All([d == N for d in vol.shape])

3D Refinement
5

Thanks @olibclarke. Used your comments from this to fix it: Errors in using an imported volume. Used an ab-initio volume and performed the molmap #1 12 onGrid #2. (#1- PDB model for density map generation, #2- ab initio volume) The density map generated this way doesn’t lead to the error.

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