------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [6073, 737]: Comparing 1up8_A and 1d2t_A, based on their crossing files. There are 36 (24 H + 12 S) secondary structure elements in 1up8_A, of which 29 satisfy the size requirements. There are 12 (12 H + 0 S) secondary structure elements in 1d2t_A, of which 10 satisfy the size requirements. 7.25016 [ 2.50399] ((5 . 8) (8 . 10) (10 . 11) (12 . 12)) 11.313 {0/2:6} B:0 7.25101 [ 2.52435] ((23 . 7) (26 . 9) (28 . 11) (29 . 12)) 17.836 {0/5:6} B:0 7.25124 [ 2.52964] ((22 . 3) (26 . 7) (29 . 10) (30 . 12)) 18.749 {0/5:6} B:0 7.27588 [ 2.97871] ((20 . 3) (22 . 4) (26 . 8) (29 . 11)) 14.080 {1/4:6} B:0 7.41266 [ 4.14599] ((20 . 3) (22 . 5) (27 . 10) (29 . 11)) 12.782 {2/5:6} B:0 SIMILARITY (1/min{score1}): 0.3058 [and 1/min{score2}: 0.5924] [6073, 5348]: Comparing 1up8_A and 1qi9_A, based on their crossing files. There are 36 (24 H + 12 S) secondary structure elements in 1up8_A, of which 29 satisfy the size requirements. There are 35 (25 H + 10 S) secondary structure elements in 1qi9_A, of which 24 satisfy the size requirements. 1.45236 [ 1.20415] ((1 . 1) (3 . 3) (4 . 4) (8 . 7) (10 . 9) (17 . 13) (18 . 14) (20 . 15) (22 . 16) (23 . 17) (26 . 20) (27 . 21) (29 . 23) (30 . 25) (31 . 27) (32 . 28) (33 . 29) (34 . 30) (35 . 31) (36 . 32)) 2.134 {6/146:190} B:0 1.83705 [ 1.70786] ((1 . 1) (3 . 3) (4 . 4) (8 . 9) (17 . 13) (18 . 14) (20 . 15) (22 . 16) (23 . 17) (26 . 20) (27 . 21) (29 . 23) (30 . 25) (31 . 27) (32 . 28) (33 . 29) (34 . 30) (35 . 31) (36 . 32)) 3.041 {20/128:171} B:0 1.92147 [ 1.81072] ((1 . 1) (3 . 3) (4 . 4) (8 . 7) (10 . 11) (17 . 13) (18 . 14) (20 . 15) (22 . 16) (23 . 17) (26 . 20) (27 . 21) (29 . 23) (30 . 25) (32 . 28) (33 . 29) (34 . 30) (35 . 32) (36 . 33)) 3.400 {22/130:171} B:0 2.00365 [ 1.92635] ((1 . 1) (3 . 3) (4 . 4) (8 . 7) (10 . 9) (17 . 13) (18 . 14) (20 . 15) (22 . 16) (23 . 17) (26 . 20) (27 . 21) (29 . 23) (30 . 25) (31 . 27) (32 . 28) (33 . 29) (34 . 30) (35 . 32) (36 . 33)) 2.486 {27/146:190} B:0 2.11421 [ 2.03347] ((1 . 1) (3 . 3) (4 . 4) (8 . 7) (10 . 9) (17 . 13) (18 . 14) (20 . 15) (22 . 16) (23 . 17) (26 . 20) (27 . 21) (29 . 23) (30 . 25) (31 . 27) (33 . 29) (34 . 30) (35 . 32) (36 . 33)) 2.507 {25/128:171} B:0 SIMILARITY (1/min{score1}): 0.6885 [and 1/min{score2}: 0.8305] [6073, 6073]: Comparing 1up8_A and 1up8_A, based on their crossing files. There are 36 (24 H + 12 S) secondary structure elements in 1up8_A, of which 29 satisfy the size requirements. There are 36 (24 H + 12 S) secondary structure elements in 1up8_A, of which 29 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (3 . 3) (4 . 4) (5 . 5) (7 . 7) (8 . 8) (10 . 10) (12 . 12) (14 . 14) (15 . 15) (16 . 16) (17 . 17) (18 . 18) (19 . 19) (20 . 20) (21 . 21) (22 . 22) (23 . 23) (26 . 26) (27 . 27) (28 . 28) (29 . 29) (30 . 30) (31 . 31) (32 . 32) (33 . 33) (34 . 34) (35 . 35) (36 . 36)) 0.000 {0/326:406} B:0 1.17056 [ 1.17056] ((1 . 1) (3 . 3) (4 . 4) (5 . 5) (7 . 7) (8 . 8) (10 . 10) (12 . 12) (14 . 14) (16 . 16) (17 . 17) (18 . 18) (19 . 19) (20 . 20) (21 . 21) (22 . 22) (23 . 23) (26 . 26) (27 . 27) (28 . 28) (29 . 29) (30 . 30) (33 . 33) (34 . 34) (36 . 35)) 1.086 {12/236:300} B:0 1.17056 [ 1.17056] ((1 . 1) (3 . 3) (4 . 4) (5 . 5) (7 . 7) (8 . 8) (10 . 10) (12 . 12) (14 . 14) (16 . 16) (17 . 17) (18 . 18) (19 . 19) (20 . 20) (21 . 21) (22 . 22) (23 . 23) (26 . 26) (27 . 27) (28 . 28) (29 . 29) (30 . 30) (33 . 33) (34 . 34) (35 . 36)) 1.086 {12/236:300} B:0 1.72630 [ 1.72630] ((1 . 1) (4 . 3) (8 . 8) (10 . 10) (12 . 12) (17 . 17) (19 . 19) (20 . 20) (21 . 21) (22 . 22) (23 . 23) (26 . 26) (27 . 28) (29 . 29) (30 . 30) (31 . 31) (33 . 33) (34 . 34)) 3.487 {15/124:153} B:0 7.25031 [ 7.25031] ((20 . 8) (23 . 12) (28 . 20) (30 . 23)) 13.254 {0/5:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [6073, 6313]: Comparing 1up8_A and 1vns, based on their crossing files. There are 36 (24 H + 12 S) secondary structure elements in 1up8_A, of which 29 satisfy the size requirements. There are 31 (23 H + 8 S) secondary structure elements in 1vns, of which 21 satisfy the size requirements. 5.80007 [ 4.20019] ((20 . 12) (22 . 13) (23 . 14) (26 . 15) (33 . 24)) 7.796 {0/7:10} B:0 5.80029 [ 4.20077] ((8 . 2) (27 . 5) (29 . 6) (33 . 14) (34 . 17)) 11.048 {0/0:10} B:0 7.25014 [ 5.25037] ((5 . 2) (19 . 8) (21 . 9) (34 . 24)) 10.862 {0/4:6} B:0 7.25018 [ 5.25048] ((5 . 12) (8 . 14) (10 . 15) (22 . 24)) 11.622 {0/4:6} B:0 7.25021 [ 5.25055] ((1 . 5) (3 . 6) (23 . 17) (30 . 30)) 12.001 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.3447 [and 1/min{score2}: 0.4754] -------------------------------------------------------------------------------------------------------------------------