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    Thanks a lot for your reply.

    I tried again following your suggestion, to put my interest component as the last one. But there was no improvement.

    the options were’
    -in:file:s xxx.pdb
    -run:min_type dfpmin_armijo_nonmonotone
    -in:file:frag3 aaxxxx03_05.200_v1_3
    -flexible_chain F
    -flexible_start_resnum 1
    -flexible_stop_resnum 44
    -AnchoredDesign:perturb_temp 0.8
    -AnchoredDesign:refine_temp 0.8
    -AnchoredDesign:refine_repack_cycles 10
    -AnchoredDesign:perturb_cycles 500
    -AnchoredDesign:refine_cycles 100
    -nstruct 1′

    One difference is that my ‘floppy tail’ is localized in N-terminal. Could it be the possible reason? Thanks for any further suggestion.