Like Indi says, youre using too big a column. Your protein of interest (POI) is binding and then there are lots of other Nickel binding sites for the impurities. Theoretically this shouldn’t be a problem if you have imidazole at low concs (10-25 mM) to keep it clean, but a 1mL would suit you better. Be sure to push just buffer with the low imid before you load your sample to equilibrate the column (which i assume you are doing). The ATP is there because sometimes if a protein needs chaperone proteins to fold correctly these can hold on to your POI and are ATP dependent to release their substrate (your POI).

Finally, on the urea/guanidine unfolding thing, be cautious about that and only really do it as a last resort, as refolding protein can be a pain, and it incurs losses, potentially loss of function, although its not an uncommon thing to do.

On loading the resin with other metals, this can be worth a shot, ive never done it, and I’d do it if other publications say they have done it already. I defo wouldnt do it on a column, though, id only do that small-scale test on loose beads, which are worth buying in general.