Hi Luca,
When you select a base pair or stacking pair in Selection Editor, find checkbox "Enabled" on the left side. Uncheck it. Note that you can select all base pairs and uncheck it once. Do the same for stacking pairs. This will disable each annotation.
Another way:
Refinement settings tab -> All parameters -> Search parameters, enter "nucleic_acid". Locate 3 "Enabled" checkboxes and uncheck them. This will turn off nucleic acids SS restraints even if they are present in .eff file (no need to delete/disable them).
For completeness, command-line argument to do this is "nucleic_acid.enabled=False". If it is True (default) and there is no nucleic acid SS annotations (you deleted all of them), Phenix will try to find them before refinement. This is what you observed.
To make sure you did not have nucleic acid SS restraints in refinement, locate something like:
==============================
395 hydrogen bonds defined for protein.
1135 hydrogen bond angles defined for protein.
Restraints generated for nucleic acids:
0 hydrogen bonds
0 hydrogen bond angles
0 basepair planarities
0 basepair parallelities
0 stacking parallelities
Total time for adding SS restraints: 1.35
==============================
in the log-file.
Best regards,
Oleg Sobolev.