Hi Rhys, In Refmac, you can change the weighting of the Xray terms vs the geometry restraints rather than use what is automatically assigned. Have you tried this? In Phenix you can use secondary structure restraints (probably you can do this in Refmac too, but I haven't tried) and try checking the box optimize stereochemistry/Xray weight. This will probably help if your over fitting is moving things into density but making the geometry sub optimal.
Regards Christine On Wed, Jul 12, 2017 at 4:17 PM, Rhys Grinter <rhys.grin...@monash.edu> wrote: > Dear All, > > I'm currently in the process of refining a low(ish) resolution structure > at 3.2 Ang, with a fair level of anisotropy. I processed the data through > the anisotropy server (https://services.mbi.ucla.edu/anisoscale/), which > elliptically truncated the data to 4.0, 3.8 and 3.2 Ang. This really > improved the maps and allowed me to trace the majority of the chain and > build most side chains. > > The R-factors are reasonable (0.29 work and 0.35 free respectively). but > I'm having trouble with over fitting in refinement as I continue to refine. > What parameters/restraints would the community generally use when refining > this kind of structure? Additionally Refmac doesn't seem to read the > structure factors from the anisotropy server output file properly, giving > vastly inflated R values and strange looking maps. > > Cheers, > > Rhys > > -- > Dr Rhys Grinter > Sir Henry Wellcome Fellow > Monash University > +61 (0)3 9902 9213 <+61%203%209902%209213> > +61 (0)403 896 767 <+61%20403%20896%20767> >
