Hi Jan,

Did you run your DEN refinement with optimize=True? If you haven't run the grid optimization, it's unlikely that you found the optimal gamma/weight pair for your specific case.

Also, I would recommend not using reference model restraints while running DEN refinement. This could potentially prevent your model from "deforming", if you are restraining it to be the same as a reference model.

To use a reference file with DEN, you would use:

den.reference_file="path_to_reference_file"

That will handle the chainID/resID matching automatically, and correctly use your reference in a DEN context.

Jeff

On Wed, Oct 2, 2013 at 4:43 PM, Jan van Agthoven <[email protected]> wrote:

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
reference.params

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?

Thanks,
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