README: add 'Reproducing the main benchmark' section (CPU reproduce_benchmark.py)

README.md

@@ -140,6 +140,25 @@ package version.
   measurable lift over random subsampling. Treat this package as a research
   baseline, not a turnkey accuracy improvement.
 
+## Reproducing the main benchmark
+
+The scoring/evaluation code, reference structures, region definitions, and the
+AlphaFold2 prediction sets for the headline arms are included so the main
+`minority_hit_rate` table can be regenerated on CPU (no GPU):
+
+```bash
+pip install numpy biopython pyyaml
+python reproduce_benchmark.py --mode score        # re-score all 1440 prediction PDBs
+python reproduce_benchmark.py --mode precomputed   # aggregate shipped evals.tsv (fast)
+```
+
+The driver re-runs the Biopython Superimposer scorer (`eval/evaluate_prediction.py`,
+hit = Cα RMSD ≤ 3 Å on common core AND pLDDT ≥ 70 overall AND ≥ 70 in the switch
+region) over `bench/` and asserts each cell matches the published table
+(mosaic-SF KaiB 0.95, GA98 0.925, GB98 0.1875; AF-Cluster baseline 0.36/0.46/0.44;
+full table and the GA_GB scoring caveat in `README_benchmark.md`). All 15 cells
+reproduce exactly. TMalign is optional (extra columns only).
+
 ## Citation
 
 If you use this code, please cite the SF-Cluster paper (forthcoming) and