HHblits output different with MSA output

[CryoSky]

To whom it may concern, I tried to use HHblits with the following command: /home/sj52/dependency/hh-suite/build/bin/hhblits -i query_1.fasta -o query.hhr -oa3m query.a3m -Z 50 -B 50 -d /home/sj52/dependency/database/pdb70

The input sequence is: IELAPGHKCNITLQDSVAELELFDVQPLQSGDYTCQVSNE

But I found the query.a3m only includes my input sequence while query.hhr looks good and it finds more than 40 templates. Could anyone kindly explain why this difference happens? I have read the Github wiki but I'm sorry I cannot understand the difference between the final MSA and hhr outputs.

Besides, I found some cases query.a3m can generate MSA but starts with Uniprot ID. However, hhr file starts from PDB id. Could anyone kindly tell me how to convert the output of query.a3m to PDB ID?

I'm using ubuntu 16LTS system. Best wishes, Shikai