Speed problem when running RosettaLigand ligand docking

Hello, I am trying to do protein design using a protocol derived from RosettaLigand ligand docking.

When I run Rosetta Design as the following command line, everything seems correct and there are output structures (pdb files). The problem is that it takes ages to get the results. In average, it will take 15~20 mins to get one models. For 1000 models, it spent 9 days. I think there is something wrong, but I don't know how to solve it.

$ rosetta_scripts.linuxgccrelease @design_1anf.options -parser:protocol design_1anf.xml -extra_res_fa ../step1_prep/malt.params -s "../step1_prep/1anf_r_relaxed.pdb ../step1_prep/malt_positioned.pdb" -nstruct 1000 -out:file:scorefile design_results_1anf.sc > design_1anf.log

During the preparing step, I generate 100 ligand conformers by RDkit.

This is my design script (design_1anf.xml):

 <ROSETTASCRIPTS>
    <SCOREFXNS>
        <ScoreFunction name="ligand_soft_rep" weights="ligand_soft_rep"/>
        <ScoreFunction name="hard_rep" weights="ligandprime"/>
    </SCOREFXNS>
    <TASKOPERATIONS>
        <DetectProteinLigandInterface name="design_interface" cut1="6.0" cut2="8.0" cut3="10.0" cut4="12.0" design="1" resfile="1anf.resfile"/> # see Note 19
    </TASKOPERATIONS>
    <LIGAND_AREAS>
        <LigandArea name="docking_sidechain" chain="X" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true" minimize_ligand="10"/>
        <LigandArea name="final_sidechain" chain="X" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true"/>
        <LigandArea name="final_backbone" chain="X" cutoff="7.0" add_nbr_radius="false" all_atom_mode="true" Calpha_restraints="0.3"/>
    </LIGAND_AREAS>
    <INTERFACE_BUILDERS>
        <InterfaceBuilder name="side_chain_for_docking" ligand_areas="docking_sidechain"/>
        <InterfaceBuilder name="side_chain_for_final" ligand_areas="final_sidechain"/>
        <InterfaceBuilder name="backbone" ligand_areas="final_backbone" extension_window="3"/>
    </INTERFACE_BUILDERS>
    <MOVEMAP_BUILDERS>
        <MoveMapBuilder name="docking" sc_interface="side_chain_for_docking" minimize_water="true"/>
        <MoveMapBuilder name="final" sc_interface="side_chain_for_final" bb_interface="backbone" minimize_water="true"/>
    </MOVEMAP_BUILDERS>
    <SCORINGGRIDS ligand_chain="X" width="15"> # see Note 20
        <ClassicGrid grid_name="vdw" weight="1.0"/>
    </SCORINGGRIDS>
    <MOVERS>

    <FavorNativeResidue name="favor_native" bonus="1.00"/> # see Notes 21 and 22

    <Transform name="transform" chain="X" box_size="5.0" move_distance="0.1" angle="5" cycles="500" repeats="1" temperature="5" rmsd="4.0"/> # see
Note 23
    <HighResDocker name="high_res_docker" cycles="6" repack_every_Nth="3" scorefxn="ligand_soft_rep" movemap_builder="docking"/>
    <PackRotamersMover name="designinterface" scorefxn="hard_rep" task_operations="design_interface"/>
    <FinalMinimizer name="final" scorefxn="hard_rep" movemap_builder="final"/>
    <InterfaceScoreCalculator name="add_scores" chains="X" scorefxn="hard_rep"/>
    <ParsedProtocol name="low_res_dock">
        <Add mover_name="transform"/>
    </ParsedProtocol>
    <ParsedProtocol name="high_res_dock">
        <Add mover_name="high_res_docker"/>
        <Add mover_name="final"/>
    </ParsedProtocol>
    </MOVERS>
    <PROTOCOLS>
        <Add mover_name="favor_native"/>
        <Add mover_name="low_res_dock"/>
        <Add mover_name="designinterface"/> # see Note 24
        <Add mover_name="high_res_dock"/>
        <Add mover_name="add_scores"/>
    </PROTOCOLS>
</ROSETTASCRIPTS>

Thanks very much in advance!