Outputs Overview

When AlphaFold completes a prediction run, it generates the following output files and directories:

• msas directory: Contains the multiple sequence alignments used as input for the model.
• features.pkl: A machine-readable pickle file containing input features extracted from the MSA and templates.
• ranking_debug.json: Stores the ranking information used to order the five model outputs.
• relax_metrics.json: Contains metrics from the AMBER relaxation step.
• timings.json: Records runtime information for different stages of the prediction pipeline.

Each of the five models produces:

• A ranked PDB structure
• A relaxed PDB structure
• An unrelaxed PDB structure
• A corresponding .pkl file containing model data