------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [6637, 347]: Comparing 7odc_A and 1bd0_A, based on their crossing files. There are 36 (17 H + 19 S) secondary structure elements in 7odc_A, of which 13 satisfy the size requirements. There are 37 (16 H + 21 S) secondary structure elements in 1bd0_A, of which 14 satisfy the size requirements. 2.48371 [ 2.59945] ((4 . 1) (25 . 22) (26 . 26) (30 . 31) (32 . 32) (35 . 36)) 5.746 {2/10:15} B:0 2.60023 [ 2.80018] ((4 . 1) (25 . 21) (30 . 31) (32 . 32) (35 . 36)) 5.685 {0/6:10} B:0 2.60034 [ 2.80028] ((4 . 1) (25 . 21) (31 . 31) (32 . 32) (35 . 36)) 6.308 {0/6:10} B:0 3.25059 [ 3.50047] ((26 . 22) (29 . 29) (30 . 30) (32 . 31)) 8.527 {0/4:6} B:0 3.25165 [ 3.50132] ((25 . 26) (27 . 28) (30 . 32) (31 . 33)) 11.037 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.4026 [and 1/min{score2}: 0.3847] [6637, 1054]: Comparing 7odc_A and 1e79_A, based on their crossing files. There are 36 (17 H + 19 S) secondary structure elements in 7odc_A, of which 13 satisfy the size requirements. There are 38 (21 H + 17 S) secondary structure elements in 1e79_A, of which 6 satisfy the size requirements. 3.25226 [ 1.52248] ((29 . 1) (30 . 2) (32 . 3) (35 . 5)) 11.942 {0/5:6} B:0 5.20962 [ 5.01014] ((26 . 1) (29 . 4) (30 . 5) (32 . 7)) 6.160 {2/4:6} B:0 3.25027 [ 1.50274] ((25 . 2) (26 . 1) (29 . 5) (30 . 7)) 7.023 {0/4:6} B:1 4.37866 [ 4.01973] ((25 . 2) (26 . 1) (30 . 3) (31 . 4)) 6.395 {2/5:6} B:1 2.16719 [ 1.00530] ((25 . 2) (26 . 1) (29 . 3) (30 . 7) (31 . 4) (32 . 5)) 6.118 {0/13:15} B:2 SIMILARITY (1/min{score1}): 0.4614 [and 1/min{score2}: 0.9947] [6637, 1057]: Comparing 7odc_A and 1e79_D, based on their crossing files. There are 36 (17 H + 19 S) secondary structure elements in 7odc_A, of which 13 satisfy the size requirements. There are 37 (19 H + 18 S) secondary structure elements in 1e79_D, of which 6 satisfy the size requirements. 3.25234 [ 1.52325] ((29 . 1) (30 . 2) (32 . 3) (35 . 5)) 12.046 {0/5:6} B:0 5.20963 [ 5.01014] ((26 . 1) (29 . 4) (30 . 5) (32 . 6)) 6.333 {2/4:6} B:0 2.60132 [ 1.21319] ((25 . 5) (26 . 2) (30 . 1) (31 . 3) (32 . 4)) 8.828 {0/9:10} B:2 5.41958 [ 5.38623] ((25 . 1) (26 . 2) (29 . 5) (30 . 4) (31 . 3) (32 . 6)) 4.915 {7/13:15} B:2 SIMILARITY (1/min{score1}): 0.3844 [and 1/min{score2}: 0.8243] [6637, 2226]: Comparing 7odc_A and 1hkv_A, based on their crossing files. There are 36 (17 H + 19 S) secondary structure elements in 7odc_A, of which 13 satisfy the size requirements. There are 43 (17 H + 26 S) secondary structure elements in 1hkv_A, of which 16 satisfy the size requirements. 1.92780 [ 2.32482] ((26 . 32) (27 . 33) (29 . 35) (30 . 36) (31 . 37) (32 . 38) (35 . 41)) 2.538 {2/17:21} B:0 2.17174 [ 2.66939] ((25 . 30) (26 . 32) (27 . 33) (29 . 35) (32 . 38) (35 . 41)) 4.994 {1/15:15} B:0 2.29323 [ 2.73783] ((25 . 31) (26 . 32) (27 . 33) (29 . 35) (32 . 38) (35 . 41)) 5.694 {2/13:15} B:0 3.25051 [ 4.00028] ((26 . 31) (29 . 34) (30 . 35) (32 . 36)) 8.243 {0/3:6} B:0 3.25055 [ 4.00029] ((25 . 32) (26 . 34) (29 . 37) (30 . 38)) 8.385 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.5187 [and 1/min{score2}: 0.4301] [6637, 3366]: Comparing 7odc_A and 1knw_A, based on their crossing files. There are 36 (17 H + 19 S) secondary structure elements in 7odc_A, of which 13 satisfy the size requirements. There are 33 (14 H + 19 S) secondary structure elements in 1knw_A, of which 13 satisfy the size requirements. 2.17305 [ 2.17305] ((26 . 24) (27 . 25) (29 . 27) (31 . 28) (32 . 29) (35 . 31)) 2.345 {1/14:15} B:0 2.60010 [ 2.60010] ((3 . 1) (25 . 22) (27 . 25) (29 . 27) (35 . 31)) 4.606 {0/10:10} B:0 3.25060 [ 3.25060] ((25 . 24) (26 . 26) (29 . 28) (30 . 29)) 8.564 {0/3:6} B:0 3.25127 [ 3.25127] ((3 . 1) (4 . 2) (30 . 26) (32 . 27)) 10.342 {0/4:6} B:0 3.36193 [ 3.36193] ((25 . 26) (29 . 29) (32 . 31) (36 . 33)) 10.443 {1/5:6} B:0 SIMILARITY (1/min{score1}): 0.4602 [and 1/min{score2}: 0.4602] [6637, 6234]: Comparing 7odc_A and 1vhe_A, based on their crossing files. There are 36 (17 H + 19 S) secondary structure elements in 7odc_A, of which 13 satisfy the size requirements. There are 30 (12 H + 18 S) secondary structure elements in 1vhe_A, of which 8 satisfy the size requirements. 2.60040 [ 1.60170] ((25 . 6) (27 . 8) (29 . 10) (31 . 13) (32 . 15)) 6.543 {0/9:10} B:0 2.63413 [ 1.73209] ((25 . 6) (26 . 7) (27 . 8) (30 . 13) (32 . 15)) 4.418 {1/8:10} B:0 3.25016 [ 2.00069] ((26 . 6) (29 . 9) (30 . 10) (32 . 13)) 6.163 {0/4:6} B:0 3.25148 [ 2.00634] ((29 . 6) (30 . 7) (32 . 9) (35 . 13)) 10.750 {0/5:6} B:0 6.12520 [ 6.01847] ((25 . 7) (27 . 8) (29 . 13) (32 . 15)) 6.960 {3/5:6} B:0 SIMILARITY (1/min{score1}): 0.5370 [and 1/min{score2}: 0.8590] [6637, 6241]: Comparing 7odc_A and 1vho_A, based on their crossing files. There are 36 (17 H + 19 S) secondary structure elements in 7odc_A, of which 13 satisfy the size requirements. There are 26 (9 H + 17 S) secondary structure elements in 1vho_A, of which 7 satisfy the size requirements. 2.60032 [ 1.40203] ((25 . 6) (26 . 7) (29 . 9) (30 . 11) (32 . 13)) 6.186 {0/8:10} B:0 3.25053 [ 1.75339] ((25 . 7) (26 . 8) (29 . 11) (30 . 13)) 8.315 {0/3:6} B:0 2.60024 [ 1.40156] ((25 . 6) (26 . 7) (30 . 11) (31 . 8) (32 . 13)) 5.788 {0/9:10} B:1 3.25051 [ 1.75324] ((1 . 9) (2 . 8) (3 . 10) (4 . 11)) 8.218 {0/4:6} B:1 3.25057 [ 1.75367] ((29 . 6) (30 . 7) (31 . 9) (32 . 8)) 8.482 {0/4:6} B:1 SIMILARITY (1/min{score1}): 0.3846 [and 1/min{score2}: 0.7135] [6637, 6637]: Comparing 7odc_A and 7odc_A, based on their crossing files. There are 36 (17 H + 19 S) secondary structure elements in 7odc_A, of which 13 satisfy the size requirements. There are 36 (17 H + 19 S) secondary structure elements in 7odc_A, of which 13 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (25 . 25) (26 . 26) (27 . 27) (29 . 29) (30 . 30) (31 . 31) (32 . 32) (35 . 35) (36 . 36)) 0.000 {0/69:78} B:0 2.17853 [ 2.17853] ((3 . 3) (4 . 4) (27 . 27) (30 . 31) (35 . 35) (36 . 36)) 4.095 {1/12:15} B:0 2.17853 [ 2.17853] ((3 . 3) (4 . 4) (27 . 27) (31 . 30) (35 . 35) (36 . 36)) 4.095 {1/12:15} B:0 2.80276 [ 2.80276] ((3 . 3) (25 . 26) (27 . 27) (35 . 35) (36 . 36)) 5.178 {2/10:10} B:0 3.30491 [ 3.30491] ((3 . 3) (26 . 25) (27 . 27) (36 . 36)) 5.807 {1/6:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] -------------------------------------------------------------------------------------------------------------------------