------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [5792, 1084]: Comparing 1scz_A and 1eaf, based on their crossing files. There are 21 (10 H + 11 S) secondary structure elements in 1scz_A, of which 19 satisfy the size requirements. There are 22 (11 H + 11 S) secondary structure elements in 1eaf, of which 17 satisfy the size requirements. 1.27856 [ 1.18294] ((1 . 2) (2 . 3) (3 . 4) (5 . 6) (6 . 8) (7 . 9) (8 . 10) (9 . 11) (10 . 12) (13 . 15) (15 . 17) (17 . 18) (18 . 19) (19 . 20) (20 . 21) (21 . 22)) 2.617 {9/99:120} B:0 1.28736 [ 1.21599] ((1 . 2) (2 . 3) (3 . 4) (4 . 5) (5 . 6) (6 . 8) (7 . 9) (8 . 10) (9 . 11) (10 . 12) (13 . 15) (15 . 17) (17 . 18) (18 . 19) (19 . 20) (20 . 21) (21 . 22)) 2.643 {12/115:136} B:0 2.37505 [ 2.12506] ((1 . 2) (2 . 3) (5 . 6) (9 . 11) (13 . 15) (17 . 17) (20 . 21) (21 . 22)) 3.554 {0/24:28} B:0 3.80010 [ 3.40014] ((1 . 2) (2 . 3) (3 . 5) (13 . 15) (15 . 18)) 6.135 {0/10:10} B:0 3.80706 [ 3.40985] ((1 . 2) (2 . 3) (4 . 4) (13 . 15) (17 . 17)) 6.698 {1/9:10} B:0 SIMILARITY (1/min{score1}): 0.7821 [and 1/min{score2}: 0.8454] [5792, 3537]: Comparing 1scz_A and 1l5a_A, based on their crossing files. There are 21 (10 H + 11 S) secondary structure elements in 1scz_A, of which 19 satisfy the size requirements. There are 28 (15 H + 13 S) secondary structure elements in 1l5a_A, of which 11 satisfy the size requirements. 2.66612 [ 2.39487] ((2 . 2) (5 . 3) (6 . 5) (7 . 6) (15 . 7) (16 . 8) (17 . 9) (19 . 10) (20 . 11)) 5.343 {4/17:36} B:0 4.19732 [ 4.02399] ((1 . 1) (2 . 2) (5 . 3) (17 . 7) (18 . 9) (19 . 10) (20 . 11)) 8.979 {4/10:21} B:0 4.27330 [ 4.23574] ((1 . 1) (2 . 2) (5 . 3) (6 . 5) (7 . 6) (15 . 7) (16 . 8) (17 . 9) (19 . 10) (20 . 11)) 7.374 {11/26:45} B:0 4.75008 [ 2.75041] ((3 . 1) (10 . 7) (13 . 8) (15 . 10)) 6.861 {0/3:6} B:0 4.75019 [ 2.75100] ((2 . 2) (15 . 7) (16 . 8) (17 . 9)) 8.603 {0/1:6} B:0 SIMILARITY (1/min{score1}): 0.3751 [and 1/min{score2}: 0.5451] [5792, 3538]: Comparing 1scz_A and 1l5a_A, based on their crossing files. There are 21 (10 H + 11 S) secondary structure elements in 1scz_A, of which 19 satisfy the size requirements. There are 28 (15 H + 13 S) secondary structure elements in 1l5a_A, of which 14 satisfy the size requirements. 1.90050 [ 1.40126] ((2 . 15) (3 . 16) (5 . 17) (8 . 18) (10 . 20) (13 . 21) (15 . 23) (17 . 25) (19 . 26) (20 . 27)) 5.486 {0/37:45} B:0 1.92273 [ 1.45457] ((2 . 15) (3 . 16) (5 . 17) (8 . 18) (10 . 20) (13 . 21) (15 . 23) (17 . 25) (19 . 26) (21 . 27)) 6.588 {3/34:45} B:0 2.11152 [ 1.55658] ((2 . 15) (5 . 17) (8 . 18) (10 . 20) (13 . 21) (15 . 23) (17 . 25) (19 . 26) (20 . 27)) 5.640 {0/28:36} B:0 2.80772 [ 2.69761] ((2 . 15) (3 . 16) (5 . 17) (8 . 18) (12 . 21) (15 . 23) (17 . 25) (19 . 26) (20 . 27) (21 . 28)) 5.828 {9/34:45} B:0 2.96983 [ 2.82602] ((2 . 15) (3 . 16) (5 . 17) (8 . 18) (12 . 21) (15 . 23) (17 . 25) (19 . 26) (20 . 27)) 5.630 {8/29:36} B:0 SIMILARITY (1/min{score1}): 0.5262 [and 1/min{score2}: 0.7136] [5792, 4312]: Comparing 1scz_A and 1nm8_A, based on their crossing files. There are 21 (10 H + 11 S) secondary structure elements in 1scz_A, of which 19 satisfy the size requirements. There are 39 (21 H + 18 S) secondary structure elements in 1nm8_A, of which 22 satisfy the size requirements. 3.80052 [ 4.40033] ((12 . 16) (15 . 18) (17 . 20) (19 . 21) (20 . 22)) 9.290 {0/8:10} B:0 3.80063 [ 4.40041] ((1 . 15) (5 . 19) (8 . 20) (10 . 21) (13 . 22)) 9.769 {0/9:10} B:0 3.80876 [ 4.40565] ((1 . 15) (5 . 19) (8 . 20) (13 . 22) (16 . 24)) 12.761 {1/9:10} B:0 3.81931 [ 4.41248] ((1 . 15) (5 . 19) (9 . 20) (10 . 21) (13 . 22)) 9.138 {1/7:10} B:0 3.83483 [ 4.42257] ((2 . 5) (7 . 11) (9 . 12) (10 . 13) (13 . 14)) 6.927 {1/6:10} B:0 SIMILARITY (1/min{score1}): 0.3532 [and 1/min{score2}: 0.3441] [5792, 4313]: Comparing 1scz_A and 1nm8_A, based on their crossing files. There are 21 (10 H + 11 S) secondary structure elements in 1scz_A, of which 19 satisfy the size requirements. There are 39 (21 H + 18 S) secondary structure elements in 1nm8_A, of which 14 satisfy the size requirements. 1.72807 [ 1.27473] ((2 . 25) (3 . 26) (5 . 27) (9 . 28) (10 . 29) (12 . 30) (13 . 31) (15 . 35) (17 . 37) (19 . 38) (20 . 39)) 5.464 {1/43:55} B:0 1.72821 [ 1.27507] ((2 . 25) (3 . 26) (5 . 27) (8 . 28) (10 . 29) (12 . 30) (13 . 31) (15 . 35) (17 . 37) (19 . 38) (20 . 39)) 5.728 {1/43:55} B:0 2.26725 [ 2.11861] ((2 . 25) (3 . 26) (5 . 27) (8 . 28) (9 . 29) (12 . 30) (13 . 31) (15 . 35) (17 . 37) (19 . 38) (20 . 39)) 5.855 {9/44:55} B:0 2.52028 [ 2.36256] ((2 . 25) (3 . 26) (5 . 27) (8 . 28) (9 . 29) (13 . 31) (15 . 35) (17 . 37) (19 . 38) (20 . 39)) 5.881 {8/35:45} B:0 3.16684 [ 2.33376] ((2 . 25) (5 . 27) (12 . 30) (13 . 31) (17 . 35) (19 . 36)) 6.152 {0/11:15} B:0 SIMILARITY (1/min{score1}): 0.5787 [and 1/min{score2}: 0.7845] [5792, 5792]: Comparing 1scz_A and 1scz_A, based on their crossing files. There are 21 (10 H + 11 S) secondary structure elements in 1scz_A, of which 19 satisfy the size requirements. There are 21 (10 H + 11 S) secondary structure elements in 1scz_A, of which 19 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (12 . 12) (13 . 13) (15 . 15) (16 . 16) (17 . 17) (18 . 18) (19 . 19) (20 . 20) (21 . 21)) 0.000 {0/148:171} B:0 1.05777 [ 1.05777] ((1 . 1) (2 . 2) (3 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (12 . 12) (13 . 13) (15 . 15) (16 . 16) (17 . 17) (18 . 18) (19 . 19) (20 . 20) (21 . 21)) 3.135 {4/130:153} B:0 3.90668 [ 3.90668] ((1 . 1) (2 . 2) (3 . 4) (15 . 17) (18 . 18)) 6.855 {2/9:10} B:0 3.90668 [ 3.90668] ((1 . 1) (2 . 2) (4 . 3) (17 . 15) (18 . 18)) 6.855 {2/9:10} B:0 4.75053 [ 4.75053] ((12 . 4) (13 . 5) (17 . 10) (19 . 15)) 11.056 {0/4:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [5792, 6561]: Comparing 1scz_A and 3cla, based on their crossing files. There are 21 (10 H + 11 S) secondary structure elements in 1scz_A, of which 19 satisfy the size requirements. There are 16 (6 H + 10 S) secondary structure elements in 3cla, of which 15 satisfy the size requirements. 1.46576 [ 1.16238] ((2 . 3) (3 . 4) (5 . 5) (6 . 7) (7 . 8) (9 . 9) (10 . 10) (13 . 11) (15 . 12) (17 . 13) (18 . 14) (19 . 15) (20 . 16)) 4.193 {3/64:78} B:0 1.58362 [ 1.25058] ((2 . 3) (3 . 4) (5 . 5) (6 . 7) (7 . 8) (9 . 9) (10 . 10) (13 . 11) (15 . 12) (17 . 13) (19 . 15) (20 . 16)) 3.857 {1/54:66} B:0 1.90015 [ 1.50030] ((2 . 3) (3 . 4) (5 . 5) (8 . 9) (10 . 10) (13 . 11) (15 . 12) (17 . 13) (19 . 15) (20 . 16)) 4.027 {0/38:45} B:0 1.90038 [ 1.50077] ((2 . 3) (5 . 5) (6 . 7) (7 . 8) (8 . 9) (13 . 11) (15 . 12) (17 . 13) (19 . 15) (20 . 16)) 3.707 {1/34:45} B:0 1.92956 [ 1.82413] ((2 . 3) (3 . 4) (5 . 5) (6 . 7) (7 . 8) (8 . 9) (9 . 10) (13 . 11) (15 . 12) (17 . 13) (18 . 14) (19 . 15) (20 . 16)) 4.321 {11/63:78} B:0 SIMILARITY (1/min{score1}): 0.6822 [and 1/min{score2}: 0.8603] -------------------------------------------------------------------------------------------------------------------------