The output from the build script gives a max distance of 104.7 Å. With a 15 Å padding, that's a 120 Å cell. Truncating that gives: same residue as (-x-y-z<103.923 and -x-y+z<103.923 and -x+y-z<103.923 and -x+y+z<103.923 and +x-y-z<103.923 and +x-y+z<103.923 and +x+y-z<103.923 and +x+y+z<103.923 and x < 69.282 and x > -69.282 and y < 69.282 and y > -69.282 and z < 69.282 and z > -69.282 and noh) cellBasisVector1 69.282 -69.282 -69.282 cellBasisVector2 -69.282 69.282 -69.282 cellBasisVector3 -69.282 -69.282 69.282 CRYST1 69.282 69.282 69.282 109.47 109.47 109.47 P 1 1 graphics top color 1 graphics top line {0 0 0} {69.282 -69.282 -69.282} width 5 graphics top color 7 graphics top line {0 0 0} {-69.282 69.282 -69.282} width 5 graphics top color 0 graphics top line {0 0 0} {-69.282 -69.282 69.282} width 5 Add 120.158 ions in leap (the system has volume 1.33022e-21 liters)