Hi Eike, at this resolution R-factors are expected to be lower. If you send me data and model files (as well as ligand CIF files, if any) then I can have a look! Please send files off mailing list (to my email directly). Pavel On 2/27/14, 10:39 AM, Eike Schulz wrote:
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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