Even clean installation doesn't solve this. Here is a long thread about this http://forums.macrumors.com/threads/macbook-pro-2015-with-osx-el-capitan-10-11-4 -system-wide-freeze.1963711/ . In 10.11.3 everything worked flawlessly. This issue is related probably to newest broadwell intel chips. I will try what you suggested, but i think that it will not fix this issue.
Here is my etrecheck report:
EtreCheck version: 2.9.11 (264)
Report generated 2016-05-03 12:41:13
Download EtreCheck from https://etrecheck.com
Runtime 1:33
Performance: Excellent
Click the [Support] links for help with non-Apple products.
Click the [Details] links for more information about that line.
Problem: Apps are crashing
Hardware Information: ⓘ
MacBook Pro (Retina, 13-inch, Early 2015)
[Technical Specifications] - [User Guide] - [Warranty & Service]
MacBook Pro - model: MacBookPro12,1
1 2,7 GHz Intel Core i5 CPU: 2-core
8 GB RAM Not upgradeable
BANK 0/DIMM0
4 GB DDR3 1867 MHz ok
BANK 1/DIMM0
4 GB DDR3 1867 MHz ok
Bluetooth: Good - Handoff/Airdrop2 supported
Wireless: en0: 802.11 a/b/g/n/ac
Battery: Health = Normal - Cycle count = 7
Video Information: ⓘ
Intel Iris Graphics 6100
Color LCD 2880 x 1800
BenQ GW2470 1920 x 1080
System Software: ⓘ
OS X El Capitan 10.11.4 (15E65) - Time since boot: about 5 hours
Disk Information: ⓘ
APPLE SSD SM0128G disk0 : (121,33 GB) (Solid State - TRIM: Yes)
EFI (disk0s1) <not mounted> : 210 MB
Recovery HD (disk0s3) <not mounted> [Recovery]: 650 MB
Macintosh HD (disk1) / : 120.10 GB (80.13 GB free)
Core Storage: disk0s2 120.47 GB Online
USB Information: ⓘ
Apple Card Reader 129,79 GB
Transcend (disk2s1) /Volumes/Transcend : 129.77 GB (63.34 GB free)
Broadcom Corp. Bluetooth USB Host Controller
Thunderbolt Information: ⓘ
Apple Inc. thunderbolt_bus
Apple Inc. Thunderbolt to Gigabit Ethernet Adapter
Gatekeeper: ⓘ
Mac App Store and identified developers
Kernel Extensions: ⓘ
/Library/Application Support/VirtualBox
[loaded] org.virtualbox.kext.VBoxDrv (5.0.16 - 2016-04-08) [Support]
[loaded] org.virtualbox.kext.VBoxNetAdp (5.0.16 - 2016-04-08) [Support]
[loaded] org.virtualbox.kext.VBoxNetFlt (5.0.16 - 2016-04-08) [Support]
[loaded] org.virtualbox.kext.VBoxUSB (5.0.16 - 2016-04-08) [Support]
System Launch Agents: ⓘ
[not loaded] 7 Apple tasks
[loaded] 155 Apple tasks
[running] 76 Apple tasks
System Launch Daemons: ⓘ
[not loaded] 46 Apple tasks
[loaded] 156 Apple tasks
[running] 87 Apple tasks
Launch Agents: ⓘ
[loaded] com.oracle.java.Java-Updater.plist (2016-04-01) [Support]
Launch Daemons: ⓘ
[loaded] com.oracle.java.Helper-Tool.plist (2016-04-01) [Support]
[loaded] com.transcend.TSRecoverHandlerHelp.plist (2016-04-01) [Support]
[running] com.transcend.TSSleepHandlerHelp.plist (2016-04-01) [Support]
[loaded] com.transcend.TSTRIMHandlerHelp.plist (2016-04-01) [Support]
[not loaded] org.virtualbox.startup.plist (2016-04-08) [Support]
User Launch Agents: ⓘ
[loaded] com.bittorrent.uTorrent.plist (2016-04-01) [Support]
[loaded] com.google.keystone.agent.plist (2016-04-01) [Support]
User Login Items: ⓘ
Dropbox Application (/Applications/Dropbox.app)
Other Apps: ⓘ
[running] com.etresoft.EtreCheck.158112
[running] com.getdropbox.dropbox.66272
[running] com.google.Chrome.243232
[running] com.install4j.1106-5897-7327-6550.5.236192
[running] com.sublimetext.3.59232
[loaded] 405 Apple tasks
[running] 192 Apple tasks
Internet Plug-ins: ⓘ
QuickTime Plugin: 7.7.3 (2016-03-12)
Unity Web Player: UnityPlayer version 5.3.4f1 - SDK 10.6 (2016-03-11) [Support]
JavaAppletPlugin: Java 8 Update 91 build 14 (2016-04-20) Check version
Default Browser: 601 - SDK 10.11 (2016-03-12)
3rd Party Preference Panes: ⓘ
Java (2016-04-20) [Support]
TeXDistPrefPane (2016-04-01) [Support]
Time Machine: ⓘ
Time Machine not configured!
Top Processes by CPU: ⓘ
9% Google Chrome Helper(12)
3% Google Chrome
2% kernel_task
2% fontd
2% WindowServer
Top Processes by Memory: ⓘ
1.92 GB Google Chrome Helper(12)
947 MB kernel_task
434 MB realJavaApplicationStub
229 MB Google Chrome
213 MB Finder
Virtual Memory Information: ⓘ
59 MB Free RAM
7.94 GB Used RAM (1.60 GB Cached)
130 MB Swap Used
Diagnostics Information: ⓘ
May 3, 2016, 07:32:36 AM Self test - passed
May 1, 2016, 04:55:37 PM /Library/Logs/DiagnosticReports/5KPlayer_2016-05-01-165537_[redacted].hang
/Applications/5KPlayer.app/Contents/MacOS/5KPlayer
May 1, 2016, 04:54:25 PM /Library/Logs/DiagnosticReports/5KPlayer_2016-05-01-165425_[redacted].hang
Apr 30, 2016, 09:10:22 PM /Library/Logs/DiagnosticReports/5KPlayer_2016-04-30-211022_[redacted].hang