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RESULT-CHANGING: Refinement: fewer weight and displacement trials, each family tried further only where its first members ask for it

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Counted on the 368 refinements of the rc181 full battery (fee8ffa) which trial of each stage was kept,
and replayed each stage's decision without the trials left out here:

- Ladder: B refined first at the middle rung only, at the other two where it comes within two ties of
  B held there. B held was kept by 281 of 364 ladders; the rule changed the rung kept on 4 (within
  0.006 R-free at the ladder) and leaves out 412 of 1236 B-refined ladder trials.
- Ladder NCS rungs: at the rung the trials without NCS chose and the next looser one only. On 198
  ladders with copies NCS was never kept at any other rung: 232 of 594 NCS trials left out, no pick
  changed.
- Trajectory: the X-ray weight halved only in the first step (from the ladder's coarse rung). No later
  step kept the halved weight (0 of 91).
- Displacements: the 2-segment TLS cut dropped (6 choices changed, none by more than 0.001); the model's
  own TLS groups tried only where one body per chain or the finest cut lowers R-free from where the
  weights ended, the cuts between those only where also the finest fits the free set better than one
  body per chain (as before), and the U at its balanced weight only where the U at a quarter of it
  lowers R-free. Replayed: 7 of 364 choices changed (max +0.0026, mean +0.00001), 2315 -> 1527
  displacement trials.

The late trials still run ahead where the slots take them all at once (small models: no extra wave);
results do not depend on the slots or cards.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01HVeDQqN9qRD57vnShzTC37
This commit is contained in:
leonarski_fandClaude Opus 5.5 committed 2026-10-28 08:42:44 +01:00
1 parent 4b9ef226ef
commit 73e86d5e7d
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image_analysis/structure_refinement/Refinement.cpp
+80 -35
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@@ -1871,8 +1871,9 @@ AdpHypothesis TlsHypothesis(const Context &ctx, std::string name, std::vector<st
// The displacement models the refinement chooses among once its weights are chosen, from the model as it stands: the
// TLS bodies of the model's own groups (`input`, where it has them); one body per chain of at least MIN_TLS_ATOMS
// refinable atoms, and the chains cut into 2, 4, 8 and 16 TLSMD segments of at least MIN_TLS_RESIDUES residues
// (TlsSegments) - each cut a hypothesis where it differs from the one before; and a U per atom.
// refinable atoms, and the chains cut into 4, 8 and 16 TLSMD segments of at least MIN_TLS_RESIDUES residues
// (TlsSegments) - each cut a hypothesis where it differs from the one before; and a U per atom. (Cut into 2, the
// chains changed the choice on 6 of 364 refinements of the battery, none by more than 0.001 in R-free.)
std::vector<AdpHypothesis> AdpHypotheses(const Context &ctx, const RefinementTopology &topo,
const std::vector<TlsBody> &input) {
constexpr size_t MIN_TLS_ATOMS = 50;
@@ -1912,7 +1913,7 @@ std::vector<AdpHypothesis> AdpHypotheses(const Context &ctx, const RefinementTop
const std::vector<gemmi::Position> pos = ctx.Positions();
const std::vector<double> b = ctx.B();
size_t last = 0;
for (int k : {1, 2, 4, 8, 16}) {
for (int k : {1, 4, 8, 16}) {
std::vector<std::vector<int>> groups;
for (const std::vector<std::vector<int>> &residues : chains) {
std::vector<int> starts = TlsSegments(residues, pos, b, k, MIN_TLS_RESIDUES);
@@ -2384,6 +2385,7 @@ RefinementResult RefineOnce(const gemmi::Structure &placed, const std::vector<Me
// Trials whose need is decided by others are run with them where the slots take them all at once, and left
// out where it is decided they were not needed - with their evaluations, which do not count: the outcome and
// the count are the same whatever the slots.
auto ahead = [&](size_t trials) { return trial_slots.size() >= trials; };
int ahead_evaluations = 0;
auto drop_ahead = [&](TrialOutcome &o) {
ahead_evaluations += o.evaluations;
@@ -2417,8 +2419,12 @@ RefinementResult RefineOnce(const gemmi::Structure &placed, const std::vector<Me
// 1. The weights from the placed model: the ladder's rungs, tighter geometry first, each with the B factors
// held and refined at their own balanced weight; where there are copies, each rung without NCS restraints
// and then with them - those with them at the B factors' weight the rungs without chose, which NCS does
// not change (on 39 refinements of 21 structures with copies it never did; the X-ray weight it does) - run
// ahead at every B weight where the slots take them.
// not change (on 39 refinements of 21 structures with copies it never did; the X-ray weight it does), and
// at the rung they chose and the next looser one (on 198 refinements of the battery with copies, NCS was
// never kept at any other).
// The B factors are refined first at the middle rung only, and at the others where that comes within two
// ties of holding them there: on 364 refinements of the battery B held was kept by 281, and the rule
// changed the rung kept on 4 (all within 0.006 in R-free).
std::vector<TrialWeights> ladder;
for (double rung : settings.weight_ladder)
for (double adp : settings.adp_ladder) {
@@ -2439,20 +2445,38 @@ RefinementResult RefineOnce(const gemmi::Structure &placed, const std::vector<Me
if (these(ladder[i]))
outcomes[i] = std::move(ran[m++]);
};
const bool ncs_ahead = ncs_p != nullptr && trial_slots.size() >= ladder.size();
run_ladder([&](const TrialWeights &l) { return l.ncs == 0 || ncs_ahead; });
const double mid = w0 * settings.weight_ladder[settings.weight_ladder.size() / 2];
auto first = [&](const TrialWeights &l) { return l.ncs == 0 && (l.adp == 0 || l.w == mid); };
const bool all_ahead = ahead(ladder.size());
run_ladder([&](const TrialWeights &l) { return first(l) || all_ahead; });
// B refined against B held at the middle rung (where both ran)
const TrialOutcome *held = nullptr, *refined = nullptr;
for (size_t i = 0; i < ladder.size(); i++)
if (ladder[i].w == mid && ladder[i].ncs == 0)
(ladder[i].adp == 0 ? held : refined) = &outcomes[i];
const bool refine_b = held == nullptr || refined == nullptr ||
(refined->ran && refined->trial.within_bounds &&
(!held->trial.within_bounds || refined->trial.r_free < held->trial.r_free + 2 * R_FREE_TIE));
auto rest_b = [&](const TrialWeights &l) { return l.ncs == 0 && !first(l); };
if (refine_b && !all_ahead)
run_ladder(rest_b);
// the best of those without NCS restraints, those with them set aside
std::vector<TrialOutcome> with_ncs(ladder.size());
for (size_t i = 0; i < ladder.size(); i++)
if (ladder[i].ncs > 0)
if (ladder[i].ncs > 0 || (!refine_b && rest_b(ladder[i])))
std::swap(with_ncs[i], outcomes[i]);
if (const int b = best_of(outcomes); ncs_p != nullptr && b >= 0) {
const double adp = outcomes[b].trial.adp_weight;
const double adp = outcomes[b].trial.adp_weight, w = outcomes[b].trial.weight;
double looser = w;
for (double rung : settings.weight_ladder)
if (w0 * rung > w && (looser == w || w0 * rung < looser))
looser = w0 * rung;
auto these = [&](const TrialWeights &l) { return l.ncs > 0 && l.adp == adp && (l.w == w || l.w == looser); };
for (size_t i = 0; i < ladder.size(); i++)
if (ladder[i].ncs > 0 && ladder[i].adp == adp)
if (these(ladder[i]))
std::swap(with_ncs[i], outcomes[i]);
if (!ncs_ahead)
run_ladder([&](const TrialWeights &l) { return l.ncs > 0 && l.adp == adp; });
if (!all_ahead)
run_ladder(these);
}
for (TrialOutcome &o : with_ncs)
drop_ahead(o);
@@ -2462,10 +2486,11 @@ RefinementResult RefineOnce(const gemmi::Structure &placed, const std::vector<Me
state = std::move(outcomes[k]);
// 2. The trajectory: steps of a few macro-cycles from where the last one ended, each trying the weights as they
// are and, in turn, the positions' X-ray weight halved and doubled (halved: the geometry loosens as the
// model improves at one weight, until it leaves the bounds) and the B factors' divided and multiplied by
// four; where there are copies, also the NCS restraints changed: switched on where they are off, and in
// turn tightened and loosened (to off beyond NCS_SIGMA_MAX) where they are on.
// are and, in turn, the positions' X-ray weight halved and doubled (halved only in the first step, from the
// ladder's coarse rung: on 364 refinements of the battery no later step kept it, of 91 that tried it) and
// the B factors' divided and multiplied by four; where there are copies, also the NCS restraints changed:
// switched on where they are off, and in turn tightened and loosened (to off beyond NCS_SIGMA_MAX) where
// they are on.
// A step is taken while it lowers R-free or R-work by more than the tie and its R-free stays within the tie
// of the best so far; the trajectory ends at its best step (on a deposited model, whose free set it was
// fitted to, R-work falls while R-free rises, and it ends where it began).
@@ -2484,7 +2509,8 @@ RefinementResult RefineOnce(const gemmi::Structure &placed, const std::vector<Me
trials.push_back({w, adp / 4, ncs_s});
trials.push_back({w, 4 * adp, ncs_s});
} else {
trials.push_back({w / 2, adp, ncs_s});
if (step == 0)
trials.push_back({w / 2, adp, ncs_s});
if (2 * w <= w_max)
trials.push_back({2 * w, adp, ncs_s});
}
@@ -2810,10 +2836,11 @@ RefinementResult RefineOnce(const gemmi::Structure &placed, const std::vector<Me
// R-free (beyond the tie) and the -ln L of the free reflections are lower: the free set is the test of the
// parameters it adds.
// Following Merritt (2012) Acta Cryst. D68, 468-477 (the displacement model the data support, decided by test)
// The trials that would not change the choice are left out: the TLS cuts between one body per chain and the
// finest are tried only where the finest fits the free set better than one body per chain (run ahead where
// the slots take them), and the U at four times its balanced weight not at all (on 49 refinements of 33
// structures, no choice taken changed).
// The trials that would not change the choice are left out: the model's own TLS groups are tried only where
// one body per chain or the finest cut lowers R-free, the cuts between those only where also the finest
// fits the free set better, the U at its balanced weight only where the U at a quarter of it lowers R-free
// (run ahead where the slots take them), and the U at four times its balanced weight not at all (on 49
// refinements of 33 structures, no choice taken changed).
if (settings.adp_hypotheses && state.ran && !ctx.Cancelled()) {
const RefinementStage adp_stage("adp_hypotheses");
ctx.SetPositions(state.pos);
@@ -2842,19 +2869,22 @@ RefinementResult RefineOnce(const gemmi::Structure &placed, const std::vector<Me
ctx.SetAniso(keep);
}
const double ncs_s = state.trial.ncs_sigma;
// every trial in order of trust; those between one TLS body per chain and the finest cut run after the
// others where those ask for them
// every trial in order of trust; the model's own TLS groups and the cuts between one TLS body per chain
// and the finest, and the U at its balanced weight, run after the others where those ask for them
std::vector<TrialWeights> trials;
std::vector<const AdpHypothesis *> which;
int coarsest = -1, finest = -1;
int own = -1, coarsest = -1, finest = -1, u_quarter = -1;
for (const AdpHypothesis &h : hyps) {
if (h.kind == AdpHypothesis::Kind::Anisotropic) {
u_quarter = static_cast<int>(trials.size());
for (double f : {0.25, 1.0}) {
trials.push_back({w, u_w0 * f, ncs_s});
which.push_back(&h);
}
} else {
if (h.segments > 0) {
if (h.segments == 0)
own = static_cast<int>(trials.size());
else {
if (coarsest < 0)
coarsest = static_cast<int>(trials.size());
finest = static_cast<int>(trials.size());
@@ -2866,6 +2896,10 @@ RefinementResult RefineOnce(const gemmi::Structure &placed, const std::vector<Me
std::vector<char> later(trials.size(), 0);
for (int k = coarsest + 1; k < finest; k++)
later[k] = 1;
if (own >= 0 && coarsest >= 0)
later[own] = 1;
if (u_quarter >= 0)
later[u_quarter + 1] = 1;
outcomes.assign(trials.size(), TrialOutcome());
auto run = [&](const std::vector<char> &these) {
std::vector<TrialWeights> t;
@@ -2875,27 +2909,38 @@ RefinementResult RefineOnce(const gemmi::Structure &placed, const std::vector<Me
t.push_back(trials[k]);
h.push_back(which[k]);
}
if (t.empty())
return;
std::vector<TrialOutcome> ran = RunTrials(trial_slots, t, refinable, state.pos, state.b, state.aniso,
&state.fit, settings.macro_cycles + 1, settings, ncs_p, h);
for (size_t k = 0, m = 0; k < trials.size(); k++)
if (these[k])
outcomes[k] = std::move(ran[m++]);
};
const bool later_ahead = trial_slots.size() >= trials.size();
const bool later_ahead = ahead(trials.size());
std::vector<char> now(trials.size());
for (size_t k = 0; k < trials.size(); k++)
now[k] = !later[k] || later_ahead;
run(now);
auto fits_better = [&](int a, int b) {
return outcomes[a].ran && outcomes[b].ran && outcomes[a].trial.nll_free < outcomes[b].trial.nll_free;
// the model's own groups where one body per chain or the finest cut lowers R-free from where the weights
// ended, the cuts between where also the finest fits the free set better than one body per chain, the U
// at its balanced weight where the U at a quarter of it lowers R-free (on 364 refinements of the battery
// that changed the choice on 7, none by more than 0.003 in R-free, and left out 6 in 10 of these trials)
auto lowers = [&](int k) {
return k >= 0 && outcomes[k].ran && outcomes[k].trial.within_bounds &&
outcomes[k].trial.r_free < state.trial.r_free;
};
if (finest > coarsest + 1 && fits_better(finest, coarsest)) {
if (!later_ahead)
run(later);
} else
for (size_t k = 0; k < trials.size(); k++)
if (later[k])
drop_ahead(outcomes[k]);
const bool tls = lowers(coarsest) || lowers(finest), u_full = lowers(u_quarter);
const bool cuts = tls && finest > coarsest && outcomes[finest].ran && outcomes[coarsest].ran &&
outcomes[finest].trial.nll_free < outcomes[coarsest].trial.nll_free;
std::vector<char> needed(trials.size(), 0);
for (int k = 0; k < static_cast<int>(trials.size()); k++)
needed[k] = later[k] && (k == u_quarter + 1 ? u_full : k == own ? tls : cuts);
if (!later_ahead)
run(needed);
for (size_t k = 0; k < trials.size(); k++)
if (later[k] && !needed[k])
drop_ahead(outcomes[k]);
int best = -1; // where the weights ended
auto trial = [&](int k) -> const RefinementWeightTrial & { return k < 0 ? state.trial : outcomes[k].trial; };
for (size_t k = 0; k < outcomes.size(); k++) {