[phenixbb] High B-factors and High Clash Score

[Pavel Afonine]

Hi Edwin,

it's hard to tell without seeing the files. If you send me your most 
current model and data then I can have a look.

Pavel

On 7/24/15 14:13, Edwin Lazo wrote:
> Hi all,
>
> I am refining a structure that diffracted to 3.5 Angstroms and 
> contains 6 monomers in the ASU. It is noteworthy to mention, in 
> certain monomers, half their residues are missing (in other words no 
> density). Initial b-factors after molrep were 118.585, R=0.32, and 
> Rfree=0.40. Initial refinement was done with refmac and:
>
> mean b-value=117.344
> R=0.31
> Rfree=0.40
>
> Refinement with Phenix 
> (phenix-installer-dev-2054-intel-linux-2.6-x86_64-centos5) was 
> performed and the Ramachandran plot was bad:
>
> OUTLIERS : 6.52  %
> ALLOWED  : 13.67 %
> FAVORED  : 79.82 %
> ROTAMER OUTLIERS : 7.18 %
> CBETA DEVIATIONS : 8
>
> And final R=0.38 and Rfree=0.41.
>
> I then improved Ramachandran plot in coot and follow Pavel's suggestion:
>
> /- add H atoms: />>//>>/phenix.reduce model.pdb > model_H.pdb />>//>>/- then run a quick geometry regularization: *(**T**his part I **did in 
> coot. phenix.**pdb**tools model_H.pdb --geom and phenix.pdbt**ools 
> model_H.pdb --geometry**-**restraints do not work)* />>//>>/phenix.pdbtools model_H.pdb --geom />>//>>/- then strip off H: />>//>>/phenix.reduce -trim model_H_regularized.pdb > start.pdb />>//>>/- then run refinement using NCS and Ramachandran plot restraints: />>//>>/phenix.refine start.pdb def_data.mtz main.ncs=true --overwrite />>/output.prefix=def2 main.number_of_mac=5 ramachandran_restraints=true />>/rama_potential=emsley strategy=individual_sites+**individual_adp />>//>>/- then take outcome of previous refinement and run the same refinement />>/plus weights optimization: />>//>>/phenix.refine def2_001.pdb def_data.mtz main.ncs=true --overwrite />>/output.prefix=def3 main.number_of_mac=5 ramachandran_restraints=true />>/rama_potential=emsley strategy=individual_sites+**individual_adp />>/optimize_xyz=true nproc=6 /My current stats are as follows: Final 
> R=0.35Final Rfree=0.38ALL-ATOM CLASHSCORE : 173.74RAMACHANDRAN 
> PLOT:OUTLIERS : 2.27 %ALLOWED : 4.61 %FAVORED : 93.13 %ROTAMER 
> OUTLIERS : 36.26 %CBETA DEVIATIONS : 6Wilson B-Value: 108.4Mean 
> B-value: 108.997I am unsure how to proceed from here. I am planning on 
> removing some side chains which have no density and then refining with 
> Rama. restraints. I can also send my mtz and pdb if that would help. 
> The stats when I processed the data are as follows from xia2 -3d (xds, 
> xscale): High resolution limit 3.50 15.65 3.50Low resolution limit 
> 109.96 109.96 3.59Completeness 94.1 90.5 91.5Multiplicity 4.8 5.1 
> 3.2I/sigma 11.3 26.5 2.4Rmerge 0.118 0.068 0.458Rmeas(I) 0.144 0.080 
> 0.605Rmeas(I+/-) 0.144 0.083 0.584Rpim(I) 0.062 0.036 0.311Rpim(I+/-) 
> 0.081 0.047 0.358CC half 0.992 0.994 0.791Wilson B factor 
> 90.052Anomalous completeness 86.9 93.6 71.3Anomalous multiplicity 2.4 
> 3.0 1.8Anomalous correlation -0.262 -0.440 -0.052Anomalous slope 1.005 
> 0.000 0.000Total observations 169836 2234 7765Total unique 35071 442 
> 2464Assuming spacegroup: P 21 21 21Unit cell:73.010 180.780 
> 219.91090.000 90.000 90.000
> Any help would greatly be appreciated,
> -- 
> Edwin Lazo
> Scientific Associate
> Life Science and Biomedical Technology Research Resource
> National Synchrotron Light Source II Building 745
> Upton, NY 11973
> Office:(631)344-7247
> Fax:(631)344-5059
>
>
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