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<p>Hi,<br>
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<p>I'm trying to follow the protocol described in White et al., <span style="color: rgb(115, 115, 115); font-family: Georgia, Times, serif; font-size: 13px; font-style: italic; background-color: rgb(255, 255, 255);">Structural principles of SNARE complex recognition
by the AAA+ protein NSF</span> e-life 2018 <br>
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<p><a href="https://elifesciences.org/articles/38888">https://elifesciences.org/articles/38888</a><br>
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<p>Here is the pertinent paragraph:<br>
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<p>"T<span style="color: rgb(33, 33, 33); font-family: "Noto Serif", serif; font-size: 16px; background-color: rgb(255, 255, 255);">o improve the Ramachandran statistics and geometry of the models, a two-parameter grid search of real space refinements was performed
in which 3–5 macrocycles of global minimization and local grid search were performed in the presence of secondary structure restraints. First, a grid refinement search was performed for both target functions with around 1000 refinements each. For the </span><em>emsley</em><span style="color: rgb(33, 33, 33); font-family: "Noto Serif", serif; font-size: 16px; background-color: rgb(255, 255, 255);"> target
function, </span><em>rama_weight</em><span style="color: rgb(33, 33, 33); font-family: "Noto Serif", serif; font-size: 16px; background-color: rgb(255, 255, 255);"> and </span><em>scale_allowed</em><span style="color: rgb(33, 33, 33); font-family: "Noto Serif", serif; font-size: 16px; background-color: rgb(255, 255, 255);"> were
varied from 0.01 to 300; for the </span><em>oldfield</em><span style="color: rgb(33, 33, 33); font-family: "Noto Serif", serif; font-size: 16px; background-color: rgb(255, 255, 255);"> target function, a grid of refinements was performed over </span><em>plot_cutoff</em><span style="color: rgb(33, 33, 33); font-family: "Noto Serif", serif; font-size: 16px; background-color: rgb(255, 255, 255);"> values
from 0.01 to 1.0 and </span><em>weight_scale</em><span style="color: rgb(33, 33, 33); font-family: "Noto Serif", serif; font-size: 16px; background-color: rgb(255, 255, 255);"> values from 0.1 to 300. Results were judged empirically and based primarily on
a balance between </span><em>CC<span style="box-sizing: border-box; font-size: 12px; line-height: 0; position: relative; vertical-align: baseline; bottom: -0.25em;">mask</span></em><span style="color: rgb(33, 33, 33); font-family: "Noto Serif", serif; font-size: 16px; background-color: rgb(255, 255, 255);"> and
a minimal fraction of residues flagged by the program CaBLAM (</span><a href="https://elifesciences.org/articles/38888#bib37" data-behaviour-initialised="true" style="box-sizing: border-box; background-color: rgb(255, 255, 255); color: rgb(33, 33, 33); text-decoration-line: none; border-bottom: 1px dotted rgb(33, 33, 33); font-family: "Noto Serif", serif; font-size: 16px;">Richardson
et al., 2018</a><span style="color: rgb(33, 33, 33); font-family: "Noto Serif", serif; font-size: 16px; background-color: rgb(255, 255, 255);">) because focusing on the fraction of residues with favored </span><em>CC<span style="box-sizing: border-box; font-size: 12px; line-height: 0; position: relative; vertical-align: baseline; bottom: -0.25em;">mask</span></em><span style="color: rgb(33, 33, 33); font-family: "Noto Serif", serif; font-size: 16px; background-color: rgb(255, 255, 255);"> and
Ramachandran statistics alone often resulted in unrealistic models with serious problems (</span><a href="https://elifesciences.org/articles/38888#fig12" data-behaviour-initialised="true" style="box-sizing: border-box; background-color: rgb(255, 255, 255); color: rgb(33, 33, 33); text-decoration-line: none; border-bottom: 1px dotted rgb(33, 33, 33); font-family: "Noto Serif", serif; font-size: 16px;">Figure
12</a><span style="color: rgb(33, 33, 33); font-family: "Noto Serif", serif; font-size: 16px; background-color: rgb(255, 255, 255);">, </span><a href="https://elifesciences.org/articles/38888#table2" data-behaviour-initialised="true" style="box-sizing: border-box; background-color: rgb(255, 255, 255); color: rgb(33, 33, 33); text-decoration-line: none; border-bottom: 1px dotted rgb(33, 33, 33); font-family: "Noto Serif", serif; font-size: 16px;">Table
2</a><span style="color: rgb(33, 33, 33); font-family: "Noto Serif", serif; font-size: 16px; background-color: rgb(255, 255, 255);">).</span>"<br>
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<p>There are no differences in the refined structures regardless of what parameters I change. Attached is the input file I use for phenix.real_space_refine (1.18.2​). Altering the oldfield weight_scale (0.1 to 300) and plot_cutoff (0.1 to 0.5) makes no difference.
Any help is highly appreciated. <br>
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<p>Best wishes,<br>
Reza<br>
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Reza Khayat, PhD
<div>Associate Professor </div>
<div>City College of New York</div>
<div>Department of Chemistry and Biochemistry</div>
<div>New York, NY 10031</div>
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