Supplementary Use of ARP/wARP

After restrained refinement is complete and before using the graphics it is worth knowing which parts of the model should be corrected.
ARP/wARP can be used for this purpose.

arp_warp XYZIN input.BRK MAPIN1 3Fo-2Fc.MAP XYZOUT temp << eof
MODE UPDATE ALLATOMS
CELL number number number number number number
SYMMETRY number/string
RESOLUTION number number
REMOVE ATOMS 50 CUTSIGMA 1.0
END
eof

The output of this job will contain a list of the 50 worst (from ARP/wARP 's point of view) atoms which do not agree with the electron density. These atoms should be inspected first. The input MAPIN1 should be the $(3F_o-2F_c / 2mF_o-D_Fc,\alpha_c)$ map.