[phenixbb] Increase in R/R(free) after phenix.real_space_refine

Nathaniel Echols nechols at lbl.gov
Fri Sep 19 13:22:59 PDT 2014

Global real-space refinement simply isn't very useful at high resolution,
and you shouldn't need a large radius of convergence when the R-free is
already 13%.  I'm a big fan of automating everything possible, but this is
one case where fixing the sidechains manually in Coot (which should do an
excellent job) is by far the easiest option.  Once you fix the sidechains
the C-beta outliers will probably disappear.

PS. A common reason for C-beta deviations at high resolution is residues
with alternate conformations being split at C-beta rather than splitting
the entire residue, which allows the backbone to move to accommodate the
optimal placement of the sidechain (rather than straining the geometry to
get the sidechain atoms to fit the density).  Always split the entire
residue - the backbone is almost never rigid in disordered regions.

On Fri, Sep 19, 2014 at 1:11 PM, George Devaniranjan <devaniranjan at gmail.com
> wrote:

> Hi,
> I refined (phenix.refine)  a 1.0Å structure but it had a few CB outliers
> and some rotamer outliers.
> I decided to try real_space_refine, to check if they could be fixed (given
> that it has a higher radius of convergence).
> (using run=local_grid_search+minimization_global in real_space_refine)
> But, the R/R(free) increased from 11.39/13.24( for the refine model) to
> 16.51/17.55 (real_space_refine model).
> It seemed a big increase, when I looked at the map against the structure
> the protein itself seemed fine.
> The rotamers outliers had decreased, the CB outliers were fixed..etc
> The solvent fit to the density had worsened in COOT.
> What am I doing wrong? Any suggestions, advice would be much appreciated.
> Thank you,
> George
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