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
