From e021c8dfbc034646de4d97a608855e799d974de0 Mon Sep 17 00:00:00 2001 From: Filip Leonarski Date: Tue, 27 Oct 2026 14:12:18 +0100 Subject: [PATCH] battery: the refine arm gets three protein sets and a ribosome 193L (tetragonal lysozyme 1.33 A, Na+ and Cl-), 1EXR (Ca2+-calmodulin 1.0 A, four EF-hand Ca2+), 1K4C (KcsA in high K+, 2.0 A, the selectivity-filter K+ sites) and 4YBB (E. coli 70S ribosome 2.1 A, tag "large", to show that a ribosome refines at all). All X-ray with deposited structure factors. 4YBB on an RTX 5080 (16 GB): completes on the GPU, 489,290 atoms with riding hydrogens, 3.06 M reflections; wall 2:09, peak GPU memory 7.4 GB, peak host RSS 6.9 GB; R-free 0.2876 as given, 0.2782 after placement, 0.2808 final (deposited 0.2338). Co-Authored-By: Claude Opus 5.5 Claude-Session: https://claude.ai/code/session_01HVeDQqN9qRD57vnShzTC37 --- tools/battery/README.md | 2 ++ tools/battery/refine.json | 10 +++++++--- 2 files changed, 9 insertions(+), 3 deletions(-) diff --git a/tools/battery/README.md b/tools/battery/README.md index b000f8c5e..ae62c0ddf 100644 --- a/tools/battery/README.md +++ b/tools/battery/README.md @@ -540,6 +540,8 @@ scored. Run it on its own (`--arm refine`) or beside the others (`--arm open,ref A row is an id and why the entry is there: `{"id": "1hr2", "tags": [...], "why": "..."}`. Public depositions only; the PDB ID may be named. To add one, add the row - nothing else is needed. +The set tagged `large` (4ybb, a 70S ribosome of ~490,000 atoms with its riding hydrogens) is there to show that +a ribosome refines at all: about two minutes and 7 GB of GPU memory on a 16 GB card, 7 GB of host memory. ### The REFMAC model check (open arm, opt-in) diff --git a/tools/battery/refine.json b/tools/battery/refine.json index d0fa58cd6..82b114216 100644 --- a/tools/battery/refine.json +++ b/tools/battery/refine.json @@ -1,4 +1,8 @@ {"arm": "refine", "sets": [ - {"id": "1hr2", "tags": ["rna", "mg"], "why": "Tetrahymena group I intron P4-P6 domain (J5/5a hinge mutant), 2.25 A, P212121, two molecules, 42 Mg2+ and 265 waters in the deposition (buffer MgCl2, Na cacodylate, NaCl, spermine); its Mg2+ sites are re-examined in the Cat_Wiz paper (Naleem et al. 2026, Nucleic Acids Res. 54, gkag120, Table 3) and its stacked-purine N7/O6 site in Leonarski et al. 2017 (Nucleic Acids Res. 45, 987-1004)"}, - {"id": "2r8s", "tags": ["rna", "protein", "mg"], "why": "the same P4-P6 domain bound to a synthetic Fab, 1.95 A, ammonium acetate and MgCl2 in the drop; Leonarski et al. 2017 (Nucleic Acids Res. 45, 987-1004) note that a water replaces the Mg2+ of 1HR2's stacked-purine N7/O6 site here"} -]} + {"id": "1hr2", "tags": ["rna", "mg"], "why": "Tetrahymena group I intron P4-P6 domain (J5/5a hinge mutant), 2.25 A, P212121, two molecules, 42 Mg2+ and 265 waters in the deposition (buffer MgCl2, Na cacodylate, NaCl, spermine); its Mg2+ sites are re-examined in the Cat_Wiz paper (Naleem et al. 2026, Nucleic Acids Res. 54, gkag120, Table 3) and its stacked-purine N7/O6 site in Leonarski et al. 2017 (Nucleic Acids Res. 45, 987-1004)"}, + {"id": "2r8s", "tags": ["rna", "protein", "mg"], "why": "the same P4-P6 domain bound to a synthetic Fab, 1.95 A, ammonium acetate and MgCl2 in the drop; Leonarski et al. 2017 (Nucleic Acids Res. 45, 987-1004) note that a water replaces the Mg2+ of 1HR2's stacked-purine N7/O6 site here"}, + {"id": "193l", "tags": ["protein", "na", "cl"], "why": "tetragonal hen egg-white lysozyme, 1.33 A, P43212, crystallised from NaCl: the classic Na+ site (loop 60-73) and Cl- sites of lysozyme; a standard test protein"}, + {"id": "1exr", "tags": ["protein", "ca"], "why": "calmodulin with four Ca2+ in its EF hands, 1.0 A (Wilson & Brunger 2000, J. Mol. Biol. 301, 1237-1256): Ca2+ sites of carboxylate-rich, well-determined pentagonal-bipyramidal geometry"}, + {"id": "1k4c", "tags": ["protein", "k"], "why": "the KcsA potassium channel with a Fab, 2.0 A, in high K+ (Zhou et al. 2001, Nature 414, 43-48): the K+ sites of the selectivity filter, eight carbonyl O each"}, + {"id": "4ybb", "tags": ["rna", "protein", "mg", "large"], "why": "the E. coli 70S ribosome, 2.1 A, two ribosomes in the asymmetric unit, ~295,000 atoms with Mg2+ and Zn2+ (Noeske et al. 2015, Nat. Struct. Mol. Biol. 22, 336-341): whether a ribosome refines at all"} +]} \ No newline at end of file