The IRA custodian should do the calculation for you. You must explicitly request a "return of contribution," not a regular distribution, of the amount of the excess contribution. The custodian must calculate the gain or loss attributable to the amount of contribution being returned and distribute the adjusted amount.
If you want to check the custodian's calculations, see CFR 1.408-11 for the details of the calculation:
https://www.law.cornell.edu/cfr/text/26/1.408-11
