[phenixbb] question in geometry refinement

Noelia Bernardo García xnoelia at iqfr.csic.es
Thu Jan 26 03:04:55 PST 2017

Dear colleagues,

I am dealing with the refinement of a protein with 5 monomers in the asymmetric unit at 2.2 Å resolution. Four of them have correct geometry and good density map, however, the fifth molecule has poor density and bad geometry. Ramachandran plot is presents 91.05% (favored), 3.23 % (outliers). 
I have modified the occupancy of the molecule, the refinement results in 0.8 occupancy for this chain. I also tried to refined the structure without this chain, but the R values increased and the density map indicated that it should be there. I would like to refine this chain fixing the geometry of the others which are correct. Do you have any ideas about how to proceed?

Some info:
Protein residues 305 
5 monomers in the a.u 
Space group C121 a=151.390, b= 67.81,  c=155.420Å, 94.53º
R value 0.23 / Rfree 0.28
Many thanks,


Noelia Bernardo García, PhD
Instituto de Química Física "Rocasolano"
Spanish National Research Council (CSIC)
c/ Serrano 119
28006 Madrid (Spain)
Phone: +34-91 561 94 00 (ext. 961107)
e-mail: xnoelia at iqfr.csic.es

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