<html>
<head>
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
Hi Noelia,<br>
<br>
it sounds like that molecule (the 5th) may be disordered and the
fact that its occupancy refines to 0.8 is a good indication of
this.. I suggest you do your best fixing outliers manually, then run
refinement with <br>
- Ramachandran plot restraints enabled (you can apply them to all
model or to just that 5th molecule only);<br>
- weights optimization (it runs much slower but if you can use
multiple CPUs that will speed it up);<br>
- may be secondary structure restraints (that will rely on SS
annotation provided in HELIX/SHEET records, so make sure it is
correct if you choose to use it).<br>
<br>
If this does not help please feel free to send me files and I will
have a look to see what else can be done!<br>
<br>
Good luck (and I guess I'll see you at Crystallography School in
Madrid in May?),<br>
Pavel<br>
<br>
<blockquote
cite="mid:E9CAC6E5-033E-478B-B187-5528B9B30153@iqfr.csic.es"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
<div style="margin: 0px;">Dear colleagues,</div>
<div style="margin: 0px; min-height: 14px;"><br>
</div>
<div style="margin: 0px;">I am dealing with the refinement of a
protein with 5 monomers in the asymmetric unit at 2.2 Å
resolution. Four of them have correct geometry and good density
map, however, the fifth molecule has poor density and bad
geometry. Ramachandran plot is presents 91.05% (favored), 3.23 %
(outliers). </div>
<div style="margin: 0px;">I have modified the occupancy of the
molecule, the refinement results in 0.8 occupancy for this
chain. I also tried to refined the structure without this chain,
but the R values increased and the density map indicated that it
should be there. I would like to refine this chain fixing the
geometry of the others which are correct. Do you have any ideas
about how to proceed?</div>
<div style="margin: 0px; min-height: 14px;"><br>
</div>
<div style="margin: 0px; min-height: 14px;"><br>
</div>
<div style="margin: 0px;">Some info:</div>
<div style="margin: 0px;">Protein residues 305 </div>
<div style="margin: 0px;">5 monomers in the a.u </div>
<div style="margin: 0px;">Space group C121 a=151.390, b= 67.81,
c=155.420Å, 94.53º</div>
<div style="margin: 0px;">R value 0.23 / Rfree 0.28</div>
<p style="margin: 0px; min-height: 14px;"> <br
class="webkit-block-placeholder">
</p>
<div style="margin: 0px;">Many thanks,</div>
<div style="margin: 0px;"><br>
</div>
<div style="margin: 0px;">Noelia</div>
</blockquote>
</body>
</html>