Hello YeBin,
Modeller states that you have more aminoacids in the alignment
than in the pdb-file (353/352), and if you compare the fasta-sequence
and the pdb-file you will find a lysine (K) at the C-terminus
that is not present in the pdb-file. Delete the K from your
alignment or change it to a "-" and Modeller should work fine.
Remember that there might no be all aminoacids present in
a pdb-file for structural reasons: loops at the surface may
be highly mobile, and can therefore often not be solved by
crystallography, and that means you will have a gap in the
structure. Before modelling, check the sequence.
You can use DeepView to write out the aminoacids present in
the pdb-file by loading the protein and then saving the sequence
in FASTA-format.
Best wishes,
Thorsten