In terms of map-to-model validation, in Supplementary Figs. S3(a) and S3(b) we present Q-score and FSC-Q metrics, respectively, showing the agreement between the ensemble cryo-EM map and the structural model derived from it. In most areas the agreement is very good, with the exception of the receptor-binding domain (RBD) and substantial parts of the N-terminal domain (NTD), as expected from their higher flexibility.