The protein does not have missing residues, in the Model missing residues windows all the options are disabled. For this either the log window or a pop-up can notify the user. Or in the explorer window the Modelling Refinement section can be disabled.
As there were a few non-standard residues left in the structure, the structure patcher was not able to generate the final model. Log window showing:
So regarding the non-standard residues, the user can be notified beforehand.
Version: 2.3 BioIn OS: Windows Machine: PIPL05 Input PDB ID: 5M8L
So regarding the non-standard residues, the user can be notified beforehand.