First suggestion - use WEIGHT AUTO in REFMAC - you may have restrained
the geometry too tightly..
And have you tried TLS ?
And at what level do you see no density - remember sigma levels in
maps need to vary with B factor - very easy to achieve this with COOT..
Eleanor
JOE CRYSTAL wrote:
> Dear all,
>
>
> I am refining a structure at 2.0 A. The water molecules have been
> added using arp/warp resulting Rwork/Rfree=21/26% (about 370 HOH for
> 360 residues). After 10 cycles of refmac refinement (wt 0.3),
> Rwork/Rfree went up about 1.5% to 22.5/27.5%. I did some minor
> adjustments and add/delete water in Coot followed by 10 cycles refmac
> refinement, but Rwork/Rfree are still around 22.5/27.5%. I also
> noticed a few side chains without density. Will setting those atoms
> to 0 occupancy or high B factor or mutating to Ala help decrease Rfree
> substantially? If not, is there any better strategies to lower down R
> factors? I will be very appreciative if you have any suggestions or
> comments to offer. Thank you in advance.
>
>
> Best,
>
>
> Joe
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