particle coverage

variable x0 equal 0.0
variable x1 equal 10
variable y0 equal 0.0
variable y1 equal 10
variable z0 equal 0.0
variable z1 equal 10

variable regx0 equal -0.0001+${x0}
variable regx1 equal 0.0001+${x1}
variable regy0 equal -0.0001+${y0}
variable regy1 equal 0.0001+${y1}
variable regz0 equal -0.0001+${z0}
variable regz1 equal 0.0001+${z1}

lattice sc .6
region sim_reg block ${regx0} ${regx1} ${regy0} ${regy1} ${regz0} ${regz1} units box ##simulation box
region insParticles block ${x0} ${x1} ${y0} ${y1} ${z0} ${z1} units box ##region in which our particles are generated

create_box 2 sim_reg

variable binSize equal .1
neighbor ${binSize} bin

variable neighDelay equal 0
variable neighOne equal 500000
variable neighPage equal 10000000
neigh_modify delay ${neighDelay} one ${neighOne} page ${neighPage}

#######################################################################
variable dia_NMC_1 equal 0.1
variable dia_NMC_2 equal 4

#############################################################
#Create atoms in the sim_reg box

create_atoms 1 region sim_reg
#mass 1 1.0
set atom 1 diameter ${dia_NMC_1}

run 1

################################################################
#Delete atoms part one

region sphere_outside sphere 5.0 5.0 5.0 5 side out #try it out with 4 may be
delete_atoms region sphere_outside
run 1

################################################################
#Delete atoms part two

region sphere_inside sphere 5.0 5.0 5.0 4.5 side in
delete_atoms region sphere_inside
run 1
##########################################################

# Create a big particle
create_atoms 2 single 5.0 5.0 5.0

# Set diameter of the big particle
set atom 2 diameter ${dia_NMC_2}

run 1

As you can see in the picture, the small particles should cover the big particle but is not happening. A particle is generated in the centre. But when I am changing the diameter of the particle, it is not changing. Another particle from the corner which is already deleted, that diameter is changing. When I comment on the delete atom parts, I can create the big particle properly.
Can someone please help me how can I solve the problem?