Hello Charles and all,
I want to refine a protein against RDC's and have been following the
scripts in gb3_rdc and other examples. The protocol I followed is very
similar to the protocol given in the scripts but just to check a few
things, I have not done any minimization in the catesian space but only in
the torsional space. I observe that there are peptide bond planarity
violations (omega torsional angle) in that.
That is odd as I thought IVM only uses phi and psi only as coordinates. The
starting structure does not have any omega angle discrepancies. But the
refined structures have it. Can you please let me know where should I be
looking for the possible cause of error?
Thanks
Santhosh
ps: attaching are the violations in the refined structures along with the
original torsional angles. I can attach the exact script if you want to.
Amino acid Int. Phi Psi Omega Chi1-5
1 MET ( 1 )A 999.9 154.9 179.7 57.1 -175.1 -145.2
2 GLN ( 2 )A -95.8 142.4 178.0 -69.9 -69.0 -19.8
3 ILE ( 3 )A -131.5 165.4 179.7 61.5 168.2
4 PHE ( 4 )A -124.4 139.9 177.5 -61.2 -80.0
5 VAL ( 5 )A -122.9 123.7 179.0 -175.4
6 LYS ( 6 )A -100.1 142.3 179.6 -89.1 180.0 179.4 53.5
7 THR ( 7 )A -101.8 166.0 180.0 71.2
8 LEU ( 8 )A -64.0 -19.6 -178.8 -59.3 175.7
9 THR ( 9 )A -93.3 -0.0 177.5 67.1
10 GLY ( 10 )A 94.6 13.9 179.7
11 LYS ( 11 )A -90.2 144.9 178.5 -170.0 180.0 -179.8 62.1
12 THR ( 12 )A -118.0 127.9 178.9 -60.0
13 ILE ( 13 )A -111.6 139.0 178.6 -37.5 -172.7
14 THR ( 14 )A -105.1 132.0 -179.2 -59.0
15 LEU ( 15 )A -127.3 150.3 176.4 -58.2 170.5
16 GLU ( 16 )A -101.0 122.2 -178.5 -179.6 180.0 9.6
17 VAL ( 17 )A -140.0 168.0 177.4 -62.3
18 GLU ( 18 )A -118.5 150.9 -179.3 -67.4 -77.4 -81.5
19 PRO ( 19 )A -58.1 -24.2 -179.2
20 SER ( 20 )A -85.3 -1.8 178.6 50.4
21 ASP ( 21 )A -70.5 143.3 178.3 -77.5 -19.6
22 THR ( 22 )A -86.3 157.2 178.1 61.9
23 ILE ( 23 )A -62.0 -39.7 178.2 -65.6 -57.5
24 GLU ( 24 )A -60.0 -38.3 179.9 -179.4 178.6 9.4
25 ASN ( 25 )A -66.2 -40.1 179.2 -70.0 23.0
26 VAL ( 26 )A -62.9 -43.7 179.0 172.5
27 LYS ( 27 )A -60.0 -40.0 -179.1 -69.4 -144.6 -159.9 -63.4
28 ALA ( 28 )A -62.5 -37.8 178.9
29 LYS ( 29 )A -65.7 -39.0 177.7 -70.0 180.0 -180.0 -96.0
30 ILE ( 30 )A -65.0 -40.0 179.8 -70.0 -178.7
31 GLN ( 31 )A -60.1 -44.1 -178.8 178.4 178.5 2.2
32 ASP ( 32 )A -60.4 -40.6 -177.6 -178.0 -20.0
33 LYS ( 33 )A -81.7 -40.3 -174.8 -55.5 -135.1 -174.5 178.1
34 GLU ( 34 )A -110.8 -14.9 178.2 -65.3 -70.1 -20.0
35 GLY ( 35 )A 82.4 11.2 -179.7
36 ILE ( 36 )A -86.4 117.0 179.7 -51.4 155.4
37 PRO ( 37 )A -58.8 134.8 -179.5
38 PRO ( 38 )A -49.4 -31.4 -178.4
39 ASP ( 39 )A -71.0 -16.3 -179.4 -70.0 -27.0
40 GLN ( 40 )A -100.0 1.8 -178.0 -69.1 -176.9 -29.9
41 GLN ( 41 )A -108.0 139.5 176.4 -73.9 -177.4 65.5
42 ARG ( 42 )A -126.2 123.9 -179.1 -72.6 180.0 180.0 -157.5 -8.3
43 LEU ( 43 )A -105.7 130.1 -179.7 -69.3 171.6
44 ILE ( 44 )A -123.2 138.1 177.7 -81.1 91.4
45 PHE ( 45 )A -139.3 127.1 -179.8 177.8 77.9
46 ALA ( 46 )A 50.0 39.2 176.9
47 GLY ( 47 )A 82.0 0.0 -179.0
48 LYS ( 48 )A -112.2 139.3 178.2 -50.0 -179.8 -65.6 -157.0
49 GLN ( 49 )A -79.4 129.0 -179.0 -167.4 170.0 -80.0
50 LEU ( 50 )A -86.9 136.5 -179.3 -50.9 176.6
51 GLU ( 51 )A -91.2 149.9 -177.7 -70.0 180.0 -10.0
52 ASP ( 52 )A -68.8 -20.0 -179.1 -67.6 16.6
53 GLY ( 53 )A -94.0 3.5 179.5
54 ARG ( 54 )A -110.1 165.9 179.7 -62.7 -56.4 -163.4 -81.4 -29.5
55 THR ( 55 )A -107.5 167.4 178.4 63.9
56 LEU ( 56 )A -59.9 -42.9 -178.4 -61.9 172.8
57 SER ( 57 )A -61.9 -30.3 -179.6 60.9
58 ASP ( 58 )A -62.1 -29.0 -179.9 -69.1 -20.1
59 TYR ( 59 )A -99.9 13.8 -179.9 -71.5 -78.5
60 ASN ( 60 )A 50.1 40.0 178.2 -60.1 -50.0
61 ILE ( 61 )A -81.0 121.5 -177.1 -65.2 173.8
62 GLN ( 62 )A -107.5 169.1 -178.5 -70.0 177.8 70.1
63 LYS ( 63 )A -51.1 141.2 -179.0 55.6 -174.1 179.9 170.6
64 GLU ( 64 )A 66.7 23.4 176.0 -64.1 -170.6 -15.8
65 SER ( 65 )A -76.8 148.7 179.5 -72.3
66 THR ( 66 )A -112.8 124.0 177.4 -60.0
67 LEU ( 67 )A -105.2 157.4 179.1 -53.1 87.8
68 HIS ( 68 )A -112.3 134.1 -179.7 -68.7 90.0
69 LEU ( 69 )A -106.2 132.7 178.8 180.0 73.7
70 VAL ( 70 )A -120.7 144.8 -179.2 153.9
71 LEU ( 71 )A -109.9 140.0 -179.9 -50.1 -180.0
72 ARG ( 72 )A -119.2 130.1 180.0 179.5 172.9 170.0 -139.4 54.0
73 LEU ( 73 )A -120.0 128.7 179.6 -65.6 167.7
74 ARG ( 74 )A -69.8 -39.9 180.0 -63.5 -80.0 -170.9 122.3 -81.5
75 GLY ( 75 )A -89.9 -180.0 -180.0
76 GLY ( 76 )A 167.1 999.9 999.9Example violations:
(atom-i |atom-j |atom-k |atom-L ) angle
equil. delta energy const. period
(A 13 O |A 13 C |A 14 N |A 14 CA ) -8.473
0.000 8.473 10.934 500.000 0
(A 14 HN |A 14 N |A 13 C |A 13 CA ) -8.461
0.000 8.461 10.904 500.000 0
(A 13 CA |A 13 C |A 14 N |A 14 CA ) 171.554
180.000 8.446 10.865 500.000 0
(A 14 O |A 14 C |A 15 N |A 15 CA ) 6.952
0.000 -6.952 7.361 500.000 0
(A 15 HN |A 15 N |A 14 C |A 14 CA ) 6.777
0.000 -6.777 6.995 500.000 0
(A 14 CA |A 14 C |A 15 N |A 15 CA ) -173.100
180.000 -6.900 7.252 500.000 0
(A 33 O |A 33 C |A 34 N |A 34 CA ) 8.242
0.000 -8.242 10.346 500.000 0
(A 34 HN |A 34 N |A 33 C |A 33 CA ) 8.398
0.000 -8.398 10.742 500.000 0
(A 33 CA |A 33 C |A 34 N |A 34 CA ) -171.650
180.000 -8.350 10.620 500.000 0
(A 36 O |A 36 C |A 37 N |A 37 CA ) -6.011
0.000 6.011 5.503 500.000 0
(A 36 CA |A 36 C |A 37 N |A 37 CA ) 174.017
180.000 5.983 5.453 500.000 0
(A 41 O |A 41 C |A 42 N |A 42 CA ) -8.389
0.000 8.389 10.720 500.000 0
(A 42 HN |A 42 N |A 41 C |A 41 CA ) -8.451
0.000 8.451 10.878 500.000 0
(A 41 CA |A 41 C |A 42 N |A 42 CA ) 171.594
180.000 8.406 10.763 500.000 0
(A 42 O |A 42 C |A 43 N |A 43 CA ) 7.124
0.000 -7.124 7.730 500.000 0
(A 43 HN |A 43 N |A 42 C |A 42 CA ) 7.133
0.000 -7.133 7.750 500.000 0
(A 42 CA |A 42 C |A 43 N |A 43 CA ) -172.866
180.000 -7.134 7.751 500.000 0
(atom-i |atom-j |atom-k |atom-L ) angle
equil. delta energy const. period
(A 13 O |A 13 C |A 14 N |A 14 CA ) -8.572
0.000 8.572 11.192 500.000 0
(A 14 HN |A 14 N |A 13 C |A 13 CA ) -8.560
0.000 8.560 11.161 500.000 0
(A 13 CA |A 13 C |A 14 N |A 14 CA ) 171.455
180.000 8.545 11.122 500.000 0
(A 14 O |A 14 C |A 15 N |A 15 CA ) 7.106
0.000 -7.106 7.691 500.000 0
(A 15 HN |A 15 N |A 14 C |A 14 CA ) 6.931
0.000 -6.931 7.317 500.000 0
(A 14 CA |A 14 C |A 15 N |A 15 CA ) -172.946
180.000 -7.054 7.579 500.000 0
(A 33 O |A 33 C |A 34 N |A 34 CA ) 8.749
0.000 -8.749 11.659 500.000 0
(A 34 HN |A 34 N |A 33 C |A 33 CA ) 8.905
0.000 -8.905 12.079 500.000 0
(A 33 CA |A 33 C |A 34 N |A 34 CA ) -171.142
180.000 -8.858 11.950 500.000 0
(A 36 O |A 36 C |A 37 N |A 37 CA ) -5.987
0.000 5.987 5.458 500.000 0
(A 36 CA |A 36 C |A 37 N |A 37 CA ) 174.041
180.000 5.959 5.409 500.000 0
(A 41 O |A 41 C |A 42 N |A 42 CA ) -8.198
0.000 8.198 10.236 500.000 0
(A 42 HN |A 42 N |A 41 C |A 41 CA ) -8.260
0.000 8.260 10.390 500.000 0
(A 41 CA |A 41 C |A 42 N |A 42 CA ) 171.785
180.000 8.215 10.278 500.000 0
(A 42 O |A 42 C |A 43 N |A 43 CA ) 6.830
0.000 -6.830 7.105 500.000 0
(A 43 HN |A 43 N |A 42 C |A 42 CA ) 6.839
0.000 -6.839 7.124 500.000 0
(A 42 CA |A 42 C |A 43 N |A 43 CA ) -173.160
180.000 -6.840 7.125 500.000 0
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