Substituting phenix.python into build shell scripts
  update_options.sh
  update_ResidueType_enum_files.sh

  Phenix modules found : /usr/local/phenix-1.21-5207/modules/phenix
False
/usr/local/Rosetta-3.14/rosetta.source.release-371/main/source

  ~> phenix.python scons.py bin mode=release extras=python  -j 1

scons: Reading SConscript files ...
Running versioning script ... Release package detected, using rosetta/main/.release.json to acquire version information...
Done. (0.0 seconds)
Number of option files updated: 0
Total 4680 options.
Finished updating ResidueProperty code
-- no changes needed
Finished updating VariantType code
-- no changes needed
scons: done reading SConscript files.
scons: Building targets ...
g++ -o build/src/release/linux/4.18/64/x86/gcc/8/python/core/scoring/cryst/PhenixInterface.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/include/python2.7 src/core/scoring/cryst/PhenixInterface.cc
src/core/scoring/cryst/PhenixInterface.cc: In constructor 'core::scoring::cryst::PhenixInterface::PhenixInterface()':
src/core/scoring/cryst/PhenixInterface.cc:66:20: error: 'basic::options' has not been declared
  mtzfile_ = basic::options::option[ basic::options::OptionKeys::cryst::mtzfile ]();
                    ^~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:66:44: error: 'basic::options' has not been declared
  mtzfile_ = basic::options::option[ basic::options::OptionKeys::cryst::mtzfile ]();
                                            ^~~~~~~
src/core/scoring/cryst/PhenixInterface.cc: In member function 'void core::scoring::cryst::PhenixInterface::fitBfactors(core::pose::Pose&)':
src/core/scoring/cryst/PhenixInterface.cc:215:14: error: 'initialize_disulfide_bonds' is not a member of 'core::pose'
  core::pose::initialize_disulfide_bonds( pose );
              ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:222:19: error: aggregate 'core::pose::Pose pose_asu' has incomplete type and cannot be defined
  core::pose::Pose pose_asu;
                   ^~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:223:14: error: 'core::pose::symmetry' has not been declared
  core::pose::symmetry::extract_asymmetric_unit(pose, pose_asu);
              ^~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:225:2: error: 'fix_bfactorsH' was not declared in this scope
  fix_bfactorsH( pose_asu );
  ^~~~~~~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:225:2: note: suggested alternative: 'fitBfactors'
  fix_bfactorsH( pose_asu );
  ^~~~~~~~~~~~~
  fitBfactors
src/core/scoring/cryst/PhenixInterface.cc:226:2: error: 'fix_bfactorsMissing' was not declared in this scope
  fix_bfactorsMissing( pose_asu );
  ^~~~~~~~~~~~~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc: In member function 'PyObject* core::scoring::cryst::PhenixInterface::pose_to_pycoords(const core::pose::Pose&)':
src/core/scoring/cryst/PhenixInterface.cc:377:30: error: 'symmetry' is not a namespace-name
  using namespace core::pose::symmetry;
                              ^~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:377:38: error: expected namespace-name before ';' token
  using namespace core::pose::symmetry;
                                      ^
src/core/scoring/cryst/PhenixInterface.cc:378:24: error: 'core::conformation' has not been declared
  using namespace core::conformation::symmetry;
                        ^~~~~~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:378:38: error: 'symmetry' is not a namespace-name
  using namespace core::conformation::symmetry;
                                      ^~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:378:46: error: expected namespace-name before ';' token
  using namespace core::conformation::symmetry;
                                              ^
src/core/scoring/cryst/PhenixInterface.cc:383:7: error: 'is_symmetric' was not declared in this scope
  if ( is_symmetric( pose ) ) {
       ^~~~~~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:384:3: error: 'SymmetricConformation' was not declared in this scope
   SymmetricConformation const & symm_conf (
   ^~~~~~~~~~~~~~~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:386:3: error: 'SymmetryInfoCOP' was not declared in this scope
   SymmetryInfoCOP symm_info( symm_conf.Symmetry_Info() );
   ^~~~~~~~~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:388:26: error: 'symm_info' was not declared in this scope
   for ( int i=1; i<=(int)symm_info->num_total_residues_without_pseudo(); ++i ) {
                          ^~~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:388:26: note: suggested alternative: 'symlink'
   for ( int i=1; i<=(int)symm_info->num_total_residues_without_pseudo(); ++i ) {
                          ^~~~~~~~~
                          symlink
src/core/scoring/cryst/PhenixInterface.cc:389:9: error: invalid use of incomplete type 'const class core::pose::Pose'
    if ( pose.residue(i).aa() == core::chemical::aa_vrt ) continue;
         ^~~~
In file included from src/core/scoring/cryst/PhenixInterface.hh:23,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
src/core/pose/Pose.fwd.hh:25:7: note: forward declaration of 'class core::pose::Pose'
 class Pose;
       ^~~~
src/core/scoring/cryst/PhenixInterface.cc:389:39: error: 'core::chemical' has not been declared
    if ( pose.residue(i).aa() == core::chemical::aa_vrt ) continue;
                                       ^~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:392:10: error: 'core::conformation' has not been declared
    core::conformation::Residue const &rsd_i = pose.residue(i);
          ^~~~~~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:395:28: error: invalid use of incomplete type 'const class core::pose::Pose'
    bool ignore_cys_hg = ( !pose.residue(i).has_variant_type( core::chemical::DISULFIDE ) &&
                            ^~~~
In file included from src/core/scoring/cryst/PhenixInterface.hh:23,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
src/core/pose/Pose.fwd.hh:25:7: note: forward declaration of 'class core::pose::Pose'
 class Pose;
       ^~~~
src/core/scoring/cryst/PhenixInterface.cc:395:68: error: 'core::chemical' has not been declared
    bool ignore_cys_hg = ( !pose.residue(i).has_variant_type( core::chemical::DISULFIDE ) &&
                                                                    ^~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:396:14: error: invalid use of incomplete type 'using element_type = class core::pose::Pose' {aka 'class core::pose::Pose'}
     ref_pose_->residue(i).has_variant_type( core::chemical::DISULFIDE ) );
              ^~
In file included from src/core/scoring/cryst/PhenixInterface.hh:23,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
src/core/pose/Pose.fwd.hh:25:7: note: forward declaration of 'using element_type = class core::pose::Pose' {aka 'class core::pose::Pose'}
 class Pose;
       ^~~~
src/core/scoring/cryst/PhenixInterface.cc:396:51: error: 'core::chemical' has not been declared
     ref_pose_->residue(i).has_variant_type( core::chemical::DISULFIDE ) );
                                                   ^~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:397:24: error: invalid use of incomplete type 'const class core::pose::Pose'
    bool add_cys_hg = ( pose.residue(i).has_variant_type( core::chemical::DISULFIDE ) &&
                        ^~~~
In file included from src/core/scoring/cryst/PhenixInterface.hh:23,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
src/core/pose/Pose.fwd.hh:25:7: note: forward declaration of 'class core::pose::Pose'
 class Pose;
       ^~~~
src/core/scoring/cryst/PhenixInterface.cc:397:64: error: 'core::chemical' has not been declared
    bool add_cys_hg = ( pose.residue(i).has_variant_type( core::chemical::DISULFIDE ) &&
                                                                ^~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:398:15: error: invalid use of incomplete type 'using element_type = class core::pose::Pose' {aka 'class core::pose::Pose'}
     !ref_pose_->residue(i).has_variant_type( core::chemical::DISULFIDE ) );
               ^~
In file included from src/core/scoring/cryst/PhenixInterface.hh:23,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
src/core/pose/Pose.fwd.hh:25:7: note: forward declaration of 'using element_type = class core::pose::Pose' {aka 'class core::pose::Pose'}
 class Pose;
       ^~~~
src/core/scoring/cryst/PhenixInterface.cc:398:52: error: 'core::chemical' has not been declared
     !ref_pose_->residue(i).has_variant_type( core::chemical::DISULFIDE ) );
                                                    ^~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:400:27: error: 'rsd_i' was not declared in this scope
    for ( int j=1; j<=(int)rsd_i.natoms(); ++j ) {
                           ^~~~~
src/core/scoring/cryst/PhenixInterface.cc:401:10: error: invalid use of incomplete type 'const class core::pose::Pose'
     if ( pose.residue_type(i).atom_name(j) == " CEN" ) continue;
          ^~~~
In file included from src/core/scoring/cryst/PhenixInterface.hh:23,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
src/core/pose/Pose.fwd.hh:25:7: note: forward declaration of 'class core::pose::Pose'
 class Pose;
       ^~~~
src/core/scoring/cryst/PhenixInterface.cc:402:10: error: invalid use of incomplete type 'const class core::pose::Pose'
     if ( pose.residue_type(i).atom_type(j).is_virtual() ) continue;
          ^~~~
In file included from src/core/scoring/cryst/PhenixInterface.hh:23,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
src/core/pose/Pose.fwd.hh:25:7: note: forward declaration of 'class core::pose::Pose'
 class Pose;
       ^~~~
src/core/scoring/cryst/PhenixInterface.cc:404:27: error: invalid use of incomplete type 'const class core::pose::Pose'
     if ( ignore_cys_hg && pose.residue(i).atom_name(j) == " HG " ) {
                           ^~~~
In file included from src/core/scoring/cryst/PhenixInterface.hh:23,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
src/core/pose/Pose.fwd.hh:25:7: note: forward declaration of 'class core::pose::Pose'
 class Pose;
       ^~~~
src/core/scoring/cryst/PhenixInterface.cc:416:53: error: 'rsd_i' was not declared in this scope
     utility::vector1< std::string > variant_types = rsd_i.type().properties().get_list_of_variants();
                                                     ^~~~~
src/core/scoring/cryst/PhenixInterface.cc:420:5: error: 'chemical' has not been declared
     chemical::ResidueTypeSetCOP residue_type_set = pose.residue_type_set_for_pose();
     ^~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:421:5: error: 'chemical' has not been declared
     chemical::ResidueTypeCOP replacement_type( residue_type_set->get_representative_type_name3( rsd_i.type().name3(), variant_types ) );
     ^~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:422:10: error: 'replacement_type' was not declared in this scope
     if ( replacement_type ) {
          ^~~~~~~~~~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:423:6: error: 'conformation' has not been declared
      conformation::ResidueOP new_res = conformation::ResidueFactory::create_residue( *replacement_type, rsd_i, pose.conformation() );
      ^~~~~~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:424:66: error: 'new_res' was not declared in this scope
      copy_residue_coordinates_and_rebuild_missing_atoms( rsd_i, *new_res, pose.conformation() );
                                                                  ^~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:424:75: error: invalid use of incomplete type 'const class core::pose::Pose'
      copy_residue_coordinates_and_rebuild_missing_atoms( rsd_i, *new_res, pose.conformation() );
                                                                           ^~~~
In file included from src/core/scoring/cryst/PhenixInterface.hh:23,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
src/core/pose/Pose.fwd.hh:25:7: note: forward declaration of 'class core::pose::Pose'
 class Pose;
       ^~~~
src/core/scoring/cryst/PhenixInterface.cc:424:6: error: 'copy_residue_coordinates_and_rebuild_missing_atoms' was not declared in this scope
      copy_residue_coordinates_and_rebuild_missing_atoms( rsd_i, *new_res, pose.conformation() );
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:428:33: error: invalid use of incomplete type 'using element_type = class core::pose::Pose' {aka 'class core::pose::Pose'}
      coords.push_back( ref_pose_->residue(i).xyz( ref_pose_->residue(i).atom_index(" HG ")) );
                                 ^~
In file included from src/core/scoring/cryst/PhenixInterface.hh:23,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
src/core/pose/Pose.fwd.hh:25:7: note: forward declaration of 'using element_type = class core::pose::Pose' {aka 'class core::pose::Pose'}
 class Pose;
       ^~~~
src/core/scoring/cryst/PhenixInterface.cc:428:60: error: invalid use of incomplete type 'using element_type = class core::pose::Pose' {aka 'class core::pose::Pose'}
      coords.push_back( ref_pose_->residue(i).xyz( ref_pose_->residue(i).atom_index(" HG ")) );
                                                            ^~
In file included from src/core/scoring/cryst/PhenixInterface.hh:23,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
src/core/pose/Pose.fwd.hh:25:7: note: forward declaration of 'using element_type = class core::pose::Pose' {aka 'class core::pose::Pose'}
 class Pose;
       ^~~~
src/core/scoring/cryst/PhenixInterface.cc:433:26: error: invalid use of incomplete type 'const class core::pose::Pose'
   for ( int i=1; i<=(int)pose.size(); ++i ) {
                          ^~~~
In file included from src/core/scoring/cryst/PhenixInterface.hh:23,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
src/core/pose/Pose.fwd.hh:25:7: note: forward declaration of 'class core::pose::Pose'
 class Pose;
       ^~~~
src/core/scoring/cryst/PhenixInterface.cc:434:9: error: invalid use of incomplete type 'const class core::pose::Pose'
    if ( pose.residue(i).aa() == core::chemical::aa_vrt ) continue;
         ^~~~
In file included from src/core/scoring/cryst/PhenixInterface.hh:23,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
src/core/pose/Pose.fwd.hh:25:7: note: forward declaration of 'class core::pose::Pose'
 class Pose;
       ^~~~
src/core/scoring/cryst/PhenixInterface.cc:434:39: error: 'core::chemical' has not been declared
    if ( pose.residue(i).aa() == core::chemical::aa_vrt ) continue;
                                       ^~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:435:10: error: 'core::conformation' has not been declared
    core::conformation::Residue const &rsd_i = pose.residue(i);
          ^~~~~~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:436:27: error: 'rsd_i' was not declared in this scope
    for ( int j=1; j<=(int)rsd_i.natoms(); ++j ) {
                           ^~~~~
src/core/scoring/cryst/PhenixInterface.cc:437:10: error: invalid use of incomplete type 'const class core::pose::Pose'
     if ( pose.residue_type(i).atom_name(j) == " CEN" ) continue;
          ^~~~
In file included from src/core/scoring/cryst/PhenixInterface.hh:23,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
src/core/pose/Pose.fwd.hh:25:7: note: forward declaration of 'class core::pose::Pose'
 class Pose;
       ^~~~
src/core/scoring/cryst/PhenixInterface.cc:438:10: error: invalid use of incomplete type 'const class core::pose::Pose'
     if ( pose.residue_type(i).atom_type(j).is_virtual() ) continue;
          ^~~~
In file included from src/core/scoring/cryst/PhenixInterface.hh:23,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
src/core/pose/Pose.fwd.hh:25:7: note: forward declaration of 'class core::pose::Pose'
 class Pose;
       ^~~~
src/core/scoring/cryst/PhenixInterface.cc:454:75: error: no match for 'operator[]' (operand types are '__gnu_cxx::__alloc_traits<std::allocator<numeric::xyzVector<double> >, numeric::xyzVector<double> >::value_type' {aka 'numeric::xyzVector<double>'} and 'int')
   PyList_SetItem( pCoords, 3*(i-1)+0, PyFloat_FromDouble( (float)coords[i][0]) );
                                                                           ^
src/core/scoring/cryst/PhenixInterface.cc:455:75: error: no match for 'operator[]' (operand types are '__gnu_cxx::__alloc_traits<std::allocator<numeric::xyzVector<double> >, numeric::xyzVector<double> >::value_type' {aka 'numeric::xyzVector<double>'} and 'int')
   PyList_SetItem( pCoords, 3*(i-1)+1, PyFloat_FromDouble( (float)coords[i][1]) );
                                                                           ^
src/core/scoring/cryst/PhenixInterface.cc:456:75: error: no match for 'operator[]' (operand types are '__gnu_cxx::__alloc_traits<std::allocator<numeric::xyzVector<double> >, numeric::xyzVector<double> >::value_type' {aka 'numeric::xyzVector<double>'} and 'int')
   PyList_SetItem( pCoords, 3*(i-1)+2, PyFloat_FromDouble( (float)coords[i][2]) );
                                                                           ^
src/core/scoring/cryst/PhenixInterface.cc: In member function 'void core::scoring::cryst::PhenixInterface::pylist_to_grads(const core::pose::Pose&, PyObject*, utility::vector1<utility::vector1<numeric::xyzVector<double> > >&)':
src/core/scoring/cryst/PhenixInterface.cc:468:30: error: 'symmetry' is not a namespace-name
  using namespace core::pose::symmetry;
                              ^~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:468:38: error: expected namespace-name before ';' token
  using namespace core::pose::symmetry;
                                      ^
src/core/scoring/cryst/PhenixInterface.cc:469:24: error: 'core::conformation' has not been declared
  using namespace core::conformation::symmetry;
                        ^~~~~~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:469:38: error: 'symmetry' is not a namespace-name
  using namespace core::conformation::symmetry;
                                      ^~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:469:46: error: expected namespace-name before ';' token
  using namespace core::conformation::symmetry;
                                              ^
src/core/scoring/cryst/PhenixInterface.cc:473:2: error: 'SymmetryInfoCOP' was not declared in this scope
  SymmetryInfoCOP symm_info;
  ^~~~~~~~~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:474:18: error: invalid use of incomplete type 'const class core::pose::Pose'
  int nres = (int)pose.size();
                  ^~~~
In file included from src/core/scoring/cryst/PhenixInterface.hh:23,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
src/core/pose/Pose.fwd.hh:25:7: note: forward declaration of 'class core::pose::Pose'
 class Pose;
       ^~~~
src/core/scoring/cryst/PhenixInterface.cc:475:19: error: 'core::pose::symmetry' has not been declared
  if ( core::pose::symmetry::is_symmetric(pose) ) {
                   ^~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:476:9: error: 'core::conformation' has not been declared
   core::conformation::symmetry::SymmetricConformation const & SymmConf (
         ^~~~~~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:478:3: error: 'symm_info' was not declared in this scope
   symm_info = SymmConf.Symmetry_Info();
   ^~~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:478:3: note: suggested alternative: 'symlink'
   symm_info = SymmConf.Symmetry_Info();
   ^~~~~~~~~
   symlink
src/core/scoring/cryst/PhenixInterface.cc:478:15: error: 'SymmConf' was not declared in this scope
   symm_info = SymmConf.Symmetry_Info();
               ^~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:478:15: note: suggested alternative: 'sysconf'
   symm_info = SymmConf.Symmetry_Info();
               ^~~~~~~~
               sysconf
src/core/scoring/cryst/PhenixInterface.cc:484:25: error: invalid use of incomplete type 'const class core::pose::Pose'
  for ( int i=1; i<=(int)pose.size(); ++i ) {
                         ^~~~
In file included from src/core/scoring/cryst/PhenixInterface.hh:23,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
src/core/pose/Pose.fwd.hh:25:7: note: forward declaration of 'class core::pose::Pose'
 class Pose;
       ^~~~
src/core/scoring/cryst/PhenixInterface.cc:485:8: error: invalid use of incomplete type 'const class core::pose::Pose'
   if ( pose.residue(i).aa() == core::chemical::aa_vrt ) continue;
        ^~~~
In file included from src/core/scoring/cryst/PhenixInterface.hh:23,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
src/core/pose/Pose.fwd.hh:25:7: note: forward declaration of 'class core::pose::Pose'
 class Pose;
       ^~~~
src/core/scoring/cryst/PhenixInterface.cc:485:38: error: 'core::chemical' has not been declared
   if ( pose.residue(i).aa() == core::chemical::aa_vrt ) continue;
                                      ^~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:486:8: error: 'symm_info' was not declared in this scope
   if ( symm_info && !symm_info->bb_is_independent(i) ) continue;
        ^~~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:486:8: note: suggested alternative: 'symlink'
   if ( symm_info && !symm_info->bb_is_independent(i) ) continue;
        ^~~~~~~~~
        symlink
src/core/scoring/cryst/PhenixInterface.cc:488:9: error: 'core::conformation' has not been declared
   core::conformation::Residue const &rsd_i = pose.residue(i);
         ^~~~~~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:491:27: error: invalid use of incomplete type 'const class core::pose::Pose'
   bool ignore_cys_hg = ( !pose.residue(i).has_variant_type( core::chemical::DISULFIDE ) &&
                           ^~~~
In file included from src/core/scoring/cryst/PhenixInterface.hh:23,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
src/core/pose/Pose.fwd.hh:25:7: note: forward declaration of 'class core::pose::Pose'
 class Pose;
       ^~~~
src/core/scoring/cryst/PhenixInterface.cc:491:67: error: 'core::chemical' has not been declared
   bool ignore_cys_hg = ( !pose.residue(i).has_variant_type( core::chemical::DISULFIDE ) &&
                                                                   ^~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:492:13: error: invalid use of incomplete type 'using element_type = class core::pose::Pose' {aka 'class core::pose::Pose'}
    ref_pose_->residue(i).has_variant_type( core::chemical::DISULFIDE ) );
             ^~
In file included from src/core/scoring/cryst/PhenixInterface.hh:23,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
src/core/pose/Pose.fwd.hh:25:7: note: forward declaration of 'using element_type = class core::pose::Pose' {aka 'class core::pose::Pose'}
 class Pose;
       ^~~~
src/core/scoring/cryst/PhenixInterface.cc:492:50: error: 'core::chemical' has not been declared
    ref_pose_->residue(i).has_variant_type( core::chemical::DISULFIDE ) );
                                                  ^~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:493:23: error: invalid use of incomplete type 'const class core::pose::Pose'
   bool add_cys_hg = ( pose.residue(i).has_variant_type( core::chemical::DISULFIDE ) &&
                       ^~~~
In file included from src/core/scoring/cryst/PhenixInterface.hh:23,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
src/core/pose/Pose.fwd.hh:25:7: note: forward declaration of 'class core::pose::Pose'
 class Pose;
       ^~~~
src/core/scoring/cryst/PhenixInterface.cc:493:63: error: 'core::chemical' has not been declared
   bool add_cys_hg = ( pose.residue(i).has_variant_type( core::chemical::DISULFIDE ) &&
                                                               ^~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:494:14: error: invalid use of incomplete type 'using element_type = class core::pose::Pose' {aka 'class core::pose::Pose'}
    !ref_pose_->residue(i).has_variant_type( core::chemical::DISULFIDE ) );
              ^~
In file included from src/core/scoring/cryst/PhenixInterface.hh:23,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
src/core/pose/Pose.fwd.hh:25:7: note: forward declaration of 'using element_type = class core::pose::Pose' {aka 'class core::pose::Pose'}
 class Pose;
       ^~~~
src/core/scoring/cryst/PhenixInterface.cc:494:51: error: 'core::chemical' has not been declared
    !ref_pose_->residue(i).has_variant_type( core::chemical::DISULFIDE ) );
                                                   ^~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:496:20: error: 'rsd_i' was not declared in this scope
   grads[i].resize( rsd_i.natoms() );
                    ^~~~~
src/core/scoring/cryst/PhenixInterface.cc:498:9: error: invalid use of incomplete type 'const class core::pose::Pose'
    if ( pose.residue_type(i).atom_type(j).is_virtual() ) {
         ^~~~
In file included from src/core/scoring/cryst/PhenixInterface.hh:23,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
src/core/pose/Pose.fwd.hh:25:7: note: forward declaration of 'class core::pose::Pose'
 class Pose;
       ^~~~
src/core/scoring/cryst/PhenixInterface.cc:499:16: error: no match for 'operator[]' (operand types are '__gnu_cxx::__alloc_traits<std::allocator<numeric::xyzVector<double> >, numeric::xyzVector<double> >::value_type' {aka 'numeric::xyzVector<double>'} and 'int')
     grads[i][j][0] = grads[i][j][1] = grads[i][j][2] = 0; // placeholder
                ^
src/core/scoring/cryst/PhenixInterface.cc:499:33: error: no match for 'operator[]' (operand types are '__gnu_cxx::__alloc_traits<std::allocator<numeric::xyzVector<double> >, numeric::xyzVector<double> >::value_type' {aka 'numeric::xyzVector<double>'} and 'int')
     grads[i][j][0] = grads[i][j][1] = grads[i][j][2] = 0; // placeholder
                                 ^
src/core/scoring/cryst/PhenixInterface.cc:499:50: error: no match for 'operator[]' (operand types are '__gnu_cxx::__alloc_traits<std::allocator<numeric::xyzVector<double> >, numeric::xyzVector<double> >::value_type' {aka 'numeric::xyzVector<double>'} and 'int')
     grads[i][j][0] = grads[i][j][1] = grads[i][j][2] = 0; // placeholder
                                                  ^
src/core/scoring/cryst/PhenixInterface.cc:500:16: error: invalid use of incomplete type 'const class core::pose::Pose'
    } else if ( pose.residue_type(i).atom_name(j) == " CEN" ) {
                ^~~~
In file included from src/core/scoring/cryst/PhenixInterface.hh:23,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
src/core/pose/Pose.fwd.hh:25:7: note: forward declaration of 'class core::pose::Pose'
 class Pose;
       ^~~~
src/core/scoring/cryst/PhenixInterface.cc:501:16: error: no match for 'operator[]' (operand types are '__gnu_cxx::__alloc_traits<std::allocator<numeric::xyzVector<double> >, numeric::xyzVector<double> >::value_type' {aka 'numeric::xyzVector<double>'} and 'int')
     grads[i][j][0] = grads[i][j][1] = grads[i][j][2] = 0; // placeholder
                ^
src/core/scoring/cryst/PhenixInterface.cc:501:33: error: no match for 'operator[]' (operand types are '__gnu_cxx::__alloc_traits<std::allocator<numeric::xyzVector<double> >, numeric::xyzVector<double> >::value_type' {aka 'numeric::xyzVector<double>'} and 'int')
     grads[i][j][0] = grads[i][j][1] = grads[i][j][2] = 0; // placeholder
                                 ^
src/core/scoring/cryst/PhenixInterface.cc:501:50: error: no match for 'operator[]' (operand types are '__gnu_cxx::__alloc_traits<std::allocator<numeric::xyzVector<double> >, numeric::xyzVector<double> >::value_type' {aka 'numeric::xyzVector<double>'} and 'int')
     grads[i][j][0] = grads[i][j][1] = grads[i][j][2] = 0; // placeholder
                                                  ^
src/core/scoring/cryst/PhenixInterface.cc:502:33: error: invalid use of incomplete type 'const class core::pose::Pose'
    } else if ( ignore_cys_hg && pose.residue(i).atom_name(j) == " HG " ) {
                                 ^~~~
In file included from src/core/scoring/cryst/PhenixInterface.hh:23,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
src/core/pose/Pose.fwd.hh:25:7: note: forward declaration of 'class core::pose::Pose'
 class Pose;
       ^~~~
src/core/scoring/cryst/PhenixInterface.cc:503:16: error: no match for 'operator[]' (operand types are '__gnu_cxx::__alloc_traits<std::allocator<numeric::xyzVector<double> >, numeric::xyzVector<double> >::value_type' {aka 'numeric::xyzVector<double>'} and 'int')
     grads[i][j][0] = grads[i][j][1] = grads[i][j][2] = 0; // placeholder
                ^
src/core/scoring/cryst/PhenixInterface.cc:503:33: error: no match for 'operator[]' (operand types are '__gnu_cxx::__alloc_traits<std::allocator<numeric::xyzVector<double> >, numeric::xyzVector<double> >::value_type' {aka 'numeric::xyzVector<double>'} and 'int')
     grads[i][j][0] = grads[i][j][1] = grads[i][j][2] = 0; // placeholder
                                 ^
src/core/scoring/cryst/PhenixInterface.cc:503:50: error: no match for 'operator[]' (operand types are '__gnu_cxx::__alloc_traits<std::allocator<numeric::xyzVector<double> >, numeric::xyzVector<double> >::value_type' {aka 'numeric::xyzVector<double>'} and 'int')
     grads[i][j][0] = grads[i][j][1] = grads[i][j][2] = 0; // placeholder
                                                  ^
src/core/scoring/cryst/PhenixInterface.cc:513:16: error: no match for 'operator[]' (operand types are '__gnu_cxx::__alloc_traits<std::allocator<numeric::xyzVector<double> >, numeric::xyzVector<double> >::value_type' {aka 'numeric::xyzVector<double>'} and 'int')
     grads[i][j][0] = PyFloat_AsDouble( gx );
                ^
src/core/scoring/cryst/PhenixInterface.cc:514:16: error: no match for 'operator[]' (operand types are '__gnu_cxx::__alloc_traits<std::allocator<numeric::xyzVector<double> >, numeric::xyzVector<double> >::value_type' {aka 'numeric::xyzVector<double>'} and 'int')
     grads[i][j][1] = PyFloat_AsDouble( gy );
                ^
src/core/scoring/cryst/PhenixInterface.cc:515:16: error: no match for 'operator[]' (operand types are '__gnu_cxx::__alloc_traits<std::allocator<numeric::xyzVector<double> >, numeric::xyzVector<double> >::value_type' {aka 'numeric::xyzVector<double>'} and 'int')
     grads[i][j][2] = PyFloat_AsDouble( gz );
                ^
src/core/scoring/cryst/PhenixInterface.cc: In member function 'void core::scoring::cryst::PhenixInterface::stealBfactorsFromFile(core::pose::Pose&, std::__cxx11::string)':
src/core/scoring/cryst/PhenixInterface.cc:538:19: error: aggregate 'core::pose::Pose pose_asu' has incomplete type and cannot be defined
  core::pose::Pose pose_asu;
                   ^~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:539:14: error: 'core::pose::symmetry' has not been declared
  core::pose::symmetry::extract_asymmetric_unit(pose, pose_asu);
              ^~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:542:23: error: variable 'std::ifstream PDBIN' has initializer but incomplete type
  std::ifstream PDBIN( filename.c_str() , std::ifstream::in );
                       ^~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:542:57: error: incomplete type 'std::ifstream' {aka 'std::basic_ifstream<char>'} used in nested name specifier
  std::ifstream PDBIN( filename.c_str() , std::ifstream::in );
                                                         ^~
src/core/scoring/cryst/PhenixInterface.cc:557:29: error: invalid use of incomplete type 'class core::pose::Pose'
   core::Size residALT_ros = pose.pdb_info()->pdb2pose( chainid[0], resid, icode[0] );
                             ^~~~
In file included from src/core/scoring/cryst/PhenixInterface.hh:23,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
src/core/pose/Pose.fwd.hh:25:7: note: forward declaration of 'class core::pose::Pose'
 class Pose;
       ^~~~
src/core/scoring/cryst/PhenixInterface.cc:566:74: error: invalid use of incomplete type 'class core::pose::Pose'
    TR << "error finding res! " << resid << chainid << " first res = " << pose.pdb_info()->pose2pdb(1) << std::endl;
                                                                          ^~~~
In file included from src/core/scoring/cryst/PhenixInterface.hh:23,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
src/core/pose/Pose.fwd.hh:25:7: note: forward declaration of 'class core::pose::Pose'
 class Pose;
       ^~~~
src/core/scoring/cryst/PhenixInterface.cc:573:15: error: 'basic::options' has not been declared
   if ( basic::options::option[ basic::options::OptionKeys::inout::output_alternate_atomids ].value() ) {
               ^~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:573:39: error: 'basic::options' has not been declared
   if ( basic::options::option[ basic::options::OptionKeys::inout::output_alternate_atomids ].value() ) {
                                       ^~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:585:3: error: invalid use of incomplete type 'class core::pose::Pose'
   pose.pdb_info()->temperature( resid_ros, atmid, B );
   ^~~~
In file included from src/core/scoring/cryst/PhenixInterface.hh:23,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
src/core/pose/Pose.fwd.hh:25:7: note: forward declaration of 'class core::pose::Pose'
 class Pose;
       ^~~~
src/core/scoring/cryst/PhenixInterface.cc:589:2: error: 'fix_bfactorsH' was not declared in this scope
  fix_bfactorsH( pose );
  ^~~~~~~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:589:2: note: suggested alternative: 'fitBfactors'
  fix_bfactorsH( pose );
  ^~~~~~~~~~~~~
  fitBfactors
src/core/scoring/cryst/PhenixInterface.cc: In member function 'void core::scoring::cryst::PhenixInterface::initialize_target_evaluator(const core::pose::Pose&, std::__cxx11::string)':
src/core/scoring/cryst/PhenixInterface.cc:872:15: error: 'basic::options' has not been declared
  if ( !basic::options::option[ basic::options::OptionKeys::cryst::crystal_refine ].value() ) {
               ^~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:872:39: error: 'basic::options' has not been declared
  if ( !basic::options::option[ basic::options::OptionKeys::cryst::crystal_refine ].value() ) {
                                       ^~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:885:8: error: invalid use of incomplete type 'const class core::pose::Pose'
  if ( !pose.pdb_info() || pose.pdb_info()->crystinfo().A()*pose.pdb_info()->crystinfo().B()*pose.pdb_info()->crystinfo().C() == 0 ) {
        ^~~~
In file included from src/core/scoring/cryst/PhenixInterface.hh:23,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
src/core/pose/Pose.fwd.hh:25:7: note: forward declaration of 'class core::pose::Pose'
 class Pose;
       ^~~~
src/core/scoring/cryst/PhenixInterface.cc:885:27: error: invalid use of incomplete type 'const class core::pose::Pose'
  if ( !pose.pdb_info() || pose.pdb_info()->crystinfo().A()*pose.pdb_info()->crystinfo().B()*pose.pdb_info()->crystinfo().C() == 0 ) {
                           ^~~~
In file included from src/core/scoring/cryst/PhenixInterface.hh:23,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
src/core/pose/Pose.fwd.hh:25:7: note: forward declaration of 'class core::pose::Pose'
 class Pose;
       ^~~~
src/core/scoring/cryst/PhenixInterface.cc:885:60: error: invalid use of incomplete type 'const class core::pose::Pose'
  if ( !pose.pdb_info() || pose.pdb_info()->crystinfo().A()*pose.pdb_info()->crystinfo().B()*pose.pdb_info()->crystinfo().C() == 0 ) {
                                                            ^~~~
In file included from src/core/scoring/cryst/PhenixInterface.hh:23,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
src/core/pose/Pose.fwd.hh:25:7: note: forward declaration of 'class core::pose::Pose'
 class Pose;
       ^~~~
src/core/scoring/cryst/PhenixInterface.cc:885:93: error: invalid use of incomplete type 'const class core::pose::Pose'
  if ( !pose.pdb_info() || pose.pdb_info()->crystinfo().A()*pose.pdb_info()->crystinfo().B()*pose.pdb_info()->crystinfo().C() == 0 ) {
                                                                                             ^~~~
In file included from src/core/scoring/cryst/PhenixInterface.hh:23,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
src/core/pose/Pose.fwd.hh:25:7: note: forward declaration of 'class core::pose::Pose'
 class Pose;
       ^~~~
src/core/scoring/cryst/PhenixInterface.cc:891:19: error: aggregate 'core::pose::Pose pose_asu' has incomplete type and cannot be defined
  core::pose::Pose pose_asu;
                   ^~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:893:19: error: 'core::pose::symmetry' has not been declared
  if ( core::pose::symmetry::is_symmetric(pose) ) {
                   ^~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:894:15: error: 'core::pose::symmetry' has not been declared
   core::pose::symmetry::extract_asymmetric_unit(pose, pose_asu);
               ^~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:899:50: error: 'ScoreFunction' is not a member of 'core::scoring'
   pose_asu.energies().scoring_end(core::scoring::ScoreFunction());
                                                  ^~~~~~~~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:902:14: error: 'initialize_disulfide_bonds' is not a member of 'core::pose'
  core::pose::initialize_disulfide_bonds( pose_asu ); //fpd
              ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
                 from src/utility/vectorL.hh:26,
                 from src/utility/vector1.hh:23,
                 from src/core/scoring/cryst/PhenixInterface.hh:26,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
/usr/include/c++/8/bits/stl_vector.h: In instantiation of 'std::vector<_Tp, _Alloc>::size_type std::vector<_Tp, _Alloc>::size() const [with _Tp = numeric::xyzVector<double>; _Alloc = std::allocator<numeric::xyzVector<double> >; std::vector<_Tp, _Alloc>::size_type = long unsigned int]':
src/core/scoring/cryst/PhenixInterface.cc:449:45:   required from here
/usr/include/c++/8/bits/stl_vector.h:806:50: error: invalid use of incomplete type 'class numeric::xyzVector<double>'
       { return size_type(this->_M_impl._M_finish - this->_M_impl._M_start); }
                          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
In file included from src/core/types.hh:19,
                 from src/core/scoring/cryst/PhenixInterface.hh:22,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
src/numeric/xyzVector.fwd.hh:28:28: note: declaration of 'class numeric::xyzVector<double>'
 template< typename > class xyzVector;
                            ^~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
                 from src/utility/vectorL.hh:26,
                 from src/utility/vector1.hh:23,
                 from src/core/scoring/cryst/PhenixInterface.hh:26,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
/usr/include/c++/8/bits/stl_vector.h: In instantiation of 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](std::vector<_Tp, _Alloc>::size_type) [with _Tp = numeric::xyzVector<double>; _Alloc = std::allocator<numeric::xyzVector<double> >; std::vector<_Tp, _Alloc>::reference = numeric::xyzVector<double>&; std::vector<_Tp, _Alloc>::size_type = long unsigned int]':
src/utility/vectorL.hh:429:28:   required from 'utility::vectorL<<anonymous>, T, A>::reference utility::vectorL<<anonymous>, T, A>::operator[](utility::vectorL<<anonymous>, T, A>::index_type) [with long int L = 1; T = numeric::xyzVector<double>; A = std::allocator<numeric::xyzVector<double> >; utility::vectorL<<anonymous>, T, A>::reference = numeric::xyzVector<double>&; utility::vectorL<<anonymous>, T, A>::index_type = long unsigned int]'
src/core/scoring/cryst/PhenixInterface.cc:454:74:   required from here
/usr/include/c++/8/bits/stl_vector.h:933:34: error: invalid use of incomplete type 'class numeric::xyzVector<double>'
  return *(this->_M_impl._M_start + __n);
          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
In file included from src/core/types.hh:19,
                 from src/core/scoring/cryst/PhenixInterface.hh:22,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
src/numeric/xyzVector.fwd.hh:28:28: note: declaration of 'class numeric::xyzVector<double>'
 template< typename > class xyzVector;
                            ^~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
                 from src/utility/vectorL.hh:26,
                 from src/utility/vector1.hh:23,
                 from src/core/scoring/cryst/PhenixInterface.hh:26,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
/usr/include/c++/8/bits/stl_vector.h: In instantiation of 'std::_Vector_base<_Tp, _Alloc>::~_Vector_base() [with _Tp = numeric::xyzVector<double>; _Alloc = std::allocator<numeric::xyzVector<double> >]':
/usr/include/c++/8/bits/stl_vector.h:570:7:   required from 'std::vector<_Tp, _Alloc>::~vector() [with _Tp = numeric::xyzVector<double>; _Alloc = std::allocator<numeric::xyzVector<double> >]'
src/utility/vectorL.hh:232:2:   required from 'utility::vector1<T, A>::vector1(const allocator_type&) [with T = numeric::xyzVector<double>; A = std::allocator<numeric::xyzVector<double> >; utility::vector1<T, A>::allocator_type = std::allocator<numeric::xyzVector<double> >]'
src/core/scoring/cryst/PhenixInterface.cc:381:55:   required from here
/usr/include/c++/8/bits/stl_vector.h:286:35: error: invalid use of incomplete type 'class numeric::xyzVector<double>'
         _M_impl._M_end_of_storage - _M_impl._M_start);
         ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
In file included from src/core/types.hh:19,
                 from src/core/scoring/cryst/PhenixInterface.hh:22,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
src/numeric/xyzVector.fwd.hh:28:28: note: declaration of 'class numeric::xyzVector<double>'
 template< typename > class xyzVector;
                            ^~~~~~~~~
In file included from /usr/include/c++/8/memory:64,
                 from src/utility/pointer/std/owning_ptr.hh:20,
                 from src/utility/pointer/owning_ptr.hh:15,
                 from src/utility/pointer/std/access_ptr.hh:21,
                 from src/utility/pointer/access_ptr.hh:15,
                 from src/core/pose/Pose.fwd.hh:17,
                 from src/core/scoring/cryst/PhenixInterface.hh:23,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
/usr/include/c++/8/bits/stl_construct.h: In instantiation of 'void std::_Destroy(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = numeric::xyzVector<double>*]':
/usr/include/c++/8/bits/stl_construct.h:206:15:   required from 'void std::_Destroy(_ForwardIterator, _ForwardIterator, std::allocator<_T2>&) [with _ForwardIterator = numeric::xyzVector<double>*; _Tp = numeric::xyzVector<double>]'
/usr/include/c++/8/bits/stl_vector.h:567:15:   required from 'std::vector<_Tp, _Alloc>::~vector() [with _Tp = numeric::xyzVector<double>; _Alloc = std::allocator<numeric::xyzVector<double> >]'
src/utility/vectorL.hh:232:2:   required from 'utility::vector1<T, A>::vector1(const allocator_type&) [with T = numeric::xyzVector<double>; A = std::allocator<numeric::xyzVector<double> >; utility::vector1<T, A>::allocator_type = std::allocator<numeric::xyzVector<double> >]'
src/core/scoring/cryst/PhenixInterface.cc:381:55:   required from here
/usr/include/c++/8/bits/stl_construct.h:133:21: error: static assertion failed: value type is destructible
       static_assert(is_destructible<_Value_type>::value,
                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_construct.h:137:11: error: invalid use of incomplete type 'std::iterator_traits<numeric::xyzVector<double>*>::value_type' {aka 'class numeric::xyzVector<double>'}
       std::_Destroy_aux<__has_trivial_destructor(_Value_type)>::
       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  __destroy(__first, __last);
  ~~~~~~~~~^~~~~~~~~~~~~~~~~
In file included from src/core/types.hh:19,
                 from src/core/scoring/cryst/PhenixInterface.hh:22,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
src/numeric/xyzVector.fwd.hh:28:28: note: declaration of 'std::iterator_traits<numeric::xyzVector<double>*>::value_type' {aka 'class numeric::xyzVector<double>'}
 template< typename > class xyzVector;
                            ^~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
                 from src/utility/vectorL.hh:26,
                 from src/utility/vector1.hh:23,
                 from src/core/scoring/cryst/PhenixInterface.hh:26,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
/usr/include/c++/8/bits/stl_vector.h: In instantiation of 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = numeric::xyzVector<double>; _Alloc = std::allocator<numeric::xyzVector<double> >; std::size_t = long unsigned int]':
/usr/include/c++/8/bits/stl_vector.h:260:9:   required from 'std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = numeric::xyzVector<double>; _Alloc = std::allocator<numeric::xyzVector<double> >; std::size_t = long unsigned int; std::_Vector_base<_Tp, _Alloc>::allocator_type = std::allocator<numeric::xyzVector<double> >]'
/usr/include/c++/8/bits/stl_vector.h:460:61:   required from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = numeric::xyzVector<double>; _Alloc = std::allocator<numeric::xyzVector<double> >]'
src/utility/vectorL.hh:147:12:   required from 'utility::vectorL<<anonymous>, T, A>::vectorL(const utility::vectorL<<anonymous>, T, A>&) [with long int L = 1; T = numeric::xyzVector<double>; A = std::allocator<numeric::xyzVector<double> >]'
src/utility/vector1.hh:135:12:   required from 'utility::vector1<T, A>::vector1(const utility::vector1<T, A>&) [with T = numeric::xyzVector<double>; A = std::allocator<numeric::xyzVector<double> >]'
/usr/include/c++/8/bits/stl_construct.h:75:7:   [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
/usr/include/c++/8/bits/stl_uninitialized.h:134:15:   required from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = const utility::vector1<numeric::xyzVector<double> >*; _ForwardIterator = utility::vector1<numeric::xyzVector<double> >*]'
/usr/include/c++/8/bits/stl_uninitialized.h:289:37:   required from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = const utility::vector1<numeric::xyzVector<double> >*; _ForwardIterator = utility::vector1<numeric::xyzVector<double> >*; _Tp = utility::vector1<numeric::xyzVector<double> >]'
/usr/include/c++/8/bits/stl_uninitialized.h:311:2:   required from '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = utility::vector1<numeric::xyzVector<double> >*; _ForwardIterator = utility::vector1<numeric::xyzVector<double> >*; _Allocator = std::allocator<utility::vector1<numeric::xyzVector<double> > >]'
/usr/include/c++/8/bits/vector.tcc:611:44:   required from 'void std::vector<_Tp, _Alloc>::_M_default_append(std::vector<_Tp, _Alloc>::size_type) [with _Tp = utility::vector1<numeric::xyzVector<double> >; _Alloc = std::allocator<utility::vector1<numeric::xyzVector<double> > >; std::vector<_Tp, _Alloc>::size_type = long unsigned int]'
/usr/include/c++/8/bits/stl_vector.h:827:4:   required from 'void std::vector<_Tp, _Alloc>::resize(std::vector<_Tp, _Alloc>::size_type) [with _Tp = utility::vector1<numeric::xyzVector<double> >; _Alloc = std::allocator<utility::vector1<numeric::xyzVector<double> > >; std::vector<_Tp, _Alloc>::size_type = long unsigned int]'
src/core/scoring/cryst/PhenixInterface.cc:482:21:   required from here
/usr/include/c++/8/bits/stl_vector.h:313:59: error: invalid use of incomplete type 'class numeric::xyzVector<double>'
  this->_M_impl._M_end_of_storage = this->_M_impl._M_start + __n;
                                    ~~~~~~~~~~~~~~~~~~~~~~~^~~~~
In file included from src/core/types.hh:19,
                 from src/core/scoring/cryst/PhenixInterface.hh:22,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
src/numeric/xyzVector.fwd.hh:28:28: note: declaration of 'class numeric::xyzVector<double>'
 template< typename > class xyzVector;
                            ^~~~~~~~~
In file included from /usr/include/c++/8/memory:65,
                 from src/utility/pointer/std/owning_ptr.hh:20,
                 from src/utility/pointer/owning_ptr.hh:15,
                 from src/utility/pointer/std/access_ptr.hh:21,
                 from src/utility/pointer/access_ptr.hh:15,
                 from src/core/pose/Pose.fwd.hh:17,
                 from src/core/scoring/cryst/PhenixInterface.hh:23,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
/usr/include/c++/8/bits/stl_uninitialized.h: In instantiation of '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const numeric::xyzVector<double>*, std::vector<numeric::xyzVector<double>, std::allocator<numeric::xyzVector<double> > > >; _ForwardIterator = numeric::xyzVector<double>*]':
/usr/include/c++/8/bits/stl_uninitialized.h:289:37:   required from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const numeric::xyzVector<double>*, std::vector<numeric::xyzVector<double>, std::allocator<numeric::xyzVector<double> > > >; _ForwardIterator = numeric::xyzVector<double>*; _Tp = numeric::xyzVector<double>]'
/usr/include/c++/8/bits/stl_vector.h:463:31:   required from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = numeric::xyzVector<double>; _Alloc = std::allocator<numeric::xyzVector<double> >]'
src/utility/vectorL.hh:147:12:   required from 'utility::vectorL<<anonymous>, T, A>::vectorL(const utility::vectorL<<anonymous>, T, A>&) [with long int L = 1; T = numeric::xyzVector<double>; A = std::allocator<numeric::xyzVector<double> >]'
src/utility/vector1.hh:135:12:   required from 'utility::vector1<T, A>::vector1(const utility::vector1<T, A>&) [with T = numeric::xyzVector<double>; A = std::allocator<numeric::xyzVector<double> >]'
/usr/include/c++/8/bits/stl_construct.h:75:7:   [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
/usr/include/c++/8/bits/stl_uninitialized.h:134:15:   required from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = const utility::vector1<numeric::xyzVector<double> >*; _ForwardIterator = utility::vector1<numeric::xyzVector<double> >*]'
/usr/include/c++/8/bits/stl_uninitialized.h:289:37:   required from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = const utility::vector1<numeric::xyzVector<double> >*; _ForwardIterator = utility::vector1<numeric::xyzVector<double> >*; _Tp = utility::vector1<numeric::xyzVector<double> >]'
/usr/include/c++/8/bits/stl_uninitialized.h:311:2:   required from '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = utility::vector1<numeric::xyzVector<double> >*; _ForwardIterator = utility::vector1<numeric::xyzVector<double> >*; _Allocator = std::allocator<utility::vector1<numeric::xyzVector<double> > >]'
/usr/include/c++/8/bits/vector.tcc:611:44:   required from 'void std::vector<_Tp, _Alloc>::_M_default_append(std::vector<_Tp, _Alloc>::size_type) [with _Tp = utility::vector1<numeric::xyzVector<double> >; _Alloc = std::allocator<utility::vector1<numeric::xyzVector<double> > >; std::vector<_Tp, _Alloc>::size_type = long unsigned int]'
/usr/include/c++/8/bits/stl_vector.h:827:4:   required from 'void std::vector<_Tp, _Alloc>::resize(std::vector<_Tp, _Alloc>::size_type) [with _Tp = utility::vector1<numeric::xyzVector<double> >; _Alloc = std::allocator<utility::vector1<numeric::xyzVector<double> > >; std::vector<_Tp, _Alloc>::size_type = long unsigned int]'
src/core/scoring/cryst/PhenixInterface.cc:482:21:   required from here
/usr/include/c++/8/bits/stl_uninitialized.h:132:12: error: invalid use of incomplete type 'std::__iterator_traits<__gnu_cxx::__normal_iterator<const numeric::xyzVector<double>*, std::vector<numeric::xyzVector<double>, std::allocator<numeric::xyzVector<double> > > >, void>::value_type' {aka 'class numeric::xyzVector<double>'}
       return std::__uninitialized_copy<__is_trivial(_ValueType1)
                                        ~~~~~~~~~~~~~~~~~~~~~~~~~
            && __is_trivial(_ValueType2)
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from src/core/types.hh:19,
                 from src/core/scoring/cryst/PhenixInterface.hh:22,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
src/numeric/xyzVector.fwd.hh:28:28: note: declaration of 'std::__iterator_traits<__gnu_cxx::__normal_iterator<const numeric::xyzVector<double>*, std::vector<numeric::xyzVector<double>, std::allocator<numeric::xyzVector<double> > > >, void>::value_type' {aka 'class numeric::xyzVector<double>'}
 template< typename > class xyzVector;
                            ^~~~~~~~~
In file included from /usr/include/c++/8/memory:65,
                 from src/utility/pointer/std/owning_ptr.hh:20,
                 from src/utility/pointer/owning_ptr.hh:15,
                 from src/utility/pointer/std/access_ptr.hh:21,
                 from src/utility/pointer/access_ptr.hh:15,
                 from src/core/pose/Pose.fwd.hh:17,
                 from src/core/scoring/cryst/PhenixInterface.hh:23,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
/usr/include/c++/8/bits/stl_uninitialized.h:132:12: error: invalid use of incomplete type 'std::iterator_traits<numeric::xyzVector<double>*>::value_type' {aka 'class numeric::xyzVector<double>'}
       return std::__uninitialized_copy<__is_trivial(_ValueType1)
                                        ~~~~~~~~~~~~~~~~~~~~~~~~~
            && __is_trivial(_ValueType2)
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from src/core/types.hh:19,
                 from src/core/scoring/cryst/PhenixInterface.hh:22,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
src/numeric/xyzVector.fwd.hh:28:28: note: declaration of 'std::iterator_traits<numeric::xyzVector<double>*>::value_type' {aka 'class numeric::xyzVector<double>'}
 template< typename > class xyzVector;
                            ^~~~~~~~~
In file included from /usr/include/c++/8/x86_64-redhat-linux/bits/c++allocator.h:33,
                 from /usr/include/c++/8/bits/allocator.h:46,
                 from /usr/include/c++/8/memory:63,
                 from src/utility/pointer/std/owning_ptr.hh:20,
                 from src/utility/pointer/owning_ptr.hh:15,
                 from src/utility/pointer/std/access_ptr.hh:21,
                 from src/utility/pointer/access_ptr.hh:15,
                 from src/core/pose/Pose.fwd.hh:17,
                 from src/core/scoring/cryst/PhenixInterface.hh:23,
                 from src/core/scoring/cryst/PhenixInterface.cc:15:
/usr/include/c++/8/ext/new_allocator.h: In instantiation of '_Tp* __gnu_cxx::new_allocator<_Tp>::allocate(__gnu_cxx::new_allocator<_Tp>::size_type, const void*) [with _Tp = numeric::xyzVector<double>; __gnu_cxx::new_allocator<_Tp>::pointer = numeric::xyzVector<double>*; __gnu_cxx::new_allocator<_Tp>::size_type = long unsigned int]':
/usr/include/c++/8/bits/alloc_traits.h:436:32:   required from 'static _Tp* std::allocator_traits<std::allocator<_Tp1> >::allocate(std::allocator_traits<std::allocator<_Tp1> >::allocator_type&, std::allocator_traits<std::allocator<_Tp1> >::size_type) [with _Tp = numeric::xyzVector<double>; std::allocator_traits<std::allocator<_Tp1> >::pointer = numeric::xyzVector<double>*; std::allocator_traits<std::allocator<_Tp1> >::allocator_type = std::allocator<numeric::xyzVector<double> >; std::allocator_traits<std::allocator<_Tp1> >::size_type = long unsigned int]'
/usr/include/c++/8/bits/stl_vector.h:296:33:   required from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = numeric::xyzVector<double>; _Alloc = std::allocator<numeric::xyzVector<double> >; std::_Vector_base<_Tp, _Alloc>::pointer = numeric::xyzVector<double>*; std::size_t = long unsigned int]'
/usr/include/c++/8/bits/stl_vector.h:311:33:   required from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = numeric::xyzVector<double>; _Alloc = std::allocator<numeric::xyzVector<double> >; std::size_t = long unsigned int]'
/usr/include/c++/8/bits/stl_vector.h:260:9:   required from 'std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = numeric::xyzVector<double>; _Alloc = std::allocator<numeric::xyzVector<double> >; std::size_t = long unsigned int; std::_Vector_base<_Tp, _Alloc>::allocator_type = std::allocator<numeric::xyzVector<double> >]'
/usr/include/c++/8/bits/stl_vector.h:460:61:   required from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = numeric::xyzVector<double>; _Alloc = std::allocator<numeric::xyzVector<double> >]'
src/utility/vectorL.hh:147:12:   [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
/usr/include/c++/8/bits/stl_uninitialized.h:134:15:   required from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = const utility::vector1<numeric::xyzVector<double> >*; _ForwardIterator = utility::vector1<numeric::xyzVector<double> >*]'
/usr/include/c++/8/bits/stl_uninitialized.h:289:37:   required from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = const utility::vector1<numeric::xyzVector<double> >*; _ForwardIterator = utility::vector1<numeric::xyzVector<double> >*; _Tp = utility::vector1<numeric::xyzVector<double> >]'
/usr/include/c++/8/bits/stl_uninitialized.h:311:2:   required from '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = utility::vector1<numeric::xyzVector<double> >*; _ForwardIterator = utility::vector1<numeric::xyzVector<double> >*; _Allocator = std::allocator<utility::vector1<numeric::xyzVector<double> > >]'
/usr/include/c++/8/bits/vector.tcc:611:44:   required from 'void std::vector<_Tp, _Alloc>::_M_default_append(std::vector<_Tp, _Alloc>::size_type) [with _Tp = utility::vector1<numeric::xyzVector<double> >; _Alloc = std::allocator<utility::vector1<numeric::xyzVector<double> > >; std::vector<_Tp, _Alloc>::size_type = long unsigned int]'
/usr/include/c++/8/bits/stl_vector.h:827:4:   required from 'void std::vector<_Tp, _Alloc>::resize(std::vector<_Tp, _Alloc>::size_type) [with _Tp = utility::vector1<numeric::xyzVector<double> >; _Alloc = std::allocator<utility::vector1<numeric::xyzVector<double> > >; std::vector<_Tp, _Alloc>::size_type = long unsigned int]'
src/core/scoring/cryst/PhenixInterface.cc:482:21:   required from here
/usr/include/c++/8/ext/new_allocator.h:111:48: error: invalid application of 'sizeof' to incomplete type 'numeric::xyzVector<double>'
  return static_cast<_Tp*>(::operator new(__n * sizeof(_Tp)));
                                                ^~~~~~~~~~~
/usr/include/c++/8/ext/new_allocator.h: In instantiation of '__gnu_cxx::new_allocator<_Tp>::size_type __gnu_cxx::new_allocator<_Tp>::max_size() const [with _Tp = numeric::xyzVector<double>; __gnu_cxx::new_allocator<_Tp>::size_type = long unsigned int]':
/usr/include/c++/8/ext/new_allocator.h:101:18:   required from '_Tp* __gnu_cxx::new_allocator<_Tp>::allocate(__gnu_cxx::new_allocator<_Tp>::size_type, const void*) [with _Tp = numeric::xyzVector<double>; __gnu_cxx::new_allocator<_Tp>::pointer = numeric::xyzVector<double>*; __gnu_cxx::new_allocator<_Tp>::size_type = long unsigned int]'
/usr/include/c++/8/bits/alloc_traits.h:436:32:   required from 'static _Tp* std::allocator_traits<std::allocator<_Tp1> >::allocate(std::allocator_traits<std::allocator<_Tp1> >::allocator_type&, std::allocator_traits<std::allocator<_Tp1> >::size_type) [with _Tp = numeric::xyzVector<double>; std::allocator_traits<std::allocator<_Tp1> >::pointer = numeric::xyzVector<double>*; std::allocator_traits<std::allocator<_Tp1> >::allocator_type = std::allocator<numeric::xyzVector<double> >; std::allocator_traits<std::allocator<_Tp1> >::size_type = long unsigned int]'
/usr/include/c++/8/bits/stl_vector.h:296:33:   required from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = numeric::xyzVector<double>; _Alloc = std::allocator<numeric::xyzVector<double> >; std::_Vector_base<_Tp, _Alloc>::pointer = numeric::xyzVector<double>*; std::size_t = long unsigned int]'
/usr/include/c++/8/bits/stl_vector.h:311:33:   required from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = numeric::xyzVector<double>; _Alloc = std::allocator<numeric::xyzVector<double> >; std::size_t = long unsigned int]'
/usr/include/c++/8/bits/stl_vector.h:260:9:   required from 'std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = numeric::xyzVector<double>; _Alloc = std::allocator<numeric::xyzVector<double> >; std::size_t = long unsigned int; std::_Vector_base<_Tp, _Alloc>::allocator_type = std::allocator<numeric::xyzVector<double> >]'
/usr/include/c++/8/bits/stl_vector.h:460:61:   [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
/usr/include/c++/8/bits/stl_uninitialized.h:134:15:   required from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = const utility::vector1<numeric::xyzVector<double> >*; _ForwardIterator = utility::vector1<numeric::xyzVector<double> >*]'
/usr/include/c++/8/bits/stl_uninitialized.h:289:37:   required from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = const utility::vector1<numeric::xyzVector<double> >*; _ForwardIterator = utility::vector1<numeric::xyzVector<double> >*; _Tp = utility::vector1<numeric::xyzVector<double> >]'
/usr/include/c++/8/bits/stl_uninitialized.h:311:2:   required from '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = utility::vector1<numeric::xyzVector<double> >*; _ForwardIterator = utility::vector1<numeric::xyzVector<double> >*; _Allocator = std::allocator<utility::vector1<numeric::xyzVector<double> > >]'
/usr/include/c++/8/bits/vector.tcc:611:44:   required from 'void std::vector<_Tp, _Alloc>::_M_default_append(std::vector<_Tp, _Alloc>::size_type) [with _Tp = utility::vector1<numeric::xyzVector<double> >; _Alloc = std::allocator<utility::vector1<numeric::xyzVector<double> > >; std::vector<_Tp, _Alloc>::size_type = long unsigned int]'
/usr/include/c++/8/bits/stl_vector.h:827:4:   required from 'void std::vector<_Tp, _Alloc>::resize(std::vector<_Tp, _Alloc>::size_type) [with _Tp = utility::vector1<numeric::xyzVector<double> >; _Alloc = std::allocator<utility::vector1<numeric::xyzVector<double> > >; std::vector<_Tp, _Alloc>::size_type = long unsigned int]'
src/core/scoring/cryst/PhenixInterface.cc:482:21:   required from here
/usr/include/c++/8/ext/new_allocator.h:130:29: error: invalid application of 'sizeof' to incomplete type 'numeric::xyzVector<double>'
       { return size_t(-1) / sizeof(_Tp); }
                             ^~~~~~~~~~~
scons: *** [build/src/release/linux/4.18/64/x86/gcc/8/python/core/scoring/cryst/PhenixInterface.os] Error 1
scons: building terminated because of errors.