Real-space refinement is not run by default at this resolution, so no need to turn it off explicitly. Pavel On 11/7/13 2:53 PM, Nathaniel Echols wrote:

Try turning off real space refinement:

refine.strategy=individual_sites+individual_adp+occupancies

(and at this resolution, anomalous_group refinement of the seleniums would probably also be useful, but you'd have to use the anomalous data as input.)

-Nat

On Thu, Nov 7, 2013 at 1:12 PM, Mark Wilson mailto:[email protected]> wrote:

Dear PHENIX users and developers, I am refining a structure containing SeMet residues at atomic (1.05 Å) resolution. The model was initially refined in Refmac5 and behaved as expected (i.e. reasonable R factors and agreement with maps). I've used this final Refmac5 model as a starting point for refinement in PHENIX 1.8.4 with standard settings, as below.

phenix.refine data.mtz \ refinement.input.xray_data.labels="F, SIGF" model.pdb \ main.use_experimental_phases=false \ refinement.main.number_of_macro_cycles=5 output.prefix="model_refine"> phenix_refine_1.log

Strangely, the conformations of the MSE residues are changed quite significantly after refinement in PHENIX, departing both from electron density and from the prior model. Any help would be appreciated. Best regards, Mark

Mark A. Wilson Associate Professor Department of Biochemistry/Redox Biology Center University of Nebraska N118 Beadle Center 1901 Vine Street Lincoln, NE 68588 (402) 472-3626 tel:%28402%29%20472-3626 [email protected] mailto:[email protected]

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