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.


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