------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [2684, 1046]: Comparing 1j0a_A and 1e5x_A, based on their crossing files. There are 25 (15 H + 10 S) secondary structure elements in 1j0a_A, of which 23 satisfy the size requirements. There are 33 (20 H + 13 S) secondary structure elements in 1e5x_A, of which 30 satisfy the size requirements. 1.19860 [ 1.52280] ((2 . 8) (3 . 9) (4 . 10) (6 . 11) (7 . 12) (8 . 13) (9 . 14) (10 . 16) (11 . 17) (12 . 18) (13 . 19) (15 . 21) (16 . 22) (17 . 23) (18 . 24) (20 . 27) (21 . 28) (22 . 29) (23 . 30) (25 . 31)) 3.085 {11/147:190} B:0 1.21225 [ 1.48672] ((2 . 8) (3 . 9) (4 . 10) (6 . 11) (7 . 12) (8 . 13) (9 . 14) (10 . 16) (11 . 17) (12 . 18) (13 . 19) (15 . 21) (16 . 22) (17 . 23) (18 . 24) (19 . 26) (20 . 27) (21 . 28) (22 . 29) (23 . 30) (25 . 31)) 3.891 {15/163:210} B:0 1.87079 [ 1.95179] ((1 . 4) (2 . 8) (3 . 9) (4 . 10) (6 . 11) (7 . 12) (8 . 13) (9 . 14) (10 . 16) (11 . 17) (12 . 18) (13 . 19) (15 . 21) (16 . 22) (17 . 23) (18 . 24) (19 . 26) (20 . 27) (21 . 28) (22 . 29) (23 . 30) (25 . 31)) 4.255 {33/181:231} B:0 3.83334 [ 5.00000] ((9 . 12) (11 . 14) (15 . 21) (16 . 22) (17 . 23) (23 . 30)) 3.124 {0/12:15} B:0 3.83335 [ 5.00001] ((6 . 21) (7 . 22) (8 . 23) (9 . 24) (10 . 25) (11 . 27)) 3.657 {0/8:15} B:0 SIMILARITY (1/min{score1}): 0.8343 [and 1/min{score2}: 0.6726] [2684, 1370]: Comparing 1j0a_A and 1f2d_A, based on their crossing files. There are 25 (15 H + 10 S) secondary structure elements in 1j0a_A, of which 23 satisfy the size requirements. There are 26 (16 H + 10 S) secondary structure elements in 1f2d_A, of which 23 satisfy the size requirements. 1.19980 [ 1.19980] ((2 . 1) (3 . 2) (4 . 3) (6 . 5) (7 . 7) (8 . 8) (9 . 9) (10 . 11) (11 . 12) (12 . 13) (13 . 14) (15 . 16) (16 . 17) (17 . 18) (18 . 20) (19 . 21) (21 . 23) (22 . 24) (23 . 25) (24 . 26)) 2.818 {11/146:190} B:0 1.22232 [ 1.22232] ((2 . 1) (3 . 2) (4 . 3) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 11) (11 . 12) (12 . 13) (13 . 14) (15 . 16) (16 . 17) (17 . 18) (18 . 20) (19 . 21) (21 . 23) (22 . 24) (23 . 25) (24 . 26)) 2.844 {12/144:190} B:0 2.30014 [ 2.30014] ((9 . 12) (15 . 16) (16 . 17) (17 . 18) (18 . 20) (19 . 21) (21 . 23) (22 . 24) (23 . 25) (24 . 26)) 2.897 {1/36:45} B:0 2.95327 [ 2.95327] ((2 . 9) (6 . 16) (7 . 17) (8 . 18) (9 . 20) (10 . 21) (12 . 24) (13 . 25)) 6.845 {2/12:28} B:0 3.03029 [ 3.03029] ((2 . 1) (3 . 2) (4 . 3) (7 . 7) (8 . 8) (9 . 9) (18 . 17) (20 . 20)) 2.550 {4/20:28} B:0 SIMILARITY (1/min{score1}): 0.8335 [and 1/min{score2}: 0.8335] [2684, 2684]: Comparing 1j0a_A and 1j0a_A, based on their crossing files. There are 25 (15 H + 10 S) secondary structure elements in 1j0a_A, of which 23 satisfy the size requirements. There are 25 (15 H + 10 S) secondary structure elements in 1j0a_A, of which 23 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12) (13 . 13) (15 . 15) (16 . 16) (17 . 17) (18 . 18) (19 . 19) (20 . 20) (21 . 21) (22 . 22) (23 . 23) (24 . 24) (25 . 25)) 0.000 {0/209:253} B:0 4.60004 [ 4.60004] ((11 . 2) (15 . 6) (16 . 7) (17 . 8) (18 . 9)) 5.613 {0/6:10} B:0 4.60004 [ 4.60004] ((2 . 11) (6 . 15) (7 . 16) (8 . 17) (9 . 18)) 5.613 {0/6:10} B:0 4.60006 [ 4.60006] ((15 . 6) (16 . 7) (17 . 8) (18 . 9) (20 . 13)) 6.349 {0/3:10} B:0 4.60006 [ 4.60006] ((6 . 15) (7 . 16) (8 . 17) (9 . 18) (13 . 20)) 6.349 {0/3:10} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [2684, 3340]: Comparing 1j0a_A and 1kl7_A, based on their crossing files. There are 25 (15 H + 10 S) secondary structure elements in 1j0a_A, of which 23 satisfy the size requirements. There are 37 (23 H + 14 S) secondary structure elements in 1kl7_A, of which 30 satisfy the size requirements. 1.31730 [ 1.63116] ((1 . 5) (4 . 8) (6 . 9) (7 . 10) (8 . 11) (9 . 12) (10 . 13) (11 . 14) (12 . 15) (15 . 16) (16 . 17) (17 . 18) (18 . 19) (20 . 27) (21 . 28) (22 . 29) (23 . 30) (24 . 31) (25 . 32)) 4.021 {13/135:171} B:0 1.48269 [ 1.68943] ((1 . 5) (4 . 8) (6 . 9) (7 . 10) (8 . 11) (9 . 12) (10 . 13) (11 . 14) (12 . 15) (15 . 16) (16 . 17) (17 . 18) (18 . 19) (19 . 23) (20 . 27) (21 . 28) (22 . 29) (23 . 30) (24 . 31) (25 . 32)) 4.488 {20/151:190} B:0 1.57759 [ 1.78982] ((4 . 8) (6 . 9) (7 . 10) (8 . 11) (9 . 12) (10 . 13) (11 . 14) (12 . 15) (15 . 16) (16 . 17) (17 . 18) (18 . 19) (19 . 23) (20 . 27) (21 . 28) (22 . 29) (23 . 30) (24 . 31) (25 . 32)) 4.195 {19/134:171} B:0 3.83336 [ 5.00001] ((15 . 18) (21 . 28) (22 . 29) (23 . 30) (24 . 31) (25 . 32)) 4.245 {0/14:15} B:0 3.83337 [ 5.00002] ((1 . 5) (6 . 9) (9 . 10) (18 . 17) (19 . 18) (20 . 19)) 4.785 {0/10:15} B:0 SIMILARITY (1/min{score1}): 0.7591 [and 1/min{score2}: 0.6131] [2684, 4495]: Comparing 1j0a_A and 1o58_A, based on their crossing files. There are 25 (15 H + 10 S) secondary structure elements in 1j0a_A, of which 23 satisfy the size requirements. There are 22 (13 H + 9 S) secondary structure elements in 1o58_A, of which 19 satisfy the size requirements. 2.55581 [ 2.11156] ((2 . 2) (4 . 3) (6 . 5) (7 . 6) (8 . 7) (9 . 8) (11 . 10) (16 . 16) (20 . 18)) 2.602 {1/28:36} B:0 2.87557 [ 2.37601] ((9 . 6) (15 . 12) (16 . 14) (17 . 15) (18 . 16) (21 . 19) (22 . 20) (23 . 21)) 3.700 {1/21:28} B:0 3.83334 [ 3.16668] ((6 . 5) (7 . 6) (8 . 7) (9 . 10) (16 . 16) (20 . 18)) 3.232 {0/12:15} B:0 4.60006 [ 3.80011] ((6 . 13) (7 . 14) (8 . 15) (9 . 16) (13 . 18)) 6.261 {0/5:10} B:0 4.60013 [ 3.80023] ((6 . 12) (7 . 14) (8 . 15) (9 . 16) (13 . 18)) 7.564 {0/5:10} B:0 SIMILARITY (1/min{score1}): 0.7273 [and 1/min{score2}: 0.8652] [2684, 5138]: Comparing 1j0a_A and 1pwh_A, based on their crossing files. There are 25 (15 H + 10 S) secondary structure elements in 1j0a_A, of which 23 satisfy the size requirements. There are 25 (15 H + 10 S) secondary structure elements in 1pwh_A, of which 23 satisfy the size requirements. 1.18756 [ 1.18756] ((2 . 1) (3 . 2) (4 . 3) (6 . 5) (7 . 6) (8 . 7) (9 . 8) (10 . 9) (11 . 10) (12 . 11) (13 . 12) (15 . 13) (16 . 14) (17 . 15) (18 . 16) (20 . 20) (21 . 21) (22 . 22) (23 . 24) (25 . 25)) 2.696 {10/143:190} B:0 1.19993 [ 1.19993] ((2 . 1) (3 . 2) (4 . 3) (6 . 5) (7 . 6) (8 . 7) (9 . 8) (10 . 9) (11 . 10) (12 . 11) (13 . 12) (15 . 13) (16 . 14) (17 . 15) (18 . 16) (19 . 19) (20 . 20) (21 . 21) (22 . 22) (23 . 24) (25 . 25)) 3.350 {14/157:210} B:0 1.77107 [ 1.77107] ((2 . 1) (3 . 2) (4 . 3) (6 . 5) (7 . 6) (8 . 7) (9 . 8) (11 . 10) (15 . 13) (16 . 16) (20 . 20) (21 . 21) (23 . 24)) 2.535 {3/67:78} B:0 2.57043 [ 2.57043] ((3 . 2) (6 . 5) (7 . 6) (8 . 7) (9 . 10) (16 . 16) (20 . 20) (21 . 21) (23 . 24)) 3.101 {3/30:36} B:0 2.87535 [ 2.87535] ((3 . 2) (6 . 5) (7 . 8) (8 . 9) (9 . 10) (16 . 16) (20 . 20) (23 . 24)) 3.892 {1/24:28} B:0 SIMILARITY (1/min{score1}): 0.8421 [and 1/min{score2}: 0.8421] [2684, 5404]: Comparing 1j0a_A and 1qop_B, based on their crossing files. There are 25 (15 H + 10 S) secondary structure elements in 1j0a_A, of which 23 satisfy the size requirements. There are 33 (19 H + 14 S) secondary structure elements in 1qop_B, of which 28 satisfy the size requirements. 1.15535 [ 1.40298] ((2 . 5) (3 . 6) (4 . 7) (6 . 9) (7 . 10) (8 . 11) (9 . 12) (10 . 14) (11 . 15) (12 . 16) (13 . 17) (15 . 19) (16 . 20) (17 . 21) (18 . 22) (20 . 29) (21 . 30) (22 . 31) (23 . 32) (24 . 33)) 3.283 {6/143:190} B:0 1.15572 [ 1.40318] ((2 . 5) (3 . 6) (4 . 7) (6 . 9) (7 . 10) (8 . 11) (9 . 12) (10 . 14) (11 . 15) (12 . 16) (13 . 17) (15 . 18) (16 . 20) (17 . 21) (18 . 22) (20 . 29) (21 . 30) (22 . 31) (23 . 32) (24 . 33)) 3.793 {6/142:190} B:0 1.15964 [ 1.40538] ((2 . 5) (3 . 6) (4 . 7) (6 . 9) (7 . 10) (8 . 11) (9 . 12) (10 . 14) (11 . 15) (12 . 16) (13 . 17) (15 . 19) (16 . 20) (17 . 21) (18 . 22) (20 . 29) (21 . 30) (22 . 31) (23 . 32) (25 . 33)) 3.362 {7/143:190} B:0 1.16009 [ 1.40563] ((2 . 5) (3 . 6) (4 . 7) (6 . 9) (7 . 10) (8 . 11) (9 . 12) (10 . 14) (11 . 15) (12 . 16) (13 . 17) (15 . 18) (16 . 20) (17 . 21) (18 . 22) (20 . 29) (21 . 30) (22 . 31) (23 . 32) (25 . 33)) 3.792 {7/142:190} B:0 1.17794 [ 1.38191] ((2 . 5) (3 . 6) (4 . 7) (6 . 9) (7 . 10) (8 . 11) (9 . 12) (10 . 14) (11 . 15) (12 . 16) (13 . 17) (15 . 19) (16 . 20) (17 . 21) (18 . 22) (19 . 28) (20 . 29) (21 . 30) (22 . 31) (23 . 32) (25 . 33)) 4.045 {13/156:210} B:0 SIMILARITY (1/min{score1}): 0.8655 [and 1/min{score2}: 0.7236] [2684, 5895]: Comparing 1j0a_A and 1tdj, based on their crossing files. There are 25 (15 H + 10 S) secondary structure elements in 1j0a_A, of which 23 satisfy the size requirements. There are 38 (20 H + 18 S) secondary structure elements in 1tdj, of which 22 satisfy the size requirements. 1.29042 [ 1.24765] ((2 . 3) (3 . 4) (4 . 5) (6 . 7) (7 . 8) (8 . 9) (9 . 10) (10 . 11) (11 . 12) (12 . 13) (15 . 15) (16 . 16) (17 . 17) (18 . 18) (20 . 21) (21 . 22) (22 . 23) (23 . 24) (25 . 25)) 3.014 {12/135:171} B:0 1.32872 [ 1.29726] ((2 . 3) (3 . 4) (4 . 5) (6 . 7) (7 . 8) (8 . 9) (9 . 10) (10 . 11) (11 . 12) (12 . 13) (15 . 15) (16 . 16) (17 . 17) (18 . 18) (19 . 20) (20 . 21) (21 . 22) (22 . 23) (23 . 24) (25 . 25)) 3.410 {16/148:190} B:0 3.28573 [ 3.14287] ((3 . 4) (6 . 7) (7 . 8) (8 . 9) (15 . 17) (20 . 21) (23 . 24)) 3.227 {0/19:21} B:0 3.28683 [ 3.14413] ((10 . 9) (12 . 13) (15 . 15) (16 . 16) (17 . 17) (18 . 18) (23 . 24)) 4.423 {1/16:21} B:0 3.29067 [ 3.14852] ((15 . 7) (16 . 8) (17 . 9) (18 . 10) (19 . 11) (20 . 12) (25 . 19)) 6.134 {1/11:21} B:0 SIMILARITY (1/min{score1}): 0.7749 [and 1/min{score2}: 0.8015] [2684, 6189]: Comparing 1j0a_A and 1v7c_A, based on their crossing files. There are 25 (15 H + 10 S) secondary structure elements in 1j0a_A, of which 23 satisfy the size requirements. There are 29 (18 H + 11 S) secondary structure elements in 1v7c_A, of which 23 satisfy the size requirements. 1.33562 [ 1.33562] ((2 . 2) (4 . 4) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12) (15 . 14) (16 . 15) (17 . 16) (18 . 17) (20 . 22) (21 . 23) (22 . 24) (23 . 25) (25 . 27)) 2.627 {10/118:153} B:0 1.36726 [ 1.36726] ((2 . 2) (4 . 4) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12) (15 . 14) (16 . 15) (17 . 16) (18 . 17) (19 . 21) (20 . 22) (21 . 23) (22 . 24) (23 . 25) (25 . 27)) 3.517 {14/130:171} B:0 1.40098 [ 1.40098] ((2 . 2) (4 . 4) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12) (15 . 14) (16 . 15) (17 . 16) (18 . 17) (20 . 22) (21 . 23) (22 . 24) (23 . 25) (24 . 27)) 2.895 {12/115:153} B:0 1.40236 [ 1.40236] ((2 . 2) (3 . 3) (4 . 4) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12) (15 . 14) (16 . 15) (17 . 16) (18 . 17) (20 . 22) (21 . 23) (22 . 24) (23 . 25) (25 . 27)) 2.983 {15/131:171} B:0 2.89348 [ 2.89348] ((6 . 6) (7 . 7) (8 . 8) (16 . 17) (20 . 22) (21 . 23) (22 . 24) (23 . 25)) 2.542 {3/26:28} B:0 SIMILARITY (1/min{score1}): 0.7487 [and 1/min{score2}: 0.7487] -------------------------------------------------------------------------------------------------------------------------