read_te_290E> Number of residues in the alignment and pdb files are
different: 836 834
For alignment entry: 1 1iax
x (mismatch at alignment position 835)
Please check your alignment file header to be sure you correctly specified
the starting and ending residue numbers and chains. The alignment sequence
must match that from the atom file exactly.
You should follow the advice in the error message, and check your
alignment file header. Your header tells Modeller to read residues 11:A
through 438:B from your PDB file, so it's not going to read the HETATMs,
which come after 438:B. Fix your alignment header.
BTW, your PDB file contains 4 HETAMs (two SO4 and two PLP) but your
alignment sequence contains only two.