[phenixbb] FAQ high res refinement

Pavel Afonine pafonine at lbl.gov
Thu Feb 27 10:59:49 PST 2014


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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