Quantitative theoretical studies of long-range electron transfer are still rare, and reliable computational methods to analyze these reactions are still being developed. We re-examined electron transfer reactions in ruthenium-modified cytochrome b562 derivatives focusing on accurate calculation of statistical average of electron transfer rates that are dominated by a small fraction of accessible protein conformations. We performed a series of ab initio calculations of donor/acceptor interactions over protein fragments sampled from long molecular dynamic trajectories and compared computed electron transfer rates to available experimental data. Our approach takes into account cofactor electronic structure and effects of solvation on the donor-acceptor interactions. It allows predicting absolute values of electron transfer rates in contrast to other computational methodologies that give only qualitative results. Our calculations reproduced with a good accuracy experimental electron transfer rates. We also found that electron transfer in some of the cytochrome b562 derivatives is dominated by "shortcut" conformations, where donor/acceptor interactions are mediated by nonbonded interactions of Ru ligands with protein surface groups. Several derivatives adopt long-lived conformations with the Ru complex interacting with negatively charged protein residues that are characterized by shorter Ru-Fe distances and higher ET rates. We argue that quantitative theoretical analysis is essential for detailed understanding of protein electron transfer and mechanisms of biological redox reactions.