Dear Pieter;
If I read correctly the last 3 sentences of the log file you obtained:
> malign3d_> Initial framework positions: 9 > fit2xyz_E> number of equivalent positions < 3: 0 > recover__> MODELLER_STATUS >= CONTROL: 1 1
It seems that you tryed to used malign3d with 9 sequences but you told us that you have only 8 structures. That is probably the problem, because Malign3D works only with structures. Here you included the sequence to model, that crashed Modeller. Please Check you top file again.
Eric
-- Eric FEYFANT Laboratory of Molecular Biophysics (SALI Lab) The Rockefeller Univ, Box 270 1230 York Ave | New York NY 10021 | USA | Phone: (212) 327 7206 | Fax: (212) 327 7540 E-mail: eric@flute.rockefeller.edu www-homepage:http://salilab.org/~eric/