1. Department of Microbiology and Immunology, Stanford University School of Medicine , 291 Campus Drive, Stanford, CA 94305 , USA
2. Department of Chemistry, Stanford University , 450 Serra Mall, Stanford, CA 94305 , USA
3. Department of Bioengineering, Stanford University , 450 Serra Mall, Stanford, CA 94305 , USA
4. Department of Structural Biology, University of Pittsburgh , 4200 Fifth Ave, Pittsburgh, PA 15260 , USA
5. Leiden Institute of Advanced Computer Science, Leiden University , Rapenburg 70, 2311 EZ Leiden , The Netherlands
6. Department of Pediatrics––Infectious Diseases, Stanford University School of Medicine , 291 Campus Drive, Stanford, CA 94305 , USA
7. Department of Mathematics, University of California , Berkeley, CA 94720 , USA
8. Center for Advanced Mathematics for Energy Research Application (CAMERA), Lawrence Berkeley National Laboratory , 1 Cyclotron Rd, Berkeley, CA 94720 , USA
9. Division of Cryo-EM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University , Menlo Park, CA 94305 , USA