CERES

CERES re-refines deposited cryo-electron microscopy (cryo-EM) atomic models to improve model–map agreement and validation metrics for structures in the Protein Data Bank (PDB).

Key Features:

• Automatic re-refinement: Targets previously deposited atomic structures with map resolutions better than 5 Ångströms for systematic re-refinement.
• Phenix integration: Utilizes current versions of Phenix tools, including phenix.real_space_refine, to perform refinements.
• Real-space refinement: Enhances models against experimental real-space maps to improve structural details.
• Validation metrics: Computes robust validation metrics tailored for low-resolution cryo-EM data to evaluate model quality.
• Standardized reporting: Produces a comprehensive summary format termed "cryo-EM Table 1" that encapsulates experimental details and validation metrics.
• Continuous model improvement: Provides a mechanism to iteratively improve deposited models within the PDB.

Scientific Applications:

• Model fidelity improvement: Enhances the accuracy and model–map agreement of cryo-EM-derived atomic models for downstream structural analyses.
• Standardized evaluation and reporting: Enables consistent reporting of experimental details and validation metrics for cryo-EM structures using the "cryo-EM Table 1" format.
• Support for structural biology research: Supplies refined models and validation data that underpin research applications dependent on high-quality cryo-EM structures.

Methodology:

Automatically re-refines deposited structures with map resolutions better than 5 Ångströms using current Phenix tools (including phenix.real_space_refine) against real-space maps and computes validation metrics, producing a "cryo-EM Table 1" summary.