although in this platform we have the possibility to get up to 60 Gbp of data, I got only 47 Gbp, so my first question is what is the probable reason for this that I have not used the whole capacity of sequencing?

Under-clustering, which means you did not load the optimal amount of DNA.

Does not it show that my TF did not have more binding sites to be sequenced?

What does that mean? Are these numbers obtained after all filtering steps? Do you have a lot of PCR duplicates that indicate the saturation for each library might already be reached? Please be more precise. Best would be to present the flagstat results after filtering the BAM file for MAPQ > 20, removing PCR duplicates and keeping only primary alignments. Samtools can do all that filtering, e.g. samtools view -q 20 -f 0 -F 1284 -o filtered.bam your.bam given you marked duplicates before, e.g. using samblaster. is this simply the "raw" result which could mean that libraries have not been properly balanced so some are overrepresented in the pool you loaded while others (such as your TF ones) are underrepresented. That probably comes down to inaccurate quantification. How did you do it, Bioanalyzer, qPCR, if at all? What kind of input, chromatin or IgG? You should perform some library complexity estimates, such as with preseq and then show the results.