diff --git a/moldesign/_tests/data/3b5x.cif.bz2 b/moldesign/_tests/data/3b5x.cif.bz2
new file mode 100644
index 0000000..05dd98b
Binary files /dev/null and b/moldesign/_tests/data/3b5x.cif.bz2 differ
diff --git a/moldesign/_tests/test_pdb_processing.py b/moldesign/_tests/test_pdb_processing.py
index 701112e..c7febe4 100644
--- a/moldesign/_tests/test_pdb_processing.py
+++ b/moldesign/_tests/test_pdb_processing.py
@@ -129,6 +129,13 @@ def test_single_chain_2p8w():
     assert mol.chains['C'].num_residues == 1
     assert mol.chains['C'].residues['GNP843'].num_atoms == 32
 
+    
+def test_missing_atoms_3b5x():
+    mol = mdt.read(get_data_path('3b5x.cif.bz2'))
+    assert mol.num_chains == 2
+    assert mol.num_atoms == 1144
+    assert mol.num_residues == 1144
+
 
 MISSINGRES_2JAJ = [('A', 'GLY', -4), ('A', 'PRO', -3), ('A', 'LEU', -2), ('A', 'GLY', -1),
                    ('A', 'MET', 0), ('A', 'ALA', 1), ('A', 'GLY', 2), ('A', 'LEU', 3),
diff --git a/moldesign/molecules/residue.py b/moldesign/molecules/residue.py
index 4bcc05e..b8325e9 100644
--- a/moldesign/molecules/residue.py
+++ b/moldesign/molecules/residue.py
@@ -247,11 +247,10 @@ def _is_ending_residue(self):
         except KeyError:
             # If we're here, the residue is missing some atoms. We'll fall back to checking the
             # next residues in line
-            if self.index == len(self.molecule.residues):
+            if self.index == len(self.molecule.residues) - 1:
                 return True
             else:
-                print('WARNING: %s is missing expected atoms. Attempting to infer chain end' % \
-                    self)
+                print('WARNING: %s is missing expected atoms. Attempting to infer chain end' % self)
                 nextres = self.molecule.residues[self.index + 1]
                 return not self._same_polymer(nextres)