already a while ago I have noticed that modeller tends to produce what I
would call spaghetti proteins (containing knots and other fancy
structures) when it is supplied with multiple templates that are far
from the target (35 % or less) and also quite diverse among each other.
However, Modeller 9 seems to suffer more from this effect than the
previous versions
Just to resolve this for the benefit of the modeller_usage list: a bug
in Modeller 9v1 caused the original template structures to be used in
the generation of its initial model. This is different from the Modeller
8 behavior, in which the templates were first modified by
alignment.check() (which does all pairwise superpositions). The Modeller
8 behavior has been restored in the new Modeller release, 9v2.