I have recently solved a structure at 2.71A resolution using CCP4 (Refmac5) with R and R free of 22 and 29 respectively. The model is nicely fitted in the map and everything looks except in some loop region where the map is not fitted well. I just finished modelling and checked ramachandran plot which is showing unreasonably high number of outliers (12%) with only 65% in the favoured region. I am thinking to use phenix_refine with simulated annaeling and using the option fix bad chain rotamers. What else i can do aprt from this. i will be highly thankful for the suggestions. Apart from this can anyone let me know how

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INTEKHAB ALAM
LABORATORY OF STRUCTURAL BIOINFORMATICS
KOREA UNIVERSITY, SEOUL