Comparing HIS with propka2 and propka3

[chiendarret]

I am new to propka3 (3.4.0 on linux). With an ensemble of nucleotides and proteins (a sphere of 30A cut around the "small molecule" ligand of interest from a huge ensemble, without capping) I am trying to assign the protonation of HIS at pH 7.0 for MD in solution.
I can only compare directly a few HIS

PROPKA2:
HIS 13E 1.22 6.50
HIS 17E 6.43 6.50
HIS 152G 6.43 6.50
HIS 158G 4.47 6.50
HIS 5B 6.36 6.50
HIS 28C 3.17 6.50
HIS 39C 3.96 6.50
HIS 40C 2.15 6.50
HIS 41C 4.88 6.50
HIS 49C 9.11 6.50
HIS 62C 6.08 6.50
HIS 23D 7.02 6.50
HIS 59D 6.67 6.50
HIS 90D 6.60 6.50

PROPKA3:
HIS 13 E 0.89 6.50
HIS 17 E 5.25 6.50
HIS 158 G 4.20 6.50
HIS 5 B 5.48 6.50
for the other ones I am in a trouble:
HIS NE2 C 1.07 5.00 NAR
HIS NE2 C -3.60 5.00 NAR
HIS NE2 C 0.86 5.00 NAR
HIS ND1 C 0.69 5.00 NAR
HIS NE2 C 3.25 5.00 NAR
HIS NE2 C 4.94 5.00 NAR
HIS NE2 D 4.45 5.00 NAR
HIS NE2 D 4.50 5.00 NAR
HIS ND1 D 5.49 5.00 NAR

I also noticed that for protein residues at the end of chains, without capping, propka3 complains about missing atoms (while none is missing, except capping), while propka2 ignores them.

Should I forget about propka2? However, how to locate the HISs lacking residue number in the propka3 list?

thanks
francesco pietra