------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [5025, 282]: Comparing 1pj5_A and 1b37_A, based on their crossing files. There are 74 (31 H + 43 S) secondary structure elements in 1pj5_A, of which 8 satisfy the size requirements. There are 38 (16 H + 22 S) secondary structure elements in 1b37_A, of which 9 satisfy the size requirements. 1.33443 [ 1.50077] ((24 . 27) (26 . 28) (28 . 29) (29 . 30) (33 . 32) (35 . 33)) 5.112 {0/11:15} B:0 1.33654 [ 1.50225] ((24 . 27) (26 . 28) (28 . 29) (29 . 30) (33 . 32) (35 . 34)) 6.687 {0/11:15} B:0 1.33672 [ 1.50238] ((24 . 26) (26 . 28) (28 . 29) (29 . 30) (33 . 32) (35 . 34)) 6.778 {0/11:15} B:0 1.60015 [ 1.80011] ((24 . 27) (26 . 28) (28 . 29) (29 . 30) (33 . 32)) 3.568 {0/7:10} B:0 1.60118 [ 1.80083] ((24 . 26) (26 . 28) (28 . 29) (29 . 30) (33 . 32)) 5.967 {0/7:10} B:0 SIMILARITY (1/min{score1}): 0.7494 [and 1/min{score2}: 0.6663] [5025, 503]: Comparing 1pj5_A and 1c0p_A, based on their crossing files. There are 74 (31 H + 43 S) secondary structure elements in 1pj5_A, of which 8 satisfy the size requirements. There are 28 (12 H + 16 S) secondary structure elements in 1c0p_A, of which 6 satisfy the size requirements. 1.33337 [ 1.00008] ((24 . 17) (26 . 18) (28 . 19) (29 . 20) (33 . 22) (35 . 25)) 2.119 {0/10:15} B:0 2.00371 [ 1.50875] ((28 . 17) (29 . 18) (33 . 22) (35 . 25)) 9.400 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.7500 [and 1/min{score2}: 0.9999] [5025, 757]: Comparing 1pj5_A and 1d5t_A, based on their crossing files. There are 74 (31 H + 43 S) secondary structure elements in 1pj5_A, of which 8 satisfy the size requirements. There are 39 (20 H + 19 S) secondary structure elements in 1d5t_A, of which 6 satisfy the size requirements. 1.33338 [ 1.00012] ((24 . 30) (26 . 31) (28 . 33) (29 . 35) (33 . 36) (35 . 37)) 2.356 {0/10:15} B:0 2.92496 [ 2.87914] ((24 . 30) (26 . 31) (29 . 33) (33 . 36) (35 . 37)) 3.616 {2/7:10} B:0 2.01135 [ 1.52642] ((24 . 33) (25 . 36) (26 . 35) (29 . 37)) 12.447 {0/3:6} B:1 2.00123 [ 1.50291] ((24 . 37) (26 . 33) (28 . 35) (29 . 30)) 7.126 {0/3:6} B:2 SIMILARITY (1/min{score1}): 0.7500 [and 1/min{score2}: 0.9999] [5025, 1202]: Comparing 1pj5_A and 1el5_A, based on their crossing files. There are 74 (31 H + 43 S) secondary structure elements in 1pj5_A, of which 8 satisfy the size requirements. There are 36 (13 H + 23 S) secondary structure elements in 1el5_A, of which 6 satisfy the size requirements. 1.33337 [ 1.00009] ((24 . 21) (26 . 24) (28 . 25) (29 . 26) (33 . 28) (35 . 30)) 2.201 {0/11:15} B:0 SIMILARITY (1/min{score1}): 0.7500 [and 1/min{score2}: 0.9999] [5025, 1440]: Comparing 1pj5_A and 1f8r_A, based on their crossing files. There are 74 (31 H + 43 S) secondary structure elements in 1pj5_A, of which 8 satisfy the size requirements. There are 46 (23 H + 23 S) secondary structure elements in 1f8r_A, of which 9 satisfy the size requirements. 1.17561 [ 1.30908] ((24 . 32) (25 . 33) (26 . 34) (28 . 35) (29 . 36) (33 . 38) (35 . 40)) 4.566 {1/15:21} B:0 1.33392 [ 1.50041] ((24 . 32) (26 . 34) (28 . 35) (29 . 36) (33 . 38) (35 . 40)) 4.366 {0/11:15} B:0 1.60042 [ 1.80030] ((24 . 32) (26 . 34) (28 . 35) (29 . 36) (35 . 40)) 4.611 {0/6:10} B:0 3.43668 [ 3.49451] ((29 . 34) (33 . 38) (34 . 39) (35 . 40)) 7.029 {2/6:6} B:0 SIMILARITY (1/min{score1}): 0.8506 [and 1/min{score2}: 0.7639] [5025, 1897]: Comparing 1pj5_A and 1gpe_A, based on their crossing files. There are 74 (31 H + 43 S) secondary structure elements in 1pj5_A, of which 8 satisfy the size requirements. There are 52 (26 H + 26 S) secondary structure elements in 1gpe_A, of which 14 satisfy the size requirements. 1.93846 [ 2.52427] ((24 . 32) (26 . 34) (28 . 39) (29 . 40) (34 . 45) (35 . 46)) 6.719 {2/11:15} B:0 2.00859 [ 3.50161] ((24 . 39) (26 . 41) (28 . 43) (34 . 48)) 11.604 {0/3:6} B:0 2.37913 [ 3.58999] ((28 . 39) (29 . 40) (34 . 45) (35 . 46)) 7.093 {1/5:6} B:0 4.06457 [ 4.49157] ((26 . 40) (28 . 41) (33 . 45) (35 . 46)) 15.730 {2/5:6} B:0 5.03219 [ 5.27679] ((24 . 32) (26 . 34) (33 . 38) (35 . 40)) 11.347 {2/4:6} B:0 SIMILARITY (1/min{score1}): 0.5159 [and 1/min{score2}: 0.3962] [5025, 3061]: Comparing 1pj5_A and 1ju2_A, based on their crossing files. There are 74 (31 H + 43 S) secondary structure elements in 1pj5_A, of which 8 satisfy the size requirements. There are 44 (17 H + 27 S) secondary structure elements in 1ju2_A, of which 9 satisfy the size requirements. 2.72435 [ 2.83630] ((24 . 31) (29 . 34) (33 . 37) (34 . 38)) 6.327 {1/4:6} B:0 4.06146 [ 4.09692] ((24 . 32) (29 . 34) (33 . 37) (34 . 38)) 8.981 {2/5:6} B:0 5.03206 [ 5.05085] ((24 . 30) (26 . 31) (28 . 32) (29 . 33)) 10.506 {1/2:6} B:0 7.50958 [ 7.51525] ((26 . 31) (28 . 32) (29 . 33) (35 . 35)) 10.589 {3/4:6} B:0 1.56080 [ 1.62432] ((24 . 30) (26 . 32) (28 . 33) (29 . 34) (33 . 37) (34 . 38) (35 . 31)) 8.039 {2/14:21} B:1 SIMILARITY (1/min{score1}): 0.6407 [and 1/min{score2}: 0.6156] [5025, 3114]: Comparing 1pj5_A and 1k0i_A, based on their crossing files. There are 74 (31 H + 43 S) secondary structure elements in 1pj5_A, of which 8 satisfy the size requirements. There are 38 (17 H + 21 S) secondary structure elements in 1k0i_A, of which 8 satisfy the size requirements. 1.33419 [ 1.33419] ((24 . 22) (26 . 23) (28 . 24) (29 . 25) (33 . 27) (35 . 29)) 4.798 {0/10:15} B:0 4.06234 [ 4.06234] ((28 . 21) (29 . 22) (34 . 27) (35 . 29)) 12.193 {2/5:6} B:0 SIMILARITY (1/min{score1}): 0.7495 [and 1/min{score2}: 0.7495] [5025, 3271]: Comparing 1pj5_A and 1kdg_A, based on their crossing files. There are 74 (31 H + 43 S) secondary structure elements in 1pj5_A, of which 8 satisfy the size requirements. There are 46 (27 H + 19 S) secondary structure elements in 1kdg_A, of which 11 satisfy the size requirements. 2.00120 [ 2.75046] ((26 . 33) (28 . 34) (29 . 36) (35 . 41)) 7.087 {0/4:6} B:0 2.38020 [ 2.92589] ((24 . 34) (26 . 36) (33 . 39) (34 . 42)) 8.910 {1/5:6} B:0 4.06150 [ 4.20718] ((26 . 34) (29 . 36) (33 . 39) (35 . 41)) 9.226 {2/5:6} B:0 5.03198 [ 5.11092] ((24 . 36) (26 . 37) (28 . 38) (33 . 42)) 9.833 {2/4:6} B:0 6.01861 [ 6.06530] ((26 . 33) (28 . 34) (34 . 39) (35 . 41)) 10.034 {3/5:6} B:0 SIMILARITY (1/min{score1}): 0.4997 [and 1/min{score2}: 0.3636] [5025, 3729]: Comparing 1pj5_A and 1ltx_R, based on their crossing files. There are 74 (31 H + 43 S) secondary structure elements in 1pj5_A, of which 8 satisfy the size requirements. There are 42 (20 H + 22 S) secondary structure elements in 1ltx_R, of which 6 satisfy the size requirements. 1.33366 [ 1.00078] ((24 . 32) (26 . 33) (28 . 34) (29 . 36) (33 . 37) (35 . 39)) 3.782 {0/10:15} B:0 6.68033 [ 6.67114] ((26 . 32) (28 . 33) (29 . 34) (35 . 39)) 11.189 {2/3:6} B:0 7.50951 [ 7.50304] ((26 . 32) (28 . 33) (29 . 34) (33 . 37)) 8.248 {3/4:6} B:0 2.00706 [ 1.51654] ((24 . 34) (25 . 37) (26 . 36) (29 . 39)) 11.044 {0/2:6} B:1 1.60090 [ 1.20212] ((24 . 33) (26 . 32) (28 . 36) (29 . 34) (34 . 37)) 5.569 {0/7:10} B:2 SIMILARITY (1/min{score1}): 0.7498 [and 1/min{score2}: 0.9992] [5025, 4128]: Comparing 1pj5_A and 1n4w_A, based on their crossing files. There are 74 (31 H + 43 S) secondary structure elements in 1pj5_A, of which 8 satisfy the size requirements. There are 35 (16 H + 19 S) secondary structure elements in 1n4w_A, of which 7 satisfy the size requirements. 1.60103 [ 1.40154] ((24 . 24) (26 . 25) (28 . 26) (29 . 27) (33 . 30)) 5.772 {0/6:10} B:0 2.00132 [ 1.75197] ((26 . 24) (28 . 25) (29 . 26) (34 . 30)) 7.254 {0/3:6} B:0 5.03267 [ 5.01963] ((26 . 27) (28 . 28) (29 . 29) (33 . 30)) 13.428 {2/4:6} B:0 7.50949 [ 7.50558] ((24 . 24) (26 . 26) (29 . 27) (33 . 30)) 7.394 {3/4:6} B:0 7.50952 [ 7.50561] ((24 . 25) (26 . 26) (28 . 27) (33 . 30)) 9.001 {3/4:6} B:0 SIMILARITY (1/min{score1}): 0.6246 [and 1/min{score2}: 0.7135] [5025, 4238]: Comparing 1pj5_A and 1ng4_A, based on their crossing files. There are 74 (31 H + 43 S) secondary structure elements in 1pj5_A, of which 8 satisfy the size requirements. There are 31 (13 H + 18 S) secondary structure elements in 1ng4_A, of which 7 satisfy the size requirements. 1.14289 [ 1.00005] ((24 . 20) (26 . 21) (28 . 22) (29 . 23) (33 . 25) (34 . 26) (35 . 27)) 1.923 {0/16:21} B:0 1.60353 [ 1.40526] ((28 . 20) (29 . 21) (33 . 25) (34 . 26) (35 . 27)) 7.855 {0/8:10} B:0 2.00089 [ 1.75133] ((26 . 20) (28 . 21) (29 . 22) (33 . 26)) 6.578 {0/4:6} B:0 1.60036 [ 1.40054] ((28 . 22) (29 . 21) (33 . 25) (34 . 26) (35 . 27)) 4.442 {0/9:10} B:1 1.60250 [ 1.40373] ((24 . 21) (26 . 20) (28 . 23) (29 . 22) (34 . 25)) 7.204 {0/6:10} B:2 SIMILARITY (1/min{score1}): 0.8750 [and 1/min{score2}: 0.9999] [5025, 5025]: Comparing 1pj5_A and 1pj5_A, based on their crossing files. There are 74 (31 H + 43 S) secondary structure elements in 1pj5_A, of which 8 satisfy the size requirements. There are 74 (31 H + 43 S) secondary structure elements in 1pj5_A, of which 8 satisfy the size requirements. 1.00000 [ 1.00000] ((24 . 24) (25 . 25) (26 . 26) (28 . 28) (29 . 29) (33 . 33) (34 . 34) (35 . 35)) 0.000 {0/23:28} B:0 5.03171 [ 5.03171] ((24 . 24) (25 . 25) (26 . 28) (35 . 35)) 4.107 {2/4:6} B:0 5.03171 [ 5.03171] ((24 . 24) (25 . 25) (28 . 26) (35 . 35)) 4.107 {2/4:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [5025, 5058]: Comparing 1pj5_A and 1pn0_A, based on their crossing files. There are 74 (31 H + 43 S) secondary structure elements in 1pj5_A, of which 8 satisfy the size requirements. There are 49 (20 H + 29 S) secondary structure elements in 1pn0_A, of which 8 satisfy the size requirements. 1.33391 [ 1.33391] ((24 . 22) (26 . 23) (28 . 24) (29 . 25) (33 . 26) (35 . 28)) 4.356 {0/10:15} B:0 1.33613 [ 1.33613] ((24 . 22) (26 . 23) (28 . 24) (29 . 25) (33 . 26) (35 . 27)) 6.460 {0/10:15} B:0 1.60007 [ 1.60007] ((26 . 23) (28 . 24) (29 . 25) (33 . 26) (35 . 28)) 2.921 {0/7:10} B:0 1.60108 [ 1.60108] ((26 . 23) (28 . 24) (29 . 25) (33 . 26) (35 . 27)) 5.831 {0/7:10} B:0 2.00279 [ 2.00279] ((28 . 22) (29 . 23) (33 . 26) (35 . 27)) 8.754 {0/5:6} B:0 SIMILARITY (1/min{score1}): 0.7497 [and 1/min{score2}: 0.7497] [5025, 5761]: Comparing 1pj5_A and 1s3e_A, based on their crossing files. There are 74 (31 H + 43 S) secondary structure elements in 1pj5_A, of which 8 satisfy the size requirements. There are 44 (23 H + 21 S) secondary structure elements in 1s3e_A, of which 8 satisfy the size requirements. 1.33383 [ 1.33383] ((24 . 28) (26 . 30) (28 . 31) (29 . 32) (33 . 34) (35 . 36)) 4.190 {0/9:15} B:0 1.60025 [ 1.60025] ((24 . 28) (28 . 31) (29 . 32) (33 . 34) (35 . 36)) 4.035 {0/6:10} B:0 1.64453 [ 1.64453] ((24 . 28) (25 . 29) (26 . 30) (28 . 31) (29 . 32) (33 . 34) (35 . 36)) 4.504 {2/13:21} B:0 5.00365 [ 5.00365] ((24 . 28) (26 . 30) (28 . 31) (29 . 32) (33 . 29) (34 . 34) (35 . 36)) 9.406 {7/14:21} B:1 SIMILARITY (1/min{score1}): 0.7497 [and 1/min{score2}: 0.7497] [5025, 5804]: Comparing 1pj5_A and 1sez_A, based on their crossing files. There are 74 (31 H + 43 S) secondary structure elements in 1pj5_A, of which 8 satisfy the size requirements. There are 43 (22 H + 21 S) secondary structure elements in 1sez_A, of which 8 satisfy the size requirements. 1.33353 [ 1.33353] ((24 . 29) (26 . 31) (28 . 33) (29 . 36) (33 . 38) (35 . 39)) 3.344 {0/9:15} B:0 1.60011 [ 1.60011] ((24 . 29) (26 . 31) (28 . 33) (29 . 36) (33 . 38)) 3.296 {0/6:10} B:0 2.00319 [ 2.00319] ((24 . 31) (25 . 32) (26 . 33) (28 . 36)) 9.048 {0/2:6} B:0 5.03174 [ 5.03174] ((24 . 29) (26 . 33) (29 . 36) (33 . 38)) 6.234 {2/4:6} B:0 SIMILARITY (1/min{score1}): 0.7499 [and 1/min{score2}: 0.7499] [5025, 6215]: Comparing 1pj5_A and 1ve9_A, based on their crossing files. There are 74 (31 H + 43 S) secondary structure elements in 1pj5_A, of which 8 satisfy the size requirements. There are 28 (13 H + 15 S) secondary structure elements in 1ve9_A, of which 7 satisfy the size requirements. 1.14289 [ 1.00005] ((24 . 17) (26 . 18) (28 . 19) (29 . 20) (33 . 22) (34 . 23) (35 . 24)) 1.940 {0/16:21} B:0 1.60338 [ 1.40503] ((28 . 17) (29 . 18) (33 . 22) (34 . 23) (35 . 24)) 7.768 {0/8:10} B:0 3.43647 [ 3.39493] ((24 . 17) (26 . 18) (29 . 19) (35 . 24)) 3.747 {1/3:6} B:0 4.06129 [ 4.03635] ((26 . 17) (33 . 22) (34 . 23) (35 . 24)) 7.748 {2/5:6} B:0 5.03171 [ 5.01866] ((29 . 19) (33 . 22) (34 . 23) (35 . 24)) 4.301 {3/6:6} B:0 SIMILARITY (1/min{score1}): 0.8750 [and 1/min{score2}: 0.9999] -------------------------------------------------------------------------------------------------------------------------