XChem fragment hits are detected and modelled using the PanDDA paradigm (Pearce et al, 2016), which explicitly treats the low occupancy binding of fragments as a superposition of bound and unbound states. This requires on the one hand a 3D density background correction to detect and model fragments; and on the other to model both bound and unbound states for refinement (Pearce et al, 2017).
These corrected density maps are named "Event maps", and are the primary evidence for the fragment models. They are deposited in the PDB along with the refined models and diffraction data; however, the existing validation processes of the PDB do not yet correctly account for these data, and consequently the validation reports flag up several of the structures as extreme outliers.
Instead, to check the electron density evidence for the fragment hits, consult the density and model quality evidence presented here, where the data that explain the model are collated in easily reviewable form. This is a stop-gap solution while we work with the PDB to simplify the process of accessing this evidence directly on their pages.
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