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. 2023 Jun 3;14:3217. doi: 10.1038/s41467-023-39031-1

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 6 — a, c, e Box-whisker plots of CC_box (a), CC_mask (c), and CC_peaks (e) for the average maps of half-maps, the maps processed by DeepEMhancer, LocScale, LocSpiral, phenix.auto_sharpen, phenix.resolve_cryo_em (density modification) and EMReady (n = 25 individual test cases). The center line is the median, the cross is the mean, lower and upper hinges represent the first and third quartile, the whiskers stretch to 1.5 times the interquartile range from the corresponding hinge, and the outliers are plotted as diamonds. Dashed lines stand for the average CC values of deposited half-maps. b, d, f Comparison of CC_box (b), CC_mask (d), and CC_peaks (f) between the deposited map and EMReady-processed map on each test case. Source data are provided as a Source Data file.