Thank you very much for your suggestions. I will try all these options and let you know the results. Rongjin = = = = = = = = On 2010-04-14 12:03:10 You wrote = = = = = = = = 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.