------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [4656, 754]: Comparing 1ohe_A and 1d5r_A, based on their crossing files. There are 24 (15 H + 9 S) secondary structure elements in 1ohe_A, of which 13 satisfy the size requirements. There are 23 (8 H + 15 S) secondary structure elements in 1d5r_A, of which 10 satisfy the size requirements. 1.30010 [ 1.00023] ((13 . 1) (14 . 2) (15 . 3) (16 . 4) (18 . 5) (19 . 6) (20 . 7) (21 . 8) (22 . 9) (23 . 10)) 2.779 {0/31:45} B:0 1.30095 [ 1.00208] ((13 . 1) (14 . 2) (15 . 3) (16 . 4) (18 . 5) (19 . 6) (20 . 7) (21 . 8) (22 . 9) (24 . 10)) 4.838 {0/30:45} B:0 2.60023 [ 2.00051] ((15 . 3) (18 . 4) (19 . 6) (20 . 7) (24 . 10)) 5.717 {0/6:10} B:0 2.60168 [ 2.00368] ((15 . 3) (16 . 5) (17 . 6) (20 . 7) (23 . 10)) 9.378 {0/5:10} B:0 3.25020 [ 2.50043] ((16 . 2) (17 . 3) (18 . 4) (21 . 6)) 6.474 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.7692 [and 1/min{score2}: 0.9998] [4656, 1604]: Comparing 1ohe_A and 1fpz_A, based on their crossing files. There are 24 (15 H + 9 S) secondary structure elements in 1ohe_A, of which 13 satisfy the size requirements. There are 16 (9 H + 7 S) secondary structure elements in 1fpz_A, of which 13 satisfy the size requirements. 1.18202 [ 1.18202] ((13 . 1) (14 . 3) (15 . 6) (16 . 7) (17 . 9) (18 . 10) (19 . 11) (20 . 12) (21 . 13) (22 . 14) (23 . 15)) 3.047 {0/36:55} B:0 1.18220 [ 1.18220] ((13 . 1) (14 . 3) (15 . 6) (16 . 7) (17 . 9) (18 . 10) (19 . 11) (20 . 12) (21 . 13) (22 . 14) (23 . 16)) 3.583 {0/36:55} B:0 2.60019 [ 2.60019] ((14 . 7) (15 . 9) (16 . 10) (20 . 12) (23 . 16)) 5.458 {0/2:10} B:0 3.25001 [ 3.25001] ((18 . 3) (19 . 6) (20 . 7) (21 . 9)) 2.794 {0/4:6} B:0 3.25058 [ 3.25058] ((16 . 3) (17 . 6) (19 . 9) (21 . 11)) 8.486 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.8460 [and 1/min{score2}: 0.8460] [4656, 1725]: Comparing 1ohe_A and 1g4u_S, based on their crossing files. There are 24 (15 H + 9 S) secondary structure elements in 1ohe_A, of which 13 satisfy the size requirements. There are 23 (14 H + 9 S) secondary structure elements in 1g4u_S, of which 15 satisfy the size requirements. 1.30037 [ 1.50024] ((13 . 10) (14 . 11) (15 . 12) (16 . 13) (18 . 18) (19 . 19) (20 . 20) (21 . 21) (22 . 22) (23 . 23)) 3.812 {0/30:45} B:0 2.16693 [ 2.50017] ((14 . 13) (18 . 18) (19 . 19) (20 . 20) (21 . 21) (22 . 22)) 5.138 {0/11:15} B:0 2.60032 [ 3.00021] ((13 . 10) (14 . 11) (15 . 12) (16 . 13) (20 . 18)) 6.218 {0/6:10} B:0 3.25004 [ 3.75002] ((16 . 18) (19 . 19) (20 . 20) (23 . 23)) 4.298 {0/4:6} B:0 3.25005 [ 3.75003] ((13 . 15) (14 . 16) (16 . 18) (18 . 20)) 4.683 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.7690 [and 1/min{score2}: 0.6666] [4656, 2436]: Comparing 1ohe_A and 1i9s_A, based on their crossing files. There are 24 (15 H + 9 S) secondary structure elements in 1ohe_A, of which 13 satisfy the size requirements. There are 14 (10 H + 4 S) secondary structure elements in 1i9s_A, of which 12 satisfy the size requirements. 1.30001 [ 1.20001] ((14 . 1) (15 . 4) (16 . 5) (17 . 6) (18 . 7) (19 . 8) (20 . 9) (21 . 10) (22 . 11) (23 . 12)) 1.494 {0/25:45} B:0 1.44540 [ 1.33455] ((14 . 1) (15 . 4) (16 . 5) (17 . 6) (18 . 7) (19 . 8) (20 . 9) (21 . 10) (24 . 12)) 5.242 {0/14:36} B:0 2.00193 [ 1.89159] ((15 . 6) (16 . 7) (19 . 8) (20 . 9) (21 . 10) (22 . 11) (23 . 12)) 3.112 {2/14:21} B:0 3.25002 [ 3.00003] ((16 . 1) (19 . 4) (20 . 5) (21 . 6)) 3.754 {0/0:6} B:0 3.25040 [ 3.00050] ((14 . 5) (16 . 7) (17 . 8) (19 . 10)) 7.722 {0/1:6} B:0 SIMILARITY (1/min{score1}): 0.7692 [and 1/min{score2}: 0.8333] [4656, 2959]: Comparing 1ohe_A and 1jln_A, based on their crossing files. There are 24 (15 H + 9 S) secondary structure elements in 1ohe_A, of which 13 satisfy the size requirements. There are 22 (12 H + 10 S) secondary structure elements in 1jln_A, of which 17 satisfy the size requirements. 1.30027 [ 1.70012] ((13 . 8) (14 . 10) (15 . 11) (16 . 12) (18 . 16) (19 . 17) (20 . 18) (21 . 19) (22 . 21) (23 . 22)) 3.527 {0/28:45} B:0 2.16676 [ 2.83338] ((16 . 16) (19 . 17) (20 . 18) (21 . 19) (22 . 21) (23 . 22)) 3.972 {0/11:15} B:0 2.16731 [ 2.83362] ((18 . 16) (19 . 17) (20 . 18) (21 . 19) (22 . 21) (24 . 22)) 6.438 {0/12:15} B:0 2.46578 [ 2.52613] ((11 . 5) (13 . 8) (14 . 10) (15 . 11) (16 . 12) (18 . 15) (19 . 17) (20 . 18) (21 . 19) (22 . 21) (23 . 22)) 4.939 {9/37:55} B:0 2.54455 [ 2.62414] ((13 . 8) (14 . 10) (15 . 11) (16 . 12) (18 . 15) (19 . 17) (20 . 18) (21 . 19) (22 . 21) (23 . 22)) 3.977 {7/28:45} B:0 SIMILARITY (1/min{score1}): 0.7691 [and 1/min{score2}: 0.6013] [4656, 3585]: Comparing 1ohe_A and 1lar_A, based on their crossing files. There are 24 (15 H + 9 S) secondary structure elements in 1ohe_A, of which 13 satisfy the size requirements. There are 39 (17 H + 22 S) secondary structure elements in 1lar_A, of which 17 satisfy the size requirements. 1.30016 [ 1.70007] ((13 . 5) (14 . 6) (15 . 7) (16 . 8) (18 . 14) (19 . 15) (20 . 16) (21 . 17) (22 . 18) (23 . 19)) 3.099 {0/29:45} B:0 2.16672 [ 2.83336] ((16 . 14) (19 . 15) (20 . 16) (21 . 17) (22 . 18) (23 . 19)) 3.513 {0/11:15} B:0 2.16716 [ 2.83356] ((18 . 14) (19 . 15) (20 . 16) (21 . 17) (22 . 18) (24 . 19)) 6.033 {0/12:15} B:0 2.60015 [ 3.40007] ((13 . 5) (14 . 6) (15 . 7) (16 . 8) (20 . 14)) 5.109 {0/6:10} B:0 2.60023 [ 3.40010] ((13 . 11) (14 . 12) (16 . 14) (17 . 15) (18 . 16)) 5.708 {0/7:10} B:0 SIMILARITY (1/min{score1}): 0.7691 [and 1/min{score2}: 0.5882] [4656, 3754]: Comparing 1ohe_A and 1lw3_A, based on their crossing files. There are 24 (15 H + 9 S) secondary structure elements in 1ohe_A, of which 13 satisfy the size requirements. There are 40 (24 H + 16 S) secondary structure elements in 1lw3_A, of which 22 satisfy the size requirements. 1.18341 [ 2.00033] ((11 . 19) (13 . 21) (14 . 22) (15 . 23) (16 . 24) (18 . 26) (19 . 29) (20 . 30) (21 . 31) (22 . 33) (23 . 35)) 3.989 {1/35:55} B:0 1.30151 [ 2.20031] ((11 . 19) (13 . 21) (14 . 22) (16 . 24) (18 . 26) (19 . 29) (20 . 30) (21 . 31) (22 . 33) (23 . 35)) 3.973 {1/32:45} B:0 1.30223 [ 2.20046] ((11 . 19) (13 . 21) (14 . 22) (15 . 23) (16 . 24) (18 . 26) (19 . 29) (20 . 30) (21 . 31) (23 . 35)) 3.866 {1/28:45} B:0 2.60004 [ 4.40001] ((16 . 26) (19 . 29) (20 . 30) (21 . 31) (22 . 33)) 3.793 {0/6:10} B:0 2.60014 [ 4.40003] ((11 . 19) (15 . 23) (16 . 24) (18 . 26) (23 . 31)) 5.004 {0/7:10} B:0 SIMILARITY (1/min{score1}): 0.8450 [and 1/min{score2}: 0.4999] [4656, 3768]: Comparing 1ohe_A and 1lyv_A, based on their crossing files. There are 24 (15 H + 9 S) secondary structure elements in 1ohe_A, of which 13 satisfy the size requirements. There are 19 (11 H + 8 S) secondary structure elements in 1lyv_A, of which 15 satisfy the size requirements. 1.30050 [ 1.50033] ((13 . 3) (14 . 4) (15 . 5) (16 . 6) (18 . 12) (19 . 13) (20 . 15) (21 . 16) (22 . 18) (23 . 19)) 4.125 {0/29:45} B:0 1.30282 [ 1.50184] ((13 . 3) (14 . 4) (15 . 5) (16 . 6) (18 . 12) (19 . 13) (20 . 15) (21 . 16) (22 . 18) (24 . 19)) 6.355 {0/27:45} B:0 2.16680 [ 2.50009] ((16 . 12) (19 . 13) (20 . 15) (21 . 16) (22 . 18) (23 . 19)) 4.353 {0/12:15} B:0 2.16808 [ 2.50092] ((16 . 12) (17 . 13) (20 . 15) (21 . 16) (22 . 18) (23 . 19)) 7.838 {0/11:15} B:0 2.16866 [ 2.50130] ((14 . 10) (16 . 12) (19 . 13) (20 . 15) (21 . 16) (22 . 18)) 8.545 {0/10:15} B:0 SIMILARITY (1/min{score1}): 0.7689 [and 1/min{score2}: 0.6665] [4656, 3963]: Comparing 1ohe_A and 1mkp, based on their crossing files. There are 24 (15 H + 9 S) secondary structure elements in 1ohe_A, of which 13 satisfy the size requirements. There are 11 (5 H + 6 S) secondary structure elements in 1mkp, of which 11 satisfy the size requirements. 1.30003 [ 1.10006] ((13 . 1) (14 . 2) (15 . 3) (16 . 4) (18 . 6) (19 . 7) (20 . 8) (21 . 9) (22 . 10) (23 . 11)) 2.116 {0/30:45} B:0 1.44447 [ 1.22227] ((13 . 1) (14 . 2) (15 . 3) (18 . 6) (19 . 7) (20 . 8) (21 . 9) (22 . 10) (23 . 11)) 2.171 {0/24:36} B:0 1.44549 [ 1.22394] ((13 . 1) (14 . 2) (15 . 3) (16 . 4) (18 . 6) (19 . 7) (20 . 8) (21 . 9) (24 . 11)) 5.358 {0/19:36} B:0 2.60086 [ 2.20142] ((13 . 1) (14 . 2) (15 . 3) (16 . 6) (17 . 7)) 7.941 {0/8:10} B:0 3.25044 [ 2.75073] ((15 . 3) (16 . 6) (17 . 7) (18 . 8)) 7.941 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.7692 [and 1/min{score2}: 0.9090] [4656, 4655]: Comparing 1ohe_A and 1ohe_A, based on their crossing files. There are 24 (15 H + 9 S) secondary structure elements in 1ohe_A, of which 13 satisfy the size requirements. There are 24 (15 H + 9 S) secondary structure elements in 1ohe_A, of which 9 satisfy the size requirements. 1.62505 [ 1.12515] ((13 . 2) (14 . 3) (16 . 4) (19 . 5) (20 . 7) (21 . 8) (22 . 9) (23 . 10)) 2.727 {0/19:28} B:0 1.62539 [ 1.12617] ((13 . 2) (14 . 3) (16 . 4) (19 . 5) (20 . 7) (21 . 8) (22 . 9) (24 . 10)) 4.569 {0/19:28} B:0 2.16905 [ 1.50714] ((13 . 2) (14 . 3) (16 . 4) (17 . 5) (18 . 7) (23 . 10)) 8.930 {0/8:15} B:0 2.60003 [ 1.80008] ((18 . 4) (19 . 5) (20 . 7) (21 . 8) (22 . 9)) 3.289 {0/9:10} B:0 2.60123 [ 1.80370] ((16 . 4) (17 . 5) (20 . 7) (21 . 8) (22 . 9)) 8.678 {0/7:10} B:0 SIMILARITY (1/min{score1}): 0.6154 [and 1/min{score2}: 0.8888] [4656, 4656]: Comparing 1ohe_A and 1ohe_A, based on their crossing files. There are 24 (15 H + 9 S) secondary structure elements in 1ohe_A, of which 13 satisfy the size requirements. There are 24 (15 H + 9 S) secondary structure elements in 1ohe_A, of which 13 satisfy the size requirements. 1.00000 [ 1.00000] ((11 . 11) (13 . 13) (14 . 14) (15 . 15) (16 . 16) (17 . 17) (18 . 18) (19 . 19) (20 . 20) (21 . 21) (22 . 22) (23 . 23) (24 . 24)) 0.000 {0/56:78} B:0 2.16686 [ 2.16686] ((11 . 11) (15 . 15) (17 . 17) (19 . 19) (20 . 20) (23 . 24)) 4.738 {0/8:15} B:0 2.60070 [ 2.60070] ((14 . 16) (15 . 17) (16 . 18) (17 . 19) (19 . 21)) 7.545 {0/2:10} B:0 2.60070 [ 2.60070] ((16 . 14) (17 . 15) (18 . 16) (19 . 17) (21 . 19)) 7.545 {0/2:10} B:0 3.25001 [ 3.25001] ((18 . 14) (19 . 15) (20 . 16) (21 . 17)) 2.943 {0/4:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [4656, 4857]: Comparing 1ohe_A and 1p15_A, based on their crossing files. There are 24 (15 H + 9 S) secondary structure elements in 1ohe_A, of which 13 satisfy the size requirements. There are 16 (6 H + 10 S) secondary structure elements in 1p15_A, of which 11 satisfy the size requirements. 1.30007 [ 1.10011] ((13 . 2) (14 . 3) (15 . 4) (16 . 5) (18 . 11) (19 . 12) (20 . 13) (21 . 14) (22 . 15) (23 . 16)) 2.508 {0/29:45} B:0 1.30104 [ 1.10171] ((13 . 2) (14 . 3) (15 . 4) (16 . 5) (18 . 11) (19 . 12) (20 . 13) (21 . 14) (22 . 15) (24 . 16)) 4.947 {0/31:45} B:0 1.44447 [ 1.22227] ((13 . 2) (14 . 3) (15 . 4) (16 . 5) (18 . 11) (19 . 12) (20 . 13) (21 . 14) (22 . 15)) 2.217 {0/24:36} B:0 2.16672 [ 1.83342] ((16 . 11) (19 . 12) (20 . 13) (21 . 14) (22 . 15) (23 . 16)) 3.414 {0/12:15} B:0 2.16798 [ 1.83549] ((16 . 11) (17 . 12) (20 . 13) (21 . 14) (22 . 15) (23 . 16)) 7.689 {0/11:15} B:0 SIMILARITY (1/min{score1}): 0.7692 [and 1/min{score2}: 0.9090] [4656, 4948]: Comparing 1ohe_A and 1pa1_A, based on their crossing files. There are 24 (15 H + 9 S) secondary structure elements in 1ohe_A, of which 13 satisfy the size requirements. There are 22 (11 H + 11 S) secondary structure elements in 1pa1_A, of which 18 satisfy the size requirements. 1.30042 [ 1.80016] ((13 . 6) (14 . 7) (15 . 8) (16 . 9) (18 . 15) (19 . 16) (20 . 17) (21 . 18) (22 . 20) (23 . 21)) 3.933 {0/29:45} B:0 2.16678 [ 3.00004] ((16 . 15) (19 . 16) (20 . 17) (21 . 18) (22 . 20) (23 . 21)) 4.192 {0/11:15} B:0 2.16709 [ 3.00016] ((18 . 15) (19 . 16) (20 . 17) (21 . 18) (22 . 20) (24 . 21)) 5.800 {0/12:15} B:0 2.46313 [ 2.58207] ((13 . 6) (14 . 7) (15 . 8) (16 . 9) (18 . 14) (19 . 16) (20 . 17) (21 . 18) (22 . 20) (23 . 21)) 4.318 {7/29:45} B:0 2.60026 [ 3.60010] ((13 . 6) (14 . 7) (15 . 8) (16 . 9) (20 . 15)) 5.871 {0/5:10} B:0 SIMILARITY (1/min{score1}): 0.7690 [and 1/min{score2}: 0.5555] [4656, 5573]: Comparing 1ohe_A and 1r6h_A, based on their crossing files. There are 24 (15 H + 9 S) secondary structure elements in 1ohe_A, of which 13 satisfy the size requirements. There are 11 (6 H + 5 S) secondary structure elements in 1r6h_A, of which 11 satisfy the size requirements. 1.18209 [ 1.00045] ((13 . 1) (14 . 2) (15 . 3) (16 . 4) (17 . 5) (18 . 6) (19 . 7) (20 . 8) (21 . 9) (22 . 10) (23 . 11)) 3.303 {0/30:55} B:0 1.30117 [ 1.10194] ((13 . 1) (14 . 2) (15 . 3) (16 . 4) (17 . 5) (18 . 6) (19 . 7) (20 . 8) (21 . 9) (24 . 11)) 5.102 {0/19:45} B:0 2.43228 [ 2.40773] ((13 . 1) (14 . 2) (15 . 3) (16 . 4) (17 . 5) (18 . 6) (19 . 7) (20 . 8) (21 . 9) (23 . 10)) 4.468 {5/21:45} B:0 2.43240 [ 2.40785] ((13 . 1) (14 . 2) (15 . 3) (16 . 4) (17 . 5) (18 . 6) (19 . 7) (20 . 8) (21 . 10) (24 . 11)) 5.371 {5/21:45} B:0 3.25006 [ 2.75009] ((14 . 4) (15 . 5) (16 . 6) (19 . 9)) 4.763 {0/1:6} B:0 SIMILARITY (1/min{score1}): 0.8460 [and 1/min{score2}: 0.9995] [4656, 6243]: Comparing 1ohe_A and 1vhr_A, based on their crossing files. There are 24 (15 H + 9 S) secondary structure elements in 1ohe_A, of which 13 satisfy the size requirements. There are 13 (8 H + 5 S) secondary structure elements in 1vhr_A, of which 12 satisfy the size requirements. 1.18187 [ 1.09097] ((13 . 2) (14 . 3) (15 . 5) (16 . 6) (17 . 7) (18 . 8) (19 . 9) (20 . 10) (21 . 11) (22 . 12) (23 . 13)) 2.166 {0/35:55} B:0 1.30005 [ 1.20006] ((13 . 2) (14 . 3) (15 . 5) (16 . 6) (17 . 7) (18 . 8) (19 . 9) (20 . 10) (21 . 11) (23 . 13)) 2.257 {0/25:45} B:0 2.16669 [ 2.00004] ((16 . 8) (19 . 9) (20 . 10) (21 . 11) (22 . 12) (23 . 13)) 2.941 {0/11:15} B:0 2.60012 [ 2.40015] ((15 . 7) (16 . 8) (19 . 9) (20 . 10) (23 . 13)) 4.809 {0/3:10} B:0 3.25001 [ 3.00002] ((14 . 8) (15 . 9) (16 . 10) (17 . 11)) 3.373 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.8461 [and 1/min{score2}: 0.9166] [4656, 6530]: Comparing 1ohe_A and 2shp_A, based on their crossing files. There are 24 (15 H + 9 S) secondary structure elements in 1ohe_A, of which 13 satisfy the size requirements. There are 37 (13 H + 24 S) secondary structure elements in 2shp_A, of which 17 satisfy the size requirements. 1.30031 [ 1.70014] ((13 . 22) (14 . 23) (15 . 24) (16 . 25) (18 . 31) (19 . 32) (20 . 33) (21 . 34) (22 . 36) (23 . 37)) 3.655 {0/31:45} B:0 2.16674 [ 2.83337] ((16 . 31) (19 . 32) (20 . 33) (21 . 34) (22 . 36) (23 . 37)) 3.792 {0/12:15} B:0 2.16723 [ 2.83358] ((18 . 31) (19 . 32) (20 . 33) (21 . 34) (22 . 36) (24 . 37)) 6.217 {0/12:15} B:0 2.31777 [ 2.42101] ((13 . 22) (14 . 23) (15 . 24) (16 . 25) (18 . 30) (19 . 32) (20 . 33) (21 . 34) (22 . 36) (23 . 37)) 4.118 {7/31:45} B:0 2.60018 [ 3.40008] ((13 . 22) (14 . 23) (15 . 24) (16 . 25) (20 . 31)) 5.375 {0/6:10} B:0 SIMILARITY (1/min{score1}): 0.7690 [and 1/min{score2}: 0.5882] -------------------------------------------------------------------------------------------------------------------------