Test: linux.gcc.static.build.release 「view this page in B3 βῆτα server」
Branch: rosetta:commits 「revision: №20703」
Test files: 「file-system-view」 「file-list-view」
Daemon: nobu-4     Started at: 2025-04-01 15:12:10     Run time: 0:01:54      State: failed


Running: /home/benchmark/prefix/nobu-4/linux/python-3.9.gcc/99a1a29fd465f86265a7c5b92d75dbcd/bin/python3.9 ./scons.py bin cxx=gcc extras=static mode=release -j64 scons: Reading SConscript files ... Running versioning script ... Done. (0.1 seconds) Number of option files updated: 0 Total 4710 options. Updating submodules needed for compilation. Finished updating ResidueProperty code -- no changes needed Finished updating VariantType code -- no changes needed scons: done reading SConscript files. scons: Building targets ... ar rc build/src/release/linux/5.4/64/x86/gcc/4.8/static/libprotocols_c.6.a build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/flexpep_docking/FlexPepDockingAbInitio.o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/flexpep_docking/FlexPepDockingFlags.o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/flexpep_docking/FlexPepDockingLowRes.o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/flexpep_docking/FlexPepDockingPoseMetrics.o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/flexpep_docking/FlexPepDockingProtocol.o ranlib build/src/release/linux/5.4/64/x86/gcc/4.8/static/libprotocols_c.6.a g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/protein_grid/ProteinGrid.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/protein_grid/ProteinGrid.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/topology_broker/SymmetryClaimer.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/topology_broker/SymmetryClaimer.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/topology_broker/TemplateFragmentClaimer.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/topology_broker/TemplateFragmentClaimer.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/topology_broker/TemplateJumpClaimer.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/topology_broker/TemplateJumpClaimer.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/topology_broker/TopologyBroker.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/topology_broker/TopologyBroker.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/topology_broker/TopologyClaimer.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/topology_broker/TopologyClaimer.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/topology_broker/TopologyClaimerFactory.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/topology_broker/TopologyClaimerFactory.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/topology_broker/util.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/topology_broker/util.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/topology_broker/claims/DofClaim.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/topology_broker/claims/DofClaim.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/trRosetta_protocols/constraint_generators/trRosettaConstraintGenerator.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/trRosetta_protocols/constraint_generators/trRosettaConstraintGenerator.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/trRosetta_protocols/movers/trRosettaProtocolMover.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/trRosetta_protocols/movers/trRosettaProtocolMover.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/protein_mpnn/ProteinMPNN.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/protein_mpnn/ProteinMPNN.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/protein_mpnn/util.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/protein_mpnn/util.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/protein_mpnn/ProteinMPNNMover.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/protein_mpnn/ProteinMPNNMover.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/protein_mpnn/ProteinMPNNProbabilitiesMetric.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/protein_mpnn/ProteinMPNNProbabilitiesMetric.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/fold_from_loops/filters/RmsdFromResidueSelectorFilter.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/fold_from_loops/filters/RmsdFromResidueSelectorFilter.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/fold_from_loops/filters/ScorePoseSegmentFromResidueSelectorFilter.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/fold_from_loops/filters/ScorePoseSegmentFromResidueSelectorFilter.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/fold_from_loops/filters/ConstraintFulfilmentFilter.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/fold_from_loops/filters/ConstraintFulfilmentFilter.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/fold_from_loops/selectors/ProteinResidueSelector.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/fold_from_loops/selectors/ProteinResidueSelector.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/fold_from_loops/selectors/CutpointResidueSelector.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/fold_from_loops/selectors/CutpointResidueSelector.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/fold_from_loops/selectors/ConstraintResidueSelector.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/fold_from_loops/selectors/ConstraintResidueSelector.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/fold_from_loops/constraint_generator/SegmentedAtomPairConstraintGenerator.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/fold_from_loops/constraint_generator/SegmentedAtomPairConstraintGenerator.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/fold_from_loops/constraint_generator/AutomaticSheetConstraintGenerator.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/fold_from_loops/constraint_generator/AutomaticSheetConstraintGenerator.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/fold_from_loops/movers/AlignByResidueSelectorMover.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/fold_from_loops/movers/AlignByResidueSelectorMover.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/fold_from_loops/movers/DisplayPoseLabelsMover.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/fold_from_loops/movers/DisplayPoseLabelsMover.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/fold_from_loops/movers/LabelPoseFromResidueSelectorMover.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/fold_from_loops/movers/LabelPoseFromResidueSelectorMover.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/fold_from_loops/movers/ReleaseConstraintFromResidueMover.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/fold_from_loops/movers/ReleaseConstraintFromResidueMover.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/fold_from_loops/movers/SplitAndMixPoseMover.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/fold_from_loops/movers/SplitAndMixPoseMover.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/fold_from_loops/movers/ResidueLabelsToPymolSelectionMover.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/fold_from_loops/movers/ResidueLabelsToPymolSelectionMover.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/fold_from_loops/movers/SavePDBInfoMover.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/fold_from_loops/movers/SavePDBInfoMover.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/fold_from_loops/movers/MoveMapFactoryToNamedMoveMapMover.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/fold_from_loops/movers/MoveMapFactoryToNamedMoveMapMover.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/fold_from_loops/movers/NubInitioLoopClosureMover.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/fold_from_loops/movers/NubInitioLoopClosureMover.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/fold_from_loops/utils/utils.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/fold_from_loops/utils/utils.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/fold_from_loops/utils/Nub.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/fold_from_loops/utils/Nub.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/fold_from_loops/NubInitioMover.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/fold_from_loops/NubInitioMover.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/cyclic_peptide/CrankshaftFlipMover.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/cyclic_peptide/CrankshaftFlipMover.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/cyclic_peptide/CreateAngleConstraint.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/cyclic_peptide/CreateAngleConstraint.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/cyclic_peptide/CreateDistanceConstraint.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/cyclic_peptide/CreateDistanceConstraint.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/cyclic_peptide/CreateTorsionConstraint.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/cyclic_peptide/CreateTorsionConstraint.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/cyclic_peptide/CrosslinkerMover.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/cyclic_peptide/CrosslinkerMover.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/cyclic_peptide/CycpepRigidBodyPermutationMover.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/cyclic_peptide/CycpepRigidBodyPermutationMover.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/cyclic_peptide/CycpepSymmetryFilter.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/cyclic_peptide/CycpepSymmetryFilter.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/cyclic_peptide/FlipChiralityMover.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/cyclic_peptide/FlipChiralityMover.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/cyclic_peptide/OversaturatedHbondAcceptorFilter.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/cyclic_peptide/OversaturatedHbondAcceptorFilter.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/cyclic_peptide/PeptideCyclizeMover.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/cyclic_peptide/PeptideCyclizeMover.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/cyclic_peptide/PeptideInternalHbondsFilter.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/cyclic_peptide/PeptideInternalHbondsFilter.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/cyclic_peptide/PeptideInternalHbondsMetric.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/cyclic_peptide/PeptideInternalHbondsMetric.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/cyclic_peptide/PeptideStubMover.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/cyclic_peptide/PeptideStubMover.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/cyclic_peptide/RamaMutationSelector.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/cyclic_peptide/RamaMutationSelector.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/cyclic_peptide/SymmetricCycpepAlign.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/cyclic_peptide/SymmetricCycpepAlign.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/cyclic_peptide/TryDisulfPermutations.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/cyclic_peptide/TryDisulfPermutations.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/cyclic_peptide/crosslinker/1_4_BBMB_Helper.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/cyclic_peptide/crosslinker/1_4_BBMB_Helper.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/cyclic_peptide/crosslinker/CrosslinkerMoverHelper.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/cyclic_peptide/crosslinker/CrosslinkerMoverHelper.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/cyclic_peptide/crosslinker/Lanthionine_Helper.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/cyclic_peptide/crosslinker/Lanthionine_Helper.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/cyclic_peptide/crosslinker/lanthionine_util.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/cyclic_peptide/crosslinker/lanthionine_util.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/cyclic_peptide/crosslinker/Metal_HelperBase.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/cyclic_peptide/crosslinker/Metal_HelperBase.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/cyclic_peptide/crosslinker/OctahedralMetal_Helper.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/cyclic_peptide/crosslinker/OctahedralMetal_Helper.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/cyclic_peptide/crosslinker/SquarePlanarMetal_Helper.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/cyclic_peptide/crosslinker/SquarePlanarMetal_Helper.cc src/protocols/protein_grid/ProteinGrid.cc: In member function 'void protocols::protein_grid::ProteinGrid::placed_ligand_space_fill_analysis(core::conformation::ResidueOP)': src/protocols/protein_grid/ProteinGrid.cc:651:52: error: 'atom_num' was not declared in this scope core::Real atom_lj_radius = ligresOP->atom_type(atom_num).lj_radius(); ^ src/protocols/protein_grid/ProteinGrid.cc: In function 'void protocols::protein_grid::export_protein_matrix_to_pdb(std::string)': src/protocols/protein_grid/ProteinGrid.cc:975:83: error: 'fullness_ratio_' was not declared in this scope std::string matrix_pdb_name = pdb_name_prefix + "_WholeRatio_" + std::to_string(fullness_ratio_); ^ src/protocols/protein_grid/ProteinGrid.cc:978:6: error: 'using_sub_area_' was not declared in this scope if(using_sub_area_) ^ src/protocols/protein_grid/ProteinGrid.cc:980:70: error: 'sub_fullness_ratio_' was not declared in this scope matrix_pdb_name = matrix_pdb_name + "_SubRatio_" + std::to_string(sub_fullness_ratio_); ^ src/protocols/protein_grid/ProteinGrid.cc:989:64: error: 'export_protein_matrix_to_pose' was not declared in this scope core::pose::Pose matrix_pose = export_protein_matrix_to_pose(); ^ src/protocols/protein_grid/ProteinGrid.cc:995:28: error: 'working_pose_' was not declared in this scope core::pose::add_comment(*working_pose_, "Corresponding space fill matrix file:", matrix_pdb_name); ^ g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/cyclic_peptide/crosslinker/SquarePyramidalMetal_Helper.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/cyclic_peptide/crosslinker/SquarePyramidalMetal_Helper.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/cyclic_peptide/crosslinker/TBMB_Helper.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/cyclic_peptide/crosslinker/TBMB_Helper.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/cyclic_peptide/crosslinker/TetrahedralMetal_Helper.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/cyclic_peptide/crosslinker/TetrahedralMetal_Helper.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/cyclic_peptide/crosslinker/Thioether_Helper.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/cyclic_peptide/crosslinker/Thioether_Helper.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/cyclic_peptide/crosslinker/thioether_util.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/cyclic_peptide/crosslinker/thioether_util.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/cyclic_peptide/crosslinker/TrigonalPlanarMetal_Helper.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/cyclic_peptide/crosslinker/TrigonalPlanarMetal_Helper.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/cyclic_peptide/crosslinker/TrigonalPyramidalMetal_Helper.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/cyclic_peptide/crosslinker/TrigonalPyramidalMetal_Helper.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/cyclic_peptide/crosslinker/TMA_Helper.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/cyclic_peptide/crosslinker/TMA_Helper.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/denovo_design/util.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/denovo_design/util.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/denovo_design/architects/BetaSheetArchitect.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/denovo_design/architects/BetaSheetArchitect.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/denovo_design/architects/BlueprintArchitect.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/denovo_design/architects/BlueprintArchitect.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/denovo_design/architects/CompoundArchitect.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/denovo_design/architects/CompoundArchitect.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/denovo_design/architects/DeNovoArchitect.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/denovo_design/architects/DeNovoArchitect.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/denovo_design/architects/DeNovoArchitectFactory.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/denovo_design/architects/DeNovoArchitectFactory.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/denovo_design/architects/HelixArchitect.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/denovo_design/architects/HelixArchitect.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/denovo_design/architects/MotifArchitect.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/denovo_design/architects/MotifArchitect.cc g++ -o build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/denovo_design/architects/PoseArchitect.o -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 -Werror -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/denovo_design/architects/PoseArchitect.cc scons: *** [build/src/release/linux/5.4/64/x86/gcc/4.8/static/protocols/protein_grid/ProteinGrid.o] Error 1 scons: building terminated because of errors.
{}