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<h1 class="title">Refinement at high resolution (higher than approx. 1.0 Angstrom)</h1>
<p>Guidelines for structure refinement at high resolution:</p>
<blockquote>
<ul>
<li><p class="first">make sure the model contains hydrogen atoms. If not, <tt class="docutils literal"><span class="pre">phenix.reduce</span></tt>
can be used to add them:</p>
<pre class="literal-block">
% phenix.reduce model.pdb > model_h.pdb
</pre>
<p>By default, <tt class="docutils literal"><span class="pre">phenix.refine</span></tt> will refine positions of H atoms as riding
model (H atom will exactly follow the atom it is attached to). Note that
<tt class="docutils literal"><span class="pre">phenix.refine</span></tt> can also refine individual coordinates of H atoms (can be
used for small molecules at ultra-high resolutions or for refinement
against neutron data). This is governed by
<tt class="docutils literal"><span class="pre">hydrogens.refine_sites</span> <span class="pre">=</span> <span class="pre">individual</span> <span class="pre">*riding</span></tt> keyword and the default is
to use riding model. <tt class="docutils literal"><span class="pre">hydrogens.refine_adp</span></tt> defines how hydrogens'
B-factors are refined (default is to refine one group B for all H atoms).
At high resolution one should definitely try to use <tt class="docutils literal"><span class="pre">one_b_per_molecule</span></tt>
or even <tt class="docutils literal"><span class="pre">individual</span></tt> choice (resolution permitting). Similar strategy
should be used for refinement of H's occupancies,
<tt class="docutils literal"><span class="pre">hydrogens.refine_occupancies</span></tt> keyword.</p>
</li>
<li><p class="first">most of the atoms should be refined with anisotropic ADP. Exceptions could
be model parts with high B-factors), atoms in alternative conformations,
hydrogens and solvent molecules. However, at resolutions higher than 1.0A
it's worth of trying to refine solvent with anisotropic ADP.</p>
</li>
<li><p class="first">it is a good idea to constantly monitor the existing solvent molecules and
check for new ones by using <tt class="docutils literal"><span class="pre">ordered_solvent=true</span></tt> keyword. If it's
decided to refine waters with anisotropic ADP then make sure that the newly
added ones are also anisotropic; use
<tt class="docutils literal"><span class="pre">ordered_solvent.new_solvent=anisotropic</span></tt> (default is <tt class="docutils literal"><span class="pre">isotropic</span></tt>). One
can also ask <tt class="docutils literal"><span class="pre">phenix.refine</span></tt> to refine occupancies of water:
<tt class="docutils literal"><span class="pre">ordered_solvent.refine_occupancies=true</span></tt> (default is False).</p>
</li>
<li><p class="first">at high resolution the alternative conformations can be visible for more
than 20% of residues. <tt class="docutils literal"><span class="pre">phenix.refine</span></tt> automatically recognizes atoms in
alternative conformations (based on PDB records) and by default does
constrained refinement of occupancies for these atoms. Please note, that
<tt class="docutils literal"><span class="pre">phenix.refine</span></tt> does not build or create the fragments in alternative
conformations; the atoms in alternative conformations should be properly
defined in input PDB file (using conformer identifiers) (if actually found
in a structure).</p>
</li>
<li><p class="first">the default weights for stereochemical and ADP restraints are most likely
too tight at this resolution, so most likely the corresponding values need
to be relaxed. Use <tt class="docutils literal"><span class="pre">wxc_scale</span></tt> and <tt class="docutils literal"><span class="pre">wxu_scale</span></tt> for this; lower values,
like 1/2, 1/3, 1/4, ... etc of the default ones should be tried.
<tt class="docutils literal"><span class="pre">phenix.refine</span></tt> allows automatically optimize these values (
<tt class="docutils literal"><span class="pre">optimize_wxc=True</span></tt> and <tt class="docutils literal"><span class="pre">optimize_wxu=True</span></tt>), however this is a very
slow task so it may be considered for an over night run or even longer.
At ultra-high resolutions (approx. 0.8A or higher) a complete unrestrained
refinement should be definitely tried out for well ordered parts of the
model (single conformations, low B-factors).</p>
</li>
<li><p class="first">at ultra-high resolution the residual maps show the electron density
redistribution due to bonds formation as density peaks at interatomic bonds.
<tt class="docutils literal"><span class="pre">phenix.refine</span></tt> has specific tools to model this density called IAS
models (Afonine et al, Acta Cryst. (2007). D63, 1194-1197).</p>
</li>
</ul>
</blockquote>
<p>This example illustrates most of the above points:</p>
<pre class="literal-block">
% phenix.refine model_h.pdb data.mtz high_res.params
</pre>
<p>where the file <tt class="docutils literal"><span class="pre">high_res.params</span></tt> contains following lines (for more parameters
under each scope look at complete list of parameters):</p>
<pre class="literal-block">
refinement.main {
number_of_macro_cycles = 5
ordered_solvent=true
}
refinement.refine {
adp {
individual {
isotropic = element H
anisotropic = not element H
}
}
}
refinement.target_weights {
wxc_scale = 0.25
wxu_scale = 0.3
}
refinement.hydrogens {
refine_sites = individual *riding
refine_adp = *one_b_per_residue one_b_per_molecule individual
refine_occupancies = *one_q_per_residue one_q_per_molecule individual
}
refinement {
ordered_solvent {
mode = auto filter_only *every_macro_cycle
new_solvent = isotropic *anisotropic
refine_occupancies = True
}
}
</pre>
<p>In the example above <tt class="docutils literal"><span class="pre">phenix.refine</span></tt> will perform 5 macro-cycles with ordered
solvent update (add/remove) every macro-cycles, all atoms including newly added
water will be refined with anisotropic B-factors (except hydrogens), riding
model will be used for positional refinement of H atoms, one occupancy and
isotropic B-factor will be refined per all hydrogens within a residue,
occupancies of waters will be refined as well, the default stereochemistry and
ADP restraints weights are scaled down by the factors of 0.25 and 0.3
respectively. If starting model is far enough from the "final" one, more
macro-cycles may be required (than 5 used in this example).</p>
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