Here we compare the result of fitting the source model (ribosome maturation protein SBDS, PDB: 5AN9 chain J) to the density map (ribosome maturation protein SBDS, EMDB: 3146) by Flex-EM (red) (a), MDFF (green) (b), and our method (purple) (c). The target model (ribosome maturation protein SBDS, PDB: 5ANB chain J) is colored cyan. (d) Shown here is the overlap of the fitted source model by Flex-EM, MDFF, and our method. A zoomed-in view can be found in Fig. S5. To see this figure in color, go online.