A significant missing part of the model are ordered water molecules (some can be clearly seen in the electron density maps). This is to be expected at this resolution (1.8A). We would proceed with much more caution if the resolution of the data were significantly lower (2.5A or worse). Water molecules are automatically picked using the CNS task file water_pick.inp:
cns_solve < water_pick.inp > water_pick.out [6.5 minutes]
The automated picking located 69 water molecules (or ions) at a sigma level greater than 4 in a sigma-A weighted differece map:
REMARK coordinates from water picking REMARK 69 waters picked at level greater than 4.0 REMARK in (1 m|Fo| - 1 D|Fc|)e^(i phi_calc) cross-val. sigmaa map REMARK peak selection criteria: hbond REMARK peaks closer than 2.6 A or further than 4.0 A were deleted REMARK but peaks 2.0 A from oxygen or nitrogen were kept REMARK peaks further than 3.2 A from a oxygen or nitrogen were deleted REMARK map resolution: 500 - 1.8 A REMARK starting r= 0.2755 free_r= 0.2992 REMARK final r= 0.2568 free_r= 0.2809 REMARK sg= P2(1)2(1)2(1) a= 65.508 b= 72.216 c= 45.035 alpha= 90 beta= 90 gamma= 90
The B-factors and coordinates for the water molecules were refined in the water picking script. In some cases it might be useful to perform refinement of all B-factors and coordinates after the water picking, especially if a large number of waters were found. We will proceed to a final look at model statistics and maps (see next section).