<div dir="ltr">Hi,<div><br></div><div>Here are some suggestions:</div><div><br></div><div>1) For the offending residues, check the TLS groups. Maybe you can exclude these residues from the TLS groups (using isotropic Bs for these residues only) or come up with a better assignment.<br></div><div>2) From your description, it sounds like you refined XYZ, B, TLS and occupancies right after MR. You could refine XYZ and B first, adding TLS and occupancies later.</div><div>3) 1.5 Å resolution is typically the "border" for using individual anisotropic ADP's. So you might want to try using anisotropic ADPs instead of TLS. There is no guarantee that it'll work, but why not give it a try.</div><div>4) Unrelated to B or TLS: Check the distance between the oxygen of the peptide unit (which is pushed out of density) and the nitrogen from the symmetry related molecule. I circled the interaction in red in your figure. The distance should be around 2.7-3.5 Å. I cannot tell from looking at the screenshot. If it is shorter, nonbonded restraints could push the atoms apart. </div><div><br></div><div>Best wishes,</div><div><br></div><div>Dorothee</div><div><br></div><div><div><img src="cid:ii_juycuq1z0" alt="bolb.jpg" width="562" height="351"><br></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Apr 26, 2019 at 5:41 AM Sam Tang <<a href="mailto:samtys0910@gmail.com">samtys0910@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div dir="ltr"><div dir="ltr">Hello,<br clear="all"><div><div dir="ltr" class="gmail-m_-6042032943916548139gmail_signature"><div dir="ltr"><div dir="ltr"><div style="font-size:12.7273px"><br></div></div></div></div></div><div><font color="#000000"><span style="font-size:12.7273px">I am refining a structure solved to 1.5A by MR. Rw/Rf were 0.17/0.22 which seem acceptable to me. At the very beginning part of the protein the electron density is a bit wobbly. I am able to build the residues into the positive densities. But after phenix.refine the chain always shifts away a bit and leaves the green blobs there. </span></font></div><div><br></div><div>(Photo: <a href="https://drive.google.com/open?id=1UngAJuEUt1S0LwPybMJLw2E1xA4cNM3R" target="_blank">https://drive.google.com/open?id=1UngAJuEUt1S0LwPybMJLw2E1xA4cNM3R</a>)<br></div><div><br></div><div>I am thinking if this can be solved by adjusting the target weights. Or can I apply certain restraints only to those few residues?</div><div><br></div><div>I refined XYZ (reciprocal space), XYZ (real space), individual B-factors, TLS and occupancies.</div><div><br></div><div>Thanks in advance.</div><div><br></div><div>Regards</div><div><br></div><div>Sam</div></div></div></div>
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