I have solved a structure of protein with ligand at 2.7 and 2.8 A. Both have ligand bound in it as i soaked it. 

For the first structure i soaked for lesser time and lesser concentration of ligand and solved it at 2.7 A resolution. Although the ligand has good density (2Fo-Fc at 0.9 sigma) but it is little unconnected from its middle portion. Its RSCC value is 0.76 and B-factor of 70.0. Overall completeness of structure is > 91%. So If i decrease the occupancy of ligand here, will it improve the ligand statistics esp. the Real space R-value??

However for the second structure, i soaked for longer time and higher ligand concentration, so the ligand is perfect with clear 2Fo-Fc map at 1.2 sigma and Fo-Fc map at 2.8 sigma along with well defined simulated annealing and composite omit maps. The RSCC value is 0.81 with B-factor of 40.1.The only issue is the overall completeness of the structure is 88%. But if i get evrything OK at this completeness, den can i consider the second structure with ligand as the correct one??

Thanks in advance.

Monica