Just finished a round of refinement.  Rfree went up about 1% and R went down a bit.  I am wondering what happened here.  Also Rfree always went down after TLS refinement but always went up a lot more after the individual ADP refinement.  Is there anything I can do here?  Should I use weaker B restraints?  I tried to assign a wxu_scale value.  But phenix.refine automatically adjust it to 1.81 every time.

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R-factors, x-ray target values and norm of gradient of x-ray target

stage     r-work r-free  xray_target_w  xray_target_t

   0    :  0.3982 0.5701   6.156859e+00   6.238509e+00

   1_bss:  0.2008 0.2494   5.949117e+00   6.088855e+00

   1_xyz:  0.2030 0.2497   5.953829e+00   6.091696e+00

   1_adp:  0.1998 0.2559   5.952833e+00   6.099340e+00

   2_bss:  0.1996 0.2557   5.952517e+00   6.099196e+00

   2_xyz:  0.1984 0.2576   5.953246e+00   6.104085e+00

   2_adp:  0.1974 0.2578   5.950434e+00   6.102336e+00

   3_bss:  0.1972 0.2574   5.950333e+00   6.102222e+00

   3_xyz:  0.1997 0.2576   5.956524e+00   6.103647e+00

   3_adp:  0.1987 0.2590   5.955554e+00   6.104434e+00

   3_bss:  0.1986 0.2588   5.955445e+00   6.104227e+00

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Weights for target T = Exray * wxc * wxc_scale + Echem * wc and

angles between gradient vectors, eg. (d_Exray/d_sites, d_Echem/d_sites)

stage              wxc          wxu  wxc_sc  wxu_sc /_gxc,gc /_gxu,gu

   0    :    5.5611e-01   7.2249e-01   0.050   1.810   96.334  101.736

   1_bss:    5.5611e-01   7.2249e-01   0.050   1.810   96.334  101.736

   1_xyz:    4.5001e-01   6.1023e-01   0.050   1.810   96.591  102.016

   1_adp:    4.5001e-01   6.1023e-01   0.050   1.810   96.591  102.016

   2_bss:    4.5001e-01   6.1023e-01   0.050   1.810   96.591  102.016

   2_xyz:    5.1326e-01   6.5356e-01   0.050   1.810  112.802  141.393

   2_adp:    5.1326e-01   6.5356e-01   0.050   1.810  112.802  141.393

   3_bss:    5.1326e-01   6.5356e-01   0.050   1.810  112.802  141.393

   3_xyz:    3.3568e-01   7.0695e-01   0.050   1.810  111.975  135.760

   3_adp:    3.3568e-01   7.0695e-01   0.050   1.810  111.975  135.760

   3_bss:    3.3568e-01   7.0695e-01   0.050   1.810  111.975  135.760

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Jianghai