------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [1511, 1511]: Comparing 1fit and 1fit, based on their crossing files. There are 12 (5 H + 7 S) secondary structure elements in 1fit, of which 9 satisfy the size requirements. There are 12 (5 H + 7 S) secondary structure elements in 1fit, of which 9 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (2 . 2) (4 . 4) (5 . 5) (6 . 6) (8 . 8) (9 . 9) (11 . 11) (12 . 12)) 0.000 {0/30:36} B:0 3.49448 [ 3.49448] ((6 . 4) (8 . 8) (11 . 9) (12 . 12)) 6.811 {1/3:6} B:0 3.49448 [ 3.49448] ((4 . 6) (8 . 8) (9 . 11) (12 . 12)) 6.811 {1/3:6} B:0 5.02087 [ 5.02087] ((1 . 2) (8 . 8) (9 . 9) (11 . 11) (12 . 12)) 3.345 {4/8:10} B:0 5.02087 [ 5.02087] ((4 . 5) (8 . 8) (9 . 9) (11 . 11) (12 . 12)) 4.033 {4/8:10} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [1511, 1960]: Comparing 1fit and 1guq_A, based on their crossing files. There are 12 (5 H + 7 S) secondary structure elements in 1fit, of which 9 satisfy the size requirements. There are 26 (11 H + 15 S) secondary structure elements in 1guq_A, of which 10 satisfy the size requirements. 1.80010 [ 2.00008] ((5 . 4) (6 . 6) (8 . 8) (9 . 9) (11 . 11)) 3.557 {0/5:10} B:0 2.25008 [ 2.50006] ((6 . 6) (8 . 8) (9 . 9) (11 . 11)) 3.914 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.5555 [and 1/min{score2}: 0.5000] [1511, 1961]: Comparing 1fit and 1guq_A, based on their crossing files. There are 12 (5 H + 7 S) secondary structure elements in 1fit, of which 9 satisfy the size requirements. There are 26 (11 H + 15 S) secondary structure elements in 1guq_A, of which 11 satisfy the size requirements. 1.32512 [ 1.59355] ((4 . 14) (5 . 15) (6 . 16) (8 . 18) (9 . 19) (11 . 20) (12 . 25)) 2.484 {1/13:21} B:0 1.50003 [ 1.83335] ((4 . 14) (5 . 15) (6 . 16) (8 . 18) (9 . 19) (11 . 20)) 2.312 {0/7:15} B:0 2.25090 [ 2.75049] ((8 . 18) (9 . 19) (11 . 21) (12 . 25)) 7.198 {0/3:6} B:0 2.25112 [ 2.75062] ((1 . 15) (2 . 16) (8 . 18) (12 . 25)) 7.612 {0/3:6} B:0 2.25116 [ 2.75064] ((1 . 15) (4 . 16) (8 . 18) (12 . 25)) 7.675 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.7546 [and 1/min{score2}: 0.6275] [1511, 3390]: Comparing 1fit and 1kpf, based on their crossing files. There are 12 (5 H + 7 S) secondary structure elements in 1fit, of which 9 satisfy the size requirements. There are 9 (4 H + 5 S) secondary structure elements in 1kpf, of which 8 satisfy the size requirements. 1.50004 [ 1.33339] ((4 . 2) (5 . 3) (6 . 4) (8 . 6) (9 . 7) (11 . 9)) 2.485 {0/8:15} B:0 1.80003 [ 1.60005] ((5 . 3) (6 . 4) (8 . 6) (9 . 7) (11 . 9)) 2.676 {0/4:10} B:0 7.50622 [ 7.50388] ((5 . 2) (6 . 4) (8 . 6) (9 . 7) (11 . 9)) 4.431 {3/4:10} B:0 10.00640 [10.00400] ((4 . 3) (8 . 6) (9 . 7) (11 . 9)) 5.519 {3/3:6} B:0 SIMILARITY (1/min{score1}): 0.6666 [and 1/min{score2}: 0.7500] [1511, 3580]: Comparing 1fit and 1l9v_A, based on their crossing files. There are 12 (5 H + 7 S) secondary structure elements in 1fit, of which 9 satisfy the size requirements. There are 24 (15 H + 9 S) secondary structure elements in 1l9v_A, of which 10 satisfy the size requirements. 1.50010 [ 1.66674] ((4 . 14) (5 . 15) (6 . 17) (8 . 18) (9 . 19) (11 . 20)) 3.092 {0/8:15} B:0 1.80007 [ 2.00005] ((5 . 15) (6 . 17) (8 . 18) (9 . 19) (11 . 20)) 3.166 {0/4:10} B:0 2.25052 [ 2.50038] ((1 . 17) (5 . 19) (6 . 20) (8 . 22)) 6.273 {0/2:6} B:0 5.05052 [ 5.07639] ((6 . 15) (8 . 18) (9 . 19) (11 . 20)) 5.608 {1/2:6} B:0 7.51515 [ 7.52305] ((5 . 14) (8 . 18) (9 . 19) (11 . 20)) 5.798 {3/4:6} B:0 SIMILARITY (1/min{score1}): 0.6666 [and 1/min{score2}: 0.6000] [1511, 5849]: Comparing 1fit and 1st0_A, based on their crossing files. There are 12 (5 H + 7 S) secondary structure elements in 1fit, of which 9 satisfy the size requirements. There are 27 (13 H + 14 S) secondary structure elements in 1st0_A, of which 15 satisfy the size requirements. 1.50005 [ 2.50001] ((4 . 15) (5 . 16) (6 . 17) (8 . 19) (9 . 21) (11 . 22)) 2.542 {0/7:15} B:0 2.54141 [ 3.82404] ((4 . 21) (5 . 22) (8 . 24) (9 . 26)) 8.675 {1/5:6} B:0 3.49510 [ 4.23394] ((1 . 21) (2 . 22) (4 . 23) (8 . 27)) 9.771 {2/6:6} B:0 6.02953 [ 6.21692] ((4 . 21) (5 . 22) (9 . 26) (12 . 19)) 8.405 {3/5:6} B:1 1.51654 [ 2.50362] ((4 . 22) (5 . 21) (8 . 11) (9 . 10) (11 . 26) (12 . 19)) 11.043 {0/12:15} B:4 SIMILARITY (1/min{score1}): 0.6666 [and 1/min{score2}: 0.4000] -------------------------------------------------------------------------------------------------------------------------