I'm no statistician, but here's what I've got:
well if it was 1 in 100,000 then you'd only have 10 in a million. That alone would elevate the men to an elite status. Far too rare and valuable to do barbaric tests, and too few to service every woman in the population. That doesn't work for this game.
In the average population, you can assume about 25% are under the age of 15 - though this should be lower since the Chimera virus reduced births for a number of years. On average, there's about as many men as there are women.
So, in a population of 1,000,000 you'd have about 250,000 people under 15, give or take, leaving an adult population of around 750,000. Split in half, that 375,000 men.
1% Fertility = 1 man for every 10 women.
.1% = 1 man for every 100,000 women
In a population of 1 million, with roughly 370,000 males there would be 375 fertile males at .1%. At .5% you'd be looking at 1,850.
I would think .5% is your number. 1,850 isn't rare and valuable enough to avoid testing on the men, or keeping those who are "working class" as breeding stock - though I would suggest quarters that are slightly better than prison cells, they are, after all, important to the future of humanity and you don't want unnecessary deaths. At 1,850 that leaves about 202 females per male, which again, I think probably works for the game.