SG search: gate the systematic-absence test on intensity, not just I/sigma

The monoclinic 2_1 screw was missed on EP_cs_02-10 and EP_cs_01-17 (adopted P2
instead of P2_1). The 0k0-odd reflections are correctly measured as weak (~0.1-1%
of 0k0-even, matching XDS), but their merged sigmas are ~2x too small, so their
I/sigma clears the present_i_over_sigma cut and they count as screw-axis
violations - the search then falls back to the symmorphic group.

Add a resolution-normalised intensity E^2 = I / <I>(shell), computed from
equal-count resolution shells, and require a reflection to reach present_e_squared
(0.3) as well as present_i_over_sigma before it counts as violating a predicted
absence. This only tightens "present", so it cannot manufacture a screw whose
predicted-absent class carries real intensity (a symmorphic crystal's axial
reflections sit at E^2 ~ 1 and still register as violations).

On the 18-crystal rotation battery this recovers the screw on EP_cs_02-10 and
EP_cs_01-17 (-> P2_1) and, as a side effect, on MyoB (-> P2_1), pding4_001
(-> P4_122/P4_322) and pding4_003 (-> P2_2_2_1) - all confirmed by genuine absences
in the reference intensities (absent class at 0.02-0.76% of the allowed class),
which the old sigma-only test also missed. The other 13 crystals, indexing rate
and ISa are unchanged; the screw-free control (Ins_I -> I23/I2_13) is unaffected.

Add a regression test that reproduces the under-estimated-sigma screw and checks
the gate recovers it (and that disabling the gate reproduces the miss).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

tests/SearchSpaceGroupTest.cpp

@@ -146,4 +146,48 @@ TEST_CASE("SearchSpaceGroup detects synthetic space groups") {
             CHECK(std::find(accepted.begin(), accepted.end(), tc.expected_short_name) != accepted.end());
         }
     }
+}
+
+// Regression: a real screw axis whose systematically-absent reflections carry a genuinely weak
+// intensity but an UNDER-estimated sigma (so their I/sigma clears the "present" cut) must still be
+// found. Reproduces the monoclinic 2_1 miss on EP_cs_02-10 / EP_cs_01-17, where the merged sigmas on
+// the 0k0-odd reflections were ~2x too small and faked screw-axis violations. The E^2 intensity gate
+// (present_e_squared) is what keeps those reflections classified absent.
+TEST_CASE("SearchSpaceGroup finds a screw axis despite under-estimated sigmas on absent reflections") {
+    const gemmi::SpaceGroup& sg = gemmi::get_spacegroup_by_name("P 1 21 1");
+    auto merged = GenerateMergedReflectionsForSpaceGroup(sg, 18);
+
+    // Every systematically-absent (0k0, k odd) reflection: small-but-nonzero intensity (~2% of a
+    // normal reflection) with a far-too-small sigma, so I/sigma ~ 27 fakes a "present" reflection.
+    const gemmi::GroupOps gops = sg.operations();
+    int absent_count = 0;
+    for (auto& r : merged) {
+        const gemmi::Op::Miller hkl{{r.h, r.k, r.l}};
+        if (gops.is_systematically_absent(hkl)) {
+            r.I = 8.0f;
+            r.sigma = 0.3f;
+            ++absent_count;
+        }
+    }
+    REQUIRE(absent_count >= 8);   // enough predicted-absent reflections to be trusted
+
+    SearchSpaceGroupOptions opt;
+    opt.merge_friedel = true;
+
+    SECTION("intensity gate on (default): screw recovered") {
+        const auto result = SearchSpaceGroup(merged, opt);
+        INFO(SearchSpaceGroupResultToText(result));
+        REQUIRE(result.best_space_group.has_value());
+        CHECK(result.best_space_group->short_name() == "P21");
+    }
+
+    SECTION("intensity gate off (I/sigma only): the screw is missed") {
+        // Documents the failure the gate fixes: with I/sigma alone the too-small sigmas fake
+        // violations and the search falls back to the symmorphic group.
+        opt.present_e_squared = 0.0;
+        const auto result = SearchSpaceGroup(merged, opt);
+        INFO(SearchSpaceGroupResultToText(result));
+        REQUIRE(result.best_space_group.has_value());
+        CHECK(result.best_space_group->short_name() == "P2");
+    }
 }