PyCharm 3.x Flake8 Configuration XML

flake8.xml

<toolSet name="Code Checking">
  <tool name="Flake8" showInMainMenu="true" showInEditor="true" showInProject="true" showInSearchPopup="true" disabled="false" useConsole="true" showConsoleOnStdOut="false" showConsoleOnStdErr="false" synchronizeAfterRun="true">
    <exec>
      <option name="COMMAND" value="/usr/local/bin/flake8" />
      <option name="PARAMETERS" value="--max-complexity 10 $FilePath$" />
      <option name="WORKING_DIRECTORY" value="$ProjectFileDir$" />
    </exec>
    <filter>
      <option name="NAME" value="Filter 1" />
      <option name="DESCRIPTION" />
      <option name="REGEXP" value="$FILE_PATH$\:$LINE$\:$COLUMN$\:.*" />
    </filter>
    <filter>
      <option name="NAME" value="Filter 2" />
      <option name="DESCRIPTION" />
      <option name="REGEXP" value="$FILE_PATH$\:$LINE$\:.*" />
    </filter>
  </tool>
</toolSet>

@ssbarnea you must to add a output filter containing the regular expression $FILE_PATH$\:$LINE$\:$COLUMN$\:.* working in pycharm CE 2016.3.2