Thanks everyone.
First, I checked my data and showed almost no anisotropy.
Second, I tried both refmac and phenix, had the similar results.
Third, ncs may be the key... I re-processed hkl and cut the resolution and did ncs=true. It first generated error message and suggested to put distance limit upto 3. Then now the gap between R and Rfree is reasonable (.2834 and .3361 without substrate and water).
However I tried my previous pdb that has everything with old mtz file, Final R-work = 0.2389, R-free = 0.3158. In this case, I had to expand my limit upto 6.
I still need to look more or do further refine from newly generated mtz file though, (sorry that's why I was late for responding.... I wanted to confirm it). Anyway, seemingly setting up 'ncs' as Pavel mentioned is most possible answer to my case.
Thanks again.
YoungJin
----- Original Message -----
From: "Kendall Nettles"
Thanks for your suggestions, Phill. When I did Ramachandran analysis, it shows 96.60% in preferred region and 2.62% in allowed regions, and 0.79% is in outlier. Geometry looks Ok. I also did optimize_wxc and optimize_wxu, and tls option. it didn't help much. Now I am trying to scale down.
Thanks again.
Young-Jin
0. Use Molprobity or the Validation tools in Coot to look at your structure and see what errors you can fix. 1. What is your geometry like ? Try reducing wxc_scale (try wxc_scale=0.5) and see what happens. 2. What is the variation of B-factors across bonds ? Try reducing wxu_scale - perhaps wxu_scale=0.5 or less. 2a. phenix.refine is autocratic about wxu_scale if you're using TLS so setting it yourself does not help. 3. Since R-free of 0.298 is a little high for a 2.5 Angstrom structure, you should carefully check your model. Perhaps you have a high proportion of disordered structure, which can cause this. If you feel that your model is correct, you could explore using TLS on your model. Potential TLS groups can be found using the TLSMD server at: http://skuld.bmsc.washington.edu/~tlsmd/ although the results should always be filtered through a common-sense definition of domain/group boundaries (e.g. don't break in the middle of helices unless there's a good reason to).
Phil Jeffrey Princeton
Young-Jin Cho wrote:
Hi everyone, I recently got a diffraction data and am trying to refine it. The question is whatever I did the gap between R and Rfree stay far away: .2140/.2982 around 2.5 A resolution. (water added and isotropic(individual_adp) and so on). Although I am redoing with many different approaches, if anyone can give me any comments or suggestions, it would be helpful.
Thanks in advance,
Young-Jin