You should delete the 1099-R and re-enter it. When asked if 'any or all of this distribution if RMD' indicate Yes. For the RMD amount, if you don't know the amount, you can enter an amount equal to or less than the distribution, depending on the Code(s) in Box 7. You may have Form 5498 reporting the amount.
This will remove the RMD Excess Accumulation Worksheet from your return.
Neither the IRS or TurboTax know what your RMD should be. The IRS expects you and/or your plan administrator to handle this properly. You can take your RMD from one or from several accounts. Here's more info on IRS Requirements for RMD's.
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