Group isotropic (one isotropic B per selected model part).Restrained individual isotropic, anisotropic, mixed.Atomic Displacement Parameters (ADP) refinement:.Reference model, Ramachandran plot restraints Restraints specific to low-resolution refinement: secondary structure,.NCS: global (Cartesian), local (torsion), constraints ("strict" NCS).Fixing (not refining) coordinates of any selected part of the structure.Adding custom (user-defined) restraints (bonds, angles, etc).Selective removing of stereochemistry restraints.LBFGS minimization, Cartesian or torsion Simulated Annealing.Restrained or unrestrained individual, in real or reciprocal space.Automatic multiple-zone rigid-body refinement with a large convergence radius.Acta Crystallogr D Biol Crystallogr 69, 625-34 (2013). Bulk-solvent and overall scaling revisited: faster calculations, improved results.Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution.Acta Crystallogr D Biol Crystallogr 68, 352-67 (2012). Towards automated crystallographic structure refinement with phenix.refine.Making sure atom charge is used in refinementĬitation reference and comprehensive methodology details.Refining with anomalous data (or what phenix.refine does with Fobs+ and Fobs-).Suppressing the output of certain files.Using phenix.refine to calculate structure factors.Ignoring test (free) flags in refinement.Refinement using FFT or direct structure factor calculation algorithm.Modifying the initial model before refinement starts.Default refinement with user specified X-ray target function.Bulk solvent correction and anisotropic scaling.Setting the resolution range for the refinement.Creating R-free flags (if not present in the input reflection files).
Changing the number of refinement cycles and minimizer iterations.Examples of frequently used refinement protocols, common problems.Refinement at high resolution (higher than approx.Neutron and joint X-ray and neutron refinement.Refinement of Atomic Displacement Parameters (ADP or B-factors).Giving parameters on the command line or in files.Remark on using amplitudes (Fobs) vs intensities (Iobs).Citation reference and comprehensive methodology details.
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