Firstly I want to ask why my rules.v4 looks so complicated after using: iptables -F. I thought it will be empty after flushing:
# Generated by iptables-save v1.6.0 on Tue Jan 9 21:25:13 2018
*filter
:INPUT ACCEPT [76:4024]
:FORWARD ACCEPT [0:0]
:OUTPUT ACCEPT [1:40]
:ufw-after-forward - [0:0]
:ufw-after-input - [0:0]
:ufw-after-logging-forward - [0:0]
:ufw-after-logging-input - [0:0]
:ufw-after-logging-output - [0:0]
:ufw-after-output - [0:0]
:ufw-before-forward - [0:0]
:ufw-before-input - [0:0]
:ufw-before-logging-forward - [0:0]
:ufw-before-logging-input - [0:0]
:ufw-before-logging-output - [0:0]
:ufw-before-output - [0:0]
:ufw-logging-allow - [0:0]
:ufw-logging-deny - [0:0]
:ufw-not-local - [0:0]
:ufw-reject-forward - [0:0]
:ufw-reject-input - [0:0]
:ufw-reject-output - [0:0]
:ufw-skip-to-policy-forward - [0:0]
:ufw-skip-to-policy-input - [0:0]
:ufw-skip-to-policy-output - [0:0]
:ufw-track-forward - [0:0]
:ufw-track-input - [0:0]
:ufw-track-output - [0:0]
:ufw-user-forward - [0:0]
:ufw-user-input - [0:0]
:ufw-user-limit - [0:0]
:ufw-user-limit-accept - [0:0]
:ufw-user-logging-forward - [0:0]
:ufw-user-logging-input - [0:0]
:ufw-user-logging-output - [0:0]
:ufw-user-output - [0:0]
-A INPUT -i enp3s0 -p udp -m udp --dport 67 -j ACCEPT
-A INPUT -i enp3s0 -p tcp -m tcp --dport 67 -j ACCEPT
-A INPUT -i enp3s0 -p udp -m udp --dport 53 -j ACCEPT
-A INPUT -i enp3s0 -p tcp -m tcp --dport 53 -j ACCEPT
-A INPUT -i enp2s0 -p udp -m udp --dport 67 -j ACCEPT
-A INPUT -i enp2s0 -p tcp -m tcp --dport 67 -j ACCEPT
-A INPUT -i enp2s0 -p udp -m udp --dport 53 -j ACCEPT
-A INPUT -i enp2s0 -p tcp -m tcp --dport 53 -j ACCEPT
-A INPUT -j ufw-before-logging-input
-A INPUT -j ufw-before-input
-A INPUT -j ufw-after-input
-A INPUT -j ufw-after-logging-input
-A INPUT -j ufw-reject-input
-A INPUT -j ufw-track-input
-A FORWARD -d 10.42.0.0/24 -o enp3s0 -m state --state RELATED,ESTABLISHED -j ACCEPT
-A FORWARD -s 10.42.0.0/24 -i enp3s0 -j ACCEPT
-A FORWARD -i enp3s0 -o enp3s0 -j ACCEPT
-A FORWARD -o enp3s0 -j REJECT --reject-with icmp-port-unreachable
-A FORWARD -i enp3s0 -j REJECT --reject-with icmp-port-unreachable
-A FORWARD -d 10.42.1.0/24 -o enp2s0 -m state --state RELATED,ESTABLISHED -j ACCEPT
-A FORWARD -s 10.42.1.0/24 -i enp2s0 -j ACCEPT
-A FORWARD -i enp2s0 -o enp2s0 -j ACCEPT
-A FORWARD -o enp2s0 -j REJECT --reject-with icmp-port-unreachable
-A FORWARD -i enp2s0 -j REJECT --reject-with icmp-port-unreachable
-A FORWARD -j ufw-before-logging-forward
-A FORWARD -j ufw-before-forward
-A FORWARD -j ufw-after-forward
-A FORWARD -j ufw-after-logging-forward
-A FORWARD -j ufw-reject-forward
-A FORWARD -j ufw-track-forward
-A OUTPUT -j ufw-before-logging-output
-A OUTPUT -j ufw-before-output
-A OUTPUT -j ufw-after-output
-A OUTPUT -j ufw-after-logging-output
-A OUTPUT -j ufw-reject-output
-A OUTPUT -j ufw-track-output
-A ufw-after-input -p udp -m udp --dport 137 -j ufw-skip-to-policy-input
-A ufw-after-input -p udp -m udp --dport 138 -j ufw-skip-to-policy-input
-A ufw-after-input -p tcp -m tcp --dport 139 -j ufw-skip-to-policy-input
-A ufw-after-input -p tcp -m tcp --dport 445 -j ufw-skip-to-policy-input
-A ufw-after-input -p udp -m udp --dport 67 -j ufw-skip-to-policy-input
-A ufw-after-input -p udp -m udp --dport 68 -j ufw-skip-to-policy-input
-A ufw-after-input -m addrtype --dst-type BROADCAST -j ufw-skip-to-policy-input
-A ufw-after-logging-forward -m limit --limit 3/min --limit-burst 10 -j LOG --log-prefix "[UFW BLOCK] "
-A ufw-after-logging-input -m limit --limit 3/min --limit-burst 10 -j LOG --log-prefix "[UFW BLOCK] "
-A ufw-before-forward -m conntrack --ctstate RELATED,ESTABLISHED -j ACCEPT
-A ufw-before-forward -p icmp -m icmp --icmp-type 3 -j ACCEPT
-A ufw-before-forward -p icmp -m icmp --icmp-type 4 -j ACCEPT
-A ufw-before-forward -p icmp -m icmp --icmp-type 11 -j ACCEPT
-A ufw-before-forward -p icmp -m icmp --icmp-type 12 -j ACCEPT
-A ufw-before-forward -p icmp -m icmp --icmp-type 8 -j ACCEPT
-A ufw-before-forward -j ufw-user-forward
-A ufw-before-input -i lo -j ACCEPT
-A ufw-before-input -m conntrack --ctstate RELATED,ESTABLISHED -j ACCEPT
-A ufw-before-input -m conntrack --ctstate INVALID -j ufw-logging-deny
-A ufw-before-input -m conntrack --ctstate INVALID -j DROP
-A ufw-before-input -p icmp -m icmp --icmp-type 3 -j ACCEPT
-A ufw-before-input -p icmp -m icmp --icmp-type 4 -j ACCEPT
-A ufw-before-input -p icmp -m icmp --icmp-type 11 -j ACCEPT
-A ufw-before-input -p icmp -m icmp --icmp-type 12 -j ACCEPT
-A ufw-before-input -p icmp -m icmp --icmp-type 8 -j ACCEPT
-A ufw-before-input -p udp -m udp --sport 67 --dport 68 -j ACCEPT
-A ufw-before-input -j ufw-not-local
-A ufw-before-input -d 224.0.0.251/32 -p udp -m udp --dport 5353 -j ACCEPT
-A ufw-before-input -d 239.255.255.250/32 -p udp -m udp --dport 1900 -j ACCEPT
-A ufw-before-input -j ufw-user-input
-A ufw-before-output -o lo -j ACCEPT
-A ufw-before-output -m conntrack --ctstate RELATED,ESTABLISHED -j ACCEPT
-A ufw-before-output -j ufw-user-output
-A ufw-logging-allow -m limit --limit 3/min --limit-burst 10 -j LOG --log-prefix "[UFW ALLOW] "
-A ufw-logging-deny -m conntrack --ctstate INVALID -m limit --limit 3/min --limit-burst 10 -j RETURN
-A ufw-logging-deny -m limit --limit 3/min --limit-burst 10 -j LOG --log-prefix "[UFW BLOCK] "
-A ufw-not-local -m addrtype --dst-type LOCAL -j RETURN
-A ufw-not-local -m addrtype --dst-type MULTICAST -j RETURN
-A ufw-not-local -m addrtype --dst-type BROADCAST -j RETURN
-A ufw-not-local -m limit --limit 3/min --limit-burst 10 -j ufw-logging-deny
-A ufw-not-local -j DROP
-A ufw-skip-to-policy-forward -j DROP
-A ufw-skip-to-policy-input -j DROP
-A ufw-skip-to-policy-output -j ACCEPT
-A ufw-track-output -p tcp -m conntrack --ctstate NEW -j ACCEPT
-A ufw-track-output -p udp -m conntrack --ctstate NEW -j ACCEPT
-A ufw-user-limit -m limit --limit 3/min -j LOG --log-prefix "[UFW LIMIT BLOCK] "
-A ufw-user-limit -j REJECT --reject-with icmp-port-unreachable
-A ufw-user-limit-accept -j ACCEPT
COMMIT
# Completed on Tue Jan 9 21:25:13 2018
# Generated by iptables-save v1.6.0 on Tue Jan 9 21:25:13 2018
*nat
:PREROUTING ACCEPT [306:30491]
:INPUT ACCEPT [79:4750]
:OUTPUT ACCEPT [128:10004]
:POSTROUTING ACCEPT [122:8932]
-A POSTROUTING -s 10.42.0.0/24 ! -d 10.42.0.0/24 -j MASQUERADE
-A POSTROUTING -s 10.42.1.0/24 ! -d 10.42.1.0/24 -j MASQUERADE
COMMIT
# Completed on Tue Jan 9 21:25:13 2018
Second question - I need iptables to rate limit new connections on specific port (limit not per ip, but all new attempts if there are too many of them), at the same time don't block any traffic that doesn't come to that specific port. All examples I saw on the internet use DROP for default INPUT policy, but that don't suit me.
Update: I run game server on port 45000 (it uses tcp and upd protocol)and recently I had problems with bot spam. Bots are trying to connect to my server from all over the world using hundreds of proxys. Game server plugins successfully blocked them, but this attack become much stronger lately and now it cause lags. Ideally I wanted to block access to this port based on geolocation and allow only 5-10 countries, but thats complicated. Another option is to rate-limit new connections to that port while keeping already existing. Of course it sertanly will block normal players trying to join during attack, but at least those who already play can do it without extreme lagging. My server isn't large (30 players max) so I assume rate limit to 30 new connections to port 45000 per 30 seconds will be fine.