[phenixbb] Weird occupancy values in HySS

Pavel Afonine pafonine at lbl.gov
Thu Sep 21 14:36:10 PDT 2017

Hi Dominic,

I don't think you should interpret occupancy values at phasing stage too 
literally. The sites may be partially occupied or belong to other 
chemical species, etc. It doesn't matter as long as you get phasing 
solved. Where it does matter is later in refinement but then restraints 
or constraints will be applied to refining parameters and you will be 
getting meaningful parameter values.


On 9/21/17 12:35, Dominic Gilzer wrote:
> Dear everybody,
> I am using Phenix HySS to solve the substructure of an iodine soak. I 
> tried several high resolution cut-offs and a varying amount of heavy 
> atoms to search for, but consistently get occupancies of > 1.0.
> Has anyone noticed such values for occupancies before, and by chance 
> knows how or why these occur?
> Best regards,
> Dominic

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