The paper introduces phenix.refine, a program within the PHENIX package that supports crystallographic structure refinement using a wide range of model parameterizations and experimental data resolutions. It highlights the program's automation features, flexibility, and extensive customization options. The refinement process is divided into three main parts: initialization, macro-cycle, and output. The initialization step processes input data, selects refinement strategies, and performs consistency checks. The macro-cycle is the main body of the refinement, where specific steps are tailored to optimize particular parameters. The output includes the refined model, electron-density maps, and statistics. The paper also discusses specific tools for refinement at subatomic and low resolutions, emphasizing the importance of completing the model and incorporating additional information to improve refinement results.The paper introduces phenix.refine, a program within the PHENIX package that supports crystallographic structure refinement using a wide range of model parameterizations and experimental data resolutions. It highlights the program's automation features, flexibility, and extensive customization options. The refinement process is divided into three main parts: initialization, macro-cycle, and output. The initialization step processes input data, selects refinement strategies, and performs consistency checks. The macro-cycle is the main body of the refinement, where specific steps are tailored to optimize particular parameters. The output includes the refined model, electron-density maps, and statistics. The paper also discusses specific tools for refinement at subatomic and low resolutions, emphasizing the importance of completing the model and incorporating additional information to improve refinement results.