Remodel has lots of design features, but you can choose to not use them, say you wouldn’t run it with “-find_neighbors -design_neighbors” and a blueprint with a “ALLAA” resfile code at any position. For loops you will have to use “-generic_aa G”, however, for Remodel to work.
Remodel uses real fragments, so it is not totally made up. And actually, you can add posttranslational modifications that exist in vivo but the expression system did not add, so you could make a model more real than the structure (just playing devil’s advocate here for fun).
Although it may pay to check for DG or DP amino acids pairs in your loops as they do funny things in vivo (isoaspartate and self-cleavage), which obviously Remodel knows nothing about.
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