<font class="Apple-style-span" size="4">Dear all,</font><div><font class="Apple-style-span" size="4"><br></font></div><div><font class="Apple-style-span" size="4">I have been stuck in the problem for a while. I appreciate any suggestions.</font></div>
<div><font class="Apple-style-span" size="4"><br></font></div><div><font class="Apple-style-span" size="4"><span class="Apple-style-span">I have two </span><span class="Apple-style-span">zinc binding domain in my 3A structure which are Cys4 type. The geometry is OK for one domain, but it is not refined properly in the other one.</span></font></div>
<div><span class="Apple-style-span"><font class="Apple-style-span" size="4"><br></font></span></div><div><span class="Apple-style-span"><font class="Apple-style-span" size="4">The problems during phenix refinement are</font></span></div>
<div><span class="Apple-style-span"><font class="Apple-style-span" size="4">1. Zinc is always refined to position ~0.5A off from its correct position</font></span></div><div><font class="Apple-style-span" size="4">2. The refined bond lengths of four Cys-Zn are all below 2.3</font></div>
<div><font class="Apple-style-span" size="4">3. Sometimes, distances between SG atoms of nearby cysteines are too close, and coot just connect them as disulfate bond.</font></div><div><font class="Apple-style-span" size="4">4. Sometimes, I get the following message showing that all bond angles are outliers with >8 sigmas, I listed part of the outliers.</font></div>
<div> </div><div><div><font class="Apple-style-span" color="#3333ff">Top angle outliers (sorted by deviation):</font></div><div><font class="Apple-style-span" color="#3333ff">atoms ideal model difference deviation (sigma)</font></div>
<div><font class="Apple-style-span" color="#3333ff">----------------------------------------------------------------------------</font></div><div><font class="Apple-style-span" color="#3333ff"> SG CYS D1204 57.894 104.470 46.576 9.32</font></div>
<div><font class="Apple-style-span" color="#3333ff">ZN ZN D2001 </font></div><div><font class="Apple-style-span" color="#3333ff"> SG CYS D1112 </font></div><div><font class="Apple-style-span" color="#3333ff"><br>
</font></div><div><font class="Apple-style-span" color="#3333ff"> SG CYS D1201 50.842 92.496 41.654 8.33</font></div><div><font class="Apple-style-span" color="#3333ff">ZN ZN D2001 </font></div>
<div><font class="Apple-style-span" color="#3333ff"> SG CYS D1204 </font></div><div><font class="Apple-style-span" color="#3333ff"><br></font></div><div><font class="Apple-style-span" color="#3333ff"> SG CYS D1204 126.952 92.496 -34.455 -6.89</font></div>
<div><font class="Apple-style-span" color="#3333ff">ZN ZN D2001 </font></div><div><font class="Apple-style-span" color="#3333ff"> SG CYS D1201 </font></div><div><font class="Apple-style-span" color="#3333ff"><br>
</font></div><div><font class="Apple-style-span" color="#3333ff"> SG CYS D1201 52.183 86.105 33.922 6.78</font></div><div><font class="Apple-style-span" color="#3333ff">ZN ZN D2001 </font></div>
<div><font class="Apple-style-span" color="#3333ff"> SG CYS D1112 </font></div><div><font class="Apple-style-span" color="#3333ff"><br></font></div><div><font class="Apple-style-span" color="#3333ff"> SG CYS D1194 152.275 119.729 -32.546 -6.51</font></div>
<div><font class="Apple-style-span" color="#3333ff">ZN ZN D2001 </font></div><div><font class="Apple-style-span" color="#3333ff"> SG CYS D1112 </font></div><div><font class="Apple-style-span" color="#3333ff"><br>
</font></div><div><font class="Apple-style-span" color="#3333ff"> SG CYS D1112 89.273 119.729 30.456 6.09</font></div><div><font class="Apple-style-span" color="#3333ff">ZN ZN D2001 </font></div>
<div><font class="Apple-style-span" color="#3333ff"> SG CYS D1194 </font></div><div><font class="Apple-style-span" size="4"><br></font></div></div><div><font class="Apple-style-span" size="4">I also post my metal.edit file for refinement </font></div>
<div><font class="Apple-style-span" size="4"><br></font></div><div><div><font class="Apple-style-span" color="#3333ff">refinement.geometry_restraints.edits {</font></div><div><font class="Apple-style-span" color="#3333ff"> bond {</font></div>
<div><font class="Apple-style-span" color="#3333ff"> action = *add</font></div><div><font class="Apple-style-span" color="#3333ff"> atom_selection_1 = name ZN and chain D and resname ZN and resseq 2001</font></div>
<div><font class="Apple-style-span" color="#3333ff"> atom_selection_2 = name SG and chain D and resname CYS and resseq 1201</font></div><div><font class="Apple-style-span" color="#3333ff"> distance_ideal = 2.310000</font></div>
<div><font class="Apple-style-span" color="#3333ff"> sigma = 0.100</font></div><div><font class="Apple-style-span" color="#3333ff"> }</font></div><div><font class="Apple-style-span" color="#3333ff">}</font></div><div>
<font class="Apple-style-span" color="#3333ff"><br></font></div><div><font class="Apple-style-span" color="#3333ff">refinement.geometry_restraints.edits {</font></div><div><font class="Apple-style-span" color="#3333ff"> bond {</font></div>
<div><font class="Apple-style-span" color="#3333ff"> action = *add</font></div><div><font class="Apple-style-span" color="#3333ff"> atom_selection_1 = name ZN and chain D and resname ZN and resseq 2001</font></div>
<div><font class="Apple-style-span" color="#3333ff"> atom_selection_2 = name SG and chain D and resname CYS and resseq 1194</font></div><div><font class="Apple-style-span" color="#3333ff"> distance_ideal = 2.310000</font></div>
<div><font class="Apple-style-span" color="#3333ff"> sigma = 0.100</font></div><div><font class="Apple-style-span" color="#3333ff"> }</font></div><div><font class="Apple-style-span" color="#3333ff">}</font></div><div>
<font class="Apple-style-span" color="#3333ff"><br></font></div><div><font class="Apple-style-span" color="#3333ff">refinement.geometry_restraints.edits {</font></div><div><font class="Apple-style-span" color="#3333ff"> bond {</font></div>
<div><font class="Apple-style-span" color="#3333ff"> action = *add</font></div><div><font class="Apple-style-span" color="#3333ff"> atom_selection_1 = name ZN and chain D and resname ZN and resseq 2001</font></div>
<div><font class="Apple-style-span" color="#3333ff"> atom_selection_2 = name SG and chain D and resname CYS and resseq 1112</font></div><div><font class="Apple-style-span" color="#3333ff"> distance_ideal = 2.310000</font></div>
<div><font class="Apple-style-span" color="#3333ff"> sigma = 0.100</font></div><div><font class="Apple-style-span" color="#3333ff"> }</font></div><div><font class="Apple-style-span" color="#3333ff">}</font></div><div>
<font class="Apple-style-span" color="#3333ff"><br></font></div><div><font class="Apple-style-span" color="#3333ff">refinement.geometry_restraints.edits {</font></div><div><font class="Apple-style-span" color="#3333ff"> bond {</font></div>
<div><font class="Apple-style-span" color="#3333ff"> action = *add</font></div><div><font class="Apple-style-span" color="#3333ff"> atom_selection_1 = name ZN and chain D and resname ZN and resseq 2001</font></div>
<div><font class="Apple-style-span" color="#3333ff"> atom_selection_2 = name SG and chain D and resname CYS and resseq 1204</font></div><div><font class="Apple-style-span" color="#3333ff"> distance_ideal = 2.310000</font></div>
<div><font class="Apple-style-span" color="#3333ff"> sigma = 0.100</font></div><div><font class="Apple-style-span" color="#3333ff"> }</font></div><div><font class="Apple-style-span" color="#3333ff">}</font></div><div>
<font class="Apple-style-span" color="#3333ff"><br></font></div><div><font class="Apple-style-span" color="#3333ff">refinement.geometry_restraints.edits {</font></div><div><font class="Apple-style-span" color="#3333ff"> angle {</font></div>
<div><font class="Apple-style-span" color="#3333ff"> action = *add</font></div><div><font class="Apple-style-span" color="#3333ff"> atom_selection_1 = name SG and chain D and resname CYS and resseq 1194</font></div>
<div><font class="Apple-style-span" color="#3333ff"> atom_selection_2 = name ZN and chain D and resname ZN and resseq 2001</font></div><div><font class="Apple-style-span" color="#3333ff"> atom_selection_3 = name SG and chain D and resname CYS and resseq 1201</font></div>
<div><font class="Apple-style-span" color="#3333ff"> angle_ideal = 112.172178</font></div><div><font class="Apple-style-span" color="#3333ff"> sigma = 5</font></div><div><font class="Apple-style-span" color="#3333ff"> }</font></div>
<div><font class="Apple-style-span" color="#3333ff">}</font></div><div><font class="Apple-style-span" color="#3333ff"><br></font></div><div><font class="Apple-style-span" color="#3333ff">refinement.geometry_restraints.edits {</font></div>
<div><font class="Apple-style-span" color="#3333ff"> angle {</font></div><div><font class="Apple-style-span" color="#3333ff"> action = *add</font></div><div><font class="Apple-style-span" color="#3333ff"> atom_selection_1 = name SG and chain D and resname CYS and resseq 1112</font></div>
<div><font class="Apple-style-span" color="#3333ff"> atom_selection_2 = name ZN and chain D and resname ZN and resseq 2001</font></div><div><font class="Apple-style-span" color="#3333ff"> atom_selection_3 = name SG and chain D and resname CYS and resseq 1201</font></div>
<div><font class="Apple-style-span" color="#3333ff"> angle_ideal = 87.092184</font></div><div><font class="Apple-style-span" color="#3333ff"> sigma = 5</font></div><div><font class="Apple-style-span" color="#3333ff"> }</font></div>
<div><font class="Apple-style-span" color="#3333ff">}</font></div><div><font class="Apple-style-span" color="#3333ff"><br></font></div><div><font class="Apple-style-span" color="#3333ff">refinement.geometry_restraints.edits {</font></div>
<div><font class="Apple-style-span" color="#3333ff"> angle {</font></div><div><font class="Apple-style-span" color="#3333ff"> action = *add</font></div><div><font class="Apple-style-span" color="#3333ff"> atom_selection_1 = name SG and chain D and resname CYS and resseq 1112</font></div>
<div><font class="Apple-style-span" color="#3333ff"> atom_selection_2 = name ZN and chain D and resname ZN and resseq 2001</font></div><div><font class="Apple-style-span" color="#3333ff"> atom_selection_3 = name SG and chain D and resname CYS and resseq 1194</font></div>
<div><font class="Apple-style-span" color="#3333ff"> angle_ideal = 118.116518</font></div><div><font class="Apple-style-span" color="#3333ff"> sigma = 5</font></div><div><font class="Apple-style-span" color="#3333ff"> }</font></div>
<div><font class="Apple-style-span" color="#3333ff">}</font></div><div><font class="Apple-style-span" color="#3333ff"><br></font></div><div><font class="Apple-style-span" color="#3333ff">refinement.geometry_restraints.edits {</font></div>
<div><font class="Apple-style-span" color="#3333ff"> angle {</font></div><div><font class="Apple-style-span" color="#3333ff"> action = *add</font></div><div><font class="Apple-style-span" color="#3333ff"> atom_selection_1 = name SG and chain D and resname CYS and resseq 1204</font></div>
<div><font class="Apple-style-span" color="#3333ff"> atom_selection_2 = name ZN and chain D and resname ZN and resseq 2001</font></div><div><font class="Apple-style-span" color="#3333ff"> atom_selection_3 = name SG and chain D and resname CYS and resseq 1201</font></div>
<div><font class="Apple-style-span" color="#3333ff"> angle_ideal = 91.677138</font></div><div><font class="Apple-style-span" color="#3333ff"> sigma = 5</font></div><div><font class="Apple-style-span" color="#3333ff"> }</font></div>
<div><font class="Apple-style-span" color="#3333ff">}</font></div><div><font class="Apple-style-span" color="#3333ff"><br></font></div><div><font class="Apple-style-span" color="#3333ff">refinement.geometry_restraints.edits {</font></div>
<div><font class="Apple-style-span" color="#3333ff"> angle {</font></div><div><font class="Apple-style-span" color="#3333ff"> action = *add</font></div><div><font class="Apple-style-span" color="#3333ff"> atom_selection_1 = name SG and chain D and resname CYS and resseq 1204</font></div>
<div><font class="Apple-style-span" color="#3333ff"> atom_selection_2 = name ZN and chain D and resname ZN and resseq 2001</font></div><div><font class="Apple-style-span" color="#3333ff"> atom_selection_3 = name SG and chain D and resname CYS and resseq 1194</font></div>
<div><font class="Apple-style-span" color="#3333ff"> angle_ideal = 130.829256</font></div><div><font class="Apple-style-span" color="#3333ff"> sigma = 5</font></div><div><font class="Apple-style-span" color="#3333ff"> }</font></div>
<div><font class="Apple-style-span" color="#3333ff">}</font></div><div><font class="Apple-style-span" color="#3333ff"><br></font></div><div><font class="Apple-style-span" color="#3333ff">refinement.geometry_restraints.edits {</font></div>
<div><font class="Apple-style-span" color="#3333ff"> angle {</font></div><div><font class="Apple-style-span" color="#3333ff"> action = *add</font></div><div><font class="Apple-style-span" color="#3333ff"> atom_selection_1 = name SG and chain D and resname CYS and resseq 1204</font></div>
<div><font class="Apple-style-span" color="#3333ff"> atom_selection_2 = name ZN and chain D and resname ZN and resseq 2001</font></div><div><font class="Apple-style-span" color="#3333ff"> atom_selection_3 = name SG and chain D and resname CYS and resseq 1112</font></div>
<div><font class="Apple-style-span" color="#3333ff"> angle_ideal = 104.886672</font></div><div><font class="Apple-style-span" color="#3333ff"> sigma = 5</font></div><div><font class="Apple-style-span" color="#3333ff"> }</font></div>
<div><font class="Apple-style-span" color="#3333ff">}</font></div><div><br></div><div><br></div><div><font class="Apple-style-span" size="4">Questions, </font></div><div><font class="Apple-style-span" size="4">1. Why the ideal bond angle are different in the metal.edit file and final model ? How does phenix determine the ideal bond_angle?</font></div>
<div><font class="Apple-style-span" size="4"> For example, in the metal.edit file</font></div><div><font class="Apple-style-span" color="#3333ff"><font class="Apple-style-span" size="4"> </font>atom_selection_1 = name SG and chain D and resname CYS and resseq 1204</font></div>
<div><font class="Apple-style-span" color="#3333ff"> atom_selection_2 = name ZN and chain D and resname ZN and resseq 2001</font></div><div><font class="Apple-style-span" color="#3333ff"> atom_selection_3 = name SG and chain D and resname CYS and resseq 1112</font></div>
<div><font class="Apple-style-span" color="#3333ff"> The angle_ideal = 104.886672 </font></div><div><br></div><div><font class="Apple-style-span" size="4">But in the final model</font></div><div><font class="Apple-style-span" size="4"> </font></div>
<div><div><font class="Apple-style-span" color="#3333ff">atoms ideal model difference deviation (sigma)</font></div><div><font class="Apple-style-span" color="#3333ff">----------------------------------------------------------------------------</font></div>
<div><font class="Apple-style-span" color="#3333ff"> SG CYS D1204 57.894 104.470 46.576 9.32</font></div><div><font class="Apple-style-span" color="#3333ff">ZN ZN D2001 </font></div>
<div><font class="Apple-style-span" color="#3333ff"> SG CYS D1112 </font></div></div><div style="font-size: large; "><br></div></div><div style="font-size: large; ">2. Do I need to put the following LINK in the pdb header to run refinement?</div>
<div><font class="Apple-style-span" color="#3333ff">LINK ZN ZN D2001 SG CYS D1201 1555 1555 2.34 </font></div><div><font class="Apple-style-span" color="#3333ff">LINK ZN ZN D2001 SG CYS D1112 1555 1555 2.33 </font></div>
<div><font class="Apple-style-span" color="#3333ff">LINK ZN ZN D2001 SG CYS D1194 1555 1555 2.38 </font></div><div><font class="Apple-style-span" color="#3333ff">LINK ZN ZN D2001 SG CYS D1204 1555 1555 2.37</font></div>
<div><br></div><div><font class="Apple-style-span" size="4">3. After phenix refinement, the output pdb doesn't contain these LINK lines no matter what the inpout pdb is. Does phenix_refine use these restrains of LINK lines?</font></div>
<div><font class="Apple-style-span" size="4"><br></font></div><div><font class="Apple-style-span" size="4">Thanks.</font></div><div><font class="Apple-style-span" size="4"><br></font></div><div><font class="Apple-style-span" size="4">Yu Zhang</font></div>
<div><font class="Apple-style-span" size="4">Postdoc fellow</font></div><div><font class="Apple-style-span" size="4">Rutgers University</font></div>