The optimization process and recommendations:

1. Create Optimal Indexes (modified query below): The recommended indexes are an integral part of this optimization effort and should be created before testing the execution duration of the optimized query.
2. Explicitly ORDER BY After GROUP BY (modified query below): By default, the database sorts all 'GROUP BY col1, col2, ...' queries as if you specified 'ORDER BY col1, col2, ...' in the query as well. If a query includes a GROUP BY clause but you want to avoid the overhead of sorting the result, you can suppress sorting by specifying 'ORDER BY NULL'.
3. Replace In Subquery With Correlated Exists (modified query below): In many cases, an EXISTS subquery with a correlated condition will perform better than a non correlated IN subquery.

Optimal indexes for this query:

ALTER TABLE `STATUS` ADD INDEX `status_idx_group_id_user_id` (`group_id`,`user_id`);
ALTER TABLE `STATUS` ADD INDEX `status_idx_user_id_project_id` (`user_id`,`project_id`);

The optimized query:

SELECT
        STATUS.user_id 
    FROM
        STATUS 
    WHERE
        STATUS.group_id = 1 
        AND NOT EXISTS (
            SELECT
                1 
            FROM
                STATUS AS STATUS1 
            WHERE
                (
                    STATUS1.project_id = 2
                ) 
                AND (
                    STATUS.user_id = STATUS1.user_id
                ) 
            GROUP BY
                STATUS1.user_id 
            ORDER BY
                NULL
        ) 
    GROUP BY
        STATUS.user_id 
    ORDER BY
        NULL