[phenixbb] phenix.refine wxc weight

rainfieldcn rainfieldcn at gmail.com
Fri Jan 17 14:14:00 PST 2014


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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