Checking your imagination: applications of the free R value.

By Gerard J. Kleywegt, A. Brunger. 1996

GJK thanks Dr T Alwyn Jones for many stimulating discussion concerning model quality, validation and the free R value, and Dr Randy J Read for suggesting the test with a backward-traced model containing NCS. ATB thanks Drs P Adams, FT Burling, P Gros, J-S Jiang, RJ Read, LM Rice, and ALU Roberts for stimulating discussions about cross-validation in crystallography. GJK acknowledges support from Uppsala University and the European Union (through grant number BIO4-CT96-0189 to Dr TA Jones, Uppsala). ATB acknowledges support from the National Science Foundation (grant number BIR-9514819).

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Citations in the corpus

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix (2019, methodology): “If Rfree increases while Rwork decreases, the model might be incorrectly parameterized or the refinement strategy needs to be revised (Kleywegt & Brünger, 1996). phenix.refine reports Rwork and Rfree values after refinement; R-factor plots show how the values change during the refinement run.”
The PDB_REDO server for macromolecular structure model optimization (2014, methodology): “In PDB_REDO, k-fold cross-validation (Picard & Cook, 1984; Kleywegt & Brünger, 1996) is used if the test set is smaller than 500 reflections.”
Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution (2012, unknown): “Traditional global validation metrics such as Rwork and Rfree (Brünger, 1992b) are increasingly less sensitive to local changes in the model as resolution decreases (Murshudov et al., 1997; Kleywegt & Brünger, 1996), making model validation difficult.”