[phenixbb] Refining atoms on special positions

Oliver Clarke clarke at wehi.EDU.AU
Thu May 7 00:36:18 PDT 2009


I'm running phenix.refine v1.4-3, and I'm refining a 3.3A structure  
that has potassium ions present on a crystallographic fourfold axis. I  
believe (based on previous refinement in REFMAC5.5), that these ions  
are at full occupancy, so I set the occupancy of each ion to 1.

Despite this, there is still a lot (several 7-10sigma peaks in the Fo- 
Fc) of unexplained positive density, the potassium ions do not  
converge to their previously refined positions, and their B-factors  
refine upwards to values several times higher than the surrounding  
protein. When the same structure is refined in refmac (with ion  
occupancy set to 0.25), there is little to no unexplained density and  
the R/Rfree are substantially lower (21.9/25.9 as against 24.5/31)

Does anyone have any ideas/suggestions as to what might be going on?


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