diff --git a/pdbfixer/pdbfixer.py b/pdbfixer/pdbfixer.py
index d1ac03e..1e376fc 100644
--- a/pdbfixer/pdbfixer.py
+++ b/pdbfixer/pdbfixer.py
@@ -389,7 +389,7 @@ def _addAtomsToTopology(self, heavyAtomsOnly, omitUnknownMolecules):
 
                 # Create the new residue and add existing heavy atoms.
 
-                newResidue = newTopology.addResidue(residue.name, newChain, residue.id)
+                newResidue = newTopology.addResidue(residue.name, newChain, residue.id, residue.insertionCode)
                 for atom in residue.atoms():
                     if not heavyAtomsOnly or (atom.element is not None and atom.element != hydrogen):
                         if atom.name == 'OXT' and (chain.index, indexInChain+1) in self.missingResidues:
@@ -510,7 +510,7 @@ def _addMissingResiduesToChain(self, chain, residueNames, startPosition, endPosi
 
             # Create the new residue.
 
-            newResidue = chain.topology.addResidue(residueName, chain, "%d" % ((firstIndex+i)%10000))
+            newResidue = chain.topology.addResidue(residueName, chain, "%d" % (firstIndex+i))
             fraction = (i+1.0)/(numResidues+1.0)
             translate = startPosition + (endPosition-startPosition)*fraction + loopHeight*math.sin(fraction*math.pi)*loopDirection
             templateAtoms = list(template.topology.atoms())
@@ -569,7 +569,7 @@ def removeChains(self, chainIndices=None, chainIds=None):
 
         return
 
-    def findMissingResidues(self):
+    def findMissingResidues(self,chainWithGapsOverride=None):
         """Find residues that are missing from the structure.
 
         The results are stored into the missingResidues field, which is a dict.  Each key is a tuple consisting of
@@ -587,13 +587,33 @@ def findMissingResidues(self):
         chains = [c for c in self.topology.chains() if len(list(c.residues())) > 0]
         chainWithGaps = {}
 
+        # This is PDBFixer's best guess for what might appear in a SEQRES
+
+        knownResidues = set(self.templates.keys()) | set(substitutions.keys())
+        for s in self.sequences:
+            knownResidues.update(s.residues)
+
         # Find the sequence of each chain, with gaps for missing residues.
 
         for chain in chains:
-            minResidue = min(int(r.id) for r in chain.residues())
-            maxResidue = max(int(r.id) for r in chain.residues())
-            residues = [None]*(maxResidue-minResidue+1)
+            if chainWithGapsOverride:
+                if chain.id in chainWithGapsOverride:
+                    chainWithGaps[chain] = chainWithGapsOverride[chain.id]
+                continue
+
+            seqresResidues = []
             for r in chain.residues():
+                if r.name in knownResidues:
+                    seqresResidues.append(r)
+                else:
+                    # assume that everything that follows is a ligand/water
+                    break
+
+            if len(seqresResidues) == 0: continue
+            minResidue = min(int(r.id) for r in seqresResidues)
+            maxResidue = max(int(r.id) for r in seqresResidues)
+            residues = [None]*(maxResidue-minResidue+1)
+            for r in seqresResidues:
                 residues[int(r.id)-minResidue] = r.name
             chainWithGaps[chain] = residues
 
@@ -607,6 +627,8 @@ def findMissingResidues(self):
                     continue
                 if chain in chainSequence:
                     continue
+                if chain not in chainWithGaps:
+                    continue
                 for offset in range(len(sequence.residues)-len(chainWithGaps[chain])+1):
                     if all(a == b or b == None for a,b in zip(sequence.residues[offset:], chainWithGaps[chain])):
                         chainSequence[chain] = sequence