Hi,
I would like to support Dr Yamashita's statement and emphasize that
Arg side chains really do deviate from planarity from time to time, and
it is possible that your side chain is an "outlier" because it really is
non-planar. In the paper Yamashita mentioned ("Arginine off-kilter:
guanidinium is not as planar as restraints denote.", Acta Cryst. 2020,
D76, 1159-1166) we gave as one example Arg 242 in 2xfr in which the
chi-5 angle is 22 deg from planarity and completely supported by its
density.
When you have an "outlier" in a model despite restraints you should
not simply increase the weights but try to understand what is driving
your model away from the restraint. Something about your structure is
fighting against the restraint and understanding what that is is the
key. Maybe there is an error in some nearby side chain creating a bad
contact or maybe something else. Maybe it is reality peeking through.
Simply increasing the weight only hides the issue and may actually
create its own error in your model. (The hardest errors to identify are
those that are inappropriately consistent with the validation criteria!)
Dale Tronrud
On 8/17/2023 8:03 AM, Keitaro Yamashita wrote:
Hi,
I assume the planarity you mentioned is what is discussed in Moriarty
et al (2020) https://doi.org/10.1107/S2059798320013534
As shown there, it is known to have some deviation. In Refmac (or in
the CCP4 monomer library) it is restrained using a torsion angle with
5 degree sigma instead of the planarity restraint. You can tighten the
restraint using an even smaller sigma. The keyword could be:
restr tors include resi ARG name chi5 sigma 2.0
By the way, did you mean by "outliers" those from the PDB validation
report? I have had a feeling that their criterion is a bit too strict.
Could anyone from the PDB tell how the outlier of the ARG sidechain is
calculated?
Best regards,
Keitaro
On Thu, 17 Aug 2023 at 15:02, Vladyslav Yadrykhinsky
<vladyslav.yadrykhin...@student.uib.no> wrote:
Hello,
I am refining a structure and I have ARG planarity outliers in the sidechain.
Could someone please tell me how should I set the planarity restraint in
REFMAC5 (version 5.8.0403) to correct them?
Should I use: plane [value1] [value2] in the advanced settings? If so, what
values 1 and 2 should be? My current weight restraints are 0.128....
Please let me know if you need more information and I will appreciate any
assistance on the matter.
Best regards,
Vladyslav
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