Two points:
1. B-factors tend to differ lots between NCS copies, so you want to set
those restraints rather low (at least, I always do, by default)
2. NCS groups tend to need a far more fine-grained description than just
plonking in the whole domain. For structures in my lab, we often see
that tight NCS "does not work" -- until the group definitions are
selected more carefully.
Cheers
phx
Nicholas Keep wrote:
> I am refining a low (3A) resolution structure of a 3 domain protein.
> There are 4 copies in the ASU. I have been applying tight NCS
> restraints by domain in refmac and have pulled the weak MR solution
> down to Rfree below 30 (just).
>
> However my question is that in 2 of the 4 copies one of the domains is
> very poorly resolved. I can lower Rfree by around 0.5% by omitting
> the domains from the PDB entirely or not applying the NCS restraints
> to these copies of the domain. Clearly they are there and should
> resemble the moderately well resolved copies by coordinates but the
> way Bfactor restraints are applied between NCS copies seems to be the
> issue. If tight restraints are included the B factors are much lower
> (30-40) rather than 60-80 for the poor domains.
>
> I was wondering if there is a theoretically correct way to treat this?
>
> Would applying TLS scaling to each domain lead to the residual B
> factors being more balanced?
> Can a B factor offset be applied to the NCS restraints or could I only
> apply a coordinate restraint not a B factor restraint between certain
> copies?
>
> Comments welcomed especially from Garib.
>
> Happy New Year
> Nick
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