[phenixbb] FAQ high res refinement
Eike Schulz
eike.schulz at embl.de
Thu Feb 27 10:39:25 PST 2014
>
> Dear all,
>
> I am currently refining a rather well resolved protein at 0.97Å. However, even
> after many cycles of refinement the R-factors are stuck at around Rwork/Rfree
> 14.5/16.5. Considering number of aa, Rmerge (3.5%) and resolution this seems
> to be too high. I assume 10 25 macrocycles should be enough for effective
> weight refinement in phenix, however no improvement of the R-factors.
>
> A quick run with default settings in competitor software 'R' yields >2% better
> R-factors.
>
> I would appreciate suggestion how to improve my refinement protocol, values
> differing from default are listed below.
>
> Thank you very much in advance
>
> Eike
>
>
>
>
>
>
> refine {
> adp {
> individual {
> isotropic = element H
> anisotropic = not element H
> }
> group_adp_refinement_mode = one_adp_group_per_residue \
> *two_adp_groups_per_residue group_selection
> }
> }
> main {
> apply_overall_isotropic_scale_to_adp = False
> nqh_flips = False
> ordered_solvent = True
> place_ions = True
> number_of_macro_cycles = 10
> hydrogen_bonds = True
> use_convergence_test = True
> target = auto *ml mlhl ml_sad ls
> random_seed = 3326496
> wavelength = 0.885611
> nproc = 4
> }
> hydrogens {
> refine = individual *riding Auto
> }
> tls {
> find_automatically = False
> one_residue_one_group = False
> }
> ordered_solvent {
> mode = second_half filter_only every_macro_cycle \
> *every_macro_cycle_after_first
> h_bond_min_mac = 1
> h_bond_min_sol = 1
> h_bond_max = 6
> refine_occupancies = True
> new_solvent = isotropic *anisotropic
> b_iso_min = 0
> }
> peak_search {
> max_number_of_peaks = 1303
> }
> target_weights {
> optimize_xyz_weight = True
> optimize_adp_weight = True
> wxc_scale = 0.2
> wxu_scale = 0.2
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