------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [3045, 370]: Comparing 1jsc_A and 1bfd, based on their crossing files. There are 47 (27 H + 20 S) secondary structure elements in 1jsc_A, of which 13 satisfy the size requirements. There are 41 (23 H + 18 S) secondary structure elements in 1bfd, of which 12 satisfy the size requirements. 1.19468 [ 1.10717] ((19 . 16) (20 . 17) (22 . 19) (23 . 20) (24 . 21) (25 . 22) (26 . 23) (30 . 24) (31 . 25) (32 . 26) (33 . 27)) 2.826 {2/37:55} B:0 1.30003 [ 1.20004] ((19 . 16) (20 . 17) (22 . 19) (23 . 20) (24 . 21) (26 . 23) (30 . 24) (31 . 25) (32 . 26) (33 . 27)) 2.115 {0/30:45} B:0 1.62505 [ 1.50007] ((19 . 16) (20 . 17) (22 . 19) (23 . 20) (24 . 21) (26 . 23) (30 . 26) (33 . 27)) 2.773 {0/18:28} B:0 1.62506 [ 1.50008] ((19 . 16) (20 . 17) (24 . 20) (26 . 23) (30 . 24) (31 . 25) (32 . 26) (33 . 27)) 2.896 {0/18:28} B:0 2.16671 [ 2.00005] ((23 . 17) (24 . 20) (30 . 24) (31 . 25) (32 . 26) (33 . 27)) 3.213 {0/9:15} B:0 SIMILARITY (1/min{score1}): 0.8370 [and 1/min{score2}: 0.9032] [3045, 747]: Comparing 1jsc_A and 1d4o_A, based on their crossing files. There are 47 (27 H + 20 S) secondary structure elements in 1jsc_A, of which 13 satisfy the size requirements. There are 17 (11 H + 6 S) secondary structure elements in 1d4o_A, of which 12 satisfy the size requirements. 1.31526 [ 1.21928] ((19 . 1) (20 . 2) (22 . 4) (23 . 5) (24 . 8) (25 . 9) (26 . 10) (30 . 14) (32 . 16) (33 . 17)) 3.192 {2/33:45} B:0 1.47278 [ 1.36898] ((19 . 1) (20 . 2) (22 . 4) (23 . 5) (25 . 9) (26 . 10) (30 . 14) (32 . 16) (33 . 17)) 3.239 {2/26:36} B:0 2.16669 [ 2.00003] ((20 . 5) (24 . 8) (25 . 9) (26 . 10) (32 . 16) (33 . 17)) 2.857 {0/11:15} B:0 2.33560 [ 2.20686] ((19 . 1) (20 . 2) (22 . 4) (23 . 5) (25 . 9) (32 . 14)) 3.809 {2/12:15} B:0 2.63416 [ 2.44311] ((19 . 1) (20 . 2) (22 . 4) (29 . 9) (32 . 14)) 4.718 {1/8:10} B:0 SIMILARITY (1/min{score1}): 0.7603 [and 1/min{score2}: 0.8202] [3045, 842]: Comparing 1jsc_A and 1dhs, based on their crossing files. There are 47 (27 H + 20 S) secondary structure elements in 1jsc_A, of which 13 satisfy the size requirements. There are 26 (17 H + 9 S) secondary structure elements in 1dhs, of which 23 satisfy the size requirements. 1.30027 [ 2.30005] ((19 . 4) (20 . 5) (22 . 7) (23 . 8) (25 . 19) (26 . 20) (30 . 22) (31 . 23) (32 . 24) (33 . 25)) 3.525 {0/27:45} B:0 1.44448 [ 2.55556] ((19 . 4) (20 . 5) (22 . 7) (23 . 8) (25 . 19) (26 . 20) (30 . 22) (32 . 24) (33 . 25)) 2.283 {0/21:36} B:0 2.60039 [ 4.60007] ((20 . 20) (22 . 21) (23 . 22) (26 . 24) (29 . 26)) 6.498 {0/4:10} B:0 2.70351 [ 4.61971] ((20 . 20) (22 . 21) (24 . 24) (25 . 25) (29 . 26)) 4.675 {1/6:10} B:0 3.25008 [ 5.75002] ((19 . 21) (20 . 22) (22 . 23) (23 . 24)) 5.245 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.7691 [and 1/min{score2}: 0.4500] [3045, 2765]: Comparing 1jsc_A and 1j8f_A, based on their crossing files. There are 47 (27 H + 20 S) secondary structure elements in 1jsc_A, of which 13 satisfy the size requirements. There are 24 (15 H + 9 S) secondary structure elements in 1j8f_A, of which 22 satisfy the size requirements. 1.30155 [ 2.20032] ((19 . 2) (20 . 3) (22 . 8) (23 . 9) (24 . 12) (25 . 17) (26 . 18) (30 . 20) (32 . 22) (33 . 23)) 3.037 {1/30:45} B:0 2.18602 [ 3.67071] ((25 . 17) (26 . 18) (30 . 20) (32 . 22) (33 . 23) (34 . 24)) 9.317 {1/11:15} B:0 2.60013 [ 4.40003] ((20 . 9) (23 . 12) (29 . 17) (30 . 18) (32 . 20)) 4.962 {0/8:10} B:0 2.60042 [ 4.40009] ((19 . 8) (20 . 9) (29 . 17) (30 . 18) (32 . 20)) 6.645 {0/6:10} B:0 2.60079 [ 4.40016] ((19 . 5) (24 . 9) (25 . 10) (29 . 15) (30 . 16)) 7.769 {0/8:10} B:0 SIMILARITY (1/min{score1}): 0.7683 [and 1/min{score2}: 0.5235] [3045, 3045]: Comparing 1jsc_A and 1jsc_A, based on their crossing files. There are 47 (27 H + 20 S) secondary structure elements in 1jsc_A, of which 13 satisfy the size requirements. There are 47 (27 H + 20 S) secondary structure elements in 1jsc_A, of which 13 satisfy the size requirements. 1.00000 [ 1.00000] ((19 . 19) (20 . 20) (22 . 22) (23 . 23) (24 . 24) (25 . 25) (26 . 26) (29 . 29) (30 . 30) (31 . 31) (32 . 32) (33 . 33) (34 . 34)) 0.000 {0/61:78} B:0 1.08333 [ 1.08333] ((19 . 19) (20 . 20) (22 . 22) (23 . 23) (24 . 24) (25 . 25) (26 . 26) (29 . 29) (30 . 30) (31 . 31) (32 . 32) (33 . 33)) 0.000 {0/50:66} B:0 1.08334 [ 1.08334] ((19 . 19) (20 . 20) (22 . 22) (24 . 23) (25 . 25) (26 . 26) (29 . 29) (30 . 30) (31 . 31) (32 . 32) (33 . 33) (34 . 34)) 1.326 {0/51:66} B:0 1.08334 [ 1.08334] ((19 . 19) (20 . 20) (22 . 22) (23 . 24) (25 . 25) (26 . 26) (29 . 29) (30 . 30) (31 . 31) (32 . 32) (33 . 33) (34 . 34)) 1.326 {0/51:66} B:0 2.16670 [ 2.16670] ((19 . 19) (20 . 20) (22 . 22) (24 . 23) (25 . 25) (32 . 30)) 3.176 {0/12:15} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [3045, 3802]: Comparing 1jsc_A and 1m2k_A, based on their crossing files. There are 47 (27 H + 20 S) secondary structure elements in 1jsc_A, of which 13 satisfy the size requirements. There are 22 (12 H + 10 S) secondary structure elements in 1m2k_A, of which 19 satisfy the size requirements. 1.19288 [ 1.73085] ((19 . 1) (20 . 2) (22 . 8) (23 . 9) (24 . 11) (25 . 16) (26 . 17) (29 . 18) (30 . 19) (32 . 21) (33 . 22)) 4.230 {2/39:55} B:0 1.30576 [ 1.67195] ((19 . 1) (20 . 2) (22 . 8) (23 . 9) (24 . 11) (25 . 16) (26 . 17) (29 . 18) (30 . 19) (31 . 20) (32 . 21) (33 . 22)) 4.359 {5/45:66} B:0 2.16670 [ 3.16668] ((20 . 9) (25 . 16) (26 . 17) (30 . 19) (32 . 21) (33 . 22)) 3.015 {0/9:15} B:0 2.16697 [ 3.16676] ((20 . 9) (22 . 10) (23 . 11) (29 . 16) (30 . 17) (32 . 19)) 5.323 {0/10:15} B:0 2.60004 [ 3.80001] ((20 . 9) (22 . 10) (25 . 16) (30 . 19) (32 . 21)) 3.702 {0/7:10} B:0 SIMILARITY (1/min{score1}): 0.8383 [and 1/min{score2}: 0.5981] [3045, 4562]: Comparing 1jsc_A and 1o97_D, based on their crossing files. There are 47 (27 H + 20 S) secondary structure elements in 1jsc_A, of which 13 satisfy the size requirements. There are 30 (12 H + 18 S) secondary structure elements in 1o97_D, of which 10 satisfy the size requirements. 1.65242 [ 1.30767] ((20 . 19) (22 . 21) (23 . 22) (26 . 25) (30 . 27) (31 . 28) (32 . 29) (33 . 30)) 2.300 {1/12:28} B:0 3.06873 [ 2.93653] ((20 . 19) (22 . 21) (23 . 22) (25 . 26) (26 . 27) (30 . 29)) 4.232 {2/7:15} B:0 3.25002 [ 2.50005] ((26 . 22) (30 . 25) (31 . 26) (32 . 27)) 3.856 {0/0:6} B:0 3.25042 [ 2.50093] ((23 . 19) (31 . 26) (32 . 27) (33 . 28)) 7.861 {0/0:6} B:0 3.25059 [ 2.50130] ((20 . 22) (23 . 25) (24 . 27) (26 . 29)) 8.537 {0/1:6} B:0 SIMILARITY (1/min{score1}): 0.6152 [and 1/min{score2}: 0.7993] [3045, 4795]: Comparing 1jsc_A and 1ovm_A, based on their crossing files. There are 47 (27 H + 20 S) secondary structure elements in 1jsc_A, of which 13 satisfy the size requirements. There are 43 (25 H + 18 S) secondary structure elements in 1ovm_A, of which 12 satisfy the size requirements. 1.68040 [ 1.56919] ((19 . 15) (20 . 16) (23 . 19) (25 . 22) (26 . 23) (30 . 24) (32 . 26) (33 . 27)) 2.541 {2/20:28} B:0 1.86310 [ 1.72185] ((19 . 15) (20 . 16) (24 . 19) (25 . 22) (26 . 23) (30 . 24) (32 . 26)) 2.732 {1/16:21} B:0 2.04527 [ 1.94256] ((19 . 15) (20 . 16) (24 . 19) (26 . 23) (30 . 24) (32 . 26) (33 . 27)) 2.954 {2/13:21} B:0 2.18332 [ 2.02108] ((19 . 15) (23 . 16) (24 . 19) (30 . 24) (32 . 26) (33 . 27)) 3.530 {1/11:15} B:0 2.19084 [ 2.03055] ((19 . 15) (20 . 16) (22 . 18) (23 . 19) (25 . 22) (26 . 23)) 2.035 {1/10:15} B:0 SIMILARITY (1/min{score1}): 0.5951 [and 1/min{score2}: 0.6373] [3045, 4847]: Comparing 1jsc_A and 1ozh_A, based on their crossing files. There are 47 (27 H + 20 S) secondary structure elements in 1jsc_A, of which 13 satisfy the size requirements. There are 48 (27 H + 21 S) secondary structure elements in 1ozh_A, of which 12 satisfy the size requirements. 1.22312 [ 1.14247] ((19 . 18) (20 . 19) (22 . 21) (23 . 22) (24 . 24) (25 . 25) (26 . 26) (30 . 29) (32 . 30) (33 . 31) (34 . 32)) 2.601 {3/41:55} B:0 1.44665 [ 1.33614] ((19 . 18) (20 . 19) (22 . 21) (23 . 22) (24 . 24) (25 . 25) (26 . 26) (30 . 30) (33 . 31)) 2.911 {1/25:36} B:0 1.54327 [ 1.45484] ((19 . 18) (20 . 19) (22 . 21) (24 . 22) (25 . 25) (30 . 29) (32 . 30) (33 . 31) (34 . 32)) 3.143 {3/28:36} B:0 1.86382 [ 1.72276] ((23 . 19) (24 . 22) (29 . 25) (30 . 29) (32 . 30) (33 . 31) (34 . 32)) 5.977 {1/16:21} B:0 2.16674 [ 2.00010] ((19 . 18) (20 . 19) (23 . 24) (25 . 25) (26 . 26) (30 . 30)) 3.786 {0/12:15} B:0 SIMILARITY (1/min{score1}): 0.8176 [and 1/min{score2}: 0.8753] [3045, 5072]: Comparing 1jsc_A and 1pox_A, based on their crossing files. There are 47 (27 H + 20 S) secondary structure elements in 1jsc_A, of which 13 satisfy the size requirements. There are 46 (27 H + 19 S) secondary structure elements in 1pox_A, of which 13 satisfy the size requirements. 1.18271 [ 1.18271] ((19 . 18) (20 . 19) (22 . 21) (23 . 22) (25 . 24) (26 . 25) (30 . 26) (31 . 27) (32 . 28) (33 . 29) (34 . 30)) 2.912 {1/38:55} B:0 1.30105 [ 1.30105] ((19 . 18) (20 . 19) (24 . 22) (25 . 24) (26 . 25) (30 . 26) (31 . 27) (32 . 28) (33 . 29) (34 . 30)) 3.275 {1/34:45} B:0 1.44476 [ 1.44476] ((19 . 18) (20 . 19) (22 . 21) (23 . 22) (25 . 24) (26 . 25) (30 . 28) (33 . 29) (34 . 30)) 3.967 {0/26:36} B:0 1.85770 [ 1.85770] ((24 . 22) (29 . 24) (30 . 26) (31 . 27) (32 . 28) (33 . 29) (34 . 30)) 5.523 {0/16:21} B:0 2.16675 [ 2.16675] ((19 . 18) (20 . 19) (23 . 22) (25 . 24) (26 . 26) (30 . 28)) 3.816 {0/12:15} B:0 SIMILARITY (1/min{score1}): 0.8455 [and 1/min{score2}: 0.8455] [3045, 5124]: Comparing 1jsc_A and 1pvd_A, based on their crossing files. There are 47 (27 H + 20 S) secondary structure elements in 1jsc_A, of which 13 satisfy the size requirements. There are 44 (23 H + 21 S) secondary structure elements in 1pvd_A, of which 14 satisfy the size requirements. 1.85722 [ 2.00006] ((19 . 16) (20 . 17) (24 . 20) (25 . 23) (26 . 24) (32 . 27) (33 . 28)) 3.331 {0/17:21} B:0 2.18330 [ 2.34669] ((19 . 16) (20 . 17) (22 . 19) (23 . 22) (25 . 23) (26 . 25)) 3.229 {1/11:15} B:0 2.54451 [ 2.55933] ((19 . 16) (20 . 17) (22 . 19) (23 . 20) (24 . 22) (25 . 23) (26 . 24) (30 . 25) (32 . 26) (33 . 28)) 2.708 {8/32:45} B:0 2.60072 [ 2.80057] ((23 . 17) (24 . 20) (26 . 22) (30 . 25) (32 . 27)) 7.582 {0/5:10} B:0 2.65736 [ 2.84630] ((20 . 17) (24 . 20) (30 . 25) (32 . 27) (33 . 28)) 3.692 {1/7:10} B:0 SIMILARITY (1/min{score1}): 0.5384 [and 1/min{score2}: 0.5000] [3045, 5172]: Comparing 1jsc_A and 1q14_A, based on their crossing files. There are 47 (27 H + 20 S) secondary structure elements in 1jsc_A, of which 13 satisfy the size requirements. There are 24 (15 H + 9 S) secondary structure elements in 1q14_A, of which 22 satisfy the size requirements. 1.19383 [ 2.00251] ((19 . 1) (20 . 2) (22 . 7) (23 . 8) (24 . 11) (25 . 16) (26 . 17) (29 . 18) (30 . 19) (32 . 21) (33 . 22)) 5.221 {2/39:55} B:0 1.30146 [ 2.20030] ((19 . 1) (20 . 2) (22 . 7) (23 . 8) (24 . 11) (25 . 16) (26 . 17) (30 . 19) (32 . 21) (33 . 22)) 2.423 {1/30:45} B:0 3.25004 [ 5.50001] ((20 . 8) (29 . 16) (30 . 17) (32 . 19)) 4.302 {0/5:6} B:0 3.25005 [ 5.50001] ((20 . 8) (23 . 11) (29 . 16) (30 . 17)) 4.684 {0/5:6} B:0 3.25018 [ 5.50004] ((24 . 8) (25 . 9) (26 . 11) (33 . 16)) 6.304 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.8376 [and 1/min{score2}: 0.4994] [3045, 5771]: Comparing 1jsc_A and 1s5p_A, based on their crossing files. There are 47 (27 H + 20 S) secondary structure elements in 1jsc_A, of which 13 satisfy the size requirements. There are 22 (9 H + 13 S) secondary structure elements in 1s5p_A, of which 16 satisfy the size requirements. 1.45252 [ 1.78213] ((20 . 1) (22 . 8) (23 . 9) (25 . 16) (26 . 17) (29 . 19) (30 . 20) (32 . 21) (33 . 22)) 3.712 {1/18:36} B:0 2.16669 [ 2.66668] ((20 . 9) (25 . 16) (26 . 17) (30 . 20) (32 . 21) (33 . 22)) 2.745 {0/9:15} B:0 2.60010 [ 3.20005] ((20 . 9) (22 . 10) (29 . 16) (30 . 17) (32 . 20)) 4.582 {0/7:10} B:0 2.60032 [ 3.20017] ((19 . 8) (20 . 9) (29 . 16) (30 . 17) (32 . 20)) 6.215 {0/7:10} B:0 3.25003 [ 4.00002] ((19 . 16) (20 . 17) (22 . 19) (23 . 21)) 4.155 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.6903 [and 1/min{score2}: 0.5885] [3045, 6075]: Comparing 1jsc_A and 1upa_A, based on their crossing files. There are 47 (27 H + 20 S) secondary structure elements in 1jsc_A, of which 13 satisfy the size requirements. There are 47 (28 H + 19 S) secondary structure elements in 1upa_A, of which 14 satisfy the size requirements. 1.22338 [ 1.30644] ((19 . 16) (20 . 17) (22 . 19) (23 . 20) (24 . 21) (25 . 23) (26 . 24) (30 . 27) (32 . 28) (33 . 29) (34 . 30)) 3.605 {3/41:55} B:0 1.30109 [ 1.40087] ((19 . 16) (20 . 17) (22 . 19) (23 . 20) (24 . 21) (25 . 23) (26 . 24) (30 . 27) (32 . 28) (33 . 29)) 1.386 {1/32:45} B:0 2.16667 [ 2.33334] ((19 . 16) (20 . 17) (24 . 20) (30 . 27) (32 . 28) (33 . 29)) 2.121 {0/12:15} B:0 2.18327 [ 2.34667] ((19 . 16) (20 . 17) (22 . 19) (23 . 21) (25 . 23) (26 . 24)) 2.284 {1/11:15} B:0 2.70363 [ 2.88419] ((20 . 17) (22 . 23) (23 . 24) (24 . 27) (29 . 29)) 5.745 {1/6:10} B:0 SIMILARITY (1/min{score1}): 0.8174 [and 1/min{score2}: 0.7654] [3045, 6376]: Comparing 1jsc_A and 1zpd_A, based on their crossing files. There are 47 (27 H + 20 S) secondary structure elements in 1jsc_A, of which 13 satisfy the size requirements. There are 46 (26 H + 20 S) secondary structure elements in 1zpd_A, of which 13 satisfy the size requirements. 1.19039 [ 1.19039] ((19 . 16) (20 . 17) (22 . 18) (23 . 19) (24 . 21) (25 . 23) (26 . 24) (30 . 26) (32 . 28) (33 . 29) (34 . 30)) 2.496 {2/41:55} B:0 1.31932 [ 1.31932] ((19 . 16) (20 . 17) (22 . 18) (23 . 19) (24 . 21) (25 . 23) (26 . 24) (30 . 26) (32 . 28) (33 . 29)) 2.196 {2/31:45} B:0 1.67099 [ 1.67099] ((19 . 16) (20 . 17) (22 . 18) (24 . 19) (25 . 23) (30 . 26) (32 . 28) (33 . 29)) 2.682 {2/21:28} B:0 2.29166 [ 2.29166] ((19 . 16) (20 . 17) (22 . 18) (23 . 19) (24 . 21) (25 . 23) (26 . 24) (30 . 26) (32 . 27) (33 . 29) (34 . 30)) 2.625 {9/40:55} B:0 2.63406 [ 2.63406] ((19 . 16) (20 . 17) (23 . 21) (25 . 23) (26 . 24)) 2.559 {1/8:10} B:0 SIMILARITY (1/min{score1}): 0.8401 [and 1/min{score2}: 0.8401] -------------------------------------------------------------------------------------------------------------------------