After you file

For 2024, you need to report an excess contribution of $1000 to a Roth IRA and pay the 6% penalty.

 

For 2025, you can remove $1000 of your current year IRA contributions, tell the custodian to process a removal of excess contributions.  They will also send you the net attributed income, which will be taxable on your 2025 return (they will send a 1099-R).  Then the 2024 excess will get used up in the 2025 limit. 

 

Or you can withdraw $1000 from the Roth IRA as a regular withdrawal.  It won't be taxable as long as it represents a return of contributions (you have not already withdrawn all your contributions).   By withdrawing that $1000, the excess will be cleared off the form 5329 for 2025 when you file your return.