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Figure 10
Amber refinement produces better hydrogen bonds and van der Waals contacts as well as removing somewhat more steric clashes. (a) The Asn182 helix-cap region in PDB entry 3g8L at 2.5 Å resolution, with numerous clashes and other outliers. (b) CDL/E&H refinement makes large improvements, removing most clashes and all other outliers. (c) Amber refinement does even better, removing all clashes and most small overlaps (yellow) and optimizing to produce more hydrogen bonds and favorable van der Waals contacts (green and blue dots).

Journal logoSTRUCTURAL
BIOLOGY
ISSN: 2059-7983
Volume 76| Part 1| January 2020| Pages 51-62
https://doi.org/10.1107/S2059798319015134
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