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Figure 2
(a, b) PDB entry 1ol1 and (c, d) PDB entry 3waz after 20 cycles of geometry optimization using the Servalcat REFMAC5 controller (a, c) without and (bd) with the alias mechanism. Since the monomers CIR (a, b) and ORP (c, d) do not follow the standard nomenclature, their chemistry is not properly recognized without the alias mechanism (missing hydrogen atoms in peptide bonds and missing restraints other than bond length). The ideal bond angles in the CCP4-ML are CA—C—N, 115.9°; C—N—CA, 122.1° (for a peptide link); O3′—P—OP2, 108.5°; O3′—P—O5′, 101.1° (for a phosphodiester link). Images were created using PyMOL (version 2.4; Schrödinger).

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