in a Modeller-generated .rsr file, I have lines like this one:
R 9 3 4 25 8 18 2 5 4 4 7 9 10 12 9
10 12 14 0.1295 0.3250 0.5455 -1.0908 -0.7138
-1.1903 2.5360 -2.3 3880 387 2.5656 0.0908 0.1065
0.2059 0.2164 0.5271 0.3072 -0.2541 3880 -0.4199
-0.6670
I suppose it's a restraint on phi-psi angles, but I cant find a
description for Feature "4" (third number in first line) in the Modeller
documentation (http://salilab.org/modeller/manual/node447.html).
Yes, you are correct - it's a phi-psi restraint. Feature 4 is the same
as feature 3 (it's a dihedral angle). (There are complicated historical
reasons why there are two identical dihedral angle features.)
Moreover, why are there two features for this restraint (numb_feat=2)
The two features are the two dihedral angles (phi and psi).
and what does Modal2 = 5 stand for?
Actually for this mathematical form Modal2 is not used, so you can
ignore it. Only Modality is used, which is the number of terms in the
binormal.
Are restraints of this type (i.e. Group=25, dihedral) always generated
by default (Modeller version>= 9.5)?
Yes, automodel generates these restraints for each residue that has both
a phi and a psi angle (so the termini in each chain are excluded).