The output side of C6, without R5 will have the clock signal on it with the mean DC level of this signal situated at earth. So if the AC signal has a 1 microsecond 5V positive pulse with a 9 micro second "0", on the output side of C6 will have a signal of +4.5V going down to -.5V. i.e. the area of the pulse above the 0V line will equal the area below it. R5 puts some bias on the signal to compensate for this. In my example the bias should be +.5V. It would be easier and better to replace R5 with a diode, cathode to earth, This will clamp the most negative part of the pulse train to the diodes forward conduction voltage, -.7V? IRRESPECTIVE of the shape of the pulse train.
Frank