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. 2021 Feb 4;18(2):156–164. doi: 10.1038/s41592-020-01051-w

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© The Author(s) 2021

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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Extended Data Fig. 2 — a, Mis-modeled peptide (identified by red ball at carbonyl oxgen position) is flagged by two successive CaBLAM outliers (magenta dihedrals), a bad clash (hot-pink spikes), and a bond-angle outlier (not shown), but no Ramachandran outlier. b, Correctly modeled peptide, involving a near-180° flip of the central peptide to achieve regular α-helical conformation. Ser 38 of T1/APOF model 60_1 is shown in (a); model 35_1 shown in (b). This example illustrates the most easily correctable situations: (1) for a CaBLAM outlier inside helix or β-sheet, regularize the secondary structure; (2) for two successive CaBLAM outliers, try flipping the central peptide. Molecular graphics were generated using KiNG. Note that sidechains are truncated by graphics clipping.