Macromolecular refinement of X-ray and cryoelectron microscopy structures with Phenix/OPLS3e for improved structure and ligand quality

With the advent of the resolution revolution in cryoelectron microscopy (cryo-EM), low-resolution refinement is common, and likewise increases the need for a reliable force field. Here, we report on the incorporation of the OPLS3e force field with the VSGB2.1 solvation model in the structure determination package Phenix. Our results show significantly improved structure quality and reduced ligand strain at lower resolution for X-ray refinement. For refinement of cryo-EM-based structures, we find comparable quality structures, goodness-of-fit, and reduced ligand strain. We also show how structure quality and ligand strain are related to the map-model cross-correlation as a function of data weight, and how that can detect overfitting. Signs of overfitting are found in over half of our cryo-EM dataset, which can be remedied by a re-refinement at a lower data weight. Finally, a start-to-end script for refining structures with Phenix/OPLS3e is available in the Schrodinger 2020-3 distribution.

Automated summary

With the resolution revolution in cryo-EM, the need for a reliable force field is increasing. Incorporating the OPLS3e force field with the VSGB2.1 solvation model in Phenix has shown improved structure quality and reduced ligand strain for X-ray and cryo-EM refinement. Overfitting can be detected by examining the map-model cross-correlation as a function of data weight, and remedied by re-refinement at a lower data weight in cryo-EM structures.