[phenixbb] DEN refinement

Jan van Agthoven janccp4 at gmail.com
Wed Oct 2 13:43:47 PDT 2013

Hi everyone,
I ran a DEN refinement of my low resolution structure (3.6) to improve
my model. I typed in the following command:

phenix.den_refine model.pdb data.mtz den.reference_file=reference.pdb

with reference.params saying:

refinement.reference_model.reference_group {
     reference = chain A and resseq 1:953
     selection = chain A and resseq 1:953
refinement.reference_model.reference_group {
     reference = chain B and resseq 1:687
     selection = chain B and resseq 1:687

because the reference file only contains chain A and chain B.

Unfortunately I obtained much worse R factors then with a regular refinement:

Start R-work = 0.2798, R-free = 0.3176
Final R-work = 0.3733, R-free = 0.4089

Does someone have an idea what could have go wrong?


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