(a)A local rotational search around a segmented Apoferritin map (EMD:20026, 1.75Å). The top 10 fits by cross-correlation (CC) score are considered, out of 100 fits with evenly sampled orientations around the protein center. The plot, top left, shows CC and Q-scores plotted for each of the 10 top fits. CC and Q-scores are both lower for incorrect placements of the model. (b) Cross-correlation scores before and after real-space refinement with Phenix – the scores increase after refinement in all cases. (c) Q-scores also increase in all cases after refinement. The maps and models for which Q-scores are calculated are listed in Table 1.