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PreprintCC BYbioRxiv

Decision benchmarking of cryo-EM re-refinement

  • X. Yi1
  • X. Zhang
  • L. Zhang
  • J. Yi1
  1. 1INTOSYN AI Labs
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Abstract

Map fit is widely used in cryo-EM re-refinement. We benchmarked selection against retaining the deposited model (no operation), using packed-side-chain agreement with higher-resolution references. In a prespecified 3.0-3.6 [A] cohort (167 entries, 131 sequence groups), highest-correlation selection increased {chi}1 disagreement by 2.4{degrees} (95% interval 2.1-2.7{degrees}), with positive loss in 91% of groups. Group-weighted fractions with >20{degrees} increases and decreases were 7.2% and 3.7%; the fraction exceeding 1 [A] local side-chain RMSD rose by 2.4 percentage points. Selection by a half map withheld from re-refinement increased disagreement (2.29{degrees}; 1.70-2.97{degrees}; 99 entries). In 53 prespecified within-study low/high-resolution pairs, loss was 3.43{degrees} (2.85-4.02{degrees}), positive in 50 pairs; half-map loss was 2.35{degrees} (1.60-3.21{degrees}; 44 pairs). Primum provides fixed cohorts, residue sets and scoring tools to benchmark refiners and selection rules against no operation.

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Cite

BibTeXRIS
BibTeX
@misc{yi2026decision,
  title = {{Decision benchmarking of cryo-EM re-refinement}},
  author = {X. Yi and X. Zhang and L. Zhang and J. Yi},
  howpublished = {bioRxiv},
  year = {2026},
  month = oct,
  doi = {10.64898/2026.10.31.763284},
  url = {https://www.biorxiv.org/content/10.64898/2026.10.31.763284v1},
  note = {CC BY},
}
RIS
TY  - UNPB
TI  - Decision benchmarking of cryo-EM re-refinement
AU  - X. Yi
AU  - X. Zhang
AU  - L. Zhang
AU  - J. Yi
PY  - 2026
DA  - 2026/10/31
PB  - bioRxiv
DO  - 10.64898/2026.10.31.763284
UR  - https://www.biorxiv.org/content/10.64898/2026.10.31.763284v1
AB  - Map fit is widely used in cryo-EM re-refinement. We benchmarked selection against retaining the deposited model (no operation), using packed-side-chain agreement with higher-resolution references. In a prespecified 3.0-3.6 [A] cohort (167 entries, 131 sequence groups), highest-correlation selection increased {chi}1 disagreement by 2.4{degrees} (95% interval 2.1-2.7{degrees}), with positive loss in 91% of groups. Group-weighted fractions with >20{degrees} increases and decreases were 7.2% and 3.7%; the fraction exceeding 1 [A] local side-chain RMSD rose by 2.4 percentage points. Selection by a half map withheld from re-refinement increased disagreement (2.29{degrees}; 1.70-2.97{degrees}; 99 entries). In 53 prespecified within-study low/high-resolution pairs, loss was 3.43{degrees} (2.85-4.02{degrees}), positive in 50 pairs; half-map loss was 2.35{degrees} (1.60-3.21{degrees}; 44 pairs). Primum provides fixed cohorts, residue sets and scoring tools to benchmark refiners and selection rules against no operation.
ER  -