<i>REFMAC</i>5 for the refinement of macromolecular crystal structures

TLDR

The paper describes the components of REFMAC5, a macromolecular crystallographic refinement program distributed with the CCP4 suite. REFMAC5 employs likelihood‑based refinement with data‑specific functions, automated twinning handling, TLS and anisotropic ADP refinement, and a suite of chemical restraints and parameterization options. The program achieves reliable models down to 4 Å using advanced restraints and long‑range ADP restraints, and is presented as a flexible, highly optimized package suitable for the full resolution range of macromolecular crystallography.

Abstract

This paper describes various components of the macromolecular crystallographic refinement program REFMAC5, which is distributed as part of the CCP4 suite. REFMAC5 utilizes different likelihood functions depending on the diffraction data employed (amplitudes or intensities), the presence of twinning and the availability of SAD/SIRAS experimental diffraction data. To ensure chemical and structural integrity of the refined model, REFMAC5 offers several classes of restraints and choices of model parameterization. Reliable models at resolutions at least as low as 4 Å can be achieved thanks to low-resolution refinement tools such as secondary-structure restraints, restraints to known homologous structures, automatic global and local NCS restraints, `jelly-body' restraints and the use of novel long-range restraints on atomic displacement parameters (ADPs) based on the Kullback-Leibler divergence. REFMAC5 additionally offers TLS parameterization and, when high-resolution data are available, fast refinement of anisotropic ADPs. Refinement in the presence of twinning is performed in a fully automated fashion. REFMAC5 is a flexible and highly optimized refinement package that is ideally suited for refinement across the entire resolution spectrum encountered in macromolecular crystallography.