------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [2742, 539]: Comparing 1j5x_A and 1c7q_A, based on their crossing files. There are 25 (16 H + 9 S) secondary structure elements in 1j5x_A, of which 23 satisfy the size requirements. There are 33 (23 H + 10 S) secondary structure elements in 1c7q_A, of which 31 satisfy the size requirements. 1.21922 [ 1.58004] ((2 . 6) (3 . 7) (4 . 8) (5 . 9) (6 . 11) (8 . 13) (9 . 14) (10 . 16) (11 . 17) (12 . 18) (13 . 19) (14 . 20) (16 . 22) (17 . 23) (18 . 24) (19 . 25) (21 . 27) (22 . 29) (23 . 30) (24 . 31)) 5.742 {8/98:190} B:0 1.30660 [ 1.57951] ((1 . 5) (2 . 6) (3 . 7) (4 . 8) (5 . 9) (6 . 11) (8 . 13) (9 . 14) (10 . 16) (11 . 17) (12 . 18) (13 . 19) (14 . 20) (16 . 22) (17 . 23) (18 . 24) (19 . 25) (21 . 27) (22 . 29) (23 . 30) (25 . 31)) 5.245 {11/100:210} B:0 1.39651 [ 1.63311] ((2 . 6) (3 . 7) (4 . 8) (5 . 9) (6 . 11) (7 . 12) (8 . 13) (9 . 14) (10 . 16) (11 . 17) (12 . 18) (13 . 19) (14 . 20) (16 . 22) (17 . 23) (18 . 24) (19 . 25) (21 . 27) (22 . 29) (23 . 30) (25 . 31)) 5.577 {13/105:210} B:0 1.43881 [ 1.66011] ((2 . 6) (3 . 7) (4 . 8) (5 . 9) (6 . 11) (7 . 12) (8 . 13) (9 . 14) (10 . 16) (11 . 17) (12 . 18) (13 . 19) (14 . 20) (16 . 22) (17 . 23) (18 . 24) (19 . 25) (21 . 27) (22 . 29) (23 . 30) (24 . 31)) 6.229 {14/108:210} B:0 1.26506 [ 1.60187] ((2 . 4) (3 . 6) (4 . 8) (5 . 9) (6 . 11) (8 . 13) (9 . 14) (10 . 16) (11 . 17) (12 . 18) (14 . 20) (16 . 22) (17 . 23) (18 . 24) (19 . 25) (21 . 27) (22 . 29) (23 . 30) (24 . 31) (25 . 21)) 7.144 {9/96:190} B:1 SIMILARITY (1/min{score1}): 0.8202 [and 1/min{score2}: 0.6577] [2742, 2447]: Comparing 1j5x_A and 1iat_A, based on their crossing files. There are 25 (16 H + 9 S) secondary structure elements in 1j5x_A, of which 23 satisfy the size requirements. There are 43 (30 H + 13 S) secondary structure elements in 1iat_A, of which 35 satisfy the size requirements. 1.34647 [ 1.81771] ((2 . 9) (3 . 12) (4 . 13) (5 . 14) (6 . 15) (7 . 16) (8 . 18) (9 . 19) (10 . 21) (12 . 24) (13 . 26) (14 . 27) (16 . 30) (17 . 32) (18 . 33) (19 . 34) (21 . 36) (22 . 37) (23 . 40) (25 . 41)) 5.476 {10/90:190} B:0 1.13644 [ 1.67890] ((1 . 9) (2 . 8) (3 . 12) (4 . 13) (5 . 14) (6 . 15) (8 . 18) (9 . 19) (10 . 21) (11 . 22) (12 . 24) (13 . 26) (14 . 27) (16 . 30) (17 . 32) (18 . 33) (19 . 34) (21 . 36) (22 . 37) (23 . 40) (25 . 41)) 6.287 {7/104:210} B:1 1.36097 [ 2.06112] ((2 . 8) (3 . 12) (4 . 13) (5 . 14) (6 . 15) (8 . 18) (9 . 19) (10 . 21) (12 . 24) (13 . 9) (14 . 29) (16 . 30) (17 . 32) (21 . 36) (22 . 37) (23 . 40) (24 . 41)) 7.502 {3/71:136} B:1 1.81285 [ 2.03286] ((1 . 9) (2 . 27) (3 . 12) (4 . 13) (5 . 14) (6 . 15) (8 . 18) (9 . 19) (10 . 21) (11 . 22) (12 . 24) (13 . 26) (14 . 29) (16 . 30) (17 . 32) (18 . 33) (19 . 34) (21 . 36) (22 . 37) (23 . 40) (25 . 41)) 6.911 {18/103:210} B:1 2.04467 [ 2.20770] ((1 . 9) (2 . 27) (3 . 12) (4 . 13) (5 . 14) (6 . 15) (7 . 16) (8 . 18) (9 . 19) (10 . 21) (12 . 24) (13 . 26) (14 . 29) (16 . 30) (17 . 32) (18 . 33) (19 . 34) (21 . 36) (22 . 37) (23 . 40) (25 . 41)) 7.118 {21/105:210} B:1 SIMILARITY (1/min{score1}): 0.8897 [and 1/min{score2}: 0.5970] [2742, 2742]: Comparing 1j5x_A and 1j5x_A, based on their crossing files. There are 25 (16 H + 9 S) secondary structure elements in 1j5x_A, of which 23 satisfy the size requirements. There are 25 (16 H + 9 S) secondary structure elements in 1j5x_A, of which 23 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) (10 . 10) (11 . 11) (12 . 12) (13 . 13) (14 . 14) (16 . 16) (17 . 17) (18 . 18) (19 . 19) (21 . 21) (22 . 22) (23 . 23) (24 . 24) (25 . 25)) 0.000 {0/157:253} B:0 3.28573 [ 3.28573] ((4 . 16) (5 . 17) (6 . 18) (8 . 21) (9 . 22) (12 . 23) (13 . 25)) 3.629 {0/8:21} B:0 3.28573 [ 3.28573] ((16 . 4) (17 . 5) (18 . 6) (21 . 8) (22 . 9) (23 . 12) (25 . 13)) 3.629 {0/8:21} B:0 3.28575 [ 3.28575] ((2 . 2) (6 . 8) (8 . 10) (9 . 11) (10 . 12) (16 . 18) (22 . 22)) 4.144 {0/9:21} B:0 3.28575 [ 3.28575] ((2 . 2) (8 . 6) (10 . 8) (11 . 9) (12 . 10) (18 . 16) (22 . 22)) 4.144 {0/9:21} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [2742, 3821]: Comparing 1j5x_A and 1m3s_A, based on their crossing files. There are 25 (16 H + 9 S) secondary structure elements in 1j5x_A, of which 23 satisfy the size requirements. There are 11 (6 H + 5 S) secondary structure elements in 1m3s_A, of which 11 satisfy the size requirements. 2.30986 [ 1.18128] ((2 . 1) (4 . 3) (5 . 4) (6 . 5) (8 . 6) (9 . 7) (10 . 8) (11 . 9) (12 . 10) (13 . 11)) 2.746 {2/24:45} B:0 2.49764 [ 1.87634] ((1 . 1) (4 . 3) (5 . 4) (6 . 5) (8 . 6) (9 . 7) (10 . 8) (11 . 9) (12 . 10) (13 . 11)) 3.658 {4/22:45} B:0 2.56780 [ 1.32208] ((2 . 1) (5 . 4) (6 . 5) (8 . 6) (9 . 7) (10 . 8) (11 . 9) (12 . 10) (13 . 11)) 2.789 {2/21:36} B:0 3.83334 [ 1.83341] ((2 . 1) (6 . 3) (8 . 6) (9 . 7) (10 . 8) (12 . 10)) 3.332 {0/7:15} B:0 3.99606 [ 2.66398] ((16 . 3) (17 . 4) (18 . 5) (21 . 6) (22 . 7) (25 . 11)) 4.196 {1/4:15} B:0 SIMILARITY (1/min{score1}): 0.4329 [and 1/min{score2}: 0.8465] [2742, 3996]: Comparing 1j5x_A and 1moq, based on their crossing files. There are 25 (16 H + 9 S) secondary structure elements in 1j5x_A, of which 23 satisfy the size requirements. There are 28 (16 H + 12 S) secondary structure elements in 1moq, of which 24 satisfy the size requirements. 1.09685 [ 1.14428] ((1 . 1) (2 . 2) (4 . 7) (5 . 8) (6 . 9) (7 . 10) (8 . 11) (9 . 12) (10 . 13) (11 . 14) (12 . 15) (13 . 16) (14 . 17) (16 . 19) (17 . 20) (18 . 21) (19 . 22) (21 . 23) (22 . 24) (23 . 27) (25 . 28)) 3.739 {3/110:210} B:0 1.91667 [ 2.00001] ((4 . 7) (5 . 8) (6 . 9) (7 . 10) (8 . 11) (9 . 12) (10 . 13) (11 . 14) (12 . 15) (13 . 16) (18 . 19) (22 . 24)) 1.913 {0/33:66} B:0 1.91668 [ 2.00001] ((1 . 1) (2 . 2) (4 . 7) (5 . 8) (6 . 9) (7 . 10) (8 . 11) (9 . 12) (10 . 13) (11 . 14) (12 . 15) (13 . 16)) 1.992 {0/39:66} B:0 1.91668 [ 2.00001] ((1 . 1) (2 . 2) (5 . 8) (6 . 9) (7 . 10) (8 . 11) (9 . 12) (10 . 13) (11 . 14) (12 . 15) (13 . 16) (18 . 19)) 2.233 {0/39:66} B:0 1.91673 [ 2.00005] ((4 . 7) (5 . 8) (8 . 13) (9 . 14) (10 . 15) (13 . 16) (16 . 19) (17 . 20) (18 . 21) (21 . 23) (22 . 24) (23 . 25)) 3.247 {0/30:66} B:0 SIMILARITY (1/min{score1}): 0.9117 [and 1/min{score2}: 0.8739] [2742, 4365]: Comparing 1j5x_A and 1nri_A, based on their crossing files. There are 25 (16 H + 9 S) secondary structure elements in 1j5x_A, of which 23 satisfy the size requirements. There are 18 (13 H + 5 S) secondary structure elements in 1nri_A, of which 15 satisfy the size requirements. 2.30108 [ 1.50388] ((2 . 4) (4 . 6) (5 . 7) (6 . 8) (8 . 12) (9 . 13) (10 . 14) (11 . 15) (12 . 16) (13 . 17)) 2.961 {1/21:45} B:0 2.30251 [ 1.50900] ((1 . 4) (4 . 6) (5 . 7) (6 . 8) (8 . 12) (9 . 13) (10 . 14) (11 . 15) (12 . 16) (13 . 17)) 3.699 {1/17:45} B:0 2.57112 [ 1.72060] ((13 . 4) (14 . 5) (16 . 6) (17 . 7) (18 . 8) (21 . 12) (22 . 13) (23 . 14) (25 . 17)) 7.502 {1/10:36} B:0 2.87565 [ 1.87734] ((13 . 4) (14 . 5) (16 . 6) (17 . 7) (18 . 8) (21 . 12) (23 . 14) (25 . 17)) 7.979 {0/8:28} B:0 2.90295 [ 2.45086] ((14 . 4) (16 . 6) (17 . 7) (18 . 8) (19 . 11) (21 . 12) (22 . 13) (23 . 14) (25 . 17)) 4.086 {3/13:36} B:0 SIMILARITY (1/min{score1}): 0.4779 [and 1/min{score2}: 0.7300] [2742, 6266]: Comparing 1j5x_A and 1vim_A, based on their crossing files. There are 25 (16 H + 9 S) secondary structure elements in 1j5x_A, of which 23 satisfy the size requirements. There are 13 (8 H + 5 S) secondary structure elements in 1vim_A, of which 13 satisfy the size requirements. 2.09819 [ 1.22041] ((2 . 1) (3 . 2) (4 . 3) (5 . 4) (6 . 5) (8 . 6) (9 . 7) (10 . 8) (11 . 9) (12 . 10) (13 . 12)) 4.663 {2/28:55} B:0 2.30064 [ 1.30352] ((2 . 1) (4 . 3) (5 . 4) (6 . 5) (8 . 6) (9 . 7) (10 . 8) (11 . 9) (12 . 10) (13 . 12)) 2.787 {1/24:45} B:0 2.30134 [ 1.30734] ((1 . 1) (4 . 3) (5 . 4) (6 . 5) (8 . 6) (9 . 7) (10 . 8) (11 . 9) (12 . 10) (13 . 12)) 3.596 {1/20:45} B:0 2.82585 [ 2.24646] ((13 . 1) (14 . 2) (16 . 3) (17 . 4) (18 . 5) (21 . 6) (22 . 7) (23 . 8) (24 . 12)) 6.662 {3/14:36} B:0 3.28573 [ 1.85720] ((2 . 1) (6 . 3) (8 . 6) (9 . 7) (10 . 8) (11 . 9) (12 . 10)) 3.170 {0/9:21} B:0 SIMILARITY (1/min{score1}): 0.4766 [and 1/min{score2}: 0.8194] -------------------------------------------------------------------------------------------------------------------------