Let's say I'm modelling a protein with one molecule of 150 residues in the asymmetric unit, in P4 symmetry. So total number of residues 4x150=600. When I input the sequence of just the asymmetric unit (150 residues), I get:
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WARNING: 450 unknown residues were encountered, TYR assumed
To me, the expected behaviour would be to propagate the sequence of the asymmetric unit to all the symmetry mates.
The workaround is just to duplicate the sequence four times in the input but still give 150 residues in the asymmetric unit, which keeps the program happy but isn't noted in the manual. I'm a bit nervous doing that knowing it's already surprised me here, so it might be better to not give a sequence at all.
I feel it's worth reporting in case someone else runs into this. A symmetric solution with different form factors in one of the symmetry mates doesn't make sense in any situation I can think of.