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.

Optimal indexes for this query:

ALTER TABLE `building` ADD INDEX `building_idx_id` (`id`);
ALTER TABLE `building_floor` ADD INDEX `building_floor_idx_id` (`id`);
ALTER TABLE `department` ADD INDEX `department_idx_id` (`id`);
ALTER TABLE `security_clearance` ADD INDEX `security_clearance_idx_id` (`id`);

The optimized query:

SELECT
        employee.id,
        employee.name,
        employee.position,
        security_clearance.id,
        security_clearance.description,
        department.id,
        department.name,
        building.id,
        building.name,
        building_floor.id,
        building_floor.clearance_working_hours,
        building_floor.clearance_non_working_hours 
    FROM
        employee 
    LEFT JOIN
        department 
            ON employee.department = department.id 
    LEFT JOIN
        building_floor 
            ON department.id = building_floor.id 
    LEFT JOIN
        building 
            ON building_floor.building_id = building.id 
    LEFT JOIN
        security_clearance 
            ON employee.clearance_id = security_clearance.id 
            AND building_floor.clearance_working_hours = security_clearance.id 
            AND building_floor.clearance_non_working_hours = security_clearance.id