I am calculating the RSA with psa module of JOY package for a structure solved with NMR. During the process I am getting many warning messages in terminal of :

Warning: too many atoms in L position 3 -- found 14 expected 8

Warning: unknown atom type HD11 in residue LEU at position 3, using default radius

I get these warnings for almost all the atoms of my structure,and the final output of the psa file most residues are followed with a '!' (meaning not all atoms were found in that sidechain).

I have searched along the literature and in the documentation of joy to understand these warnings but did not find an answer.

My question: Is the output still correct with that many warnings and '!' sign or is there any previous step or pdb reparation step that must be performed before?

Thank you so much!