The most common reason for this is that GraphEnt chose a completely wrong value (on the low side, ie must be increased) for the F000 term. You can correct this by editing the MAXENT_AUTO.IN file, add a line with the F000 keyword (see 7.1.4), and re-executing the program with GraphEnt MAXENT_AUTO.IN (see also discussion in 8.1).
Other possible reasons are : (i) Seriously underestimated standard deviations (see keyword TARGet, page ), (ii) Completely wrong scaling of data (on the high side, ie you must downscale them, see keyword SCALe, page ), (iii) Doing a low resolution run with strong data throughout the resolution range used for the calculation, and, (iv) Calculating an isomorphous difference Patterson function for a markedly non-isomorphous derivative (see also page ).
Case (iii) is one of GraphEnt's deficiencies : the program should adjust the size of grid depending on the data quality, instead of using a fixed correspondence between the range of hkl indeces and the grid size that it will chose. There is a solution however : if your GraphEnt map shows contours that are not smooth (and maybe you also see peak-splitting), then, edit the MAXENT_AUTO.IN file in your current directory, increase the grid size given in the GRID keyword (see page ), and re-run the program by giving GraphEnt MAXENT_AUTO.IN.