<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><span id="OLK_SRC_BODY_SECTION"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; "><div><div><font class="Apple-style-span" face="Consolas"><br>Dear all, </font></div><div><font class="Apple-style-span" face="Consolas"><br></font></div><div><font class="Apple-style-span" face="Consolas">I am currently refining a rather well resolved protein at 0.97�. However, even after many cycles of refinement the R-factors are stuck at around Rwork/Rfree 14.5/16.5. Considering number of aa, Rmerge (3.5%) and resolution this seems to be too high. </font><span class="Apple-style-span" style="font-family: Consolas; ">I assume 10 – 25 macrocycles should be enough for effective weight refinement in phenix, however no improvement of the R-factors. </span></div><div><font class="Apple-style-span" face="Consolas"><br></font></div><div><font class="Apple-style-span" face="Consolas">A quick run with default settings in competitor software 'R' yields >2% better R-factors. </font></div><div><font class="Apple-style-span" face="Consolas"><br></font></div><div><span class="Apple-style-span" style="font-family: Consolas; ">I would appreciate suggestion how to improve my refinement protocol, values differing from default are listed below. </span></div><div><span class="Apple-style-span" style="font-family: Consolas; "><br></span></div><div><span class="Apple-style-span" style="font-family: Consolas; ">Thank you very much in advance</span></div><div><span class="Apple-style-span" style="font-family: Consolas; "><br></span></div><div><span class="Apple-style-span" style="font-family: Consolas; ">Eike</span></div><div><span class="Apple-style-span" style="font-family: Consolas; "><br></span></div><div><span class="Apple-style-span" style="font-family: Consolas; "><br></span></div><div><font class="Apple-style-span" face="Consolas"><br></font></div><div><font class="Apple-style-span" face="Consolas"><br></font></div><div><font class="Apple-style-span" face="Consolas"> </font></div><div><font class="Apple-style-span" face="Consolas"><br></font></div><div><font class="Apple-style-span" face="Consolas">refine {</font></div><div><font class="Apple-style-span" face="Consolas"> adp {</font></div><div><font class="Apple-style-span" face="Consolas"> individual {</font></div><div><font class="Apple-style-span" face="Consolas"> isotropic = element H</font></div><div><font class="Apple-style-span" face="Consolas"> anisotropic = not element H</font></div><div><font class="Apple-style-span" face="Consolas"> }</font></div><div><font class="Apple-style-span" face="Consolas"> group_adp_refinement_mode = one_adp_group_per_residue \</font></div><div><font class="Apple-style-span" face="Consolas"> *two_adp_groups_per_residue group_selection</font></div><div><font class="Apple-style-span" face="Consolas"> }</font></div><div><font class="Apple-style-span" face="Consolas"> }</font></div><div><font class="Apple-style-span" face="Consolas"> main {</font></div><div><font class="Apple-style-span" face="Consolas"> apply_overall_isotropic_scale_to_adp = False</font></div><div><font class="Apple-style-span" face="Consolas"> nqh_flips = False</font></div><div><font class="Apple-style-span" face="Consolas"> ordered_solvent = True</font></div><div><font class="Apple-style-span" face="Consolas"> place_ions = True</font></div><div><font class="Apple-style-span" face="Consolas"> number_of_macro_cycles = 10</font></div><div><font class="Apple-style-span" face="Consolas"> hydrogen_bonds = True</font></div><div><font class="Apple-style-span" face="Consolas"> use_convergence_test = True</font></div><div><font class="Apple-style-span" face="Consolas"> target = auto *ml mlhl ml_sad ls</font></div><div><font class="Apple-style-span" face="Consolas"> random_seed = 3326496</font></div><div><font class="Apple-style-span" face="Consolas"> wavelength = 0.885611</font></div><div><font class="Apple-style-span" face="Consolas"> nproc = 4</font></div><div><font class="Apple-style-span" face="Consolas"> }</font></div><div><font class="Apple-style-span" face="Consolas"> hydrogens {</font></div><div><font class="Apple-style-span" face="Consolas"> refine = individual *riding Auto</font></div><div><font class="Apple-style-span" face="Consolas"> }</font></div><div><font class="Apple-style-span" face="Consolas"> tls {</font></div><div><font class="Apple-style-span" face="Consolas"> find_automatically = False</font></div><div><font class="Apple-style-span" face="Consolas"> one_residue_one_group = False</font></div><div><font class="Apple-style-span" face="Consolas"> }</font></div><div><font class="Apple-style-span" face="Consolas"> ordered_solvent {</font></div><div><font class="Apple-style-span" face="Consolas"> mode = second_half filter_only every_macro_cycle \</font></div><div><font class="Apple-style-span" face="Consolas"> *every_macro_cycle_after_first</font></div><div><font class="Apple-style-span" face="Consolas"> h_bond_min_mac = 1</font></div><div><font class="Apple-style-span" face="Consolas"> h_bond_min_sol = 1</font></div><div><font class="Apple-style-span" face="Consolas"> h_bond_max = 6</font></div><div><font class="Apple-style-span" face="Consolas"> refine_occupancies = True</font></div><div><font class="Apple-style-span" face="Consolas"> new_solvent = isotropic *anisotropic</font></div><div><font class="Apple-style-span" face="Consolas"> b_iso_min = 0</font></div><div><font class="Apple-style-span" face="Consolas"> }</font></div><div><font class="Apple-style-span" face="Consolas"> peak_search {</font></div><div><font class="Apple-style-span" face="Consolas"> max_number_of_peaks = 1303</font></div><div><font class="Apple-style-span" face="Consolas"> }</font></div><div><font class="Apple-style-span" face="Consolas"> target_weights {</font></div><div><font class="Apple-style-span" face="Consolas"> optimize_xyz_weight = True</font></div><div><font class="Apple-style-span" face="Consolas"> optimize_adp_weight = True</font></div><div><font class="Apple-style-span" face="Consolas"> wxc_scale = 0.2</font></div><div><font class="Apple-style-span" face="Consolas"> wxu_scale = 0.2</font></div></div></div></div></blockquote></span></body></html>