Clarify ProteinInterfaceDesign “randomness”

Hello, I am using the following protocol, modified from the design raf-rac interface demo, to design a protien protein interface. I ran 2 designs in parallel using nstruct = 1,000 and ran SequenceProfile.py to analyze and found that the results were the same for each. Therefore I wondering exactly how the sequence space is "randomly" searched to identify mutations and how likely these mutations will be to give a more favorable interface in vitro. Thanks in advance

</SCOREFXNS>

        <FILTERS>

    <Ddg name=ddg_binding threshold=0 scorefxn=REF2015 repeats=3 repack=1/>

    DDG filter computes binding score for the complex

    (threshold=0 only allows complexes with negative binding score)

    (repeats=3 calculates binding score three times and returns average)

    (repack=1 repack complex in both bound and unbound states to calculate binding score)

    <Sasa name=sasa threshold=800/>

    SASA filter computes interface solvent-accessible surface area

    (threshold=800 only allows complexes with greater than 800 Å^2

    as per Janin et al., Quarterly Reviews of Biophysics, 2008)

  </FILTERS>

        <TASKOPERATIONS>

                <RestrictResiduesToRepacking name=nodesign residues=/>

                <ProteinInterfaceDesign name=design repack_chain1=1 repack_chain2=1 design_chain1=0 design_chain2=1 interface_distance_cutoff=8/>

                <InitializeFromCommandline name=cmdline/>

                Reads command line options

        </TASKOPERATIONS>

        <MOVERS>

                <FavorNativeResidue name=Fav bonus=1/>

                <Docking name=dock1 fullatom=1 local_refine=1/>

                Runs local refinement stage of full atom docking

                <PackRotamersMover name=packrot scorefxn=REF2015 task_operations=design,cmdline/>

                Runs protein interface design

                <MinMover name=min scorefxn=REF2015 chi=1 bb=1 type=dfpmin_armijo_nonmonotone tolerance=0.01/>

                Runs full atom side-chain and backbone minimization

        </MOVERS>

        <PROTOCOLS>

                Runs movers and filters in this order

                <Add mover_name=Fav/>

                <Add mover_name=dock1/>

                <Add mover_name=packrot/>

                <Add mover_name=min/>

                <Add filter_name=ddg_binding/>

                <Add filter_name=sasa/>

        </PROTOCOLS>

</dock_design>