diff --git a/Testing/Data/SystemTest/BenzeneBinWidthCASTEP.nxs.md5 b/Testing/Data/SystemTest/BenzeneBinWidthCASTEP.nxs.md5
index 949f9d5f2af3e83b1e89d822ef2eb3a0df69e725..2894a7a5302ff03cd1c872e49b07f5d72b8a4563 100644
--- a/Testing/Data/SystemTest/BenzeneBinWidthCASTEP.nxs.md5
+++ b/Testing/Data/SystemTest/BenzeneBinWidthCASTEP.nxs.md5
@@ -1 +1 @@
-9f52c317a2ed01f26514b539139df5e6
+8c4c9164cbd6256b8fe558a8cc5aab2f
diff --git a/Testing/Data/SystemTest/C6H5Cl-Gaussian.nxs.md5 b/Testing/Data/SystemTest/C6H5Cl-Gaussian.nxs.md5
index e536bb4ffd8ce11e9dabbf3d9e0ebdf562ba1a41..f1e705becf4e102b0739c5c63ce4866db79d13b1 100644
--- a/Testing/Data/SystemTest/C6H5Cl-Gaussian.nxs.md5
+++ b/Testing/Data/SystemTest/C6H5Cl-Gaussian.nxs.md5
@@ -1 +1 @@
-f1f62461da1f6153030a035259e45467
+426766659eb52b2cdca5f4c452269af6
diff --git a/Testing/Data/SystemTest/Crystalb3lypScratchAbins.nxs.md5 b/Testing/Data/SystemTest/Crystalb3lypScratchAbins.nxs.md5
index 167594df65ab6078343181770947c26d8977d7fe..a0d98fe4b09cffb5488c18105b9027db37d5f7b9 100644
--- a/Testing/Data/SystemTest/Crystalb3lypScratchAbins.nxs.md5
+++ b/Testing/Data/SystemTest/Crystalb3lypScratchAbins.nxs.md5
@@ -1 +1 @@
-388422e55d7804eba97f0c9e62e1bf1a
+a9184f96367d95daf4e4b21368a7b18f
diff --git a/Testing/Data/SystemTest/LiOH_H2O_2D2O_CASTEP.nxs.md5 b/Testing/Data/SystemTest/LiOH_H2O_2D2O_CASTEP.nxs.md5
index 6ef1265575d0c6645cbb282b5a6c7a5d8f5ecabb..5956bfd094e88d5fcad42ad7746e9775f1224bea 100644
--- a/Testing/Data/SystemTest/LiOH_H2O_2D2O_CASTEP.nxs.md5
+++ b/Testing/Data/SystemTest/LiOH_H2O_2D2O_CASTEP.nxs.md5
@@ -1 +1 @@
-6ec344e29194b881cfc567a566135818
+19a30c2a011dfd8553cb2673d32b8446
diff --git a/Testing/Data/SystemTest/Mapi.nxs.md5 b/Testing/Data/SystemTest/Mapi.nxs.md5
index b8e145e075e4dac86e18cfd722fe6a580ed4733a..e50d1cd23342658649c99602eb4eff419f0ac0e2 100644
--- a/Testing/Data/SystemTest/Mapi.nxs.md5
+++ b/Testing/Data/SystemTest/Mapi.nxs.md5
@@ -1 +1 @@
-c308b28f6a48285ce7a9bc24fc34829f
+bb780cfae9584657a059862dcfbb65ee
diff --git a/Testing/Data/SystemTest/Na2SiF6.nxs.md5 b/Testing/Data/SystemTest/Na2SiF6.nxs.md5
deleted file mode 100644
index 616c744a04dd978666324982220990c82678cabb..0000000000000000000000000000000000000000
--- a/Testing/Data/SystemTest/Na2SiF6.nxs.md5
+++ /dev/null
@@ -1 +0,0 @@
-f17d1f28923a94a1b097806d044321e2
diff --git a/Testing/Data/SystemTest/Na2SiF6_CASTEP.nxs.md5 b/Testing/Data/SystemTest/Na2SiF6_CASTEP.nxs.md5
index 305960b322405e9ba3a95424658c01271b135479..406a60d0ad2b5df99d2273ebe8444bf26f6d7c35 100644
--- a/Testing/Data/SystemTest/Na2SiF6_CASTEP.nxs.md5
+++ b/Testing/Data/SystemTest/Na2SiF6_CASTEP.nxs.md5
@@ -1 +1 @@
-ee9b47071de97a4712bf904a2d8019fd
+6a9ebb184ce6cbad194d2f4217e8e6c2
diff --git a/Testing/Data/SystemTest/Na2SiF6_DMOL3.nxs.md5 b/Testing/Data/SystemTest/Na2SiF6_DMOL3.nxs.md5
index 5d3b5fb9143b009e41e953160528adf0bf94a6b5..17ae498c9f66c478e2779493ba53b437b8cd1b8e 100644
--- a/Testing/Data/SystemTest/Na2SiF6_DMOL3.nxs.md5
+++ b/Testing/Data/SystemTest/Na2SiF6_DMOL3.nxs.md5
@@ -1 +1 @@
-68ea153bd8dac8c5b40a15e65fb6dac1
+23947afbbcec326052018f34551993a3
diff --git a/Testing/Data/SystemTest/TolueneLargerOrderAbins.nxs.md5 b/Testing/Data/SystemTest/TolueneLargerOrderAbins.nxs.md5
index 58f23181f720f18df14ffabf7cc12fcf33028188..6f162e65e2187871e7d09931033ba4c62dc8501c 100644
--- a/Testing/Data/SystemTest/TolueneLargerOrderAbins.nxs.md5
+++ b/Testing/Data/SystemTest/TolueneLargerOrderAbins.nxs.md5
@@ -1 +1 @@
-62ea5e1a6155f84b479a1947e9c38622
+7031da500c989b8ee3b7e884ab12426c
diff --git a/Testing/Data/SystemTest/TolueneScale.nxs.md5 b/Testing/Data/SystemTest/TolueneScale.nxs.md5
index 34ac1914c0ea7499cc7f68d8bffecddc8332c7da..9e1652d98002743d739737cb348e7c1e0fb74546 100644
--- a/Testing/Data/SystemTest/TolueneScale.nxs.md5
+++ b/Testing/Data/SystemTest/TolueneScale.nxs.md5
@@ -1 +1 @@
-e481f1052eb404a39bd7bb2197d2e6cd
+d1a0e156844c6459d230763742e21080
diff --git a/Testing/Data/SystemTest/TolueneScratchAbins.nxs.md5 b/Testing/Data/SystemTest/TolueneScratchAbins.nxs.md5
index 05c4de8bd3ab955f92764092c50114fa6830482a..ffd48113c4d5f8b80826ad666eca4a60f2c17b97 100644
--- a/Testing/Data/SystemTest/TolueneScratchAbins.nxs.md5
+++ b/Testing/Data/SystemTest/TolueneScratchAbins.nxs.md5
@@ -1 +1 @@
-57009dcbb2f5ec83f760d6f732a27cbf
+ab23cd079e36f46dd610dc22a9d8beac
diff --git a/Testing/Data/SystemTest/TolueneSmallerOrderAbins.nxs.md5 b/Testing/Data/SystemTest/TolueneSmallerOrderAbins.nxs.md5
index 042253d6bbfa168d994072eae2f122d21b74a5b9..7306501d648bc3762f2d8b4404b12a6234137571 100644
--- a/Testing/Data/SystemTest/TolueneSmallerOrderAbins.nxs.md5
+++ b/Testing/Data/SystemTest/TolueneSmallerOrderAbins.nxs.md5
@@ -1 +1 @@
-52247e506e1d99794a14561353791670
+6864e54cc20afed4303eb4d977137913
diff --git a/Testing/Data/SystemTest/TolueneTAbins.nxs.md5 b/Testing/Data/SystemTest/TolueneTAbins.nxs.md5
index da81bd3f49f6d852250a2aa8a928f048d41ac19a..c73aee7c27bcb71fa3f32305aaba2f0102a37f93 100644
--- a/Testing/Data/SystemTest/TolueneTAbins.nxs.md5
+++ b/Testing/Data/SystemTest/TolueneTAbins.nxs.md5
@@ -1 +1 @@
-11926b88b484b4731a0f95f5dfcf21af
+3423d4b0e7c111a829cfac95c81fc350
diff --git a/docs/source/concepts/AbinsImplementation.rst b/docs/source/concepts/AbinsImplementation.rst
index ab88934a783e53affa612b1088dc62a1291a41d5..21463d62ab41ec4302c7e7f666b425dabc09800e 100644
--- a/docs/source/concepts/AbinsImplementation.rst
+++ b/docs/source/concepts/AbinsImplementation.rst
@@ -134,6 +134,14 @@ result scaling and splitting into atomic contributions.
 System tests
 ~~~~~~~~~~~~
 System tests are defined in *Testing/SystemTests/tests/analysis/AbinsTest.py*.
-These tests compare the output workspaces of Abins runs with reference Nexus files.
+These tests compare the output workspaces of Abins runs with reference Nexus files,
+using the standard setup described in
+`the main developer docs <http://developer.mantidproject.org/SystemTests.html>`_.
+The reference data will need to be changed when major updates to Abins
+impact the output results; the simplest way to obtain the new
+reference files is to run the system tests, which will save Nexus
+files from the failed system tests. These should be inspected to
+verify that all changes were expected and understood as consequences
+of changes to Abins.
 
 .. categories:: Concepts