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<p>Hi Juliana,</p>
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<div class="WordSection1">After running phenix real space refine
with different refinement strategies.� My map-model FSC curve
has some interesting features:<o:p></o:p>
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It does not starts at 1 as it does the map FSC curve, is
that ok?� What could be causing this?</li>
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<p>which one is it? Is it FSC(half_map1, half_map2) or
FSC(experimental_map, model_map) ?<br>
</p>
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It has a dip around 5-6�, this deep can be a bit up or down
depending the refinement strategy I use, therefore the FSC
model at 0.5 can cut the resolution at 3.9 or 6 �. What this
deep mean?� Am I doing something wrong in the refinement?</li>
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<p>How different these models are?<br>
</p>
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The mask and unmask curves completely overlap, is that ok?</li>
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<p>This suggests to me the map is probably already masked or somehow
'normalized'..<br>
</p>
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Also, my refinement shows a high clash score (15-20), if I
change the nonbonded_weight parameter from 100 (default) to
higher values the clash score decreases but the FSC curves
gets lower them the FSC curve crosses the 0.5 cutoff at 6A.</li>
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<p>When it comes to clashscore, generally the lower the better but
zero is not the goal.<br>
</p>
<p>Looking at one of screenshots I see you have 2.42% of atoms with
occupancy less than 1. Do you really see partially occupied atoms
in 4A resolution map? Unlikely! So.. please check those out!</p>
<p>I can run more diagnostics for you if you share maps and models
(off-list of course!).<br>
</p>
<p>Pavel</p>
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