Question or Issue
I'm hosting a server, but it lags quite often, but I'm unable to understand the reason.
The world is almost new (about 24h) so there are not many objects that could cause lag.

Modpack Version

Enigmatica 2 Expert 1.49

Additional Context

The hardware is:
CPU: Xeon Gold 6140 (18c/36t)
RAM: 32Gb DDR4

It uses less than the 10% of the CPU and 5.5-6Gb of RAM.

[21:28:30] [Server thread/WARN] [minecraft/MinecraftServer]: Can't keep up! Did the system time change, or is the server overloaded? Running 14490ms behind, skipping 289 tick(s)

[21:28:42] [Server thread/WARN] [minecraft/MinecraftServer]: Can't keep up! Did the system time change, or is the server overloaded? Running 8318ms behind, skipping 166 tick(s)
[21:29:11] [Server thread/WARN] [minecraft/MinecraftServer]: Can't keep up! Did the system time change, or is the server overloaded? Running 16261ms behind, skipping 325 tick(s)
[21:29:15] [Server thread/WARN] [minecraft/MinecraftServer]: Can't keep up! Did the system time change, or is the server overloaded? Running 3861ms behind, skipping 77 tick(s)
[21:29:40] [Server thread/WARN] [minecraft/MinecraftServer]: Can't keep up! Did the system time change, or is the server overloaded? Running 14603ms behind, skipping 292 tick(s)
[21:29:51] [Server thread/WARN] [minecraft/MinecraftServer]: Can't keep up! Did the system time change, or is the server overloaded? Running 6893ms behind, skipping 137 tick(s)
[21:30:18] [Server thread/WARN] [minecraft/MinecraftServer]: Can't keep up! Did the system time change, or is the server overloaded? Running 15683ms behind, skipping 313 tick(s)
[21:30:22] [Server thread/WARN] [minecraft/MinecraftServer]: Can't keep up! Did the system time change, or is the server overloaded? Running 3920ms behind, skipping 78 tick(s)
[21:30:48] [Server thread/WARN] [minecraft/MinecraftServer]: Can't keep up! Did the system time change, or is the server overloaded? Running 15106ms behind, skipping 302 tick(s)
[21:30:52] [Server thread/WARN] [minecraft/MinecraftServer]: Can't keep up! Did the system time change, or is the server overloaded? Running 4180ms behind, skipping 83 tick(s)
[21:31:20] [Server thread/WARN] [minecraft/MinecraftServer]: Can't keep up! Did the system time change, or is the server overloaded? Running 15516ms behind, skipping 310 tick(s)
[21:31:24] [Server thread/WARN] [minecraft/MinecraftServer]: Can't keep up! Did the system time change, or is the server overloaded? Running 3986ms behind, skipping 79 tick(s)
[21:31:52] [Server thread/WARN] [minecraft/MinecraftServer]: Can't keep up! Did the system time change, or is the server overloaded? Running 17221ms behind, skipping 344 tick(s)
[21:31:57] [Server thread/WARN] [minecraft/MinecraftServer]: Can't keep up! Did the system time change, or is the server overloaded? Running 4256ms behind, skipping 85 tick(s)
[21:32:26] [Server thread/WARN] [minecraft/MinecraftServer]: Can't keep up! Did the system time change, or is the server overloaded? Running 16858ms behind, skipping 337 tick(s)
[21:32:30] [Server thread/WARN] [minecraft/MinecraftServer]: Can't keep up! Did the system time change, or is the server overloaded? Running 4157ms behind, skipping 83 tick(s)
[21:32:59] [Server thread/WARN] [minecraft/MinecraftServer]: Can't keep up! Did the system time change, or is the server overloaded? Running 16873ms behind, skipping 337 tick(s)
[21:33:03] [Server thread/WARN] [minecraft/MinecraftServer]: Can't keep up! Did the system time change, or is the server overloaded? Running 4013ms behind, skipping 80 tick(s)
[21:33:37] [Server thread/WARN] [minecraft/MinecraftServer]: Can't keep up! Did the system time change, or is the server overloaded? Running 20121ms behind, skipping 402 tick(s)
[21:33:42] [Server thread/WARN] [minecraft/MinecraftServer]: Can't keep up! Did the system time change, or is the server overloaded? Running 4425ms behind, skipping 88 tick(s)
[21:34:14] [Server thread/WARN] [minecraft/MinecraftServer]: Can't keep up! Did the system time change, or is the server overloaded? Running 18922ms behind, skipping 378 tick(s)
[21:34:18] [Server thread/WARN] [minecraft/MinecraftServer]: Can't keep up! Did the system time change, or is the server overloaded? Running 4159ms behind, skipping 83 tick(s)
[21:34:51] [Server thread/WARN] [minecraft/MinecraftServer]: Can't keep up! Did the system time change, or is the server overloaded? Running 19981ms behind, skipping 399 tick(s)
[21:34:55] [Server thread/WARN] [minecraft/MinecraftServer]: Can't keep up! Did the system time change, or is the server overloaded? Running 4331ms behind, skipping 86 tick(s)
[21:35:23] [Server thread/WARN] [minecraft/MinecraftServer]: Can't keep up! Did the system time change, or is the server overloaded? Running 15967ms behind, skipping 319 tick(s)
[21:35:28] [Server thread/WARN] [minecraft/MinecraftServer]: Can't keep up! Did the system time change, or is the server overloaded? Running 4209ms behind, skipping 84 tick(s)
[21:35:58] [Server thread/WARN] [minecraft/MinecraftServer]: Can't keep up! Did the system time change, or is the server overloaded? Running 17925ms behind, skipping 358 tick(s)
[21:36:02] [Server thread/WARN] [minecraft/MinecraftServer]: Can't keep up! Did the system time change, or is the server overloaded? Running 4593ms behind, skipping 91 tick(s)

ist possible, your CPU is too weak ? 2.3 GHz, i think Minecraft uses Only 1-2 CPU Cores, so your CPU is Good, but not for Minecraft? I run our Server on a I 7700K with 4.5 GHz, works Smooth. And Ram i have 16 But, for this Pack i use 8 GB. Or look if it is in Turbo Modus, watch in Windows Energy Managment, Use High Performance, so it goes not under your max. of 3.7 GHz

Minecraft can only utilize 1 CPU Core, so that is probably what is causing you trouble, as t3rraz suggests.
What is the TPS of the server?

Sometimes a newly generated world will generate something tick intensive in the spawn chunks, making the server laggy almost immediately. I suggest installing Tick Profiler and LagGoggles, and trying to find the cause of lag :)