We acknowledge the support from the Advanced Computing and e-Science group at the Institute of Physics of Cantabria (IFCA–CSIC–UC) as well as the Barcelona Supercomputer Center (access project BCV-2020-2-0005). The authors acknowledge the support and the use of resources of Instruct, a Landmark ESFRI project (Instruct Access Project ID11775). Author contributions were as follows. Roberto Melero and COSS performed all of the image analysis in Scipion, while BF performed equivalent work in the principal component analysis and JLV in the local resolution analysis. MM and Roberto Marabini were in charge of structural modeling, while Pablo Chacon performed the flexible fittings and incorporated important sections of the manuscript. ER-A performed the map-to-model analysis as well as generating the sharpened cryo-EM maps, while RS-G also worked in new sharpening methods and DH performed the elastic inter-class analysis. Pablo Conesa, YF-R, LdC and PL were in charge of the IT hardware and software support. JMcL and DW supplied the images and provided advice throughout the work. HT, COSS and JMC conceptualized the work, with JMC writing the manuscript, which was complemented by all other authors. PC, JMcL, HT and JMC were responsible for the funding. The authors declare no conflicts of interest.