------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [1786, 1786]: Comparing 1ga6_A and 1ga6_A, based on their crossing files. There are 30 (12 H + 18 S) secondary structure elements in 1ga6_A, of which 24 satisfy the size requirements. There are 30 (12 H + 18 S) secondary structure elements in 1ga6_A, of which 24 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (10 . 10) (11 . 11) (12 . 12) (14 . 14) (15 . 15) (16 . 16) (17 . 17) (18 . 18) (19 . 19) (20 . 20) (21 . 21) (23 . 23) (24 . 24) (25 . 25) (26 . 26) (30 . 30)) 0.000 {0/226:276} B:0 1.24111 [ 1.24111] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (11 . 11) (12 . 12) (14 . 14) (15 . 15) (16 . 16) (17 . 17) (20 . 18) (21 . 21) (23 . 23) (24 . 24) (25 . 25) (26 . 26) (30 . 30)) 1.221 {15/166:210} B:0 1.24111 [ 1.24111] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (11 . 11) (12 . 12) (14 . 14) (15 . 15) (16 . 16) (17 . 17) (18 . 20) (21 . 21) (23 . 23) (24 . 24) (25 . 25) (26 . 26) (30 . 30)) 1.221 {15/166:210} B:0 4.80001 [ 4.80001] ((1 . 1) (3 . 3) (5 . 5) (8 . 6) (30 . 30)) 4.023 {0/8:10} B:0 4.80001 [ 4.80001] ((1 . 1) (3 . 3) (5 . 5) (6 . 8) (30 . 30)) 4.023 {0/8:10} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [1786, 1793]: Comparing 1ga6_A and 1gci, based on their crossing files. There are 30 (12 H + 18 S) secondary structure elements in 1ga6_A, of which 24 satisfy the size requirements. There are 18 (9 H + 9 S) secondary structure elements in 1gci, of which 18 satisfy the size requirements. 1.50035 [ 1.12583] ((1 . 1) (2 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (11 . 9) (12 . 10) (14 . 11) (21 . 12) (23 . 13) (24 . 14) (25 . 15) (26 . 16) (30 . 18)) 3.673 {2/95:120} B:0 1.60018 [ 1.20044] ((2 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (11 . 9) (12 . 10) (14 . 11) (21 . 12) (23 . 13) (24 . 14) (25 . 15) (26 . 16) (30 . 18)) 3.679 {1/81:105} B:0 1.60034 [ 1.20080] ((1 . 1) (2 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (11 . 9) (12 . 10) (14 . 11) (21 . 12) (23 . 13) (24 . 14) (25 . 15) (30 . 18)) 3.370 {2/82:105} B:0 1.74739 [ 1.35984] ((1 . 2) (2 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (11 . 9) (12 . 10) (14 . 11) (21 . 12) (23 . 13) (24 . 14) (25 . 15)) 3.956 {6/66:91} B:0 1.90601 [ 1.71830] ((2 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (11 . 9) (12 . 10) (18 . 11) (21 . 12) (23 . 13) (24 . 14) (25 . 15) (26 . 16) (30 . 18)) 4.953 {13/81:105} B:0 SIMILARITY (1/min{score1}): 0.6665 [and 1/min{score2}: 0.8882] [1786, 1944]: Comparing 1ga6_A and 1gt9_1, based on their crossing files. There are 30 (12 H + 18 S) secondary structure elements in 1ga6_A, of which 24 satisfy the size requirements. There are 30 (13 H + 17 S) secondary structure elements in 1gt9_1, of which 21 satisfy the size requirements. 1.26400 [ 1.10651] ((1 . 2) (2 . 3) (3 . 4) (4 . 5) (5 . 6) (6 . 7) (7 . 8) (8 . 9) (11 . 12) (12 . 13) (14 . 16) (15 . 17) (19 . 20) (21 . 22) (23 . 23) (24 . 24) (25 . 25) (26 . 26) (30 . 30)) 2.093 {4/141:171} B:0 1.33336 [ 1.16671] ((1 . 2) (2 . 3) (3 . 4) (4 . 5) (5 . 6) (6 . 7) (7 . 8) (8 . 9) (11 . 12) (12 . 13) (14 . 16) (15 . 17) (19 . 20) (21 . 22) (24 . 24) (25 . 25) (26 . 26) (30 . 30)) 1.945 {1/125:153} B:0 1.33344 [ 1.16682] ((1 . 2) (2 . 3) (3 . 4) (4 . 5) (5 . 6) (6 . 7) (7 . 8) (8 . 9) (11 . 12) (12 . 13) (14 . 16) (15 . 17) (21 . 22) (23 . 23) (24 . 24) (25 . 25) (26 . 26) (30 . 30)) 2.123 {2/124:153} B:0 4.00012 [ 3.50019] ((7 . 6) (11 . 12) (19 . 20) (25 . 25) (26 . 26) (30 . 30)) 6.762 {0/11:15} B:0 4.80354 [ 4.20528] ((7 . 6) (11 . 12) (19 . 20) (23 . 23) (30 . 30)) 7.296 {1/9:10} B:0 SIMILARITY (1/min{score1}): 0.7969 [and 1/min{score2}: 0.9037] [1786, 2456]: Comparing 1ga6_A and 1ic6_A, based on their crossing files. There are 30 (12 H + 18 S) secondary structure elements in 1ga6_A, of which 24 satisfy the size requirements. There are 23 (8 H + 15 S) secondary structure elements in 1ic6_A, of which 16 satisfy the size requirements. 1.60033 [ 1.06778] ((1 . 2) (2 . 4) (4 . 6) (5 . 7) (6 . 8) (7 . 9) (8 . 10) (11 . 12) (12 . 13) (14 . 16) (21 . 17) (23 . 18) (24 . 19) (25 . 20) (26 . 21)) 3.409 {2/83:105} B:0 2.00032 [ 1.33442] ((2 . 4) (4 . 6) (5 . 7) (6 . 8) (7 . 9) (8 . 10) (11 . 12) (12 . 13) (20 . 17) (24 . 19) (25 . 20) (26 . 21)) 5.101 {0/46:66} B:0 2.12890 [ 1.92074] ((2 . 4) (4 . 6) (5 . 7) (6 . 8) (7 . 9) (8 . 10) (11 . 12) (12 . 13) (18 . 16) (21 . 17) (23 . 18) (24 . 19) (25 . 20) (26 . 21)) 4.935 {13/70:91} B:0 2.12914 [ 1.92107] ((2 . 4) (4 . 6) (5 . 7) (6 . 8) (7 . 9) (8 . 10) (11 . 12) (12 . 13) (18 . 16) (20 . 17) (23 . 18) (24 . 19) (25 . 20) (26 . 21)) 5.897 {13/70:91} B:0 2.40004 [ 1.60013] ((1 . 2) (2 . 4) (4 . 6) (5 . 7) (6 . 8) (7 . 9) (8 . 10) (11 . 12) (12 . 13) (14 . 17)) 3.451 {0/30:45} B:0 SIMILARITY (1/min{score1}): 0.6249 [and 1/min{score2}: 0.9365] [1786, 5568]: Comparing 1ga6_A and 1r64_A, based on their crossing files. There are 30 (12 H + 18 S) secondary structure elements in 1ga6_A, of which 24 satisfy the size requirements. There are 33 (14 H + 19 S) secondary structure elements in 1r64_A, of which 18 satisfy the size requirements. 1.60059 [ 1.20140] ((1 . 2) (2 . 4) (5 . 6) (6 . 7) (7 . 8) (8 . 9) (11 . 10) (12 . 12) (14 . 14) (21 . 15) (23 . 16) (24 . 17) (25 . 18) (26 . 19) (30 . 21)) 4.413 {2/80:105} B:0 1.60083 [ 1.20197] ((1 . 2) (2 . 4) (5 . 6) (6 . 7) (7 . 8) (8 . 9) (11 . 10) (12 . 12) (20 . 14) (21 . 15) (23 . 16) (24 . 17) (25 . 18) (26 . 19) (30 . 21)) 4.997 {2/79:105} B:0 1.71440 [ 1.28599] ((2 . 4) (5 . 6) (6 . 7) (7 . 8) (8 . 9) (11 . 10) (12 . 12) (14 . 14) (21 . 15) (23 . 16) (24 . 17) (25 . 18) (26 . 19) (30 . 21)) 3.348 {1/68:91} B:0 1.71520 [ 1.28788] ((1 . 2) (2 . 4) (5 . 6) (6 . 7) (7 . 8) (8 . 9) (11 . 10) (12 . 12) (20 . 14) (21 . 15) (23 . 16) (25 . 18) (26 . 19) (30 . 21)) 5.063 {2/66:91} B:0 1.84625 [ 1.38484] ((2 . 4) (5 . 6) (6 . 7) (7 . 8) (8 . 9) (11 . 10) (12 . 12) (14 . 14) (21 . 15) (23 . 16) (24 . 17) (25 . 18) (30 . 21)) 3.103 {1/57:78} B:0 SIMILARITY (1/min{score1}): 0.6248 [and 1/min{score2}: 0.8324] -------------------------------------------------------------------------------------------------------------------------