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 (1.9A). 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 [18 minutes]
The automated picking located 40 water molecules (or ions) at a sigma level greater than 4 in a sigma-A weighted, phase combined difference map:
REMARK coordinates from water picking REMARK 40 waters picked at level greater than 4 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 - 1.9 A REMARK starting r= 0.2669 free_r= 0.2971 REMARK final r= 0.2582 free_r= 0.2883 REMARK sg= P6 a= 115.996 b= 115.996 c= 44.130 alpha= 90 beta= 90 gamma= 120
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).