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<DIV><FONT face=宋体 size=2><FONT face="Times New Roman"><FONT size=3>Thank you
very much for your suggestions. I will try all these options and let you
know</FONT></FONT></FONT></DIV>
<DIV><FONT face=宋体 size=2><FONT face="Times New Roman"><FONT size=3>the results.
</FONT></FONT></FONT></DIV>
<DIV><FONT face=宋体 size=2><FONT face="Times New Roman"><FONT
size=3></FONT></FONT></FONT> </DIV>
<DIV><FONT face=宋体 size=2><FONT face="Times New Roman"><FONT size=3>Rongjin
</FONT></DIV>
<DIV><FONT face=宋体 size=2></FONT> </DIV>
<DIV><FONT face=宋体 size=2></FONT> </DIV></FONT></FONT>
<DIV><FONT size=2><FONT face="Times New Roman"><FONT color=#666666>= = = = = = =
= <FONT color=#000000>On </FONT></FONT>2010-04-14 12:03:10 You
wrote <FONT color=#666666>= = = = = = = = </FONT></FONT></FONT></DIV>
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<BLOCKQUOTE
style="PADDING-RIGHT: 0px; PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #000000 2px solid; MARGIN-RIGHT: 0px">Hi
Rongjin,<BR><BR>
<BLOCKQUOTE cite=mid:201004141009505787450@foxmail.com type="cite">
<DIV>
<DIV><FONT face="Times New Roman">I am refining another 3.3 A
resolution structure. In coot I manually adjusted the
model</FONT></DIV>
<DIV><FONT face="Times New Roman">to have >95% residues
in preferred region in ramanchandran plot, but after
refinement </FONT></DIV>
<DIV><FONT face="Times New Roman">in Phenix only </FONT><FONT
face="Times New Roman"><80% residues in the preferred region and a
lot more in the outlier region.</FONT></DIV>
<DIV><FONT face="Times New Roman">This was wen I used the default
refinement parameters "phenix.refine mtz_file pdb_file".</FONT></DIV>
<DIV><FONT face="Times New Roman">R and R_free are 0.22/0.27 in this
case.</FONT></DIV></DIV></BLOCKQUOTE><BR>you may want to
consider:<BR><BR>- using secondary structure restraints;<BR>- tightening
restraints (using wxc_scale=...);<BR>- using H atoms in refinement;<BR>-
doing some quick geometry regularization before refinement;<BR>- fixing
manually and excluding from refinement certain parts of your
model.<BR><BR>You need to experiment and find empirically which
combination of the above options works in your case. I would appreciate
if you share your experience with this and tell us what worked for your
in the
end.<BR><BR>Pavel.<BR><BR></BLOCKQUOTE></TD></TR></TBODY></TABLE></FONT></DIV></DIV></BODY></HTML>