RNA-Puzzles was launched in 2011 as a collaborative effort dedicated to advancing and improving RNA 3D structure prediction. The automatic evaluation protocols for comparisons between prediction and experiment developed within RNA-Puzzles are applied to the 2024 CASP16 competition. The scores evaluate stereochemical parameters, Watson-Crick pairs, non-Watson-Crick pairs and base stacking in addition to standard global parameters such as RMSD, TM-score, GDT, or lDDT. Several targets were particularly difficult owing to their size or multimerization. Although predictions with good metrics on secondary structure can yield acceptable global folds, these are not sufficient to guarantee the chemical precision, or the correct identification of residues involved in the non-Watson-Crick interactions that are critical for the three-dimensional architecture and the biological function of the RNAs.