On the page http://salilab.org/modeller/tutorial/iterative.html
the tutorial says
"The insertion between position 85 and 88 of the alignment was placed in
the middle of an α-helix in the template (the "9" characters on the
first line below the sequence mark the helices). Moving the insertion to
the end of the α-helix may improve the model."
But in the two PAP examples on the page I cannot see any difference at
positions 85 - 88. What am I missing here?
Good catch! There was actually a mistake in that first alignment, which
has now been corrected.