (11 . 8)) 6.033 {0/0:6} B:0 4.25014 [ 2.00131] ((7 . 3) (8 . 4) (10 . 7) (11 . 8)) 7.248 {0/0:6} B:0 6.92642 [ 6.68018] ((12 . 4) (13 . 6) (14 . 7) (15 . 8)) 8.150 {2/3:6} B:0 10.08061 [10.00402] ((6 . 3) (8 . 5) (10 . 7) (11 . 8)) 9.200 {1/1:6} B:0 SIMILARITY (1/min{score1}): 0.2353 [and 1/min{score2}: 0.4998] [119, 4783]: Comparing 1afr_A and 1otk_A, based on their crossing files. There are 19 (17 H + 2 S) secondary structure elements in 1afr_A, of which 17 satisfy the size requirements. There are 12 (12 H + 0 S) secondary structure elements in 1otk_A, of which 9 satisfy the size requirements. 2.13058 [ 1.16097] ((6 . 1) (8 . 2) (9 . 3) (10 . 6) (11 . 7) (12 . 8) (13 . 9) (14 . 10)) 5.810 {1/15:28} B:0 2.45521 [ 1.43869] ((7 . 1) (8 . 2) (10 . 6) (11 . 7) (12 . 8) (13 . 9) (14 . 10)) 6.513 {1/9:21} B:0 2.83369 [ 1.50238] ((7 . 1) (8 . 2) (10 . 6) (11 . 7) (13 . 9) (14 . 10)) 6.780 {0/6:15} B:0 4.25069 [ 2.25464] ((8 . 1) (11 . 6) (14 . 8) (15 . 10)) 10.858 {0/1:6} B:0 4.25116 [ 2.25778] ((8 . 1) (9 . 2) (11 . 6) (18 . 12)) 12.360 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.4694 [and 1/min{score2}: 0.8613] [119, 6297]: Comparing 1afr_A and 1vjx_A, based on their crossing files. There are 19 (17 H + 2 S) secondary structure elements in 1afr_A, of which 17 satisfy the size requirements. There are 6 (6 H + 0 S) secondary structure elements in 1vjx_A, of which 6 satisfy the size requirements. 4.25004 [ 1.50086] ((6 . 1) (8 . 2) (10 . 5) (11 . 6)) 5.246 {0/1:6} B:0 4.25011 [ 1.50244] ((7 . 1) (8 . 2) (10 . 5) (11 . 6)) 6.822 {0/0:6} B:0 4.25057 [ 1.51273] ((10 . 1) (11 . 2) (14 . 5) (15 . 6)) 10.334 {0/0:6} B:0 3.40016 [ 1.20372] ((5 . 3) (6 . 1) (8 . 2) (10 . 5) (11 . 6)) 6.412 {0/5:10} B:1 3.40065 [ 1.21442] ((7 . 1) (8 . 2) (10 . 5) (11 . 6) (12 . 4)) 9.030 {0/2:10} B:1 SIMILARITY (1/min{score1}): 0.2941 [and 1/min{score2}: 0.8308] -------------------------------------------------------------------------------------------------------------------------