------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [2074, 350]: Comparing 1h4a_X and 1bd7_A, based on their crossing files. There are 19 (5 H + 14 S) secondary structure elements in 1h4a_X, of which 8 satisfy the size requirements. There are 20 (6 H + 14 S) secondary structure elements in 1bd7_A, of which 17 satisfy the size requirements. 1.14290 [ 2.42858] ((1 . 11) (3 . 13) (4 . 15) (5 . 16) (6 . 17) (7 . 18) (9 . 20)) 2.051 {0/10:21} B:0 1.30673 [ 2.17324] ((1 . 1) (3 . 2) (4 . 4) (5 . 5) (6 . 7) (7 . 8) (8 . 9) (9 . 10)) 1.333 {2/17:28} B:0 2.00039 [ 4.25004] ((1 . 13) (4 . 16) (6 . 18) (7 . 20)) 5.349 {0/1:6} B:0 2.00041 [ 4.25004] ((3 . 11) (5 . 15) (7 . 17) (9 . 18)) 5.425 {0/1:6} B:0 2.00048 [ 4.25005] ((1 . 2) (4 . 5) (6 . 8) (7 . 10)) 5.630 {0/1:6} B:0 SIMILARITY (1/min{score1}): 0.8750 [and 1/min{score2}: 0.4601] [2074, 498]: Comparing 1h4a_X and 1c01_A, based on their crossing files. There are 19 (5 H + 14 S) secondary structure elements in 1h4a_X, of which 8 satisfy the size requirements. There are 8 (1 H + 7 S) secondary structure elements in 1c01_A, of which 7 satisfy the size requirements. 1.33348 [ 1.16688] ((1 . 1) (3 . 2) (4 . 4) (5 . 5) (6 . 7) (9 . 8)) 3.078 {0/8:15} B:0 2.00025 [ 1.75037] ((4 . 1) (6 . 3) (7 . 4) (9 . 5)) 4.777 {0/1:6} B:0 2.00077 [ 1.75116] ((3 . 3) (4 . 5) (5 . 7) (7 . 8)) 6.350 {0/2:6} B:0 2.00078 [ 1.75116] ((3 . 1) (4 . 3) (5 . 4) (6 . 5)) 6.361 {0/2:6} B:0 2.00210 [ 1.75314] ((3 . 3) (4 . 5) (5 . 7) (6 . 8)) 8.153 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.7795 [and 1/min{score2}: 0.8570] [2074, 1824]: Comparing 1h4a_X and 1gh5_A, based on their crossing files. There are 19 (5 H + 14 S) secondary structure elements in 1h4a_X, of which 8 satisfy the size requirements. There are 9 (0 H + 9 S) secondary structure elements in 1gh5_A, of which 7 satisfy the size requirements. 1.14301 [ 1.00024] ((1 . 2) (3 . 3) (4 . 5) (5 . 6) (6 . 7) (7 . 8) (9 . 9)) 2.803 {0/7:21} B:0 2.00035 [ 1.75052] ((1 . 3) (4 . 6) (6 . 8) (7 . 9)) 5.194 {0/1:6} B:0 2.00050 [ 1.75074] ((1 . 3) (4 . 6) (5 . 7) (7 . 9)) 5.680 {0/1:6} B:0 2.00062 [ 1.75093] ((3 . 2) (5 . 5) (7 . 7) (9 . 8)) 6.012 {0/1:6} B:0 2.00071 [ 1.75106] ((4 . 5) (5 . 6) (7 . 7) (9 . 9)) 6.220 {0/0:6} B:0 SIMILARITY (1/min{score1}): 0.8749 [and 1/min{score2}: 0.9998] [2074, 2074]: Comparing 1h4a_X and 1h4a_X, based on their crossing files. There are 19 (5 H + 14 S) secondary structure elements in 1h4a_X, of which 8 satisfy the size requirements. There are 19 (5 H + 14 S) secondary structure elements in 1h4a_X, of which 8 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9)) 0.000 {0/18:28} B:0 2.00051 [ 2.00051] ((3 . 1) (5 . 4) (7 . 6) (9 . 7)) 5.717 {0/1:6} B:0 2.00051 [ 2.00051] ((1 . 3) (4 . 5) (6 . 7) (7 . 9)) 5.717 {0/1:6} B:0 3.37688 [ 3.37688] ((1 . 1) (3 . 3) (5 . 5) (6 . 6) (9 . 7)) 6.417 {2/6:10} B:0 3.37688 [ 3.37688] ((1 . 1) (3 . 3) (5 . 5) (6 . 6) (7 . 9)) 6.417 {2/6:10} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [2074, 2075]: Comparing 1h4a_X and 1h4a_X, based on their crossing files. There are 19 (5 H + 14 S) secondary structure elements in 1h4a_X, of which 8 satisfy the size requirements. There are 19 (5 H + 14 S) secondary structure elements in 1h4a_X, of which 8 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 10) (3 . 12) (4 . 14) (5 . 15) (6 . 16) (7 . 17) (8 . 18) (9 . 19)) 0.810 {0/18:28} B:0 2.00054 [ 2.00054] ((3 . 10) (5 . 14) (7 . 16) (9 . 17)) 5.790 {0/1:6} B:0 2.00054 [ 2.00054] ((1 . 12) (4 . 15) (6 . 17) (7 . 19)) 5.793 {0/1:6} B:0 2.00494 [ 2.00494] ((3 . 14) (4 . 16) (5 . 17) (6 . 19)) 10.096 {0/3:6} B:0 3.37689 [ 3.37689] ((1 . 10) (3 . 12) (5 . 15) (6 . 16) (9 . 17)) 6.460 {2/6:10} B:0 SIMILARITY (1/min{score1}): 0.9999 [and 1/min{score2}: 0.9999] [2074, 2181]: Comparing 1h4a_X and 1hdf_A, based on their crossing files. There are 19 (5 H + 14 S) secondary structure elements in 1h4a_X, of which 8 satisfy the size requirements. There are 13 (4 H + 9 S) secondary structure elements in 1hdf_A, of which 9 satisfy the size requirements. 1.03630 [ 1.15100] ((1 . 2) (3 . 4) (4 . 7) (5 . 8) (6 . 10) (7 . 11) (8 . 12) (9 . 13)) 2.609 {1/16:28} B:0 1.14294 [ 1.28577] ((1 . 2) (3 . 4) (4 . 7) (5 . 8) (6 . 10) (7 . 11) (9 . 13)) 2.361 {0/9:21} B:0 2.00053 [ 2.25037] ((3 . 2) (5 . 7) (7 . 10) (9 . 11)) 5.767 {0/1:6} B:0 2.00078 [ 2.25055] ((1 . 1) (4 . 4) (6 . 7) (9 . 10)) 6.364 {0/3:6} B:0 2.00082 [ 2.25058] ((1 . 7) (3 . 8) (4 . 11) (5 . 13)) 6.445 {0/0:6} B:0 SIMILARITY (1/min{score1}): 0.9650 [and 1/min{score2}: 0.8688] [2074, 4348]: Comparing 1h4a_X and 1nps_A, based on their crossing files. There are 19 (5 H + 14 S) secondary structure elements in 1h4a_X, of which 8 satisfy the size requirements. There are 9 (2 H + 7 S) secondary structure elements in 1nps_A, of which 9 satisfy the size requirements. 1.33336 [ 1.50002] ((1 . 1) (3 . 2) (4 . 5) (5 . 6) (6 . 7) (9 . 9)) 2.011 {0/8:15} B:0 2.00031 [ 2.25021] ((4 . 1) (6 . 3) (7 . 5) (9 . 6)) 5.031 {0/0:6} B:0 2.00290 [ 2.25204] ((1 . 3) (3 . 5) (4 . 7) (6 . 9)) 8.834 {0/2:6} B:0 5.01306 [ 5.02087] ((1 . 2) (4 . 5) (5 . 6) (6 . 7) (9 . 9)) 3.902 {2/4:10} B:0 1.26048 [ 1.32969] ((1 . 6) (3 . 7) (4 . 9) (5 . 1) (6 . 2) (7 . 3) (8 . 4) (9 . 5)) 1.674 {2/18:28} B:1 SIMILARITY (1/min{score1}): 0.7934 [and 1/min{score2}: 0.7521] [2074, 4691]: Comparing 1h4a_X and 1oki_A, based on their crossing files. There are 19 (5 H + 14 S) secondary structure elements in 1h4a_X, of which 8 satisfy the size requirements. There are 19 (5 H + 14 S) secondary structure elements in 1oki_A, of which 7 satisfy the size requirements. 1.14286 [ 1.00000] ((1 . 1) (3 . 2) (4 . 3) (5 . 4) (6 . 6) (7 . 7) (9 . 9)) 0.942 {0/10:21} B:0 2.00047 [ 1.75070] ((3 . 1) (5 . 3) (7 . 6) (9 . 7)) 5.608 {0/1:6} B:0 2.00051 [ 1.75076] ((1 . 2) (4 . 4) (6 . 7) (7 . 9)) 5.709 {0/1:6} B:0 3.37689 [ 3.35914] ((1 . 1) (3 . 2) (5 . 4) (6 . 6) (9 . 7)) 6.446 {2/6:10} B:0 2.00082 [ 1.75122] ((1 . 2) (3 . 1) (5 . 3) (6 . 4)) 6.441 {0/3:6} B:1 SIMILARITY (1/min{score1}): 0.8750 [and 1/min{score2}: 0.9999] [2074, 4692]: Comparing 1h4a_X and 1oki_A, based on their crossing files. There are 19 (5 H + 14 S) secondary structure elements in 1h4a_X, of which 8 satisfy the size requirements. There are 19 (5 H + 14 S) secondary structure elements in 1oki_A, of which 9 satisfy the size requirements. 1.02868 [ 1.14546] ((1 . 10) (3 . 12) (4 . 14) (5 . 15) (6 . 16) (7 . 17) (8 . 18) (9 . 19)) 0.611 {1/17:28} B:0 2.00046 [ 2.25032] ((1 . 12) (4 . 15) (6 . 17) (7 . 19)) 5.565 {0/1:6} B:0 2.00053 [ 2.25037] ((3 . 10) (5 . 14) (7 . 16) (9 . 17)) 5.771 {0/1:6} B:0 6.68015 [ 6.68821] ((1 . 12) (3 . 14) (8 . 18) (9 . 19)) 6.501 {2/3:6} B:0 10.00401 [10.00642] ((1 . 14) (3 . 16) (4 . 17) (5 . 19)) 8.020 {2/2:6} B:0 SIMILARITY (1/min{score1}): 0.9721 [and 1/min{score2}: 0.8730] [2074, 6335]: Comparing 1h4a_X and 1wkt, based on their crossing files. There are 19 (5 H + 14 S) secondary structure elements in 1h4a_X, of which 8 satisfy the size requirements. There are 7 (0 H + 7 S) secondary structure elements in 1wkt, of which 6 satisfy the size requirements. 1.33347 [ 1.00031] ((1 . 1) (4 . 3) (5 . 4) (6 . 5) (7 . 6) (9 . 7)) 3.011 {0/4:15} B:0 1.60072 [ 1.20171] ((1 . 1) (3 . 3) (6 . 5) (7 . 6) (9 . 7)) 5.282 {0/3:10} B:0 1.60134 [ 1.20316] ((1 . 1) (4 . 3) (5 . 4) (7 . 5) (9 . 7)) 6.158 {0/1:10} B:0 2.00069 [ 1.50163] ((1 . 3) (3 . 4) (4 . 6) (5 . 7)) 6.167 {0/2:6} B:0 2.00107 [ 1.50254] ((3 . 3) (4 . 4) (6 . 6) (7 . 7)) 6.891 {0/1:6} B:0 SIMILARITY (1/min{score1}): 0.7499 [and 1/min{score2}: 0.9997] -------------------------------------------------------------------------------------------------------------------------