------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [912, 154]: Comparing 1dq3_A and 1am2, based on their crossing files. There are 44 (14 H + 30 S) secondary structure elements in 1dq3_A, of which 17 satisfy the size requirements. There are 20 (5 H + 15 S) secondary structure elements in 1am2, of which 16 satisfy the size requirements. 1.71899 [ 1.65505] ((2 . 2) (3 . 3) (8 . 5) (9 . 6) (10 . 7) (11 . 8) (13 . 10) (41 . 16) (42 . 18) (43 . 19) (44 . 20)) 6.631 {5/38:55} B:0 2.42599 [ 2.41489] ((2 . 2) (3 . 3) (6 . 5) (9 . 6) (10 . 7) (11 . 8) (12 . 9) (13 . 10) (40 . 14) (41 . 17) (42 . 18) (43 . 19) (44 . 20)) 5.176 {14/59:78} B:0 4.25005 [ 4.00006] ((2 . 7) (3 . 8) (5 . 9) (6 . 10)) 5.691 {0/3:6} B:0 4.25007 [ 4.00009] ((2 . 2) (3 . 3) (10 . 9) (11 . 10)) 6.222 {0/4:6} B:0 4.25023 [ 4.00027] ((2 . 2) (3 . 3) (9 . 8) (10 . 9)) 8.207 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.5817 [and 1/min{score2}: 0.6042] [912, 198]: Comparing 1dq3_A and 1at0, based on their crossing files. There are 44 (14 H + 30 S) secondary structure elements in 1dq3_A, of which 17 satisfy the size requirements. There are 17 (2 H + 15 S) secondary structure elements in 1at0, of which 15 satisfy the size requirements. 1.43057 [ 1.27006] ((2 . 1) (3 . 2) (7 . 4) (8 . 5) (10 . 7) (11 . 8) (12 . 9) (13 . 10) (41 . 13) (42 . 15) (43 . 16) (44 . 17)) 4.774 {3/48:66} B:0 1.56312 [ 1.38908] ((2 . 1) (3 . 2) (7 . 4) (8 . 5) (11 . 8) (12 . 9) (13 . 10) (41 . 13) (42 . 15) (43 . 16) (44 . 17)) 4.264 {3/42:55} B:0 1.59968 [ 1.52416] ((2 . 1) (3 . 2) (7 . 4) (8 . 5) (9 . 6) (10 . 7) (11 . 8) (12 . 9) (13 . 10) (41 . 14) (42 . 15) (43 . 16) (44 . 17)) 4.169 {8/58:78} B:0 1.65935 [ 1.56476] ((2 . 1) (7 . 4) (8 . 5) (9 . 6) (10 . 7) (11 . 8) (12 . 9) (13 . 10) (41 . 14) (42 . 15) (43 . 16) (44 . 17)) 4.174 {7/51:66} B:0 2.48198 [ 2.21905] ((7 . 4) (8 . 5) (9 . 6) (10 . 7) (11 . 8) (12 . 9) (13 . 10)) 3.344 {2/15:21} B:0 SIMILARITY (1/min{score1}): 0.6990 [and 1/min{score2}: 0.7874] [912, 912]: Comparing 1dq3_A and 1dq3_A, based on their crossing files. There are 44 (14 H + 30 S) secondary structure elements in 1dq3_A, of which 17 satisfy the size requirements. There are 44 (14 H + 30 S) secondary structure elements in 1dq3_A, of which 17 satisfy the size requirements. 1.00000 [ 1.00000] ((2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12) (13 . 13) (40 . 40) (41 . 41) (42 . 42) (43 . 43) (44 . 44)) 0.000 {0/121:136} B:0 4.25004 [ 4.25004] ((10 . 5) (11 . 6) (12 . 7) (13 . 8)) 5.229 {0/5:6} B:0 4.25004 [ 4.25004] ((5 . 10) (6 . 11) (7 . 12) (8 . 13)) 5.229 {0/5:6} B:0 4.25023 [ 4.25023] ((6 . 9) (7 . 10) (10 . 13) (41 . 44)) 8.216 {0/4:6} B:0 4.25057 [ 4.25057] ((5 . 7) (6 . 8) (8 . 10) (9 . 11)) 10.368 {0/4:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [912, 1904]: Comparing 1dq3_A and 1gpp_A, based on their crossing files. There are 44 (14 H + 30 S) secondary structure elements in 1dq3_A, of which 17 satisfy the size requirements. There are 26 (6 H + 20 S) secondary structure elements in 1gpp_A, of which 21 satisfy the size requirements. 3.54644 [ 4.28051] ((4 . 16) (7 . 20) (8 . 22) (9 . 23) (10 . 24)) 10.226 {2/9:10} B:0 3.76189 [ 4.40878] ((8 . 6) (9 . 7) (10 . 8) (11 . 9) (12 . 10)) 3.358 {2/7:10} B:0 4.00435 [ 4.56600] ((10 . 2) (11 . 3) (12 . 5) (13 . 6) (41 . 24)) 6.421 {2/6:10} B:0 4.25002 [ 5.25001] ((2 . 5) (3 . 6) (5 . 8) (6 . 9)) 4.723 {0/1:6} B:0 4.25028 [ 5.25015] ((2 . 11) (3 . 12) (6 . 14) (9 . 17)) 8.687 {0/0:6} B:0 SIMILARITY (1/min{score1}): 0.6520 [and 1/min{score2}: 0.5708] [912, 3933]: Comparing 1dq3_A and 1mi8_A, based on their crossing files. There are 44 (14 H + 30 S) secondary structure elements in 1dq3_A, of which 17 satisfy the size requirements. There are 18 (2 H + 16 S) secondary structure elements in 1mi8_A, of which 16 satisfy the size requirements. 1.31843 [ 1.26409] ((2 . 2) (3 . 3) (4 . 4) (7 . 5) (8 . 6) (9 . 7) (10 . 8) (11 . 9) (12 . 10) (13 . 11) (41 . 15) (42 . 16) (43 . 17) (44 . 18)) 3.352 {7/73:91} B:0 1.32386 [ 1.27025] ((2 . 2) (3 . 3) (4 . 4) (7 . 5) (8 . 6) (9 . 7) (10 . 8) (11 . 9) (12 . 10) (13 . 11) (41 . 14) (42 . 16) (43 . 17) (44 . 18)) 4.051 {7/72:91} B:0 2.55331 [ 2.43250] ((7 . 5) (8 . 6) (9 . 7) (10 . 8) (11 . 9) (12 . 10) (13 . 11)) 1.908 {3/18:21} B:0 3.41559 [ 3.21866] ((3 . 8) (7 . 13) (8 . 14) (9 . 15) (10 . 16)) 6.409 {1/8:10} B:0 4.25007 [ 4.00009] ((2 . 10) (3 . 11) (6 . 15) (7 . 16)) 6.199 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.7585 [and 1/min{score2}: 0.7911] -------------------------------------------------------------------------------------------------------------------------