[phenixbb] Bulk solvent scaling problems

seglynn seglynn at MIT.EDU
Tue Sep 25 12:08:09 PDT 2007

Dear all,

I am using phenix.refine for the first time to refine a 4.5A structure solved by
MR with individual sites (stretching things a bit, I know) and a grouped ADP per
domain. Below are the R-factor per cycle stats:

REMARK ------------------------------------------------------------------------
REMARK  R-factors, x-ray target values and norm of gradient of x-ray target
REMARK  stage     r-work r-free  xray_target_w  xray_target_t
REMARK    0    :  0.6464 0.6186   7.101344e+00   7.091899e+00
REMARK    1_bss:  0.3955 0.4006   6.825652e+00   6.806242e+00
REMARK    1_xyz:  0.3200 0.3622   6.675328e+00   6.720706e+00
REMARK    1_adp:  0.3201 0.3622   6.674498e+00   6.719426e+00
REMARK    2_bss:  0.3539 0.3804   6.736883e+00   6.752128e+00
REMARK    2_xyz:  0.3067 0.3427   6.639056e+00   6.687071e+00
REMARK    2_adp:  0.3062 0.3423   6.638917e+00   6.687168e+00
REMARK    3_bss:  0.3357 0.3685   6.706475e+00   6.735398e+00
REMARK    3_xyz:  0.3082 0.3469   6.652536e+00   6.702364e+00
REMARK    3_adp:  0.3076 0.3468   6.652984e+00   6.703972e+00
REMARK    3_bss:  0.3286 0.3659   6.701854e+00   6.743421e+00
REMARK ------------------------------------------------------------------------

You can see that after the intial scaling, each cycle of bulk solvent scaling
and anisotropy correction leads to an increase in R-factors of ~2%. Has
anyone seen this behaviour before and maybe suggest a solution? Alternatively,
is there a way I can turn off the final cycle of bulk solvent scaling before
outputting the pdb and maps?

Thanks in advance,

Steve Glynn

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