Hi Kiran,
LACS is statistics-based,
that is your assignment may be fine even though LACS flagged it as
outlier. So, if you think they are fine if they look consistent in all
of your spectra and other assignments from nearby residues and atoms.
I
recommend using c3 two-letter-code for the first run in this case.
Also, you may overcome some of the problem you see in NOESY analysis
step in the Ponderosa Client if you unfold NOESY with circular shift
function -cs when you process with nmrPipe.
Proton completeness is the indicator of your proton assignment completeness that is calculated by 100.0(%) * (# of assigned protons) / (# of all available protons to assign). So if they are low, that means you probably do not have enough chemical shift information to calculate structure.