I had the same issue (MacOS Catalina 10.15.7 and the same phenix version).
The fix was:
In PHENIX Home screen, click on Preferences, then click on the graphics
tab, in the Coot path box point it to the coot.app as in
(/Applications/ccp4-8.0/coot.app) instead of
(/Applications/ccp4-8.0/bin/coot)

I must point that someone else in the lab has a similar issue using MacOS
Mojave 10.14.6 and the fix above works for the restrain problem but the
connection to Phenix is lost

Best
Ricardo

On Sun, Aug 7, 2022 at 2:09 AM Cryo EM <cryoemfa...@gmail.com> wrote:

> Hi everyone,
>
> I am using Coot 0.9.8.3 EL (ccp4) on my iMac M1 with MacOS Monterey. The
> phenix version I am using is 1.20.1-4487.
>
> At the end of validation run or real space refinement for my cryo-EM map,
> I want to fix the problems in the model interactively by the "open in coot"
> button displayed in phenix. As soon as I click on the problems list in
> phenix, coot takes me to that atom but I am not able to do any local real
> space refinement in coot since it complains about the missing restrains for
> even standard amino acids and nucleotides (screenshot attached).
>
> Please note that coot alone (when not connected to phenix) works for me
> flawlessly. I guess it has something to do with missing monomer library
> path in coot when connected to phenix but I am unable to fix this. Can
> someone please redirect me to the solution?
>
> Regards and thanks!
>
>
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-- 
Ricardo A. P. de P√°dua
HHMI Research Specialist
Kern Lab
Brandeis University, Waltham, MA

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