The organization has not been established as a private foundation with the IRS. Only private foundations can file Form 990-PF.
The organization must establish itself as a private foundation to file a 990-PF return. Two possibilities would have led to the rejection of the form. The organization might have filed Form 1023 seeking exemption status, and wouldn't have heard back from the IRS. Or, the organization wouldn't have filed Form 1023 at all.
If you have filed your Form 1023 application with IRS, you need to wait until the IRS grants exempt status to the organization before filing Form 990-PF. Or, you can paper file the form by checking the box "exemption application is pending", and mailing it to the address as found here. If the IRS has rejected the return despite the organization having the exempt status, then we suggest you contact the e-help Desk Toll-Free Number 1-866-255-0654.