diff --git a/docs/source/manual/file_formats/reference_file.rst b/docs/source/manual/file_formats/reference_file.rst
index f2240df62..0f90a8a9f 100644
--- a/docs/source/manual/file_formats/reference_file.rst
+++ b/docs/source/manual/file_formats/reference_file.rst
@@ -17,60 +17,111 @@ An example of the file is shown as follows.
 Date: Mon Sep  9 16:41:53 2024
 
 #the instance names are given during netlist generation
-references:
-- module: grid_io_top
-  count: 1
-  instances:
-    - grid_io_top_1__2_
-- module: grid_io_right
-  count: 1
-  instances:
-    - grid_io_right_2__1_
-- module: grid_io_bottom
-  count: 1
-  instances:
-    - grid_io_bottom_1__0_
-- module: grid_io_left
-  count: 1
-  instances:
-    - grid_io_left_0__1_
-- module: grid_clb
-  count: 1
-  instances:
-    - grid_clb_1__1_
-- module: sb_0__0_
-  count: 1
-  instances:
-    - sb_0__0_
-- module: sb_0__1_
-  count: 1
-  instances:
-    - sb_0__1_
-- module: sb_1__0_
-  count: 1
-  instances:
-    - sb_1__0_
-- module: sb_1__1_
-  count: 1
-  instances:
-    - sb_1__1_
-- module: cbx_1__0_
-  count: 1
-  instances:
-    - cbx_1__0_
-- module: cbx_1__1_
-  count: 1
-  instances:
-    - cbx_1__1_
-- module: cby_0__1_
-  count: 1
-  instances:
-    - cby_0__1_
-- module: cby_1__1_
-  count: 1
-  instances:
-    - cby_1__1_
-          direct_interc
+
+  references:
+    - module: grid_io_top
+
+      count: 1
+
+      instances:
+
+        - grid_io_top_1__2_
+
+    - module: grid_io_right
+
+      count: 1
+
+      instances:
+
+        - grid_io_right_2__1_
+
+    - module: grid_io_bottom
+
+      count: 1
+
+      instances:
+
+        - grid_io_bottom_1__0_
+
+    - module: grid_io_left
+
+      count: 1
+
+      instances:
+
+        - grid_io_left_0__1_
+
+    - module: grid_clb
+
+      count: 1
+
+      instances:
+
+        - grid_clb_1__1_
+
+    - module: sb_0__0_
+
+      count: 1
+
+      instances:
+
+        - sb_0__0_
+
+    - module: sb_0__1_
+
+      count: 1
+
+      instances:
+
+        - sb_0__1_
+
+    - module: sb_1__0_
+
+      count: 1
+
+      instances:
+
+        - sb_1__0_
+
+    - module: sb_1__1_
+
+      count: 1
+
+      instances:
+
+        - sb_1__1_
+
+    - module: cbx_1__0_
+
+      count: 1
+
+      instances:
+
+        - cbx_1__0_
+
+    - module: cbx_1__1_
+
+      count: 1
+
+      instances:
+
+        - cbx_1__1_
+
+    - module: cby_0__1_
+
+      count: 1
+
+      instances:
+
+        - cby_0__1_
+
+    - module: cby_1__1_
+
+      count: 1
+
+      instances:
+
+        - cby_1__1_
 
 In this example, the parent module is ``fpga_top``.
 The child modules under ``fpga_top`` are ``grid_io_top``, ``grid_io_right``, and etc.