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Flowchart showing the overall scheme for restrained refinement of models against EM data. ProSMART generates three classes of restraint: (i) reference restraints, (ii) helical fragment restraints and (iii) secondary-structure hydrogen-bond restraints (which include helix, sheet and loop restraints). Alongside reciprocal-space refinement in REFMAC, real-space refinement tools in Coot can be used to optimize the fit to density.
