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Figure 5
Differing responses of CDL/E&H versus Amber refinement to the misfitting of a water into what should be a side-chain N atom in an arginine residue. Neither result here is acceptable, but if the incorrect water is deleted (d) then both methods do a very good job of moving the guanidinium correctly back into its density. MolProbity markup for Figs. 5–10: clusters of hot pink spikes represent clashes, pillows of green dots represent hydrogen bonds, red or blue springs or fans represent larger or smaller bond-length or angle outliers, magenta spheres represent Cβ deviations, gold side chains represent rotamer outliers, green Cα–Cα lines represent Ramachandran outliers and magenta lines along the CO–CO dihedral represent CaBLAM outliers. Relevantly moving O or N atoms are emphasized with red or blue spheres.

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