rugnux: raise default min-captured-fraction to 0.7 (recover weak F-cubic space groups)

The de-novo space-group search runs its point-group correlation only on reflections
with I/sigma >= 3, but the Diederichs error model floors merged I/sigma at the
asymptotic ISa = 1/b. On a weakly-diffracting crystal a few edge-of-sweep truncated
fulls (rocking curve captured far below 1) inflate the error-model b term, dropping
ISa below 3 so no reflection clears the gate: every operator gets zero pairs and the
point group collapses to P1 (or a low subgroup). The chi^2 self-consistency guard is
likewise corrupted by those zingers.

Raising the rotation default of --min-captured-fraction from 0.5 to 0.7 drops those
partiality-extrapolated fulls, lifting ISa back above the gate and cleaning the
intensity statistics, so the search recovers the true symmetry. On the F-cubic Benas
crystals: Benas_3 P4 -> F432 (CC1/2 78% -> 98%) and Benas_7 P1 -> P6122 (CC1/2 40% ->
99%). Benas_7's data supports hexagonal P6122, not cubic F432 - the cubic 3-fold/4-folds
fail the merge self-consistency test - matching XDS.

Full /data/rotation_test battery: every other crystal keeps its exact space group; the
only cost is a little multiplicity from the extra dropped edge-fulls on a few weak/
narrow-sweep crystals (worst completeness -7% on EP_cs_01-24, whose CC1/2 nonetheless
rises), while several crystals' CC1/2 improve.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

tools/rugnux_cli.cpp

@@ -87,7 +87,7 @@ void print_usage() {
     std::cout << "   --resolution-shells <num>       Number of resolution shells in the reported statistics table (default: 10)" << std::endl;
     std::cout << "   --min-partiality <num>          Minimum partiality to accept reflection (default: 0.02)" << std::endl;
     std::cout << "   --capture-uncertainty <num>     rot3d: systematic sigma ~num*(1-captured_fraction)*I on under-captured fulls (default: 1.0 for rot3d, 0 otherwise)" << std::endl;
-    std::cout << "   --min-captured-fraction <num>   rot3d: drop a combined full whose rocking curve was captured below this fraction (edge-of-sweep truncated fulls) (default: 0.5 for rotation, 0 otherwise; 0 = off)" << std::endl;
+    std::cout << "   --min-captured-fraction <num>   rot3d: drop a combined full whose rocking curve was captured below this fraction (edge-of-sweep truncated fulls) (default: 0.7 for rotation, 0 otherwise; 0 = off)" << std::endl;
     std::cout << "   --mosaicity <num>               Diagnostic: fix the scaling mosaicity (deg) instead of the per-image seed" << std::endl;
     std::cout << "   --reject-outliers <num>         Per-observation merge outlier rejection, N sigma from the per-reflection median (default: 6 for rot3d, XDS/DIALS-style; 0 = off)" << std::endl;
     std::cout << "   --reject-delta-cchalf <num>     Per-crystal CC1/2-delta rejection: drop images with deltaCChalf below mean - N*stddev (default: off; e.g. 2.5)" << std::endl;
@@ -931,7 +931,7 @@ int main(int argc, char **argv) {
         scaling_settings.RefineB(refine_bfactor);
         scaling_settings.MinPartiality(min_partiality);
         scaling_settings.MinCapturedFraction(min_captured_fraction_arg.value_or(
-            (experiment.GetGoniometer().has_value() && !force_still) ? 0.5 : 0.0));
+            (experiment.GetGoniometer().has_value() && !force_still) ? 0.7 : 0.0));
         scaling_settings.MinCCForImage(min_image_cc / 100.0);   // --min-image-cc is percent; the setting is a fraction
         if (intensity_format)
             scaling_settings.FileFormat(intensity_format.value());
@@ -1200,9 +1200,12 @@ int main(int argc, char **argv) {
     scaling_settings.RefineB(refine_bfactor);
     scaling_settings.MinPartiality(min_partiality);
     // Drop edge-of-sweep truncated fulls (rocking curve captured < this fraction) from the rot3d combine.
-    // Defaults ON (0.5) for rotation - removes the low-capture fulls that inflate low-res R-meas and
-    // slightly bias accuracy; off for non-rot3d (no combine). An explicit --min-captured-fraction wins.
-    scaling_settings.MinCapturedFraction(min_captured_fraction_arg.value_or(rotation_indexing ? 0.5 : 0.0));
+    // Defaults ON (0.7) for rotation - removes the low-capture fulls that inflate low-res R-meas and
+    // slightly bias accuracy; off for non-rot3d (no combine). 0.7 (rather than 0.5) also strips the
+    // partiality-extrapolated fulls that dominate the intensity second moment on weakly-diffracting
+    // crystals, so the de-novo space-group search is no longer starved by the error-model I/sigma floor
+    // (e.g. F-cubic Benas_3 -> F432, Benas_7 -> P6122 instead of P1). An explicit --min-captured-fraction wins.
+    scaling_settings.MinCapturedFraction(min_captured_fraction_arg.value_or(rotation_indexing ? 0.7 : 0.0));
     // Capture-aware systematic sigma defaults ON (1.0) for the rot3d combine - it down-weights the
     // over-extrapolated under-captured fulls and, with the mosaicity fix, lifts rotation ISa/anomalous
     // substantially. Off for non-rot3d (no combine). An explicit --capture-uncertainty always wins.