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The vast majority of complex structures are currently accomplished using the Independent Atom Model (IAM), in which atoms are assumed to be spherical, and no chemical bonds exist. Emerging quantum crystallography methods process the same experimental data in better approximation, allowing for deformation of electron density resulting from different types of chemical bonds. This presentation provides several examples of macrocyclic complexes of Fe, Co, Ni, and Cu refined using Tonto and NoSpherA2 software packages. The most visible improvement over existing IAM procedures is reasonable positions of hydrogen atoms; the precision of bond distances is also significantly improved.