[phenixbb] Phenix real space refine problems

Pavel Afonine pafonine at lbl.gov
Tue Jul 16 11:32:31 PDT 2019

Hi Gyles,

please send me files off list (model before and after refinement, data 
and ligand cif if used; also indicate affected residues) and I will 


On 7/16/19 04:13, Gyles Cozier wrote:
> Good afternoon,
> I have been having issues with the last 3 versions of Phenix (1.14, 
> 1.15 and 1.16) when the XYZ(real-space) option is selected, version 
> 1.13 was the last one that doesn't have this problem for me. This 
> seems to place too much weight on correcting rotamer 'outliers' at the 
> expense of fitting to the density. The proteins that I work on have 
> always had some residues that consistently are identified as rotamer 
> outliers, but these latest versions 'correct' just about all of them 
> (typically from 1% down to 0.1%). The resulting structures show clear 
> movement of the sidechains out of what should be their density. Image 
> 1 (after using 1.13) and 2 (after using 1.14, 1.15 or 1.16) show a 
> really bad example where the Arg sidechain even gets broken apart to 
> be moved into the stronger density of a neighbouring symmetry Gln. 
> Image 3 (after using 1.13) and 4 (after using 1.14, 1.15 or 1.16) is a 
> more subtle example, but although the residue is no longer a rotamer 
> outlier after refinement using 1.16, it clearly does not fit the 
> density as well as after using 1.13. These subtle changes are 
> particularly worrying, as they could easily be missed when checking 
> the structure after refinement. Other members of the group have also 
> noticed this problem for different proteins.
> So currently I have a choice of either using version 1.13 (which with 
> Onedep no longer accepting pdb files makes things a bit inconvenient 
> as is nice to use the latest version for getting the mmcif and 
> validation), or to use 1.16, but switch off the XYZ(real-space).
> Has anyone else noticed this happening? Found a solution to the problem?
> Thank you for any suggestions,
> Gyles Cozier.
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