Hi Intekhab, are all these outliers coming from that poorly modeled loop? If not (if yes - try to improve the loop first), here are a quick things to try: 1) try adding H and refine with optimize_wxc=true; 2) do "1)" after some geometry regularization; 3) try using secondary structure restraints; 4) try without SA; 5) fix all outliers manually in Coot and re-run the refinement. What happens then? 6) try manually some stricter weights (more impact on restraints) by using a number of smaller values of wxc_scale. If nothing helps you can send me the data and model and I will have a look. Of course I don't have a magic stick and can't promise to fix it... Just in case I may spot something that may help... Remember, a ramachandran or rotamer outlier is not necessarily wrong (example on page #22,25 here: http://www.phenix-online.org/presentations/latest/pavel_validation.pdf) but each of them must be explained and enough of evidence has to be provided to support your explanations (I'm speaking of final structure at publication stage). Pavel. On 8/13/10 12:44 AM, intekhab alam wrote:
Hi there 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
-- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL