diff --git a/configure.ac b/configure.ac
index 199f423..d852eea 100644
--- a/configure.ac
+++ b/configure.ac
@@ -2,7 +2,7 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ([2.69])
-AC_INIT([xssp], [3.0.9], [Coos.Baakman@radboudumc.nl])
+AC_INIT([xssp], [3.0.10], [Coos.Baakman@radboudumc.nl])
 AM_INIT_AUTOMAKE([subdir-objects])
 AC_CONFIG_SRCDIR([config.h.in])
 AC_CONFIG_HEADERS([config.h])
diff --git a/src/align-2d.h b/src/align-2d.h
index 658734c..fcb9e9b 100644
--- a/src/align-2d.h
+++ b/src/align-2d.h
@@ -39,24 +39,24 @@ struct entry
     , m_seq(seq)
     , m_weight(weight) {}
 
-  uint32 nr() const { return m_nr; }
+  int64 nr() const { return m_nr; }
   float weight() const { return m_weight; }
   uint32 length() const { return static_cast<uint32>(m_seq.length()); }
 
-  void insert_gap(uint32 pos);
+  void insert_gap(int64 pos);
   void append_gap();
 
-  void remove_gap(uint32 pos);
+  void remove_gap(int64 pos);
 
   void remove_gaps();
   void dump_positions() { m_positions.clear(); }
 
-  uint32 m_nr;
+  int64 m_nr;
   std::string m_id;
   sequence m_seq;
   sec_structure m_ss;
   float m_weight;
-  std::vector<int16> m_positions;
+  std::vector<int64> m_positions;
 };
 
 // --------------------------------------------------------------------
diff --git a/src/blast.cpp b/src/blast.cpp
index 20beca6..42d6fd3 100644
--- a/src/blast.cpp
+++ b/src/blast.cpp
@@ -41,7 +41,7 @@ const uint32
   kGappedDropOffFinal    = 25,
   kGapTrigger        = 22,
 
-  kMaxSequenceLength    = std::numeric_limits<uint16>::max();
+  kMaxSequenceLength    = std::numeric_limits<uint32>::max();
 
 const int32
   kHitWindow        = 40;
@@ -826,8 +826,8 @@ class WordHitIterator
 
   struct Entry
   {
-    uint16 mCount;
-    uint16 mDataOffset;
+    uint32 mCount;
+    uint32 mDataOffset;
   };
 
   public:
@@ -838,7 +838,7 @@ class WordHitIterator
   struct WordHitIteratorStaticData
   {
     std::vector<Entry> mLookup;
-    std::vector<uint16> mOffsets;
+    std::vector<uint32> mOffsets;
   };
 
   WordHitIterator(const WordHitIteratorStaticData& inStaticData)
@@ -858,19 +858,19 @@ class WordHitIterator
                    WordHitIteratorStaticData& outStaticData);
 
   void Reset(const sequence& inTarget);
-  bool Next(uint16& outQueryOffset, uint16& outTargetOffset);
+  bool Next(uint32& outQueryOffset, uint32& outTargetOffset);
   uint32 Index() const { return mIndex; }
 
   private:
 
   const uint8* mTargetCurrent;
   const uint8* mTargetEnd;
-  uint16 mTargetOffset;
+  uint32 mTargetOffset;
   const std::vector<Entry>& mLookup;
-  const std::vector<uint16>& mOffsets;
+  const std::vector<uint32>& mOffsets;
   uint32 mIndex;
-  const uint16* mOffset;
-  uint16 mCount;
+  const uint32* mOffset;
+  uint32 mCount;
 };
 
 template<> const uint32 WordHitIterator<2>::kMask = 0x0001F;
@@ -886,9 +886,9 @@ void WordHitIterator<WORDSIZE>::Init(const sequence& inQuery,
   uint64 N = IWord::kMaxWordIndex;
   size_t M = 0;
 
-  std::vector<std::vector<uint16>> test(N);
+  std::vector<std::vector<uint32>> test(N);
 
-  for (uint16 i = 0; i < inQuery.length() - WORDSIZE + 1; ++i)
+  for (uint32 i = 0; i < inQuery.length() - WORDSIZE + 1; ++i)
   {
     IWord w(inQuery.c_str() + i);
 
@@ -903,14 +903,14 @@ void WordHitIterator<WORDSIZE>::Init(const sequence& inQuery,
   }
 
   outStaticData.mLookup = std::vector<Entry>(N);
-  outStaticData.mOffsets = std::vector<uint16>(M);
+  outStaticData.mOffsets = std::vector<uint32>(M);
 
-  uint16* data = &outStaticData.mOffsets[0];
+  uint32* data = &outStaticData.mOffsets[0];
 
   for (uint32 i = 0; i < N; ++i)
   {
-    outStaticData.mLookup[i].mCount = static_cast<uint16>(test[i].size());
-    outStaticData.mLookup[i].mDataOffset = static_cast<uint16>(
+    outStaticData.mLookup[i].mCount = static_cast<uint32>(test[i].size());
+    outStaticData.mLookup[i].mDataOffset = static_cast<uint32>(
         data - &outStaticData.mOffsets[0]);
 
     for (uint32 j = 0; j < outStaticData.mLookup[i].mCount; ++j)
@@ -940,8 +940,8 @@ void WordHitIterator<WORDSIZE>::Reset(const sequence& inTarget)
 }
 
 template<int WORDSIZE>
-bool WordHitIterator<WORDSIZE>::Next(uint16& outQueryOffset,
-                                     uint16& outTargetOffset)
+bool WordHitIterator<WORDSIZE>::Next(uint32& outQueryOffset,
+                                     uint32& outTargetOffset)
 {
   bool result = false;
 
@@ -999,7 +999,7 @@ struct DiagonalStartTable
     std::fill(mTable, mTable + n, -inTargetLength);
   }
 
-  int32&  operator()(uint16 inQueryOffset, uint16 inTargetOffset)
+  int32&  operator()(uint32 inQueryOffset, uint32 inTargetOffset)
   {
     return mTable[mTargetLength - inTargetOffset + inQueryOffset];
   }
@@ -1501,7 +1501,7 @@ void BlastQuery<WORDSIZE>::SearchPart(const char* inFasta, size_t inLength,
     iter.Reset(target);
     diagonals.Reset(queryLength, static_cast<int32>(target.length()));
 
-    uint16 queryOffset, targetOffset;
+    uint32 queryOffset, targetOffset;
     while (iter.Next(queryOffset, targetOffset))
     {
       ++hitsToDb;
diff --git a/src/dssp.cpp b/src/dssp.cpp
index 39a1985..74b2a8f 100644
--- a/src/dssp.cpp
+++ b/src/dssp.cpp
@@ -79,7 +79,7 @@ std::string ResidueToDSSPLine(const MResidue& residue)
   char chirality;
   std::tie(alpha,chirality) = residue.Alpha();
 
-  uint32 bp[2] = {};
+  int64 bp[2] = {};
   char bridgelabel[2] = { ' ', ' ' };
   for (uint32 i = 0; i < 2; ++i)
   {
@@ -107,13 +107,13 @@ std::string ResidueToDSSPLine(const MResidue& residue)
 
     if (acceptors[i].residue != nullptr)
     {
-      int32 d = acceptors[i].residue->GetNumber() - residue.GetNumber();
+      int64 d = acceptors[i].residue->GetNumber() - residue.GetNumber();
       NHO[i] = (boost::format("%d,%3.1f") % d % acceptors[i].energy).str();
     }
 
     if (donors[i].residue != nullptr)
     {
-      int32 d = donors[i].residue->GetNumber() - residue.GetNumber();
+      int64 d = donors[i].residue->GetNumber() - residue.GetNumber();
       ONH[i] = (boost::format("%d,%3.1f") % d % donors[i].energy).str();
     }
   }
@@ -229,7 +229,9 @@ void WriteDSSP(MProtein& protein, std::ostream& os)
   foreach (const MChain* chain, protein.GetChains())
   {
     foreach (const MResidue* residue, chain->GetResidues())
+    {
       residues.push_back(residue);
+    }
   }
 
   // keep residues sorted by residue number as assigned during reading the PDB file
diff --git a/src/hssp-nt.cpp b/src/hssp-nt.cpp
index 5fcfea7..0ba8b30 100644
--- a/src/hssp-nt.cpp
+++ b/src/hssp-nt.cpp
@@ -103,7 +103,7 @@ float calculateDistance(const sequence& a, const sequence& b)
         M += B(x - 1, y - 1);
 
       float s;
-      uint16 i = 0;
+      uint32 i = 0;
       if (a[x] == b[y])
         i = 1;
 
@@ -160,8 +160,8 @@ struct MResInfo
   uint8 m_letter;
   std::string m_chain_id,
               m_auth_chain_id;
-  uint32 m_seq_nr;
-  int32 m_pdb_nr;
+  int64 m_seq_nr;
+  int64 m_pdb_nr;
   std::string m_ins_code;
   MSecondaryStructure m_ss;
   std::string m_dssp;
@@ -372,7 +372,7 @@ MProfile::MProfile(const MChain& inChain, const sequence& inSequence,
   const std::vector<MResidue*>& residues = m_chain.GetResidues();
   std::vector<MResidue*>::const_iterator ri = residues.begin();
 
-  uint32 seq_nr = 1;
+  int64 seq_nr = 1;
   for (uint32 i = 0; i < inSequence.length(); ++i)
   {
     assert(ri != residues.end());
diff --git a/src/structure.cpp b/src/structure.cpp
index 196c69a..fdf0b32 100644
--- a/src/structure.cpp
+++ b/src/structure.cpp
@@ -980,7 +980,7 @@ void MChain::WritePDB(std::ostream& os)
   os << (ter % (last->GetCAlpha().mSerial + 1) % kResidueInfo[last->GetType()].name % mChainID % last->GetNumber() % ' ') << std::endl;
 }
 
-const MResidue* MChain::GetResidueBySeqNumber(uint16 inSeqNumber,
+const MResidue* MChain::GetResidueBySeqNumber(int64 inSeqNumber,
                                               const std::string& inInsertionCode) const
 {
   const auto r = find_if(mResidues.begin(), mResidues.end(),
@@ -1002,7 +1002,7 @@ void MChain::GetSequence(std::string& outSequence) const
 struct MResidueID
 {
   std::string chain;
-  uint16 seqNumber;
+  int64 seqNumber;
   std::string insertionCode;
 
   bool operator<(const MResidueID& o) const
@@ -1160,12 +1160,12 @@ void MProtein::ReadPDB(std::istream& is, bool cAlphaOnly)
       std::pair<MResidueID,MResidueID> ssbond;
 
       ssbond.first.chain = line[15];
-      ssbond.first.seqNumber = boost::lexical_cast<uint16>(
+      ssbond.first.seqNumber = boost::lexical_cast<int64>(
           ba::trim_copy(line.substr(16, 5)));
       ssbond.first.insertionCode = line[21];
 
       ssbond.second.chain = line[29];
-      ssbond.second.seqNumber = boost::lexical_cast<uint16>(
+      ssbond.second.seqNumber = boost::lexical_cast<int64>(
           ba::trim_copy(line.substr(30, 5)));
       ssbond.second.insertionCode = line[35];
 
@@ -1220,7 +1220,7 @@ void MProtein::ReadPDB(std::istream& is, bool cAlphaOnly)
       atom.mChainID = line[21];
       atom.mAuthChainID = atom.mChainID;
       //  23 - 26  Integer resSeq Residue sequence number.
-      atom.mResSeq = boost::lexical_cast<int16>(
+      atom.mResSeq = boost::lexical_cast<int64>(
           ba::trim_copy(line.substr(22, 4)));
       //  27    AChar iCode Code for insertion of residues.
       atom.mICode = line.substr(26, 1);
@@ -1432,7 +1432,7 @@ void MProtein::ReadmmCIF(std::istream& is, bool cAlphaOnly)
       continue;
 
     ssbond.first.chain = ss["ptnr1_label_asym_id"];
-    ssbond.first.seqNumber = boost::lexical_cast<uint16>(
+    ssbond.first.seqNumber = boost::lexical_cast<int64>(
         ss["ptnr1_label_seq_id"]);
     ssbond.first.insertionCode = ss["pdbx_ptnr1_PDB_ins_code"];
     if (ssbond.first.insertionCode == "?")
@@ -1442,7 +1442,7 @@ void MProtein::ReadmmCIF(std::istream& is, bool cAlphaOnly)
       continue;
 
     ssbond.second.chain = ss["ptnr2_label_asym_id"];
-    ssbond.second.seqNumber = boost::lexical_cast<uint16>(
+    ssbond.second.seqNumber = boost::lexical_cast<int64>(
         ss["ptnr2_label_seq_id"]);
     ssbond.second.insertionCode = ss["pdbx_ptnr2_PDB_ins_code"];
     if (ssbond.second.insertionCode == "?")
@@ -1455,7 +1455,7 @@ void MProtein::ReadmmCIF(std::istream& is, bool cAlphaOnly)
   char firstAltLoc = 0;
 
   // remap label_seq_id to auth_seq_id
-  std::map<std::string, std::map<int,int> > seq_id_map;
+  std::map<std::string, std::map<int64,int64> > seq_id_map;
 
   bool hasModelNum = false;
   int modelNum = 0;
@@ -1488,7 +1488,7 @@ void MProtein::ReadmmCIF(std::istream& is, bool cAlphaOnly)
     if (label_seq_id == "?" or label_seq_id == ".")
       seq_id_map[a.mChainID][a.mResSeq] = a.mResSeq;
     else
-      seq_id_map[a.mChainID][boost::lexical_cast<int16>(label_seq_id)] = a.mResSeq;
+      seq_id_map[a.mChainID][boost::lexical_cast<int64>(label_seq_id)] = a.mResSeq;
 
     a.mLoc.mX = ParseFloat(atom["Cartn_x"]);
     a.mLoc.mY = ParseFloat(atom["Cartn_y"]);
@@ -1545,7 +1545,9 @@ void MProtein::ReadmmCIF(std::istream& is, bool cAlphaOnly)
   }
 
   if (not atoms.empty())
+  {
     AddResidue(atoms);
+  }
 
   // map the sulfur bridges
   uint32 ssbondNr = 1;
@@ -1647,7 +1649,7 @@ void MProtein::GetStatistics(uint32& outNrOfResidues, uint32& outNrOfChains,
         if (donor[i].residue != nullptr and donor[i].energy < kMaxHBondEnergy)
         {
           ++outNrOfHBonds;
-          int32 k = donor[i].residue->GetNumber() - r->GetNumber();
+          int64 k = donor[i].residue->GetNumber() - r->GetNumber();
           if (k >= -5 and k <= 5)
             outNrOfHBondsPerDistance[k + 5] += 1;
         }
@@ -1725,7 +1727,7 @@ void MProtein::AddResidue(const std::vector<MAtom>& inAtoms)
     if (not residues.empty())
       prev = residues.back();
 
-    int32 resNumber = mResidueCount + mChains.size() + mChainBreaks;
+    int64 resNumber = mResidueCount + mChains.size() + mChainBreaks;
     MResidue* r = new MResidue(resNumber, prev, inAtoms);
     // check for chain breaks
     if (prev != nullptr and not prev->ValidDistance(*r))
@@ -1794,8 +1796,10 @@ void MProtein::CalculateSecondaryStructure(bool inPreferPiHelices)
   std::vector<MResidue*> residues;
   residues.reserve(mResidueCount);
   foreach (const MChain* chain, mChains)
+  {
     residues.insert(residues.end(), chain->GetResidues().begin(),
                     chain->GetResidues().end());
+  }
 
   if (VERBOSE)
     std::cerr << "using " << residues.size() << " residues" << std::endl;
@@ -2254,7 +2258,7 @@ void MProtein::SetChain(const std::string& inChainID, const MChain& inChain)
 
 // Non-const overload, implemented in terms of the const overload
 MResidue* MProtein::GetResidue(const std::string& inChainID,
-                               uint16 inSeqNumber,
+                               int64 inSeqNumber,
                                const std::string& inInsertionCode)
 {
   return const_cast<MResidue *>( static_cast<const MProtein &>( *this ).GetResidue(
@@ -2266,7 +2270,7 @@ MResidue* MProtein::GetResidue(const std::string& inChainID,
 
 // Const overload
 const MResidue* MProtein::GetResidue(const std::string& inChainID,
-                                     uint16 inSeqNumber,
+                                     int64 inSeqNumber,
                                      const std::string& inInsertionCode) const
 {
   const MChain& chain = GetChain(inChainID);
@@ -2287,7 +2291,7 @@ void MProtein::GetCAlphaLocations(const std::string& inChainID,
 }
 
 MPoint MProtein::GetCAlphaPosition(const std::string& inChainID,
-                                   int16 inPDBResSeq) const
+                                   int64 inPDBResSeq) const
 {
   std::string chainID = inChainID;
   if (chainID.empty())
diff --git a/src/structure.h b/src/structure.h
index 849729d..c82a6ba 100644
--- a/src/structure.h
+++ b/src/structure.h
@@ -225,11 +225,11 @@ class MResidue
   // bridge functions
   MBridgeType      TestBridge(MResidue* inResidue) const;
 
-  int16        GetSeqNumber() const    { return mSeqNumber; }
+  int64        GetSeqNumber() const    { return mSeqNumber; }
   std::string      GetInsertionCode() const  { return mInsertionCode; }
 
-  void        SetNumber(uint16 inNumber)  { mNumber = inNumber; }
-  uint16        GetNumber() const      { return mNumber; }
+  void        SetNumber(int64 inNumber)  { mNumber = inNumber; }
+  int64        GetNumber() const      { return mNumber; }
 
   void        Translate(const MPoint& inTranslation);
   void        Rotate(const MQuaternion& inRotation);
@@ -265,7 +265,7 @@ class MResidue
   std::string      mChainID;
   MResidue*      mPrev;
   MResidue*      mNext;
-  int32        mSeqNumber, mNumber;
+  int64        mSeqNumber, mNumber;
   std::string      mInsertionCode;
   MResidueType    mType;
   uint8        mSSBridgeNr;
@@ -302,7 +302,7 @@ class MChain
   std::string GetAuthChainID(void) const;
   void SetAuthChainID(const std::string &inAuthChainID);
 
-  const MResidue*      GetResidueBySeqNumber(uint16 inSeqNumber,
+  const MResidue*      GetResidueBySeqNumber(int64 inSeqNumber,
                                              const std::string& inInsertionCode) const;
 
   void        GetSequence(std::string& outSequence) const;
@@ -354,7 +354,7 @@ class MProtein
   void GetCAlphaLocations(const std::string& inChainID,
                                  std::vector<MPoint>& outPoints) const;
   MPoint        GetCAlphaPosition(const std::string& inChainID,
-                                  int16 inPDBResSeq) const;
+                                  int64 inPDBResSeq) const;
 
   void        GetSequence(const std::string& inChainID,
                           entry& outEntry) const;
@@ -384,10 +384,10 @@ class MProtein
   template<class OutputIterator>
   void        GetSequences(OutputIterator outSequences) const;
 
-  MResidue* GetResidue(const std::string& inChainID, uint16 inSeqNumber,
+  MResidue* GetResidue(const std::string& inChainID, int64 inSeqNumber,
                        const std::string& inInsertionCode);
 
-  const MResidue* GetResidue(const std::string& inChainID, uint16 inSeqNumber,
+  const MResidue* GetResidue(const std::string& inChainID, int64 inSeqNumber,
                              const std::string& inInsertionCode) const;
 
   // statistics