Hi Rongjin,

I am refining another 3.3 A resolution structure. In coot I manually adjusted the model

to have >95% residues in preferred region in ramanchandran plot, but after refinement  

in Phenix only <80% residues in the preferred region and a lot more in the outlier region.

This was wen I used the default refinement parameters "phenix.refine mtz_file pdb_file".

R and R_free are 0.22/0.27 in this case.

you may want to consider:

- using secondary structure restraints;
- tightening restraints (using wxc_scale=...);
- using H atoms in refinement;
- doing some quick geometry regularization before refinement;
- fixing manually and excluding from refinement certain parts of your model.

You need to experiment and find empirically which combination of the above options works in your case. I would appreciate if you share your experience with this and tell us what worked for your in the end.

Pavel.