Is a potential outcome of discussion surrounding this question that you decide not to apply at all? Because if you're still going to apply regardless, then I don't really see the point of asking. You failed step 3, a test that examines some of the more practical aspects of basic medicine. It's not a good look. It will likely have an effect on your application. That said, I'm sure there are people out there who have failed step 3 and gone on to obtain residency positions. Apply and see what happens.
By the way, when used to discuss issues of change, affect is a verb, and effect is a noun. The former should have been used in your question.
And yes, effect can be a verb too, as a synonym for 'cause' or 'bring about'.