Refinement: the likelihood's D and beta searches by Newton's method; D on the working set from the last fit's

Deterministic, rounding changes. The per-bin ML fit took 4 rounds x (40 + 40) golden-section steps on the
free set and a 50-step golden section for D on the working set - each step a Bessel I0/I1 per row, ~4.6M per
Refit at 92k reflections, 27-37% of a trial's wall on the high-resolution sets. Each one-dimensional search is
now a safeguarded Newton iteration on the analytic first and second derivatives (bracketed on the sign of the
derivative, bisection where a step leaves the bracket or the curvature is not positive), within the same
brackets; the free-set alternation keeps its 4 rounds from the moments, so beta is the one it was (a converged
joint fit was tried: the 4 rounds are not converged in the low-resolution bins, and converging them moves
6iu9's FOM by -0.003, so it was not kept). D on the working set starts from the bin's D of the context's
previous Refit (XrayRowModel::bin_d), restored with a trial's fit and cleared at a trial's first Refit, so a
trial depends on nothing its slot ran before (side by side = one at a time, md5).

14 parity sets, score only: R-work/R-free identical to 4 digits, mean |FOM - REFMAC| 0.01186 -> 0.01186,
D within 1e-5 and var within 1e-4 (relative) per reflection. refit.ml (TIMING sum, -N 8): 5reo 1.47 -> 0.11 s,
5f6m 3.88 -> 0.26, 9yl4 1.37 -> 0.11, 5f6m MD start 4.97 -> 0.46. Wall: 5reo 2.03 -> 1.75, 5f6m 3.45 -> 2.60,
9yl4 7.99 -> 7.36, 7d98 4.04 -> 3.78, 5f6m MD start 6.10 -> 4.82 s. 5f6m MD starts 01-04 median R-free
0.1693 -> 0.1692.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
(cherry picked from commit a91511945e0ccd7145a93877c0c231e87f86fb44)

image_analysis/structure_refinement/Refinement.cpp

@@ -1048,8 +1048,12 @@ TrialOutcome RunTrial(TrialSlot slot, const std::vector<int> &refinable, const s
         PlaceRiders(ctx, topo);
         if (cycle == 0 && fit != nullptr)
             ctx.Restore(*fit);
-        else
+        else {
+            // a trial's likelihood fit starts from nothing the slot's previous trial left
+            if (cycle == 0)
+                ctx.rows.bin_d.clear();
             ctx.Refit();
+        }
         if (adp_w > 0)
             ctx.MoveOverallB();
         {