Hello, <br><br>I&#39;m using phenix.refine for the first time and have some problem to get it reach reasonable rmsd bonds (0.012-0.015) and angles (1.5-1.8).<br>I set the bonds rmsd_max and angles rmsd_max to these values and try different values for: <br>
wxc_scale (from default 0.5 downto 0.015),  wxu_scale (from default 1 down to 0.03), wc (from default 1 up to 8), with and without optimising wxc wxu.<br>Whatever the parameters, phenix never reached final rmsd better than 0.022 and 2.2.<br>
I refine the structure with refmac so far, but need to refine the occupancies (so phenix).<br>Am I doing something wrong? Should I just use phenix to refine only the occupancy (I am actually doing it)?<br>Any help or comment are welcome. <br>
<br>Some information: <br>space group: P21, 2 molecules (180 aa) / au, 510 waters, about 20% alternate conformations,<br>ligand covalently link to the protein (correct dictionary and link parameters for refmac or phenix -add link to cif),<br>
resolution: 1.32, refine xyz for all, Baniso for all (refmac), ncs not used, R 13.6 Rfree 17.7 fom 0.913 rmsd 0.012 1.56 (last refmac)<br><br>phenix version 1.6 289 (gui)<br><br>Best regards, <br>Lionel<br><br>