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