Re: [ccp4bb] A question of density

[Bernhard Rupp]

A few figures in BMC re truncation effects:

 

http://www.ruppweb.org/Garland/gallery/Ch9/pages/Biomolecular_Crystallography_Fig_9-05_PART1.htm

http://www.ruppweb.org/Garland/gallery/Ch9/pages/Biomolecular_Crystallography_Fig_9-05_PART2.htm

http://www.ruppweb.org/Garland/gallery/Ch10/pages/Biomolecular_Crystallography_Fig_10-10.htm

 

Best, BR

 

From: CCP4 bulletin board  On Behalf Of 
0c2488af9525-dmarc-requ...@jiscmail.ac.uk
Sent: Thursday, March 5, 2020 12:21
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] A question of density

 

Hello, not sure if anyone has mentioned series termination errors in the 
vicinity of electron dense atoms. The attached is from Glusker & Trueblood and 
might be of interest.

Jon Cooper

 

On 5 Mar 2020 19:00, Jessica Besaw mailto:jbesaw1...@gmail.com> > wrote:

Hello Matthias,

 

Excellent point. Most of the the ordered water are easily visible at 2 rmsd. 
The central disordered (or partially occupied) water becomes visible only at 
1.3 - 1.4 rmsd, and it is very visible at 1 rmsd (which I have displayed all of 
the maps). In your opinion, do you think this would be noise? 

 

Jessica

 

On Wed, 4 Mar 2020 at 12:45, Barone, Matthias mailto:bar...@fmp-berlin.de> > wrote:

hey Jessica

a tip that might come up later on anyway: once you put every reasonable bit 
into the desity, what I like to to when facing such blobbs: I take a well 
defined water out to create a diff density at a position where I know it is 
real. Having a feeling of how much you have to contour the diff density at that 
point can give you a good feeling how much of noise is actually in your density 
right in between the waters..?

best, matthias

 

Dr. Matthias Barone

AG Kuehne, Rational Drug Design

Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
Robert-Rössle-Strasse 10
13125 Berlin

Germany
Phone: +49 (0)30 94793-284

  _  

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> 
> on behalf of Jessica Besaw mailto:jbesaw1...@gmail.com> >
Sent: Wednesday, March 4, 2020 6:42:34 PM
To: CCP4BB@JISCMAIL.AC.UK  
Subject: Re: [ccp4bb] A question of density 

 

Hey Nukri, 

 

Here are the details: Rwork/Rfree = 0.21 / 0.23 for a 2 Angstrom structure

 

I absolutely agree with you on the refinement. I did previously do that, and I 
attached the picture. 

 

What is the BB?

 

Cheers!

 

Jessica 

 

 

 

 

 

 

On Wed, 4 Mar 2020 at 12:20, Nukri Sanishvili mailto:sannu...@gmail.com> > wrote:

Hi Jessica,

You do not say how well is the rest of the structure refined. 

First, you should refine the structure best you can, without placing anything 
in the unclear blob of your interest so to obtain the best possible phases and 
hopefully improve the blob density as well.

Then you should let the BB see what that density looks like. Looking at only 
the list of possibilities has very little value without seeing the density 
itself.

Best wishes,

Nukri

 

On Wed, Mar 4, 2020 at 11:10 AM Jessica Besaw mailto:jbesaw1...@gmail.com> > wrote:

Hello friends,  

 

I have a "blob" of density in an active site of my protein. 

 

I am struggling to determine if I should place a water in this spot, if I 
should model it as a disordered water, if the density may be a ligand that I 
have not considered, or if it should be left as unaccounted for density. I 
would like to publish this structure without compromising the science.

 

I have attached several possibilities that I have considered below. 

 

Any suggestions would be appreciated.

 

Cheers!

 

Jessica Besaw

 

 

 

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Re: [ccp4bb] A question of density

[Dale Tronrud]

On 3/5/2020 11:00 AM, Jessica Besaw wrote:
> Hello Matthias,
> 
> Excellent point. Most of the the ordered water are easily visible at 2
> rmsd. The central disordered (or partially occupied) water becomes
> visible only at 1.3 - 1.4 rmsd, and it is very visible at 1 rmsd (which
> I have displayed all of the maps). In your opinion, do you think this
> would be noise? 

   "Noise" is a word that I hate.  Usually it is just a label we put on
something that we want an excuse to ignore.  If you decide to ignore
something you should be honest and have a specific reason.

   Personally, I think it is sufficient reason to not place an atom when
you are unsure if an atom should be placed.  With the density you have
shown, it is hard to imagine a consistent model that contains a
partially occupied water molecule in this little peak.  That "water
molecule" would be inconsistent with full occupancy of the atom to the
left, but that atom already has the lowest B factor when refined at full
occupancy.  These two atoms are too close together to both be present in
the same unit cell.

   Without a reasonable atomic model in mind, you can't build a
reasonable model.  Building a model is not simply the task of placing
atoms in peaks.  The resulting structure has to make physical sense.
What hydrogen bonding network are you proposing to exist when this rare
conformation is present?

   If you don't have confidence in a model, don't build it.  You will be
left with this little difference map peak, and you will take a tiny hit
on your R values.  Them's the breaks!  Putting in an atom you don't
believe would give you those slightly smaller R values, but is that
honest?   It seems to me that building a model that doesn't make
chemical sense just to lower R values borders on deception.

   Whether that makes this peak "noise" is irrelevant.  Maybe in five or
ten years someone will come up with a new tool for building overlapping,
partially occupied, water networks and this peak will be explained.
Would that change if this peak is "noise" or not?  All we have now is a
peak that we don't have a good way to interpret.

Dale Tronrud


> 
> Jessica
> 
> On Wed, 4 Mar 2020 at 12:45, Barone, Matthias  > wrote:
> 
> hey Jessica
> 
> a tip that might come up later on anyway: once you put every
> reasonable bit into the desity, what I like to to when facing such
> blobbs: I take a well defined water out to create a diff density at
> a position where I know it is real. Having a feeling of how much you
> have to contour the diff density at that point can give you a good
> feeling how much of noise is actually in your density right in
> between the waters..?
> 
> best, matthias
> 
> 
> Dr. Matthias Barone
> 
> AG Kuehne, Rational Drug Design
> 
> Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
> Robert-Rössle-Strasse 10
> 13125 Berlin
> 
> Germany
> Phone: +49 (0)30 94793-284
> 
> 
> *From:* CCP4 bulletin board  > on behalf of Jessica Besaw
> mailto:jbesaw1...@gmail.com>>
> *Sent:* Wednesday, March 4, 2020 6:42:34 PM
> *To:* CCP4BB@JISCMAIL.AC.UK 
> *Subject:* Re: [ccp4bb] A question of density
>  
> Hey Nukri,
> 
> Here are the details: Rwork/Rfree = 0.21 / 0.23 for a 2 Angstrom
> structure
> 
> I absolutely agree with you on the refinement. I did previously do
> that, and I attached the picture. 
> 
> What is the BB?
> 
> Cheers!
> 
> Jessica 
> 
> 
> 
> 
> 
> 
> On Wed, 4 Mar 2020 at 12:20, Nukri Sanishvili  > wrote:
> 
> Hi Jessica,
> You do not say how well is the rest of the structure refined.
> First, you should refine the structure best you can, without
> placing anything in the unclear blob of your interest so to
> obtain the best possible phases and hopefully improve the blob
> density as well.
> Then you should let the BB see what that density looks like.
> Looking at only the list of possibilities has very little value
> without seeing the density itself.
> Best wishes,
> Nukri
> 
> On Wed, Mar 4, 2020 at 11:10 AM Jessica Besaw
> mailto:jbesaw1...@gmail.com>> wrote:
> 
> Hello friends, 
> 
> I have a "blob" of density in an active site of my protein. 
> 
> I am struggling to determine if I should place a water in
> this spot, if I should model it as a disordered water, if
> the density may be a ligand that I have not considered, or
> if it should be left as unaccounted for density. I would
> like to publish this structure without compromising the science.
> 
> I have attached several possibilities 

Re: [ccp4bb] [3dem] Which resolution?

[Kay Diederichs]

Dear James,

important and educational points! This triggers some thoughts ...

The one point where I don't quite agree is with "What about filtering out the 
noise?  An ideal noise suppression filter has the same shape as the signal (I 
found that in Numerical Recipes), and the shape of the signal from a 
macromolecule is a Gaussian in reciprocal space (aka straight line on a Wilson 
plot). This is true, by the way, for both a molecule packed into a crystal or 
free in solution.  So, the ideal noise-suppression filter is simply applying a 
B factor.  "

I think we can do better than that. We should use the knowledge about the 
actual signal and its noise (which we measure) as a weighting factor, rather 
than that of the theoretical signal (the straight line in the Wilson plot), for 
the purpose of noise suppression. Formula 13.3.6 in Numerical Recipes (3rd ed., 
2007), which gives the optimal (Wiener) filter to be used for weighting, is 
phi(f) = S(f)^2/(S(f)^2 + N(f)^2)  . But at high resolution, this is just 
CC1/2: see Box 1 of reference (1) - the formula CC1/2 = 1/(1 + 2/(I/sigma)^2 
can be written as CC1/2 = ^2/(^2 + 2 ^2) where sigma is the 
estimate of the noise in I ; don't know right now why there is a factor of 2).  
This goes to zero at the resolution where the signal goes to zero, and is near 
one in the resolution range in which we have good knowledge of the signal. 
(I only thought about this today, and I also considered CC* as a weighting 
factor, as I understand is suggested by Rosenthal and Henderson, J.Mol.Biol. 
2003, but I cannot convince myself currently that this is right. Anyway, the 
shape of the CC* curve as a function of resolution matches that of CC1/2)
In other words, we should be able to suppress the noise by multiplying the 
Fourier coefficients used for map calculation with (a smooth 
resolution-dependent approximation of) CC1/2. This should allow to sharpen, 
with the best noise suppression we can get.

Thinking about this, we are already typically using weighted Fourier 
coefficients of the form 2mFobs-DFcalc for map calculation. Aren't these 
already weighted in the correct way? I think not - those m and D weights are 
calculated from estimates of model (in-)accuracy and (in-)completeness, but 
don't properly take the measurement errors into account. Of course, since noisy 
data make the sigmaA values worse, the noise in the data influences sigmaA, but 
not in the functionally correct form. To my understanding, the correct way to 
take account of both model and data errors is given by reference (2), which - 
to my knowledge - is not yet implemented except in PHASER. 

Hope this makes sense!

Kay

References:
(1) Karplus & Diederichs (2015) Assessing and maximizing data quality in 
macromolecular crystallography.
Curr. Opin. Struct. Biol. 34, 60-68 . PDF at 
https://www.biologie.uni-konstanz.de/typo3temp/secure_downloads/82815/0/2b10c9e6f9a28129e1b119d21aeeab217c918bb1/Karplus2015_CurrOpinStructBiol.pdf
(2) RJ Read, AJ McCoy (2016) A log-likelihood-gain intensity target for 
crystallographic phasing that accounts for experimental error. Acta 
Crystallographica Section D: Structural Biology 72 (3), 375-387 
https://scripts.iucr.org/cgi-bin/paper?dz5382

On Thu, 5 Mar 2020 01:11:33 +0100, James Holton  wrote:

>
>The funny thing is, although we generally regard resolution as a primary
>indicator of data quality the appearance of a density map at the classic
>"1-sigma" contour has very little to do with resolution, and everything
>to do with the B factor.
>
>Seriously, try it. Take any structure you like, set all the B factors to
>30 with PDBSET, calculate a map with SFALL or phenix.fmodel and have a
>look at the density of tyrosine (Tyr) side chains.  Even if you
>calculate structure factors all the way out to 1.0 A the holes in the
>Tyr rings look exactly the same: just barely starting to form.  This is
>because the structure factors from atoms with B=30 are essentially zero
>out at 1.0 A, and adding zeroes does not change the map.  You can adjust
>the contour level, of course, and solvent content will have some effect
>on where the "1-sigma" contour lies, but generally B=30 is the point
>where Tyr side chains start to form their holes.  Traditionally, this is
>attributed to 1.8A resolution, but it is really at B=30.  The point
>where waters first start to poke out above the 1-sigma contour is at
>B=60, despite being generally attributed to d=2.7A.
>
>Now, of course, if you cut off this B=30 data at 3.5A then the Tyr side
>chains become blobs, but that is equivalent to collecting data with the
>detector way too far away and losing your high-resolution spots off the
>edges.  I have seen a few people do that, but not usually for a
>published structure.  Most people fight very hard for those faint,
>barely-existing high-angle spots.  But why do we do that if the map is
>going to look the same anyway?  The reason is because resolution and B
>factors are linked.
>
>Resolution 

Re: [ccp4bb] A question of density

[Dale Tronrud]

   Series termination is a problem when you leave out Fourier
coefficients that have significant amplitude.  Back in the old days when
we cut data aggressively it was something to worry about.  Now that most
everyone integrates down to very weak intensities it shouldn't be much
of a problem.

   Besides, as Glusker and Tureblood noted, a peak in a difference map
(the green blob in this discussion) cannot be caused by series
termination.  If there is series termination the shape of a difference
map peak can be affected, but not the presence of the peak itself.

Dale Tronrud

On 3/5/2020 12:20 PM, 0c2488af9525-dmarc-requ...@jiscmail.ac.uk wrote:
> Hello, not sure if anyone has mentioned series termination errors in the
> vicinity of electron dense atoms. The attached is from Glusker &
> Trueblood and might be of interest.
> 
> Jon Cooper
> 
> On 5 Mar 2020 19:00, Jessica Besaw  wrote:
> 
> Hello Matthias,
> 
> Excellent point. Most of the the ordered water are easily visible at
> 2 rmsd. The central disordered (or partially occupied) water becomes
> visible only at 1.3 - 1.4 rmsd, and it is very visible at 1 rmsd
> (which I have displayed all of the maps). In your opinion, do you
> think this would be noise? 
> 
> Jessica
> 
> On Wed, 4 Mar 2020 at 12:45, Barone, Matthias  > wrote:
> 
> hey Jessica
> 
> a tip that might come up later on anyway: once you put every
> reasonable bit into the desity, what I like to to when facing
> such blobbs: I take a well defined water out to create a diff
> density at a position where I know it is real. Having a feeling
> of how much you have to contour the diff density at that point
> can give you a good feeling how much of noise is actually in
> your density right in between the waters..?
> 
> best, matthias
> 
> 
> Dr. Matthias Barone
> 
> AG Kuehne, Rational Drug Design
> 
> Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
> Robert-Rössle-Strasse 10
> 13125 Berlin
> 
> Germany
> Phone: +49 (0)30 94793-284
> 
> 
> 
> *From:* CCP4 bulletin board  > on behalf of Jessica Besaw
> mailto:jbesaw1...@gmail.com>>
> *Sent:* Wednesday, March 4, 2020 6:42:34 PM
> *To:* CCP4BB@JISCMAIL.AC.UK 
> *Subject:* Re: [ccp4bb] A question of density
>  
> Hey Nukri,
> 
> Here are the details: Rwork/Rfree = 0.21 / 0.23 for a 2 Angstrom
> structure
> 
> I absolutely agree with you on the refinement. I did previously
> do that, and I attached the picture. 
> 
> What is the BB?
> 
> Cheers!
> 
> Jessica 
> 
> 
> 
> 
> 
> 
> On Wed, 4 Mar 2020 at 12:20, Nukri Sanishvili
> mailto:sannu...@gmail.com>> wrote:
> 
> Hi Jessica,
> You do not say how well is the rest of the structure refined.
> First, you should refine the structure best you can, without
> placing anything in the unclear blob of your interest so to
> obtain the best possible phases and hopefully improve the
> blob density as well.
> Then you should let the BB see what that density looks like.
> Looking at only the list of possibilities has very little
> value without seeing the density itself.
> Best wishes,
> Nukri
> 
> On Wed, Mar 4, 2020 at 11:10 AM Jessica Besaw
> mailto:jbesaw1...@gmail.com>> wrote:
> 
> Hello friends, 
> 
> I have a "blob" of density in an active site of my protein. 
> 
> I am struggling to determine if I should place a water
> in this spot, if I should model it as a disordered
> water, if the density may be a ligand that I have not
> considered, or if it should be left as unaccounted for
> density. I would like to publish this structure without
> compromising the science.
> 
> I have attached several possibilities that I have
> considered below. 
> 
> Any suggestions would be appreciated.
> 
> Cheers!
> 
> Jessica Besaw
> 
> 
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following
> link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 
> 
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> 

Re: [ccp4bb] A question of density

[Jessica Besaw]

Hello Matthias,

Excellent point. Most of the the ordered water are easily visible at 2
rmsd. The central disordered (or partially occupied) water becomes visible
only at 1.3 - 1.4 rmsd, and it is very visible at 1 rmsd (which I have
displayed all of the maps). In your opinion, do you think this would be
noise?

Jessica

On Wed, 4 Mar 2020 at 12:45, Barone, Matthias  wrote:

> hey Jessica
>
> a tip that might come up later on anyway: once you put every reasonable
> bit into the desity, what I like to to when facing such blobbs: I take a
> well defined water out to create a diff density at a position where I know
> it is real. Having a feeling of how much you have to contour the diff
> density at that point can give you a good feeling how much of noise is
> actually in your density right in between the waters..?
>
> best, matthias
>
>
> Dr. Matthias Barone
>
> AG Kuehne, Rational Drug Design
>
> Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
> Robert-Rössle-Strasse 10
> 13125 Berlin
>
> Germany
> Phone: +49 (0)30 94793-284
> --
> *From:* CCP4 bulletin board  on behalf of Jessica
> Besaw 
> *Sent:* Wednesday, March 4, 2020 6:42:34 PM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] A question of density
>
> Hey Nukri,
>
> Here are the details: Rwork/Rfree = 0.21 / 0.23 for a 2 Angstrom structure
>
> I absolutely agree with you on the refinement. I did previously do that,
> and I attached the picture.
>
> What is the BB?
>
> Cheers!
>
> Jessica
>
>
>
>
>
>
> On Wed, 4 Mar 2020 at 12:20, Nukri Sanishvili  wrote:
>
>> Hi Jessica,
>> You do not say how well is the rest of the structure refined.
>> First, you should refine the structure best you can, without placing
>> anything in the unclear blob of your interest so to obtain the best
>> possible phases and hopefully improve the blob density as well.
>> Then you should let the BB see what that density looks like. Looking at
>> only the list of possibilities has very little value without seeing the
>> density itself.
>> Best wishes,
>> Nukri
>>
>> On Wed, Mar 4, 2020 at 11:10 AM Jessica Besaw 
>> wrote:
>>
>>> Hello friends,
>>>
>>> I have a "blob" of density in an active site of my protein.
>>>
>>> I am struggling to determine if I should place a water in this spot, if
>>> I should model it as a disordered water, if the density may be a ligand
>>> that I have not considered, or if it should be left as unaccounted for
>>> density. I would like to publish this structure without compromising the
>>> science.
>>>
>>> I have attached several possibilities that I have considered below.
>>>
>>> Any suggestions would be appreciated.
>>>
>>> Cheers!
>>>
>>> Jessica Besaw
>>>
>>>
>>>
>>> --
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>>
>>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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[ccp4bb] Postdoc position on eye-disease structural biology at Stanford University

[Soichi Wakatsuki]

Dear all,

Prof. Vinit Mahajan’s group in Department of Ophthalmology, Stanford 
School of Medicine is seeking applications for a postdoctoral fellow 
position from ambitious, enthusiastic, and recent Ph.D. holders or 
graduate students who are expecting to finish his/her graduate degree in 
structural biology, biophysics, biochemistry, bioengineering, molecular 
cell biology, or pharmaceutics. The successful candidate will be a 
structural biologist with strong interests in biomedical, translational, 
and pharmaceutical sciences, who can carry out one or few structural 
biology projects for eye disease proteins. Dr. Mahajan is a 
physician/surgeon, and a scientist, who is the vice chair for research 
and the director of Molecular Surgery Program of the Stanford’s Byers 
Eye Institute. He runs a large interdisciplinary group of scientists and 
clinicians, who are actively seeking for therapeutics and cure for eye 
patients (https://mahajanlab.stanford.edu/).


Mahajan group is pursuing structural biology research focused on eye 
diseases in a close collaboration with Prof. Soichi Wakatsuki, 
Structural Biology Department, Stanford School of Medicine and SLAC 
National Accelerator Laboratory 
(http://med.stanford.edu/wakatsukilab.html). Dr. Wakatsuki’s interests 
cover protein-protein interactions (Comerci & Herrmann et al. Nat. Comm. 
2019; Herrmann et al. PNAS 2019), enzyme dynamics (Stoffel et al. PNAS 
2019), and structure-based drug design (Hwang et. al., Nat. Comm. 2018).


Both Drs. Mahajan and Wakatsuki are members of Stanford BioX and ChEM-H, 
interdisciplinary institutes encompassing three Stanford Schools: 
Medicine, Chemistry, and Engineering. This provides a truly 
interdisciplinary research environment at the crossroad of medical 
science, structural biology and state-of-the art bioimaging 
technologies. The two groups collaborate closely on structural biology 
research on eye disease proteins. See one of our recent publications on 
the structure-function investigation of a cysteine protease: Calpain-5 
(Velez et al. Cell Reports 2020). Other ophthalmologic structural 
biology work includes: 1) targeted structure-functionomics for eye 
diseases; and 2) structure-based drug design for retinal degeneration.


SLAC provides state-of-the-art multi-modal structural biology 
technologies covering a wide range of spatiotemporal resolutions. SLAC 
hosts large scale infrastructures: SSRL Structural Molecular Biology 
(SMB), and Linac Coherent Light Source (LC/LS) providing synchrotron and 
X-ray beams for crystallography, scattering and spectroscopy, and 
Stanford-SLAC CryoEM Center (S2C2) providing access to the cryoelectron 
microscopy (Cryo-EM) instruments for both single particle structural 
analysis and tomography (CryoET).


_*Qualifications:*_ Ph.D. or equivalent degree in the relevant fields 
within the last 3 years. English proficiency is mandatory. Familiarity 
with one or more of structural biology techniques, including X-ray 
crystallography, small angle X-ray scattering, cryoEM/ET, 
biocomputation, and hybrid methods, as well as strong background and 
experiences in sample preparation and characterization. The applicant 
must be a good team player. Experiences in scientific writing and grant 
application to US funding agencies are plus.


*_Deadline:_* as soon as the position is filled.

*_Contacts: _*  Prof. Vinit Mahajan (vinit.maha...@stanford.edu)
                    Prof. Soichi Wakatsuki (soichi.wakats...@stanford.edu)

See the following websites for more information:
BioX: https://biox.stanford.edu/
SSRL: https://www-ssrl.slac.stanford.edu/
SSRL-SMB: https://www-ssrl.slac.stanford.edu/smb/index.html/
LCLS: https://lcls.slac.stanford.edu/
S2C2: https://cryoem.slac.stanford.edu/s2c2/

With best wishes

Vinit Mahajan and Soichi Wakatsuki

#

Soichi Wakatsuki, Ph.D.
Professor of Photon Science
SLAC National Accelerator Laboratory
2575 Sand Hill Road, MS 69
Menlo Park, CA   94025-7015
Tel: 1-650-926-4147, Fax:1-650-926-4100

Professor of Structural Biology
School of Medicine
Stanford University
James H. Clark Center W250A
318 Campus Drive
Stanford, CA   94305-5014
Tel: 1-650-723-8404
e-mail: soichi.wakats...@stanford.edu





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