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/