Macromolecular TLS refinement in REFMAC at moderate resolutions.

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Overview of the CCP4 suite and current developments (2011, methodology): “REFMAC5 will refine atomic coordinates and atomic isotropic or anisotropic displacement parameters (Murshudov et al., 1999), as well as group parameters for rigid-body refinement and TLS refinement (Winn et al., 2001, 2003).”
The Phenix Software for Automated Determination of Macromolecular Structures (2011, methodology): “As the data to parameter ratio approaches unity or worse, it is necessary to apply other constraints, such as refinement of coordinates in torsion angle space[46], or refinement of atomic displacements as constrained rigid groups with the translation-libration-screw (TLS) formulism[54, 55].”
D3R Grand Challenge 2: Blind Prediction of Protein-Ligand Poses, Affinity Rankings, and Relative Binding Free Energies (2017, methodology): “FXR structures were determined at Roche by molecular replacement with PHASER [23], using a set of previously determined in-house FXR structures as models, and the solution with the best log-likelihood gain was used as starting model for rebuilding and refinement in Refmac5 [24] or BUSTER [25].”
Structural insights into the assembly of the histone deacetylase-associated Sin3L/Rpd3L corepressor complex (2015, methodology): “Iterative rounds of model building and refinement were performed using Coot (58) and Refmac5 (59), respectively.”