------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [4505, 1077]: Comparing 1o5z_A and 1e8c_A, based on their crossing files. There are 36 (19 H + 17 S) secondary structure elements in 1o5z_A, of which 10 satisfy the size requirements. There are 43 (19 H + 24 S) secondary structure elements in 1e8c_A, of which 12 satisfy the size requirements. 1.00027 [ 1.20016] ((25 . 30) (26 . 31) (27 . 32) (28 . 33) (29 . 34) (30 . 35) (31 . 36) (33 . 39) (34 . 40) (35 . 43)) 2.906 {0/21:45} B:0 1.11118 [ 1.33337] ((25 . 30) (26 . 31) (27 . 32) (28 . 33) (29 . 34) (30 . 35) (31 . 36) (33 . 39) (34 . 40)) 2.196 {0/17:36} B:0 2.00087 [ 2.40050] ((28 . 31) (29 . 32) (30 . 33) (31 . 34) (34 . 35)) 6.532 {0/1:10} B:0 2.00119 [ 2.40069] ((26 . 35) (27 . 36) (29 . 39) (30 . 40) (31 . 43)) 7.071 {0/5:10} B:0 2.00121 [ 2.40070] ((30 . 31) (31 . 32) (33 . 34) (34 . 35) (35 . 36)) 7.099 {0/5:10} B:0 SIMILARITY (1/min{score1}): 0.9997 [and 1/min{score2}: 0.8332] [4505, 1820]: Comparing 1o5z_A and 1gg4_A, based on their crossing files. There are 36 (19 H + 17 S) secondary structure elements in 1o5z_A, of which 10 satisfy the size requirements. There are 39 (17 H + 22 S) secondary structure elements in 1gg4_A, of which 11 satisfy the size requirements. 1.00584 [ 1.10440] ((25 . 28) (26 . 29) (27 . 30) (28 . 31) (29 . 32) (30 . 33) (31 . 34) (33 . 36) (34 . 37) (35 . 39)) 3.243 {1/26:45} B:0 1.11131 [ 1.22237] ((25 . 28) (26 . 29) (27 . 30) (28 . 31) (29 . 32) (30 . 33) (33 . 36) (34 . 37) (35 . 39)) 2.913 {0/19:36} B:0 1.11141 [ 1.22245] ((25 . 28) (26 . 29) (27 . 30) (28 . 31) (29 . 32) (30 . 33) (31 . 34) (34 . 37) (35 . 39)) 3.227 {0/22:36} B:0 2.00011 [ 2.20008] ((26 . 31) (27 . 32) (28 . 33) (29 . 34) (30 . 35)) 3.858 {0/2:10} B:0 2.00015 [ 2.20011] ((27 . 32) (28 . 33) (29 . 34) (30 . 35) (33 . 39)) 4.224 {0/1:10} B:0 SIMILARITY (1/min{score1}): 0.9942 [and 1/min{score2}: 0.9055] [4505, 2749]: Comparing 1o5z_A and 1j6u_A, based on their crossing files. There are 36 (19 H + 17 S) secondary structure elements in 1o5z_A, of which 10 satisfy the size requirements. There are 37 (16 H + 21 S) secondary structure elements in 1j6u_A, of which 11 satisfy the size requirements. 1.13926 [ 1.21072] ((25 . 27) (26 . 28) (27 . 29) (28 . 30) (29 . 31) (30 . 32) (31 . 33) (33 . 35) (34 . 36) (35 . 37)) 3.178 {2/22:45} B:0 1.14576 [ 1.24863] ((25 . 27) (26 . 28) (27 . 29) (28 . 30) (29 . 31) (30 . 32) (33 . 35) (34 . 36) (35 . 37)) 3.225 {1/15:36} B:0 2.00117 [ 2.20088] ((30 . 28) (31 . 29) (33 . 31) (34 . 32) (35 . 33)) 7.035 {0/5:10} B:0 2.00257 [ 2.20193] ((27 . 29) (28 . 32) (30 . 34) (31 . 35) (33 . 37)) 8.568 {0/2:10} B:0 2.00489 [ 2.20367] ((26 . 30) (27 . 31) (28 . 32) (29 . 33) (31 . 37)) 10.070 {0/5:10} B:0 SIMILARITY (1/min{score1}): 0.8997 [and 1/min{score2}: 0.8260] [4505, 2818]: Comparing 1o5z_A and 1jbw_A, based on their crossing files. There are 36 (19 H + 17 S) secondary structure elements in 1o5z_A, of which 10 satisfy the size requirements. There are 32 (16 H + 16 S) secondary structure elements in 1jbw_A, of which 9 satisfy the size requirements. 1.12245 [ 1.01543] ((25 . 24) (26 . 25) (27 . 26) (28 . 27) (29 . 28) (30 . 29) (33 . 30) (34 . 31) (35 . 32)) 2.568 {1/20:36} B:0 1.25306 [ 1.12919] ((25 . 24) (26 . 25) (27 . 26) (28 . 27) (29 . 28) (30 . 29) (31 . 30) (34 . 31)) 6.299 {0/12:28} B:0 1.60483 [ 1.51014] ((27 . 26) (28 . 27) (29 . 28) (30 . 29) (31 . 30) (34 . 31) (35 . 32)) 6.469 {1/8:21} B:0 1.66695 [ 1.50038] ((28 . 25) (29 . 26) (30 . 27) (31 . 28) (33 . 30) (34 . 31)) 4.296 {0/0:15} B:0 2.50008 [ 2.25011] ((26 . 29) (27 . 30) (28 . 31) (29 . 32)) 4.221 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.8909 [and 1/min{score2}: 0.9848] [4505, 4505]: Comparing 1o5z_A and 1o5z_A, based on their crossing files. There are 36 (19 H + 17 S) secondary structure elements in 1o5z_A, of which 10 satisfy the size requirements. There are 36 (19 H + 17 S) secondary structure elements in 1o5z_A, of which 10 satisfy the size requirements. 1.00000 [ 1.00000] ((25 . 25) (26 . 26) (27 . 27) (28 . 28) (29 . 29) (30 . 30) (31 . 31) (33 . 33) (34 . 34) (35 . 35)) 0.000 {0/28:45} B:0 1.43070 [ 1.43070] ((27 . 27) (28 . 28) (29 . 29) (30 . 30) (31 . 33) (34 . 34) (35 . 35)) 6.355 {0/8:21} B:0 1.66843 [ 1.66843] ((27 . 27) (28 . 28) (30 . 30) (33 . 31) (34 . 34) (35 . 35)) 6.807 {0/7:15} B:0 2.00183 [ 2.00183] ((27 . 27) (28 . 30) (29 . 31) (31 . 33) (34 . 34)) 7.876 {0/1:10} B:0 2.00256 [ 2.00256] ((27 . 29) (28 . 30) (29 . 31) (30 . 34) (31 . 35)) 8.563 {0/2:10} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [4505, 4880]: Comparing 1o5z_A and 1p3d_A, based on their crossing files. There are 36 (19 H + 17 S) secondary structure elements in 1o5z_A, of which 10 satisfy the size requirements. There are 40 (18 H + 22 S) secondary structure elements in 1p3d_A, of which 12 satisfy the size requirements. 1.10356 [ 1.26451] ((25 . 29) (26 . 30) (27 . 31) (28 . 32) (29 . 34) (30 . 35) (31 . 36) (33 . 38) (34 . 39) (35 . 40)) 2.759 {2/24:45} B:0 1.66925 [ 2.00150] ((25 . 29) (26 . 30) (27 . 31) (28 . 32) (30 . 35) (33 . 36)) 7.487 {0/9:15} B:0 2.00113 [ 2.40066] ((27 . 36) (28 . 37) (29 . 38) (30 . 39) (31 . 40)) 6.984 {0/3:10} B:0 2.00115 [ 2.40066] ((27 . 34) (28 . 35) (29 . 36) (30 . 37) (31 . 38)) 7.005 {0/2:10} B:0 2.00155 [ 2.40090] ((30 . 30) (31 . 31) (33 . 34) (34 . 35) (35 . 36)) 7.550 {0/5:10} B:0 SIMILARITY (1/min{score1}): 0.9062 [and 1/min{score2}: 0.7908] [4505, 6554]: Comparing 1o5z_A and 2uag_A, based on their crossing files. There are 36 (19 H + 17 S) secondary structure elements in 1o5z_A, of which 10 satisfy the size requirements. There are 40 (20 H + 20 S) secondary structure elements in 2uag_A, of which 11 satisfy the size requirements. 1.02323 [ 1.11764] ((25 . 29) (26 . 30) (27 . 31) (28 . 32) (29 . 33) (30 . 34) (31 . 35) (33 . 38) (34 . 39) (35 . 40)) 2.820 {1/18:45} B:0 1.11126 [ 1.22233] ((25 . 29) (26 . 30) (27 . 31) (28 . 32) (29 . 33) (30 . 34) (31 . 35) (33 . 38) (34 . 39)) 2.686 {0/13:36} B:0 1.14591 [ 1.24874] ((25 . 29) (26 . 30) (27 . 31) (28 . 34) (29 . 35) (30 . 37) (33 . 38) (34 . 39) (35 . 40)) 3.594 {1/15:36} B:0 1.66912 [ 1.83518] ((27 . 31) (28 . 32) (29 . 33) (30 . 34) (31 . 38) (34 . 39)) 7.394 {0/1:15} B:0 2.00086 [ 2.20065] ((26 . 34) (27 . 35) (29 . 38) (30 . 39) (31 . 40)) 6.525 {0/5:10} B:0 SIMILARITY (1/min{score1}): 0.9773 [and 1/min{score2}: 0.8947] -------------------------------------------------------------------------------------------------------------------------