[edit: In case it's not obvious: Add the 2*pi factor in both places where f/w_n appears, in your formula for theta.]
I think you are asking why the solid curves in your plot are significantly different from the corresponding dashed lines in the same plot. The legend in the plot is mis-sized, so it is not possible to determine exactly what curve is what, from the plot as it appears in your post.
I think you need to add a factor of 2*pi in your equation for theta (dashed line plot), as explained below:
The dashed lines in the plot are generated by
semilogx(f,thdeg,'--','Linewidth', 2);
Unrecognized function or variable 'f'.
where the phase angle estimate thetadeg=(180/pi)*theta, where theta is given by
theta=-atan(1/ksi*(2*((f)/(w_n))+sqrt(4-ksi^2)))-atan(1/ksi*(2*((f)/(w_n))-sqrt(4-ksi^2)));
You say you were using equation 3, which is
Notice how equation 3 has
, but you have f/w_n. Replace f with 2*pi*f. Your ksi corresponds to α in equation 3:
ksi=((c*R_L*(R(ii)+R_S)+L)/(R(ii)+R_S+R_L))*w_n/2
I do not have the necessary information to check whether this formula for ksi is correct.
Your w_n corresponds to
in equation 3. w_n=sqrt((R(ii)+R_S+R_L)/(c*L*R_L))
I do not have the necessary information to check whether this formula for w_n is correct.
The solid curves in the plot are generated by .
where model is a state space model defined by
where A,B,C,D are given by
A = [-1/(R_L*c) 1/c;-1/L -(R(ii)+R_S)/L];
I do not know if the equations you have provided for A,B,C,D are a correct interpretation of the second order low pass active filter which is described by equation 3 in the paper you cited.