------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [2896, 70]: Comparing 1jix_A and 1a8i, based on their crossing files. There are 33 (20 H + 13 S) secondary structure elements in 1jix_A, of which 25 satisfy the size requirements. There are 66 (41 H + 25 S) secondary structure elements in 1a8i, of which 56 satisfy the size requirements. 1.51784 [ 2.83209] ((1 . 5) (2 . 11) (3 . 12) (4 . 21) (7 . 25) (8 . 26) (9 . 28) (11 . 23) (13 . 37) (15 . 41) (17 . 47) (19 . 48) (20 . 49) (22 . 51) (23 . 52) (24 . 53) (26 . 54) (27 . 55) (31 . 63) (32 . 64)) 6.670 {17/131:190} B:1 1.56928 [ 2.51190] ((1 . 5) (2 . 11) (3 . 12) (4 . 21) (7 . 25) (8 . 26) (9 . 28) (11 . 31) (13 . 37) (14 . 38) (15 . 41) (17 . 47) (19 . 48) (20 . 49) (22 . 51) (23 . 52) (24 . 53) (25 . 56) (26 . 54) (27 . 55) (31 . 63) (32 . 64) (33 . 66)) 5.380 {26/177:253} B:1 1.59199 [ 3.30626] ((1 . 5) (2 . 11) (3 . 12) (4 . 21) (7 . 25) (9 . 28) (15 . 35) (17 . 47) (19 . 50) (20 . 49) (22 . 51) (23 . 52) (24 . 53) (26 . 54) (27 . 55) (31 . 63) (32 . 64)) 6.198 {11/96:136} B:1 2.31853 [ 2.88433] ((1 . 5) (2 . 11) (3 . 12) (4 . 21) (7 . 25) (8 . 26) (9 . 28) (11 . 31) (13 . 37) (15 . 41) (17 . 47) (19 . 48) (20 . 49) (22 . 51) (23 . 52) (24 . 53) (25 . 59) (26 . 54) (27 . 55) (31 . 63) (32 . 64) (33 . 66)) 5.893 {37/162:231} B:1 3.02972 [ 5.66326] ((1 . 5) (3 . 21) (7 . 25) (9 . 28) (13 . 37) (15 . 41) (16 . 11) (17 . 13) (31 . 50) (33 . 66)) 5.667 {7/27:45} B:1 SIMILARITY (1/min{score1}): 0.6927 [and 1/min{score2}: 0.4061] [2896, 1348]: Comparing 1jix_A and 1f0k_A, based on their crossing files. There are 33 (20 H + 13 S) secondary structure elements in 1jix_A, of which 25 satisfy the size requirements. There are 30 (17 H + 13 S) secondary structure elements in 1f0k_A, of which 28 satisfy the size requirements. 2.77960 [ 3.11241] ((1 . 16) (2 . 17) (3 . 18) (4 . 20) (7 . 22) (8 . 23) (9 . 24) (13 . 26) (33 . 28)) 3.958 {1/16:36} B:0 3.12715 [ 3.50153] ((17 . 16) (19 . 17) (20 . 18) (23 . 21) (24 . 22) (26 . 23) (27 . 24) (32 . 29)) 3.539 {1/14:28} B:0 3.30657 [ 3.35952] ((1 . 1) (2 . 2) (3 . 3) (7 . 8) (8 . 9) (9 . 10) (13 . 12) (17 . 22) (24 . 24) (26 . 25) (27 . 26) (31 . 28) (32 . 29)) 5.263 {17/53:78} B:0 3.57183 [ 4.00029] ((16 . 15) (17 . 16) (19 . 17) (20 . 18) (23 . 21) (24 . 22) (27 . 26)) 8.337 {0/11:21} B:0 5.00001 [ 5.60001] ((2 . 2) (9 . 8) (13 . 10) (15 . 12) (27 . 24)) 4.525 {0/8:10} B:0 SIMILARITY (1/min{score1}): 0.4760 [and 1/min{score2}: 0.4263] [2896, 2510]: Comparing 1jix_A and 1iir_A, based on their crossing files. There are 33 (20 H + 13 S) secondary structure elements in 1jix_A, of which 25 satisfy the size requirements. There are 30 (17 H + 13 S) secondary structure elements in 1iir_A, of which 26 satisfy the size requirements. 2.77784 [ 2.88894] ((1 . 17) (2 . 18) (3 . 19) (4 . 21) (7 . 23) (8 . 24) (9 . 25) (13 . 27) (33 . 28)) 4.323 {0/18:36} B:0 3.12503 [ 3.25003] ((17 . 17) (19 . 18) (20 . 19) (22 . 21) (23 . 22) (24 . 23) (27 . 27) (31 . 28)) 3.998 {0/16:28} B:0 3.12504 [ 3.25003] ((1 . 17) (2 . 18) (3 . 19) (7 . 23) (8 . 24) (9 . 25) (13 . 27) (33 . 28)) 4.100 {0/13:28} B:0 3.44317 [ 3.50350] ((1 . 17) (2 . 18) (3 . 19) (4 . 21) (7 . 23) (8 . 24) (9 . 25) (13 . 27) (16 . 28)) 5.387 {6/20:36} B:0 2.39045 [ 2.39971] ((1 . 1) (2 . 2) (3 . 3) (4 . 5) (7 . 7) (8 . 8) (9 . 9) (14 . 11) (17 . 17) (20 . 19) (22 . 21) (23 . 22) (24 . 23) (25 . 26) (26 . 24) (27 . 27) (31 . 28) (32 . 29) (33 . 30)) 5.406 {28/120:171} B:1 SIMILARITY (1/min{score1}): 0.5633 [and 1/min{score2}: 0.5498] [2896, 2896]: Comparing 1jix_A and 1jix_A, based on their crossing files. There are 33 (20 H + 13 S) secondary structure elements in 1jix_A, of which 25 satisfy the size requirements. There are 33 (20 H + 13 S) secondary structure elements in 1jix_A, of which 25 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (13 . 13) (14 . 14) (15 . 15) (16 . 16) (17 . 17) (19 . 19) (20 . 20) (22 . 22) (23 . 23) (24 . 24) (25 . 25) (26 . 26) (27 . 27) (31 . 31) (32 . 32) (33 . 33)) 0.000 {0/243:300} B:0 3.12500 [ 3.12500] ((1 . 1) (2 . 2) (8 . 8) (9 . 9) (15 . 13) (17 . 17) (19 . 19) (27 . 27)) 1.510 {0/22:28} B:0 3.12500 [ 3.12500] ((1 . 1) (2 . 2) (8 . 8) (9 . 9) (13 . 15) (17 . 17) (19 . 19) (27 . 27)) 1.510 {0/22:28} B:0 3.12629 [ 3.12629] ((17 . 1) (19 . 2) (20 . 3) (22 . 4) (24 . 7) (26 . 8) (27 . 9) (31 . 33)) 4.198 {1/16:28} B:0 3.12629 [ 3.12629] ((1 . 17) (2 . 19) (3 . 20) (4 . 22) (7 . 24) (8 . 26) (9 . 27) (33 . 31)) 4.198 {1/16:28} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [2896, 5101]: Comparing 1jix_A and 1psw_A, based on their crossing files. There are 33 (20 H + 13 S) secondary structure elements in 1jix_A, of which 25 satisfy the size requirements. There are 28 (16 H + 12 S) secondary structure elements in 1psw_A, of which 25 satisfy the size requirements. 2.30943 [ 2.30943] ((1 . 1) (2 . 2) (3 . 3) (4 . 5) (7 . 7) (8 . 8) (17 . 15) (19 . 17) (20 . 18) (22 . 21) (23 . 22) (24 . 23) (26 . 24) (27 . 25) (31 . 28)) 5.799 {16/75:105} B:0 2.61535 [ 2.61535] ((16 . 2) (17 . 15) (19 . 17) (20 . 18) (22 . 21) (23 . 22) (24 . 23) (26 . 24) (27 . 25) (31 . 28)) 4.799 {4/24:45} B:0 2.77792 [ 2.77792] ((17 . 1) (19 . 2) (20 . 3) (22 . 5) (23 . 6) (24 . 7) (26 . 8) (27 . 9) (31 . 11)) 5.325 {0/19:36} B:0 2.77857 [ 2.77857] ((1 . 15) (2 . 17) (3 . 18) (4 . 21) (7 . 23) (8 . 24) (9 . 25) (13 . 26) (33 . 28)) 4.325 {1/20:36} B:0 3.12501 [ 3.12501] ((17 . 1) (19 . 2) (20 . 3) (22 . 5) (23 . 6) (24 . 7) (26 . 8) (27 . 9)) 3.273 {0/14:28} B:0 SIMILARITY (1/min{score1}): 0.6184 [and 1/min{score2}: 0.6184] [2896, 6080]: Comparing 1jix_A and 1uqt_A, based on their crossing files. There are 33 (20 H + 13 S) secondary structure elements in 1jix_A, of which 25 satisfy the size requirements. There are 38 (22 H + 16 S) secondary structure elements in 1uqt_A, of which 35 satisfy the size requirements. 2.73956 [ 3.39047] ((15 . 1) (17 . 23) (19 . 25) (20 . 27) (22 . 29) (23 . 30) (24 . 31) (26 . 32) (27 . 33) (31 . 36) (32 . 37)) 4.396 {7/30:55} B:0 1.44660 [ 1.73768] ((1 . 1) (2 . 2) (3 . 3) (4 . 5) (7 . 10) (8 . 12) (9 . 13) (13 . 16) (14 . 17) (15 . 20) (17 . 23) (19 . 25) (20 . 27) (22 . 29) (23 . 30) (24 . 31) (25 . 34) (26 . 32) (27 . 33) (31 . 36) (32 . 37) (33 . 38)) 5.068 {20/156:231} B:1 2.23000 [ 2.34883] ((1 . 1) (2 . 2) (3 . 4) (4 . 5) (7 . 10) (9 . 13) (13 . 16) (14 . 17) (15 . 20) (17 . 23) (19 . 25) (20 . 27) (22 . 29) (23 . 30) (24 . 31) (25 . 34) (26 . 32) (27 . 33) (31 . 36) (32 . 37) (33 . 38)) 4.664 {31/142:210} B:1 2.50075 [ 3.50027] ((16 . 28) (17 . 31) (19 . 32) (20 . 33) (22 . 35) (23 . 36) (24 . 23) (26 . 25) (27 . 27) (31 . 30)) 5.185 {1/23:45} B:1 1.31120 [ 1.66548] ((1 . 1) (2 . 2) (3 . 3) (4 . 5) (7 . 10) (9 . 13) (11 . 9) (13 . 16) (14 . 17) (15 . 20) (17 . 23) (19 . 25) (20 . 27) (22 . 29) (23 . 30) (24 . 31) (25 . 34) (26 . 32) (27 . 33) (31 . 36) (32 . 37) (33 . 38)) 5.487 {17/160:231} B:2 SIMILARITY (1/min{score1}): 0.7627 [and 1/min{score2}: 0.6004] [2896, 6170]: Comparing 1jix_A and 1v4v_A, based on their crossing files. There are 33 (20 H + 13 S) secondary structure elements in 1jix_A, of which 25 satisfy the size requirements. There are 30 (17 H + 13 S) secondary structure elements in 1v4v_A, of which 28 satisfy the size requirements. 1.73217 [ 1.82679] ((1 . 1) (2 . 2) (3 . 3) (7 . 7) (8 . 8) (9 . 9) (13 . 11) (15 . 14) (16 . 15) (17 . 16) (19 . 17) (20 . 19) (23 . 22) (24 . 23) (26 . 24) (27 . 25) (31 . 28) (32 . 29)) 5.204 {15/99:153} B:0 1.83946 [ 1.91977] ((1 . 1) (2 . 2) (3 . 3) (7 . 7) (8 . 8) (9 . 9) (13 . 11) (16 . 15) (17 . 16) (19 . 17) (20 . 19) (22 . 21) (23 . 22) (24 . 23) (26 . 24) (27 . 25) (31 . 28) (32 . 29)) 5.270 {17/102:153} B:0 2.31263 [ 2.57413] ((2 . 2) (17 . 16) (19 . 18) (20 . 19) (22 . 21) (23 . 22) (24 . 23) (26 . 24) (27 . 25) (31 . 28) (32 . 29)) 4.781 {4/34:55} B:0 2.50821 [ 2.53502] ((1 . 1) (2 . 2) (3 . 3) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (13 . 11) (14 . 12) (15 . 14) (16 . 15) (17 . 16) (20 . 19) (22 . 21) (23 . 22) (24 . 23) (25 . 26) (31 . 28) (33 . 30)) 5.838 {30/122:171} B:0 2.52411 [ 2.81725] ((17 . 16) (19 . 18) (20 . 19) (22 . 21) (23 . 22) (24 . 23) (26 . 24) (27 . 25) (31 . 28) (32 . 29)) 4.199 {3/27:45} B:0 SIMILARITY (1/min{score1}): 0.6688 [and 1/min{score2}: 0.6211] -------------------------------------------------------------------------------------------------------------------------