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<br>
Thank you Nigel,<br>
<br>
Rama-Z "before" (amber energy minimization):<br>
Rama-Z (Ramachandran plot Z-score):<br>
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z|
< 3; good |Rama-Z| < 2.<br>
Scores for whole/helix/sheet/loop are scaled independently;<br>
therefore, the values are not related in a simple manner.<br>
whole: -0.32 (0.86), residues: 62<br>
helix: 0.09 (1.50), residues: 12<br>
sheet: None (None), residues: 0<br>
loop : -0.27 (0.70), residues: 50<br>
<br>
after phenix.geometry_minimization<br>
whole: -3.20 (0.87), residues: 62<br>
helix: None (None), residues: 0<br>
sheet: -3.03 (1.30), residues: 12<br>
loop : -2.05 (0.72), residues: 50<br>
<br>
repeated with cdl=False<br>
whole: -3.35 (0.90), residues: 62<br>
helix: None (None), residues: 0<br>
sheet: -4.51 (1.09), residues: 10<br>
loop : -1.90 (0.75), residues: 52<br>
<br>
<br>
<br>
pdbs and logs are tarballed here:<br>
<a class="moz-txt-link-freetext" href="https://bl831.als.lbl.gov/~jamesh/bugreports/phenixmin_070721.tgz">https://bl831.als.lbl.gov/~jamesh/bugreports/phenixmin_070721.tgz</a><br>
<br>
<br>
<div class="moz-cite-prefix">On 7/8/2021 11:16 AM, Nigel Moriarty
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CANkP=2dJAVCW+HXp6CfuMW+Z0eqM19B9+LbRESDM4CLV-wL1rA@mail.gmail.com">
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<div dir="ltr">James
<div><br>
</div>
<div>This is very interesting from a different perspective but I
should point out a few things.</div>
<div><br>
</div>
<div>1. The CDL, which is the default, changes the backbone
bonds and angles based on phi/psi. Maybe in geometry
minimisation this is causing the "whirlygig." Can you check
with cdl=False?</div>
<div><br>
</div>
<div>2. In a recent pub
<ol
style="color:rgb(0,0,0);font-family:verdana,helvetica,arial,sans-serif;font-size:21.6px">
<li>Sobolev OV, Afonine PV, Moriarty NW, Hekkelman ML,
Joosten RP, Perrakis A, Adams PD: <b>A Global Ramachandran
Score Identifies Protein Structures with Unlikely
Stereochemistry.</b> <a
href="http://dx.doi.org/10.1016/j.str.2020.08.005"
style="text-decoration-line:none" moz-do-not-send="true"><i>Structure</i> 2020, <b>28</b>:1249-1258.e2.</a> [PMID:
32857966] [PMCID: PMC7642142]</li>
</ol>
<div><font face="verdana, helvetica, arial, sans-serif"
color="#000000"><span style="font-size:21.6px">we argue
that percent favoured is not an accurate measure of Rama
health. Could also provide these numbers?</span></font></div>
<div><font face="verdana, helvetica, arial, sans-serif"
color="#000000"><span style="font-size:21.6px"><br>
</span></font></div>
<div>
<div dir="ltr" class="gmail_signature"
data-smartmail="gmail_signature">
<div dir="ltr">
<div>
<div dir="ltr">
<div dir="ltr"><font face="arial, sans-serif">Cheers</font>
<div><font face="arial, sans-serif"><br>
</font></div>
<div><font face="arial, sans-serif">Nigel</font>
<div><font face="arial, sans-serif"><br>
</font></div>
<div><font face="arial, sans-serif">---</font></div>
<div><font face="arial, sans-serif">Nigel W.
Moriarty<br>
Building 33R0349, Molecular Biophysics and
Integrated Bioimaging</font></div>
<div><font face="arial, sans-serif">Lawrence
Berkeley National Laboratory</font><br>
<font face="arial, sans-serif">Berkeley, CA
94720-8235</font><br>
<font face="arial, sans-serif">Phone :
510-486-5709 Email : <a class="moz-txt-link-abbreviated" href="mailto:NWMoriarty@LBL.gov">NWMoriarty@LBL.gov</a><br>
Fax : 510-486-5909 Web : <a
href="http://CCI.LBL.gov" target="_blank"
moz-do-not-send="true">CCI.LBL.gov</a></font></div>
</div>
<div><font face="arial, sans-serif"><span
style="color:rgb(73,74,76)">ORCID : </span><font
color="#494a4c"><a
href="https://orcid.org/0000-0001-8857-9464"
target="_blank" moz-do-not-send="true">orcid.org/0000-0001-8857-9464</a></font></font><br>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br>
</div>
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<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Thu, Jul 8, 2021 at 10:28
AM James Holton <<a href="mailto:jmholton@lbl.gov"
moz-do-not-send="true">jmholton@lbl.gov</a>> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div> Thank you Pavel for your prompt response!<br>
<br>
I agree with everything you wrote below, and that is a good
point about 2nd derivatives. <br>
<br>
However, what I'm seeing is the opposite of what you might
predict. See below. <br>
<br>
<div>On 7/7/2021 11:27 PM, Pavel Afonine wrote:<br>
</div>
<blockquote type="cite">Hi James, <br>
<br>
thanks for email and sharing your observations! <br>
<br>
<blockquote type="cite">Greetings all, and I hope this
little observation helps improve things somehow. <br>
<br>
I did not expect this result, but there it is. My
MolProbity score goes from 0.7 to 1.9 after a run of
phenix.geometry_minimization <br>
<br>
I started with an AMBER-minimized model (based on 1aho),
and that got me my best MolProbity score so far (0.7).
But, even with hydrogens and waters removed the
geometry_minimization run increases the clashscore from
0 to 3.1 and Ramachandran favored drops from 98% to 88%
with one residue reaching the outlier level. <br>
</blockquote>
<br>
It is not a secret that 'standard geometry restraints'
used in Phenix and alike (read Refmac, etc) are very
simplistic. They are not aware of main chain preferential
conformations (Ramachandran plot), favorable side chain
rotamer conformations. They don't even have any
electrostatic/attraction terms -- only anti-bumping
repulsion! Standard geometry restraints won't like any NCI
(non-covalent interaction) and likely will make
interacting atoms break apart rather than stay close
together interacting. <br>
</blockquote>
<br>
Yes, there's the rub: I'm not seeing "interacting atoms
break apart", but rather they are being smashed together.
Torsion angles are also being twisted out of allowed regions
of the Ramachandran plot. <br>
<br>
All this with the x-ray term turned off!<br>
<br>
<blockquote type="cite">With this in mind any high quality
(high-resolution) atomic model or the one optimized using
sufficiently high-level QM is going to have a more
realistic geometry than the result of geometry
regularization against very simplistic restraints target.
An example: <br>
<br>
<a
href="https://journals.iucr.org/d/issues/2020/12/00/lp5048/lp5048.pdf"
target="_blank" moz-do-not-send="true">https://journals.iucr.org/d/issues/2020/12/00/lp5048/lp5048.pdf</a>
<br>
<br>
and previous papers on the topic. <br>
</blockquote>
<br>
I agree, but what doesn't make sense to me is how the
"simplistic restraints" of phenix.geometry_minimization
would be so inconsistent with the "simplistic restraints" in
phenix.molprobity ?<br>
<br>
What I am doing here is starting with an energy-minimized
model of a 1.0 A structure (1aho). It's not a fancy QM, just
the ff14SB potential in AMBER. I get my best molprobity
scores this way, but I need an x-ray refinement program like
phenix.refine to compare these models with reality. It
troubles me that the "geometry" in the x-ray refinement
program all by itself messes up my molprobity score.<br>
<br>
<blockquote type="cite"> <br>
<blockquote type="cite">Just for comparison, with refmac5
in "refi type ideal" mode I see the MolProbity rise to
1.13, but Clashscore remains zero, some Ramas go from
favored to allowed, but none rise to the level of
outliers. <br>
</blockquote>
<br>
I believe this is because of the nature of minimizer used.
Refmac uses 2nd derivative based one, which in a nutshell
means it can move the model much less (just a bit in
vicinity of a local minimum) than any program that uses
gradients only (like Phenix). <br>
</blockquote>
good point.<br>
<br>
So, what should I do to stabilize
phenix.geometry_minimization? Crank up the non-bonded
weight? Restrain to starting coordinates?<br>
<br>
<blockquote type="cite">
<blockquote type="cite">Files and logs here: <br>
<a
href="https://bl831.als.lbl.gov/~jamesh/bugreports/phenixmin_070721.tgz"
target="_blank" moz-do-not-send="true">https://bl831.als.lbl.gov/~jamesh/bugreports/phenixmin_070721.tgz</a>
<br>
<br>
I suspect this might have something to do with library
values for main-chain bonds and angles? They do seem to
vary between programs. Phenix having the shortest CA-CA
distance by up to 0.08 A. After running thorough
minimization on a poly-A peptide I get: <br>
bond amber refmac phenix shelxl Stryer <br>
C-N 1.330 1.339 1.331 1.325 1.32 <br>
N-CA 1.462 1.482 1.455 1.454 1.47 <br>
CA-C 1.542 1.534 1.521 1.546 1.53 <br>
CA-CA 3.862 3.874 <font color="#ff0000"><b>3.794</b></font>
3.854 <br>
<br>
So, which one is "right" ? <br>
</blockquote>
<br>
I'd say they are all the same, within their 'sigmas' which
are from memory about 0.02A: <br>
</blockquote>
I note that 3.874 - 3.794 = 0.08 > 0.02<br>
<br>
This brings me to my pet theory. I think what is going on
is small errors like this build up a considerable amount of
tension in the long main chain. For this 64-mer, the contour
length of the main chain after idealization is ~5 A shorter
after phenix.geometry_minimization than it is after shelxl
or amber. That 5 A has to come from somewhere. Without
stretching bonds or bending angles the only thing left to do
is twisting torsions. A kind of "whirlygig" effect.<br>
<br>
The question is: is the phenix CA-CA distance too short? Or
is the amber CA-CA distance too long?<br>
<br>
Shall we vote?<br>
<br>
-James<br>
<br>
<br>
</div>
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