Just remember - most Ramachandran outliers are due to errors in the environment - eg: maybe some side chains clash hence refinement tries to move things to accommodate that bad feature, etc etc etc...

At that resolution it is inevitable you will have some level of mis-interpretation ..

4% outliers does not surprise me.

EDSTATS is a useful tool to find things such as pep flips - you can access it most simply from CCP4 GUI2 .

But unless the outliers are in a important part of the structure I would suggest checking, then living with them.

Eleanor

On 2 July 2017 at 16:31, Rajesh Kumar <[log in to unmask]> wrote:

Dear Meytal,

PHENIX-REFINE has an option for Ramachandran outlier refine. If you check this on, it will do the work. But after this refinement, you must check every residues to make sure residues are in the density.

Thank you
Rajesh

---xxxxx----
With regards
Rajesh K. Harijan, Ph.D.
Schramm Laboratory
Albert Einstein College of Medicine
1300 Morris Park Ave., Bronx, NY 10461
Tel: 718.430.2777 | Fax: 718.430.8565

On Sun, Jul 2, 2017 at 7:26 AM, Meytal Galilee <[log in to unmask]> wrote:
Dear all,
I am refining a 2.76A structure using refmac5.
I keep fixing the Ramachandran outliers down to 18 (1.9%), however, upon restrained refinement, the outliers increase back to 35.
Do you have any suggestions how can I fix my structure?
Thanks,
Meytal Galilee