------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [801, 306]: Comparing 1dcz_A and 1b6r_A, based on their crossing files. There are 7 (0 H + 7 S) secondary structure elements in 1dcz_A, of which 6 satisfy the size requirements. There are 31 (15 H + 16 S) secondary structure elements in 1b6r_A, of which 6 satisfy the size requirements. NO SIMILARITY! [801, 355]: Comparing 1dcz_A and 1bdo, based on their crossing files. There are 7 (0 H + 7 S) secondary structure elements in 1dcz_A, of which 6 satisfy the size requirements. There are 8 (0 H + 8 S) secondary structure elements in 1bdo, of which 6 satisfy the size requirements. 1.00003 [ 1.00003] ((1 . 1) (2 . 2) (4 . 4) (5 . 5) (6 . 6) (7 . 8)) 1.619 {0/11:15} B:0 4.01964 [ 4.01964] ((1 . 1) (2 . 2) (5 . 4) (7 . 8)) 3.868 {2/5:6} B:0 SIMILARITY (1/min{score1}): 0.9999 [and 1/min{score2}: 0.9999] [801, 801]: Comparing 1dcz_A and 1dcz_A, based on their crossing files. There are 7 (0 H + 7 S) secondary structure elements in 1dcz_A, of which 6 satisfy the size requirements. There are 7 (0 H + 7 S) secondary structure elements in 1dcz_A, of which 6 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (2 . 2) (4 . 4) (5 . 5) (6 . 6) (7 . 7)) 0.000 {0/12:15} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [801, 949]: Comparing 1dcz_A and 1dv1_A, based on their crossing files. There are 7 (0 H + 7 S) secondary structure elements in 1dcz_A, of which 6 satisfy the size requirements. There are 37 (18 H + 19 S) secondary structure elements in 1dv1_A, of which 7 satisfy the size requirements. NO SIMILARITY! [801, 1906]: Comparing 1dcz_A and 1gpr, based on their crossing files. There are 7 (0 H + 7 S) secondary structure elements in 1dcz_A, of which 6 satisfy the size requirements. There are 17 (4 H + 13 S) secondary structure elements in 1gpr, of which 13 satisfy the size requirements. 1.00006 [ 2.16667] ((1 . 5) (2 . 6) (4 . 7) (5 . 8) (6 . 10) (7 . 12)) 2.001 {0/8:15} B:0 1.50277 [ 3.25027] ((1 . 8) (2 . 10) (4 . 12) (6 . 14)) 7.040 {0/2:6} B:0 1.50713 [ 3.25071] ((1 . 1) (4 . 5) (5 . 6) (7 . 8)) 8.929 {0/3:6} B:0 2.14525 [ 3.36150] ((1 . 8) (2 . 10) (6 . 14) (7 . 15)) 9.355 {1/5:6} B:0 1.50106 [ 3.25010] ((1 . 4) (4 . 8) (6 . 17) (7 . 15)) 5.530 {0/3:6} B:1 SIMILARITY (1/min{score1}): 0.9999 [and 1/min{score2}: 0.4615] [801, 1942]: Comparing 1dcz_A and 1gso_A, based on their crossing files. There are 7 (0 H + 7 S) secondary structure elements in 1dcz_A, of which 6 satisfy the size requirements. There are 37 (16 H + 21 S) secondary structure elements in 1gso_A, of which 7 satisfy the size requirements. NO SIMILARITY! [801, 2287]: Comparing 1dcz_A and 1htp, based on their crossing files. There are 7 (0 H + 7 S) secondary structure elements in 1dcz_A, of which 6 satisfy the size requirements. There are 14 (5 H + 9 S) secondary structure elements in 1htp, of which 12 satisfy the size requirements. 1.00022 [ 2.00003] ((1 . 3) (2 . 5) (4 . 7) (5 . 8) (6 . 9) (7 . 12)) 2.763 {0/10:15} B:0 2.14410 [ 3.13887] ((1 . 2) (4 . 5) (5 . 7) (6 . 8)) 8.267 {1/5:6} B:0 5.01010 [ 5.15468] ((4 . 2) (5 . 3) (6 . 5) (7 . 7)) 4.204 {1/2:6} B:0 5.01021 [ 5.15478] ((2 . 2) (4 . 3) (5 . 5) (7 . 8)) 7.851 {1/2:6} B:0 1.00019 [ 2.00002] ((1 . 8) (2 . 9) (4 . 12) (5 . 3) (6 . 5) (7 . 7)) 2.641 {0/9:15} B:1 SIMILARITY (1/min{score1}): 0.9998 [and 1/min{score2}: 0.5000] [801, 2672]: Comparing 1dcz_A and 1iyu, based on their crossing files. There are 7 (0 H + 7 S) secondary structure elements in 1dcz_A, of which 6 satisfy the size requirements. There are 7 (0 H + 7 S) secondary structure elements in 1iyu, of which 7 satisfy the size requirements. 1.00010 [ 1.16673] ((1 . 1) (2 . 2) (4 . 3) (5 . 4) (6 . 5) (7 . 7)) 2.253 {0/11:15} B:0 SIMILARITY (1/min{score1}): 0.9999 [and 1/min{score2}: 0.8571] [801, 3217]: Comparing 1dcz_A and 1k8m_A, based on their crossing files. There are 7 (0 H + 7 S) secondary structure elements in 1dcz_A, of which 6 satisfy the size requirements. There are 8 (0 H + 8 S) secondary structure elements in 1k8m_A, of which 6 satisfy the size requirements. 1.18927 [ 1.18927] ((1 . 1) (2 . 2) (4 . 4) (5 . 5) (6 . 6) (7 . 8)) 2.295 {1/10:15} B:0 1.58044 [ 1.58044] ((2 . 2) (4 . 4) (5 . 5) (6 . 6) (7 . 8)) 2.224 {1/7:10} B:0 2.14426 [ 2.14426] ((1 . 2) (2 . 4) (4 . 5) (6 . 8)) 8.450 {1/5:6} B:0 2.57742 [ 2.57742] ((1 . 1) (2 . 2) (5 . 4) (7 . 8)) 4.340 {1/4:6} B:0 SIMILARITY (1/min{score1}): 0.8409 [and 1/min{score2}: 0.8409] [801, 3324]: Comparing 1dcz_A and 1kjq_A, based on their crossing files. There are 7 (0 H + 7 S) secondary structure elements in 1dcz_A, of which 6 satisfy the size requirements. There are 36 (14 H + 22 S) secondary structure elements in 1kjq_A, of which 8 satisfy the size requirements. 3.34725 [ 3.37673] ((2 . 32) (4 . 34) (5 . 28) (6 . 30) (7 . 36)) 3.120 {1/3:10} B:1 6.67100 [ 6.68019] ((1 . 30) (2 . 32) (4 . 34) (5 . 33)) 8.557 {2/3:6} B:1 1.20078 [ 1.60033] ((1 . 36) (2 . 32) (4 . 34) (5 . 28) (7 . 30)) 4.331 {0/1:10} B:2 SIMILARITY (1/min{score1}): 0.8328 [and 1/min{score2}: 0.6249] [801, 5482]: Comparing 1dcz_A and 1qwy_A, based on their crossing files. There are 7 (0 H + 7 S) secondary structure elements in 1dcz_A, of which 6 satisfy the size requirements. There are 26 (6 H + 20 S) secondary structure elements in 1qwy_A, of which 15 satisfy the size requirements. 1.20011 [ 3.00001] ((1 . 15) (2 . 16) (4 . 17) (5 . 18) (7 . 21)) 2.646 {0/3:10} B:0 1.50143 [ 3.75009] ((1 . 1) (2 . 2) (4 . 4) (5 . 5)) 5.966 {0/3:6} B:0 1.50625 [ 3.75040] ((1 . 16) (2 . 17) (4 . 18) (6 . 21)) 8.636 {0/2:6} B:0 5.01021 [ 5.35581] ((1 . 14) (2 . 15) (4 . 17) (7 . 21)) 7.923 {2/4:6} B:0 7.50302 [ 7.61456] ((1 . 14) (2 . 15) (4 . 17) (5 . 16)) 7.350 {3/4:6} B:1 SIMILARITY (1/min{score1}): 0.8333 [and 1/min{score2}: 0.3333] -------------------------------------------------------------------------------------------------------------------------