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You might also try minimizing the starting structure before running the design (then run design with regular weights and with soft_rep_design, separately).
A cmd line I like to use before doing any design on a crystal structure is:
rosetta.gcc -relax -farlx -minimize -sc_only -read_all_chains -use_pdb_numbering -multi_chain -use_input_sc -fa_input [-find_disulf -read_hetero_h2o] -ex1 -ex1aro -ex2 -s 1NAT.pdb [-decoystats] -fa_output -nstruct 1
(I put the optional flags in [ brackets ] ie not for every situation, though they won’t hurt anything).