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Hi Eike,<br>
<br>
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).<br>
<br>
Pavel<br>
<br>
<br>
<div class="moz-cite-prefix">On 2/27/14, 10:39 AM, Eike Schulz
wrote:<br>
</div>
<blockquote cite="mid:CF3544DC.2DB28%25eike.schulz@embl.de"
type="cite"><span id="OLK_SRC_BODY_SECTION">
<blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE"
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<div style="word-wrap: break-word; -webkit-nbsp-mode: space;
-webkit-line-break: after-white-space; color: rgb(0, 0,
0); font-size: 14px; ">
<div>
<div><font class="Apple-style-span" face="Consolas"><br>
Dear all, </font></div>
<div><font class="Apple-style-span" face="Consolas"><br>
</font></div>
<div><font class="Apple-style-span" face="Consolas">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. </font><span
class="Apple-style-span" style="font-family:
Consolas; ">I assume 10 – 25 macrocycles should be
enough for effective weight refinement in phenix,
however no improvement of the R-factors. </span></div>
<div><font class="Apple-style-span" face="Consolas"><br>
</font></div>
<div><font class="Apple-style-span" face="Consolas">A
quick run with default settings in competitor
software 'R' yields >2% better R-factors. </font></div>
<div><font class="Apple-style-span" face="Consolas"><br>
</font></div>
<div><span class="Apple-style-span" style="font-family:
Consolas; ">I would appreciate suggestion how to
improve my refinement protocol, values differing
from default are listed below. </span></div>
<div><span class="Apple-style-span" style="font-family:
Consolas; "><br>
</span></div>
<div><span class="Apple-style-span" style="font-family:
Consolas; ">Thank you very much in advance</span></div>
<div><span class="Apple-style-span" style="font-family:
Consolas; "><br>
</span></div>
<div><span class="Apple-style-span" style="font-family:
Consolas; ">Eike</span></div>
<div><span class="Apple-style-span" style="font-family:
Consolas; "><br>
</span></div>
<div><span class="Apple-style-span" style="font-family:
Consolas; "><br>
</span></div>
<div><font class="Apple-style-span" face="Consolas"><br>
</font></div>
<div><font class="Apple-style-span" face="Consolas"><br>
</font></div>
<div><font class="Apple-style-span" face="Consolas"> </font></div>
<div><font class="Apple-style-span" face="Consolas"><br>
</font></div>
<div><font class="Apple-style-span" face="Consolas">refine
{</font></div>
<div><font class="Apple-style-span" face="Consolas">
adp {</font></div>
<div><font class="Apple-style-span" face="Consolas">
individual {</font></div>
<div><font class="Apple-style-span" face="Consolas">
isotropic = element H</font></div>
<div><font class="Apple-style-span" face="Consolas">
anisotropic = not element H</font></div>
<div><font class="Apple-style-span" face="Consolas">
}</font></div>
<div><font class="Apple-style-span" face="Consolas">
group_adp_refinement_mode =
one_adp_group_per_residue \</font></div>
<div><font class="Apple-style-span" face="Consolas">
*two_adp_groups_per_residue group_selection</font></div>
<div><font class="Apple-style-span" face="Consolas">
}</font></div>
<div><font class="Apple-style-span" face="Consolas"> }</font></div>
<div><font class="Apple-style-span" face="Consolas">
main {</font></div>
<div><font class="Apple-style-span" face="Consolas">
apply_overall_isotropic_scale_to_adp = False</font></div>
<div><font class="Apple-style-span" face="Consolas">
nqh_flips = False</font></div>
<div><font class="Apple-style-span" face="Consolas">
ordered_solvent = True</font></div>
<div><font class="Apple-style-span" face="Consolas">
place_ions = True</font></div>
<div><font class="Apple-style-span" face="Consolas">
number_of_macro_cycles = 10</font></div>
<div><font class="Apple-style-span" face="Consolas">
hydrogen_bonds = True</font></div>
<div><font class="Apple-style-span" face="Consolas">
use_convergence_test = True</font></div>
<div><font class="Apple-style-span" face="Consolas">
target = auto *ml mlhl ml_sad ls</font></div>
<div><font class="Apple-style-span" face="Consolas">
random_seed = 3326496</font></div>
<div><font class="Apple-style-span" face="Consolas">
wavelength = 0.885611</font></div>
<div><font class="Apple-style-span" face="Consolas">
nproc = 4</font></div>
<div><font class="Apple-style-span" face="Consolas"> }</font></div>
<div><font class="Apple-style-span" face="Consolas">
hydrogens {</font></div>
<div><font class="Apple-style-span" face="Consolas">
refine = individual *riding Auto</font></div>
<div><font class="Apple-style-span" face="Consolas"> }</font></div>
<div><font class="Apple-style-span" face="Consolas">
tls {</font></div>
<div><font class="Apple-style-span" face="Consolas">
find_automatically = False</font></div>
<div><font class="Apple-style-span" face="Consolas">
one_residue_one_group = False</font></div>
<div><font class="Apple-style-span" face="Consolas"> }</font></div>
<div><font class="Apple-style-span" face="Consolas">
ordered_solvent {</font></div>
<div><font class="Apple-style-span" face="Consolas">
mode = second_half filter_only every_macro_cycle \</font></div>
<div><font class="Apple-style-span" face="Consolas">
*every_macro_cycle_after_first</font></div>
<div><font class="Apple-style-span" face="Consolas">
h_bond_min_mac = 1</font></div>
<div><font class="Apple-style-span" face="Consolas">
h_bond_min_sol = 1</font></div>
<div><font class="Apple-style-span" face="Consolas">
h_bond_max = 6</font></div>
<div><font class="Apple-style-span" face="Consolas">
refine_occupancies = True</font></div>
<div><font class="Apple-style-span" face="Consolas">
new_solvent = isotropic *anisotropic</font></div>
<div><font class="Apple-style-span" face="Consolas">
b_iso_min = 0</font></div>
<div><font class="Apple-style-span" face="Consolas"> }</font></div>
<div><font class="Apple-style-span" face="Consolas">
peak_search {</font></div>
<div><font class="Apple-style-span" face="Consolas">
max_number_of_peaks = 1303</font></div>
<div><font class="Apple-style-span" face="Consolas"> }</font></div>
<div><font class="Apple-style-span" face="Consolas">
target_weights {</font></div>
<div><font class="Apple-style-span" face="Consolas">
optimize_xyz_weight = True</font></div>
<div><font class="Apple-style-span" face="Consolas">
optimize_adp_weight = True</font></div>
<div><font class="Apple-style-span" face="Consolas">
wxc_scale = 0.2</font></div>
<div><font class="Apple-style-span" face="Consolas">
wxu_scale = 0.2</font></div>
</div>
</div>
</div>
</blockquote>
</span>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
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</pre>
</blockquote>
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