Your sequence file should be 1 copy of the unique sequence.
Your search model should be either your original search model, or probably better, any one copy of a placed and already refined model (just take your A chain from your existing solution and call it a search model).
Your fixed_model consists of the 5 placed copies you already have.
Your value of ncs_copies is 1 if you are using a fixed_model to hold the 5 existing copies.
This approach assumes that the 6th copy is not that similar to the other 5 and NCS averaging will not be useful. Note that there is an alternative approach to do all this that involves specifying the translations and Euler angles of the 5 placed copies. This alternative method will apply NCS to all 6 copies and will work much better than the way described above if all copies actually are very similar. Probably the way described here is better for your case because you get the advantage of using the refined positions of the first 5 copies to get an accurate description of most of the cell contents and as mentioned below the 6th copy ma not be similar.
Note also that the chances of success are low because you already tried to find the 6th copy with Phaser and it didn't work. MR-rosetta could possibly work if the 6th copy is just in a different conformation. If it is disordered or otherwise not visible...it is not likely to work.
You might also just look very carefully in your 2mFo-DFc map for any indication of where the 6th molecule may be located. If you can see a hint of it, a real-space search may be worth trying instead of further molecular replacement. Also extensive auto-building could possibly show you where the 6th copy is located.
If you want to try the alternative approach, see here:
under this description:
fixed_ensemblesIf you already know the placement of one or more molecules you can specify them as fixed ensembles. NOTE 1: you are specifying location and orientation of one or more copies of the search model NOTE 2: you cannot specify use_all_plausible_sg if you have fixed ensembles
fixed_ensembleID_list = NoneEnter the word 'ensemble_1' to indicate that you want to specify a copy of your search model that is to be fixed. To specify more than one placement just say 'ensemble_1' more than once. For example if you
....
Let me know if that doesn't do it or if I gave you any of the parameters incorrectly.
All the best,
Tom T