It is possible that at that resolution, individual b's are overfitting due to n:p ratios.
Also, it is shocking how good these R- and molprobity values are--is it MR with an excellent search model, I guess?
JPK
-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Tristan Croll
Sent: Wednesday, March 23, 2016 4:55 AM
To: [log in to unmask]
Subject: Re: [ccp4bb] Surprisingly large discrepancy between PHENIX and REFMAC R/Rfree
A thought that just came up in conversation with a colleague: in moving from Phenix to Refmac I imported the _refine_data.mtz file using the ccp4i2 interface with default settings. Is there the possibility of a mix-up with the free set here?
Tristan Croll
Lecturer
Faculty of Health
School of Biomedical Sciences
Institute of Health and Biomedical Engineering Queensland University of Technology
60 Musk Ave
Kelvin Grove QLD 4059 Australia
+61 7 3138 6443
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> On 23 Mar 2016, at 6:17 PM, Tristan Croll <[log in to unmask]> wrote:
>
> Re-sending the below with CC to the bulletin board, and adding the following (very) surprising observation. After jelly-body refinement in Refmac with NCS, TLS and isotropic B-factors I have:
>
> Refmac: 0.194/0.240
> DCC: 0.194/0.214 (!)
> Phenix: 0.189/0.207 (!!)
>
> Very odd behaviour indeed - but I'm not complaining.
>
> ________________________________________
> From: Tristan Croll
> Sent: Wednesday, 23 March 2016 6:02 PM
> To: Robbie P. Joosten
> Subject: Re: [ccp4bb] Surprisingly large discrepancy between PHENIX
> and REFMAC R/Rfree
>
> Hi Robbie,
>
> I've tried giving phenix.model_vs_data the coordinates with and without the TLS contribution added to the output B-factors - it doesn't appear to make any difference in this case. I also just ran the same coordinates past the wwPDB validation server (DCC) as a third opinion. I have:
>
> Refmac: 0.250/0.258
> Phenix: 0.233/0.271
> DCC: 0.244/0.284
>
> I've also started a refinement using the original B-factors from Phenix and without hydrogens as suggested by Schara. It's currently reporting 0.2278/0.2366 before positional refinement, which also seems a little implausible. Seems to be a bit of a strange edge case... for what it's worth, though, when I let the refinement go to completion it's very well behaved in terms of geometry. MolProbity score after jelly-body refinement is 1.28 (vs. 1.55 starting from the same coordinates in Phenix).
>
> Cheers,
>
> Tristan
>
>
> ________________________________________
> From: Robbie P. Joosten <[log in to unmask]>
> Sent: Wednesday, 23 March 2016 5:38 PM
> To: Tristan Croll
> Subject: RE: [ccp4bb] Surprisingly large discrepancy between PHENIX
> and REFMAC R/Rfree
>
> Hi Tristan,
>
> Did you feed phenix.model_vs_data the Refmac output with residual or
> with total B-factors? That can make a lot of difference, particularly
> since the residual B-factors are all 30 (hence the small R-factor
> gap). I'm not sure how well phenix.model_vs_data deals with the B-factor ambiguity.
> A more subtle difference is in the solvent mask parameters, Refmac and
> Phenix use different probe and shrinkage sizes by default. Again, I
> don't know if the Refmac values are recognized in model_vs_data.
>
> For what it's worth, I get these differences between refinement
> programs a lot, in both directions. The change in R-factor is gap is
> still intriguing though.
>
> Cheers,
> Robbie
>
>> -----Original Message-----
>> From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of
>> Tristan Croll
>> Sent: Wednesday, March 23, 2016 07:32
>> To: [log in to unmask]
>> Subject: Re: [ccp4bb] Surprisingly large discrepancy between PHENIX
>> and REFMAC R/Rfree
>>
>> Sorry... mental lapse. Make that 59% solvent content - right in the
>> middle
> of
>> normal... which makes it all the more curious why the two programs
> disagree
>> so dramatically on the R-factors. Running things in the reverse
>> direction,
> if I
>> take the model refined with a fresh TLS model in REFMAC (with no
>> coordinate refinement) to reported 0.250/0.258 (0.8% gap) and run
>> phenix.model_vs_data on it, it re-computes the R factors as
>> 0.233/0.271 (3.8% gap, and 1.3% higher Rfree). Is this surprising to
>> anyone else, or
> am I
>> just being naive?
>>
>>
>>
>>
>> ________________________________
>>
>> From: CCP4 bulletin board <[log in to unmask]> on behalf of
>> Tristan Croll <[log in to unmask]>
>> Sent: Wednesday, 23 March 2016 3:16 PM
>> To: [log in to unmask]
>> Subject: [ccp4bb] Surprisingly large discrepancy between PHENIX and
>> REFMAC R/Rfree
>>
>>
>> Hi all,
>>
>>
>>
>>
>> I'm currently scratching my head over a large, low-resolution
>> structure
> (3.75
>> Angstroms, 4148 residues in the AU with 2-fold NCS). Perhaps its most
>> distinguishing feature is the very low solvent content - about 18% water.
>>
>>
>> I've been refining it up to this point in Phenix, and my last
>> refinement
> came
>> to Rwork/Rfree = 21.5/26.6 (with TLS + restrained individual B-factor
>> refinement) or 23.0/27.4 (with TLS-only) with very good geometry. Not
>> bad for the resolution, but the original model refined to 17.4/24.2
>> (also in Phenix). For comparison, I've just started a run in REFMAC5
>> starting from
> my
>> latest coordinates, with jelly-body and NCS restraints and resetting
>> the
> B-
>> factors to a constant with 5 rounds of TLS refinement prior to
>> positional refinement. To my surprise, after just the TLS refinement
>> (with no change
> in
>> coordinates), REFMAC was reporting R/Rfree = 25.05/25.84 - a *far*
>> cry
> from
>> what Phenix calculated. After the first ten rounds of positional
> refinement
>> it's currently at 20.5/24.5 - which seems promising, but what I'm
>> most interested in is the remarkably different R-factor calculations
>> from
> identical
>> coordinates between the two packages. My (perhaps naive) suspicion is
>> that this combination of low resolution and very low solvent content
>> is leading
> to
>> poor bulk solvent modelling, but I wonder if anyone else could
>> provide
> some
>> suggestions?
>>
>>
>>
>>
>> Best regards,
>>
>>
>> Tristan
>>
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