[phenixbb] phenix.refine wxc weight

[Pavel Afonine]

Hello Lei,

I don't have answer but if you send me data and model files then I will 
have a look and may be I notice something worth taking care of.

Pavel


On 1/17/14, 2:14 PM, rainfieldcn wrote:
> Hi All,
> I am doing refinement on some low resolution structures ( around 4A ).
> I used wxc_scale=0.15 before on phenix.refine: 1.8.2_1309
> I got:
> REMARK 3 DEVIATIONS FROM IDEAL VALUES.
> REMARK 3 RMSD MAX COUNT
> REMARK 3 BOND : 0.006 0.048 24993
> REMARK 3 ANGLE : 1.049 11.841 33849
> REMARK 3 CHIRALITY : 0.044 0.323 3843
> REMARK 3 PLANARITY : 0.005 0.053 4276
> REMARK 3 DIHEDRAL : 14.080 87.581 8889
> REMARK 3 MIN NONBONDED DISTANCE : 2.098
> REMARK 3 MOLPROBITY STATISTICS.
> REMARK 3 ALL-ATOM CLASHSCORE : 10.49
> REMARK 3 RAMACHANDRAN PLOT:
> REMARK 3 OUTLIERS : 0.10 %
> REMARK 3 ALLOWED : 3.84 %
> REMARK 3 FAVORED : 96.06 %
> REMARK 3 ROTAMER OUTLIERS : 3.87 %
> REMARK 3 CBETA DEVIATIONS : 0
> now, phenix is updated to phenix.refine: 1.8.4_1496.
> and I got:
> REMARK 3 DEVIATIONS FROM IDEAL VALUES.
> REMARK 3 RMSD MAX COUNT
> REMARK 3 BOND : 0.016 0.237 24993
> REMARK 3 ANGLE : 2.262 36.773 33853
> REMARK 3 CHIRALITY : 0.099 2.724 3847
> REMARK 3 PLANARITY : 0.010 0.102 4280
> REMARK 3 DIHEDRAL : 14.585 89.962 8889
> REMARK 3 MIN NONBONDED DISTANCE : 1.923
> REMARK 3 MOLPROBITY STATISTICS.
> REMARK 3 ALL-ATOM CLASHSCORE : 17.57
> REMARK 3 RAMACHANDRAN PLOT:
> REMARK 3 OUTLIERS : 0.32 %
> REMARK 3 ALLOWED : 4.07 %
> REMARK 3 FAVORED : 95.61 %
> REMARK 3 ROTAMER OUTLIERS : 4.22 %
> REMARK 3 CBETA DEVIATIONS : 39
> So I am wondering if there is some bug in phenix.refine that wxc_scale
> doesn't work?
> Thanks,
> Lei
>
>
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