For find_ncs_from_density the shape of the molecule itself is not so important. What matters is if there is some local part of the molecule that is recognizable in both copies.  So I would try default parameters first.  I assume you did that and it didn't give you a useful answer...so then I would do these things:

1. try many locations :  n_center_use=20

This is the best option...it will try 20 times using density at 20 different locations to search.  If you have an older version of phenix you may need to download a nightly build to do this.

2. Try varying the resolution

3. Try varying the angular spacing of the search (delta_phi)

All the best,

Tom T