Iterative model building, structure refinement and density modification with the<i>PHENIX AutoBuild</i>wizard

TLDR

The PHENIX AutoBuild wizard automates iterative model building, structure refinement, and density modification using RESOLVE and phenix.refine. Its model‑completion algorithms perform loop building, chain crossovers between models, and side‑chain optimization. Application to 48 structures (1.1–3.2 Å) yielded a mean R factor of 0.24 and free R of 0.29, with performance largely independent of resolution and driven by starting density quality, while recent updates added automated NCS detection, model‑completion, and solvent picking.

Abstract

The PHENIX AutoBuild wizard is a highly automated tool for iterative model building, structure refinement and density modification using RESOLVE model building, RESOLVE statistical density modification and phenix.refine structure refinement. Recent advances in the AutoBuild wizard and phenix.refine include automated detection and application of NCS from models as they are built, extensive model-completion algorithms and automated solvent-molecule picking. Model-completion algorithms in the AutoBuild wizard include loop building, crossovers between chains in different models of a structure and side-chain optimization. The AutoBuild wizard has been applied to a set of 48 structures at resolutions ranging from 1.1 to 3.2 A, resulting in a mean R factor of 0.24 and a mean free R factor of 0.29. The R factor of the final model is dependent on the quality of the starting electron density and is relatively independent of resolution.