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I had a similar problem to what you describe. In my case the dataset was severely anisotropic (2.6A, 3.4A, 4.6A in each axis). The R factors were stuck similar to yours but the map looked good. I was told by someone with a much better appreciation of the theory than myself that the anisotropy was causing the problem.

It would be interesting to know from an expert in anisotropy e.g. the creators of UCLA anisotropy server or Startaniso whether anisotropy can cause this problem and whether there is any way around it.

Cheers, Paul

Paul Steven Miller (PhD)
Postdoctoral Researcher
University of Oxford
Wellcome Trust Centre for Human Genetics
Division of Structural Biology
Roosevelt Drive
Oxford
OX3 7BN


---- Original message ----

Date: Fri, 13 Oct 2017 10:30:22 +0200
From: CCP4 bulletin board <[log in to unmask]> (on behalf of Gianluca Cioci <[log in to unmask]>)
Subject: [ccp4bb] High R/Rfree after MR  
To: [log in to unmask]

  Dear All,
  I am trying to refine a structure at 3.3A. Model has
  60% identity to the target. Maps look OK (for 3.3A)
  and rebuilding in Coot is relatively
  straightforward. However, after some rebuilding
  cycles the R factors are stuck at 0.37/0.39
  (REFMAC). 
  XTRIAGE tells me that everything is normal (no twin,
  98% completeness, R=3.5% in the low resolution bin),
  perhaps some anisotropy is present. 
  I have already refined 2 homologous structures at
  resolutions going from 3.2 to 3.8 and there were no
  problems (final R ~ 0.21/0.24). 
  Any advice ?
  Thanks,
  GIA