No subject
Tue Sep 25 15:04:34 PDT 2012
econd reflection)?<br>
<br>
Check out <a href=3D"http://strucbio.biologie.uni-konstanz.de/ccp4wiki/inde=
x.php/Refinement#what_can_go_wrong_in_refinement.3F" target=3D"_blank">http=
://strucbio.biologie.uni-<u></u>konstanz.de/ccp4wiki/index.<u></u>php/Refin=
ement#what_can_go_<u></u>wrong_in_refinement.3F</a><br>
<br>
If, after thorough attempts, you fail to find the solution, upload your cur=
rent model, sequence and raw data frames to a Dropbox folder and post the l=
ink here - there may be people who succeed in processing the data nicely, o=
r otherwise can identify the problem based on the data (rather than based o=
n your description only).<br>
<br>
HTH,<br>
<br>
Kay<br>
<br>
Am 18.04.14 01:25, schrieb <a href=3D"mailto:phenixbb-request at phenix-online=
.org" target=3D"_blank">phenixbb-request at phenix-<u></u>online.org</a>:<br>
<blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1p=
x #ccc solid;padding-left:1ex">
Date: Thu, 17 Apr 2014 16:25:00 -0700<br>
From: Yarrow Madrona<<a href=3D"mailto:amadrona at uci.edu" target=3D"_blan=
k">amadrona at uci.edu</a>><br>
To: PHENIX user mailing list<<a href=3D"mailto:phenixbb at phenix-online.or=
g" target=3D"_blank">phenixbb at phenix-online.<u></u>org</a>><br>
Subject: [phenixbb] Stalled refinement<br>
Message-ID:<br>
=C2=A0 =C2=A0 =C2=A0 =C2=A0 <<a href=3D"mailto:CAMHjG6bPE4q1xWidpE2VwFMJ=
9qLSqjtLRuLMM1ef9vWBHBfZKg at mail.gmail.com" target=3D"_blank">CAMHjG6bPE4q1x=
WidpE2VwFMJ9qLS<u></u>qjtLRuLMM1ef9vWBHBfZKg at mail.<u></u>gmail.com</a>><=
br>
Content-Type: text/plain; charset=3D"utf-8"<div><div class=3D"h5"=
><br>
<br>
Hello,<br>
<br>
I using the latest stable build of phenx.refine (1.8.4) I recently<br>
collected data, processed and obtained an MR solution using phaser. I am<br=
>
stuck trying to refine with an Rfree sitting at 40%<br>
<br>
I really want to know if the high Rfree is due to poor data quality or if<b=
r>
non-crystallographic symmetry involving a near perfect two fold rotation<br=
>
between the two molecules in the ASU could somehow impede refinement. Stats=
<br>
and other information is below. Thank you for any help you can give.<br>
<br>
-Yarrow<br>
<br>
<br>
Visually, the quality of the data is marginal at best (streaky/ice rings in=
<br>
many frames) despite good processing stats from XDS. Processing with mosflm=
<br>
or HKL2000 managed to index but failed pretty bad in integration and<br>
scaling.<br>
<br>
Phaser gave high TFZ scores for 2 molecules in the asu (see below).<br>
<br>
Density for a cholesterol like ligand shows up even though not present in<b=
r>
the search model.<br>
<br>
MolRep Self rotation shows rotational symmetry.<br>
<a href=3D"https://www.dropbox.com/s/2zsajl5o091k50r/CYP142A2-032814_21_rf%=
20copy.pdf" target=3D"_blank">https://www.dropbox.com/s/<u></u>2zsajl5o091k=
50r/CYP142A2-<u></u>032814_21_rf%20copy.pdf</a><br>
<br>
The 2 molecules in the ASU are related by almost a 2 fold rotation:<br>
<br>
Rotation matrix for chain A to chain B:<br>
<br>
new_ncs_group<br>
rota_matrix =C2=A0 =C2=A01.0000 =C2=A0 =C2=A00.0000 =C2=A0 =C2=A00.0000<br>
rota_matrix =C2=A0 =C2=A00.0000 =C2=A0 =C2=A01.0000 =C2=A0 =C2=A00.0000<br>
rota_matrix =C2=A0 =C2=A00.0000 =C2=A0 =C2=A00.0000 =C2=A0 =C2=A01.0000<br>
tran_orth =C2=A0 =C2=A0 0.0000 =C2=A0 =C2=A00.0000 =C2=A0 =C2=A00.0000<br>
<br>
center_orth =C2=A0 15.2016 =C2=A0 =C2=A00.5245 =C2=A0 33.7070<br>
<br>
rota_matrix =C2=A0 -0.9860 =C2=A0 -0.1636 =C2=A0 -0.0309<br>
rota_matrix =C2=A0 -0.1659 =C2=A0 =C2=A00.9511 =C2=A0 =C2=A00.2605<br>
rota_matrix =C2=A0 -0.0132 =C2=A0 =C2=A00.2620 =C2=A0 -0.9650<br>
tran_orth =C2=A0 =C2=A0 =C2=A034.3310 =C2=A0-24.0033 =C2=A0107.0457<br>
<br>
center_orth =C2=A0 15.7607 =C2=A0 =C2=A07.2426 =C2=A0 77.7512<br>
<br>
RMSD, B onto A =3D 0.0007 after phaser<br>
RMSD, B onto A =3D 0.347 after one round of refinement in phenix<br>
<br>
<br>
Refinement using aniostropically corrected data (ucla web server:<br>
<a href=3D"http://Services.mbi.ucla.edu/anisoscale" target=3D"_blank">Servi=
ces.mbi.ucla.edu/<u></u>anisoscale</a>) did not improve the Rfree in refine=
ment.<br>
<br>
<br>
Statistics are listed below:<br>
<br>
UNIT CELL: 51.487 88.923 89.592 90 97.15 90 P21<br>
<br>
RESOLUTION =C2=A0 =C2=A0 NUMBER OF REFLECTIONS =C2=A0 =C2=A0COMPLETENESS R-=
FACTOR =C2=A0R-FACTOR<br>
COMPARED I/SIGMA =C2=A0 R-meas =C2=A0CC(1/2) =C2=A0Anomal =C2=A0SigAno =C2=
=A0 Nano<br>
=C2=A0 =C2=A0 LIMIT =C2=A0 =C2=A0 OBSERVED =C2=A0UNIQUE =C2=A0POSSIBLE =C2=
=A0 =C2=A0 OF DATA =C2=A0 observed =C2=A0expected<br>
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=
=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 Corr<br>
<br>
=C2=A0 =C2=A0 =C2=A0 5.99 =C2=A0 =C2=A0 =C2=A0 =C2=A08280 =C2=A0 =C2=A01927=
=C2=A0 =C2=A0 =C2=A02087 =C2=A0 =C2=A0 =C2=A0 92.3% =C2=A0 =C2=A0 =C2=A0 3=
.1% =C2=A0 =C2=A0 =C2=A03.3%<br>
=C2=A0 =C2=A08246 =C2=A0 35.09 =C2=A0 =C2=A0 =C2=A03.5% =C2=A0 =C2=A099.8* =
=C2=A0 =C2=A020* =C2=A0 0.909 =C2=A0 =C2=A01296<br>
=C2=A0 =C2=A0 =C2=A0 4.30 =C2=A0 =C2=A0 =C2=A0 14606 =C2=A0 =C2=A03401 =C2=
=A0 =C2=A0 =C2=A03487 =C2=A0 =C2=A0 =C2=A0 97.5% =C2=A0 =C2=A0 =C2=A0 3.3% =
=C2=A0 =C2=A0 =C2=A03.5%<br>
=C2=A0 14580 =C2=A0 33.37 =C2=A0 =C2=A0 =C2=A03.8% =C2=A0 =C2=A099.9* =C2=
=A0 =C2=A011* =C2=A0 0.843 =C2=A0 =C2=A02273<br>
=C2=A0 =C2=A0 =C2=A0 3.53 =C2=A0 =C2=A0 =C2=A0 17961 =C2=A0 =C2=A04244 =C2=
=A0 =C2=A0 =C2=A04445 =C2=A0 =C2=A0 =C2=A0 95.5% =C2=A0 =C2=A0 =C2=A0 3.8% =
=C2=A0 =C2=A0 =C2=A03.9%<br></div></div><div class=3D"">
=C2=A0 17944 =C2=A0 31.11 =C2=A0 =C2=A0 =C2=A04.4% =C2=A0 =C2=A099.8* =C2=
=A0 =C2=A0-2 =C2=A0 =C2=A00.789 =C2=A0 =C2=A02721<br>
=C2=A0 =C2=A0 =C2=A0 3.06 =C2=A0 =C2=A0 =C2=A0 21954 =C2=A0 =C2=A05068 =C2=
=A0 =C2=A0 =C2=A05221 =C2=A0 =C2=A0 =C2=A0 97.1% =C2=A0 =C2=A0 =C2=A0 4.9% =
=C2=A0 =C2=A0 =C2=A05.1%<br>
=C2=A0 21933 =C2=A0 24.81 =C2=A0 =C2=A0 =C2=A05.6% =C2=A0 =C2=A099.7* =C2=
=A0 =C2=A0-2 =C2=A0 =C2=A00.780 =C2=A0 =C2=A03455<br>
=C2=A0 =C2=A0 =C2=A0 2.74 =C2=A0 =C2=A0 =C2=A0 25741 =C2=A0 =C2=A05830 =C2=
=A0 =C2=A0 =C2=A05933 =C2=A0 =C2=A0 =C2=A0 98.3% =C2=A0 =C2=A0 =C2=A0 7.6% =
=C2=A0 =C2=A0 =C2=A07.6%<br>
=C2=A0 25713 =C2=A0 18.88 =C2=A0 =C2=A0 =C2=A08.6% =C2=A0 =C2=A099.5* =C2=
=A0 =C2=A0-2 =C2=A0 =C2=A00.782 =C2=A0 =C2=A04165<br>
=C2=A0 =C2=A0 =C2=A0 2.51 =C2=A0 =C2=A0 =C2=A0 27859 =C2=A0 =C2=A06311 =C2=
=A0 =C2=A0 =C2=A06483 =C2=A0 =C2=A0 =C2=A0 97.3% =C2=A0 =C2=A0 =C2=A010.8% =
=C2=A0 =C2=A0 10.8%<br>
=C2=A0 27824 =C2=A0 14.06 =C2=A0 =C2=A0 12.3% =C2=A0 =C2=A099.1* =C2=A0 =C2=
=A0-2 =C2=A0 =C2=A00.774 =C2=A0 =C2=A04385<br>
=C2=A0 =C2=A0 =C2=A0 2.32 =C2=A0 =C2=A0 =C2=A0 31336 =C2=A0 =C2=A06979 =C2=
=A0 =C2=A0 =C2=A07084 =C2=A0 =C2=A0 =C2=A0 98.5% =C2=A0 =C2=A0 =C2=A014.9% =
=C2=A0 =C2=A0 15.3%<br>
=C2=A0 31296 =C2=A0 10.49 =C2=A0 =C2=A0 16.8% =C2=A0 =C2=A098.5* =C2=A0 =C2=
=A0-4 =C2=A0 =C2=A00.748 =C2=A0 =C2=A05095<br>
=C2=A0 =C2=A0 =C2=A0 2.17 =C2=A0 =C2=A0 =C2=A0 32396 =C2=A0 =C2=A07347 =C2=
=A0 =C2=A0 =C2=A07567 =C2=A0 =C2=A0 =C2=A0 97.1% =C2=A0 =C2=A0 =C2=A022.3% =
=C2=A0 =C2=A0 22.7%<br>
=C2=A0 32341 =C2=A0 =C2=A07.46 =C2=A0 =C2=A0 25.4% =C2=A0 =C2=A097.3* =C2=
=A0 =C2=A0-7 =C2=A0 =C2=A00.728 =C2=A0 =C2=A05055<br>
=C2=A0 =C2=A0 =C2=A0 2.05 =C2=A0 =C2=A0 =C2=A0 32254 =C2=A0 =C2=A07339 =C2=
=A0 =C2=A0 =C2=A08047 =C2=A0 =C2=A0 =C2=A0 91.2% =C2=A0 =C2=A0 =C2=A033.1% =
=C2=A0 =C2=A0 33.5%<br>
=C2=A0 32075 =C2=A0 =C2=A05.06 =C2=A0 =C2=A0 37.5% =C2=A0 =C2=A094.8* =C2=
=A0 =C2=A0-6 =C2=A0 =C2=A00.724 =C2=A0 =C2=A05155<br>
=C2=A0 =C2=A0 =C2=A0total =C2=A0 =C2=A0 =C2=A0212387 =C2=A0 48446 =C2=A0 =
=C2=A0 50354 =C2=A0 =C2=A0 =C2=A0 96.2% =C2=A0 =C2=A0 =C2=A0 7.8% =C2=A0 =
=C2=A0 =C2=A07.9%<br>
211952 =C2=A0 16.57 =C2=A0 =C2=A0 =C2=A08.8% =C2=A0 =C2=A099.7* =C2=A0 =C2=
=A0-3 =C2=A0 =C2=A00.768 =C2=A0 33600<br>
<br></div><div class=3D"">
Processing with mosflm or HKL2000 managed to index but failed pretty bad in=
<br>
integration and scaling.<br>
<br>
<br></div><div class=3D"">
Phaser:<br>
<br>
SOLU SET RFZ=3D27.5 TFZ=3D24.2 PAK=3D0 LLG=3D1711 RF++ TFZ=3D64.6 PAK=3D0 L=
LG=3D3610<br>
LLG=3D4865<br></div>
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------------------------------<br>
</blockquote>
<br>
</blockquote></div><br></div>
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