$q->whereNotIn('order_stage_id',[99,4])
->orWhere(function($query) {
    $query->whereNotIn('order_stage_id',[99,4])
        ->orWhere('reference_number', 'like', '%'.$request->key.'%')
        ->orWhere('seller_remark', 'like', '%'.$request->key.'%')
        ->orWhere('companies.name', 'like', '%'.$request->key.'%')
        ->orWhere('users.name', 'like', '%'.$request->key.'%');
});

$q->whereNotIn('order_stage_id',[99,4])
    ->orWhere(function($query) {

    $query->whereNotIn('order_stage_id',[99,4])
        ->where(function($query) {

        $query->where('column_1', 'like', '%XXX%')
            ->orWhere('column_2', 'like', '%XXX%')
            ->orWhere('column_2', 'like', '%XXX%');
    });
});