[phenixbb] Occupancy refinement of secondary conformation doesn't add up to 1.00

Pavel Afonine pafonine at lbl.gov
Sat Jun 14 12:36:52 PDT 2014

Hi Ben,

> I do a refinement of a glycoprotein that has a NAG-NAG attached to an 
> Asn. The data set is very high resolution and I am positive there is 
> indication of a secondary conformation of the entire attachement.
> I modeled a second conformation in Coot and run my refinement, with 
> the "adjust occupancy" option checked. After initially setting both 
> occupancies to 0.5, I am puzzled to see one of the NAGs to be refined 
> to 0.45 (conformer A) and 0.75 (conformer B) occupancy .. For the 
> other NAG, and indeed all amino acid residues, things always add up 
> like they should.
> Additionally to this, I was wondering if there was an easy option to 
> restrain each conformer of the entire Asn-NAG-NAG group to have 
> uniform occupancies -- i.e. the Asn and both NAGs of conformer A to 
> have identical occupancy.

I'm pretty sure the problem stems from incorrectly formatted PDB file 
(perhaps TER records inserted between conformations/residue, etc..). If 
you send me PDB file or just a fraction of it with residues/ligands in 
question I will tell what exactly is the root of the problem.

More information about how phenix.refine does occupancy refinement:


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