> 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?
Looking at the planeRMSD values of ARG side chains in several
validation report XML files, I now suppose they use {CD, NE, CZ, NH1,
NH2} plane (not sure if hydrogen is there) and calculate the rms
deviation from the plane. So far I did not see outlier value smaller
than 0.07, which may be the criterion. Anyway this is not actually a
plane, so I wish they would switch to a more reasonable metric.
I totally agree with others. Outliers always should be inspected, and
one should try to fix it when it turns out actually wrong. Please
change the sigma only when you think it is really needed (apologise
for not saying this earlier).
Best regards,
Keitaro
On Thu, 17 Aug 2023 at 16:03, Keitaro Yamashita
<kyamash...@mrc-lmb.cam.ac.uk> 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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