------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [3058, 149]: Comparing 1jtk_A and 1aln, based on their crossing files. There are 11 (6 H + 5 S) secondary structure elements in 1jtk_A, of which 8 satisfy the size requirements. There are 25 (15 H + 10 S) secondary structure elements in 1aln, of which 11 satisfy the size requirements. 1.14289 [ 1.57144] ((1 . 6) (2 . 7) (3 . 8) (5 . 10) (6 . 11) (7 . 12) (8 . 14)) 1.923 {0/12:21} B:0 1.33336 [ 1.83334] ((1 . 6) (2 . 7) (3 . 8) (6 . 11) (7 . 12) (8 . 14)) 2.023 {0/7:15} B:0 2.00027 [ 2.75010] ((1 . 6) (3 . 11) (5 . 12) (6 . 14)) 4.871 {0/4:6} B:0 2.00103 [ 2.75040] ((1 . 2) (6 . 8) (7 . 10) (8 . 11)) 6.818 {0/3:6} B:0 2.00306 [ 2.75118] ((1 . 1) (5 . 6) (6 . 7) (9 . 11)) 8.954 {0/5:6} B:0 SIMILARITY (1/min{score1}): 0.8750 [and 1/min{score2}: 0.6364] [3058, 150]: Comparing 1jtk_A and 1aln, based on their crossing files. There are 11 (6 H + 5 S) secondary structure elements in 1jtk_A, of which 8 satisfy the size requirements. There are 25 (15 H + 10 S) secondary structure elements in 1aln, of which 8 satisfy the size requirements. 1.14288 [ 1.14288] ((1 . 18) (2 . 19) (3 . 20) (5 . 21) (6 . 23) (7 . 24) (8 . 25)) 1.754 {0/11:21} B:0 2.00008 [ 2.00008] ((1 . 18) (3 . 23) (5 . 24) (6 . 25)) 3.610 {0/3:6} B:0 3.43656 [ 3.43656] ((1 . 18) (2 . 20) (5 . 24) (6 . 25)) 5.904 {1/3:6} B:0 5.03202 [ 5.03202] ((1 . 17) (6 . 20) (7 . 21) (8 . 23)) 10.211 {1/2:6} B:0 10.00401 [10.00401] ((1 . 21) (3 . 23) (5 . 24) (6 . 25)) 8.034 {3/3:6} B:0 SIMILARITY (1/min{score1}): 0.8750 [and 1/min{score2}: 0.8750] [3058, 1772]: Comparing 1jtk_A and 1g8m_A, based on their crossing files. There are 11 (6 H + 5 S) secondary structure elements in 1jtk_A, of which 8 satisfy the size requirements. There are 48 (26 H + 22 S) secondary structure elements in 1g8m_A, of which 30 satisfy the size requirements. 1.14323 [ 4.28572] ((1 . 20) (2 . 21) (3 . 22) (5 . 25) (6 . 26) (7 . 27) (8 . 28)) 3.475 {0/10:21} B:0 1.60013 [ 6.00000] ((3 . 44) (5 . 45) (6 . 46) (7 . 47) (8 . 48)) 3.468 {0/3:10} B:0 1.60021 [ 6.00000] ((3 . 26) (5 . 27) (6 . 28) (7 . 29) (8 . 30)) 3.879 {0/2:10} B:0 1.60025 [ 6.00000] ((1 . 20) (5 . 27) (6 . 28) (7 . 29) (8 . 30)) 4.049 {0/4:10} B:0 1.60052 [ 6.00001] ((1 . 20) (5 . 25) (6 . 26) (7 . 29) (8 . 30)) 4.856 {0/5:10} B:0 SIMILARITY (1/min{score1}): 0.9994 [and 1/min{score2}: 0.2667] [3058, 3058]: Comparing 1jtk_A and 1jtk_A, based on their crossing files. There are 11 (6 H + 5 S) secondary structure elements in 1jtk_A, of which 8 satisfy the size requirements. There are 11 (6 H + 5 S) secondary structure elements in 1jtk_A, of which 8 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (2 . 2) (3 . 3) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9)) 0.000 {0/18:28} B:0 2.00013 [ 2.00013] ((1 . 1) (3 . 6) (5 . 7) (6 . 8)) 4.073 {0/3:6} B:0 2.00013 [ 2.00013] ((1 . 1) (6 . 3) (7 . 5) (8 . 6)) 4.073 {0/3:6} B:0 3.37672 [ 3.37672] ((1 . 1) (2 . 3) (5 . 5) (6 . 6) (7 . 7)) 2.820 {2/6:10} B:0 3.37672 [ 3.37672] ((1 . 1) (3 . 2) (5 . 5) (6 . 6) (7 . 7)) 2.820 {2/6:10} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [3058, 4664]: Comparing 1jtk_A and 1oi0_A, based on their crossing files. There are 11 (6 H + 5 S) secondary structure elements in 1jtk_A, of which 8 satisfy the size requirements. There are 11 (2 H + 9 S) secondary structure elements in 1oi0_A, of which 7 satisfy the size requirements. 1.14335 [ 1.00073] ((1 . 2) (2 . 3) (3 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9)) 3.726 {0/11:21} B:0 1.33353 [ 1.16696] ((2 . 3) (3 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9)) 3.327 {0/6:15} B:0 1.33354 [ 1.16698] ((1 . 2) (2 . 3) (6 . 6) (7 . 7) (8 . 8) (9 . 9)) 3.384 {0/7:15} B:0 2.00015 [ 1.75022] ((1 . 2) (2 . 3) (3 . 5) (6 . 8)) 4.211 {0/3:6} B:0 2.00019 [ 1.75028] ((1 . 2) (3 . 6) (5 . 7) (6 . 8)) 4.448 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.8746 [and 1/min{score2}: 0.9993] [3058, 4913]: Comparing 1jtk_A and 1p6o_A, based on their crossing files. There are 11 (6 H + 5 S) secondary structure elements in 1jtk_A, of which 8 satisfy the size requirements. There are 13 (8 H + 5 S) secondary structure elements in 1p6o_A, of which 13 satisfy the size requirements. 1.14297 [ 1.85717] ((1 . 1) (2 . 2) (3 . 3) (5 . 5) (6 . 7) (7 . 8) (8 . 9)) 2.600 {0/11:21} B:0 2.00009 [ 3.25002] ((1 . 1) (6 . 9) (7 . 10) (8 . 11)) 3.664 {0/3:6} B:0 2.00010 [ 3.25002] ((3 . 7) (5 . 8) (6 . 9) (8 . 11)) 3.780 {0/2:6} B:0 2.00015 [ 3.25003] ((1 . 1) (5 . 8) (6 . 9) (8 . 11)) 4.179 {0/4:6} B:0 2.00112 [ 3.25026] ((1 . 1) (5 . 4) (6 . 7) (7 . 8)) 6.958 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.8749 [and 1/min{score2}: 0.5385] -------------------------------------------------------------------------------------------------------------------------