diff --git a/tools/battery/README.md b/tools/battery/README.md
index 18bec5d32..6b31188fa 100644
--- a/tools/battery/README.md
+++ b/tools/battery/README.md
@@ -130,13 +130,17 @@ everything else on the machine competes with it.
 
 ### The model check (open arm)
 
-If `tools/battery/model_check.py` is present, each open-arm merge (`p.mtz`) is also scored
-against the deposited model: `model_check.check(mtz, pdb_id, workdir)` returns R-free and R-work
-of the deposited model against our data, plus the deposited R-free. The runner records these as
-`rfree`, `rwork`, `rfree_deposited`, `rfree_ratio`, `model_status` and `model_reason`, and the
-report plots their ratio. The check is on by default when the module exists. Without the module
-the fields stay null. The PDB entry is the set id up to the first `_`, so `6h2p_native` is checked
-as `6h2p`. Small-molecule sets are skipped.
+`tools/battery/model_check.py` scores each open-arm merge (`p.mtz`) against the deposited model,
+unmodified (ligands, waters and hydrogens kept): REFMAC's rigid-body mode, R-factors taken before
+any shift, the data reindexed into the model's setting and reduced to the deposited space group.
+Our own free set was mostly work reflections for the depositor, so `rfree` reads low. The fair
+comparison is `rfree_depflags` (our data on the depositor's free set) against `rfree_depdata` (the
+depositor's structure factors, same free set, same protocol); `rfree_ratio` is that ratio, and the
+report plots it. It is null when the entry deposited no structure factors with a free set.
+`rfree_deposited` is the value in the entry, often from twin or full refinement. The runner records
+`rfree`, `rwork`, `rfree_deposited`, `rfree_depflags`, `rfree_depdata`, `rfree_ratio`,
+`model_status` and `model_reason`. The check is on by default when the module exists. The PDB entry
+is the set id up to the first `_`, so `6h2p_native` is checked as `6h2p`. Small-molecule sets are skipped.
 
 `model_sweep.py` is a different tool: it runs `rugnux --model` over the open arm (same inputs, same
 site config) and compares the R-free that rugnux itself reports with the published value. It needs
@@ -179,7 +183,7 @@ This is a flat list with one object per set, and every arm uses the same keys. M
 | `d_min_ref_rule`, `d_min_xds` | XDS arms: how `d_min_ref` was derived (below), and the range XDS merged |
 | `r_meas`, `cc_half`, `isa`, `completeness`, `multiplicity`, `i_over_sigma`, `indexing_rate`, `images` | from rugnux's `_report.txt` |
 | `r_meas_ref`, `cc_half_ref`, `isa_ref`, `completeness_ref` | XDS's overall values, over XDS's own range |
-| `rfree`, `rwork`, `rfree_deposited`, `rfree_ratio`, `model_status`, `model_reason` | the model check (open arm) |
+| `rfree`, `rwork`, `rfree_deposited`, `rfree_depflags`, `rfree_depdata`, `rfree_ratio`, `model_status`, `model_reason` | the model check (open arm) |
 | `wall_s`, `rugnux_wall_s`, `elapsed_s`, `exit_code`, `gpu_others`, `rugnux_verdict` | timing (`wall_s` is rugnux's own WALL_TIME, not the time spent waiting for the GPU queue), the exit code, other GPU processes seen before the set, and rugnux's own verdict line |
 
 ## The report
diff --git a/tools/battery/battery.py b/tools/battery/battery.py
index ceed6ed20..b369d949e 100644
--- a/tools/battery/battery.py
+++ b/tools/battery/battery.py
@@ -191,7 +191,7 @@ def run_one(run_dir, binary, e, opts):
     os.makedirs(wd)
     row = {"set": e["id"], "arm": e["arm"], "tags": e.get("tags", []), "input": e["input_path"],
            "gpu_others": gpu_others(), "rfree": None, "rwork": None, "rfree_deposited": None,
-           "rfree_ratio": None, "model_status": None, "model_reason": None}
+           "rfree_depflags": None, "rfree_depdata": None, "rfree_ratio": None, "model_status": None, "model_reason": None}
     if not os.path.exists(e["input_path"]):
         row.update(score.judge(e, {}, "no input"), exit_code=None, elapsed_s=None, wall_s=None, cmd=None)
         return row
@@ -221,7 +221,8 @@ def run_one(run_dir, binary, e, opts):
 def check_model(e, wd):
     """R-free of the deposited model against this run's merge (model_check.py). A set id may
     carry a suffix (6h2p_native); the PDB entry is the part before it."""
-    out = {"rfree": None, "rwork": None, "rfree_deposited": None, "rfree_ratio": None}
+    out = {"rfree": None, "rwork": None, "rfree_deposited": None, "rfree_depflags": None,
+           "rfree_depdata": None, "rfree_ratio": None}
     pdb = e["id"].split("_")[0]
     mtz = os.path.join(wd, "p.mtz")
     if not PDB_ID.match(pdb):
@@ -232,10 +233,14 @@ def check_model(e, wd):
         res = model_check.check(mtz, pdb, os.path.join(wd, "model_check"))
     except Exception as ex:          # a failing check must not lose the set's processing result
         return dict(out, model_status="error", model_reason=f"{type(ex).__name__}: {ex}"[:300])
-    out.update({k: res.get(k) for k in ("rfree", "rwork", "rfree_deposited")},
+    out.update({k: res.get(k) for k in ("rfree", "rwork", "rfree_deposited", "rfree_depflags",
+                                        "rfree_depdata")},
                model_status=res.get("status"), model_reason=res.get("reason"))
-    if out["rfree"] and out["rfree_deposited"]:
-        out["rfree_ratio"] = round(out["rfree"] / out["rfree_deposited"], 4)
+    # The fair ratio: our merge and the depositor's structure factors, both scored on the
+    # depositor's free set by the same protocol. Our own free set was mostly work reflections
+    # for the depositor, so R_free on it reads low.
+    if out["rfree_depflags"] and out["rfree_depdata"]:
+        out["rfree_ratio"] = round(out["rfree_depflags"] / out["rfree_depdata"], 4)
     return out
 
 
diff --git a/tools/battery/report.py b/tools/battery/report.py
index fb4f6eef6..0acad8427 100644
--- a/tools/battery/report.py
+++ b/tools/battery/report.py
@@ -268,12 +268,13 @@ def build(run_dir, baseline=None, allow_incomplete=False):
                     f"{arm}: d_min(rugnux) / d_min(reference), one point per set, sorted; below 1 = "
                     "finer than the reference")
     pts = [(r["set"], r["rfree_ratio"], r["verdict"],
-            f"R_free {r['rfree']:.3f} vs deposited {r['rfree_deposited']:.3f}")
+            f"R_free {r['rfree_depflags']:.3f} vs {r['rfree_depdata']:.3f} on the deposited data")
            for r in res if r.get("rfree_ratio")]
     if pts:
         doc.svg(ratio_dots(pts, "R_free ratio"),
-                "open: R_free of the deposited model against our merge / the deposited R_free, one "
-                "point per set, sorted; below 1 = our data fit the model better")
+                "open: R_free of the deposited model against our merge / against the deposited structure "
+                "factors, both on the depositor's free set with the same protocol, one point per set, "
+                "sorted; below 1 = our data fit the model better")
 
     derived = [r for r in res if (r.get("d_min_ref_rule") or "xds_range") != "xds_range"]
     if derived: