The tom cat smell definitely goes - one of my rescue cats was "done" just before I got him & I was horrified that his pee smelt "Tom". It took 1 or 2 weeks to go, but now there's no smell (thankfully)! I was told the same as someone else mentioned - it takes about 6 weeks to get rid of all the hormones in their body - he should have calmed down a lot before that though
