Clashscore and average B
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
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
Hello Pavel and Robert
Thanks for your replies. After re-investigating the model we didn't find
any major issues and the electron densities are fitted pretty well. Even
the ligand shows strong density on a SA-omit map. So I think we will stop
at this stage and take this model for further analysis.
Thanks again!
Sam
On Sat, 6 Apr 2019 at 03:30, Pavel Afonine
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
participants (2)
-
Pavel Afonine -
Sam Tang