Fig. 3: Refinement of the CERES benchmark.

a Benchmark comparison using CCC, between the initial (PDB-deposited) models (blue), the CERES re-refined models (green), and TEMPy-ReFF refinement-based model (orange), separated by resolution bands of 1 Å. We evaluated n = 229 individual models. The central line in each boxplot defines the median value, the bounds of each box define the upper and lower quartiles and the whiskers define 1.5 times the interquartile range (IQR). Outliers (points outside this 1.5*IQR range) are marked with rhombus symbols. The individual score for each model is marked with a black point. b Benchmark comparison of the same 229 models using MolProbity score, the colouring and layout of the boxplot is the same as in a. c Comparison between the refinement of the ABC methionine transporter (PDB ID: 7MC0, EMDB ID: 23572, resolution 3.3 Å) with TEMPy-ReFF and the corresponding models from PDB and CERES. For all subpanels the colouring matches that used in a. The left panel shows the overlaid models within the cryo-EM map, which is rendered as a transparent surface. The central panels show the SMOCf scores for residues from chains A (upper panel) and B (lower panel). The left-hand panels show zoomed-in views of sections of chain A (upper panel) and B (lower panel) as highlighted in the respective SMOCf plots with black outlined boxes.