------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [3853, 978]: Comparing 1m65_A and 1dys_A, based on their crossing files. There are 20 (12 H + 8 S) secondary structure elements in 1m65_A, of which 14 satisfy the size requirements. There are 23 (13 H + 10 S) secondary structure elements in 1dys_A, of which 18 satisfy the size requirements. 1.40265 [ 1.80125] ((3 . 4) (4 . 5) (6 . 6) (7 . 9) (8 . 10) (9 . 12) (11 . 15) (12 . 16) (13 . 18) (14 . 19)) 5.390 {1/28:45} B:0 1.40402 [ 1.80190] ((2 . 9) (3 . 10) (4 . 12) (6 . 13) (7 . 15) (8 . 16) (9 . 17) (11 . 18) (12 . 19) (14 . 22)) 6.546 {1/28:45} B:0 1.41941 [ 1.80925] ((3 . 4) (4 . 5) (6 . 6) (7 . 9) (8 . 10) (9 . 12) (12 . 13) (13 . 15) (14 . 16) (16 . 18)) 6.019 {2/30:45} B:0 1.55932 [ 2.00177] ((2 . 9) (3 . 10) (4 . 12) (6 . 13) (7 . 15) (8 . 16) (9 . 18) (12 . 19) (14 . 22)) 6.097 {1/23:36} B:0 2.00151 [ 2.57214] ((8 . 4) (9 . 5) (11 . 9) (12 . 10) (13 . 12) (14 . 13) (16 . 15)) 7.504 {0/11:21} B:0 SIMILARITY (1/min{score1}): 0.7818 [and 1/min{score2}: 0.6100] [3853, 3131]: Comparing 1m65_A and 1k1x_A, based on their crossing files. There are 20 (12 H + 8 S) secondary structure elements in 1m65_A, of which 14 satisfy the size requirements. There are 53 (27 H + 26 S) secondary structure elements in 1k1x_A, of which 25 satisfy the size requirements. 1.66011 [ 2.55801] ((3 . 1) (4 . 2) (6 . 4) (7 . 6) (8 . 7) (9 . 9) (12 . 10) (13 . 12) (14 . 13) (20 . 23)) 6.805 {5/36:45} B:0 1.78854 [ 3.13197] ((2 . 3) (3 . 4) (4 . 5) (6 . 7) (7 . 9) (9 . 12) (12 . 13) (16 . 25)) 6.729 {2/21:28} B:0 2.00503 [ 3.57231] ((4 . 3) (6 . 4) (7 . 6) (8 . 7) (9 . 9) (12 . 13) (14 . 17)) 4.924 {1/16:21} B:0 2.33375 [ 4.16674] ((2 . 9) (3 . 10) (6 . 13) (8 . 17) (9 . 19) (13 . 23)) 6.107 {0/12:15} B:0 2.34045 [ 4.16792] ((3 . 1) (6 . 4) (8 . 7) (11 . 9) (13 . 12) (14 . 13)) 5.413 {1/13:15} B:0 SIMILARITY (1/min{score1}): 0.7789 [and 1/min{score2}: 0.4396] [3853, 3853]: Comparing 1m65_A and 1m65_A, based on their crossing files. There are 20 (12 H + 8 S) secondary structure elements in 1m65_A, of which 14 satisfy the size requirements. There are 20 (12 H + 8 S) secondary structure elements in 1m65_A, of which 14 satisfy the size requirements. 1.00000 [ 1.00000] ((2 . 2) (3 . 3) (4 . 4) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (11 . 11) (12 . 12) (13 . 13) (14 . 14) (16 . 16) (19 . 19) (20 . 20)) 0.000 {0/79:91} B:0 1.55564 [ 1.55564] ((2 . 2) (3 . 3) (4 . 4) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (11 . 13) (12 . 14)) 3.043 {0/26:36} B:0 1.55564 [ 1.55564] ((2 . 2) (3 . 3) (4 . 4) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (13 . 11) (14 . 12)) 3.043 {0/26:36} B:0 1.89467 [ 1.89467] ((2 . 4) (3 . 6) (6 . 8) (7 . 9) (8 . 12) (12 . 14) (13 . 19) (16 . 20)) 7.558 {3/22:28} B:0 2.00768 [ 2.00768] ((2 . 4) (3 . 6) (6 . 8) (7 . 9) (8 . 12) (12 . 14) (13 . 19)) 7.552 {1/15:21} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [3853, 4432]: Comparing 1m65_A and 1ny1_A, based on their crossing files. There are 20 (12 H + 8 S) secondary structure elements in 1m65_A, of which 14 satisfy the size requirements. There are 21 (12 H + 9 S) secondary structure elements in 1ny1_A, of which 14 satisfy the size requirements. 2.80013 [ 2.80013] ((4 . 4) (6 . 5) (8 . 8) (9 . 10) (13 . 14)) 5.183 {0/6:10} B:0 2.80017 [ 2.80017] ((7 . 2) (12 . 5) (13 . 7) (14 . 8) (16 . 10)) 5.580 {0/8:10} B:0 2.80025 [ 2.80025] ((4 . 6) (6 . 8) (7 . 10) (9 . 14) (14 . 18)) 6.181 {0/6:10} B:0 2.80034 [ 2.80034] ((12 . 5) (13 . 7) (14 . 8) (16 . 10) (20 . 14)) 6.629 {0/8:10} B:0 2.80086 [ 2.80086] ((3 . 5) (6 . 8) (7 . 10) (12 . 18) (13 . 19)) 8.384 {0/6:10} B:0 SIMILARITY (1/min{score1}): 0.7794 [and 1/min{score2}: 0.7794] [3853, 4594]: Comparing 1m65_A and 1oc7_A, based on their crossing files. There are 20 (12 H + 8 S) secondary structure elements in 1m65_A, of which 14 satisfy the size requirements. There are 21 (13 H + 8 S) secondary structure elements in 1oc7_A, of which 17 satisfy the size requirements. 1.40162 [ 1.70091] ((2 . 7) (3 . 8) (4 . 9) (6 . 10) (7 . 12) (8 . 13) (9 . 14) (11 . 17) (12 . 18) (14 . 19)) 5.848 {0/27:45} B:0 1.55880 [ 1.89070] ((2 . 7) (3 . 10) (4 . 12) (6 . 13) (7 . 14) (8 . 15) (9 . 17) (12 . 18) (14 . 19)) 6.258 {1/25:36} B:0 1.55952 [ 1.89111] ((2 . 9) (3 . 10) (4 . 12) (6 . 13) (7 . 14) (8 . 15) (9 . 17) (12 . 18) (14 . 19)) 6.647 {1/24:36} B:0 2.00037 [ 2.42878] ((3 . 8) (4 . 9) (6 . 10) (8 . 13) (11 . 14) (13 . 17) (14 . 18)) 5.278 {0/14:21} B:0 2.33356 [ 2.83346] ((4 . 9) (6 . 10) (8 . 13) (9 . 14) (13 . 17) (14 . 18)) 5.267 {0/9:15} B:0 SIMILARITY (1/min{score1}): 0.7565 [and 1/min{score2}: 0.6354] [3853, 5477]: Comparing 1m65_A and 1qwn_A, based on their crossing files. There are 20 (12 H + 8 S) secondary structure elements in 1m65_A, of which 14 satisfy the size requirements. There are 74 (25 H + 49 S) secondary structure elements in 1qwn_A, of which 22 satisfy the size requirements. 2.34673 [ 3.67014] ((3 . 4) (8 . 7) (11 . 11) (12 . 12) (13 . 13) (14 . 14)) 3.960 {1/11:15} B:0 2.80009 [ 4.40002] ((4 . 6) (6 . 7) (8 . 10) (9 . 11) (12 . 14)) 4.730 {0/5:10} B:0 2.80010 [ 4.40003] ((3 . 4) (4 . 6) (6 . 7) (9 . 11) (12 . 14)) 4.880 {0/6:10} B:0 2.80012 [ 4.40003] ((3 . 12) (4 . 13) (8 . 17) (14 . 22) (16 . 23)) 5.155 {0/7:10} B:0 2.80021 [ 4.40005] ((2 . 13) (3 . 14) (6 . 17) (11 . 21) (13 . 23)) 5.894 {0/8:10} B:0 SIMILARITY (1/min{score1}): 0.7803 [and 1/min{score2}: 0.5234] [3853, 5919]: Comparing 1m65_A and 1tml, based on their crossing files. There are 20 (12 H + 8 S) secondary structure elements in 1m65_A, of which 14 satisfy the size requirements. There are 17 (10 H + 7 S) secondary structure elements in 1tml, of which 16 satisfy the size requirements. 1.27695 [ 1.45738] ((2 . 4) (3 . 5) (4 . 6) (6 . 7) (7 . 9) (8 . 10) (9 . 11) (11 . 14) (12 . 15) (14 . 16) (16 . 17)) 6.920 {0/38:55} B:0 1.40139 [ 1.60093] ((2 . 4) (3 . 5) (4 . 6) (6 . 7) (7 . 9) (8 . 10) (9 . 11) (11 . 14) (12 . 15) (14 . 16)) 5.629 {0/29:45} B:0 1.40188 [ 1.60126] ((2 . 4) (3 . 5) (4 . 6) (6 . 7) (7 . 9) (8 . 10) (9 . 11) (12 . 13) (13 . 14) (14 . 15)) 6.064 {0/30:45} B:0 1.40419 [ 1.60281] ((2 . 4) (3 . 7) (4 . 9) (6 . 10) (7 . 11) (8 . 13) (9 . 14) (12 . 15) (14 . 16) (16 . 17)) 7.054 {1/33:45} B:0 1.42187 [ 1.61479] ((3 . 3) (4 . 4) (6 . 5) (7 . 6) (8 . 7) (9 . 9) (11 . 11) (12 . 13) (13 . 14) (14 . 15)) 5.978 {2/29:45} B:0 SIMILARITY (1/min{score1}): 0.8509 [and 1/min{score2}: 0.7468] [3853, 6000]: Comparing 1m65_A and 1ufa_A, based on their crossing files. There are 20 (12 H + 8 S) secondary structure elements in 1m65_A, of which 14 satisfy the size requirements. There are 40 (26 H + 14 S) secondary structure elements in 1ufa_A, of which 22 satisfy the size requirements. 2.00371 [ 3.14381] ((2 . 16) (3 . 17) (6 . 21) (11 . 27) (12 . 28) (13 . 30) (14 . 31)) 6.278 {1/18:21} B:0 2.33367 [ 3.66675] ((2 . 16) (3 . 17) (6 . 21) (9 . 27) (12 . 28) (13 . 30)) 5.786 {0/12:15} B:0 2.80010 [ 4.40003] ((4 . 16) (6 . 17) (8 . 21) (14 . 28) (19 . 32)) 4.909 {0/8:10} B:0 2.80061 [ 4.40016] ((6 . 21) (9 . 27) (12 . 28) (13 . 30) (14 . 31)) 7.712 {0/9:10} B:0 2.81162 [ 4.40301] ((2 . 11) (6 . 17) (8 . 21) (13 . 27) (14 . 28)) 6.443 {1/10:10} B:0 SIMILARITY (1/min{score1}): 0.8386 [and 1/min{score2}: 0.5434] -------------------------------------------------------------------------------------------------------------------------