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