From owner-chemistry@ccl.net Fri Mar 15 05:37:01 2013 From: "Herbert Fruchtl herbert.fruchtl]_[st-andrews.ac.uk" To: CCL Subject: CCL:G: DFT and MP2 Message-Id: <-48410-130315052624-7288-DbkfCvGELU+8KEzi7UlWSQ**server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-9; format=flowed Date: Fri, 15 Mar 2013 09:26:00 +0000 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl^st-andrews.ac.uk] That's useful in showing that it is probably a memory problem. The scientific result is of course meaningless. MP2 (like all post-HF methods) is more sensitive to basis set size than DFT, and 6-31g* is really the bare minimum. Generally, for DFT energy/gradient a few GB memory are usually enough, and I have seen cases where more memory slowed things down. For MP2 (and DFT frequencies) you should give it as much memory as possible. It's semidirect, and even if it doesn't fail, it will need more passes of integral calculation if there is less memory available. HTH, Herbert On 15/03/13 01:53, Serdar Badoğlu serdarbadoglu() gmail.com wrote: > I haven't seen such a message. > > Finally there's hope for me. I have changed the command line as # opt freq > mp2/3-21g geom=connectivity, memory settings stayed the same. Finished > successfully in 20 minutes. > > > On Thu, Mar 14, 2013 at 10:07 PM, Reis Heribert hreis*eie.gr > > wrote: > > I don't think that will help. What Sam means is that the memory you assign > (%mem=1GB) is too small for the MP2 transformation. You should use much more > %mem (say 10GB), if you can, and if it is the problem. Usually the messages > in that case is sth like 'not enough memory do do one orbital in the MP2 > transformation' or so. > > I still would like to see the output before the dumped stuff. > > I guess you are you using a 64bit compiled Gaussian? > > Heribert > > > > On Thu, Mar 14, 2013 at 9:51 AM, Serdar Badoğlu serdarbadoglu.^^^.gmail.com > > wrote: > > %mem=1GB and %nproc=4 for me. I have 12 GB physical memory and Gaussian > running on a hdd which has over 100 GB free space. I always use "default > name" option with full path for chk files. At the moment another try is > running. This time I have used the chk file of previous calculation as a > new input. > > > > On Thu, Mar 14, 2013 at 6:55 PM, Abrash, Sam sabrash.:.richmond.edu > > wrote: > > That error also comes when there is working file that is larger than > the allotted memory. You should check the %mem keyword to make sure > enough memory has been allotted. MP2 is much more memory intensive > than DFT. > > Sam > > Samuel A. Abrash > Department of Chemistry > Coordinator, Environmental Studies Progrram > University of Richmond > Richmond, VA 23173 > Phone (Gottwald): 804-289-8248 > Phone (International Center): 804-484-1473 > Fax: 804-287-1897 > E-mail: sabrash,+,richmond.edu ,+,richmond.edu > > Web-page: > http://www.richmond.edu/~sabrash > "That's one of the tragedies of this life, that the men who are most > in need of a beating are always enormous." Rudy Valee, as J. D. > Hackensacker, III, in the Preston Sturges Film "The Palm Beach Story" > > > From: owner-chemistry+sabrash==richmond.edu > ,+,ccl.net > [mailto:owner-chemistry+sabrash > ==richmond.edu > ,+,ccl.net ] On Behalf Of Reis > Heribert hreis]![eie.gr > Sent: Thursday, March 14, 2013 11:39 AM > To: Abrash, Sam > Subject: CCL: DFT and MP2 > > Dear Serdar, > That looks like an file-IO problem. Can you include a bit more of > the end of the file, so that one can see which link produced the error? > Heribert > > On Thu, Mar 14, 2013 at 3:25 AM, Serdar Badoglu > serdarbadoglu^^^gmail.com > |a|ccl.net >> wrote: > > Sent to CCL by: "Serdar Badoglu" [serdarbadoglu[a]gmail.com > ] > Hi CCLers, > > I need to renew my DFT calculations with MP2. I had no problems > while I was > calculating the same molecule at B3LYP/6-31G* and 6-311++G** levels. > But at > MP2 level no matter what I have done I get errors. I've tried to distort > slightly the input geometry, but no change. I've tried to increase > the number > of cycles (maxcycle keyword), again no change. Can you suggest any other > solution to get rid of this problem? > > The end of the log file reads: > > dumping /fiocom/, unit = 3 NFiles = 1 SizExt = 524288 WInBlk = > 512 > defal = T LstWrd = 67072 FType=2 FMxFil=10000 > > Number 0 > Base 20480 > End 67072 > End1 67072 > Wr Pntr 20480 > Rd Pntr 20480 > Length 46592 > Error termination in NtrErr: > NtrErr Called from FileIO. > > Regards. > > Serdar Badoglu > Gazi University > > > > -= This is automatically added to each message by the mailing script > =-
> > E-mail to subscribers: CHEMISTRY|a|ccl.net > |a|ccl.net > > or use:E-mail to administrators: > CHEMISTRY-REQUEST|a|ccl.net > |a|ccl.net > or > usehttp://www.ccl.net/chemistry/sub_unsub.shtml > Content-Type: text/html; charset"us-ascii" > Content-Transfer-Encoding: quoted-printable > > xmlns:o="urn:schemas-microsoft-com:office:office" > xmlns:w="urn:schemas-microsoft-com:office:word" > xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" > xmlns="http://www.w3.org/TR/REC-html40"> > > > > > > >
>

That error also comes > when there is working file that is larger than the allotted > memory.  You should check the %mem keyword to make sure enough > memory has been allotted. MP2 is much more memory intensive than > DFT.

>

style="color:blue"> 

>

Sam

>

style="color:blue"> 

>

Samuel A. Abrash
> Department of Chemistry

>

Coordinator, > Environmental Studies Progrram
> University of Richmond
> Richmond, VA 23173
> Phone (Gottwald):  804-289-8248 >

>

Phone (International > Center): 804-484-1473
> Fax:  804-287-1897
> E-mail:  sabrash,+,richmond.edu >
> Web-page:  href="http://oncampus.richmond.edu/~sabrash">http://www.richmond.edu/~sabrash

>

"That's one of > the tragedies of this life, that the men who are most in need of a > beating are always enormous." Rudy Valee, as J. D. > Hackensacker, III, in the Preston Sturges Film "The Palm Beach > Story"

>

style="color:blue"> 

>

style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From: style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> > owner-chemistry+sabrash==richmond.edu > ,+,ccl.net > [mailto:owner-chemistry& > #43;sabrash==richmond.edu > ,+,ccl.net ] > On Behalf Of Reis Heribert hreis]![eie.gr
> Sent: Thursday, March 14, 2013 11:39 AM
> To: Abrash, Sam
> Subject: CCL: DFT and MP2

>

 

>
>
>
>

Dear Serdar,

>
>

That looks like an > file-IO problem. Can you include a bit more of the end of the file, > so that one can see which link produced the error?

>
>

Heribert

>
>

 

>
>

On Thu, Mar 14, 2013 at 3:25 AM, Serdar Badoglu > serdarbadoglu^^^gmail.com > < target="_blank">owner-chemistry|a|ccl.net > > wrote:

>


> Sent to CCL by: "Serdar  Badoglu" [serdarbadoglu[a] href="http://gmail.com" target="_blank">gmail.com > ]
> Hi CCLers,
>
> I need to renew my DFT calculations with MP2. I had no problems > while I was
> calculating the same molecule at B3LYP/6-31G* and 6-311++G** > levels. But at
> MP2 level no matter what I have done I get errors. I've tried to > distort
> slightly the input geometry, but no change. I've tried to increase > the number
> of cycles (maxcycle keyword), again no change. Can you suggest any > other
> solution to get rid of this problem?
>
> The end of the log file reads:
>
> dumping /fiocom/, unit = 3 NFiles =     1 SizExt =   >  524288 WInBlk =
> 512
>                   >  defal = T LstWrd =       67072 FType=2 > FMxFil=10000
>
>  Number           0
>  Base         20480
>  End          67072
>  End1         67072
>  Wr Pntr      20480
>  Rd Pntr      20480
>  Length       46592
>  Error termination in NtrErr:
>  NtrErr Called from FileIO.
>
> Regards.
>
> Serdar Badoglu
> Gazi University
>
>
>
> -= This is automatically added to each message by the mailing script > =-<br
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>
>
>
> > > > > > > -- > Serdar BADOĞLU, Ph.D. > Gazi Üniversitesi Fizik Bölümü > > > > > > -- > Serdar BADOĞLU, Ph.D. > Gazi Üniversitesi Fizik Bölümü -- Herbert Fruchtl Senior Scientific Computing Officer School of Chemistry, School of Mathematics and Statistics University of St Andrews -- The University of St Andrews is a charity registered in Scotland: No SC013532 From owner-chemistry@ccl.net Fri Mar 15 07:50:00 2013 From: "Stephan Ehrlich stephan.ehrlich]_[uni-muenster.de" To: CCL Subject: CCL:G: DFT and MP2 Message-Id: <-48411-130315043108-4847-OenTPwSdQbDjvZ4Tm3BsSQ]![server.ccl.net> X-Original-From: "Stephan Ehrlich" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes Date: Fri, 15 Mar 2013 09:31:00 +0100 MIME-Version: 1.0 Sent to CCL by: "Stephan Ehrlich" [stephan.ehrlich],[uni-muenster.de] Dear Serdar, while it apparently solves your technical problem, I would strongly discourage you from trusting the results of an MP2/3-21g calculation. The basis is much too small and does not account for correlation properly. It also completely lacks polarization functions. Using it will lead to large basis set superposition and incompleteness errors (BSSE and BSIE). I would suggest a basis set of at least triple-zeta quality, with polarization functions (and augmented with diffuse functions when you are looking at non-covalent interactions). As an example, the correlation-consistent basis sets by Dunning and co-workers (e.g. cc-pVTZ and aug-cc-pVTZ in this case) fulfill these criteria. I am no Gaussian expert, but sure that they are implemented in Gaussian. Cheers and good luck, Stephan. On Fri, 15 Mar 2013 02:53:00 +0100, Serdar BadoÄŸlu serdarbadoglu() gmail.com wrote: > I haven't seen such a message. > > Finally there's hope for me. I have changed the command line as # opt > freq > mp2/3-21g geom=connectivity, memory settings stayed the same. Finished > successfully in 20 minutes. ____________________________________________________________ Stephan Ehrlich (stephan.ehrlich^^^thch.uni-bonn.de) Mulliken Center for Theoretical Chemistry Institut fuer Physikalische und Theoretische Chemie Universitaet Bonn, Beringstr. 4, D-53115 Bonn, Germany ____________________________________________________________ From owner-chemistry@ccl.net Fri Mar 15 09:56:00 2013 From: "Diana O Rourke diana.orourke*certara.com" To: CCL Subject: CCL: Webinar: Designing and Optimizing Drugs Against Multiple Parameters Message-Id: <-48412-130315074221-10672-OEvQ4LBIfQEyMQCxyQ2k8A ~ server.ccl.net> X-Original-From: "Diana O Rourke" Date: Fri, 15 Mar 2013 07:42:20 -0400 Sent to CCL by: "Diana O Rourke" [diana.orourke * certara.com] Successful drug discovery often requires optimization against a set of biological and physical properties. If you are a medicinal or computational chemist interested in multi-criteria drug design, we invite you to register for the complimentary webinar: Designing and Optimizing Drugs Against Multiple Parameters. Date: March 21 Time: 11AM New York/8AM San Francisco/4PM London/5PM Paris Register: http://bit.ly/16wMxmz In the webinar, we will describe a multi-parameter approach (Muse) that is suitable for both ligand- and receptor-based de novo design and studies. The presentation will include discussion of how multiple design criteria, including pharmacophoric similarity, shape similarity, and ADME related properties (e.g. Lipinski properties, polar surface area, similarity to off- targets, etc..) can be used to guide the evolution of structures which meet multiple design criteria. Examples for both ligand- and structure-based design will be shown, and a live demo of Muse will be used to illustrate the simple workflow for multi-criteria design. Hope to see you online! Diana O'Rourke Marketing Director Certara www.certara.com From owner-chemistry@ccl.net Fri Mar 15 14:30:00 2013 From: "=?UTF-8?Q?Serdar_Bado=C4=9Flu?= serdarbadoglu!A!gmail.com" To: CCL Subject: CCL:G: DFT and MP2 Message-Id: <-48413-130315132345-10002-TQG0Wh3ZoJEEHk3aykjpKw .. server.ccl.net> X-Original-From: =?UTF-8?Q?Serdar_Bado=C4=9Flu?= Content-Type: multipart/alternative; boundary=20cf303ea1d45c306a04d7f9e619 Date: Fri, 15 Mar 2013 19:23:38 +0200 MIME-Version: 1.0 Sent to CCL by: =?UTF-8?Q?Serdar_Bado=C4=9Flu?= [serdarbadoglu++gmail.com] --20cf303ea1d45c306a04d7f9e619 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable 6-31G* worked. I have observed that I get error when I add diffuse functions on heavy atoms. But I need them. I was aimed to do my calculations with 6-311++G** basis set, because that was the set I have used in my DFT calculations and I want to see the difference between both methods. I'll try to reach that level by increasing the polarity and diffuse functions step by step until I reach the limits of my pc. Thank you all. On Fri, Mar 15, 2013 at 10:31 AM, Stephan Ehrlich stephan.ehrlich]_[ uni-muenster.de wrote: > > Sent to CCL by: "Stephan Ehrlich" [stephan.ehrlich],[uni-**muenster.de > ] > Dear Serdar, > > while it apparently solves your technical problem, I would strongly > discourage > you from trusting the results of an MP2/3-21g calculation. The basis is > much > too small and does not account for correlation properly. > It also completely lacks polarization functions. Using it will lead to > large basis set > superposition and incompleteness errors (BSSE and BSIE). > I would suggest a basis set of at least triple-zeta quality, with > polarization > functions (and augmented with diffuse functions when you are looking at > non-covalent > interactions). As an example, the correlation-consistent basis sets by > Dunning and co-workers > (e.g. cc-pVTZ and aug-cc-pVTZ in this case) fulfill these criteria. I am > no Gaussian expert, > but sure that they are implemented in Gaussian. > > Cheers and good luck, > > Stephan. > > > > On Fri, 15 Mar 2013 02:53:00 +0100, Serdar Bado=C4=9Flu serdarbadoglu() > gmail.com wrote: > > I haven't seen such a message. >> >> Finally there's hope for me. I have changed the command line as # opt fr= eq >> mp2/3-21g geom=3Dconnectivity, memory settings stayed the same. Finished >> successfully in 20 minutes. >> > > ______________________________**______________________________ > Stephan Ehrlich (stephan.ehrlich__thch.uni-**bonn.de > ) > Mulliken Center for Theoretical Chemistry > Institut fuer Physikalische und Theoretische Chemie > Universitaet Bonn, Beringstr. 4, D-53115 Bonn, Germany > ______________________________**______________________________ > > > > > -=3D This is automatically added to each message by the mailing script = =3D-> http://www.ccl.net/cgi-bin/**ccl/send_ccl_message http://www.ccl.net/cgi-bin/**ccl/send_ccl_message > Job: http://www.ccl.net/**jobsConferences: > http://server.ccl.net/**chemistry/announcements/**conferences/ > > > Search Messages: http://www.ccl.net/chemistry/**searchccl/index.shtml http://www.ccl.net/spammers.**txt > > RTFI: http://www.ccl.net/chemistry/**aboutccl/instructions/ > > > --=20 Serdar BADO=C4=9ELU, Ph.D. Gazi =C3=9Cniversitesi Fizik B=C3=B6l=C3=BCm=C3=BC --20cf303ea1d45c306a04d7f9e619 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

6-31G* worked. I have observed that I get error when I = add diffuse functions on heavy atoms. But I need them. I was aimed to do my= calculations with 6-311++G** basis set, because that was the set I have us= ed in my DFT calculations and I want to see the difference between both met= hods. I'll try to reach that level by increasing the polarity and diffu= se functions step by step until I reach the limits of my pc.

Thank you all.


= On Fri, Mar 15, 2013 at 10:31 AM, Stephan Ehrlich stephan.ehrlich]_[uni-muenster.de <owner-chemistry=ccl= .net> wrote:

Sent to CCL by: "Stephan Ehrlich" [stephan.ehrlich],[uni-muenster.de]
Dear Serdar,

while it apparently solves your technical problem, I would strongly discour= age
you from trusting the results of an MP2/3-21g calculation. The basis is muc= h
too small and does not account for correlation properly.
It also completely lacks polarization functions. Using it will lead to larg= e basis set
superposition and incompleteness errors (BSSE and BSIE).
I would suggest a basis set of at least triple-zeta quality, with polarizat= ion
functions (and augmented with diffuse functions when you are looking at non= -covalent
interactions). As an example, the correlation-consistent basis sets by Dunn= ing and co-workers
(e.g. cc-pVTZ and aug-cc-pVTZ in this case) fulfill these criteria. I am no= Gaussian expert,
but sure that they are implemented in Gaussian.

Cheers and good luck,

Stephan.



On Fri, 15 Mar 2013 02:53:00 +0100, Serdar Bado=C4=9Flu serdarbadoglu()
gmail.com <owner-chemistry__ccl.ne= t> wrote:

I haven't seen such a message.

Finally there's hope for me. I have changed the command line as # opt f= req
mp2/3-21g geom=3Dconnectivity, memory settings stayed the same. Finished successfully in 20 minutes.

____________________________________________________________
Stephan Ehrlich (stephan.ehrlich__thch.uni-bonn.de)
Mulliken Center for Theoretical Chemistry
Institut fuer Physikalische und Theoretische Chemie
Universitaet Bonn, Beringstr. 4, D-53115 Bonn, Germany
____________________________________________________________




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--
= Serdar BADO=C4=9ELU, Ph.D.
Gazi =C3=9Cniversitesi Fizik B=C3=B6l=C3=BCm= =C3=BC
--20cf303ea1d45c306a04d7f9e619-- From owner-chemistry@ccl.net Fri Mar 15 16:08:00 2013 From: "Abrash, Sam sabrash#%#richmond.edu" To: CCL Subject: CCL: DFT and MP2 Message-Id: <-48414-130315153747-22336-rj5zPdTk2MIxX34XXBHuwg _ server.ccl.net> X-Original-From: "Abrash, Sam" Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_A7C78D2AEE62DB40B9CB1ADE9D5990A23342F920QUORRArichmonde_" Date: Fri, 15 Mar 2013 19:37:39 +0000 MIME-Version: 1.0 Sent to CCL by: "Abrash, Sam" [sabrash..richmond.edu] --_000_A7C78D2AEE62DB40B9CB1ADE9D5990A23342F920QUORRArichmonde_ Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: base64 QmVmb3JlIHlvdSBnaXZlIHVwIGluY3JlYXNlICVtZW0gdG8gJW1lbT0xMEdCIG9yIHdoYXRldmVy IHRoZSBsYXJnZXN0IHlvdXIgY29tcHV0ZXIgd2lsbCBhbGxvdy4NCg0KU2FtdWVsIEEuIEFicmFz aA0KRGVwYXJ0bWVudCBvZiBDaGVtaXN0cnkNCkNvb3JkaW5hdG9yLCBFbnZpcm9ubWVudGFsIFN0 dWRpZXMgUHJvZ3JyYW0NClVuaXZlcnNpdHkgb2YgUmljaG1vbmQNClJpY2htb25kLCBWQSAyMzE3 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nG5pdmVyc2l0ZXNpIEZpemlrIELDtmzDvG3DvDxvOnA+PC9vOnA+PC9wPg0KPC9kaXY+DQo8L2Jv ZHk+DQo8L2h0bWw+DQo= --_000_A7C78D2AEE62DB40B9CB1ADE9D5990A23342F920QUORRArichmonde_-- From owner-chemistry@ccl.net Fri Mar 15 21:00:00 2013 From: "David Lowell Mobley dmobley() uci.edu" To: CCL Subject: CCL: SAMPL4 molecular modelling challenge invitation Message-Id: <-48415-130315171228-8921-jaEmQoKaxaNeptGDzKHjhA*_*server.ccl.net> X-Original-From: "David Lowell Mobley" Date: Fri, 15 Mar 2013 17:12:26 -0400 Sent to CCL by: "David Lowell Mobley" [dmobley()uci.edu] Dear Colleagues, We are writing to invite your participation in the upcoming Statistical Assessment of Modeling of Proteins and Ligands (SAMPL) challenge, now in its 4th edition. This challenge provides an opportunity for blind tests of computational methods for binding and hydration prediction as detailed below. Historically, a heavy focus of this meeting has been on free energy techniques for these applications, though other approaches are welcome as well. Our challenge this year includes protein-ligand binding, host-guest binding, and hydration free energy components. We expect to have representatives of a variety of major approaches and techniques participating, and would be delighted to have you or others in your group participate as well. Please pass this invitation along to anyone else who might be interested. The hydration free energy and host-guest aspects of the challenge have already started, and the protein-ligand component is just about to begin, so now is an ideal time to get involved. To sign up for SAMPL4, please indicate your interest at http://sampl.eyesopen.com (create an account to register and be notified as the data becomes available beginning in February; re-visit the site later to download the appropriate data and submit your predictions). A full description of the challenge is also available there, as well as at the end of this e-mail. Please contact us if you have any questions. And don't hesitate to pass along this announcement to anyone you know who may be interested. Sincerely, David Mobley (UC Irvine) Tom Peat (CSIRO) Vijay Pande (Stanford) John Chodera (MSKCC) Michael Gilson (UC San Diego) Building on a series of successful blind challenges for computational chemistry, the SAMPL4 challenge will have hydration free energy, host-guest, and binding free prediction components. As with previous SAMPL challenges, the opportunity for blind predictions is available and the SAMPL project will culminate with a science meeting in September, 2013. In the host-guest prediction component, participants will be provided with the chemical structures of the host molecule and a set of guest molecules. In the present round, we will focus on two hosts. The first is CB7, which avoids the complexities encountered in SAMPL3 for a cucurbituril derivative with four carboxyl groups. The guests will be commercially available compounds expected to span a range of affinities. The experiments will yield relative binding affinities (via NMR and potentially supplemented by ITC), through competitive binding experiments, for the sake of experimental convenience. For a second host, we will focus on a basket-shaped octa-acid host studied by the Gibb lab, and experimental data will be similar (spanning ~10 guests, all charged carboxylic acids), but with affinities measured by ITC. This challenge aspect has already started. Protein-ligand binding prediction will focus on a set of HIV integrase inhibitors with affinities in the micromolar range. Nearly 400 compounds have been tested, and roughly 100 of these are known to bind with ~70 high-resolution crystal structures available. Challenge aspects will focus on three main categories for binding: (1) virtual screening, where participants attempt to identify the binders out of a small library of compounds; (2) binding mode prediction, where participants attempt to predict binding modes or binding modes and affinities; and (3) affinity prediction, where participants attempt to predict affinities (or relative affinities) given binding modes. Participation in challenge aspect (3) precludes participation in (1) or (2) unless the aspects are done sequentially. We are grateful to Avexa Ltd, Australia for the data. This challenge aspect will begin shortly. Hydration free energy prediction will focus on a dataset of around 50 small molecules with hydration free energies curated by J. Peter Guthrie, as in previous SAMPL challenges. This challenge aspect has already started. The SAMPL4 meeting will take place September 20, 2013, at Stanford University. To give slightly more information on the data for the HIV integrase portion of the challenge, roughly 20 of the structures have already been published, so these compounds will be included in the challenge for purposes of completeness but will not be included in ranking of overall results, though participants may include these in their analysis. Compounds range from fragment-like to drug-size (~135 to 700 Da) and span a variety of chemistries. Binding affinity data is not necessarily available for all compounds, so tests #2 and #3 may focus on a smaller subset of compounds, though additional data is still being collected. Binding covers three different binding sites and affinities are often relatively weak, typically in the micromolar range. Crystal structures range from 1.65 to 2.15 angstrom resolution with good completeness and redundancy (98-100% complete, 5-fold redundancy in the data).