The two models have to match the alignment sequences, and the problem
here is that while your alignment file header specifies only single
chains (1:H through 216:H in 1ck0, and 1:H through 211:H in 1e4w) when
you read the models you don't ask for those same ranges, so by default
Modeller reads all chains. To fix this you need to specify model_segment
when you read in the models, i.e.
Of course, this is a little error prone because you have to specify
everything twice. But fortunately the alignment object remembers the
residue:chain range specified in the alignment header, so you can
simplify this to: