------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [2958, 846]: Comparing 1jlj_A and 1di6_A, based on their crossing files. There are 15 (9 H + 6 S) secondary structure elements in 1jlj_A, of which 14 satisfy the size requirements. There are 16 (8 H + 8 S) secondary structure elements in 1di6_A, of which 14 satisfy the size requirements. 1.16671 [ 1.16671] ((1 . 1) (3 . 2) (4 . 3) (5 . 4) (6 . 5) (7 . 6) (9 . 8) (10 . 9) (11 . 10) (12 . 11) (13 . 12) (14 . 15)) 2.107 {0/43:66} B:0 1.27277 [ 1.27277] ((1 . 1) (3 . 2) (4 . 3) (5 . 4) (6 . 5) (7 . 6) (9 . 8) (11 . 10) (12 . 11) (13 . 12) (14 . 15)) 2.145 {0/34:55} B:0 1.98748 [ 1.98748] ((1 . 1) (3 . 2) (4 . 3) (5 . 4) (6 . 5) (7 . 6) (9 . 8) (11 . 11) (13 . 12) (14 . 15)) 2.968 {5/27:45} B:0 2.80039 [ 2.80039] ((1 . 5) (3 . 6) (5 . 9) (6 . 11) (7 . 12)) 6.901 {0/3:10} B:0 2.80045 [ 2.80045] ((3 . 2) (4 . 3) (5 . 4) (6 . 5) (14 . 12)) 7.144 {0/5:10} B:0 SIMILARITY (1/min{score1}): 0.8571 [and 1/min{score2}: 0.8571] [2958, 2958]: Comparing 1jlj_A and 1jlj_A, based on their crossing files. There are 15 (9 H + 6 S) secondary structure elements in 1jlj_A, of which 14 satisfy the size requirements. There are 15 (9 H + 6 S) secondary structure elements in 1jlj_A, of which 14 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (9 . 9) (10 . 10) (11 . 11) (12 . 12) (13 . 13) (14 . 14) (15 . 15)) 0.000 {0/66:91} B:0 1.16867 [ 1.16867] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (9 . 9) (11 . 11) (12 . 12) (13 . 13) (15 . 14)) 5.099 {1/45:66} B:0 1.75073 [ 1.75073] ((1 . 1) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (9 . 9) (10 . 10) (14 . 15)) 5.661 {0/18:28} B:0 3.16780 [ 3.16780] ((1 . 4) (3 . 5) (4 . 6) (5 . 7) (10 . 14)) 10.316 {1/4:10} B:0 3.16780 [ 3.16780] ((4 . 1) (5 . 3) (6 . 4) (7 . 5) (14 . 10)) 10.316 {1/4:10} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [2958, 3967]: Comparing 1jlj_A and 1mkz_A, based on their crossing files. There are 15 (9 H + 6 S) secondary structure elements in 1jlj_A, of which 14 satisfy the size requirements. There are 15 (9 H + 6 S) secondary structure elements in 1mkz_A, of which 12 satisfy the size requirements. 1.16795 [ 1.00203] ((1 . 1) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (9 . 9) (10 . 10) (11 . 11) (12 . 12) (13 . 13) (14 . 14)) 3.465 {1/36:66} B:0 1.27274 [ 1.09093] ((1 . 1) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (9 . 9) (10 . 10) (11 . 11) (12 . 12) (13 . 13)) 1.663 {0/33:55} B:0 1.27567 [ 1.09556] ((1 . 1) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (9 . 9) (11 . 11) (12 . 12) (13 . 13) (14 . 14)) 3.557 {1/26:55} B:0 1.55562 [ 1.33343] ((1 . 1) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (9 . 9) (10 . 10) (13 . 14)) 2.771 {0/20:36} B:0 2.33394 [ 2.00097] ((1 . 1) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (14 . 13)) 6.717 {0/1:15} B:0 SIMILARITY (1/min{score1}): 0.8562 [and 1/min{score2}: 0.9980] [2958, 6147]: Comparing 1jlj_A and 1uz5_A, based on their crossing files. There are 15 (9 H + 6 S) secondary structure elements in 1jlj_A, of which 14 satisfy the size requirements. There are 37 (11 H + 26 S) secondary structure elements in 1uz5_A, of which 11 satisfy the size requirements. 1.44216 [ 1.18142] ((1 . 18) (3 . 21) (4 . 22) (5 . 23) (6 . 24) (7 . 25) (11 . 28) (12 . 29) (13 . 30) (14 . 31)) 3.285 {2/24:45} B:0 1.55557 [ 1.22226] ((1 . 18) (3 . 21) (4 . 22) (5 . 23) (6 . 24) (7 . 25) (11 . 28) (12 . 29) (13 . 30)) 2.000 {0/19:36} B:0 1.64836 [ 1.39241] ((1 . 18) (3 . 21) (4 . 22) (5 . 23) (6 . 24) (7 . 25) (11 . 28) (12 . 29) (13 . 31)) 3.831 {2/18:36} B:0 2.33357 [ 1.83383] ((1 . 18) (3 . 21) (4 . 22) (5 . 23) (7 . 25) (10 . 30)) 5.312 {0/8:15} B:0 2.80045 [ 2.20093] ((1 . 18) (3 . 21) (4 . 22) (5 . 23) (10 . 31)) 7.143 {0/2:10} B:0 SIMILARITY (1/min{score1}): 0.6934 [and 1/min{score2}: 0.8464] -------------------------------------------------------------------------------------------------------------------------