------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [809, 809]: Comparing 1ddz_A and 1ddz_A, based on their crossing files. There are 32 (22 H + 10 S) secondary structure elements in 1ddz_A, of which 15 satisfy the size requirements. There are 32 (22 H + 10 S) secondary structure elements in 1ddz_A, of which 15 satisfy the size requirements. 1.00000 [ 1.00000] ((18 . 18) (19 . 19) (20 . 20) (21 . 21) (22 . 22) (23 . 23) (24 . 24) (25 . 25) (26 . 26) (27 . 27) (28 . 28) (29 . 29) (30 . 30) (31 . 31) (32 . 32)) 0.000 {0/84:105} B:0 1.25190 [ 1.25190] ((19 . 18) (21 . 21) (23 . 23) (24 . 24) (25 . 25) (26 . 26) (27 . 27) (28 . 28) (29 . 29) (30 . 30) (31 . 31) (32 . 32)) 5.387 {1/47:66} B:0 1.36529 [ 1.36529] ((19 . 18) (21 . 21) (23 . 23) (24 . 24) (25 . 25) (26 . 26) (27 . 27) (29 . 29) (30 . 30) (31 . 31) (32 . 32)) 5.346 {1/39:55} B:0 2.50000 [ 2.50000] ((18 . 18) (21 . 23) (24 . 24) (25 . 25) (29 . 29) (30 . 30)) 1.798 {0/8:15} B:0 2.50036 [ 2.50036] ((19 . 18) (23 . 21) (24 . 24) (25 . 25) (29 . 29) (30 . 30)) 6.186 {0/7:15} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [809, 1194]: Comparing 1ddz_A and 1ekj_A, based on their crossing files. There are 32 (22 H + 10 S) secondary structure elements in 1ddz_A, of which 15 satisfy the size requirements. There are 16 (11 H + 5 S) secondary structure elements in 1ekj_A, of which 13 satisfy the size requirements. 1.22559 [ 1.10366] ((19 . 1) (20 . 2) (21 . 3) (23 . 6) (24 . 8) (25 . 9) (26 . 10) (27 . 11) (28 . 12) (29 . 13) (30 . 14) (31 . 15) (32 . 16)) 3.103 {5/60:78} B:0 1.29593 [ 1.15122] ((19 . 1) (20 . 2) (21 . 3) (23 . 6) (24 . 8) (25 . 9) (26 . 10) (27 . 11) (29 . 13) (30 . 14) (31 . 15) (32 . 16)) 2.562 {4/51:66} B:0 1.51019 [ 1.31554] ((21 . 3) (23 . 6) (24 . 8) (25 . 9) (26 . 10) (27 . 12) (29 . 13) (30 . 14) (31 . 15) (32 . 16)) 4.044 {2/33:45} B:0 1.66771 [ 1.44605] ((21 . 6) (24 . 8) (25 . 9) (26 . 10) (27 . 11) (29 . 13) (30 . 14) (31 . 15) (32 . 16)) 2.434 {1/27:36} B:0 2.52504 [ 2.20470] ((19 . 1) (20 . 2) (21 . 3) (23 . 6) (25 . 9) (30 . 13)) 8.056 {1/9:15} B:0 SIMILARITY (1/min{score1}): 0.8159 [and 1/min{score2}: 0.9061] [809, 1731]: Comparing 1ddz_A and 1g5c_A, based on their crossing files. There are 32 (22 H + 10 S) secondary structure elements in 1ddz_A, of which 15 satisfy the size requirements. There are 13 (8 H + 5 S) secondary structure elements in 1g5c_A, of which 11 satisfy the size requirements. 1.66699 [ 1.22304] ((21 . 3) (22 . 5) (23 . 6) (24 . 7) (25 . 8) (27 . 10) (29 . 11) (31 . 12) (32 . 13)) 4.454 {0/26:36} B:0 2.50007 [ 1.83351] ((23 . 3) (24 . 7) (25 . 8) (29 . 11) (31 . 12) (32 . 13)) 4.091 {0/8:15} B:0 2.50114 [ 1.83621] ((23 . 3) (24 . 5) (25 . 8) (29 . 11) (31 . 12) (32 . 13)) 8.264 {0/8:15} B:0 3.75187 [ 2.75473] ((24 . 5) (25 . 6) (27 . 7) (30 . 10)) 12.681 {0/4:6} B:0 3.93825 [ 3.16222] ((24 . 1) (26 . 5) (28 . 7) (30 . 9)) 22.249 {1/4:6} B:0 SIMILARITY (1/min{score1}): 0.5999 [and 1/min{score2}: 0.8176] [809, 2414]: Comparing 1ddz_A and 1i6p_A, based on their crossing files. There are 32 (22 H + 10 S) secondary structure elements in 1ddz_A, of which 15 satisfy the size requirements. There are 14 (9 H + 5 S) secondary structure elements in 1i6p_A, of which 14 satisfy the size requirements. 1.16340 [ 1.08863] ((19 . 1) (20 . 2) (21 . 3) (22 . 4) (23 . 5) (24 . 6) (25 . 7) (26 . 8) (27 . 9) (29 . 10) (30 . 11) (31 . 12) (32 . 13)) 2.805 {3/61:78} B:0 1.26508 [ 1.18510] ((19 . 1) (20 . 2) (21 . 3) (22 . 4) (23 . 5) (24 . 6) (25 . 7) (26 . 8) (27 . 9) (29 . 10) (30 . 11) (31 . 12)) 1.884 {3/51:66} B:0 1.37264 [ 1.28377] ((18 . 1) (20 . 2) (21 . 3) (23 . 5) (24 . 6) (25 . 7) (26 . 8) (27 . 9) (29 . 10) (30 . 11) (31 . 12)) 6.235 {2/39:55} B:0 1.50213 [ 1.40262] ((18 . 1) (21 . 3) (23 . 5) (24 . 6) (25 . 7) (26 . 8) (27 . 9) (29 . 10) (30 . 11) (31 . 12)) 5.568 {1/29:45} B:0 1.66976 [ 1.55936] ((18 . 1) (21 . 3) (23 . 5) (24 . 6) (25 . 7) (26 . 8) (27 . 9) (29 . 10) (30 . 11)) 5.577 {1/22:36} B:0 SIMILARITY (1/min{score1}): 0.8905 [and 1/min{score2}: 0.9416] [809, 6524]: Comparing 1ddz_A and 2rsl_A, based on their crossing files. There are 32 (22 H + 10 S) secondary structure elements in 1ddz_A, of which 15 satisfy the size requirements. There are 11 (6 H + 5 S) secondary structure elements in 2rsl_A, of which 8 satisfy the size requirements. 2.14343 [ 1.14660] ((21 . 1) (22 . 2) (23 . 4) (24 . 5) (25 . 6) (30 . 8) (31 . 9)) 6.195 {0/8:21} B:0 2.14344 [ 1.14668] ((21 . 1) (22 . 2) (23 . 4) (24 . 5) (25 . 6) (29 . 8) (31 . 9)) 6.229 {0/7:21} B:0 2.50048 [ 1.33650] ((21 . 1) (22 . 2) (23 . 4) (25 . 6) (27 . 8) (31 . 9)) 6.667 {0/7:15} B:0 3.00024 [ 1.60160] ((21 . 1) (22 . 2) (23 . 4) (25 . 6) (27 . 8)) 6.445 {0/3:10} B:0 3.75002 [ 2.00014] ((21 . 1) (23 . 4) (24 . 5) (25 . 9)) 4.172 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.4665 [and 1/min{score2}: 0.8721] -------------------------------------------------------------------------------------------------------------------------