Subdomains as subfolders with requests using mod_rewrite? - .htaccess

Question

I want to do my subdomains working with subdirectories without redirection.
I write this:
RewriteCond %{HTTP_HOST} ^(www\.)?mysubdomain\.site\.com$ [NC]
RewriteCond %{REQUEST_URI} !^/cities/mysubdomain/
RewriteRule ^(.*)$ /cities/mysubdomain/$1%{REQUEST_URI} [L]
It works good with mysubdomain.site.com, but all files inside directory not working. For example mysubdomain.site.com/robots.txt open site.com/robots.txt not site.com/cities/subdomain/robots.txt (that what I want)
Can you help with explanation?
My current .htaccess is:
Options -Indexes
ErrorDocument 404 /404.php
<IfModule mod_php5.c>
php_flag allow_call_time_pass_reference 1
php_flag session.use_trans_sid off
#php_value display_errors 1
#php_value mbstring.func_overload 2
#php_value mbstring.internal_encoding UTF-8
</IfModule>
<IfModule mod_rewrite.c>
Options +FollowSymLinks
RewriteEngine On
RewriteBase /
RewriteCond %{THE_REQUEST} ^[A-Z]{3,9}\ /index\.php\ HTTP/
RewriteRule ^index\.php$ http://example.com [R=301,L]
# sub-domain redirect
RewriteCond %{HTTP_HOST} ^(www\.)?sub\.example\.com$ [NC]
RewriteCond %{REQUEST_URI} !^/cities/barnaul/ [NC]
RewriteRule ^(.*)$ /cities/barnaul/$1 [L,QSA]
# sub-domain redirect
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-l
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_FILENAME} !/bitrix/urlrewrite.php$
RewriteRule ^(.*)$ /bitrix/urlrewrite.php [L]
RewriteRule .* - [E=REMOTE_USER:%{HTTP:Authorization}]
</IfModule>
<IfModule mod_expires.c>
ExpiresActive on
ExpiresByType image/jpeg "access plus 3 day"
ExpiresByType image/gif "access plus 3 day"
</IfModule>
RewriteCond %{HTTP_HOST} ^www.example.com$ [NC]
RewriteRule ^(.*)$ http://example.com$1 [R=301,L]
Redirect 301 /cities/sms-sending-samara.php http://sub.example.com
Redirect 301 /information/sms_directing.php http://example.com/#sms_directing
Redirect 301 /sitemap_000.xml http://example.com/sitemap.xml
Redirect 301 /information/information.php http://example.com/information/
Redirect 301 /help/%D0%9C%D0%BE%D0%B4%D1%83%D0%BB%D1%8C%201%D0%A1%20v8.2.pdf http://example.com/api/modul_1c.php
Redirect 301 /help/Модуль%201С%20v8.2.pdf http://example.com/api/modul_1c.php
Redirect 301 /api/modul.php http://example.com/api/modul_1c.php
Redirect 301 /help/HTTP.pdf http://example.com/api/prot_http.php
Redirect 301 /help/SMPP.pdf http://example.com/api/prot_smpp.php
Redirect 301 /help/SMTP.pdf http://example.com/api/prot_smtp.php
Redirect 301 /help/SOAP.pdf http://example.com/api/prot_soap.php
Redirect 301 /help/XML.pdf http://example.com/api/prot_xml.php
Redirect 301 /API/prot_http.php http://example.com/api/prot_http.php
Redirect 301 /API/prot_smpp.php http://example.com/api/prot_smpp.php
Redirect 301 /API/prot_smtp.php http://example.com/api/prot_smtp.php
Redirect 301 /API/prot_soap.php http://example.com/api/prot_soap.php
Redirect 301 /API/prot_xml.php http://example.com/api/prot_xml.php
Redirect 301 /rassilka_sms_internet.html http://example.com/rassilka_sms_cherez_internet.html
Redirect 301 /sms_rassilka_cherez_internet_01.html http://example.com/rassilka_sms_cherez_internet.html
Redirect 301 /internet_rassilka_sms.html http://example.com/rassilka_sms_cherez_internet.html
Redirect 301 /sms_uvedomlenie_2.html http://example.com/sms_uvedomlenie.html
Redirect 301 /sms_uslugi_2.html http://example.com/sms_uslugi.html
Redirect 301 /sms_rassilka_reklamy_01.html http://example.com/sms_rassilka_reklamy.html
Redirect 301 /sms_rassilka_03.html http://example.com
Redirect 301 /sms_rassilka.html http://example.com
Redirect 301 /rassilka_sms_02.html http://example.com
Redirect 301 /rassilki_sms_01.html http://example.com
Redirect 301 /sms_reklama.html http://example.com/information/reklama.php
Redirect 301 /sms_rassilka_deshevo.html http://example.com/rassilka_sms_deshego.html
Redirect 301 /sms_rassilka_deshevo01.html http://example.com/rassilka_sms_deshego.html
Redirect 301 /rassilka_sms_internet.html http://example.com/rassilka_sms_cherez_internet.html
Redirect 301 /programma_cmc.html http://example.com/programma_sms.html
Redirect 301 /korporativnye_sms.htm http://example.com/korporativnye_sms.html
Redirect 301 /information/sector/index.php http://example.com/reshenia/
Redirect 301 /massovaya_rassilka_sms.html http://example.com
Redirect 301 /API/ http://example.com/api/
Redirect 301 /API http://example.com/api/
Redirect 301 /sms_trafik.htm http://example.com/smstrafik.html
Redirect 301 /sms_shluz.htm http://example.com/smsshluz.html
Redirect 301 /sms_trafik.html http://example.com/smstrafik.html
Redirect 301 /sms_shluz.html http://example.com/smsshluz.html
Redirect 301 /information/sms_reklama.php http://example.com/information/reklama.php
Redirect 301 /rassilka_ http://example.com
Redirect 301 /information/ackciya.php http://example.com/information/post_akciya.php
Redirect 301 /information/akciya.php http://example.com/information/post_akciya.php
Redirect 301 /information/sector/gov/ http://example.com/reshenia/gosstruktury/
Redirect 301 /information/sector/ http://example.com/reshenia/
Redirect 301 /information/MMS_directing.php http://example.com
Redirect 301 /information/WAP_directing.php http://example.com
Redirect 301 /information/voice_directing.php http://example.com
Redirect 301 /mobilny_marketing.html http://example.com/mobilnymarketing.html
Redirect 301 /cities/sms-sending-belgorod.php http://sub.example.com
AddDefaultCharset cp1251