[phenixbb] Clashscore and average B

[Sam Tang]

Hello.

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 but two numbers raised
my concern. First is the clashscore of 7.7, which is below minimum of other
structures shown by Polygon. 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'.
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?
(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?

PS - it may be worth mentioning the structure contains a OMU nucleotide.
The .cif file I used was generated by elbow. The nucleotide looks normal in
coot w.r.t. contact or B-value.

Thanks a lot!

Sam
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