What is the ruling on taking possession of an apartment purchased by one's father with money borrowed through usury, and is it possible to atone for that while keeping the apartment?

It is permissible for you to accept the apartment gifted to you by your father, because most of the money paid for it is from the father's own funds, and the percentage of usury in it is small. This falls under the ruling of mixed money in which the proportion of the unlawful is minimal. It is advisable to repay the usurious debt and repent to Allah from usurious transactions.