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. Author manuscript; available in PMC: 2018 Oct 10.
Published in final edited form as: J Chem Theory Comput. 2017 Sep 26;13(10):5131–5145. doi: 10.1021/acs.jctc.7b00464

Figure 12.

Figure 12

(a) EMRinger score for the ab initio start models (pink) and the models after three rounds of iterative Rosetta-MD refinement using 4 Å density maps (black) (b) ab initio start structure of 2LLY (yellow) overlapped with the 4 Å density map (black mesh). Side chain mismatches and deviation from the densities can been seen. (c) The final refined 2LLY model (blue) overlapped with the 4 Å density map (black mesh). Three residues with benzene rings, PHE 87, HIS 99 and TRP 130, were misaligned with the density map in the ab initio start model but were well converged into the density map in the final refined model (highlighted in black boxes). (d) Zoomed in side chain residue overlaps; the native coordinates (red), the ab initio starting model coordinates (yellow) and the final refined model coordinates (blue). Side chains were well aligned with the density and overlapped with the native side chain coordinates in the refined model.