Abstract
The assessment of CASP models for utility in molecular replacement is a
measure of their use in a valuable real-world application. In CASP7, the
metric for molecular replacement assessment involved full
likelihood-based molecular replacement searches; however, this
restricted the assessable targets to crystal structures with only one
copy of the target in the asymmetric unit, and to those where the search
found the correct pose. In CASP10, full molecular replacement searches
were replaced by likelihood-based rigid-body refinement of models
superimposed on the target using the LGA algorithm, with the metric
being the refined likelihood (LLG) score. This enabled multi-copy
targets and very poor models to be evaluated, but a significant further
issue remained: the requirement of diffraction data for assessment. We
introduce here the relative-expected-LLG (reLLG), which is independent
of diffraction data. This reLLG is also independent of any crystal form,
and can be calculated regardless of the source of the target, be it
X-ray, NMR or cryo-EM. We calibrate the reLLG against the LLG for
targets in CASP14, showing that it is a robust measure of both model and
group ranking. Like the LLG, the reLLG shows that accurate coordinate
error estimates add substantial value to predicted models. We find that
refinement by CASP groups can often convert an inadequate initial model
into a successful MR search model. Consistent with findings from others,
we show that the AlphaFold2 models are sufficiently good, and reliably
so, to surpass other current model generation strategies for attempting
molecular replacement phasing.