Well, it turns out that result *was* too good to be true - but looking at the (attached) stdout from the mtz import job, I'm quite confused as to what's going on. First we have the cmtzsplit job, which appears to correctly split working and free reflections into separate files (full paths stripped out for easier reading):
cmtzsplit -mtzin .../struct_refine_data_1.mtz -mtzout .../job_1/OBSOUT.mtz -colin F-obs,SIGF-obs -colout F,SIGF -mtzout .../job_1/job_1/FREEOUT.mtz -colin R-free-flags -colout FREER > .../job_1/job_1/log_mtzsplit.txt
... except that FREEOUT .mtz goes into /job_1/job_1 whereas OBSOUT.mtz simply goes into /job_1. These free reflections are apparently discarded, because the next command is:
freerflag HKLIN .../job_1/OBSOUT.mtz HKLOUT .../job_1/job_2/hklout.mtz < .../job_1/job_2/com.txt > .../job_1/job_2/log.txt
followed by
cmtzsplit -mtzin .../job_1/job_2/hklout.mtz -mtzout .../job_1/FREEOUT.mtz -colin FreeR_flag -colout FREER >.../job_1/job_2/log_mtzsplit.txt
which creates an entirely *new* free set culled out of the working set created by the first cmtzsplit command. Something seems quite wrong here.
Best regards,
Tristan
________________________________________
From: CCP4 bulletin board <[log in to unmask]> on behalf of Tristan Croll <[log in to unmask]>
Sent: Wednesday, 23 March 2016 6:54 PM
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
This email and its attachments (if any) contain confidential information intended for use by the addressee and may be privileged. We do not waive any confidentiality, privilege or copyright associated with the email or the attachments. If you are not the intended addressee, you must not use, transmit, disclose or copy the email or any attachments. If you receive this email by mistake, please notify the sender immediately and delete the original email.
> 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
>>
runTask sys.argv ['/usr/local/ccp4-7.0/ccp4-7.0/share/ccp4i2/bin/runTask.py', '/mnt/crollt/docs/CCP4I2/CCP4_JOBS/job_1/input_params.xml']
loadVersion 0.0.5
Running QApplication to support asyncronous sub-processes
Starting Project Manager
Current schema version: ('0.1.17', '30-01-2015')
CCP4i2 opening database file /home/tristan/.CCP4I2/db/database.sqlite
updateDbSchema 0.1.17 30-01-2015
Starting Project Manager - DONE
SYMINFO file set to /usr/local/ccp4-7.0/ccp4-7.0/lib/data/syminfo.lib
extractMtzData listOfCells [{'a': 99.01, 'c': 142.86, 'b': 215.01, 'beta': 110.11, 'alpha': 90.0, 'gamma': 90.0}, {'a': 99.01, 'c': 142.86, 'b': 215.01, 'beta': 110.11, 'alpha': 90.0, 'gamma': 90.0}]
Imported file of format: mtz merged
SYMINFO file set to /usr/local/ccp4-7.0/ccp4-7.0/lib/data/syminfo.lib
extractMtzData listOfCells [{'a': 99.01, 'c': 142.86, 'b': 215.01, 'beta': 110.11, 'alpha': 90.0, 'gamma': 90.0}, {'a': 99.01, 'c': 142.86, 'b': 215.01, 'beta': 110.11, 'alpha': 90.0, 'gamma': 90.0}]
SYMINFO file set to /usr/local/ccp4-7.0/ccp4-7.0/lib/data/syminfo.lib
SYMINFO file set to /usr/local/ccp4-7.0/ccp4-7.0/lib/data/syminfo.lib
PROCESSMANAGER running command:
/usr/local/ccp4-7.0/ccp4-7.0/bin/cmtzsplit -mtzin /mnt/crollt/docs/CCP4I2/CCP4_IMPORTED_FILES/struct_refine_data_1.mtz -mtzout /mnt/crollt/docs/CCP4I2/CCP4_JOBS/job_1/OBSOUT.mtz -colin F-obs,SIGF-obs -colout F,SIGF -mtzout /mnt/crollt/docs/CCP4I2/CCP4_JOBS/job_1/job_1/FREEOUT.mtz -colin R-free-flags -colout FREER > /mnt/crollt/docs/CCP4I2/CCP4_JOBS/job_1/job_1/log_mtzsplit.txt
Process finished: 1 exit code: 0 exit status: 0 time: 14:19:31 23/Mar/2016
splitHklout DONE
CPluginScript.reportStatus struct_1_1 0 True <CCP4PluginScript.CDatabaseHandler instance at 0x7f42d2d0de18>
SYMINFO file set to /usr/local/ccp4-7.0/ccp4-7.0/lib/data/syminfo.lib
Recording file in database matches existing HKLOUT /mnt/crollt/docs/CCP4I2/CCP4_IMPORTED_FILES/struct_refine_data_1.mtz 6f52fd3cf0ae11e5ae7b2c27d7ee09da 309e0c30f0ae11e5ae7b2c27d7ee09da
Error report from extracting output data to database
None -ERROR- CDbApi:127 Attempting to create file record for file not in job directory
/mnt/crollt/docs/CCP4I2/CCP4_JOBS/job_1/OBSOUT.mtz expected in /mnt/crollt/docs/CCP4I2/CCP4_JOBS/job_1/job_1
OBSOUT {'dbFileId': None, 'contentFlag': 4, 'baseName': 'OBSOUT.mtz', 'project': '2379d66af0ae11e5ae7b2c27d7ee09da', 'subType': 1, 'annotation': 'Reflections from struct_refine_data_1', 'relPath': 'CCP4_JOBS/job_1'}
SYMINFO file set to /usr/local/ccp4-7.0/ccp4-7.0/lib/data/syminfo.lib
SYMINFO file set to /usr/local/ccp4-7.0/ccp4-7.0/lib/data/syminfo.lib
CExePathList.setupExeLookup {}
PROCESSMANAGER running command:
/usr/local/ccp4-7.0/ccp4-7.0/bin/freerflag HKLIN /mnt/crollt/docs/CCP4I2/CCP4_JOBS/job_1/OBSOUT.mtz HKLOUT /mnt/crollt/docs/CCP4I2/CCP4_JOBS/job_1/job_2/hklout.mtz < /mnt/crollt/docs/CCP4I2/CCP4_JOBS/job_1/job_2/com.txt > /mnt/crollt/docs/CCP4I2/CCP4_JOBS/job_1/job_2/log.txt
Process finished: 2 exit code: 0 exit status: 0 time: 14:19:32 23/Mar/2016
PROCESSMANAGER running command:
/usr/local/ccp4-7.0/ccp4-7.0/bin/cmtzsplit -mtzin /mnt/crollt/docs/CCP4I2/CCP4_JOBS/job_1/job_2/hklout.mtz -mtzout /mnt/crollt/docs/CCP4I2/CCP4_JOBS/job_1/FREEOUT.mtz -colin FreeR_flag -colout FREER > /mnt/crollt/docs/CCP4I2/CCP4_JOBS/job_1/job_2/log_mtzsplit.txt
Process finished: 3 exit code: 0 exit status: 0 time: 14:19:32 23/Mar/2016
splitHklout DONE
CPluginScript.reportStatus struct_1_2 0 True <CCP4PluginScript.CDatabaseHandler instance at 0x7f42d2d0de18>
CCP4Utils.getProgramVersion m1 (' Comment line--- # Task 1.2 freerflag running /usr/local/ccp4-7.0/ccp4-7.0/bin/', '')
SYMINFO file set to /usr/local/ccp4-7.0/ccp4-7.0/lib/data/syminfo.lib
Error report from extracting output data to database
None -ERROR- CDbApi:127 Attempting to create file record for file not in job directory
/mnt/crollt/docs/CCP4I2/CCP4_JOBS/job_1/FREEOUT.mtz expected in /mnt/crollt/docs/CCP4I2/CCP4_JOBS/job_1/job_2
process1 self.container.inputData {'DATASETNAME': 'dataset', 'HKLIN_FREER_COLUMN': '', 'SPACEGROUPCELL': '{\'cell\': "{\'a\': \'99.01\', \'c\': \'142.86\', \'b\': \'215.01\', \'beta\': \'110.11\', \'alpha\': \'90.0\', \'gamma\': \'90.0\'}", \'spaceGroup\': \'P 1 21 1\'}', 'CRYSTALNAME': 'crystal', 'HKLIN': '/mnt/crollt/docs/CCP4I2/CCP4_IMPORTED_FILES/struct_refine_data_1.mtz', 'HKLIN_OBS': '/mnt/crollt/docs/CCP4I2/CCP4_JOBS/job_1/HKLIN_OBS-observed_data.mtz', 'WAVELENGTH': '1.0', 'HKLIN_OBS_COLUMNS': 'F-obs,SIGF-obs', 'HKLIN_OBS_CONTENT_FLAG': '4'}
unmergedList 1 [{'crystalName': '', 'dataset': '', 'cell': "{'a': 'None', 'c': 'None', 'b': 'None', 'beta': 'None', 'alpha': 'None', 'gamma': 'None'}", 'excludeSelection': '', 'file': '/mnt/crollt/docs/CCP4I2/CCP4_IMPORTED_FILES/struct_refine_data_1.mtz', 'wavelength': 'None'}]
self.container.inputData {'DATASETNAME': 'dataset', 'HKLIN_FREER_COLUMN': '', 'SPACEGROUPCELL': '{\'cell\': "{\'a\': \'99.01\', \'c\': \'142.86\', \'b\': \'215.01\', \'beta\': \'110.11\', \'alpha\': \'90.0\', \'gamma\': \'90.0\'}", \'spaceGroup\': \'P 1 21 1\'}', 'CRYSTALNAME': 'crystal', 'HKLIN': '/mnt/crollt/docs/CCP4I2/CCP4_IMPORTED_FILES/struct_refine_data_1.mtz', 'HKLIN_OBS': '/mnt/crollt/docs/CCP4I2/CCP4_JOBS/job_1/HKLIN_OBS-observed_data.mtz', 'WAVELENGTH': '1.0', 'HKLIN_OBS_COLUMNS': 'F-obs,SIGF-obs', 'HKLIN_OBS_CONTENT_FLAG': '4'}
self.container.inputData.SPACEGROUPCELL {'cell': "{'a': '99.01', 'c': '142.86', 'b': '215.01', 'beta': '110.11', 'alpha': '90.0', 'gamma': '90.0'}", 'spaceGroup': 'P 1 21 1'}
unmergedList 4 [{'crystalName': 'crystal', 'dataset': 'dataset', 'cell': "{'a': '99.01', 'c': '142.86', 'b': '215.01', 'beta': '110.11', 'alpha': '90.0', 'gamma': '90.0'}", 'excludeSelection': '', 'file': '/mnt/crollt/docs/CCP4I2/CCP4_IMPORTED_FILES/struct_refine_data_1.mtz', 'wavelength': '1.0'}]
### Starting aimless pipeline ###
### Running pointless ###
PROCESSMANAGER running command:
/usr/local/ccp4-7.0/ccp4-7.0/bin/pointless XMLOUT /mnt/crollt/docs/CCP4I2/CCP4_JOBS/job_1/job_3/job_1/program.xml < /mnt/crollt/docs/CCP4I2/CCP4_JOBS/job_1/job_3/job_1/com.txt > /mnt/crollt/docs/CCP4I2/CCP4_JOBS/job_1/job_3/job_1/log.txt
Process finished: 4 exit code: 0 exit status: 0 time: 14:19:34 23/Mar/2016
CPluginScript.reportStatus struct_1_3_1 0 True <CCP4PluginScript.CDatabaseHandler instance at 0x7f42d2d0de18>
CCP4Utils.getProgramVersion m1 ('# Task 1.3.1 pointless running /usr/local/ccp4-7.0/ccp4-7.0/bin/', '')
process_aimless
### Running aimless ###
PROCESSMANAGER running command:
/usr/local/ccp4-7.0/ccp4-7.0/bin/aimless XMLOUT /mnt/crollt/docs/CCP4I2/CCP4_JOBS/job_1/job_3/job_2/program.xml HKLIN /mnt/crollt/docs/CCP4I2/CCP4_JOBS/job_1/job_3/job_1/MTZUNMERGEDOUT.mtz SCALES /mnt/crollt/docs/CCP4I2/CCP4_JOBS/job_1/job_3/job_2/SCALES.scales ROGUES /mnt/crollt/docs/CCP4I2/CCP4_JOBS/job_1/job_3/job_2/ROGUES.log NORMPLOT /mnt/crollt/docs/CCP4I2/CCP4_JOBS/job_1/job_3/job_2/NORMPLOT.xmgr ANOMPLOT /mnt/crollt/docs/CCP4I2/CCP4_JOBS/job_1/job_3/job_2/ANOMPLOT.xmgr CORRELPLOT /mnt/crollt/docs/CCP4I2/CCP4_JOBS/job_1/job_3/job_2/CORRELPLOT.xmgr ROGUEPLOT /mnt/crollt/docs/CCP4I2/CCP4_JOBS/job_1/job_3/job_2/ROGUEPLOT.xmgr HKLOUT /mnt/crollt/docs/CCP4I2/CCP4_JOBS/job_1/job_3/job_2/HKLOUT.mtz < /mnt/crollt/docs/CCP4I2/CCP4_JOBS/job_1/job_3/job_2/com.txt > /mnt/crollt/docs/CCP4I2/CCP4_JOBS/job_1/job_3/job_2/log.txt
Process finished: 5 exit code: 0 exit status: 0 time: 14:19:36 23/Mar/2016
CPluginScript.reportStatus struct_1_3_2 0 True <CCP4PluginScript.CDatabaseHandler instance at 0x7f42d2d0de18>
CCP4Utils.getProgramVersion m1 ('# Task 1.3.2 aimless running /usr/local/ccp4-7.0/ccp4-7.0/bin/', '')
Error report from extracting output data to database
None -WARNING- CDbApi:173 Possible job output file does not exist
SCALES /mnt/crollt/docs/CCP4I2/CCP4_JOBS/job_1/job_3/job_2/SCALES.scales
process_cycle_ctruncate MTZMERGEDOUT [/mnt/crollt/docs/CCP4I2/CCP4_JOBS/job_1/job_3/job_2/HKLOUT.mtz]
### Running ctruncate on file /mnt/crollt/docs/CCP4I2/CCP4_JOBS/job_1/job_3/job_2/HKLOUT.mtz ###
PROCESSMANAGER running command:
/usr/local/ccp4-7.0/ccp4-7.0/bin/ctruncate -hklin /mnt/crollt/docs/CCP4I2/CCP4_JOBS/job_1/job_3/job_2/HKLOUT.mtz -hklout /mnt/crollt/docs/CCP4I2/CCP4_JOBS/job_1/job_3/job_3/HKLOUT.mtz -colano /*/*/[I(+),SIGI(+),I(-),SIGI(-)] -colin /*/*/[IMEAN,SIGIMEAN] -xmlout /mnt/crollt/docs/CCP4I2/CCP4_JOBS/job_1/job_3/job_3/program.xml > /mnt/crollt/docs/CCP4I2/CCP4_JOBS/job_1/job_3/job_3/log.txt
Process finished: 6 exit code: 0 exit status: 0 time: 14:19:53 23/Mar/2016
PROCESSMANAGER running command:
/usr/local/ccp4-7.0/ccp4-7.0/bin/cmtzsplit -mtzin /mnt/crollt/docs/CCP4I2/CCP4_JOBS/job_1/job_3/job_3/HKLOUT.mtz -mtzout /mnt/crollt/docs/CCP4I2/CCP4_JOBS/job_1/job_3/HKLOUT_0-observed_data.mtz -colin I(+),SIGI(+),I(-),SIGI(-) -colout Iplus,SIGIplus,Iminus,SIGIminus -mtzout /mnt/crollt/docs/CCP4I2/CCP4_JOBS/job_1/job_3/HKLOUT_0-observed_data_asIMEAN.mtz -colin IMEAN,SIGIMEAN -colout I,SIGI > /mnt/crollt/docs/CCP4I2/CCP4_JOBS/job_1/job_3/job_3/cmtzsplit.log
Process finished: 7 exit code: 0 exit status: 0 time: 14:19:53 23/Mar/2016
SYMINFO file set to /usr/local/ccp4-7.0/ccp4-7.0/lib/data/syminfo.lib
CPluginScript.reportStatus struct_1_3_3 0 True <CCP4PluginScript.CDatabaseHandler instance at 0x7f42d2d0de18>
CCP4Utils.getProgramVersion m1 (' ### CCP4 7.0.006: ', ' version 1.17.9 : 01/03/16##')
Error report from extracting output data to database
None -ERROR- CDbApi:127 Attempting to create file record for file not in job directory
/mnt/crollt/docs/CCP4I2/CCP4_JOBS/job_1/job_3/HKLOUT_0-observed_data.mtz expected in /mnt/crollt/docs/CCP4I2/CCP4_JOBS/job_1/job_3/job_3
None -ERROR- CDbApi:127 Attempting to create file record for file not in job directory
/mnt/crollt/docs/CCP4I2/CCP4_JOBS/job_1/job_3/HKLOUT_0-observed_data_asIMEAN.mtz expected in /mnt/crollt/docs/CCP4I2/CCP4_JOBS/job_1/job_3/job_3
Datasets processed so far: 1
Datasets failed so far: 0
process_finish
aimless_pipe.process_finish spacegroup P 1 21 1
aimless_pip.process_finish
CPluginScript.reportStatus struct_1_3 0 True <CCP4PluginScript.CDatabaseHandler instance at 0x7f42d2d0de18>
Saving key:value pairs {'spaceGroup': 'P 1 21 1', 'rMeas': 0.0, 'highResLimit': 3.75}
Done saving key:value pairs
import_merged.nearlyDone
SYMINFO file set to /usr/local/ccp4-7.0/ccp4-7.0/lib/data/syminfo.lib
CPluginScript.reportStatus struct_1 {'finishStatus': 0, 'pid': None, 'jobId': '71c7f090f0ae11e583392c27d7ee09da'} True <CCP4PluginScript.CDatabaseHandler instance at 0x7f42d2d0de18>
Failed adding program version to parent job None None
SYMINFO file set to /usr/local/ccp4-7.0/ccp4-7.0/lib/data/syminfo.lib
getProgramVersions None None {'ctruncate': '1.17.9', 'freerflag': None, 'pointless': None, 'aimless': None}
quitThread <CCP4PluginScript.CRunPlugin object at 0x7f42c7f730e8>
|
