phenix.real_space_refine: a tool for refinement a model against a map

Description

The program refines a model into a map. The map can be derived from X-ray or neutron crystallography, or Electron Microscopy, and its quality can be from very good to poor. The goal is to obtain a model that fits map as good as possible and that has a meaningful geometry (no stereochemically impossible outliers, such as Ramachandran plot outliers, etc that are not justified by the map).

Contact author

For questions, bug reports, feature requests: Pavel Afonine (PAfonine@lbl.gov)

Features

• Fast gradient-driven minimization of combined map and restraints target
• Local grid search based fit to fix rotamer outliers or poor map-to-model fit
• Morphing (map guided rigid body shifts of small continuous model fragments)
• Simulated Annealing refinement
• Rigid-body refinement
• Restraints: Standard set: bond, angle, planarity, chirality, dihedral, nonbonded repulsion. Extra restraints: Ramachandran plot (two options: "oldfield" and "emsley"), C-beta deviations, rotamer, secondary structure, starting position
• Fast and fully automated restraints/map weight optimization
• Support for maps having non-zero origin
• Efficient handling of high-order NCS
• Map can be provided as CCP4 formatted map or as MTZ file with Fourier map coefficients
• ADP (B-factors) can be refined against the map
• Fast calculations
• Input PDB file may contain full molecule or only one NCS copy and NCS operators (that generate whole molecule from one NCS copy). NCS operators need to be stored as MTRIX records in PDB file header

Usage examples

1. Running with default settings:

   phenix.real_space_refine model.pdb map.ccp4
   
   phenix.real_space_refine model.pdb map_coefficients.mtz
   

   This will do several macro-cycles of global real-space refinement with secondary structure, rotamer, Ramachandran plot and C-beta deviations restraints enabled.

2. Disabling secondary structure, rotamer and Ramachandran plot restraints:

   phenix.real_space_refine model.pdb map.ccp4 \
   secondary_structure.enabled=False use_rotamer_restraints=False \
   ramachandran_restraints=False
   

3. Request output model to have bond and angle rmsd from ideal not greater than certain values:

   phenix.real_space_refine model.pdb map.ccp4 target_bonds_rmsd=0.01 \
   target_angles_rmsd=1.0
   

4. Specify which Fourier map coefficients to use:

   phenix.real_space_refine model.pdb map.mtz label='2FOFCWT,PH2FOFCWT'
   

5. Run refinement using global minimization (default), local fitting, morphing, and simulated annealing:

   phenix.real_space_refine model.pdb map.ccp4 \
   run=minimization_global+local_grid_search+morphing+simulated_annealing
   

6. If PDB file contains unknown to Phenix ligand a ligand CIF file needs to be provided. Ligand CIF file can be obtained using one of corresponding tools in Phenix (see documentation for more details). Once CIF file is available it can be used as following:

   phenix.real_space_refine model.pdb map.ccp4 ligands.cif
   

7. Group ADP (B-factor) refinement. Currently only one option availbale: restrained group ADP refinement with two B-factors per residue (one for main and one for side chains):

   phenix.real_space_refine model.pdb map.mtz run=adp
   

Notes

• Secondary structure (SS) restraints strongly rely on correct SS annotation. If SHEET and HELIX records are available in PDB file header then they will be used to enforce SS as defined. Incorrect SHEET and HELIX records are very likely to result in incorrect refined structure. If SHEET and HELIX records are not present in PDB file header and SS restraints are enabled then KSDSSP tool will be used internally to annotate SS and use it as restraints. The outcome of KSDSSP strongly depends on input model quality: for a model with gross errors SS annotation may be inaccurate resulting in poorly refine model.
• Including local fitting, morphing, or simulated annealing ( local_grid_search+morphing+simulated_annealing) into refinement may significantly increase runtime.
• It is possible to extract a box with map and model in it and do refinement inside of that box. To extract box with map and model use phenix.map_box command (see Phenix documentation for more details).
• It is important that information provided in CRYST1 record in PDB file (if provided) matches box information of CCP4 formatted map or crystal symmetry information in MTZ file (whatever used).

References

• P.V. Afonine, J.J. Headd, T.C. Terwilliger & P.D. Adams. Computational Crystallography Newsletter (2013). Volume 4, Part 2, 43-44. http://phenix-online.org/newsletter/CCN_2013_07.pdf