Hi Sam,
I am refining a structure with Phenix.refine and encounter an issue which I appreciate your comments. The structure is in P1 and refined to 36A-3A. Rw/Rf = 23.9%/29.1%, RMS bonds 0.002, RMS angles 0.544, Ramachandran favoured 97.5%. The statistics is acceptable to me
This look fine to me too!
but two numbers raised my concern. First is the clashscore of 7.7, which is below minimum of other structures shown by Polygon.
The lower, the better. So this is good! If it's lower than the others (as shown by Polygon) then you are doing better on this one!
Second is an average B of 37, with a minimum of 9.2. When I checked again in Coot (Average Temp fact. analysis), none of the residues or water look abnormal. I refined both individual and group B-factors and applied 'Optimize X-ray/adp weight'.
This looks fine too.
So my questions are: (1) if a clashscore too high means a lot of bad contacts, how do you comprehend a clashscore too low? How can I modify my strategy to get around?
It can't be "too low". Zero means you don't have any single steric clash, which is good.
(2) is there an acceptable low value of B? (I sort of went through a similar thread in phenixbb appeared 9 years ago but seems the discussion did not come to a conclusion). Any advice I should reliax or tighten the adp restraints?
Check out recent thread on ccp4bb: "acceptable difference between Average B-factor and Wilson B". Bottom line, I think what you have is just fine, unless you meaningfully and clearly define "low". Pavel