------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [125, 125]: Comparing 1agr_E and 1agr_E, based on their crossing files. There are 9 (9 H + 0 S) secondary structure elements in 1agr_E, of which 9 satisfy the size requirements. There are 9 (9 H + 0 S) secondary structure elements in 1agr_E, of which 9 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9)) 0.000 {0/34:36} B:0 1.28641 [ 1.28641] ((3 . 2) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9)) 4.435 {0/19:21} B:0 1.80030 [ 1.80030] ((2 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7)) 4.630 {0/8:10} B:0 2.25980 [ 2.25980] ((1 . 4) (3 . 5) (4 . 6) (5 . 7)) 13.100 {0/3:6} B:0 2.25980 [ 2.25980] ((4 . 1) (5 . 3) (6 . 4) (7 . 5)) 13.100 {0/3:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [125, 1216]: Comparing 1agr_E and 1emu_A, based on their crossing files. There are 9 (9 H + 0 S) secondary structure elements in 1agr_E, of which 9 satisfy the size requirements. There are 10 (10 H + 0 S) secondary structure elements in 1emu_A, of which 10 satisfy the size requirements. 1.00188 [ 1.11248] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 7) (7 . 8) (8 . 9) (9 . 10)) 1.416 {1/34:36} B:0 1.51912 [ 1.68070] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (9 . 9)) 3.685 {1/14:15} B:0 1.51968 [ 1.68111] ((2 . 3) (5 . 5) (6 . 7) (7 . 8) (8 . 9) (9 . 10)) 5.141 {1/14:15} B:0 2.25592 [ 2.50432] ((3 . 6) (4 . 7) (5 . 8) (6 . 10)) 11.541 {0/4:6} B:0 2.25691 [ 2.50505] ((5 . 3) (6 . 4) (7 . 5) (9 . 7)) 11.999 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.9981 [and 1/min{score2}: 0.8989] [125, 1606]: Comparing 1agr_E and 1fqi_A, based on their crossing files. There are 9 (9 H + 0 S) secondary structure elements in 1agr_E, of which 9 satisfy the size requirements. There are 9 (9 H + 0 S) secondary structure elements in 1fqi_A, of which 9 satisfy the size requirements. 1.00271 [ 1.00271] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9)) 1.385 {1/31:36} B:0 2.26036 [ 2.26036] ((1 . 4) (3 . 5) (4 . 6) (5 . 7)) 13.284 {0/4:6} B:0 2.26071 [ 2.26071] ((4 . 1) (5 . 3) (6 . 4) (7 . 5)) 13.395 {0/2:6} B:0 2.83923 [ 2.83923] ((3 . 5) (4 . 6) (5 . 7) (6 . 9)) 11.765 {1/4:6} B:0 SIMILARITY (1/min{score1}): 0.9973 [and 1/min{score2}: 0.9973] [125, 2286]: Comparing 1agr_E and 1htj_F, based on their crossing files. There are 9 (9 H + 0 S) secondary structure elements in 1agr_E, of which 9 satisfy the size requirements. There are 11 (11 H + 0 S) secondary structure elements in 1htj_F, of which 11 satisfy the size requirements. 1.30024 [ 1.57946] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7)) 4.421 {1/17:21} B:0 2.25088 [ 2.75048] ((1 . 2) (2 . 3) (3 . 4) (4 . 5)) 7.170 {0/4:6} B:0 2.25295 [ 2.75162] ((1 . 5) (2 . 6) (6 . 10) (7 . 11)) 9.695 {0/5:6} B:0 2.25534 [ 2.75293] ((3 . 7) (4 . 9) (5 . 10) (6 . 11)) 11.247 {0/3:6} B:0 2.25690 [ 2.75379] ((5 . 3) (6 . 4) (7 . 5) (9 . 6)) 11.993 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.7691 [and 1/min{score2}: 0.6331] [125, 2443]: Comparing 1agr_E and 1iap_A, based on their crossing files. There are 9 (9 H + 0 S) secondary structure elements in 1agr_E, of which 9 satisfy the size requirements. There are 10 (10 H + 0 S) secondary structure elements in 1iap_A, of which 10 satisfy the size requirements. 1.13274 [ 1.25566] ((2 . 1) (3 . 2) (4 . 3) (5 . 4) (6 . 5) (7 . 6) (8 . 7) (9 . 8)) 5.541 {1/24:28} B:0 2.25217 [ 2.50158] ((3 . 7) (4 . 8) (5 . 9) (6 . 10)) 8.975 {0/3:6} B:0 2.25423 [ 2.50308] ((1 . 5) (2 . 6) (4 . 8) (5 . 9)) 10.606 {0/5:6} B:0 2.25490 [ 2.50358] ((5 . 2) (6 . 3) (7 . 4) (9 . 5)) 11.009 {0/3:6} B:0 2.25705 [ 2.50515] ((1 . 4) (3 . 5) (4 . 6) (8 . 10)) 12.061 {0/5:6} B:0 SIMILARITY (1/min{score1}): 0.8828 [and 1/min{score2}: 0.7964] [125, 4716]: Comparing 1agr_E and 1omw_A, based on their crossing files. There are 9 (9 H + 0 S) secondary structure elements in 1agr_E, of which 9 satisfy the size requirements. There are 45 (28 H + 17 S) secondary structure elements in 1omw_A, of which 10 satisfy the size requirements. 1.13173 [ 1.25492] ((2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 7) (7 . 8) (8 . 9) (9 . 10)) 3.726 {1/23:28} B:0 1.28577 [ 1.42861] ((2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 7) (7 . 8) (8 . 9)) 2.388 {0/17:21} B:0 1.50113 [ 1.66749] ((2 . 3) (4 . 4) (5 . 6) (6 . 7) (7 . 8) (8 . 9)) 5.624 {0/12:15} B:0 1.80033 [ 2.00024] ((2 . 3) (5 . 6) (6 . 7) (7 . 8) (8 . 9)) 4.754 {0/8:10} B:0 2.25209 [ 2.50152] ((5 . 3) (6 . 4) (7 . 5) (8 . 6)) 8.891 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.8836 [and 1/min{score2}: 0.7969] -------------------------------------------------------------------------------------------------------------------------